The Simulation of Ionic Charge Transport in Biological Ion Channels: An Introduction to Numerical Methods
暂无分享,去创建一个
[1] J. C. Poggendorf. Annalen der Physik und Chemie , 1829 .
[2] M. Muir. Physical Chemistry , 1888, Nature.
[3] G. G. Stokes. "J." , 1890, The New Yale Book of Quotations.
[4] P. P. Ewald. Die Berechnung optischer und elektrostatischer Gitterpotentiale , 1921 .
[5] E. M.,et al. Statistical Mechanics , 2021, Manual for Theoretical Chemistry.
[6] F. Young. Biochemistry , 1955, The Indian Medical Gazette.
[7] A. Booth. Numerical Methods , 1957, Nature.
[8] C. Q. Lee,et al. The Computer Journal , 1958, Nature.
[9] B. A. Carré,et al. The Determination of the Optimum Accelerating Factor for Successive Over-relaxation , 1961, Comput. J..
[10] G. V. Chester,et al. Solid-State Physics , 1962, Nature.
[11] B. B. Owen,et al. The Physical Chemistry of Electrolytic Solutions , 1963 .
[12] H. Gummel. A self-consistent iterative scheme for one-dimensional steady state transistor calculations , 1964 .
[13] R. Korotev. Method , 1966, Understanding Religion.
[14] R. P. Bell,et al. Modern Electrochemistry , 1966, Nature.
[15] R W Hockney,et al. Computer Simulation Using Particles , 1966 .
[16] Stuart A. Rice,et al. The Statistical Mechanics of Simple Liquids , 1966 .
[17] L. Verlet. Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules , 1967 .
[18] B. F. Oscillator. Large-Signal Analysis of a Silicon Read Diode Oscillator , 1969 .
[19] H. Gummel,et al. Large-signal analysis of a silicon Read diode oscillator , 1969 .
[20] D. A. Dunnett. Classical Electrodynamics , 2020, Nature.
[21] Harold L. Friedman,et al. Study of a Refined Model for Aqueous 1‐1 Electrolytes , 1971 .
[22] D. Urry. The gramicidin A transmembrane channel: a proposed pi(L,D) helix. , 1971, Proceedings of the National Academy of Sciences of the United States of America.
[23] Louis A. Hageman,et al. Iterative Solution of Large Linear Systems. , 1971 .
[24] Åke Björck,et al. Numerical Methods , 1995, Handbook of Marine Craft Hydrodynamics and Motion Control.
[25] D. Ermak. A computer simulation of charged particles in solution. I. Technique and equilibrium properties , 1975 .
[26] B. Sakmann,et al. Single-channel currents recorded from membrane of denervated frog muscle fibres , 1976, Nature.
[27] Harold L. Friedman,et al. Brownian dynamics: Its application to ionic solutions , 1977 .
[28] D. Brandt,et al. Multi-level adaptive solutions to boundary-value problems math comptr , 1977 .
[29] G. Torrie,et al. Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling , 1977 .
[30] H. Grubin. The physics of semiconductor devices , 1979, IEEE Journal of Quantum Electronics.
[31] Achi Brandt,et al. Multigrid solvers on parallel computers , 1981 .
[32] H. Berendsen,et al. Interaction Models for Water in Relation to Protein Hydration , 1981 .
[33] D. Heyes,et al. Electrostatic potentials and fields in infinite point charge lattices , 1981 .
[34] L. Ehrlich. An Ad Hoc SOR Method , 1981 .
[35] Martin H. Schultz,et al. Elliptic problem solvers , 1981 .
[36] Electrostatic modeling of ion pores. Energy barriers and electric field profiles. , 1982, Biophysical journal.
[37] W. L. Jorgensen. Revised TIPS for simulations of liquid water and aqueous solutions , 1982 .
[38] W. L. Jorgensen,et al. Comparison of simple potential functions for simulating liquid water , 1983 .
[39] Peter C. Jordan. Electrostatic modeling of ion pores. II. Effects attributable to the membrane dipole potential. , 1983, Biophysical journal.
[40] S. Swain. Handbook of Stochastic Methods for Physics, Chemistry and the Natural Sciences , 1984 .
[41] Peter C. Jordan,et al. Molecular dynamics simulation of cation motion in water-filled gramicidinlike pores. , 1984, Biophysical journal.
