Monte Carlo Simulation Of Proteins And Study Of Membrane Behavior

In this thesis, we develop Monte Carlo Algorithm for all-atom protein simula-tion, with combination of a efficient backbone sampling method and a side-chain sampling method. In chapter two. we describe Monte Carlo Algortihm and the conformation sampling method in detail. implement them in a high-accuracy pro-tein modeling pacage. Rosetta. and run a series benchmark for confirming our algorithm. In chaper three. the density of states of trpzip2has been explored at all-atom level. Replica exchange Monte Carlo method was used for sufficient sampling over a wide range of temperature. Micro-canonical anlaysis was per-formed to confirm that the phase transition behavior of this two-state folder is first-order-like. Canonical analysis of heat capacity suggests that hydrogen bond-ing interaction exerts a considerable positive influence on folding cooperativity, in contrast, hydrophobic interaction is insufficient for high degree of folding cooper-ativity. Furthermore, we explain physical nature of the folding process from free energy landscape perspective and extensively analyse of hydrogen bonding and stacking energy.Another part of this thesis is the study of the behavior of lipid bilayers. which contains:1. Study of a pore in bilayer membrane using Dissipative Parti-cle Dynamics Simulation,2. Study of the dynamics of disk-to-vesicle transforma-tion using Dissipative Particle Dynamics Simulation and coarse-grained Molecular Dynamics Simulation.3. Study of the system that tubular membrane confining collidal particles using analytical method and simulation. In chapter four, we de-velop a DPD model for simulating bilayer system. Extensive simulation of lipid membrane with different projected surface area were performed, thus we investi-gate the relationship between surface tension calculated by stress tensor and that by fluctuation. We compare our result to previous theory and simulation and try to clarify some conflicts between them. We also find a simple model that can calculate line tension with membrane bending rigidity and membrane thickness, the simulation data agrees with the model then we propose a new computational method for mesuring bending rigidity. In chapter five, with the same membrane model, we study the folding kinetics of transition from disk membrane to vesicle. The scaling behavior of closing time as function of the size of disk is calculated. Then we investigate the effects of temperature and viscosity on the closing time. In chapter six. we study the system that tubular membrane confining collidal par-itcles theoretically and introduce temperature with Monte Carlo simulation. We find that themal fluctuation exerts significant influence to the phase transition behavior. We also perform Langevin simulation with a coarse-grained membrane model to study tubular membrane confining a Janus particle.