Related papers: On the origin of diverse time scales in the protei…
A large number of water models exists for molecular simulations. They differ in the ability to reproduce specific features of real water instead of others, like the correct temperature for the density maximum or the diffusion coefficient.…
Studying the changed water dynamics in the hydration layers of biomolecules is an important step towards fuller understanding of their function and mechanisms, but has shown to be quite difficult. The measurement of the time-dependent…
We perform lengthy molecular dynamics simulations of the SPC/E model of water to investigate the dynamics under pressure at many temperatures and compare with experimental measurements. We calculate the isochrones of the diffusion constant…
Biomembranes, which are mainly composed of neutral and charged lipids, exhibit a large variety of functional structures and dynamics. Here, we report a coarse-grained molecular dynamics (MD) simulation of the phase separation and…
We study slow dynamics of particles moving in a matrix of immobile obstacles using molecular dynamics simulations. The glass transition point decreases drastically as the obstacle density increases. At higher obstacle densities, the…
Many biological processes are supported by special molecules, called motor proteins or molecular motors, that transport cellular cargoes along linear protein filaments and can reversibly associate to their tracks. Stimulated by these…
Protein dynamics has been investigated on a wide range of time scales. Nano- and picosecond dynamics have been assigned to local fluctuations, while slower dynamics have been attributed to larger conformational changes. However, it is…
Using molecular dynamics simulations, we investigate the relation between the dynamic transitions of biomolecules (lysozyme and DNA) and the dynamic and thermodynamic properties of hydration water. We find that the dynamic transition of the…
Biological membranes are self-assembled complex fluid interfaces that host proteins, molecular motors and other macromolecules essential for cellular function. These membranes have a distinct in-plane fluid response with a surface viscosity…
We present a fluctuating hydrodynamic description of an active lattice gas model with excluded volume interactions that exhibits motility-induced phase separation under appropriate conditions. For quasi-one dimension and higher, stability…
The authors study the short-time dynamics of helix-forming polypeptide chains using an all-atom representation of the molecules and an implicit solvation model to approximate the interaction with the surrounding solvent. The results confirm…
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. Proteins are peptide chains decorated by amino…
Biomolecular condensates play essential roles in cellular processes, and recent efforts have focused on understanding their assembly and rational design principles. In this study, we have employed an explicit-solvent minimal statistical…
The understanding of dynamics and functioning of biological membranes and in particular of membrane embedded proteins is one of the most fundamental problems and challenges in modern biology and biophysics. In particular the impact of…
We have conducted a triple-scale simulation of liquid water by concurrently coupling atomistic, mesoscopic, and continuum models of the liquid. The presented triple-scale hydrodynamic solver for molecular liquids enables the insertion of…
Protein dynamics is a fundamental element to comprehend their biological functions. However, a theoretical picture providing microscopic-detail explanation of its relevant features is still missing. One of the outmost relevant properties…
The time-dependent relaxation of a dynamical system may exhibit a power-law behavior that is superimposed by log-periodic oscillations. Sornette [Phys. Rep. 297, 239 (1998)] showed that this behavior can be explained by a discrete scale…
Colloidal gels are out-of-equilibrium structures, made up of a rarefied network of colloidal particles. Comparing experiments to numerical simulations, with hydrodynamic interactions switched off, we demonstrate the crucial role of the…
We propose a framework for describing the dynamics associated with the adsorption of small molecules to liquid-vapor interfaces, using an intermediate resolution between traditional continuum theories that are bereft of molecular detail and…
Hydrophobic hydration plays a crucial role in self-assembly processes over multiple length-scales, but the extrapolation of molecular-scale models to larger length-scale hydration phenomena is sometimes not warranted. Scaled-particle…