[42] H. Berendsen,et al. A consistent empirical potential for water–protein interactions , 1984 .
[43] G. Baccarani,et al. An investigation of steady-state velocity overshoot in silicon , 1985 .
[44] D. Levitt. Strong electrolyte continuum theory solution for equilibrium profiles, diffusion limitation, and conductance in charged ion channels. , 1985, Biophysical journal.
[45] C. W. Gardiner,et al. Handbook of stochastic methods - for physics, chemistry and the natural sciences, Second Edition , 1986, Springer series in synergetics.
[46] C. Birdsall,et al. Plasma Physics via Computer Simulation , 2018 .
[47] Michael A. Wilson,et al. Molecular dynamics test of the Brownian description of Na+ motion in water , 1985 .
[48] Wolfgang Hackbusch,et al. Multi-grid methods and applications , 1985, Springer series in computational mathematics.
[49] H. F. Jordan,et al. Is SOR Color-Blind? , 1986 .
[50] T. Straatsma,et al. THE MISSING TERM IN EFFECTIVE PAIR POTENTIALS , 1987 .
[51] Leslie Greengard,et al. A fast algorithm for particle simulations , 1987 .
[52] Peter C. Jordan,et al. Electrostatic modeling of ion pores. Multipolar sources. , 1987, Biophysical chemistry.
[53] D. Levitt. Exact continuum solution for a channel that can be occupied by two ions. , 1987, Biophysical journal.
[54] C. Brooks. Computer simulation of liquids , 1989 .
[55] E Jakobsson,et al. Water and polypeptide conformations in the gramicidin channel. A molecular dynamics study. , 1989, Biophysical journal.
[56] Ronald M. Levy,et al. Computer simulations of the dielectric properties of water: Studies of the simple point charge and transferrable intermolecular potential models , 1989 .
[57] N. Karasawa,et al. Acceleration of convergence for lattice sums , 1989 .
[58] Peter C. Jordan,et al. How does vestibule surface charge affect ion conduction and toxin binding in a sodium channel? , 1990, Biophysical journal.
[59] M Karplus,et al. Ion transport in a model gramicidin channel. Structure and thermodynamics. , 1991, Biophysical journal.
[60] J. Mccammon,et al. Time-correlation analysis of simulated water motion in flexible and rigid gramicidin channels. , 1991, Biophysical journal.
[61] Arieh Warshel,et al. A local reaction field method for fast evaluation of long‐range electrostatic interactions in molecular simulations , 1992 .
[62] Mark E. Tuckerman,et al. Reversible multiple time scale molecular dynamics , 1992 .
[63] W. Goddard,et al. Atomic level simulations on a million particles: The cell multipole method for Coulomb and London nonbond interactions , 1992 .
[64] E Jakobsson,et al. The nature of ion and water barrier crossings in a simulated ion channel. , 1993, Biophysical journal.
[65] S. Vandewalle. Parallel multigrid waveform relaxation for parabolic problems , 1993 .
[66] Randal R Ketchem,et al. High-resolution conformation of gramicidin A in a lipid bilayer by solid-state NMR. , 1993, Science.
[67] J. Molenaar. Multigrid methods for semiconductor device simulation , 1993 .
[68] T. Darden,et al. Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .
[69] Martin Head-Gordon,et al. Derivation and efficient implementation of the fast multipole method , 1994 .
[70] D. Beglov,et al. Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations , 1994 .
[71] Steven J. Stuart,et al. Dynamical fluctuating charge force fields: Application to liquid water , 1994 .
[72] L Greengard,et al. Fast Algorithms for Classical Physics , 1994, Science.
[73] A. Karshikoff,et al. Electrostatic properties of two porin channels from Escherichia coli. , 1994, Journal of molecular biology.
[74] Richard J. Needs,et al. An Optimized Ewald Method for Long-Ranged Potentials , 1994 .
[75] Wolfgang Fichtner,et al. Memory Aspects and Performance of Iterative Solvers , 1994, SIAM J. Sci. Comput..
[76] Jiro Shimada,et al. Performance of fast multipole methods for calculating electrostatic interactions in biomacromolecular simulations , 1994, J. Comput. Chem..
[77] B. Honig,et al. Classical electrostatics in biology and chemistry. , 1995, Science.
[78] T. Darden,et al. A smooth particle mesh Ewald method , 1995 .
