trunk/openmdDocs/openmdDoc.bib

%% This BibTeX bibliography file was created using BibDesk.
%% http://bibdesk.sourceforge.net/


%% Created for Dan Gezelter at 2015-03-16 17:03:45 -0400 


%% Saved with string encoding Unicode (UTF-8) 


@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.}}


@incollection{Shoemake:1994uq,
        Acmid = {180915},
        Address = {San Diego, CA, USA},
        Author = {Shoemake, Ken},
        Chapter = {Fiber Bundle Twist Reduction},
        Date-Added = {2015-03-16 18:03:08 +0000},
        Date-Modified = {2015-03-16 18:03:12 +0000},
        Editor = {Heckbert, Paul S.},
        Isbn = {0-12-336155-9},
        Numpages = {7},
        Pages = {230--236},
        Publisher = {Academic Press Professional, Inc.},
        Title = {Graphics Gems IV},
        Url = {http://dl.acm.org/citation.cfm?id=180895.180915},
        Year = {1994},
        Bdsk-Url-1 = {http://dl.acm.org/citation.cfm?id=180895.180915}}

@article{Kallmann:2008fk,
        Author = {Kallmann, Marcelo},
        Date-Added = {2015-03-16 17:59:57 +0000},
        Date-Modified = {2015-03-16 17:59:57 +0000},
        Doi = {10.1002/cav.176},
        Issn = {1546-427X},
        Journal = {Computer Animation and Virtual Worlds},
        Keywords = {analytical inverse kinematics, character animation, reaching},
        Number = {2},
        Pages = {79--91},
        Publisher = {John Wiley & Sons, Ltd.},
        Title = {Analytical inverse kinematics with body posture control},
        Url = {http://dx.doi.org/10.1002/cav.176},
        Volume = {19},
        Year = {2008},
        Bdsk-Url-1 = {http://dx.doi.org/10.1002/cav.176}}

@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,
        Author = {R.~E. Jones and D.~H. Templeton},
        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,
        Address = {Malabar, Florida},
        Author = {B.~J. Berne and R. Pecora},
        Publisher = {Robert E. Krieger Publishing Company, Inc.},
        Title = {Dynamic Light Scattering},
        Year = 1990}

@article{Evans77,
        Author = {D.~J. Evans},
        Journal = {Mol. Phys.},
        Pages = {317-325},
        Title = {On the representation of orientation space},
        Volume = 34,
        Year = 1977}

@article{Tuckerman92,
        Author = {M. Tuckerman and B.~J. Berne and G.~J. Martyna},
        Journal = jcp,
        Pages = {1990-2001},
        Title = {Reversible multiple time scale molecular dynamics},
        Volume = 97,
        Year = 1992}

@book{Hansen86,
        Address = {London},
        Author = {J.~P. Hansen and I.~R. McDonald},
        Chapter = 7,
        Pages = {199-206},
        Publisher = {Academic Press},
        Title = {Theory of Simple Liquids},
        Year = 1986}

@article{Angelani98,
        Author = {L. Angelani and G. Parisi and G. Ruocco and G. Viliani},
        Journal = prl,
        Number = 21,
        Pages = {4648-4651},
        Title = {Connected Network of Minima as a Model Glass: Long Time Dynamics},
        Volume = 81,
        Year = 1998}

@article{Stillinger82,
        Author = {F.~H. Stillinger and T.~A. Weber},
        Journal = pra,
        Number = 2,
        Pages = {978-989},
        Title = {Hidden structure in liquids},
        Volume = 25,
        Year = 1982}

@article{Stillinger83,
        Author = {F.~H. Stillinger and T.~A. Weber},
        Journal = pra,
        Number = 4,
        Pages = {2408-2416},
        Title = {Dynamics of structural transitions in liquids},
        Volume = 28,
        Year = 1983}

@article{Weber84,
        Author = {T.~A. Weber and F.~H. Stillinger},
        Journal = jcp,
        Number = 6,
        Pages = {2742-2746},
        Title = {The effect of density on the inherent structure in liquids},
        Volume = 80,
        Year = 1984}

@article{Stillinger85,
        Author = {F.~H. Stillinger and T.~A. Weber},
        Journal = jcp,
        Number = 9,
        Pages = {4767-4775},
        Title = {Inherent structure theory of liquids in the hard-sphere limit},
        Volume = 83,
        Year = 1985}

@article{Stillinger98,
        Author = {S. Sastry and P.~G. Debenedetti and F.~H. Stillinger},
        Journal = {Nature},
        Pages = {554-557},
        Title = {Signatures of distinct dynamical regimes in the energy landscape of a glass-forming liquid},
        Volume = 393,
        Year = 1998}

@article{Parkhurst75a,
        Author = {H.~J. {Parkhurst, Jr.} and J. Jonas},
        Journal = jcp,
        Number = 6,
        Pages = {2698-2704},
        Title = {Dense liquids. I. The effect of density and temperature on viscosity of tetramethylsilane and benzene-$\mbox{D}_6$},
        Volume = 63,
        Year = 1975}

@article{Parkhurst75b,
        Author = {H.~J. {Parkhurst, Jr.} and J. Jonas},
        Journal = jcp,
        Number = 6,
        Pages = {2705-2709},
        Title = {Dense liquids. II. The effect of density and temperature on viscosity of tetramethylsilane and benzene},
        Volume = 63,
        Year = 1975}

@article{Forester97,
        Author = {T.~R. Forester and W. Smith and J.~H.~R. Clarke},
        Journal = {J. Chem. Soc. - Faraday Transactions},
        Pages = {613-619},
        Title = {Antibiotic activity of valinomycin - Molecular dynamics simulations involving the water/membrane interface},
        Volume = 93,
        Year = 1997}

@article{Tieleman98,
        Author = {D.~P. Tieleman and H.~J.~C. Berendsen},
        Journal = bj,
        Pages = {2786-2801},
        Title = {A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer},
        Volume = 74,
        Year = 1998}

@article{Cascales98,
        Author = {J.~J.~L. Cascales and J.~G.~H. Cifre and J.~G. de~la~Torre},
        Journal = {J. Phys. Chem. B},
        Pages = {625-631},
        Title = {Anaesthetic mechanism on a model biological membrane: A molecular dynamics simulation study},
        Volume = 102,
        Year = 1998}

@article{Bassolino95,
        Author = {D. Bassolino and H.~E. Alper and T.~R. Stouch},
        Journal = {J. Am. Chem. Soc.},
        Pages = {4118-4129},
        Title = {MECHANISM OF SOLUTE DIFFUSION THROUGH LIPID BILAYER-MEMBRANES BY MOLECULAR-DYNAMICS SIMULATION},
        Volume = 117,
        Year = 1995}

@article{Alper95,
        Author = {H.~E. Alper and T.~R. Stouch},
        Journal = {J. Phys. Chem.},
        Pages = {5724-5731},
        Title = {ORIENTATION AND DIFFUSION OF A DRUG ANALOG IN BIOMEMBRANES - MOLECULAR-DYNAMICS SIMULATIONS},
        Volume = 99,
        Year = 1995}

@article{Sok92,
        Author = {R.~M. Sok and H.~J.~C. Berendsen and W.~F. {van~Gunsteren}},
        Journal = {J. Chem. Phys.},
        Pages = {4699-4704},
        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,
        Pages = {3649},
        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,
        Pages = 4695,
        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},
        Pages = {1935-1939},
        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},
        Pages = {124-134},
        Title = {Algorithms for quantum computation: discrete logarithms and factoring},
        Year = 1994}

@article{Feynman82,
        Author = {R.~P. Feynman},
        Journal = {Int. J. Theor. Phys.},
        Pages = {467-488},
        Title = {Simulating physics with computers},
        Volume = 21,
        Year = 1982}

