Related papers: Multicanonical Chain Growth Algorithm
A Monte Carlo method is given to compute the binding affinity of a ligand to a protein. The method involves extending configuration space by a discrete variable indicating whether the ligand is bound to the protein and a special Monte Carlo…
We calculate the efficiency of a rejection-free dynamic Monte Carlo method for $d$-dimensional off-lattice homogeneous particles interacting through a repulsive power-law potential $r^{-p}$. Theoretically we find the algorithmic efficiency…
We show how to generalize the Lattice Switch Monte Carlo method to calculate the phase diagram of a binary system. A global coordinate transformation is combined with a modification of particle diameters, enabling the multi-component system…
Real-space quantum Monte Carlo is used to calculate the total atomization energy of benzene. In contrast to orbital-space methods common in quantum chemistry, real-space methods allow results at near the complete-basis-set limit to be…
An efficient method for computing thermodynamic equilibrium states at the micromagnetic length scale is introduced, using the Markov chain Monte Carlo method. Trial moves include not only rotations of vectors, but also a change in their…
In this text, we implement a monte carlo algorithm to study thermodynamic properties of ice. Our program, written in Python, is open-sourced and available at https://github.com/AKnightWing/ColdAsIce. We develop a novel scheme to compute the…
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 Monte-Carlo approach to proton stopping in warm dense matter is implemented into an existing particle-in-cell code. The model is based on multiple binary-collisions among electron-electron, electron-ion and ion-ion, taking into account…
We propose a new Monte Carlo method for efficiently sampling trajectories with fixed initial and final conditions in a system with discrete degrees of freedom. The method can be applied to any stochastic process with local interactions,…
We provide a complete thermodynamic solution of a 1D hopping model in the presence of a random potential by obtaining the density of states. Since the partition function is related to the density of states by a Laplace transform, the…
It is a long-standing challenge to accurately and efficiently compute thermodynamic quantities of many-body systems at thermal equilibrium. The conventional methods, e.g., Markov chain Monte Carlo, require many steps to equilibrate. The…
We combine the principle of gauge invariance with extrinsic string geometry to develop a lattice model that can be employed to theoretically describe properties of chiral, unbranched homopolymers. We find that in its low temperature phase…
We perform simulations for long hard-sphere polymer chains using a recently developed binary-tree based Monte Carlo method. Systems in two to five dimensions with free and periodic boundary conditions and up to $10^7$ repeat units are…
We present a novel implementation of the parallel tempering Monte Carlo method in a multicanonical ensemble. Multicanonical weights are derived by a self-consistent iterative process using a Boltzmann inversion of global energy histograms.…
Starting from a master equation in a quantum Hamilton form we study analytically a nonequilibrium system which is coupled locally to two heat bathes at different temperatures. Based on a lattice gas description an evolution equation for the…
We develop the hybrid Monte Carlo method for simulations of single off-lattice polymer chains. We discuss implementation and choice of simulation parameters in some detail. The performance of the algorithm is tested on models for…
We determined scaling laws for the numerical effort to find the optimal configurations of a simple model potential energy surface (PES) with a perfect funnel structure that reflects key characteristics of the protein interactions.…
We present a study of the parallel tempering (replica exchange) Monte Carlo method, with special focus on the feedback-optimized parallel tempering algorithm, used for generating an optimal set of simulation temperatures. This method is…
Restricted path integral Monte Carlo simulations are used to calculate the equilibrium properties of hydrogen in the density and temperature range of $9.83 \times 10^{-4}\rm \leq \rho \leq 0.153 \rm gcm^{-3}$ and $5000 \leq T \leq 250 000…
We translate the problem of calculating the entropy of a set of binary configurations/signals into a sequence of supervised classification tasks. Subsequently, one can use virtually any machine learning classification algorithm for…