trunk/xDissertation/dissertation.bib

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@string{acp = {Adv. Chem. Phys.}}

@string{bj = {Biophys. J.}}

@string{ccp5 = {CCP5 Information Quarterly}}

@string{cp = {Chem. Phys.}}

@string{cpl = {Chem. Phys. Lett.}}

@string{jacs = {J. Am. Chem. Soc.}}

@string{jcc = {J. Comp. Chem.}}

@string{jcop = {J. Comp. Phys.}}

@string{jcp = {J. Chem. Phys.}}

@string{jml = {J. Mol. Liq.}}

@string{jmb = {J. Mol. Bio.}}

@string{jpc = {J. Phys. Chem.}}

@string{jpca = {J. Phys. Chem. A}}

@string{jpcb = {J. Phys. Chem. B}}

@string{mp = {Mol. Phys.}}

@string{pams = {Proc. Am. Math Soc.}}

@string{pccp = {Phys. Chem. Chem. Phys.}}

@string{pnas = {Proc. Natl. Acad. Sci. USA}}

@string{pr = {Phys. Rev.}}

@string{pra = {Phys. Rev. A}}

@string{prb = {Phys. Rev. B}}

@string{pre = {Phys. Rev. E}}

@string{prl = {Phys. Rev. Lett.}}

@string{rmp = {Rev. Mod. Phys.}}

@string{cpc = "Comp. Phys. Comm."}

@article{Peters:1999uq,
        Abstract = {The Fokker-Planck (FP) equation describing the dynamics of a single Brownian particle near a fixed external surface is derived using the multiple-time-scales perturbation method, previously used by Cukier and Deutch and Nienhuis in the absence of any external surfaces, and Piasecki ei LII. for two Brownian spheres in a hard fluid. The FP equation includes an explicit expression for the (time-independent) particle friction tensor in terms of the force autocorrelation Function and equilibrium average force on the particle by the surrounding fluid and in the presence of a fixed external surface. such as an adsorbate. The scaling and perturbation analysis given here also shows that the Force autocorrelation function must decay rapidly on the zeroth-order time scale tau(0), which physically requires N-Kn much less than 1, where N-Kn is the Knudsen number (ratio of the length scale for fluid intermolecular interactions to the Brownian particle length scale). This restricts the theory given here to liquid systems where N-Kn much less than 1. For a specified particle configuration with respect to the external surface, equilibrium canonical molecular dynamics (MD) calculations are conducted, as shown here, in order to obtain numerical values of the friction tensor from the force autocorrelation expression. Molecular dynamics computations of the friction tensor for a single spherical particle in the absence of a fixed external surface are shown to recover Stokes' law for various types of fluid molecule-particle interaction potentials. Analytical studies of the static force correlation function also demonstrate the remarkable principle of force-time parity whereby the particle friction coefficient is nearly independent of the fluid molecule-particle interaction potential. Molecular dynamics computations of the friction tensor for a single spherical particle near a fixed external spherical surface (adsorbate) demonstrate a breakdown in continuum hydrodynamic results at close particle surface separation distances on the order of several molecular diameters.},
        Author = {Peters, MH},
        Date-Added = {2008-03-13 16:54:59 -0400},
        Date-Modified = {2008-03-13 16:56:54 -0400},
        Journal = {Journal of Statistical Physics},
        Keywords = {Brownian particle; Fokker Planck equation; adsorption; molecular friction; force autocorrelation function; molecular dynamics},
        Pages = {557-586},
        Timescited = {0},
        Title = {Fokker-Planck equation, molecular friction, and molecular dynamics for Brownian particle transport near external solid surfaces},
        Volume = {94},
        Year = {1999}}

@article{Peters:1999qy,
        Abstract = {The Fokker-Planck equation and molecular-based grand friction tensor are derived for the problem of rotational and translational motions of a structured Brownian particle, including the presence of a structured wall. Using the method of multiple time scales, it is shown that the time independent, grand friction tensor for the Brownian particle includes, in a general way, terms that account fur the fluid molecular mediated interactions with the wall. The resulting Fokker-Planck equation has important applications in processes involving site-specific adsorption of macromolecules, such as affinity chromotography, biological separations, and numerous cellular processes involving attachment of macromolecules. (C) 1999 American Institute of Physics. [S0021-9606(98)51748-5].},
        Author = {Peters, MH},
        Date-Added = {2008-03-13 16:54:59 -0400},
        Date-Modified = {2008-03-13 16:56:44 -0400},
        Journal = jcp,
        Pages = {528-538},
        Timescited = {0},
        Title = {Fokker-Planck equation and the grand molecular friction tensor for coupled rotational and translational motions of structured Brownian particles near structured surfaces},
        Volume = {110},
        Year = {1999}}

@article{Peters:2000fk,
        Abstract = {Beginning with the molecular-based Fokker-Planck equation obtained previously [M. H. Peters, J. Chem. Phys. 110, 528 (1999); J. Stat. Phys. 94, 557 (1999)], the Smoluchowski diffusion equation is derived here to describe the spatial and orientational dynamics of molecularly structured macromolecules near molecularly structured surfaces. The formal scaling and perturbation methods employed allow the establishment of definite limits on the use of the Smoluchowski equation when surfaces are present. It is shown that the Smoluchowski equation reduces to that given previously [D. W. Condiff and J. S. Dahler, J. Chem. Phys. 44, 3988 (1966)] in the absence of external surfaces. A specific example application is given involving a spherical macromolecule with electrostatic charge segments near a planar surface with an arbitrary charge distribution. Finally, we show that the short-time solution to the Smoluchowski equation obtained here yields a Brownian dynamics method consistent with that given previously [E. Dickinson, S. A. Allison, and J. A. McCammon, J. Chem. Soc. Faraday Trans. 2 81, 591 (1985)] for orientable, interacting Brownian particles. This study has applications to problems involving site-specific adsorption of orientable, structured Brownian particles, such as association or adsorption of biological macromolecules to cellular surfaces and enzyme-substrate docking kinetics, to name a few. (C) 2000 American Institute of Physics. [S0021-9606(00)50112-3].},
        Author = {Peters, MH},
        Date-Added = {2008-03-13 16:54:59 -0400},
        Date-Modified = {2008-03-13 16:56:20 -0400},
        Journal = jcp,
        Pages = {5488-5498},
        Timescited = {0},
        Title = {The Smoluchowski diffusion equation for structured macromolecules near structured surfaces},
        Volume = {112},
        Year = {2000}}

@article{Nienhuis:1970lr,
        Abstract = { A quantummechanical system consisting of N light bath particles and one heavy Brownian linear rotator is considered. By employing the multiple time scale technique and the Wigner representation of quantummechanics, a Fokker-Planck equation for the motion of the Brownian particle is derived. Some properties of this equation are briefly discussed.},
        Author = {Nienhuis, G. },
        Date-Added = {2008-03-13 16:53:44 -0400},
        Date-Modified = {2008-03-13 16:53:44 -0400},
        Journal = {Physica},
        Number = {1},
        Pages = {26--48},
        Title = {On the microscopic theory of Brownian motion with a rotational degree of freedom},
        Ty = {JOUR},
        Url = {http://www.sciencedirect.com/science/article/B6X42-46D224N-BW/2/0e1b39b5a20e979c5fa5e1f560de6413},
        Volume = {49},
        Year = {1970},
        Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6X42-46D224N-BW/2/0e1b39b5a20e979c5fa5e1f560de6413}}

@article{SunX._jp0762020,
        Affiliation = {Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556},
        Author = {Sun, X. and Gezelter, J.D.},
        Date-Added = {2008-02-15 13:48:18 -0500},
        Date-Modified = {2008-02-15 13:48:18 -0500},
        Issn = {1520-6106},
        Journal = jpcb,
        Number = {7},
        Pages = {1968-1975},
        Title = {Dipolar Ordering in the Ripple Phases of Molecular-Scale Models of Lipid Membranes},
        Url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0762020},
        Volume = {112},
        Year = {2008},
        Bdsk-Url-1 = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/jp0762020}}

@book{Schlick2002,
        Address = {Secaucus, NJ, USA},
        Author = {Tamar Schlick},
        Date-Added = {2008-02-12 16:52:19 -0500},
        Date-Modified = {2008-02-12 16:53:15 -0500},
        Isbn = {038795404X},
        Publisher = {Springer-Verlag New York, Inc.},
        Title = {Molecular Modeling and Simulation: An Interdisciplinary Guide},
        Year = {2002}}

@article{Chun:2000fj,
        Abstract = {A modeling approach that can significantly speed up the dynamics simulation of large molecular systems is presented herein. A multigranular modeling approach, whereby different parts of the molecule are modeled at different levels of detail, is enabled by substructuring. Substructuring the molecular system is accomplished by collecting groups of atoms into rigid or flexible bodies. Body flexibility is modeled by a truncated set of body-based modes. This approach allows for the elimination of the high-frequency harmonic motion while capturing the low-frequency anharmonic motion of interest. This results in the use of larger integration step sizes, substantially reducing the computational time required for a given dynamic simulation. The method also includes the use of a multiple time scale (MTS) integration scheme. Speed increases of 5- to 30-fold over atomistic simulations have been realized in various applications of the method. (C) 2000 John Wiley \& Sons, Inc.},
        Author = {Chun, HM and Padilla, CE and Chin, DN and Watanabe, M and Karlov, VI and Alper, HE and Soosaar, K and Blair, KB and Becker, OM and Caves, LSD and Nagle, R and Haney, DN and Farmer, BL},
        Date-Added = {2008-01-22 10:38:33 -0500},
        Date-Modified = {2008-01-22 10:38:49 -0500},
        Keywords = {molecular dynamics; normal modes; anharmonicity; macromolecules; numerical integrators},
        Journal = jcc,
        Pages = {159--184},
        Timescited = 0,
        Title = {{MBO(N)D:} A multibody method for long-time molecular dynamics simulations},
        Volume = 21,
        Year = 2000}

@article{Fogolari:1996lr,
        Abstract = {In an effort to reduce the number of degrees of freedom necessary to describe a polypeptide chain we analyze the statistical behavior of polypeptide chains when represented as C alpha chains, C alpha chains with C beta atoms attached, and C alpha chains with rotational ellipsoids as models of side chains. A statistical analysis on a restricted data set of 75 unrelated protein structures is performed. The comparison of the database distributions with those obtained by model calculation on very short polypeptide stretches allows the dissection of local versus nonlocal features of the distributions. The database distribution of the bend angles of polypeptide chains of pseudo bonded C alpha atoms spans a restricted range of values and shows a bimodal structure. On the other hand, the torsion angles of the C alpha chain may assume almost all possible values. The distribution is bimodal, but with a much broader probability distribution than for bend angles. The C alpha - C beta vectors may be taken as representative of the orientation of the lateral chain, as the direction of the bond is close to the direction of the vector joining C alpha to the ad hoc defined center of the "steric mass" of the side chain. Interestingly, both the bend angle defined by C alpha i-C alpha i+1-C beta i+1 and the torsional angle offset of the pseudo-dihedral C alpha i-C alpha i+1-C alpha i+2-C beta i+2 with respect to C alpha i-C alpha i+1-C alpha i+2-C alpha i+3 span a limited range of values. The latter results show that it is possible to give a more realistic representation of polypeptide chains without introducing additional degrees of freedom, i.e., by just adding to the C alpha chain a C beta with given side-chain properties. However, a more realistic description of side chains may be attained by modeling side chains as rotational ellipsoids that have roughly the same orientation and steric hindrance. To this end, we define the steric mass of an atom as proportional to its van der Waals volume and we calculate the side-chain inertia ellipsoid assuming that the steric mass of each atom is uniformly distributed within its van der Waals volume. Finally, we define the rotational ellipsoid representing the side chain as the uniform density ellipsoid possessing the same rotationally averaged inertia tensor of the side chain. The statistics of ellipsoid parameters support the possibility of representing a side chain via an ellipsoid, independently of the local conformation. To make this description useful for molecular modeling we describe ellipsoid-ellipsoid interactions via a Lennard-Jones potential that preserves the repulsive core of the interacting ellipsoids and takes into account their mutual orientation. Tests are performed for two different forms of the interaction potential on a set of high-resolution protein structures. Results are encouraging, in view of the drastic simplifications that were introduced.},
        Address = {Dipartimento di Scienze e Tecnologie Biomediche, Universita di Udine, Italy.},
        Au = {Fogolari, F and Esposito, G and Viglino, P and Cattarinussi, S},
        Author = {Fogolari, F and Esposito, G and Viglino, P and Cattarinussi, S},
        Da = {19960924},
        Date-Added = {2008-01-22 10:19:04 -0500},
        Date-Modified = {2008-01-22 10:19:09 -0500},
        Dcom = {19960924},
        Edat = {1996/03/01},
        Issn = {0006-3495 (Print)},
        Jid = {0370626},
        Journal = {Biophys J},
        Jt = {Biophysical journal},
        Language = {eng},
        Lr = {20071115},
        Mh = {Amino Acids/chemistry; Biophysics; Carbon/chemistry; Databases, Factual; Evaluation Studies as Topic; *Models, Molecular; Molecular Structure; Peptides/*chemistry; *Protein Conformation; Software; Thermodynamics},
        Mhda = {1996/03/01 00:01},
        Number = {3},
        Own = {NLM},
        Pages = {1183--1197},
        Pl = {UNITED STATES},
        Pmid = {8785277},
        Pst = {ppublish},
        Pt = {Journal Article},
        Pubm = {Print},
        Rn = {0 (Amino Acids); 0 (Peptides); 7440-44-0 (Carbon)},
        Sb = {IM},
        So = {Biophys J. 1996 Mar;70(3):1183-97. },
        Stat = {MEDLINE},
        Title = {Modeling of polypeptide chains as C alpha chains, C alpha chains with C beta, and C alpha chains with ellipsoidal lateral chains.},
        Volume = {70},
        Year = {1996}}

@inbook{Ramachandran1996,
        Address = {Providence, Rhode Island},
        author = {Gomathi Ramachandran and Tamar Schlick},
        Chapter = {Beyond optimization: Simulating the dynamics of supercoiled DNA by a macroscopic model},
        Date-Added = {2008-01-22 10:03:42 -0500},
        Date-Modified = {2008-01-22 10:06:57 -0500},
        Editor = {P. M. Pardalos and D. Shalloway and G. Xue},
        Pages = {215-231},
        Publisher = {American Mathematical Society},
        Series = {DIMACS Series in Discrete Mathematics and Theoretical Computer Science},
        Title = {Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding},
        Volume = {23},
        Year = {1996}}

@article{FIXMAN:1986lr,
        Author = {Fixman, M},
        Date-Added = {2008-01-22 09:59:29 -0500},
        Date-Modified = {2008-01-22 09:59:35 -0500},
        Journal = {Macromolecules},
        Pages = {1204-1207},
        Timescited = {0},
        Title = {CONSTRUCTION OF LANGEVIN FORCES IN THE SIMULATION OF HYDRODYNAMIC INTERACTION},
        Volume = {19},
        Year = {1986}}

@article{Berendsen87,
        Author = {H.~J.~C. Berendsen and J.~R. Grigera and T.~P. Straatsma},
        Date-Added = {2008-01-22 09:53:15 -0500},
        Date-Modified = {2008-01-22 09:53:15 -0500},
        Journal = jpc,
        Pages = {6269-6271},
        Title = {The Missing Term in Effective Pair Potentials},
        Volume = 91,
        Year = 1987}

@incollection{Berendsen81,
        Address = {Dordrecht},
        Author = {H.~J.~C. Berendsen and J.~P.~M. Postma and W.~F. {van~Gunsteren} and J. Hermans},
        Booktitle = {Intermolecular Forces},
        Date-Added = {2008-01-22 09:52:49 -0500},
        Date-Modified = {2008-01-22 09:52:49 -0500},
        Editor = {B. Pullman},
        Pages = {331-342},
        Publisher = {Reidel},
        Title = {Simple Point Charge Water},
        Year = 1981}

@article{Stillinger74,
        Author = {F.~H. Stillinger and A. Rahman},
        Date-Added = {2008-01-22 09:51:43 -0500},
        Date-Modified = {2008-01-22 09:51:43 -0500},
        Journal = jcp,
        Number = 4,
        Pages = {1545-1557},
        Title = {Improved simulation of liquid water by molecular dynamics},
        Volume = 60,
        Year = 1974}

@article{Torre:1983lr,
        Author = {{Garc\'{i}a de la Torre}, Jose and Rodes, Vicente},
        Date-Added = {2008-01-11 16:16:43 -0500},
        Date-Modified = {2008-01-11 16:16:43 -0500},
        Journal = jcp,
        Journal1 = {The Journal of Chemical Physics},
        Journal2 = {J. Chem. Phys.},
        Keywords = {polymers; molecular models; hydrodynamics; rotation; interactions; macromolecules},
        Number = 5,
        Pages = {2454--2460},
        Publisher = {AIP},
        Title = {Effects from bead size and hydrodynamic interactions on the translational and rotational coefficients of macromolecular bead models},
        Ty = {JOUR},
        Url = {http://link.aip.org/link/?JCP/79/2454/1},
        Volume = 79,
        Year = 1983,
        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/79/2454/1}}

@article{PhysRev.119.53,
        Author = {Favro, L. Dale},
        Date-Added = {2008-01-09 16:57:02 -0500},
        Date-Modified = {2008-01-09 16:57:02 -0500},
        Doi = {10.1103/PhysRev.119.53},
        Journal = {Phys. Rev.},
        Month = {Jul},
        Number = 1,
        Numpages = 9,
        Pages = {53--62},
        Publisher = {American Physical Society},
        Title = {Theory of the Rotational Brownian Motion of a Free Rigid Body},
        Volume = 119,
        Year = 1960,
        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRev.119.53}}

@article{hess:209,
        Author = {Berk Hess},
        Date-Added = {2008-01-08 16:41:06 -0500},
        Date-Modified = {2008-01-08 16:41:06 -0500},
        Doi = {10.1063/1.1421362},
        Journal = jcp,
        Keywords = {viscosity; molecular dynamics method; liquid theory; shear flow},
        Number = 1,
        Pages = {209-217},
        Publisher = {AIP},
        Title = {Determining the shear viscosity of model liquids from molecular dynamics simulations},
        Url = {http://link.aip.org/link/?JCP/116/209/1},
        Volume = 116,
        Year = 2002,
        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/116/209/1},
        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.1421362}}

@article{Garcia-de-la-Torre:1997qy,
        Abstract = {Single-valued hydrodynamic coefficients of a rigid particle can be calculated from existing theories and computer programs for either bead models or ellipsoids. Starting from these coefficients, we review the procedures for the calculation of complex solution properties depending on rotational diffusion, such as the decays of electric birefringence and fluorescence anisotropy. We also describe the calculation of the scattering from factor of bead models. The hydrodynamic coefficients and solution properties can be combined to give universal, shape-dependent functions, which were initially intended for ellipsoidal particles, and are extended here for the most general case. We have implemented all three developments in a new computer program. SOLPRO, for calculation of SOLution PROperties, which can be linked to existing software for bead models or ellipsoids.},
        Address = {Departamento de Quimica Fisica Universidad de Murcia, Spain. jgt{\char64}fcu,um.es},
        Au = {{Garc\'{i}a de la Torre}, Jose and Carrasco, B and Harding, SE},
        Author = {{Garc\'{i}a de la Torre}, Jose and Carrasco, B and Harding, S E},
        Da = 19970709,
        Date-Added = {2008-01-08 15:45:31 -0500},
        Date-Modified = {2008-01-08 15:46:57 -0500},
        Dcom = 19970709,
        Edat = {1997/01/01},
        Issn = {0175-7571 (Print)},
        Jid = 8409413,
        Journal = {Eur Biophys J},
        Jt = {European biophysics journal : EBJ},
        Keywords = {Birefringence; Fluorescence Polarization; Humans; Immunoglobulin G/chemistry; Models, Structural; *Protein Conformation; Proteins/*chemistry; Scattering, Radiation; *Software; Ultracentrifugation/methods},
        Language = {eng},
        Lr = 20061115,
        Mhda = {1997/01/01 00:01},
        Number = {5-6},
        Own = {NLM},
        Pages = {361--372},
        Pl = {GERMANY},
        Pmid = 9213556,
        Pst = {ppublish},
        Pt = {Journal Article; Research Support, Non-U.S. Gov't},
        Pubm = {Print},
        Rn = {0 (Immunoglobulin G); 0 (Proteins)},
        Sb = {IM},
        So = {Eur Biophys J. 1997;25(5-6):361-72.},
        Stat = {MEDLINE},
        Title = {SOLPRO: theory and computer program for the prediction of SOLution PROperties of rigid macromolecules and bioparticles.},
        Volume = 25,
        Year = 1997}

@article{Ravichandran:1999fk,
        Abstract = {Detailed molecular dynamics simulations of the rotational and the translational motions of Gay-Berne ellipsoids in a sea of Lennard-Jones spheres have been carried out. It is found that while the translational motion of an ellipsoid is isotropic at low density, it becomes increasingly anisotropic with density until the ratio of the parallel to the perpendicular diffusion coefficients becomes nearly equal to the value of the aspect ratio at high density. The latter is in agreement with the prediction of Navier-Stokes hydrodynamics with slip boundary condition. The product of the translational diffusion coefficient and the rotational correlation time also attains a hydrodynamic-like density independent behavior only at high density. The reorientational correlation function becomes nonexponential at high density and low temperature where it also develops a slow decay. The perpendicular component of the velocity time correlation function exhibits a clear double minimum, only at high density, which becomes more pronounced as the aspect ratio is increased. (C) 1999 American Institute of Physics. [S0021-9606(99)51440-2].},
        Author = {Ravichandran, S and Bagchi, B},
        Date-Added = {2008-01-08 15:24:48 -0500},
        Date-Modified = {2008-01-08 15:25:41 -0500},
        Journal = jcp,
        Pages = {7505-7511},
        Title = {Anisotropic diffusion of nonspherical molecules in dense liquids: A molecular dynamics simulation of isolated ellipsoids in the sea of spheres},
        Volume = 111,
        Year = 1999}

@article{TANG:1993lr,
        Abstract = {Translational friction coefficients of hard prolate ellipsoids (having aspect ratios of 1-10) have been calculated by solving the linearized Navier-Stokes equations of hydrodynamics, using the method of Faxen's theorem. When the stick boundary condition was used, the present results reproduce the famous work of Lamb. The new information derived from this study arises from the analysis of the friction under the influence of the slip hydrodynamic boundary condition. It was found that the slip friction perpendicular to the long axis of the prolate ellipsoid increases monotonically with aspect ratio, whereas the parallel component of the friction decreases monotonically to an apparent limiting value. The ratio f(perpendicular to)/f(parallel to) of friction coefficients perpendicular and parallel to the long axis of the particle, calculated using slip hydrodynamics, scales roughly as the aspect ratio of the ellipsoid, in accord with the findings from an Enskog (uncorrelated binary collision) kinetic theory of hard ellipsoids and from the estimate derived from molecular dynamics. In contrast, f(perpendicular to)/f(parallel to) derived by means of stick hydrodynamics shows a weak dependence on the aspect ratio and disagrees with kinetic theory and molecular dynamics findings.},
        Author = {Tang, SA and Evans, GT},
        Date-Added = {2008-01-08 15:23:42 -0500},
        Date-Modified = {2008-01-08 15:24:09 -0500},
        Journal = mp,
        Pages = {1443-1457},
        Title = {A CRITIQUE OF SLIP AND STICK HYDRODYNAMICS FOR ELLIPSOIDAL BODIES},
        Volume = 80,
        Year = 1993}

@article{Schmidt:2003kx,
        Abstract = {Using molecular dynamics computer simulation, we have calculated the velocity autocorrelation function and diffusion constant for a spherical solute in a dense fluid of spherical solvent particles. The size and mass of the solute particle are related in such a way that we can naturally approach the Brownian limit (when the solute becomes much larger and more massive than the solvent particles). We find that as long as the solute radius is interpreted as an effective hydrodynamic radius, the Stokes-Einstein law with slip boundary conditions is satisfied as the Brownian limit is approached (specifically, when the solute is roughly 100 times more massive than the solvent particles). In contrast, the Stokes-Einstein law is not satisfied for a tagged particle of the neat solvent. We also find that in the Brownian limit the amplitude of the long-time tail of the solute's velocity autocorrelation function is in good agreement with theoretical hydrodynamic predictions. When the solvent density is substantially lower than the triple density, the Stokes-Einstein law is no longer satisfied, and the amplitude of the long-time tail is not in good agreement with theoretical predictions, signaling the breakdown of hydrodynamics. (C) 2003 American Institute of Physics.},
        Author = {Schmidt, JR and Skinner, JL},
        Date-Added = {2008-01-08 15:12:53 -0500},
        Date-Modified = {2008-01-08 15:13:21 -0500},
        Doi = {DOI 10.1063/1.1610442},
        Journal = jcp,
        Pages = {8062-8068},
        Title = {Hydrodynamic boundary conditions, the Stokes-Einstein law, and long-time tails in the Brownian limit},
        Volume = 119,
        Year = 2003,
        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.1610442}}

