trunk/openmdDocs/openmdDoc.bib

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%% http://bibdesk.sourceforge.net/


%% Created for Dan Gezelter at 2014-04-18 13:55:22 -0400 


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

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

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

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

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

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

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

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

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

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

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

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

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

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

@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.}}


@article{Berne:1972pb,
        Author = {Berne, Bruce J. and Pechukas, Philip},
        Date-Added = {2014-04-18 17:55:18 +0000},
        Date-Modified = {2014-04-18 17:55:18 +0000},
        Doi = {http://dx.doi.org/10.1063/1.1677837},
        Journal = {J. Chem. Phys.},
        Number = {8},
        Pages = {4213-4216},
        Title = {Gaussian Model Potentials for Molecular Interactions},
        Url = {http://scitation.aip.org/content/aip/journal/jcp/56/8/10.1063/1.1677837},
        Volume = {56},
        Year = {1972},
        Bdsk-Url-1 = {http://scitation.aip.org/content/aip/journal/jcp/56/8/10.1063/1.1677837},
        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.1677837}}

@article{Cleaver:1996rt,
        Author = {Cleaver, Douglas J. and Care, Christopher M. and Allen, Michael P. and Neal, Maureen P.},
        Date-Added = {2014-04-18 17:54:57 +0000},
        Date-Modified = {2014-04-18 17:54:57 +0000},
        Doi = {10.1103/PhysRevE.54.559},
        Issue = {1},
        Journal = {Phys. Rev. E},
        Month = {Jul},
        Numpages = {0},
        Pages = {559--567},
        Publisher = {American Physical Society},
        Title = {Extension and generalization of the Gay-Berne potential},
        Url = {http://link.aps.org/doi/10.1103/PhysRevE.54.559},
        Volume = {54},
        Year = {1996},
        Bdsk-Url-1 = {http://link.aps.org/doi/10.1103/PhysRevE.54.559},
        Bdsk-Url-2 = {http://dx.doi.org/10.1103/PhysRevE.54.559}}

@article{Kushick:1976xy,
        Author = {Kushick, J. and Berne, Bruce J.},
        Date-Added = {2014-04-18 17:54:44 +0000},
        Date-Modified = {2014-04-18 17:54:44 +0000},
        Doi = {http://dx.doi.org/10.1063/1.432403},
        Journal = {J. Chem. Phys.},
        Number = {4},
        Pages = {1362-1367},
        Title = {Computer simulation of anisotropic molecular fluids},
        Url = {http://scitation.aip.org/content/aip/journal/jcp/64/4/10.1063/1.432403},
        Volume = {64},
        Year = {1976},
        Bdsk-Url-1 = {http://scitation.aip.org/content/aip/journal/jcp/64/4/10.1063/1.432403},
        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.432403}}

@article{Gay:1981yu,
        Author = {Gay, J. G. and Berne, B. J.},
        Date-Added = {2014-04-18 17:54:23 +0000},
        Date-Modified = {2014-04-18 17:54:23 +0000},
        Doi = {http://dx.doi.org/10.1063/1.441483},
        Journal = {J. Chem. Phys.},
        Number = {6},
        Pages = {3316-3319},
        Title = {Modification of the overlap potential to mimic a linear site--site potential},
        Url = {http://scitation.aip.org/content/aip/journal/jcp/74/6/10.1063/1.441483},
        Volume = {74},
        Year = {1981},
        Bdsk-Url-1 = {http://scitation.aip.org/content/aip/journal/jcp/74/6/10.1063/1.441483},
        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.441483}}

@article{Luckhurst:1990fy,
        Author = {Luckhurst, G. R. and Stephens, R. A. and Phippen, R. W.},
        Date-Added = {2014-04-18 17:54:23 +0000},
        Date-Modified = {2014-04-18 17:54:23 +0000},
        Doi = {10.1080/02678299008047361},
        Eprint = {http://www.tandfonline.com/doi/pdf/10.1080/02678299008047361},
        Journal = {Liquid Crystals},
        Number = {4},
        Pages = {451-464},
        Title = {Computer simulation studies of anisotropic systems. XIX. Mesophases formed by the Gay-Berne model mesogen},
        Url = {http://www.tandfonline.com/doi/abs/10.1080/02678299008047361},
        Volume = {8},
        Year = {1990},
        Bdsk-Url-1 = {http://www.tandfonline.com/doi/abs/10.1080/02678299008047361},
        Bdsk-Url-2 = {http://dx.doi.org/10.1080/02678299008047361}}

@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 = {2014-04-18 17:53:52 +0000},
        Date-Modified = {2014-04-18 17:53:52 +0000},
        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}}

@article{Golubkov06,
        Author = {Pavel A. Golubkov and Rengyu Ren},
        Date-Added = {2014-04-18 17:53:44 +0000},
        Date-Modified = {2014-04-18 17:53:44 +0000},
        Journal = jcp,
        Pages = 064103,
        Title = {Generalized coarse-grained model based on point multipole and Gay-Berne potentials},
        Volume = 125,
        Year = 2006}

