相关论文: The structure of MESSI biological systems

Signatures of glassy dynamics have been identified experimentally for a rich variety of materials in which molecular networks provide rigidity. Here we present a theoretical framework to study the glassy behavior of both passive and active…

Multistationarity, underlies biochemical switching and cellular decision-making. We study how multistationarity in the sequential n-site phosphorylation-dephosphorylation cycle is affected when only some species are open, meaning allowed to…

Under the assumption of mass-action kinetics, a dynamical system may be induced by several different reaction networks and/or parameters. It is therefore possible for a mass-action system to exhibit complex-balancing dynamics without being…

Many biochemical and industrial applications involve complicated networks of simultaneously occurring chemical reactions. Under the assumption of mass action kinetics, the dynamics of these chemical reaction networks are governed by systems…

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…

Multisite protein phosphorylation plays a prominent role in intracellular processes like signal transduction, cell-cycle control and nuclear signal integration. Many proteins are phosphorylated in a sequential and distributive way at more…

We study diffusion-driven pattern-formation in networks of networks, a class of multilayer systems, where different layers have the same topology, but different internal dynamics. Agents are assumed to disperse within a layer by undergoing…

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…

The formation and regulation of macromolecular complexes provides the backbone of most cellular processes, including gene regulation and signal transduction. The inherent complexity of assembling macromolecular structures makes current…

This work concerns the question of how two important dynamical properties, oscillations and bistability, emerge in an important biological signaling network. Specifically, we consider a model for dual-site phosphorylation and…

One of the aims of systems biology is to build multiple layered and multiple scale models of living systems which can efficiently describe phenomena occurring at various level of resolution. Such models should consist of layers of various…

We propose and analyze a nonlinear age-structured multi-species model that serves as a unifying framework for ecological and biotechnological systems in complex environments (microbial communities, bioreactors, and others). The formulation…

Coexistence of different dynamical phases is a hallmark of glassy dynamics. This is well-studied in classical systems where the underlying theoretical framework is that of large deviation theory. The presence of a similar phase coexistence…

Gene regulatory networks with dynamics characterized by multiple stable states underlie cell fate-decisions. Quantitative models that can link molecular-level knowledge of gene regulation to a global understanding of network dynamics have…

Mathematical approaches from dynamical systems theory are used in a range of fields. This includes biology where they are used to describe processes such as protein-protein interaction and gene regulatory networks. As such networks increase…

Multistationarity in molecular systems underlies switch-like responses in cellular decision making. Determining whether and when a system displays multistationarity is in general a difficult problem. In this work we completely determine the…

Many recent generative models make use of neural networks to transform the probability distribution of a simple low-dimensional noise process into the complex distribution of the data. This raises the question of whether biological networks…

We study families of chemical reaction networks whose positive steady states are toric, and therefore can be parameterized by monomials. Families are constructed algorithmically from a core network; we show that if a family member is…

In this paper we present a network model to study the impact of spatial distribution of constituents, coupling between them and diffusive processes in the context of biological situations. The model is in terms of network of mobile elements…

Tensor network methods have proved to be highly effective in addressing a wide variety of physical scenarios, including those lacking an intrinsic one-dimensional geometry. In such contexts, it is possible for the problem to exhibit a weak…