Folding and Unfolding Simulations of a Three-Stranded Beta-Sheet Protein

Understanding the folding processes of a protein into its three-dimensional native structure only with its amino-acid sequence information is a long-standing challenge in modern science. Two- hundred independent folding simulations (starting from non-native conformations) and two- hundred independent unfolding simulations (starting from the folded native structure) are performed using the united-residue force field and Metropolis Monte Carlo algorithm for betanova (three-stranded antiparallel beta-sheet protein). From these extensive computer simulations, two representative folding pathways and two representative unfolding pathways are obtained in the reaction coordinates such as the fraction of native contacts, the radius of gyration, and the root- mean-square deviation. The folding pathways and the unfolding pathways are similar each other. The largest deviation between the folding pathways and the unfolding pathways results from the root-mean-square deviation near the folded native structure. In general, unfolding computer simulations could capture the essentials of folding simulations.

Advances in the kinetics of heat and mass transfer in near-continuous complex flows

The study of macro continuous flow has a long history.Simultaneously,the exploration of heat and mass transfer in small systems with a particle number of several hundred or less has gained significant interest in the fields of statistical physics and nonlinear science.However,due to absence of suitable methods,the understanding of mesoscale behavior situated between the aforementioned two scenarios,which challenges the physical function of traditional continuous fluid theory and exceeds the simulation capability of microscopic molecular dynamics method,remains considerably deficient.This greatly restricts the evaluation of effects of mesoscale behavior and impedes the development of corresponding regulation techniques.To access the mesoscale behaviors,there are two ways:from large to small and from small to large.Given the necessity to interface with the prevailing macroscopic continuous modeling currently used in the mechanical engineering community,our study of mesoscale behavior begins from the side closer to the macroscopic continuum,that is from large to small.Focusing on some fundamental challenges encountered in modeling and analysis of near-continuous flows,we review the research progress of discrete Boltzmann method(DBM).The ideas and schemes of DBM in coarse-grained modeling and complex physical field analysis are introduced.The relationships,particularly the differences,between DBM and traditional fluid modeling as well as other kinetic methods are discussed.After verification and validation of the method,some applied researches including the development of various physical functions associated with discrete and non-equilibrium effects are illustrated.Future directions of DBM related studies are indicated.

Computer Simulation Study of Biopolymer Betanova

Betanova is a monomeric, three-stranded antiparallel beta-sheet protein with twenty residues. The pathways between the folded native structure and unfolded conformations of betanova are studied using UNRES force field and the most popular computer simulation method, Metropolis Monte Carlo algorithm. At a fixed temperature, 100 Monte Carlo simulations are performed, starting from the folded native structure, and the pathways are obtained at two different temperatures.

Cooperation in an asymmetric volunteer's dilemma game with relatedness

What motivates some members of a social group to voluntarily incur costs in order to provide for the common good? This question lies at the heart of theoretical and empirical studies of cooperative behavior. This is also the question that underlies the classic volunteer's dilemma model, which has been previously explored in scenarios where group members are related or interact asym- metrically. Here we present a model that combines asymmetry and relatedness, showing that the probability of volunteerism in such systems depends closely on both the degree of asymmetry and level of relatedness between interacting individuals. As has been shown in previous volunteer's dilemma models, the payoff ratio and overall group size also influence the probability of volunteerism. The probability of volunteerism decreases with increasing group size or decreasing cost-to-benefit ratio of the coplayers; in the presence of asymmetrical interactions, subordinate players were more likely to offer public goods than the dominant player. More asymmetrical interactions decrease the probability of volunteerism of the dominant player; overall volunteerism increases with increasing relatedness.

Simple black holes with anisotropic fluid

We study a spherically symmetric spacetime made of an anisotropic fluid whose radial equation-of-state is given by p_1=-ρ. This case allows analytic solutions and is a good example for studying the static configuration of a black hole plus matter. For a given equation-of-state parameter w_2 = p_2/ρ for angular directions, we find the exact solutions of the Einstein equation described by two parameters. We classify the solutions into six types based on the behavior of the metric function. Depending on the parameters, the solutions can have event and cosmological horizons. One of the solution types corresponds to a generalization of the Reissner-Nordstr(o|¨)m black hole, the thermodynamic properties for which are obtained in a simple form. The solutions are stable under radial perturbations.