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Enzyme kinetics has historically been described by deterministic models, with the Michaelis-Menten (MM) equation serving as a paradigm. However, recent experimental and theoretical advances have made it clear that stochastic fluctuations,…
We study the asymptotic behavior of multiscale stochastic spatial gene networks. Multiscaling takes into account the difference of abundance between molecules , and captures the dynamic of rare species at a mesoscopic level. We introduce an…
Stochastic thermodynamics provides a framework for describing small systems like colloids or biomolecules driven out of equilibrium but still in contact with a heat bath. Both, a first-law like energy balance involving exchanged heat and…
We investigate a class of stochastic chemical reaction networks with $n{\ge}1$ chemical species $S_1$, \ldots, $S_n$, and whose complexes are only of the form $k_iS_i$, $i{=}1$,\ldots, $n$, where $(k_i)$ are integers. The time evolution of…
Systems in which a short-ranged attraction and long-ranged repulsion compete are intrinsically frustrated, leading their structure and dynamics to be dominated either by mesoscopic order or by metastable disorder. Here we report the latter…
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…
All living things exhibit adaptations that enable them to survive and reproduce in the natural environment that they inhabit. From a biological standpoint, it has long been understood that adaptation comes from natural selection, whereby…
We introduce a stochastic agent-based model for the flocking dynamics of self-propelled particles that exhibit velocity-alignment interactions with neighbours within their field of view. The stochasticity in the dynamics of the model arises…
Based on laboratory based growth of plant-like structures from inorganic materials, we present new theory for the emergence of plant structure at a range of scales dictated by levels of ionization (charge density), which can be traced…
Chemically fueled supramolecular systems can exhibit complex, time-dependent behaviors reminiscent of living matter when maintained far from equilibrium by continuous energy or fuel consumption. Here, we introduce a minimal…
We consider stochastic descriptions of chemical reaction networks in which there are both fast and slow reactions, and for which the time scales are widely separated. We develop a computational algorithm that produces the generator of the…
Conservation laws are time-invariant properties that constrain many physical systems. For systems of chemical reactions, the law of mass conservation constrains how atoms flow between chemical species. Chemical reaction networks can display…
Explaining the origin of life requires us to explain how self-replication arises. To be specific, how can a self-replicating entity develop spontaneously from a chemical reaction system in which no reaction is self-replicating? Previously…
Originating from the pioneering study of Alan Turing, the bifurcation analysis predicting spatial pattern formation from a spatially uniform state for diffusing morphogens or chemical species that interact through nonlinear reactions is a…
We consider birth and death stochastic dynamics of particle systems with attractive interaction. The heuristic generator of the dynamics has a constant birth rate and density dependent decreasing death rate. The corresponding statistical…
The intrinsic length scales of a reaction diffusion system (Gierer-Meinhardt model)is varied by quasi-statically changing the diffusion constant of the activator and a transition from rolls to hexagon is detected. The transition is…
Chemotaxis describes the movement of an organism, such as single or multi-cellular organisms and bacteria, in response to a chemical stimulus. Two widely used models to describe the phenomenon are the celebrated Keller-Segel equation and a…
Nonequilibrium thermodynamics (NET) investigates processes in systems out of global equilibrium. On a mesoscopic level, it provides a statistical dynamic description of various complex phenomena such as chemical reactions, ion transport,…
Randomness is an unavoidable feature of the intracellular environment due to chemical reactants being present in low copy number. That phenomenon, predicted by Delbr\"uck long ago \cite{delbruck40}, has been detected in both prokaryotic…
We consider a stochastic model, called the replicator coalescent, describing a system of blocks of $k$ different types which undergo pairwise mergers at rates depending on the block types: with rate $C_{i,j}$ blocks of type $i$ and $j$…