相关论文: Unfolding Rates for the Diffusion-Collision Model
Extensive numerical simulation are reported for the structure and dynamics of large clusters on metal(100) surfaces. Different types of perimeter hopping processes makes center-of-mass of the cluster to follow a a random walk trajectory.…
The proposal of this paper is to provide a simple angular random walk model to build up polypeptide structures, which encompass properties of dihedral angles of folded proteins. From this model, structures will be built with lengths ranging…
DNA hairpin molecules with periodic base sequences can be expected to exhibit a regular coarse-grained free energy landscape (FEL) as function of the number of open base pairs and applied mechanical force. Using a commonly employed model,…
A receding-front model for drying of porous material is proposed that explains their drying-rate curves based on the dynamics of the evaporation front. The falling-rate regime is attributed to the slowing down of the front's propagation…
Despite many advances in computational modeling of protein structures, these methods have not been widely utilized by experimental structural biologists. Two major obstacles are preventing the transition from a purely-experimental to a…
A general theoretical framework is developed using free energy functional methods to understand the effects of heterogeneity in the folding of a well-designed protein. Native energetic heterogeneity arising from non-uniformity in native…
We study the statistical mechanics of RNA secondary structures designed to have an attraction between two different types of structures as a model system for heteropolymer aggregation. The competition between the branching entropy of the…
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…
A scattering model is developed for ultracold molecular collisions, which allows inelastic processes, chemical reactions, and complex formation to be treated in a unified way. All these scattering processes and various combinations of them…
The Boltzmann equation for $d$-dimensional inelastic Maxwell models is considered to determine the collisional moments of second, third and fourth degree in a granular binary mixture. These collisional moments are exactly evaluated in terms…
Diffusion coefficients are essential microphysics input for modeling white dwarf evolution, as they impact phase separation at crystallization and sedimentary heat sources. Present schemes for computing diffusion coefficients are accurate…
The bulk nuclear matter produced in heavy ion collisions carries a multitude of conserved quantum numbers: electric charge, baryon number, and strangeness. Therefore, the diffusion processes associated to these conserved charges cannot…
First shells of hydration and bulk solvent plays a crucial role in the folding of proteins. Here, the role of water in the dynamics of proteins has been investigated using a theoretical protein-solvent model and a statistical physics…
Utilizing a partitioning method based on equal (or unequal) probabilities -- without incorporating the alpha-cluster ($\alpha$-cluster) model -- allows for the derivation of diverse topological configurations of nuclear fragments resulting…
A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…
Diffusion of particles through an heterogenous obstacle line is modeled as a two-dimensional diffusion problem with a one--directional nonlinear convective drift and is examined using two-scale asymptotic analysis. At the scale where the…
The formation of chain-folded structures from the melt is observed in molecular dynamics simulations resembling the lamellae of polymer crystals. Crystallization and subsequent melting temperatures are related linearly to the inverse…
We investigate, both experimentally and theoretically, the bifurcation to alternans in heart tissue. Previously, this phenomenon has been modeled either as a smooth or as border-collision period-doubling bifurcation. Using a new…
An asymmetric exclusion model on an open chain with random rates for hopping particles, where overtaking is also possible, is studied numerically and by computer simulation. The phase structure of the model and the density profiles near the…
The structures of proteins exhibit secondary elements composed of helices and loops. Comparison of several water-only hydrophobicity scales with the functionalities of two repeat proteins shows that these secondary elements possess…