Related papers: A Vectorized Algorithm for Molecular Dynamics of S…
We consider dynamically constrained Monte-Carlo dynamics and show that this leads to the generation of long ranged effective interactions. This allows us to construct a local algorithm for the simulation of charged systems without ever…
In the simulation of biological molecules, it is customary to impose constraints on the fastest degrees of freedom to increase the time step. The evaluation of the involved constraint forces must be performed in an efficient manner, for…
An ensemble of directed macromolecules on a lattice is considered, where the constituting molecules are chosen as a random sequence of N different types. The same type of molecules experiences a hard-core (exclusion) interaction. We study…
Numerous algorithms and parallelisations have been developed for short-range particle simulations; however, none are optimally performant for all scenarios. Such a concept led to the prior development of the particle simulation library…
We present the efficient and universal numerical method for simulation of interacting quantum gas kinetics on a finite momentum lattice, based on the Boltzmann equation for occupation numbers. Usually, the study of models with two-particle…
We introduce a novel quantum algorithm for the lattice Boltzmann method (LBM) based on the one-step simplified LBM. The structure of the algorithm allows for more flexibility in modelling different physics in contrast to earlier quantum…
Contrary to conventional wisdom, the construction of clusters on a lattice can easily be vectorized, namely over each ``generation'' in a breadth first search. This applies directly to, e.g., the {\it single cluster} variant of the…
This study presents a novel quantum algorithm for lattice gas automata simulation with a single time step, demonstrating logarithmic complexity in terms of $CX$ gates. The algorithm is composed of three main steps: collision, mapping, and…
We develop a theoretical and computational approach to deal with systems that involve a disparate range of spatio-temporal scales, such as those comprised of colloidal particles or polymers moving in a fluidic molecular environment. Our…
Patchy particles is the name given to a large class of systems of mesoscopic particles characterized by a repulsive core and a discrete number of short-range and highly directional interaction sites. Numerical simulations have contributed…
Polynomial approximations to the inverse of the fermion matrix are used to filter the dynamics of the upper energy scales in HMC simulations. The use of a multiple time-scale integration scheme allows the filtered pseudofermions to be…
This paper presents an improved immersed moving boundary model (IBM) for solving complex fluid-particle interactions in a coupled lattice Boltzmann method (LBM) and an adhesive discrete element method (DEM), using the "partially saturated…
In this paper we continue the study of the derivation of different types of kinetic equations which arise from scaling limits of interacting particle systems. We began this study in \cite{NVW}. More precisely, we consider the derivation of…
A grand canonical Monte Carlo (MC) algorithm is presented for studying the lattice gas model (LGM) of multiple protein sequence alignment, which coherently combines long-range interactions and variable-length insertions. MC simulations are…
We propose a method of simulating efficiently many-body interacting fermion lattice models in trapped ions, including highly nonlinear interactions in arbitrary spatial dimensions and for arbitrarily distant couplings. We map products of…
This paper constructs a new interacting particle system on a two--dimensional lattice with geometric jumps near a boundary which partially reflects the particles. The projection to each horizontal level is Markov, and on every level the…
In many real-world scenarios, the underlying random fluctuations are non-Gaussian, particularly in contexts where heavy-tailed data distributions arise. A typical example of such non-Gaussian phenomena calls for L\'evy noise, which…
Lattice gas algorithms (LGA) are a class of algorithms including, in chronological order, binary lattice gas cellular automata (LGCA), integer lattice gas algorithms (ILGA) and lattice Boltzmann method (LBM). They are largely used for…
We present a multi-scale lattice Boltzmann scheme, which adaptively refines particles' velocity space. Different velocity sets, i.e., higher- and lower-order lattices, are consistently and efficiently coupled, allowing us to use the…
Human blood flow is a multi-scale problem: in first approximation, blood is a dense suspension of plasma and deformable red cells. Physiological vessel diameters range from about one to thousands of cell radii. Current computational models…