Related papers: On the origin of diverse time scales in the protei…
There is a growing interest since the 1990s to understand the squeezing and shear behaviors of liquid films at nanometer scale by the atomic force microscope (AFM) measurement. We carry out all-atom contact-mode AFM simulations in a…
The current computational study investigates the changes in solvation dynamics of water when introducing hydrophobic side chains to the molecular probe N-methyl-6-oxyquinolinium betaine. High precision transient fluorescence and absorption…
Different hypotheses have been proposed to explain the mechanism for the extremely low friction coefficient of carbon coatings and its undesired dependence on air humidity. A decisive atomistic insight is still lacking because of the…
Molecular dynamics (MD) simulations are powerful tools for elucidating the macroscopic physical properties of materials from microscopic atomic behaviors. However, the massive, high-dimensional datasets generated by MD simulations pose a…
Over times shorter than that required for relaxation of enthalpy, a liquid can exhibit striking heterogeneities. The picture of these heterogeneities is complex with transient patches of rigidity, irregular yet persistent, intersected by…
Structure and dynamics of water remain a challenge. Resolving the properties of hydrogen bonding lies at the heart of this puzzle. Here we employ ab initio Molecular Dynamics (AIMD) simulations over a wide temperature range. The total…
We present a ``coarse molecular dynamics'' approach and apply it to studying the kinetics and thermodynamics of a peptide fragment dissolved in water. Short bursts of appropriately initialized simulations are used to infer the deterministic…
The density of a protein molecule is a key property within a variety of experimental techniques. We present a computational method for determining protein mass density that explicitly incorporates hydration effects. Our approach uses…
In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…
Dynamic structuring of water is a key player in a large class of processes underlying biochemical and technological developments today, the latter often involving electric fields. However, the anisotropic coupling between the water…
Using molecular dynamics simulations, we study the slow dynamics of supercooled liquids confined in a random matrix of immobile obstacles. We study the dynamical crossover from glass-like to Lorentz-gas-like behavior in terms of the density…
The process of drying is a simple physical mechanism that drives a system to relax from one equilibrium point to another. The native states of the constituent particles in the droplets can be linked to the emergent morphological patterns…
The low-frequency collective vibrational modes in proteins as well as the protein-water interface have been suggested as dominant factors controlling the efficiency of biochemical reactions and biological energy transport. It is thus…
This is a short survey on recent results obtained by the authors on dynamical phase transitions of interacting particle systems. We consider particle systems with exclusion dynamics, but it is conjectured that our results should hold for a…
A theoretical approach is developed to quantify hydrophobic hydration and interactions on a molecular scale, with the goal of gaining insight into the molecular origins of hydrophobic effects. The model is based on the fundamental relation…
We describe a recent multiscale approach based on the concurrent coupling of constrained molecular dynamics for long biomolecules with a mesoscopic lattice Boltzmann treatment of solvent hydrodynamics. The multiscale approach is based on a…
By performing molecular dynamics simulations with up to 132 million coarse-grained particles in half-micron sized boxes, we show that hydrodynamics quantitatively explains the finite-size effects on diffusion of lipids, proteins, and carbon…
Molecular dynamics simulations of SPC/E water confined in a Silica pore are presented. The simulations have been performed at different hydration levels and temperatures to study the single-particle dynamics. Due to the confinement and to…
The dynamic behavior of a hard-sphere colloidal suspension was studied by X-ray Photon Correlation Spectroscopy and Small Angle X-ray Scattering over a wide range of particle volume fractions. The short-time mobility of the particles was…
The mobility of water molecules confined in a silica pore is studied by computer simulation in the low hydration regime, where most of the molecules reside close to the hydrophilic substrate. A layer analysis of the single particle dynamics…