Related papers: Linear Response Theory of Evolved Metabolic System…
A reaction-diffusion system with mass conservation modelling cell polarity is considered. A range of the parameters is found where the solution converges exponentially to the constant equilibrium and the $\omega$-limit set of the solution…
We study the current response to periodic driving of a crucial biochemical reaction network, namely, substrate inhibition. We focus on the conversion rate of substrate into product under time-varying metabolic conditions, modeled by a…
Phenotypically structured equations arise in population biology to describe the interaction of species with their environment that brings the nutrients. This interaction usually leads to selection of the fittest individuals. Models used in…
In this paper, a general framework for the analysis of a connection between the training of artificial neural networks via the dynamics of Markov chains and the approximation of conservation law equations is proposed. This framework allows…
The paper analyses stochastic systems describing reacting molecular systems with a combination of two types of state spaces, a finite-dimensional, and an infinite dimenional part. As a typical situation consider the interaction of larger…
The metabolic activity of microbes has played an essential role in the evolution and persistence of life on Earth. Microbial metabolism plays a primary role in the flow of carbon, nitrogen and other elements through the biosphere on a…
The accurate determination of transport coefficients in numerical simulations is becoming increasingly important in a wide range of applications. Here we consider the linear response in systems driven away from thermal equilibrium into a…
We study how local equilibrium, and linear response predictions of transport coefficients are violated as systems move far from equilibrium. This is done by studying heat flow in classical lattice models with and without bulk transport…
Integrated global food system analysis is hampered by the fragmentation of data among food types, processes, and scales. Studies also often neglect the connection to human metabolism -- the ultimate driver of food demand. Here we use a…
We address the issue of the validity of linear response theory for a closed quantum system subject to a periodic external driving. Linear response theory (LRT) predicts energy absorption at frequencies of the external driving where the…
Most microorganisms regulate their cell size. We review here some of the mathematical formulations of the problem of cell size regulation. We focus on coarse-grained stochastic models and the statistics they generate. We review the…
Understanding the organization of reaction fluxes in cellular metabolism from the stoichiometry and the topology of the underlying biochemical network is a central issue in systems biology. In this task, it is important to devise reasonable…
Background. Emerging technologies now allow for mass spectrometry based profiling of up to thousands of small molecule metabolites (metabolomics) in an increasing number of biosamples. While offering great promise for revealing insight into…
As an effective method to deliver external materials into biological cells, microinjection has been widely applied in the biomedical field. However, the cognition of cell mechanical property is still inadequate, which greatly limits the…
A recent experiment driving colloids electromagnetically, by B\'erut et al. [2014 Europhys. Lett. 107, 60004], is an ideal paradigm for illustrating a linear response theory for nonequilibrium overdamped systems including hydrodynamic…
The adiabatic theorem refers to a setup where an evolution equation contains a time-dependent parameter whose change is very slow, measured by a vanishing parameter $\epsilon$. Under suitable assumptions the solution of the…
Metabolic pathways are fundamental maps in biochemistry that detail how molecules are transformed through various reactions. The complexity of metabolic network, where a single compound can play a part in multiple pathways, poses a…
The metabolic processes complexity is at the heart of energy conversion in living organisms and forms a huge obstacle to develop tractable thermodynamic metabolism models. By raising our analysis to a higher level of abstraction, we develop…
Metabolic networks are known to be scale free but the evolutionary origin of this structural property is not clearly understood. One way of studying the dynamical process is to compare the metabolic networks of species that have arisen at…
The study of biological cells in terms of mesoscopic, nonequilibrium, nonlinear, stochastic dynamics of open chemical systems provides a paradigm for other complex, self-organizing systems with ultra-fast stochastic fluctuations, short-time…