@article{Schmidt:2004fj,
        Abstract = {Using molecular dynamics computer simulation, we have calculated the velocity autocorrelation function and diffusion constant for a variety of solutes in a dense fluid of spherical solvent particles. We explore the effects of surface roughness of the solute on the resulting hydrodynamic boundary condition as we naturally approach the Brownian limit (when the solute becomes much larger and more massive than the solvent particles). We find that when the solute and solvent interact through a purely repulsive isotropic potential, in the Brownian limit the Stokes-Einstein law is satisfied with slip boundary conditions. However, when surface roughness is introduced through an anisotropic solute-solvent interaction potential, we find that the Stokes-Einstein law is satisfied with stick boundary conditions. In addition, when the attractive strength of a short-range isotropic solute-solvent potential is increased, the solute becomes dressed with solvent particles, making it effectively rough, and so stick boundary conditions are again recovered.},
        Author = {Schmidt, JR and Skinner, JL},
        Date-Added = {2008-01-08 15:12:53 -0500},
        Date-Modified = {2008-01-08 15:13:20 -0500},
        Doi = {DOI 10.1021/jp037185r},
        Journal = jpcb,
        Pages = {6767-6771},
        Title = {Brownian motion of a rough sphere and the Stokes-Einstein Law},
        Volume = 108,
        Year = 2004,
        Bdsk-Url-1 = {http://dx.doi.org/10.1021/jp037185r}}

@article{Klein01,
        Author = {J.~C. Shelley andf M.~Y. Shelley and R.~C. Reeder and S. Bandyopadhyay and M.~L. Klein},
        Date-Added = {2008-01-08 14:58:56 -0500},
        Date-Modified = {2008-01-08 14:58:56 -0500},
        Journal = {J. Phys. Chem. B},
        Pages = {4464-4470},
        Title = {A Coarse Grain Model for Phospholipid Simulations},
        Volume = 105,
        Year = 2001}

@article{Berardi98,
        Author = {R. Berardi and C. Fava and C. Zannoni},
        Date-Added = {2008-01-08 14:58:56 -0500},
        Date-Modified = {2008-01-08 14:58:56 -0500},
        Journal = cpl,
        Pages = {8-14},
        Title = {A Gay-Berne potential for dissimilar biaxial particles},
        Volume = 297,
        Year = 1998}

@article{Hura00,
        Author = {G. Hura and J.~M. Sorenson and R.~M. Glaeser and T. Head-Gordon},
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@article{Benninger:2005qy,
        Abstract = {The plasma membrane of cells is an ordered environment, giving rise to anisotropic orientation and restricted motion of molecules and proteins residing in the membrane. At the same time as being an organized matrix of defined structure, the cell membrane is heterogeneous and dynamic. Here we present a method where we use fluorescence imaging of linear dichroism to measure the orientation of molecules relative to the cell membrane. By detecting linear dichroism as well as fluorescence anisotropy, the orientation parameters are separated from dynamic properties such as rotational diffusion and homo energy transfer (energy migration). The sensitivity of the technique is enhanced by using two-photon excitation for higher photo-selection compared to single photon excitation. We show here that we can accurately image lipid organization in whole cell membranes and in delicate structures such as membrane nanotubes connecting two cells. The speed of our wide-field imaging system makes it possible to image changes in orientation and anisotropy occurring on a subsecond timescale. This is demonstrated by time-lapse studies showing that cholesterol depletion rapidly disrupts the orientation of a fluorophore located within the hydrophobic region of the cell membrane but not of a surface bound probe. This is consistent with cholesterol having an important role in stabilizing and ordering the lipid tails within the plasma membrane. },
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        Author = {Benninger, Richard K. P. and Onfelt, Bjorn and Neil, Mark A. A. and Davis, Daniel M. and French, Paul M. W.},
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        Title = {Fluorescence Imaging of Two-Photon Linear Dichroism: Cholesterol Depletion Disrupts Molecular Orientation in Cell Membranes},
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        Url = {http://www.biophysj.org/cgi/content/abstract/88/1/609},
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        Year = 2005,
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@article{NorbertKucerka04012005,
        Abstract = {Quantitative structures of the fully hydrated fluid phases of dimyristoylphosphatidylcholine (DMPC) and dilauroylphosphatidylcholine (DLPC) were obtained at 30{degrees}C. Data for the relative form factors F(qz) for DMPC were obtained using a combination of four methods. 1), Volumetric data provided F(0). 2), Diffuse x-ray scattering from oriented stacks of bilayers provided relative form factors |F(qz)| for high qz, 0.22 < qz < 0.8 A-1. 3), X-ray scattering from extruded unilamellar vesicles with diameter 600 A provided |F(qz)| for low qz, 0.1 < qz < 0.3 A-1. 4), Previous measurements using a liquid crystallographic x-ray method provided |F(2{pi}h/D)| for h = 1 and 2 for a range of nearly fully hydrated D-spacings. The data from method 4 overlap and validate the new unilamellar vesicles data for DMPC, so method 4 is not required for DLPC or future studies. We used hybrid electron density models to obtain structural results from these form factors. Comparison of the model electron density profiles with that of gel phase DMPC provides areas per lipid A, 60.6 {+/-} 0.5 A2 for DMPC and 63.2 {+/-} 0.5 A2 for DLPC. Constraints on the model provided by volume measurements and component volumes obtained from simulations put the electron density profiles {rho}(z) and the corresponding form factors F(qz) on absolute scales. Various thicknesses, such as the hydrophobic thickness and the steric thickness, are obtained and compared to literature values.
},
        Author = {Kucerka, Norbert and Liu, Yufeng and Chu, Nanjun and Petrache, Horia I. and Tristram-Nagle, Stephanie and Nagle, John F.},
        Date-Added = {2008-01-08 14:58:56 -0500},
        Date-Modified = {2008-01-08 14:59:02 -0500},
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        Pages = {2626-2637},
        Title = {{Structure of Fully Hydrated Fluid Phase DMPC and DLPC Lipid Bilayers Using X-Ray Scattering from Oriented Multilamellar Arrays and from Unilamellar Vesicles}},
        Url = {http://www.biophysj.org/cgi/content/abstract/88/4/2626},
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        Year = 2005,
        Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/88/4/2626},
        Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.104.056606}}

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        Journal = {Physik Z.},
        Number = {297-309},
        Title = {Uber Schwingungen in Raumgittern},
        Volume = 13,
        Year = 1912}

@incollection{Angell85,
        Address = {Springfield, VA},
        Author = {C.~A. Angell},
        Booktitle = {Relaxations in Complex Systems},
        Date-Added = {2008-01-08 14:58:56 -0500},
        Date-Modified = {2008-01-08 14:59:03 -0500},
        Editor = {K.~Ngai and G.~B. Wright},
        Pages = 1,
        Publisher = {National Technical Information Service, U.S. Department of Commerce},
        Title = {unknown},
        Year = 1985}

@article{Ribeiro98,
        Author = {M.~C.~C. Ribeiro and P.~A. Madden},
        Date-Added = {2008-01-08 14:58:56 -0500},
        Date-Modified = {2008-01-08 14:59:03 -0500},
        Journal = jcp,
        Pages = {3256-3263},
        Title = {Unstable Modes in Ionic Melts},
        Volume = 108,
        Year = 1998}

@article{Mutz1991,
        Author = {Mutz, M. and Bensimon, D. and Brienne, M. J.},
        Date-Added = {2008-01-08 14:58:56 -0500},
        Date-Modified = {2008-01-08 14:59:03 -0500},
        Doi = {10.1103/PhysRevLett.67.923},
        Journal = {Phys. Rev. Lett.},
        Month = {Aug},
        Number = 7,
        Numpages = 3,
        Pages = {923--926},
        Publisher = {American Physical Society},
        Title = {Wrinkling transition in partially polymerized vesicles},
        Volume = 67,
        Year = 1991,
        Bdsk-Url-1 = {http://dx.doi.org/10.1103/PhysRevLett.67.923}}

@article{Wendt78,
        Author = {H. Wendt and F.~F. Abraham},
        Date-Added = {2008-01-08 14:58:56 -0500},
        Date-Modified = {2008-01-08 14:59:03 -0500},
        Journal = prl,
        Pages = 1244,
        Volume = 41,
        Year = 1978}

@unpublished{Truhlar00,
        Author = {D.~G. Truhlar and A. Kohen},
        Date-Added = {2008-01-08 14:58:56 -0500},
        Date-Modified = {2008-01-08 14:59:03 -0500},
        Note = {private correspondence},
        Year = 2000}

@article{Dwyer1977,
        Author = {D.~J. Dwyer and G.~W. Simmons and R.~P. Wei},
        Date-Added = {2008-01-08 14:58:56 -0500},
        Date-Modified = {2008-01-08 14:59:03 -0500},
        Journal = {Surf. Sci.},
        Pages = 617,
        Volume = 64,
        Year = 1977}

@article{Macritche78,
        Author = {F. MacRitche},
        Date-Added = {2008-01-08 14:58:56 -0500},
        Date-Modified = {2008-01-08 14:59:03 -0500},
        Journal = {Adv. Protein Chem.},
        Pages = 283,
        Volume = 32,
        Year = 1978}

@article{Feder80,
        Author = {J. Feder},
        Date-Added = {2008-01-08 14:58:56 -0500},
        Date-Modified = {2008-01-08 14:59:03 -0500},
        Journal = {J. Theor. Biol.},
        Pages = 237,
        Volume = 87,
        Year = 1980}

@article{Ramsden93,
        Author = {J.~J. Ramsden},
        Date-Added = {2008-01-08 14:58:56 -0500},
        Date-Modified = {2008-01-08 14:59:03 -0500},
        Journal = prl,
        Pages = 295,
        Volume = 71,
        Year = 1993}

@article{Egelhoff89,
        Author = {W.~F. Egelhoff and I. Jacob},
        Date-Added = {2008-01-08 14:58:56 -0500},
        Date-Modified = {2008-01-08 14:59:03 -0500},
        Journal = prl,
        Pages = 921,
        Volume = 62,
        Year = 1989}

@article{Dobson1987,
        Author = {B.~W. Dobson},
        Date-Added = {2008-01-08 14:58:56 -0500},
        Date-Modified = {2008-01-08 14:59:03 -0500},
        Journal = prb,
        Pages = 1068,
        Volume = 36,
        Year = 1987}

@article{Davis:1969uq,
        Abstract = { Exact solutions of the Stokes equations are derived for the case of two unequal spheres slowly rotating or translating perpendicular to their line of centers in a quiescent, unbounded viscous fluid, following Wakiya[16]. Numerical results are presented for the force and torque coefficients for size ratios from 1[middle dot]0 to 10[middle dot]0, and separations down to 0[middle dot]001 times the radius of the smaller.},
        Author = {Davis, M. H.},
        Date-Added = {2008-01-08 14:57:14 -0500},
        Date-Modified = {2008-01-08 14:57:14 -0500},
        Journal = {Chemical Engineering Science},
        Number = 12,
        Pages = {1769--1776},
        Title = {The slow translation and rotation of two unequal spheres in a viscous fluid},
        Ty = {JOUR},
        Url = {http://www.sciencedirect.com/science/article/B6TFK-445H8BM-84/2/b34951283900cdde792ec1309ec51565},
        Volume = 24,
        Year = 1969,
        Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TFK-445H8BM-84/2/b34951283900cdde792ec1309ec51565}}

@article{Stimson:1926qy,
        Author = {Stimson, M and Jeffery, GB},
        Date-Added = {2008-01-08 14:51:23 -0500},
        Date-Modified = {2008-01-08 14:51:35 -0500},
        Journal = {Proceedings of the Royal Society of London Series A-Containing Papers of a Mathematical and Physical Character},
        Pages = {110-116},
        Title = {The motion of two spheres in a viscous fluid},
        Volume = 111,
        Year = 1926}

@article{Orlandi:2006fk,
        Abstract = {Liquid crystal phases formed by bent-shaped (or {\tt{}"{}}banana{\tt{}"{}}) molecules are currently of great interest. Here we investigate by Monte Carlo computer simulations the phases formed by rigid banana molecules modeled combining three Gay-Berne sites and containing either one central or two lateral and transversal dipoles. We show that changing the dipole position and orientation has a profound effect on the mesophase stability and molecular organization. In particular, we find a uniaxial nematic phase only for off-center dipolar models and tilted phases only for the one with terminal dipoles.},
        Address = {Dipartimento di Chimica Fisica e Inorganica, and INSTM, Universita di Bologna, Viale Risorgimento 4, 40136 Bologna, Italy.},
        Au = {Orlandi, S and Berardi, R and Steltzer, J and Zannoni, C},
        Author = {Orlandi, Silvia and Berardi, Roberto and Steltzer, Joachim and Zannoni, Claudio},
        Da = 20060407,
        Date-Added = {2008-01-08 14:47:56 -0500},
        Date-Modified = {2008-01-08 14:48:06 -0500},
        Dcom = 20070727,
        Doi = {10.1063/1.2176622},
        Edat = {2006/04/08 09:00},
        Issn = {0021-9606 (Print)},
        Jid = 0375360,
        Journal = {J Chem Phys},
        Jt = {The Journal of chemical physics},
        Language = {eng},
        Mhda = {2006/04/08 09:01},
        Number = 12,
        Own = {NLM},
        Pages = 124907,
        Pl = {United States},
        Pmid = 16599725,
        Pst = {ppublish},
        Pt = {Journal Article},
        Pubm = {Print},
        So = {J Chem Phys. 2006 Mar 28;124(12):124907.},
        Stat = {PubMed-not-MEDLINE},
        Title = {A Monte Carlo study of the mesophases formed by polar bent-shaped molecules.},
        Volume = 124,
        Year = 2006,
        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.2176622}}

@article{sun:031602,
        Author = {Xiuquan Sun and J. Daniel Gezelter},
        Date-Added = {2008-01-08 14:42:33 -0500},
        Date-Modified = {2008-01-08 14:42:33 -0500},
        Doi = {10.1103/PhysRevE.75.031602},
        Eid = 031602,
        Journal = {Physical Review E (Statistical, Nonlinear, and Soft Matter Physics)},
        Keywords = {lattice theory; membranes},
        Number = 3,
        Numpages = 7,
        Pages = 031602,
        Publisher = {APS},
        Title = {Spontaneous corrugation of dipolar membranes},
        Url = {http://link.aps.org/abstract/PRE/v75/e031602},
        Volume = 75,
        Year = 2007,
        Bdsk-Url-1 = {http://link.aps.org/abstract/PRE/v75/e031602},
        Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevE.75.031602}}

@article{Ortega:2007lr,
        Abstract = {The equivalent radius for any solution property is the radius of a spherical particle having the same value of solution property as that of the macromolecule under consideration. Equivalent radii for different properties present a dependence on size and shape that are more similar than the values of the properties themselves. Furthermore, the ratios of equivalent radii of two properties depend on the conformation (shape or flexibility), but not on the absolute sizes. We define equivalent radii and their ratios, and describe their evaluation for some common models of rigid and flexible macromolecules. Using radii and ratios, we have devised procedures to fit macromolecular models to experimental properties, allowing the determination of the model parameters. Using these quantities, we can construct target functions for an equilibrated, unbiased optimization. The procedures, which have been implemented in public-domain computer programs, are illustrated for rigid, globular proteins, and the rodlike tobacco mosaic virus, and for semiflexible, wormlike heparin molecules.},
        Address = {Departamento de Quimica Fisica, Facultad de Quimica, Universidad de Murcia, 30071 Murcia, Spain.},
        Au = {Ortega, A and {Garc\'{i}a de la Torre}, Jose},
        Author = {Ortega, A and {Garc\'{i}a de la Torre}, Jose},
        Da = 20070813,
        Date-Added = {2008-01-08 14:38:03 -0500},
        Date-Modified = {2008-01-08 14:38:49 -0500},
        Dcom = 20071017,
        Dep = 20070724,
        Doi = {10.1021/bm700473f},
        Edat = {2007/07/25 09:00},
        Issn = {1525-7797 (Print)},
        Jid = 100892849,
        Journal = {Biomacromolecules},
        Jt = {Biomacromolecules},
        Keywords = {Computer Simulation; Heparin/chemistry; Macromolecular Substances/*chemistry; *Models, Chemical; *Models, Molecular; Molecular Conformation; Particle Size; Protein Conformation; Proteins/chemistry; Software; Solutions},
        Language = {eng},
        Mhda = {2007/10/18 09:00},
        Number = 8,
        Own = {NLM},
        Pages = {2464--2475},
        Phst = {2007/07/24 {$[$}aheadofprint{$]$}},
        Pl = {United States},
        Pmid = 17645309,
        Pst = {ppublish},
        Pt = {Journal Article; Research Support, Non-U.S. Gov't},
        Pubm = {Print-Electronic},
        Rn = {0 (Macromolecular Substances); 0 (Proteins); 0 (Solutions); 9005-49-6 (Heparin)},
        Sb = {IM},
        So = {Biomacromolecules. 2007 Aug;8(8):2464-75. Epub 2007 Jul 24.},
        Stat = {MEDLINE},
        Title = {Equivalent radii and ratios of radii from solution properties as indicators of macromolecular conformation, shape, and flexibility.},
        Volume = 8,
        Year = 2007,
        Bdsk-Url-1 = {http://dx.doi.org/10.1021/bm700473f}}

@article{Torre2003,
        Abstract = {While the prediction of hydrodynamic properties of rigid particles
    is nowadays feasible using simple and efficient computer programs,
    the calculation of such properties and, in general, the dynamic
    behavior of flexible macromolecules has not reached a similar situation.
    Although the theories are available, usually the computational work
    is done using solutions specific for each problem. We intend to
    develop computer programs that would greatly facilitate the task
    of predicting solution behavior of flexible macromolecules. In this
    paper, we first present an overview of the two approaches that are
    most practical: the Monte Carlo rigid-body treatment, and the Brownian
    dynamics simulation technique. The Monte Carlo procedure is based
    on the calculation of properties for instantaneous conformations
    of the macromolecule that are regarded as if they were instantaneously
    rigid. We describe how a Monte Carlo program can be interfaced to
    the programs in the HYDRO suite for rigid particles, and provide
    an example of such calculation, for a hypothetical particle: a protein
    with two domains connected by a flexible linker. We also describe
    briefly the essentials of Brownian dynamics, and propose a general
    mechanical model that includes several kinds of intramolecular interactions,
    such as bending, internal rotation, excluded volume effects, etc.
    We provide an example of the application of this methodology to
    the dynamics of a semiflexible, wormlike DNA.},
        Annote = {724XK Times Cited:6 Cited References Count:64},
        Author = {{Garc\'{i}a de la Torre}, Jose and H. E. Sanchez and A. Ortega and J. G. Hernandez and M. X. Fernandes and F. G. Diaz and M. C. L. Martinez},
        Issn = {0175-7571},
        Journal = {European Biophysics Journal with Biophysics Letters},
        Month = {Aug},
        Number = 5,
        Pages = {477-486},
        Title = {Calculation of the solution properties of flexible macromolecules: methods and applications},
        Uri = {<Go to ISI>://000185513400011},
        Volume = 32,
        Year = 2003}

@article{Alakent2005,
        Abstract = {Time series analysis tools are employed on the principal modes obtained
    from the C-alpha trajectories from two independent molecular-dynamics
    simulations of alpha-amylase inhibitor (tendamistat). Fluctuations
    inside an energy minimum (intraminimum motions), transitions between
    minima (interminimum motions), and relaxations in different hierarchical
    energy levels are investigated and compared with those encountered
    in vacuum by using different sampling window sizes and intervals.
    The low-frequency low-indexed mode relationship, established in
    vacuum, is also encountered in water, which shows the reliability
    of the important dynamics information offered by principal components
    analysis in water. It has been shown that examining a short data
    collection period (100 ps) may result in a high population of overdamped
    modes, while some of the low-frequency oscillations (< 10 cm(-1))
    can be captured in water by using a longer data collection period
    (1200 ps). Simultaneous analysis of short and long sampling window
    sizes gives the following picture of the effect of water on protein
    dynamics. Water makes the protein lose its memory: future conformations
    are less dependent on previous conformations due to the lowering
    of energy barriers in hierarchical levels of the energy landscape.
    In short-time dynamics (< 10 ps), damping factors extracted from
    time series model parameters are lowered. For tendamistat, the friction
    coefficient in the Langevin equation is found to be around 40-60
    cm(-1) for the low-indexed modes, compatible with literature. The
    fact that water has increased the friction and that on the other
    hand has lubrication effect at first sight contradicts. However,
    this comes about because water enhances the transitions between
    minima and forces the protein to reduce its already inherent inability
    to maintain oscillations observed in vacuum. Some of the frequencies
    lower than 10 cm(-1) are found to be overdamped, while those higher
    than 20 cm(-1) are slightly increased. As for the long-time dynamics
    in water, it is found that random-walk motion is maintained for
    approximately 200 ps (about five times of that in vacuum) in the
    low-indexed modes, showing the lowering of energy barriers between
    the higher-level minima.},
        Annote = {973OH Times Cited:1 Cited References Count:33},
        Author = {B. Alakent and M. C. Camurdan and P. Doruker},
        Issn = {0021-9606},
        Journal = jcp,
        Month = {Oct 8},
        Number = 14,
        Pages = {-},
        Title = {Hierarchical structure of the energy landscape of proteins revisited by time series analysis. II. Investigation of explicit solvent effects},
        Uri = {<Go to ISI>://000232532000064},
        Volume = 123,
        Year = 2005}

@book{Alexander1987,
        Address = {New York},
        Author = {C. Alexander},
        Publisher = {Oxford University Press},
        Title = {A Pattern Language: Towns, Buildings, Construction},
        Year = 1987}

@book{Allen1987,
        Address = {New York},
        Author = {M.~P. Allen and D.~J. Tildesley},
        Publisher = {Oxford University Press},
        Title = {Computer Simulations of Liquids},
        Year = 1987}

@article{Allison1991,
        Abstract = {A Brownian dynamics algorithm is developed to simulate dynamics experiments
    of rigid macromolecules. It is applied to polarized dynamic light
    scattering from rodlike sturctures and from a model of a DNA fragment
    (762 base pairs). A number of rod cases are examined in which the
    translational anisotropy is increased form zero to a large value.
    Simulated first cumulants as well as amplitudes and lifetimes of
    the dynamic form factor are compared with predictions of analytic
    theories and found to be in very good agreement with them. For DNA
    fragments 762 base pairs in length or longer, translational anisotropy
    does not contribute significantly to dynamic light scattering. In
    a comparison of rigid and flexible simulations on semistiff models
    of this fragment, it is shown directly that flexing contributes
    to the faster decay processes probed by light scattering and that
    the flexible model studies are in good agreement with experiment.},
        Annote = {Eu814 Times Cited:8 Cited References Count:32},
        Author = {S. A. Allison},
        Issn = {0024-9297},
        Journal = {Macromolecules},
        Month = {Jan 21},
        Number = 2,
        Pages = {530-536},
        Title = {A Brownian Dynamics Algorithm for Arbitrary Rigid Bodies - Application to Polarized Dynamic Light-Scattering},
        Uri = {<Go to ISI>://A1991EU81400029},
        Volume = 24,
        Year = 1991}

@article{Andersen1983,
        Annote = {Rq238 Times Cited:559 Cited References Count:14},
        Author = {H. C. Andersen},
        Issn = {0021-9991},
        Journal = jcop,
        Number = 1,
        Pages = {24-34},
        Title = {Rattle - a Velocity Version of the Shake Algorithm for Molecular-Dynamics Calculations},
        Uri = {<Go to ISI>://A1983RQ23800002},
        Volume = 52,
        Year = 1983}

