Related papers: Linear Response Theory of Evolved Metabolic System…
Cellular metabolism, the integrated interconversion of thousands of metabolic substrates through enzyme-catalyzed biochemical reactions, is the most investigated complex intercellular web of molecular interactions. While the topological…
The linear response of a dynamical system refers to changes to properties of the system when small external perturbations are applied. We consider the little-studied question of selecting an optimal perturbation so as to (i) maximise the…
Lately, experimental research on microbial symbioses based on nutrient exchange and interdependence has yielded a number of interesting findings, however an in-depth mathematical description of the exact underlying dynamics of such…
The metabolic network plays a crucial role in regulating bacterial metabolism and growth, but it is subject to inherent molecular stochasticity. Previous studies have utilized flux balance analysis and the maximum entropy method to predict…
Quantitative studies of cell metabolism are often based on large chemical reaction network models. A steady state approach is suited to analyze phenomena on the timescale of cell growth and circumvents the problem of incomplete experimental…
We have developed a coarse-grained formulation for modeling the dynamic behavior of cells quantitatively, based on stochasticity and heterogeneity, rather than on biochemical reactions. We treat each reaction as a continuous-time stochastic…
Perturbations are ubiquitous in metabolism. A central tool to understand and control their influence on metabolic networks is sensitivity analysis, which investigates how the network responds to external perturbations. We follow here a…
One of the major characteristics of living organisms is metabolic rate, which is the amount of energy produced per unit of time. When the mass of organisms increases, the metabolic rate also increases (usually as a power function of mass),…
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…
How biological networks achieve robust control despite relying on imperfect, local information remains an important open question. Here, we identify thermodynamic constraints that can curtail non-equilibrium steady-state responses so…
Understanding how systems respond to external perturbations is fundamental to statistical physics. For systems far from equilibrium, a general framework for response remains elusive. While progress has been made on the linear response of…
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…
Understanding the emergent behavior of chemical reaction networks (CRNs) is a fundamental aspect of biology and its origin from inanimate matter. A closed CRN monotonically tends to thermal equilibrium, but when it is opened to external…
Linear response theory asserts that sufficiently small external biases produce currents proportional to the applied force and forms the theoretical foundation of nonequilibrium transport. Here we demonstrate that linear response can break…
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 investigate the stability properties of two different classes of metabolic cycles using a combination of analytical and computational methods. Using principles from structural kinetic modeling (SKM), we show that the stability of…
We cast the metabolism of interacting cells within a statistical mechanics framework considering both, the actual phenotypic capacities of each cell and its interaction with its neighbors. Reaction fluxes will be the components of…
Simple ideas, endowed from the mathematical theory of control, are used in order to analyze in general grounds the human immune system. The general principles are minimization of the pathogen load and economy of resources. They should…
This paper studies a chemotaxis system where cells move in response to a chemical signal within a confined habitat. The model includes external source terms that combine local and nonlocal growth with dampening effects. The main focus is on…
The origin and shape of metabolic scaling has been controversial since Kleiber found that basal metabolic rate of animals seemed to vary as a power law of their body mass with exponent 3/4, instead of 2/3, as a surface-to-volume argument…