Related papers: Molecular Dynamics Simulations of Cytochrome c un-…
Monte Carlo simulation studies of reverse micelles of an anionic surfactant, sodium AOT, in a non-polar solvent provide strong evidence that, in the absence of water, these clusters are charge ordered polyhedral shells. The stabilizing…
We study the dynamics of hydration water/protein association in folded proteins, using lysozyme and myoglobin as examples. Extensive molecular dynamics simulations are performed to identify underlying mechanisms of the dynamical transition…
We investigate the presence of structural collective motions on a picosecond time scale for the heme protein, cytochrome c, as a function of oxidation and hydration, using terahertz (THz) time-domain spectroscopy and molecular dynamics…
Elucidation of possible pathways between folded (native) and unfolded states of a protein is a challenging task, as the intermediates are often hard to detect. Here we alter the solvent environment in a controlled manner by choosing two…
The growth of a methane hydrate seed within a silica slit pore of fixed width has been studied using AllAtom Molecular Dynamics (AA-MD). An AA force field has been used to describe the molecules of the solid silica substrate, with a-quartz…
We study four citrate synthase homodimeric proteins within a structure-based coarse-grained model. Two of these proteins come from thermophilic bacteria, one from a cryophilic bacterium and one from a mesophilic organism; three are in the…
We study the structural changes occurring in the isotropic phase of the C$_{12}$=EO$_6$/H$_2$O lyotropic mixture (up to 35% surfactant weight concentration) upon increasing the concentration and temperature, from small individual micelles…
A molecular dynamics simulation of water confined in a silica pore is performed in order to compare it with recent experimental results on water confined in porous Vycor glass at room temperature. A cylindrical pore of 40 A is created…
We study theoretically the thermodynamics, over a broad temperature range (5 C to 125 C), related to hydrated water upon protein unfolding. The hydration effect is modeled as interacting dipoles in an external field, mimicking the influence…
We propose a simple microscopic model of molecular dynamics simulation to study orientational glass in three dimensions. We present simulation results for mixtures of mildly anisotropic particles and spherical impurities. We realize fcc…
In the present work we study and compare unfolding of a small protein, chicken villin headpiece (HP-36) in two different aqueous binary mixtures, namely water-ethanol (EtOH) and water-dimethyl sulphoxide (DMSO). In both the binary mixtures,…
We use molecular dynamics computer simulations and nuclear magnetic resonance experiments to investigate the dynamics of water at interfaces of molecular roughness and low mobility. We find that, when approaching such interfaces, the…
Proteins work only if folded in their native state, but changes in temperature T and pressure P induce their unfolding. Therefore for each protein there is a stability region (SR) in the T-P thermodynamic plane outside which the biomolecule…
Normal micelle aggregates of amphiphilic surfactant in aqueous solvent are formed by a process of entropically driven self-assembly. The self-assembly of reverse micelles from amphiphilic surfactant in non-polar solvent in the presence of…
A growing number of proteins have been shown to adopt knotted folds. Yet the biological roles and biophysical properties of these knots remain poorly understood. We have used protein engineering and atomic force microscopy to explore…
We developed a new mechanical model for determining the compression and shear mechanical behavior of four different hemoglobin structures. Previous studies on hemoglobin structures have focused primarily on overall mechanical behavior;…
The molecular mechanism of the solvent motion that is required to instigate the protein structural relaxation above a critical hydration level or transition temperature has yet to be determined. In this work we use quasi-elastic neutron…
The viscosity of AOT/water/decane water-in-oil microemulsions exhibits a well-known maximum as a function of water/AOT molar ratio, which is usually attributed to increased attractions among nearly spherical droplets. The maximum can be…
We embark on a quest to identify small molecules in the chemical space that can potentially violate Hund's rule. Utilizing twelve TDDFT approximations and the ADC(2) many-body method, we report the energies of S$_1$ and T$_1$ excited states…
We study the behavior of five proteins at the air-water and oil-water interfaces by all-atom molecular dynamics. The proteins are found to get distorted when pinned to the interface. This behavior is consistent with the phenomenological way…