--- trunk/tengDissertation/dissertation.bib 2006/04/04 04:33:23 2691 +++ trunk/tengDissertation/dissertation.bib 2006/06/07 01:49:15 2807 @@ -1,2111 +1,3114 @@ -@string{jcp = "J. Chem. Phys."} -@string{cpl = "Chem. Phys. Lett."} -@string{jpc = "J. Phys. Chem."} -@string{jpcA = "J. Phys. Chem. A"} -@string{jpcB = "J. Phys. Chem. B"} -@string{cp = "Chem. Phys."} -@string{acp = "Adv. Chem. Phys."} -@string{pra = "Phys. Rev. A"} -@string{prb = "Phys. Rev. B"} -@string{pre = "Phys. Rev. E"} -@string{prl = "Phys. Rev. Lett."} -@string{rmp = "Rev. Mod. Phys."} -@string{jml = "J. Mol. Liq."} -@string{mp = "Mol. Phys."} -@string{pnas = "Proc. Natl. Acad. Sci. USA"} -@string{jacs = "J. Am. Chem. Soc."} - -@Book{Berne90, - author = {B.~J. Berne and R. Pecora}, - title = {Dynamic Light Scattering}, - publisher = {Robert E. Krieger Publishing Company, Inc.}, - year = 1990, - address = {Malabar, Florida} -} - -@Article{Evans77, - author = {D.~J. 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Chem. Soc. - Faraday Transactions}, - year = 1997, - volume = 93, - pages = {613-619} -} - -@Article{Tieleman98, - author = {D.~P. Tieleman and H.~J.~C. Berendsen}, - title = {A molecular dynamics study of the pores formed by - Escherichia coli OmpF porin in a fully hydrated - palmitoyloleoylphosphatidylcholine bilayer}, - journal = {Biophys. J.}, - year = 1998, - volume = 74, - pages = {2786-2801} -} - -@Article{Cascales98, - author = {J.~J.~L. Cascales and J.~G.~H. Cifre and J.~G. de~la~Torre}, - title = {Anaesthetic mechanism on a model biological - membrane: A molecular dynamics simulation study}, - journal = {J. Phys. Chem. B}, - year = 1998, - volume = 102, - pages = {625-631} -} - -@Article{Bassolino95, - author = {D. Bassolino and H.~E. Alper and T.~R. Stouch}, - title = {MECHANISM OF SOLUTE DIFFUSION THROUGH LIPID - BILAYER-MEMBRANES BY MOLECULAR-DYNAMICS SIMULATION}, - journal = {J. Am. Chem. Soc.}, - year = 1995, - volume = 117, - pages = {4118-4129} -} - -@Article{Alper95, - author = {H.~E. Alper and T.~R. Stouch}, - title = {ORIENTATION AND DIFFUSION OF A DRUG ANALOG IN - BIOMEMBRANES - MOLECULAR-DYNAMICS SIMULATIONS}, - journal = {J. Phys. Chem.}, - year = 1995, - volume = 99, - pages = {5724-5731} -} - -@Article{Sok92, - author = {R.~M. Sok and H.~J.~C. Berendsen and W.~F. van~Gunsteren}, - title = {MOLECULAR-DYNAMICS SIMULATION OF THE TRANSPORT OF - SMALL MOLECULES ACROSS A POLYMER MEMBRANE}, - journal = {J. Chem. Phys.}, - year = 1992, - volume = 96, - pages = {4699-4704} -} - -@Article{Rabani99, - author = {E. Rabani and J.~D. Gezelter and B.~J. Berne}, - title = {Direct Observation of Stretched-Exponential - Relaxation in Low-Temperature Lennard-Jones Systems - Using the Cage Correlation Function}, - journal = prl, - year = {1999}, - volume = 82, - pages = {3649} -} - -@Article{Rabani97, - author = {E. Rabani and J.~D. Gezelter and B.~J. 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Berne}, - title = {Can imaginary instantaneous normal mode frequencies - predict barriers to self-diffusion?}, - journal = jcp, - year = 1997, - volume = 107, - pages = 4618 -} - -@Article{Zwanzig83, - author = {R. Zwanzig}, - title = {On the relation between self-diffusion and viscosity - of liquids}, - journal = jcp, - year = 1983, - volume = 79, - pages = {4507-4508} -} - -@Article{Zwanzig88, - author = {R. Zwanzig}, - title = {Diffusion in rough potential}, - journal = {Proc. Natl. Acad. Sci. USA}, - year = 1988, - volume = 85, - pages = 2029 -} - -@Article{Stillinger95, - author = {F.~H. Stillinger}, - title = {A Topographic View of Supercooled Liquids and Glass - Formation}, - journal = {Science}, - year = 1995, - volume = 267, - pages = {1935-1939} -} - -@InCollection{Angell85, - author = {C.~A. Angell}, - title = {unknown}, - booktitle = {Relaxations in Complex Systems}, - publisher = {National Technical Information Service, - U.S. Department of Commerce}, - year = 1985, - editor = {K.~Ngai and G.~B. Wright}, - address = {Springfield, VA}, - pages = 1 -} - -@Article{Bembenek96, - author = {S.~D. Bembenek and B.~B. Laird}, - title = {The role of localization in glasses and supercooled liquids}, - journal = jcp, - year = 1996, - volume = 104, - pages = 5199 -} - -@Article{Sun97, - author = {X. Sun and W.~H. Miller}, - title = {Semiclassical initial value representation for - electronically nonadiabatic molecular dynamics}, - journal = jcp, - year = 1997, - volume = 106, - pages = 6346 -} - -@Article{Spath96, - author = {B.~W. Spath and W.~H. 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II. Intermediate - scattering function and dynamic susceptibility}, - journal = pre, - year = 1995, - volume = 52, - pages = {4134-4153} -} - -@InProceedings{Gotze89, - author = "W. G{\"{o}}tze", - title = "Aspects of Structural Glass Transitions", - editor = "J.~P. Hansen and D. Levesque and J. Zinn-Justin", - volume = "I", - pages = "287-503", - booktitle = "Liquids, Freezing and Glass Transitions", - year = 1989, - publisher = "North-Holland", - address = "Amsterdam" -} - -@Article{Sun97a, - author = "X. Sun and W.~H. Miller", - title = {Mixed semiclassical-classical approaches to the - dynamics of complex molecular systems}, - journal = jcp, - year = 1997, - pages = 916 -} - -@Article{Keshavamurthy94, - author = "S. Keshavamurthy and W.~H. Miller", - title = "ivr", - journal = cpl, - year = 1994, - volume = 218, - pages = 189 -} - -@Article{Billing75, - author = "G.~D. Billing", - title = "ehrenfest", - journal = cpl, - year = 1975, - volume = 30, - pages = 391 -} - -@Article{Chang90, - author = {Y.-T. Chang and W.~H. Miller}, - title = {An Empirical Valence Bond Model for Constructing - Global Potential Energy Surfaces for Chemical - Reactions of Polyatomic Molecular Systems}, - journal = jpc, - year = 1990, - volume = 94, - pages = {5884-5888} -} +This file was created with JabRef 2.0.1. +Encoding: GBK -@Article{Shor94, - author = {P.W. Shor}, - title = {Algorithms for quantum computation: discrete - logarithms and factoring}, - journal = {Proceedings of the 35th Annual Symposium -on Foundations of Computer Science}, - year = 1994, - pages = {124-134} -} - -@Article{Feynman82, - author = {R.~P. Feynman}, - title = {Simulating physics with computers}, - journal = {Int. J. Theor. Phys.}, - year = 1982, - volume = 21, - pages = {467-488} -} - -@Article{Grover97, - author = {L.~K. 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Sleator and J.~A. Smolin and H. Weinfurter", - title = {elementary gates for quantum computation}, - journal = {Phys. Rev. A}, - year = 1995, - volume = 52, - pages = {3457-3467} -} - -@Article{Small97, - author = {T. Reinot and J.~M. Hayes and G.~J. Small}, - 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}, - journal = jcp, - year = 1997, - volume = 106, - pages = {457-466} -} - -@Article{Laflamme96, - author = {R. Laflamme and C. Miquel and J.~P. Paz and W.~H. Zurek}, - title = {A perfect quantum error correcting code: 5 bit code - correcting a general 1 qubit error to encode 1 qubit - of information}, - journal = prl, - year = 1996, - volume = 98, - pages = 77 -} - -@Article{Shor95, - author = {P.~W. Shor}, - title = {SCHEME FOR REDUCING DECOHERENCE IN QUANTUM COMPUTER MEMORY}, - journal = {Phys. Rev. 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VanHoek and - T.~H. Haines and D.~W. Deamer}, - title = {Permeation of protons, potassium ions, and small - polar molecules through phospholipid bilayers as a - function of membrane thickness}, - journal = {Biophys. J.}, - year = 1996, - volume = 70, - pages = {339-348} -} - -@Article{Little96, - author = {H.~J. Little}, - title = {How has molecular pharmacology contributed to our - understanding of the mechanism(s) of general - anesthesia?}, - journal = {Pharmacology \& Therapeutics}, - year = 1996, - volume = 69, - pages = {37-58} -} - -@Article{McKinnon92, - author = {S.~J. McKinnon and S.~L. Whittenburg and B. Brooks}, - title = {Nonequilibrium Molecular Dynamics Simulation of - Oxygen Diffusion through Hexadecane Monolayers with - Varying Concentrations of Cholesterol}, - journal = jpc, - year = 1992, - volume = 96, - pages = {10497-10506} -} - -@Article{Venable93, - author = {R.~M. Venable and Y. Zhang and B.~J. Hardy and - R.~W. Pastor}, - title = {Molecular Dynamics Simulations of a Lipid Bilayer - and of Hexadecane: An Investigation of Membrane Fluidity}, - journal = {Science}, - year = 1993, - volume = 262, - pages = {223-226} -} - -@Article{Essmann99, - author = {U. Essmann and M.~L. Berkowitz}, - title = {Dynamical properties of phospholipid bilayers from - computer simulation}, - journal = {Biophys. J.}, - year = 1999, - volume = 76, - pages = {2081-2089} -} - -@Article{Tu98, - author = {K.~C. Tu and M. Tarek and M.~L. Klein and D. Scharf}, - title = {Effects of anesthetics on the structure of a - phospholipid bilayer: Molecular dynamics - investigation of halothane in the hydrated liquid - crystal phase of dipalmitoylphosphatidylcholine}, - journal = {Biophys. J.}, - year = 1998, - volume = 75, - pages = {2123-2134} -} - -@Article{Pomes96, - author = {R. Pomes and B. 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Pechukas}, - title = {Gaussian Model Potentials for Molecular Interactions}, - journal = jcp, - year = 1972, - volume = 56, - pages = {4213-4216} -} - -@Article{Perram96, - author = {J.~W. Perram and J. Rasmussen and E. Praestgaard and - J.~L. Lebowitz}, - title = {Ellipsoid contact potential: Theory and relation to - overlap potentials}, - journal = pre, - year = 1996, - volume = 54, - pages = {6565-6572} -} - -@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}, - title = {A second generation force field for the simulation - of proteins and nucleic acids}, - journal = jacs, - year = 1995, - volume = 117, - pages = {5179-5197} +@ARTICLE{Torre2003, + author = {J. G. {de la Torre} and H. E. Sanchez and A. Ortega and J. G. Hernandez + and M. X. Fernandes and F. G. Diaz and M. C. L. Martinez}, + title = {Calculation of the solution properties of flexible macromolecules: + methods and applications}, + journal = {European Biophysics Journal with Biophysics Letters}, + year = {2003}, + volume = {32}, + pages = {477-486}, + number = {5}, + month = {Aug}, + abstract = {While the prediction of hydrodynamic properties of rigid particles + is nowadays feasible using simple and efficient computer programs, + the calculation of such properties and, in general, the dynamic + behavior of flexible macromolecules has not reached a similar situation. + Although the theories are available, usually the computational work + is done using solutions specific for each problem. We intend to + develop computer programs that would greatly facilitate the task + of predicting solution behavior of flexible macromolecules. In this + paper, we first present an overview of the two approaches that are + most practical: the Monte Carlo rigid-body treatment, and the Brownian + dynamics simulation technique. The Monte Carlo procedure is based + on the calculation of properties for instantaneous conformations + of the macromolecule that are regarded as if they were instantaneously + rigid. We describe how a Monte Carlo program can be interfaced to + the programs in the HYDRO suite for rigid particles, and provide + an example of such calculation, for a hypothetical particle: a protein + with two domains connected by a flexible linker. We also describe + briefly the essentials of Brownian dynamics, and propose a general + mechanical model that includes several kinds of intramolecular interactions, + such as bending, internal rotation, excluded volume effects, etc. + We provide an example of the application of this methodology to + the dynamics of a semiflexible, wormlike DNA.}, + annote = {724XK Times Cited:6 Cited References Count:64}, + issn = {0175-7571}, + uri = {://000185513400011}, } -@Article{Brooks83, - author = {B.~R. Brooks and R.~E. Bruccoleri and B.~D. Olafson - and D.~J. States and S. Swaminathan and M. Karplus}, - title = {{\sc charmm}: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations}, - journal = {J. Comp. Chem.}, - year = 1983, - volume = 4, - pages = {187-217} +@ARTICLE{Alakent2005, + author = {B. Alakent and M. C. Camurdan and P. Doruker}, + title = {Hierarchical structure of the energy landscape of proteins revisited + by time series analysis. II. Investigation of explicit solvent effects}, + journal = {Journal of Chemical Physics}, + year = {2005}, + volume = {123}, + pages = {-}, + number = {14}, + month = {Oct 8}, + abstract = {Time series analysis tools are employed on the principal modes obtained + from the C-alpha trajectories from two independent molecular-dynamics + simulations of alpha-amylase inhibitor (tendamistat). Fluctuations + inside an energy minimum (intraminimum motions), transitions between + minima (interminimum motions), and relaxations in different hierarchical + energy levels are investigated and compared with those encountered + in vacuum by using different sampling window sizes and intervals. + The low-frequency low-indexed mode relationship, established in + vacuum, is also encountered in water, which shows the reliability + of the important dynamics information offered by principal components + analysis in water. It has been shown that examining a short data + collection period (100 ps) may result in a high population of overdamped + modes, while some of the low-frequency oscillations (< 10 cm(-1)) + can be captured in water by using a longer data collection period + (1200 ps). Simultaneous analysis of short and long sampling window + sizes gives the following picture of the effect of water on protein + dynamics. Water makes the protein lose its memory: future conformations + are less dependent on previous conformations due to the lowering + of energy barriers in hierarchical levels of the energy landscape. + In short-time dynamics (< 10 ps), damping factors extracted from + time series model parameters are lowered. For tendamistat, the friction + coefficient in the Langevin equation is found to be around 40-60 + cm(-1) for the low-indexed modes, compatible with literature. The + fact that water has increased the friction and that on the other + hand has lubrication effect at first sight contradicts. However, + this comes about because water enhances the transitions between + minima and forces the protein to reduce its already inherent inability + to maintain oscillations observed in vacuum. Some of the frequencies + lower than 10 cm(-1) are found to be overdamped, while those higher + than 20 cm(-1) are slightly increased. As for the long-time dynamics + in water, it is found that random-walk motion is maintained for + approximately 200 ps (about five times of that in vacuum) in the + low-indexed modes, showing the lowering of energy barriers between + the higher-level minima.}, + annote = {973OH Times Cited:1 Cited References Count:33}, + issn = {0021-9606}, + uri = {://000232532000064}, } -@InCollection{MacKerell98, - author = {A.~D. {MacKerell, Jr.} and B. Brooks and - C.~L. {Brooks III} and L. Nilsson and B. Roux and - Y. Won and and M. Karplus}, - title = {{\sc charmm}: The Energy Function and Its Parameterization - with an Overview of the Program}, - booktitle = {The Encyclopedia of Computational Chemistry}, - pages = {271-277}, - publisher = {John Wiley \& Sons}, - year = 1998, - editor = {P.~v.~R. {Schleyer, {\it et al.}}}, - volume = 1, - address = {New York} +@BOOK{Alexander1987, + title = {A Pattern Language: Towns, Buildings, Construction}, + publisher = {Oxford University Press}, + year = {1987}, + author = {C. Alexander}, + address = {New York}, } -@InCollection{Jorgensen98, - author = {W.~L. Jorgensen}, - title = {OPLS Force Fields}, - booktitle = {The Encyclopedia of Computational Chemistry}, - pages = {1986-1989}, - publisher = {John Wiley \& Sons}, - year = 1998, - editor = {P.~v.~R. {Schleyer, {\it et al.}}}, - volume = 3, - address = {New York} +@BOOK{Allen1987, + title = {Computer Simulations of Liquids}, + publisher = {Oxford University Press}, + year = {1987}, + author = {M.~P. Allen and D.~J. Tildesley}, + address = {New York}, } -@Article{Rabani2000, - author = {E. Rabani and J.~D. Gezelter and B.~J. Berne}, - title = {Reply to `Comment on ``Direct Observation of - Stretched-Exponential Relaxation in Low-Temperature - Lennard-Jones Systems Using th eCage Correlation - Function'' '}, - journal = prl, - year = 2000, - volume = 85, - pages = 467 +@ARTICLE{Allison1991, + author = {S. A. Allison}, + title = {A Brownian Dynamics Algorithm for Arbitrary Rigid Bodies - Application + to Polarized Dynamic Light-Scattering}, + journal = {Macromolecules}, + year = {1991}, + volume = {24}, + pages = {530-536}, + number = {2}, + month = {Jan 21}, + abstract = {A Brownian dynamics algorithm is developed to simulate dynamics experiments + of rigid macromolecules. It is applied to polarized dynamic light + scattering from rodlike sturctures and from a model of a DNA fragment + (762 base pairs). A number of rod cases are examined in which the + translational anisotropy is increased form zero to a large value. + Simulated first cumulants as well as amplitudes and lifetimes of + the dynamic form factor are compared with predictions of analytic + theories and found to be in very good agreement with them. For DNA + fragments 762 base pairs in length or longer, translational anisotropy + does not contribute significantly to dynamic light scattering. In + a comparison of rigid and flexible simulations on semistiff models + of this fragment, it is shown directly that flexing contributes + to the faster decay processes probed by light scattering and that + the flexible model studies are in good agreement with experiment.}, + annote = {Eu814 Times Cited:8 Cited References Count:32}, + issn = {0024-9297}, + uri = {://A1991EU81400029}, } -@Book{Cevc87, - author = {G. Cevc and D. Marsh}, - title = {Phospholipid Bilayers}, - publisher = {John Wiley \& Sons}, - year = 1987, - address = {New York} +@ARTICLE{Andersen1983, + author = {H. C. Andersen}, + title = {Rattle - a Velocity Version of the Shake Algorithm for Molecular-Dynamics + Calculations}, + journal = {Journal of Computational Physics}, + year = {1983}, + volume = {52}, + pages = {24-34}, + number = {1}, + annote = {Rq238 Times Cited:559 Cited References Count:14}, + issn = {0021-9991}, + uri = {://A1983RQ23800002}, } -@Article{Janiak79, - author = {M.~J. Janiak and D.~M. Small and G.~G. Shipley}, - title = {Temperature and Compositional Dependence of the - Structure of Hydrated Dimyristoyl Lecithin}, - journal = {J. Biol. Chem.}, - year = 1979, - volume = 254, - pages = {6068-6078} +@ARTICLE{Auerbach2005, + author = {A. Auerbach}, + title = {Gating of acetylcholine receptor channels: Brownian motion across + a broad transition state}, + journal = {Proceedings of the National Academy of Sciences of the United States + of America}, + year = {2005}, + volume = {102}, + pages = {1408-1412}, + number = {5}, + month = {Feb 1}, + abstract = {Acetylcholine receptor channels (AChRs) are proteins that switch between + stable #closed# and #open# conformations. In patch clamp recordings, + diliganded AChR gating appears to be a simple, two-state reaction. + However, mutagenesis studies indicate that during gating dozens + of residues across the protein move asynchronously and are organized + into rigid body gating domains (#blocks#). Moreover, there is an + upper limit to the apparent channel opening rate constant. These + observations suggest that the gating reaction has a broad, corrugated + transition state region, with the maximum opening rate reflecting, + in part, the mean first-passage time across this ensemble. Simulations + reveal that a flat, isotropic energy profile for the transition + state can account for many of the essential features of AChR gating. + With this mechanism, concerted, local structural transitions that + occur on the broad transition state ensemble give rise to fractional + measures of reaction progress (Phi values) determined by rate-equilibrium + free energy relationship analysis. The results suggest that the + coarse-grained AChR gating conformational change propagates through + the protein with dynamics that are governed by the Brownian motion + of individual gating blocks.}, + annote = {895QF Times Cited:9 Cited References Count:33}, + issn = {0027-8424}, + uri = {://000226877300030}, } -@Book{Tobias90, - author = {Sheila Tobias}, - title = {They're not Dumb. They're Different: Stalking the - Second Tier}, - publisher = {Research Corp.}, - year = 1990, - address = {Tucson} +@ARTICLE{Baber1995, + author = {J. Baber and J. F. Ellena and D. S. Cafiso}, + title = {Distribution of General-Anesthetics in Phospholipid-Bilayers Determined + Using H-2 Nmr and H-1-H-1 Noe Spectroscopy}, + journal = {Biochemistry}, + year = {1995}, + volume = {34}, + pages = {6533-6539}, + number = {19}, + month = {May 16}, + abstract = {The effect of the general anesthetics halothane, enflurane, and isoflurane + on hydrocarbon chain packing in palmitoyl(d(31))oleoylphosphatidylcholine + membranes in the liquid crystalline phase was investigated using + H-2 NMR. Upon the addition of the anesthetics, the first five methylene + units near the interface generally show a very small increase in + segmental order, while segments deeper within the bilayer show a + small decrease in segmental order. From the H-2 NMR results, the + chain length for the perdeuterated palmitoyl chain in the absence + of anesthetic was found to be 12.35 Angstrom. Upon the addition + of halothane enflurane, or isoflurane, the acyl chain undergoes + slight contractions of 0.11, 0.20, or 0.16 Angstrom, respectively, + at 50 mol % anesthetic. A simple model was used to estimate the + relative amounts of anesthetic located near the interface and deeper + in the bilayer hydrocarbon region, and only a slight preference + for an interfacial location was observed. Intermolecular H-1-H-1 + nuclear Overhauser effects (NOEs) were measured between phospholipid + and halothane protons. These NOEs are consistent with the intramembrane + location of the anesthetics suggested by the H-2 NMR data. In addition, + the NOE data indicate that anesthetics prefer the interfacial and + hydrocarbon regions of the membrane and are not found in high concentrations + in the phospholipid headgroup.}, + annote = {Qz716 Times Cited:38 Cited References Count:37}, + issn = {0006-2960}, + uri = {://A1995QZ71600035}, } -@Article{Mazur92, - author = {E. Mazur}, - title = {Qualitative vs. Quantititative Thinking: Are we - teaching the right thing? }, - journal = {Optics and Photonics News}, - year = 1992, - volume = 3, - pages = 38 +@ARTICLE{Banerjee2004, + author = {D. Banerjee and B. C. Bag and S. K. Banik and D. S. Ray}, + title = {Solution of quantum Langevin equation: Approximations, theoretical + and numerical aspects}, + journal = {Journal of Chemical Physics}, + year = {2004}, + volume = {120}, + pages = {8960-8972}, + number = {19}, + month = {May 15}, + abstract = {Based on a coherent state representation of noise operator and an + ensemble averaging procedure using Wigner canonical thermal distribution + for harmonic oscillators, a generalized quantum Langevin equation + has been recently developed [Phys. Rev. E 65, 021109 (2002); 66, + 051106 (2002)] to derive the equations of motion for probability + distribution functions in c-number phase-space. We extend the treatment + to explore several systematic approximation schemes for the solutions + of the Langevin equation for nonlinear potentials for a wide range + of noise correlation, strength and temperature down to the vacuum + limit. The method is exemplified by an analytic application to harmonic + oscillator for arbitrary memory kernel and with the help of a numerical + calculation of barrier crossing, in a cubic potential to demonstrate + the quantum Kramers' turnover and the quantum Arrhenius plot. (C) + 2004 American Institute of Physics.