Monte Carlo simulations of self-avoiding random walks surrounded by aligned rods on a square lattice and a simple cubic lattice were performed to address the topological constraints involved for dilute solutions of flexible polymers in a highly oriented nematic solvent. The nematic constraint exerted by the solvent is modelled by requiring that the distance between nearest neighbour chain segme...

The scattering function and radius of gyration of an ideal polymer network are calculated depending on the strength of the bonds that form the crosslinks. Our calculations are based on an exact theorem for the characteristic function of a polydisperse phantom network that allows for treating the crosslinks between pairs of randomly selected monomers as quenched variables without resorting to re...

In this work, we compare the results of molecular dynamics simulations involving the application of three generalized Born (GB) models to 10 different proteins. The three GB models, the Still, HCT, and modified analytical generalized Born models, were implemented in the computationally efficient gromacs package. The performance of each model was assessed from the backbone rms deviation from the...

Human plasma low density lipoproteins (LDL) were deuterated in the phospholipid headgroup region by exchange with phosphatidylcholine-N(CD3)3-apolipoprotein A complexes. The exchange was associated with a net transfer of phosphatidylcholine to LDL leading to an increase in total phospholipid content by 27%. Practically all of the endogenous phosphatidylcholine including lysophosphatidylcholine,...

In Escherichia coli, SecA is a large, multifunctional protein that is a vital component of the general protein secretion pathway. In its membrane-bound form it functions as the motor component of the protein translocase, perhaps through successive rounds of membrane insertion and ATP hydrolysis. To understand both the energy conversion process and translocase assembly, we have used contrast-mat...

Although recent spectroscopic studies of chemically denatured proteins hint at significant nonrandom residual structure, the results of extensive small angle X-ray scattering studies suggest random coil behavior, calling for a coherent understanding of these seemingly contradicting observations. Here, we report the results of a Monte Carlo study of the effects of two types of local structures, ...

We perform extensive coarse-grained (CG) Langevin dynamics simulations of intrinsically disordered proteins (IDPs), which possess fluctuating conformational statistics between that for excluded volume random walks and collapsed globules. Our CG model includes repulsive steric, attractive hydrophobic, and electrostatic interactions between residues and is calibrated to a large collection of sing...

Confocal Raman spectroscopy has been implemented within the molecularly thin films of a surface forces apparatus. Applying this technique to an initial system, we investigate the confinement and shear-induced changes in the Raman spectra of poly(dimethylsiloxane) (PDMS) liquids confined between atomically smooth mica surfaces at thicknesses less than the unperturbed radius of gyration of the po...