Related papers: Molecular Diversity and Network Complexity in Grow…
There is a widening recognition that cancer cells are products of complex developmental processes. Carcinogenesis and metastasis formation are increasingly described as systems-level, network phenomena. Here we propose that malignant…
Complex networks have recently attracted much interest due to their prevalence in nature and our daily lives [1, 2]. A critical property of a network is its resilience to random breakdown and failure [3-6], typically studied as a…
The path toward the emergence of life in our biosphere involved several key events allowing for the persistence, reproduction and evolution of molecular systems. All these processes took place in a given environmental context and required…
Molecular biology features numerous complexes of proteins that coordinate in an interlocking fashion to fulfill different functions. Adaptive evolution explains some of this complexity, but needn't be the default when neutral explanations…
Explaining the origin of life requires us to explain how self-replication arises. To be specific, how can a self-replicating entity develop spontaneously from a chemical reaction system in which no reaction is self-replicating? Previously…
Investigating the emergence of a particular cell type is a recurring theme in models of growing cellular populations. The evolution of resistance to therapy is a classic example. Common questions are: when does the cell type first occur,…
We investigate the properties of large random conservative chemical reaction networks composed of elementary reactions endowed with either mass-action or saturating kinetics, assigning kinetic parameters in a thermodynamically-consistent…
We present a simple mathematical model that captures the evolutionary capabilities of a prebiotic compartment or protocell. In the model the protocell contains an autocatalytic set whose chemical dynamics is coupled to the growth-division…
Complex networks can be used to represent complex systems which originate in the real world. Here we study a transformation of these complex networks into simplicial complexes, where cliques represent the simplices of the complex. We extend…
This paper presents a real-time simulation involving ''protozoan-like'' cells that evolve by natural selection in a physical 2D ecosystem. Selection pressure is exerted via the requirements to collect mass and energy from the surroundings…
Complex network theory provides a unifying framework for the study of structured dynamic systems. The current literature emphasizes a widely reported phenomenon of intermittent interaction among network vertices. In this paper, we introduce…
Complex systems often have features that can be modeled by advanced mathematical tools [1]. Of special interests are the features of complex systems that have a network structure as such systems are important for modeling technological and…
In a cell or microorganism the processes that generate mass, energy, information transfer, and cell fate specification are seamlessly integrated through a complex network of various cellular constituents and reactions. However, despite the…
Many of the chemical reactions that take place within a living cell are irreversible. Due to evolutionary pressures, the number of allowable reactions within these systems are highly constrained and thus the resulting metabolic networks…
Living organisms must respond to environmental changes. Generally, accurate and rapid responses are provided by simple, unidirectional networks that connect inputs with outputs. Besides accuracy and speed, biological responses should also…
Living organisms rely on molecular networks, such as gene circuits and signaling pathways, for information processing and robust decision-making in crowded, noisy environments. Recent advances show that interacting biomolecules…
Systems of dynamical interactions between competing species can be used to model many complex systems, and can be mathematically described by {\em random} networks. Understanding how patterns of activity arise in such systems is important…
Distinct channels of interaction in a complex networked system define network layers, which co-exist and co-operate for the system's function. Towards realistic modeling and understanding such multiplex systems, we introduce and study a…
A reaction network is a chemical system involving multiple reactions and chemical species. Stochastic models of such networks treat the system as a continuous time Markov chain on the number of molecules of each species with reactions as…
Introduction: While the origin and evolution of proteins remain mysterious, advances in evolutionary genomics and systems biology are facilitating the historical exploration of the structure, function and organization of proteins and…