Calculation of conformation-dependent biomolecular forces. Academic Article

abstract

• 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.

authors

• Hwang, Wonmuk

published proceedings

• J Chem Phys

author list (cited authors)

• Hwang, W.

citation count

• 11

complete list of authors

• Hwang, Wonmuk

publication date

• November 2007

publisher

• AIP Publishing  Publisher

published in

• Journal of Chemical Physics  Journal

keywords

• Chemistry, Physical
• Computer Simulation
• Entropy
• Hot Temperature
• Microscopy, Atomic Force
• Models, Statistical
• Models, Theoretical
• Normal Distribution
• Polymers
• Protein Conformation
• Software
• Temperature
• Thermodynamics

PubMed Central ID

• 17994854

Digital Object Identifier (DOI)

• 10.1063/1.2784557

start page

• 175104

end page

• 175104

volume

• 127

issue

• 17

URL

• http%3A%2F%2Fdx.doi.org%2F10.1063%2F1.2784557