arXiv subjects

Eduardo R. Mendoza

Publications and source records attributed to Eduardo R. Mendoza.

29 records · Page 2Linked to original sources

arXiv2020

A computational approach to concentration robustness in power law kinetic systems of Shinar-Feinberg type

There have been recent theoretic results that provide sufficient conditions for the existence of a species displaying absolute concentration robustness (ACR) in a power law kinetic (PLK) system. One such result involves the detection of ACR among networks of high deficiency by considering a lower deficiency subnetwork with ACR as a local property. In turn, this "smaller" subnetwork serves as a "building block" for the larger ACR-possessing network. Here, with this theorem as foundation, we construct an algorithm that systematically checks ACR in a PLK system. By slightly modifying the algorithm, we also provide a procedure that identifies balanced concentration robustness (BCR), a weaker form of concentration robustness than ACR, in a PLK system.

physics.chem-ph↗

arXiv2020

Positive Equilibria of Hill-Type Kinetic Systems

This work introduces a novel approach to study properties of positive equilibria of a chemical reaction network $\mathscr{N}$ endowed with Hill-type kinetics $K$, called a Hill-type kinetic (HTK) system $\left(\mathscr{N},K\right)$, including their multiplicity and concentration robustness in a species. We associate a unique positive linear combination of power-law kinetic systems called poly-PL kinetic (PYK) system $\left( {\mathscr{N},{K_\text{PY}}} \right)$ to the given HTK system. The associated system has the key property that its equilibria sets coincide with those of the Hill-type system, i.e., ${E_ + }\left( {\mathscr{N},K} \right) = {E_ + }\left( {\mathscr{N},{K_\text{PY}}} \right)$ and ${Z_ + }\left( {\mathscr{N},K} \right) = {Z_ + }\left( {\mathscr{N},{K_\text{PY}}} \right)$. This allows us to identify two novel subsets of the Hill-type kinetics, called PL-equilibrated and PL-complex balanced kinetics, to which recent results on absolute concentration robustness (ACR) of species and complex balancing at positive equilibria of power-law (PL) kinetic systems can be applied. Our main results also include the Shinar-Feinberg ACR Theorem for PL-equilibrated HT-RDK systems (i.e., subset of complex factorizable HTK systems), which establishes a foundation for the analysis of ACR in HTK systems, and the extension of the results of Müller and Regensburger on generalized mass action systems to PL-complex balanced HT-RDK systems. In addition, we derive the theory of balanced concentration robustness (BCR) in an analogous manner to ACR for PL-equilibrated systems. Finally, we provide further extensions of our results to a more general class of kinetics, which includes quotients of poly-PL functions.

math.DS↗

arXiv2020

A Computational Approach to Multistationarity in Poly-PL Kinetic Systems

One important question that interests those who work in chemical reaction network theory (CRNT) is this: Does the system obtained from a reaction network admit a positive equilibrium and if it does, can there be more than one within a stoichiometric class? The higher deficiency algorithm (HDA) of Ji and Feinberg provided a method of determining the multistationarity capacity of a CRN with mass action kinetics (MAK). An extension of this, called Multistationarity Algorithm (MSA), recently came into the scene tackling CRNs with power law kinetics (PLK), a kinetic system which is more general (having MAK systems as a special case). For this paper, we provide a computational approach to study the multistationarity feature of reaction networks endowed with kinetics which are non-negative linear combinations of power law functions called poly-PL kinetics (PYK). The idea is to use MSA and combine it with a transformation called STAR-MSC (i.e., $S$-invariant Termwise Addition of Reactions via Maximal Stoichiometric Coefficients) producing PLKs that are dynamically equivalent to PYKs. This leads us to being able to determinine the multistationarity capacity of a much larger class of kinetic systems. We show that if the transformed dynamically equivalent PLK system is multistationary for a stoichiometric class for a set of particular rate constants, then so is its original corresponding PYK system. Moreover, the monostationarity property of the transformed PLK system also implies the monostationarity property of the original PYK system.

