相关论文: Simulation, Experiment, and Evolution: Understandi…

Motivation: Protein folding is a dynamic process during which a protein's amino acid sequence undergoes a series of 3-dimensional (3D) conformational changes en route to reaching a native 3D structure; the resulting 3D structural…

To what extent do general features of folding/unfolding kinetics of small globular proteins follow from their thermodynamic properties? To address this question, we investigate a new simplifed protein chain model that embodies a cooperative…

Random packings of stiff rods are self-supporting mechanical structures stabilized by long range interactions induced by contacts. To understand the geometrical and topological complexity of the packings, we first deploy X-ray computerized…

Proteins are polymerized by cyclic machines called ribosome which use their messenger RNA (mRNA) track also as the corresponding template and the process is called translation. We explore, in depth and detail, the stochastic nature of the…

A coarse-grained variational model is used to investigate the polymer dynamics of barrier crossing for a diverse set of two-state folding proteins. The model gives reliable folding rate predictions provided excluded volume terms that induce…

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,…

Mechanical unfolding and refolding of ubiquitin are studied by Monte Carlo simulations of a Go model with binary variables. The exponential dependence of the time constants on the force is verified, and folding and unfolding lengths are…

Nucleation processes are at the heart of a large number of phenomena, from cloud formation to protein crystallization. A recently emerging area where nucleation is highly relevant is the initiation of filamentous protein self-assembly, a…

We consider six different secondary structures of proteins and construct two types of Go-type off-lattice models: with the steric constraints and without. The basic aminoacid-aminoacid potential is Lennard Jones for the native contacts and…

A major challenge in molecular simulations is to describe denaturant-dependent folding of proteins order to make direct comparisons with {\it in vitro} experiments. We use the molecular transfer model, which is currently the only method…

Protein folding is a problem of large interest since it concerns the mechanism by which the genetic information is translated into proteins with well defined three-dimensional (3D) structures and functions. Recently theoretical models have…

Computational prediction of RNA structures is an important problem in computational structural biology. Studies of RNA structure formation often assume that the process starts from a fully synthesized sequence. Experimental evidence,…

This manuscript reviews recent results of large scale shell model calculations on N=Z nuclei. The topics discussed include the role proton-neutron pairing on the binding energies of pf-shell nuclei and his influence on backbending rotors;…

We inquire how structure emerges during the process of protein folding. For this we scrutinise col- lective many-atom motions during all-atom molecular dynamics simulations. We introduce, develop and employ various topological techniques,…

Reactive pathways to nucleation in a three-dimensional Ising model at 60% of the critical temperature are studied using transition path sampling of single spin flip Monte Carlo dynamics. Analysis of the transition state ensemble (TSE)…

Proteins must fold quickly to acquire their biologically functional three-dimensional native structures. Hence, these are mainly stabilized by local contacts, while intricate topologies such as knots are rare. Here, we reveal the existence…

Self-assembly of proteins is a biological phenomenon which gives rise to spontaneous formation of amyloid fibrils or polymers. The starting point of this phase, called nucleation exhibits an important variability among replicated…

A spherical model of skeleton with junctions is investigated by Monte Carlo simulations. The model is governed by one-dimensional bending energy. The results indicate that the model undergoes a first-order transition separating the smooth…

A Monte Carlo method is used in order to simulate the competition between the molecular relaxation and crystallization times in the formation of a glass. The results show that nucleation is avoided during supercooling and produce…

We study the conformation and scaling properties of a self-avoiding fluid membrane, subject to an osmotic pressure $p$, by means of Monte Carlo simulations. Using finite size scaling methods in combination with a histogram reweighting…