}, + annote = {816YY Times Cited:8 Cited References Count:35}, + issn = {0021-9606}, + uri = {://000221146400009}, } -@Book{Mazur97, - author = {Eric Mazur}, - title = {Peer Instruction: A User's Manual}, - publisher = {Prentice Hall}, - year = 1997, - address = {New Jersey} +@ARTICLE{Barojas1973, + author = {J. Barojas and D. Levesque}, + title = {Simulation of Diatomic Homonuclear Liquids}, + journal = {Phys. Rev. A}, + year = {1973}, + volume = {7}, + pages = {1092-1105}, } -@Article{Wigner55, - author = {E.~P. Wigner}, - title = {Characteristic Vectors of Bordered Matrices with - Infinite Dimensions}, - journal = {Annals of Mathematics}, - year = 1955, - volume = 62, - pages = {548-564} +@ARTICLE{Barth1998, + author = {E. Barth and T. Schlick}, + title = {Overcoming stability limitations in biomolecular dynamics. I. Combining + force splitting via extrapolation with Langevin dynamics in LN}, + journal = {Journal of Chemical Physics}, + year = {1998}, + volume = {109}, + pages = {1617-1632}, + number = {5}, + month = {Aug 1}, + abstract = {We present an efficient new method termed LN for propagating biomolecular + dynamics according to the Langevin equation that arose fortuitously + upon analysis of the range of harmonic validity of our normal-mode + scheme LIN. LN combines force linearization with force splitting + techniques and disposes of LIN'S computationally intensive minimization + (anharmonic correction) component. Unlike the competitive multiple-timestepping + (MTS) schemes today-formulated to be symplectic and time-reversible-LN + merges the slow and fast forces via extrapolation rather than impulses; + the Langevin heat bath prevents systematic energy drifts. This combination + succeeds in achieving more significant speedups than these MTS methods + which are Limited by resonance artifacts to an outer timestep less + than some integer multiple of half the period of the fastest motion + (around 4-5 fs for biomolecules). We show that LN achieves very + good agreement with small-timestep solutions of the Langevin equation + in terms of thermodynamics (energy means and variances), geometry, + and dynamics (spectral densities) for two proteins in vacuum and + a large water system. Significantly, the frequency of updating the + slow forces extends to 48 fs or more, resulting in speedup factors + exceeding 10. The implementation of LN in any program that employs + force-splitting computations is straightforward, with only partial + second-derivative information required, as well as sparse Hessian/vector + multiplication routines. The linearization part of LN could even + be replaced by direct evaluation of the fast components. The application + of LN to biomolecular dynamics is well suited for configurational + sampling, thermodynamic, and structural questions. (C) 1998 American + Institute of Physics.}, + annote = {105HH Times Cited:29 Cited References Count:49}, + issn = {0021-9606}, + uri = {://000075066300006}, } -@Article{Gaukel98, - author = {C. Gaukel and H.~R. Schober}, - title = {Diffusion Mechanisms in under-cooled Binary Metal - Liquids of $\mbox{Zr}_{67}\mbox{Cu}_{33}$}, - journal = {Solid State Comm.}, - year = 1998, - volume = 107, - pages = {1-5} +@ARTICLE{Batcho2001, + author = {P. F. Batcho and T. Schlick}, + title = {Special stability advantages of position-Verlet over velocity-Verlet + in multiple-time step integration}, + journal = {Journal of Chemical Physics}, + year = {2001}, + volume = {115}, + pages = {4019-4029}, + number = {9}, + month = {Sep 1}, + abstract = {We present an analysis for a simple two-component harmonic oscillator + that compares the use of position-Verlet to velocity-Verlet for + multiple-time step integration. The numerical stability analysis + based on the impulse-Verlet splitting shows that position-Verlet + has enhanced stability, in terms of the largest allowable time step, + for cases where an ample separation of time scales exists. Numerical + investigations confirm the advantages of the position-Verlet scheme + when used for the fastest time scales of the system. Applications + to a biomolecule. a solvated protein, for both Newtonian and Langevin + dynamics echo these trends over large outer time-step regimes. (C) + 2001 American Institute of Physics.}, + annote = {469KV Times Cited:6 Cited References Count:30}, + issn = {0021-9606}, + uri = {://000170813800005}, } -@Article{Qi99, - author = {Y. Qi and T. \c{C}a\v{g}in and Y. - Kimura and W.~A. {Goddard III}}, - title = {Molecular-dynamics simulations of glass formation - and crystallization in binary liquid metals: $\mbox{Cu-Ag}$ - and $\mbox{Cu-Ni}$}, - journal = prb, - year = 1999, - volume = 59, - number = 5, - pages = {3527-3533} +@ARTICLE{Bates2005, + author = {M. A. Bates and G. R. Luckhurst}, + title = {Biaxial nematic phases and V-shaped molecules: A Monte Carlo simulation + study}, + journal = {Physical Review E}, + year = {2005}, + volume = {72}, + pages = {-}, + number = {5}, + month = {Nov}, + abstract = {Inspired by recent claims that compounds composed of V-shaped molecules + can exhibit the elusive biaxial nematic phase, we have developed + a generic simulation model for such systems. This contains the features + of the molecule that are essential to its liquid crystal behavior, + namely the anisotropies of the two arms and the angle between them. + The behavior of the model has been investigated using Monte Carlo + simulations for a wide range of these structural parameters. This + allows us to establish the relationship between the V-shaped molecule + and its ability to form a biaxial nematic phase. Of particular importance + are the criteria of geometry and the relative anisotropy necessary + for the system to exhibit a Landau point, at which the biaxial nematic + is formed directly from the isotropic phase. The simulations have + also been used to determine the orientational order parameters for + a selection of molecular axes. These are especially important because + they reveal the phase symmetry and are connected to the experimental + determination of this. The simulation results show that, whereas + some positions are extremely sensitive to the phase biaxiality, + others are totally blind to this.}, + annote = {Part 1 988LQ Times Cited:0 Cited References Count:38}, + issn = {1539-3755}, + uri = {://000233603100030}, } -@Article{Khorunzhy97, - author = {A. Khorunzhy and G.~J. Rodgers}, - title = {Eigenvalue distribution of large dilute random matrices}, - journal = {J. Math. Phys.}, - year = 1997, - volume = 38, - pages = {3300-3320} +@ARTICLE{Beard2003, + author = {D. A. Beard and T. Schlick}, + title = {Unbiased rotational moves for rigid-body dynamics}, + journal = {Biophysical Journal}, + year = {2003}, + volume = {85}, + pages = {2973-2976}, + number = {5}, + month = {Nov 1}, + abstract = {We introduce an unbiased protocol for performing rotational moves + in rigid-body dynamics simulations. This approach - based on the + analytic solution for the rotational equations of motion for an + orthogonal coordinate system at constant angular velocity - removes + deficiencies that have been largely ignored in Brownian dynamics + simulations, namely errors for finite rotations that result from + applying the noncommuting rotational matrices in an arbitrary order. + Our algorithm should thus replace standard approaches to rotate + local coordinate frames in Langevin and Brownian dynamics simulations.}, + annote = {736UA Times Cited:0 Cited References Count:11}, + issn = {0006-3495}, + uri = {://000186190500018}, } -@Article{Rodgers88, - author = {G.~J. Rodgers and A. Bray}, - title = {Density of States of a Sparse Random Matrix}, - journal = {Phys. Rev. B}, - year = 1988, - volume = 37, - pages = 355703562 +@ARTICLE{Beloborodov1998, + author = {I. S. Beloborodov and V. Y. Orekhov and A. S. Arseniev}, + title = {Effect of coupling between rotational and translational Brownian + motions on NMR spin relaxation: Consideration using green function + of rigid body diffusion}, + journal = {Journal of Magnetic Resonance}, + year = {1998}, + volume = {132}, + pages = {328-329}, + number = {2}, + month = {Jun}, + abstract = {Using the Green function of arbitrary rigid Brownian diffusion (Goldstein, + Biopolymers 33, 409-436, 1993), it was analytically shown that coupling + between translation and rotation diffusion degrees of freedom does + not affect the correlation functions relevant to the NMR intramolecular + relaxation. It follows that spectral densities usually used for + the anisotropic rotation diffusion (Woessner, J. Chem. Phys. 37, + 647-654, 1962) can be regarded as exact in respect to the rotation-translation + coupling for the spin system connected with a rigid body. (C) 1998 + Academic Press.}, + annote = {Zu605 Times Cited:2 Cited References Count:6}, + issn = {1090-7807}, + uri = {://000074214800017}, } -@Article{Rodgers90, - author = {G.~J. Rodgers and C. {De Dominicis}}, - title = {Density of states of sparse random matrices}, - journal = {J. Phys. A: Math. Gen.}, - year = 1990, - volume = 23, - pages = {1567-1573} +@ARTICLE{Berardi1996, + author = {R. Berardi and S. Orlandi and C. Zannoni}, + title = {Antiphase structures in polar smectic liquid crystals and their molecular + origin}, + journal = {Chemical Physics Letters}, + year = {1996}, + volume = {261}, + pages = {357-362}, + number = {3}, + month = {Oct 18}, + abstract = {We demonstrate that the overall molecular dipole organization in a + smectic liquid crystal formed of polar molecules can be strongly + influenced by the position of the dipole in the molecule. We study + by large scale Monte Carlo simulations systems of attractive-repulsive + ''Gay-Berne'' elongated ellipsoids with an axial dipole at the center + or near the end of the molecule and we show that monolayer smectic + liquid crystals and modulated antiferroelectric bilayer stripe domains + similar to the experimentally observed ''antiphase'' structures + are obtained in the two cases.}, + annote = {Vn637 Times Cited:49 Cited References Count:26}, + issn = {0009-2614}, + uri = {://A1996VN63700023}, } -@InProceedings{Barker80, - author = {J.~A. Barker}, - title = {Reaction field method for polar fluids}, - booktitle = {The problem of long-range forces in the computer - simulation of condensed matter}, - pages = {45-6}, - year = 1980, - editor = {D. Ceperley}, - volume = 9, - series = {NRCC Workshop Proceedings} +@ARTICLE{Berkov2005, + author = {D. V. Berkov and N. L. Gorn}, + title = {Magnetization precession due to a spin-polarized current in a thin + nanoelement: Numerical simulation study}, + journal = {Physical Review B}, + year = {2005}, + volume = {72}, + pages = {-}, + number = {9}, + month = {Sep}, + abstract = {In this paper a detailed numerical study (in frames of the Slonczewski + formalism) of magnetization oscillations driven by a spin-polarized + current through a thin elliptical nanoelement is presented. We show + that a sophisticated micromagnetic model, where a polycrystalline + structure of a nanoelement is taken into account, can explain qualitatively + all most important features of the magnetization oscillation spectra + recently observed experimentally [S. I. Kiselev , Nature 425, 380 + (2003)], namely, existence of several equidistant spectral bands, + sharp onset and abrupt disappearance of magnetization oscillations + with increasing current, absence of the out-of-plane regime predicted + by a macrospin model, and the relation between frequencies of so-called + small-angle and quasichaotic oscillations. However, a quantitative + agreement with experimental results (especially concerning the frequency + of quasichaotic oscillations) could not be achieved in the region + of reasonable parameter values, indicating that further model refinement + is necessary for a complete understanding of the spin-driven magnetization + precession even in this relatively simple experimental situation.}, + annote = {969IT Times Cited:2 Cited References Count:55}, + issn = {1098-0121}, + uri = {://000232228500058}, } -@Article{Smith82, - author = {W. Smith}, - title = {Point multipoles in the Ewald summation}, - journal = {CCP5 Quarterly}, - year = 1982, - volume = 4, - pages = {13-25} +@ARTICLE{Berkov2005a, + author = {D. V. Berkov and N. L. Gorn}, + title = {Stochastic dynamic simulations of fast remagnetization processes: + recent advances and applications}, + journal = {Journal of Magnetism and Magnetic Materials}, + year = {2005}, + volume = {290}, + pages = {442-448}, + month = {Apr}, + abstract = {Numerical simulations of fast remagnetization processes using stochastic + dynamics are widely used to study various magnetic systems. In this + paper, we first address several crucial methodological problems + of such simulations: (i) the influence of finite-element discretization + on simulated dynamics, (ii) choice between Ito and Stratonovich + stochastic calculi by the solution of micromagnetic stochastic equations + of motion and (iii) non-trivial correlation properties of the random + (thermal) field. Next, we discuss several examples to demonstrate + the great potential of the Langevin dynamics for studying fast remagnetization + processes in technically relevant applications: we present numerical + analysis of equilibrium magnon spectra in patterned structures, + study thermal noise effects on the magnetization dynamics of nanoelements + in pulsed fields and show some results for a remagnetization dynamics + induced by a spin-polarized current. (c) 2004 Elsevier B.V. All + rights reserved.}, + annote = {Part 1 Sp. Iss. SI 922KU Times Cited:2 Cited References Count:25}, + issn = {0304-8853}, + uri = {://000228837600109}, } -@Article{Daw84, - author = {M.~S. Daw and M.~I. Baskes}, - title = {Embedded-atom method: Derivation and application to - impurities, surfaces, and other defects in metals}, - journal = prb, - year = 1984, - volume = 29, - number = 12, - pages = {6443-6453} +@ARTICLE{Berkov2002, + author = {D. V. Berkov and N. L. Gorn and P. Gornert}, + title = {Magnetization dynamics in nanoparticle systems: Numerical simulation + using Langevin dynamics}, + journal = {Physica Status Solidi a-Applied Research}, + year = {2002}, + volume = {189}, + pages = {409-421}, + number = {2}, + month = {Feb 16}, + abstract = {We report on recent progress achieved by the development of numerical + methods based on the stochastic (Langevin) dynamics applied to systems + of interacting magnetic nanoparticles. The method enables direct + simulations of the trajectories of magnetic moments taking into + account (i) all relevant interactions, (ii) precession dynamics, + and (iii) temperature fluctuations included via the random (thermal) + field. We present several novel results obtained using new methods + developed for the solution of the Langevin equations. In particular, + we have investigated magnetic nanodots and disordered granular systems + of single-domain magnetic particles. For the first case we have + calculated the spectrum and the spatial distribution of spin excitations. + For the second system the complex ac susceptibility chi(omega, T) + for various particle concentrations and particle anisotropies were + computed and compared with numerous experimental results.}, + annote = {526TF Times Cited:4 Cited References Count:37}, + issn = {0031-8965}, + uri = {://000174145200026}, } - -@Article{Chen90, - author = {A.~P. Sutton and J. Chen}, - title = {Long-Range $\mbox{Finnis Sinclair}$ Potentials}, - journal = {Phil. Mag. Lett.}, - year = 1990, - volume = 61, - pages = {139-146} +@ARTICLE{Bernal1980, + author = {J.M. Bernal and J. G. {de la Torre}}, + title = {Transport Properties and Hydrodynamic Centers of Rigid Macromolecules + with Arbitrary Shape}, + journal = {Biopolymers}, + year = {1980}, + volume = {19}, + pages = {751-766}, } -@Article{Lu97, - author = {J. Lu and J.~A. Szpunar}, - title = {Applications of the embedded-atom method to glass - formation and crystallization of liquid and glass - transition-metal nickel}, - journal = {Phil. Mag. A}, - year = {1997}, - volume = {75}, - pages = {1057-1066}, +@ARTICLE{Brunger1984, + author = {A. Brunger and C. L. Brooks and M. Karplus}, + title = {Stochastic Boundary-Conditions for Molecular-Dynamics Simulations + of St2 Water}, + journal = {Chemical Physics Letters}, + year = {1984}, + volume = {105}, + pages = {495-500}, + number = {5}, + annote = {Sm173 Times Cited:143 Cited References Count:22}, + issn = {0009-2614}, + uri = {://A1984SM17300007}, } -@Article{Shlesinger99, - author = {M.~F. Shlesinger and J. Klafter and G. Zumofen}, - title = {Above, below, and beyond Brownian motion}, - journal = {Am. J. Phys.}, - year = 1999, - volume = 67, - pages = {1253-1259} +@ARTICLE{Budd1999, + author = {C. J. Budd and G. J. Collins and W. Z. Huang and R. D. Russell}, + title = {Self-similar numerical solutions of the porous-medium equation using + moving mesh methods}, + journal = {Philosophical Transactions of the Royal Society of London Series + a-Mathematical Physical and Engineering Sciences}, + year = {1999}, + volume = {357}, + pages = {1047-1077}, + number = {1754}, + month = {Apr 15}, + abstract = {This paper examines a synthesis of adaptive mesh methods with the + use of symmetry to study a partial differential equation. In particular, + it considers methods which admit discrete self-similar solutions, + examining the convergence of these to the true self-similar solution + as well as their stability. Special attention is given to the nonlinear + diffusion equation describing flow in a porous medium.}, + annote = {199EE Times Cited:4 Cited References Count:14}, + issn = {1364-503X}, + uri = {://000080466800005}, } -@Article{Klafter96, - author = {J. Klafter and M. Shlesinger and G. Zumofen}, - title = {Beyond Brownian Motion}, - journal = {Physics Today}, - year = 1996, - volume = 49, - pages = {33-39} +@ARTICLE{Camp1999, + author = {P. J. Camp and M. P. Allen and A. J. Masters}, + title = {Theory and computer simulation of bent-core molecules}, + journal = {Journal of Chemical Physics}, + year = {1999}, + volume = {111}, + pages = {9871-9881}, + number = {21}, + month = {Dec 1}, + abstract = {Fluids of hard bent-core molecules have been studied using theory + and computer simulation. The molecules are composed of two hard + spherocylinders, with length-to-breadth ratio L/D, joined by their + ends at an angle 180 degrees - gamma. For L/D = 2 and gamma = 0,10,20 + degrees, the simulations show isotropic, nematic, smectic, and solid + phases. For L/D = 2 and gamma = 30 degrees, only isotropic, nematic, + and solid phases are in evidence, which suggests that there is a + nematic-smectic-solid triple point at an angle in the range 20 degrees + < gamma < 30 degrees. In all of the orientationally ordered fluid + phases the order is purely uniaxial. For gamma = 10 degrees and + 20 degrees, at the studied densities, the solid is also uniaxially + ordered, whilst for gamma = 30 degrees the solid layers are biaxially + ordered. For L/D = 2 and gamma = 60 degrees and 90 degrees we find + no spontaneous orientational ordering. This is shown to be due to + the interlocking of dimer pairs which precludes alignment. We find + similar results for L/D = 9.5 and gamma = 72 degrees, where an isotropic-biaxial + nematic transition is predicted by Onsager theory. Simulations in + the biaxial nematic phase show it to be at least mechanically stable + with respect to the isotropic phase, however. We have compared the + quasi-exact simulation results in the isotropic phase with the predicted + equations of state from three theories: the virial expansion containing + the second and third virial coefficients; the Parsons-Lee equation + of state; an application of Wertheim's theory of associating fluids + in the limit of infinite attractive association energy. For all + of the molecule elongations and geometries we have simulated, the + Wertheim theory proved to be the most accurate. Interestingly, the + isotropic equation of state is virtually independent of the dimer + bond angle-a feature that is also reflected in the lack of variation + with angle of the calculated second and third virial coefficients. + (C) 1999 American Institute of Physics. [S0021-9606(99)50445-5].}, + annote = {255TC Times Cited:24 Cited References Count:38}, + issn = {0021-9606}, + uri = {://000083685400056}, } -@Article{Blumen83, - author = {A. Blumen and J. Klafter and G. Zumofen}, - title = {Recombination in amorphous materials as a - continuous-time random-walk problem}, - journal = {Phys. Rev. B}, - year = 1983, - volume = 27, - pages = {3429-3435} +@ARTICLE{Care2005, + author = {C. M. Care and D. J. Cleaver}, + title = {Computer simulation of liquid crystals}, + journal = {Reports on Progress in Physics}, + year = {2005}, + volume = {68}, + pages = {2665-2700}, + number = {11}, + month = {Nov}, + abstract = {A review is presented of molecular and mesoscopic computer simulations + of liquid crystalline systems. Molecular simulation approaches applied + to such systems are described, and the key findings for bulk phase + behaviour are reported. Following this, recently developed lattice + Boltzmann approaches to the mesoscale modelling of nemato-dynanics + are reviewed. This paper concludes with a discussion of possible + areas for future development in this field.}, + annote = {989TU Times Cited:2 Cited References Count:258}, + issn = {0034-4885}, + uri = {://000233697600004}, } -@Article{Klafter94, - author = {J. Klafter and G. Zumofen}, - title = {Probability Distributions for Continuous-Time Random - Walks with Long Tails}, - journal = jpc, - year = 1994, - volume = 98, - pages = {7366-7370} +@ARTICLE{Carrasco1999, + author = {B. Carrasco and J. G. {de la Torre}}, + title = {Hydrodynamic properties of rigid particles: Comparison of different + modeling and computational procedures}, + journal = {Biophysical Journal}, + year = {1999}, + volume = {76}, + pages = {3044-3057}, + number = {6}, + month = {Jun}, + abstract = {The hydrodynamic properties of rigid particles are calculated from + models composed of spherical elements (beads) using theories developed + by Kirkwood, Bloomfield, and their coworkers. Bead models have usually + been built in such a way that the beads fill the volume occupied + by the particles. Sometimes the beads are few and of varying sizes + (bead models in the strict sense), and other times there are many + small beads (filling models). Because hydrodynamic friction takes + place at the molecular surface, another possibility is to use shell + models, as originally proposed by Bloomfield. In this work, we have + developed procedures to build models of the various kinds, and we + describe the theory and methods for calculating their hydrodynamic + properties, including approximate methods that may be needed to + treat models with a very large number of elements. By combining + the various possibilities of model building and hydrodynamic calculation, + several strategies can be designed. We have made a quantitative + comparison of the performance of the various strategies by applying + them to some test cases, for which the properties are known a priori. + We provide guidelines and computational tools for bead modeling.