Related papers: Dynamic metabolic resource allocation based on the…
During overflow metabolism, cells excrete glycolytic byproducts when growing under aerobic conditions in a seemingly wasteful fashion. While potentially advantageous for microbes with finite oxidative capacity, its role in higher organisms…
The world is full of systems of distributed agents, collaborating and competing in complex ways: firms and workers specialise within economies, neurons adapt their tuning across brain circuits, and species compete and coexist within…
Reaction-diffusion systems offer a powerful framework for understanding self-organized patterns in biological systems, yet controlling these patterns remains a significant challenge. As a consequence, we present a rigorous framework of…
Model usage is the central challenge of model-based reinforcement learning. Although dynamics model based on deep neural networks provide good generalization for single step prediction, such ability is over exploited when it is used to…
We study the problem of synthesizing a policy that maximizes the entropy of a Markov decision process (MDP) subject to a temporal logic constraint. Such a policy minimizes the predictability of the paths it generates, or dually, maximizes…
Conventional harvesting problems for natural resources often assume physiological homogeneity of the body length/weight among individuals. However, such assumptions generally are not valid in real-world problems, where heterogeneity plays…
The maximum entropy principle from statistical mechanics states that a closed system attains an equilibrium distribution that maximizes its entropy. We first show that for graphs with fixed number of edges one can define a stochastic edge…
In this article, we focus on a periodic resource allocation problem applied to a dynamical system which comes from a biological system. More precisely, we consider a system with $N$ resources and $N$ activities, each activity use the…
The effective use of limited resources for controlling spreading processes on networks is of prime significance in diverse contexts, ranging from the identification of "influential spreaders" for maximizing information dissemination and…
This paper aims to introduce a concept of an equilibrium point of a dynamical system which will call it almost global asymptotically stable. A biological prey-predator model is also analyzed with a modification function growth in prey…
Microbes require several complex organic molecules for growth. A species may obtain a required factor by taking up molecules released by other species or by synthesizing the molecule. The patterns of uptake and synthesis set a flow of…
Living systems continuously transform matter and energy through the chemical processes that constitute their metabolism. The overall metabolic rate of an organism correlates positively with its body mass, however both the exact scaling…
Models of networks play a major role in explaining and reproducing empirically observed patterns. Suitable models can be used to randomize an observed network while preserving some of its features, or to generate synthetic graphs whose…
Reaction-diffusion equations are commonly used to model a diverse array of complex systems, including biological, chemical, and physical processes. Typically, these models are phenomenological, requiring the fitting of parameters to…
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…
This paper studies the dynamic programming principle using the measurable selection method for stochastic control of continuous processes. The novelty of this work is to incorporate intermediate expectation constraints on the canonical…
Biological molecular machines convert free energy between different forms in cells, often at high efficiency. Optimal control theory provides a framework to elucidate design principles governing energetically efficient driving. Here, we use…
Mathematical modeling of disease outbreaks can infer the future trajectory of an epidemic, which can inform policy decisions. Another task is inferring the origin of a disease, which is relatively difficult with current mathematical models.…
Understanding design principles of complex cellular organization is one of the major challenges in biology. Recent analysis of the large-scale cellular organization has revealed the scale-free nature and robustness of metabolic and protein…
Self-organization creates new order and shifts sub-boundaries while reorganizing energy and entropy within a control volume. This article examines pathway selection and tests whether maximizing the entropy generation rate can forecast…