@article{kuang:AuThl,
        Author = {Kuang, Shenyu and Gezelter, J. Daniel},
        Date-Added = {2012-08-20 20:52:32 +0000},
        Date-Modified = {2012-08-20 20:52:32 +0000},
        Doi = {10.1021/jp2073478},
        Eprint = {http://pubs.acs.org/doi/pdf/10.1021/jp2073478},
        Journal = {J. Phys. Chem. C},
        Number = {45},
        Pages = {22475-22483},
        Title = {Simulating Interfacial Thermal Conductance at Metal-Solvent Interfaces: The Role of Chemical Capping Agents},
        Url = {http://pubs.acs.org/doi/abs/10.1021/jp2073478},
        Volume = {115},
        Year = {2011},
        Bdsk-Url-1 = {http://pubs.acs.org/doi/abs/10.1021/jp2073478},
        Bdsk-Url-2 = {http://dx.doi.org/10.1021/jp2073478}}

@article{2012MolPh.110..691K,
        Adsnote = {Provided by the SAO/NASA Astrophysics Data System},
        Adsurl = {http://adsabs.harvard.edu/abs/2012MolPh.110..691K},
        Author = {{Kuang}, S. and {Gezelter}, J.~D.},
        Date-Added = {2012-08-20 20:48:58 +0000},
        Date-Modified = {2012-08-20 20:48:58 +0000},
        Doi = {10.1080/00268976.2012.680512},
        Journal = {Molecular Physics},
        Month = may,
        Pages = {691-701},
        Title = {{Velocity shearing and scaling RNEMD: a minimally perturbing method for simulating temperature and momentum gradients}},
        Volume = 110,
        Year = 2012,
        Bdsk-Url-1 = {http://dx.doi.org/10.1080/00268976.2012.680512}}

@article{kuang:164101,
        Author = {Shenyu Kuang and J. Daniel Gezelter},
        Date-Added = {2012-08-20 19:01:18 +0000},
        Date-Modified = {2012-08-20 19:01:18 +0000},
        Doi = {10.1063/1.3499947},
        Eid = {164101},
        Journal = {J. Chem. Phys.},
        Keywords = {linear momentum; molecular dynamics method; thermal conductivity; total energy; viscosity},
        Number = {16},
        Numpages = {9},
        Pages = {164101},
        Publisher = {AIP},
        Title = {A gentler approach to RNEMD: Nonisotropic velocity scaling for computing thermal conductivity and shear viscosity},
        Url = {http://link.aip.org/link/?JCP/133/164101/1},
        Volume = {133},
        Year = {2010},
        Bdsk-Url-1 = {http://link.aip.org/link/?JCP/133/164101/1},
        Bdsk-Url-2 = {http://dx.doi.org/10.1063/1.3499947}}

@article{Maginn:2010,
        Abstract = {The reverse nonequilibrium molecular dynamics
                  (RNEMD) method calculates the shear viscosity of a
                  fluid by imposing a nonphysical exchange of momentum
                  and measuring the resulting shear velocity
                  gradient. In this study we investigate the range of
                  momentum flux values over which RNEMD yields usable
                  (linear) velocity gradients. We find that nonlinear
                  velocity profiles result primarily from gradients in
                  fluid temperature and density. The temperature
                  gradient results from conversion of heat into bulk
                  kinetic energy, which is transformed back into heat
                  elsewhere via viscous heating. An expression is
                  derived to predict the temperature profile resulting
                  from a specified momentum flux for a given fluid and
                  simulation cell. Although primarily bounded above,
                  we also describe milder low-flux limitations. RNEMD
                  results for a Lennard-Jones fluid agree with
                  equilibrium molecular dynamics and conventional
                  nonequilibrium molecular dynamics calculations at
                  low shear, but RNEMD underpredicts viscosity
                  relative to conventional NEMD at high shear.},
        Address = {CIRCULATION \& FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA},
        Affiliation = {Tenney, CM (Reprint Author), Univ Notre Dame, Dept Chem \& Biomol Engn, 182 Fitzpatrick Hall, Notre Dame, IN 46556 USA. {[}Tenney, Craig M.; Maginn, Edward J.] Univ Notre Dame, Dept Chem \& Biomol Engn, Notre Dame, IN 46556 USA.},
        Article-Number = {014103},
        Author = {Tenney, Craig M. and Maginn, Edward J.},
        Author-Email = {ed@nd.edu},
        Date-Added = {2012-08-20 18:56:53 +0000},
        Date-Modified = {2012-08-20 18:56:53 +0000},
        Doc-Delivery-Number = {542DQ},
        Doi = {10.1063/1.3276454},
        Funding-Acknowledgement = {U.S. Department of Energy {[}DE-FG36-08G088020]},
        Funding-Text = {Support for this work was provided by the U.S. Department of Energy (Grant No. DE-FG36-08G088020)},
        Issn = {0021-9606},
        Journal = {J. Chem. Phys.},
        Journal-Iso = {J. Chem. Phys.},
        Keywords = {Lennard-Jones potential; molecular dynamics method; Navier-Stokes equations; viscosity},
        Keywords-Plus = {CURRENT AUTOCORRELATION-FUNCTION; IONIC LIQUID; SIMULATIONS; TEMPERATURE},
        Language = {English},
        Month = {JAN 7},
        Number = {1},
        Number-Of-Cited-References = {20},
        Pages = {014103},
        Publisher = {AMER INST PHYSICS},
        Subject-Category = {Physics, Atomic, Molecular \& Chemical},
        Times-Cited = {0},
        Title = {Limitations and recommendations for the calculation of shear viscosity using reverse nonequilibrium molecular dynamics},
        Type = {Article},
        Unique-Id = {ISI:000273472300004},
        Volume = {132},
        Year = {2010},
        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.3276454}}

