相关论文: Accelerating flux balance calculations in genome-s…
Comprehensive and confident identifications of metabolites and other chemicals in complex samples will revolutionize our understanding of the role these chemically diverse molecules play in biological systems. Despite recent advances,…
This paper introduces a novel constraint adaptive filtering algorithm based on a relative logarithmic cost function which is termed as Constrained Least Mean Logarithmic Square (CLMLS). The proposed CLMLS algorithm elegantly adjusts the…
The behavior of some stochastic chemical reaction networks is largely unaffected by slight inaccuracies in reaction rates. We formalize the robustness of state probabilities to reaction rate deviations, and describe a formal connection…
The metabolic state of a cell, comprising fluxes, metabolite concentrations and enzyme levels, is shaped by a compromise between metabolic benefit and enzyme cost. This hypothesis and its consequences can be studied by computational models…
In the modeling of complex biological systems, the use of power-law models (such as S-systems and GMA systems) often provides a remarkable accuracy over several orders of magnitude in concentrations, an unusually broad range not fully…
Despite their topological complexity almost all functional properties of metabolic networks can be derived from steady-state dynamics. Indeed, many theoretical investigations (like flux-balance analysis) rely on extracting function from…
Bayesian multinomial logistic-normal (MLN) models are popular for the analysis of sequence count data (e.g., microbiome or gene expression data) due to their ability to model multivariate count data with complex covariance structure.…
We present the Distributed and Localized Model Predictive Control (DLMPC) algorithm for large-scale structured linear systems, wherein only local state and model information needs to be exchanged between subsystems for the computation and…
As an essential attribute of organic compounds, polarity has a profound influence on many molecular properties such as solubility and phase transition temperature. Thin layer chromatography (TLC) represents a commonly used technique for…
Real-world (bio)chemical processes often exhibit stochastic dynamics with non-trivial correlations and state-dependent fluctuations. Model predictive control (MPC) often must consider these fluctuations to achieve reliable performance.…
The high penetration of distributed energy resources, resulting in backfeed of power at the transmission and distribution interface, is causing conventional underfrequency load shedding (UFLS) schemes to become nonconforming. Adaptive…
In the wake of the intense effort made for the experimental CILEX project, numerical simulation cam- paigns have been carried out in order to finalize the design of the facility and to identify optimal laser and plasma parameters. These…
Modeling the dynamical flows on networks of biomolecular machines often entails computing node populations and edge fluxes with Master Equations and correlating machine performance with entropy production. But this alone is not sufficient…
Learning to integrate non-linear equations from highly resolved direct numerical simulations (DNSs) has seen recent interest for reducing the computational load for fluid simulations. Here, we focus on determining a flux-limiter for shock…
We develop a novel data-driven framework as an alternative to dynamic flux balance analysis, bypassing the demand for deep domain knowledge and manual efforts to formulate the optimization problem. The proposed framework is end-to-end,…
This paper presents a load balancing strategy for reaction rate evaluation and chemistry integration in reacting flow simulations. The large disparity in scales during combustion introduces stiffness in the numerical integration of the PDEs…
In topology optimization of compliant mechanisms, the specific placement of boundary conditions strongly affects the resulting material distribution and performance of the design. At the same time, the most effective locations of the loads…
We introduce a rigorous method to microscopically compute the observables which characterize the thermodynamics and kinetics of rare macromolecular transitions for which it is possible to identify a priori a slow reaction coordinate. In…
This paper proposes an optimization-based task and motion planning framework, named "Logic Network Flow", that integrates temporal logic specifications into mixed-integer programs for efficient robot planning. Inspired by the…
Chemical kinetic models are an essential component in the development and optimisation of combustion devices through their coupling to multi-dimensional simulations such as computational fluid dynamics (CFD). Low-dimensional kinetic models…