math.DS↗

arXiv2020

Robustness in power law kinetic systems with reactant-determined interactions

Robustness against the presence of environmental disruptions can be observed in many systems of chemical reaction network. However, identifying the underlying components of a system that give rise to robustness is often elusive. The influential work of Shinar and Feinberg established simple yet subtle network-based conditions for absolute concentration robustness (ACR), a phenomena in which a species in a mass-action system has the same concentration for any steady state the network may admit. In this contribution, we extend this result to embrace kinetic systems more general than mass-action systems, namely, power-law kinetic systems with reactant-determined interactions (denoted by "PL-RDK"). In PL-RDK, the kinetic order vectors (which we call "interactions") of reactions with the same reactant complex are identical. As illustration, we considered a scenario in the pre-industrial state of global carbon cycle. A power-law approximation of the dynamical system of this scenario is found to be dynamically equivalent to an ACR-possessing PL-RDK system.

math.DS↗

arXiv2020

Absolute concentration robustness in power law kinetic systems

Absolute concentration robustness (ACR) is a condition wherein a species in a chemical kinetic system possesses the same value for any positive steady state the network may admit regardless of initial conditions. Thus far, results on ACR center on chemical kinetic systems with deficiency one. In this contribution, we use the idea of dynamic equivalence of chemical reaction networks to derive novel results that guarantee ACR for some classes of power law kinetic systems with deficiency zero. Furthermore, using network decomposition, we identify ACR in higher deficiency networks (i.e. deficiency $\geq$ 2) by considering the presence of a low deficiency subnetwork with ACR. Network decomposition also enabled us to recognize and define a weaker form of concentration robustness than ACR, which we named as `balanced concentration robustness'. Finally, we also discuss and emphasize our view of ACR as a primarily kinetic character rather than a condition that arises from structural sources.

math.DS↗

arXiv2020

Chemical reaction network decompositions and realizations of S-systems

This paper presents novel decomposition classes of chemical reaction networks (CRNs) derived from S-system kinetics. Based on the network decomposition theory initiated by Feinberg in 1987, we introduce the concept of incidence independent decompositions and develop the theory of $\mathscr{C}$- and $\mathscr{C}^*$- decompositions which partition the set of complexes and the set of nonzero complexes respectively, including their structure theorems in terms of linkage classes. Analogous to Feinberg's independent decomposition, we demonstrate the important relationship between sets of complex balance equilibria for an incidence independent decomposition of weakly reversible subnetworks for any kinetics. We show that the $\mathscr{C}^*$-decompositions are also incidence independent. We also introduce in this paper a new realization for an S-system that is analyzed using a newly defined class of species coverable CRNs. This led to the extension of the deficiency formula and characterization of fundamental decompositions of species decomposable reaction networks.

math.DS↗

arXiv2020

Fundamental Decompositions and Multistationarity of Power-Law Kinetic Systems

The fundamental decomposition of a chemical reaction network (also called its "$\mathscr{F}$-decomposition") is the set of subnetworks generated by the partition of its set of reactions into the "fundamental classes" introduced by Ji and Feinberg in 2011 as the basis of their "higher deficiency algorithm" for mass action systems. The first part of this paper studies the properties of the $\mathscr{F}$-decomposition, in particular, its independence (i.e., the network's stoichiometric subspace is the direct sum of the subnetworks' stoichiometric subspaces) and its incidence-independence (i.e., the image of the network's incidence map is the direct sum of the incidence maps' images of the subnetworks). We derive necessary and sufficient conditions for these properties and identify network classes where the $\mathscr{F}$-decomposition coincides with other known decompositions. The second part of the paper applies the above-mentioned results to improve the Multistationarity Algorithm for power-law kinetic systems (MSA), a general computational approach that we introduced in previous work. We show that for systems with non-reactant determined interactions but with an independent $\mathscr{F}$-decomposition, the transformation to a dynamically equivalent system with reactant-determined interactions -- required in the original MSA -- is not necessary. We illustrate this improvement with the subnetwork of Schmitz's carbon cycle model recently analyzed by Fortun et al.

