相关论文: Thermal Motions of the E. Coli Glucose-Galactose B…

We simulate the electrical properties of a device realized by a G protein coupled receptor (GPCR), embedded in its membrane and in contact with two metallic electrodes through which an external voltage is applied. To this purpose, recently,…

We describe a novel coarse-grained simulation method for modelling the dynamics of globular macromolecules, such as proteins. The macromolecule is treated as a continuum that is subject to thermal fluctuations. The model includes a…

We present a novel Monte Carlo simulation of protein folding, in which all heavy atoms are represented as interacting hard spheres. This model includes all degrees of freedom relevant to folding - all sidechain and backbone torsions - and…

A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model, are used to carry out long (several $\mu$s) simulation and study folding transition and transport of proteins…

Molecular dynamic (MD) simulations are applied to investigate the dependency of the kinetic friction coefficient on the temperature at the nano-scale. The system is comprised of an aluminum spherical particle consisting of 32000 atoms in an…

The elastic properties of semiflexible polymers are of great importance in biology. There are experiments on biopolymers like double stranded DNA, which twist and stretch single molecules to probe their elastic properties. It is known that…

Using analytical calculations and computer simulations we consider both the lateral diffusion of a membrane protein and the fluctuation spectrum of the membrane in which the protein is embedded. The membrane protein interacts with the…

Due to the time-scale limitations of all-atom simulation of proteins, there has been substantial interest in coarse-grained approaches. Some methods, like "Resolution Exchange," [E. Lyman et al., Phys. Rev. Lett. 96, 028105 (2006)] can…

Native extracellular matrices (ECMs), such as those of the human brain and other neural tissues, exhibit networks of molecular interactions between specific matrix proteins and other tissue components. Guided by these naturally…

The spatiotemporal oscillation patterns of the proteins MinD and MinE are used by the bacterium E. coli to sense its own geometry. Strikingly, both computer simulations and experiments have recently shown that for the same geometry of the…

We introduce an approach for performing "very long" computer simulations of the dynamics of simplified, folded proteins. Using an alpha-carbon protein model and a fine grid to mimic continuum computations at increased speed, we perform…

With increasing interest in the use of glassy carbon (GC) for a wide variety of application areas, the need for developing fundamental understanding of its mechanical properties has come to the forefront. Further, recent theoretical and…

The coil-globule transition has been studied for A-B copolymer chains both by means of lattice Monte Carlo simulations using bond fluctuation algorithm and by a numerical self-consistent field method. Copolymer chains of fixed length with A…

After a brief review of the protein folding quantum theory and a short discussion on its experimental evidences the mechanism of glucose transport across membrane is studied from the point of quantum conformational transition. The…

In this article the notion of metabolic turnover is revisited in the light of recent results of out-of-equilibrium thermodynamics. By means of Monte Carlo methods we perform an exact uniform sampling of the steady state fluxes in a genome…

Mechanical stretching of six proteins is studied through molecular dynamics simulations. The model is Go-like, with Lennard-Jones interactions at native contacts. Low temperature unfolding scenarios are remarkably complex and sensitive to…

We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…

Considerable insight into the functional activity of proteins and enzymes can be obtained by studying the low-energy conformational distortions that the biopolymer can sustain. We carry out the characterization of these large scale…

The description of carrier dynamics in spatially confined semiconductor nanocrystals (NCs), which have enhanced electron-hole and exciton-phonon interactions, is a great challenge for modern computational science. These NCs typically…

We investigate the motion of a colloidal particle driven out of equilibrium by an external torque. We use the molecular dynamics simulation that is alternative to the numerical integration approach based on the Langevin equation and is…