Related papers: Linear Response Theory of Evolved Metabolic System…
We distinguish a mechanical representation of the world in terms of point masses with positions and momenta and the chemical representation of the world in terms of populations of different individuals, each with intrinsic stochasticity,…
One of the aims of systems biology is to build multiple layered and multiple scale models of living systems which can efficiently describe phenomena occurring at various level of resolution. Such models should consist of layers of various…
Chemical reaction networks underpin biological and physical phenomena across scales, from microbial interactions to planetary atmosphere dynamics. Bacterial communities exhibit complex competitive interactions for resources, human organs…
It has long been hypothesized that futile cycles in cellular metabolism are involved in the regulation of biochemical pathways. Following the work of Newsholme and Crabtree, we develop a quantitative theory for this idea based on…
Many mathematical models for biological phenomena, such as the spread of diseases, are based on reaction-diffusion equations for densities of interacting cell populations. We present a consistent derivation of reaction-diffusion equations…
It is shown that the dual to the linear programming problem that arises in constraint-based models of metabolism can be given a thermodynamic interpretation in which the shadow prices are chemical potential analogues, and the objective is…
As the quantification of metabolism, nonequilibrium steady states play a central role in living matter, but are beyond the purview of equilibrium statistical mechanics. Here we develop a fermionic theory of nonequilibrium steady states in…
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…
Living systems are forced away from thermodynamic equilibrium by exchange of mass and energy with their environment. In order to model a biochemical reaction network in a non-equilibrium state one requires a mathematical formulation to…
A major goal of modern computational biology is to simulate the collective behaviour of large cell populations starting from the intricate web of molecular interactions occurring at the microscopic level. In this paper we describe a…
Nonlinear density response theory is revisited focusing on the harmonically perturbed finite temperature uniform electron gas. Within the non-interacting limit, brute force quantum kinetic theory calculations for the quadratic, cubic,…
We study the multi-species replicator model with linear fitness and random fitness matrices of various classes. By means of numerical resolution of the replicator equations, we determine the survival probability of a species in terms of its…
We consider the electrons of a molecule in the adiabatic time-dependent density functional theory approximation. We establish the well-posedness of the time evolution and its linear response close to a non-degenerate ground state, and prove…
One of the major research questions regarding human microbiome studies is the feasibility of designing interventions that modulate the composition of the microbiome to promote health and cure disease. This requires extensive understanding…
Controlling complex reaction networks is a fundamental challenge in the fields of physics, biology, and systems engineering. Here, we prove a general principle for catalytic reaction systems with kinetics where the reaction order and the…
Basing on the theory of Feynman's influence functional and its hierarchical equations of motion, we develop a linear response theory for quantum open systems. Our theory provides an effective way to calculate dynamical observables of a…
We introduce a comprehensive analytical benchmark, relying on Fokker-Planck formalism, to study microbial dynamics in presence of both biotic and abiotic forces. In equilibrium, we observe a balance between the two kinds of forces, leading…
System-level properties of metabolic networks may be the direct product of natural selection or arise as a by-product of selection on other properties. Here we study the effect of direct selective pressure for growth or viability in…
The Green-Kubo relation, the Einstein relation, and the fluctuation-response relation are representative universal relations among measurable quantities that are valid in the linear response regime. We provide pedagogical proofs of these…
Intracellular protein patterns govern essential cellular functions by dynamically redistributing proteins between membrane-bound and cytosolic states, conserving their total numbers. This review presents a theoretical framework for…