Related papers: Depth dependent dynamics in the hydration shell of…
When a liquid is rapidly cooled below its melting point without inducing crystallization, its dynamics slow down significantly without noticeable structural changes. Elucidating the origin of this slowdown has been a long-standing…
We have performed a multicanonical molecular dynamics simulation on a simple model protein.We have studied a model protein composed of charged, hydrophobic, and neutral spherical bead monomers.Since the hydrophobic interaction is considered…
Hydrostatic pressure is a common perturbation to probe the conformations of proteins. There are two common forms of pressure dependent potentials of mean force (PMFs) derived from hydrophobic molecules available for the coarse grained…
In this work, we have carried out molecular dynamics (MD) simulation techniques to study the diffusion coefficient of interlayer molecules at different temperature. Within the wider context of water dynamics in soils, and with a particular…
The formation of a spanning hydrogen-bonded network of hydration water is found to occur via a 2D percolation transition in various systems: smooth hydrophilic surfaces, the surface of a single protein molecule, protein powder and diluted…
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…
We report the combined results of molecular dynamics simulations and theoretical calculations concerning various dynamical arrest transitions in a model system representing a dipolar fluid, namely, N (softcore) rigid spheres interacting…
Molecular dynamics simulations are carried out to explore the dynamical crossover phenomenon in strongly confined and mildly supercooled water in graphene oxide nanopores. In contrast to studies where confinement is used to study the…
The dynamical glass transition is typically taken to be the temperature at which a glassy liquid is no longer able to equilibrate on experimental timescales. Consequently, the physical properties of these systems just above or below the…
Mossbauer spectroscopy and neutron scattering measurements on proteins embedded in solvents including water and aqueous mixtures have emphasized the observation of the distinctive temperature dependence of the atomic mean square…
A mode-coupling theory for the slow single-particle dynamics in fluids adsorbed in disordered porous media is derived, which complements previous work on the collective dynamics [V. Krakoviack, Phys. Rev. E 75, 031503 (2007)]. Its…
We investigate dynamical heterogeneities in the collective relaxation of a concentrated microgel system, for which the packing fraction can be conveniently varied by changing the temperature. The packing fraction dependent mechanical…
We propose a universal elastic energy for proteins, which depends only on the radius of gyration $R_{g}$ and the residue number $N$. It is constructed using physical arguments based on the hydrophobic effect and hydrogen bonding. Adjustable…
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…
We incorporate hydrodynamic interactions in a structure-based model of ubiquitin and demonstrate that the hydrodynamic coupling may reduce the peak force when stretching the protein at constant speed, especially at larger speeds.…
Biological adhesion is a critical mechanical function of complex organisms operating at multiple scales. At the cellular scale, cell-cell adhesion is remarkably tunable to enable both cohesion and malleability during development,…
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…
Time-resolved single-molecule biophysical experiments yield data that contain a wealth of dynamic information, in addition to the equilibrium distributions derived from histograms of the time series. In typical force spectroscopic setups…
Concentrated aqueous solutions of the protein lysozyme undergo a liquid solid transition upon a temperature quench into the unstable spinodal region below a characteristic arrest temperature of Tf=15C. We use video microscopy and…
A coarse-grained off-lattice model that is not biased in any way to the native state is proposed to fold proteins. To predict the native structure in a reasonable time, the model has included the essential effects of water in an effective…