Related papers: Accelerating flux balance calculations in genome-s…
Metabolic scaling is one of the most important patterns in biology. Theory explaining the 3/4-power size-scaling of biological metabolic rate does not predict the non-linear scaling observed for smaller life forms. Here we present a new…
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…
This paper proposes an optimization-based task and motion planning framework, named "Logic Network Flow", to integrate signal temporal logic (STL) specifications into efficient mixed-binary linear programmings. In this framework, temporal…
The uniform sampling of convex polytopes is an interesting computational problem with many applications in inference from linear constraints, but the performances of sampling algorithms can be affected by ill-conditioning. This is the case…
The design of genome-scale constraint-based metabolic networks has steadily advanced, with an increasing number of successful cases achieving growth-coupled production, in which the biosynthesis of key metabolites is linked to cell growth.…
Life is a nonequilibrium phenomenon: metabolism provides a continuous supply of energy that drives nearly all cellular processes. However, very little is known about how much energy different cellular processes use, i.e. their energetic…
In this work we propose a novel algorithmic strategy that allows for an efficient characterization of the whole set of stable fluxes compatible with the metabolic constraints. The algorithm, based on the well-known Bethe approximation,…
We discuss chemical reaction networks and metabolic pathways based on stoichiometric network analysis, and introduce deformed toric ideal constraints by the algebraic geometrical approach. This paper concerns steady state flux of chemical…
The performance and efficiency of distributed machine learning (ML) depends significantly on how long it takes for nodes to exchange state changes. Overly-aggressive attempts to reduce communication often sacrifice final model accuracy and…
Gaining insights from realistic dynamical models of biochemical systems can be challenging given their large number of state variables. Model reduction techniques can mitigate this by decreasing complexity by mapping the model onto a…
We explore methods to use thermostatically controlled loads (TCLs), such as water heaters and air conditioners, to provide ancillary services by assisting in balancing generation and load. We show that by adding simple imbedded instructions…
Quantum--Mechanical methods that are both computationally fast and accurate are not yet available for electronic excitations having charge transfer character. In this work, we present a significant step forward towards this goal for those…
Temporal gene expression data (Wen, et. al.) was analyzed using the recently introduced inverse modeling technique of Embedded Complex Logistic Maps (ECLM). Preliminary results indicate scale-free structure in the gene regulatory network…
We present an unsupervised data processing workflow that is specifically designed to obtain a fast conformational clustering of long molecular dynamics simulation trajectories. In this approach we combine two dimensionality reduction…
We present two modifications of the standard cell list algorithm for nonequilibrium molecular dynamics simulations of homogeneous, linear flows. When such a flow is modeled with periodic boundary conditions, the simulation box deforms with…
The regulation of metabolic activity by tuning enzyme expression levels is crucial to sustain cellular growth in changing environments. Metabolic networks are often studied at steady state using constraint-based models and optimization…
Moment dynamics in stochastic chemical kinetics often involve an infinite chain of coupled equations, where lower-order moments depend on higher-order ones, making them analytically intractable. Moment bounding via semidefinite programming…
We cast the metabolism of interacting cells within a statistical mechanics framework considering both, the actual phenotypic capacities of each cell and its interaction with its neighbors. Reaction fluxes will be the components of…
Metabolic fluxes in cells are governed by physical, physiological, and economic principles. Here I assume an optimal allocation of enzyme resources and postulate a general principle for metabolism: each enzyme must convert less valuable…
Molecular profiling data (e.g., gene expression) has been used for clinical risk prediction and biomarker discovery. However, it is necessary to integrate other prior knowledge like biological pathways or gene interaction networks to…