}, + annote = {200TT Times Cited:46 Cited References Count:57}, + issn = {0006-3495}, + uri = {://000080556700016}, } - -@Article{Dzugutov92, - author = {M. Dzugutov}, - title = {Glass formation in a simple monatomic liquid with - icosahedral inherent local order}, - journal = pra, - year = 1992, - volume = 46, - pages = {R2984-R2987} +@ARTICLE{Chandra1999, + author = {A. Chandra and T. Ichiye}, + title = {Dynamical properties of the soft sticky dipole model of water: Molecular + dynamics simulations}, + journal = {Journal of Chemical Physics}, + year = {1999}, + volume = {111}, + pages = {2701-2709}, + number = {6}, + month = {Aug 8}, + abstract = {Dynamical properties of the soft sticky dipole (SSD) model of water + are calculated by means of molecular dynamics simulations. Since + this is not a simple point model, the forces and torques arising + from the SSD potential are derived here. Simulations are carried + out in the microcanonical ensemble employing the Ewald method for + the electrostatic interactions. Various time correlation functions + and dynamical quantities associated with the translational and rotational + motion of water molecules are evaluated and compared with those + of two other commonly used models of liquid water, namely the transferable + intermolecular potential-three points (TIP3P) and simple point charge/extended + (SPC/E) models, and also with experiments. The dynamical properties + of the SSD water model are found to be in good agreement with the + experimental results and appear to be better than the TIP3P and + SPC/E models in most cases, as has been previously shown for its + thermodynamic, structural, and dielectric properties. Also, molecular + dynamics simulations of the SSD model are found to run much faster + than TIP3P, SPC/E, and other multisite models. (C) 1999 American + Institute of Physics. [S0021-9606(99)51430-X].}, + annote = {221EN Times Cited:14 Cited References Count:66}, + issn = {0021-9606}, + uri = {://000081711200038}, } -@Article{Moore94, - author = {P. Moore and T. Keyes}, - title = {Normal Mode Analysis of Liquid $\mbox{CS}_2$: Velocity - Correlation Functions and Self-Diffusion Constants}, - journal = jcp, - year = 1994, - volume = 100, - pages = 6709 +@ARTICLE{Channell1990, + author = {P. J. Channell and C. Scovel}, + title = {Symplectic Integration of Hamiltonian-Systems}, + journal = {Nonlinearity}, + year = {1990}, + volume = {3}, + pages = {231-259}, + number = {2}, + month = {may}, + annote = {Dk631 Times Cited:152 Cited References Count:34}, + issn = {0951-7715}, + uri = {://A1990DK63100001}, } -@Article{Seeley89, - author = {G. Seeley and T. Keyes}, - title = {Normal-mode analysis of liquid-state dynamics}, - journal = jcp, - year = 1989, - volume = 91, - pages = {5581-5586} +@ARTICLE{Chen2003, + author = {B. Chen and F. Solis}, + title = {Explicit mixed finite order Runge-Kutta methods}, + journal = {Applied Numerical Mathematics}, + year = {2003}, + volume = {44}, + pages = {21-30}, + number = {1-2}, + month = {Jan}, + abstract = {We investigate the asymptotic behavior of systems of nonlinear differential + equations and introduce a family of mixed methods from combinations + of explicit Runge-Kutta methods. These methods have better stability + behavior than traditional Runge-Kutta methods and generally extend + the range of validity of the calculated solutions. These methods + also give a way of determining if the numerical solutions are real + or spurious. Emphasis is put on examples coming from mathematical + models in ecology. (C) 2002 IMACS. Published by Elsevier Science + B.V. All rights reserved.}, + annote = {633ZD Times Cited:0 Cited References Count:9}, + issn = {0168-9274}, + uri = {://000180314200002}, } -@Article{Madan90, - author = {B. Madan and T. Keyes and G. Seeley}, - title = {Diffusion in supercooled liquids via normal mode - analysis}, - journal = jcp, - year = 1990, - volume = 92, - pages = {7565-7569} +@ARTICLE{Cheung2004, + author = {D. L. Cheung and S. J. Clark and M. R. Wilson}, + title = {Calculation of flexoelectric coefficients for a nematic liquid crystal + by atomistic simulation}, + journal = {Journal of Chemical Physics}, + year = {2004}, + volume = {121}, + pages = {9131-9139}, + number = {18}, + month = {Nov 8}, + abstract = {Equilibrium molecular dynamics calculations have been performed for + the liquid crystal molecule n-4-(trans-4-n-pentylcyclohexyl)benzonitrile + (PCH5) using a fully atomistic model. Simulation data have been + obtained for a series of temperatures in the nematic phase. The + simulation data have been used to calculate the flexoelectric coefficients + e(s) and e(b) using the linear response formalism of Osipov and + Nemtsov [M. A. Osipov and V. B. Nemtsov, Sov. Phys. Crstallogr. + 31, 125 (1986)]. The temperature and order parameter dependence + of e(s) and e(b) are examined, as are separate contributions from + different intermolecular interactions. Values of e(s) and e(b) calculated + from simulation are consistent with those found from experiment. + (C) 2004 American Institute of Physics.}, + annote = {866UM Times Cited:4 Cited References Count:61}, + issn = {0021-9606}, + uri = {://000224798900053}, } -@Article{Madan91, - author = {B. Madan and T. Keyes and G. Seeley}, - title = {Normal mode analysis of the velocity correlation - function in supercooled liquids}, - journal = jcp, - year = 1991, - volume = 94, - pages = {6762-6769} +@ARTICLE{Cheung2002, + author = {D. L. Cheung and S. J. Clark and M. R. Wilson}, + title = {Calculation of the rotational viscosity of a nematic liquid crystal}, + journal = {Chemical Physics Letters}, + year = {2002}, + volume = {356}, + pages = {140-146}, + number = {1-2}, + month = {Apr 15}, + abstract = {Equilibrium molecular dynamics calculations have been performed for + the liquid crystal molecule n-4-(trans-4-npentylcyclohexyl)benzonitrile + (PCH5) using a fully atomistic model. Simulation data has been obtained + for a series of temperatures in the nematic phase. The rotational + viscosity co-efficient gamma(1), has been calculated using the angular + velocity correlation function of the nematic director, n, the mean + squared diffusion of n and statistical mechanical methods based + on the rotational diffusion co-efficient. We find good agreement + between the first two methods and experimental values. (C) 2002 + Published by Elsevier Science B.V.}, + annote = {547KF Times Cited:8 Cited References Count:31}, + issn = {0009-2614}, + uri = {://000175331000020}, } -@Article{Buchner92, - author = {M. Buchner, B.~M. Ladanyi and R.~M. Stratt}, - title = {The short-time dynamics of molecular - liquids. Instantaneous-normal-mode theory}, - journal = jcp, - year = 1992, - volume = 97, - pages = {8522-8535} +@ARTICLE{Chin2004, + author = {S. A. Chin}, + title = {Dynamical multiple-time stepping methods for overcoming resonance + instabilities}, + journal = {Journal of Chemical Physics}, + year = {2004}, + volume = {120}, + pages = {8-13}, + number = {1}, + month = {Jan 1}, + abstract = {Current molecular dynamics simulations of biomolecules using multiple + time steps to update the slowly changing force are hampered by instabilities + beginning at time steps near the half period of the fastest vibrating + mode. These #resonance# instabilities have became a critical barrier + preventing the long time simulation of biomolecular dynamics. Attempts + to tame these instabilities by altering the slowly changing force + and efforts to damp them out by Langevin dynamics do not address + the fundamental cause of these instabilities. In this work, we trace + the instability to the nonanalytic character of the underlying spectrum + and show that a correct splitting of the Hamiltonian, which renders + the spectrum analytic, restores stability. The resulting Hamiltonian + dictates that in addition to updating the momentum due to the slowly + changing force, one must also update the position with a modified + mass. Thus multiple-time stepping must be done dynamically. (C) + 2004 American Institute of Physics.}, + annote = {757TK Times Cited:1 Cited References Count:22}, + issn = {0021-9606}, + uri = {://000187577400003}, } -@Article{Wan94, - author = {Yi. Wan and R.~M. Stratt}, - title = {Liquid theory for the instantaneous normal modes of - a liquid}, - journal = jcp, - year = 1994, - volume = 100, - pages = {5123-5138} +@ARTICLE{Cook2000, + author = {M. J. Cook and M. R. Wilson}, + title = {Simulation studies of dipole correlation in the isotropic liquid + phase}, + journal = {Liquid Crystals}, + year = {2000}, + volume = {27}, + pages = {1573-1583}, + number = {12}, + month = {Dec}, + abstract = {The Kirkwood correlation factor g(1) determines the preference for + local parallel or antiparallel dipole association in the isotropic + phase. Calamitic mesogens with longitudinal dipole moments and Kirkwood + factors greater than 1 have an enhanced effective dipole moment + along the molecular long axis. This leads to higher values of Delta + epsilon in the nematic phase. This paper describes state-of-the-art + molecular dynamics simulations of two calamitic mesogens 4-(trans-4-n-pentylcyclohexyl)benzonitrile + (PCH5) and 4-(trans-4-n-pentylcyclohexyl) chlorobenzene (PCH5-Cl) + in the isotropic liquid phase using an all-atom force field and + taking long range electrostatics into account using an Ewald summation. + Using this methodology, PCH5 is seen to prefer antiparallel dipole + alignment with a negative g(1) and PCH5-Cl is seen to prefer parallel + dipole alignment with a positive g(1); this is in accordance with + experimental dielectric measurements. Analysis of the molecular + dynamics trajectories allows an assessment of why these molecules + behave differently.}, + annote = {376BF Times Cited:10 Cited References Count:16}, + issn = {0267-8292}, + uri = {://000165437800002}, } -@article{Stratt95, - author = {R.~M. Stratt}, - title = {The instantaneous normal modes of liquids}, - journal = {Acc. Chem. Res.}, - year = 1995, - volume = 28, - pages = {201-207} +@ARTICLE{Cui2003, + author = {B. X. Cui and M. Y. Shen and K. F. Freed}, + title = {Folding and misfolding of the papillomavirus E6 interacting peptide + E6ap}, + journal = {Proceedings of the National Academy of Sciences of the United States + of America}, + year = {2003}, + volume = {100}, + pages = {7087-7092}, + number = {12}, + month = {Jun 10}, + abstract = {All-atom Langevin dynamics simulations have been performed to study + the folding pathways of the 18-residue binding domain fragment E6ap + of the human papillomavirus E6 interacting peptide. Six independent + folding trajectories, with a total duration of nearly 2 mus, all + lead to the same native state in which the E6ap adopts a fluctuating + a-helix structure in the central portion (Ser-4-Leu-13) but with + very flexible N and C termini. Simulations starting from different + core configurations exhibit the E6ap folding dynamics as either + a two- or three-state folder with an intermediate misfolded state. + The essential leucine hydrophobic core (Leu-9, Leu-12, and Leu-13) + is well conserved in the native-state structure but absent in the + intermediate structure, suggesting that the leucine core is not + only essential for the binding activity of E6ap but also important + for the stability of the native structure. The free energy landscape + reveals a significant barrier between the basins separating the + native and misfolded states. We also discuss the various underlying + forces that drive the peptide into its native state.}, + annote = {689LC Times Cited:3 Cited References Count:48}, + issn = {0027-8424}, + uri = {://000183493500037}, } -@Article{Nitzan95, - author = {G.~V. Vijayadamodar and A. Nitzan}, - title = {On the application of instantaneous normal mode - analysis to long time dynamics of liquids}, - journal = jcp, - year = 1995, - volume = 103, - pages = {2169-2177} -} - -@Article{Ribeiro98, - author = "M.~C.~C. Ribeiro and P.~A. Madden", - title = "Unstable Modes in Ionic Melts", - journal = jcp, - year = 1998, - volume = 108, - pages = {3256-3263} -} - -@Article{Keyes98a, - author = {T. Keyes and W.-X. Li and U.~Z{\"{u}}rcher}, - title = {Comment on a critique of the instantaneous normal - mode (INM) approach to diffusion - (J. Chem. Phys. {\bf 107}, 4618 (1997))}, - journal = jcp, - year = 1998, - volume = 109, - pages = {4693-4694} -} - -@Article{Alemany98, - author = {M.~M.~G. Alemany and C. Rey and L.~J. Gallego}, - title = {Transport coefficients of liquid transition metals: - A computer simulation study using the embedded atom - model}, - journal = jcp, - year = 1998, - volume = 109, - pages = {5175-5176} +@ARTICLE{Denisov2003, + author = {S. I. Denisov and T. V. Lyutyy and K. N. Trohidou}, + title = {Magnetic relaxation in finite two-dimensional nanoparticle ensembles}, + journal = {Physical Review B}, + year = {2003}, + volume = {67}, + pages = {-}, + number = {1}, + month = {Jan 1}, + abstract = {We study the slow phase of thermally activated magnetic relaxation + in finite two-dimensional ensembles of dipolar interacting ferromagnetic + nanoparticles whose easy axes of magnetization are perpendicular + to the distribution plane. We develop a method to numerically simulate + the magnetic relaxation for the case that the smallest heights of + the potential barriers between the equilibrium directions of the + nanoparticle magnetic moments are much larger than the thermal energy. + Within this framework, we analyze in detail the role that the correlations + of the nanoparticle magnetic moments and the finite size of the + nanoparticle ensemble play in magnetic relaxation.}, + annote = {642XH Times Cited:11 Cited References Count:31}, + issn = {1098-0121}, + uri = {://000180830400056}, } -@Article{Belonoshko00, - author = {A.~B. Belonoshko and R. Ahuja and O. Eriksson and - B. Johansson}, - title = {Quasi ab initio molecular dynamic study of Cu melting}, - journal = prb, - year = 2000, - volume = 61, - pages = {3838-3844} +@ARTICLE{Derreumaux1998, + author = {P. Derreumaux and T. Schlick}, + title = {The loop opening/closing motion of the enzyme triosephosphate isomerase}, + journal = {Biophysical Journal}, + year = {1998}, + volume = {74}, + pages = {72-81}, + number = {1}, + month = {Jan}, + abstract = {To explore the origin of the large-scale motion of triosephosphate + isomerase's flexible loop (residues 166 to 176) at the active site, + several simulation protocols are employed both for the free enzyme + in vacuo and for the free enzyme with some solvent modeling: high-temperature + Langevin dynamics simulations, sampling by a #dynamics##driver# + approach, and potential-energy surface calculations. Our focus is + on obtaining the energy barrier to the enzyme's motion and establishing + the nature of the loop movement. Previous calculations did not determine + this energy barrier and the effect of solvent on the barrier. High-temperature + molecular dynamics simulations and crystallographic studies have + suggested a rigid-body motion with two hinges located at both ends + of the loop; Brownian dynamics simulations at room temperature pointed + to a very flexible behavior. The present simulations and analyses + reveal that although solute/solvent hydrogen bonds play a crucial + role in lowering the energy along the pathway, there still remains + a high activation barrier, This finding clearly indicates that, + if the loop opens and closes in the absence of a substrate at standard + conditions (e.g., room temperature, appropriate concentration of + isomerase), the time scale for transition is not in the nanosecond + but rather the microsecond range. Our results also indicate that + in the context of spontaneous opening in the free enzyme, the motion + is of rigid-body type and that the specific interaction between + residues Ala(176) and Tyr(208) plays a crucial role in the loop + opening/closing mechanism.}, + annote = {Zl046 Times Cited:30 Cited References Count:29}, + issn = {0006-3495}, + uri = {://000073393400009}, } -@Article{Banhart92, - author = {J. Banhart and H. Ebert and R. Kuentzler and - J. Voitl\"{a}nder}, - title = {Electronic properties of single-phased metastable - Ag-Cu alloys}, - journal = prb, - year = 1992, - volume = 46, - pages = {9968-9975} +@ARTICLE{Dullweber1997, + author = {A. Dullweber and B. Leimkuhler and R. McLachlan}, + title = {Symplectic splitting methods for rigid body molecular dynamics}, + journal = {Journal of Chemical Physics}, + year = {1997}, + volume = {107}, + pages = {5840-5851}, + number = {15}, + month = {Oct 15}, + abstract = {Rigid body molecular models possess symplectic structure and time-reversal + symmetry. Standard numerical integration methods destroy both properties, + introducing nonphysical dynamical behavior such as numerically induced + dissipative states and drift in the energy during long term simulations. + This article describes the construction, implementation, and practical + application of fast explicit symplectic-reversible integrators for + multiple rigid body molecular simulations, These methods use a reduction + to Euler equations for the free rigid body, together with a symplectic + splitting technique. In every time step, the orientational dynamics + of each rigid body is integrated by a sequence of planar rotations. + Besides preserving the symplectic and reversible structures of the + flow, this scheme accurately conserves the total angular momentum + of a system of interacting rigid bodies. Excellent energy conservation + fan be obtained relative to traditional methods, especially in long-time + simulations. The method is implemented in a research code, ORIENT + and compared with a quaternion/extrapolation scheme for the TIP4P + model of water. Our experiments show that the symplectic-reversible + scheme is far superior to the more traditional quaternion method. + (C) 1997 American Institute of Physics.}, + annote = {Ya587 Times Cited:35 Cited References Count:32}, + issn = {0021-9606}, + uri = {://A1997YA58700024}, } -@Article{Wendt78, - author = {H. Wendt and F.~F. Abraham}, - title = {}, - journal = prl, - year = 1978, - volume = 41, - pages = 1244 +@BOOK{Gamma1994, + title = {Design Patterns: Elements of Reusable Object-Oriented Software}, + publisher = {Perason Education}, + year = {1994}, + author = {E. Gamma, R. Helm, R. Johnson and J. Vlissides}, + address = {London}, + chapter = {7}, } -@Article{Lewis91, - author = {L.~J. Lewis}, - title = {Atomic dynamics through the glass transition}, - journal = prb, - year = 1991, - volume = 44, - pages = {4245-4254} +@ARTICLE{Edwards2005, + author = {S. A. Edwards and D. R. M. Williams}, + title = {Stretching a single diblock copolymer in a selective solvent: Langevin + dynamics simulations}, + journal = {Macromolecules}, + year = {2005}, + volume = {38}, + pages = {10590-10595}, + number = {25}, + month = {Dec 13}, + abstract = {Using the Langevin dynamics technique, we have carried out simulations + of a single-chain flexible diblock copolymer. The polymer consists + of two blocks of equal length, one very poorly solvated and the + other close to theta-conditions. We study what happens when such + a polymer is stretched, for a range of different stretching speeds, + and correlate our observations with features in the plot of force + vs extension. We find that at slow speeds this force profile does + not increase monotonically, in disagreement with earlier predictions, + and that at high speeds there is a strong dependence on which end + of the polymer is pulled, as well as a high level of hysteresis.}, + annote = {992EC Times Cited:0 Cited References Count:13}, + issn = {0024-9297}, + uri = {://000233866200035}, } -@Article{Liu92, - author = {R.~S. Liu and D.~W. Qi and S. Wang}, - title = {Subpeaks of structure factors for rapidly quenched metals}, - journal = prb, - year = 1992, - volume = 45, - pages = {451-453} +@ARTICLE{Egberts1988, + author = {E. Egberts and H. J. C. Berendsen}, + title = {Molecular-Dynamics Simulation of a Smectic Liquid-Crystal with Atomic + Detail}, + journal = {Journal of Chemical Physics}, + year = {1988}, + volume = {89}, + pages = {3718-3732}, + number = {6}, + month = {Sep 15}, + annote = {Q0188 Times Cited:219 Cited References Count:43}, + issn = {0021-9606}, + uri = {://A1988Q018800036}, } -@Book{pliny, - author = {Pliny}, - title = {Hist. Nat.}, - publisher = { }, - year = { }, - volume = {XXXVI} +@ARTICLE{Ermak1978, + author = {D. L. Ermak and J. A. Mccammon}, + title = {Brownian Dynamics with Hydrodynamic Interactions}, + journal = {Journal of Chemical Physics}, + year = {1978}, + volume = {69}, + pages = {1352-1360}, + number = {4}, + annote = {Fp216 Times Cited:785 Cited References Count:42}, + issn = {0021-9606}, + uri = {://A1978FP21600004}, } -@Article{Anheuser94, - author = {K. Anheuser and J.P. Northover}, - title = {Silver plating of Roman and Celtic coins from Britan - a technical study}, - journal = {Brit. Num. J.}, - year = 1994, - volume = 64, - pages = 22 +@ARTICLE{Evans1977, + author = {D. J. Evans}, + title = {Representation of Orientation Space}, + journal = {Molecular Physics}, + year = {1977}, + volume = {34}, + pages = {317-325}, + number = {2}, + annote = {Ds757 Times Cited:271 Cited References Count:18}, + issn = {0026-8976}, + uri = {://A1977DS75700002}, } -@Article{Pense92, - author = {A. W. Pense}, - title = {The Decline and Fall of the Roman Denarius}, - journal = {Mat. Char.