@article{MullerPlathe:1997xw,
        Abstract = {A nonequilibrium molecular dynamics method for
                  calculating the thermal conductivity is
                  presented. It reverses the usual cause and effect
                  picture. The ``effect,'' the heat flux, is imposed
                  on the system and the ``cause,'' the temperature
                  gradient is obtained from the simulation. Besides
                  being very simple to implement, the scheme offers
                  several advantages such as compatibility with
                  periodic boundary conditions, conservation of total
                  energy and total linear momentum, and the sampling
                  of a rapidly converging quantity (temperature
                  gradient) rather than a slowly converging one (heat
                  flux). The scheme is tested on the Lennard-Jones
                  fluid. (C) 1997 American Institute of Physics.},
        Address = {WOODBURY},
        Author = {M\"{u}ller-Plathe, F.},
        Cited-Reference-Count = {13},
        Date = {APR 8},
        Date-Added = {2012-08-20 18:53:56 +0000},
        Date-Modified = {2012-08-20 18:53:56 +0000},
        Document-Type = {Article},
        Isi = {ISI:A1997WR62000032},
        Isi-Document-Delivery-Number = {WR620},
        Iso-Source-Abbreviation = {J. Chem. Phys.},
        Issn = {0021-9606},
        Journal = jcp,
        Language = {English},
        Month = {Apr},
        Number = {14},
        Page-Count = {4},
        Pages = {6082--6085},
        Publication-Type = {J},
        Publisher = {AMER INST PHYSICS},
        Publisher-Address = {CIRCULATION FULFILLMENT DIV, 500 SUNNYSIDE BLVD, WOODBURY, NY 11797-2999},
        Reprint-Address = {MullerPlathe, F, MAX PLANCK INST POLYMER RES, D-55128 MAINZ, GERMANY.},
        Source = {J CHEM PHYS},
        Subject-Category = {Physics, Atomic, Molecular & Chemical},
        Times-Cited = {106},
        Title = {A simple nonequilibrium molecular dynamics method for calculating the thermal conductivity},
        Volume = {106},
        Year = {1997}}

@article{ISI:000080382700030,
        Abstract = {A nonequilibrium method for calculating the shear
                  viscosity is presented. It reverses the
                  cause-and-effect picture customarily used in
                  nonequilibrium molecular dynamics: the effect, the
                  momentum flux or stress, is imposed, whereas the
                  cause, the velocity gradient or shear rate, is
                  obtained from the simulation. It differs from other
                  Norton-ensemble methods by the way in which the
                  steady-state momentum flux is maintained. This
                  method involves a simple exchange of particle
                  momenta, which is easy to implement. Moreover, it
                  can be made to conserve the total energy as well as
                  the total linear momentum, so no coupling to an
                  external temperature bath is needed. The resulting
                  raw data, the velocity profile, is a robust and
                  rapidly converging property. The method is tested on
                  the Lennard-Jones fluid near its triple point. It
                  yields a viscosity of 3.2-3.3, in Lennard-Jones
                  reduced units, in agreement with literature
                  results. {[}S1063-651X(99)03105-0].},
        Address = {ONE PHYSICS ELLIPSE, COLLEGE PK, MD 20740-3844 USA},
        Affiliation = {Muller-Plathe, F (Reprint Author), Max Planck Inst Polymerforsch, Ackermannweg 10, D-55128 Mainz, Germany. Max Planck Inst Polymerforsch, D-55128 Mainz, Germany.},
        Author = {M\"{u}ller-Plathe, F},
        Date-Added = {2012-08-20 18:52:38 +0000},
        Date-Modified = {2012-08-20 18:52:38 +0000},
        Doc-Delivery-Number = {197TX},
        Issn = {1063-651X},
        Journal = {Phys. Rev. E},
        Journal-Iso = {Phys. Rev. E},
        Language = {English},
        Month = {MAY},
        Number = {5, Part A},
        Number-Of-Cited-References = {17},
        Pages = {4894-4898},
        Publisher = {AMERICAN PHYSICAL SOC},
        Subject-Category = {Physics, Fluids \& Plasmas; Physics, Mathematical},
        Times-Cited = {57},
        Title = {Reversing the perturbation in nonequilibrium molecular dynamics: An easy way to calculate the shear viscosity of fluids},
        Type = {Article},
        Unique-Id = {ISI:000080382700030},
        Volume = {59},
        Year = {1999}}

@article{Vardeman2011,
        Author = {Vardeman, Charles F. II and Stocker, Kelsey M. and Gezelter, J. Daniel},
        Date-Added = {2011-05-11 11:18:00 -0400},
        Date-Modified = {2011-05-11 11:18:00 -0400},
        Journal = {J. Chem. Theory Comput.},
        Keywords = {Langevin Hull},
        Pages = {834-842},
        Title = {The Langevin Hull: Constant pressure and temperature dynamics for nonperiodic systems},
        Volume = {7},
        Year = {2011},
        Bdsk-File-1 = {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}}

