Related papers: Control principles of metabolic networks
Mathematical and computational models can assist in gaining an understanding of cell behavior at many levels of organization. Here, we review models in the literature that focus on eukaryotic cell motility at 3 size scales: intracellular…
Living systems are capable of locomotion, reconfiguration, and replication. To perform these tasks, cells spatiotemporally coordinate the interactions of force-generating, "active" molecules that create and manipulate non-equilibrium…
Given the large size and complexity of most biochemical regulation and signaling networks, there is a non-trivial relationship between the micro-level logic of component interactions and the observed macro-dynamics. Here we address this…
We consider the problem of inferring the probability distribution of flux configurations in metabolic network models from empirical flux data. For the simple case in which experimental averages are to be retrieved, data are described by a…
The genetic regulatory network (GRN) plays a key role in controlling the response of the cell to changes in the environment. Although the structure of GRNs has been the subject of many studies, their large scale structure in the light of…
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…
Identity, response to external stimuli, and spatial architecture of a living system are central topics of molecular biology. Presently, they are largely seen as a result of the interplay between a gene repertoire and the regulatory…
Biological systems perform an astonishing array of dynamical processes -- including development and repair, regulation, behavior and motor control, sensing and signaling, and adaptation, among others. Powered by the transduction of stored…
This paper serves as a framework for designing advanced models for drug action on metabolism. Drug treatment may affect metabolism by either enhancing or inhibiting metabolic reactions comprising a metabolic network. We introduce the…
Many cellular processes involve information processing and decision making. We can probe these processes at increasing molecular detail. The analysis of heterogeneous data remains a challenge that requires new ways of thinking about cells…
Metabolic networks have two properties that are generally regarded as unrelated: One, they have metabolic reactions whose single knockout is lethal for the organism, and two, they have correlated sets of reactions forming functional…
Macromolecules occupy between 34 and 44% of the cell cytoplasm, about half the maximum pack- ing density of spheres in three dimension. Yet, there is no clear understanding of what is special about this value. To address this fundamental…
Understanding deaths and life-death boundaries of cells is a fundamental challenge in biological sciences. In this study, we present a theoretical framework for investigating cell death. We conceptualize cell death as a controllability…
Self-regulation of living tissue as an example of self-organization phenomena in active fractal systems of biological, ecological, and social nature is under consideration. The characteristic feature of these systems is the absence of any…
The emerging field at the intersection of quantitative biology, network modeling, and control theory has enjoyed significant progress in recent years. This Special Issue brings together a selection of papers on complementary approaches to…
Networks of biochemical reactions, like cellular metabolic networks, are kept in non-equilibrium steady states by the exchange fluxes connecting them to the environment. In most cases, feasible flux configurations can be derived from…
Metabolic heterogeneity is widely recognised as the next challenge in our understanding of non-genetic variation. A growing body of evidence suggests that metabolic heterogeneity may result from the inherent stochasticity of intracellular…
A blood cell lineage consists of several consecutive developmental stages from the pluripotent or multipotent stem cell to a particular stage of terminally differentiated cells. There is considerable interest in identifying the key…
In living cells, biochemical reactions are catalyzed by specific enzymes and connect to one another by sharing substrates and products, forming complex networks. In our previous studies, we established a framework determining the responses…
Energy-based modelling brings engineering insight to the understanding of biomolecular systems. It is shown how well-established control engineering concepts, such as loop-gain, arise from energy feedback loops and are therefore amenable to…