相关论文: A Linear Reciprocal Relationship Between Robustnes…

The ambitious and ultimate research purpose in Systems Biology is the understanding and modelling of the cell's system. Although a vast number of models have been developed in order to extract biological knowledge from complex systems…

The goal of this paper is to outline a scenario of emerging stochasticity in high-dimensional highly nonlinear systems, such as genetic regulatory networks (GRN). We focus attention on the fact that in such systems confluence of all the…

Inside individual cells, expression of genes is stochastic across organisms ranging from bacterial to human cells. A ubiquitous feature of stochastic expression is burst-like synthesis of gene products, which drives considerable…

Rigidity is an emergent property of materials - it is not a feature of individual components that comprise the structure, but instead arises from interactions between many constituent parts. Recently, it has been recognized that…

Granular packings under constant shear stress display below the Coulomb limit, a logarithmic creep dynamics. However the addition of small stress modulations induces a linear creep regime characterized by an effective viscous response.…

We study the evolutionary robustness of strategies in infinitely repeated prisoners' dilemma games in which players make mistakes with a small probability and are patient. The evolutionary process we consider is given by the replicator…

We present a model of the evolution of control systems in a genome under environmental constraints. The model conceptually follows the Jacob and Monod model of gene control. Genes contain control elements which respond to the internal state…

Rheological responses are the most relevant features to describe soft matter. So far, such constitutive relations are still not well understood in terms of small scale properties, although this knowledge would help the design of synthetic…

The functioning of a living cell is largely determined by the structure of its regulatory network, comprising non-linear interactions between regulatory genes. An important factor for the stability and evolvability of such regulatory…

Life systems are complex and hierarchical, with diverse components at different scales, yet they sustain themselves, grow, and evolve over time. How can a theory of such complex biological states be developed? Here we note that for a…

In this paper, we use the framework of infinitesimal homeostasis to study general design principles for the occurrence of homeostasis in gene regulatory networks. We assume that the dynamics of the genes explicitly includes both…

We propose a three dimensional mechanical model of embryonic tissue dynamics. Mechanically coupled adherent cells are represented as particles interconnected with elastic beams which can exert non-central forces and torques. Tissue…

The dynamical properties and mechanical functions of amorphous materials are governed by their microscopic structures, particularly the elasticity of the interaction networks, which is generally complicated by structural heterogeneity. This…

The plasticity property of biological neural networks allows them to perform learning and optimize their behavior by changing their configuration. Inspired by biology, plasticity can be modeled in artificial neural networks by using Hebbian…

Biological systems must be robust for stable function against perturbations, but robustness alone is not sufficient. The ability to switch between appropriate states (phenotypes) in response to different conditions is essential for…

We evolve network topology of an asymmetrically connected threshold network by a simple local rewiring rule: quiet nodes grow links, active nodes lose links. This leads to convergence of the average connectivity of the network towards the…

In contrast to the neutral population cycles of the deterministic mean-field Lotka--Volterra rate equations, including spatial structure and stochastic noise in models for predator-prey interactions yields complex spatio-temporal structures…

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…

In natural ecosystems, species can be characterized by the nonlinear density-dependent self-regulation of their growth profile. Species of many taxa show a substantial density-dependent reduction for low population size. Nevertheless, many…

Conformational barcodes tag functional sites of proteins, and are decoded by interacting molecules transmitting the incoming signal. Conformational barcodes are modified by all co-occurring allosteric events induced by post-translational…