@misc{Qhull,
        Date-Added = {2010-11-24 13:59:33 -0500},
        Date-Modified = {2011-05-11 11:15:50 -0400},
        Note = {Software Library Is Available From the National Science and Technology Research Center for Computation and Visualization of Geometric Structures (The Geometry Center), University of Minnesota. $\mathtt{http://www.qhull.org}$},
        Title = {Qhull},
        Year = 1993}

@article{Sun:2008fk,
        Abstract = {We present an algorithm for carrying out Langevin dynamics simulations on complex rigid bodies by incorporating the hydrodynamic resistance tensors for arbitrary shapes into an advanced rotational integration scheme. The integrator gives quantitative agreement with both analytic and approximate hydrodynamic theories for a number of model rigid bodies and works well at reproducing the solute dynamical properties (diffusion constants and orientational relaxation times) obtained from explicitly solvated simulations. (C) 2008 American Institute of Physics.},
        Address = {CIRCULATION \& FULFILLMENT DIV, 2 HUNTINGTON QUADRANGLE, STE 1 N O 1, MELVILLE, NY 11747-4501 USA},
        Author = {Sun, Xiuquan and Lin, Teng and Gezelter, J. Daniel},
        Date-Added = {2010-11-24 13:59:02 -0500},
        Date-Modified = {2010-11-24 14:02:09 -0500},
        Doi = {DOI 10.1063/1.2936991},
        Isi = {000256936700007},
        Isi-Recid = {171639081},
        Isi-Ref-Recids = {74848920 50663994 119330651 134477260 22939933 131802420 114632880 64190493 55802797 21189309 75892319 21406638 110293282 113408519 96782216 130078852 17359022 100665361 113671463 49951397 123367767 123367728 154386980 102422498 35241737 32391149 6325223 127852571 58929276 95157449 32334819 42562624 12736689 163240533 130556111 122778971 51825394 49588888 145030437 101277182 101670714 148588118 73818708 142688207 124629108 18817706 103995016 149522882 50793 47098 109491995 114073447 108180005 98728780 112132273 16915130 31384453 127055599 134786719 131544581 124299358 1555937 160750161 85968524 163240534},
        Journal = {J. Chem. Phys.},
        Number = {23},
        Pages = {234107},
        Publisher = {AMER INST PHYSICS},
        Times-Cited = {2},
        Title = {Langevin dynamics for rigid bodies of arbitrary shape},
        Volume = {128},
        Year = {2008},
        Bdsk-Url-1 = {http://gateway.isiknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=Alerting&SrcApp=Alerting&DestApp=WOS&DestLinkType=FullRecord;KeyUT=000256936700007}}

@article{Kohanoff:2005qm,
        Abstract = {We present a method for simulating clusters or, molecules subjected to an external pressure, which is exerted by a pressure-transmitting medium. It is based on the canoninical Langevin thermostat, but extended in such a way that the Brownian forces are allowed to operate only from the region exterior to the cluster. We show that the frictional force of the Langevin thermostat is linked to the pressure of the reservoir in a unique way, and that this property manifests itself when the particle it acts upon is not pointlike but has finite dimensions. By choosing appropriately the strength of the random forces and the friction coefficient, both temperature and pressure can be controlled independently. We illustrate the capabilities of this new method by calculating the compressibility of small gold clusters under pressure.},
        Address = {PO BOX 10 11 61, D-69451 WEINHEIM, GERMANY},
        Author = {Kohanoff, J and Caro, A and Finnis, MW},
        Date = {SEP 5 2005},
        Date-Added = {2010-11-22 12:24:56 -0500},
        Date-Modified = {2010-11-22 12:24:56 -0500},
        Doi = {DOI 10.1002/cphc.200400607},
        Journal = {ChemPhysChem},
        Keywords = {clusters; gold; nanostructures; pressure; simulation},
        Pages = {1848-1852},
        Publisher = {WILEY-V C H VERLAG GMBH},
        Timescited = {2},
        Title = {An isothermal-isobaric Langevin thermostat for simulating nanoparticles under pressure: Application to Au clusters},
        Volume = {6},
        Year = {2005},
        Bdsk-Url-1 = {http://dx.doi.org/10.1002/cphc.200400607}}

@article{springerlink:10.1007/BF00977785,
        Author = {Lee, D. T. and Schachter, B. J.},
        Date-Added = {2010-11-22 12:24:49 -0500},
        Date-Modified = {2010-11-22 12:24:49 -0500},
        Issn = {0885-7458},
        Issue = {3},
        Journal = {International Journal of Parallel Programming},
        Keyword = {Computer Science},
        Note = {10.1007/BF00977785},
        Pages = {219-242},
        Publisher = {Springer Netherlands},
        Title = {Two algorithms for constructing a Delaunay triangulation},
        Url = {http://dx.doi.org/10.1007/BF00977785},
        Volume = {9},
        Year = {1980},
        Bdsk-Url-1 = {http://dx.doi.org/10.1007/BF00977785}}

