Related papers: Accelerating flux balance calculations in genome-s…
Metabolomic data sets provide a direct read-out of cellular phenotypes and are increasingly generated to study biological questions. Our previous work revealed the potential of analyzing extracellular metabolomic data in the context of the…
Biological systems are governed by coupled interactions between intracellular metabolism and bioreactor operation that span multiple time scales. Constraint-based metabolic models are widely used to describe intracellular metabolism, but…
Metabolic reactions of single-cell organisms are routinely observed to become dispensable or even incapable of carrying activity under certain circumstances. Yet, the mechanisms as well as the range of conditions and phenotypes associated…
Despite the significant progress made in recent years, the computation of the complete set of elementary flux modes of large or even genome-scale metabolic networks is still impossible. We introduce a novel approach to speed up the…
Dynamic flux balance analysis uses a quasi-steady state assumption to calculate an organism's metabolic activity at each time-step of a dynamic simulation, using the well-known technique of flux balance analysis. For microbial communities,…
Accurately modeling chemical reactions at the atomistic level requires high-level electronic structure theory due to the presence of unpaired electrons and the need to properly describe bond breaking and making energetics. Commonly used…
Approximate computing is an effective computing paradigm for improving the energy efficiency of error-tolerant applications. Approximate logic synthesis (ALS) is an automatic process to generate approximate circuits with reduced area,…
Lightweight Temporal Compression (LTC) is among the lossy stream compression methods that provide the highest compression rate for the lowest CPU and memory consumption. As such, it is well suited to compress data streams in…
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…
Linear optimal power flow (LOPF) algorithms use a linearization of the alternating current (AC) load flow equations to optimize generator dispatch in a network subject to the loading constraints of the network branches. Common algorithms…
This work focus on how to stabilize and lossless model compression, aiming to reduce model complexity and enhance efficiency without sacrificing performance due to compression errors. A key challenge is effectively leveraging compression…
In this paper we present a variant of the Calculus of Looping Sequences (CLS for short) with global and local rewrite rules. While global rules, as in CLS, are applied anywhere in a given term, local rules can only be applied in the…
Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run…
This paper presents an efficient suboptimal model predictive control (MPC) algorithm for nonlinear switched systems subject to minimum dwell time constraints (MTC). While MTC are required for most physical systems due to stability, power…
There is currently much interest in the development of improved trajectory-based methods for the simulation of nonadiabatic processes in complex systems. An important goal for such methods is the accurate calculation of the rate constant…
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…
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.…
We consider a novel approach for the enhancement of fluid mixing via pure stirring strategies building upon the Least Action Principle (LAP) for incompressible flows. The LAP is formally analogous to the Benamou--Brenier formulation of…
Cells generally convert nutrient resources to useful products via energy transduction. Accordingly, the thermodynamic efficiency of this conversion process is one of the most essential characteristics of living organisms. However, although…
How biological networks achieve robust control despite relying on imperfect, local information remains an important open question. Here, we identify thermodynamic constraints that can curtail non-equilibrium steady-state responses so…