Concept
Equilibrium thermodynamics
Related publications (43)
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 PORTFOLIO2021Equilibrium and non-equilibrium furanose selection in the ribose isomerisation network
Paolo De Los Rios, Daniel Maria Busiello, Shiling Liang, Francesco Piazza
The exclusive presence of beta -D-ribofuranose in nucleic acids is still a conundrum in prebiotic chemistry, given that pyranose species are substantially more stable at equilibrium. However, a precise characterisation of the relative furanose/pyranose fra ...
NATURE RESEARCH2021Repair or Degrade: the Thermodynamic Dilemma of Cellular Protein Quality-Control
Paolo De Los Rios, Pierre Goloubinoff, Satyam Tiwari, Mathieu Rebeaud, Bruno Claude Daniel Fauvet
Life is a non-equilibrium phenomenon. Owing to their high free energy content, the macromolecules of life tend to spontaneously react with ambient oxygen and water and turn into more stable inorganic molecules. A similar thermodynamic picture applies to th ...
FRONTIERS MEDIA SA2021Large-scale kinetic metabolic models of Pseudomonas putida KT2440 for consistent design of metabolic engineering strategies
Vassily Hatzimanikatis, Ljubisa Miskovic, Milenko Tokic
Background: Pseudomonas putida is a promising candidate for the industrial production of biofuels and biochemicals because of its high tolerance to toxic compounds and its ability to grow on a wide variety of substrates. Engineering this organism for impro ...
2020The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models
Vassily Hatzimanikatis, Pierre Guy Rémy Salvy
Systems biology has long been interested in models capturing both metabolism and expression in a cell. We propose here an implementation of the metabolism and expression model formalism (ME-models), which we call ETFL, for Expression and Thermodynamics Flu ...
2020A Mixed-Integer Linear Programming Formulation for Optimizing Multi-Scale Material and Energy Integration
François Maréchal, Ivan Daniel Kantor, Hür Ebuzer Bütün
This research presents a mathematical formulation for optimizing integration of complex industrial systems from the level of unit operations to processes, entire plants, and finally to considering industrial symbiosis opportunities between plants. The fram ...
2020Synthesis of grid compliant substitute natural gas from a representative biogas mixture in a hybrid Ni/Ru catalysed reactor
Andreas Züttel, Emanuele Moioli, Marco Calizzi, Robin Tobias Andreas Mutschler, Alexandre Borsay
We demonstrate biogas upgrading towards full CO2 conversion in mild conditions in a three-step reactor system using Ru- and Ni-based catalysts. In each of the three reactor stages, the temperature is carefully controlled, thus optimizing the reaction therm ...
2020Thermochemical 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 SOC2019Enhanced 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 ...
2019Chaperones convert the energy from ATP into the nonequilibrium stabilization of native proteins
Paolo De Los Rios, Alessandro Barducci, Pierre Goloubinoff, Bruno Claude Daniel Fauvet, Alberto Stefano Sassi
During and after protein translation, molecular chaperones require ATP hydrolysis to favor the native folding of their substrates and, under stress, to avoid aggregation and revert misfolding. Why do some chaperones need ATP, and what are the consequences ...
2018