@article{Auerbach2005,
        Abstract = {Acetylcholine receptor channels (AChRs) are proteins that switch between
    stable #closed# and #open# conformations. In patch clamp recordings,
    diliganded AChR gating appears to be a simple, two-state reaction.
    However, mutagenesis studies indicate that during gating dozens
    of residues across the protein move asynchronously and are organized
    into rigid body gating domains (#blocks#). Moreover, there is an
    upper limit to the apparent channel opening rate constant. These
    observations suggest that the gating reaction has a broad, corrugated
    transition state region, with the maximum opening rate reflecting,
    in part, the mean first-passage time across this ensemble. Simulations
    reveal that a flat, isotropic energy profile for the transition
    state can account for many of the essential features of AChR gating.
    With this mechanism, concerted, local structural transitions that
    occur on the broad transition state ensemble give rise to fractional
    measures of reaction progress (Phi values) determined by rate-equilibrium
    free energy relationship analysis. The results suggest that the
    coarse-grained AChR gating conformational change propagates through
    the protein with dynamics that are governed by the Brownian motion
    of individual gating blocks.},
        Annote = {895QF Times Cited:9 Cited References Count:33},
        Author = {A. Auerbach},
        Issn = {0027-8424},
        Journal = pnas,
        Month = {Feb 1},
        Number = 5,
        Pages = {1408-1412},
        Title = {Gating of acetylcholine receptor channels: Brownian motion across a broad transition state},
        Uri = {<Go to ISI>://000226877300030},
        Volume = 102,
        Year = 2005}

@article{Baber1995,
        Abstract = {The effect of the general anesthetics halothane, enflurane, and isoflurane
    on hydrocarbon chain packing in palmitoyl(d(31))oleoylphosphatidylcholine
    membranes in the liquid crystalline phase was investigated using
    H-2 NMR. Upon the addition of the anesthetics, the first five methylene
    units near the interface generally show a very small increase in
    segmental order, while segments deeper within the bilayer show a
    small decrease in segmental order. From the H-2 NMR results, the
    chain length for the perdeuterated palmitoyl chain in the absence
    of anesthetic was found to be 12.35 Angstrom. Upon the addition
    of halothane enflurane, or isoflurane, the acyl chain undergoes
    slight contractions of 0.11, 0.20, or 0.16 Angstrom, respectively,
    at 50 mol % anesthetic. A simple model was used to estimate the
    relative amounts of anesthetic located near the interface and deeper
    in the bilayer hydrocarbon region, and only a slight preference
    for an interfacial location was observed. Intermolecular H-1-H-1
    nuclear Overhauser effects (NOEs) were measured between phospholipid
    and halothane protons. These NOEs are consistent with the intramembrane
    location of the anesthetics suggested by the H-2 NMR data. In addition,
    the NOE data indicate that anesthetics prefer the interfacial and
    hydrocarbon regions of the membrane and are not found in high concentrations
    in the phospholipid headgroup.},
        Annote = {Qz716 Times Cited:38 Cited References Count:37},
        Author = {J. Baber and J. F. Ellena and D. S. Cafiso},
        Issn = {0006-2960},
        Journal = {Biochemistry},
        Month = {May 16},
        Number = 19,
        Pages = {6533-6539},
        Title = {Distribution of General-Anesthetics in Phospholipid-Bilayers Determined Using H-2 Nmr and H-1-H-1 Noe Spectroscopy},
        Uri = {<Go to ISI>://A1995QZ71600035},
        Volume = 34,
        Year = 1995}

@article{Banerjee2004,
        Abstract = {Based on a coherent state representation of noise operator and an
    ensemble averaging procedure using Wigner canonical thermal distribution
    for harmonic oscillators, a generalized quantum Langevin equation
    has been recently developed [Phys. Rev. E 65, 021109 (2002); 66,
    051106 (2002)] to derive the equations of motion for probability
    distribution functions in c-number phase-space. We extend the treatment
    to explore several systematic approximation schemes for the solutions
    of the Langevin equation for nonlinear potentials for a wide range
    of noise correlation, strength and temperature down to the vacuum
    limit. The method is exemplified by an analytic application to harmonic
    oscillator for arbitrary memory kernel and with the help of a numerical
    calculation of barrier crossing, in a cubic potential to demonstrate
    the quantum Kramers' turnover and the quantum Arrhenius plot. (C)
    2004 American Institute of Physics.},
        Annote = {816YY Times Cited:8 Cited References Count:35},
        Author = {D. Banerjee and B. C. Bag and S. K. Banik and D. S. Ray},
        Issn = {0021-9606},
        Journal = jcp,
        Month = {May 15},
        Number = 19,
        Pages = {8960-8972},
        Title = {Solution of quantum Langevin equation: Approximations, theoretical and numerical aspects},
        Uri = {<Go to ISI>://000221146400009},
        Volume = 120,
        Year = 2004}

@article{Barojas1973,
        Author = {J. Barojas and D. Levesque},
        Journal = {Phys. Rev. A},
        Pages = {1092-1105},
        Title = {Simulation of Diatomic Homonuclear Liquids},
        Volume = 7,
        Year = 1973}

@article{Barth1998,
        Abstract = {We present an efficient new method termed LN for propagating biomolecular
    dynamics according to the Langevin equation that arose fortuitously
    upon analysis of the range of harmonic validity of our normal-mode
    scheme LIN. LN combines force linearization with force splitting
    techniques and disposes of LIN'S computationally intensive minimization
    (anharmonic correction) component. Unlike the competitive multiple-timestepping
    (MTS) schemes today-formulated to be symplectic and time-reversible-LN
    merges the slow and fast forces via extrapolation rather than impulses;
    the Langevin heat bath prevents systematic energy drifts. This combination
    succeeds in achieving more significant speedups than these MTS methods
    which are Limited by resonance artifacts to an outer timestep less
    than some integer multiple of half the period of the fastest motion
    (around 4-5 fs for biomolecules). We show that LN achieves very
    good agreement with small-timestep solutions of the Langevin equation
    in terms of thermodynamics (energy means and variances), geometry,
    and dynamics (spectral densities) for two proteins in vacuum and
    a large water system. Significantly, the frequency of updating the
    slow forces extends to 48 fs or more, resulting in speedup factors
    exceeding 10. The implementation of LN in any program that employs
    force-splitting computations is straightforward, with only partial
    second-derivative information required, as well as sparse Hessian/vector
    multiplication routines. The linearization part of LN could even
    be replaced by direct evaluation of the fast components. The application
    of LN to biomolecular dynamics is well suited for configurational
    sampling, thermodynamic, and structural questions. (C) 1998 American
    Institute of Physics.},
        Annote = {105HH Times Cited:29 Cited References Count:49},
        Author = {E. Barth and T. Schlick},
        Issn = {0021-9606},
        Journal = jcp,
        Month = {Aug 1},
        Number = 5,
        Pages = {1617-1632},
        Title = {Overcoming stability limitations in biomolecular dynamics. I. Combining force splitting via extrapolation with Langevin dynamics in LN},
        Uri = {<Go to ISI>://000075066300006},
        Volume = 109,
        Year = 1998}

@article{Batcho2001,
        Abstract = {We present an analysis for a simple two-component harmonic oscillator
    that compares the use of position-Verlet to velocity-Verlet for
    multiple-time step integration. The numerical stability analysis
    based on the impulse-Verlet splitting shows that position-Verlet
    has enhanced stability, in terms of the largest allowable time step,
    for cases where an ample separation of time scales exists. Numerical
    investigations confirm the advantages of the position-Verlet scheme
    when used for the fastest time scales of the system. Applications
    to a biomolecule. a solvated protein, for both Newtonian and Langevin
    dynamics echo these trends over large outer time-step regimes. (C)
    2001 American Institute of Physics.},
        Annote = {469KV Times Cited:6 Cited References Count:30},
        Author = {P. F. Batcho and T. Schlick},
        Issn = {0021-9606},
        Journal = jcp,
        Month = {Sep 1},
        Number = 9,
        Pages = {4019-4029},
        Title = {Special stability advantages of position-Verlet over velocity-Verlet in multiple-time step integration},
        Uri = {<Go to ISI>://000170813800005},
        Volume = 115,
        Year = 2001}

@article{Bates2005,
        Abstract = {Inspired by recent claims that compounds composed of V-shaped molecules
    can exhibit the elusive biaxial nematic phase, we have developed
    a generic simulation model for such systems. This contains the features
    of the molecule that are essential to its liquid crystal behavior,
    namely the anisotropies of the two arms and the angle between them.
    The behavior of the model has been investigated using Monte Carlo
    simulations for a wide range of these structural parameters. This
    allows us to establish the relationship between the V-shaped molecule
    and its ability to form a biaxial nematic phase. Of particular importance
    are the criteria of geometry and the relative anisotropy necessary
    for the system to exhibit a Landau point, at which the biaxial nematic
    is formed directly from the isotropic phase. The simulations have
    also been used to determine the orientational order parameters for
    a selection of molecular axes. These are especially important because
    they reveal the phase symmetry and are connected to the experimental
    determination of this. The simulation results show that, whereas
    some positions are extremely sensitive to the phase biaxiality,
    others are totally blind to this.},
        Annote = {Part 1 988LQ Times Cited:0 Cited References Count:38},
        Author = {M. A. Bates and G. R. Luckhurst},
        Issn = {1539-3755},
        Journal = {Physical Review E},
        Month = {Nov},
        Number = 5,
        Pages = {-},
        Title = {Biaxial nematic phases and V-shaped molecules: A Monte Carlo simulation study},
        Uri = {<Go to ISI>://000233603100030},
        Volume = 72,
        Year = 2005}

@article{Beard2003,
        Abstract = {We introduce an unbiased protocol for performing rotational moves
    in rigid-body dynamics simulations. This approach - based on the
    analytic solution for the rotational equations of motion for an
    orthogonal coordinate system at constant angular velocity - removes
    deficiencies that have been largely ignored in Brownian dynamics
    simulations, namely errors for finite rotations that result from
    applying the noncommuting rotational matrices in an arbitrary order.
    Our algorithm should thus replace standard approaches to rotate
    local coordinate frames in Langevin and Brownian dynamics simulations.},
        Annote = {736UA Times Cited:0 Cited References Count:11},
        Author = {D. A. Beard and T. Schlick},
        Issn = {0006-3495},
        Journal = bj,
        Month = {Nov 1},
        Number = 5,
        Pages = {2973-2976},
        Title = {Unbiased rotational moves for rigid-body dynamics},
        Uri = {<Go to ISI>://000186190500018},
        Volume = 85,
        Year = 2003}

@article{Beloborodov1998,
        Abstract = {Using the Green function of arbitrary rigid Brownian diffusion (Goldstein,
    Biopolymers 33, 409-436, 1993), it was analytically shown that coupling
    between translation and rotation diffusion degrees of freedom does
    not affect the correlation functions relevant to the NMR intramolecular
    relaxation. It follows that spectral densities usually used for
    the anisotropic rotation diffusion (Woessner, J. Chem. Phys. 37,
    647-654, 1962) can be regarded as exact in respect to the rotation-translation
    coupling for the spin system connected with a rigid body. (C) 1998
    Academic Press.},
        Annote = {Zu605 Times Cited:2 Cited References Count:6},
        Author = {I. S. Beloborodov and V. Y. Orekhov and A. S. Arseniev},
        Issn = {1090-7807},
        Journal = {Journal of Magnetic Resonance},
        Month = {Jun},
        Number = 2,
        Pages = {328-329},
        Title = {Effect of coupling between rotational and translational Brownian motions on NMR spin relaxation: Consideration using green function of rigid body diffusion},
        Uri = {<Go to ISI>://000074214800017},
        Volume = 132,
        Year = 1998}

@article{Berardi1996,
        Abstract = {We demonstrate that the overall molecular dipole organization in a
    smectic liquid crystal formed of polar molecules can be strongly
    influenced by the position of the dipole in the molecule. We study
    by large scale Monte Carlo simulations systems of attractive-repulsive
    ''Gay-Berne'' elongated ellipsoids with an axial dipole at the center
    or near the end of the molecule and we show that monolayer smectic
    liquid crystals and modulated antiferroelectric bilayer stripe domains
    similar to the experimentally observed ''antiphase'' structures
    are obtained in the two cases.},
        Annote = {Vn637 Times Cited:49 Cited References Count:26},
        Author = {R. Berardi and S. Orlandi and C. Zannoni},
        Issn = {0009-2614},
        Journal = {Chemical Physics Letters},
        Month = {Oct 18},
        Number = 3,
        Pages = {357-362},
        Title = {Antiphase structures in polar smectic liquid crystals and their molecular origin},
        Uri = {<Go to ISI>://A1996VN63700023},
        Volume = 261,
        Year = 1996}

@article{Berkov2005,
        Abstract = {In this paper a detailed numerical study (in frames of the Slonczewski
    formalism) of magnetization oscillations driven by a spin-polarized
    current through a thin elliptical nanoelement is presented. We show
    that a sophisticated micromagnetic model, where a polycrystalline
    structure of a nanoelement is taken into account, can explain qualitatively
    all most important features of the magnetization oscillation spectra
    recently observed experimentally [S. I. Kiselev , Nature 425, 380
    (2003)], namely, existence of several equidistant spectral bands,
    sharp onset and abrupt disappearance of magnetization oscillations
    with increasing current, absence of the out-of-plane regime predicted
    by a macrospin model, and the relation between frequencies of so-called
    small-angle and quasichaotic oscillations. However, a quantitative
    agreement with experimental results (especially concerning the frequency
    of quasichaotic oscillations) could not be achieved in the region
    of reasonable parameter values, indicating that further model refinement
    is necessary for a complete understanding of the spin-driven magnetization
    precession even in this relatively simple experimental situation.},
        Annote = {969IT Times Cited:2 Cited References Count:55},
        Author = {D. V. Berkov and N. L. Gorn},
        Issn = {1098-0121},
        Journal = {Physical Review B},
        Month = {Sep},
        Number = 9,
        Pages = {-},
        Title = {Magnetization precession due to a spin-polarized current in a thin nanoelement: Numerical simulation study},
        Uri = {<Go to ISI>://000232228500058},
        Volume = 72,
        Year = 2005}

@article{Berkov2005a,
        Abstract = {Numerical simulations of fast remagnetization processes using stochastic
    dynamics are widely used to study various magnetic systems. In this
    paper, we first address several crucial methodological problems
    of such simulations: (i) the influence of finite-element discretization
    on simulated dynamics, (ii) choice between Ito and Stratonovich
    stochastic calculi by the solution of micromagnetic stochastic equations
    of motion and (iii) non-trivial correlation properties of the random
    (thermal) field. Next, we discuss several examples to demonstrate
    the great potential of the Langevin dynamics for studying fast remagnetization
    processes in technically relevant applications: we present numerical
    analysis of equilibrium magnon spectra in patterned structures,
    study thermal noise effects on the magnetization dynamics of nanoelements
    in pulsed fields and show some results for a remagnetization dynamics
    induced by a spin-polarized current. (c) 2004 Elsevier B.V. All
    rights reserved.},
        Annote = {Part 1 Sp. Iss. SI 922KU Times Cited:2 Cited References Count:25},
        Author = {D. V. Berkov and N. L. Gorn},
        Issn = {0304-8853},
        Journal = {Journal of Magnetism and Magnetic Materials},
        Month = {Apr},
        Pages = {442-448},
        Title = {Stochastic dynamic simulations of fast remagnetization processes: recent advances and applications},
        Uri = {<Go to ISI>://000228837600109},
        Volume = 290,
        Year = 2005}

@article{Berkov2002,
        Abstract = {We report on recent progress achieved by the development of numerical
    methods based on the stochastic (Langevin) dynamics applied to systems
    of interacting magnetic nanoparticles. The method enables direct
    simulations of the trajectories of magnetic moments taking into
    account (i) all relevant interactions, (ii) precession dynamics,
    and (iii) temperature fluctuations included via the random (thermal)
    field. We present several novel results obtained using new methods
    developed for the solution of the Langevin equations. In particular,
    we have investigated magnetic nanodots and disordered granular systems
    of single-domain magnetic particles. For the first case we have
    calculated the spectrum and the spatial distribution of spin excitations.
    For the second system the complex ac susceptibility chi(omega, T)
    for various particle concentrations and particle anisotropies were
    computed and compared with numerous experimental results.},
        Annote = {526TF Times Cited:4 Cited References Count:37},
        Author = {D. V. Berkov and N. L. Gorn and P. Gornert},
        Issn = {0031-8965},
        Journal = {Physica Status Solidi a-Applied Research},
        Month = {Feb 16},
        Number = 2,
        Pages = {409-421},
        Title = {Magnetization dynamics in nanoparticle systems: Numerical simulation using Langevin dynamics},
        Uri = {<Go to ISI>://000174145200026},
        Volume = 189,
        Year = 2002}

@article{Bernal1980,
        Author = {J.M. Bernal and {Garc\'{i}a de la Torre}, Jose},
        Journal = {Biopolymers},
        Pages = {751-766},
        Title = {Transport Properties and Hydrodynamic Centers of Rigid Macromolecules with Arbitrary Shape},
        Volume = 19,
        Year = 1980}

@article{Brenner1967,
        Author = {H. Brenner},
        Journal = {J. Collid. Int. Sci.},
        Pages = {407-436},
        Title = {Coupling between the Translational and Rotational Brownian Motions of Rigid Particles of Arbitrary shape},
        Volume = 23,
        Year = 1967}

@article{Brooks1983,
        Annote = {Qp423 Times Cited:6414 Cited References Count:96},
        Author = {B. R. Brooks and R. E. Bruccoleri and B. D. Olafson and D. J. States and S. Swaminathan and M. Karplus},
        Issn = {0192-8651},
        Journal = jcc,
        Number = 2,
        Pages = {187-217},
        Title = {Charmm - a Program for Macromolecular Energy, Minimization, and Dynamics Calculations},
        Uri = {<Go to ISI>://A1983QP42300010},
        Volume = 4,
        Year = 1983}

@article{Brunger1984,
        Annote = {Sm173 Times Cited:143 Cited References Count:22},
        Author = {A. Brunger and C. L. Brooks and M. Karplus},
        Issn = {0009-2614},
        Journal = {Chemical Physics Letters},
        Number = 5,
        Pages = {495-500},
        Title = {Stochastic Boundary-Conditions for Molecular-Dynamics Simulations of St2 Water},
        Uri = {<Go to ISI>://A1984SM17300007},
        Volume = 105,
        Year = 1984}

@article{Budd1999,
        Abstract = {This paper examines a synthesis of adaptive mesh methods with the
    use of symmetry to study a partial differential equation. In particular,
    it considers methods which admit discrete self-similar solutions,
    examining the convergence of these to the true self-similar solution
    as well as their stability. Special attention is given to the nonlinear
    diffusion equation describing flow in a porous medium.},
        Annote = {199EE Times Cited:4 Cited References Count:14},
        Author = {C. J. Budd and G. J. Collins and W. Z. Huang and R. D. Russell},
        Issn = {1364-503X},
        Journal = {Philosophical Transactions of the Royal Society of London Series a-Mathematical Physical and Engineering Sciences},
        Month = {Apr 15},
        Number = 1754,
        Pages = {1047-1077},
        Title = {Self-similar numerical solutions of the porous-medium equation using moving mesh methods},
        Uri = {<Go to ISI>://000080466800005},
        Volume = 357,
        Year = 1999}

@article{Camp1999,
        Abstract = {Fluids of hard bent-core molecules have been studied using theory
    and computer simulation. The molecules are composed of two hard
    spherocylinders, with length-to-breadth ratio L/D, joined by their
    ends at an angle 180 degrees - gamma. For L/D = 2 and gamma = 0,10,20
    degrees, the simulations show isotropic, nematic, smectic, and solid
    phases. For L/D = 2 and gamma = 30 degrees, only isotropic, nematic,
    and solid phases are in evidence, which suggests that there is a
    nematic-smectic-solid triple point at an angle in the range 20 degrees
    < gamma < 30 degrees. In all of the orientationally ordered fluid
    phases the order is purely uniaxial. For gamma = 10 degrees and
    20 degrees, at the studied densities, the solid is also uniaxially
    ordered, whilst for gamma = 30 degrees the solid layers are biaxially
    ordered. For L/D = 2 and gamma = 60 degrees and 90 degrees we find
    no spontaneous orientational ordering. This is shown to be due to
    the interlocking of dimer pairs which precludes alignment. We find
    similar results for L/D = 9.5 and gamma = 72 degrees, where an isotropic-biaxial
    nematic transition is predicted by Onsager theory. Simulations in
    the biaxial nematic phase show it to be at least mechanically stable
    with respect to the isotropic phase, however. We have compared the
    quasi-exact simulation results in the isotropic phase with the predicted
    equations of state from three theories: the virial expansion containing
    the second and third virial coefficients; the Parsons-Lee equation
    of state; an application of Wertheim's theory of associating fluids
    in the limit of infinite attractive association energy. For all
    of the molecule elongations and geometries we have simulated, the
    Wertheim theory proved to be the most accurate. Interestingly, the
    isotropic equation of state is virtually independent of the dimer
    bond angle-a feature that is also reflected in the lack of variation
    with angle of the calculated second and third virial coefficients.
    (C) 1999 American Institute of Physics. [S0021-9606(99)50445-5].},
        Annote = {255TC Times Cited:24 Cited References Count:38},
        Author = {P. J. Camp and M. P. Allen and A. J. Masters},
        Issn = {0021-9606},
        Journal = jcp,
        Month = {Dec 1},
        Number = 21,
        Pages = {9871-9881},
        Title = {Theory and computer simulation of bent-core molecules},
        Uri = {<Go to ISI>://000083685400056},
        Volume = 111,
        Year = 1999}

@article{Care2005,
        Abstract = {A review is presented of molecular and mesoscopic computer simulations
    of liquid crystalline systems. Molecular simulation approaches applied
    to such systems are described, and the key findings for bulk phase
    behaviour are reported. Following this, recently developed lattice
    Boltzmann approaches to the mesoscale modelling of nemato-dynanics
    are reviewed. This paper concludes with a discussion of possible
    areas for future development in this field.},
        Annote = {989TU Times Cited:2 Cited References Count:258},
        Author = {C. M. Care and D. J. Cleaver},
        Issn = {0034-4885},
        Journal = {Reports on Progress in Physics},
        Month = {Nov},
        Number = 11,
        Pages = {2665-2700},
        Title = {Computer simulation of liquid crystals},
        Uri = {<Go to ISI>://000233697600004},
        Volume = 68,
        Year = 2005}

@article{Carrasco1999,
        Abstract = {The hydrodynamic properties of rigid particles are calculated from
    models composed of spherical elements (beads) using theories developed
    by Kirkwood, Bloomfield, and their coworkers. Bead models have usually
    been built in such a way that the beads fill the volume occupied
    by the particles. Sometimes the beads are few and of varying sizes
    (bead models in the strict sense), and other times there are many
    small beads (filling models). Because hydrodynamic friction takes
    place at the molecular surface, another possibility is to use shell
    models, as originally proposed by Bloomfield. In this work, we have
    developed procedures to build models of the various kinds, and we
    describe the theory and methods for calculating their hydrodynamic
    properties, including approximate methods that may be needed to
    treat models with a very large number of elements. By combining
    the various possibilities of model building and hydrodynamic calculation,
    several strategies can be designed. We have made a quantitative
    comparison of the performance of the various strategies by applying
    them to some test cases, for which the properties are known a priori.
    We provide guidelines and computational tools for bead modeling.},
        Annote = {200TT Times Cited:46 Cited References Count:57},
        Author = {B. Carrasco and {Garc\'{i}a de la Torre}, Jose},
        Issn = {0006-3495},
        Journal = bj,
        Month = {Jun},
        Number = 6,
        Pages = {3044-3057},
        Title = {Hydrodynamic properties of rigid particles: Comparison of different modeling and computational procedures},
        Uri = {<Go to ISI>://000080556700016},
        Volume = 76,
        Year = 1999}

