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We develop a formalism for calculating probabilities for the outcomes of stellar dynamical interactions, based on results from $N$-body scattering experiments. We focus here on encounters involving up to six particles and calculate…
For conventional smoothed particle hydrodynamics (SPH), obtaining the static solution of a problem is time-consuming. To address this drawback, we propose an efficient dynamic relaxation method by adding large artificial-viscosity-based…
Quantum-chemical simulations are essential for predicting energies of chemical reactions. Accurately solving the many-body Schr\"odinger equation for reagent and product states of most relevant chemical process is, however, unfeasible.…
Highly specific spatiotemporal interactions between cognate molecular partners essentially sustain all biochemical transactions in the living matter. That such an exquisite level of accuracy may result from encountering forces solely driven…
Efficient analysis and simulation of multiscale stochastic systems of chemical kinetics is an ongoing area for research, and is the source of many theoretical and computational challenges. In this paper, we present a significant improvement…
We consider the problem of efficiently performing simulation and inference for stochastic kinetic models. Whilst it is possible to work directly with the resulting Markov jump process, computational cost can be prohibitive for networks of…
Machine learning (ML) strategies are opening the door to faster computer simulations, allowing us to simulate more realistic colloidal systems. Since the interactions in colloidal systems are often highly many-body, stemming from e.g.…
Recently, a method was developed for implementing arbitrary short-range nucleon-nucleon correlations in Monte Carlo sampled nuclei (as well as deformations of the 1-body nuclear density). We use this method to implement realistic 2-body…
We present a new particle-based (discrete element) numerical method for the simulation of granular dynamics, with application to motions of particles on small solar system body and planetary surfaces. The method employs the parallel N-body…
The dynamic cavity method provides the most efficient way to evaluate probabilities of dynamic trajectories in systems of stochastic units with unidirectional sparse interactions. It is closely related to sum-product algorithms widely used…
In scenarios involving text classification where the number of classes is large (in multiples of 10000s) and training samples for each class are few and often verbose, nearest neighbor methods are effective but very slow in computing a…
We show that finite-range alternatives to the standard long-range BKS pair potential for silica might be used in molecular dynamics simulations. We study two such models that can be efficiently simulated since no Ewald summation is…
The simulation of complex stochastic network dynamics arising, for instance, from models of coupled biomolecular processes remains computationally challenging. Often, the necessity to scan a models' dynamics over a large parameter space…
A version of the time-parallel algorithm parareal is analyzed and applied to stochastic models in chemical kinetics. A fast predictor at the macroscopic scale (evaluated in serial) is available in the form of the usual reaction rate…
Finding a reduction of complex, high-dimensional dynamics to its essential, low-dimensional "heart" remains a challenging yet necessary prerequisite for designing efficient numerical approaches. Machine learning methods have the potential…
Classical Molecular Dynamics (MD) simulations provide insight on the properties of many soft-matter systems. In some situations it is interesting to model the creation of chemical bonds, a process that is not part of the MD framework. In…
In this paper we present a method for exact generation of multivariate samples with pre-specified marginal distributions and a given correlation matrix, based on a mixture of Fr\'echet-Hoeffding bounds and marginal products. The bivariate…
In this paper, three efficient ensemble algorithms are proposed for fast-solving the random fluid-fluid interaction model. Such a model can be simplified as coupling two heat equations with random diffusion coefficients and a friction…
A novel Stochastic Event-Driven Molecular Dynamics (SEDMD) algorithm is developed for the simulation of polymer chains suspended in a solvent. The polymers are represented as chains of hard spheres tethered by square wells and interact with…
Quasi two-dimensional Coulomb systems have drawn widespread interest. The reduced symmetry of these systems leads to complex collective behaviors, yet simultaneously poses significant challenges for particle-based simulations. In this…