Publication
pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis
Publications associées (68)
Growth and investigation of Argon thin films adsorbed on graphite by means of Ultrafast Electron Diffraction
Starting from our big universe to the microscopic world, phase transitions play an important role in nature. Just after the Big Bang our universe experienced multiple phase transitions, from high-temperature plasma to the matter we know today.Phase transit ...
EPFL2023Individual and combined benefits of different nonequilibrium proofreading mechanisms
Paolo De Los Rios, Daniel Maria Busiello, Stefano Zamuner, Adélaïde Alice Mohr
Genome duplication, transcription, and translation are among many crucial cellular processes that need to be performed with high fidelity. However, those extremely low error rates cannot be explained with simple equilibrium thermodynamic considerations. Th ...
College Pk2023Experimental and theoretical thermodynamic studies in Ba2MgReO6-the ground state in the context of Jahn-Teller effect
Henrik Moodysson Rønnow, Ivica Zivkovic, Jana Pásztorová
We address the degeneracy of the ground state multiplet on the 5d(1) Re6+ ion in double perovskite Ba2MgReO6 using a combination of specific heat measurements and density functional calculations. For Ba2MgReO6, two different ground state multiplets have pr ...
IOP Publishing Ltd2023Controlling surface effects in extremely high aspect ratio gold plasmonic electrodes
Olivier Martin, Christian Santschi, Marco Riccardi
Nanofabrication is key to many technological advances, especially the challenge of merging nanophotonics with electronics. Here, we investigate the fabrication process of plasmonic interdigitated gold electrodes having a very high aspect ratio (i.e. long a ...
ELSEVIER2022A 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 PORTFOLIO2021Analysis of human metabolism by reducing the complexity of the genome-scale models using redHUMAN
Vassily Hatzimanikatis, Meriç Ataman, Maria Masid Barcon
Altered metabolism is associated with many human diseases. Human genome-scale metabolic models (GEMs) were reconstructed within systems biology to study the biochemistry occurring in human cells. However, the complexity of these networks hinders a consiste ...
2020Large-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 ...
2020Optimization methods and objective functions for analysis of metabolic network models
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 ...
EPFL2020Membraneless organelles: phasing out of equilibrium
Over the past years, liquid-liquid phase separation (LLPS) has emerged as a ubiquitous principle of cellular organization implicated in many biological processes ranging from gene expression to cell division. The formation of biological condensates, like t ...
PORTLAND PRESS LTD2020redLips: a comprehensive mechanistic model of the lipid metabolic network of yeast
Vassily Hatzimanikatis, Sofia Tsouka
Over the last decades, yeast has become a key model organism for the study of lipid biochemistry. Because the regulation of lipids has been closely linked to various physiopathologies, the study of these biomolecules could lead to new diagnostics and treat ...
OXFORD UNIV PRESS2020