Related papers: A theoretical basis for cell deaths
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…
A novel mechanism for cell differentiation is proposed, based on the dynamic clustering in a globally coupled chaotic system. A simple model with metabolic reaction, active transport of chemicals from media, and cell division is found to…
Metabolic networks perform some of the most fundamental functions in living cells, including energy transduction and building block biosynthesis. While these are the best characterized networks in living systems, understanding their…
Dynamics maintaining diversity of cell types in a multi-cellular system are studied in relationship with the plasticity of cellular states. First, we introduce a new theoretical framework, reaction-diffusion system on `chemical species…
Cell tracking is a key computational task in live-cell microscopy, but fully automated analysis of high-throughput imaging requires reliable and, thus, uncertainty-aware data analysis tools, as the amount of data recorded within a single…
Engineering biology requires precise control of biomolecular circuits, and Cybergenetics is the field dedicated to achieving this goal. A significant challenge in developing controllers for cellular functions is designing systems that can…
This paper presents a novel framework for the modeling of biological networks. It makes use of recent tools analyzing the robust satisfaction of properties of (hybrid) dynamical systems. The main challenge of this approach as applied to…
Whole-cell modelling is constrained by the laws of nature in general and the laws of thermodynamics in particular. This paper shows how one prolific source of information, stoichiometric models of biomolecular systems, can be integrated…
The organization of live cells to tissues is associated with the mechanical interaction between cells, which is mediated through their elastic environment. We model cells as spherical active force dipoles surrounded by an infinite elastic…
Our knowledge of how individual cells self-organize to form complex multicellular systems is being revolutionized by a data outburst, coming from high-throughput experimental breakthroughs such as single-cell RNA sequencing and spatially…
Understanding how fluctuations propagate across spatial scales is central to our understanding of inanimate matter from turbulence to critical phenomena. In contrast to physical systems, biological systems are organized into a hierarchy of…
Quantitative studies of cell metabolism are often based on large chemical reaction network models. A steady state approach is suited to analyze phenomena on the timescale of cell growth and circumvents the problem of incomplete experimental…
The properties and fundamental limits of chemical computers have recently attracted significant interest as a model of computation, an unifying principle of cellular organisation and in the context of bio-engineering. As of yet, research in…
Current efforts in the biomedical sciences and related interdisciplinary fields are focused on gaining a molecular understanding of health and disease, which is a problem of daunting complexity that spans many orders of magnitude in…
How do cellular automata behave in the limit of a very large number of cells? Is there a continuum limit with simple properties? We attack this problem by mapping certain classes of automata to quantum field theories for which powerful…
The biological cell exhibits a fantastic range of behaviors, but ultimately these are governed by a handful of physical and chemical principles. Here we explore simple theory, known for decades and based on the simple thermodynamics of…
Cell populations invade through a combination of proliferation and motility. Proliferation depends on the internal timing of cell division: how long cells take to complete the cell cycle. This timing varies substantially within (and across)…
The paper analyses stochastic systems describing reacting molecular systems with a combination of two types of state spaces, a finite-dimensional, and an infinite dimenional part. As a typical situation consider the interaction of larger…
Cellular automata are a set of computational models in discrete space that have a discrete time evolution defined by neighbourhood rules. They are used to simulate many complex systems in physics and science in general. In this work,…
What determines whether an organism or collective will survive under particular conditions? This question is asked across the life sciences when determining adaptive fit, developing efficacious treatments for diseases, and assessing the…