Publications related to Thermodynamics-based Metabolite Sensitivity Analysis in metabolic networks

Related publications (37)

Nicotinamide mononucleotide restores impaired metabolism, endothelial cell proliferation and angiogenesis in old sedentary male mice

Aging is accompanied by a decline in neovascularization potential and increased susceptibility to ischemic injury. Here, we confirm the age-related impaired neovascularization following ischemic leg injury and impaired angiogenesis. The age-related deficit ...

2025

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

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

Evangelia Vagena

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

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

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

White dwarfs as a probe of exceptionally light QCD axions

Stefan Stelzl

We study the effects of exceptionally light QCD axions on the stellar configuration of white dwarfs. At finite baryon density, the nonderivative coupling of the axion to nucleons displaces the axion from its invacuum minimum, which implies a reduction of t ...

American Physical Society2024

A framework for understanding collective microbiome metabolism

Martin Ackermann

Microbiome metabolism underlies numerous vital ecosystem functions. Individual microbiome members often perform partial catabolism of substrates or do not express all of the metabolic functions required for growth. Microbiome members can complement each ot ...

NATURE PORTFOLIO2024

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

Soliton gas: Theory, numerics, and experiments

Andrey Gelash

The concept of soliton gas was introduced in 1971 by Zakharov as an infinite collection of weakly interacting solitons in the framework of Korteweg-de Vries (KdV) equation. In this theoretical construction of a diluted (rarefied) soliton gas, solitons with ...

Amer Physical Soc2024

Rational strain design with minimal phenotype perturbation

Vassily Hatzimanikatis, Ljubisa Miskovic, Daniel Robert Weilandt, Bharath Narayanan

Devising genetic interventions for desired cellular phenotypes remains challenging regarding time and resources. Kinetic models can accelerate this task by simulating metabolic responses to genetic perturbations. However, exhaustive design evaluations with ...

Nature Portfolio2024

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

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

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

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

Influence of temperature on phase assemblages of belite-ye'elimite cement

Karen Scrivener, Diana Londoño Zuluaga, Natechanok Chitvoranund

This paper studies the effect of temperature on the phase assemblages of belite-ye'elimite cement. A comparison is made between thermodynamic modelling and experimental data at 28 and 180 days of hydration at 5, 20, 40, and 60 degrees C. The fast reaction ...

Pergamon-Elsevier Science Ltd2023

Many-body physics with strongly interacting fermions coupled to light

Victor Youri Helson

This thesis reports on the realization of the first experiments conducted with superfluid, strongly interacting Fermi gases of 6Li coupled to the light field of an optical cavity. In the scope of existing ultracold atomic platforms, this is the first time ...

EPFL2023

Expanding computational biochemistry towards complex and non-natural compounds

Anastasia Sveshnikova

In the beginning was the metabolism. The biochemical processes that make life possible transformed the soup of chemicals into the life on Earth we know today. Since then, living organisms have evolved, and life on Earth has become more complex. Living orga ...

EPFL2023

Optimal enzyme utilization suggests that concentrations and thermodynamics determine binding mechanisms and enzyme saturations

Vassily Hatzimanikatis, Daniel Robert Weilandt, Asli Sahin

One of the main challenges hampering the development of kinetic models is the lack of kinetic parameters for many enzymatic reactions. Here, the authors introduce a framework to explore the catalytically optimal operating conditions of any complex enzyme m ...

Nature Portfolio2023

Improving time-resolution and sensitivity of in situ X-ray photoelectron spectroscopy of a powder catalyst by modulated excitation

Oliver Kröcher, Davide Ferri, Filippo Buttignol

Ambient pressure X-ray photoelectron spectroscopy (APXPS) is a powerful tool to characterize the surface structure of heterogeneous catalysts in situ. In order to improve the time resolution and the signal-to-noise (S/N) ratio of photoemission spectra, we ...

ROYAL SOC CHEMISTRY2023