Related papers: Unbiased sampling of globular lattice proteins in …
We propose that a tunable generalized three-dimensional Hofstadter Hamiltonian can be realized by engineering the Raman-assisted hopping of ultracold atoms in a cubic optical lattice. The Hamiltonian describes a periodic lattice system…
We introduce a Hamiltonian Monte Carlo (HMC) methodology based on a randomized selection of integration times, referred to as eHMC, where "e" stands for empirical. The approach relies on an offline calibration phase that leverages…
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,…
A recent reformulation [1] of the problem of Coulomb gases in the presence of a dynamical dielectric medium showed that finite temperature simulations of such systems can be accomplished on the basis of completely local Hamiltonians on a…
We find the exact solution of three interacting friendly directed walks on the square lattice in the bulk, modelling a system of homopolymers that can undergo gelation by introducing two distinct interaction parameters that differentiate…
We have simulated the three-dimensional Heisenberg model on simple cubic lattices, using the single-cluster Monte Carlo update algorithm. The expected pronounced reduction of critical slowing down at the phase transition is verified. This…
We study the path behavior of the symmetric walk on some special comb-type subsets of ${\mathbb Z}^2$ which are obtained from ${\mathbb Z}^2$ by generalizing the comb having finitely many horizontal lines instead of one.
We investigate the one-dimensional Hubbard model with a confining potential, which may describe cold fermionic atoms trapped in an optical lattice. Combining the variational Monte Carlo simulations with the new stochastic reconfiguration…
We have developed a technique to accelerate the acquisition of effectively uncorrelated configurations for off-lattice models of dense polymer melts which makes use of both parallel tempering and large scale Monte Carlo moves. The method is…
A unique feature of the hybrid quantum Monte Carlo (HQMC) method is the potential to simulate negative sign free lattice fermion models with subcubic scaling in system size. Here we will revisit the algorithm for various models. We will…
We analyze response of a macromolecule near to a substrate; the substrate is tiled in the sequential and specific manner so that repeat units of the macromolecule may have different response on its adsorption in different directions onto…
Systems Biology is a fundamental field and paradigm that introduces a new era in Biology. The crux of its functionality and usefulness relies on metabolic networks that model the reactions occurring inside an organism and provide the means…
The performance of Hamiltonian Monte Carlo simulations crucially depends on both the integration timestep and the number of integration steps. We present an adaptive general-purpose framework to automatically tune such parameters, based on…
Elastic systems that are spatially heterogeneous in their mechanical response pose special challenges for molecular simulations. Standard methods for sampling thermal fluctuations of a system's size and shape proceed through a series of…
Two-component submonolayer growth on triangular lattice is qualitatively studied by kinetic Monte Carlo techniques. The hopping barrier governing surface diffusion of the atoms is estimated with an improved formula and using realistic pair…
We show that an isometric action of a torsion-free uniform lattice $\Gamma$ on hyperbolic space $\mathbb{H}^n$ can be metrically approximated by geometric actions of $\Gamma$ on $\mathrm{CAT}(0)$ cube complexes, provided that either $n$ is…
This paper studies a non-random-walk Markov Chain Monte Carlo method, namely the Hamiltonian Monte Carlo (HMC) method in the context of Subset Simulation used for structural reliability analysis. The HMC method relies on a deterministic…
We assume that the protein folding process follows two autonomous steps: the conformational search for the native, mainly ruled by the hydrophobic effect; and, the final adjustment stage, which eventually gives stability to the native. Our…
We analyze Riemannian Hamiltonian Monte Carlo (RHMC) for sampling a polytope defined by $m$ inequalities in $\R^n$ endowed with the metric defined by the Hessian of a convex barrier function. The advantage of RHMC over Euclidean methods…
Coulomb and log-gases are exchangeable singular Boltzmann-Gibbs measures appearing in mathematical physics at many places, in particular in random matrix theory. We explore experimentally an efficient numerical method for simulating such…