@article{Chandra1999,
        Abstract = {Dynamical properties of the soft sticky dipole (SSD) model of water
    are calculated by means of molecular dynamics simulations. Since
    this is not a simple point model, the forces and torques arising
    from the SSD potential are derived here. Simulations are carried
    out in the microcanonical ensemble employing the Ewald method for
    the electrostatic interactions. Various time correlation functions
    and dynamical quantities associated with the translational and rotational
    motion of water molecules are evaluated and compared with those
    of two other commonly used models of liquid water, namely the transferable
    intermolecular potential-three points (TIP3P) and simple point charge/extended
    (SPC/E) models, and also with experiments. The dynamical properties
    of the SSD water model are found to be in good agreement with the
    experimental results and appear to be better than the TIP3P and
    SPC/E models in most cases, as has been previously shown for its
    thermodynamic, structural, and dielectric properties. Also, molecular
    dynamics simulations of the SSD model are found to run much faster
    than TIP3P, SPC/E, and other multisite models. (C) 1999 American
    Institute of Physics. [S0021-9606(99)51430-X].},
        Annote = {221EN Times Cited:14 Cited References Count:66},
        Author = {A. Chandra and T. Ichiye},
        Issn = {0021-9606},
        Journal = jcp,
        Month = {Aug 8},
        Number = 6,
        Pages = {2701-2709},
        Title = {Dynamical properties of the soft sticky dipole model of water: Molecular dynamics simulations},
        Uri = {<Go to ISI>://000081711200038},
        Volume = 111,
        Year = 1999}

@article{Channell1990,
        Annote = {Dk631 Times Cited:152 Cited References Count:34},
        Author = {P. J. Channell and C. Scovel},
        Issn = {0951-7715},
        Journal = {Nonlinearity},
        Month = {may},
        Number = 2,
        Pages = {231-259},
        Title = {Symplectic Integration of Hamiltonian-Systems},
        Uri = {<Go to ISI>://A1990DK63100001},
        Volume = 3,
        Year = 1990}

@article{Chen2003,
        Abstract = {We investigate the asymptotic behavior of systems of nonlinear differential
    equations and introduce a family of mixed methods from combinations
    of explicit Runge-Kutta methods. These methods have better stability
    behavior than traditional Runge-Kutta methods and generally extend
    the range of validity of the calculated solutions. These methods
    also give a way of determining if the numerical solutions are real
    or spurious. Emphasis is put on examples coming from mathematical
    models in ecology. (C) 2002 IMACS. Published by Elsevier Science
    B.V. All rights reserved.},
        Annote = {633ZD Times Cited:0 Cited References Count:9},
        Author = {B. Chen and F. Solis},
        Issn = {0168-9274},
        Journal = {Applied Numerical Mathematics},
        Month = {Jan},
        Number = {1-2},
        Pages = {21-30},
        Title = {Explicit mixed finite order Runge-Kutta methods},
        Uri = {<Go to ISI>://000180314200002},
        Volume = 44,
        Year = 2003}

@article{Cheung2004,
        Abstract = {Equilibrium molecular dynamics calculations have been performed for
    the liquid crystal molecule n-4-(trans-4-n-pentylcyclohexyl)benzonitrile
    (PCH5) using a fully atomistic model. Simulation data have been
    obtained for a series of temperatures in the nematic phase. The
    simulation data have been used to calculate the flexoelectric coefficients
    e(s) and e(b) using the linear response formalism of Osipov and
    Nemtsov [M. A. Osipov and V. B. Nemtsov, Sov. Phys. Crstallogr.
    31, 125 (1986)]. The temperature and order parameter dependence
    of e(s) and e(b) are examined, as are separate contributions from
    different intermolecular interactions. Values of e(s) and e(b) calculated
    from simulation are consistent with those found from experiment.
    (C) 2004 American Institute of Physics.},
        Annote = {866UM Times Cited:4 Cited References Count:61},
        Author = {D. L. Cheung and S. J. Clark and M. R. Wilson},
        Issn = {0021-9606},
        Journal = jcp,
        Month = {Nov 8},
        Number = 18,
        Pages = {9131-9139},
        Title = {Calculation of flexoelectric coefficients for a nematic liquid crystal by atomistic simulation},
        Uri = {<Go to ISI>://000224798900053},
        Volume = 121,
        Year = 2004}

@article{Cheung2002,
        Abstract = {Equilibrium molecular dynamics calculations have been performed for
    the liquid crystal molecule n-4-(trans-4-npentylcyclohexyl)benzonitrile
    (PCH5) using a fully atomistic model. Simulation data has been obtained
    for a series of temperatures in the nematic phase. The rotational
    viscosity co-efficient gamma(1), has been calculated using the angular
    velocity correlation function of the nematic director, n, the mean
    squared diffusion of n and statistical mechanical methods based
    on the rotational diffusion co-efficient. We find good agreement
    between the first two methods and experimental values. (C) 2002
    Published by Elsevier Science B.V.},
        Annote = {547KF Times Cited:8 Cited References Count:31},
        Author = {D. L. Cheung and S. J. Clark and M. R. Wilson},
        Issn = {0009-2614},
        Journal = {Chemical Physics Letters},
        Month = {Apr 15},
        Number = {1-2},
        Pages = {140-146},
        Title = {Calculation of the rotational viscosity of a nematic liquid crystal},
        Uri = {<Go to ISI>://000175331000020},
        Volume = 356,
        Year = 2002}

@article{Chin2004,
        Abstract = {Current molecular dynamics simulations of biomolecules using multiple
    time steps to update the slowly changing force are hampered by instabilities
    beginning at time steps near the half period of the fastest vibrating
    mode. These #resonance# instabilities have became a critical barrier
    preventing the long time simulation of biomolecular dynamics. Attempts
    to tame these instabilities by altering the slowly changing force
    and efforts to damp them out by Langevin dynamics do not address
    the fundamental cause of these instabilities. In this work, we trace
    the instability to the nonanalytic character of the underlying spectrum
    and show that a correct splitting of the Hamiltonian, which renders
    the spectrum analytic, restores stability. The resulting Hamiltonian
    dictates that in addition to updating the momentum due to the slowly
    changing force, one must also update the position with a modified
    mass. Thus multiple-time stepping must be done dynamically. (C)
    2004 American Institute of Physics.},
        Annote = {757TK Times Cited:1 Cited References Count:22},
        Author = {S. A. Chin},
        Issn = {0021-9606},
        Journal = jcp,
        Month = {Jan 1},
        Number = 1,
        Pages = {8-13},
        Title = {Dynamical multiple-time stepping methods for overcoming resonance instabilities},
        Uri = {<Go to ISI>://000187577400003},
        Volume = 120,
        Year = 2004}

@article{Cook2000,
        Abstract = {The Kirkwood correlation factor g(1) determines the preference for
    local parallel or antiparallel dipole association in the isotropic
    phase. Calamitic mesogens with longitudinal dipole moments and Kirkwood
    factors greater than 1 have an enhanced effective dipole moment
    along the molecular long axis. This leads to higher values of Delta
    epsilon in the nematic phase. This paper describes state-of-the-art
    molecular dynamics simulations of two calamitic mesogens 4-(trans-4-n-pentylcyclohexyl)benzonitrile
    (PCH5) and 4-(trans-4-n-pentylcyclohexyl) chlorobenzene (PCH5-Cl)
    in the isotropic liquid phase using an all-atom force field and
    taking long range electrostatics into account using an Ewald summation.
    Using this methodology, PCH5 is seen to prefer antiparallel dipole
    alignment with a negative g(1) and PCH5-Cl is seen to prefer parallel
    dipole alignment with a positive g(1); this is in accordance with
    experimental dielectric measurements. Analysis of the molecular
    dynamics trajectories allows an assessment of why these molecules
    behave differently.},
        Annote = {376BF Times Cited:10 Cited References Count:16},
        Author = {M. J. Cook and M. R. Wilson},
        Issn = {0267-8292},
        Journal = {Liquid Crystals},
        Month = {Dec},
        Number = 12,
        Pages = {1573-1583},
        Title = {Simulation studies of dipole correlation in the isotropic liquid phase},
        Uri = {<Go to ISI>://000165437800002},
        Volume = 27,
        Year = 2000}

@article{Cui2003,
        Abstract = {All-atom Langevin dynamics simulations have been performed to study
    the folding pathways of the 18-residue binding domain fragment E6ap
    of the human papillomavirus E6 interacting peptide. Six independent
    folding trajectories, with a total duration of nearly 2 mus, all
    lead to the same native state in which the E6ap adopts a fluctuating
    a-helix structure in the central portion (Ser-4-Leu-13) but with
    very flexible N and C termini. Simulations starting from different
    core configurations exhibit the E6ap folding dynamics as either
    a two- or three-state folder with an intermediate misfolded state.
    The essential leucine hydrophobic core (Leu-9, Leu-12, and Leu-13)
    is well conserved in the native-state structure but absent in the
    intermediate structure, suggesting that the leucine core is not
    only essential for the binding activity of E6ap but also important
    for the stability of the native structure. The free energy landscape
    reveals a significant barrier between the basins separating the
    native and misfolded states. We also discuss the various underlying
    forces that drive the peptide into its native state.},
        Annote = {689LC Times Cited:3 Cited References Count:48},
        Author = {B. X. Cui and M. Y. Shen and K. F. Freed},
        Issn = {0027-8424},
        Journal = pnas,
        Month = {Jun 10},
        Number = 12,
        Pages = {7087-7092},
        Title = {Folding and misfolding of the papillomavirus E6 interacting peptide E6ap},
        Uri = {<Go to ISI>://000183493500037},
        Volume = 100,
        Year = 2003}

@article{Denisov2003,
        Abstract = {We study the slow phase of thermally activated magnetic relaxation
    in finite two-dimensional ensembles of dipolar interacting ferromagnetic
    nanoparticles whose easy axes of magnetization are perpendicular
    to the distribution plane. We develop a method to numerically simulate
    the magnetic relaxation for the case that the smallest heights of
    the potential barriers between the equilibrium directions of the
    nanoparticle magnetic moments are much larger than the thermal energy.
    Within this framework, we analyze in detail the role that the correlations
    of the nanoparticle magnetic moments and the finite size of the
    nanoparticle ensemble play in magnetic relaxation.},
        Annote = {642XH Times Cited:11 Cited References Count:31},
        Author = {S. I. Denisov and T. V. Lyutyy and K. N. Trohidou},
        Issn = {1098-0121},
        Journal = {Physical Review B},
        Month = {Jan 1},
        Number = 1,
        Pages = {-},
        Title = {Magnetic relaxation in finite two-dimensional nanoparticle ensembles},
        Uri = {<Go to ISI>://000180830400056},
        Volume = 67,
        Year = 2003}

@article{Derreumaux1998,
        Abstract = {To explore the origin of the large-scale motion of triosephosphate
    isomerase's flexible loop (residues 166 to 176) at the active site,
    several simulation protocols are employed both for the free enzyme
    in vacuo and for the free enzyme with some solvent modeling: high-temperature
    Langevin dynamics simulations, sampling by a #dynamics##driver#
    approach, and potential-energy surface calculations. Our focus is
    on obtaining the energy barrier to the enzyme's motion and establishing
    the nature of the loop movement. Previous calculations did not determine
    this energy barrier and the effect of solvent on the barrier. High-temperature
    molecular dynamics simulations and crystallographic studies have
    suggested a rigid-body motion with two hinges located at both ends
    of the loop; Brownian dynamics simulations at room temperature pointed
    to a very flexible behavior. The present simulations and analyses
    reveal that although solute/solvent hydrogen bonds play a crucial
    role in lowering the energy along the pathway, there still remains
    a high activation barrier, This finding clearly indicates that,
    if the loop opens and closes in the absence of a substrate at standard
    conditions (e.g., room temperature, appropriate concentration of
    isomerase), the time scale for transition is not in the nanosecond
    but rather the microsecond range. Our results also indicate that
    in the context of spontaneous opening in the free enzyme, the motion
    is of rigid-body type and that the specific interaction between
    residues Ala(176) and Tyr(208) plays a crucial role in the loop
    opening/closing mechanism.},
        Annote = {Zl046 Times Cited:30 Cited References Count:29},
        Author = {P. Derreumaux and T. Schlick},
        Issn = {0006-3495},
        Journal = bj,
        Month = {Jan},
        Number = 1,
        Pages = {72-81},
        Title = {The loop opening/closing motion of the enzyme triosephosphate isomerase},
        Uri = {<Go to ISI>://000073393400009},
        Volume = 74,
        Year = 1998}

@article{Dullweber1997,
        Abstract = {Rigid body molecular models possess symplectic structure and time-reversal
    symmetry. Standard numerical integration methods destroy both properties,
    introducing nonphysical dynamical behavior such as numerically induced
    dissipative states and drift in the energy during long term simulations.
    This article describes the construction, implementation, and practical
    application of fast explicit symplectic-reversible integrators for
    multiple rigid body molecular simulations, These methods use a reduction
    to Euler equations for the free rigid body, together with a symplectic
    splitting technique. In every time step, the orientational dynamics
    of each rigid body is integrated by a sequence of planar rotations.
    Besides preserving the symplectic and reversible structures of the
    flow, this scheme accurately conserves the total angular momentum
    of a system of interacting rigid bodies. Excellent energy conservation
    fan be obtained relative to traditional methods, especially in long-time
    simulations. The method is implemented in a research code, ORIENT
    and compared with a quaternion/extrapolation scheme for the TIP4P
    model of water. Our experiments show that the symplectic-reversible
    scheme is far superior to the more traditional quaternion method.
    (C) 1997 American Institute of Physics.},
        Annote = {Ya587 Times Cited:35 Cited References Count:32},
        Author = {A. Dullweber and B. Leimkuhler and R. McLachlan},
        Issn = {0021-9606},
        Journal = jcp,
        Month = {Oct 15},
        Number = 15,
        Pages = {5840-5851},
        Title = {Symplectic splitting methods for rigid body molecular dynamics},
        Uri = {<Go to ISI>://A1997YA58700024},
        Volume = 107,
        Year = 1997}

@book{Gamma1994,
        Address = {London},
        Author = {E. Gamma, R. Helm, R. Johnson and J. Vlissides},
        Chapter = 7,
        Publisher = {Perason Education},
        Title = {Design Patterns: Elements of Reusable Object-Oriented Software},
        Year = 1994}

@article{Edwards2005,
        Abstract = {Using the Langevin dynamics technique, we have carried out simulations
    of a single-chain flexible diblock copolymer. The polymer consists
    of two blocks of equal length, one very poorly solvated and the
    other close to theta-conditions. We study what happens when such
    a polymer is stretched, for a range of different stretching speeds,
    and correlate our observations with features in the plot of force
    vs extension. We find that at slow speeds this force profile does
    not increase monotonically, in disagreement with earlier predictions,
    and that at high speeds there is a strong dependence on which end
    of the polymer is pulled, as well as a high level of hysteresis.},
        Annote = {992EC Times Cited:0 Cited References Count:13},
        Author = {S. A. Edwards and D. R. M. Williams},
        Issn = {0024-9297},
        Journal = {Macromolecules},
        Month = {Dec 13},
        Number = 25,
        Pages = {10590-10595},
        Title = {Stretching a single diblock copolymer in a selective solvent: Langevin dynamics simulations},
        Uri = {<Go to ISI>://000233866200035},
        Volume = 38,
        Year = 2005}

@article{Egberts1988,
        Annote = {Q0188 Times Cited:219 Cited References Count:43},
        Author = {E. Egberts and H. J. C. Berendsen},
        Issn = {0021-9606},
        Journal = jcp,
        Month = {Sep 15},
        Number = 6,
        Pages = {3718-3732},
        Title = {Molecular-Dynamics Simulation of a Smectic Liquid-Crystal with Atomic Detail},
        Uri = {<Go to ISI>://A1988Q018800036},
        Volume = 89,
        Year = 1988}

@article{Ermak1978,
        Annote = {Fp216 Times Cited:785 Cited References Count:42},
        Author = {D. L. Ermak and J. A. Mccammon},
        Issn = {0021-9606},
        Journal = jcp,
        Number = 4,
        Pages = {1352-1360},
        Title = {Brownian Dynamics with Hydrodynamic Interactions},
        Uri = {<Go to ISI>://A1978FP21600004},
        Volume = 69,
        Year = 1978}

@article{Evans1977,
        Annote = {Ds757 Times Cited:271 Cited References Count:18},
        Author = {D. J. Evans},
        Issn = {0026-8976},
        Journal = mp,
        Number = 2,
        Pages = {317-325},
        Title = {Representation of Orientation Space},
        Uri = {<Go to ISI>://A1977DS75700002},
        Volume = 34,
        Year = 1977}

@article{Fennell2004,
        Abstract = {The density maximum and temperature dependence of the self-diffusion
    constant were investigated for the soft sticky dipole (SSD) water
    model and two related reparametrizations of this single-point model.
    A combination of microcanonical and isobaric-isothermal molecular
    dynamics simulations was used to calculate these properties, both
    with and without the use of reaction field to handle long-range
    electrostatics. The isobaric-isothermal simulations of the melting
    of both ice-I-h and ice-I-c showed a density maximum near 260 K.
    In most cases, the use of the reaction field resulted in calculated
    densities which were significantly lower than experimental densities.
    Analysis of self-diffusion constants shows that the original SSD
    model captures the transport properties of experimental water very
    well in both the normal and supercooled liquid regimes. We also
    present our reparametrized versions of SSD for use both with the
    reaction field or without any long-range electrostatic corrections.
    These are called the SSD/RF and SSD/E models, respectively. These
    modified models were shown to maintain or improve upon the experimental
    agreement with the structural and transport properties that can
    be obtained with either the original SSD or the density-corrected
    version of the original model (SSD1). Additionally, a novel low-density
    ice structure is presented which appears to be the most stable ice
    structure for the entire SSD family. (C) 2004 American Institute
    of Physics.},
        Annote = {816YY Times Cited:5 Cited References Count:39},
        Author = {C. J. Fennell and J. D. Gezelter},
        Issn = {0021-9606},
        Journal = jcp,
        Month = {May 15},
        Number = 19,
        Pages = {9175-9184},
        Title = {On the structural and transport properties of the soft sticky dipole and related single-point water models},
        Uri = {<Go to ISI>://000221146400032},
        Volume = 120,
        Year = 2004}

@article{Fernandes2002,
        Abstract = {We have developed a Brownian dynamics simulation algorithm to generate
    Brownian trajectories of an isolated, rigid particle of arbitrary
    shape in the presence of electric fields or any other external agents.
    Starting from the generalized diffusion tensor, which can be calculated
    with the existing HYDRO software, the new program BROWNRIG (including
    a case-specific subprogram for the external agent) carries out a
    simulation that is analyzed later to extract the observable dynamic
    properties. We provide a variety of examples of utilization of this
    method, which serve as tests of its performance, and also illustrate
    its applicability. Examples include free diffusion, transport in
    an electric field, and diffusion in a restricting environment.},
        Annote = {633AD Times Cited:2 Cited References Count:43},
        Author = {M. X. Fernandes and {Garc\'{i}a de la Torre}, Jose},
        Issn = {0006-3495},
        Journal = bj,
        Month = {Dec},
        Number = 6,
        Pages = {3039-3048},
        Title = {Brownian dynamics simulation of rigid particles of arbitrary shape in external fields},
        Uri = {<Go to ISI>://000180256300012},
        Volume = 83,
        Year = 2002}

@book{Frenkel1996,
        Address = {New York},
        Author = {D. Frenkel and B. Smit},
        Publisher = {Academic Press},
        Title = {Understanding Molecular Simulation : From Algorithms to Applications},
        Year = 1996}

@article{Gay1981,
        Annote = {Lj347 Times Cited:482 Cited References Count:13},
        Author = {J. G. Gay and B. J. Berne},
        Issn = {0021-9606},
        Journal = jcp,
        Number = 6,
        Pages = {3316-3319},
        Title = {Modification of the Overlap Potential to Mimic a Linear Site-Site Potential},
        Uri = {<Go to ISI>://A1981LJ34700029},
        Volume = 74,
        Year = 1981}

@article{Gelin1999,
        Abstract = {To investigate the influence of inertial effects on the dynamics of
    an assembly of beads subjected to rigid constraints and placed in
    a buffer medium, a convenient method to introduce suitable generalized
    coordinates is presented. Without any restriction on the nature
    of the soft forces involved (both stochastic and deterministic),
    pertinent Langevin equations are derived. Provided that the Brownian
    forces are Gaussian and Markovian, the corresponding Fokker-Planck
    equation (FPE) is obtained in the complete phase space of generalized
    coordinates and momenta. The correct short time behavior for correlation
    functions (CFs) of generalized coordinates is established, and the
    diffusion equation with memory (DEM) is deduced from the FPE in
    the high friction Limit. The DEM is invoked to perform illustrative
    calculations in two dimensions of the orientational CFs for once
    broken nonrigid rods immobilized on a surface. These calculations
    reveal that the CFs under certain conditions exhibit an oscillatory
    behavior, which is irreproducible within the standard diffusion
    equation. Several methods are considered for the approximate solution
    of the DEM, and their application to three dimensional DEMs is discussed.},
        Annote = {257MM Times Cited:2 Cited References Count:82},
        Author = {M. F. Gelin},
        Issn = {1022-1344},
        Journal = {Macromolecular Theory and Simulations},
        Month = {Nov},
        Number = 6,
        Pages = {529-543},
        Title = {Inertial effects in the Brownian dynamics with rigid constraints},
        Uri = {<Go to ISI>://000083785700002},
        Volume = 8,
        Year = 1999}

@article{Goetz1998,
        Author = {R. Goetz and R. Lipowsky},
        Journal = jcp,
        Number = 17,
        Pages = 7397,
        Title = {Computer simulations of bilayer membranes: Self-assembly and interfacial tension},
        Volume = 108,
        Year = 1998}

@book{Goldstein2001,
        Address = {San Francisco},
        Author = {H. Goldstein and C. Poole and J. Safko},
        Edition = {3rd},
        Publisher = {Addison Wesley},
        Title = {Classical Mechanics},
        Year = 2001}

@article{Gray2003,
        Abstract = {Protein-protein docking algorithms provide a means to elucidate structural
    details for presently unknown complexes. Here, we present and evaluate
    a new method to predict protein-protein complexes from the coordinates
    of the unbound monomer components. The method employs a low-resolution,
    rigid-body, Monte Carlo search followed by simultaneous optimization
    of backbone displacement and side-chain conformations using Monte
    Carlo minimization. Up to 10(5) independent simulations are carried
    out, and the resulting #decoys# are ranked using an energy function
    dominated by van der Waals interactions, an implicit solvation model,
    and an orientation-dependent hydrogen bonding potential. Top-ranking
    decoys are clustered to select the final predictions. Small-perturbation
    studies reveal the formation of binding funnels in 42 of 54 cases
    using coordinates derived from the bound complexes and in 32 of
    54 cases using independently determined coordinates of one or both
    monomers. Experimental binding affinities correlate with the calculated
    score function and explain the predictive success or failure of
    many targets. Global searches using one or both unbound components
    predict at least 25% of the native residue-residue contacts in 28
    of the 32 cases where binding funnels exist. The results suggest
    that the method may soon be useful for generating models of biologically
    important complexes from the structures of the isolated components,
    but they also highlight the challenges that must be met to achieve
    consistent and accurate prediction of protein-protein interactions.
    (C) 2003 Elsevier Ltd. All rights reserved.},
        Annote = {704QL Times Cited:48 Cited References Count:60},
        Author = {J. J. Gray and S. Moughon and C. Wang and O. Schueler-Furman and B. Kuhlman and C. A. Rohl and D. Baker},
        Issn = {0022-2836},
        Journal = jmb,
        Month = {Aug 1},
        Number = 1,
        Pages = {281-299},
        Title = {Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations},
        Uri = {<Go to ISI>://000184351300022},
        Volume = 331,
        Year = 2003}

@article{Greengard1994,
        Abstract = {Some of the recently developed fast summation methods that have arisen
    in scientific computing are described. These methods require an
    amount of work proportional to N or N log N to evaluate all pairwise
    interactions in an ensemble of N particles. Traditional methods,
    by contrast, require an amount of work proportional to N-2. AS a
    result, large-scale simulations can be carried out using only modest
    computer resources. In combination with supercomputers, it is possible
    to address questions that were previously out of reach. Problems
    from diffusion, gravitation, and wave propagation are considered.},
        Annote = {Pb499 Times Cited:99 Cited References Count:44},
        Author = {L. Greengard},
        Issn = {0036-8075},
        Journal = {Science},
        Month = {Aug 12},
        Number = 5174,
        Pages = {909-914},
        Title = {Fast Algorithms for Classical Physics},
        Uri = {<Go to ISI>://A1994PB49900031},
        Volume = 265,
        Year = 1994}

