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We investigate the stability properties of two different classes of metabolic cycles using a combination of analytical and computational methods. Using principles from structural kinetic modeling (SKM), we show that the stability of…
The emergence of life from inanimate matter presents a thermodynamic challenge: the Second Law of Thermodynamics dictates a global trend towards disorder, yet life constitutes localized pockets of profound organization. This paper presents…
In complex systems, the interplay between nonlinear and stochastic dynamics, e.g., J. Monod's necessity and chance, gives rise to an evolutionary process in Darwinian sense, in terms of discrete jumps among attractors, with punctuated…
The dynamical behavior of two types of non-equilibrium systems is discussed: $(a)$ two-dimensional cellular structures, and $(b)$ living polymers. Simple models governing their evolution are introduced and steady state distributions (cell…
Natural systems are inextricably affected by noise. Within recent decades, the manner in which noise affects the collective behavior of self-organized systems, specifically, has garnered considerable interest from researchers and developers…
Control schemes for dynamical systems typically involve stabilizing unstable periodic orbits. In this paper we introduce a new paradigm of control that involves `trapping' the dynamics arbitrarily close to any desired trajectory. This is…
The possibility that evolutionary forces -- together with a few fundamental factors such as thermodynamic constraints, specific computational features enabling information processing, and ecological processes -- might constrain the logic of…
Biological and advanced cyberphysical control systems often have limited, sparse, uncertain, and distributed communication and computing in addition to sensing and actuation. Fortunately, the corresponding plants and performance…
The population dynamics and stability of ecosystems of interacting species is studied from the perspective of non-equilibrium thermodynamics by assuming that species, through their biotic and abiotic interactions, are units of entropy…
Life is commonly described as a self-organized, far-from-equilibrium process that maintains internal order by consuming free energy and exporting entropy. This thermodynamic view underlies diverse theoretical frameworks -- from autopoiesis…
Run-and-tumble particles constitute one of the simplest models of self-propelled active matter, and provide an ideal playground to the understanding of out-of-equilibrium systems. We consider an idealized setup where one such particle is…
Order can spontaneously emerge from seemingly noisy interactions between biological agents, like a flock of birds changing their direction of flight in unison, without a leader or an external cue. We are interested in the generic conditions…
My goal is to study the dynamics of the Universe from a relational perspective based on the happening of events in temporal relation to each other and their respective points of reference. Accordingly, the flow of time was modeled as the…
Networks of limit cycle oscillators can show intricate patterns of synchronization such as splay states and cluster synchronization. Here we analyze dynamical states that display a continuum of seemingly independent splay clusters. Each…
The complexity of many biological, social and technological systems stems from the richness of the interactions among their units. Over the past decades, a great variety of complex systems has been successfully described as networks whose…
The Turing patterning mechanism is believed to underly the formation of repetitive structures in development, such as zebrafish stripes and mammalian digits, but it has proved difficult to isolate the specific biochemical species…
Many natural and engineered dynamical systems, including all living objects, exhibit signatures of what can be called spontaneous dynamical long-range order (DLRO). This order's omnipresence has long been recognized by the scientific…
Biological systems exhibit large-scale self-organized dynamics and structures which enable organisms to perform the functions of life. The field of active matter strives to develop and understand microscopically-driven nonequilibrium…
Modeling dynamical systems and unraveling their underlying causal relationships is central to many domains in the natural sciences. Various physical systems, such as those arising in cell biology, are inherently high-dimensional and…
Species or population that proliferate faster than others become dominant in numbers. Catalysis allows catalytic sets within a molecular reaction network to dominate the non catalytic parts of the network by processing most of the available…