}, - year = 1992, - volume = 29, - pages = 213 +@ARTICLE{Fennell2004, + author = {C. J. Fennell and J. D. Gezelter}, + title = {On the structural and transport properties of the soft sticky dipole + and related single-point water models}, + journal = {Journal of Chemical Physics}, + year = {2004}, + volume = {120}, + pages = {9175-9184}, + number = {19}, + month = {May 15}, + abstract = {The density maximum and temperature dependence of the self-diffusion + constant were investigated for the soft sticky dipole (SSD) water + model and two related reparametrizations of this single-point model. + A combination of microcanonical and isobaric-isothermal molecular + dynamics simulations was used to calculate these properties, both + with and without the use of reaction field to handle long-range + electrostatics. The isobaric-isothermal simulations of the melting + of both ice-I-h and ice-I-c showed a density maximum near 260 K. + In most cases, the use of the reaction field resulted in calculated + densities which were significantly lower than experimental densities. + Analysis of self-diffusion constants shows that the original SSD + model captures the transport properties of experimental water very + well in both the normal and supercooled liquid regimes. We also + present our reparametrized versions of SSD for use both with the + reaction field or without any long-range electrostatic corrections. + These are called the SSD/RF and SSD/E models, respectively. These + modified models were shown to maintain or improve upon the experimental + agreement with the structural and transport properties that can + be obtained with either the original SSD or the density-corrected + version of the original model (SSD1). Additionally, a novel low-density + ice structure is presented which appears to be the most stable ice + structure for the entire SSD family. (C) 2004 American Institute + of Physics.}, + annote = {816YY Times Cited:5 Cited References Count:39}, + issn = {0021-9606}, + uri = {://000221146400032}, } -@Article{Ngai81, - author = {K.~L. Ngai and F.-S. Liu}, - title = {Dispersive diffusion transport and noise, - time-dependent diffusion coefficient, generalized - Einstein-Nernst relation, and dispersive - diffusion-controlled unimolecular and bimolecular - reactions}, - journal = prb, - year = 1981, - volume = 24, - pages = {1049-1065} +@ARTICLE{Fernandes2002, + author = {M. X. Fernandes and J. G. {de la Torre}}, + title = {Brownian dynamics simulation of rigid particles of arbitrary shape + in external fields}, + journal = {Biophysical Journal}, + year = {2002}, + volume = {83}, + pages = {3039-3048}, + number = {6}, + month = {Dec}, + abstract = {We have developed a Brownian dynamics simulation algorithm to generate + Brownian trajectories of an isolated, rigid particle of arbitrary + shape in the presence of electric fields or any other external agents. + Starting from the generalized diffusion tensor, which can be calculated + with the existing HYDRO software, the new program BROWNRIG (including + a case-specific subprogram for the external agent) carries out a + simulation that is analyzed later to extract the observable dynamic + properties. We provide a variety of examples of utilization of this + method, which serve as tests of its performance, and also illustrate + its applicability. Examples include free diffusion, transport in + an electric field, and diffusion in a restricting environment.}, + annote = {633AD Times Cited:2 Cited References Count:43}, + issn = {0006-3495}, + uri = {://000180256300012}, } -@Unpublished{Truhlar00, - author = {D.~G. Truhlar and A. Kohen}, - note = {private correspondence} +@BOOK{Frenkel1996, + title = {Understanding Molecular Simulation : From Algorithms to Applications}, + publisher = {Academic Press}, + year = {1996}, + author = {D. Frenkel and B. Smit}, + address = {New York}, } -@Article{Truhlar78, - author = {Donald G. Truhlar}, - title = {Interpretation of the Activation Energy}, - journal = {J. Chem. Ed.}, - year = 1978, - volume = 55, - pages = 309 +@ARTICLE{Gay1981, + author = {J. G. Gay and B. J. Berne}, + title = {Modification of the Overlap Potential to Mimic a Linear Site-Site + Potential}, + journal = {Journal of Chemical Physics}, + year = {1981}, + volume = {74}, + pages = {3316-3319}, + number = {6}, + annote = {Lj347 Times Cited:482 Cited References Count:13}, + issn = {0021-9606}, + uri = {://A1981LJ34700029}, } -@Book{Tolman27, - author = {R. C. Tolman}, - title = {Statistical Mechanics with Applications to Physics and Chemistry}, - chapter = {}, - publisher = {Chemical Catalog Co.}, - address = {New York}, - year = 1927, - pages = {260-270} +@ARTICLE{Gelin1999, + author = {M. F. Gelin}, + title = {Inertial effects in the Brownian dynamics with rigid constraints}, + journal = {Macromolecular Theory and Simulations}, + year = {1999}, + volume = {8}, + pages = {529-543}, + number = {6}, + month = {Nov}, + abstract = {To investigate the influence of inertial effects on the dynamics of + an assembly of beads subjected to rigid constraints and placed in + a buffer medium, a convenient method to introduce suitable generalized + coordinates is presented. Without any restriction on the nature + of the soft forces involved (both stochastic and deterministic), + pertinent Langevin equations are derived. Provided that the Brownian + forces are Gaussian and Markovian, the corresponding Fokker-Planck + equation (FPE) is obtained in the complete phase space of generalized + coordinates and momenta. The correct short time behavior for correlation + functions (CFs) of generalized coordinates is established, and the + diffusion equation with memory (DEM) is deduced from the FPE in + the high friction Limit. The DEM is invoked to perform illustrative + calculations in two dimensions of the orientational CFs for once + broken nonrigid rods immobilized on a surface. These calculations + reveal that the CFs under certain conditions exhibit an oscillatory + behavior, which is irreproducible within the standard diffusion + equation. Several methods are considered for the approximate solution + of the DEM, and their application to three dimensional DEMs is discussed.}, + annote = {257MM Times Cited:2 Cited References Count:82}, + issn = {1022-1344}, + uri = {://000083785700002}, } -@Article{Tolman20, - author = {R. C. Tolman}, - title = {Statistical Mechanics Applied to Chemical Kinetics}, - journal = jacs, - year = 1920, - volume = 42, - pages = 2506 +@BOOK{Goldstein2001, + title = {Classical Mechanics}, + publisher = {Addison Wesley}, + year = {2001}, + author = {H. Goldstein and C. Poole and J. Safko}, + address = {San Francisco}, + edition = {3rd}, } -@Article{Nagel96, - author = {M.D. Ediger and C.A. Angell and Sidney R. Nagel}, - title = {Supercooled Liquids and Glasses}, - journal = jpc, - year = 1996, - volume = 100, - pages = 13200 +@ARTICLE{Gray2003, + author = {J. J. Gray and S. Moughon and C. Wang and O. Schueler-Furman and + B. Kuhlman and C. A. Rohl and D. Baker}, + title = {Protein-protein docking with simultaneous optimization of rigid-body + displacement and side-chain conformations}, + journal = {Journal of Molecular Biology}, + year = {2003}, + volume = {331}, + pages = {281-299}, + number = {1}, + month = {Aug 1}, + abstract = {Protein-protein docking algorithms provide a means to elucidate structural + details for presently unknown complexes. Here, we present and evaluate + a new method to predict protein-protein complexes from the coordinates + of the unbound monomer components. The method employs a low-resolution, + rigid-body, Monte Carlo search followed by simultaneous optimization + of backbone displacement and side-chain conformations using Monte + Carlo minimization. Up to 10(5) independent simulations are carried + out, and the resulting #decoys# are ranked using an energy function + dominated by van der Waals interactions, an implicit solvation model, + and an orientation-dependent hydrogen bonding potential. Top-ranking + decoys are clustered to select the final predictions. Small-perturbation + studies reveal the formation of binding funnels in 42 of 54 cases + using coordinates derived from the bound complexes and in 32 of + 54 cases using independently determined coordinates of one or both + monomers. Experimental binding affinities correlate with the calculated + score function and explain the predictive success or failure of + many targets. Global searches using one or both unbound components + predict at least 25% of the native residue-residue contacts in 28 + of the 32 cases where binding funnels exist. The results suggest + that the method may soon be useful for generating models of biologically + important complexes from the structures of the isolated components, + but they also highlight the challenges that must be met to achieve + consistent and accurate prediction of protein-protein interactions. + (C) 2003 Elsevier Ltd. All rights reserved.}, + annote = {704QL Times Cited:48 Cited References Count:60}, + issn = {0022-2836}, + uri = {://000184351300022}, } -@InBook{Blumen86, - author = {A. Blumen and J. Klafter and G. Zumofen}, - editor = {Luciano Peitronero and E. Tosatti}, - title = {Fractals in Physics}, - chapter = {Reactions in Disordered Media Modelled by Fractals}, - publisher = {North-Holland}, - year = 1986, - series = {International Symposium on Fractals in Physics}, - address = {Amsterdam}, - pages = 399 +@ARTICLE{Greengard1994, + author = {L. Greengard}, + title = {Fast Algorithms for Classical Physics}, + journal = {Science}, + year = {1994}, + volume = {265}, + pages = {909-914}, + number = {5174}, + month = {Aug 12}, + abstract = {Some of the recently developed fast summation methods that have arisen + in scientific computing are described. These methods require an + amount of work proportional to N or N log N to evaluate all pairwise + interactions in an ensemble of N particles. Traditional methods, + by contrast, require an amount of work proportional to N-2. AS a + result, large-scale simulations can be carried out using only modest + computer resources. In combination with supercomputers, it is possible + to address questions that were previously out of reach. Problems + from diffusion, gravitation, and wave propagation are considered.}, + annote = {Pb499 Times Cited:99 Cited References Count:44}, + issn = {0036-8075}, + uri = {://A1994PB49900031}, } -@Article{Shlesinger84, - author = {M.~F. Shlesinger and E.~W. Montroll}, - title = {On the Williams-Watts function of dielectric relaxation}, - journal = {Proc. Natl. Acad. Sci. USA}, - year = 1984, - volume = 81, - pages = {1280-1283} +@ARTICLE{Greengard1987, + author = {L. Greengard and V. Rokhlin}, + title = {A Fast Algorithm for Particle Simulations}, + journal = {Journal of Computational Physics}, + year = {1987}, + volume = {73}, + pages = {325-348}, + number = {2}, + month = {Dec}, + annote = {L0498 Times Cited:899 Cited References Count:7}, + issn = {0021-9991}, + uri = {://A1987L049800006}, } -@Article{Klafter86, - author = {J. Klafter and M.~F. Shlesinger}, - title = {On the relationship among three theories of - relaxation in disordered systems}, - journal = {Proc. Natl. Acad. Sci. USA}, - year = 1986, - volume = 83, - pages = {848-851} +@ARTICLE{Hairer1997, + author = {E. Hairer and C. Lubich}, + title = {The life-span of backward error analysis for numerical integrators}, + journal = {Numerische Mathematik}, + year = {1997}, + volume = {76}, + pages = {441-462}, + number = {4}, + month = {Jun}, + abstract = {Backward error analysis is a useful tool for the study of numerical + approximations to ordinary differential equations. The numerical + solution is formally interpreted as the exact solution of a perturbed + differential equation, given as a formal and usually divergent series + in powers of the step size. For a rigorous analysis, this series + has to be truncated. In this article we study the influence of this + truncation to the difference between the numerical solution and + the exact solution of the perturbed differential equation. Results + on the long-time behaviour of numerical solutions are obtained in + this way. We present applications to the numerical phase portrait + near hyperbolic equilibrium points, to asymptotically stable periodic + orbits and Hopf bifurcation, and to energy conservation and approximation + of invariant tori in Hamiltonian systems.}, + annote = {Xj488 Times Cited:50 Cited References Count:19}, + issn = {0029-599X}, + uri = {://A1997XJ48800002}, } -@Article{Li2001, - author = {Z. Li and M. Lieberman and W. Hill}, - title = {{\sc xps} and {\sc sers} Study of Silicon Phthalocyanine - Monolayers: umbrella vs. octopus design strategies - for formation of oriented {\sc sam}s}, - journal = {Langmuir}, - year = 2001, - volume = 17, - pages = {4887-4894} +@ARTICLE{Hao1993, + author = {M. H. Hao and M. R. Pincus and S. Rackovsky and H. A. Scheraga}, + title = {Unfolding and Refolding of the Native Structure of Bovine Pancreatic + Trypsin-Inhibitor Studied by Computer-Simulations}, + journal = {Biochemistry}, + year = {1993}, + volume = {32}, + pages = {9614-9631}, + number = {37}, + month = {Sep 21}, + abstract = {A new procedure for studying the folding and unfolding of proteins, + with an application to bovine pancreatic trypsin inhibitor (BPTI), + is reported. The unfolding and refolding of the native structure + of the protein are characterized by the dimensions of the protein, + expressed in terms of the three principal radii of the structure + considered as an ellipsoid. A dynamic equation, describing the variations + of the principal radii on the unfolding path, and a numerical procedure + to solve this equation are proposed. Expanded and distorted conformations + are refolded to the native structure by a dimensional-constraint + energy minimization procedure. A unique and reproducible unfolding + pathway for an intermediate of BPTI lacking the [30,51] disulfide + bond is obtained. The resulting unfolded conformations are extended; + they contain near-native local structure, but their longest principal + radii are more than 2.5 times greater than that of the native structure. + The most interesting finding is that the majority of expanded conformations, + generated under various conditions, can be refolded closely to the + native structure, as measured by the correct overall chain fold, + by the rms deviations from the native structure of only 1.9-3.1 + angstrom, and by the energy differences of about 10 kcal/mol from + the native structure. Introduction of the [30,51] disulfide bond + at this stage, followed by minimization, improves the closeness + of the refolded structures to the native structure, reducing the + rms deviations to 0.9-2.0 angstrom. The unique refolding of these + expanded structures over such a large conformational space implies + that the folding is strongly dictated by the interactions in the + amino acid sequence of BPTI. The simulations indicate that, under + conditions that favor a compact structure as mimicked by the volume + constraints in our algorithm; the expanded conformations have a + strong tendency to move toward the native structure; therefore, + they probably would be favorable folding intermediates. The results + presented here support a general model for protein folding, i.e., + progressive formation of partially folded structural units, followed + by collapse to the compact native structure. The general applicability + of the procedure is also discussed.}, + annote = {Ly294 Times Cited:27 Cited References Count:57}, + issn = {0006-2960}, + uri = {://A1993LY29400014}, } -@Article{Evans1993, - author = {J.~W. Evans}, - title = {Random and Cooperative Sequential Adsorption}, - journal = rmp, - year = 1993, - volume = 65, - pages = {1281-1329} +@ARTICLE{Hinsen2000, + author = {K. Hinsen and A. J. Petrescu and S. Dellerue and M. C. Bellissent-Funel + and G. R. Kneller}, + title = {Harmonicity in slow protein dynamics}, + journal = {Chemical Physics}, + year = {2000}, + volume = {261}, + pages = {25-37}, + number = {1-2}, + month = {Nov 1}, + abstract = {The slow dynamics of proteins around its native folded state is usually + described by diffusion in a strongly anharmonic potential. In this + paper, we try to understand the form and origin of the anharmonicities, + with the principal aim of gaining a better understanding of the + principal motion types, but also in order to develop more efficient + numerical methods for simulating neutron scattering spectra of large + proteins. First, we decompose a molecular dynamics (MD) trajectory + of 1.5 ns for a C-phycocyanin dimer surrounded by a layer of water + into three contributions that we expect to be independent: the global + motion of the residues, the rigid-body motion of the sidechains + relative to the backbone, and the internal deformations of the sidechains. + We show that they are indeed almost independent by verifying the + factorization of the incoherent intermediate scattering function. + Then, we show that the global residue motions, which include all + large-scale backbone motions, can be reproduced by a simple harmonic + model which contains two contributions: a short-time vibrational + term, described by a standard normal mode calculation in a local + minimum, and a long-time diffusive term, described by Brownian motion + in an effective harmonic potential. The potential and the friction + constants were fitted to the MD data. The major anharmonic contribution + to the incoherent intermediate scattering function comes from the + rigid-body diffusion of the sidechains. This model can be used to + calculate scattering functions for large proteins and for long-time + scales very efficiently, and thus provides a useful complement to + MD simulations, which are best suited for detailed studies on smaller + systems or for shorter time scales. (C) 2000 Elsevier Science B.V. + All rights reserved.}, + annote = {Sp. Iss. SI 368MT Times Cited:16 Cited References Count:31}, + issn = {0301-0104}, + uri = {://000090121700003}, } - -@Article{Dwyer1977, - author = {D.~J. Dwyer and G.~W. Simmons and R.~P. Wei}, - title = {}, - journal = {Surf. Sci.}, - year = 1977, - volume = 64, - pages = 617 +@ARTICLE{Ho1992, + author = {C. Ho and C. D. Stubbs}, + title = {Hydration at the Membrane Protein-Lipid Interface}, + journal = {Biophysical Journal}, + year = {1992}, + volume = {63}, + pages = {897-902}, + number = {4}, + month = {Oct}, + abstract = {Evidence has been found for the existence water at the protein-lipid + hydrophobic interface ot the membrane proteins, gramicidin and apocytochrome + C, using two related fluorescence spectroscopic approaches. The + first approach exploited the fact that the presence of water in + the excited state solvent cage of a fluorophore increases the rate + of decay. For 1,6-diphenyl-1,3,5-hexatriene (DPH) and 1-palmitoyl-2-[[2-[4-(6-phenyl-trans-1,3,5-hexatrienyl) + phenyl]ethyl]carbonyl]-3-sn-PC (DPH-PC), where the fluorophores + are located in the hydrophobic core of the lipid bilayer, the introduction + of gramicidin reduced the fluorescence lifetime, indicative of an + increased presence of water in the bilayer. Since a high protein:lipid + ratio was used, the fluorophores were forced to be adjacent to the + protein hydrophobic surface, hence the presence of water in this + region could be inferred. Cholesterol is known to reduce the water + content of lipid bilayers and this effect was maintained at the + protein-lipid interface with both gramicidin and apocytochrome C, + again suggesting hydration in this region. The second approach was + to use the fluorescence enhancement induced by exchanging deuterium + oxide (D2O) for H2O. Both the fluorescence intensities of trimethylammonium-DPH, + located in the lipid head group region, and of the gramicidin intrinsic + tryptophans were greater in a D2O buffer compared with H2O, showing + that the fluorophores were exposed to water in the bilayer at the + protein-lipid interface. In the presence of cholesterol the fluorescence + intensity ratio of D2O to H2O decreased, indicating a removal of + water by the cholesterol, in keeping with the lifetime data. Altered + hydration at the protein-lipid interface could affect conformation, + thereby offering a new route by which membrane protein functioning + may be modified.}, + annote = {Ju251 Times Cited:55 Cited References Count:44}, + issn = {0006-3495}, + uri = {://A1992JU25100002}, } -@Article{Macritche1978, - author = {F. MacRitche}, - title = {}, - journal = {Adv. Protein Chem.}, - year = 1978, - volume = 32, - pages = 283 +@BOOK{Hockney1981, + title = {Computer Simulation Using Particles}, + publisher = {McGraw-Hill}, + year = {1981}, + author = {R.W. Hockney and J.W. Eastwood}, + address = {New York}, } -@Article{Feder1980, - author = {J. Feder}, - title = {}, - journal = {J. Theor. Biol.}, - year = 1980, - volume = 87, - pages = 237 +@ARTICLE{Hoover1985, + author = {W. G. Hoover}, + title = {Canonical Dynamics - Equilibrium Phase-Space Distributions}, + journal = {Physical Review A}, + year = {1985}, + volume = {31}, + pages = {1695-1697}, + number = {3}, + annote = {Acr30 Times Cited:1809 Cited References Count:11}, + issn = {1050-2947}, + uri = {://A1985ACR3000056}, } -@Article{Ramsden1993, - author = {J.~J. Ramsden}, - title = {}, - journal = prl, - year = 1993, - volume = 71, - pages = 295 +@ARTICLE{Huh2004, + author = {Y. Huh and N. M. Cann}, + title = {Discrimination in isotropic, nematic, and smectic phases of chiral + calamitic molecules: A computer simulation study}, + journal = {Journal of Chemical Physics}, + year = {2004}, + volume = {121}, + pages = {10299-10308}, + number = {20}, + month = {Nov 22}, + abstract = {Racemic fluids of chiral calamitic molecules are investigated with + molecular dynamics simulations. In particular, the phase behavior + as a function of density is examined for eight racemates. The relationship + between chiral discrimination and orientational order in the phase + is explored. We find that the transition from the isotropic phase + to a liquid crystal phase is accompanied by an increase in chiral + discrimination, as measured by differences in radial distributions. + Among ordered phases, discrimination is largest for smectic phases + with a significant preference for heterochiral contact within the + layers. (C) 2004 American Institute of Physics.}, + annote = {870FJ Times Cited:0 Cited References Count:63}, + issn = {0021-9606}, + uri = {://000225042700059}, } - -@Article{Egelhoff1989, - author = {W.~F. Egelhoff and I. Jacob}, - title = {}, - journal = prl, - year = 1989, - volume = 62, - pages = 921 +@ARTICLE{Izaguirre2001, + author = {J. A. Izaguirre and D. P. Catarello and J. M. Wozniak and R. D. Skeel}, + title = {Langevin stabilization of molecular dynamics}, + journal = {Journal of Chemical Physics}, + year = {2001}, + volume = {114}, + pages = {2090-2098}, + number = {5}, + month = {Feb 1}, + abstract = {In this paper we show the possibility of using very mild stochastic + damping to stabilize long time step integrators for Newtonian molecular + dynamics. More specifically, stable and accurate integrations are + obtained for damping coefficients that are only a few percent of + the natural decay rate of processes of interest, such as the velocity + autocorrelation function. Two new multiple time stepping integrators, + Langevin Molly (LM) and Brunger-Brooks-Karplus-Molly (BBK-M), are + introduced in this paper. Both use the mollified impulse method + for the Newtonian term. LM uses a discretization of the Langevin + equation that is exact for the constant force, and BBK-M uses the + popular Brunger-Brooks-Karplus integrator (BBK). These integrators, + along with an extrapolative method called LN, are evaluated across + a wide range of damping coefficient values. When large damping coefficients + are used, as one would for the implicit modeling of solvent molecules, + the method LN is superior, with LM closely following. However, with + mild damping of 0.2 ps(-1), LM produces the best results, allowing + long time steps of 14 fs in simulations containing explicitly modeled + flexible water. With BBK-M and the same damping coefficient, time + steps of 12 fs are possible for the same system. Similar results + are obtained for a solvated protein-DNA simulation of estrogen receptor + ER with estrogen response element ERE. A parallel version of BBK-M + runs nearly three times faster than the Verlet-I/r-RESPA (reversible + reference system propagator algorithm) when using the largest stable + time step on each one, and it also parallelizes well. The computation + of diffusion coefficients for flexible water and ER/ERE shows that + when mild damping of up to 0.2 ps-1 is used the dynamics are not + significantly distorted. (C) 2001 American Institute of Physics.