相关论文: Folding in lattice models with side chains

Extensive Monte Carlo simulations are performed to analyze a recent neutron diffraction experiment on a distorted triangular lattice compound RbCoBr$_3$. We consider a spin-lattice model, where both spin and lattice are Ising variables.…

We study the thermodynamics and kinetics of folding for a small peptide. Our data rely on Monte Carlo simulations where the interactions among all atoms are taken into account. Monte Carlo kinetics is used to study folding of the peptide at…

We consider Monte Carlo algorithms for the simulation of charged lattice gases with purely local dynamics. We study the mobility of particles as a function of temperature and show that the poor mobility of particles at low temperatures is…

The simulation of a protein's folding process is often done via stochastic local search, which requires a procedure to apply structural changes onto a given conformation. Here, we introduce a constraint-based approach to enumerate lattice…

Semiflexible macromolecules in dilute solution under very good solvent conditions are modeled by self-avoiding walks on the simple cubic lattice ($d=3$ dimensions) and square lattice ($d=2$ dimensions), varying chain stiffness by an energy…

The effectiveness of the recently developed Fixed-Node Quantum Monte Carlo method for lattice fermions, developed by van Leeuwen and co-workers, is tested by applying it to the 1D Kondo lattice, an example of a one-dimensional model with a…

The equilibrium properties of hard rod monolayers are investigated in a lattice model (where position and orientation of a rod are restricted to discrete values) as well as in an off--lattice model featuring spherocylinders with continuous…

Using Monte Carlo simulations, we study the properties of an elastic triangular lattice subject to a random background potential. As the cooling rate is reduced, we observe a rather sudden crossover between two different glass phases, one…

We study the phase diagram of the Kondo-lattice model with nearest-neighbor hopping in the square lattice by means of the variational Monte Carlo technique. Specifically, we analyze a wide class of variational wave functions that allow…

We have used kinetic Monte Carlo simulations to study the kinetics of unfolding of cross-linked polymer chains under mechanical loading. As the ends of a chain are pulled apart, the force transmitted by each crosslink increases until it…

This paper considers the Monte Carlo dynamics of random dimer coverings of the square lattice, which can be mapped to a rough interface model. Two kinds of slow modes are identified, associated respectively with long-wavelength fluctuations…

Computational experiments are used to show that grain boundary mobility is independent of driving force in a two-dimensional, square-lattice Ising model with Metropolis kinetics. This is established over the entire Monte Carlo temperature…

Compact polymers are self-avoiding random walks which visit every site on a lattice. This polymer model is used widely for studying statistical problems inspired by protein folding. One difficulty with using compact polymers to perform…

We apply the exchange Monte Carlo method to the ordering dynamics of the three-state Potts model with the conserved order parameter. Even for the deeply quenched case to low temperatures, we have observed a rapid domain growth; we have…

The extended Hubbard Hamiltonian is a widely accepted model for uncovering the effects of strong correlations on the phase diagram of low-dimensional systems, and a variety of theoretical techniques have been applied to it. In this paper…

We investigate the dynamics of a single semiflexible filament, under the action of a compressing force, using numerical simulations and scaling arguments. The force is applied along the end to end vector at one extremity of the filament,…

Monte Carlo simulations of a simple lattice model of protein folding show two distinct regimes depending on the chain length. The first regime well describes the folding of small protein sequences and its kinetic counterpart appears to be…

Monte Carlo simulations of a Miyazawa-Jernigan lattice-polymer model indicate that, depending on the native's structure geometry, the model exhibits two broad classes of folding mechanisms for two-state folders. Folding to native structures…

We theoretically investigate the kinetics of the folding transition of a single semiflexible polymer. In the folding transition, the growth rate decrease with an increase in the number of monomers in a collapsed domain, suggesting that the…

We study a harmonic triangular lattice, which relaxes in the presence of a weak, short-wavelength periodic potential. Monte Carlo simulations reveal that the elastic lattice has only short-ranged positional correlations, despite the absence…