Related papers: Global Sensitivity Analysis of Biochemical Reactio…
Inferring parameters of models of biochemical kinetics from single-cell data remains challenging because of the uncertainty arising from the intractability of the likelihood function of stochastic reaction networks. Such uncertainty falls…
Partial measurements of biochemical reaction networks are ubiquitous and limit our ability to reconstruct the topology of the reaction network and the strength of the interactions amongst both the observed and the unobserved molecular…
In this paper we introduce a new representation for the multistationarity region of a reaction network, using polynomial superlevel sets. The advantages of using this polynomial superlevel set representation over the already existing…
Recent work of M.D. Johnston et al. has produced sufficient conditions on the structure of a chemical reaction network which guarantee that the corresponding discrete state space system exhibits an extinction event. The conditions consist…
We study biochemical reaction networks capable of product discrimination inspired by biological proofreading mechanisms. At equilibrium, product discrimination, the selective formation of a "correct" product with respect to an "incorrect…
We present a novel method for identifying a biochemical reaction network based on multiple sets of estimated reaction rates in the corresponding reaction rate equations arriving from various (possibly different) experiments. The current…
A common method for analyzing the effects of molecular noise in chemical reaction networks is to approximate the underlying chemical master equation by a Fokker-Planck equation, and to study the statistics of the associated chemical…
In the scope of discrete finite-state models of interacting components, we present a novel algorithm for identifying sets of local states of components whose activity is necessary for the reachability of a given local state. If all the…
A large variety of dynamical systems, such as chemical and biomolecular systems, can be seen as networks of nonlinear entities. Prediction, control, and identification of such nonlinear networks require knowledge of the state of the system.…
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…
Chemical reaction networks (CRN) comprise an important class of models to understand biological functions such as cellular information processing, the robustness and control of metabolic pathways, circadian rhythms, and many more. However,…
Computing pseudospectra of non-normal matrices is essential for understanding the stability and transient behavior of dynamical systems. Such analysis is critical in applications including fluid dynamics, control systems, and differential…
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…
Biochemical models that exhibit bistability are of interest to biologists and mathematicians alike. Chemical reaction network theory can provide sufficient conditions for the existence of bistability, and on the other hand can rule out the…
Simulation of biomolecular networks is now indispensable for studying biological systems, from small reaction networks to large ensembles of cells. Here we present a novel approach for stochastic simulation of networks embedded in the…
We consider the problem of learning data-driven replicas for stiff systems of ordinary differential equations arising in chemical kinetics that can be evaluated with high computational efficiency. We first focus on training emulators for…
Parametrized polynomial ordinary differential equation systems are broadly used for modeling, specially in the study of biochemical reaction networks under the assumption of mass-action kinetics. Understanding the qualitative behavior of…
Many biochemical and industrial applications involve complicated networks of simultaneously occurring chemical reactions. Under the assumption of mass action kinetics, the dynamics of these chemical reaction networks are governed by systems…
We consider a three-node half-duplex Gaussian relay network where two nodes (say $a$, $b$) want to communicate with each other and the third node acts as a relay for this twoway communication. Outer bounds and achievable rate regions for…
Retrosynthesis is one of the fundamental problems in organic chemistry. The task is to identify reactants that can be used to synthesize a specified product molecule. Recently, computer-aided retrosynthesis is finding renewed interest from…