[79] R. Eisenberg,et al. Diffusion as a chemical reaction: Stochastic trajectories between fixed concentrations , 1995 .
[80] R. Eisenberg,et al. Hydrodynamic model of temperature change in open ionic channels. , 1995, Biophysical journal.
[81] B. Sakmann,et al. Single-Channel Recording , 1995, Springer US.
[82] B. Roux,et al. Structure, energetics, and dynamics of lipid–protein interactions: A molecular dynamics study of the gramicidin A channel in a DMPC bilayer , 1996, Proteins.
[83] K Schulten,et al. VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.
[84] B. Wallace,et al. Solution structure of a parallel left-handed double-helical gramicidin-A determined by 2D 1H NMR. , 1996, Journal of molecular biology.
[85] J. Board,et al. Ewald summation techniques in perspective: a survey , 1996 .
[86] Jim Glosli,et al. Comments on P3M, FMM, and the Ewald method for large periodic Coulombic systems , 1996 .
[87] P. Turq,et al. REAL IONIC SOLUTIONS IN THE MEAN SPHERICAL APPROXIMATION. 1. SIMPLE SALTS IN THE PRIMITIVE MODEL , 1996 .
[88] R. S. Eisenberg,et al. Computing the Field in Proteins and Channels , 2010, 1009.2857.
[89] K. C. Lee,et al. Macromolecular structural elucidation with solid-state NMR-derived orientational constraints , 1996, Journal of biomolecular NMR.
[90] Frederick E. Petry,et al. Principles and Applications , 1997 .
[91] L. Shen,et al. Transmembrane helix structure, dynamics, and interactions: multi-nanosecond molecular dynamics simulations. , 1997, Biophysical journal.
[92] E Jakobsson,et al. Computer simulation studies of biological membranes: progress, promise and pitfalls. , 1997, Trends in biochemical sciences.
[93] Christian Holm,et al. How to mesh up Ewald sums. I. A theoretical and numerical comparison of various particle mesh routines , 1998 .
[94] Christopher M. Snowden,et al. Introduction To Semiconductor Device Modelling , 1998 .
[95] B. Eisenberg,et al. Anomalous mole fraction effect, electrostatics, and binding in ionic channels. , 1998, Biophysical journal.
[96] B. Chait,et al. The structure of the potassium channel: molecular basis of K+ conduction and selectivity. , 1998, Science.
[97] M S Sansom,et al. Lipid properties and the orientation of aromatic residues in OmpF, influenza M2, and alamethicin systems: molecular dynamics simulations. , 1998, Biochemistry.
[98] H. Berendsen,et al. A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer. , 1998, Biophysical journal.
[99] Gerhard Hummer,et al. Molecular Theories and Simulation of Ions and Polar Molecules in Water , 1998 .
[100] S. Chung,et al. Brownian dynamics study of ion transport in the vestibule of membrane channels. , 1998, Biophysical journal.
[101] E Jakobsson,et al. Using theory and simulation to understand permeation and selectivity in ion channels. , 1998, Methods.
[102] B. Roux,et al. Statistical mechanical equilibrium theory of selective ion channels. , 1999, Biophysical journal.
[103] A. Nitzan,et al. A lattice relaxation algorithm for three-dimensional Poisson-Nernst-Planck theory with application to ion transport through the gramicidin A channel. , 1999, Biophysical journal.
[104] Shin-Ho Chung,et al. The effect of hydrophobic and hydrophilic channel walls on the structure and diffusion of water and ions , 1999 .
[105] T. Weiss,et al. Theoretical analysis of hydrophobic matching and membrane-mediated interactions in lipid bilayers containing gramicidin. , 1999, Biophysical journal.
[106] Herman J. C. Berendsen,et al. Molecular Dynamics Simulations: The Limits and Beyond , 1999, Computational Molecular Dynamics.
[107] T. E. Thompson,et al. Monte Carlo simulation of two-component bilayers: DMPC/DSPC mixtures. , 1999, Biophysical journal.
[108] Sean Conlan,et al. Stochastic sensing of organic analytes by a pore-forming protein containing a molecular adapter , 1999, Nature.
[109] C. Caldwell. Mathematics of Computation , 1999 .
[110] E. Jakobsson,et al. Simulation study of a gramicidin/lipid bilayer system in excess water and lipid. II. Rates and mechanisms of water transport. , 1999, Biophysical journal.
