Related papers: Computing Biomolecular System Steady-states
Many natural and man-made network systems need to maintain certain patterns, such as working at equilibria or limit cycles, to function properly. Thus, the ability to stabilize such patterns is crucial. Most of the existing studies on…
Binding and unbinding of ligands to specific sites of a macromolecule are one of the most elementary molecular interactions inside the cell that embody the computational processes of biological regulations. The interaction between…
Modeling dynamical biological systems is key for understanding, predicting, and controlling complex biological behaviors. Traditional methods for identifying governing equations, such as ordinary differential equations (ODEs), typically…
In a recent experiment [Vochezer {\it et al.,} Phys. Rev. Lett. \textbf{120}, 073602 (2018)], a novel kind of hybrid atom-opto-mechanical system has been realized by coupling atoms in a lattice to a membrane. While such system promises a…
The modelling and analysis of biological systems has deep roots in Mathematics, specifically in the field of ordinary differential equations (ODEs). Alternative approaches based on formal calculi, often derived from process algebras or term…
A model of multicellular systems with several types of cells is developed from the phase field model. The model is presented as a set of partial differential equations of the field variables, each of which expresses the shape of one cell.…
Cell-fate transition can be modeled by ordinary differential equations (ODEs) which describe the behavior of several molecules in interaction, and for which each stable equilibrium corresponds to a possible phenotype (or 'biological…
We present a modelling framework for the dynamics of cells structured by the concentration of a micromolecule they contain. We derive general equations for the evolution of the cell population and of the extra-cellular concentration of the…
An iterative approach is introduced, which allows the efficient solution of the hierarchical equations of motion (HEOM) for the steady state of open quantum systems. The approach combines the method of matrix equations with an efficient…
Direct simulation of biomolecular dynamics in thermal equilibrium is challenging due to the metastable nature of conformation dynamics and the computational cost of molecular dynamics. Biased or enhanced sampling methods may improve the…
We introduce a unifying and generalizing framework for complex and detailed balanced steady states in chemical reaction network theory. To this end, we generalize the graph commonly used to represent a reaction network. Specifically, we…
As the quantification of metabolism, nonequilibrium steady states play a central role in living matter, but are beyond the purview of equilibrium statistical mechanics. Here we develop a fermionic theory of nonequilibrium steady states in…
Modeling of biomolecular systems plays an essential role in understanding biological processes, such as ionic flow across channels, protein modification or interaction, and cell signaling. The continuum model described by the…
Cellular bioelectricity describes the biological phenomenon in which cells in living tissue generate and maintain patterns of voltage gradients induced by differing concentrations of charged ions. A growing body of research suggests that…
Communication between cells is realized by exchange of biochemical substances. Due to internal organization of living systems and variability of external parameters, the exchange is heavily influenced by perturbations of various parameters…
A biological regulatory network can be modeled as a discrete function that contains all available information on network component interactions. From this function we can derive a graph representation of the network structure as well as of…
We derive and simulate a mathematical model for mechanotransduction related to the Rho GTPase signalling pathway. The model addresses the bidirectional coupling between signalling processes and cell mechanics. A numerical method based on…
The primary objective of this paper is to highlight the need for and benefits of studying the steady state and dynamic response of power systems using three phase integrated transmission and distribution (T&D) system models (hereafter…
It is shown that the equilibrium Generalized Mean Spherical Model of fluid structure may be extended to nonequilibrium states with equation of state information used in equilibrium replaced by an exact condition on the two-body distribution…
Dynamical systems describe the changes in processes that arise naturally from their underlying physical principles, such as the laws of motion or the conservation of mass, energy or momentum. These models facilitate a causal explanation for…