@article{Grover97,
        Author = {L.~K. Grover},
        Journal = prl,
        Pages = {4709-4712},
        Title = {Quantum computers can search arbitrarily large databases by a single query},
        Volume = 79,
        Year = 1997}

@article{Chuang98,
        Author = {I. Chuang and N. Gershenfeld and M. Kubinec},
        Journal = prl,
        Pages = {3408-3411},
        Title = {Experimental Implementation of Fast Quantum Searching},
        Volume = 80,
        Year = 1998}

@article{Monroe95,
        Author = {C. Monroe and D.~M. Meekhof and B.~E. King and W.~M. Itano and D.~J. Wineland},
        Journal = prl,
        Pages = 4714,
        Title = {Demonstration of a fundamental quantum logic gate},
        Volume = 75,
        Year = 1995}

@article{Lent93,
        Author = {C.~S. Lent and P.~D. Tougaw and W.~Porod and G.~H. Bernstein},
        Journal = {Nanotechnology},
        Pages = {49-57},
        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,
        Author = {R. Laflamme and C. Miquel and J.~P. Paz and W.~H. Zurek},
        Journal = prl,
        Pages = 77,
        Title = {A perfect quantum error correcting code: 5 bit code correcting a general 1 qubit error to encode 1 qubit of information},
        Volume = 98,
        Year = 1996}

@article{Shor95,
        Author = {P.~W. Shor},
        Journal = {Phys. Rev. A},
        Pages = {2493-2496},
        Title = {SCHEME FOR REDUCING DECOHERENCE IN QUANTUM COMPUTER MEMORY},
        Volume = 52,
        Year = 1995}

@article{Calderbank96,
        Author = {A.~R. Calderbank and P.~W. Shor},
        Journal = {Phys. Rev. A},
        Pages = {1098-1105},
        Title = {Good quantum error-correcting codes exist},
        Volume = 54,
        Year = 1996}

@article{Steane96,
        Author = {A.~M. Steane},
        Journal = prl,
        Pages = {793-797},
        Title = {Error correcting codes in quantum theory},
        Volume = 77,
        Year = 1996}

@article{Gezelter95,
        Author = {J.~D. Gezelter and W.~H. Miller},
        Journal = jcp,
        Pages = {7868-7876},
        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},
        Pages = {171-177},
        Title = {PERMEABILITY OF LIPID BILAYERS TO AMINO-ACIDS AND PHOSPHATE},
        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},
        Journal = jpc,
        Pages = {10497-10506},
        Title = {Nonequilibrium Molecular Dynamics Simulation of Oxygen Diffusion through Hexadecane Monolayers with Varying Concentrations of Cholesterol},
        Volume = 96,
        Year = 1992}

@article{Venable93,
        Author = {R.~M. Venable and Y. Zhang and B.~J. Hardy and R.~W. Pastor},
        Journal = {Science},
        Pages = {223-226},
        Title = {Molecular Dynamics Simulations of a Lipid Bilayer and of Hexadecane: An Investigation of Membrane Fluidity},
        Volume = 262,
        Year = 1993}

@article{Essmann99,
        Author = {U. Essmann and M.~L. Berkowitz},
        Journal = bj,
        Pages = {2081-2089},
        Title = {Dynamical properties of phospholipid bilayers from computer simulation},
        Volume = 76,
        Year = 1999}

@article{Tu98,
        Author = {K.~C. Tu and M. Tarek and M.~L. Klein and D. Scharf},
        Journal = bj,
        Pages = {2123-2134},
        Title = {Effects of anesthetics on the structure of a phospholipid bilayer: Molecular dynamics investigation of halothane in the hydrated liquid crystal phase of dipalmitoylphosphatidylcholine},
        Volume = 75,
        Year = 1998}

@article{Pomes96,
        Author = {R. Pomes and B. Roux},
        Journal = bj,
        Pages = {19-39},
        Title = {Structure and dynamics of a proton wire: A theoretical study of H+ translocation along the single-file water chain in the gramicidin a channel},
        Volume = 71,
        Year = 1996}

@article{Duwez60,
        Author = {P. Duwez and R.~H. Willens and W. {Klement~Jr.}},
        Journal = {J. Appl. Phys.},
        Pages = {1136-1137},
        Title = {Continuous Series of Metastable Solid Solutions in Silver-Copper Alloys},
        Volume = 31,
        Year = 1960}

@article{Peker93,
        Author = {A. Peker and W.~L. Johnson},
        Journal = {Appl. Phys. Lett.},
        Pages = {2342-2344},
        Title = {A highly processable metallic-glass - $\mbox{Zr}_{41.2}\mbox{Ti}_{13.8}\mbox{Cu}_{12.5}\mbox{Ni}_{10.0}\mbox{Be}_{22.5}$},
        Volume = 63,
        Year = 1993}

@article{ChoiYim97,
        Author = {H. Choi-Yim and W.~L. Johnson},
        Journal = {Appl. Phys. Lett.},
        Pages = {3808-3810},
        Title = {Bulk metallic glass matrix composites},
        Volume = 71,
        Year = 1997}

@article{Sun96,
        Author = {X. Sun and S. Schneider and U. Geyer and W.~L. Johnson and M.~A. Nicolet},
        Journal = {J. Mater. Res.},
        Pages = {2738-2743},
        Title = {Oxidation and crystallization of an amorphous $\mbox{Zr}_{60}\mbox{Al}_{15}\mbox{Ni}_{25}$ alloy},
        Volume = 11,
        Year = 1996}

@article{Heller93,
        Author = {H. Heller and M. Schaefer and K. Schulten},
        Journal = jpc,
        Pages = {8343-8360},
        Title = {MOLECULAR DYNAMICS SIMULATION OF A BILAYER OF 200 LIPIDS IN THE GEL AND IN THE LIQUID-CRYSTAL PHASES},
        Volume = 97,
        Year = 1993}

@article{Berardi96,
        Author = {R. Berardi and S. Orlandi and C Zannoni},
        Journal = cpl,
        Pages = {357-362},
        Title = {Antiphase structures in polar smectic liquid crystals and their molecular origin},
        Volume = 261,
        Year = 1996}

@article{Berardi99,
        Author = {R. Berardi and S. Orlandi and C. Zannoni},
        Journal = {Int. J. Mod. Phys. C},
        Pages = {477-484},
        Title = {Monte Carlo simulations of rod-like Gay-Berne mesogens with transverse dipoles},
        Volume = 10,
        Year = 1999}

@article{Pasterny2000,
        Author = {K. Pasterny and E. Gwozdz and A. Brodka},
        Journal = {J. Mol. Liq.},
        Pages = {173-184},
        Title = {Properties of a model liquid crystal: Polar Gay-Berne particles},
        Volume = 85,
        Year = 2000}

@article{Jorgensen83,
        Author = {W.~L. Jorgensen and J. Chandrasekhar and J.~D. Madura and R.~W. Impey and M.~L. Klein},
        Journal = jcp,
        Pages = {926-935},
        Title = {COMPARISON OF SIMPLE POTENTIAL FUNCTIONS FOR SIMULATING LIQUID WATER},
        Volume = 79,
        Year = 1983}

@article{Berardi98,
        Author = {R. Berardi and C. Fava and C. Zannoni},
        Journal = cpl,
        Pages = {8-14},
        Title = {A Gay-Berne potential for dissimilar biaxial particles},
        Volume = 297,
        Year = 1998}

