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Current questions in ecology revolve around instabilities in the dynamics on spatial networks and particularly the effect of node heterogeneity. We extend the Master Stability Function formalism to inhomogeneous biregular networks having…
Enzymes show two distinct transport behaviors in the presence of their substrates in solution. First, their diffusivity enhances with increasing substrate concentration. In addition, enzymes perform directional motion toward regions with…
The spatial organization of enzymes often plays a crucial role in the functionality and efficiency of enzymatic pathways. To fully understand the design and operation of enzymatic pathways, it is therefore crucial to understand how the…
Understanding and modeling enzyme-substrate interactions is crucial for catalytic mechanism research, enzyme engineering, and metabolic engineering. Although a large number of predictive methods have emerged, they do not incorporate prior…
A biological system achieve homeostasis when there is a regulated quantity that is maintained within a narrow range of values. Here we consider homeostasis as a phenomenon of network dynamics. In this context, we improve a general theory…
The robustness of an ecological network quantifies the resilience of the ecosystem it represents to species loss. It corresponds to the proportion of species that are disconnected from the rest of the network when extinctions occur…
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…
A kinetic system has an absolute concentration robustness (ACR) for a molecular species if its concentration remains the same in every positive steady state of the system. Just recently, a condition that sufficiently guarantees the…
Homeostasis occurs in a biological system when a chosen output variable remains approximately constant despite changes in an input variable. In this work we specifically focus on biological systems which may be represented as chemical…
A reaction system exhibits "absolute concentration robustness" (ACR) in some species if the positive steady-state value of that species does not depend on initial conditions. Mathematically, this means that the positive part of the variety…
The active sites of enzymes consist of residues necessary for catalysis, and structurally important non-catalytic residues that together maintain the architecture and function of the active site. Examples of evolutionary interactions…
The concept of allostery in which macromolecules switch between two different conformations is a central theme in biological processes ranging from gene regulation to cell signaling to enzymology. Allosteric enzymes pervade metabolic…
Complex networks have been shown to be robust against random structural perturbations, but vulnerable against targeted attacks. Robustness analysis usually simulates the removal of individual or sets of nodes, followed by the assessment of…
This paper is Part II of a two-part series devoting to the study of systematic measures in a complex bio-network modeled by a system of ordinary differential equations. In this part, we quantify several systematic measures of a biological…
Recent studies on the evolutionary dynamics of the Prisoner's Dilemma game in scale-free networks have demonstrated that the heterogeneity of the network interconnections enhances the evolutionary success of cooperation. In this paper we…
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,…
We examine the stochastic dynamics of two enzymes that are mechanically coupled to each other, e.g., through an elastic substrate or a fluid medium. The enzymes undergo conformational changes during their catalytic cycle, which itself is…
This paper studies a networked bivirus model, in which two competing viruses spread across a network of interconnected populations; each node represents a population with a large number of individuals. The viruses may spread through…
This work addresses whether a reaction network, taken with mass-action kinetics, is multistationary, that is, admits more than one positive steady state in some stoichiometric compatibility class. We build on previous work on the effect…
Robustness to genetic or environmental disturbances is often considered as a key property of living systems. Yet, in spite of being discussed since the 1950s, how robustness emerges from the complexity of genetic architectures and how it…