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When describing the low-energy physics of bosons in a double-well potential with a high barrier between the wells and sufficiently weak atom-atom interactions, one can to a good approximation ignore the high energy states and thereby obtain…
A general framework for performing event-driven simulations of systems with semi-flexible or rigid bodies interacting under impulsive torques and forces is outlined. Two different approaches are presented. In the first, the dynamics and…
The linked cell list algorithm is an essential part of molecular simulation software, both molecular dynamics and Monte Carlo. Though it scales linearly with the number of particles, there has been a constant interest in increasing its…
A model of a device is proposed and related theoretical calculation is performed to study the weak interactions among neutral atoms and molecules. In this model 3-body collisions among the neutral particles occur repeatedly in a trap.…
Three-body correlations in three-body exotic atoms are studied with simple models that consist of three bosons interacting through a superposition of long- and short-range potentials. We discuss the correlations among particles by comparing…
Molecular dynamics simulations are performed for a finite non-relativistic system of particles with Lennard-Jones potential. We study the effect of liquid-gas mixed phase on particle number fluctuations in coordinate subspace. A metastable…
We calculate the effective three-body force for bosons interacting with each other by a two-body potential tuned to a narrow zero crossing in any dimension. We use the standard two-channel model parametrized by the background atom-atom…
Mathematical and computational models can assist in gaining an understanding of cell behavior at many levels of organization. Here, we review models in the literature that focus on eukaryotic cell motility at 3 size scales: intracellular…
Recent advances in random-walk particle-tracking have enabled direct simulation of mixing and reactions on particles by allowing the particles to interact with each other using a multi-point mass transfer scheme. The mass transfer scheme…
The introduction of optical tweezers for trapping atoms has opened remarkable opportunities for manipulating few-body systems. Here, we present the first bottom-up assembly of atom triads. We directly observe atom loss through inelastic…
We developed a general theoretical approach and a user-ready computer code that permit to study the dynamics of collisional energy transfer and ro-vibrational energy exchange in complex molecule-molecule collisions. The method is a mixture…
We show that polar molecules driven by microwave fields give naturally rise to strong three-body interactions, while the two-particle interaction can be independently controlled and even switched off. The derivation of these effective…
We present the bond-calculus, a process algebra for modelling biological and chemical systems featuring nonlinear dynamics, multiway interactions, and dynamic bonding of agents. Mathematical models based on differential equations have been…
Massively-parallel molecular dynamics simulation is applied to systems containing electrolytes, vapour-liquid interfaces, and biomolecules in contact with water-oil interfaces. Novel molecular models of alkali halide salts are presented and…
This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization…
Analyzing the motion of multiple biological agents, be it cells or individual animals, is pivotal for the understanding of complex collective behaviors. With the advent of advanced microscopy, detailed images of complex tissue formations…
We implement a three-body potential to model associative bond swaps, and release it as part of the HOOMD-blue software. The use of a three-body potential to model swaps has been proven to be effective and has recently provided useful…
A molecule traveling in a realistic propagation environment can experience stochastic interactions with other molecules and the environment boundary. The statistical behavior of some isolated phenomena, such as dilute unbounded molecular…
We propose a stroboscopic method to dynamically decouple the effects of two-body atom-atom interactions for ultracold atoms, and realize a system dominated by elastic three-body interactions. Using this method, we show that it is possible…
Many cell functions require a concerted effort from multiple membrane proteins, for example, for signaling, cell division, and endocytosis. One contribution to their successful self-organization stems from the membrane deformations that…