Related papers: Reversible Interacting-Particle Reaction Dynamics
Intrinsically disordered proteins (IDPs) constitute a broad set of proteins with few uniting and many diverging properties. IDPs-and intrinsically disordered regions (IDRs) interspersed between folded domains-are generally characterized as…
In particle-based stochastic reaction-diffusion models, reaction rate and placement kernels are used to decide the probability per time a reaction can occur between reactant particles, and to decide where product particles should be placed.…
Reversible to irreversible (R-IR) transitions arise in numerous periodically driven collectively interacting systems that, after a certain number of driving cycles, organize into a reversible state where the particle trajectories repeat, or…
We describe collective-move Monte Carlo algorithms designed to approximate the overdamped dynamics of self-assembling nanoscale components equipped with strong, short-ranged and anisotropic interactions. Conventional Monte Carlo simulations…
Robotics demands simulation that can reason about the diversity of real-world physical interactions, from rigid to deformable objects and fluids. Current simulators address this by stitching together multiple subsolvers for different…
Interacting particle systems play a key role in science and engineering. Access to the governing particle interaction law is fundamental for a complete understanding of such systems. However, the inherent system complexity keeps the…
Hybrid molecular dynamics/Monte Carlo simulations used to study melts of unentangled, thermoreversibly associating supramolecular polymers. In this first of a series of papers, we describe and validate a model that is effective in…
Dissipative particle dynamics (DPD) does not conserve energy and this precludes its use in the study of thermal processes in complex fluids. We present here a generalization of DPD that incorporates an internal energy and a temperature…
Physics-based differentiable rendering (PBDR) has become an efficient method in computer vision, graphics, and machine learning for addressing an array of inverse problems. PBDR allows patterns to be generated from perceptions which can be…
Particle-based stochastic reaction-diffusion (PBSRD) models are a popular approach for capturing stochasticity in reaction and transport processes across biological systems. In some contexts, the overdamped approximation inherent in such…
Two-dimensional relativistic particle-in-cell (PIC) simulations of radiative magnetic reconnection in pair plasmas with multiple interacting current sheets are carried out to mimic the dynamics in high-energy astrophysical environments,…
Real-life control tasks involve matters of various substances---rigid or soft bodies, liquid, gas---each with distinct physical behaviors. This poses challenges to traditional rigid-body physics engines. Particle-based simulators have been…
A competitive (2+1)-dimensional model of deposit formation, based on the combination of random sequential absorption deposition (RSAD), ballistic deposition (BD) and random deposition (RD) models, is proposed. This model was named as…
There exist methods for determining effective conservative interactions in coarse grained particle based mesoscopic simulations. The resulting models can be used to capture thermal equilibrium behavior, but in the model system we study do…
Intelligent agents need a physical understanding of the world to predict the impact of their actions in the future. While learning-based models of the environment dynamics have contributed to significant improvements in sample efficiency…
The conditions under which stochastic systems of infinitely many interacting particles can maintain sufficient spatial order to move coherently along a time-periodic orbit, thereby breaking the time-translation invariance of the underlying…
This paper tackles the task of goal-conditioned dynamic manipulation of deformable objects. This task is highly challenging due to its complex dynamics (introduced by object deformation and high-speed action) and strict task requirements…
The paradigm that the primary amino acid sequence prescribes structure and thus function has for a long time been central to the understanding of protein science. Though the theory is supported by the behaviour of most structured proteins,…
The exact equations of motion for microscopic density of classical many-body system with account of inter-particle retarded interactions are derived. It is shown that interactions retardation leads to irreversible behaviour of many-body…
Cross-reactions and other systematic issues generated by the coupling of functional chemical subsystems pose the largest challenge for assembling a viable protocell in the laboratory. Our current work seeks to identify and clarify such key…