Related papers: Remark on Protein Collapse from a Random Walk
A global picture of a random particle movement is given by the convex hull of the visited points. We obtained numerically the probability distributions of the volume and surface of the convex hulls of a selection of three types of…
We study secondary structures of random RNA molecules by means of a renormalized field theory based on an expansion in the sequence disorder. We show that there is a continuous phase transition from a molten phase at higher temperatures to…
The effect of topology on the collapse transition and instantaneous shape of an energy polydisperse polymer (a model heteropolymer) is studied by means of computer simulations. In particular, we consider three different chain topology,…
We discuss multiscale simulations of long biopolymer translocation through wide nanopores that can accommodate multiple polymer strands. The simulations provide clear evidence of folding quantization, namely, the translocation proceeds…
We study the evolution of a random walker on a conservative dynamic random environment composed of independent particles performing simple symmetric random walks, generalizing results of [16] to higher dimensions and more general transition…
We find the collapse of columns of granular rods to show range of behaviors that depends on particle aspect ratio (length $L$ to diameter $d$) and initial pile geometry (height/radius). For all aspect ratios $L/d$ below 24 there exists a…
By means of continuous space Monte Carlo simulation we study conformational structures formed by star and comb heteropolymers during kinetics of folding from the coil to the globule, as well as the corresponding equilibrium states on going…
We present a statistical model of a dilute polymer solution in good solvent in the presence of low-molecular weight cosolvent. We investigate the conformational changes of the polymer induced by a change of the cosolvent concentration and…
Suspensions of swimming particles exhibit complex collective behaviors driven by hydrodynamic interactions, showing persistent large-scale flows and long-range correlations. While heavily studied, it remains unclear how such structures…
The mechanism of cold- and pressure-denaturation are matter of debate. Some models propose that when denaturation occurs more hydrogen bonds between the molecules of hydration water are formed. Other models identify the cause in the density…
The size distribution of ionized regions during the epoch of reionization -- a key ingredient in understanding the HI power spectrum observable by 21cm experiments -- can be modelled analytically using the excursion set formalism of random…
We propose a general theory to describe the distribution of protein-folding transition paths. We show that transition paths follow a predictable sequence of high-free-energy transient states that are separated by free-energy barriers. Each…
Collapse, or a gravitational-like phase transition is studied in a microcanonical ensemble of particles with an attractive $1/r^{\alpha}$ potential. A mean field continuous integral equation is used to determine a saddle-point density…
The branching annihilating random walk is studied on a random graph whose sites have uniform number of neighbors (z). The Monte Carlo simulations in agreement with the generalized mean-field analysis indicate that the concentration decreses…
We simulate a model of repulsively interacting colloids on a commensurate two-dimensional triangular pinning substrate where the amount of heterogeneous motion that appears at melting can be controlled systematically by turning off a…
We propose a simple mean-field theory for the structure of ring polymer melts. By combining the notion of topological volume fraction and a classical van der Waals theory of fluids, we take into account many body effects of topological…
We have performed chain-growth simulations of minimalistic hybrid lattice models for polymers interacting with interfaces of attractive solid substrates in order to gain insights into the conformational transitions of the polymers in the…
We study, in d-dimensions, the random walker with geometrically shrinking step sizes at each hop. We emphasize the integrated quantities such as expectation values, cumulants and moments rather than a direct study of the probability…
We show that non-entangled polymers display an elastic-like behaviour at a macroscopic scale (probed at some 0.100 mm thickness) up to at least hundred degrees above the glass transition temperature. This observation, found under…
Dimerization and subsequent aggregation of polymers and biopolymers often occur under nonequilibrium conditions. When the initial state of the polymer is not collapsed or the final folded native state, the dynamics of dimerization can…