@article{Gay81,
        Author = {J.~G. Gay and B.~J. Berne},
        Journal = jcp,
        Pages = {3316-3319},
        Title = {MODIFICATION OF THE OVERLAP POTENTIAL TO MIMIC A LINEAR SITE-SITE POTENTIAL},
        Volume = 74,
        Year = 1981}

@article{Perram96,
        Author = {J.~W. Perram and J. Rasmussen and E. Praestgaard and J.~L. Lebowitz},
        Journal = pre,
        Pages = {6565-6572},
        Title = {Ellipsoid contact potential: Theory and relation to overlap potentials},
        Volume = 54,
        Year = 1996}

@article{Cornell95,
        Author = {W.~D. Cornell and P. Cieplak and C.~I. Bayly and I.~R. Gould and K.~M. {Merz, Jr.} and D.~M. Ferguson and D.~C. Spellmeyer and T. Fox and J.~W. Caldwell and P.~A. Kollman},
        Journal = jacs,
        Pages = {5179-5197},
        Title = {A second generation force field for the simulation of proteins and nucleic acids},
        Volume = 117,
        Year = 1995}

@article{Brooks83,
        Author = {B.~R. Brooks and R.~E. Bruccoleri and B.~D. Olafson and D.~J. States and S. Swaminathan and M. Karplus},
        Journal = jcc,
        Pages = {187-217},
        Title = {{\sc charmm}: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations},
        Volume = 4,
        Year = 1983}

@incollection{MacKerell98,
        Address = {New York},
        Author = {A.~D. {MacKerell, Jr.} and B. Brooks and C.~L. {Brooks III} and L. Nilsson and B. Roux and Y. Won and M. Karplus},
        Booktitle = {The Encyclopedia of Computational Chemistry},
        Editor = {P.~v.~R. {Schleyer, {\it et al.}}},
        Pages = {271-277},
        Publisher = {John Wiley \& Sons},
        Title = {{\sc charmm}: The Energy Function and Its Parameterization with an Overview of the Program},
        Volume = 1,
        Year = 1998}

@incollection{Jorgensen98,
        Address = {New York},
        Author = {W.~L. Jorgensen},
        Booktitle = {The Encyclopedia of Computational Chemistry},
        Editor = {P.~v.~R. {Schleyer, {\it et al.}}},
        Pages = {1986-1989},
        Publisher = {John Wiley \& Sons},
        Title = {OPLS Force Fields},
        Volume = 3,
        Year = 1998}

@article{Rabani2000,
        Author = {E. Rabani and J.~D. Gezelter and B.~J. Berne},
        Journal = prl,
        Pages = 467,
        Title = {Reply to `Comment on ``Direct Observation of Stretched-Exponential Relaxation in Low-Temperature Lennard-Jones Systems Using th eCage Correlation Function'' '},
        Volume = 85,
        Year = 2000}

@book{Cevc87,
        Address = {New York},
        Author = {G. Cevc and D. Marsh},
        Publisher = {John Wiley \& Sons},
        Title = {Phospholipid Bilayers},
        Year = 1987}

@article{Janiak79,
        Author = {M.~J. Janiak and D.~M. Small and G.~G. Shipley},
        Journal = {J. Biol. Chem.},
        Pages = {6068-6078},
        Title = {Temperature and Compositional Dependence of the Structure of Hydrated Dimyristoyl Lecithin},
        Volume = 254,
        Year = 1979}

@book{Tobias90,
        Address = {Tucson},
        Author = {Sheila Tobias},
        Publisher = {Research Corp.},
        Title = {They're not Dumb. They're Different: Stalking the Second Tier},
        Year = 1990}

@article{Mazur92,
        Author = {E. Mazur},
        Journal = {Optics and Photonics News},
        Pages = 38,
        Title = {Qualitative vs. Quantititative Thinking: Are we teaching the right thing?},
        Volume = 3,
        Year = 1992}

@book{Mazur97,
        Address = {New Jersey},
        Author = {Eric Mazur},
        Publisher = {Prentice Hall},
        Title = {Peer Instruction: A User's Manual},
        Year = 1997}

@article{Wigner55,
        Author = {E.~P. Wigner},
        Journal = {Annals of Mathematics},
        Pages = {548-564},
        Title = {Characteristic Vectors of Bordered Matrices with Infinite Dimensions},
        Volume = 62,
        Year = 1955}

@article{Gaukel98,
        Author = {C. Gaukel and H.~R. Schober},
        Journal = {Solid State Comm.},
        Pages = {1-5},
        Title = {Diffusion Mechanisms in under-cooled Binary Metal Liquids of $\mbox{Zr}_{67}\mbox{Cu}_{33}$},
        Volume = 107,
        Year = 1998}

@article{Qi99,
        Author = {Y. Qi and T. \c{C}a\v{g}in and Y. Kimura and W.~A. {Goddard III}},
        Journal = prb,
        Number = 5,
        Pages = {3527-3533},
        Title = {Molecular-dynamics simulations of glass formation and crystallization in binary liquid metals: $\mbox{Cu-Ag}$ and $\mbox{Cu-Ni}$},
        Volume = 59,
        Year = 1999}

@article{Khorunzhy97,
        Author = {A. Khorunzhy and G.~J. Rodgers},
        Journal = {J. Math. Phys.},
        Pages = {3300-3320},
        Title = {Eigenvalue distribution of large dilute random matrices},
        Volume = 38,
        Year = 1997}

@article{Rodgers88,
        Author = {G.~J. Rodgers and A. Bray},
        Journal = {Phys. Rev. B},
        Pages = 355703562,
        Title = {Density of States of a Sparse Random Matrix},
        Volume = 37,
        Year = 1988}

@article{Rodgers90,
        Author = {G.~J. Rodgers and C. {De Dominicis}},
        Journal = {J. Phys. A: Math. Gen.},
        Pages = {1567-1573},
        Title = {Density of states of sparse random matrices},
        Volume = 23,
        Year = 1990}

@inproceedings{Barker80,
        Author = {J.~A. Barker},
        Booktitle = {The problem of long-range forces in the computer simulation of condensed matter},
        Editor = {D. Ceperley},
        Pages = {45-6},
        Series = {NRCC Workshop Proceedings},
        Title = {Reaction field method for polar fluids},
        Volume = 9,
        Year = 1980}

@article{Smith82,
        Author = {W. Smith},
        Journal = {CCP5 Quarterly},
        Pages = {13-25},
        Title = {Point multipoles in the Ewald summation},
        Volume = 4,
        Year = 1982}

@article{Daw84,
        Author = {M.~S. Daw and M.~I. Baskes},
        Journal = prb,
        Number = 12,
        Pages = {6443-6453},
        Title = {Embedded-atom method: Derivation and application to impurities, surfaces, and other defects in metals},
        Volume = 29,
        Year = 1984}

@article{Chen90,
        Author = {A.~P. Sutton and J. Chen},
        Journal = {Phil. Mag. Lett.},
        Pages = {139-146},
        Title = {Long-Range $\mbox{Finnis Sinclair}$ Potentials},
        Volume = 61,
        Year = 1990}

@article{Lu97,
        Author = {J. Lu and J.~A. Szpunar},
        Journal = {Phil. Mag. A},
        Pages = {1057-1066},
        Title = {Applications of the embedded-atom method to glass formation and crystallization of liquid and glass transition-metal nickel},
        Volume = {75},
        Year = {1997}}

@article{Shlesinger99,
        Author = {M.~F. Shlesinger and J. Klafter and G. Zumofen},
        Journal = {Am. J. Phys.},
        Pages = {1253-1259},
        Title = {Above, below, and beyond Brownian motion},
        Volume = 67,
        Year = 1999}

@article{Klafter96,
        Author = {J. Klafter and M. Shlesinger and G. Zumofen},
        Journal = {Physics Today},
        Pages = {33-39},
        Title = {Beyond Brownian Motion},
        Volume = 49,
        Year = 1996}

