Related papers: On Natural Genetic Engineering: Structural Dynamis…
We consider evolution of a large population, where fitness of each organism is defined by many phenotypical traits. These traits result from expression of many genes. We propose a new model of gene regulation, where gene expression is…
The dynamics of gene regulatory networks is governed by the interaction between deterministic biochemical reactions and molecular noise. To understand how gene regulatory networks process information during cell state transitions, we study…
Gene regulatory network (GRN) modeling is a well-established theoretical framework for the study of cell-fate specification during developmental processes. Recently, dynamical models of GRNs have been taken as a basis for formalizing the…
The NK model has been used widely to explore aspects of natural evolution and complex systems. This paper introduces a modified form of the NK model for exploring distributed control in complex systems such as organisations, social…
Effective control of biological systems can often be achieved through the control of a surprisingly small number of distinct variables. We bring clarity to such results using the formalism of Boolean dynamical networks, analyzing the…
Based on a recently proposed non-equilibrium mechanism for spatial pattern formation [cond-mat/0312366] we study how morphogenesis can be controlled by locally coupled discrete dynamical networks, similar to gene regulation networks of…
Biological systems operate under persistent noise, which can alter system states and induce transitions between attractors. Here, we study the attractor dynamics of Boolean networks focusing on the transitions between attractors induced by…
Boolean networks (BNs) are widely used to model the qualitative dynamics of biological systems. Besides the logical rules determining the evolution of each component with respect to the state of its regulators, the scheduling of component…
We provide a rigorous solution to the problem of constructing a structural evolution for a network of coupled identical dynamical units that switches between specified topologies without constraints on their structure. The evolution of the…
Characterization of the differences between biological and random networks can reveal the design principles that enable the robust realization of crucial biological functions including the establishment of different cell types. Previous…
Metabolic networks consist of linked functional components, or modules. The mechanism underlying metabolic network modularity is of great interest not only to researchers of basic science but also to those in fields of engineering. Previous…
The dynamical organization in the presence of noise of a Boolean neural network with random connections is analyzed. For low levels of noise, the system reaches a stationary state in which the majority of its elements acquire the same…
The study of the interplay between the structure and dynamics of complex multilevel systems is a pressing challenge nowadays. In this paper, we use a semi-annealed approximation to study the stability properties of Random Boolean Networks…
Modelling genetic phenomena affecting biological traits is important for the development of agriculture as it allows breeders to predict the potential of breeding for certain traits. One such phenomenon is heterosis or hybrid vigor:…
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…
Discrete dynamical models underpin systems biology, but we still lack substrate-agnostic diagnostics for identifying finite-horizon dynamical signatures that may be relevant to open-ended evolution (OEE), such as the recurrent production of…
We present a rigorous mathematical framework for analyzing dynamics of a broad class of Boolean network models. We use this framework to provide the first formal proof of many of the standard critical transition results in Boolean network…
The relationship between the properties of a dynamical system and the structure of its defining equations has long been studied in many contexts. Here we study this problem for the class of conjunctive (resp. disjunctive) Boolean networks,…
Understanding design principles of molecular interaction networks is an important goal of molecular systems biology. Some insights have been gained into features of their network topology through the discovery of graph theoretic patterns…
While modern deep networks have demonstrated remarkable versatility, their training dynamics remain poorly understood--often driven more by empirical tweaks than architectural insight. This paper investigates how internal structural choices…