@article{delaunay,
        Author = {B. Delaunay},
        Date-Added = {2010-11-22 12:24:45 -0500},
        Date-Modified = {2010-11-22 12:24:45 -0500},
        Journal = {Bull. Acad. Science USSR VII:Class. Sci. Mat. Nat.},
        Pages = {793-800},
        Title = {Sur la sph{\`e}re vide},
        Year = {1934}}

@article{EDELSBRUNNER:1994oq,
        Abstract = {Frequently, data in scientific computing is in its abstract form a finite point set in space, and it is sometimes useful or required to compute what one might call the ''shape'' of the set. For that purpose, this article introduces the formal notion of the family of alpha-shapes of a finite point set in R3. Each shape is a well-defined polytope, derived from the Delaunay triangulation of the point set, with a parameter alpha is-an-element-of R controlling the desired level of detail. An algorithm is presented that constructs the entire family of shapes for a given set of size n in time O(n2), worst case. A robust implementation of the algorithm is discussed, and several applications in the area of scientific computing are mentioned.},
        Address = {1515 BROADWAY, NEW YORK, NY 10036},
        Author = {Edelsbrunner, H and Mucke, E.~P.},
        Date = {JAN 1994},
        Date-Added = {2010-11-22 12:24:34 -0500},
        Date-Modified = {2010-11-22 12:24:34 -0500},
        Journal = {ACM Transactions On Graphics},
        Keywords = {COMPUTATIONAL GRAPHICS; DELAUNAY TRIANGULATIONS; GEOMETRIC ALGORITHMS; POINT SETS; POLYTOPES; ROBUST IMPLEMENTATION; SCIENTIFIC COMPUTING; SCIENTIFIC VISUALIZATION; SIMPLICIAL COMPLEXES; SIMULATED PERTURBATION; 3-DIMENSIONAL SPACE},
        Pages = {43-72},
        Publisher = {ASSOC COMPUTING MACHINERY},
        Timescited = {270},
        Title = {3-DIMENSIONAL ALPHA-SHAPES},
        Volume = {13},
        Year = {1994}}

@article{Barber96,
        Author = {C.~B. Barber and D.~P. Dobkin and H.~T. Huhdanpaa},
        Date-Added = {2010-11-22 12:24:25 -0500},
        Date-Modified = {2010-11-22 12:24:25 -0500},
        Journal = {ACM Trans. Math. Software},
        Pages = {469-483},
        Title = {The Quickhull Algorithm for Convex Hulls},
        Volume = 22,
        Year = 1996}

@book{Schlick2002,
        Address = {Secaucus, NJ, USA},
        Author = {Tamar Schlick},
        Date-Added = {2010-11-22 12:24:11 -0500},
        Date-Modified = {2010-11-22 12:24:11 -0500},
        Isbn = {038795404X},
        Publisher = {Springer-Verlag New York, Inc.},
        Title = {Molecular Modeling and Simulation: An Interdisciplinary Guide},
        Year = {2002}}

@article{GarciadelaTorreJ2002,
        Affiliation = {Departamento de Qu{\'\i}mica F{\'\i}sica, Facultad de Qu{\'\i}mica, Universidad de Murcia, 30071 Murcia, Spain},
        Author = {{Garc\'{i}a de la Torre}, Jose and Carrasco, B.},
        Date-Added = {2010-11-22 12:23:52 -0500},
        Date-Modified = {2010-11-22 12:23:52 -0500},
        Journal = {Biopolymers},
        Number = {3},
        Pages = {163-167},
        Title = {Hydrodynamic Properties of Rigid Macromolecules Composed of Ellipsoidal and Cylindrical Subunits},
        Volume = {63},
        Year = {2002}}

@article{Garcia-de-la-Torre:2001wd,
        Abstract = { The calculation of hydrodynamic and other solution properties of rigid macromolecules, using bead-shell model methodologies, requires the specification of the macromolecular shape in a format that can be interfaced with existing programs for hydrodynamic computations. Here, a procedure is presented for such a structural specification that is applicable to arbitrarily shaped particles. A computer program (), in which the user inserts the code needed to determine the structure, produces an structural file that is interpreted by another program () which is in charge of the computation of properties. As simple and yet illustrative examples we consider two cases: (1) dimeric structures composed of ellipsoidal subunits; and (2) toroidal structures, presenting simple equations that predict the properties of toroids with varying radial ratios.},
        Author = {{Garc\'{i}a de la Torre}, Jose},
        Date-Added = {2010-11-22 12:23:48 -0500},
        Date-Modified = {2010-11-22 12:23:48 -0500},
        Journal = {Biophysical Chemistry},
        Keywords = {Rigid macromolecules; Hydrodynamic properties; Bead-shell model; Three-dimensional structure},
        Number = {3},
        Pages = {265--274},
        Title = {Building hydrodynamic bead-shell models for rigid bioparticles of arbitrary shape},
        Ty = {JOUR},
        Url = {http://www.sciencedirect.com/science/article/B6TFB-44XJKW6-8/1/376af59f3b89aecd8486b1c6186b0953},
        Volume = {94},
        Year = {2001},
        Bdsk-Url-1 = {http://www.sciencedirect.com/science/article/B6TFB-44XJKW6-8/1/376af59f3b89aecd8486b1c6186b0953}}

