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A diffuse-interface model for microstructure with an arbitrary number of components and phases was developed from basic thermodynamic and kinetic principles and formalized within a variational framework. The model includes a composition…
Diffusion is a fundamental phenomenon that occurs ubiquitously in nature and remains the subject of continuous research interest. Understanding diffusion is a key to understanding leaving systems. In this Chapter, I discuss diffusion of…
The separation of substances into different phases is ubiquitous in nature and important scientifically and technologically. This phenomenon may become drastically different if the species involved, whether molecules or supramolecular…
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,…
We propose a principle of consistency between different hierarchical levels of biological systems. Given a consistency between molecule replication and cell reproduction, universal statistical laws on cellular chemical abundances are…
This paper investigates the competition of two species in a heterogeneous environment subject to the effect of harvesting. The most realistic harvesting case is connected with the intrinsic growth rate, and the harvesting functions are…
In many biological systems, natural selection acts simultaneously on multiple levels of organization. This scenario typically presents an evolutionary conflict between the incentive of individuals to cheat and the collective incentive to…
The activity of biological cells is primarily based on chemical reactions and typically modeled as a reaction-diffusion system. Cells are, however, highly crowded with macromolecules, including a variety of molecular machines such as…
Virtually every biological function emerges through the organization of molecules in time and space. Consequently, a major challenge in statistical physics is to uncover the universal principles governing macromolecular self-organization…
Developing new molecular compounds is crucial to address pressing challenges, from health to environmental sustainability. However, exploring the molecular space to discover new molecules is difficult due to the vastness of the space. Here…
This is the first of two papers where we discuss the limits imposed by competition to the biodiversity of species communities. In this first paper we study the coexistence of competing species at the fixed point of population dynamic…
Based on a non-equilibrium mechanism for spatial pattern formation we study how position information can be controlled by locally coupled discrete dynamical networks, similar to gene regulation networks of cells in a developing…
All life, including cells and artificial protocells, must integrate diverse molecules into a single unit in order to reproduce. Despite expected pressure to evolve a simple system with the fastest replication speed, the mechanism by which…
We seek models for the genotype evolution of agricultural animals, animals involved in primary production processes. Classical models for genotype evolution have tended to be very simple in order that analytic methods may be employed in…
We analyze evolutionary dynamics in a confluent, branching cellular population, such as in a growing duct, vasculature, or in a branching microbial colony. We focus on the coarse-grained features of the evolution and build a statistical…
Models of coordinated behavior of populations living in the same environment are introduced for the cases when they either compete with each other, or they both gain by mutual interactions, or finally when one hunts the other one. The…
How large ecosystems can create and maintain the remarkable biodiversity we see in nature is probably one of the biggest open questions in science, attracting attention from different fields, from Theoretical Ecology to Mathematics and…
Mechanisms of immunity, and of the host-pathogen interactions in general are among the most fundamental problems of medicine, ecology, and evolution studies. Here, we present a microscopic, protein-level, sequence-based model of immune…
We discuss several continuum cell-cell adhesion models based on the underlying microscopic assumptions. We propose an improvement on these models leading to sharp fronts and intermingling invasion fronts between different cell type…
Phase separation has emerged as an essential concept for the spatial organization inside biological cells. However, despite the clear relevance to virtually all physiological functions, we understand surprisingly little about what phases…