Related papers: Computing Biomolecular System Steady-states
This work presents the development, analysis and numerical simulations of a biophysical model for 3D cell deformation and movement, which couples biochemical reactions and biomechanical forces. We propose a mechanobiochemical model which…
During the last decades, significant advances have been made in the area of power system stability and control. Nevertheless, when this analysis is carried out by means of decentralized conditions in a general network, it has been based on…
We propose a general classification of nonequilibrium steady states in terms of their stationary probability distribution and the associated probability currents. The stationary probabilities can be represented graph-theoretically as…
Metabolic flux balance analyses are a standard tool in analysing metabolic reaction rates compatible with measurements, steady-state and the metabolic reaction network stoichiometry. Flux analysis methods commonly place unrealistic…
We introduce a novel frequency-dependent incoherent pump scheme with a square-shaped spectrum as a way to study strongly correlated photons in arrays of coupled nonlinear resonators. This scheme can be implemented via a reservoir of…
Complex network dynamics have been analyzed with models of systems of coupled switches or systems of coupled oscillators. However, many complex systems are composed of components with diverse dynamics whose interactions drive the system's…
Quantitative modeling has become an essential tool in modern biophysics, driven by advances in both experimental techniques and theoretical frameworks. Powerful high-resolution techniques now provide detailed datasets spanning molecular to…
We consider the problem of embedding a dynamic network, to obtain time-evolving vector representations of each node, which can then be used to describe changes in behaviour of individual nodes, communities, or the entire graph. Given this…
The equivalent split-circuit formulation is a novel approach that has recently been applied to a range of power system related problems. As a result, a linear and a nonlinear method for power system state estimation with simultaneous…
We comment on some recent, yet unpublished results concerning instabilities in complex systems and their applications. In particular, we briefly describe main observations during extensive computer simulations of two lattice nonequilibrium…
Reaction diffusion systems with Turing instability and mass conservation are studied. In such systems, abrupt decays of stripes follow quasi-stationary states in sequence. At steady state, the distance between stripes is much longer than…
Tissue homeostasis, the biological process of maintaining a steady state in tissue via control of cell proliferation, death, and metabolic function, is essential for the development, growth, maintenance, and proper function of living…
We consider an aggregation model for two interacting species. The coupling between the species is via their velocities, that incorporate self- and cross-interactions. Our main interest is categorizing the possible steady states of the…
We use molecular dynamics simulations to compute the Lyapunov spectra of many-particle systems resembling simple fluids in thermal equilibrium and in non-equilibrium stationary states. Here we review some of the most interesting results and…
We consider a problem from biological network analysis of determining regions in a parameter space over which there are multiple steady states for positive real values of variables and parameters. We describe multiple approaches to address…
In this paper we analyze a coupled system between a transport equation and an ordinary differential equation with time delay (which is a simplified version of a model for kidney blood flow control). Through a careful spectral analysis we…
An analysis is made of a moving disturbance using a directed cyclic graph. A statistical approach is used to calculate the alternative positions in space and state of the disturbance with a defined observed time. The probability for a…
The mathematical modelling of biological systems has historically followed one of two approaches: comprehensive and minimal. In comprehensive models, the involved biological pathways are modelled independently, then brought together as an…
We have considered the complexity and asymptotic stability in the process of biochemical substance exchange in a coupled ring of cells. We have used coupled maps to model this process. It includes the coupling parameter, cell affinity and…
We propose an electrolyser model for steady-state load flow analysis of multi-carrier energy networks, where the electrolyser is capable of producing hydrogen gas and heat. We show that there are boundary conditions that lead to a…