Related papers: Flow rate of transport network controls uniform me…
Flux of rigid or soft particles (such as drops, vesicles, red blood cells, etc.) in a channel is a complex function of particle concentration, which depends on the details of induced dissipation and suspension structure due to hydrodynamic…
Numerous networks, such as transportation, distribution and delivery networks optimize their designs in order to increase efficiency and lower costs, improving the stability of its intended functions, etc. Networks that distribute goods,…
Accurately determining and classifying the structure of complex networks is the focus of much current research. One class of network of particular interest are metabolic pathways, which have previously been studied from a graph theoretical…
Metabolism plays a central role in cell physiology because it provides the molecular machinery for growth. At the genome-scale, metabolism is made up of thousands of reactions interacting with one another. Untangling this complexity is key…
Transport networks are crucial to the functioning of natural and technological systems. Nature features transport networks that are adaptive over a vast range of parameters, thus providing an impressive level of robustness in supply.…
We consider a basic model of a dynamical distribution network, modeled as a directed graph with storage variables corresponding to every vertex and flow inputs corresponding to every edge, subject to unknown but constant inflows and…
Flux analysis is a class of constraint-based approaches to the study of biochemical reaction networks: they are based on determining the reaction flux configurations compatible with given stoichiometric and thermodynamic constraints. One of…
Living organisms produce metabolites of many types via their metabolisms. Especially, flavonoids, a kind of secondary metabolites, of plant species are interesting examples. Since plant species are believed to have specific flavonoids with…
Modeling traffic distribution and extracting optimal flows in multilayer networks is of utmost importance to design efficient multi-modal network infrastructures. Recent results based on optimal transport theory provide powerful and…
Many situations in physics, biology, and engineering consist of the transport of some physical quantity through a network of narrow channels. The ability of a network to transport such a quantity in every direction can be described by the…
Network flow is a powerful mathematical framework to systematically explore the relationship between structure and function in biological, social, and technological networks. We introduce a new pipelining model of flow through networks…
The ribosome flow model with input and output (RFMIO) is a deterministic dynamical system that has been used to study the flow of ribosomes during mRNA translation. The RFMIO and its variants encapsulate important properties that are…
Transport is an important function in many network systems and understanding its behavior on biological, social, and technological networks is crucial for a wide range of applications. However, it is a property that is not well-understood…
Understanding design principles of complex cellular organization is one of the major challenges in biology. Recent analysis of the large-scale cellular organization has revealed the scale-free nature and robustness of metabolic and protein…
The survival and proliferation of cells and organisms require a highly coordinated allocation of cellular resources to ensure the efficient synthesis of cellular components. In particular, the total enzymatic capacity for cellular…
The regulation of metabolic activity by tuning enzyme expression levels is crucial to sustain cellular growth in changing environments. Metabolic networks are often studied at steady state using constraint-based models and optimization…
We present a model for continuous cell culture coupling intra-cellular metabolism to extracellular variables describing the state of the bioreactor, taking into account the growth capacity of the cell and the impact of toxic byproduct…
We derive a monotonicity property for general, transient flows of a commodity transferred throughout a network, where the flow is characterized by density and mass flux dynamics on the edges with density continuity and mass balance…
Despite their topological complexity almost all functional properties of metabolic networks can be derived from steady-state dynamics. Indeed, many theoretical investigations (like flux-balance analysis) rely on extracting function from…
The ubiquity of modules in biological networks may result from an evolutionary benefit of a modular organization. For instance, modularity may increase the rate of adaptive evolution, because modules can be easily combined into new…