Publications associées à Modeling of uncertainties in biochemical reactions

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

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

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

Stefano Mischler, Laura Brambilla

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

CONTROL OF HYPERBOLIC AND PARABOLIC EQUATIONS ON NETWORKS AND SINGULAR LIMITS

Nicola De Nitti

vanishing viscosity, networks. This work has received funding from the Alexander von Humboldt-Professorship program, the Transregio 154 Project "Mathematical Modelling, Simulation and Optimization Using the Example of Gas Networks" of the DFG, the grant PI ...

Amer Inst Mathematical Sciences-Aims2024

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

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

An explainability framework for deep learning on chemical reactions exemplified by enzyme-catalysed reaction classification

Daniel Probst

Assigning or proposing a catalysing enzyme given a chemical or biochemical reaction is of great interest to life sciences and chemistry alike. The exploration and design of metabolic pathways and the challenge of finding more sustainable enzyme-catalysed a ...

2023

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

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

Individual and combined benefits of different nonequilibrium proofreading mechanisms

Paolo De Los Rios, Adélaïde Alice Mohr, Stefano Zamuner, Daniel Maria Busiello

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

Inferring free-energy barriers and kinetic rates from molecular dynamics via underdamped Langevin models

Fabio Pietrucci, Sara Bonella, David Daniel Girardier

Rare events include many of the most interesting transformation processes in condensed matter, from phase transitions to biomolecular conformational changes to chemical reactions. Access to the corresponding mechanisms, free-energy landscapes and kinetic r ...

Aip Publishing2023

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

Karen Scrivener, Barbara Lothenbach, Natechanok Chitvoranund, Diana Londoño Zuluaga

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

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

Reinforcement learning approach to control an inverted pendulum: A general framework for educational purposes

Jesus Sanchez Rodriguez

Machine learning is often cited as a new paradigm in control theory, but is also often viewed as empirical and less intuitive for students than classical model-based methods. This is particularly the case for reinforcement learning, an approach that does n ...

PUBLIC LIBRARY SCIENCE2023

Optimized numerical solutions of SIRDVW multiage model controlling SARS-CoV-2 vaccine roll out: An application to the Italian scenario

Alfio Quarteroni, Nicola Parolini, Luca Dede'

In the context of SARS-CoV-2 pandemic, mathematical modelling has played a funda-mental role for making forecasts, simulating scenarios and evaluating the impact of pre-ventive political, social and pharmaceutical measures. Optimal control theory represent ...

KEAI PUBLISHING LTD2023

Computational tools and resources for designing new pathways to small molecules

Vassily Hatzimanikatis, Anastasia Sveshnikova

The metabolic engineering community relies on computational methods for pathway design to produce important small molecules in microbial hosts. Metabolic network databases are continuously curated and updated with known and novel reactions that expand the ...

CURRENT BIOLOGY LTD2022

Dissecting the role of the asparagine synthesis in acute liver injury

Yu Sun

Amino acids are some of the main building stones of life used in a variety of biological processes, such as protein synthesis, energy metabolism or even as precursors for hormone synthesis. How-ever, some of them also participate and coordinate certain cel ...

EPFL2022

Precipitation, Characterization, Kinetic, and Thermodynamic Modelling of Synthetic C-S-H Systems (C-S-H, CASH, CSH+$)

Maya Nicole Harris

This thesis investigates the effects of aluminates, sulfates, and heterogeneous substrates on the nucleation and growth of synthetic calcium-silicate-hydrates (C-S-H) produced by dropwise precipitation. The use of synthetic C-S-H, separate from other cemen ...

EPFL2022

Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx

Vassily Hatzimanikatis, Jasmin Maria Hafner, Victor Luc Etienne Viterbo, Anastasia Sveshnikova

Metabolic "dark matter" describes currently unknown metabolic processes, which form a blind spot in our general understanding of metabolism and slow down the development of biosynthetic cell factories and naturally derived pharmaceuticals. Mapping the dark ...

Nature Portfolio2022

Unified Green's function approach for spectral and thermodynamic properties from algorithmic inversion of dynamical potentials

Nicola Marzari, Tommaso Chiarotti, Andrea Ferretti

Dynamical potentials appear in many advanced electronic-structure methods, including self-energies from many-body perturbation theory, dynamical mean-field theory, electronic-transport formulations, and many embedding approaches. Here, we propose a novel t ...

AMER PHYSICAL SOC2022