Related papers: Energy gradients as potential drivers of pre-cellu…
Understanding how species persist under interacting stressors is a central challenge in ecology. We develop a spatially explicit reaction-diffusion framework to investigate competing species in landscapes shaped by climate variability,…
Spatial self-organization emerges in distributed systems exhibiting local interactions when nonlinearities and the appropriate propagation of signals are at work. These kinds of phenomena can be modeled with different frameworks, typically…
The interactions between diffusing molecules and membrane-bound receptors drive numerous cellular processes. In this work, we develop a spatial model of molecular interactions with membrane receptors by homogenizing the cell membrane and…
Spatial systems with heterogeneities are ubiquitous in nature, from precipitation, temperature and soil gradients controlling vegetation growth to morphogen gradients controlling gene expression in embryos. Such systems, generally described…
Phase separating systems that are maintained away from thermodynamic equilibrium via molecular processes represent a class of active systems, which we call active emulsions. These systems are driven by external energy input for example…
Abridged abstract: Inert interactions between randomly moving entities and spatial disorder play a crucial role in quantifying the diffusive properties of a system. These interactions affect only the movement of the entities, and examples…
Resource competition is a fundamental interaction in natural communities.However little is known about competition in spatial environments where organisms are able to regulate resource distributions. Here, we analyze the competition of two…
Self-generated gradients (SGG) provide robust steering cues that guide cells in their long-distance expeditions during embryonic development, immune response, and cancer metastasis. Cells generate their own local, dynamic gradients by…
Virtually all cells use energy and ion-specific membrane pumps to maintain large transmembrane gradients of Na$^+$, K$^+$, Cl$^-$, Mg$^{++}$, and Ca$^{++}$. Although they consume up to 1/3 of a cell's energy budget, the corresponding…
Temperature gradients represent energy sources that can be harvested to generate steady reaction or transport fluxes. Technological developments could lead to the transfer of free energy from heat sources and sinks to chemical systems for…
We consider various modeling levels for spatially homogeneous chemical reaction systems, namely the chemical master equation, the chemical Langevin dynamics, and the reaction-rate equation. Throughout we restrict our study to the case where…
Aggregation-diffusion equations are foundational tools for modelling biological aggregations. Their principal use is to link the collective movement mechanisms of organisms to their emergent space use patterns in a concrete mathematical…
Biomolecular condensates play a crucial role in the spatial organization of living matter. These membrane-less organelles, resulting from liquid-liquid phase separation, operate far from thermodynamic equilibrium, with their size and…
A great number of biological organisms live in aqueous environments. Major evolutionary transitions, including the emergence of life itself, likely occurred in such environments. While the chemical aspects of the role of water in biology…
Cells are constantly exposed to diverse stimuli-chemical, mechanical, or electrical-that guide their movement. In physiological conditions, these signals often overlap, as seen during infections, where neutrophils and dendritic cells…
The dynamical characterization of proteins is crucial to understand protein function. From a microscopic point of view, protein dynamics is governed by the local atomic interactions that, in turn, trigger the functional conformational…
The fundamental processes of biological development are governed by multiple signaling molecules that create non-uniform concentration profiles known as morphogen gradients. It is widely believed that the establishment of morphogen…
An equilibrated model glass-forming liquid is studied by mapping successive configurations produced by molecular dynamics simulation onto a time series of inherent structures (local minima in the potential energy). Using this ``inherent…
We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…
The capacity to sense gradients efficiently and acquire information about the ambient environment confers many advantages like facilitating movement toward nutrient sources or away from toxic chemicals. The amplified dispersal evinced by…