相关论文: Unfolding Rates for the Diffusion-Collision Model
By providing new insights into the distribution of a protein's torsion angles, recent statistical models for this data have pointed the way to more efficient methods for protein structure prediction. Most current approaches have…
Reaction-diffusion systems have been proposed as a model for pattern formation and morphogenesis. The Fickian diffusion typically employed in these constructions model the Brownian motion of particles. The biological and chemical elements…
We study the unfolding of a single polymer chain due to an external force. We use a simplified model which allows to perform all calculations in closed form without assuming a Boltzmann-Gibbs form for the equilibrium distribution.…
An anisotropic random barrier model is presented, in which the transition probabilities in different directions have different probability density functions. At low temperatures, the anisotropic long--time diffusion coefficients, obtained…
We investigate the influence of nearby two-level systems on the dynamics of a qubit. The intrinsic decoherence is given by a coupling of both the qubit and the two-level systems to a heat bath. Assuming weak interactions between the qubit…
We recently introduced a physical model [Hoang et al., P. Natl. Acad. Sci. USA (2004), Banavar et al., Phys. Rev. E (2004)] for proteins which incorporates, in an approximate manner, several key features such as the inherent anisotropy of a…
Diffusion plays a key role in microstructure evolution at multicomponent alloys: diffusion controls the kinetics of phase transformations and alloy homogenization. This study aims at developing computationally efficient approaches to…
Mechanical unfolding of the fourth domain of Distyostelium discoideum filamin (DDFLN4) was studied in detail using the C$_{\alpha}$-Go model. We show that unfolding pathways of this protein depend on the pulling speed. The agreement between…
We analyze collisional decoherence of atoms or molecules prepared in a coherent superposition of nondegenerate internal states at ultralow temperatures and placed in an ultracold buffer gas. Our analysis is applicable for an arbitrary bath…
A reduced protein model with five to six atoms per amino acid and five amino acid types is developed and tested on a three-helix-bundle protein, a 46-amino acid fragment from staphylococcal protein A. The model does not rely on the widely…
The freeze-out process in heavy ion collisions is driven by the competition between the scattering rate and the expansion rate of the matter. We analyse the expansion rate $\Theta$ (often called Hubble flow) in relativistic heavy ion…
To analyze hydration effects on macromolecular diffusion, the friction coefficients of macromolecules were examined using molecular dynamics simulations with an all-atom model. In the present study, a method was introduced to decompose the…
Rock formations are very often characterized by the presence of fractures that have grown subcritically over geological time scales and under evolving stress fields. In mechanically layered systems, such fractures can either become…
Proteins are linear chain molecules that play a central role in life and health. Protein native state folds are modular assemblies of space-filling building blocks of {\alpha}-helices, \{beta}-sheets and tight turns. Here we deduce the…
Equations that govern the temperature-dependence of the rate constants, Gibbs energies,enthalpies, entropies and heat capacities of activation for folding and unfolding of spontaneously-folding fixed two-state systems have been derived…
We consider a single-species diffusion-limited annihilation reaction with reactants confined to a two-dimensional surface with one arbitrarily large dimension and the other comparable in size to interparticle distances. This situation could…
Bulk matter produced in heavy ion collisions has multiple conserved quantum numbers like baryon number, strangeness and electric charge. The diffusion process of these charges can be described by a diffusion matrix describing the…
Explicit analytical expressions for the drag and diffusion coefficients of a spherical particle attached to the interface between two immiscible fluids are constructed for the case of a small viscosity ratio between the fluid phases. The…
Incomplete release profiles of protein delivery systems can be caused by unfolding and denaturation of proteins due to protein-biomaterial interactions. This paper investigates the mechanisms causing incomplete release of the wound healing…
Effect of molecular crowding and confinement experienced by protein in the cell during unfolding has been studied by modeling a linear polymer chain on a percolation cluster. It is known that internal structure of the cell changes in time,…