相关论文: 13CFLUX -- Third-generation high-performance engin…
Metabolic flux analysis using 13C labeled substrates is an important tool for metabolic engineering. Although it has now been evolving for more than ten years, metabolic flux analysis has still not reached the limits of its application.…
Isotopically non-stationary metabolic flux analysis (INST $^{13}$C-MFA) provides unique insights into cellular physiology but is typically limited by low throughput and high experimental costs. Here, we present a miniaturized and automated…
Metabolic flux balance analyses are a standard tool in analysing metabolic reaction rates compatible with measurements, steady-state and the metabolic reaction network stoichiometry. Flux analysis methods commonly place unrealistic…
13C-Metabolic Flux Analysis (13C-MFA) and Flux Balance Analysis (FBA) are widely used to investigate the operation of biochemical networks in both biological and biotechnological research. Both of these methods use metabolic reaction…
Accurate quantification of intracellular metabolic fluxes is central to systems biology and biotechnology. Flux estimation relies on biochemical network models, with $^{13}$C metabolic flux analysis (MFA) being the state-of-the-art…
Carbon isotope labeling method is a standard metabolic engineering tool for flux quantification in living cells. To cope with the high dimensionality of isotope labeling systems, diverse algorithms have been developed to reduce the number…
A major theme in constraint-based modeling is unifying experimental data, such as biochemical information about the reactions that can occur in a system or the composition and localization of enzyme complexes, with highthroughput data…
Comprehension of metabolic pathways is considerably enhanced by metabolic flux analysis (MFA-ILE) in isotope labeling experiments. The balance equations are given by hundreds of algebraic (stationary MFA) or ordinary differential equations…
Machine learning (ML) is increasingly becoming a common tool in computational chemistry. At the same time, the rapid development of ML methods requires a flexible software framework for designing custom workflows. MLatom 3 is a program…
Topology Optimization (TO) holds the promise of designing next-generation compact and efficient fluidic devices. However, the inherent complexity of fluid-based TO systems, characterized by multiphysics nonlinear interactions, poses…
Numerical simulations are ubiquitous in mathematics and computational science. Several industrial and clinical applications entail modeling complex multiphysics systems that evolve over a variety of spatial and temporal scales. This study…
Motivation: Flow Injection Analysis coupled to High-Resolution Mass Spectrometry (FIA-HRMS) is a promising approach for high-throughput metabolomics. FIA-HRMS data, however, cannot be preprocessed with current software tools which rely on…
$\textit{A priori}$ prediction of phase stability of materials is a challenging practice, requiring knowledge of all energetically-competing structures at formation conditions. Large materials repositories $\unicode{x2014}$ housing…
Building a virtual cell capable of accurately simulating cellular behaviors in silico has long been a dream in computational biology. We introduce CellFlux, an image-generative model that simulates cellular morphology changes induced by…
We demonstrate how three-dimensional fluid flow simulations can be carried out on the Cellular Automata Machine 8 (CAM-8), a special-purpose computer for cellular-automata computations. The principal algorithmic innovation is the use of a…
Transformers are central to advances in artificial intelligence (AI), excelling in fields ranging from computer vision to natural language processing. Despite their success, their large parameter count and computational demands challenge…
Quite generally, constraint-based metabolic flux analysis describes the space of viable flux configurations for a metabolic network as a high-dimensional polytope defined by the linear constraints that enforce the balancing of production…
The paper describes capabilities of numerical simulation of liquid flows with solid and/or gas admixtures in centrifugal pumps using modern commercial CFD software packages, with the purpose to predict performance curves of the pumps…
In this paper we study the liveness of several MUTEX solutions by representing them as processes in PAFAS s, a CCS-like process algebra with a specific operator for modelling non-blocking reading behaviours. Verification is carried out…
Computational fluid dynamics (CFD) is an important tool for the simulation of the cardiovascular function and dysfunction. Due to the complexity of the anatomy, the transitional regime of blood flow in the heart, and the strong mutual…