Related papers: Homeostatic Mechanisms in Biological Systems
With the formal construction of a thermodynamic spring, I describe the mechanics, energetics, entropy, and kinetics of a binary mechanical model system. A protein that transitions between two metastable structural states behaves as a…
Recent computational experiments have demonstrated the spontaneous emergence of self-replicating programs across universal automata, artificial chemistries, and self-modifying code systems. Remarkably, these results arise without explicit…
We describe a mechanism for pronounced biochemical oscillations, relevant to microscopic systems, such as the intracellular environment. This mechanism operates for reaction schemes which, when modeled using deterministic rate equations,…
Feedback loops are essential for regulating cell proliferation and maintaining the delicate balance between cell division and cell death. Thanks to the exact solution of a few simple models of cell growth it is by now clear that stochastic…
Ergodicity and output controllability have been shown to be fundamental concepts for the analysis and synthetic design of closed-loop stochastic reaction networks, as exemplified by the use of antithetic integral feedback controllers. In…
Understanding mechanosensitivity, i.e. how cells sense the stiffness of their environment is very important, yet there is a fundamental difficulty in understanding its mechanism: to measure an elastic modulus one requires two points of…
One popular assumption regarding biological systems is that traits have evolved to be optimized with respect to function. This is a standard goal in evolutionary computation, and while not always embraced in the biological sciences, is an…
Controlling stochastic reactions networks is a challenging problem with important implications in various fields such as systems and synthetic biology. Various regulation motifs have been discovered or posited over the recent years, the…
We propose that operator induction serves as an adequate model of perception. We explain how to reduce universal agent models to operator induction. We propose a universal measure of operator induction fitness, and show how it can be used…
Hemostasis and thrombosis are often thought as two sides of the same clotting mechanism whereas hemostasis is a natural protective mechanism to prevent bleeding and thrombosis is a blood clot abnormally formulated inside a blood vessel,…
Quantifying energy flows at nanometer scales promises to guide future research in a variety of disciplines, from microscopic control and manipulation, to autonomously operating molecular machines. A general understanding of the…
Perfect adaptation is a phenomenon whereby the output variables of a system can maintain certain values despite external disturbances. Robust perfect adaptation (RPA) refers to an adaptation property that does not require fine-tuning of…
Based on extensive study of a dynamical systems model of the development of a cell society, a novel theory for stem cell differentiation and its regulation is proposed as the ``chaos hypothesis''. Two fundamental features of stem cell…
Living cells use readout molecules to record the state of receptor proteins, similar to measurements or copies in typical computational devices. But is this analogy rigorous? Can cells be optimally efficient, and if not, why? We show that,…
Auto-regulatory feedback loops are one of the most common network motifs. A wide variety of stochastic models have been constructed to understand how the fluctuations in protein numbers in these loops are influenced by the kinetic…
Biomolecular feedback systems are now a central application area of interest within control theory. While classical control techniques provide invaluable insight into the function and design of both natural and synthetic biomolecular…
We consider stochastic models of chemical reaction networks with time dependent input rates and several types of molecules. We prove that, in despite of strong time dependence of input rates, there is a kind of homeostasis phenomenon: far…
In this paper we report that notions of topological protection can be applied to stationary configurations that are driven far from equilibrium by active, dissipative processes. We show this for physically two disparate cases : stochastic…
Pluripotent embryonic stem cells are of paramount importance for biomedical research thanks to their innate ability for self-renewal and differentiation into all major cell lines. The fateful decision to exit or remain in the pluripotent…
The similarity between neural and immune networks has been known for decades, but so far we did not understand the mechanism that allows the immune system, unlike associative neural networks, to recall and execute a large number of…