Related papers: The Stability of Boolean Networks with Generalized…
We investigate how classifiers for Boolean networks (BNs) can be constructed and modified under constraints. A typical constraint is to observe only states in attractors or even more specifically steady states of BNs. Steady states of BNs…
Inferring dynamic biochemical networks is one of the main challenges in systems biology. Given experimental data, the objective is to identify the rules of interaction among the different entities of the network. However, the number of…
We describe systems using Kauffman and similar networks. They are directed funct ioning networks consisting of finite number of nodes with finite number of discr ete states evaluated in synchronous mode of discrete time. In this paper we…
Robustness to mutations and noise has been shown to evolve through stabilizing selection for optimal phenotypes in model gene regulatory networks. The ability to evolve robust mutants is known to depend on the network architecture. How do…
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…
Many natural and man-made network systems need to maintain certain patterns, such as working at equilibria or limit cycles, to function properly. Thus, the ability to stabilize such patterns is crucial. Most of the existing studies on…
The controllability of networked sampled-data systems with zero-order holders on the control and transmission channels is explored, where single- and multi-rate sampling patterns are considered, respectively. The effects of sampling on the…
Biological processes, including cell differentiation, organism development, and disease progression, can be interpreted as attractors (fixed points or limit cycles) of an underlying networked dynamical system. In this paper, we study the…
A Boolean network (BN) is called observable if any initial state can be uniquely determined from the output sequence. In the existing literature on observability of BNs, there is almost no research on the relationship between the number of…
Progress in cell type reprogramming has revived the interest in Waddington's concept of the epigenetic landscape. Recently researchers developed the quasi-potential theory to represent the Waddington's landscape. The Quasi-potential U(x),…
In this report, we present a formal approach that addresses the problem of emergence of phase transitions in stochastic and attractive nonlinear threshold Boolean automata networks. Nonlinear networks considered are informally defined on…
Boolean Networks and their dynamics are of great interest as abstract modeling schemes in various disciplines, ranging from biology to computer science. Whereas parallel update schemes have been studied extensively in past years, the level…
Based on a non-equilibrium mechanism for spatial pattern formation we study how position information can be controlled by locally coupled discrete dynamical networks, similar to gene regulation networks of cells in a developing…
A dynamical system, called a binary closed chain of contours, is studied. The dynamica system belongs to the class of Buslaev networks. The system contains $N$ {\it contours.} There two cells and a particle in each contour. There two…
An abelian network is a collection of communicating automata whose state transitions and message passing each satisfy a local commutativity condition. This paper is a continuation of the abelian networks series of Bond and Levine (2016),…
In this paper, a necessary and sufficient condition for the controllability of networked systems with heterogeneous dynamics is established where the nodes are higher dimensional linear time invariant systems and the network topology is…
In this paper, we focus on the study of quotients of Boolean control networks (BCNs) with the motivation that they might serve as smaller models that still carry enough information about the original network. Given a BCN and an equivalence…
We observe deterministic chaos in a simple network of electronic logic gates that are not regulated by a clocking signal. The resulting power spectrum is ultra-wide-band, extending from dc to beyond 2 GHz. The observed behavior is…
We introduce a numerical method to study random Boolean networks with asynchronous stochas- tic update. Each node in the network of states starts with equal occupation probability and this probability distribution then evolves to a steady…
Interactions between genes and gene products give rise to complex circuits that enable cells to process information and respond to external signals. Theoretical studies often describe these interactions using continuous, stochastic, or…