[111] P. Phale,et al. Brownian dynamics simulation of ion flow through porin channels. , 1999, Journal of molecular biology.
[112] Benedict Leimkuhler,et al. Computational Molecular Dynamics: Challenges, Methods, Ideas: Proceedings of the 2nd International Symposium on Algorithms for Macromolecular Modellin , 1999 .
[113] L. Yang,et al. Experimental evidence for hydrophobic matching and membrane-mediated interactions in lipid bilayers containing gramicidin. , 1999, Biophysical journal.
[114] Tamar Schlick,et al. Some Failures and Successes of Long-Timestep Approaches to Biomolecular Simulations , 1999, Computational Molecular Dynamics.
[115] M S Sansom,et al. Alamethicin helices in a bilayer and in solution: molecular dynamics simulations. , 1999, Biophysical journal.
[116] Simulation study of a gramicidin/lipid bilayer system in excess water and lipid. I. Structure of the molecular complex. , 1999, Biophysical journal.
[117] Benedict Leimkuhler,et al. Computational Molecular Dynamics: Challenges, Methods, Ideas , 1999, Computational Molecular Dynamics.
[118] Harry A. Stern,et al. Fluctuating Charge, Polarizable Dipole, and Combined Models: Parameterization from ab Initio Quantum Chemistry , 1999 .
[119] A. Smondyrev,et al. Structure of dipalmitoylphosphatidylcholine/cholesterol bilayer at low and high cholesterol concentrations: molecular dynamics simulation. , 1999, Biophysical journal.
[120] R. MacKinnon,et al. The cavity and pore helices in the KcsA K+ channel: electrostatic stabilization of monovalent cations. , 1999, Science.
[121] U. Essmann,et al. Dynamical properties of phospholipid bilayers from computer simulation. , 1999, Biophysical journal.
[122] Ruhong Zhou,et al. Parametrizing a polarizable force field from ab initio data. I. The fluctuating point charge model , 1999 .
[123] E Jakobsson,et al. Combined Monte Carlo and molecular dynamics simulation of fully hydrated dioleyl and palmitoyl-oleyl phosphatidylcholine lipid bilayers. , 1999, Biophysical journal.
[124] S H Chung,et al. Test of Poisson-Nernst-Planck Theory in Ion Channels , 1999, The Journal of general physiology.
[125] E. von Kitzing,et al. (In)validity of the constant field and constant currents assumptions in theories of ion transport. , 1999, Biophysical journal.
[126] Christian Holm,et al. How to Mesh up Ewald Sums , 2000 .
[127] R. L. Rowley,et al. A corrected 3D Ewald calculation of the low effective temperature properties of the electrochemical interface , 2000 .
[128] J. Nagle,et al. Lipid bilayer structure. , 2000, Current opinion in structural biology.
[129] Uwe Hollerbach,et al. Predicting Function from Structure Using the Poisson−Nernst−Planck Equations: Sodium Current in the Gramicidin A Channel , 2000 .
[130] E. Lindahl,et al. Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations. , 2000, Biophysical journal.
[131] B. Roux,et al. A combined molecular dynamics and diffusion model of single proton conduction through gramicidin. , 2000, Biophysical journal.
[132] B. Eisenberg,et al. Binding and selectivity in L-type calcium channels: a mean spherical approximation. , 2000, Biophysical journal.
[133] W. Im,et al. A Grand Canonical Monte Carlo-Brownian dynamics algorithm for simulating ion channels. , 2000, Biophysical journal.
[134] M. Kurnikova,et al. Three-dimensional Poisson-Nernst-Planck theory studies: influence of membrane electrostatics on gramicidin A channel conductance. , 2000, Biophysical journal.
[135] Serge Durand-Vidal,et al. Electrolytes at interfaces , 2000 .
[136] D. Busath,et al. Monte Carlo Simulations of the Mechanism for Channel Selectivity: The Competition between Volume Exclusion and Charge Neutrality , 2000 .
[137] Shin-Ho Chung,et al. Tests of continuum theories as models of ion channels. II. Poisson-Nernst-Planck theory versus brownian dynamics. , 2000, Biophysical journal.
[138] A. Kierzek,et al. Cluster Formation in Aqueous Electrolyte Solutions Observed by Dynamic Light Scattering , 2000 .
[139] B. Roux,et al. Molecular dynamics of the KcsA K(+) channel in a bilayer membrane. , 2000, Biophysical journal.
