Related papers: The protein dynamical transition is independent of…
A four states phase diagram for protein folding as a function of temperature and solvent quality is derived from an improved 2-d lattice model taking into account the temperature dependence of the hydrophobic effect. The phase diagram…
We conduct experiments on two-dimensional packings of colloidal thermosensitive hydrogel particles whose packing fraction can be tuned above the jamming transition by varying the temperature. By measuring displacement correlations between…
Experimental observations suggest that proteins follow different pathways under different environmental conditions. We perform molecular dynamics simulations of a model of the SH3 domain over a broad range of temperatures, and identify…
Single-molecule atomic force spectroscopy probes elastic properties of titin, ubiquitin and other relevant proteins. We explain bioprotein folding dynamics under both length- and force-clamp by modeling polyprotein modules as particles in a…
The paper is devoted to a systematic account of the theory of conformational dynamics of protein molecules. As an example of application of this theory, we provide a complete analytical description of experiments on the kinetics of CO…
A coarse grained model of a random polypeptide chain, with only discrete torsional degrees of freedom and Hookean springs connecting pairs of hydrophobic residues is shown to display stretched exponential relaxation under Metropolis…
We present results for the kinetics of phase separation in solid binary mixtures ($A_1+A_2$) from Monte Carlo simulations of the Ising model in two dimensions. The simulation results are understood via appropriate application of the…
We present a detailed dynamic light scattering study on the phase separation in the ocular lens emerging during cold cataract development. Cold cataract is a phase separation effect that proceeds via spinodal decomposition of the lens…
Using a large scale molecular dynamics computer simulation we investigate the dynamics of a supercooled melt of SiO_2. We find that with increasing temperature the temperature dependence of the diffusion constants crosses over from an…
Ultrafast, time-resolved spectroscopies enable the direct observation of non-equilibrium processes in condensed-phase systems and have revealed key insights into energy transport, hydrogen-bond dynamics, and vibrational coupling. While ab…
We construct a Hamiltonian for a single domain protein where the contact enthalpy and the chain entropy decrease linearly with the number of native contacts. The hydration effect upon protein unfolding is included by modeling water as ideal…
We use computer simulations to study the microscopic dynamics of an athermal assembly of soft particles near the fluid-to-solid, jamming transition. Borrowing tools developed to study dynamic heterogeneity near glass transitions, we…
The rates of protein folding with photon absorption or emission and the cross section of photon -protein inelastic scattering are calculated from the quantum folding theory by use of standard field-theoretical method. All these protein…
In the present paper we present results of calculations obtained with the use of the theoretical method described in our preceding paper [1] and perform detail analysis of alpha helix-random coil transition in alanine polypeptides of…
We elucidate the physics of the dynamical transition via 10-100ns molecular dynamics simulations at temperatures spanning 160-300K. By tracking the energy fluctuations, we show that the protein dynamical transition is marked by a cross-over…
A simple and surprisingly accurate description of spectral diffusion in deeply frozen globular proteins is constructed directly using the concept of ultrametricity of protein dynamics. Earlier the similar concept has been used for…
The femtosecond optical pump-probe technique was used to study dynamics of photoexcited electrons and coherent optical phonons in transition metals Zn and Cd as a function of temperature and excitation level. The optical response in time…
Langevin dynamical simulations are performed to investigate the depinning dynamics of a two-dimensional solid dusty plasma, which is modulated by one-dimensional nonlinear deformed periodic substrates, and also driven by the combination of…
This letter investigates the molecular dynamics of inelastic disks without external forcing. By introducing a new observation frame with a rescaled time, we observe the virtual steady states converted from asymptotic energy dissipation…
Fragility index and cooperativity length characterizing the molecular mobility in the amorphous phase are for the first time calculated in drawn polylactide (PLA). The microstructure of the samples is investigated from wide-angle X-ray…