Related papers: Unbiased sampling of globular lattice proteins in …
In this manuscript, we describe a new configurational bias Monte Carlo technique for the simulation of peptides. We focus on the biologically relevant cases of linear and cyclic peptides. Our approach leads to an efficient,…
The HP model of protein folding, where the chain exists in a free medium, is investigated using a parallel Monte Carlo scheme based upon Wang-Landau sampling. Expanding on the work of Wust and Landau by introducing a lesser known replica…
With its systematic exploration of probability distributions, Hamiltonian Monte Carlo is a potent Markov Chain Monte Carlo technique; it is an approach, however, ultimately contingent on the choice of a suitable Hamiltonian function. By…
We present a new Monte Carlo algorithm that produces results of high accuracy with reduced simulational effort. Independent random walks are performed (concurrently or serially) in different, restricted ranges of energy, and the resultant…
We study the equilibrium properties of a flexible homopolymer where consecutive monomers are represented by impenetrable hard spheres that are tangent to each other, and non-consecutive monomers interact via a square-well potential. To this…
We develop a new elementary move for simulations of polymer chains in torsion angle space. The method is flexible and easy to implement. Tentative updates are drawn from a (conformation-dependent) Gaussian distribution that favors…
Accelerated algorithms for simulating the morphological evolution of strained heteroeptiaxy based on a ball and spring lattice model in three dimensions are explained. We derive exact Green's function formalisms for boundary values in the…
Using fermionic representation of spin degrees of freedom within the Popov-Fedotov approach we develop an algorithm for Monte Carlo sampling of skeleton Feynman diagrams for Heisenberg type models. Our scheme works without modifications for…
A simple lattice model is used to study compaction in granular media. As in real experiments, we consider a series of taps separated by large enough waiting times. The relaxation of the density exhibits the characteristic inverse…
We applied our previously developed library-based Monte Carlo (LBMC) to equilibrium sampling of several implicitly solvated all-atom peptides. LBMC can perform equilibrium sampling of molecules using the pre-calculated statistical libraries…
We present a technique that enables the evaluation of perturbative expansions based on one-loop-renormalized vertices up to large expansion orders. Specifically, we show how to compute large-order corrections to the random phase…
In this work we introduce a worldline based fermion Monte Carlo algorithm for studying few body quantum mechanics of self-interacting fermions in the Hamiltonian lattice formulation. Our motivation to construct the method comes from our…
We have exactly enumerated all sequences and conformations of HP proteins with chains of up to 19 monomers on the simple cubic lattice. For two variants of the hydrophobic-polar (HP) model, where only two types of monomers are…
We consider dynamically constrained Monte-Carlo dynamics and show that this leads to the generation of long ranged effective interactions. This allows us to construct a local algorithm for the simulation of charged systems without ever…
We perform a numerical study of a new microcanonical polymer model on the three dimensional cubic lattice, consisting of ideal chains whose range and number of nearest-neighbor contacts are fixed to given values. Our simulations suggest an…
We describe a class of "bare bones" models of homopolymers which undergo coil-globule collapse and proteins which fold into their native states in free space or into denatured states when captured by an attractive substrate as the…
We present a novel and open-source implementation of the worm algorithm, which is an algorithm to simulate Bose-Hubbard and sign-positive spin models using a path integral representation of the partition function. The code can deal with…
We present a new lattice Monte Carlo approach developed for studying large numbers of strongly interacting nonrelativistic fermions, and apply it to a dilute gas of unitary fermions confined to a harmonic trap. Our lattice action is highly…
Hamiltonian Monte Carlo (HMC) has been widely adopted in the statistics community because of its ability to sample high-dimensional distributions much more efficiently than other Metropolis-based methods. Despite this, HMC often performs…
Polymer chains undergoing a continuous adsorption-desorption transition are studied through extensive computer simulations. A three-dimensional self-avoiding walk lattice model of a polymer chain grafted onto a surface has been treated for…