相关论文: Engineering reaction-diffusion networks with prope…
Turing's mechanism is often invoked to explain periodic patterns in nature, although direct experimental support is scarce. Turing patterns form in reaction-diffusion systems when the activating species diffuse much slower than the…
For continuous-time Markov chains and open unimolecular chemical reaction networks, we prove that any two stationary currents are linearly related upon perturbations of a single edge's transition rates, arbitrarily far from equilibrium. We…
Many biological decision-making processes can be viewed as performing a classification task over a set of inputs, using various chemical and physical processes as "biological hardware." In this context, it is important to understand the…
Diffusion dynamics in multiplex networks can model a diverse number of real-world processes. In some specific configurations of these systems, the super-diffusion phenomenon arises, in which the diffusion is faster in the multiplex network…
To unveil the logic of cell from a level of chemical reaction dynamics, we need to clarify how ensemble of chemicals can autonomously produce the set of chemical, without assuming a specific external control echanism. A cell consists of a…
A general methodology is proposed to engineer a system of interacting components (particles) which is able to self-regulate their concentrations in order to produce any prescribed output in response to a particular input. The methodology is…
We develop a model-independent reduction method of chemical reaction systems based on the stoichiometry, which determines their network topology. A subnetwork can be eliminated systematically to give a reduced system with fewer degrees of…
Qualitative attributes of the region between order and disorder are examined to explore models of genetic and protein networks. Results show how the connectivity of vertices and the strength of their connections are related and how their…
The reaction-diffusion models have been extensively applied to explain the mechanism of pattern formations in early embryogenesis based on geometrically confined microtissues consisting of human pluripotent stem cells. Recently, mechanical…
Biomolecular processes are typically modeled using chemical reaction networks coupled to infinitely large chemical reservoirs. A difference in chemical potential between these reservoirs can drive the system into a non-equilibrium steady…
Which reaction networks, when taken with mass-action kinetics, have the capacity for multiple steady states? There is no complete answer to this question, but over the last 40 years various criteria have been developed that can answer this…
Recurrent networks are a special class of artificial neural systems that use their internal states to perform computing tasks for machine learning. One of its state-of-the-art developments, i.e. reservoir computing (RC), uses the internal…
Diffusion involving atom transport from one location to another governs many important processes and behaviors such as precipitation and phase nucleation. Local chemical complexity in compositionally complex alloys poses challenges for…
We report the first study of a network of connected enzyme-catalyzed reactions, with added chemical and enzymatic processes that incorporate the recently developed biochemical filtering steps into the functioning of this biocatalytic…
We develop a general classification of the nature of the instabilities yielding spatial organization in open nonideal reaction-diffusion systems, based on linear stability analysis. This encompasses dynamics where chemical species diffuse,…
Many important phenomena in biochemistry and biology exploit dynamical features such as multi-stability, oscillations, and chaos. Construction of novel chemical systems with such rich dynamics is a challenging problem central to the fields…
This paper proposes the Ricci-flow equation from Riemannian geometry as a general geometric framework for various nonlinear reaction-diffusion systems (and related dissipative solitons) in mathematical biology. More precisely, we propose a…
New checkable criteria for persistence of chemical reaction networks are proposed, which extend and complement those obtained by the authors in previous work. The new results allow the consideration of reaction rates which are time-varying,…
Reaction networks are widely used models to describe biochemical processes. Stochastic fluctuations in the counts of biological macromolecules have amplified consequences due to their small population sizes. This makes it necessary to favor…
General conditions are established under which reaction-cross-diffusion systems can undergo spatiotemporal pattern-forming instabilities. Recent work has focused on designing systems theoretically and experimentally to exhibit patterns with…