@article{JoseGarciadelaTorre02012000,
        Abstract = {The solution properties, including hydrodynamic quantities and the radius of gyration, of globular proteins are calculated from their detailed, atomic-level structure, using bead-modeling methodologies described in our previous article (Carrasco and Garcia de la Torre, 1999, Biophys. J. 76:3044-3057). We review how this goal has been pursued by other authors in the past. Our procedure starts from a list of atomic coordinates, from which we build a primary hydrodynamic model by replacing nonhydrogen atoms with spherical elements of some fixed radius. The resulting particle, consisting of overlapping spheres, is in turn represented by a shell model treated as described in our previous work. We have applied this procedure to a set of 13 proteins. For each protein, the atomic element radius is adjusted, to fit all of the hydrodynamic properties, taking values close to 3 A, with deviations that fall within the error of experimental data. Some differences are found in the atomic element radius found for each protein, which can be explained in terms of protein hydration. A computational shortcut makes the procedure feasible, even in personal computers. All of the model-building and calculations are carried out with a HYDROPRO public-domain computer program.
},
        Author = {{Garc\'{i}a de la Torre}, Jose and Huertas, Maria L. and Carrasco, Beatriz},
        Date-Added = {2010-11-22 12:23:36 -0500},
        Date-Modified = {2010-11-22 12:23:36 -0500},
        Eprint = {http://www.biophysj.org/cgi/reprint/78/2/719.pdf},
        Journal = bj,
        Number = {2},
        Pages = {719-730},
        Title = {{Calculation of Hydrodynamic Properties of Globular Proteins from Their Atomic-Level Structure}},
        Url = {http://www.biophysj.org/cgi/content/abstract/78/2/719},
        Volume = {78},
        Year = {2000},
        Bdsk-Url-1 = {http://www.biophysj.org/cgi/content/abstract/78/2/719}}

@article{Fennell06,
        Author = {C.~J. Fennell and J.~D. Gezelter},
        Date-Added = {2008-05-16 10:19:01 -0400},
        Date-Modified = {2008-05-16 10:19:01 -0400},
        Doi = {10.1063/1.2206581},
        Journal = jcp,
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/MyPapers/Fennell_PairwiseSummationMethods_06.pdf},
        Number = {23},
        Pages = {234104(12)},
        Rating = {5},
        Read = {Yes},
        Title = {Is the \uppercase{E}wald summation still necessary? \uppercase{P}airwise alternatives to the accepted standard for long-range electrostatics},
        Volume = {124},
        Year = {2006},
        Bdsk-Url-1 = {http://dx.doi.org/10.1063/1.2206581}}

@article{Heyes81,
        Author = {D.~M. Heyes},
        Date-Added = {2008-05-16 10:18:50 -0400},
        Date-Modified = {2008-05-16 10:18:50 -0400},
        Journal = jcp,
        Keywords = {Empty Keywords},
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Heyes_CoulombChargeSpreading_81.pdf},
        Number = {3},
        Pages = {1924-1929},
        Title = {Electrostatic potentials and fields in infinite point charge lattices},
        Volume = {74},
        Year = {1981}}

@article{Jones56,
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        Date-Added = {2008-05-16 10:18:41 -0400},
        Date-Modified = {2008-05-16 10:18:41 -0400},
        Journal = jcp,
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/TheoryTechniques/Ewald/Jones_ChargeShapeFunctions_56.pdf},
        Number = {5},
        Pages = {1062-1063},
        Title = {Optimum Atomic Shape for \uppercase{B}ertaut Series},
        Volume = {25},
        Year = {1956}}

@book{Allen87,
        Address = {New York},
        Author = {M.~P. Allen and D.~J. Tildesley},
        Date-Added = {2008-05-16 10:18:32 -0400},
        Date-Modified = {2008-05-16 10:18:32 -0400},
        Publisher = {Oxford University Press},
        Title = {Computer Simulations of Liquids},
        Year = 1987}

@article{Wolf99,
        Author = {D. Wolf and P. Keblinski and S.~R. Phillpot and J. Eggebrecht},
        Date-Added = {2008-05-16 10:18:22 -0400},
        Date-Modified = {2008-05-16 10:18:22 -0400},
        Journal = jcp,
        Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/Wolf_Potential/Wolf_electroCorr_99.pdf},
        Number = {17},
        Pages = {8254-8282},
        Rating = {0},
        Read = {No},
        Title = {Exact method for the simulation of Coulombic systems by spherically truncated, pairwise $r^{-1}$ summation},
        Volume = {110},
        Year = {1999}}

@book{Berne90,
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        Year = 1990}

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        Year = 1977}

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        Volume = 97,
        Year = 1992}

@book{Hansen86,
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        Year = 1986}

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        Year = 1982}

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        Year = 1983}

@article{Weber84,
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        Year = 1984}

@article{Stillinger85,
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        Year = 1985}

@article{Stillinger98,
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        Year = 1998}

@article{Parkhurst75a,
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        Year = 1975}

@article{Parkhurst75b,
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        Year = 1975}

@article{Forester97,
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@article{Tieleman98,
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        Title = {A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer},
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        Year = 1998}

@article{Cascales98,
        Author = {J.~J.~L. Cascales and J.~G.~H. Cifre and J.~G. de~la~Torre},
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        Year = 1998}

