Free Energy of Deformation of the Radius of Gyration in Semiflexible Chains

Abstract

The distribution function P(S) of the radius of gyration S, the corresponding elastic free energy A(S) and the mean force $\left\langle f \right\rangle (S)$ were computed from simulations based on the wormlike chain (WLC) model. The relation of the S‐conjugated elastic functions to the analogous functions based on the chain vector R and their connection to the statistical‐mechanics ensembles was elucidated. Simulation data revealed that available analytical functions for P(S) fail to predict the behavior of semiflexible chains. When the power‐law function P(S) was used instead, the exponents sizeably raised with stiffness at chain expansion. The exponents deduced from elastic compression of a chain agreed fairly with the scaling exponents for chain confinement into a sphere.magnified image

Free Energy of Polymers Confined in Open and Closed Cavities

“…When the radius of equivalent sphere R g is considered equal to the cavity radius D , the compression part the free energy of deformation of the radius of gyration A ( R g ) is closely related to the confinement free energy Δ A R . The present simulation model was recently used25 to compute the free energy function A ( R g ) for EV chains. From the simulation of flexible ( b = 0) chains the effective scaling exponent x = −3.15 was found25 to govern the compression part of the function A ( R g ).…”

“…The present simulation model was recently used25 to compute the free energy function A ( R g ) for EV chains. From the simulation of flexible ( b = 0) chains the effective scaling exponent x = −3.15 was found25 to govern the compression part of the function A ( R g ). In semiflexible chains of stiffness b = 20 this exponent x in the A ( R g ) function was reduced to the value around −2.…”

Folding of Polyalanine into Helical Hairpins

“…The hairpins in DNA are usually formed on unwinding the double helix and subsequent complementary base-pairing within one folded DNA strand. However, the simulation results [21] imply that in the narrow channels the undisrupted structure of double-helix DNA can be bent into double-or multiple-leg hairpins. Inherent tendency of long-chain PA to form the compact hairpin-like structures in vacuum and non-polar media demonstrated above for homopolymer peptide PA is directly relevant to the organization of integral membrane proteins.…”

Stiffening Transition in Semiflexible Cyclic Macromolecules

“…There are indications that at a certain stiffness of finitely long linear polymers the intrachain interactions vanish as the spatial distance between monomer units along the polymer backbone becomes too large. [12,13] …”