Related papers: Computing equilibrium concentrations for large het…
A natural condition on the structure of the underlying chemical reaction network, namely weak reversibility, is shown to guarantee the existence of an equilibrium (steady state) in each positive stoichiometric compatibility class for the…
The detailed balance property is a fundamental property that must be satisfied in all the macroscopic systems with a well defined temperature at each point. On the other hand, many biochemical networks work in non-equilibrium conditions and…
Biological systems are driven by intricate interactions among the complex array of molecules that comprise the cell. Many methods have been developed to reconstruct network models of those interactions. These methods often draw on large…
Motivated by problems from Chemical Reaction Network Theory, we investigate whether steady state ideals of reversible reaction networks are generated by binomials. We take an algebraic approach considering, besides concentrations of…
Motivation: A Chemical Reaction Network (CRN) is a set of chemical reactions, which can be very complex and difficult to analyze. Indeed, dynamical properties of CRNs can be described by a set of non-linear differential equations that…
It has recently been shown that structural conditions on the reaction network, rather than a 'fine-tuning' of system parameters, often suffice to impart 'absolute concentration robustness' on a wide class of biologically relevant,…
The ability to achieve coordinated behavior -- engineered or emergent -- on networked systems has attracted widespread interest over several fields. This interest has led to remarkable advances in developing a theoretical understanding of…
Let $\Omega$ be a nonempty closed and convex subset of a uniformly smooth and uniformly convex real Banach space $\mathcal{X}$ with dual space $\mathcal{X}^*$. This article presents a hybrid algorithm for finding a common element of the set…
The modern thermodynamics of discrete systems is based on graph theory, which provides both algebraic methods to define observables and a geometric intuition of their meaning and role. However, because chemical reactions are usually…
Linear mixed models with large imbalanced crossed random effects structures pose severe computational problems for maximum likelihood estimation and for Bayesian analysis. The costs can grow as fast as $N^{3/2}$ when there are N…
We consider nonlinear reaction systems satisfying mass-action kinetics with slow and fast reactions. It is known that the fast-reaction-rate limit can be described by an ODE with Lagrange multipliers and a set of nonlinear constraints that…
Chemical reactions often proceed through the formation and the consumption of intermediate species. An example is the creation and subsequent degradation of the substrate-enzyme complexes in an enzymatic reaction. In this paper we provide a…
We consider the problem of distributed learning, where a network of agents collectively aim to agree on a hypothesis that best explains a set of distributed observations of conditionally independent random processes. We propose a…
In this paper, it is presented a methodology for implementing arbitrarily constructed time-homogenous Markov chains with biochemical systems. Not only discrete but also continuous-time Markov chains are allowed to be computed. By employing…
The quasi-steady state approximation and time-scale separation are commonly applied methods to simplify models of biochemical reaction networks based on ordinary differential equations (ODEs). The concentrations of the "fast" species are…
The study of Chemical Reaction Networks (CRN's) is a very active field. Earlier well-known results \cite{Feinberg:def_01:87, Anderson:product_dist:10} identify a topological quantity called deficiency, for any CRN, which, when exactly equal…
Dynamical systems arising from chemical reaction networks with mass action kinetics are the subject of chemical reaction network theory (CRNT). In particular, this theory provides statements about uniqueness, existence, and stability of…
This paper addresses the distributed Nash Equilibrium seeking problem for aggregative games, where legitimate players' decisions are affected by potential malicious players. To describe players' behavior, we introduce a novel heterogeneous…
Recently, Ogita and Aishima proposed an efficient eigendecomposition refinement algorithm for the symmetric eigenproblem. Their basic algorithm involves division by the difference of two approximate eigenvalues, and can become unstable when…
For the investigation of chemical reaction networks, the efficient and accurate determination of all relevant intermediates and elementary reactions is mandatory. The complexity of such a network may grow rapidly, in particular if reactive…