Publications associées à A genetic algorithm based design and experimental characterization of a highly thermostable metalloprotein

Data from: Optimal blade pitch control for enhanced vertical-axis wind turbine performance

Sébastien Le Fouest, Karen Ann J Mulleners

This directory contains open-source data obtained using a single-bladed H-type vertical-axis wind turbine prototype with individual blade pitching. This data results from the optimisation of the blade's pitching kinematics using a genetic algorithm at two ...

Zenodo2024

Opportunities and challenges in design and optimization of protein function

Bruno Emanuel Ferreira De Sousa Correia, Casper Alexander Goverde

The field of protein design has made remarkable progress over the past decade. Historically, the low reliability of purely structure-based design methods limited their application, but recent strategies that combine structure-based and sequence-based calcu ...

Nature Portfolio2024

Augmented Memory: Sample-Efficient Generative Molecular Design with Reinforcement Learning

Philippe Schwaller, Jeff Guo

Sample efficiency is a fundamental challenge in de novo molecular design. Ideally, molecular generative models should learn to satisfy a desired objective under minimal calls to oracles (computational property predictors). This problem becomes more apparen ...

Amer Chemical Soc2024

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

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

Genetic Algorithms for the Discovery of Homogeneous Catalysts

Anne-Clémence Corminboeuf, Puck Elisabeth van Gerwen, Simone Gallarati, Rubén Laplaza Solanas, Alexandre Alain Schöpfer

In this account, we discuss the use of genetic algorithms in the inverse design process of homogeneous catalysts for chemical transformations. We describe the main components of evolutionary experiments, specifically the nature of the fitness function to o ...

2023

A combined genetic algorithm and active learning approach to build and test surrogate models in Process Systems Engineering

François Maréchal, Julia Granacher

In Process Systems Engineering, computationally-demanding models are frequent and plentiful. Handling such complexity in an optimization framework in a fast and reliable way is essential, not only for generating meaningful solutions but also for providing ...

Pergamon-Elsevier Science Ltd2023

Wind farm power density optimization according to the area size using a novel self-adaptive genetic algorithm

Fernando Porté Agel, Nicolas Otto Kirchner Bossi

This work studies the power density (PD) optimization in wind farms, and its sensitivity to the available area size. A novel genetic algorithm (PDGA) is introduced, which optimizes PD and the turbine layout, by self-adapting to the PD and to the solutions ...

Pergamon-Elsevier Science Ltd2023

Optimization of elastic wave propagation in a reconfigurable medium by genetic algorithms with adaptive mutation probability

Romain Christophe Rémy Fleury, Janez Rus

We introduce a reconfigurable medium for the manipulation of elastic propagation properties of Lamb waves. It is based on a shape memory polymer (SMP) with temperature-dependent Young's modulus. Waves are excited by a laser pulse and detected by a laser vi ...

IOP Publishing Ltd2023

Advancing Computational Chemistry with Stochastic and Artificial Intelligence Approaches

Justin Villard

Computational chemistry aims to simulate reactions and molecular properties at the atomic scale, advancing the design of novel compounds and materials with economic, environmental, and societal implications. However, the field relies on approximate quantum ...

EPFL2023

De novo design of protein interactions with learned surface fingerprints

Henning Paul-Julius Stahlberg, Didier Trono, Priscilla Turelli, Charlène Mireille Raymonde Raclot, Sandrine Madeleine Suzanne Georgeon, Beat Fierz, Aaron Simone Petruzzella, Anthony Marchand, Bruno Emanuel Ferreira De Sousa Correia, Elisa Oricchio, Zander Harteveld, Pablo Gainza Cirauqui, Freyr Sverrisson, Andreas Scheck, Sarah Wehrle, Stéphane Rosset, Alexandra Krina Van Hall-Beauvais, Alexandra Teslenko, Jane Marsden, Michael Bronstein, Casper Alexander Goverde, Stephen Michael Buckley, Dongchun Ni, Martin Pacesa

Physical interactions between proteins are essential for most biological processes governing life. However, the molecular determinants of such interactions have been challenging to understand, even as genomic, proteomic and structural data increase. This k ...

2023

A Geometric Transformer for Structural Biology: Development and Applications of the Protein Structure Transformer

Lucien Fabrice Krapp

Proteins, the central building blocks of life, play pivotal roles in nearly every biological function. To do so, these macromolecular structures interact with their surrounding environment in complex ways, leading to diverse functional behaviors. The predi ...

EPFL2023

Generative power of a protein language model trained on multiple sequence alignments

Umberto Lupo, Anne-Florence Raphaëlle Bitbol, Damiano Sgarbossa

Computational models starting from large ensembles of evolutionarily related protein sequences capture a representation of protein families and learn constraints associated to protein structure and function. They thus open the possibility for generating no ...

eLIFE SCIENCES PUBL LTD2023

De novo designed proteins: a study in engineering novel folds and functions

Alexandra Krina Van Hall-Beauvais

Proteins control nearly every facet of life on a molecular level. Proteins are formed from linear strings of amino acids, which fold into three-dimensional structures that can enact functions. Evolution has created highly efficient proteins in diverse fold ...

EPFL2023

De novo protein design by inversion of the AlphaFold structure prediction network

Bruno Emanuel Ferreira De Sousa Correia, Stéphane Rosset, Casper Alexander Goverde, Benedict Dieter Gregor Wolf, Hamed Khakzad

De novo protein design enhances our understanding of the principles that govern protein folding and interactions, and has the potential to revolutionize biotechnology through the engineering of novel protein functionalities. Despite recent progress in comp ...

2023

Screening for drivers of SARS-CoV-2 uptake

Christoph Merten, Alexis Louis Autour

Genetic and cellular drivers of the cellular uptake of SARS-CoV-2 can be screened at high throughput via droplet microfluidics and size-exclusion methods for the analysis of the formation of fusions between cells expressing the virus's spike protein and ce ...

Nature Portfolio2023

Byzantine-Resilient Learning Beyond Gradients: Distributing Evolutionary Search

Rachid Guerraoui, Andrei Kucharavy, Matteo Monti

Modern machine learning (ML) models are capable of impressive performances. However, their prowess is not due only to the improvements in their architecture and training algorithms but also to a drastic increase in computational power used to train them.|S ...

Assoc Computing Machinery2023

Integrated electronics for time-of-flight positron emission tomography photodetectors

Andrada Alexandra Muntean

Positron emission tomography is a nuclear imaging technique well known for its use in oncology for cancer diagnosis and staging. A PET scanner is a complex machine which comprises photodetectors placed in a ring configuration that detect gamma photons gen ...

EPFL2023

PROBING INTRACELLULAR ELASTICITY WITH MINIMAL-HESSIAN REGISTRATION

Michaël Unser

We propose an image-based elastography method to measure the heterogeneous stiffness inside a cell and its nucleus. It uses a widely accessible setup consisting of plate compression imaged with fluorescence microscopy. Our framework recovers a spatial map ...

IEEE2023

Wind farm layout and unconstrained hub height optimization using genetic algorithms applied to different power densities

Fernando Porté Agel, Nicolas Otto Kirchner Bossi

LES and wind tunnel studies have shown significant benefit when allowing turbines (T) in a wind farm to adopt different heights. This work presents two new genetic algorithms (GA) that perform wind farm layout optimization (WFLO) involving continuous and t ...

2022