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Coupled cluster theory is a vital cornerstone of electronic structure theory and is being applied to ever-larger systems. Stochastic approaches to quantum chemistry have grown in importance and offer compelling advantages over traditional…
By mixing the target posterior distribution with a surrogate distribution, of which the normalizing constant is tractable, we propose a method for estimating the marginal likelihood using the Wang-Landau algorithm. We show that a faster…
Obtaining a good load balance is a significant challenge in scaling up lattice-Boltzmann simulations of realistic sparse problems to the exascale. Here we analyze the effect of weighted decomposition on the performance of the HemeLB…
We introduce an algorithm to systematically improve the efficiency of parallel tempering Monte Carlo simulations by optimizing the simulated temperature set. Our approach is closely related to a recently introduced adaptive algorithm that…
Molecular dynamics (MD) simulations are widely used to study large-scale molecular systems. HPC systems are ideal platforms to run these studies, however, reaching the necessary simulation timescale to detect rare processes is challenging,…
Mean-field, ensemble-chain, and adaptive samplers have historically been viewed as distinct approaches to Monte Carlo sampling. In this paper, we present a unifying {two-system} framework that brings all three under one roof. In our…
We discuss two topics that we have encountered in our lattice-Boltzmann simulations of complex fluids: the sizes of droplets in particle-stabilised emulsions and deformable particles in fluid flow. The common factor in these seemingly…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
Monte Carlo simulation has been performed in one-dimensional Lebwohl-Lasher model and two dimensional XY-model using the Wang-Landau and the Wang-Landau-Transition-Matrix Monte Carlo methods. Random walk has been performed in the…
To evaluate the effectiveness of machine learning in systems with competing interactions, we developed a self-learning quantum Monte Carlo (SLQMC) method to simulate the phase transition in the classical Holstein-spin-fermion model. In…
Sampling-based methods for motion planning, which capture the structure of the robot's free space via (typically random) sampling, have gained popularity due to their scalability, simplicity, and for offering global guarantees, such as…
We present phase diagrams, free-energy landscapes, and order-parameter distributions for a model spin-crossover material with a two-step transition between the high-spin and low-spin states (a square-lattice Ising model with…
Assuming a steady-state condition within a cell, metabolic fluxes satisfy an under-determined linear system of stoichiometric equations. Characterizing the space of fluxes that satisfy such equations along with given bounds (and possibly…
We present a simple, parallel and distributed algorithm for setting up and partitioning a sparse representation of a regular discretized simulation domain. This method is scalable for a large number of processes even for complex geometries…
The Multilevel Monte Carlo (MLMC) method has proven to be an effective variance-reduction statistical method for Uncertainty Quantification (UQ) in Partial Differential Equation (PDE) models, combining model computations at different levels…
The multi-level hp-refinement scheme is a powerful extension of the finite element method that allows local mesh adaptation without the trouble of constraining hanging nodes. This is achieved through hierarchical high-order overlay meshes,…
We discuss a sampling algorithm which generates flat histogram in energy. In combination with transition matrix Monte Carlo, the density of states and derived quantities such as entropy and free energy as a function of temperature can be…
Hamiltonian Monte Carlo (HMC) algorithms which combine numerical approximation of Hamiltonian dynamics on finite intervals with stochastic refreshment and Metropolis correction are popular sampling schemes, but it is known that they may…
In simulations of crystals, unlike liquids or gases, it may happen that the properties of the studied system depend not only on the volume of the simulation cell but also on its shape. For such cases it is desirable to change the shape of…
The Quantum Monte Carlo (QMC) method can yield the imaginary-time dependence of a correlation function $C(\tau)$ of an operator $\hat O$. The analytic continuation to real-time proceeds by means of a "numerical inversion" of these data to…