@article{Blumen83,
        Author = {A. Blumen and J. Klafter and G. Zumofen},
        Journal = {Phys. Rev. B},
        Pages = {3429-3435},
        Title = {Recombination in amorphous materials as a continuous-time random-walk problem},
        Volume = 27,
        Year = 1983}

@article{Klafter94,
        Author = {J. Klafter and G. Zumofen},
        Journal = jpc,
        Pages = {7366-7370},
        Title = {Probability Distributions for Continuous-Time Random Walks with Long Tails},
        Volume = 98,
        Year = 1994}

@article{Dzugutov92,
        Author = {M. Dzugutov},
        Journal = pra,
        Pages = {R2984-R2987},
        Title = {Glass formation in a simple monatomic liquid with icosahedral inherent local order},
        Volume = 46,
        Year = 1992}

@article{Moore94,
        Author = {P. Moore and T. Keyes},
        Journal = jcp,
        Pages = 6709,
        Title = {Normal Mode Analysis of Liquid $\mbox{CS}_2$: Velocity Correlation Functions and Self-Diffusion Constants},
        Volume = 100,
        Year = 1994}

@article{Seeley89,
        Author = {G. Seeley and T. Keyes},
        Journal = jcp,
        Pages = {5581-5586},
        Title = {Normal-mode analysis of liquid-state dynamics},
        Volume = 91,
        Year = 1989}

@article{Madan90,
        Author = {B. Madan and T. Keyes and G. Seeley},
        Journal = jcp,
        Pages = {7565-7569},
        Title = {Diffusion in supercooled liquids via normal mode analysis},
        Volume = 92,
        Year = 1990}

@article{Madan91,
        Author = {B. Madan and T. Keyes and G. Seeley},
        Journal = jcp,
        Pages = {6762-6769},
        Title = {Normal mode analysis of the velocity correlation function in supercooled liquids},
        Volume = 94,
        Year = 1991}

@article{Buchner92,
        Author = {M. Buchner, B.~M. Ladanyi and R.~M. Stratt},
        Journal = jcp,
        Pages = {8522-8535},
        Title = {The short-time dynamics of molecular liquids. Instantaneous-normal-mode theory},
        Volume = 97,
        Year = 1992}

@article{Wan94,
        Author = {Yi. Wan and R.~M. Stratt},
        Journal = jcp,
        Pages = {5123-5138},
        Title = {Liquid theory for the instantaneous normal modes of a liquid},
        Volume = 100,
        Year = 1994}

@article{Stratt95,
        Author = {R.~M. Stratt},
        Journal = {Acc. Chem. Res.},
        Pages = {201-207},
        Title = {The instantaneous normal modes of liquids},
        Volume = 28,
        Year = 1995}

@article{Nitzan95,
        Author = {G.~V. Vijayadamodar and A. Nitzan},
        Journal = jcp,
        Pages = {2169-2177},
        Title = {On the application of instantaneous normal mode analysis to long time dynamics of liquids},
        Volume = 103,
        Year = 1995}

@article{Ribeiro98,
        Author = {M.~C.~C. Ribeiro and P.~A. Madden},
        Journal = jcp,
        Pages = {3256-3263},
        Title = {Unstable Modes in Ionic Melts},
        Volume = 108,
        Year = 1998}

@article{Keyes98a,
        Author = {T. Keyes and W.-X. Li and U.~Z{\"{u}}rcher},
        Journal = jcp,
        Pages = {4693-4694},
        Title = {Comment on a critique of the instantaneous normal mode (INM) approach to diffusion (J. Chem. Phys. {\bf 107}, 4618 (1997))},
        Volume = 109,
        Year = 1998}

@article{Alemany98,
        Author = {M.~M.~G. Alemany and C. Rey and L.~J. Gallego},
        Journal = jcp,
        Pages = {5175-5176},
        Title = {Transport coefficients of liquid transition metals: A computer simulation study using the embedded atom model},
        Volume = 109,
        Year = 1998}

@article{Belonoshko00,
        Author = {A.~B. Belonoshko and R. Ahuja and O. Eriksson and B. Johansson},
        Journal = prb,
        Pages = {3838-3844},
        Title = {Quasi ab initio molecular dynamic study of Cu melting},
        Volume = 61,
        Year = 2000}

@article{Banhart92,
        Author = {J. Banhart and H. Ebert and R. Kuentzler and J. Voitl\"{a}nder},
        Journal = prb,
        Pages = {9968-9975},
        Title = {Electronic properties of single-phased metastable Ag-Cu alloys},
        Volume = 46,
        Year = 1992}

@article{Wendt78,
        Author = {H. Wendt and F.~F. Abraham},
        Journal = prl,
        Pages = 1244,
        Volume = 41,
        Year = 1978}

@article{Lewis91,
        Author = {L.~J. Lewis},
        Journal = prb,
        Pages = {4245-4254},
        Title = {Atomic dynamics through the glass transition},
        Volume = 44,
        Year = 1991}

@article{Liu92,
        Author = {R.~S. Liu and D.~W. Qi and S. Wang},
        Journal = prb,
        Pages = {451-453},
        Title = {Subpeaks of structure factors for rapidly quenched metals},
        Volume = 45,
        Year = 1992}

@book{pliny,
        Author = {Pliny},
        Title = {Hist. Nat.},
        Volume = {XXXVI}}

@article{Anheuser94,
        Author = {K. Anheuser and J.P. Northover},
        Journal = {Brit. Num. J.},
        Pages = 22,
        Title = {Silver plating of Roman and Celtic coins from Britan - a technical study},
        Volume = 64,
        Year = 1994}

@article{Pense92,
        Author = {A. W. Pense},
        Journal = {Mat. Char.},
        Pages = 213,
        Title = {The Decline and Fall of the Roman Denarius},
        Volume = 29,
        Year = 1992}

@article{Ngai81,
        Author = {K.~L. Ngai and F.-S. Liu},
        Journal = prb,
        Pages = {1049-1065},
        Title = {Dispersive diffusion transport and noise, time-dependent diffusion coefficient, generalized Einstein-Nernst relation, and dispersive diffusion-controlled unimolecular and bimolecular reactions},
        Volume = 24,
        Year = 1981}

@unpublished{Truhlar00,
        Author = {D.~G. Truhlar and A. Kohen},
        Note = {private correspondence}}

@article{Truhlar78,
        Author = {Donald G. Truhlar},
        Journal = {J. Chem. Ed.},
        Pages = 309,
        Title = {Interpretation of the Activation Energy},
        Volume = 55,
        Year = 1978}

@book{Tolman27,
        Address = {New York},
        Author = {R. C. Tolman},
        Pages = {260-270},
        Publisher = {Chemical Catalog Co.},
        Title = {Statistical Mechanics with Applications to Physics and Chemistry},
        Year = 1927}

@article{Tolman20,
        Author = {R. C. Tolman},
        Journal = jacs,
        Pages = 2506,
        Title = {Statistical Mechanics Applied to Chemical Kinetics},
        Volume = 42,
        Year = 1920}

@article{Nagel96,
        Author = {M.D. Ediger and C.A. Angell and Sidney R. Nagel},
        Journal = jpc,
        Pages = 13200,
        Title = {Supercooled Liquids and Glasses},
        Volume = 100,
        Year = 1996}

@inbook{Blumen86,
        Address = {Amsterdam},
        Author = {A. Blumen and J. Klafter and G. Zumofen},
        Chapter = {Reactions in Disordered Media Modelled by Fractals},
        Editor = {Luciano Peitronero and E. Tosatti},
        Pages = 399,
        Publisher = {North-Holland},
        Series = {International Symposium on Fractals in Physics},
        Title = {Fractals in Physics},
        Year = 1986}

