Related papers: Linear Response Theory of Evolved Metabolic System…
We study the qualitative behavior of a model to represent local regulation in a metabolic network. The model is based on the end-product control structure introduced in [A. Goelzer, F. Bekkal Brikci, I. Martin-Verstraete et al., BMC Syst…
Dynamical systems are often subject to forcing or changes in their governing parameters and it is of interest to study how this affects their statistical properties. A prominent real-life example of this class of problems is the…
Finite-time coherent sets represent minimally mixing objects in general nonlinear dynamics, and are spatially mobile features that are the most predictable in the medium term. When the dynamical system is subjected to small parameter…
Adaptive control in biological systems, such as intestinal immunity, remains poorly understood despite detailed knowledge of underlying regulatory networks. We propose an alternative framework based on stochastic martingale turnover, in…
Understanding how nonequilibrium systems respond to perturbations is a central challenge in physics. In this work, we establish mutual linearity in nonequilibrium overdamped Langevin systems. This theory provides a framework for controlling…
Cell growth in size is a complex process coordinated by intrinsic and environmental signals. In a recent work [Tzur et al., Science, 2009, 325:167-171], size distributions in an exponentially growing population of mammalian cells were used…
Virtually every biological rate depends on temperature, yet the resulting rate-temperature relationships often deviate strongly from simple Arrhenius behavior. In this first part of a two-part review, we survey phenomenological models used…
We propose a discrete model to determine the metabolic scaling exponent based on Fibonacci growth patterns and discrete biological development phases. In contrast to continuous fractal models such as the West-Brown-Enquist (WBE) theory, the…
Vertex Models, as used to describe cellular tissue, have an energy controlled by deviations of each cell area and perimeter from target values. The constrained nonlinear relation between area and perimeter leads to new mechanical response.…
To maintain homeostasis, living cells process information with networks of interacting molecules. Traditional models for cellular information processing have focused on networks of chemical reactions between molecules. Here, we describe how…
Organisms have evolved a variety of mechanisms to cope with the unpredictability of environmental conditions, and yet mainstream models of metabolic regulation are typically based on strict optimality principles that do not account for…
The dynamics governing the evolution of a many body system is constrained by a nonabelian local symmetry. We obtain a general form of the global macroscopic conditions assuring that at the microscopic level the evolution respects the…
Linear response theory has found many applications in statistical physics. One of these is to compute minimal-work protocols that drive nonequilibrium systems between different thermodynamic states, which are useful for designing engineered…
The classical macroscopic chemotaxis equations have previously been derived from an individual-based description of the tactic response of cells that use a "run-and-tumble" strategy in response to environmental cues. Here we derive…
A binary fluid mixture in contact with lateral particle reservoirs is considered. By imposing different particle concentrations in these reservoirs, the system can be maintained under controlled non-equilibrium conditions. Previous…
We study a statistical model describing the steady state distribution of the fluxes in a metabolic network. The resulting model on continuous variables can be solved by the cavity method. In particular analytical tractability is possible…
Understanding the pathways through which diet affects human metabolism is a central task in nutritional epidemiology. This article proposes novel methodology to identify food items associated with blood metabolites in two cohorts of…
Equations of motion that recognize biochemical patterns are described. The equations are partial differential equations in a continuous multiple component system in which adequate initial and boundary conditions are given. The biochemical…
We design the controls of physical systems that are faced by uncertainties. The system dynamics are described by random hyperbolic balance laws. The control aims to steer the system to a desired state under uncertainties. We propose a…
Understanding the links between diet, metabolic changes, and health outcomes is a key focus in nutritional science and broader biological research. Analyzing relationships, such as those between ultra-processed food (UPF) intake and…