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        Title = {MECHANISM OF SOLUTE DIFFUSION THROUGH LIPID BILAYER-MEMBRANES BY MOLECULAR-DYNAMICS SIMULATION},
        Volume = 117,
        Year = 1995}

@article{Alper95,
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        Title = {ORIENTATION AND DIFFUSION OF A DRUG ANALOG IN BIOMEMBRANES - MOLECULAR-DYNAMICS SIMULATIONS},
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        Year = 1995}

@article{Sok92,
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        Title = {MOLECULAR-DYNAMICS SIMULATION OF THE TRANSPORT OF SMALL MOLECULES ACROSS A POLYMER MEMBRANE},
        Volume = 96,
        Year = 1992}

@article{Rabani99,
        Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
        Journal = prl,
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        Title = {Direct Observation of Stretched-Exponential Relaxation in Low-Temperature Lennard-Jones Systems Using the Cage Correlation Function},
        Volume = 82,
        Year = {1999}}

@article{Rabani97,
        Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
        Journal = {J. Chem. Phys.},
        Pages = {6867-6876},
        Title = {Calculating the hopping rate for self-diffusion on rough potential energy surfaces: Cage correlations},
        Volume = 107,
        Year = 1997}

@article{Gezelter99,
        Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
        Journal = jcp,
        Pages = 3444,
        Title = {Methods for calculating the hopping rate for orientational and spatial diffusion in a molecular liquid: $\mbox{CS}_{2}$},
        Volume = 110,
        Year = 1999}

@article{Gezelter98a,
        Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
        Journal = jcp,
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        Title = {Response to 'Comment on a Critique of the Instantaneous Normal Mode (INM) Approach to Diffusion'},
        Volume = 109,
        Year = 1998}

@article{Gezelter97,
        Author = {J.~D. Gezelter and E. Rabani and B.~J. Berne},
        Journal = jcp,
        Pages = 4618,
        Title = {Can imaginary instantaneous normal mode frequencies predict barriers to self-diffusion?},
        Volume = 107,
        Year = 1997}

@article{Zwanzig83,
        Author = {R. Zwanzig},
        Journal = jcp,
        Pages = {4507-4508},
        Title = {On the relation between self-diffusion and viscosity of liquids},
        Volume = 79,
        Year = 1983}

@article{Zwanzig88,
        Author = {R. Zwanzig},
        Journal = {Proc. Natl. Acad. Sci. USA},
        Pages = 2029,
        Title = {Diffusion in rough potential},
        Volume = 85,
        Year = 1988}

@article{Stillinger95,
        Author = {F.~H. Stillinger},
        Journal = {Science},
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        Title = {A Topographic View of Supercooled Liquids and Glass Formation},
        Volume = 267,
        Year = 1995}

@incollection{Angell85,
        Address = {Springfield, VA},
        Author = {C.~A. Angell},
        Booktitle = {Relaxations in Complex Systems},
        Editor = {K.~Ngai and G.~B. Wright},
        Pages = 1,
        Publisher = {National Technical Information Service, U.S. Department of Commerce},
        Title = {unknown},
        Year = 1985}

@article{Bembenek96,
        Author = {S.~D. Bembenek and B.~B. Laird},
        Journal = jcp,
        Pages = 5199,
        Title = {The role of localization in glasses and supercooled liquids},
        Volume = 104,
        Year = 1996}

@article{Sun97,
        Author = {X. Sun and W.~H. Miller},
        Journal = jcp,
        Pages = 6346,
        Title = {Semiclassical initial value representation for electronically nonadiabatic molecular dynamics},
        Volume = 106,
        Year = 1997}

@article{Spath96,
        Author = {B.~W. Spath and W.~H. Miller},
        Journal = jcp,
        Pages = 95,
        Title = {SEMICLASSICAL CALCULATION OF CUMULATIVE REACTION PROBABILITIES},
        Volume = 104,
        Year = 1996}

@book{Warshel91,
        Address = {New York},
        Author = {Arieh Warshel},
        Publisher = {Wiley},
        Title = {Computer modeling of chemical reactions in enzymes and solutions},
        Year = 1991}

@article{Vuilleumier97,
        Author = {Rodolphe Vuilleumier and Daniel Borgis},
        Journal = jpc,
        Title = {Molecular Dynamics of an excess proton in water using a non-additive valence bond force field},
        Volume = {in press},
        Year = 1997}

@article{Kob95a,
        Author = {W. Kob and H.~C. Andersen},
        Journal = pre,
        Pages = {4626-4641},
        Title = {Testing mode-coupling theory for a supercooled binary Lennard-Jones mixtures: The van Hove corraltion function},
        Volume = 51,
        Year = 1995}

@article{Kob95b,
        Author = {W. Kob and H.~C. Andersen},
        Journal = pre,
        Pages = {4134-4153},
        Title = {Testing mode-coupling theory for a supercooled binary Lennard-Jones mixtures. II. Intermediate scattering function and dynamic susceptibility},
        Volume = 52,
        Year = 1995}

@inproceedings{Gotze89,
        Address = {Amsterdam},
        Author = {W. G{\"{o}}tze},
        Booktitle = {Liquids, Freezing and Glass Transitions},
        Editor = {J.~P. Hansen and D. Levesque and J. Zinn-Justin},
        Pages = {287-503},
        Publisher = {North-Holland},
        Title = {Aspects of Structural Glass Transitions},
        Volume = {I},
        Year = 1989}