[140] S. Feller,et al. Molecular dynamics simulations of lipid bilayers , 2000 .
[141] R. L. Rowley,et al. Molecular dynamics simulation of continuous current flow through a model biological membrane channel. , 2001, Physical review letters.
[142] D. Busath,et al. Monte Carlo Study of the Effect of Ion and Channel Size on the Selectivity of a Model Calcium Channel , 2001 .
[143] Robert S. Eisenberg,et al. Two- and Three-Dimensional Poisson–Nernst–Planck Simulations of Current Flow Through Gramicidin A , 2002, J. Sci. Comput..
[144] R. MacKinnon,et al. Chemistry of ion coordination and hydration revealed by a K+ channel–Fab complex at 2.0 Å resolution , 2001, Nature.
[145] J. F. Hinton,et al. Structures of gramicidins A, B, and C incorporated into sodium dodecyl sulfate micelles. , 2001, Biochemistry.
[146] H. Bayley,et al. Stochastic sensors inspired by biology , 2001, Nature.
[147] E. Jakobsson,et al. Hierarchical approach to predicting permeation in ion channels. , 2001, Biophysical journal.
[148] J. Valverde. Molecular Modelling: Principles and Applications , 2001 .
[149] D Henderson,et al. Model channel ion currents in NaCl-extended simple point charge water solution with applied-field molecular dynamics. , 2001, Biophysical journal.
[150] G. R. Smith,et al. Simulation approaches to ion channel structure–function relationships , 2001, Quarterly Reviews of Biophysics.
[151] B. Roux,et al. Energetics of ion conduction through the K + channel , 2022 .
[152] T. Halgren,et al. Polarizable force fields. , 2001, Current opinion in structural biology.
[153] Alexander D. MacKerell,et al. Computational Biochemistry and Biophysics , 2001 .
[154] Graham R. Smith,et al. Setting up and optimization of membrane protein simulations , 2002, European Biophysics Journal.
[155] R. Eisenberg,et al. Combining computational chemistry and computational electronics to understand protein ion channels , 2002 .
[156] Shin-Ho Chung,et al. Reservoir boundaries in Brownian dynamics simulations of ion channels. , 2002, Biophysical Journal.
[157] G. Yellen. The voltage-gated potassium channels and their relatives , 2002, Nature.
[158] Helmut Grubmüller,et al. Water permeation through gramicidin A: desformylation and the double helix: a molecular dynamics study. , 2002, Biophysical journal.
[159] R. L. Rowley,et al. Permeation of ions through a model biological channel: effect of periodic boundary conditions and cell size , 2002 .
[160] Youxing Jiang,et al. Crystal structure and mechanism of a calcium-gated potassium channel , 2002, Nature.
[161] Godehard Sutmann,et al. Long-Range Interactions in Many-Particle Simulation , 2002 .
[162] Shin-Ho Chung,et al. Continuum electrostatics fails to describe ion permeation in the gramicidin channel. , 2002, Biophysical journal.
[163] W. Im,et al. Ions and counterions in a biological channel: a molecular dynamics simulation of OmpF porin from Escherichia coli in an explicit membrane with 1 M KCl aqueous salt solution. , 2002, Journal of molecular biology.
[164] Benoît Roux,et al. On the potential functions used in molecular dynamics simulations of ion channels. , 2002, Biophysical journal.
[165] T. Schlick,et al. Efficient multiple-time-step integrators with distance-based force splitting for particle-mesh-Ewald molecular dynamics simulations , 2002 .
[166] Ansgar Philippsen,et al. Imaging the electrostatic potential of transmembrane channels: atomic probe microscopy of OmpF porin. , 2002, Biophysical journal.
[167] P. Clancy,et al. Effects of the Ewald sum on the free energy of the extended simple point charge model for water , 2002 .
[168] W. Im,et al. Ion permeation and selectivity of OmpF porin: a theoretical study based on molecular dynamics, Brownian dynamics, and continuum electrodiffusion theory. , 2002, Journal of molecular biology.
[169] H. L. Scott,et al. Modeling the lipid component of membranes. , 2002, Current opinion in structural biology.
[170] T. Schlick. Molecular modeling and simulation , 2002 .
[171] K. M. Armstrong,et al. On the origin of closing flickers in gramicidin channels: a new hypothesis. , 2002, Biophysical journal.
