Related papers: Entropy, Ergodicity and Stem Cell Multipotency
Nowadays, multiscale modelling is recognized as the most suitable way to study biological processes. Indeed, almost every phenomenon in nature exhibits a multiscale behaviour, i.e., it is the outcome of interactions that occur at different…
Extrachromosomal DNA (ecDNA) can drive oncogene amplification, gene expression and intratumor heterogeneity, representing a major force in cancer initiation and progression. The phenomenon becomes even more intricate as distinct types of…
Active contributions to fluctuations are a direct consequence of metabolic energy consumption in living cells. Such metabolic processes continuously create active forces, which deform the membrane to control motility, proliferation as well…
We propose a three dimensional mechanical model of embryonic tissue dynamics. Mechanically coupled adherent cells are represented as particles interconnected with elastic beams which can exert non-central forces and torques. Tissue…
How are granular details of stochastic growth and division of individual cells reflected in smooth deterministic growth of population numbers? We provide an integrated, multiscale perspective of microbial growth dynamics by formulating a…
Understanding the relationship between spontaneous stochastic fluctuations and the topology of the underlying gene regulatory network is of fundamental importance for the study of single-cell stochastic gene expression. Here by solving the…
The complexity of gene regulatory networks in multicellular organisms makes interpretable low-dimensional models highly desirable. An attractive geometric picture, attributed to Waddington, visualizes the differentiation of a cell into…
A change in a stochastic system has three representations: Probabilistic, statistical, and informational: (i) is based on random variable $u(\omega)\to\tilde{u}(\omega)$; this induces (ii) the probability distributions $F_u(x)\to…
While there has been a keen interest in studying computation at the edge of chaos for dynamical systems undergoing a phase transition, this has come under question for cellular automata. We show that for continuously deformed cellular…
The interrelationships of the fundamental biological processes natural selection, mutation, and stochastic drift are quantified by the entropy rate of Moran processes with mutation, measuring the long-run variation of a Markov process. The…
In this paper we revisit the concept of mobility entropy. Over time, the structure of spatial interactions among urban centres tends to become more complex and evolves from centralised models to more scattered origin and destination…
Can one demonstrate quantitative effects of diversity within a system comprised of distinct individuals on the performance of the system as a whole? Assuming that individuals can be different, we develop a model to interpolate between…
We define the concept of dependence among multiple variables using maximum entropy techniques and introduce a graphical notation to denote the dependencies. Direct inference of information theoretic quantities from data uncovers…
In an attempt to explain the uniqueness of the coding mechanism of living cells as contrasted with multi-species structure of ecosystems we examine two models of individuals with some replicative properties. In the first model the system…
Biochemical signaling cascades transmit intracellular information while dissipating energy under nonequilibrium conditions. We model a cascade as a code string and apply information-entropy ideas to quantify an optimal transmission rate. A…
Phenotypic heterogeneity is a most fascinating property of a population of cells, which shows the differences among individuals even with the same genetic background and extracellular environmental conditions. However, the lack of…
In this paper I describe a cellular automaton model of a multi-species ecosystem, suitable for the study of emergent properties of macroevolution. Unlike majority of ecological models, the number of coexisting species is not fixed. Starting…
We are interested in modeling some two-level population dynamics, resulting from the interplay of ecological interactions and phenotypic variation of individuals (or hosts) and the evolution of cells (or parasites) of two types living in…
In this article, we will see a new approach to study the impact of a small microscopic population of cancer cells on a macroscopic population of healthy cells, with an example inspired by pathological hematopoiesis. Hematopoiesis is the…
Adaptive control in biological systems, such as intestinal immunity, remains poorly understood despite detailed knowledge of underlying regulatory networks. We propose an alternative framework based on stochastic martingale turnover, in…