Molecular dynamics simulation of a generic polymer model is applied to study melts of polymers with di†erent types of intrinsic sti†ness. Important static observables of the single chain such as gyration radius or persistence length are determined. Additionally we investigate the overall static melt structure including pair correlation function, structure function and orientational correlation ...

Molecular dynamics simulation of a generic polymer model is applied to study melts of polymers with diierent types of intrinsic stiiness. Important static observables of the single chain such as gyration radius or persistence length are determined. Additionally we investigate the overall static melt structure including pair correlation function, structure function and orientational correlation ...

We consider dilute non-adsorbed polymers grafted at an impenetrable surface and compute several quantities which characterize the polymer shape: the asphericity and the ratios of the eigenvalues of the radius-of-gyration tensor. The results are only slightly different from those obtained for polymers in the bulk, showing that the surface has little influence on the polymer shape.

Time-resolved small-angle x-ray scattering was used to measure the radius of gyration of cytochrome c after initiation of folding by a pH jump. Submillisecond time resolution was obtained with a microfabricated diffusional mixer and synchrotron radiation. The results show that the protein first collapses to compact denatured structures before folding very fast to the native state.

Molecular dynamic simulation is a powerful method that monitors all variations in the atomic level in explicit solvent. By this method we can calculate many chemical and biochemical properties of large scale biological systems. In this work all-atom molecular dynamics simulation of polyalanine (PA) was investigated in the presence of 0.224, 0.448, 0.673, 0.897 and 1.122 M of guanidinium chlorid...

This paper uncovers novel and specific dynamical mechanisms that initiate large-amplitude collective motions in polyatomic molecules. These mechanisms are understood in terms of intramolecular energy transfer between modes and driving forces. Structural transition dynamics of a six-atom cluster between a symmetric and an elongated isomer is highlighted as an illustrative example of what is a ge...

Upon transfer from strongly denaturing to native conditions, proteins undergo a collapse that either precedes folding or occurs simultaneously with it. This collapse is similar to the well known coil-globule transition of polymers. Here we employ single-molecule fluorescence methods to fully characterize the equilibrium coil-globule transition in the denatured state of the IgG-binding domain of...

Published data on the characterization of unfolded proteins in dilute solutions in aqueous guanidine hydrochloride are analyzed to show that the data are not fit by either the random flight or wormlike chain models for linear chains. The analysis includes data on the intrinsic viscosity, root-mean-square radius of gyration, from small-angle X-ray scattering, and hydrodynamic radius, from the tr...

Apparent electrostatic persistence lengths (i.e., those found by substituting the perturbed for the unperturbed mean-square gyration radius in the wormlike chain theory) obtained from static light scattering for variably ionized acrylamideJsodium acrylate copolymers varied approximately as the inverse square root of the ionic strength, C,, and linearly with fractional ionization. While this doe...