Related papers: Extended Pattern Recognition Scheme for Self-learn…
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…
An efficient simulation-based methodology is proposed for the rolling window estimation of state space models, called particle rolling Markov chain Monte Carlo (MCMC) with double block sampling. In our method, which is based on Sequential…
Self-organized monolayers of highly flexible \Frechet dendrons were deposited on graphite surfaces by solution casting. Scanning tunneling microscopy (STM) reveals an unprecedented variety of patterns with up to seven stable hierarchical…
We describe the Monte Carlo (MC) simulation package of the `2K-CAPTURE' setup and discuss the agreement of its output with data. The `2K-CAPTURE' MC simulates the energy loss of particles in detector and components of the passive shield and…
We extend the applicability range of fermionic path integral Monte Carlo simulations to heavier elements and lower temperatures by introducing various localized nodal surfaces. Hartree-Fock nodes yield the most accurate prediction for…
This review article is intended as a practical guide for newcomers to the field of kinetic Monte Carlo (KMC) simulations, and specifically to lattice KMC simulations as prevalently used for surface and interface applications. We will…
We present the completion of a data analysis pipeline that self-consistently separates global 21-cm signals from large systematics using a pattern recognition technique. In the first paper of this series, we obtain optimal basis vectors…
The shape evolution of two-dimensional islands under electromigration-driven periphery diffusion is studied by kinetic Monte Carlo (KMC) simulations and continuum theory. The energetics of the KMC model is adapted to the Cu(100) surface,…
Kinetic Monte Carlo (KMC) is a powerful method for simulation of diffusion processes in various systems. The accuracy of the method, however, relies on the extent of details used for the parameterization of the model. Migration barriers are…
The following electromagnetism (EM) inverse problem is addressed. It consists in estimating local radioelectric properties of materials recovering an object from global EM scattering measurements, at various incidences and wave frequencies.…
We propose a general way to construct an effective Hamiltonian in the Self-learning Monte Carlo method (SLMC), which speeds up Monte Carlo simulations by training an effective model to propose uncorrelated configurations in the Markov…
A class of Monte Carlo algorithms which incorporate absorbing Markov chains is presented. In a particular limit, the lowest-order of these algorithms reduces to the $n$-fold way algorithm. These algorithms are applied to study the escape…
I present a strategy for unsupervised manifold learning on local atomic environments in molecular simulations based on simple rotation- and permutation-invariant three-body features. These features are highly descriptive, generalize to…
We introduce Preconditioned Monte Carlo (PMC), a novel Monte Carlo method for Bayesian inference that facilitates efficient sampling of probability distributions with non-trivial geometry. PMC utilises a Normalising Flow (NF) in order to…
State space models (SSM) have been widely applied for the analysis and visualization of large sequential datasets. Sequential Monte Carlo (SMC) is a very popular particle-based method to sample latent states from intractable posteriors.…
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…
Amphiphilic molecules spontaneously form self-assembled structures of various shapes depending on their molecular structures, the temperature, and other physical conditions. The functionalities of these structures are dictated by their…
The shell-model Monte Carlo (SMMC) technique transforms the traditional nuclear shell-model problem into a path-integral over auxiliary fields. We describe below the method and its applications to four physics issues: calculations of sdpf-…
Owing to the advances in computational techniques and the increase in computational power, atomistic simulations of materials can simulate large systems with higher accuracy. Complex phenomena can be observed in such state-of-the-art…
Image-based sequencing of mRNA makes it possible to see where in a tissue sample a given gene is active, and thus discern large numbers of different cell types in parallel. This is crucial for gaining a better understanding of tissue…