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The notion of (auto) catalytic networks has become a cornerstone in understanding the possibility of a sudden dramatic increase of diversity in biological evolution as well as in the evolution of social and economical systems. Here we study…
A number of microorganisms leave persistent trails while moving along surfaces. For single-cell organisms, the trail-mediated self-interaction will influence its dynamics. It has been discussed recently [Kranz \textit{et al.} Phys. Rev.…
We reveal several distinct regimes of the relaxation dynamics of a small quantum system coupled to an environment within the plane of the dissipation strength and the reservoir temperature. This is achieved by discriminating between…
The emergence of self-sustaining autocatalytic networks in chemical reaction systems has been studied as a possible mechanism for modelling how living systems first arose. It has been known for several decades that such networks will form…
Singularities in macroscopic systems at discontinuous phase transitions are replaced in finite systems by sharp but continuous changes. Both the energy differences between metastable and stable phases and the energy barriers separating…
We perform molecular dynamics simulation of a small number of particles in a box with periodic boundary conditions from a view point of chaotic dynamical systems. There is a transition at a critical energy E_c that each particle is confined…
We formulate the large deviations for a class of two scale chemical kinetic processes motivated from biological applications. The result is successfully applied to treat a genetic switching model with positive feedbacks. The corresponding…
Motivated by the study of rare events for a typical genetic switching model in systems biology, in this paper we aim to establish the general two-scale large deviations for chemical reaction systems. We build a formal approach to explicitly…
A system formed by a crowded environment of catalytic obstacles and complex oscillatory chemical reactions is inquired. The obstacles are static spheres of equal radius, which are placed in a random way. The chemical reactions are carried…
Density-dependent diffusion is a widespread phenomenon in nature. We have examined the density-dependent diffusion behavior of some biological processes such as tumor growth and invasion [23]. Here, we extend our previous work by developing…
Molecular search phenomena are observed in a variety of chemical and biological systems. During the search the participating particles frequently move in complex inhomogeneous environments with random transitions between different dynamic…
Mechanical interactions between biological cells may be mediated by secreted products, making them dependent on the local particle density. Here, we explore the generic physics of density-dependent attractive interactions. We show using…
We investigate the propagation of random fluctuations through biochemical networks in which the concentrations of species are large enough so that the unperturbed problem is well-described by ordinary differential equation. We characterize…
Understanding how biological homochirality emerged remains a challenge for the researchers interested in the origin of life. During the last decades, stable non-racemic steady states of nonequilibrium chemical systems have been discussed as…
We analyzed the stochastic behavior of systems controlled by autocatalytic reaction A+X -> X+X, X+X -> A+X, X -> B provided that the distribution of reacting particles in the system volume is uniform, i.e. the point model of reaction…
Colloidal mixtures represent a versatile model system to study transport in complex environments. They allow for a systematic variation of the control parameters, namely size ratio, total volume fraction and composition. We study the…
In this paper, we investigate a mathematical modeling of biochemical processes which makes it possible to determine the adaptation of a biosystem to open environmental conditions.
Simulating percolation and critical phenomena of labelled species inside films composed of single-component linear homogeneous macromolecules using molecular Monte Carlo method in 3 dimensions, we study dependence of these conducting…
Heterogeneity in gene expression across isogenic cell populations can give rise to phenotypic diversity, even when cells are in homogenous environments. This diversity arises from the discrete, stochastic nature of biochemical reactions,…
An overview of the behavior of materials at high pressure is presented, starting from the effects on single atoms driving electronic transitions and changes in periodic trends. A range of high-pressure-induced phenomena in the solid state…