Dynamic coupling between coordinates in a model for biomolecular isomerization.
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Aaron R Dinner | Ao Ma | Ambarish Nag | A. Nag | Ao Ma | A. Dinner
[1] C. Dellago,et al. Reaction coordinates of biomolecular isomerization. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[2] J. Onuchic,et al. DIFFUSIVE DYNAMICS OF THE REACTION COORDINATE FOR PROTEIN FOLDING FUNNELS , 1996, cond-mat/9601091.
[3] A. Berezhkovskii,et al. One-dimensional reaction coordinates for diffusive activated rate processes in many dimensions. , 2005, The Journal of chemical physics.
[4] Arup K Chakraborty,et al. Atomistic understanding of kinetic pathways for single base-pair binding and unbinding in DNA , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[5] Martin Karplus,et al. A POSITION DEPENDENT FRICTION MODEL FOR SOLUTION REACTIONS IN THE HIGH FRICTION REGIME : PROTON TRANSFER IN TRIOSEPHOSPHATE ISOMERASE (TIM) , 1996 .
[6] G. Hummer,et al. Conformational diffusion and helix formation kinetics. , 2000, Physical review letters.
[7] Berend Smit,et al. Molecular Dynamics Simulations , 2002 .
[8] C. Dellago,et al. Transition path sampling and the calculation of rate constants , 1998 .
[9] B. Berne,et al. Spatial dependence of time‐dependent friction for pair diffusion in a simple fluid , 1990 .
[10] B. Brooks,et al. An analysis of the accuracy of Langevin and molecular dynamics algorithms , 1988 .
[11] B. Berg,et al. Multicanonical algorithms for first order phase transitions , 1991 .
[12] A. H. Klahn,et al. References and Notes , 2022 .
[13] 宁北芳,et al. 疟原虫var基因转换速率变化导致抗原变异[英]/Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A , 2005 .
[14] M. Karplus,et al. A Comprehensive Analytical Treatment of Continuum Electrostatics , 1996 .
[15] D. Landau,et al. Efficient, multiple-range random walk algorithm to calculate the density of states. , 2000, Physical review letters.
[16] F A Gianturco,et al. Vibrational excitation of CF4 by electron impact: a computational analysis , 2005 .
[17] Vijay S Pande,et al. One-dimensional reaction coordinate and the corresponding potential of mean force from commitment probability distribution. , 2005, The journal of physical chemistry. B.
[18] R. Hochstrasser,et al. Two-dimensional infrared spectroscopy: a promising new method for the time resolution of structures. , 2001, Current opinion in structural biology.
[19] M. Karplus,et al. Simulation of activation free energies in molecular systems , 1996 .
[20] John E. Straub,et al. Dynamic friction on rigid and flexible bonds , 1990 .
[21] Bernard Pettitt,et al. Stochastic dynamics simulations of the alanine dipeptide using a solvent-modified potential energy surface , 1993 .
[22] David Chandler,et al. Statistical mechanics of isomerization dynamics in liquids and the transition state approximation , 1978 .
[23] Berend Smit,et al. Understanding Molecular Simulation , 2001 .
[24] Benoît Roux,et al. Conformational Flexibility of o-Phosphorylcholine and o-Phosphorylethanolamine: A Molecular Dynamics Study of Solvation Effects , 1994 .
[25] M. Karplus,et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .
[26] Gerhard Hummer,et al. Unveiling functional protein motions with picosecond x-ray crystallography and molecular dynamics simulations. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[27] J. Langer. Statistical theory of the decay of metastable states , 1969 .
[28] X. Xie,et al. Single-molecule enzymatic dynamics. , 1998, Science.
[29] Berend Smit,et al. Understanding molecular simulation: from algorithms to applications , 1996 .
[30] Aaron R Dinner,et al. Automatic method for identifying reaction coordinates in complex systems. , 2005, The journal of physical chemistry. B.
[31] 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.
[32] V. Pande,et al. On the transition coordinate for protein folding , 1998 .
[33] M. Karplus,et al. THE THERMODYNAMICS AND KINETICS OF PROTEIN FOLDING : A LATTICE MODEL ANALYSIS OF MULTIPLE PATHWAYS WITH INTERMEDIATES , 1999 .
[34] H. Kramers. Brownian motion in a field of force and the diffusion model of chemical reactions , 1940 .
[35] Jianping Wang,et al. Two-dimensional infrared spectroscopy of the alanine dipeptide in aqueous solution. , 2005, The journal of physical chemistry. B.
[36] F. Calvo,et al. Sampling along reaction coordinates with the Wang-Landau method , 2002, cond-mat/0205428.
[37] D. Chandler,et al. Grid-Flux Method for Learning the Solvent Contribution to the Mechanisms of Reactions , 2003 .
[38] F. Young. Biochemistry , 1955, The Indian Medical Gazette.
[39] B. Berne,et al. Calculation of dynamic friction on intramolecular degrees of freedom , 1987 .
[40] H Frauenfelder,et al. Dynamics of ligand binding to myoglobin. , 1975, Biochemistry.
[41] Edward Harder,et al. On the Calculation of Diffusion Coefficients in Confined Fluids and Interfaces with an Application to the Liquid-Vapor Interface of Water † , 2003 .
[42] M. Karplus,et al. Dynamics of ligand binding to heme proteins. , 1979, Journal of molecular biology.
[43] Aaron R. Dinner,et al. Monte Carlo simulations of biomolecules: The MC module in CHARMM , 2006, J. Comput. Chem..
[44] P. Hänggi,et al. Reaction-rate theory: fifty years after Kramers , 1990 .