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Motivated by recent understandings in the stochastic natures of gene expression, biochemical signaling, and spontaneous reversible epigenetic switchings, we study a simple deterministic cell population dynamics in which subpopulations grow…
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…
We consider a size-structured model for cell division and address the question of determining the division (birth) rate from the measured stable size distribution of the population. We formulate such question as an inverse problem for an…
Mechanical stresses stemming from environmental factors are a key determinant of cellular behavior and physiology. Yet, the role of self-induced biomechanical stresses in growing bacterial colonies has remained largely unexplored. Here, we…
Current mathematical frameworks for predicting the flux state and macromolecular composition of the cell do not rely on thermodynamic constraints to determine the spontaneous direction of reactions. These predictions may be biologically…
Natural selection has shaped the evolution of cells and multi-cellular organisms such that social cooperation can often be preferred over an individualistic approach to metabolic regulation. This paper extends a framework for dynamic…
Nearly all cell models explicitly or implicitly deal with the biophysical constraints that must be respected for life to persist. Despite this, there is almost no systematicity in how these constraints are implemented, and we lack a…
Cells control their size to cope with noise during growth and division. Eukaryotic cells exhibiting "sizer" control (targeting a specific size before dividing) may rely on molecular concentration thresholds, but simple implementations of…
This paper investigates the role of size in biological organisms. More specifically, how the energy demand, expressed by the metabolic rate, changes according to the mass of an organism. Empirical evidence suggests a power-law relation…
We cast the metabolism of interacting cells within a statistical mechanics framework considering both, the actual phenotypic capacities of each cell and its interaction with its neighbors. Reaction fluxes will be the components of…
The mechanism by which cells measure the dimension of the organ in which they are embedded, and slow down their growth when the final size is reached, is a long-standing problem of developmental biology. The role of mechanics in this…
In exponential population growth, variability in the timing of individual division events and environmental factors (including stochastic inoculation) compound to produce variable growth trajectories. In several stochastic models of…
Understanding the organization of reaction fluxes in cellular metabolism from the stoichiometry and the topology of the underlying biochemical network is a central issue in systems biology. In this task, it is important to devise reasonable…
The mechanism of bacterial cell size control has been a mystery for decades, which involves the well-coordinated growth and division in the cell cycle. The revolutionary modern techniques of microfluidics and the advanced live imaging…
Optimization-based models have been used to predict cellular behavior for over 25 years. The constraints in these models are derived from genome annotations, measured macro-molecular composition of cells, and by measuring the cell's growth…
Modelling, analysing and inferring triggering mechanisms in population reproduction is fundamental in many biological applications. It is also an active and growing research domain in mathematical biology. In this chapter, we review the…
Cell migration is crucial to many physiological and pathological processes. During migration, a cell adapts its morphology, including the overall morphology and nucleus morphology, in response to various cues in complex microenvironments,…
Recent studies at individual cell resolution have revealed phenotypic heterogeneity in nominally clonal tumor cell populations. The heterogeneity affects cell growth behaviors, which can result in departure from the idealized uniform…
We study the Stochastic Thermodynamics of cell growth and division using a theoretical framework based on branching processes with resetting. Cell division may be split into two sub-processes: branching, by which a given cell gives birth to…
The metabolic network plays a crucial role in regulating bacterial metabolism and growth, but it is subject to inherent molecular stochasticity. Previous studies have utilized flux balance analysis and the maximum entropy method to predict…