相关论文: Flux cost functions and optimal metabolic states

Many biological functions require the dynamics to be necessarily driven out-of-equilibrium. In contrast, in various contexts, a nonequilibrium dynamics at fast timescales can be described by an effective equilibrium dynamics at a slower…

It is known that Flux Corrected Transport algorithms can produce entropy-violating solutions of hyperbolic conservation laws. Our purpose is to design flux correction with maximal antidiffusive fluxes to obtain entropy solutions of scalar…

When simulating runaway electron dynamics in tokamak disruptions, fluid models with lower numerical cost are often preferred to more accurate kinetic models. The aim of this work is to compare fluid and kinetic simulations of a large…

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…

Molecular motors play pivotal roles in organizing the interior of cells. A motor efficient in cargo transport would move along cytoskeletal filaments with a high speed and a minimal error in transport distance (or time) while consuming a…

Functional data analysis in a mixed-effects model framework is done using operator calculus. In this approach the functional parameters are treated as serially correlated effects giving an alternative to the penalized likelihood approach,…

To fully leverage the multi-task optimization paradigm for accelerating the solution of expensive scheduling problems, this study has effectively tackled three vital concerns. The primary issue is identifying auxiliary tasks that closely…

As an example for the optimization of unstable flows, we present an economics-based method for deciding the optimal rates at which vehicles are allowed to enter a highway. It exploits the naturally occuring fluctuations of traffic flow and…

Quantitative studies of cell metabolism are often based on large chemical reaction network models. A steady state approach is suited to analyze phenomena on the timescale of cell growth and circumvents the problem of incomplete experimental…

Elastic network models (ENMs) are valuable and efficient tools for characterizing the collective internal dynamics of proteins based on the knowledge of their native structures. The increasing evidence that the biological functionality of…

The mechanics of crawling cells on a substrate is investigated by using a minimal model that satisfies the force-free condition. A cell is described by two subcellular elements connected by a linear actuator that changes the length of the…

We study the problem of the optimal execution of a large trade in the presence of nonlinear transient impact. We propose an approach based on homotopy analysis, whereby a well behaved initial strategy is continuously deformed to lower the…

Developing high-performance and energy-efficient algorithms for maximum matchings is becoming increasingly important in social network analysis, computational sciences, scheduling, and others. In this work, we propose the first maximum…

We present a novel flow-based kinetic approach, inspired by continuous normalizing flows, for plasma simulation that unifies the complementary strengths of direct Vlasov solvers and particle-based methods. By tracking the distribution…

In this note, we introduce a class of indicators that enable to compute efficiently optimal transport plans associated to arbitrary distributions of $N$ demands and $N$ supplies in $\mathbf{R}$ in the case where the cost function is…

Finite volume methods are proposed for computing approximate pathwise entropy/kinetic solutions to conservation laws with a rough path dependent flux function. For a convex flux, it is demonstrated that rough path oscillations may lead to…

Background: The rational identification of essential genes is a cornerstone of drug discovery, yet standard computational methods like Flux Balance Analysis (FBA) often struggle to produce accurate predictions in complex, redundant…

Metabolic heterogeneity is widely recognised as the next challenge in our understanding of non-genetic variation. A growing body of evidence suggests that metabolic heterogeneity may result from the inherent stochasticity of intracellular…

We consider the following inference problem: Given a set of edge-flow signals observed on a graph, lift the graph to a cell complex, such that the observed edge-flow signals can be represented as a sparse combination of gradient and curl…

A recent breakthrough in biologically-plausible normative frameworks for dimensionality reduction is based upon the similarity matching cost function and the low-rank matrix approximation problem. Despite clear biological interpretation,…