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Hamiltonian Monte Carlo (HMC) is an efficient method of simulating smooth distributions and has motivated the widely used No-U-turn Sampler (NUTS) and software Stan. We build on NUTS and the technique of "unbiased sampling" to design HMC…
Hamiltonian Monte Carlo (HMC) is a popular sampling method in Bayesian inference. Recently, Heng & Jacob (2019) studied Metropolis HMC with couplings for unbiased Monte Carlo estimation, establishing a generic parallelizable scheme for HMC.…
We present a scalable Bayesian framework for the analysis of confocal fluorescence spectroscopy data, addressing key limitations in traditional fluorescence correlation spectroscopy methods. Our framework captures molecular motion,…
We study the first order phase transition of the fixed-connectivity triangulated surface model using the Parallel Tempering Monte Carlo (PTMC) technique on relatively large lattices. From the PTMC results, we find that the transition is…
We investigate the properties of the Hybrid Monte-Carlo algorithm (HMC) in high dimensions. HMC develops a Markov chain reversible w.r.t. a given target distribution $\Pi$ by using separable Hamiltonian dynamics with potential $-\log\Pi$.…
Honeycomb-like microstructures have been shown to exhibit local elastic buckling under compression, with three possible geometric buckling modes, or pattern transformations. The individual pattern transformations, and consequently also…
We examine the relation between the recently proposed time-dependent quantum Monte Carlo (TDQMC) method and the principles of stochastic quantization. In both TDQMC and stochastic quantization particle motion obeys stochastic guidance…
Monte Carlo methods are widely used for approximating complicated, multidimensional integrals for Bayesian inference. Population Monte Carlo (PMC) is an important class of Monte Carlo methods, which utilizes a population of proposals to…
Monte Carlo simulations are a powerful tool to investigate the thermodynamic properties of atomic systems. In practice however, sampling of the complete configuration space is often hindered by high energy barriers between different regions…
This paper presents a new Monte Carlo (MC) algorithm for time-dependent particle transport problems with global variance reduction based on automatic weight windows (WWs). The centers of WWs at a time step are defined by the solution of an…
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,…
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…
Parallel tempering is a meta-algorithm for Markov Chain Monte Carlo that uses multiple chains to sample from tempered versions of the target distribution, enhancing mixing in multi-modal distributions that are challenging for traditional…
To predict the complex chemical evolution in multicomponent alloys, it is highly desirable to have accurate atomistic simulation methods capable of reaching sufficiently large spatial and temporal scales. In this work, we advance the…
The growth rates and chemical ordering of ferroelectric alloys are studied with kinetic Monte Carlo (KMC) simulations using an electrostatic model with long-range Coulomb interactions, as a function of temperature, chemical composition, and…
Monte Carlo simulations of hard-sphere (HS) crystal grown on a square patterned wall under gravity have been performed. While previous simulations were performed with step-wise controlled gravity, in the present simulations constant gravity…
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.…
Traditional Markov Chain Monte Carlo methods suffer from low acceptance rate, slow mixing and low efficiency in high dimensions. Hamiltonian Monte Carlo resolves this issue by avoiding the random walk. Hamiltonian Monte Carlo (HMC) is a…
To synthesize diffusion MR measurements from Monte-Carlo simulation using tissue models with sizes comparable to those of scan voxels. Larger regions enable restricting structures to be modeled in greater detail and improve accuracy and…
A method is proposed for determining the line tension, which is the main physical characteristic of a three-phase contact region, by Monte-Carlo (MC) simulations. The key idea of the proposed method is that if a three-phase equilibrium…