Publication

How uncertainty in kinetic parameters affects metabolic control analysis of optimally grown E.coli

Publications associées (33)

A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics

Vassily Hatzimanikatis, Ljubisa Miskovic, Maria Masid Barcon, Mohammadomid Oftadeh, Pierre Guy Rémy Salvy

Eukaryotic organisms play an important role in industrial biotechnology, from the production of fuels and commodity chemicals to therapeutic proteins. To optimize these industrial systems, a mathematical approach can be used to integrate the description of ...

NATURE PORTFOLIO2021

Uncertainty estimation for molecular dynamics and sampling

Michele Ceriotti, Federico Grasselli, Yongbin Zhuang, Venkat Kapil, Kevin Rossi, Edgar Albert Engel, Giulio Imbalzano

Machine-learning models have emerged as a very effective strategy to sidestep time-consuming electronic-structure calculations, enabling accurate simulations of greater size, time scale, and complexity. Given the interpolative nature of these models, the r ...

2021

Characterising Structure and Stability of Materials using Machine Learning

Andrea Anelli

The search of novel materials using in-silico high-throughput screening is emerging as a fundamental step in the pipeline of materials discovery, but its low yields in terms of synthesisable structures limit its effectiveness. In order to isolate configura ...

EPFL2020

Thermochemical Stability of Hybrid Halide Perovskites

Joachim Maier, Alessandro Senocrate

This contribution discusses the chemical stability of methylammonium (MA) halide perovskites (MAPbI(3), MAPbBr(3), and MAPbCl(3)); it considers degradation processes relevant for devices (vs T, O-2, H2O, voltage, illumination) by outlining their thermodyna ...

AMER CHEMICAL SOC2019

Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models

Vassily Hatzimanikatis, Noushin Hadadi, Vikash Kumar Pandey

The ever-increasing availability of transcriptomic and metabolomic data can be used to deeply analyze and make ever-expanding predictions about biological processes, as changes in the reaction fluxes through genome-wide pathways can now be tracked. Current ...

2019

Identification of the enzymes responsible for diverse phenotypic states of yeast lipid metabolism using comprehensive mechanistic models

Sofia Tsouka

Lipids carry an important role in cell structure and function, as well as in the physiopathology of multiple diseases. Maintenance of the lipid profiles should be tightly regulated for preserving membrane permeability, cell integrity and several other func ...

2018

Mapping the diverse phenotypic states of yeast lipid metabolism to enzymes using mechanistic kinetic models

Sofia Tsouka

Lipids carry a very important role in cell structure and function, as well as in the physiopathology of many diseases. Maintenance of the lipid profiles should be tightly regulated as it is very important for preserving membrane permeability, cell integrit ...

2018

Generalized convex hull construction for materials discovery

Michele Ceriotti, Edgar Albert Engel, Andrea Anelli

Searching for novel materials involves identifying potential candidates and selecting those that have desirable properties and facile synthesis. It is relatively easy to generate large numbers of potential candidates, for instance, by computational searche ...

2018

Unravelling the precipitation pathway of biorelevant minerals: from fundamental studies to biomedical applications

Agnese Carino

The formation pathway of biominerals archetypes, namely calcium carbonate (CaC) and calcium phosphates (CaPs), was investigated using a multidisciplinary approach. The time-resolved analytical data were collected using a controlled-composition method and i ...

EPFL2018

pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis

Vassily Hatzimanikatis, Meriç Ataman, Georgios Fengos, Keng Cher Soh, Pierre Guy Rémy Salvy

Summary: pyTFA and matTFA are the first published implementations of the original TFA paper. Specifically, they include explicit formulation of Gibbs energies and metabolite concentrations, which enables straightforward integration of metabolite concentrat ...

2018

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