相关论文: The structure of MESSI biological systems
The vast majority of the literature on learning dynamical systems or stochastic processes from time series has focused on stable or ergodic systems, for both Bayesian and frequentist inference procedures. However, most real-world systems…
Discrete mesoscale network models, in which explicitly modeled polymer chains are replaced by implicit pairwise potentials, are capable of predicting the macroscale mechanical response of polymeric materials such as elastomers and gels,…
Cells can often choose among several stably heritable phenotypes. Examples are the expression of genes in eukaryotic cells where long chromosomal regions can adopt persistent and heritable silenced or active states, that may be associated…
A dynamical system obtains a wide variety of kinetic realizations, which is advantageous for the analysis of biochemical systems. A reaction network, derived from a dynamical system, may or may not possess some properties needed for a…
Microbial ecosystems are remarkably diverse, stable, and often consist of a balanced mixture of core and peripheral species. Here we propose a conceptual model exhibiting all these emergent properties in quantitative agreement with real…
The multisite phosphorylation-dephosphorylation cycle is a motif repeatedly used in cell signaling. This motif itself can generate a variety of dynamic behaviors like bistability and ultrasensitivity without direct positive feedbacks. In…
In this work, we introduce a generalized framework for multiscale state-space modeling that incorporates nested nonlinear dynamics, with a specific focus on Bayesian learning under switching regimes. Our framework captures the complex…
From molecular, cellular, to ecological systems, the modeling of biological processes often stands on the assumption that fast components immediately reach the equilibrium at each moment (quasi-steady state) and only slow components govern…
The recent discovery of universal principles underlying many complex networks occurring across a wide range of length scales in the biological world has spurred physicists in trying to understand such features using techniques from…
We introduce a mesoscopic model for natural network formation processes, acting as a bridge between the discrete and continuous network approach proposed by Hu and Cai. The models are based on a common approach where the dynamics of the…
The global dynamics of gene regulatory networks are known to show robustness to perturbations in the form of intrinsic and extrinsic noise, as well as mutations of individual genes. One molecular mechanism underlying this robustness has…
Mixture transition distribution time series models build high-order dependence through a weighted combination of first-order transition densities for each one of a specified number of lags. We present a framework to construct stationary…
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…
This paper presents an algorithm for approximating certain types of dynamical systems given by a system of ordinary delay differential equations by a Boolean network model. Often Boolean models are much simpler to understand than complex…
We propose a methodology to analyze synchronization in an ensemble of diffusively coupled multistable systems. First, we study how two bidirectionally coupled multistable oscillators synchronize and demonstrate the high complexity of the…
Neither of the two prevalent theories, namely thermodynamic stability and kinetic stability, provides a comprehensive understanding of protein folding. The thermodynamic theory is misleading because it assumes that free energy is the…
We derive a formulation of the First Law of nonequilibrium thermodynamics for biological information-processing systems by partitioning entropy in the Second Law into microscopic and mesoscopic components and by assuming that natural…
It has recently been shown that structural conditions on the reaction network, rather than a 'fine-tuning' of system parameters, often suffice to impart 'absolute concentration robustness' on a wide class of biologically relevant,…
The biological requirements for an ecosystem to develop and maintain species diversity are in general unknown. Here we consider a model ecosystem of sessile and mutually excluding organisms competing for space [Mathiesen et al. Phys. Rev.…
We present a new conjecture about a necessary condition that a (bio)chemical network has to satisfy for it to exhibit multistationarity. According to a Theorem of Feliu and Wiuf [27, 12], the conjecture is known for strictly monotonic…