Related papers: Signal duration and the time scale dependence of s…
We study delay-induced transitions in consensus dynamics on signed networks with a ring topology. The proposed model is formulated as a system of delay differential equations incorporating both cooperative and antagonistic interactions, as…
Signaling pathways are responsible for the regulation of cell processes, such as monitoring the external environment, transmitting information across membranes, and making cell fate decisions. Given the increasing amount of biological data…
Information processing in the brain requires integration of information over time. Such an integration can be achieved if signals are maintained in the network activity for the required period, as quantified by the intrinsic timescale.…
Essential life processes take place across multiple space and time scales in living organisms but understanding their mechanistic interactions remains an ongoing challenge. Advanced multiscale modeling techniques are providing new…
This work mainly investigates the mean-square stability and stabilizability for a single-input single-output networked linear feedback system. The control signal in the networked system is transmitted over an unreliable channel. In this…
Delays and stochasticity have both served as crucially valuable ingredients in mathematical descriptions of control, physical, and biological systems. In this work, we investigate how explicitly dynamical stochasticity in delays modulates…
Signaling networks are designed to sense an environmental stimulus and adapt to it. We propose and study a minimal model of signaling network that can sense and respond to external stimuli of varying strength in an adaptive manner. The…
The growing adoption of inverter-based resources (IBRs) has introduced unprecedented dynamics in power systems, resulting in oscillations across a broad spectrum of frequencies. Communication delay between the plant-level control and the…
Gene duplication is a fundamental evolutionary mechanism that contributes to biological complexity and diversity (Fortna et al., 2004). Traditionally, research has focused on the duplication of gene sequences (Zhang, 1914). However,…
Cell growth and gene expression, essential elements of all living systems, have long been the focus of biophysical interrogation. Advances in single-cell methods have invigorated theoretical studies into these processes. However, until…
Complex systems often have features that can be modeled by advanced mathematical tools [1]. Of special interests are the features of complex systems that have a network structure as such systems are important for modeling technological and…
Current molecular dynamic simulations of biomolecules using multiple time steps to update the slowingly changing force are hampered by an instability occuring at time step equal to half the period of the fastest vibrating mode. This has…
Oscillations lie at the core of many biological processes, from the cell cycle, to circadian oscillations and developmental processes. Time-keeping mechanisms are essential to enable organisms to adapt to varying conditions in environmental…
Information exchange is a critical process in all communication systems, including biological ones. The concept of retroactivity represents the loads that downstream modules apply to their upstream systems in biological circuits. This paper…
In a molecular communication network, transmitters and receivers communicate by using signalling molecules. At the receivers, the signalling molecules react, via a chain of chemical reactions, to produce output molecules. The counts of…
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…
A novel theory for cell differentiation is proposed, based on simulations with interacting artificial cells which have metabolic networks within, and divide into two when the final product is accumulated. Results of simulations with coupled…
The knowledge of cell molecular mechanisms implicated in human diseases is expanding and should be converted into guidelines for deciphering pathological cell signaling and suggesting appropriate treatment. The basic assumption is that…
Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as…
Post-translational modification (PTM) of proteins plays a key role in signal transduction, and hence significant effort has gone toward understanding how PTM networks process information. This involves, on the theory side, analyzing the…