Publications related to Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways

Collimation simulations for the FCC-ee

Tatiana Pieloni, Félix Simon Carlier, Guillaume Clément Broggi, Milica Rakic, Giovanni Iadarola, Bruce Roderik

The collimation system of the Future Circular Collider, operating with leptons (FCC-ee), must protect not only the experiments against backgrounds, but also the machine itself from beam losses. With a 17.8 MJ stored energy of the electron and positron beam ...

Iop Publishing Ltd2024

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

Development and clinical validation of computational imaging biomarkers for neurodegenerative diseases

Veronica Lily Ravano

Neurodegenerative and neuroinflammatory disorders often involve complex pathophysiological mechanisms that are â to this date â only partially understood. A more comprehensive understanding of those microstructural processes and their characterization ...

EPFL2024

From low-rank retractions to dynamical low-rank approximation and back

Daniel Kressner, Axel Elie Joseph Séguin, Gianluca Ceruti

In algorithms for solving optimization problems constrained to a smooth manifold, retractions are a well-established tool to ensure that the iterates stay on the manifold. More recently, it has been demonstrated that retractions are a useful concept for ot ...

Springer2024

SC-TPTP: An Extension of the TPTP Derivation Format for Sequent-Based Calculus

Simon Guilloud

Motivated by the transfer of proofs between proof systems, and in particular from first order automated theorem provers (ATPs) to interactive theorem provers (ITPs), we specify an extension of the TPTP derivation text format to describe proofs in first-ord ...

2024

From Sequence to Dynamics to Function: Computational Design of Allostery and Ligand Selectivity in G-Protein Coupled Receptors

Mahdi Hijazi

The phenomenon of allostery, a general property in proteins that has been heralded as "the second secret of life" remains elusive to our understanding and even more challenging to incorporate into protein design. One example of allosteric proteins with gre ...

EPFL2024

Modular segmentation, spatial analysis and visualization of volume electron microscopy datasets

Martin Weigert

Volume electron microscopy is the method of choice for the in situ interrogation of cellular ultrastructure at the nanometer scale, and with the increase in large raw image datasets generated, improving computational strategies for image segmentation and s ...

Nature Portfolio2024

Structural Insights into Electrophiles and Electrophilic Metabolites Sensing and Signaling: The Missing Information

Chloé Rogg, Yimon Aye

Native reactive electrophilic species (RES) are long-recognized regulators of pathophysiology; yet, knowledge surrounding how RES regulate context-specific biology remains limited. The latest technological advances in profiling and precision decoding of RE ...

WILEY-V C H VERLAG GMBH2023

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

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

Numerical tools for burning plasmas

Laurent Villard, Alberto Bottino, Jonathan Graves, Ben McMillan, Emmanuel Lanti, Emanuele Poli, Xiao Wang, Baruch Rofman

The software stack under development within a European coordinated effort on tools for burning plasma modelling is presented. The project is organised as a Task (TSVV Task 10) under the new E-TASC initiative (Litaudon et al 2022 Plasma Phys. Control. Fusio ...

IOP Publishing Ltd2023

Media Coverage of 3D Visual Tools Used in Urban Participatory Planning

Jens Ingensand, Thibaud Nicolas Chassin

The opportunities provided by adopting digitally-generated visual tools in urban participatory planning are compelling. These visual tools can promote interactions between authorities and citizens and among citizens. However, the urban participatory practi ...

IGI GLOBAL2023

ROSMOSE: A Web-based Optimization Tool to Aid Decision-making for the Design and Operation of Industrial and Urban Energy Systems

François Maréchal, Cédric Terrier, Daniel Alexander Florez Orrego, Michel Lopez, Meire Ellen Gorete Ribeiro Domingos

Energy efficiency is crucial for the sustainable operation of all industrial and urban sectors. However, practicing engineers have seldom access to open-source tools that can readily evaluate and compare scenarios in terms of energy consumption, cost, and ...

2023

Understanding Revision Behavior in Adaptive Writing Support Systems for Education

Tanja Christina Käser Jacober, Paola Mejia Domenzain, Luca Mouchel, Thiemo Wambsganss

Revision behavior in adaptive writing support systems is an important and relatively new area of research that can improve the design and effectiveness of these tools, and promote students' self-regulated learning (SRL). Understanding how these tools are u ...

Zenodo2023

Digital Intervention for Collaborative and Human-Centered Activities in Design-Based Learning Scenarios

Denis Gillet, Isabelle Barbara Marie-Hélène Cardia

Training science and engineering students to become responsible citizens and professionals requires novel and creative pedagogical approaches, such as design thinking. This concept relies on processes and tools to develop creativity and problem-solving ski ...

IEEE2023

Assessing the readiness of municipalities for digital process innovation

Mert Duygan

Pre-adoption phases of innovation are understudied in the innovation literature. This article addresses preadoption phases of innovation by running a prospective analysis. We assess the readiness of municipalities for the adoption of a digital tool that br ...

ELSEVIER SCI LTD2023

Evaluation of teachers’ orchestration tools usage in robotic classrooms

Pierre Dillenbourg, Sina Shahmoradi, Barbara Bruno, Aditi Kothiyal

Teachers’ self-efficacy in managing classrooms is an important consideration when it comes to bringing educational robots to classrooms. Orchestration tools support teachers by providing awareness indicators of students’ progress as well as levers to contr ...

2023

Development of a Robotic Microsurgeon for Embryonic Research

Ece Özelçi

Understanding how biological matter takes its shape is instrumental to biology, bioengineering, medicine, and bioinspired engineering. Gaining information on the principles of morphogenesis could enable clinicians to correct developmental abnormalities, ev ...

EPFL2023

Analysis of accretion disc structure and stability using open code for vertical structure

Pascale Jablonka

Detailed chemical abundances of very metal-poor (VMP; [Fe/H] < -2) stars are important for better understanding the first stars, early star formation, and chemical enrichment of galaxies. Big on-going and coming high-resolution spectroscopic surveys provid ...

OXFORD UNIV PRESS2023