@article{Shlesinger84,
        Author = {M.~F. Shlesinger and E.~W. Montroll},
        Journal = {Proc. Natl. Acad. Sci. USA},
        Pages = {1280-1283},
        Title = {On the Williams-Watts function of dielectric relaxation},
        Volume = 81,
        Year = 1984}

@article{Klafter86,
        Author = {J. Klafter and M.~F. Shlesinger},
        Journal = {Proc. Natl. Acad. Sci. USA},
        Pages = {848-851},
        Title = {On the relationship among three theories of relaxation in disordered systems},
        Volume = 83,
        Year = 1986}

@article{Li2001,
        Author = {Z. Li and M. Lieberman and W. Hill},
        Journal = {Langmuir},
        Pages = {4887-4894},
        Title = {{\sc xps} and {\sc sers} Study of Silicon Phthalocyanine Monolayers: umbrella vs. octopus design strategies for formation of oriented {\sc sam}s},
        Volume = 17,
        Year = 2001}

@article{Evans1993,
        Author = {J.~W. Evans},
        Journal = rmp,
        Pages = {1281-1329},
        Title = {Random and Cooperative Sequential Adsorption},
        Volume = 65,
        Year = 1993}

@article{Dwyer1977,
        Author = {D.~J. Dwyer and G.~W. Simmons and R.~P. Wei},
        Journal = {Surf. Sci.},
        Pages = 617,
        Volume = 64,
        Year = 1977}

@article{Macritche1978,
        Author = {F. MacRitche},
        Journal = {Adv. Protein Chem.},
        Pages = 283,
        Volume = 32,
        Year = 1978}

@article{Feder1980,
        Author = {J. Feder},
        Journal = {J. Theor. Biol.},
        Pages = 237,
        Volume = 87,
        Year = 1980}

@article{Ramsden1993,
        Author = {J.~J. Ramsden},
        Journal = prl,
        Pages = 295,
        Volume = 71,
        Year = 1993}

@article{Egelhoff1989,
        Author = {W.~F. Egelhoff and I. Jacob},
        Journal = prl,
        Pages = 921,
        Volume = 62,
        Year = 1989}

@article{Viot1992a,
        Author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot},
        Journal = jpc,
        Pages = {5212-5218},
        Title = {RANDOM SEQUENTIAL ADSORPTION OF ANISOTROPIC PARTICLES 1. JAMMING LIMIT AND ASYMPTOTIC-BEHAVIOR},
        Volume = 97,
        Year = 1992}

@article{Viot1992b,
        Author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot},
        Journal = {Physica A},
        Pages = {248-252},
        Title = {SATURATION COVERAGE IN RANDOM SEQUENTIAL ADSORPTION OF VERY ELONGATED PARTICLES},
        Volume = 191,
        Year = 1992}

@article{Dobson1987,
        Author = {B.~W. Dobson},
        Journal = prb,
        Pages = 1068,
        Volume = 36,
        Year = 1987}

@article{Boyer1995,
        Author = {D. Boyer and P. Viot and G. Tarjus and J. Talbot},
        Journal = jcp,
        Pages = 1607,
        Title = {PERCUS-$\mbox{Y}$EVICK-LIKE INTERGRAL EQUATION FOR RANDOM SEQUENTIAL ADSORPTION},
        Volume = 103,
        Year = 1995}

@article{Viot1992c,
        Author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot},
        Journal = {Physica A},
        Pages = {248-252},
        Title = {SATURATION COVERAGE OF HIGHLY ELONGATED ANISOTROPIC PARTICLES},
        Volume = 191,
        Year = 1992}

@article{Ricci1994,
        Author = {S.~M. Ricci and J. Talbot and G. Tarjus and P. Viot},
        Journal = jcp,
        Pages = 9164,
        Title = {A STRUCTURAL COMPARISON OF RANDOM SEQUENTIAL ADSORPTION AND EQUILIBRIUM CONFIGURATIONS OF SPHEROCYLINDERS},
        Volume = 101,
        Year = 1994}

@article{Semmler1998,
        Author = {M. Semmler and E.~K. Mann and J. Ricka and M. Borkovec},
        Journal = {Langmuir},
        Pages = {5127-5132},
        Title = {Diffusional Deposition of Charged Latex Particles on Water-Solid Interfaces at Low Ionic Strength},
        Volume = 14,
        Year = 1998}

@article{Solomon1986,
        Author = {H. Solomon and H. Weiner},
        Journal = {Comm. Statistics A},
        Pages = {2571-2607},
        Title = {A REVIEW OF THE PACKING PROBLEM},
        Volume = 15,
        Year = 1986}

@article{Bonnier1993,
        Author = {B. Bonnier and M. Hontebeyrie and C. Meyers},
        Journal = {Physica A},
        Pages = {1-10},
        Title = {ON THE RANDOM FILLING OF R(D) BY NONOVERLAPPING D-DIMENSIONAL CUBES},
        Volume = 198,
        Year = 1993}

@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{Dullweber1997,
        Author = {A. Dullweber and B. Leimkuhler and R. McLachlan},
        Journal = jcp,
        Number = 15,
        Pages = {5840-5851},
        Title = {Symplectic splitting methods for rigid body molecular dynamics},
        Volume = 107,
        Year = 1997}

@article{Siepmann1998,
        Author = {M. Martin and J.~I. Siepmann},
        Journal = jpcB,
        Pages = {2569-2577},
        Title = {Transferable Potentials for Phase Equilibria. 1. United-Atom Description of n-Alkanes},
        Volume = 102,
        Year = 1998}

@article{Marrink01,
        Author = {S.~J. Marrink and E. Lindahl and O. Edholm and A.~E. Mark},
        Journal = jacs,
        Pages = {8638-8639},
        Title = {Simulations of the Spontaneous Aggregation of Phospholipids into Bilayers},
        Volume = 123,
        Year = 2001}

@article{liu96:new_model,
        Author = {Y. Liu and T. Ichiye},
        Journal = jpc,
        Pages = {2723-2730},
        Title = {Soft sticky dipole potential for liquid water: a new model},
        Volume = 100,
        Year = 1996}

@article{liu96:monte_carlo,
        Author = {Y. Liu and T. Ichiye},
        Journal = cpl,
        Pages = {334-340},
        Title = {The static dielectric constant of the soft sticky dipole model of liquid water: $\mbox{Monte Carlo}$ simulation},
        Volume = 256,
        Year = 1996}

@article{chandra99:ssd_md,
        Author = {A. Chandra and T. Ichiye},
        Journal = jcp,
        Number = 6,
        Pages = {2701-2709},
        Title = {Dynamical properties of the soft sticky dipole model of water: Molecular dynamics simulation},
        Volume = 111,
        Year = 1999}

@book{allen87:csl,
        Address = {New York},
        Author = {M.~P. Allen and D.~J. Tildesley},
        Publisher = {Oxford University Press},
        Title = {Computer Simulations of Liquids},
        Year = 1987}

@book{leach01:mm,
        Address = {Harlow, England},
        Author = {A. Leach},
        Edition = {2nd},
        Publisher = {Pearson Educated Limited},
        Title = {Molecular Modeling: Principles and Applications},
        Year = 2001}

@article{katsaras00,
        Author = {J. Katsaras and S. Tristram-Nagle and Y. Liu and R.~L. Headrick and E. Fontes and P.~C. Mason and J.~F. Nagle},
        Journal = pre,
        Number = 5,
        Pages = {5668-5677},
        Title = {Clarification of the ripple phase of lecithin bilayers using fully hydrated, aligned samples},
        Volume = 61,
        Year = 2000}