@article{Greengard1987,
        Annote = {L0498 Times Cited:899 Cited References Count:7},
        Author = {L. Greengard and V. Rokhlin},
        Issn = {0021-9991},
        Journal = jcop,
        Month = {Dec},
        Number = 2,
        Pages = {325-348},
        Title = {A Fast Algorithm for Particle Simulations},
        Uri = {<Go to ISI>://A1987L049800006},
        Volume = 73,
        Year = 1987}

@article{Hairer1997,
        Abstract = {Backward error analysis is a useful tool for the study of numerical
    approximations to ordinary differential equations. The numerical
    solution is formally interpreted as the exact solution of a perturbed
    differential equation, given as a formal and usually divergent series
    in powers of the step size. For a rigorous analysis, this series
    has to be truncated. In this article we study the influence of this
    truncation to the difference between the numerical solution and
    the exact solution of the perturbed differential equation. Results
    on the long-time behaviour of numerical solutions are obtained in
    this way. We present applications to the numerical phase portrait
    near hyperbolic equilibrium points, to asymptotically stable periodic
    orbits and Hopf bifurcation, and to energy conservation and approximation
    of invariant tori in Hamiltonian systems.},
        Annote = {Xj488 Times Cited:50 Cited References Count:19},
        Author = {E. Hairer and C. Lubich},
        Issn = {0029-599X},
        Journal = {Numerische Mathematik},
        Month = {Jun},
        Number = 4,
        Pages = {441-462},
        Title = {The life-span of backward error analysis for numerical integrators},
        Uri = {<Go to ISI>://A1997XJ48800002},
        Volume = 76,
        Year = 1997}

@article{Hao1993,
        Abstract = {A new procedure for studying the folding and unfolding of proteins,
    with an application to bovine pancreatic trypsin inhibitor (BPTI),
    is reported. The unfolding and refolding of the native structure
    of the protein are characterized by the dimensions of the protein,
    expressed in terms of the three principal radii of the structure
    considered as an ellipsoid. A dynamic equation, describing the variations
    of the principal radii on the unfolding path, and a numerical procedure
    to solve this equation are proposed. Expanded and distorted conformations
    are refolded to the native structure by a dimensional-constraint
    energy minimization procedure. A unique and reproducible unfolding
    pathway for an intermediate of BPTI lacking the [30,51] disulfide
    bond is obtained. The resulting unfolded conformations are extended;
    they contain near-native local structure, but their longest principal
    radii are more than 2.5 times greater than that of the native structure.
    The most interesting finding is that the majority of expanded conformations,
    generated under various conditions, can be refolded closely to the
    native structure, as measured by the correct overall chain fold,
    by the rms deviations from the native structure of only 1.9-3.1
    angstrom, and by the energy differences of about 10 kcal/mol from
    the native structure. Introduction of the [30,51] disulfide bond
    at this stage, followed by minimization, improves the closeness
    of the refolded structures to the native structure, reducing the
    rms deviations to 0.9-2.0 angstrom. The unique refolding of these
    expanded structures over such a large conformational space implies
    that the folding is strongly dictated by the interactions in the
    amino acid sequence of BPTI. The simulations indicate that, under
    conditions that favor a compact structure as mimicked by the volume
    constraints in our algorithm; the expanded conformations have a
    strong tendency to move toward the native structure; therefore,
    they probably would be favorable folding intermediates. The results
    presented here support a general model for protein folding, i.e.,
    progressive formation of partially folded structural units, followed
    by collapse to the compact native structure. The general applicability
    of the procedure is also discussed.},
        Annote = {Ly294 Times Cited:27 Cited References Count:57},
        Author = {M. H. Hao and M. R. Pincus and S. Rackovsky and H. A. Scheraga},
        Issn = {0006-2960},
        Journal = {Biochemistry},
        Month = {Sep 21},
        Number = 37,
        Pages = {9614-9631},
        Title = {Unfolding and Refolding of the Native Structure of Bovine Pancreatic Trypsin-Inhibitor Studied by Computer-Simulations},
        Uri = {<Go to ISI>://A1993LY29400014},
        Volume = 32,
        Year = 1993}

@article{Hinsen2000,
        Abstract = {The slow dynamics of proteins around its native folded state is usually
    described by diffusion in a strongly anharmonic potential. In this
    paper, we try to understand the form and origin of the anharmonicities,
    with the principal aim of gaining a better understanding of the
    principal motion types, but also in order to develop more efficient
    numerical methods for simulating neutron scattering spectra of large
    proteins. First, we decompose a molecular dynamics (MD) trajectory
    of 1.5 ns for a C-phycocyanin dimer surrounded by a layer of water
    into three contributions that we expect to be independent: the global
    motion of the residues, the rigid-body motion of the sidechains
    relative to the backbone, and the internal deformations of the sidechains.
    We show that they are indeed almost independent by verifying the
    factorization of the incoherent intermediate scattering function.
    Then, we show that the global residue motions, which include all
    large-scale backbone motions, can be reproduced by a simple harmonic
    model which contains two contributions: a short-time vibrational
    term, described by a standard normal mode calculation in a local
    minimum, and a long-time diffusive term, described by Brownian motion
    in an effective harmonic potential. The potential and the friction
    constants were fitted to the MD data. The major anharmonic contribution
    to the incoherent intermediate scattering function comes from the
    rigid-body diffusion of the sidechains. This model can be used to
    calculate scattering functions for large proteins and for long-time
    scales very efficiently, and thus provides a useful complement to
    MD simulations, which are best suited for detailed studies on smaller
    systems or for shorter time scales. (C) 2000 Elsevier Science B.V.
    All rights reserved.},
        Annote = {Sp. Iss. SI 368MT Times Cited:16 Cited References Count:31},
        Author = {K. Hinsen and A. J. Petrescu and S. Dellerue and M. C. Bellissent-Funel and G. R. Kneller},
        Issn = {0301-0104},
        Journal = {Chemical Physics},
        Month = {Nov 1},
        Number = {1-2},
        Pages = {25-37},
        Title = {Harmonicity in slow protein dynamics},
        Uri = {<Go to ISI>://000090121700003},
        Volume = 261,
        Year = 2000}

@article{Ho1992,
        Abstract = {Evidence has been found for the existence water at the protein-lipid
    hydrophobic interface ot the membrane proteins, gramicidin and apocytochrome
    C, using two related fluorescence spectroscopic approaches. The
    first approach exploited the fact that the presence of water in
    the excited state solvent cage of a fluorophore increases the rate
    of decay. For 1,6-diphenyl-1,3,5-hexatriene (DPH) and 1-palmitoyl-2-[[2-[4-(6-phenyl-trans-1,3,5-hexatrienyl)
    phenyl]ethyl]carbonyl]-3-sn-PC (DPH-PC), where the fluorophores
    are located in the hydrophobic core of the lipid bilayer, the introduction
    of gramicidin reduced the fluorescence lifetime, indicative of an
    increased presence of water in the bilayer. Since a high protein:lipid
    ratio was used, the fluorophores were forced to be adjacent to the
    protein hydrophobic surface, hence the presence of water in this
    region could be inferred. Cholesterol is known to reduce the water
    content of lipid bilayers and this effect was maintained at the
    protein-lipid interface with both gramicidin and apocytochrome C,
    again suggesting hydration in this region. The second approach was
    to use the fluorescence enhancement induced by exchanging deuterium
    oxide (D2O) for H2O. Both the fluorescence intensities of trimethylammonium-DPH,
    located in the lipid head group region, and of the gramicidin intrinsic
    tryptophans were greater in a D2O buffer compared with H2O, showing
    that the fluorophores were exposed to water in the bilayer at the
    protein-lipid interface. In the presence of cholesterol the fluorescence
    intensity ratio of D2O to H2O decreased, indicating a removal of
    water by the cholesterol, in keeping with the lifetime data. Altered
    hydration at the protein-lipid interface could affect conformation,
    thereby offering a new route by which membrane protein functioning
    may be modified.},
        Annote = {Ju251 Times Cited:55 Cited References Count:44},
        Author = {C. Ho and C. D. Stubbs},
        Issn = {0006-3495},
        Journal = bj,
        Month = {Oct},
        Number = 4,
        Pages = {897-902},
        Title = {Hydration at the Membrane Protein-Lipid Interface},
        Uri = {<Go to ISI>://A1992JU25100002},
        Volume = 63,
        Year = 1992}

@book{Hockney1981,
        Address = {New York},
        Author = {R.W. Hockney and J.W. Eastwood},
        Publisher = {McGraw-Hill},
        Title = {Computer Simulation Using Particles},
        Year = 1981}

@article{Hoover1985,
        Annote = {Acr30 Times Cited:1809 Cited References Count:11},
        Author = {W. G. Hoover},
        Issn = {1050-2947},
        Journal = {Physical Review A},
        Number = 3,
        Pages = {1695-1697},
        Title = {Canonical Dynamics - Equilibrium Phase-Space Distributions},
        Uri = {<Go to ISI>://A1985ACR3000056},
        Volume = 31,
        Year = 1985}

@article{Huh2004,
        Abstract = {Racemic fluids of chiral calamitic molecules are investigated with
    molecular dynamics simulations. In particular, the phase behavior
    as a function of density is examined for eight racemates. The relationship
    between chiral discrimination and orientational order in the phase
    is explored. We find that the transition from the isotropic phase
    to a liquid crystal phase is accompanied by an increase in chiral
    discrimination, as measured by differences in radial distributions.
    Among ordered phases, discrimination is largest for smectic phases
    with a significant preference for heterochiral contact within the
    layers. (C) 2004 American Institute of Physics.},
        Annote = {870FJ Times Cited:0 Cited References Count:63},
        Author = {Y. Huh and N. M. Cann},
        Issn = {0021-9606},
        Journal = jcp,
        Month = {Nov 22},
        Number = 20,
        Pages = {10299-10308},
        Title = {Discrimination in isotropic, nematic, and smectic phases of chiral calamitic molecules: A computer simulation study},
        Uri = {<Go to ISI>://000225042700059},
        Volume = 121,
        Year = 2004}

@article{Humphrey1996,
        Abstract = {VMD is a molecular graphics program designed for the display and analysis
    of molecular assemblies, in particular biopolymers such as proteins
    and nucleic acids. VMD can simultaneously display any number of
    structures using a wide variety of rendering styles and coloring
    methods. Molecules are displayed as one or more ''representations,''
    in which each representation embodies a particular rendering method
    and coloring scheme for a selected subset of atoms. The atoms displayed
    in each representation are chosen using an extensive atom selection
    syntax, which includes Boolean operators and regular expressions.
    VMD provides a complete graphical user interface for program control,
    as well as a text interface using the Tcl embeddable parser to allow
    for complex scripts with variable substitution, control loops, and
    function calls. Full session logging is supported, which produces
    a VMD command script for later playback. High-resolution raster
    images of displayed molecules may be produced by generating input
    scripts for use by a number of photorealistic image-rendering applications.
    VMD has also been expressly designed with the ability to animate
    molecular dynamics (MD) simulation trajectories, imported either
    from files or from a direct connection to a running MD simulation.
    VMD is the visualization component of MDScope, a set of tools for
    interactive problem solving in structural biology, which also includes
    the parallel MD program NAMD, and the MDCOMM software used to connect
    the visualization and simulation programs. VMD is written in C++,
    using an object-oriented design; the program, including source code
    and extensive documentation, is freely available via anonymous ftp
    and through the World Wide Web.},
        Annote = {Uh515 Times Cited:1418 Cited References Count:19},
        Author = {W. Humphrey and A. Dalke and K. Schulten},
        Issn = {0263-7855},
        Journal = {Journal of Molecular Graphics},
        Month = {Feb},
        Number = 1,
        Pages = {33-\&},
        Title = {VMD: Visual molecular dynamics},
        Uri = {<Go to ISI>://A1996UH51500005},
        Volume = 14,
        Year = 1996}

@article{Izaguirre2001,
        Abstract = {In this paper we show the possibility of using very mild stochastic
    damping to stabilize long time step integrators for Newtonian molecular
    dynamics. More specifically, stable and accurate integrations are
    obtained for damping coefficients that are only a few percent of
    the natural decay rate of processes of interest, such as the velocity
    autocorrelation function. Two new multiple time stepping integrators,
    Langevin Molly (LM) and Brunger-Brooks-Karplus-Molly (BBK-M), are
    introduced in this paper. Both use the mollified impulse method
    for the Newtonian term. LM uses a discretization of the Langevin
    equation that is exact for the constant force, and BBK-M uses the
    popular Brunger-Brooks-Karplus integrator (BBK). These integrators,
    along with an extrapolative method called LN, are evaluated across
    a wide range of damping coefficient values. When large damping coefficients
    are used, as one would for the implicit modeling of solvent molecules,
    the method LN is superior, with LM closely following. However, with
    mild damping of 0.2 ps(-1), LM produces the best results, allowing
    long time steps of 14 fs in simulations containing explicitly modeled
    flexible water. With BBK-M and the same damping coefficient, time
    steps of 12 fs are possible for the same system. Similar results
    are obtained for a solvated protein-DNA simulation of estrogen receptor
    ER with estrogen response element ERE. A parallel version of BBK-M
    runs nearly three times faster than the Verlet-I/r-RESPA (reversible
    reference system propagator algorithm) when using the largest stable
    time step on each one, and it also parallelizes well. The computation
    of diffusion coefficients for flexible water and ER/ERE shows that
    when mild damping of up to 0.2 ps-1 is used the dynamics are not
    significantly distorted. (C) 2001 American Institute of Physics.},
        Annote = {397CQ Times Cited:14 Cited References Count:36},
        Author = {J. A. Izaguirre and D. P. Catarello and J. M. Wozniak and R. D. Skeel},
        Issn = {0021-9606},
        Journal = jcp,
        Month = {Feb 1},
        Number = 5,
        Pages = {2090-2098},
        Title = {Langevin stabilization of molecular dynamics},
        Uri = {<Go to ISI>://000166676100020},
        Volume = 114,
        Year = 2001}

@article{Torre1977,
        Author = {{Garc\'{i}a de la Torre}, Jose and V.~A. Bloomfield},
        Journal = {Biopolymers},
        Pages = {1747-1763},
        Title = {Hydrodynamic properties of macromolecular complexes. I. Translation},
        Volume = 16,
        Year = 1977}

@article{Kale1999,
        Abstract = {Molecular dynamics programs simulate the behavior of biomolecular
    systems, leading to understanding of their functions. However, the
    computational complexity of such simulations is enormous. Parallel
    machines provide the potential to meet this computational challenge.
    To harness this potential, it is necessary to develop a scalable
    program. It is also necessary that the program be easily modified
    by application-domain programmers. The NAMD2 program presented in
    this paper seeks to provide these desirable features. It uses spatial
    decomposition combined with force decomposition to enhance scalability.
    It uses intelligent periodic load balancing, so as to maximally
    utilize the available compute power. It is modularly organized,
    and implemented using Charm++, a parallel C++ dialect, so as to
    enhance its modifiability. It uses a combination of numerical techniques
    and algorithms to ensure that energy drifts are minimized, ensuring
    accuracy in long running calculations. NAMD2 uses a portable run-time
    framework called Converse that also supports interoperability among
    multiple parallel paradigms. As a result, different components of
    applications can be written in the most appropriate parallel paradigms.
    NAMD2 runs on most parallel machines including workstation clusters
    and has yielded speedups in excess of 180 on 220 processors. This
    paper also describes the performance obtained on some benchmark
    applications. (C) 1999 Academic Press.},
        Annote = {194FM Times Cited:373 Cited References Count:51},
        Author = {L. Kale and R. Skeel and M. Bhandarkar and R. Brunner and A. Gursoy and N. Krawetz and J. Phillips and A. Shinozaki and K. Varadarajan and K. Schulten},
        Issn = {0021-9991},
        Journal = jcop,
        Month = {May 1},
        Number = 1,
        Pages = {283-312},
        Title = {NAMD2: Greater scalability for parallel molecular dynamics},
        Uri = {<Go to ISI>://000080181500013},
        Volume = 151,
        Year = 1999}

@article{Kane2000,
        Abstract = {The purpose of this work is twofold. First, we demonstrate analytically
    that the classical Newmark family as well as related integration
    algorithms are variational in the sense of the Veselov formulation
    of discrete mechanics. Such variational algorithms are well known
    to be symplectic and momentum preserving and to often have excellent
    global energy behaviour. This analytical result is verified through
    numerical examples and is believed to be one of the primary reasons
    that this class of algorithms performs so well. Second, we develop
    algorithms for mechanical systems with forcing, and in particular,
    for dissipative systems. In this case, we develop integrators that
    are based on a discretization of the Lagrange d'Alembert principle
    as well as on a variational formulation of dissipation. It is demonstrated
    that these types of structured integrators have good numerical behaviour
    in terms of obtaining the correct amounts by which the energy changes
    over the integration run. Copyright (C) 2000 John Wiley & Sons,
    Ltd.},
        Annote = {373CJ Times Cited:30 Cited References Count:41},
        Author = {C. Kane and J. E. Marsden and M. Ortiz and M. West},
        Issn = {0029-5981},
        Journal = {International Journal for Numerical Methods in Engineering},
        Month = {Dec 10},
        Number = 10,
        Pages = {1295-1325},
        Title = {Variational integrators and the Newmark algorithm for conservative and dissipative mechanical systems},
        Uri = {<Go to ISI>://000165270600004},
        Volume = 49,
        Year = 2000}

@article{Klimov1997,
        Abstract = {The viscosity (eta) dependence of the folding rates for four sequences
    (the native state of three sequences is a beta sheet, while the
    fourth forms an alpha helix) is calculated for off-lattice models
    of proteins. Assuming that the dynamics is given by the Langevin
    equation, we show that the folding rates increase linearly at low
    viscosities eta, decrease as 1/eta at large eta, and have a maximum
    at intermediate values. The Kramers' theory of barrier crossing
    provides a quantitative fit of the numerical results. By mapping
    the simulation results to real proteins we estimate that for optimized
    sequences the time scale for forming a four turn alpha-helix topology
    is about 500 ns, whereas for beta sheet it is about 10 mu s.},
        Annote = {Xk293 Times Cited:77 Cited References Count:17},
        Author = {D. K. Klimov and D. Thirumalai},
        Issn = {0031-9007},
        Journal = prl,
        Month = {Jul 14},
        Number = 2,
        Pages = {317-320},
        Title = {Viscosity dependence of the folding rates of proteins},
        Uri = {<Go to ISI>://A1997XK29300035},
        Volume = 79,
        Year = 1997}

@article{Kol1997,
        Abstract = {Rigid-body molecular dynamics simulations typically are performed
    in a quaternion representation. The nonseparable form of the Hamiltonian
    in quaternions prevents the use of a standard leapfrog (Verlet)
    integrator, so nonsymplectic Runge-Kutta, multistep, or extrapolation
    methods are generally used, This is unfortunate since symplectic
    methods like Verlet exhibit superior energy conservation in long-time
    integrations. In this article, we describe an alternative method,
    which we call RSHAKE (for rotation-SHAKE), in which the entire rotation
    matrix is evolved (using the scheme of McLachlan and Scovel [J.
    Nonlin. Sci, 16 233 (1995)]) in tandem with the particle positions.
    We employ a fast approximate Newton solver to preserve the orthogonality
    of the rotation matrix. We test our method on a system of soft-sphere
    dipoles and compare with quaternion evolution using a 4th-order
    predictor-corrector integrator, Although the short-time error of
    the quaternion algorithm is smaller for fixed time step than that
    for RSHAKE, the quaternion scheme exhibits an energy drift which
    is not observed in simulations with RSHAKE, hence a fixed energy
    tolerance can be achieved by using a larger time step, The superiority
    of RSHAKE increases with system size. (C) 1997 American Institute
    of Physics.},
        Annote = {Xq332 Times Cited:11 Cited References Count:18},
        Author = {A. Kol and B. B. Laird and B. J. Leimkuhler},
        Issn = {0021-9606},
        Journal = jcp,
        Month = {Aug 15},
        Number = 7,
        Pages = {2580-2588},
        Title = {A symplectic method for rigid-body molecular simulation},
        Uri = {<Go to ISI>://A1997XQ33200046},
        Volume = 107,
        Year = 1997}

@article{Lansac2001,
        Abstract = {Cyanobiphenyls (nCB's) represent a useful and intensively studied
    class of mesogens. Many of the peculiar properties of nCB's (e.g.,
    the occurence of the partial bilayer smectic-A(d) phase) are thought
    to be a manifestation of short-range antiparallel association of
    neighboring molecules, resulting from strong dipole-dipole interactions
    between cyano groups. To test and extend existing models of microscopic
    ordering in nCB's, we carry out large-scale atomistic simulation
    studies of the microscopic structure and dynamics of the Sm-A(d)
    phase of 4-octyl-4'-cyanobiphenyl (8CB). We compute a variety of
    thermodynamic, structural, and dynamical properties for this material,
    and make a detailed comparison of our results with experimental
    measurements in order to validate our molecular model. Semiquantitative
    agreement with experiment is found: the smectic layer spacing and
    mass density are well reproduced, translational diffusion constants
    are similar to experiment, but the orientational ordering of alkyl
    chains is overestimated. This simulation provides a detailed picture
    of molecular conformation, smectic layer structure, and intermolecular
    correlations in Sm-A(d) 8CB, and demonstrates that pronounced short-range
    antiparallel association of molecules arising from dipole-dipole
    interactions plays a dominant role in determining the molecular-scale
    structure of 8CB.},
        Annote = {Part 1 496QF Times Cited:10 Cited References Count:60},
        Author = {Y. Lansac and M. A. Glaser and N. A. Clark},
        Issn = {1063-651X},
        Journal = {Physical Review E},
        Month = {Nov},
        Number = 5,
        Pages = {-},
        Title = {Microscopic structure and dynamics of a partial bilayer smectic liquid crystal},
        Uri = {<Go to ISI>://000172406900063},
        Volume = 6405,
        Year = 2001}

@article{Lansac2003,
        Abstract = {Recently, a new class of smectic liquid crystal phases characterized
    by the spontaneous formation of macroscopic chiral domains from
    achiral bent-core molecules has been discovered. We have carried
    out Monte Carlo simulations of a minimal hard spherocylinder dimer
    model to investigate the role of excluded volume interactions in
    determining the phase behavior of bent-core materials and to probe
    the molecular origins of polar and chiral symmetry breaking. We
    present the phase diagram of hard spherocylinder dimers of length-diameter
    ratio of 5 as a function of pressure or density and dimer opening
    angle psi. With decreasing psi, a transition from a nonpolar to
    a polar smectic A phase is observed near psi=167degrees, and the
    nematic phase becomes thermodynamically unstable for psi<135degrees.
    Free energy calculations indicate that the antipolar smectic A (SmAP(A))
    phase is more stable than the polar smectic A phase (SmAP(F)). No
    chiral smectic or biaxial nematic phases were found.},
        Annote = {Part 1 646CM Times Cited:15 Cited References Count:38},
        Author = {Y. Lansac and P. K. Maiti and N. A. Clark and M. A. Glaser},
        Issn = {1063-651X},
        Journal = {Physical Review E},
        Month = {Jan},
        Number = 1,
        Pages = {-},
        Title = {Phase behavior of bent-core molecules},
        Uri = {<Go to ISI>://000181017300042},
        Volume = 67,
        Year = 2003}

@book{Leach2001,
        Address = {Harlow, England},
        Author = {A. Leach},
        Edition = {2nd},
        Publisher = {Pearson Educated Limited},
        Title = {Molecular Modeling: Principles and Applications},
        Year = 2001}

@article{Leimkuhler1999,
        Abstract = {Reversible and adaptive integration methods based on Kustaanheimo-Stiefel
    regularization and modified Sundman transformations are applied
    to simulate general perturbed Kepler motion and to compute classical
    trajectories of atomic systems (e.g. Rydberg atoms). The new family
    of reversible adaptive regularization methods also conserves angular
    momentum and exhibits superior energy conservation and numerical
    stability in long-time integrations. The schemes are appropriate
    for scattering, for astronomical calculations of escape time and
    long-term stability, and for classical and semiclassical studies
    of atomic dynamics. The components of an algorithm for trajectory
    calculations are described. Numerical experiments illustrate the
    effectiveness of the reversible approach.},
        Annote = {199EE Times Cited:11 Cited References Count:48},
        Author = {B. Leimkuhler},
        Issn = {1364-503X},
        Journal = {Philosophical Transactions of the Royal Society of London Series a-Mathematical Physical and Engineering Sciences},
        Month = {Apr 15},
        Number = 1754,
        Pages = {1101-1133},
        Title = {Reversible adaptive regularization: perturbed Kepler motion and classical atomic trajectories},
        Uri = {<Go to ISI>://000080466800007},
        Volume = 357,
        Year = 1999}

