相关论文: Controlling the occurrence sequence of reaction mo…

Polynomial dynamical systems (DSs) can model a wide range of physical processes. A special subset of these DSs that can model chemical reactions under mass-action kinetics is called chemical dynamical systems (CDSs). A fundamental problem,…

Chemical modelling serves two purposes in dynamical models: accounting for the effect of microphysics on the dynamics and providing observable signatures. Ideally, the former must be done as part of the hydrodynamic simulation but this…

We have developed an algorithm coupling mesoscopic simulations on different levels in a hierarchy of Cartesian meshes. Based on the multiscale nature of the chemical reactions, some molecules in the system will live on a fine-grained mesh,…

This paper is centered on using chemical reaction as a computational metaphor for simultaneously solving problems. An artificial chemical reactor that can simultaneously solve instances of three unrelated problems was created. The reactor…

Molecular interactions are wired in a fascinating way resulting in complex behavior of biological systems. Theoretical modeling provides a useful framework for understanding the dynamics and the function of such networks. The complexity of…

We discuss a method of approximate model reduction for networks of biochemical reactions. This method can be applied to networks with polynomial or rational reaction rates and whose parameters are given by their orders of magnitude. In…

Digital circuits based on residue number systems have been considered to produce a pseudo-random behavior. The present work is an initial step towards the complete implementation of those systems for similar applications using quantum…

Presented with sensory challenges, living cells employ extensive noisy, fluctuating signalling and communication among themselves to compute a physiologically proper response which often results in symmetry breaking. We propose, based on…

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…

Chemical reactions are the fundamental building blocks of drug design and organic chemistry research. In recent years, there has been a growing need for a large-scale deep-learning framework that can efficiently capture the basic rules of…

Stochastic chemical systems with diffusion are modeled with a reaction-diffusion master equation. On a macroscopic level, the governing equation is a reaction-diffusion equation for the averages of the chemical species. On a mesoscopic…

Reaction-diffusion systems offer a powerful framework for understanding self-organized patterns in biological systems, yet controlling these patterns remains a significant challenge. As a consequence, we present a rigorous framework of…

The paper proposes a modular-based approach to constraint handling in process optimization and control. This is partly motivated by the recent interest in learning-based methods, e.g., within bioproduction, for which constraint handling…

A number of biological rhythms originate from networks comprised of multiple cellular oscillators. But analytical results are still lacking on the collective oscillation period of inter-coupled gene regulatory oscillators, which, as has…

Reaction systems are a computational model inspired by the bio-chemical reactions that happen inside biological cells. They have been and currently are studied for their many nice theoretical properties. They are also a useful modeling tool…

As biochemical systems may frequently suffer from limited energy resources so that internal molecular fluctuation has to be utilized to induce random rhythm, it is still a great theoretical challenge to understand the elementary principles…

Models invoking the chemical master equation are used in many areas of science, and, hence, their simulation is of interest to many researchers. The complexity of the problems at hand often requires considerable computational power, so a…

Many important applications in biochemistry, materials science, and catalysis sit squarely at the interface between quantum and statistical mechanics: coherent evolution is interrupted by discrete events, such as binding of a substrate or…

The hematopoietic system has a highly regulated and complex structure in which cells are organized to successfully create and maintain new blood cells. Feedback regulation is crucial to tightly control this system, but the specific…

We present a practical method to obtain bounds for the oscillation minima and maxima of large classes of biochemical oscillator models that generate oscillations through a negative feedback. These bounds depend on the feedback nonlinearity…