}, + annote = {397CQ Times Cited:14 Cited References Count:36}, + issn = {0021-9606}, + uri = {://000166676100020}, } - -@Article{Viot1992a, - author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot}, - title = {RANDOM SEQUENTIAL ADSORPTION OF ANISOTROPIC - PARTICLES 1. JAMMING LIMIT AND ASYMPTOTIC-BEHAVIOR}, - journal = jpc, - year = 1992, - volume = 97, - pages = {5212-5218} +@ARTICLE{Torre1977, + author = {Jose Garcia De La Torre, V.A. Bloomfield}, + title = {Hydrodynamic properties of macromolecular complexes. I. Translation}, + journal = {Biopolymers}, + year = {1977}, + volume = {16}, + pages = {1747-1763}, } -@Article{Viot1992b, - author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot}, - title = {SATURATION COVERAGE IN RANDOM SEQUENTIAL ADSORPTION - OF VERY ELONGATED PARTICLES}, - journal = {Physica A}, - year = 1992, - volume = 191, - pages = {248-252} +@ARTICLE{Kane2000, + author = {C. Kane and J. E. Marsden and M. Ortiz and M. West}, + title = {Variational integrators and the Newmark algorithm for conservative + and dissipative mechanical systems}, + journal = {International Journal for Numerical Methods in Engineering}, + year = {2000}, + volume = {49}, + pages = {1295-1325}, + number = {10}, + month = {Dec 10}, + abstract = {The purpose of this work is twofold. First, we demonstrate analytically + that the classical Newmark family as well as related integration + algorithms are variational in the sense of the Veselov formulation + of discrete mechanics. Such variational algorithms are well known + to be symplectic and momentum preserving and to often have excellent + global energy behaviour. This analytical result is verified through + numerical examples and is believed to be one of the primary reasons + that this class of algorithms performs so well. Second, we develop + algorithms for mechanical systems with forcing, and in particular, + for dissipative systems. In this case, we develop integrators that + are based on a discretization of the Lagrange d'Alembert principle + as well as on a variational formulation of dissipation. It is demonstrated + that these types of structured integrators have good numerical behaviour + in terms of obtaining the correct amounts by which the energy changes + over the integration run. Copyright (C) 2000 John Wiley & Sons, + Ltd.}, + annote = {373CJ Times Cited:30 Cited References Count:41}, + issn = {0029-5981}, + uri = {://000165270600004}, } -@Article{Dobson1987, - author = {B.~W. Dobson}, - title = {}, - journal = prb, - year = 1987, - volume = 36, - pages = 1068 +@ARTICLE{Klimov1997, + author = {D. K. Klimov and D. Thirumalai}, + title = {Viscosity dependence of the folding rates of proteins}, + journal = {Physical Review Letters}, + year = {1997}, + volume = {79}, + pages = {317-320}, + number = {2}, + month = {Jul 14}, + abstract = {The viscosity (eta) dependence of the folding rates for four sequences + (the native state of three sequences is a beta sheet, while the + fourth forms an alpha helix) is calculated for off-lattice models + of proteins. Assuming that the dynamics is given by the Langevin + equation, we show that the folding rates increase linearly at low + viscosities eta, decrease as 1/eta at large eta, and have a maximum + at intermediate values. The Kramers' theory of barrier crossing + provides a quantitative fit of the numerical results. By mapping + the simulation results to real proteins we estimate that for optimized + sequences the time scale for forming a four turn alpha-helix topology + is about 500 ns, whereas for beta sheet it is about 10 mu s.}, + annote = {Xk293 Times Cited:77 Cited References Count:17}, + issn = {0031-9007}, + uri = {://A1997XK29300035}, } -@Article{Boyer1995, - author = {D. Boyer and P. Viot and G. Tarjus and J. Talbot}, - title = {PERCUS-$\mbox{Y}$EVICK-LIKE INTERGRAL EQUATION FOR RANDOM SEQUENTIAL - ADSORPTION}, - journal = jcp, - year = 1995, - volume = 103, - pages = 1607 +@ARTICLE{Kol1997, + author = {A. Kol and B. B. Laird and B. J. Leimkuhler}, + title = {A symplectic method for rigid-body molecular simulation}, + journal = {Journal of Chemical Physics}, + year = {1997}, + volume = {107}, + pages = {2580-2588}, + number = {7}, + month = {Aug 15}, + abstract = {Rigid-body molecular dynamics simulations typically are performed + in a quaternion representation. The nonseparable form of the Hamiltonian + in quaternions prevents the use of a standard leapfrog (Verlet) + integrator, so nonsymplectic Runge-Kutta, multistep, or extrapolation + methods are generally used, This is unfortunate since symplectic + methods like Verlet exhibit superior energy conservation in long-time + integrations. In this article, we describe an alternative method, + which we call RSHAKE (for rotation-SHAKE), in which the entire rotation + matrix is evolved (using the scheme of McLachlan and Scovel [J. + Nonlin. Sci, 16 233 (1995)]) in tandem with the particle positions. + We employ a fast approximate Newton solver to preserve the orthogonality + of the rotation matrix. We test our method on a system of soft-sphere + dipoles and compare with quaternion evolution using a 4th-order + predictor-corrector integrator, Although the short-time error of + the quaternion algorithm is smaller for fixed time step than that + for RSHAKE, the quaternion scheme exhibits an energy drift which + is not observed in simulations with RSHAKE, hence a fixed energy + tolerance can be achieved by using a larger time step, The superiority + of RSHAKE increases with system size. (C) 1997 American Institute + of Physics.}, + annote = {Xq332 Times Cited:11 Cited References Count:18}, + issn = {0021-9606}, + uri = {://A1997XQ33200046}, } -@Article{Viot1992c, - author = {P. Viot and G. Tarjus and S.~M. Ricci and J. Talbot}, - title = {SATURATION COVERAGE OF HIGHLY ELONGATED ANISOTROPIC - PARTICLES}, - journal = {Physica A}, - year = 1992, - volume = 191, - pages = {248-252} +@ARTICLE{Lansac2001, + author = {Y. Lansac and M. A. Glaser and N. A. Clark}, + title = {Microscopic structure and dynamics of a partial bilayer smectic liquid + crystal}, + journal = {Physical Review E}, + year = {2001}, + volume = {6405}, + pages = {-}, + number = {5}, + month = {Nov}, + abstract = {Cyanobiphenyls (nCB's) represent a useful and intensively studied + class of mesogens. Many of the peculiar properties of nCB's (e.g., + the occurence of the partial bilayer smectic-A(d) phase) are thought + to be a manifestation of short-range antiparallel association of + neighboring molecules, resulting from strong dipole-dipole interactions + between cyano groups. To test and extend existing models of microscopic + ordering in nCB's, we carry out large-scale atomistic simulation + studies of the microscopic structure and dynamics of the Sm-A(d) + phase of 4-octyl-4'-cyanobiphenyl (8CB). We compute a variety of + thermodynamic, structural, and dynamical properties for this material, + and make a detailed comparison of our results with experimental + measurements in order to validate our molecular model. Semiquantitative + agreement with experiment is found: the smectic layer spacing and + mass density are well reproduced, translational diffusion constants + are similar to experiment, but the orientational ordering of alkyl + chains is overestimated. This simulation provides a detailed picture + of molecular conformation, smectic layer structure, and intermolecular + correlations in Sm-A(d) 8CB, and demonstrates that pronounced short-range + antiparallel association of molecules arising from dipole-dipole + interactions plays a dominant role in determining the molecular-scale + structure of 8CB.}, + annote = {Part 1 496QF Times Cited:10 Cited References Count:60}, + issn = {1063-651X}, + uri = {://000172406900063}, } -@Article{Ricci1994, - author = {S.~M. Ricci and J. Talbot and G. Tarjus and P. Viot}, - title = {A STRUCTURAL COMPARISON OF RANDOM SEQUENTIAL ADSORPTION AND - EQUILIBRIUM CONFIGURATIONS OF SPHEROCYLINDERS}, - journal = jcp, - year = 1994, - volume = 101, - pages = 9164 +@ARTICLE{Lansac2003, + author = {Y. Lansac and P. K. Maiti and N. A. Clark and M. A. Glaser}, + title = {Phase behavior of bent-core molecules}, + journal = {Physical Review E}, + year = {2003}, + volume = {67}, + pages = {-}, + number = {1}, + month = {Jan}, + abstract = {Recently, a new class of smectic liquid crystal phases characterized + by the spontaneous formation of macroscopic chiral domains from + achiral bent-core molecules has been discovered. We have carried + out Monte Carlo simulations of a minimal hard spherocylinder dimer + model to investigate the role of excluded volume interactions in + determining the phase behavior of bent-core materials and to probe + the molecular origins of polar and chiral symmetry breaking. We + present the phase diagram of hard spherocylinder dimers of length-diameter + ratio of 5 as a function of pressure or density and dimer opening + angle psi. With decreasing psi, a transition from a nonpolar to + a polar smectic A phase is observed near psi=167degrees, and the + nematic phase becomes thermodynamically unstable for psi<135degrees. + Free energy calculations indicate that the antipolar smectic A (SmAP(A)) + phase is more stable than the polar smectic A phase (SmAP(F)). No + chiral smectic or biaxial nematic phases were found.}, + annote = {Part 1 646CM Times Cited:15 Cited References Count:38}, + issn = {1063-651X}, + uri = {://000181017300042}, } -@Article{Semmler1998, - author = {M. Semmler and E.~K. Mann and J. Ricka and M. Borkovec}, - title = {Diffusional Deposition of Charged Latex Particles on - Water-Solid Interfaces at Low Ionic Strength}, - journal = {Langmuir}, - year = 1998, - volume = 14, - pages = {5127-5132} +@BOOK{Leach2001, + title = {Molecular Modeling: Principles and Applications}, + publisher = {Pearson Educated Limited}, + year = {2001}, + author = {A. Leach}, + address = {Harlow, England}, + edition = {2nd}, } -@Article{Solomon1986, - author = {H. Solomon and H. Weiner}, - title = {A REVIEW OF THE PACKING PROBLEM}, - journal = {Comm. Statistics A}, - year = 1986, - volume = 15, - pages = {2571-2607} +@ARTICLE{Leimkuhler1999, + author = {B. Leimkuhler}, + title = {Reversible adaptive regularization: perturbed Kepler motion and classical + atomic trajectories}, + journal = {Philosophical Transactions of the Royal Society of London Series + a-Mathematical Physical and Engineering Sciences}, + year = {1999}, + volume = {357}, + pages = {1101-1133}, + number = {1754}, + month = {Apr 15}, + abstract = {Reversible and adaptive integration methods based on Kustaanheimo-Stiefel + regularization and modified Sundman transformations are applied + to simulate general perturbed Kepler motion and to compute classical + trajectories of atomic systems (e.g. Rydberg atoms). The new family + of reversible adaptive regularization methods also conserves angular + momentum and exhibits superior energy conservation and numerical + stability in long-time integrations. The schemes are appropriate + for scattering, for astronomical calculations of escape time and + long-term stability, and for classical and semiclassical studies + of atomic dynamics. The components of an algorithm for trajectory + calculations are described. Numerical experiments illustrate the + effectiveness of the reversible approach.}, + annote = {199EE Times Cited:11 Cited References Count:48}, + issn = {1364-503X}, + uri = {://000080466800007}, } -@Article{Bonnier1993, - author = {B. Bonnier and M. Hontebeyrie and C. Meyers}, - title = {ON THE RANDOM FILLING OF R(D) BY NONOVERLAPPING - D-DIMENSIONAL CUBES}, - journal = {Physica A}, - year = 1993, - volume = 198, - pages = {1-10} -} - -@Book{Frenkel1996, - author = {D. Frenkel and B. Smit}, - title = {Understanding Molecular Simulation : From Algorithms - to Applications}, - publisher = {Academic Press}, - year = 1996, - address = {New York} - - +@BOOK{Leimkuhler2004, + title = {Simulating Hamiltonian Dynamics}, + publisher = {Cambridge University Press}, + year = {2004}, + author = {B. Leimkuhler and S. Reich}, + address = {Cambridge}, } -@Article{Dullweber1997, - author = {A. Dullweber and B. Leimkuhler and R. McLachlan}, - title = {Symplectic splitting methods for rigid body molecular - dynamics}, - journal = jcp, - year = 1997, - volume = 107, - number = 15, - pages = {5840-5851} +@ARTICLE{Levelut1981, + author = {A. M. Levelut and R. J. Tarento and F. Hardouin and M. F. Achard + and G. Sigaud}, + title = {Number of Sa Phases}, + journal = {Physical Review A}, + year = {1981}, + volume = {24}, + pages = {2180-2186}, + number = {4}, + annote = {Ml751 Times Cited:96 Cited References Count:16}, + issn = {1050-2947}, + uri = {://A1981ML75100057}, } -@Article{Siepmann1998, - author = {M. Martin and J.~I. Siepmann}, - title = {Transferable Potentials for Phase Equilibria. 1. United-Atom - Description of n-Alkanes}, - journal = jpcB, - year = 1998, - volume = 102, - pages = {2569-2577} +@ARTICLE{Lieb1982, + author = {W. R. Lieb and M. Kovalycsik and R. Mendelsohn}, + title = {Do Clinical-Levels of General-Anesthetics Affect Lipid Bilayers - + Evidence from Raman-Scattering}, + journal = {Biochimica Et Biophysica Acta}, + year = {1982}, + volume = {688}, + pages = {388-398}, + number = {2}, + annote = {Nu461 Times Cited:40 Cited References Count:28}, + issn = {0006-3002}, + uri = {://A1982NU46100012}, } -@Article{Marrink01, - author = {S.~J. Marrink and E. Lindahl and O. Edholm and A.~E. Mark}, - title = {Simulations of the Spontaneous Aggregation of Phospholipids - into Bilayers}, - journal = jacs, - year = 2001, - volume = 123, - pages = {8638-8639} +@ARTICLE{Link1997, + author = {D. R. Link and G. Natale and R. Shao and J. E. Maclennan and N. A. + Clark and E. Korblova and D. M. Walba}, + title = {Spontaneous formation of macroscopic chiral domains in a fluid smectic + phase of achiral molecules}, + journal = {Science}, + year = {1997}, + volume = {278}, + pages = {1924-1927}, + number = {5345}, + month = {Dec 12}, + abstract = {A smectic liquid-crystal phase made from achiral molecules with bent + cores was found to have fluid layers that exhibit two spontaneous + symmetry-breaking instabilities: polar molecular orientational ordering + about the layer normal and molecular tilt. These instabilities combine + to form a chiral layer structure with a handedness that depends + on the sign of the tilt. The bulk states are either antiferroelectric-racemic, + with the layer polar direction and handedness alternating in sign + from layer to layer, or antiferroelectric-chiral, which is of uniform + layer handedness. Both states exhibit an electric field-induced + transition from antiferroelectric to ferroelectric.}, + annote = {Yl002 Times Cited:407 Cited References Count:25}, + issn = {0036-8075}, + uri = {://A1997YL00200028}, } -@Article{liu96:new_model, - author = {Y. Liu and T. Ichiye}, - title = {Soft sticky dipole potential for liquid water: a new model}, - journal = jpc, - year = 1996, - volume = 100, - pages = {2723-2730} +@ARTICLE{Liwo2005, + author = {A. Liwo and M. Khalili and H. A. Scheraga}, + title = {Ab initio simulations of protein folding pathways by molecular dynamics + with the united-residue (UNRES) model of polypeptide chains}, + journal = {Febs Journal}, + year = {2005}, + volume = {272}, + pages = {359-360}, + month = {Jul}, + annote = {Suppl. 1 005MG Times Cited:0 Cited References Count:0}, + issn = {1742-464X}, + uri = {://000234826102043}, } -@Article{liu96:monte_carlo, - author = {Y. Liu and T. Ichiye}, - title = {The static dielectric constant of the soft sticky dipole model of liquid water: $\mbox{Monte Carlo}$ simulation}, - journal = {Chemical Physics Letters}, - year = 1996, - volume = 256, - pages = {334-340} +@ARTICLE{Luty1994, + author = {B. A. Luty and M. E. Davis and I. G. Tironi and W. F. Vangunsteren}, + title = {A Comparison of Particle-Particle, Particle-Mesh and Ewald Methods + for Calculating Electrostatic Interactions in Periodic Molecular-Systems}, + journal = {Molecular Simulation}, + year = {1994}, + volume = {14}, + pages = {11-20}, + number = {1}, + abstract = {We compare the Particle-Particle Particle-Mesh (PPPM) and Ewald methods + for calculating electrostatic interactions in periodic molecular + systems. A brief comparison of the theories shows that the methods + are very similar differing mainly in the technique which is used + to perform the ''k-space'' or mesh calculation. Because the PPPM + utilizes the highly efficient numerical Fast Fourier Transform (FFT) + method it requires significantly less computational effort than + the Ewald method and scale's almost linearly with system size.}, + annote = {Qf464 Times Cited:50 Cited References Count:20}, + issn = {0892-7022}, + uri = {://A1994QF46400002}, } -@Article{chandra99:ssd_md, - author = {A. Chandra and T. Ichiye}, - title = {Dynamical properties of the soft sticky dipole model of water: Molecular dynamics simulation}, - journal = {Journal of Chemical Physics}, - year = 1999, - volume = 111, - number = 6, - pages = {2701-2709} +@BOOK{Marion1990, + title = {Classical Dynamics of Particles and Systems}, + publisher = {Academic Press}, + year = {1990}, + author = {J.~B. Marion}, + address = {New York}, + edition = {2rd}, } -@Book{allen87:csl, - author = {M.~P. Allen and D.~J. Tildesley}, - title = {Computer Simulations of Liquids}, - publisher = {Oxford University Press}, - year = 1987, - address = {New York} +@ARTICLE{Marrink1994, + author = {S. J. Marrink and H. J. C. Berendsen}, + title = {Simulation of Water Transport through a Lipid-Membrane}, + journal = {Journal of Physical Chemistry}, + year = {1994}, + volume = {98}, + pages = {4155-4168}, + number = {15}, + month = {Apr 14}, + abstract = {To obtain insight in the process of water permeation through a lipid + membrane, we performed molecular dynamics simulations on a phospholipid + (DPPC)/water system with atomic detail. Since the actual process + of permeation is too slow to be studied directly, we deduced the + permeation rate indirectly via computation of the free energy and + diffusion rate profiles of a water molecule across the bilayer. + We conclude that the permeation of water through a lipid membrane + cannot be described adequately by a simple homogeneous solubility-diffusion + model. Both the excess free energy and the diffusion rate strongly + depend on the position in the membrane, as a result from the inhomogeneous + nature of the membrane. The calculated excess free energy profile + has a shallow slope and a maximum height of 26 kJ/mol. The diffusion + rate is highest in the middle of the membrane where the lipid density + is low. In the interfacial region almost all water molecules are + bound by the lipid headgroups, and the diffusion turns out to be + 1 order of magnitude smaller. The total transport process is essentially + determined by the free energy barrier. The rate-limiting step is + the permeation through the dense part of the lipid tails, where + the resistance is highest. We found a permeation rate of 7(+/-3) + x 10(-2) cm/s at 350 K, comparable to experimental values for DPPC + membranes, if corrected for the temperature of the simulation. Taking + the inhomogeneity of the membrane into account, we define a new + ''four-region'' model which seems to be more realistic than the + ''two-phase'' solubility-diffusion model.}, + annote = {Ng219 Times Cited:187 Cited References Count:25}, + issn = {0022-3654}, + uri = {://A1994NG21900040}, } -@Book{leach01:mm, - author = {A. Leach}, - title = {Molecular Modeling: Principles and Applications}, - publisher = {Pearson Educated Limited}, - year = 2001, - address = {Harlow, England}, - edition = {2nd} +@ARTICLE{Marsden1998, + author = {J. E. Marsden and G. W. Patrick and S. Shkoller}, + title = {Multisymplectic geometry, variational integrators, and nonlinear + PDEs}, + journal = {Communications in Mathematical Physics}, + year = {1998}, + volume = {199}, + pages = {351-395}, + number = {2}, + month = {Dec}, + abstract = {This paper presents a geometric-variational approach to continuous + and discrete mechanics and field theories. Using multisymplectic + geometry, we show that the existence of the fundamental geometric + structures as well as their preservation along solutions can be + obtained directly from the variational principle. In particular, + we prove that a unique multisymplectic structure is obtained by + taking the derivative of an action function, and use this structure + to prove covariant generalizations of conservation of symplecticity + and Noether's theorem. Natural discretization schemes for PDEs, + which have these important preservation properties, then follow + by choosing a discrete action functional. In the case of mechanics, + we recover the variational symplectic integrators of Veselov type, + while for PDEs we obtain covariant spacetime integrators which conserve + the corresponding discrete multisymplectic form as well as the discrete + momentum mappings corresponding to symmetries. We show that the + usual notion of symplecticity along an infinite-dimensional space + of fields can be naturally obtained by making a spacetime split. + All of the aspects of our method are demonstrated with a nonlinear + sine-Gordon equation, including computational results and a comparison + with other discretization schemes.}, + annote = {154RH Times Cited:88 Cited References Count:36}, + issn = {0010-3616}, + uri = {://000077902200006}, } - -@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}, - title = {Clarification of the ripple phase of lecithin bilayers using fully hydrated, aligned samples}, - journal = {Physical Review E}, - year = 2000, - volume = 61, - number = 5, - pages = {5668-5677} +@ARTICLE{McLachlan1993, + author = {R.~I McLachlan}, + title = {Explicit Lie-Poisson integration and the Euler equations}, + journal = {prl}, + year = {1993}, + volume = {71}, + pages = {3043-3046}, } -@Article{sengupta00, - author = {K. Sengupta and V.