@book{Leimkuhler2004,
        Address = {Cambridge},
        Author = {B. Leimkuhler and S. Reich},
        Publisher = {Cambridge University Press},
        Title = {Simulating Hamiltonian Dynamics},
        Year = 2004}

@article{Levelut1981,
        Annote = {Ml751 Times Cited:96 Cited References Count:16},
        Author = {A. M. Levelut and R. J. Tarento and F. Hardouin and M. F. Achard and G. Sigaud},
        Issn = {1050-2947},
        Journal = {Physical Review A},
        Number = 4,
        Pages = {2180-2186},
        Title = {Number of Sa Phases},
        Uri = {<Go to ISI>://A1981ML75100057},
        Volume = 24,
        Year = 1981}

@article{Lieb1982,
        Annote = {Nu461 Times Cited:40 Cited References Count:28},
        Author = {W. R. Lieb and M. Kovalycsik and R. Mendelsohn},
        Issn = {0006-3002},
        Journal = {Biochimica Et Biophysica Acta},
        Number = 2,
        Pages = {388-398},
        Title = {Do Clinical-Levels of General-Anesthetics Affect Lipid Bilayers - Evidence from Raman-Scattering},
        Uri = {<Go to ISI>://A1982NU46100012},
        Volume = 688,
        Year = 1982}

@article{Link1997,
        Abstract = {A smectic liquid-crystal phase made from achiral molecules with bent
    cores was found to have fluid layers that exhibit two spontaneous
    symmetry-breaking instabilities: polar molecular orientational ordering
    about the layer normal and molecular tilt. These instabilities combine
    to form a chiral layer structure with a handedness that depends
    on the sign of the tilt. The bulk states are either antiferroelectric-racemic,
    with the layer polar direction and handedness alternating in sign
    from layer to layer, or antiferroelectric-chiral, which is of uniform
    layer handedness. Both states exhibit an electric field-induced
    transition from antiferroelectric to ferroelectric.},
        Annote = {Yl002 Times Cited:407 Cited References Count:25},
        Author = {D. R. Link and G. Natale and R. Shao and J. E. Maclennan and N. A. Clark and E. Korblova and D. M. Walba},
        Issn = {0036-8075},
        Journal = {Science},
        Month = {Dec 12},
        Number = 5345,
        Pages = {1924-1927},
        Title = {Spontaneous formation of macroscopic chiral domains in a fluid smectic phase of achiral molecules},
        Uri = {<Go to ISI>://A1997YL00200028},
        Volume = 278,
        Year = 1997}

@article{Liwo2005,
        Annote = {Suppl. 1 005MG Times Cited:0 Cited References Count:0},
        Author = {A. Liwo and M. Khalili and H. A. Scheraga},
        Issn = {1742-464X},
        Journal = {Febs Journal},
        Month = {Jul},
        Pages = {359-360},
        Title = {Ab initio simulations of protein folding pathways by molecular dynamics with the united-residue (UNRES) model of polypeptide chains},
        Uri = {<Go to ISI>://000234826102043},
        Volume = 272,
        Year = 2005}

@article{Luty1994,
        Abstract = {We compare the Particle-Particle Particle-Mesh (PPPM) and Ewald methods
    for calculating electrostatic interactions in periodic molecular
    systems. A brief comparison of the theories shows that the methods
    are very similar differing mainly in the technique which is used
    to perform the ''k-space'' or mesh calculation. Because the PPPM
    utilizes the highly efficient numerical Fast Fourier Transform (FFT)
    method it requires significantly less computational effort than
    the Ewald method and scale's almost linearly with system size.},
        Annote = {Qf464 Times Cited:50 Cited References Count:20},
        Author = {B. A. Luty and M. E. Davis and I. G. Tironi and W. F. Vangunsteren},
        Issn = {0892-7022},
        Journal = {Molecular Simulation},
        Number = 1,
        Pages = {11-20},
        Title = {A Comparison of Particle-Particle, Particle-Mesh and Ewald Methods for Calculating Electrostatic Interactions in Periodic Molecular-Systems},
        Uri = {<Go to ISI>://A1994QF46400002},
        Volume = 14,
        Year = 1994}

@book{Marion1990,
        Address = {New York},
        Author = {J.~B. Marion},
        Edition = {2rd},
        Publisher = {Academic Press},
        Title = {Classical Dynamics of Particles and Systems},
        Year = 1990}

@article{Marrink1994,
        Abstract = {To obtain insight in the process of water permeation through a lipid
    membrane, we performed molecular dynamics simulations on a phospholipid
    (DPPC)/water system with atomic detail. Since the actual process
    of permeation is too slow to be studied directly, we deduced the
    permeation rate indirectly via computation of the free energy and
    diffusion rate profiles of a water molecule across the bilayer.
    We conclude that the permeation of water through a lipid membrane
    cannot be described adequately by a simple homogeneous solubility-diffusion
    model. Both the excess free energy and the diffusion rate strongly
    depend on the position in the membrane, as a result from the inhomogeneous
    nature of the membrane. The calculated excess free energy profile
    has a shallow slope and a maximum height of 26 kJ/mol. The diffusion
    rate is highest in the middle of the membrane where the lipid density
    is low. In the interfacial region almost all water molecules are
    bound by the lipid headgroups, and the diffusion turns out to be
    1 order of magnitude smaller. The total transport process is essentially
    determined by the free energy barrier. The rate-limiting step is
    the permeation through the dense part of the lipid tails, where
    the resistance is highest. We found a permeation rate of 7(+/-3)
    x 10(-2) cm/s at 350 K, comparable to experimental values for DPPC
    membranes, if corrected for the temperature of the simulation. Taking
    the inhomogeneity of the membrane into account, we define a new
    ''four-region'' model which seems to be more realistic than the
    ''two-phase'' solubility-diffusion model.},
        Annote = {Ng219 Times Cited:187 Cited References Count:25},
        Author = {S. J. Marrink and H. J. C. Berendsen},
        Issn = {0022-3654},
        Journal = {Journal of Physical Chemistry},
        Month = {Apr 14},
        Number = 15,
        Pages = {4155-4168},
        Title = {Simulation of Water Transport through a Lipid-Membrane},
        Uri = {<Go to ISI>://A1994NG21900040},
        Volume = 98,
        Year = 1994}

@article{Marrink2004,
        Author = {S.~J. Marrink and A.~H. de~Vries and A.~E. Mark},
        Journal = {J. Phys. Chem. B},
        Pages = {750-760},
        Title = {Coarse Grained Model for Semiquantitative Lipid Simulations},
        Volume = 108,
        Year = 2004}

@article{Marsden1998,
        Abstract = {This paper presents a geometric-variational approach to continuous
    and discrete mechanics and field theories. Using multisymplectic
    geometry, we show that the existence of the fundamental geometric
    structures as well as their preservation along solutions can be
    obtained directly from the variational principle. In particular,
    we prove that a unique multisymplectic structure is obtained by
    taking the derivative of an action function, and use this structure
    to prove covariant generalizations of conservation of symplecticity
    and Noether's theorem. Natural discretization schemes for PDEs,
    which have these important preservation properties, then follow
    by choosing a discrete action functional. In the case of mechanics,
    we recover the variational symplectic integrators of Veselov type,
    while for PDEs we obtain covariant spacetime integrators which conserve
    the corresponding discrete multisymplectic form as well as the discrete
    momentum mappings corresponding to symmetries. We show that the
    usual notion of symplecticity along an infinite-dimensional space
    of fields can be naturally obtained by making a spacetime split.
    All of the aspects of our method are demonstrated with a nonlinear
    sine-Gordon equation, including computational results and a comparison
    with other discretization schemes.},
        Annote = {154RH Times Cited:88 Cited References Count:36},
        Author = {J. E. Marsden and G. W. Patrick and S. Shkoller},
        Issn = {0010-3616},
        Journal = {Communications in Mathematical Physics},
        Month = {Dec},
        Number = 2,
        Pages = {351-395},
        Title = {Multisymplectic geometry, variational integrators, and nonlinear PDEs},
        Uri = {<Go to ISI>://000077902200006},
        Volume = 199,
        Year = 1998}

@article{Matthey2004,
        Abstract = {PROTOMOL is a high-performance framework in C++ for rapid prototyping
    of novel algorithms for molecular dynamics and related applications.
    Its flexibility is achieved primarily through the use of inheritance
    and design patterns (object-oriented programming): Performance is
    obtained by using templates that enable generation of efficient
    code for sections critical to performance (generic programming).
    The framework encapsulates important optimizations that can be used
    by developers, such as parallelism in the force computation. Its
    design is based on domain analysis of numerical integrators for
    molecular dynamics (MD) and of fast solvers for the force computation,
    particularly due to electrostatic interactions. Several new and
    efficient algorithms are implemented in PROTOMOL. Finally, it is
    shown that PROTOMOL'S sequential performance is excellent when compared
    to a leading MD program, and that it scales well for moderate number
    of processors. Binaries and source codes for Windows, Linux, Solaris,
    IRIX, HP-UX, and AIX platforms are available under open source license
    at http://protomol.sourceforge.net.},
        Annote = {860EP Times Cited:2 Cited References Count:52},
        Author = {T. Matthey and T. Cickovski and S. Hampton and A. Ko and Q. Ma and M. Nyerges and T. Raeder and T. Slabach and J. A. Izaguirre},
        Issn = {0098-3500},
        Journal = {Acm Transactions on Mathematical Software},
        Month = {Sep},
        Number = 3,
        Pages = {237-265},
        Title = {ProtoMol, an object-oriented framework for prototyping novel algorithms for molecular dynamics},
        Uri = {<Go to ISI>://000224325600001},
        Volume = 30,
        Year = 2004}

@article{McLachlan1993,
        Author = {R.~I McLachlan},
        Journal = {prl},
        Pages = {3043-3046},
        Title = {Explicit Lie-Poisson integration and the Euler equations},
        Volume = 71,
        Year = 1993}

@article{McLachlan1998,
        Abstract = {We give a survey and some new examples of generating functions for
    systems with symplectic structure, systems with a first integral,
    systems that preserve volume, and systems with symmetries and/or
    time-reversing symmetries. Both ODEs and maps are treated, and we
    discuss how generating functions may be used in the structure-preserving
    numerical integration of ODEs with the above properties.},
        Annote = {Yt049 Times Cited:7 Cited References Count:26},
        Author = {R. I. McLachlan and G. R. W. Quispel},
        Issn = {0167-2789},
        Journal = {Physica D},
        Month = {Jan 15},
        Number = {1-2},
        Pages = {298-309},
        Title = {Generating functions for dynamical systems with symmetries, integrals, and differential invariants},
        Uri = {<Go to ISI>://000071558900021},
        Volume = 112,
        Year = 1998}

@article{McLachlan1998a,
        Abstract = {We consider properties of flows, the relationships between them, and
    whether numerical integrators can be made to preserve these properties.
    This is done in the context of automorphisms and antiautomorphisms
    of a certain group generated by maps associated to vector fields.
    This new framework unifies several known constructions. We also
    use the concept of #covariance# of a numerical method with respect
    to a group of coordinate transformations. The main application is
    to explore the relationship between spatial symmetries, reversing
    symmetries, and time symmetry of flows and numerical integrators.},
        Annote = {Zc449 Times Cited:14 Cited References Count:33},
        Author = {R. I. McLachlan and G. R. W. Quispel and G. S. Turner},
        Issn = {0036-1429},
        Journal = {Siam Journal on Numerical Analysis},
        Month = {Apr},
        Number = 2,
        Pages = {586-599},
        Title = {Numerical integrators that preserve symmetries and reversing symmetries},
        Uri = {<Go to ISI>://000072580500010},
        Volume = 35,
        Year = 1998}

@article{McLachlan2005,
        Abstract = {In this paper we revisit the Moser-Veselov description of the free
    rigid body in body coordinates, which, in the 3 x 3 case, can be
    implemented as an explicit, second-order, integrable approximation
    of the continuous solution. By backward error analysis, we study
    the modified vector field which is integrated exactly by the discrete
    algorithm. We deduce that the discrete Moser-Veselov (DMV) is well
    approximated to higher order by time reparametrizations of the continuous
    equations (modified vector field). We use the modified vector field
    to scale the initial data of the DMV to improve the order of the
    approximation and show the equivalence of the DMV and the RATTLE
    algorithm. Numerical integration with these preprocessed initial
    data is several orders of magnitude more accurate than the original
    DMV and RATTLE approach.},
        Annote = {911NS Times Cited:0 Cited References Count:14},
        Author = {R. I. McLachlan and A. Zanna},
        Issn = {1615-3375},
        Journal = {Foundations of Computational Mathematics},
        Month = {Feb},
        Number = 1,
        Pages = {87-123},
        Title = {The discrete Moser-Veselov algorithm for the free rigid body, revisited},
        Uri = {<Go to ISI>://000228011900003},
        Volume = 5,
        Year = 2005}

@article{Meineke2005,
        Abstract = {OOPSE is a new molecular dynamics simulation program that is capable
    of efficiently integrating equations of motion for atom types with
    orientational degrees of freedom (e.g. #sticky# atoms and point
    dipoles). Transition metals can also be simulated using the embedded
    atom method (EAM) potential included in the code. Parallel simulations
    are carried out using the force-based decomposition method. Simulations
    are specified using a very simple C-based meta-data language. A
    number of advanced integrators are included, and the basic integrator
    for orientational dynamics provides substantial improvements over
    older quaternion-based schemes. (C) 2004 Wiley Periodicals, Inc.},
        Annote = {891CF Times Cited:1 Cited References Count:56},
        Author = {M. A. Meineke and C. F. Vardeman and T. Lin and C. J. Fennell and J. D. Gezelter},
        Issn = {0192-8651},
        Journal = jcc,
        Month = {Feb},
        Number = 3,
        Pages = {252-271},
        Title = {OOPSE: An object-oriented parallel simulation engine for molecular dynamics},
        Uri = {<Go to ISI>://000226558200006},
        Volume = 26,
        Year = 2005}

@article{Melchionna1993,
        Abstract = {In this paper we write down equations of motion (following the approach
    pioneered by Hoover) for an exact isothermal-isobaric molecular
    dynamics simulation, and we extend them to multiple thermostating
    rates, to a shape-varying cell and to molecular systems, coherently
    with the previous 'extended system method'. An integration scheme
    is proposed together with a numerical illustration of the method.},
        Annote = {Kq355 Times Cited:172 Cited References Count:17},
        Author = {S. Melchionna and G. Ciccotti and B. L. Holian},
        Issn = {0026-8976},
        Journal = mp,
        Month = {Feb 20},
        Number = 3,
        Pages = {533-544},
        Title = {Hoover Npt Dynamics for Systems Varying in Shape and Size},
        Uri = {<Go to ISI>://A1993KQ35500002},
        Volume = 78,
        Year = 1993}

@article{Memmer2002,
        Abstract = {The phase behaviour of achiral banana-shaped molecules was studied
    by computer simulation. The banana-shaped molecules were described
    by model intermolecular interactions based on the Gay-Berne potential.
    The characteristic molecular structure was considered by joining
    two calamitic Gay-Berne particles through a bond to form a biaxial
    molecule of point symmetry group C-2v with a suitable bending angle.
    The dependence on temperature of systems of N=1024 rigid banana-shaped
    molecules with bending angle phi=140degrees has been studied by
    means of Monte Carlo simulations in the isobaric-isothermal ensemble
    (NpT). On cooling an isotropic system, two phase transitions characterized
    by phase transition enthalpy, entropy and relative volume change
    have been observed. For the first time by computer simulation of
    a many-particle system of banana-shaped molecules, at low temperature
    an untilted smectic phase showing a global phase biaxiality and
    a spontaneous local polarization in the layers, i.e. a local polar
    arrangement of the steric dipoles, with an antiferroelectric-like
    superstructure could be proven, a phase structure which recently
    has been discovered experimentally. Additionally, at intermediate
    temperature a nematic-like phase has been proved, whereas close
    to the transition to the smectic phase hints of a spontaneous achiral
    symmetry breaking have been determined. Here, in the absence of
    a layered structure a helical superstructure has been formed. All
    phases have been characterized by visual representations of selected
    configurations, scalar and pseudoscalar correlation functions, and
    order parameters.},
        Annote = {531HT Times Cited:12 Cited References Count:37},
        Author = {R. Memmer},
        Issn = {0267-8292},
        Journal = {Liquid Crystals},
        Month = {Apr},
        Number = 4,
        Pages = {483-496},
        Title = {Liquid crystal phases of achiral banana-shaped molecules: a computer simulation study},
        Uri = {<Go to ISI>://000174410500001},
        Volume = 29,
        Year = 2002}

@article{Metropolis1949,
        Author = {N. Metropolis and S. Ulam},
        Journal = {J. Am. Stat. Ass.},
        Pages = {335-341},
        Title = {The $\mbox{Monte Carlo}$ Method},
        Volume = 44,
        Year = 1949}

@article{Mielke2004,
        Abstract = {The torque generated by RNA polymerase as it tracks along double-stranded
    DNA can potentially induce long-range structural deformations integral
    to mechanisms of biological significance in both prokaryotes and
    eukaryotes. In this paper, we introduce a dynamic computer model
    for investigating this phenomenon. Duplex DNA is represented as
    a chain of hydrodynamic beads interacting through potentials of
    linearly elastic stretching, bending, and twisting, as well as excluded
    volume. The chain, linear when relaxed, is looped to form two open
    but topologically constrained subdomains. This permits the dynamic
    introduction of torsional stress via a centrally applied torque.
    We simulate by Brownian dynamics the 100 mus response of a 477-base
    pair B-DNA template to the localized torque generated by the prokaryotic
    transcription ensemble. Following a sharp rise at early times, the
    distributed twist assumes a nearly constant value in both subdomains,
    and a succession of supercoiling deformations occurs as superhelical
    stress is increasingly partitioned to writhe. The magnitude of writhe
    surpasses that of twist before also leveling off when the structure
    reaches mechanical equilibrium with the torsional load. Superhelicity
    is simultaneously right handed in one subdomain and left handed
    in the other, as predicted by the #transcription-induced##twin-supercoiled-domain#
    model [L. F. Liu and J. C. Wang, Proc. Natl. Acad. Sci. U.S.A. 84,
    7024 (1987)]. The properties of the chain at the onset of writhing
    agree well with predictions from theory, and the generated stress
    is ample for driving secondary structural transitions in physiological
    DNA. (C) 2004 American Institute of Physics.},
        Annote = {861ZF Times Cited:3 Cited References Count:34},
        Author = {S. P. Mielke and W. H. Fink and V. V. Krishnan and N. Gronbech-Jensen and C. J. Benham},
        Issn = {0021-9606},
        Journal = jcp,
        Month = {Oct 22},
        Number = 16,
        Pages = {8104-8112},
        Title = {Transcription-driven twin supercoiling of a DNA loop: A Brownian dynamics study},
        Uri = {<Go to ISI>://000224456500064},
        Volume = 121,
        Year = 2004}

@article{Naess2001,
        Abstract = {The three Eulerian angles constitute the classical choice of generalized
    coordinates used to describe the three degrees of rotational freedom
    of a rigid body, but it has long been known that this choice yields
    singular equations of motion. The latter is also true when Eulerian
    angles are used in Brownian dynamics analyses of the angular orientation
    of single rigid bodies and segmented polymer chains. Starting from
    kinetic theory we here show that by instead employing the three
    components of Cartesian rotation vectors as the generalized coordinates
    describing angular orientation, no singularity appears in the configuration
    space diffusion equation and the associated Brownian dynamics algorithm.
    The suitability of Cartesian rotation vectors in Brownian dynamics
    simulations of segmented polymer chains with spring-like or ball-socket
    joints is discussed. (C) 2001 Elsevier Science B.V. All rights reserved.},
        Annote = {433TA Times Cited:7 Cited References Count:19},
        Author = {S. N. Naess and H. M. Adland and A. Mikkelsen and A. Elgsaeter},
        Issn = {0378-4371},
        Journal = {Physica A},
        Month = {May 15},
        Number = {3-4},
        Pages = {323-339},
        Title = {Brownian dynamics simulation of rigid bodies and segmented polymer chains. Use of Cartesian rotation vectors as the generalized coordinates describing angular orientations},
        Uri = {<Go to ISI>://000168774800005},
        Volume = 294,
        Year = 2001}

@article{Niori1996,
        Abstract = {The synthesis of a banana-shaped molecule is reported and it is found
    that the smectic phase which it forms is biaxial with the molecules
    packed in the best,direction into a layer. Because of this characteristic
    packing, spontaneous polarization appears parallel to the layer
    and switches on reversal of an applied electric field. This is the
    first obvious example of ferroelectricity in an achiral smectic
    phase and is ascribed to the C-2v symmetry of the molecular packing.},
        Annote = {Ux855 Times Cited:447 Cited References Count:18},
        Author = {T. Niori and T. Sekine and J. Watanabe and T. Furukawa and H. Takezoe},
        Issn = {0959-9428},
        Journal = {Journal of Materials Chemistry},
        Month = {Jul},
        Number = 7,
        Pages = {1231-1233},
        Title = {Distinct ferroelectric smectic liquid crystals consisting of banana shaped achiral molecules},
        Uri = {<Go to ISI>://A1996UX85500025},
        Volume = 6,
        Year = 1996}

@article{Noguchi2002,
        Abstract = {We Studied the structural changes of bilayer vesicles induced by mechanical
    forces using a Brownian dynamics simulation. Two nanoparticles,
    which interact repulsively with amphiphilic molecules, are put inside
    a vesicle. The position of one nanoparticle is fixed, and the other
    is moved by a constant force as in optical-trapping experiments.
    First, the pulled vesicle stretches into a pear or tube shape. Then
    the inner monolayer in the tube-shaped region is deformed, and a
    cylindrical structure is formed between two vesicles. After stretching
    the cylindrical region, fission occurs near the moved vesicle. Soon
    after this the cylindrical region shrinks. The trapping force similar
    to 100 pN is needed to induce the formation of the cylindrical structure
    and fission.},
        Annote = {Part 1 568PX Times Cited:5 Cited References Count:39},
        Author = {H. Noguchi and M. Takasu},
        Issn = {1063-651X},
        Journal = {Physical Review E},
        Month = {may},
        Number = 5,
        Pages = {-},
        Title = {Structural changes of pulled vesicles: A Brownian dynamics simulation},
        Uri = {<Go to ISI>://000176552300084},
        Volume = 65,
        Year = 2002}

@article{Noguchi2001,
        Abstract = {We studied the fusion dynamics of vesicles using a Brownian dynamics
    simulation. Amphiphilic molecules spontaneously form vesicles with
    a bilayer structure. Two vesicles come into contact and form a stalk
    intermediate, in which a necklike structure only connects the outer
    monolayers, as predicted by the stalk hypothesis. We have found
    a new pathway of pore opening from stalks at high temperature: the
    elliptic stalk bends and contact between the ends of the arc-shaped
    stalk leads to pore opening. On the other hand, we have clarified
    that the pore-opening process at low temperature agrees with the
    modified stalk model: a pore is induced by contact between the inner
    monolayers inside the stalk. (C) 2001 American Institute of Physics.},
        Annote = {491UW Times Cited:48 Cited References Count:25},
        Author = {H. Noguchi and M. Takasu},
        Issn = {0021-9606},
        Journal = jcp,
        Month = {Nov 22},
        Number = 20,
        Pages = {9547-9551},
        Title = {Fusion pathways of vesicles: A Brownian dynamics simulation},
        Uri = {<Go to ISI>://000172129300049},
        Volume = 115,
        Year = 2001}

@book{Olver1986,
        Address = {New York},
        Author = {P.J. Olver},
        Publisher = {Springer},
        Title = {Applications of Lie groups to differential equatitons},
        Year = 1986}

