Related papers: Reversible Interacting-Particle Reaction Dynamics
Intrinsically disordered regions (IDRs) of proteins mediate sequence-specific interactions underlying diverse cellular processes, including the formation of biomolecular condensates. Although IDRs strongly influence condensate compositions,…
Cognitive Radars (CRs) employ perception-action cycle to adapt their sensing and transmission strategies based on its' perception of the target kinematic states and mission objectives. This paper considers an inverse learning Electronic…
A hybrid mesoscopic multi-particle collision model is used to study diffusion-influenced reaction kinetics. The mesoscopic particle dynamics conserves mass, momentum and energy so that hydrodynamic effects are fully taken into account.…
The capacity of proteins to interact specifically with one another underlies our conceptual understanding of how living systems function. Systems-level study of specificity in protein-protein interactions is complicated by the fact that the…
Multiparticle collision dynamics (MPCD) is a relatively new algorithm of fluid flow simulations that has been applied mostly to flows around simple objects. One might ask how it behaves in more complex flows. Therefore, we extend MPCD to…
Relativistic magnetic reconnection is one of the most fundamental mechanisms considered responsible for the acceleration of relativistic particles in astrophysical jets and magnetospheres of compact objects. Understanding the properties of…
In this study, we present the original method for reconstructing the potential of interparticle interaction from statistically averaged structural data, namely, the radial distribution function of particles in many-particle system. This…
Modeling membrane interactions with arbitrarily shaped colloidal particles, such as environmental micro- and nanoplastics, at the cell scale remains particularly challenging, owing to the complexity of particle geometries and the need to…
Discrete particle simulations have become the standard in science and industrial applications exploring the properties of particulate systems. Most of such simulations rely on the concept of interacting spherical particles to describe the…
The mechanisms of physical and chemical interactions of low temperature plasmas with surfaces can be fruitfully explored using molecular dynamics (MD) simulations. MD simulations follow the detailed motion of sets of interacting atoms…
Multiparticle collision dynamics (MPCD) is a flexible and robust mesoscale computational technique for simulating solvent-mediated hydrodynamic interactions in soft materials. Here, we provide a critical overview of the MPCD method and…
Accurately predicting chemical reactions is essential for driving innovation in synthetic chemistry, with broad applications in medicine, manufacturing, and agriculture. At the same time, reaction prediction is a complex problem which can…
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…
Strongly interacting spins underlie many intriguing phenomena and applications ranging from magnetism to quantum information processing. Interacting spins combined with motion display exotic spin transport phenomena, such as superfluidity…
We propose a Poincare-invariant description for the effective dynamics of systems of charged particles by means of intrinsic multipole moments. To achieve this goal we study the effective dynamics of such systems within two frameworks --…
An adpative integration technique for time advancement of particle motion in the context of coupled computational fluid dynamics (CFD) - discrete element method (DEM) simulations is presented in this work. CFD-DEM models provide an accurate…
Using collision driven discrete molecular dynamics (DMD), we investigate the thermodynamics and dynamics of systems of 500 dumbbell molecules interacting by a purely repulsive ramp-like discretized potential, consisting of $n$ steps of…
A fundamental objective of materials modeling is identifying atomic structures that align with experimental observables. Conventional approaches for disordered materials involve sampling from thermodynamic ensembles and hoping for an…
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly…
Certain biochemical reactions can only be triggered after binding of a sufficient number of particles to a specific target region such as an enzyme or a protein sensor. We investigate the distribution of the reaction time, i.e., the first…