[172] Galya Orr,et al. Probing conformational changes of gramicidin ion channels by single-molecule patch-clamp fluorescence microscopy. , 2003, Biophysical journal.
[173] Donald E Elmore,et al. Investigating lipid composition effects on the mechanosensitive channel of large conductance (MscL) using molecular dynamics simulations. , 2003, Biophysical journal.
[174] S. Bezrukov,et al. Residue ionization and ion transport through OmpF channels. , 2003, Biophysical journal.
[175] Uwe Hollerbach,et al. Dielectric boundary force and its crucial role in gramicidin. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.
[176] Youxing Jiang,et al. The principle of gating charge movement in a voltage-dependent K+ channel , 2003, Nature.
[177] Steven J. Stuart,et al. Potentials and Algorithms for Incorporating Polarizability in Computer Simulations , 2003 .
[178] R. Rand,et al. The effects of gramicidin on the structure of phospholipid assemblies. , 2003, Biophysical journal.
[179] Serdar Kuyucak,et al. Gramicidin A channel as a test ground for molecular dynamics force fields. , 2003, Biophysical journal.
[180] Boaz Nadler,et al. Connecting a Discrete Ionic Simulation to a Continuum , 2003, SIAM J. Appl. Math..
[181] M. Sansom,et al. Potassium channel, ions, and water: simulation studies based on the high resolution X-ray structure of KcsA. , 2003, Biophysical journal.
[182] M. Saraniti,et al. Silicon-based ion channel sensor , 2003 .
[183] C. Brooks,et al. An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins. , 2003, Biophysical journal.
[184] G. Ciccotti,et al. Algorithms for Brownian dynamics , 2003 .
[185] Shin-Ho Chung,et al. Dielectric self-energy in Poisson-Boltzmann and Poisson-Nernst-Planck models of ion channels. , 2003, Biophysical journal.
[186] B. Roux,et al. Structure of gramicidin a in a lipid bilayer environment determined using molecular dynamics simulations and solid-state NMR data. , 2003, Journal of the American Chemical Society.
[187] M. Cadene,et al. X-ray structure of a voltage-dependent K+ channel , 2003, Nature.
[188] Abraham Nitzan,et al. The role of the dielectric barrier in narrow biological channels: a novel composite approach to modeling single-channel currents. , 2003, Biophysical journal.
[189] B. Roux,et al. Energetics of ion conduction through the gramicidin channel , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[190] B. Roux,et al. A microscopic view of ion conduction through the K+ channel , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[191] G. Lamm,et al. The Poisson–Boltzmann Equation , 2003 .
[192] Silicon-based ion channel sensor , 2004 .
[193] R. Horn,et al. Specificity of Charge-carrying Residues in the Voltage Sensor of Potassium Channels , 2004, The Journal of general physiology.
[194] Dirk Gillespie,et al. Computing induced charges in inhomogeneous dielectric media: application in a Monte Carlo simulation of complex ionic systems. , 2004, Physical review. E, Statistical, nonlinear, and soft matter physics.
[195] Peter C. Jordan,et al. Gating gramicidin channels in lipid bilayers: reaction coordinates and the mechanism of dissociation. , 2004, Biophysical journal.
[196] E. Jakobsson,et al. Ionization states of residues in OmpF and mutants: effects of dielectric constant and interactions between residues. , 2004, Biophysical journal.
[197] Peter C. Jordan,et al. Anion pathway and potential energy profiles along curvilinear bacterial ClC Cl- pores: electrostatic effects of charged residues. , 2004, Biophysical journal.
[198] Ericka Stricklin-Parker,et al. Ann , 2005 .
[199] Perspectives on Ab Initio Calculations , 2007 .
[200] A. Wallqvist,et al. Molecular Models of Water: Derivation and Description , 2007 .
[201] T. Lybrand. Computer Simulation of Biomolecular Systems Using Molecular Dynamics and Free Energy Perturbation Methods , 2007 .
[202] T. P. Straatsma,et al. Free Energy by Molecular Simulation , 2007 .
[203] Appendix: Published Force Field Parameters for Molecular Mechanics, Molecular Dynamics, and Monte Carlo Simulations , 2007 .
[204] K. Merz,et al. Computer Simulation of Lipid Systems , 2007 .
[205] R. Eisenberg. Atomic Biology, Electrostatics, and Ionic Channels , 2008, 0807.0715.