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Living cell signaling systems include multistep biochemical signaling reaction cascades (BSCs) comprising modifications of molecular signaling proteins. Substantial data on BSCs have been accumulated in the field of molecular biology and…
Feedback in sensory biochemical networks can give rise to bifurcations in cells' behavioral response. These bifurcations share many properties with thermodynamic critical points. Evidence suggests that biological systems may operate near…
Living cells are continually exposed to environmental signals that vary in time. These signals are detected and processed by biochemical networks, which are often highly stochastic. To understand how cells cope with a fluctuating…
Stochastic kinetic models of genetic expression are able to describe protein fluctuations. A comparative study of the canonical and a feedback model is given here by using stochastic simulation methods. The feedback model is skeleton model…
Biomolecules stochastically occupy different possible configurations with probabilities given by non-equilibrium steady-state distributions. These distributions are determined by the transition rate constants between different…
Stochasticity in gene expression can give rise to fluctuations in protein levels and lead to phenotypic variation across a population of genetically identical cells. Recent experiments indicate that bursting and feedback mechanisms play…
Statistical properties of environments experienced by biological signaling systems in the real world change, which necessitate adaptive responses to achieve high fidelity information transmission. One form of such adaptive response is gain…
Living organisms rely on endogenous feedback mechanisms to maintain homeostasis in the presence of uncertainty and environmental fluctuations. An emerging challenge at the interface of control systems engineering and synthetic biology is…
Living systems often function with regulatory interactions, but the question of how activity, stochasticity and regulations work together for achieving different goals still remains puzzling. We propose a stochastic model of an active…
A model for autonomous feedback control of particle transport through a large number of channels is introduced. Interactions among the particles can lead to a strong suppression of fluctuations in the particle number statistics. Within a…
Cellular behavior is governed by gene regulatory processes that are intrinsically dynamic and nonlinear, and are subject to non-negligible amounts of random fluctuations. Such conditions are ubiquitous in physical systems, where they have…
Resistive switching is one of the foremost candidates for building novel types of non-volatile random access memories. Any practical implementation of such a memory cell calls for a strong miniaturization, at which point fluctuations start…
Mesoscopic fluctuations reveal stochastic dynamics of molecules in both inanimate and living matter. We investigate how small-number fluctuations shape the collective dynamics of molecular motors using motile cilia as model system. We…
Gene products (RNAs, proteins) often occur at low molecular counts inside individual cells, and hence are subject to considerable random fluctuations (noise) in copy number over time. Not surprisingly, cells encode diverse regulatory…
Nature presents multiple intriguing examples of processes which proceed at high precision and regularity. This remarkable stability is frequently counter to modelers' experience with the inherent stochasticity of chemical reactions in the…
Cellular biology exists embedded in a world dominated by random dynamics and chance. Many vital molecules and pieces of cellular machinery diffuse within cells, moving along random trajectories as they collide with the other biomolecular…
We generalize and extend the recently proposed method to account for contributions of system size (or volume/participant) fluctuations to the experimentally measured moments of particle multiplicity distributions. We find that in the…
Chemically active systems such as living cells are maintained out of thermal equilibrium due to chemical events which generate heat and lead to active fluctuations. A key question is to understand on which time and length scales active…
Mixed positive and negative feedback loops are often found in biological systems which support oscillations. In this work we consider a prototype of such systems, which has been recently found at the core of many genetic circuits showing…
In a previous work, we presented a model that integrates cancer cell differentiation and immunotherapy, analysing a particular therapy against cancer stem cells by cytotoxic cell vaccines. As every biological system is exposed to random…