相关论文: Folding in lattice models with side chains
Physical mechanisms underlying the empirical correlation between relative contact order (CO) and folding rate among naturally-occurring small single-domain proteins are investigated by evaluating postulated interaction schemes for a set of…
Two coarse-grained models for polymer chains in dense glass-forming polymer melts are studied by computer simulation: the bond-fluctuation model on a simple cubic lattice, where a bond-length potential favors long bonds, is treated by…
We study a generalized clock model on the simple cubic lattice. The parameter of the model can be tuned such that the amplitude of the leading correction to scaling vanishes. In the main part of the study we simulate the model with $Z_8$…
A model describing the three-dimensional folding of the triangular lattice on the face-centered cubic lattice is generalized allowing the presence of defects corresponding to cuts in the two-dimensional network. The model can be expressed…
Quantum Monte Carlo method is used to look into the superconductivity in the three-leg Hubbard ladder. The enhanced correlation for the pairing across the central and edge chains, which has been predicted in the weak-coupling…
We have studied a model of self-attracting walk proposed by Sapozhnikov using Monte Carlo method. The mean square displacement $ < R^2(t) > \sim t^{2\nu}$ and the mean number of visited sites $ < S(t) > \sim t^{k}$ are calculated for one-,…
Folding properties of a two-dimensional toy protein model containing only two amino-acid types, hydrophobic and hydrophilic, respectively, are analyzed. An efficient Monte Carlo procedure is employed to ensure that the ground states are…
We consider six different secondary structures of proteins and construct two types of Go-type off-lattice models: with the steric constraints and without. The basic aminoacid-aminoacid potential is Lennard Jones for the native contacts and…
We offer simple solutions to three kinematic problems that occur in the folding of proteins. We show how to construct suitably local elementary Monte Carlo moves, how to close a loop, and how to fold a loop without breaking the bond that…
A method based on Monte Carlo sampling of the probability flows projected onto the subspace of one or more slow variables is proposed for investigation of dynamic and static properties of lattice spin systems. We illustrate the method by…
We present Monte Carlo computer simulations for melts of semiflexible randomly knotted and randomly concatenated ring polymers on the fcc lattice and in slit confinement. Through systematic variation of the slit width at fixed melt density,…
We consider equilibrium folding transitions in lattice protein models with and without side chains. A dimensionless measure, $Omega_{c}$, is introduced to quantitatively assess the degree of cooperativity in lattice models and in real…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
A theta-term, which couples to topological charge, is added to the two-dimensional lattice CP^3 model and U(1) gauge theory. Monte Carlo simulations are performed and compared to strong-coupling character expansions. In certain instances, a…
We consider two types of Go models of a protein (crambin) and study their kinetics through molecular dynamics simulations. In the first model, the residue -- residue contact interactions are selected based on a cutoff distance, $R_c$,…
We present computer simulations of a dynamic Monte Carlo algorithm for polymer chains on the FCC lattice which takes explicitly into account the possibility to overcome topological constraints by controlling the rate at which nearby polymer…
Structural fluctuations in the thermal equilibrium of the kinesin motor domain are studied using a lattice protein model with Go interactions. By means of the multi-self-overlap ensemble (MSOE) Monte Carlo method and the principal component…
We consider several multiscale-in-time kinetic Monte Carlo models, in which some variables evolve on a fast time scale, while the others evolve on a slow time scale. In the first two models we consider, a particle evolves in a…
A kinetic Ising model is analyzed where spin variables correspond to lattice cells with mobile or immobile particles. Introducing additional restrictions for the flip processes according to the n-spin facilitated kinetic Ising model and…
We present a new Monte Carlo scheme for the efficient simulation of multi-polymer systems. The method permits chains to be inserted into the system using a biased growth technique. The growth proceeds via the use of a retractable feeler,…