Related papers: Global Sensitivity Analysis of Biochemical Reactio…
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…
We define and study a class of (random) Boolean constraint satisfaction problems representing minimal feasibility constraints for networks of chemical reactions. The constraints we consider encode, respectively, for hard mass-balance…
In the presence of multiscale dynamics in a reaction network, direct simulation methods become inefficient as they can only advance the system on the smallest scale. This work presents stochastic averaging techniques to accelerate…
The recent advancements in mathematical modeling of biochemical systems have generated increased interest in sensitivity analysis methodologies. There are two primary approaches for analyzing these mathematical models: the stochastic…
The steady-state degree of a chemical reaction network is the number of complex steady-states for generic rate constants and initial conditions. One way to bound the steady-state degree is through the mixed volume of the steady-state system…
We consider the task of deciding whether an unknown qubit state falls in a prescribed neighborhood of a reference state. We assume that several copies of the unknown state are given and apply a unitary operation pairwise on them combined…
Quantum fidelity estimation is essential for benchmarking quantum states and processes on noisy quantum devices. While stabilizer operations form the foundation of fault-tolerant quantum computing, non-stabilizer resources further enable…
In chemical reaction network theory, ordinary differential equations are used to model the temporal change of chemical species concentration. As the functional form of these ordinary differential equations systems is derived from an…
Utilizing quantum computer to investigate quantum chemistry is an important research field nowadays. In addition to the ground-state problems that have been widely studied, the determination of excited-states plays a crucial role in the…
The distributive sequential n-site phosphorylation/dephosphorylation system is an important building block in networks of chemical reactions arising in molecular biology, which has been intensively studied. In the nice paper of Wang and…
Stochastic reaction networks is a powerful class of models for the representation a wide variety of population models including biochemistry. The control of such networks has been recently considered due to their important implications for…
A stochastic model for a chemical reaction network is embedded in a one-parameter family of models with species numbers and rate constants scaled by powers of the parameter. A systematic approach is developed for determining appropriate…
We study the statistical properties of the stationary firing-rate states of a neural network model with quenched disorder. The model has arbitrary size, discrete-time evolution equations and binary firing rates, while the topology and the…
The prediction of organic reaction outcomes is a fundamental problem in computational chemistry. Since a reaction may involve hundreds of atoms, fully exploring the space of possible transformations is intractable. The current solution…
Surfaces serve as highly efficient catalysts for a vast variety of chemical reactions. Typically, such surface reactions involve billions of molecules which diffuse and react over macroscopic areas. Therefore, stochastic fluctuations are…
In particle-based stochastic reaction-diffusion models, reaction rate and placement kernels are used to decide the probability per time a reaction can occur between reactant particles, and to decide where product particles should be placed.…
This paper is concerned with the global existence and stability of solution to the quasi linear hyperbolic-parabolic chemotaxis system on the half-line,which was proposed in[1] to primarily describe the formation of coherent vascular…
We develop a thermodynamic framework for closed and open chemical networks applicable to non-elementary reactions that do not need to obey mass action kinetics. It only requires the knowledge of the kinetics and of the standard chemical…
We present herein an extension of an algebraic statistical method for inferring biochemical reaction networks from experimental data, proposed recently in [3]. This extension allows us to analyze reaction networks that are not necessarily…
We present a computational method for performing structural translation, which has been studied recently in the context of analyzing the steady states and dynamical behavior of mass-action systems derived from biochemical reaction networks.…