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

Related publications (30)

Reconstruction and analysis of genome-scale metabolic networks in single organisms and microbial communities

Microorganisms are a key component in the chain of life. They are essential for agriculture, produce a large proportion of oxygen, and play a central role in the cycle of elements. Microorganisms are widely used in the production of food and alcoholic beve ...

EPFL2024

Unique corrosion behavior of an archaeological Roman iron ring: Microchemical characterization and thermodynamic considerations

Stefano Mischler

The corrosion mechanisms of a Roman iron bezel ring were investigated by in-depth characterization of its uncommon corrosion pattern and thermodynamic modelling. A silver foil and altered glass remnants were identified, covered with thick strata of magneti ...

2024

First-principles thermodynamics of precipitation in aluminum-containing refractory alloys

Anirudh Raju Natarajan

Materials for high -temperature environments are actively being investigated for deployment in aerospace and nuclear applications. This study uses computational approaches to unravel the crystallography and thermodynamics of a promising class of refractory ...

Pergamon-Elsevier Science Ltd2024

Optimality principles for the analysis of biological processes across scales: From enzyme kinetics to microbiome dynamics

Asli Sahin

Microorganisms are essential for life on Earth, performing key roles in numerous biological processes. Their influence extends across a wide spectrum, from human health and ecological balance to advancements in biotechnology and industrial applications. Th ...

EPFL2024

Contradict mechanism of long-term magnesium and sodium sulfate attacks of nano silica-modified cement mortars - Experimental and thermodynamic modeling

Qiao Wang

The mechanisms of external sulfate attack on cement mortars containing nano silica have been studied under full immersion conditions after 3 years. The sulfate degradation processes were compared between sodium sulfate and magnesium sulfate solutions with ...

Elsevier Sci Ltd2024

Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants

Wayo Matsushima, Didier Trono, Evaristo Jose Planet Letschert

Growing evidence indicates that transposable elements (TEs) play important roles in evolution by providing genomes with coding and non-coding sequences. Identification of TE-derived functional elements, however, has relied on TE annotations in individual s ...

2024

Multimodal transcriptomic atlases of mouse spinal cord injury

Matthieu Pierre Gautier

A spinal cord injury (SCI) triggers a cascade of molecular and cellular responses involving inflammatory cell infiltration and cytokine release, apoptosis, demyelination, excitotoxicity, ischemia, and the formation of a fibrotic scar surrounded by an astro ...

EPFL2024

Genome sequences of Vibrio cholerae strains isolated in the DRC between 2009 and 2012

Melanie Blokesch, Sandrine Stutzmann, Natalia Carolina Drebes Dorr, Alexandre Lemopoulos

Vibrio cholerae has caused seven cholera pandemics in the past two centuries. The seventh and ongoing pandemic has been particularly severe on the African continent. Here, we report long read-based genome sequences of six V. cholerae strains isolated in th ...

2024

On the Convergence to the Non-equilibrium Steady State of a Langevin Dynamics with Widely Separated Time Scales and Different Temperatures

Nicolas Macris, Emanuele Mingione, Diego Alberici

We study the solution of the two-temperature Fokker-Planck equation and rigorously analyse its convergence towards an explicit non-equilibrium stationary measure for long time and two widely separated time scales. The exponential rates of convergence are e ...

Springer Int Publ Ag2024

Single-mitosis dissection of acute and chronic DNA mutagenesis and repair

Christina Ernst

How chronic mutational processes and punctuated bursts of DNA damage drive evolution of the cancer genome is poorly understood. Here, we demonstrate a strategy to disentangle and quantify distinct mechanisms underlying genome evolution in single cells, dur ...

Nature Portfolio2024

The cost of adaptability: resource availability constrains functional stability under pulsed disturbances

Hannes Markus Peter

Global change exposes ecosystems to changes in the frequency, magnitude, and concomitancy of disturbances, which impact the composition and functioning of these systems. Here, we experimentally evaluate the effects of salinity disturbances and eutrophicati ...

Amer Soc Microbiology2024

A novel fatigue life prediction methodology based on energy dissipation in viscoelastic materials, synergistic effects of stress level, stress ratio, and temperature

Thomas Keller, Lulu Liu, Abdolvahid Movahedirad

This work introduces a new methodology to predict the fatigue life of viscoelastic materials by considering the creep effect on fatigue behavior under the concurrent effects of stress level, stress ratio, and temperature. The model established based on the ...

2024

Collective motion in a sheet of microswimmers

Viktor Skultéty

Self-propelled particles such as bacteria or algae swimming through a fluid are non-equilibrium systems where particle motility breaks microscopic detailed balance, often resulting in large-scale collective motion. Previous theoretical work has identified ...

Nature Portfolio2024

NMR and MS reveal characteristic metabolome atlas and optimize esophageal squamous cell carcinoma early detection

Lijing Xin

Metabolic changes precede malignant histology. However, it remains unclear whether detectable characteristic metabolome exists in esophageal squamous cell carcinoma (ESCC) tissues and biofluids for early diagnosis. Here, we conduct NMR- and MS-based metabo ...

Nature Portfolio2024

Growth and investigation of Argon thin films adsorbed on graphite by means of Ultrafast Electron Diffraction

Paolo Usai

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 transi ...

EPFL2023

Spectral and thermodynamic properties of interacting electrons with dynamical functionals

Tommaso Chiarotti

Empowered by ever-increasing computational power and algorithmic developments, electronic-structure simulations continue to drive research and innovation in materials science. In this context, ab-initio calculations offer an unbiased platform for the under ...

EPFL2023

Nature-Inspired Stalactite Nanopores for Biosensing and Energy Harvesting

Aleksandra Radenovic, Victor Carle Adrien Boureau, Andrey Chernev, Mukeshchand Thakur, Tzu-Heng Chen, Yunfei Teng, Vasily Artemov, Lucie Navratilova, Nianduo Cai

Nature provides a wide range of self-assembled structures from the nanoscale to the macroscale. Under the right thermodynamic conditions and with the appropriate material supply, structures like stalactites, icicles, and corals can grow. However, the natur ...

Wiley-V C H Verlag Gmbh2023

Individual 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 ...

Amer Physical Soc2023

Machine-learning the electronic density of states: electronic properties without quantum mechanics

Chiheb Ben Mahmoud

The electronic density of states (DOS) quantifies the distribution of the energy levels that can be occupied by electrons in a quasiparticle picture and is central to modern electronic structure theory. It also underpins the computation and interpretation ...

EPFL2023

Modeling, analysis, and design of complex biological networks

Mohammadomid Oftadeh

Automating experimental procedures has resulted in an unprecedented increase in the volume of generated data, which, in turn, has caused an accumulation of unprocessed data. As a result, the need to develop tools to analyze data systematically has been ris ...

EPFL2023