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The coupled quantum dynamics of electrons and protons is ubiquitous in many dynamical processes involving light-matter interaction, such as solar energy conversion in chemical systems and photosynthesis. A first-principles description of…
Biological systems and processes are networks of complex nonlinear regulatory interactions between nucleic acids, proteins, and metabolites. A natural way in which to represent these interaction networks is through the use of a graph. In…
In this paper, we propose a novel approach that employs kinetic equations to describe the collective dynamics emerging from graph-mediated pairwise interactions in multi-agent systems. We formally show that for large graphs and specific…
This paper applies the multibond graph approach for rigid multibody systems to model the dynamics of general spatial mechanisms. The commonly used quick return mechanism which comprises of revolute as well as prismatic joints has been…
In this paper, we present a survey of the use of graph theoretical techniques in Biology. In particular, we discuss recent work on identifying and modelling the structure of bio-molecular networks, as well as the application of centrality…
Network systems consist of subsystems and their interconnections, and provide a powerful framework for analysis, modeling and control of complex systems. However, subsystems may have high-dimensional dynamics, and the amount and nature of…
In systems characterized by a rough potential energy landscape, local energetic minima and saddles define a network of metastable states whose topology strongly influences the dynamics. Changes in temperature, causing the merging and…
From multicellular tissues to bacterial colonies, three dimensional cellular structures arise through the interaction of cellular activities and mechanical forces. Simple bacterial communities provide model systems for analyzing such…
We derive the nonequilibrium conductance matrix for open stationary Chemical Reaction Networks (CRNs) described by a deterministic mass action kinetic equation. As an illustration, we determine the nonequilibrium conductance matrix of a CRN…
Dynamical reaction-diffusion processes and meta-population models are standard modeling approaches for a wide variety of phenomena in which local quantities - such as density, potential and particles - diffuse and interact according to the…
Theoretical physics is used for a toy model of molecular biology to assess conditions that lead to the edge of chaos (EOC) in a network of biomolecules. Results can enhance our ability to understand complex diseases and their treatment or…
Adaptive networks model social, physical, technical, or biological systems as attributed graphs evolving at the level of both their topology and data. They are naturally described by graph transformation, but the majority of authors take an…
In the 20th century, individual technology products like the generator, telephone, and automobile were connected to form many of the large-scale, complex, infrastructure networks we know today: the power grid, the communication…
The physiology of voltage gated ion channels is complex and insights into their gating mechanism is incomplete. Their function is best represented by Markov models with relatively large number of distinct states that are connected by…
Biological networks are one of the most studied object in computational biology. Several methods have been developed for studying qualitative properties of biological networks. Last decade had seen the improvement of molecular techniques…
In this review, we give an introduction to the structural and functional properties of the biological networks. We focus on three major themes: topology of complex biological networks like the metabolic and protein-protein interaction…
Years ago Edwards proposed a thermodynamic description of dense granular matter, in which the grains (the `atoms' of the system) interact with inelastic forces. The approach is intriguing but is not justified from first principles, and…
The discerning behavior of living systems relies on accurate interactions selected from the lot of molecular collisions occurring in the cell. To ensure the reliability of interactions, binding partners are classically envisioned as finely…
Different approaches have been used in the development of system models. In addition, modeling and simulation approaches are essential for design, analysis, control, and diagnosis of complex systems. This work presents a Simulink model for…
Advances in bioengineering and biomedicine demand a deep understanding of the dynamic behavior of biological systems, ranging from protein pathways to complex cellular processes. Biological networks like gene regulatory networks and protein…