math.DS↗

arXiv2020

A Computational Approach to Multistationarity of Power-Law Kinetic Systems

This paper presents a computational solution to determine if a chemical reaction network endowed with power-law kinetics (PLK system) has the capacity for multistationarity, i.e., whether there exist positive rate constants such that the corresponding differential equations admit multiple positive steady states within a stoichiometric class. The approach, which is called the "Multistationarity Algorithm for PLK systems" (MSA), combines (i) the extension of the "higher deficiency algorithm" of Ji and Feinberg for mass action to PLK systems with reactant-determined interactions, and (ii) a method that transforms any PLK system to a dynamically equivalent one with reactant-determined interactions. Using this algorithm, we obtain two new results: the monostationarity of a popular model of anaerobic yeast fermentation pathway, and the multistationarity of a global carbon cycle model with climate engineering, both in the generalized mass action format of biochemical systems theory. We also provide examples of the broader scope of our approach for deficiency one PLK systems in comparison to the extension of Feinberg's "deficiency one algorithm" to such systems.

math.DS↗

arXiv2020

Structural Properties of an S-system Model of Mycobacterium Tuberculosis Gene Regulation

Magombedze and Mulder in 2013 studied the gene regulatory system of Mycobacterium Tuberculosis (Mtb) by partitioning this into three subsystems based on putative gene function and role in dormancy/latency development. Each subsystem, in the form of S-system, is represented by an embedded chemical reaction network (CRN), defined by a species subset and a reaction subset induced by the set of digraph vertices of the subsystem. For the embedded networks of S-system, we showed interesting structural properties and proved that all S-system CRNs (with at least two species) are discordant. Analyzing the subsystems as subnetworks, where arcs between vertices belonging to different subsystems are retained, we formed a digraph homomorphism from the corresponding subnetworks to the embedded networks. Lastly, we explored the modularity concept of CRN in the context of digraph.

q-bio.MN↗

arXiv2019

Species subsets and embedded networks of S-systems

Magombedze and Mulder (2013) studied the gene regulatory system of \textit{Mycobacterium Tuberculosis} (\textit{Mtb}) by partitioning this into three subsystems based on putative gene function and role in dormancy/latency development. Each subsystem, in the form of $S$-system, is represented by an embedded chemical reaction network (CRN), defined by a species subset and a reaction subset induced by the set of digraph vertices of the subsystem. Based on the network decomposition theory initiated by Feinberg in 1987, we have introduced the concept of incidence-independent and developed the theory of $\mathscr{C}$- and $\mathscr{C}^*$-decompositions including their structure theorems in terms of linkage classes. With the $S$-system CRN $\mathscr{N}$ of Magombedze and Mulder's \textit{Mtb} model, its reaction set partition induced decomposition of subnetworks that are not CRNs of $S$-system but constitute independent decomposition of $\mathscr{N}$. We have also constructed a new $S$-system CRN $\mathscr{N}^*$ for which the embedded networks are $\mathscr{C}^*$-decomposition. We have shown that subnetworks of $\mathscr{N}$ and the embedded networks (subnetworks of $\mathscr{N}^*$) are digraph homomorphisms. Lastly, we attempted to explore modularity in the context of CRN.

q-bio.MN↗

arXiv2019

Linear conjugacy of chemical kinetic systems

Two networks are said to be linearly conjugate if the solution of their dynamic equations can be transformed into each other by a positive linear transformation. The study on dynamical equivalence in chemical kinetic systems was initiated by Craciun and Pantea in 2008 and eventually led to the Johnston-Siegel Criterion for linear conjugacy (JSC). Several studies have applied Mixed Integer Linear Programming (MILP) approach to generate linear conjugates of MAK (mass action kinetic) systems, Bio-CRNs (which is a subset of hill-type kinetic systems when the network is restricted to digraphs), and PL-RDK (complex factorizable power law kinetic) systems. In this study, we present a general computational solution to construct linear conjugates of any "rate constant-interaction function decomposable" (RID) chemical kinetic systems, wherein each of its rate function is the product of a rate constant and an interaction function. We generate an extension of the JSC to the complex factorizable (CF) subset of RID kinetic systems and show that any non-complex factorizable (NF) RID kinetic system can be dynamically equivalent to a CF system via transformation. We show that linear conjugacy can be generated for any RID kinetic systems by applying the JSC to any NF kinetic system that are transformed to CF kinetic system.

math.AG↗