相关论文: Flux cost functions and optimal metabolic states
Active Flux is a recently developed numerical method for hyperbolic conservation laws. Its classical degrees of freedom are cell averages and point values at cell interfaces. These latter are shared between adjacent cells, leading to a…
Biological functionality of cellular aggregates is largely influenced by the activity and displacements of individual constituent cells. From a theoretical perspective this activity can be characterized by hydrodynamic transport…
We consider optimal distributed computation of a given function of distributed data. The input (data) nodes and the sink node that receives the function form a connected network that is described by an undirected weighted network graph. The…
We present a supervised dimensionality reduction technique called Convex Linear Discriminant Analysis (ConvexLDA). The proposed model optimizes a multi-objective cost function by balancing two complementary terms. The first term pulls the…
Cellular metabolism, the integrated interconversion of thousands of metabolic substrates through enzyme-catalyzed biochemical reactions, is the most investigated complex intercellular web of molecular interactions. While the topological…
The motility skills of phytoplankton have evolved and persisted over millions of years, primarily in response to factors such as nutrient and light availability, temperature and viscosity gradients, turbulence, and predation pressure.…
A function $F$ defined on all subsets of a finite ground set $E$ is quasi-concave if $F(X\cup Y)\geq\min\{F(X),F(Y)\}$ for all $X,Y\subset E$. Quasi-concave functions arise in many fields of mathematics and computer science such as social…
Biochemical signaling pathways can be insulated from impedance and competition effects through enzymatic "futile cycles" which consume energy, typically in the form of ATP. We hypothesize that better insulation necessarily requires higher…
Characterizing the capabilities, criticalities and response to perturbations of genome-scale metabolic networks is a basic problem with important applications. A key question concerns the identification of the potentially most harmful…
We investigate the welfare loss of continuous and discrete order matching models in blockchain-based decentralized exchanges (DEX) that utilize order books to record outstanding orders. Continuous processing matches each incoming…
We present an approach for flux analysis in process algebra models of biological systems. We perceive flux as the flow of resources in stochastic simulations. We resort to an established correspondence between event structures, a broadly…
Objective: As metabolic cost is a primary factor influencing humans' gait, we want to deepen our understanding of metabolic energy expenditure models. Therefore, this paper identifies the parameters and input variables, such as muscle or…
Numerous networks, such as transportation, distribution and delivery networks optimize their designs in order to increase efficiency and lower costs, improving the stability of its intended functions, etc. Networks that distribute goods,…
By combining methods of kinetic and density functional theory, we present a description of molecular fluids which accounts for their microscopic structure and thermodynamic properties as well as for the hydrodynamic behavior. We focus on…
Here we report on the viscosity of eukaryotic living cells as a function of the time, and on the application of stochastic models to analyze its temporal fluctuations. The viscoelastic properties of NIH/3T3 fibroblastic cells are…
This paper deals with temporal enzyme distribution in the activation of biochemical pathways. Pathway activation arises when production of a certain biomolecule is required due to changing environmental conditions. Under the premise that…
To understand cell migration, it is crucial to gain knowledge on how cells exert and integrate forces on/from their environment. A quantity of prime interest for biophysicists interested in cell movements modeling is the intracellular…
Evaluating the log-sum-exp function or the softmax function is a key step in many modern data science algorithms, notably in inference and classification. Because of the exponentials that these functions contain, the evaluation is prone to…
Given a source and a target probability measure supported on $\mathbb{R}^d$, the Monge problem asks to find the most efficient way to map one distribution to the other. This efficiency is quantified by defining a \textit{cost} function…
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. Instead, given a reconstruction, the initial value problem…