相关论文: Flux cost functions and optimal metabolic states
Metabolism and evolution are closely connected: if a mutation incurs extra energetic costs for an organism, there is a baseline selective disadvantage that may or may not be compensated for by other adaptive effects. A long-standing, but to…
Complex biological systems are very robust to genetic and environmental changes at all levels of organization. Many biological functions of Escherichia coli metabolism can be sustained against single-gene or even multiple-gene mutations by…
The Active Flux scheme is a Finite Volume scheme with additional point values distributed along the cell boundary. It is third order accurate and does not require a Riemann solver: the continuous reconstruction serves as initial data for…
Metabolic control analysis (Kacser & Burns (1973). Symp. Soc. Exp. Biol. 27, 65-104; Heinrich & Rapoport (1974). Eur. J. Biochem. 42, 89-95) was developed for the understanding of multi-enzyme networks. At the core of this approach is the…
We introduce a methodology to study the possible matter flows of an ecosystem defined by observational biomass data and realistic biological constraints. The flows belong to a polyhedron in a multi dimensional space making statistical…
We consider the shape optimization of flow fields for electrochemical cells. Our goal is to improve the cell by modifying the shape of its flow field. To do so, we introduce simulation models of the flow field with and without the porous…
Many dynamic processes such as telecommunication and transport networks can be described through discrete time series of graphs. Modelling the dynamics of such time series enables prediction of graph structure at future time steps, which…
Life and functioning of higher organisms depends on the continuous supply of metabolites to tissues and organs. What are the requirements on the transport network pervading a tissue to provide a uniform supply of nutrients, minerals, or…
Interstitial fluid flow is a feature of many solid tumours. In vitro Experiments have shown that such fluid flow can direct tumour cell movement upstream or downstream depending on the balance between the competing mechanisms of tensotaxis…
The identification of cellular objectives is one of the central topics in the research of microbial metabolic networks. In particular, the information about a cellular objective is needed in flux balance analysis which is a commonly used…
This paper studies the application of the blended dynamics approach towards distributed optimization problem where the global cost function is given by a sum of local cost functions. The benefits include (i) individual cost function need…
Resource Balance Analysis (RBA) is a framework for predicting steady-state cellular growth under resource constraints. However, classical RBA formulations are static and do not capture the dynamic regulation of biosynthetic resources or…
The purpose of this work is to develop an algorithmic optimization approach for a capacitated Multi-Commodity flow problem, where the objective is to minimize the total link costs, where the cost of each arc increases convexly with its…
Background: Genome-scale metabolic network models and constraint-based modeling techniques have become important tools for analyzing cellular metabolism. Thermodynamically infeasible cy-cles (TICs) causing unbounded metabolic flux ranges…
Enzymes show two distinct transport behaviors in the presence of their substrates in solution. First, their diffusivity enhances with increasing substrate concentration. In addition, enzymes perform directional motion toward regions with…
Analyzing big data in a highly dynamic environment becomes more and more critical because of the increasingly need for end-to-end processing of this data. Modern data flows are quite complex and there are not efficient, cost-based,…
Flux sampling is an analysis that, based on a distribution, picks randomly an efficient number of points from the solution space of a metabolic model. Unlike most constraint-based analyses, flux sampling does not require an objective…
Cells adapt their metabolic fluxes in response to changes in the environment. We present a framework for the systematic construction of flux-based graphs derived from organism-wide metabolic networks. Our graphs encode the directionality of…
We present an iterative inverse reinforcement learning algorithm to infer optimal cost functions in continuous spaces. Based on a popular maximum entropy criteria, our approach iteratively finds a weight improvement step and proposes a…
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…