Related papers: Strategies for particle resampling in PIC simulati…
Interacting particle methods are increasingly used to sample from complex and high-dimensional distributions. These stochastic particle integration techniques can be interpreted as an universal acceptance-rejection sequential particle…
Molecular Dynamics (MD) simulations are fundamental computational tools for the study of proteins and their free energy landscapes. However, sampling protein conformational changes through MD simulations is challenging due to the relatively…
One popular approach to incorporating experimental data into molecular simulations is to restrain the ensemble average of observables to their experimental values. Here I derive equations for the equilibrium distributions generated by…
Quantum annealing aims to provide a faster method for finding the minima of complicated functions, compared to classical computing, so there is an increasing interest in the relaxation dynamics of quantum spin systems. Moreover, it is known…
We present a theoretical approach to scale the artificially fast dynamics of simulated coarse-grained polymer liquids down to its realistic value. As coarse-graining affects entropy and dissipation, two factors enter the rescaling:…
We discuss a unified approach to stochastic optimization of pseudo-Boolean objective functions based on particle methods, including the cross-entropy method and simulated annealing as special cases. We point out the need for auxiliary…
A series of simulations aimed at elucidating the self-assembly dynamics of spherical virus capsids is described. This little-understood phenomenon is a fascinating example of the complex processes that occur in the simplest of organisms.…
Sequential Monte Carlo algorithms, or Particle Filters, are Bayesian filtering algorithms which propagate in time a discrete and random approximation of the a posteriori distribution of interest. Such algorithms are based on Importance…
Smoothing short-wavelength charge density variations can stabilize explicit electrostatic particle-in-cell (PIC) plasma simulations against grid heating and cold beam instabilities, which cause unphysical heating when the Debye length is…
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…
Mutually repelling particles form spontaneously ordered clusters when forced into confinement. The clusters may adopt similar spatial arrangements even if the underlying particle interactions are contrastingly different. Here we demonstrate…
We present a methodology for simulating dilute suspensions of particles settling under gravity, with the main purpose of overcoming limitations of triply periodic configurations, mainly the strong vertical correlation that hinders the study…
In complex systems with many degrees of freedom such as spin glass and biomolecular systems, conventional simulations in canonical ensemble suffer from the quasi-ergodicity problem. A simulation in generalized ensemble performs a random…
We present a scheme to efficiently simulate, with a classical computer, the dynamics of multipartite quantum systems on which the amount of entanglement (or of correlations in the case of mixed-state dynamics) is conveniently restricted.…
An algorithm and numerical code for the up-sampling of a system of particles, from a smaller to a larger number, is described. The method introduces a Poissonian `shot-noise' to the up-sampled distribution, typical of the noise statistics…
Particle-in-Cell (PIC) methods employ particle representations of unknown fields, but also employ continuum fields for other parts of the problem. Thus projection between particle and continuum bases is required. Moreover, we often need to…
Current mathematical frameworks for predicting the flux state and macromolecular composition of the cell do not rely on thermodynamic constraints to determine the spontaneous direction of reactions. These predictions may be biologically…
One way to investigate the precision of estimates likely to result from planned experiments and planned epidemiological studies is to simulate a large number of possible outcomes and analyse the sets of possible results. This appears to be…
An efficient parallelization approach to simulate optical properties of ensembles of quantum emitters in realistic electromagnetic environments is considered. It relies on balancing computing load of utilized processors and is built into…
In crowded systems, particle currents can be mediated by propagating collective excitations which are generated as rare events, are localized and have a finite lifetime. The theoretical description of such excitations is hampered by the…