Related papers: Functional State Dependence of Picosecond Protein …
Using both analytical and simulational methods, we study low-temperature nucleation rates in kinetic Ising lattice-gas models that evolve under two different Arrhenius dynamics that interpose between the Ising states a transition state…
The impact of the dispersion of the transport coefficients on the structure of the energy distribution function for charge carriers far from equilibrium has been investigated in effective-medium approximation for model densities of states.…
Since the structural transformations observed in water-ethanol binary mixtures are apparently driven by relatively weak intermolecular forces (like hydrophobicity and hydrogen bonding) that often cooperate to form self assembled structures,…
The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon…
The effect of interactions on dynamics of coupled motor proteins is investigated theoretically. A simple stochastic discrete model, that allows to calculate explicitly the dynamic properties of the system, is developed. It is shown that…
A simple model for the force-dependent unwinding and rewinding rates of the nucleosome inner turn is constructed and quantitatively compared to the results of recent measurements [A. H. Mack et al., J. Mol. Biol. 423, 687 (2012)]. First, a…
Simulations of photochemical reaction dynamics have been a challenge to the theoretical chemistry community for some time. In an effort to determine the predictive character of current approaches, we predict the results of an upcoming…
We use recently introduced three-point dynamic susceptibilities to obtain an experimental determination of the temperature evolution of the number of molecules, N_corr, that are dynamically correlated during the structural relaxation of…
We present two simplified models of protein dynamics based on Langevin's equation of motion in a viscous medium. We explore the effect of the potential energy function's symmetry on the kinetics and thermodynamics of simulated folding. We…
In structure-based models of proteins, one often assumes that folding is accomplished when all contacts are established. This assumption may frequently lead to a conceptual problem that folding takes place in a temperature region of very…
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…
In this study, the additional heat capacity which appear during the water dissociation of the proteins that are one of the soft materials, have been considered by the statistical mechanical methods. For this purpose, taking the electric…
We performed an experimental study of the temperature and doping dependence of the energy-loss function of the bilayer and trilayer Bi-cuprate family. The primary aim is to obtain information on the energy stored in the Coulomb interaction…
We present photoluminescence studies as a function of temperature from a series of conjugated polymers and a conjugated molecule with distinctly different backbone conformations. The organic materials investigated here are: planar…
Oxygen is released to living tissues via conformational changes of hemoglobin from R-state (oxyhemoglobin) to T-state (desoxyhemoglobin). The detailed mechanism of this process is not yet fully understood. We have carried out…
Experimental studies of the glassy slowdown in molecular liquids indicate that the high-temperature activation energy $E_{\infty}$ of glass-forming liquids is directly related to their glass transition temperature $T_{\text{g}}$. To further…
The time sequences of the molecular dynamics simulation for the folding process of a protein is analyzed with the inherent structure landscape which focuses on configurational dynamics of the system. Time dependent energy and entropy for…
A coarse-grained molecular dynamics model of linear polyethylene-like polymer chain system was built to investigate the responds of structure and mechanical properties during uniaxial deformation. The influence of chain length, temperature,…
What energetic and solvation effects underlie the remarkable two-state thermodynamics and folding/unfolding kinetics of small single-domain proteins? To address this question, we investigate the folding and unfolding of a hierarchy of…
Activated dynamics in a glassy system undergoing steady shear deformation is studied by numerical simulations. Our results show that the external driving force has a strong influence on the barrier crossing rate, even though the reaction…