Publications related to Computational Studies on Cellular Metabolism : From Biochemical Pathways to Complex Metabolic Networks

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

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

Live-cell imaging powered by computation

Suliana Manley

The proliferation of microscopy methods for live-cell imaging offers many new possibilities for users but can also be challenging to navigate. The prevailing challenge in live-cell fluorescence microscopy is capturing intra-cellular dynamics while preservi ...

Nature Portfolio2024

Mechanisms and functions of protein S-acylation

Françoise Gisou van der Goot Grunberg, Laurence Gouzi Abrami, Francisco De Magalhães Sarmento Ribeiro De Mesquita

Over the past two decades, protein S-acylation (often referred to as S-palmitoylation) has emerged as an important regulator of vital signalling pathways. S-Acylation is a reversible post-translational modification that involves the attachment of a fatty a ...

Nature Portfolio2024

Orchestrating chromosome conformation capture analysis with Bioconductor

Cyril Matthey-Doret

Genome-wide chromatin conformation capture assays provide formidable insights into the spatial organization of genomes. However, due to the complexity of the data structure, their integration in multi-omics workflows remains challenging. We present data st ...

Nature Research2024

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

Hausdorff dimension of fermions on a random lattice

Mattia Guerino Varrone

Geometric properties of lattice quantum gravity in two dimensions are studied numerically via Monte Carlo on Euclidean Dynamical Triangulations. A new computational method is proposed to simulate gravity coupled with fermions, which allows the study of int ...

Elsevier2024

In situ architecture of Opa1-dependent mitochondrial cristae remodeling

Juan Cruz Landoni Martin

Cristae membrane state plays a central role in regulating mitochondrial function and cellular metabolism. The protein Optic atrophy 1 (Opa1) is an important crista remodeler that exists as two forms in the mitochondrion, a membrane-anchored long form (l-Op ...

Springernature2024

The role of computational methods in cardiovascular medicine: a narrative review

Alfio Quarteroni, Luca Dede', Christian Vergara, Stefano Pagani

Background and Objective: Computational models of the cardiovascular system allow for a detailed and quantitative investigation of both physiological and pathological conditions, thanks to their ability to combine clinical-possibly patient-specific-data wi ...

Ame Publishing Company2024

A Combination Technique for Optimal Control Problems Constrained by Random PDEs

Fabio Nobile, Tommaso Vanzan

We present a combination technique based on mixed differences of both spatial approximations and quadrature formulae for the stochastic variables to solve efficiently a class of optimal control problems (OCPs) constrained by random partial differential equ ...

2024

Augmenting large language models with chemistry tools

Andres Camilo Marulanda Bran, Carlo Baldassari, Philippe Schwaller, Oliver Tobias Schilter

Large language models (LLMs) have shown strong performance in tasks across domains but struggle with chemistry-related problems. These models also lack access to external knowledge sources, limiting their usefulness in scientific applications. We introduce ...

Nature Portfolio2024

EncodingActs: Modeling, Representing and Transmitting Embodied Knowledge in Traditional Martial Arts

Yumeng Hou

EncodingActs investigates how computational methods can facilitate the transmission of multifaceted knowledge within intangible cultural heritage (ICH). ICH, characterized by living, tacit, yet complex epistemic systems, is conventionally viewed as challen ...

EPFL2024

Host cell CRISPR genomics and modelling reveal shared metabolic vulnerabilities in the intracellular development of Plasmodium falciparum and related hemoparasites

Mélanie Yvette Yolande Borteele, Vassily Hatzimanikatis, Denis Alain Henri Lucien Joly

Parasitic diseases, particularly malaria (caused by Plasmodium falciparum) and theileriosis (caused by Theileria spp.), profoundly impact global health and the socioeconomic well-being of lower-income countries. Despite recent advances, identifying host me ...

Nature Research2024

Engineering novel protein interactions with therapeutic potential using deep learning-guided surface design

Anthony Marchand

Proteins are foundational biomolecules of life playing a crucial role in a myriad of biological processes. Their function often requires interplay with other biomolecules, including proteins themselves. Protein-protein interactions (PPIs) are essential for ...

EPFL2024

Surface segregation in high-entropy alloys from alchemical machine learning

Michele Ceriotti, Sandip De, Guillaume André Jean Fraux, Arslan Mazitov, Nataliya Lopanitsyna

High-entropy alloys (HEAs), containing several metallic elements in near-equimolar proportions, have long been of interest for their unique mechanical properties. More recently, they have emerged as a promising platform for the development of novel heterog ...

Iop Publishing Ltd2024

Seeking the new, learning from the unexpected: Computational models of surprise and novelty in the brain

Alireza Modirshanechi

Human babies have a natural desire to interact with new toys and objects, through which they learn how the world around them works, e.g., that glass shatters when dropped, but a rubber ball does not. When their predictions are proven incorrect, such as whe ...

EPFL2024

A Streamline Upwind Petrov-Galerkin Reduced Order Method for Advection-Dominated Partial Differential Equations Under Optimal Control

Gianluigi Rozza, Fabio Zoccolan

In this paper we will consider distributed Linear-Quadratic Optimal Control Problems dealing with Advection-Diffusion PDEs for high values of the Peclet number. In this situation, computational instabilities occur, both for steady and unsteady cases. A Str ...

Walter De Gruyter Gmbh2024

Computational Homogenization for Inverse Design of Surface-based Inflatables

Mark Pauly, Florin Isvoranu, Francis Julian Panetta, Yingying Ren, Seiichi Eduardo Suzuki Erazo, Uday Kusupati

Surface-based inflatables are composed of two thin layers of nearly inextensible sheet material joined together along carefully selected fusing curves. During inflation, pressure forces separate the two sheets to maximize the enclosed volume. The fusing c ...

Association for Computing Machinery (ACM)2024

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

Global emergent responses of stream microbial metabolism to glacier shrinkage

Tom Ian Battin, Hannes Markus Peter, Tyler Joe Kohler, Massimo Bourquin, Michail Styllas, Nicola Deluigi

Most cryospheric ecosystems are energy limited. How their energetics will respond to climate change remains largely unknown. This is particularly true for glacier-fed streams, which interface with the cryosphere and initiate some of Earth's largest river s ...

Nature Portfolio2024