@article{sengupta00,
        Author = {K. Sengupta and V.~A. Raghunathan and J. Katsaras},
        Journal = {Europhysics Letters},
        Number = 6,
        Pages = {722-728},
        Title = {Novel structural Features of the ripple phase of phospholipids},
        Volume = 49,
        Year = 2000}

@article{venable00,
        Author = {R.~M. Venable and B.~R. Brooks and R.~W. Pastor},
        Journal = jcp,
        Number = 10,
        Pages = {4822-4832},
        Title = {Molecular dynamics simulations of gel ($L_{\beta I}$) phase lipid bilayers in constant pressure and constant surface area ensembles},
        Volume = 112,
        Year = 2000}

@article{lindahl00,
        Author = {E. Lindahl and O. Edholm},
        Journal = bj,
        Month = {July},
        Pages = {426-433},
        Title = {Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations},
        Volume = 79,
        Year = 2000}

@article{saiz02,
        Author = {L. Saiz and M. Klein},
        Journal = jcp,
        Number = 7,
        Pages = {3052-3057},
        Title = {Electrostatic interactions in a neutral model phospholipid bilayer by molecular dynamics simulations},
        Volume = 116,
        Year = 2002}

@article{stevens95,
        Author = {M.~J. Stevens and G.~S. Grest},
        Journal = pre,
        Number = 6,
        Pages = {5976-5983},
        Title = {Phase coexistence of a Stockmayer fluid in an aplied field},
        Volume = 51,
        Year = 1995}

@article{darden93:pme,
        Author = {T. Darden and D. York and L. Pedersen},
        Journal = jcp,
        Number = 12,
        Pages = {10089-10092},
        Title = {Particle mesh Ewald: An $N \log N$ method for Ewald sums in large systems},
        Volume = 98,
        Year = 1993}

@article{goetz98,
        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}

@article{marrink01:undulation,
        Author = {S.~J. Marrink and A.~E. Mark},
        Journal = jpcB,
        Pages = {6122-6127},
        Title = {Effect of undulations on surface tension in simulated bilayers},
        Volume = 105,
        Year = 2001}

@article{lindahl00:undulation,
        Author = {E. Lindahl and O. Edholm},
        Journal = bj,
        Pages = {426-433},
        Title = {Mesoscopic undulation and thickness fluctuations in lipid bilayers from molecular dynamics simulation},
        Volume = 79,
        Year = 2000}

@article{metropolis:1949,
        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{metropolis:1953,
        Author = {N. Metropolis and A.~W. Rosenbluth and M.~N. Rosenbluth and A.~H. Teller and E. Teller},
        Journal = jcp,
        Pages = {1087-1092},
        Title = {Equation of State Calculations by Fast Computing Machines},
        Volume = 21,
        Year = 1953}

@article{born:1912,
        Author = {M. Born and Th. Von~Karman},
        Journal = {Physik Z.},
        Number = {297-309},
        Title = {Uber Schwingungen in Raumgittern},
        Volume = 13,
        Year = 1912}

@book{chandler:1987,
        Author = {David Chandler},
        Publisher = {Oxford University Press},
        Title = {Introduction to Modern Statistical Mechanics},
        Year = 1987}

@article{pearlman:1995,
        Author = {David~A. Pearlman and David~A. Case and James~W. Caldwell and Wilson~S. Ross and Thomas~E. {Cheatham~III} and Steve DeBolt and David Ferguson and George Seibel and Peter Kollman},
        Journal = cpc,
        Pages = {1-41},
        Title = {{\sc amber}, a package of computer programs for applying molecular mechanics. normal mode analysis, molecular dynamics, and free energy calculations to simulate the structural and energetic properties of molecules},
        Volume = 91,
        Year = 1995}

@book{Goldstein01,
        Address = {San Francisco},
        Author = {H. Goldstein and C. Poole and J. Safko},
        Edition = {3rd},
        Publisher = {Addison Wesley},
        Title = {Classical Mechanics},
        Year = 2001}

@article{Bratko85,
        Author = {D. Bratko and L. Blum and A. Luzar},
        Journal = jcp,
        Number = 12,
        Pages = {6367-6370},
        Title = {A simple model for the intermolecular potential of water},
        Volume = 83,
        Year = 1985}

@article{Bratko95,
        Author = {L. Blum and F. Vericat and D. Bratko},
        Journal = jcp,
        Number = 3,
        Pages = {1461-1462},
        Title = {Towards an analytical model of water: The octupolar model},
        Volume = 102,
        Year = 1995}

@article{Ichiye03,
        Author = {M.-L. Tan and J.~T. Fischer and A. Chandra and B.~R. Brooks and T. Ichiye},
        Journal = cpl,
        Pages = {646-652},
        Title = {A temperature of maximum density in soft sticky dipole water},
        Volume = 376,
        Year = 2003}

@article{Soper86,
        Author = {A.~K. Soper and M.~G. Phillips},
        Journal = cp,
        Number = 1,
        Pages = {47-60},
        Title = {A new determination of the structure of water at 298K},
        Volume = 107,
        Year = 1986}

@article{plimpton95,
        Author = {S. Plimpton},
        Journal = {J. Comp. Phys.},
        Pages = {1-19},
        Title = {Fast Parallel Algorithms for Short-Range Molecular Dymanics},
        Volume = 117,
        Year = 1995}

@article{Ercolessi02,
        Author = {U. Tartaglino and E. Tosatti and D. Passerone and F. Ercolessi},
        Journal = prb,
        Pages = 241406,
        Title = {Bending strain-driven modification of surface resconstructions: Au(111)},
        Volume = 65,
        Year = 2002}

@article{Ercolessi88,
        Author = {F. Ercolessi and M. Parrinello and E. Tosatti},
        Journal = {Phil. Mag. A},
        Pages = {213-226},
        Title = {Simulation of Gold in the Glue Model.},
        Volume = 58,
        Year = 1988}

@article{Finnis84,
        Author = {M.~W Finnis and J.~E. Sinclair},
        Journal = {Phil. Mag. A},
        Pages = {45-55},
        Title = {A Simple Empirical N-Body Potential for Transition-Metals},
        Volume = 50,
        Year = 1984}

@article{FBD86,
        Author = {S.~M. Foiles and M.~I. Baskes and M.~S. Daw},
        Journal = prb,
        Number = 12,
        Pages = 7983,
        Title = {Embedded-atom-method functions for the fcc metals $\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys},
        Volume = 33,
        Year = 1986}

@article{EAM93,
        Author = {M.~S. Daw and S.~M. Foiles and M.~I. Baskes},
        Journal = {Mat. Sci. Rep.},
        Pages = {251-310},
        Title = {The embededd-atom method},
        Volume = 9,
        Year = 1993}

@article{johnson89,
        Author = {R.~A. Johnson},
        Journal = prb,
        Number = 17,
        Pages = 12554,
        Title = {Alloy models with the embedded-atom method},
        Volume = 39,
        Year = 1989}

@article{Laird97,
        Author = {A. Kol and B.~B. Laird and B.~J. Leimkuhler},
        Journal = jcp,
        Number = 7,
        Pages = {2580-2588},
        Title = {A symplectic method for rigid-body molecular simulation},
        Volume = 107,
        Year = 1997}

@article{hoover85,
        Author = {W.~G. Hoover},
        Journal = pra,
        Pages = 1695,
        Title = {Canonical dynamics: Equilibrium phase-space distributions},
        Volume = 31,
        Year = 1985}

