Related papers: On the origin of diverse time scales in the protei…
We present simulations of stochastic fluid dynamics in the vicinity of a critical endpoint belonging to the universality class of the Ising model. This study is motivated by the challenge of modeling the dynamics of critical fluctuations…
Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions…
We use molecular dynamics simulations to study the behavior of supercooled water subject to different stimuli from a diluted azobenzene hydrophobic probe. When the molecular motor does not fold, it acts as a passive probe, modifying the…
We investigate the hydrodynamic properties of a fluid simulated with a mesoscopic solvent model. Two distinct regimes are identified, the `particle regime' in which the dynamics is gas-like, and the `collective regime' where the dynamics is…
We discuss the hydrodynamic collective effects due to active protein molecules that are immersed in lipid bilayer membranes and modeled as stochastic force dipoles. We specifically take into account the presence of the bulk solvent which…
By combining methods of kinetic and density functional theory, we present a description of molecular fluids which accounts for their microscopic structure and thermodynamic properties as well as for the hydrodynamic behavior. We focus on…
We present a novel statistical mechanics formalism for the theoretical description of the process of protein folding$\leftrightarrow$unfolding transition in water environment. The formalism is based on the construction of the partition…
In order to find a measure of the dynamical features of phase separation kinetics during spinodal decomposition of a liquid binary mixture (like water and cyclohexane , water and 2,6 lutidiene or methanol and cyclohexane), we study both the…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
We develop a general framework in the renormalization-group (RG) method for extracting a mesoscopic dynamics from an evolution equation by incorporating some excited (fast) modes as additional components to the invariant manifold spanned by…
For many biological applications of molecular dynamics (MD) the importance of good sampling in conformational space makes it necessary to eliminate the fastest motions from the system in order to increase the time step. An accurate…
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…
Multiparticle collision dynamics (MPCD) enables to simulate fluid dynamics including both hydrodynamics and thermal fluctuations. Its main use concerns complex fluids, where the solvent interacts with concentrated solutes, may they be…
Motivated by the very low diffusivity recently found in ab initio simulations of liquid water, we have studied its dependence with temperature, system size, and duration of the simulations. We use ab initio molecular dynamics (AIMD),…
We report on the direct measurement of the correlation times of the protein backbone carbons and proximal waters of hydration in mechanically strained elastin by nuclear magnetic resonance methods. The experimental data indicate a decrease…
The process of protons transport in molecular water chains is of fundamental interest for many biological systems. Although many features of such systems can be analyzed using large-scale computational modeling, other features are better…
The hydrophobic effect stabilizes the native structure of proteins by minimizing the unfavourable interactions between hydrophobic residues and water through the formation of a hydrophobic core. Here we include the entropic and enthalpic…
The adsorption dynamics of a colloidal particle at a fluid interface is studied theoretically and numerically, documenting distinctly different relaxation regimes. The adsorption of a perfectly smooth particle is characterized by a fast…
Unstructured proteins can modulate cellular responses to environmental conditions by undergoing coil-globule transitions and phase separation. However, the molecular mechanisms of these phenomena still need to be fully understood. Here, we…
We present a computational investigation on the slow dynamics of a mixture of large and small soft spheres. By varying the size disparity at a moderate fixed composition different relaxation scenarios are observed for the small particles.…