Related papers: Amplified biochemical oscillations in cellular sys…
We consider a standard optomechanical system where a mechanical oscillator is coupled to a cavity mode through the radiation pressure interaction. The oscillator is coherently driven at its resonance frequency, whereas the cavity mode is…
Oscillations lie at the core of many biological processes, from the cell cycle, to circadian oscillations and developmental processes. Time-keeping mechanisms are essential to enable organisms to adapt to varying conditions in environmental…
Overdamped stochastic systems maintained far from equilibrium can display sustained oscillations with fluctuations that decrease with the system size. The correlation time of such noisy limit cycles expressed in units of the cycle period is…
Cellular processes do not follow deterministic rules; even in identical environments genetically identical cells can make random choices leading to different phenotypes. This randomness originates from fluctuations present in the…
Self-oscillations underlie many natural phenomena such as heartbeat, ocean waves, and the pulsation of variable stars. From pendulum clocks to the behavior of animal groups, self-oscillation is one of the keys to the understanding of…
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…
A natural phenomenon occurring in a living system is an outcome of the dynamics of the specific biological network underlying the phenomenon. The collective dynamics have both deterministic and stochastic components. The stochastic nature…
Gene expression is a central process to any form of life. It involves multiple temporal and functional scales that extend from specific protein-DNA interactions to the coordinated regulation of multiple genes in response to intracellular…
Natural biological systems process environmental information through both amplitude and frequency-modulated signals, yet engineered biological circuits have largely relied on amplitude-based regulation alone. Despite the prevalence of…
The dynamics of stochastic reaction networks within cells are inevitably modulated by factors considered extrinsic to the network such as for instance the fluctuations in ribsome copy numbers for a gene regulatory network. While several…
The phenomena of stochasticity in biochemical processes have been intriguing life scientists for the past few decades. We now know that living cells take advantage of stochasticity in some cases and counteract stochastic effects in others.…
Due to inherent noise in intracellular networks cellular decisions can be random, so genetically identical cells can display different phenotypic behavior even in identical environments. Most previous work in understanding the…
While noise is generally associated with uncertainties and often has a negative connotation in engineering, living organisms have evolved to adapt to (and even exploit) such uncertainty to ensure the survival of a species or implement…
Local interactions among biomolecules, and the role played by their environment, have gained increasing attention in modelling biochemical reactions. By defining the automaton of molecular perceptions, we explore an agent-based…
In recent years considerable portion of the computer science community has focused its attention on understanding living cell biochemistry and efforts to understand such complication reaction environment have spread over wide front, ranging…
How do single cell fate decisions induced by activation of key signaling proteins above threshold concentrations within a time interval are affected by stochastic fluctuations in biochemical reactions? We address this question using minimal…
Stochasticity is a key characteristic of intracellular processes such as gene regulation and chemical signalling. Therefore, characterising stochastic effects in biochemical systems is essential to understand the complex dynamics of living…
This paper investigates optimal fluctuations for chemical reaction systems with N species, M reactions, and general rate law. In the limit of large volume, large fluctuations for such models occur with overwhelming probability in the…
We study a stochastic two-species chemical reaction system with two mechanisms. One mechanism consists of chemical interactions which govern the overall drift of species amounts in the system; the other mechanism consists of resampling,…
A connection is established between discrete stochastic model describing microscopic motion of fluctuating cells, and macroscopic equations describing dynamics of cellular density. Cells move towards chemical gradient (process called…