Related papers: Crowding induced entropy-enthalpy compensation in …
In this paper, we identify a radically new viewpoint on the collective behaviour of groups of intelligent agents. We first develop a highly general abstract model for the possible future lives that these agents may encounter as a result of…
High-order phenomena play crucial roles in many systems of interest, but their analysis is often highly nontrivial. There is a rich literature providing a number of alternative information-theoretic quantities capturing high-order…
We introduce axiomatically a complete thermodynamic formalism for a single macromolecule, either with or without detailed balance, in an isothermal ambient fluid based on its stochastic dynamics. With detailed balance, the novel theory…
We show that an analogy between crowding in fluid and jammed phases of hard spheres captures the density dependence of the kissing number for a family of numerically generated jammed states. We extend this analogy to jams of mixtures of…
The capacity of proteins to interact specifically with one another underlies our conceptual understanding of how living systems function. Systems-level study of specificity in protein-protein interactions is complicated by the fact that the…
Inspired by recent experiments on the effects of cytosolic crowders on the organization of bacterial chromosomes, we consider a "feather-boa" type model chromosome in the presence of non-additive crowders, encapsulated within a cylindrical…
Making decisions freely presupposes that there is some indeterminacy in the environment and in the decision making engine. The former is reflected on the behavioral changes due to communicating: few changes indicate rigid environments;…
This paper is framed in a series of studies on attraction-repulsion chemotaxis models combining different effects: nonlinear diffusion and sensitivities and logistic sources, for the dynamics of the cell density, and consumption and/or…
How do living cells achieve sufficient abundances of functional protein complexes while minimizing promiscuous non-functional interactions? Here we study this problem using a first-principle model of the cell whose phenotypic traits are…
We present a comprehensive computational study of the collective behavior emerging from the competition between self-propulsion, excluded volume interactions and velocity-alignment in a two-dimensionnal model of active particles. We…
We consider a requester who acquires a set of data (e.g. images) that is not owned by one party. In order to collect as many data as possible, crowdsourcing mechanisms have been widely used to seek help from the crowd. However, existing…
The Minority Game (MG) is a basic multi-agent model representing a simplified and binary form of the bar attendance model of Arthur. The model has an informationally efficient phase in which the agents lack the capability of exploiting any…
The dynamics of molecular collisions in a macroscopic body are encoded by the parameter Thermodynamic entropy - a statistical measure of the number of molecular configurations that correspond to a given macrostate. Directionality in the…
The concept of entropy in statistical physics is related to the existence of irreversible macroscopic processes. In this work, we explore a recently introduced entropy formula for a class of stochastic processes with more than one absorbing…
We propose an entropic geometrical model of psycho-physical crowd dynamics (with dissipative crowd kinematics), using Feynman action-amplitude formalism that operates on three synergetic levels: macro, meso and micro. The intent is to…
There are numerous scenarios in which populations of cells migrate in crowded environments. Typical examples include wound healing, cancer growth and embryo development. In these crowded environments cells are able to interact with each…
Stochasticity is a defining feature of the pairwise forces governing interactions in biological systems-from molecular motors to cell-cell adhesion-yet its consequences on large-scale dynamics remain poorly understood. Here, we show that…
A coarse-grained variational model is used to investigate the polymer dynamics of barrier crossing for a diverse set of two-state folding proteins. The model gives reliable folding rate predictions provided excluded volume terms that induce…
We investigate, via Brownian dynamics simulations, the reaction dynamics of a simple, non-linear chemical network (the Willamowski-Rossler network) under spatial confinement and crowding conditions. Our results show that the presence of…
Proteins created by combinatorial methods in vitro are an important source of information for understanding sequence-structure-function relationships. Alignments of folded proteins from combinatorial libraries can be analyzed using methods…