Related papers: Discrete state model of a self-aggregating colloid…
In this work we present a discrete model that captures the fundamental properties of additively manufactured solids in a minimal setting. The model is based on simplified kinematics and allows for the onset of incompatible deformations…
Via molecular dynamics simulations we have studied kinetics of vapor-"solid" phase transition in an active matter model in which self-propulsion is introduced via the well-known Vicsek rule. The overall density of the particles is chosen in…
We propose a class of discrete state sampling algorithms based on Nesterov's accelerated gradient method, which extends the classical Metropolis-Hastings (MH) algorithm. The evolution of the discrete states probability distribution governed…
We study a model of diffusive oscillators whose internal states are subject to a periodic drive. These models are inspired by the dynamics of deformable particles with pulsating sizes, where repulsion leads to arrest the internal pulsation…
Motivated by recent experimental findings in chemical synthesis of colloidal particles, we draw an analogy between self-assembly processes occurring in biological systems (e.g. protein folding) and a new exciting possibility in the field of…
An example of a discrete pregeometry on a microscopic scale is introduced. The model is a directed dyadic acyclic graph. This is the particular case of a causal set. The particles in this model must be self-organized repetitive structures.…
We develop an operator-based framework to coarse-grain interacting particle systems that exhibit clustering dynamics. Starting from the particle-based transfer operator, we first construct a sequence of reduced representations: the operator…
We construct a continuum model for biological aggregations in which individuals experience long-range social attraction and short range dispersal. For the case of one spatial dimension, we study the steady states analytically and…
New insights into phase separation in colloidal suspensions are provided via a new dynamical theory based on the Polydisperse Lattice-Gas model. The model gives a simplified description of polydisperse colloids, incorporating a hard-core…
The aim of this review is to provide a concise overview of some of the generic approaches that have been developed to deal with the statistical description of large systems of interacting dissipative 'units'. The latter notion includes,…
Inspired by a PDE-ODE system of aggregation developed in the biomathematical literature, an interacting particle system representing aggregation at the level of individuals is investigated. It is proved that the empirical density of the…
A Markov state model of the dynamics of a protein-like chain immersed in an implicit hard sphere solvent is derived from first principles for a system of monomers that interact via discontinuous potentials designed to account for local…
Under certain conditions, the dynamics of coarse-grained models of solvated proteins can be described using a Markov state model, which tracks the evolution of populations of configurations. The transition rates among states that appear in…
Generative modeling over discrete structures underpins applications across deep learning, from biological sequence design and code generation to large language models, yet generation often remains sequential, relying on autoregressive…
Active colloids constitute a novel class of materials composed of colloidal-scale particles locally converting chemical energy into motility, mimicking micro-organisms. Evolving far from equilibrium, these systems display structural…
Coarse-graining techniques play a central role in reducing the complexity of stochastic models, and are typically characterised by a mapping which projects the full state of the system onto a smaller set of variables which captures the…
We study coarse-grained (group-level) alignment dynamics of individual-based animal group models for {\it heterogeneous} populations consisting of informed (on preferred directions) and uninformed individuals. The orientation of each…
Multiscale systems are ubiquitous in science and technology, but are notoriously challenging to simulate as short spatiotemporal scales must be appropriately linked to emergent bulk physics. When expensive high-dimensional dynamical systems…
We review a few representative examples of granular experiments or models where phase separation, accompanied by domain coarsening, is a relevant phenomenon. We first elucidate the intrinsic non-equilibrium, or athermal, nature of granular…
The motile micro-organisms such as E. coli, sperm, or some seaweed are usually modelled by self-propelled particles that move with the run-and-tumble process. Individual-based stochastic models are usually employed to model the aggregation…