~A. Raghunathan and J. Katsaras}, - title = {Novel structural Features of the ripple phase of phospholipids}, - journal = {Europhysics Letters}, - year = 2000, - volume = 49, - number = 6, - pages = {722-728} +@ARTICLE{McLachlan1998, + author = {R. I. McLachlan and G. R. W. Quispel}, + title = {Generating functions for dynamical systems with symmetries, integrals, + and differential invariants}, + journal = {Physica D}, + year = {1998}, + volume = {112}, + pages = {298-309}, + number = {1-2}, + month = {Jan 15}, + abstract = {We give a survey and some new examples of generating functions for + systems with symplectic structure, systems with a first integral, + systems that preserve volume, and systems with symmetries and/or + time-reversing symmetries. Both ODEs and maps are treated, and we + discuss how generating functions may be used in the structure-preserving + numerical integration of ODEs with the above properties.}, + annote = {Yt049 Times Cited:7 Cited References Count:26}, + issn = {0167-2789}, + uri = {://000071558900021}, } -@Article{venable00, - author = {R.~M. Venable and B.~R. Brooks and R.~W. Pastor}, - title = {Molecular dynamics simulations of gel ($L_{\beta I}$) phase lipid bilayers in constant pressure and constant surface area ensembles}, - journal = jcp, - year = 2000, - volume = 112, - number = 10, - pages = {4822-4832} +@ARTICLE{McLachlan1998a, + author = {R. I. McLachlan and G. R. W. Quispel and G. S. Turner}, + title = {Numerical integrators that preserve symmetries and reversing symmetries}, + journal = {Siam Journal on Numerical Analysis}, + year = {1998}, + volume = {35}, + pages = {586-599}, + number = {2}, + month = {Apr}, + abstract = {We consider properties of flows, the relationships between them, and + whether numerical integrators can be made to preserve these properties. + This is done in the context of automorphisms and antiautomorphisms + of a certain group generated by maps associated to vector fields. + This new framework unifies several known constructions. We also + use the concept of #covariance# of a numerical method with respect + to a group of coordinate transformations. The main application is + to explore the relationship between spatial symmetries, reversing + symmetries, and time symmetry of flows and numerical integrators.}, + annote = {Zc449 Times Cited:14 Cited References Count:33}, + issn = {0036-1429}, + uri = {://000072580500010}, } -@Article{lindahl00, - author = {E. Lindahl and O. Edholm}, - title = {Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations}, - journal = {Biophysical Journal}, - year = 2000, - volume = 79, - pages = {426-433}, - month = {July} +@ARTICLE{McLachlan2005, + author = {R. I. McLachlan and A. Zanna}, + title = {The discrete Moser-Veselov algorithm for the free rigid body, revisited}, + journal = {Foundations of Computational Mathematics}, + year = {2005}, + volume = {5}, + pages = {87-123}, + number = {1}, + month = {Feb}, + abstract = {In this paper we revisit the Moser-Veselov description of the free + rigid body in body coordinates, which, in the 3 x 3 case, can be + implemented as an explicit, second-order, integrable approximation + of the continuous solution. By backward error analysis, we study + the modified vector field which is integrated exactly by the discrete + algorithm. We deduce that the discrete Moser-Veselov (DMV) is well + approximated to higher order by time reparametrizations of the continuous + equations (modified vector field). We use the modified vector field + to scale the initial data of the DMV to improve the order of the + approximation and show the equivalence of the DMV and the RATTLE + algorithm. Numerical integration with these preprocessed initial + data is several orders of magnitude more accurate than the original + DMV and RATTLE approach.}, + annote = {911NS Times Cited:0 Cited References Count:14}, + issn = {1615-3375}, + uri = {://000228011900003}, } - -@Article{saiz02, - author = {L. Saiz and M. Klein}, - title = {Electrostatic interactions in a neutral model phospholipid bilayer by molecular dynamics simulations}, - journal = jcp, - year = 2002, - volume = 116, - number = 7, - pages = {3052-3057} +@ARTICLE{Melchionna1993, + author = {S. Melchionna and G. Ciccotti and B. L. Holian}, + title = {Hoover Npt Dynamics for Systems Varying in Shape and Size}, + journal = {Molecular Physics}, + year = {1993}, + volume = {78}, + pages = {533-544}, + number = {3}, + month = {Feb 20}, + abstract = {In this paper we write down equations of motion (following the approach + pioneered by Hoover) for an exact isothermal-isobaric molecular + dynamics simulation, and we extend them to multiple thermostating + rates, to a shape-varying cell and to molecular systems, coherently + with the previous 'extended system method'. An integration scheme + is proposed together with a numerical illustration of the method.}, + annote = {Kq355 Times Cited:172 Cited References Count:17}, + issn = {0026-8976}, + uri = {://A1993KQ35500002}, } -@Article{stevens95, - author = {M.~J. Stevens and G.~S. Grest}, - title = {Phase coexistence of a Stockmayer fluid in an aplied field}, - journal = {Physical Review E}, - year = 1995, - volume = 51, - number = 6, - pages = {5976-5983} +@ARTICLE{Memmer2002, + author = {R. Memmer}, + title = {Liquid crystal phases of achiral banana-shaped molecules: a computer + simulation study}, + journal = {Liquid Crystals}, + year = {2002}, + volume = {29}, + pages = {483-496}, + number = {4}, + month = {Apr}, + abstract = {The phase behaviour of achiral banana-shaped molecules was studied + by computer simulation. The banana-shaped molecules were described + by model intermolecular interactions based on the Gay-Berne potential. + The characteristic molecular structure was considered by joining + two calamitic Gay-Berne particles through a bond to form a biaxial + molecule of point symmetry group C-2v with a suitable bending angle. + The dependence on temperature of systems of N=1024 rigid banana-shaped + molecules with bending angle phi=140degrees has been studied by + means of Monte Carlo simulations in the isobaric-isothermal ensemble + (NpT). On cooling an isotropic system, two phase transitions characterized + by phase transition enthalpy, entropy and relative volume change + have been observed. For the first time by computer simulation of + a many-particle system of banana-shaped molecules, at low temperature + an untilted smectic phase showing a global phase biaxiality and + a spontaneous local polarization in the layers, i.e. a local polar + arrangement of the steric dipoles, with an antiferroelectric-like + superstructure could be proven, a phase structure which recently + has been discovered experimentally. Additionally, at intermediate + temperature a nematic-like phase has been proved, whereas close + to the transition to the smectic phase hints of a spontaneous achiral + symmetry breaking have been determined. Here, in the absence of + a layered structure a helical superstructure has been formed. All + phases have been characterized by visual representations of selected + configurations, scalar and pseudoscalar correlation functions, and + order parameters.}, + annote = {531HT Times Cited:12 Cited References Count:37}, + issn = {0267-8292}, + uri = {://000174410500001}, } -@Article{darden93:pme, - author = {T. Darden and D. York and L. Pedersen}, - title = {Particle mesh Ewald: An $N \log N$ method for Ewald sums in large systems}, - journal = {Journal of Chemical Physics}, - year = 1993, - volume = 98, - number = 12, - pages = {10089-10092} +@ARTICLE{Metropolis1949, + author = {N. Metropolis and S. Ulam}, + title = {The $\mbox{Monte Carlo}$ Method}, + journal = {J. Am. Stat. Ass.}, + year = {1949}, + volume = {44}, + pages = {335-341}, } - - -@Article{goetz98, - author = {R. Goetz and R. Lipowsky}, - title = {Computer simulations of bilayer membranes: Self-assembly and interfacial tension}, - journal = {Journal of Chemical Physics}, - year = 1998, - volume = 108, - number = 17, - pages = 7397 +@ARTICLE{Mielke2004, + author = {S. P. Mielke and W. H. Fink and V. V. Krishnan and N. Gronbech-Jensen + and C. J. Benham}, + title = {Transcription-driven twin supercoiling of a DNA loop: A Brownian + dynamics study}, + journal = {Journal of Chemical Physics}, + year = {2004}, + volume = {121}, + pages = {8104-8112}, + number = {16}, + month = {Oct 22}, + abstract = {The torque generated by RNA polymerase as it tracks along double-stranded + DNA can potentially induce long-range structural deformations integral + to mechanisms of biological significance in both prokaryotes and + eukaryotes. In this paper, we introduce a dynamic computer model + for investigating this phenomenon. Duplex DNA is represented as + a chain of hydrodynamic beads interacting through potentials of + linearly elastic stretching, bending, and twisting, as well as excluded + volume. The chain, linear when relaxed, is looped to form two open + but topologically constrained subdomains. This permits the dynamic + introduction of torsional stress via a centrally applied torque. + We simulate by Brownian dynamics the 100 mus response of a 477-base + pair B-DNA template to the localized torque generated by the prokaryotic + transcription ensemble. Following a sharp rise at early times, the + distributed twist assumes a nearly constant value in both subdomains, + and a succession of supercoiling deformations occurs as superhelical + stress is increasingly partitioned to writhe. The magnitude of writhe + surpasses that of twist before also leveling off when the structure + reaches mechanical equilibrium with the torsional load. Superhelicity + is simultaneously right handed in one subdomain and left handed + in the other, as predicted by the #transcription-induced##twin-supercoiled-domain# + model [L. F. Liu and J. C. Wang, Proc. Natl. Acad. Sci. U.S.A. 84, + 7024 (1987)]. The properties of the chain at the onset of writhing + agree well with predictions from theory, and the generated stress + is ample for driving secondary structural transitions in physiological + DNA. (C) 2004 American Institute of Physics.}, + annote = {861ZF Times Cited:3 Cited References Count:34}, + issn = {0021-9606}, + uri = {://000224456500064}, } -@Article{marrink01:undulation, - author = {S.~J. Marrink and A.~E. Mark}, - title = {Effect of undulations on surface tension in simulated bilayers}, - journal = {Journal of Physical Chemistry B}, - year = 2001, - volume = 105, - pages = {6122-6127} +@ARTICLE{Naess2001, + author = {S. N. Naess and H. M. Adland and A. Mikkelsen and A. Elgsaeter}, + title = {Brownian dynamics simulation of rigid bodies and segmented polymer + chains. Use of Cartesian rotation vectors as the generalized coordinates + describing angular orientations}, + journal = {Physica A}, + year = {2001}, + volume = {294}, + pages = {323-339}, + number = {3-4}, + month = {May 15}, + abstract = {The three Eulerian angles constitute the classical choice of generalized + coordinates used to describe the three degrees of rotational freedom + of a rigid body, but it has long been known that this choice yields + singular equations of motion. The latter is also true when Eulerian + angles are used in Brownian dynamics analyses of the angular orientation + of single rigid bodies and segmented polymer chains. Starting from + kinetic theory we here show that by instead employing the three + components of Cartesian rotation vectors as the generalized coordinates + describing angular orientation, no singularity appears in the configuration + space diffusion equation and the associated Brownian dynamics algorithm. + The suitability of Cartesian rotation vectors in Brownian dynamics + simulations of segmented polymer chains with spring-like or ball-socket + joints is discussed. (C) 2001 Elsevier Science B.V. All rights reserved.}, + annote = {433TA Times Cited:7 Cited References Count:19}, + issn = {0378-4371}, + uri = {://000168774800005}, } -@Article{lindahl00:undulation, - author = {E. Lindahl and O. Edholm}, - title = {Mesoscopic undulation and thickness fluctuations in lipid bilayers from molecular dynamics simulation}, - journal = {Biophysical Journal}, - year = 2000, - volume = 79, - pages = {426-433} +@ARTICLE{Niori1996, + author = {T. Niori and T. Sekine and J. Watanabe and T. Furukawa and H. Takezoe}, + title = {Distinct ferroelectric smectic liquid crystals consisting of banana + shaped achiral molecules}, + journal = {Journal of Materials Chemistry}, + year = {1996}, + volume = {6}, + pages = {1231-1233}, + number = {7}, + month = {Jul}, + abstract = {The synthesis of a banana-shaped molecule is reported and it is found + that the smectic phase which it forms is biaxial with the molecules + packed in the best,direction into a layer. Because of this characteristic + packing, spontaneous polarization appears parallel to the layer + and switches on reversal of an applied electric field. This is the + first obvious example of ferroelectricity in an achiral smectic + phase and is ascribed to the C-2v symmetry of the molecular packing.}, + annote = {Ux855 Times Cited:447 Cited References Count:18}, + issn = {0959-9428}, + uri = {://A1996UX85500025}, } -@Article{metropolis:1949, - author = {N. Metropolis and S. Ulam}, - title = {The $\mbox{Monte Carlo}$ Method}, - journal = {J. Am. Stat. Ass.}, - year = 1949, - volume = 44, - pages = {335-341} +@ARTICLE{Noguchi2002, + author = {H. Noguchi and M. Takasu}, + title = {Structural changes of pulled vesicles: A Brownian dynamics simulation}, + journal = {Physical Review E}, + year = {2002}, + volume = {65}, + pages = {-}, + number = {5}, + month = {may}, + abstract = {We Studied the structural changes of bilayer vesicles induced by mechanical + forces using a Brownian dynamics simulation. Two nanoparticles, + which interact repulsively with amphiphilic molecules, are put inside + a vesicle. The position of one nanoparticle is fixed, and the other + is moved by a constant force as in optical-trapping experiments. + First, the pulled vesicle stretches into a pear or tube shape. Then + the inner monolayer in the tube-shaped region is deformed, and a + cylindrical structure is formed between two vesicles. After stretching + the cylindrical region, fission occurs near the moved vesicle. Soon + after this the cylindrical region shrinks. The trapping force similar + to 100 pN is needed to induce the formation of the cylindrical structure + and fission.}, + annote = {Part 1 568PX Times Cited:5 Cited References Count:39}, + issn = {1063-651X}, + uri = {://000176552300084}, } -@Article{metropolis:1953, - author = {N. Metropolis and A.~W. Rosenbluth and M.~N. Rosenbluth and A.~H. Teller and E. Teller}, - title = {Equation of State Calculations by Fast Computing Machines}, - journal = {J. Chem. Phys.}, - year = 1953, - volume = 21, - pages = {1087-1092} +@ARTICLE{Noguchi2001, + author = {H. Noguchi and M. Takasu}, + title = {Fusion pathways of vesicles: A Brownian dynamics simulation}, + journal = {Journal of Chemical Physics}, + year = {2001}, + volume = {115}, + pages = {9547-9551}, + number = {20}, + month = {Nov 22}, + abstract = {We studied the fusion dynamics of vesicles using a Brownian dynamics + simulation. Amphiphilic molecules spontaneously form vesicles with + a bilayer structure. Two vesicles come into contact and form a stalk + intermediate, in which a necklike structure only connects the outer + monolayers, as predicted by the stalk hypothesis. We have found + a new pathway of pore opening from stalks at high temperature: the + elliptic stalk bends and contact between the ends of the arc-shaped + stalk leads to pore opening. On the other hand, we have clarified + that the pore-opening process at low temperature agrees with the + modified stalk model: a pore is induced by contact between the inner + monolayers inside the stalk. (C) 2001 American Institute of Physics.}, + annote = {491UW Times Cited:48 Cited References Count:25}, + issn = {0021-9606}, + uri = {://000172129300049}, } -@Article{born:1912, - author = {M. Born and Th. Von~Karman}, - title = {Uber Schwingungen in Raumgittern}, - journal = {Physik Z.}, - year = 1912, - volume = 13, - number = {297-309} +@BOOK{Olver1986, + title = {Applications of Lie groups to differential equatitons}, + publisher = {Springer}, + year = {1986}, + author = {P.J. Olver}, + address = {New York}, } -@Book{chandler:1987, - author = {David Chandler}, - title = {Introduction to Modern Statistical Mechanics}, - publisher = {Oxford University Press}, - year = 1987 +@ARTICLE{Omelyan1998, + author = {I. P. Omelyan}, + title = {On the numerical integration of motion for rigid polyatomics: The + modified quaternion approach}, + journal = {Computers in Physics}, + year = {1998}, + volume = {12}, + pages = {97-103}, + number = {1}, + month = {Jan-Feb}, + abstract = {A revised version of the quaternion approach for numerical integration + of the equations of motion for rigid polyatomic molecules is proposed. + The modified approach is based on a formulation of the quaternion + dynamics with constraints. This allows one to resolve the rigidity + problem rigorously using constraint forces. It is shown that the + procedure for preservation of molecular rigidity can be realized + particularly simply within the Verlet algorithm in velocity form. + We demonstrate that the method presented leads to an improved numerical + stability with respect to the usual quaternion rescaling scheme + and it is roughly as good as the cumbersome atomic-constraint technique. + (C) 1998 American Institute of Physics.}, + annote = {Yx279 Times Cited:12 Cited References Count:28}, + issn = {0894-1866}, + uri = {://000072024300025}, } - -@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}, - 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}, - journal = {Computer Physics Communications}, - year = 1995, - volume = 91, - pages = {1-41} +@ARTICLE{Omelyan1998a, + author = {I. P. Omelyan}, + title = {Algorithm for numerical integration of the rigid-body equations of + motion}, + journal = {Physical Review E}, + year = {1998}, + volume = {58}, + pages = {1169-1172}, + number = {1}, + month = {Jul}, + abstract = {An algorithm for numerical integration of the rigid-body equations + of motion is proposed. The algorithm uses the leapfrog scheme and + the quantities involved are angular velocities and orientational + variables that can be expressed in terms of either principal axes + or quaternions. Due to specific features of the algorithm, orthonormality + and unit norms of the orientational variables are integrals of motion, + despite an approximate character of the produced trajectories. It + is shown that the method presented appears to be the most efficient + among all such algorithms known.}, + annote = {101XL Times Cited:8 Cited References Count:22}, + issn = {1063-651X}, + uri = {://000074893400151}, } -@Book{Goldstein01, - author = {H. Goldstein and C. Poole and J. Safko}, - title = {Classical Mechanics}, - publisher = {Addison Wesley}, - year = 2001, - address = {San Francisco}, - edition = {3rd} +@ARTICLE{Orlandi2006, + author = {S. Orlandi and R. Berardi and J. Steltzer and C. Zannoni}, + title = {A Monte Carlo study of the mesophases formed by polar bent-shaped + molecules}, + journal = {Journal of Chemical Physics}, + year = {2006}, + volume = {124}, + pages = {-}, + number = {12}, + month = {Mar 28}, + abstract = {Liquid crystal phases formed by bent-shaped (or #banana#) molecules + are currently of great interest. Here we investigate by Monte Carlo + computer simulations the phases formed by rigid banana molecules + modeled combining three Gay-Berne sites and containing either one + central or two lateral and transversal dipoles. We show that changing + the dipole position and orientation has a profound effect on the + mesophase stability and molecular organization. In particular, we + find a uniaxial nematic phase only for off-center dipolar models + and tilted phases only for the one with terminal dipoles. (c) 2006 + American Institute of Physics.}, + annote = {028CP Times Cited:0 Cited References Count:42}, + issn = {0021-9606}, + uri = {://000236464000072}, } -@Article{Bratko85, - author = {D. Bratko and L. Blum and A. Luzar}, - title = {A simple model for the intermolecular potential of water}, - journal = jcp, - year = 1985, - volume = 83, - number = 12, - pages = {6367-6370} +@ARTICLE{Owren1992, + author = {B. Owren and M. Zennaro}, + title = {Derivation of Efficient, Continuous, Explicit Runge-Kutta Methods}, + journal = {Siam Journal on Scientific and Statistical Computing}, + year = {1992}, + volume = {13}, + pages = {1488-1501}, + number = {6}, + month = {Nov}, + abstract = {Continuous, explicit Runge-Kutta methods with the minimal number of + stages are considered. These methods are continuously differentiable + if and only if one of the stages is the FSAL evaluation. A characterization + of a subclass of these methods is developed for orders 3, 4, and + 5. It is shown how the free parameters of these methods can be used + either to minimize the continuous truncation error coefficients + or to maximize the stability region. As a representative for these + methods the fifth-order method with minimized error coefficients + is chosen, supplied with an error estimation method, and analysed + by using the DETEST software. The results are compared with a similar + implementation of the Dormand-Prince 5(4) pair with interpolant, + showing a significant advantage in the new method for the chosen + problems.}, + annote = {Ju936 Times Cited:25 Cited References Count:20}, + issn = {0196-5204}, + uri = {://A1992JU93600013}, } -@Article{Bratko95, - author = {L. Blum and F. Vericat and D. Bratko}, - title = {Towards an analytical model of water: The octupolar model}, - journal = jcp, - year = 1995, - volume = 102, - number = 3, - pages = {1461-1462} +@ARTICLE{Palacios1998, + author = {J. L. Garcia-Palacios and F. J. Lazaro}, + title = {Langevin-dynamics study of the dynamical properties of small magnetic + particles}, + journal = {Physical Review B}, + year = {1998}, + volume = {58}, + pages = {14937-14958}, + number = {22}, + month = {Dec 1}, + abstract = {The stochastic Landau-Lifshitz-Gilbert equation of motion for a classical + magnetic moment is numerically solved (properly observing the customary + interpretation of it as a Stratonovich stochastic differential equation), + in order to study the dynamics of magnetic nanoparticles. The corresponding + Langevin-dynamics approach allows for the study of the fluctuating + trajectories of individual magnetic moments, where we have encountered + remarkable phenomena in the overbarrier rotation process, such as + crossing-back or multiple crossing of the potential barrier, rooted + in the gyromagnetic nature of the system. Concerning averaged quantities, + we study the linear dynamic response of the archetypal ensemble + of noninteracting classical magnetic moments with axially symmetric + magnetic anisotropy. The results are compared with different analytical + expressions used to model the relaxation of nanoparticle ensembles, + assessing their accuracy. It has been found that, among a number + of heuristic expressions for the linear dynamic susceptibility, + only the simple formula proposed by Shliomis and Stepanov matches + the coarse features of the susceptibility reasonably. By comparing + the numerical results with the asymptotic formula of Storonkin {Sov. + Phys. Crystallogr. 