Related papers: Maximum entropy and population heterogeneity in co…

Estimation of division and death rates of lymphocytes in different conditions is vital for quantitative understanding of the immune system. Deuterium, in the form of deuterated glucose or heavy water, can be used to measure rates of…

We develop a continuous mathematical model of population dynamics that describes the sequential emergence of new genotypes under limited resources. The framework models genotype density as a nonlinear flow in mutation space, combining…

The propensity of water to remain in a metastable liquid state at temperatures below its equilibrium melting point holds significant potential for cryopreserving biological material such as tissues and organs. The benefits conferred are a…

Biomolecular condensates are small droplets forming spontaneously in biological cells via phase separation. They play a role in many cellular processes, but it is unclear how cells control them. Cellular regulation often relies on…

To maintain renewing epithelial tissues in a healthy, homeostatic state, (stem) cell divisions and differentiation need to be tightly regulated. Mechanisms of homeostatic control often rely on crowding control: cells are able to sense the…

Among the different computational approaches modelling the dynamics of isogenic cell populations, discrete stochastic models can describe with sufficient accuracy the evolution of small size populations. However, for a systematic and…

The cell cycle duration is a variable cellular phenotype that underlies long-term population growth and age structures. By analyzing the stationary solutions of a branching process with heritable cell division times, we demonstrate…

We study the interplay of population growth and evolutionary dynamics using a stochastic model based on birth and death events. In contrast to the common assumption of an independent population size, evolution can be strongly affected by…

The abundance of a species' population in an ecosystem is rarely stationary, often exhibiting large fluctuations over time. Using historical data on marine species, we show that the year-to-year fluctuations of population growth rate obey a…

Measurements of cell size dynamics have established the adder principle as a robust mechanism of cell size homeostasis. In this framework, cells add a nearly constant amount of size during each cell cycle, independent of their size at…

During overflow metabolism, cells excrete glycolytic byproducts when growing under aerobic conditions in a seemingly wasteful fashion. While potentially advantageous for microbes with finite oxidative capacity, its role in higher organisms…

This paper shows how to evolve numerically the maximum entropy probability distributions for a given set of constraints, which is a variational calculus problem. An evolutionary algorithm can obtain approximations to some well-known…

Stochastic models of sequential mutation acquisition are widely used to quantify cancer and bacterial evolution. Across manifold scenarios, recurrent research questions are: how many cells are there with $n$ alterations, and how long will…

Realistic models of biological processes typically involve interacting components on multiple scales, driven by changing environment and inherent stochasticity. Such models are often analytically and numerically intractable. We revisit a…

Biological systems are governed by coupled interactions between intracellular metabolism and bioreactor operation that span multiple time scales. Constraint-based metabolic models are widely used to describe intracellular metabolism, but…

We present a simple model for describing the dynamics of the interaction between a homogeneous population or society, and the natural resources and reserves that the society needs for its survival. The model is formulated in terms of…

A tumor can be thought of as an ecosystem, which critically means that we cannot just consider it as a collection of mutated cells but more as a complex system of many interacting cellular and microenvironmental elements. At its simplest, a…

Coevolutionary dynamics is investigated in chemical catalysis, biological evolution, social and economic systems. The dynamics of these systems can be analyzed within the unifying framework of evolutionary game theory. In this Letter, we…

We consider an exponentially growing population of cells undergoing mutations and ask about the effect of reproductive fluctuations (genetic drift) on its long-term evolution. We combine first step analysis with the stochastic dynamics of a…

Maximum entropy models are increasingly being used to describe the collective activity of neural populations with measured mean neural activities and pairwise correlations, but the full space of probability distributions consistent with…