@article{Omelyan1998,
        Abstract = {A revised version of the quaternion approach for numerical integration
    of the equations of motion for rigid polyatomic molecules is proposed.
    The modified approach is based on a formulation of the quaternion
    dynamics with constraints. This allows one to resolve the rigidity
    problem rigorously using constraint forces. It is shown that the
    procedure for preservation of molecular rigidity can be realized
    particularly simply within the Verlet algorithm in velocity form.
    We demonstrate that the method presented leads to an improved numerical
    stability with respect to the usual quaternion rescaling scheme
    and it is roughly as good as the cumbersome atomic-constraint technique.
    (C) 1998 American Institute of Physics.},
        Annote = {Yx279 Times Cited:12 Cited References Count:28},
        Author = {I. P. Omelyan},
        Issn = {0894-1866},
        Journal = {Computers in Physics},
        Month = {Jan-Feb},
        Number = 1,
        Pages = {97-103},
        Title = {On the numerical integration of motion for rigid polyatomics: The modified quaternion approach},
        Uri = {<Go to ISI>://000072024300025},
        Volume = 12,
        Year = 1998}

@article{Omelyan1998a,
        Abstract = {An algorithm for numerical integration of the rigid-body equations
    of motion is proposed. The algorithm uses the leapfrog scheme and
    the quantities involved are angular velocities and orientational
    variables that can be expressed in terms of either principal axes
    or quaternions. Due to specific features of the algorithm, orthonormality
    and unit norms of the orientational variables are integrals of motion,
    despite an approximate character of the produced trajectories. It
    is shown that the method presented appears to be the most efficient
    among all such algorithms known.},
        Annote = {101XL Times Cited:8 Cited References Count:22},
        Author = {I. P. Omelyan},
        Issn = {1063-651X},
        Journal = {Physical Review E},
        Month = {Jul},
        Number = 1,
        Pages = {1169-1172},
        Title = {Algorithm for numerical integration of the rigid-body equations of motion},
        Uri = {<Go to ISI>://000074893400151},
        Volume = 58,
        Year = 1998}

@article{Owren1992,
        Abstract = {Continuous, explicit Runge-Kutta methods with the minimal number of
    stages are considered. These methods are continuously differentiable
    if and only if one of the stages is the FSAL evaluation. A characterization
    of a subclass of these methods is developed for orders 3, 4, and
    5. It is shown how the free parameters of these methods can be used
    either to minimize the continuous truncation error coefficients
    or to maximize the stability region. As a representative for these
    methods the fifth-order method with minimized error coefficients
    is chosen, supplied with an error estimation method, and analysed
    by using the DETEST software. The results are compared with a similar
    implementation of the Dormand-Prince 5(4) pair with interpolant,
    showing a significant advantage in the new method for the chosen
    problems.},
        Annote = {Ju936 Times Cited:25 Cited References Count:20},
        Author = {B. Owren and M. Zennaro},
        Issn = {0196-5204},
        Journal = {Siam Journal on Scientific and Statistical Computing},
        Month = {Nov},
        Number = 6,
        Pages = {1488-1501},
        Title = {Derivation of Efficient, Continuous, Explicit Runge-Kutta Methods},
        Uri = {<Go to ISI>://A1992JU93600013},
        Volume = 13,
        Year = 1992}

@article{Palacios1998,
        Abstract = {The stochastic Landau-Lifshitz-Gilbert equation of motion for a classical
    magnetic moment is numerically solved (properly observing the customary
    interpretation of it as a Stratonovich stochastic differential equation),
    in order to study the dynamics of magnetic nanoparticles. The corresponding
    Langevin-dynamics approach allows for the study of the fluctuating
    trajectories of individual magnetic moments, where we have encountered
    remarkable phenomena in the overbarrier rotation process, such as
    crossing-back or multiple crossing of the potential barrier, rooted
    in the gyromagnetic nature of the system. Concerning averaged quantities,
    we study the linear dynamic response of the archetypal ensemble
    of noninteracting classical magnetic moments with axially symmetric
    magnetic anisotropy. The results are compared with different analytical
    expressions used to model the relaxation of nanoparticle ensembles,
    assessing their accuracy. It has been found that, among a number
    of heuristic expressions for the linear dynamic susceptibility,
    only the simple formula proposed by Shliomis and Stepanov matches
    the coarse features of the susceptibility reasonably. By comparing
    the numerical results with the asymptotic formula of Storonkin {Sov.
    Phys. Crystallogr. 30, 489 (1985) [Kristallografiya 30, 841 (1985)]},
    the effects of the intra-potential-well relaxation modes on the
    low-temperature longitudinal dynamic response have been assessed,
    showing their relatively small reflection in the susceptibility
    curves but their dramatic influence on the phase shifts. Comparison
    of the numerical results with the exact zero-damping expression
    for the transverse susceptibility by Garanin, Ishchenko, and Panina
    {Theor. Math. Phys. (USSR) 82, 169 (1990) [Teor. Mat. Fit. 82, 242
    (1990)]}, reveals a sizable contribution of the spread of the precession
    frequencies of the magnetic moment in the anisotropy field to the
    dynamic response at intermediate-to-high temperatures. [S0163-1829
    (98)00446-9].},
        Annote = {146XW Times Cited:66 Cited References Count:45},
        Author = {J. L. Garcia-Palacios and F. J. Lazaro},
        Issn = {0163-1829},
        Journal = {Physical Review B},
        Month = {Dec 1},
        Number = 22,
        Pages = {14937-14958},
        Title = {Langevin-dynamics study of the dynamical properties of small magnetic particles},
        Uri = {<Go to ISI>://000077460000052},
        Volume = 58,
        Year = 1998}

@article{Parr1995,
        Abstract = {Despite the parsing power of LR/LALR algorithms, e.g. YACC, programmers
    often choose to write recursive-descent parsers by hand to obtain
    increased flexibility, better error handling, and ease of debugging.
    We introduce ANTLR, a public-domain parser generator that combines
    the flexibility of hand-coded parsing with the convenience of a
    parser generator, which is a component of PCCTS. ANTLR has many
    features that make it easier to use than other language tools. Most
    important, ANTLR provides predicates which let the programmer systematically
    direct the parse via arbitrary expressions using semantic and syntactic
    context; in practice, the use of predicates eliminates the need
    to hand-tweak the ANTLR output, even for difficult parsing problems.
    ANTLR also integrates the description of lexical and syntactic analysis,
    accepts LL(k) grammars for k > 1 with extended BNF notation, and
    can automatically generate abstract syntax trees. ANTLR is widely
    used, with over 1000 registered industrial and academic users in
    37 countries. It has been ported to many popular systems such as
    the PC, Macintosh, and a variety of UNIX platforms; a commercial
    C++ front-end has been developed as a result of one of our industrial
    collaborations.},
        Annote = {Rk104 Times Cited:19 Cited References Count:10},
        Author = {T. J. Parr and R. W. Quong},
        Issn = {0038-0644},
        Journal = {Software-Practice \& Experience},
        Month = {Jul},
        Number = 7,
        Pages = {789-810},
        Title = {Antlr - a Predicated-Ll(K) Parser Generator},
        Uri = {<Go to ISI>://A1995RK10400004},
        Volume = 25,
        Year = 1995}

@article{Pastor1988,
        Annote = {T1302 Times Cited:61 Cited References Count:26},
        Author = {R. W. Pastor and B. R. Brooks and A. Szabo},
        Issn = {0026-8976},
        Journal = mp,
        Month = {Dec 20},
        Number = 6,
        Pages = {1409-1419},
        Title = {An Analysis of the Accuracy of Langevin and Molecular-Dynamics Algorithms},
        Uri = {<Go to ISI>://A1988T130200011},
        Volume = 65,
        Year = 1988}

@article{Pelzl1999,
        Annote = {220RC Times Cited:313 Cited References Count:49},
        Author = {G. Pelzl and S. Diele and W. Weissflog},
        Issn = {0935-9648},
        Journal = {Advanced Materials},
        Month = {Jul 5},
        Number = 9,
        Pages = {707-724},
        Title = {Banana-shaped compounds - A new field of liquid crystals},
        Uri = {<Go to ISI>://000081680400007},
        Volume = 11,
        Year = 1999}

@article{Perram1985,
        Annote = {Akb93 Times Cited:71 Cited References Count:12},
        Author = {J. W. Perram and M. S. Wertheim},
        Issn = {0021-9991},
        Journal = jcop,
        Number = 3,
        Pages = {409-416},
        Title = {Statistical-Mechanics of Hard Ellipsoids .1. Overlap Algorithm and the Contact Function},
        Uri = {<Go to ISI>://A1985AKB9300008},
        Volume = 58,
        Year = 1985}

@article{Rotne1969,
        Author = {F. Perrin},
        Journal = {J. Chem. Phys.},
        Pages = {4831-4837},
        Title = {Variational treatment of hydrodynamic interaction in polymers},
        Volume = 50,
        Year = 1969}

@article{Perrin1936,
        Author = {F. Perrin},
        Journal = {J. Phys. Radium},
        Pages = {1-11},
        Title = {Mouvement brownien d'un ellipsoid(II). Rotation libre et depolarisation des fluorescences. Translation et diffusion de moleculese ellipsoidales},
        Volume = 7,
        Year = 1936}

@article{Perrin1934,
        Author = {F. Perrin},
        Journal = {J. Phys. Radium},
        Pages = {497-511},
        Title = {Mouvement brownien d'un ellipsoid(I). Dispersion dielectrique pour des molecules ellipsoidales},
        Volume = 5,
        Year = 1934}

@article{Petrache2000,
        Author = {H.~I. Petrache and S.~W. Dodd and M.~F. Brown},
        Journal = bj,
        Pages = {3172-3192},
        Title = {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by $^2\text{H}$ {\sc nmr} Spectroscopy},
        Volume = 79,
        Year = 2000}

@article{Petrache1998,
        Abstract = {X-ray diffraction data taken at high instrumental resolution were
    obtained for EPC and DMPC under various osmotic pressures, primarily
    at T = 30 degrees C. The headgroup thickness D-HH was obtained from
    relative electron density profiles. By using volumetric results
    and by comparing to gel phase DPPC we obtain areas A(EPC)(F) = 69.4
    +/- 1.1 Angstrom(2) and A(DMPC)(F) = 59.7 +/- 0.2 Angstrom(2). The
    analysis also gives estimates for the areal compressibility K-A.
    The A(F) results lead to other structural results regarding membrane
    thickness and associated waters. Using the recently determined absolute
    electrons density profile of DPPC, the AF results also lead to absolute
    electron density profiles and absolute continuous transforms \F(q)\
    for EPC and DMPC, Limited measurements of temperature dependence
    show directly that fluctuations increase with increasing temperature
    and that a small decrease in bending modulus K-c accounts for the
    increased water spacing reported by Simon et al. (1995) Biophys.
    J. 69, 1473-1483. (C) 1998 Elsevier Science Ireland Ltd. All rights
    reserved.},
        Annote = {130AT Times Cited:98 Cited References Count:39},
        Author = {H. I. Petrache and S. Tristram-Nagle and J. F. Nagle},
        Issn = {0009-3084},
        Journal = {Chemistry and Physics of Lipids},
        Month = {Sep},
        Number = 1,
        Pages = {83-94},
        Title = {Fluid phase structure of EPC and DMPC bilayers},
        Uri = {<Go to ISI>://000076497600007},
        Volume = 95,
        Year = 1998}

@article{Powles1973,
        Author = {J.~G. Powles},
        Journal = {Advan. Phys.},
        Pages = {1-56},
        Title = {A general ellipsoid can not always serve as a modle for the rotational diffusion properties of arbitrary shaped rigid molecules},
        Volume = 22,
        Year = 1973}

@article{Recio2004,
        Abstract = {Protein recognition is one of the most challenging and intriguing
    problems in structural biology. Despite all the available structural,
    sequence and biophysical information about protein-protein complexes,
    the physico-chemical patterns, if any, that make a protein surface
    likely to be involved in protein-protein interactions, remain elusive.
    Here, we apply protein docking simulations and analysis of the interaction
    energy landscapes to identify protein-protein interaction sites.
    The new protocol for global docking based on multi-start global
    energy optimization of an allatom model of the ligand, with detailed
    receptor potentials and atomic solvation parameters optimized in
    a training set of 24 complexes, explores the conformational space
    around the whole receptor without restrictions. The ensembles of
    the rigid-body docking solutions generated by the simulations were
    subsequently used to project the docking energy landscapes onto
    the protein surfaces. We found that highly populated low-energy
    regions consistently corresponded to actual binding sites. The procedure
    was validated on a test set of 21 known protein-protein complexes
    not used in the training set. As much as 81% of the predicted high-propensity
    patch residues were located correctly in the native interfaces.
    This approach can guide the design of mutations on the surfaces
    of proteins, provide geometrical details of a possible interaction,
    and help to annotate protein surfaces in structural proteomics.
    (C) 2003 Elsevier Ltd. All rights reserved.},
        Annote = {763GQ Times Cited:21 Cited References Count:59},
        Author = {J. Fernandez-Recio and M. Totrov and R. Abagyan},
        Issn = {0022-2836},
        Journal = jmb,
        Month = {Jan 16},
        Number = 3,
        Pages = {843-865},
        Title = {Identification of protein-protein interaction sites from docking energy landscapes},
        Uri = {<Go to ISI>://000188066900016},
        Volume = 335,
        Year = 2004}

@article{Reddy2006,
        Abstract = {An overview on the recent developments in the field of liquid crystalline
    bent-core molecules (so-called banana liquid crystals) is given.
    After some basic issues, dealing with general aspects of the systematisation
    of the mesophases, development of polar order and chirality in this
    class of LC systems and explaining some general structure-property
    relationships, we focus on fascinating new developments in this
    field, such as modulated, undulated and columnar phases, so-called
    B7 phases, phase biaxiality, ferroelectric and antiferroelectric
    polar order in smectic and columnar phases, amplification and switching
    of chirality and the spontaneous formation of superstructural and
    supramolecular chirality.},
        Annote = {021NS Times Cited:2 Cited References Count:316},
        Author = {R. A. Reddy and C. Tschierske},
        Issn = {0959-9428},
        Journal = {Journal of Materials Chemistry},
        Number = 10,
        Pages = {907-961},
        Title = {Bent-core liquid crystals: polar order, superstructural chirality and spontaneous desymmetrisation in soft matter systems},
        Uri = {<Go to ISI>://000235990500001},
        Volume = 16,
        Year = 2006}

@article{Reich1999,
        Abstract = {Backward error analysis has become an important tool for understanding
    the long time behavior of numerical integration methods. This is
    true in particular for the integration of Hamiltonian systems where
    backward error analysis can be used to show that a symplectic method
    will conserve energy over exponentially long periods of time. Such
    results are typically based on two aspects of backward error analysis:
    (i) It can be shown that the modified vector fields have some qualitative
    properties which they share with the given problem and (ii) an estimate
    is given for the difference between the best interpolating vector
    field and the numerical method. These aspects have been investigated
    recently, for example, by Benettin and Giorgilli in [J. Statist.
    Phys., 74 (1994), pp. 1117-1143], by Hairer in [Ann. Numer. Math.,
    1 (1994), pp. 107-132], and by Hairer and Lubich in [Numer. Math.,
    76 (1997), pp. 441-462]. In this paper we aim at providing a unifying
    framework and a simplification of the existing results and corresponding
    proofs. Our approach to backward error analysis is based on a simple
    recursive definition of the modified vector fields that does not
    require explicit Taylor series expansion of the numerical method
    and the corresponding flow maps as in the above-cited works. As
    an application we discuss the long time integration of chaotic Hamiltonian
    systems and the approximation of time averages along numerically
    computed trajectories.},
        Annote = {237HV Times Cited:43 Cited References Count:41},
        Author = {S. Reich},
        Issn = {0036-1429},
        Journal = {Siam Journal on Numerical Analysis},
        Month = {Sep 8},
        Number = 5,
        Pages = {1549-1570},
        Title = {Backward error analysis for numerical integrators},
        Uri = {<Go to ISI>://000082650600010},
        Volume = 36,
        Year = 1999}

@article{Ros2005,
        Abstract = {The recent literature in the field of liquid crystals shows that banana-shaped
    mesogenic materials represent a bewitching and stimulating field
    of research that is interesting both academically and in terms of
    applications. Numerous topics are open to investigation in this
    area because of the rich phenomenology and new possibilities that
    these materials offer. The principal concepts in this area are reviewed
    along with recent results. In addition, new directions to stimulate
    further research activities are highlighted.},
        Annote = {990XA Times Cited:3 Cited References Count:72},
        Author = {M. B. Ros and J. L. Serrano and M. R. {de la Fuente} and C. L. Folcia},
        Issn = {0959-9428},
        Journal = {Journal of Materials Chemistry},
        Number = 48,
        Pages = {5093-5098},
        Title = {Banana-shaped liquid crystals: a new field to explore},
        Uri = {<Go to ISI>://000233775500001},
        Volume = 15,
        Year = 2005}

@article{Roux1991,
        Abstract = {The mobility of water, Na+. and K+ has been calculated inside a periodic
    poly-(L,D)-alanine beta-helix, a model for the interior of the gramicidin
    channel. Because of the different dynamical regimes for the three
    species (high barrier for Na+, low barrier for K+, almost free diffusion
    for water), different methods are used to calculate the mobilities.
    By use of activated dynamics and a potential of mean force determined
    previously (Roux, B.; Karplus, M. Biophys. J. 1991, 59, 961), the
    barrier crossing rate of Na+ ion is determined. The motion of Na+
    at the transition state is controlled by local interactions and
    collisions with the neighboring carbonyls and the two nearest water
    molecules. There are significant deviations from transition-state
    theory; the transmission coefficient is equal to 0.11. The water
    and K+ motions are found to be well described by a diffusive model;
    the motion of K+ appears to be controlled by the diffusion of water.
    The time-dependent friction functions of Na+ and K+ ions in the
    periodic beta-helix are calculated and analyzed by using a generalized
    Langevin equation approach. Both Na+ and K+ suffer many rapid collisions,
    and their dynamics is overdamped and noninertial. Thus, the selectivity
    sequence of ions in the beta-helix is not influenced strongly by
    their masses.},
        Annote = {Fr756 Times Cited:97 Cited References Count:65},
        Author = {B. Roux and M. Karplus},
        Issn = {0022-3654},
        Journal = {Journal of Physical Chemistry},
        Month = {Jun 13},
        Number = 12,
        Pages = {4856-4868},
        Title = {Ion-Transport in a Gramicidin-Like Channel - Dynamics and Mobility},
        Uri = {<Go to ISI>://A1991FR75600049},
        Volume = 95,
        Year = 1991}

@article{Roy2005,
        Abstract = {A vast majority of compounds with bent core or banana shaped molecules
    exhibit the phase sequence B-6-B-1-B-2 as the chain length is increased
    in a homologous series. The B-6 phase has an intercalated fluid
    lamellar structure with a layer spacing of half the molecular length.
    The B-1 phase has a two dimensionally periodic rectangular columnar
    structure. The B-2 phase has a monolayer fluid lamellar structure
    with molecules tilted with respect to the layer normal. Neglecting
    the tilt order of the molecules in the B-2 phase, we have developed
    a frustrated packing model to describe this phase sequence qualitatively.
    The model has some analogy with that of the frustrated smectics
    exhibited by highly polar rod like molecules.},
        Annote = {985FW Times Cited:0 Cited References Count:30},
        Author = {A. Roy and N. V. Madhusudana},
        Issn = {1292-8941},
        Journal = {European Physical Journal E},
        Month = {Nov},
        Number = 3,
        Pages = {253-258},
        Title = {A frustrated packing model for the B-6-B-1-SmAP(A) sequence of phases in banana shaped molecules},
        Uri = {<Go to ISI>://000233363300002},
        Volume = 18,
        Year = 2005}

@article{Ryckaert1977,
        Annote = {Cz253 Times Cited:3680 Cited References Count:7},
        Author = {J. P. Ryckaert and G. Ciccotti and H. J. C. Berendsen},
        Issn = {0021-9991},
        Journal = jcop,
        Number = 3,
        Pages = {327-341},
        Title = {Numerical-Integration of Cartesian Equations of Motion of a System with Constraints - Molecular-Dynamics of N-Alkanes},
        Uri = {<Go to ISI>://A1977CZ25300007},
        Volume = 23,
        Year = 1977}

@article{Sagui1999,
        Abstract = {Current computer simulations of biomolecules typically make use of
    classical molecular dynamics methods, as a very large number (tens
    to hundreds of thousands) of atoms are involved over timescales
    of many nanoseconds. The methodology for treating short-range bonded
    and van der Waals interactions has matured. However, long-range
    electrostatic interactions still represent a bottleneck in simulations.
    In this article, we introduce the basic issues for an accurate representation
    of the relevant electrostatic interactions. In spite of the huge
    computational time demanded by most biomolecular systems, it is
    no longer necessary to resort to uncontrolled approximations such
    as the use of cutoffs. In particular, we discuss the Ewald summation
    methods, the fast particle mesh methods, and the fast multipole
    methods. We also review recent efforts to understand the role of
    boundary conditions in systems with long-range interactions, and
    conclude with a short perspective on future trends.},
        Annote = {213KJ Times Cited:126 Cited References Count:73},
        Author = {C. Sagui and T. A. Darden},
        Issn = {1056-8700},
        Journal = {Annual Review of Biophysics and Biomolecular Structure},
        Pages = {155-179},
        Title = {Molecular dynamics simulations of biomolecules: Long-range electrostatic effects},
        Uri = {<Go to ISI>://000081271400008},
        Volume = 28,
        Year = 1999}

@article{Sandu1999,
        Abstract = {Numerical resonance artifacts have become recognized recently as a
    limiting factor to increasing the timestep in multiple-timestep
    (MTS) biomolecular dynamics simulations. At certain timesteps correlated
    to internal motions (e.g., 5 fs, around half the period of the fastest
    bond stretch, T-min), visible inaccuracies or instabilities can
    occur. Impulse-MTS schemes are vulnerable to these resonance errors
    since large energy pulses are introduced to the governing dynamics
    equations when the slow forces are evaluated. We recently showed
    that such resonance artifacts can be masked significantly by applying
    extrapolative splitting to stochastic dynamics. Theoretical and
    numerical analyses of force-splitting integrators based on the Verlet
    discretization are reported here for linear models to explain these
    observations and to suggest how to construct effective integrators
    for biomolecular dynamics that balance stability with accuracy.
    Analyses for Newtonian dynamics demonstrate the severe resonance
    patterns of the Impulse splitting, with this severity worsening
    with the outer timestep. Delta t: Constant Extrapolation is generally
    unstable, but the disturbances do not grow with Delta t. Thus. the
    stochastic extrapolative combination can counteract generic instabilities
    and largely alleviate resonances with a sufficiently strong Langevin
    heat-bath coupling (gamma), estimates for which are derived here
    based on the fastest and slowest motion periods. These resonance
    results generally hold for nonlinear test systems: a water tetramer
    and solvated protein. Proposed related approaches such as Extrapolation/Correction
    and Midpoint Extrapolation work better than Constant Extrapolation
    only for timesteps less than T-min/2. An effective extrapolative
    stochastic approach for biomolecules that balances long-timestep
    stability with good accuracy for the fast subsystem is then applied
    to a biomolecule using a three-class partitioning: the medium forces
    are treated by Midpoint Extrapolation via position Verlet, and the
    slow forces are incorporated by Constant Extrapolation. The resulting
    algorithm (LN) performs well on a solvated protein system in terms
    of thermodynamic properties and yields an order of magnitude speedup
    with respect to single-timestep Langevin trajectories. Computed
    spectral density functions also show how the Newtonian modes can
    be approximated by using a small gamma in the range Of 5-20 ps(-1).
    (C) 1999 Academic Press.},
        Annote = {194FM Times Cited:14 Cited References Count:32},
        Author = {A. Sandu and T. Schlick},
        Issn = {0021-9991},
        Journal = jcop,
        Month = {May 1},
        Number = 1,
        Pages = {74-113},
        Title = {Masking resonance artifacts in force-splitting methods for biomolecular simulations by extrapolative Langevin dynamics},
        Uri = {<Go to ISI>://000080181500004},
        Volume = 151,
        Year = 1999}

@article{Sasaki2004,
        Abstract = {Tris(2-aminoethyl) amine derivatives with appended urea and sulfonamide
    groups are shown to facilitate the translocation of fluorescent
    phospholipid probes and endogenous phosphatidylserine across vesicle
    and erythrocyte cell membranes. The synthetic translocases appear
    to operate by binding to the phospholipid head groups and forming
    lipophilic supramolecular complexes which diffuse through the non-polar
    interior of the bilayer membrane.},
        Annote = {760PX Times Cited:8 Cited References Count:25},
        Author = {Y. Sasaki and R. Shukla and B. D. Smith},
        Issn = {1477-0520},
        Journal = {Organic \& Biomolecular Chemistry},
        Number = 2,
        Pages = {214-219},
        Title = {Facilitated phosphatidylserine flip-flop across vesicle and cell membranes using urea-derived synthetic translocases},
        Uri = {<Go to ISI>://000187843800012},
        Volume = 2,
        Year = 2004}