30, 489 (1985) [Kristallografiya 30, 841 (1985)]}, + the effects of the intra-potential-well relaxation modes on the + low-temperature longitudinal dynamic response have been assessed, + showing their relatively small reflection in the susceptibility + curves but their dramatic influence on the phase shifts. Comparison + of the numerical results with the exact zero-damping expression + for the transverse susceptibility by Garanin, Ishchenko, and Panina + {Theor. Math. Phys. (USSR) 82, 169 (1990) [Teor. Mat. Fit. 82, 242 + (1990)]}, reveals a sizable contribution of the spread of the precession + frequencies of the magnetic moment in the anisotropy field to the + dynamic response at intermediate-to-high temperatures. [S0163-1829 + (98)00446-9].}, + annote = {146XW Times Cited:66 Cited References Count:45}, + issn = {0163-1829}, + uri = {://000077460000052}, } -@Article{Ichiye03, - author = {M.-L. Tan and J.~T. Fischer and A. Chandra and B.~R. Brooks - and T. Ichiye}, - title = {A temperature of maximum density in soft sticky dipole - water}, - journal = cpl, - year = 2003, - volume = 376, - pages = {646-652}, +@ARTICLE{Pastor1988, + author = {R. W. Pastor and B. R. Brooks and A. Szabo}, + title = {An Analysis of the Accuracy of Langevin and Molecular-Dynamics Algorithms}, + journal = {Molecular Physics}, + year = {1988}, + volume = {65}, + pages = {1409-1419}, + number = {6}, + month = {Dec 20}, + annote = {T1302 Times Cited:61 Cited References Count:26}, + issn = {0026-8976}, + uri = {://A1988T130200011}, } - -@Article{Soper86, - author = {A.~K. Soper and M.~G. Phillips}, - title = {A new determination of the structure of water at 298K}, - journal = cp, - year = 1986, - volume = 107, - number = 1, - pages = {47-60}, +@ARTICLE{Pelzl1999, + author = {G. Pelzl and S. Diele and W. Weissflog}, + title = {Banana-shaped compounds - A new field of liquid crystals}, + journal = {Advanced Materials}, + year = {1999}, + volume = {11}, + pages = {707-724}, + number = {9}, + month = {Jul 5}, + annote = {220RC Times Cited:313 Cited References Count:49}, + issn = {0935-9648}, + uri = {://000081680400007}, } -@Article{plimpton95, - author = {S. Plimpton}, - title = {Fast Parallel Algorithms for Short-Range Molecular Dymanics}, - journal = {J. Comp. Phys.}, - year = 1995, - volume = 117, - pages = {1-19}, +@ARTICLE{Perram1985, + author = {J. W. Perram and M. S. Wertheim}, + title = {Statistical-Mechanics of Hard Ellipsoids .1. Overlap Algorithm and + the Contact Function}, + journal = {Journal of Computational Physics}, + year = {1985}, + volume = {58}, + pages = {409-416}, + number = {3}, + annote = {Akb93 Times Cited:71 Cited References Count:12}, + issn = {0021-9991}, + uri = {://A1985AKB9300008}, } -@Article{plimpton93, - author = {S.~J. Plimpton and B.~A. Hendrickson}, - title = {Parallel Molecular Dynamics with the Embedded Atom Method}, - journal = {MRS Proceedings}, - year = 1993, - volume = 291, - pages = 37 +@ARTICLE{Rotne1969, + author = {F. Perrin}, + title = {Variational treatment of hydrodynamic interaction in polymers}, + journal = {J. Chem. Phys.}, + year = {1969}, + volume = {50}, + pages = {4831¨C4837}, } - -@Article{Ercolessi02, - author = {U. Tartaglino and E. Tosatti and D. Passerone and F. Ercolessi}, - title = {Bending strain-driven modification of surface resconstructions: Au(111)}, - journal = prb, - year = 2002, - volume = 65, - pages = 241406 +@ARTICLE{Perrin1936, + author = {F. Perrin}, + title = {Mouvement brownien d'un ellipsoid(II). Rotation libre et depolarisation + des fluorescences. Translation et diffusion de moleculese ellipsoidales}, + journal = {J. Phys. Radium}, + year = {1936}, + volume = {7}, + pages = {1-11}, } -@Article{Ercolessi88, - author = {F. Ercolessi and M. Parrinello and E. Tosatti}, - title = {Simulation of Gold in the Glue Model.}, - journal = {Philosophical Magazine A}, - year = 1988, - volume = 58, - pages = {213-226} +@ARTICLE{Perrin1934, + author = {F. Perrin}, + title = {Mouvement brownien d'un ellipsoid(I). Dispersion dielectrique pour + des molecules ellipsoidales}, + journal = {J. Phys. Radium}, + year = {1934}, + volume = {5}, + pages = {497-511}, } -@Article{Finnis84, - author = {M.~W Finnis and J.~E. Sinclair }, - title = {A Simple Empirical N-Body Potential for Transition-Metals}, - journal = {Phil. Mag. A}, - year = 1984, - volume = 50, - pages = {45-55} +@ARTICLE{Petrache1998, + author = {H. I. Petrache and S. Tristram-Nagle and J. F. Nagle}, + title = {Fluid phase structure of EPC and DMPC bilayers}, + journal = {Chemistry and Physics of Lipids}, + year = {1998}, + volume = {95}, + pages = {83-94}, + number = {1}, + month = {Sep}, + abstract = {X-ray diffraction data taken at high instrumental resolution were + obtained for EPC and DMPC under various osmotic pressures, primarily + at T = 30 degrees C. The headgroup thickness D-HH was obtained from + relative electron density profiles. By using volumetric results + and by comparing to gel phase DPPC we obtain areas A(EPC)(F) = 69.4 + +/- 1.1 Angstrom(2) and A(DMPC)(F) = 59.7 +/- 0.2 Angstrom(2). The + analysis also gives estimates for the areal compressibility K-A. + The A(F) results lead to other structural results regarding membrane + thickness and associated waters. Using the recently determined absolute + electrons density profile of DPPC, the AF results also lead to absolute + electron density profiles and absolute continuous transforms \F(q)\ + for EPC and DMPC, Limited measurements of temperature dependence + show directly that fluctuations increase with increasing temperature + and that a small decrease in bending modulus K-c accounts for the + increased water spacing reported by Simon et al. (1995) Biophys. + J. 69, 1473-1483. (C) 1998 Elsevier Science Ireland Ltd. All rights + reserved.}, + annote = {130AT Times Cited:98 Cited References Count:39}, + issn = {0009-3084}, + uri = {://000076497600007}, } -@Article{FBD86, - author = {S.~M. Foiles and M.~I. Baskes and M.~S. Daw}, - title = {Embedded-atom-method functions for the fcc metals -$\mbox{Cu, Ag, Au, Ni, Pd, Pt}$, and their alloys}, - journal = prb, - year = 1986, - volume = 33, - number = 12, - pages = 7983 +@ARTICLE{Powles1973, + author = {J.~G. Powles}, + title = {A general ellipsoid can not always serve as a modle for the rotational + diffusion properties of arbitrary shaped rigid molecules}, + journal = {Advan. Phys.}, + year = {1973}, + volume = {22}, + pages = {1-56}, } -@Article{johnson89, - author = {R.~A. Johnson}, - title = {Alloy models with the embedded-atom method}, - journal = prb, - year = 1989, - volume = 39, - number = 17, - pages = 12554 +@ARTICLE{Recio2004, + author = {J. Fernandez-Recio and M. Totrov and R. Abagyan}, + title = {Identification of protein-protein interaction sites from docking + energy landscapes}, + journal = {Journal of Molecular Biology}, + year = {2004}, + volume = {335}, + pages = {843-865}, + number = {3}, + month = {Jan 16}, + abstract = {Protein recognition is one of the most challenging and intriguing + problems in structural biology. Despite all the available structural, + sequence and biophysical information about protein-protein complexes, + the physico-chemical patterns, if any, that make a protein surface + likely to be involved in protein-protein interactions, remain elusive. + Here, we apply protein docking simulations and analysis of the interaction + energy landscapes to identify protein-protein interaction sites. + The new protocol for global docking based on multi-start global + energy optimization of an allatom model of the ligand, with detailed + receptor potentials and atomic solvation parameters optimized in + a training set of 24 complexes, explores the conformational space + around the whole receptor without restrictions. The ensembles of + the rigid-body docking solutions generated by the simulations were + subsequently used to project the docking energy landscapes onto + the protein surfaces. We found that highly populated low-energy + regions consistently corresponded to actual binding sites. The procedure + was validated on a test set of 21 known protein-protein complexes + not used in the training set. As much as 81% of the predicted high-propensity + patch residues were located correctly in the native interfaces. + This approach can guide the design of mutations on the surfaces + of proteins, provide geometrical details of a possible interaction, + and help to annotate protein surfaces in structural proteomics. + (C) 2003 Elsevier Ltd. All rights reserved.}, + annote = {763GQ Times Cited:21 Cited References Count:59}, + issn = {0022-2836}, + uri = {://000188066900016}, } -@Article{Laird97, - author = {A. Kol and B.~B. Laird and B.~J. Leimkuhler}, - title = {A symplectic method for rigid-body molecular simulation}, - journal = jcp, - year = 1997, - volume = 107, - number = 7, - pages = {2580-2588} -} - - -@Article{hoover85, - author = {W.~G. Hoover}, - title = {Canonical dynamics: Equilibrium phase-space distributions}, - journal = pra, - year = 1985, - volume = 31, - pages = 1695 -} - -@Article{Roux91, - author = {B. Roux and M. Karplus}, - title = {Ion transport in a Gramicidin-like channel: dynamics and mobility}, - journal = jpc, - year = 1991, - volume = 95, - number = 15, - pages = {4856-4868} -} - - -@Article{Marrink94, - author = {S.~J Marrink and H.~J.~C. Berendsen}, - title = {Simulation of water transport through a lipid membrane}, - journal = jpc, - year = 1994, - volume = 98, - number = 15, - pages = {4155-4168} -} - - -@Article{Daw89, - author = {Murray~S. Daw}, - title = {Model of metallic cohesion: The embedded-atom method}, - journal = {Physical Review B}, - year = 1989, - volume = 39, - pages = {7441-7452} +@ARTICLE{Reddy2006, + author = {R. A. Reddy and C. Tschierske}, + title = {Bent-core liquid crystals: polar order, superstructural chirality + and spontaneous desymmetrisation in soft matter systems}, + journal = {Journal of Materials Chemistry}, + year = {2006}, + volume = {16}, + pages = {907-961}, + number = {10}, + abstract = {An overview on the recent developments in the field of liquid crystalline + bent-core molecules (so-called banana liquid crystals) is given. + After some basic issues, dealing with general aspects of the systematisation + of the mesophases, development of polar order and chirality in this + class of LC systems and explaining some general structure-property + relationships, we focus on fascinating new developments in this + field, such as modulated, undulated and columnar phases, so-called + B7 phases, phase biaxiality, ferroelectric and antiferroelectric + polar order in smectic and columnar phases, amplification and switching + of chirality and the spontaneous formation of superstructural and + supramolecular chirality.}, + annote = {021NS Times Cited:2 Cited References Count:316}, + issn = {0959-9428}, + uri = {://000235990500001}, } -@InBook{voter, - author = {A.~F. Voter}, - editor = {J.~H. Westbrook and R.~L. Fleischer}, - title = {Intermetallic Compounds: Principles and Practice}, - chapter = 4, - publisher = {John Wiley and Sons Ltd}, - year = 1995, - volume = 1, - pages = 77 +@ARTICLE{Reich1999, + author = {S. Reich}, + title = {Backward error analysis for numerical integrators}, + journal = {Siam Journal on Numerical Analysis}, + year = {1999}, + volume = {36}, + pages = {1549-1570}, + number = {5}, + month = {Sep 8}, + abstract = {Backward error analysis has become an important tool for understanding + the long time behavior of numerical integration methods. This is + true in particular for the integration of Hamiltonian systems where + backward error analysis can be used to show that a symplectic method + will conserve energy over exponentially long periods of time. Such + results are typically based on two aspects of backward error analysis: + (i) It can be shown that the modified vector fields have some qualitative + properties which they share with the given problem and (ii) an estimate + is given for the difference between the best interpolating vector + field and the numerical method. These aspects have been investigated + recently, for example, by Benettin and Giorgilli in [J. Statist. + Phys., 74 (1994), pp. 1117-1143], by Hairer in [Ann. Numer. Math., + 1 (1994), pp. 107-132], and by Hairer and Lubich in [Numer. Math., + 76 (1997), pp. 441-462]. In this paper we aim at providing a unifying + framework and a simplification of the existing results and corresponding + proofs. Our approach to backward error analysis is based on a simple + recursive definition of the modified vector fields that does not + require explicit Taylor series expansion of the numerical method + and the corresponding flow maps as in the above-cited works. As + an application we discuss the long time integration of chaotic Hamiltonian + systems and the approximation of time averages along numerically + computed trajectories.}, + annote = {237HV Times Cited:43 Cited References Count:41}, + issn = {0036-1429}, + uri = {://000082650600010}, } -@Article{marrink:2002, - author = {S.~J. Marrink and D.~P. Teileman}, - title = {Molecular Dynamics Simulation of Spontaneous Membrane Fusion during a Cubic-Hexagonal Phase Transition}, - journal = {Biophysical Journal}, - year = 2002, - volume = 83, - pages = {2386-2392} +@ARTICLE{Ros2005, + author = {M. B. Ros and J. L. Serrano and M. R. {de la Fuente} and C. L. Folcia}, + title = {Banana-shaped liquid crystals: a new field to explore}, + journal = {Journal of Materials Chemistry}, + year = {2005}, + volume = {15}, + pages = {5093-5098}, + number = {48}, + abstract = {The recent literature in the field of liquid crystals shows that banana-shaped + mesogenic materials represent a bewitching and stimulating field + of research that is interesting both academically and in terms of + applications. Numerous topics are open to investigation in this + area because of the rich phenomenology and new possibilities that + these materials offer. The principal concepts in this area are reviewed + along with recent results. In addition, new directions to stimulate + further research activities are highlighted.}, + annote = {990XA Times Cited:3 Cited References Count:72}, + issn = {0959-9428}, + uri = {://000233775500001}, } -@Article{sum:2003, - author = {A.~K. Sum and J.~J. de~Pablo}, - title = {Molecular Simulation Study on the influence of Dimethylsulfoxide on the structure of Phospholipid Bilayers}, - journal = {Biophysical Journal}, - year = 2003, - volume = 85, - pages = {3636-3645} +@ARTICLE{Roux1991, + author = {B. Roux and M. Karplus}, + title = {Ion-Transport in a Gramicidin-Like Channel - Dynamics and Mobility}, + journal = {Journal of Physical Chemistry}, + year = {1991}, + volume = {95}, + pages = {4856-4868}, + number = {12}, + month = {Jun 13}, + abstract = {The mobility of water, Na+. and K+ has been calculated inside a periodic + poly-(L,D)-alanine beta-helix, a model for the interior of the gramicidin + channel. Because of the different dynamical regimes for the three + species (high barrier for Na+, low barrier for K+, almost free diffusion + for water), different methods are used to calculate the mobilities. + By use of activated dynamics and a potential of mean force determined + previously (Roux, B.; Karplus, M. Biophys. J. 1991, 59, 961), the + barrier crossing rate of Na+ ion is determined. The motion of Na+ + at the transition state is controlled by local interactions and + collisions with the neighboring carbonyls and the two nearest water + molecules. There are significant deviations from transition-state + theory; the transmission coefficient is equal to 0.11. The water + and K+ motions are found to be well described by a diffusive model; + the motion of K+ appears to be controlled by the diffusion of water. + The time-dependent friction functions of Na+ and K+ ions in the + periodic beta-helix are calculated and analyzed by using a generalized + Langevin equation approach. Both Na+ and K+ suffer many rapid collisions, + and their dynamics is overdamped and noninertial. Thus, the selectivity + sequence of ions in the beta-helix is not influenced strongly by + their masses.}, + annote = {Fr756 Times Cited:97 Cited References Count:65}, + issn = {0022-3654}, + uri = {://A1991FR75600049}, } -@Article{gomez:2003, - author = {J.~D. Faraldo-Gomez and G.~R. Smith and M.~S.P. Sansom}, - title = {Setting up and optimization of membrane protein simulations}, - journal = {Eur. Biophys. J.}, - year = 2002, - volume = 31, - pages = {217-227} +@ARTICLE{Roy2005, + author = {A. Roy and N. V. Madhusudana}, + title = {A frustrated packing model for the B-6-B-1-SmAP(A) sequence of phases + in banana shaped molecules}, + journal = {European Physical Journal E}, + year = {2005}, + volume = {18}, + pages = {253-258}, + number = {3}, + month = {Nov}, + abstract = {A vast majority of compounds with bent core or banana shaped molecules + exhibit the phase sequence B-6-B-1-B-2 as the chain length is increased + in a homologous series. The B-6 phase has an intercalated fluid + lamellar structure with a layer spacing of half the molecular length. + The B-1 phase has a two dimensionally periodic rectangular columnar + structure. The B-2 phase has a monolayer fluid lamellar structure + with molecules tilted with respect to the layer normal. Neglecting + the tilt order of the molecules in the B-2 phase, we have developed + a frustrated packing model to describe this phase sequence qualitatively. + The model has some analogy with that of the frustrated smectics + exhibited by highly polar rod like molecules.}, + annote = {985FW Times Cited:0 Cited References Count:30}, + issn = {1292-8941}, + uri = {://000233363300002}, } - -@Article{smondyrev:1999, - author = {A.~M. Smondyrev and M.~L. Berkowitz}, - title = {Molecular Dynamics Simulation of {\sc dppc} Bilayer in {\sc dmso}}, - journal = {Biophysical Journal}, - year = 1999, - volume = 76, - pages = {2472-2478} +@ARTICLE{Ryckaert1977, + author = {J. P. Ryckaert and G. Ciccotti and H. J. C. Berendsen}, + title = {Numerical-Integration of Cartesian Equations of Motion of a System + with Constraints - Molecular-Dynamics of N-Alkanes}, + journal = {Journal of Computational Physics}, + year = {1977}, + volume = {23}, + pages = {327-341}, + number = {3}, + annote = {Cz253 Times Cited:3680 Cited References Count:7}, + issn = {0021-9991}, + uri = {://A1977CZ25300007}, } -@Article{nina:2002, - author = {M. Nina and T. Simonson}, - title = {Molecular Dynamics of the $\text{tRNA}^{\text{Ala}}$ Acceptor Stem: Comparison between Continuum Reaction Field and Particle-Mesh Ewald Electrostatic Treatments}, - journal = {J. Phys. Chem. B}, - year = 2002, - volume = 106, - pages = {3696-3705} +@ARTICLE{Sagui1999, + author = {C. Sagui and T. A. Darden}, + title = {Molecular dynamics simulations of biomolecules: Long-range electrostatic + effects}, + journal = {Annual Review of Biophysics and Biomolecular Structure}, + year = {1999}, + volume = {28}, + pages = {155-179}, + abstract = {Current computer simulations of biomolecules typically make use of + classical molecular dynamics methods, as a very large number (tens + to hundreds of thousands) of atoms are involved over timescales + of many nanoseconds. The methodology for treating short-range bonded + and van der Waals interactions has matured. However, long-range + electrostatic interactions still represent a bottleneck in simulations. + In this article, we introduce the basic issues for an accurate representation + of the relevant electrostatic interactions. In spite of the huge + computational time demanded by most biomolecular systems, it is + no longer necessary to resort to uncontrolled approximations such + as the use of cutoffs. In particular, we discuss the Ewald summation + methods, the fast particle mesh methods, and the fast multipole + methods. We also review recent efforts to understand the role of + boundary conditions in systems with long-range interactions, and + conclude with a short perspective on future trends.}, + annote = {213KJ Times Cited:126 Cited References Count:73}, + issn = {1056-8700}, + uri = {://000081271400008}, } -@Article{norberg:2000, - author = {J. Norberg and L. Nilsson}, - title = {On the truncation of Long-Range Electrostatic Interactions in {\sc dna}}, - journal = {Biophysical Journal}, - year = 2000, - volume = 79, - pages = {1537-1553} +@ARTICLE{Sandu1999, + author = {A. Sandu and T. Schlick}, + title = {Masking resonance artifacts in force-splitting methods for biomolecular + simulations by extrapolative Langevin dynamics}, + journal = {Journal of Computational Physics}, + year = {1999}, + volume = {151}, + pages = {74-113}, + number = {1}, + month = {May 1}, + abstract = {Numerical resonance artifacts have become recognized recently as a + limiting factor to increasing the timestep in multiple-timestep + (MTS) biomolecular dynamics simulations. At certain timesteps correlated + to internal motions (e.g., 5 fs, around half the period of the fastest + bond stretch, T-min), visible inaccuracies or instabilities can + occur. Impulse-MTS schemes are vulnerable to these resonance errors + since large energy pulses are introduced to the governing dynamics + equations when the slow forces are evaluated. We recently showed + that such resonance artifacts can be masked significantly by applying + extrapolative splitting to stochastic dynamics. Theoretical and + numerical analyses of force-splitting integrators based on the Verlet + discretization are reported here for linear models to explain these + observations and to suggest how to construct effective integrators + for biomolecular dynamics that balance stability with accuracy. + Analyses for Newtonian dynamics demonstrate the severe resonance + patterns of the Impulse splitting, with this severity worsening + with the outer timestep. Delta t: Constant Extrapolation is generally + unstable, but the disturbances do not grow with Delta t. Thus. the + stochastic extrapolative combination can counteract generic instabilities + and largely alleviate resonances with a sufficiently strong Langevin + heat-bath coupling (gamma), estimates for which are derived here + based on the fastest and slowest motion periods. These resonance + results generally hold for nonlinear test systems: a water tetramer + and solvated protein. Proposed related approaches such as Extrapolation/Correction + and Midpoint Extrapolation work better than Constant Extrapolation + only for timesteps less than T-min/2. An effective extrapolative + stochastic approach for biomolecules that balances long-timestep + stability with good accuracy for the fast subsystem is then applied + to a biomolecule using a three-class partitioning: the medium forces + are treated by Midpoint Extrapolation via position Verlet, and the + slow forces are incorporated by Constant Extrapolation. The resulting + algorithm (LN) performs well on a solvated protein system in terms + of thermodynamic properties and yields an order of magnitude speedup + with respect to single-timestep Langevin trajectories. Computed + spectral density functions also show how the Newtonian modes can + be approximated by using a small gamma in the range Of 5-20 ps(-1). + (C) 1999 Academic Press.