@article{Roux91,
        Author = {B. Roux and M. Karplus},
        Journal = jpc,
        Number = 15,
        Pages = {4856-4868},
        Title = {Ion transport in a Gramicidin-like channel: dynamics and mobility},
        Volume = 95,
        Year = 1991}

@article{Marrink94,
        Author = {S.~J Marrink and H.~J.~C. Berendsen},
        Journal = jpc,
        Number = 15,
        Pages = {4155-4168},
        Title = {Simulation of water transport through a lipid membrane},
        Volume = 98,
        Year = 1994}

@article{Daw89,
        Author = {Murray~S. Daw},
        Journal = prb,
        Pages = {7441-7452},
        Title = {Model of metallic cohesion: The embedded-atom method},
        Volume = 39,
        Year = 1989}

@inbook{voter,
        Author = {A.~F. Voter},
        Chapter = 4,
        Editor = {J.~H. Westbrook and R.~L. Fleischer},
        Pages = 77,
        Publisher = {John Wiley and Sons Ltd},
        Title = {Intermetallic Compounds: Principles and Practice},
        Volume = 1,
        Year = 1995}

@article{marrink:2002,
        Author = {S.~J. Marrink and D.~P. Teileman},
        Journal = bj,
        Pages = {2386-2392},
        Title = {Molecular Dynamics Simulation of Spontaneous Membrane Fusion during a Cubic-Hexagonal Phase Transition},
        Volume = 83,
        Year = 2002}

@article{sum:2003,
        Author = {A.~K. Sum and J.~J. de~Pablo},
        Journal = bj,
        Pages = {3636-3645},
        Title = {Molecular Simulation Study on the influence of Dimethylsulfoxide on the structure of Phospholipid Bilayers},
        Volume = 85,
        Year = 2003}

@article{gomez:2003,
        Author = {J.~D. Faraldo-Gomez and G.~R. Smith and M.~S.P. Sansom},
        Journal = {Eur. Biophys. J.},
        Pages = {217-227},
        Title = {Setting up and optimization of membrane protein simulations},
        Volume = 31,
        Year = 2002}

@article{smondyrev:1999,
        Author = {A.~M. Smondyrev and M.~L. Berkowitz},
        Journal = bj,
        Pages = {2472-2478},
        Title = {Molecular Dynamics Simulation of {\sc dppc} Bilayer in {\sc dmso}},
        Volume = 76,
        Year = 1999}

@article{nina:2002,
        Author = {M. Nina and T. Simonson},
        Journal = jpcB,
        Pages = {3696-3705},
        Title = {Molecular Dynamics of the $\text{tRNA}^{\text{Ala}}$ Acceptor Stem: Comparison between Continuum Reaction Field and Particle-Mesh Ewald Electrostatic Treatments},
        Volume = 106,
        Year = 2002}

@article{norberg:2000,
        Author = {J. Norberg and L. Nilsson},
        Journal = bj,
        Pages = {1537-1553},
        Title = {On the truncation of Long-Range Electrostatic Interactions in {\sc dna}},
        Volume = 79,
        Year = 2000}

@article{patra:2003,
        Author = {M. Patra and M. Karttunen and M.~T. Hyv\"{o}nen and E. Falk and P. Lindqvist and I. Vattulainen},
        Journal = bj,
        Pages = {3636-3645},
        Title = {Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts Due to Truncating Electrostatic Interactions},
        Volume = 84,
        Year = 2003}

@article{marrink04,
        Author = {S.~J. Marrink and A.~H. {de~Vries} and A.~E. Mark},
        Journal = jpcB,
        Pages = {750-760},
        Title = {Coarse Grained Model for Semiquantitative Lipid Simulations},
        Volume = 108,
        Year = 2004}

@article{andersen83,
        Author = {H.~C. Andersen},
        Journal = {J. Comp. Phys.},
        Pages = {24-34},
        Title = {{\sc rattle}: A Velocity Version of the Shake Algorithm for Molecular Dynamics Calculations},
        Volume = 52,
        Year = 1983}

@article{hura00,
        Author = {G. Hura and J.~M. Sorenson and R.~M. Glaeser and T. Head-Gordon},
        Journal = jcp,
        Pages = {9140-9148},
        Title = {A high-quality x-ray scattering experiment on liquid water at ambient conditions},
        Volume = 113,
        Year = 2000}

@article{ryckaert77,
        Author = {J.~P. Ryckaert and G. Ciccotti and H.~J.~C. Berendsen},
        Journal = {J. Comp. Phys.},
        Pages = {327-341},
        Title = {Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes},
        Volume = 23,
        Year = 1977}

@inbook{fowles99:lagrange,
        Author = {G.~R. Fowles and G.~L. Cassiday},
        Chapter = 10,
        Edition = {6th},
        Publisher = {Saunders College Publishing},
        Title = {Analytical Mechanics},
        Year = 1999}

@article{petrache00,
        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{egberts88,
        Author = {E. Egberts and H.~J.~C. Berendsen},
        Journal = jcp,
        Pages = {3718-3732},
        Title = {Molecular Dynamics Simulation of a smectic liquid crystal with atomic detail},
        Volume = 89,
        Year = 1988}

@article{Holz00,
        Author = {M. Holz and S.~R. Heil and A. Sacco},
        Journal = {Phys. Chem. Chem. Phys.},
        Pages = {4740-4742},
        Title = {Temperature-dependent self-diffusion coefficients of water and six selected molecular liquids for calibration in accurate $^1${\sc h} {\sc nmr pfg} measurements},
        Volume = 2,
        Year = 2000}

@incollection{zannoni94,
        Author = {C. Zannoni},
        Booktitle = {The Molecular Dynamics of Liquid Crstals},
        Chapter = 6,
        Editor = {G.~R. Luckhurst and C.~A. Veracini},
        Pages = {139-169},
        Publisher = {Kluwer Academic Publishers},
        Title = {An introduction to the molecular dynamics method and to orientational dynamics in liquid crystals},
        Year = 1994}

@article{melchionna93,
        Author = {S. Melchionna and G. Ciccotti and B.~L. Holian},
        Journal = {Mol. Phys.},
        Pages = {533-544},
        Title = {Hoover {\sc npt} dynamics for systems varying in shape and size},
        Volume = 78,
        Year = 1993}

@article{fennell04,
        Author = {C.~J. Fennell and J.~D. Gezelter},
        Journal = jcp,
        Number = 19,
        Pages = {9175-9184},
        Title = {On the structural and transport properties of the soft sticky dipole(SSD) and related single point water models},
        Volume = 120,
        Year = 2004}

@article{klein01,
        Author = {J.~C. Shelley andf M.~Y. Shelley and R.~C. Reeder and S. Bandyopadhyay and M.~L. Klein},
        Journal = jpcB,
        Pages = {4464-4470},
        Title = {A coarse Grain Model for Phospholipid Simulations},
        Volume = 105,
        Year = 2001}

@article{marrink03:vesicles,
        Author = {S.~J. Marrink and A.~E. Mark},
        Journal = jacs,
        Pages = {15233-15242},
        Title = {Molecular Dynaimcs Simulation of the Formation, Structure, and Dynamics of Small Phospholipid Vesicles},
        Volume = 125,
        Year = 2003}

@article{FletcherReeves,
        Author = {R. Fletcher and C.~M. Reeves},
        Journal = {Comput. J.},
        Number = 2,
        Pages = {149-154},
        Title = {Function minimization by conjugate gradients},
        Volume = 7,
        Year = 1964}

@article{PolakRibiere,
        Author = {E. Polak and G. Ribiere},
        Journal = {Rev. Fr. Inform. Rech. Oper.},
        Pages = {35-43},
        Title = {Note sur la convergence de methodes de directions conjugees},
        Volume = {16-R1},
        Year = 1969}

