Related papers: Constrained Allocation Flux Balance Analysis
Studies by microbiologists from the 1970s provided robust estimates for the energy supply and demand of a prokaryotic cell. The amount of ATP needed to support growth was calculated from the chemical composition of the cell and known…
A model is proposed to study the process of hypoxia-induced angiogenesis in cancer cells. The model accounts for the role played by the vascular endothelial growth factor (VEGF)-A in regulating the oxygen intake. VEGF-A is dynamically…
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…
Higher levels of renewable electricity generation increase uncertainty in power system operation. To ensure secure system operation, new tools that account for this uncertainty are required. In this paper, we formulate a chance-constrained…
In the balanced allocations framework, there are $m$ jobs (balls) to be allocated to $n$ servers (bins). The goal is to minimize the gap, the difference between the maximum and the average load. Peres, Talwar and Wieder (RSA 2015) used the…
Investigation of protein self-assembly processes is important for the understanding of the growth processes of functional proteins as well as disease-causing amyloids. Inside cells, intrinsic molecular fluctuations are so high that they…
Thermodynamics constrains the flow of matter in a reaction network to occur through routes along which the Gibbs energy decreases, implying that viable steady-state flux patterns should be void of closed reaction cycles. Identifying and…
Genome-scale stoichiometric modeling of metabolism has become a standard systems biology tool for modeling cellular physiology and growth. Extensions of this approach are also emerging as a valuable avenue for predicting, understanding and…
Fluid flow has a major effect on the aggregation and fragmentation of bacterial colonies. Yet, a generic framework to understand and predict how hydrodynamics affects colony size remains elusive. This study investigates how fluid flow…
Stochastic fluctuations of molecular abundances are a ubiquitous feature of cellular processes and lead to significant cell-to-cell variability. Recent theoretical work established lower bounds for stochastic fluctuations in cells for broad…
We present a novel distributed evolutionary algorithm, KaFFPaE, to solve the Graph Partitioning Problem, which makes use of KaFFPa (Karlsruhe Fast Flow Partitioner). The use of our multilevel graph partitioner KaFFPa provides new effective…
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…
Genetic and environmental perturbation experiments have been used to study microbes in a bid to gain insight into transcriptional regulation, adaptive evolution, and other cellular dynamics. These studies have potential in enabling rational…
Simulation-based ranking and selection (R&S) is a popular technique for optimizing discrete-event systems (DESs). It evaluates the mean performance of system designs by simulation outputs and aims to identify the best system design from a…
Data analytics often involves hypothetical reasoning: repeatedly modifying the data and observing the induced effect on the computation result of a data-centric application. Recent work has proposed to leverage ideas from data provenance…
We study an optimal control problem arising from a resource allocation problem in cellular metabolism. A minimalistic model that describes the production of enzymatic vs. non-enzymatic biomass components from a single nutrient source is…
Single-cell trajectory analysis aims to reconstruct the biological developmental processes of cells as they evolve over time, leveraging temporal correlations in gene expression. During cellular development, gene expression patterns…
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…
In this paper, we develop a novel adaptation-based approach to constrained control design under multiple state and input constraints. Specifically, we introduce a method for synthesizing any number of time-varying candidate control barrier…
Traditional control-flow analysis (CFA) for higher-order languages, whether implemented by constraint-solving or abstract interpretation, introduces spurious connections between callers and callees. Two distinct invocations of a function…