Related papers: Biochemical network decomposition reveals absolute…
The theory of complex networks and of disordered systems is used to study the stability and dynamical properties of a simple model of material flow networks defined on random graphs. In particular we address instabilities that are…
We present a novel approach to represent ecological systems using reaction networks, and show how a particular framework called Chemical Organization Theory (COT) sheds new light on the longstanding complexity-stability debate. Namely, COT…
As a promising computational paradigm, occurrence of critical states in artificial and biological neural networks has attracted wide-spread attention. An often-made explicit or implicit assumption is that one single critical state is…
Unraveling the structure of complex biological networks and relating it to their functional role is an important task in systems biology. Here we attempt to characterize the functional organization of the large-scale metabolic networks of…
Network science has presented community detection as a valuable tool for revealing functional modules in complex systems rooted in the wiring architectures of complex networks. The varying procedures of community detection can produce,…
Steady state is an essential concept in reaction networks. Its stability reflects fundamental characteristics of several biological phenomena such as cellular signal transduction and gene expression. Because biochemical reactions occur at…
Zero-one biochemical reaction networks are widely recognized for their importance in analyzing signal transduction and cellular decision-making processes. Degenerate networks reveal non-standard behaviors and mark the boundary where…
We extend the traditional framework of steady state energy transduction -- typically characterized by a single input and output -- to multi-resource transduction in open chemical reaction networks (CRNs). Transduction occurs when…
The mechanical behavior of composite materials is significantly influenced by their structure and constituent materials. One emerging class of composite materials is irregular network reinforced composites (NRC's), whose reinforcing phase…
Complex networks have recently attracted much interest due to their prevalence in nature and our daily lives [1, 2]. A critical property of a network is its resilience to random breakdown and failure [3-6], typically studied as a…
Chemical reaction networks (CRNs) provide a convenient language for modelling a broad variety of biological systems. These models are commonly studied with respect to the time series they generate in deterministic or stochastic simulations.…
Understanding the structure and dynamics of biological networks is one of the important challenges in system biology. In addition, increasing amount of experimental data in biological networks necessitate the use of efficient methods to…
Chemical reaction systems are dynamical systems that arise in chemical engineering and systems biology. In this work, we consider the question of whether the minimal (in a precise sense) multistationary chemical reaction networks, which we…
Robustness of ecological flow networks under random failure of arcs is considered with respect to two different functionalities: coherence and circulation. In our previous work, we showed that each functionality is associated with a natural…
Embedding computation in biochemical environments incompatible with traditional electronics is expected to have wide-ranging impact in synthetic biology, medicine, nanofabrication and other fields. Natural biochemical systems are typically…
Motivated by recent progress on the interplay between graph theory, dynamics, and systems theory, we revisit the analysis of chemical reaction networks described by mass action kinetics. For reaction networks possessing a thermodynamic…
Backpropagation-optimized artificial neural networks, while precise, lack robustness, leading to unforeseen behaviors that affect their safety. Biological neural systems do solve some of these issues already. Unlike artificial models,…
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…
Organisms often use cyclic changes in the concentrations of chemicals species to precisely time biological functions. Underlying these biochemical clocks are chemical reactions and transport processes, which are inherently stochastic.…
We introduce a unifying and generalizing framework for complex and detailed balanced steady states in chemical reaction network theory. To this end, we generalize the graph commonly used to represent a reaction network. Specifically, we…