@article{Satoh1996,
        Abstract = {The effects of dipole-dipole interaction on mesophase formation are
    investigated with a Monte Carlo simulation using the dipolar Gay-Berne
    potential. It is shown that the dipole moment at the end of a molecule
    causes a shift in the nematic-isotropic transition toward higher
    temperature and a spread of the temperature range of the nematic
    phase and that layer structures with various interdigitations are
    formed in the smectic phase.},
        Annote = {Uq975 Times Cited:32 Cited References Count:33},
        Author = {K. Satoh and S. Mita and S. Kondo},
        Issn = {0009-2614},
        Journal = {Chemical Physics Letters},
        Month = {Jun 7},
        Number = {1-3},
        Pages = {99-104},
        Title = {Monte Carlo simulations using the dipolar Gay-Berne model: Effect of terminal dipole moment on mesophase formation},
        Uri = {<Go to ISI>://A1996UQ97500017},
        Volume = 255,
        Year = 1996}

@article{Schaps1999,
        Annote = {163EC Times Cited:0 Cited References Count:0},
        Author = {G. L. Schaps},
        Issn = {1044-789X},
        Journal = {Dr Dobbs Journal},
        Month = {Mar},
        Number = 3,
        Pages = {84-+},
        Title = {Compiler construction with ANTLR and Java - Tools for building tools},
        Uri = {<Go to ISI>://000078389200023},
        Volume = 24,
        Year = 1999}

@article{Shen2002,
        Abstract = {Met-enkephalin is one of the smallest opiate peptides. Yet, its dynamical
    structure and receptor docking mechanism are still not well understood.
    The conformational dynamics of this neuron peptide in liquid water
    are studied here by using all-atom molecular dynamics (MID) and
    implicit water Langevin dynamics (LD) simulations with AMBER potential
    functions and the three-site transferable intermolecular potential
    (TIP3P) model for water. To achieve the same simulation length in
    physical time, the full MID simulations require 200 times as much
    CPU time as the implicit water LID simulations. The solvent hydrophobicity
    and dielectric behavior are treated in the implicit solvent LD simulations
    by using a macroscopic solvation potential, a single dielectric
    constant, and atomic friction coefficients computed using the accessible
    surface area method with the TIP3P model water viscosity as determined
    here from MID simulations for pure TIP3P water. Both the local and
    the global dynamics obtained from the implicit solvent LD simulations
    agree very well with those from the explicit solvent MD simulations.
    The simulations provide insights into the conformational restrictions
    that are associated with the bioactivity of the opiate peptide dermorphin
    for the delta-receptor.},
        Annote = {540MH Times Cited:36 Cited References Count:45},
        Author = {M. Y. Shen and K. F. Freed},
        Issn = {0006-3495},
        Journal = bj,
        Month = {Apr},
        Number = 4,
        Pages = {1791-1808},
        Title = {Long time dynamics of met-enkephalin: Comparison of explicit and implicit solvent models},
        Uri = {<Go to ISI>://000174932400010},
        Volume = 82,
        Year = 2002}

@article{Shillcock2005,
        Annote = {901QJ Times Cited:9 Cited References Count:23},
        Author = {J. C. Shillcock and R. Lipowsky},
        Issn = {1476-1122},
        Journal = {Nature Materials},
        Month = {Mar},
        Number = 3,
        Pages = {225-228},
        Title = {Tension-induced fusion of bilayer membranes and vesicles},
        Uri = {<Go to ISI>://000227296700019},
        Volume = 4,
        Year = 2005}

@article{Shimada1993,
        Abstract = {To make improved treatments of electrostatic interactions in biomacromolecular
    simulations, two possibilities are considered. The first is the
    famous particle-particle and particle-mesh (PPPM) method developed
    by Hockney and Eastwood, and the second is a new one developed here
    in their spirit but by the use of the multipole expansion technique
    suggested by Ladd. It is then numerically found that the new PPPM
    method gives more accurate results for a two-particle system at
    small separation of particles. Preliminary numerical examination
    of the various computational methods for a single configuration
    of a model BPTI-water system containing about 24,000 particles indicates
    that both of the PPPM methods give far more accurate values with
    reasonable computational cost than do the conventional truncation
    methods. It is concluded the two PPPM methods are nearly comparable
    in overall performance for the many-particle systems, although the
    first method has the drawback that the accuracy in the total electrostatic
    energy is not high for configurations of charged particles randomly
    generated.},
        Annote = {Lh164 Times Cited:27 Cited References Count:47},
        Author = {J. Shimada and H. Kaneko and T. Takada},
        Issn = {0192-8651},
        Journal = jcc,
        Month = {Jul},
        Number = 7,
        Pages = {867-878},
        Title = {Efficient Calculations of Coulombic Interactions in Biomolecular Simulations with Periodic Boundary-Conditions},
        Uri = {<Go to ISI>://A1993LH16400011},
        Volume = 14,
        Year = 1993}

@article{Skeel2002,
        Abstract = {The best simple method for Newtonian molecular dynamics is indisputably
    the leapfrog Stormer-Verlet method. The appropriate generalization
    to simple Langevin dynamics is unclear. An analysis is presented
    comparing an 'impulse method' (kick; fluctuate; kick), the 1982
    method of van Gunsteren and Berendsen, and the Brunger-Brooks-Karplus
    (BBK) method. It is shown how the impulse method and the van Gunsteren-Berendsen
    methods can be implemented as efficiently as the BBK method. Other
    considerations suggest that the impulse method is the best basic
    method for simple Langevin dynamics, with the van Gunsteren-Berendsen
    method a close contender.},
        Annote = {633RX Times Cited:8 Cited References Count:22},
        Author = {R. D. Skeel and J. A. Izaguirre},
        Issn = {0026-8976},
        Journal = mp,
        Month = {Dec 20},
        Number = 24,
        Pages = {3885-3891},
        Title = {An impulse integrator for Langevin dynamics},
        Uri = {<Go to ISI>://000180297200014},
        Volume = 100,
        Year = 2002}

@article{Skeel1997,
        Abstract = {The following integration methods for special second-order ordinary
    differential equations are studied: leapfrog, implicit midpoint,
    trapezoid, Stormer-Verlet, and Cowell-Numerov. We show that all
    are members, or equivalent to members, of a one-parameter family
    of schemes. Some methods have more than one common form, and we
    discuss a systematic enumeration of these forms. We also present
    a stability and accuracy analysis based on the idea of ''modified
    equations'' and a proof of symplecticness. It follows that Cowell-Numerov
    and ''LIM2'' (a method proposed by Zhang and Schlick) are symplectic.
    A different interpretation of the values used by these integrators
    leads to higher accuracy and better energy conservation. Hence,
    we suggest that the straightforward analysis of energy conservation
    is misleading.},
        Annote = {We981 Times Cited:30 Cited References Count:35},
        Author = {R. D. Skeel and G. H. Zhang and T. Schlick},
        Issn = {1064-8275},
        Journal = {Siam Journal on Scientific Computing},
        Month = {Jan},
        Number = 1,
        Pages = {203-222},
        Title = {A family of symplectic integrators: Stability, accuracy, and molecular dynamics applications},
        Uri = {<Go to ISI>://A1997WE98100012},
        Volume = 18,
        Year = 1997}

@article{Tao2005,
        Abstract = {Recently a microscopic theory for the dynamics of suspensions of long
    thin rigid rods was presented, confirming and expanding the well-known
    theory by Doi and Edwards [The Theory of Polymer Dynamics (Clarendon,
    Oxford, 1986)] and Kuzuu [J. Phys. Soc. Jpn. 52, 3486 (1983)]. Here
    this theory is put to the test by comparing it against computer
    simulations. A Brownian dynamics simulation program was developed
    to follow the dynamics of the rods, with a length over a diameter
    ratio of 60, on the Smoluchowski time scale. The model accounts
    for excluded volume interactions between rods, but neglects hydrodynamic
    interactions. The self-rotational diffusion coefficients D-r(phi)
    of the rods were calculated by standard methods and by a new, more
    efficient method based on calculating average restoring torques.
    Collective decay of orientational order was calculated by means
    of equilibrium and nonequilibrium simulations. Our results show
    that, for the currently accessible volume fractions, the decay times
    in both cases are virtually identical. Moreover, the observed decay
    of diffusion coefficients with volume fraction is much quicker than
    predicted by the theory, which is attributed to an oversimplification
    of dynamic correlations in the theory. (c) 2005 American Institute
    of Physics.},
        Annote = {943DN Times Cited:3 Cited References Count:26},
        Author = {Y. G. Tao and W. K. {den Otter} and J. T. Padding and J. K. G. Dhont and W. J. Briels},
        Issn = {0021-9606},
        Journal = jcp,
        Month = {Jun 22},
        Number = 24,
        Pages = {-},
        Title = {Brownian dynamics simulations of the self- and collective rotational diffusion coefficients of rigid long thin rods},
        Uri = {<Go to ISI>://000230332400077},
        Volume = 122,
        Year = 2005}

@book{Tolman1979,
        Address = {New York},
        Author = {R.~C. Tolman},
        Chapter = 2,
        Pages = {19-22},
        Publisher = {Dover Publications, Inc.},
        Title = {The Principles of Statistical Mechanics},
        Year = 1979}

@article{Tu1995,
        Abstract = {We report a constant pressure and temperature molecular dynamics simulation
    of a fully hydrated liquid crystal (L(alpha) phase bilayer of dipalmitoylphosphatidylcholine
    at 50 degrees C and 28 water molecules/lipid. We have shown that
    the bilayer is stable throughout the 1550-ps simulation and have
    demonstrated convergence of the system dimensions. Several important
    aspects of the bilayer structure have been investigated and compared
    favorably with experimental results. For example, the average positions
    of specific carbon atoms along the bilayer normal agree well with
    neutron diffraction data, and the electron density profile is in
    accord with x-ray diffraction results. The hydrocarbon chain deuterium
    order parameters agree reasonably well with NMR results for the
    middles of the chains, but the simulation predicts too much order
    at the chain ends. In spite of the deviations in the order parameters,
    the hydrocarbon chain packing density appears to be essentially
    correct, inasmuch as the area/lipid and bilayer thickness are in
    agreement with the most refined experimental estimates. The deuterium
    order parameters for the glycerol and choline groups, as well as
    the phosphorus chemical shift anisotropy, are in qualitative agreement
    with those extracted from NMR measurements.},
        Annote = {Tv018 Times Cited:108 Cited References Count:34},
        Author = {K. Tu and D. J. Tobias and M. L. Klein},
        Issn = {0006-3495},
        Journal = bj,
        Month = {Dec},
        Number = 6,
        Pages = {2558-2562},
        Title = {Constant pressure and temperature molecular dynamics simulation of a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine bilayer},
        Uri = {<Go to ISI>://A1995TV01800037},
        Volume = 69,
        Year = 1995}

@article{Tuckerman1992,
        Abstract = {The Trotter factorization of the Liouville propagator is used to generate
    new reversible molecular dynamics integrators. This strategy is
    applied to derive reversible reference system propagator algorithms
    (RESPA) that greatly accelerate simulations of systems with a separation
    of time scales or with long range forces. The new algorithms have
    all of the advantages of previous RESPA integrators but are reversible,
    and more stable than those methods. These methods are applied to
    a set of paradigmatic systems and are shown to be superior to earlier
    methods. It is shown how the new RESPA methods are related to predictor-corrector
    integrators. Finally, we show how these methods can be used to accelerate
    the integration of the equations of motion of systems with Nose
    thermostats.},
        Annote = {Je891 Times Cited:680 Cited References Count:19},
        Author = {M. Tuckerman and B. J. Berne and G. J. Martyna},
        Issn = {0021-9606},
        Journal = jcp,
        Month = {Aug 1},
        Number = 3,
        Pages = {1990-2001},
        Title = {Reversible Multiple Time Scale Molecular-Dynamics},
        Uri = {<Go to ISI>://A1992JE89100044},
        Volume = 97,
        Year = 1992}

@book{Varadarajan1974,
        Address = {New York},
        Author = {V.S. Varadarajan},
        Publisher = {Prentice-Hall},
        Title = {Lie groups, Lie algebras, and their representations},
        Year = 1974}

@article{Vincent1995,
        Abstract = {We have implemented a portable parallel version of the macromolecular
    modeling package AMBER4. The message passing paradigm was used.
    All message passing constructs are compliant with the Message Passing
    Interface (MPI) standard. The molecular dynamics/minimization module
    MINMD and the free-energy perturbation module Gibbs have been implemented
    in parallel on a number of machines, including a Gray T3D, an IBM
    SP1/SP2, and a collection of networked workstations. In addition,
    the code has been tested with an MPI implementation from Argonne
    National Laboratories/Mississippi State University which runs on
    many parallel machines. The goal of this work is to decrease the
    amount of time required to perform molecular dynamics simulations.
    Performance results for a Lipid bilayer molecular dynamics simulation
    on a Gray T3D, an IBM SP1/SPZ and a Gray C90 are compared. (C) 1995
    by John Wiley & Sons, Inc.},
        Annote = {Ta403 Times Cited:16 Cited References Count:23},
        Author = {J. J. Vincent and K. M. Merz},
        Issn = {0192-8651},
        Journal = jcc,
        Month = {Nov},
        Number = 11,
        Pages = {1420-1427},
        Title = {A Highly Portable Parallel Implementation of Amber4 Using the Message-Passing Interface Standard},
        Uri = {<Go to ISI>://A1995TA40300009},
        Volume = 16,
        Year = 1995}

@article{Wegener1979,
        Author = {W.~A. Wegener, V.~J. Koester and R.~M. Dowben},
        Journal = {Proc. Natl. Acad. Sci.},
        Number = 12,
        Pages = {6356-6360},
        Title = {A general ellipsoid can not always serve as a modle for the rotational diffusion properties of arbitrary shaped rigid molecules},
        Volume = 76,
        Year = 1979}

@article{Wilson2006,
        Author = {G.~V. Wilson},
        Journal = {American Scientist},
        Title = {Where's the Real Bottleneck in Scientific Computing?},
        Volume = 94,
        Year = 2006}

@article{Withers2003,
        Abstract = {The effects of longitudinal quadrupole moments on the formation of
    liquid crystalline phases are studied by means of constant NPT Monte
    Carlo simulation methods. The popular Gay-Berne model mesogen is
    used as the reference fluid, which displays the phase sequences
    isotropic-smectic A-smectic B and isotropic-smectic B at high (T*=2.0)
    and low (T*=1.5) temperatures, respectively. With increasing quadrupole
    magnitude the smectic phases are observed to be stabilized with
    respect to the isotropic liquid, while the smectic B is destabilized
    with respect to the smectic A. At the lower temperature, a sufficiently
    large quadrupole magnitude results in the injection of the smectic
    A phase into the phase sequence and the replacement of the smectic
    B phase by the tilted smectic J phase. The nematic phase is also
    injected into the phase sequence at both temperatures considered,
    and ultimately for sufficiently large quadrupole magnitudes no coherent
    layered structures were observed. The stabilization of the smectic
    A phase supports the commonly held belief that, while the inclusion
    of polar groups is not a prerequisite for the formation of the smectic
    A phase, quadrupolar interactions help to increase the temperature
    and pressure range for which the smectic A phase is observed. The
    quality of the layered structure is worsened with increasing quadrupole
    magnitude. This behavior, along with the injection of the nematic
    phase into the phase sequence, indicate that the general tendency
    of the quadrupolar interactions is to destabilize the layered structure.
    A pressure dependence upon the smectic layer spacing is observed.
    This behavior is in much closer agreement with experimental findings
    than has been observed previously for nonpolar Gay-Berne and hard
    spherocylinder models. (C) 2003 American Institute of Physics.},
        Annote = {738EF Times Cited:3 Cited References Count:43},
        Author = {I. M. Withers},
        Issn = {0021-9606},
        Journal = jcp,
        Month = {Nov 15},
        Number = 19,
        Pages = {10209-10223},
        Title = {Effects of longitudinal quadrupoles on the phase behavior of a Gay-Berne fluid},
        Uri = {<Go to ISI>://000186273200027},
        Volume = 119,
        Year = 2003}

@article{Wolf1999,
        Abstract = {Based on a recent result showing that the net Coulomb potential in
    condensed ionic systems is rather short ranged, an exact and physically
    transparent method permitting the evaluation of the Coulomb potential
    by direct summation over the r(-1) Coulomb pair potential is presented.
    The key observation is that the problems encountered in determining
    the Coulomb energy by pairwise, spherically truncated r(-1) summation
    are a direct consequence of the fact that the system summed over
    is practically never neutral. A simple method is developed that
    achieves charge neutralization wherever the r(-1) pair potential
    is truncated. This enables the extraction of the Coulomb energy,
    forces, and stresses from a spherically truncated, usually charged
    environment in a manner that is independent of the grouping of the
    pair terms. The close connection of our approach with the Ewald
    method is demonstrated and exploited, providing an efficient method
    for the simulation of even highly disordered ionic systems by direct,
    pairwise r(-1) summation with spherical truncation at rather short
    range, i.e., a method which fully exploits the short-ranged nature
    of the interactions in ionic systems. The method is validated by
    simulations of crystals, liquids, and interfacial systems, such
    as free surfaces and grain boundaries. (C) 1999 American Institute
    of Physics. [S0021-9606(99)51517-1].},
        Annote = {189PD Times Cited:70 Cited References Count:34},
        Author = {D. Wolf and P. Keblinski and S. R. Phillpot and J. Eggebrecht},
        Issn = {0021-9606},
        Journal = jcp,
        Month = {May 1},
        Number = 17,
        Pages = {8254-8282},
        Title = {Exact method for the simulation of Coulombic systems by spherically truncated, pairwise r(-1) summation},
        Uri = {<Go to ISI>://000079913000008},
        Volume = 110,
        Year = 1999}

@article{Yoshida1990,
        Annote = {Ej798 Times Cited:492 Cited References Count:9},
        Author = {H. Yoshida},
        Issn = {0375-9601},
        Journal = {Physics Letters A},
        Month = {Nov 12},
        Number = {5-7},
        Pages = {262-268},
        Title = {Construction of Higher-Order Symplectic Integrators},
        Uri = {<Go to ISI>://A1990EJ79800009},
        Volume = 150,
        Year = 1990}

@article{Blum1972,
        Author = {L. Blum and A.~J. Torruella},
        Journal = jcp,
        Number = 1,
        Pages = {303-309},
        Title = {Computer simulations of bilayer membranes: Self-assembly and interfacial tension},
        Volume = 56,
        Year = 1972}

@article{Stone1978,
        Author = {A.~J. Stone},
        Journal = mp,
        Number = 1,
        Pages = {241-256},
        Title = {The description of bimolecular potentials, forces and torques: the S and V function expansions},
        Volume = 36,
        Year = 1978}

@article{Berardi2003,
        Author = {R. Berardi, M. Cecchini and C. Zannoni},
        Journal = jcp,
        Number = 18,
        Pages = {9933-9946},
        Title = {A Monte Carlo study of the chiral columnar organizations of dissymmetric discotic mesogens},
        Volume = 119,
        Year = 2003}

@article{Beard2000,
        Author = {D. A. Beard and T. Schlick},
        Journal = jcp,
        Number = 17,
        Pages = {7313-7322},
        Title = {Inertial Stochastic Dynamics. I. Long-time-step Methods for Langevin Dynamics},
        Volume = 112,
        Year = 2000}

@book{Hirsch1997,
        Address = {New York},
        Author = {M.W. Hirsch},
        Publisher = {Springer},
        Title = {Differential Topology},
        Year = 1997}

@book{Jost2002,
        Address = {Berlin},
        Author = {J. Jost},
        Publisher = {Springer-Verlag},
        Title = {Riemannian Geometry and Geometric Analysis},
        Year = 2002}

@book{McDuff1998,
        Address = {Oxford},
        Author = {D. McDuff and D. Salamon},
        Publisher = {Oxford Mathematical Monographs},
        Title = {Introduction to Symplectic Topology},
        Year = 1998}

@article{Matubayasi1999,
        Author = {N. Matubayasi and M. Nakahara},
        Journal = jcp,
        Number = 7,
        Pages = {3291-3301},
        Title = {Reversible molecular dynamics for rigid bodies and hybrid Monte Carlo},
        Volume = 110,
        Year = 1999}

@article{Miller2002,
        Author = {T.F. Miller III, M. Eleftheriou},
        Journal = jcp,
        Number = 20,
        Pages = {8649-8659},
        Title = {Symplectic quaternion scheme for biophysical molecular dynamics},
        Volume = 116,
        Year = 1999}

@article{McMillan1971,
        Author = {W.L. McMillan},
        Journal = jcp,
        Number = 3,
        Pages = {1238-1246},
        Title = {Simple Molecular Model for the Smectic A Phase of Liquid Crystals},
        Volume = 4,
        Year = 1971}

@article{Gilmore1974,
        Author = {R. Gilmore},
        Journal = {Journal of Mathematical Physics},
        Number = 12,
        Pages = {2090-2092},
        Title = {Baker-Campbell-Hausdorff Formulas},
        Volume = 15,
        Year = 1974}

@article{Strang1968,
        Author = {G. Strang},
        Journal = {SIAM Journal on Numerical Analysis},
        Number = 3,
        Pages = {506-517},
        Title = {On the construction and comparision of difference schemes},
        Volume = 5,
        Year = 1968}

@article{Trotter1959,
        Author = {H.F. Trotter},
        Journal = {SIAM Journal on Numerical Analysis},
        Number = 14,
        Pages = {545-551},
        Title = {On the product of semi-groups of operators},
        Volume = 10,
        Year = 1959}

@article{Cartwright1992,
        Author = {J.H.E. Cartwright and O. Piro},
        Journal = {International Journal of Bifurcation and Chaos},
        Number = 3,
        Pages = {427-449},
        Title = {The Dynamics of Runge-Kutta Methods},
        Volume = 2,
        Year = 1992}

@article{HuseyinKaya07012005,
        Abstract = {It has been demonstrated that a "near-Levinthal" cooperative mechanism, whereby the common G[o] interaction scheme is augmented by an extra favorability for the native state as a whole, can lead to apparent two-state folding/unfolding kinetics over a broad range of native stabilities in lattice models of proteins. Here such a mechanism is shown to be generalizable to a simplified continuum (off-lattice) Langevin dynamics model with a C{alpha} protein chain representation, with the resulting chevron plots exhibiting an extended quasilinear regime reminiscent of that of apparent two-state real proteins. Similarly high degrees of cooperativity are possible in G[o]-like continuum models with rudimentary pairwise desolvation barriers as well. In these models, cooperativity increases with increasing desolvation barrier height, suggesting strongly that two-state-like folding/unfolding kinetics would be achievable when the pairwise desolvation barrier becomes sufficiently high. Besides cooperativity, another generic folding property of interest that has emerged from published experiments on several apparent two-state proteins is that their folding relaxation under constant native stability (isostability) conditions is essentially Arrhenius, entailing high intrinsic enthalpic folding barriers of [~]17-30 kcal/mol. Based on a new analysis of published data on barnase, here we propose that a similar property should also apply to a certain class of non-two-state proteins that fold with chevron rollovers. However, several continuum G[o]-like constructs considered here fail to predict any significant intrinsic enthalpic folding barrier under isostability conditions; thus the physical origin of such barriers in real proteins remains to be elucidated.
},
        Author = {Kaya, Huseyin and Liu, Zhirong and Chan, Hue Sun},
        Doi = {10.1529/biophysj.104.057471},
        Eprint = {http://www.biophysj.org/cgi/reprint/89/1/520.pdf},
        Journal = {Biophys. J.},
        Number = 1,
        Pages = {520-535},
        Title = {{Chevron Behavior and Isostable Enthalpic Barriers in Protein Folding: Successes and Limitations of Simple Go-like Modeling}},
        Url = {http://www.biophysj.org/cgi/content/abstract/89/1/520},
        Volume = 89,
        Year = 2005,
        Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/89/1/520},
        Bdsk-Url-2 = {http://dx.doi.org/10.1529/biophysj.104.057471}}
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