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In active matter and living matter, such as clusters of migrating cells, collective dynamics emerges from the underlying interactions. A common assumption of theoretical descriptions of collective cell migration is that these interactions…
Understanding the complex behavior of molecular systems is fundamental to fields such as physics, materials science, and biology. Molecular dynamics (MD) simulations are crucial tools for studying atomic-level dynamics. This work focuses on…
The objective of this article is to report the parallel implementation of the 3D molecular dynamic simulation code for laser-cluster interactions. The benchmarking of the code has been done by comparing the simulation results with some of…
We present methods for exploratory studies of molecular dynamics using MATLAB. Such methods are not suitable for large scale applications, but they can be used for developement and testing of new types of interactions and other aspects of…
We present the first direct measurement of three-body interactions in a colloidal system comprised of three charged colloidal particles. Two of the particles have been confined by means of a scanned laser tweezers to a line-shaped optical…
Large molecular dynamics simulations (millions of atoms, tens of microseconds, thousands of processors) hit the strong scalability wall: simulation on twice as many processors does not take half the time. Inspired by large N-body space…
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…
Three-body and four-body interactions have been directly measured in a colloidal system comprised of three (or four) charged colloidal particles. Two of the particles have been confined by means of a scanned laser tweezers to a line-shaped…
A new approach for integration of motion in many-body systems of interacting polyatomic molecules is proposed. It is based on splitting time propagation of pseudo-variables in a modified phase space, while the real translational and…
Periodically sheared colloids at low densities demonstrate a dynamical phase transition from an inactive to active phase as the strain amplitude is increased. The inactive phase consists of no collisions/contacts between particles in the…
The organization of live cells into tissues and their subsequent biological function involves inter-cell mechanical interactions, which are mediated by their elastic environment. To model this interaction, we consider cells as spherical…
Much work has studied effective interactions between micron-sized particles carrying linkers forming reversible, inter-particle linkages. These studies allowed understanding the equilibrium properties of colloids interacting through…
We present a simple, experimentally realizable method to make coherent three-body interactions dominate the physics of an ultracold lattice gas. Our scheme employs either lattice modulation or laser-induced tunneling to reduce or turn off…
Research in cell biology is steadily contributing new knowledge about many different aspects of physiological processes like polymerization, both with respect to the involved molecular structures as well as their related function.…
To maintain homeostasis, living cells process information with networks of interacting molecules. Traditional models for cellular information processing have focused on networks of chemical reactions between molecules. Here, we describe how…
Three-phase multiphase flows are found in an extraordinarily large number of applications. Often those involve a liquid phase and a gas phase in addition to a third phase that consists of either liquid drops or solid particles, suspended in…
A simulation technique is described for quantifying the contribution of three-body interactions to the thermodynamical properties of coarse-grained representations of complex fluids. The method is based on comparing the third virial…
A variety of models for the membrane-mediated interaction of particles in lipid membranes, mostly well-established in theoretical physics, is reviewed from a mathematical perspective. We provide mathematically consistent formulations in a…
Three-body interactions have been measured among three charged colloidal particles in deionized solvent. Two of the particles have been confined to an optical line-trap while the third one was approached by means of a focused laser beam.…
We present a technique designed for parallelizing large rigid body simulations, capable of exploiting multiple CPU cores within a computer and across a network. Our approach can be applied to simulate both unilateral and bilateral…