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 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 ...

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...

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...

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...

The diffusion of fractal aggregates constructed with the method by Thouy and Jullien [J. Phys. A 27, 2953 (1994)] comprised of N(p) spherical primary particles was studied as a function of the aggregate mass and fractal dimension using molecular dynamics simulations. It is shown that finite-size effects have a strong impact on the apparent value of the diffusion coefficient (D), but these can b...

Electrokinetic phenomena in micro/nanofluidic channels have attracted considerable attention because precise control of molecular transport in liquids is required to optically and electrically capture the behavior of single molecules. However, the detailed mechanisms of polymer transport influenced by electroosmotic flows and electric fields in micro/nanofluidic channels have not yet been eluci...

We investigate the effect of various spherical nanoparticles on chain dimensions in polymer melts for high nanoparticle loading which is larger than the percolation threshold, using molecular dynamics simulations. We show that polymer chains are unperturbed by the presence of repulsive nanoparticles. In contrast polymer chains can be perturbed by the presence of attractive nanoparticles when th...