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Despite major environmental and genetic differences, microbial metabolic networks are known to generate consistent physiological outcomes across vastly different organisms. This remarkable robustness suggests that, at least in bacteria,…
Biological systems, unlike physical or chemical systems, are characterized by the very inhomogeneous distribution of their components. The immune system, in particular, is notable for self-organizing its structure. Classically, the dynamics…
Thermodynamic constraints on reactions directions are inherent in the structure of a given biochemical network. However, concrete procedures for determining feasible reaction directions for large-scale metabolic networks are not well…
Cellular ingredient concentrations can be stabilized by adjusting generation and consumption rates through multiple pathways. To explore the portion of cellular metabolism equipped with multiple pathways, we categorize individual metabolic…
From the perfect radial symmetries of radiolarian mineral skeletons to the broken symmetry of homochirality, the logic of Nature's regularities has fascinated scientists for centuries. Some of Nature's symmetries are clearly visible in…
Environmental science almost invariably proposes problems of extreme complexity, typically characterized by strongly nonlinear evolution dynamics. The systems under investigation have many degrees of freedom - which makes them complicated -…
We propose a whole-body model of the metabolism in man as well as a generalized approach for modeling metabolic networks. Using this approach, we are able to write a large metabolic network in a systematic and compact way. We demonstrate…
Cellular metabolic networks exhibit scale-free topologies with power-law degree distributions across diverse organisms. Although such topologies are often linked to mutational robustness and evolutionary advantage, their role in metabolic…
Biological and social systems are structured at multiple scales, and the incentives of individuals who interact in a group may diverge from the collective incentive of the group as a whole. Mechanisms to resolve this tension are responsible…
Studying systems where many individual bodies in motion interact with one another is a complex and interesting area. Simple mechanisms that may be determined for biological, chemical, or physical reasons can lead to astonishingly complex…
Complex systems' modeling and simulation are powerful ways to investigate a multitude of natural phenomena providing extended knowledge on their structure and behavior. However, enhanced modeling and simulation require integration of…
Due to recent advances in synthetic biology and artificial life, the origin of life is currently a hot topic of research. We review the literature and argue that the two traditionally competing "replicator-first" and "metabolism-first"…
The networks of predator-prey interactions in ecological systems are remarkably complex, but nevertheless surprisingly stable in terms of long term persistence of the system as a whole. In order to understand the mechanism driving the…
Biological systems exhibit two structural features on many levels of organization: sparseness, in which only a small fraction of possible interactions between components actually occur; and modularity - the near decomposability of the…
Molecular recognition, which is essential in processing information in biological systems, takes place in a crowded noisy biochemical environment and requires the recognition of a specific target within a background of various similar…
Understanding and modelling the complexity of the immune system is a challenge that is shared by the ImmunoComplexiT$^1$ thematic network from the RNSC. The immune system is a complex biological, adaptive, highly diversified, self-organized…
Many living and non-living complex systems can be modeled and understood as collective systems made of heterogeneous components that self-organize and generate nontrivial morphological structures and behaviors. This chapter presents a brief…
In prokaryotic genomes the number of transcriptional regulators is known to quadratically scale with the total number of protein-coding genes. Toolbox model was recently proposed to explain this scaling for metabolic enzymes and their…
Metabolic networks, formed by a series of metabolic pathways, are made of intracellular and extracellular reactions that determine the biochemical properties of a cell, and by a set of interactions that guide and regulate the activity of…
Building on the phenomenological and microscopic models reviewed in Part I, this second part focuses on network-level mechanisms that generate emergent temperature response curves. We review deterministic models in which temperature…