相关论文: Multistationarity in semi-open Phosphorylation-Dep…
Post-transductional modifications tune the functions of proteins and regulate the collective dynamics of biochemical networks that determine how cells respond to environmental signals. For example, protein phosphorylation and nitrosylation…
The utilization of multiple phosphorylation sites in regulating a biological response is ubiquitous in cell signaling. If each site contributes an additional, equivalent binding site, then one consequence of an increase in the number of…
A one dimensional stochastic exclusion process with two species of particles, $+$ and $-$, is studied where density of each species can fluctuate but the total particle density is conserved. From the exact stationary state weights we show…
Recent studies on epistatic networks of model organisms have unveiled a certain type of modular property called monochromaticity in which the networks are clusterable into functional modules that interact with each other through the same…
In this paper, we investigate the open tight-binding model with $N$ sites coupled to two reservoirs on its edges with the nonequilibrium Green function method to understand effects of open boundaries. As a result, we obtain an analytical…
In this work we identify and investigate a novel bifurcation in conserved systems. This secondary bifurcation stops active phase separation in its nonlinear regime. It is then either replaced by an extended, system-filling, spatially…
Chemical reaction systems are dynamical systems that arise in chemical engineering and systems biology. In this work, we consider the question of whether the minimal (in a precise sense) multistationary chemical reaction networks, which we…
Simple nonlinear dynamical systems with multiple stable stationary states are often taken as models for switchlike biological systems. This paper considers the interaction of multiple such simple multistable systems when they are embedded…
This work investigates the emergence of oscillations in one of the simplest cellular signaling networks exhibiting oscillations, namely, the dual-site phosphorylation and dephosphorylation network (futile cycle), in which the mechanism for…
Phosphorene and its components are highly reactive to oxygen when exposed to ambient conditions due to the presence of lone pairs of electrons on phosphorus atoms. Functionalization serves as a solution to prevent the chemical degradation…
Living cells exhibit a complex organization comprising numerous compartments, among which are RNA- and protein-rich membraneless, liquid-like organelles known as biomolecular condensates. Energy-consuming processes regulate their formation…
Mitochondrial networks exhibit a variety of complex behaviors, including coordinated cell-wide oscillations of energy states as well as a phase transition (depolarization) in response to oxidative stress. Since functional and structural…
The MAP kinase cascade is a network of enzymatic reactions arranged in layers. In each layer occurs a multiple futile cycle of phosphorylations. The fully phosphorylated substrate then serves as an enzyme for the layer below. This papers…
We investigate six operations on chemical reaction networks, all of which have been proven to preserve important dynamical properties, namely, the capacity for nondegenerate multistationarity (multiple steady states) and periodic orbits.…
This paper studies nonstationary open dynamical systems from the statistical viewpoint. By open, we mean that trajectories may escape through holes in the phase space. By nonstationary, we mean that the dynamical model itself (as well as…
Several statistical mechanical theories predict that colloidal suspensions of highly charged macroions and monovalent microions can exhibit unusual thermodynamic phase behavior when strongly deionized. Density-functional, extended…
A series of molybdenum disulfide intercalation compounds was prepared to study the effect of varying loadings of the samples with intercalated molecules. The molecules, (5,7,7,12,14,14-hexamethyl-1,4,8,11- tetraazacyclotetradeca-4,11-diene)…
This paper develops a quasispecies model where cells can adopt a two-cell survival strategy. Within this strategy, pairs of cells join together, at which point one of the cells sacrifices its own replicative ability for the sake of the…
Intercellular exchange networks are essential for the adaptive capabilities of populations of cells. While diffusional exchanges have traditionally been difficult to map, recent advances in nanotechnology enable precise probing of exchange…
We study the stirring process with $N-1$ species on a generic graph $G=(V,\mathcal{E})$ with reservoirs. The multispecies stirring process generalizes the symmetric exclusion process, which is recovered in the case $N=2$. We prove the…