@article{Voter:87,
        Author = {A.F. Voter and S.P. Chen},
        Journal = {Mat. Res. Soc. Symp. Proc.},
        Pages = {175},
        Title = {Accurate Interatomic Potentials for Ni, Al, and Ni3Al},
        Volume = {82},
        Year = {1987}}

@article{Hendrickson:95,
        Author = {Bruce Hendrickson and Steve Plimpton},
        Journal = {Journal of Parallel and Distributed Computing},
        Pages = {15-25},
        Title = {Parallel Many-body Simulations without All-to-All Communication},
        Volume = {27},
        Year = {1995}}

@inproceedings{Paradyn,
        Address = {Pittsburgh, PA},
        Author = {S.~J. Plimpton and B.~A. Hendrickson},
        Booktitle = {Materials Theory and Modelling},
        Editor = {J. Broughton and P. Bristowe and J. Newsam},
        Pages = 37,
        Publisher = {Materials Research Society},
        Series = {MRS Proceedings},
        Title = {Parallel Molecular Dynamics With the Embedded Atom Method},
        Volume = 291,
        Year = 1993}

@article{Voter:95,
        Author = {A.F. Voter},
        Journal = {Intermetallic Compounds: Principles and Practice},
        Pages = {77},
        Title = {The Embedded-Atom Method},
        Volume = {1},
        Year = {1995}}

@article{Heller:90,
        Author = {H. Heller and H. Grubmuller and K. Schulten},
        Journal = {Mol. Sim.},
        Pages = {133},
        Title = {Molecular dynamics simulation on a parallel computer},
        Volume = {5},
        Year = {1990}}

@article{smd,
        Author = {H. Grubmuller and B. Heymann and P. Tavan},
        Journal = {Science},
        Pages = {997-999},
        Title = {Ligand Binding: Molecular Mechanics Calculation of The Streptavidin-Biotin Rupture Force},
        Volume = 271,
        Year = 1996}

@book{Fox88,
        Address = {Englewood Cliffs, NJ},
        Author = {G.~C. Fox and M.~A. Johnson and G.~A Lyzenga and S.~W. Otto and J.~K. Salmon and D.~W. Walker},
        Publisher = {Prentice-Hall},
        Title = {Solving Promblems on Concurrent Processors},
        Volume = {I},
        Year = 1988}

@article{Gromacs,
        Author = {H.~J.~C. Berendsen and D. {van~der~Spoel} and R. {van~Drunen}},
        Journal = cpc,
        Pages = {43-56},
        Title = {GROMACS: A message-passing parallel molecular dynamics implementation},
        Volume = 91,
        Year = 1995}

@article{Gromacs3,
        Author = {E. Lindahl and B. Hess and D. {van~der~Spoel}},
        Journal = {J. Mol. Modelling},
        Pages = {306-317},
        Title = {GROMACS 3.0: A package for molecular simulation and trajectory analysis},
        Volume = 7,
        Year = 2001}

@article{DL_POLY,
        Author = {W. Smith and T. Forester},
        Journal = {J. Mol. Graphics},
        Number = 3,
        Pages = {136-141},
        Title = {DL_POLY_2.0: A general-purpose parallel molecular dynamics simulation package},
        Volume = 14,
        Year = 1996}

@article{Tinker,
        Author = {J.~W. Ponder and F.~M. Richards},
        Journal = jcc,
        Number = 7,
        Pages = {1016-1024},
        Title = {AN EFFICIENT NEWTON-LIKE METHOD FOR MOLECULAR MECHANICS ENERGY MINIMIZATION OF LARGE MOLECULES},
        Volume = 8,
        Year = 1987}

@article{namd,
        Author = {Laxmikant Kal\'{e} and Robert Skeel and Milind Bhandarkar and Robert Brunner and Attila Gursoy and Neal Krawetz and James Phillips and Aritomo Shinozaki and Krishnan Varadarajan and Klaus Schulten},
        Journal = {J. Comp. Phys.},
        Pages = {283-312},
        Title = {NAMD2: Greater scalability for parallel molecular dynamics},
        Volume = 151,
        Year = 1999}

@article{macromodel,
        Author = {F. Mohamadi and N.~G.~J. Richards and W.~C. Guida and R. Liskamp and M. Lipton and C. Caufield and G. Chang and T. Hendrickson and W.~C. Still},
        Journal = jcc,
        Pages = 440,
        Title = {MacroModel-An Integrated Software System for Modeling Organic and Bioorganic Molecules using Molecular Mechanics},
        Volume = 11,
        Year = 1990}

@article{Berendsen87,
        Author = {H.~J.~C. Berendsen and J.~R. Grigera and T.~P. Straatsma},
        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},
        Editor = {B. Pullman},
        Pages = 331,
        Publisher = {Reidel},
        Title = {Simple Point Charge Water},
        Year = 1981}

@article{Mahoney00,
        Author = {M.~W. Mahoney and W.~L. Jorgensen},
        Journal = jcp,
        Number = 20,
        Pages = {8910-8922},
        Title = {A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions},
        Volume = 112,
        Year = 2000}

@inproceedings{Alsing:00,
        Address = {Boston},
        Author = {Paul M. Alsing and Evangelos Coutsias and John McIver},
        Booktitle = {High Performance Computing in Engineering VI},
        Editor = {M. Ingber and H. Power and C.A. Brebbia},
        Pages = {81-90},
        Publisher = {WIT},
        Title = {The interfacial behavior of liquid water near hydrophobic surfaces: a parallel force decomposition molecular dynamics code},
        Year = {2000}}

@article{Cygan04,
        Author = {R.~T. Cygan and J.-J. Liang and A.~G. Kalinichev},
        Journal = jpcb,
        Pages = {1255-1266},
        Title = {Molecular models of hydroxide, oxyhydroxide, and clay phases and the development of a general force field},
        Volume = 108,
        Year = 2004}

@article{Frenkel84,
        Author = {D. Frenkel and A.~J.~C. Ladd},
        Journal = jcp,
        Number = 7,
        Pages = {3188-3193},
        Title = {New Monte Carlo method to compute the free energy of arbitrary solids. Application to the fcc and hcp phases of hard spheres},
        Volume = 81,
        Year = 1984}

@article{Hermens88,
        Author = {J. Hermans and A. Pathiaseril and A. Anderson},
        Journal = jacs,
        Pages = {5982-5986},
        Title = {Excess Free Energy of Liquids from Molecular Dynamics Simulations. Application to Water Models},
        Volume = 110,
        Year = 1988}

@article{Meijer90,
        Author = {E.~J. Meijer and D. Frenkel and R.~A. LeSar and A.~J.~C. Ladd},
        Journal = jcp,
        Number = 12,
        Pages = {7570-7575},
        Title = {Location of melting point at 300 K of nitrogen by Monte Carlo simulation},
        Volume = 92,
        Year = 1990}

@article{Baez95a,
        Author = {L.~A. B\`{a}ez and P. Clancy},
        Journal = mp,
        Number = 3,
        Pages = {385-396},
        Title = {Calculation of free energy for molecular crystals by thermodynamic integration},
        Volume = 86,
        Year = 1995}

@article{Vlot99,
        Author = {M.~J. Vlot and J. Huinink and J.~P. van~der~Eerden},
        Journal = jcp,
        Number = 1,
        Pages = {55-61},
        Title = {Free energy calculations on systems of rigid molecules: An application to the TIP4P model of H$_2$O},
        Volume = 110,
        Year = 1999}
Revision:	4322
Committed:	Wed Mar 25 17:23:48 2015 UTC (10 years, 1 month ago) by gezelter
File size:	84055 byte(s)
Log Message:	Updated for version 2.3