Related papers: Computing Biomolecular System Steady-states
Molecular motors are essential components for the biophysical functions of the cell. Our current quantitative understanding of how multiple motors move along a single track is not complete; even though models and theories for single motor…
In this paper we propose an existence and uniqueness theory for the solutions of a system of non-linear hyperbolic conservation laws, structured in age and maturity variables, representing a tissue environment. In particular we are…
Understanding how biochemical systems settle into stable states, such as how protein concentrations reach equilibrium, is central to explaining cellular behavior and designing synthetic biological circuits. However, existing analytical…
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…
Although coarse-grained models have been widely used to explain exotic phenomena in complex fluids, such as droplet formation in living cells, these conventional approaches often fail to capture the intricate microscopic degrees of freedom…
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…
Biological systems fundamentally exist out of equilibrium in order to preserve organized structures and processes. Many changing cellular conditions can be represented as transitions between nonequilibrium steady states, and organisms have…
Applications of stochastic models often involve the evaluation of steady-state performance, which requires solving a set of balance equations. In most cases of interest, the number of equations is infinite or even uncountable. As a result,…
A simple and efficient approximation scheme to study electronic transport characteristics of strongly correlated nano devices, molecular junctions or heterostructures out of equilibrium is provided by steady-state cluster perturbation…
In order to define the process of restrosynthesis of a new organic molecule, it is often necessary to be able to draw inspiration from that of a molecule similar to the target one of which we know such a process. To compute such a…
We show how graph theory can be combined with quantum theory to calculate the electronic structure of large complex systems. The graph formalism is general and applicable to a broad range of electronic structure methods and materials,…
This paper explores the connection between dynamical system properties and statistical physics of ensembles of such systems. Simple models are used to give novel phase transitions; particularly for finite N particle systems with many…
Motivation: Many biochemical pathways are known, but the numerous parameters required to correctly explore the dynamics of the pathways are not known. For this reason, algorithms that can make inferences by looking at the topology of a…
We consider the dynamics of a smart grid system characterized by widespread distributed generation and storage devices. We assume that agents are free to trade electric energy over the network and we focus on the emerging market dynamics.…
To develop and investigate detailed mathematical models of cellular metabolic processes is one of the primary challenges in systems biology. However, despite considerable advance in the topological analysis of metabolic networks, explicit…
In many complex systems, states and interaction structure coevolve towards a dynamic equilibrium. For the adaptive contact process, we obtain approximate expressions for the degree distributions that characterize the interaction network in…
A thermodynamically consistent particle-based model for fluid dynamics with continuous velocities and a non-ideal equation of state is presented. Excluded volume interactions are modeled by means of biased stochastic multiparticle…
Modern energy systems in vehicles and built infrastructure are governed by high-dimensional dynamics spanning multiple physical domains (e.g., electrical, thermal, mechanical) and timescales. This tutorial paper presents a graph-based…
The regulation of the cell state is a complex process involving several components. These complex dynamics can be modeled using Boolean networks, allowing us to explain the existence of different cell states and the transition between them.…
A continuum electromechanical model is proposed to describe the membrane curvature induced by electrostatic interactions in a solvated protein-membrane system. The model couples the macroscopic strain energy of membrane and the…