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A model of multicellular systems with several types of cells is developed from the phase field model. The model is presented as a set of partial differential equations of the field variables, each of which expresses the shape of one cell.…
The building of minimal self-reproducing systems with a physical embodiment (generically called protocells) is a great challenge, with implications for both theory and applied sciences. Although the classical view of a living protocell…
Phase separating systems that are maintained away from thermodynamic equilibrium via molecular processes represent a class of active systems, which we call active emulsions. These systems are driven by external energy input for example…
Living cells often need to measure chemical concentrations that vary in time. To this end, they deploy many resources, e.g. receptors, downstream signaling molecules, time and energy. Here, we present a theory for the optimal design of a…
Signaling networks are designed to sense an environmental stimulus and adapt to it. We propose and study a minimal model of signaling network that can sense and respond to external stimuli of varying strength in an adaptive manner. The…
Quantifying the outcomes of cells collisions is a crucial step in building the foundations of a kinetic theory of living matter. Here, we develop a mechanical theory of such collisions by first representing individual cells as extended…
Predictive modeling of the evolutionary dynamics of cancer is a challenge issue in computational cancer biology. In this paper, we propose a general mathematical model framework for the evolutionary dynamics of cancer with plasticity and…
We present a geometric framework to study the growth-division dynamics of cells and protocells, and demonstrate that self-reproduction emerges only when a system's growth dynamics and division strategy are mutually compatible. Using several…
Phase separation, crucial for spatially segregating biomolecules in cells, is well-understood in the simple case of a few components with pairwise interactions. Yet, biological cells challenge the simple picture in at least two ways: First,…
Morphogenesis of complex body shapes is reproducible despite the noise inherent in the underlying morphogenetic processes. However, how these morphogenetic processes work together to achieve this reproducibility remains unclear. Here, we…
Recent work on particle-based models of tissues has suggested that any finite rate of cell division and cell death is sufficient to fluidize an epithelial tissue. At the same time, experimental evidence has indicated the existence of glassy…
We present DiSH-Sim, a simulator for large discrete models of biological signal transduction pathways, capable of simulating networks with multi-valued elements in both deterministic and stochastic manner. We focus on order of update and…
We propose a generic model of eco-systems, with a {\it hierarchical} food web structure. In our computer simulations we let the eco-system evolve continuously for so long that that we can monitor extinctions as well as speciations over…
This paper presents the foundation for a decomposition theory for Boolean networks, a type of discrete dynamical system that has found a wide range of applications in the life sciences, engineering, and physics. Given a Boolean network…
Hybrid modeling provides an effective solution to cope with multiple time scales dynamics in systems biology. Among the applications of this method, one of the most important is the cell cycle regulation. The machinery of the cell cycle,…
We study the emergence of cell differentiation under the assumption of the existence of a given number of tradeoffs between genes encoding different functions. In the model the viability of colonies is determined by the capability of their…
Many biological systems are governed by difference equations and exhibit discrete-time dynamics. Examples include the size of a population when generations are non-overlapping, and the incidence of a disease when infections are recorded at…
Many intracellular processes continue to oscillate during the cell cycle. Although it is not well-understood how they are affected by discontinuities in the cellular environment, the general assumption is that oscillations remain robust…
In this work, we investigate a model of an adaptive networked dynamical system, where the coupling strengths among phase oscillators coevolve with the phase states. It is shown that in this model the oscillators can spontaneously…
Stochastic dynamics govern many important processes in cellular biology, and an underlying theoretical approach describing these dynamics is desirable to address a wealth of questions in biology and medicine. Mathematical tools exist for…