相关论文: Molecular Dynamics Simulation of Folding and Diffu…

We investigate the interplay between post-translational folding and escape of two small single-domain proteins at the ribosomal exit tunnel by using Langevin dynamics with coarse-grained models. It is shown that at temperatures lower or…

The folding kinetics of a number of sequences for off-lattice continuum model of proteins is studied using Langevin simulations at two values of the friction coefficient. We show that there is a remarkable correlation between folding times,…

The internal dynamics of macro-molecular systems is characterized by widely separated time scales, ranging from fraction of ps to ns. In ordinary molecular dynamics simulations, the elementary time step dt used to integrate the equation of…

The motion of molecules on solid surfaces is of interest for technological applications such as catalysis and lubrication, but it is also a theoretical challenge at a more fundamental level. The concept of activation barriers is very…

We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding…

We elucidate the physics of the dynamical transition via 10-100ns molecular dynamics simulations at temperatures spanning 160-300K. By tracking the energy fluctuations, we show that the protein dynamical transition is marked by a cross-over…

The goal of this PhD thesis was to characterize the properties of friction in nanotubes and from a more general point of view the understanding of the microscopic origin of friction. Indeed, the relative simplicity of the system allows us…

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…

We investigate the dynamics of polymer translocation through a nanopore using two-dimensional Langevin dynamics simulations. In the absence of external driving force, we consider a polymer which is initially placed in the middle of the pore…

Folding kinetics of a lattice model of protein is studied. It uses the Random Energy Model for the intrachain couplings and a temperature dependent free energy of solvation derived from a realistic hydration model of apolar solutes. The…

Porous materials are widely used for applications in gas storage and separation. The diffusive properties of a variety of gases in porous media can be modeled using molecular dynamics simulations that can be computationally demanding…

We study the dynamics of protein folding via statistical energy-landscape theory. In particular, we concentrate on the local-connectivity case with the folding progress described by the fraction of native conformations. We obtain…

The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk…

We investigate the translocation of stiff polymers in the presence of binding particles through a nanopore by two-dimensional Langevin dynamics simulations. We find that the mean translocation time shows a minimum as a function of the…

Diffusion in a multidimensional energy surface with minima and barriers is a problem of importance in statistical mechanics and also has wide applications, such as protein folding. To understand it in such a system, we carry out theory and…

We use a three dimensional cubic lattice model of proteins to study their properties that determine folding to the native state. The protein chain is modeled as a sequence of $N$ beads. The interactions between beads are taken from a…

The thermodynamics of proteins indicate that folding/unfolding takes place either through stable intermediates or through a two-state process without intermediates. The rather short folding times of the two-state process indicate that…

Accurate modeling of diffusive transport of nanoparticles across nanopores is a particularly challenging problem. The reason is that for such narrow pores the large surface-to-volume ratio amplifies the relevance of the nanoscopic details…

The impact of thermal fluctuations on the translocation dynamics of a polymer chain driven through a narrow pore has been investigated theoretically and by means of extensive Molecular-Dynamics (MD) simulation. The theoretical consideration…

Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…