@article{Sun97a,
        Author = {X. Sun and W.~H. Miller},
        Journal = jcp,
        Pages = 916,
        Title = {Mixed semiclassical-classical approaches to the dynamics of complex molecular systems},
        Year = 1997}

@article{Keshavamurthy94,
        Author = {S. Keshavamurthy and W.~H. Miller},
        Journal = cpl,
        Pages = 189,
        Title = {ivr},
        Volume = 218,
        Year = 1994}

@article{Billing75,
        Author = {G.~D. Billing},
        Journal = cpl,
        Pages = 391,
        Title = {ehrenfest},
        Volume = 30,
        Year = 1975}

@article{Chang90,
        Author = {Y.-T. Chang and W.~H. Miller},
        Journal = jpc,
        Pages = {5884-5888},
        Title = {An Empirical Valence Bond Model for Constructing Global Potential Energy Surfaces for Chemical Reactions of Polyatomic Molecular Systems},
        Volume = 94,
        Year = 1990}

@article{Shor94,
        Author = {P.W. Shor},
        Journal = {Proceedings of the 35th Annual Symposium on Foundations of Computer Science},
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        Title = {Algorithms for quantum computation: discrete logarithms and factoring},
        Year = 1994}

@article{Feynman82,
        Author = {R.~P. Feynman},
        Journal = {Int. J. Theor. Phys.},
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        Title = {Simulating physics with computers},
        Volume = 21,
        Year = 1982}

@article{Grover97,
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        Year = 1997}

@article{Chuang98,
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        Title = {Experimental Implementation of Fast Quantum Searching},
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        Year = 1998}

@article{Monroe95,
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        Volume = 75,
        Year = 1995}

@article{Lent93,
        Author = {C.~S. Lent and P.~D. Tougaw and W.~Porod and G.~H. Bernstein},
        Journal = {Nanotechnology},
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        Title = {Quantum Cellular Automata},
        Volume = 4,
        Year = 1993}

@article{Barenco95,
        Author = {A. Barenco and C.~H. Bennett and R. Cleve and D.~P. DiVincenzo and N. Margolus and P. Shor and T. Sleator and J.~A. Smolin and H. Weinfurter},
        Journal = {Phys. Rev. A},
        Pages = {3457-3467},
        Title = {elementary gates for quantum computation},
        Volume = 52,
        Year = 1995}

@article{Small97,
        Author = {T. Reinot and J.~M. Hayes and G.~J. Small},
        Journal = jcp,
        Pages = {457-466},
        Title = {Electronic dephasing and electron-phonon coupling of aluminum phthalocyanine tetrasulphonate in hyperquenched and annealed glassy films of ethanol and methanol over a broad temperature range},
        Volume = 106,
        Year = 1997}

@article{Laflamme96,
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        Title = {A perfect quantum error correcting code: 5 bit code correcting a general 1 qubit error to encode 1 qubit of information},
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        Year = 1996}

@article{Shor95,
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        Title = {SCHEME FOR REDUCING DECOHERENCE IN QUANTUM COMPUTER MEMORY},
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        Year = 1995}

@article{Calderbank96,
        Author = {A.~R. Calderbank and P.~W. Shor},
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        Year = 1996}

@article{Steane96,
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@article{Gezelter95,
        Author = {J.~D. Gezelter and W.~H. Miller},
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        Title = {RESONANT FEATURES IN THE ENERGY-DEPENDENCE OF THE RATE OF KETENE ISOMERIZATION},
        Volume = 103,
        Year = 1995}

@article{Chakrabarti92,
        Author = {A.~C. Chakrabarti and D.~W. Deamer},
        Journal = {Biochimica et Biophysica Acta},
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        Volume = 1111,
        Year = 1992}

@article{Paula96,
        Author = {S. Paula and A.~G. Volkov and A.~N. VanHoek and T.~H. Haines and D.~W. Deamer},
        Journal = bj,
        Pages = {339-348},
        Title = {Permeation of protons, potassium ions, and small polar molecules through phospholipid bilayers as a function of membrane thickness},
        Volume = 70,
        Year = 1996}

@article{Little96,
        Author = {H.~J. Little},
        Journal = {Pharmacology \& Therapeutics},
        Pages = {37-58},
        Title = {How has molecular pharmacology contributed to our understanding of the mechanism(s) of general anesthesia?},
        Volume = 69,
        Year = 1996}

@article{McKinnon92,
        Author = {S.~J. McKinnon and S.~L. Whittenburg and B. Brooks},
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        Title = {Nonequilibrium Molecular Dynamics Simulation of Oxygen Diffusion through Hexadecane Monolayers with Varying Concentrations of Cholesterol},
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        Year = 1992}

@article{Venable93,
        Author = {R.~M. Venable and Y. Zhang and B.~J. Hardy and R.~W. Pastor},
        Journal = {Science},
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        Year = 1993}

@article{Essmann99,
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        Year = 1999}

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        Journal = bj,
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        Year = 1998}

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        Year = 1996}

@article{Duwez60,
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        Year = 1960}

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