Related papers: Folding in lattice models with side chains
An extended Hubbard model on a two-leg ladder is numerically studied by means of the quantum Monte Carlo techniques. The model we study has the nearest-neighbor interactions which are repulsive along chains and attractive for rungs. The…
A sampling method for spin systems is presented. The spin lattice is written as the union of a nested sequence of sublattices, all but the last with conditionally independent spins, which are sampled in succession using their marginals. The…
In the present paper we revisit, theoretical and experimentally, the fall of a folded U-chain and of a pile-chain. The model calculation implies the division of the whole system into two subsystems of variable mass, allowing to explore the…
We analyze the kinematics of multigrid Monte Carlo algorithms by investigating acceptance rates for nonlocal Metropolis updates. With the help of a simple criterion we can decide whether or not a multigrid algorithm will have a chance to…
We have studied the linear resistance of a three dimensional lattice Superconductor model in the London limit London lattice model by Monte Carlo simulation of the vortex loop dynamics. We find excellent finite size scaling at the phase…
We use a three dimensional cubic lattice model of proteins to study their properties that determine folding to the native state. The protein chain is modeled as a sequence of $N$ beads. The interactions between beads are taken from a…
In recent past, experiments and simulations have suggested that apart from the solvent friction, friction arising from the protein itself plays an important role in protein folding by affecting the intra-chain loop formation dynamics. This…
If a stochastic system during some periods of its evolution can be divided into non-interacting parts, the kinetics of each part can be simulated independently. We show that this can be used in the development of efficient Monte Carlo…
RNA secondary structure folding kinetics is known to be important for the biological function of certain processes, such as the hok/sok system in E. coli. Although linear algebra provides an exact computational solution of secondary…
An effective low-energy description for multi-leg spin-1/2 Heisenberg ladders with an odd number of legs is proposed. Using a newly developed Monte Carlo loop algorithm and exact diagonalization techniques, the uniform and staggered…
Lattice-switch Monte Carlo is an efficient method for calculating the free energy difference between two solid phases, or a solid and a fluid phase. Here, we provide a brief introduction to the method, and list its applications since its…
The master equation for 12-monomer lattice heteropolymers is solved numerically and the time evolution of the occupancy of the native state is determined. At low temperatures, the median folding time follows the Arrhenius law and is…
Rigidity percolation provides an important basis for understanding the onset of mechanical stability in disordered materials. While most studies on the triangular lattice have focused on static properties at fixed bond~(site) occupation…
A model with a half boson degree of freedom per lattice site in one dimension is developed. The boson is protected from developing a gap by translation symmetry: while the left movers are at zero quasi-momentum, the associated right movers…
A `forward walking' Green's Function Monte Carlo algorithm is used to obtain expectation values for SU(3) lattice Yang-Mills theory in (3+1) dimensions. The ground state energy and Wilson loops are calculated, and the finite-size scaling…
We study dynamical aspects of three--dimensional gonihedric spins by using Monte--Carlo methods. The interest of this family of models (parametrized by one self-avoidance parameter $\kappa$) lies in their capability to show remarkably slow…
The one dimensional Kondo lattice model is investigated using Quantum Monte Carlo and transfer matrix techniques. In the strong coupling region ferromagnetic ordering is found even at large band fillings. In the weak coupling region the…
The one-dimensional fall of a folded chain with one end suspended from a rigid support and a chain falling from a resting heap on a table is studied. Because their Lagrangians contain no explicit time dependence, the falling chains are…
The solvability of the three-dimensional O($N$) scalar field theory in the large $N$ limit makes it an ideal toy model exhibiting "walking" behavior, expected in some SU($N$) gauge theories with a large number of fermion flavors. We study…
Monte Carlo simulations are used to study lattice gases of particles with extended hard cores on a two dimensional square lattice. Exclusions of one and up to five nearest neighbors (NN) are considered. These can be mapped onto hard squares…