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In order to study the stochastic Markov processes conditioned on a specific value of a time-integrated observable, the concept of ensembles of trajectories has been recently used extensively. In this paper, we consider a generic…
A multiscale theory of interacting continuum mechanics and thermodynamics of mixtures of fluids, electrodynamics, polarization and magnetization is proposed. The mechanical (reversible) part of the theory is constructed in a purely…
Since its foundations, more than one hundred years ago, the field of structural biology has strived to understand and analyze the properties of molecules and their interactions by studying the structure that they take in 3D space. However,…
Deep generative models are able to suggest new organic molecules by generating strings, trees, and graphs representing their structure. While such models allow one to generate molecules with desirable properties, they give no guarantees…
Tracer-diffusion of small molecules through dense systems of chain polymers is studied within an athermal lattice model, where hard core interactions are taken into account by means of the site exclusion principle. An approximate mapping of…
A mesoscopic multi-particle collision model for fluid dynamics is generalized to incorporate the chemical reactions among species that may diffuse at different rates. This generalization provides a means to simulate reaction-diffusion…
Over a century ago, Einstein formulated a precise mathematical model for describing Brownian motion. While this model adequately explains the diffusion of micron-sized particles in fluids, its limitations become apparent when applied to…
We develop a formalism for particle production in a field theory coupled to a strong time-dependent external source. An example of such a theory is the Color Glass Condensate. We derive a formula, in terms of cut vacuum-vacuum Feynman…
The generalized recurrence plot is a modern tool for quantification of complex spatial patterns. Its application spans the analysis of trabecular bone structures, Turing patterns, turbulent spatial plankton patterns, and fractals.…
The modelling of linear and nonlinear reaction-subdiffusion processes is more subtle than normal diffusion and causes different phenomena. The resulting equations feature a spatial Laplacian with a temporal memory term through a time…
We investigate the connections between microscopic chaos, defined on a dynamical level and arising from collisions between molecules, and diffusion, characterized by a mean square displacement proportional to the time. We use a number of…
Pattern formation in reaction-diffusion systems is of great importance in surface micro-patterning [Grzybowski et al. Soft Matter. 1, 114 (2005)], self-organization of cellular micro-organisms [Schulz et al. Annu. Rev. Microbiol. 55, 105…
We propose a technique to detect and generate patterns in a network of locally interacting dynamical systems. Central to our approach is a novel spatial superposition logic, whose semantics is defined over the quad-tree of a partitioned…
Numerical simulations of a simple reaction--diffusion model reveal a surprising variety of irregular spatio--temporal patterns. These patterns arise in response to finite--amplitude perturbations. Some of them resemble the steady irregular…
Complex systems are composed of many particles or agents that move and interact with one another. The underlying mathematical framework to model many of these systems must incorporate the spatial transport of particles and their…
Trimolecular reaction models are investigated in the compartment-based (lattice-based) framework for stochastic reaction-diffusion modelling. The formulae for the first collision time and the mean reaction time are derived for the case…
Generalized mode-coupling theory (GMCT) constitutes a systematically correctable, first-principles theory to study the dynamics of supercooled liquids and the glass transition. It is a hierarchical framework that, through the incorporation…
The Flory-Huggins theory is a well-established lattice model that is commonly used to study the mixing of distinct chemical species. It can successfully predict phase separation phenomena in blends of incompatible materials. However, it is…
Graph structures offer a versatile framework for representing diverse patterns in nature and complex systems, applicable across domains like molecular chemistry, social networks, and transportation systems. While diffusion models have…
A general theory of nucleation for colloids and macromolecules in solution is formulated within the context of fluctuating hydrodynamics. A formalism for the determination of nucleation pathways is developed and stochastic differential…