Publications associées à Equilibrium thermodynamics

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

Equilibrium and non-equilibrium furanose selection in the ribose isomerisation network

Paolo De Los Rios, Shiling Liang, Francesco Piazza, Daniel Maria Busiello

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 Research2021

Repair or Degrade: the Thermodynamic Dilemma of Cellular Protein Quality-Control

Paolo De Los Rios, Bruno Claude Daniel Fauvet, Pierre Goloubinoff, Satyam Tiwari, Mathieu Rebeaud

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 SA2021

Large-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 ...

2020

The 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 ...

Nature Research2020

A Mixed-Integer Linear Programming Formulation for Optimizing Multi-Scale Material and Energy Integration

François Maréchal, Ivan Daniel Kantor, Hür Ebuzer Bütün, Jean-Loup Sylvain Robineau

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 ...

2020

Version 1 of a sea ice module for the physics-based, detailed, multi-layer SNOWPACK model

Michael Lehning, Katherine Colby Leonard, Nander Wever

Sea ice is an important component of the global climate system. The presence of a snowpack covering sea ice can strongly modify the thermodynamic behavior of the sea ice, due to the low thermal conductivity and high albedo of snow. The snowpack can be stra ...

COPERNICUS GESELLSCHAFT MBH2020

Optimization methods and objective functions for analysis of metabolic network models

Zhaleh Hosseini

Computational studies of metabolism aim to systematically analyze the metabolic behaviour of biological systems in different conditions. Genome-scale metabolic network models (GEMs) capture the connection between elements of the network by applying stoichi ...

EPFL2020

Synthesis of grid compliant substitute natural gas from a representative biogas mixture in a hybrid Ni/Ru catalysed reactor

Andreas Züttel, Emanuele Moioli, Robin Tobias Andreas Mutschler, Marco Calizzi, 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 ...

2020

Thermochemical Stability of Hybrid Halide Perovskites

Michael Graetzel, 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 ...

2019

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

Chaperones 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

Non equilibrium thermodynamics of protein organization

Alberto Stefano Sassi

Three quarters of the thesis will be devoted to the discussion of non equilibrium systems. We show how certain biological systems cannot be described by standard thermodynamics. The reason is that the energy consumption due to the hydrolysis of ATP imposes ...

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

Investigation of nanoparticle-protein interactions with novel methods

Ahmet Bekdemir

Advancements in novel nanomaterials present promising avenue for therapeutics and diagnosis in nanomedicine. Importantly, in these applications, nanoparticles (NPs) are almost instantly coated with a complex layer of proteins in biological environment, ter ...

EPFL2018

Impact of the strength and spatial distribution of adsorption sites on methane deliverable capacity in nanoporous materials

Berend Smit, Cory Matthew Simon

The methane deliverable capacity of adsorbent materials is a critical performance metric that will determine the viability of using adsorbed natural gas (ANG) technology in vehicular applications. ARPA-E recently set a target deliverable capacity of 315 cc ...

Elsevier2017

Thermodynamics-based Metabolite Sensitivity Analysis in metabolic networks

Vassily Hatzimanikatis

The increasing availability of large metabolomics datasets enhances the need for computational methodologies that can organize the data in a way that can lead to the inference of meaningful relationships. Knowledge of the metabolic state of a cell and how ...

Elsevier2017

Navigating and Managing the Complexity of Genome Scale Metabolic Networks for Studies in Cellular Physiology and Industrial Biotechnology

Meriç Ataman

Metabolism is a network of biochemical reactions that converts carbon sources to cellu-lar fuels and building blocks. Metabolism of many organisms has been studied for many decades. These studies define metabolism as a very large and complex network. Stoic ...

EPFL2016

Combined water and energy integration in industrial processes with restricted connections

François Maréchal, Ivan Daniel Kantor, Maziar Kermani

Reducing the environmental impact of industrial processes is highly linked with decreasing consumption of natural resources, energy, and water. In the context of climate change, as discussed during the Conference of Parties in Paris (COP21), the efficient ...

2016

Non-equilibrium conformational dynamics in the function of molecular chaperones

Paolo De Los Rios, Alessandro Barducci

Why do chaperones need ATP hydrolysis to help proteins reach their native, functional states? In this review, we highlight the most recent experimental and theoretical evidences suggesting that ATP hydrolysis allows molecular chaperones to escape the bound ...

Elsevier2015