}, + annote = {194FM Times Cited:14 Cited References Count:32}, + issn = {0021-9991}, + uri = {://000080181500004}, } -@Article{patra:2003, - author = {M. Patra and M. Karttunen and M.~T. Hyv\"{o}nen and E. Falk and P. Lindqvist and I. Vattulainen}, - title = {Molecular Dynamics Simulations of Lipid Bilayers: Major Artifacts Due to Truncating Electrostatic Interactions}, - journal = {Biophysical Journal}, - year = 2003, - volume = 84, - pages = {3636-3645} +@ARTICLE{Sasaki2004, + author = {Y. Sasaki and R. Shukla and B. D. Smith}, + title = {Facilitated phosphatidylserine flip-flop across vesicle and cell + membranes using urea-derived synthetic translocases}, + journal = {Organic \& Biomolecular Chemistry}, + year = {2004}, + volume = {2}, + pages = {214-219}, + number = {2}, + abstract = {Tris(2-aminoethyl) amine derivatives with appended urea and sulfonamide + groups are shown to facilitate the translocation of fluorescent + phospholipid probes and endogenous phosphatidylserine across vesicle + and erythrocyte cell membranes. The synthetic translocases appear + to operate by binding to the phospholipid head groups and forming + lipophilic supramolecular complexes which diffuse through the non-polar + interior of the bilayer membrane.}, + annote = {760PX Times Cited:8 Cited References Count:25}, + issn = {1477-0520}, + uri = {://000187843800012}, } -@Article{marrink04, - author = {S.~J. Marrink and A.~H. de~Vries and A.~E. Mark}, - title = {Coarse Grained Model for Semiquantitative Lipid Simulations}, - journal = {J. Phys. Chem. B}, - year = 2004, - volume = 108, - pages = {750-760} +@ARTICLE{Satoh1996, + author = {K. Satoh and S. Mita and S. Kondo}, + title = {Monte Carlo simulations using the dipolar Gay-Berne model: Effect + of terminal dipole moment on mesophase formation}, + journal = {Chemical Physics Letters}, + year = {1996}, + volume = {255}, + pages = {99-104}, + number = {1-3}, + month = {Jun 7}, + abstract = {The effects of dipole-dipole interaction on mesophase formation are + investigated with a Monte Carlo simulation using the dipolar Gay-Berne + potential. It is shown that the dipole moment at the end of a molecule + causes a shift in the nematic-isotropic transition toward higher + temperature and a spread of the temperature range of the nematic + phase and that layer structures with various interdigitations are + formed in the smectic phase.}, + annote = {Uq975 Times Cited:32 Cited References Count:33}, + issn = {0009-2614}, + uri = {://A1996UQ97500017}, } -@Article{andersen83, - author = {H.~C. Andersen}, - title = {{\sc rattle}: A Velocity Version of the Shake Algorithm for Molecular Dynamics Calculations}, - journal = {Journal of Computational Physics}, - year = 1983, - volume = 52, - pages = {24-34} +@ARTICLE{Shen2002, + author = {M. Y. Shen and K. F. Freed}, + title = {Long time dynamics of met-enkephalin: Comparison of explicit and + implicit solvent models}, + journal = {Biophysical Journal}, + year = {2002}, + volume = {82}, + pages = {1791-1808}, + number = {4}, + month = {Apr}, + abstract = {Met-enkephalin is one of the smallest opiate peptides. Yet, its dynamical + structure and receptor docking mechanism are still not well understood. + The conformational dynamics of this neuron peptide in liquid water + are studied here by using all-atom molecular dynamics (MID) and + implicit water Langevin dynamics (LD) simulations with AMBER potential + functions and the three-site transferable intermolecular potential + (TIP3P) model for water. To achieve the same simulation length in + physical time, the full MID simulations require 200 times as much + CPU time as the implicit water LID simulations. The solvent hydrophobicity + and dielectric behavior are treated in the implicit solvent LD simulations + by using a macroscopic solvation potential, a single dielectric + constant, and atomic friction coefficients computed using the accessible + surface area method with the TIP3P model water viscosity as determined + here from MID simulations for pure TIP3P water. Both the local and + the global dynamics obtained from the implicit solvent LD simulations + agree very well with those from the explicit solvent MD simulations. + The simulations provide insights into the conformational restrictions + that are associated with the bioactivity of the opiate peptide dermorphin + for the delta-receptor.}, + annote = {540MH Times Cited:36 Cited References Count:45}, + issn = {0006-3495}, + uri = {://000174932400010}, } -@Article{hura00, - author = {G. Hura and J.~M. Sorenson and R.~M. Glaeser and T. Head-Gordon}, - title = {A high-quality x-ray scattering experiment on liquid water at ambient conditions}, - journal = {J. Chem. Phys.}, - year = 2000, - volume = 113, - pages = {9140-9148} +@ARTICLE{Shillcock2005, + author = {J. C. Shillcock and R. Lipowsky}, + title = {Tension-induced fusion of bilayer membranes and vesicles}, + journal = {Nature Materials}, + year = {2005}, + volume = {4}, + pages = {225-228}, + number = {3}, + month = {Mar}, + annote = {901QJ Times Cited:9 Cited References Count:23}, + issn = {1476-1122}, + uri = {://000227296700019}, } - -@Article{ryckaert77, - author = {J.~P. Ryckaert and G. Ciccotti and H.~J.~C. Berendsen}, - title = {Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes}, - journal = {Journal of Computational Physics}, - year = 1977, - volume = 23, - pages = {327-341} +@ARTICLE{Shimada1993, + author = {J. Shimada and H. Kaneko and T. Takada}, + title = {Efficient Calculations of Coulombic Interactions in Biomolecular + Simulations with Periodic Boundary-Conditions}, + journal = {Journal of Computational Chemistry}, + year = {1993}, + volume = {14}, + pages = {867-878}, + number = {7}, + month = {Jul}, + abstract = {To make improved treatments of electrostatic interactions in biomacromolecular + simulations, two possibilities are considered. The first is the + famous particle-particle and particle-mesh (PPPM) method developed + by Hockney and Eastwood, and the second is a new one developed here + in their spirit but by the use of the multipole expansion technique + suggested by Ladd. It is then numerically found that the new PPPM + method gives more accurate results for a two-particle system at + small separation of particles. Preliminary numerical examination + of the various computational methods for a single configuration + of a model BPTI-water system containing about 24,000 particles indicates + that both of the PPPM methods give far more accurate values with + reasonable computational cost than do the conventional truncation + methods. It is concluded the two PPPM methods are nearly comparable + in overall performance for the many-particle systems, although the + first method has the drawback that the accuracy in the total electrostatic + energy is not high for configurations of charged particles randomly + generated.}, + annote = {Lh164 Times Cited:27 Cited References Count:47}, + issn = {0192-8651}, + uri = {://A1993LH16400011}, } - -@InBook{fowles99:lagrange, - author = {G.~R. Fowles and G.~L. Cassiday}, - title = {Analytical Mechanics}, - chapter = 10, - publisher = {Saunders College Publishing}, - year = 1999, - edition = {6th} +@ARTICLE{Skeel2002, + author = {R. D. Skeel and J. A. Izaguirre}, + title = {An impulse integrator for Langevin dynamics}, + journal = {Molecular Physics}, + year = {2002}, + volume = {100}, + pages = {3885-3891}, + number = {24}, + month = {Dec 20}, + abstract = {The best simple method for Newtonian molecular dynamics is indisputably + the leapfrog Stormer-Verlet method. The appropriate generalization + to simple Langevin dynamics is unclear. An analysis is presented + comparing an 'impulse method' (kick; fluctuate; kick), the 1982 + method of van Gunsteren and Berendsen, and the Brunger-Brooks-Karplus + (BBK) method. It is shown how the impulse method and the van Gunsteren-Berendsen + methods can be implemented as efficiently as the BBK method. Other + considerations suggest that the impulse method is the best basic + method for simple Langevin dynamics, with the van Gunsteren-Berendsen + method a close contender.}, + annote = {633RX Times Cited:8 Cited References Count:22}, + issn = {0026-8976}, + uri = {://000180297200014}, } -@Article{petrache00, - author = {H.~I. Petrache and S.~W. Dodd and M.~F. Brown}, - title = {Area per Lipid and Acyl Length Distributions in Fluid Phosphatidylcholines Determined by $^2\text{H}$ {\sc nmr} Spectroscopy}, - journal = {Biophysical Journal}, - year = 2000, - volume = 79, - pages = {3172-3192} +@ARTICLE{Skeel1997, + author = {R. D. Skeel and G. H. Zhang and T. Schlick}, + title = {A family of symplectic integrators: Stability, accuracy, and molecular + dynamics applications}, + journal = {Siam Journal on Scientific Computing}, + year = {1997}, + volume = {18}, + pages = {203-222}, + number = {1}, + month = {Jan}, + abstract = {The following integration methods for special second-order ordinary + differential equations are studied: leapfrog, implicit midpoint, + trapezoid, Stormer-Verlet, and Cowell-Numerov. We show that all + are members, or equivalent to members, of a one-parameter family + of schemes. Some methods have more than one common form, and we + discuss a systematic enumeration of these forms. We also present + a stability and accuracy analysis based on the idea of ''modified + equations'' and a proof of symplecticness. It follows that Cowell-Numerov + and ''LIM2'' (a method proposed by Zhang and Schlick) are symplectic. + A different interpretation of the values used by these integrators + leads to higher accuracy and better energy conservation. Hence, + we suggest that the straightforward analysis of energy conservation + is misleading.}, + annote = {We981 Times Cited:30 Cited References Count:35}, + issn = {1064-8275}, + uri = {://A1997WE98100012}, } -@Article{egberts88, - author = {E. Egberts and H.~J.~C. Berendsen}, - title = {Molecular Dynamics Simulation of a smectic liquid crystal with atomic detail}, - journal = {J. Chem. Phys.}, - year = 1988, - volume = 89, - pages = {3718-3732} +@ARTICLE{Tao2005, + author = {Y. G. Tao and W. K. {den Otter} and J. T. Padding and J. K. G. Dhont + and W. J. Briels}, + title = {Brownian dynamics simulations of the self- and collective rotational + diffusion coefficients of rigid long thin rods}, + journal = {Journal of Chemical Physics}, + year = {2005}, + volume = {122}, + pages = {-}, + number = {24}, + month = {Jun 22}, + abstract = {Recently a microscopic theory for the dynamics of suspensions of long + thin rigid rods was presented, confirming and expanding the well-known + theory by Doi and Edwards [The Theory of Polymer Dynamics (Clarendon, + Oxford, 1986)] and Kuzuu [J. Phys. Soc. Jpn. 52, 3486 (1983)]. Here + this theory is put to the test by comparing it against computer + simulations. A Brownian dynamics simulation program was developed + to follow the dynamics of the rods, with a length over a diameter + ratio of 60, on the Smoluchowski time scale. The model accounts + for excluded volume interactions between rods, but neglects hydrodynamic + interactions. The self-rotational diffusion coefficients D-r(phi) + of the rods were calculated by standard methods and by a new, more + efficient method based on calculating average restoring torques. + Collective decay of orientational order was calculated by means + of equilibrium and nonequilibrium simulations. Our results show + that, for the currently accessible volume fractions, the decay times + in both cases are virtually identical. Moreover, the observed decay + of diffusion coefficients with volume fraction is much quicker than + predicted by the theory, which is attributed to an oversimplification + of dynamic correlations in the theory. (c) 2005 American Institute + of Physics.}, + annote = {943DN Times Cited:3 Cited References Count:26}, + issn = {0021-9606}, + uri = {://000230332400077}, } -@Article{Holz00, - author = {M. Holz and S.~R. Heil and A. Sacco}, - title = {Temperature-dependent self-diffusion coefficients of - water and six selected molecular liquids for calibration - in accurate $^1${\sc h} {\sc nmr pfg} measurements}, - journal = {Phys. Chem. Chem. Phys.}, - year = 2000, - volume = 2, - pages = {4740-4742}, +@BOOK{Tolman1979, + title = {The Principles of Statistical Mechanics}, + publisher = {Dover Publications, Inc.}, + year = {1979}, + author = {R.~C. Tolman}, + address = {New York}, + chapter = {2}, + pages = {19-22}, } -@InCollection{zannoni94, - author = {C. Zannoni}, - title = {An introduction to the molecular dynamics method and to orientational dynamics in liquid crystals}, - booktitle = {The Molecular Dynamics of Liquid Crstals}, - pages = {139-169}, - publisher = {Kluwer Academic Publishers}, - year = 1994, - editor = {G.~R. Luckhurst and C.~A. Veracini}, - chapter = 6 +@ARTICLE{Tu1995, + author = {K. Tu and D. J. Tobias and M. L. Klein}, + title = {Constant pressure and temperature molecular dynamics simulation of + a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine + bilayer}, + journal = {Biophysical Journal}, + year = {1995}, + volume = {69}, + pages = {2558-2562}, + number = {6}, + month = {Dec}, + abstract = {We report a constant pressure and temperature molecular dynamics simulation + of a fully hydrated liquid crystal (L(alpha) phase bilayer of dipalmitoylphosphatidylcholine + at 50 degrees C and 28 water molecules/lipid. We have shown that + the bilayer is stable throughout the 1550-ps simulation and have + demonstrated convergence of the system dimensions. Several important + aspects of the bilayer structure have been investigated and compared + favorably with experimental results. For example, the average positions + of specific carbon atoms along the bilayer normal agree well with + neutron diffraction data, and the electron density profile is in + accord with x-ray diffraction results. The hydrocarbon chain deuterium + order parameters agree reasonably well with NMR results for the + middles of the chains, but the simulation predicts too much order + at the chain ends. In spite of the deviations in the order parameters, + the hydrocarbon chain packing density appears to be essentially + correct, inasmuch as the area/lipid and bilayer thickness are in + agreement with the most refined experimental estimates. The deuterium + order parameters for the glycerol and choline groups, as well as + the phosphorus chemical shift anisotropy, are in qualitative agreement + with those extracted from NMR measurements.}, + annote = {Tv018 Times Cited:108 Cited References Count:34}, + issn = {0006-3495}, + uri = {://A1995TV01800037}, } - -@Article{melchionna93, - author = {S. Melchionna and G. Ciccotti and B.~L. Holian}, - title = {Hoover {\sc npt} dynamics for systems varying in shape and size}, - journal = {Molecular Physics}, - year = 1993, - volume = 78, - pages = {533-544} +@ARTICLE{Tuckerman1992, + author = {M. Tuckerman and B. J. Berne and G. J. Martyna}, + title = {Reversible Multiple Time Scale Molecular-Dynamics}, + journal = {Journal of Chemical Physics}, + year = {1992}, + volume = {97}, + pages = {1990-2001}, + number = {3}, + month = {Aug 1}, + abstract = {The Trotter factorization of the Liouville propagator is used to generate + new reversible molecular dynamics integrators. This strategy is + applied to derive reversible reference system propagator algorithms + (RESPA) that greatly accelerate simulations of systems with a separation + of time scales or with long range forces. The new algorithms have + all of the advantages of previous RESPA integrators but are reversible, + and more stable than those methods. These methods are applied to + a set of paradigmatic systems and are shown to be superior to earlier + methods. It is shown how the new RESPA methods are related to predictor-corrector + integrators. Finally, we show how these methods can be used to accelerate + the integration of the equations of motion of systems with Nose + thermostats.}, + annote = {Je891 Times Cited:680 Cited References Count:19}, + issn = {0021-9606}, + uri = {://A1992JE89100044}, } -@Article{fennell04, - author = {C.~J. Fennell and J.~D. Gezelter}, - title = {On the structural and transport properties of the soft sticky dipole(SSD) and related single point water models}, - journal = {J. Chem. Phys}, - year = {in press 2004} +@BOOK{Varadarajan1974, + title = {Lie groups, Lie algebras, and their representations}, + publisher = {Prentice-Hall}, + year = {1974}, + author = {V.S. Varadarajan}, + address = {New York}, } -@Article{klein01, - author = {J.~C. Shelley andf M.~Y. Shelley and R.~C. Reeder and S. Bandyopadhyay and M.~L. Klein}, - title = {A coarse Grain Model for Phospholipid Simulations}, - journal = {J. Phys. Chem. B}, - year = 2001, - volume = 105, - pages = {4464-4470} +@ARTICLE{Wegener1979, + author = {W.~A. Wegener, V.~J. Koester and R.~M. Dowben}, + title = {A general ellipsoid can not always serve as a modle for the rotational + diffusion properties of arbitrary shaped rigid molecules}, + journal = {Proc. Natl. Acad. Sci.}, + year = {1979}, + volume = {76}, + pages = {6356-6360}, + number = {12}, } - -@Article{marrink03:vesicles, - author = {S.~J. Marrink and A.~E. Mark}, - title = {Molecular Dynaimcs Simulation of the Formation, Structure, and Dynamics of Small Phospholipid Vesicles}, - journal = {J. Am. Chem. Soc.}, - year = 2003, - volume = 125, - pages = {15233-15242} +@ARTICLE{Wilson2006, + author = {G.~V. Wilson }, + title = {Where's the Real Bottleneck in Scientific Computing?}, + journal = {American Scientist}, + year = {2006}, + volume = {94}, } -@Book{gamma94, - author = {E. Gamma, R. Helm, R. Johnson and J. Vlissides}, - title = {Design Patterns: Elements of Reusable Object-Oriented Software}, - chapter = 7, - publisher = {Perason Education}, - year = 1994, - address = {London}, - pages = {199-206} +@ARTICLE{Withers2003, + author = {I. M. Withers}, + title = {Effects of longitudinal quadrupoles on the phase behavior of a Gay-Berne + fluid}, + journal = {Journal of Chemical Physics}, + year = {2003}, + volume = {119}, + pages = {10209-10223}, + number = {19}, + month = {Nov 15}, + abstract = {The effects of longitudinal quadrupole moments on the formation of + liquid crystalline phases are studied by means of constant NPT Monte + Carlo simulation methods. The popular Gay-Berne model mesogen is + used as the reference fluid, which displays the phase sequences + isotropic-smectic A-smectic B and isotropic-smectic B at high (T*=2.0) + and low (T*=1.5) temperatures, respectively. With increasing quadrupole + magnitude the smectic phases are observed to be stabilized with + respect to the isotropic liquid, while the smectic B is destabilized + with respect to the smectic A. At the lower temperature, a sufficiently + large quadrupole magnitude results in the injection of the smectic + A phase into the phase sequence and the replacement of the smectic + B phase by the tilted smectic J phase. The nematic phase is also + injected into the phase sequence at both temperatures considered, + and ultimately for sufficiently large quadrupole magnitudes no coherent + layered structures were observed. The stabilization of the smectic + A phase supports the commonly held belief that, while the inclusion + of polar groups is not a prerequisite for the formation of the smectic + A phase, quadrupolar interactions help to increase the temperature + and pressure range for which the smectic A phase is observed. The + quality of the layered structure is worsened with increasing quadrupole + magnitude. This behavior, along with the injection of the nematic + phase into the phase sequence, indicate that the general tendency + of the quadrupolar interactions is to destabilize the layered structure. + A pressure dependence upon the smectic layer spacing is observed. + This behavior is in much closer agreement with experimental findings + than has been observed previously for nonpolar Gay-Berne and hard + spherocylinder models. (C) 2003 American Institute of Physics.}, + annote = {738EF Times Cited:3 Cited References Count:43}, + issn = {0021-9606}, + uri = {://000186273200027}, } -@Book{alexander, - author = {C. Alexander}, - title = {A Pattern Language: Towns, Buildings, Construction}, - publisher = {Oxford University Press}, - year = 1987, - address = {New York} +@ARTICLE{Wolf1999, + author = {D. Wolf and P. Keblinski and S. R. Phillpot and J. Eggebrecht}, + title = {Exact method for the simulation of Coulombic systems by spherically + truncated, pairwise r(-1) summation}, + journal = {Journal of Chemical Physics}, + year = {1999}, + volume = {110}, + pages = {8254-8282}, + number = {17}, + month = {May 1}, + abstract = {Based on a recent result showing that the net Coulomb potential in + condensed ionic systems is rather short ranged, an exact and physically + transparent method permitting the evaluation of the Coulomb potential + by direct summation over the r(-1) Coulomb pair potential is presented. + The key observation is that the problems encountered in determining + the Coulomb energy by pairwise, spherically truncated r(-1) summation + are a direct consequence of the fact that the system summed over + is practically never neutral. A simple method is developed that + achieves charge neutralization wherever the r(-1) pair potential + is truncated. This enables the extraction of the Coulomb energy, + forces, and stresses from a spherically truncated, usually charged + environment in a manner that is independent of the grouping of the + pair terms. The close connection of our approach with the Ewald + method is demonstrated and exploited, providing an efficient method + for the simulation of even highly disordered ionic systems by direct, + pairwise r(-1) summation with spherical truncation at rather short + range, i.e., a method which fully exploits the short-ranged nature + of the interactions in ionic systems. The method is validated by + simulations of crystals, liquids, and interfacial systems, such + as free surfaces and grain boundaries. (C) 1999 American Institute + of Physics. [S0021-9606(99)51517-1].}, + annote = {189PD Times Cited:70 Cited References Count:34}, + issn = {0021-9606}, + uri = {://000079913000008}, } -@Article{wilson, - author = {G.~V. Wilson }, - title = {Where's the Real Bottleneck in Scientific Computing?}, - journal = {American Scientist}, - year = 2006, - volume = 94 +@ARTICLE{Yoshida1990, + author = {H. Yoshida}, + title = {Construction of Higher-Order Symplectic Integrators}, + journal = {Physics Letters A}, + year = {1990}, + volume = {150}, + pages = {262-268}, + number = {5-7}, + month = {Nov 12}, + annote = {Ej798 Times Cited:492 Cited References Count:9}, + issn = {0375-9601}, + uri = {://A1990EJ79800009}, } -@article{Meineke05, - Author = {M.~A. Meineke and C.~F. {Vardeman II} and T. Lin and C.~J. Fennell and J.~D. Gezelter}, - Date-Modified = {2006-03-05 12:37:31 -0500}, - Journal = {J. Comp. Chem.}, - Local-Url = {file://localhost/Users/cfennell/Documents/pdf_files/MyPapers/Meineke_OOPSE_05.pdf}, - Pages = {252-271}, - Title = {OOPSE: An Open Source Object-Oriented Parallel Simulation Engine for Molecular Dynamics}, - Volume = 26, - Year = 2005 -}