相关论文: The Number of Multistate Nested Canalyzing Functio…
Boolean threshold networks have recently been proposed as useful tools to model the dynamics of genetic regulatory networks, and have been successfully applied to describe the cell cycles of \textit{S. cerevisiae} and \textit{S. pombe}.…
A recent article by Weidner et al. [2021] presents a method to extract graph properties that are predictive of the dynamical behavior of multivariate, discrete models of biochemical regulation. In other words, a method that uses only…
We study critical random Boolean networks with two inputs per node that contain only canalyzing functions. We present a phenomenological theory that explains how a frozen core of nodes that are frozen on all attractors arises. This theory…
Understanding conformational change is crucial for programming and controlling the function of many mechanical systems such as allosteric enzymes and tunable metamaterials. Of particular interest is the relationship between the network…
Cell polarization is a critical process that separates molecular species into two distinct regions in prokaryotic and eukaryotic cells, guiding biological processes such as cell division and cell differentiation. Although several underlying…
The concept of limiting step gives the limit simplification: the whole network behaves as a single step. However, in its simplest form this idea is applicable only to the simplest linear cycles in steady states. For such the simplest cycles…
Developing and maintaining life requires a lot of computation. This is done by gene regulatory networks. But we have little understanding of how this computation is organized. I show that there is a direct correspondence between the…
The cell cycle is a tightly controlled process, yet its underlying genetic network shows marked differences across species. Which of the associated structural features follow solely from the ability to impose the appropriate gene expression…
The behavior of active matter under confinement poses significant challenges due to the intricate coupling between dynamics near boundaries and those in the bulk. A defining feature of active matter systems is that a substantial portion of…
Many foraging microorganisms rely upon cellular transport networks to deliver nutrients, fluid and organelles between different parts of the organism. Networked organisms ranging from filamentous fungi to slime molds demonstrate a…
Distributed function computation is the problem, for a networked system of $n$ autonomous agents, to collectively compute the value $f(v_1, \ldots, v_n)$ of some input values, each initially private to one agent in the network. Here, we…
Effective therapy of complex diseases requires control of highly non-linear complex networks that remain incompletely characterized. In particular, drug intervention can be seen as control of signaling in cellular networks. Identification…
Interactions between units in phyical, biological, technological, and social systems usually give rise to intrincate networks with non-trivial structure, which critically affects the dynamics and properties of the system. The focus of most…
Structural changes in a network representation of a system (e.g.,different experimental conditions, time evolution), can provide insight on its organization, function and on how it responds to external perturbations. The deeper…
A wide range of applications require or can benefit from collaborative behavior of a group of agents. The technical challenge addressed in this chapter is the development of a decentralized control strategy that enables each agent to…
The subject of this paper is the evolution of the concept of information processing in regular structures based on multi-level processing in nested cellular automata. The essence of the proposed model is a discrete space-time containing…
The interaction of distinct units in physical, social, biological and technological systems naturally gives rise to complex network structures. Networks have constantly been in the focus of research for the last decade, with considerable…
Boolean networks are special types of finite state time-discrete dynamical systems. A Boolean network can be described by a function from an n-dimensional vector space over the field of two elements to itself. A fundamental problem in…
The biomolecular networks underpinning cell function exhibit canalization, or the buffering of fluctuations required to function in a noisy environment. One understudied putative mechanism for canalization is the functional equivalence of a…
Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus…