Calculation of conformation-dependent biomolecular forces.
We develop a numerical scheme that calculates forces under given conformational states of a biomolecule by using a harmonic sampling potential. It can also be used for calculating the potential of mean force, as tested by random walks on Gaussian enthalpy barriers. Further, Brownian dynamics simulations of a finite-length freely jointed chain confirm the analytic expressions for its entropic elasticity that we derive. Our method, while generally applicable to many systems, will be particularly useful for studying the elasticity of biopolymers where various types of ensembles differ due to the finite size effect.
Hwang
Wonmuk
W
Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, USA. hwm@tamu.edu
D002627:Chemistry, Physical / Q000379:methods; D003198:Computer Simulation; D019277:Entropy; D006358:Hot Temperature; D018625:Microscopy, Atomic Force; D015233:Models, Statistical; D008962:Models, Theoretical; D016011:Normal Distribution; D011108:Polymers / Q000737:chemistry; D011487:Protein Conformation; D012984:Software; D013696:Temperature; D013816:Thermodynamics
D011108:Polymers