Related papers: The Virtual Patch Clamp: Imputing C. elegans Membr…

Constant potential method molecular dynamics simulation (CPM MD) enables the accurate modelling of atomistic electrode charges when studying the electrode-electrolyte interface at the nanoscale. Here we extend the theoretical framework of…

In this paper we study asymptotic properties of different data-augmentation-type Markov chain Monte Carlo algorithms sampling from mixture models comprising discrete as well as continuous random variables. Of particular interest to us is…

We present a scalable approach to performing approximate fully Bayesian inference in generic state space models. The proposed method is an alternative to particle MCMC that provides fully Bayesian inference of both the dynamic latent states…

The CP(N-1) model in 2D is an interesting toy model for 4D QCD as it possesses confinement, asymptotic freedom and a non-trivial vacuum structure. Due to the lower dimensionality and the absence of fermions, the computational cost for…

We present computer simulations of a dynamic Monte Carlo algorithm for polymer chains on the FCC lattice which takes explicitly into account the possibility to overcome topological constraints by controlling the rate at which nearby polymer…

Sequential Monte Carlo (SMC) methods offer a principled approach to Bayesian uncertainty quantification but are traditionally limited by the need for full-batch gradient evaluations. We introduce a scalable variant by incorporating…

The determination of potentials of mean force for solute insertion in a membrane by means of all-atom molecular dynamics simulations is often hampered by sampling issues. A multiscale approach to conformational sampling was recently…

The loop gas approach to lattice field theory provides an alternative, geometrical description in terms of fluctuating loops. Statistical ensembles of random loops can be efficiently generated by Monte Carlo simulations using the worm…

Many high dimensional optimization problems can be reformulated into a problem of finding theoptimal state path under an equivalent state space model setting. In this article, we present a general emulation strategy for developing a state…

Monte Carlo simulations are widely employed to measure the physical properties of glass-forming liquids in thermal equilibrium. Combined with local Monte Carlo moves, the Metropolis algorithm can also be used to simulate the relaxation…

Bayesian inference methods such as Markov Chain Monte Carlo (MCMC) typically require repeated computations of the likelihood function, but in some scenarios this is infeasible and alternative methods are needed. Simulation-based inference…

Monte Carlo simulations of coarse-grained polymers provide a useful tool to deepen the understanding of conformational and statistical properties of polymers both in physical as well as in biological systems. In this study we sample compact…

The constant potential molecular dynamics simulation method proposed by Siepmann and Sprik and reformulated later by Reed (SR-CPM) has been widely employed to investigate the metallic electrolyte/electrode interfaces, especially for…

Based on the worm algorithm in the path-integral representation, we propose a general quantum Monte Carlo algorithm suitable for parallelizing on a distributed-memory computer by domain decomposition. Of particular importance is its…

The problem of simulatability of quantum processes using classical resources plays a cornerstone role for quantum computing. Quantum circuits can be simulated classically, e.g., using Monte Carlo sampling techniques applied to…

Thanks to novel, powerful brain activity recording techniques, we can create data-driven models from thousands of recording channels and large portions of the cortex, which can improve our understanding of brain-states neuromodulation and…

Artifacts arise in the simulations of electrolytes using periodic boundary conditions (PBC). We show the origin of these artifacts are the periodic image charges and the constraint of charge neutrality inside the simulation box, both of…

A high-fidelity kinetic Monte Carlo (KMC) simulation method (T. Treeratanaphitak, M. Pritzker, N. M. Abukhdeir, Electrochim. Acta 121 (2014) 407--414) using the semi-empirical multi-body embedded-atom method (EAM) potential has been…

In this projecting work we propose a mass spectrometric patch-clamp equipment with the capillary performing both a local potential registration at the cell membrane and the analyte suction simultaneously. This paper provides a current…

Several models for the Monte Carlo simulation of Compton scattering on electrons are quantitatively evaluated with respect to a large collection of experimental data retrieved from the literature. Some of these models are currently…