Publications related to Structural alignment

Thermal transport of glasses via machine learning driven simulations

Accessing the thermal transport properties of glasses is a major issue for the design of production strategies of glass industry, as well as for the plethora of applications and devices where glasses are employed. From the computational standpoint, the che ...

Frontiers Media Sa2024

FLO:RE – A new floor system made of reused reinforced concrete and steel elements

Corentin Jean Dominique Fivet, Numa Joy Bertola, Maléna Bastien Masse, Célia Marine Küpfer

Carefully extracting reinforced concrete (RC) elements from soon-to-be demolished structures and reusing them as load-bearing components is an emerging circular low-carbon alternative to building new structures. As floor construction typically accounts for ...

IABSE2024

Quantification of Native Lignin Structural Features with Gel-Phase 2D-HSQC0 Reveals Lignin Structural Changes During Extraction

Jeremy Luterbacher, Stefania Bertella

Our ability to study and valorize the lignin fraction of biomass is hampered by the fundamental and still unmet challenge of precisely quantifying native lignin's structural features. Here, we developed a rapid elevated-temperature H-1-C-13 Heteronuclear S ...

Wiley-VCH Verlag GmbH2024

Computational Conceptual Design – Typological Exploration Of Spatial Truss Systems Through Optimization

Corentin Jean Dominique Fivet, Jonas Warmuth, Pierluigi D'Acunto

Exploring a wide range of relevant design options from the outset is crucial for every sound conceptual design process. Optimization techniques are generally employed to generate well-performing structural design options. However, focusing only on performa ...

2023

Structural topology exploration through policy-based generation of equilibrium representations

Corentin Jean Dominique Fivet, Ioannis Mirtsopoulos

Mainstream approaches to design spatial architectural forms that are structurally relevant consist either in adapting well-known and catalogued conventional types or in searching for close-to-optimum solutions of well-defined problems. Few means exist to e ...

2023

Alignment & stability challenges for FCC-ee

Léon Van Riesen-Haupt, Frank Zimmermann

In order to achieve its ultra-low vertical emittance (1 pm) and high luminosity (of up to 230 x 10(34) cm(-2) s(-1) per collision point), the e(+)e(-) Future Circular Collider (FCC-ee) requires a well-informed alignment strategy, powerful correction method ...

SPRINGER2023

De novo design of protein interactions with learned surface fingerprints

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

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

Anne-Florence Raphaëlle Bitbol, Umberto Lupo, 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

Cortical cell assemblies and their underlying connectivity: an in silico study

Michael Reimann, András Ecker, Sirio Bolaños Puchet, James Bryden Isbister, Daniela Egas Santander

Recent developments in experimental techniques have enabled simultaneous recordings from thousands of neurons, enabling the study of functional cell assemblies. However, determining the patterns of synaptic connectivity giving rise to these assemblies rema ...

2024

Impact of phylogeny on structural contact inference from protein sequence data

Anne-Florence Raphaëlle Bitbol, Umberto Lupo, Nicola Dietler

Local and global inference methods have been developed to infer structural contacts from multiple sequence alignments of homologous proteins. They rely on correlations in amino acid usage at contacting sites. Because homologous proteins share a common ance ...

ROYAL SOC2023

Prediction of post-stroke motor recovery benefits from measures of sub-acute widespread network damages

Dimitri Nestor Alice Van De Ville, Maria Giulia Preti, Elvira Pirondini, Cyprien Alban Félicien Rivier

Rivier et al. report that global measures of brain connectivity estimated by introducing virtual lesions in healthy structural connectomes significantly increase the accuracy of motor recovery prediction in stroke patients when added to focal and clinical ...

OXFORD UNIV PRESS2023

Circularity by stock in Sri Lanka: Economic necessity meets urban fabric renovation

Paolo Tombesi, Milinda Pathiraja

Persistent fiscal and political mismanagement, together with the financial pressures of the COVID-19 pandemic, have driven Sri Lanka into a social and economic crisis triggering a decrease in national foreign exchange reserves, an inability to purchase vit ...

FRONTIERS MEDIA SA2023

Revealing the Structure of Tryptophan in Microhydrated Complexes by Cold Ion Spectroscopy

Natalia Nagornova, Oleg Boyarkine, Andrei Zviagin, Ruslan Yamaletdinov, Manuel Dömer

The geometry of biomolecules isolated in the gas phaseusuallydiffers substantially from their native structures in aqueous solution,which are the only ones truly relevant to life science. To connectthe high resolution of cold ion spectroscopy that can be a ...

2023

Combining phylogeny and coevolution improves the inference of interaction partners among paralogous proteins

Anne-Florence Raphaëlle Bitbol

Author summaryWhen two protein families interact, their sequences feature statistical dependencies. First, interacting proteins tend to share a common evolutionary history. Second, maintaining structure and interactions through the course of evolution yiel ...

PUBLIC LIBRARY SCIENCE2023

Selecting Suitable Near-Native Lignins for Research

Jeremy Luterbacher

There are several methods to isolate near-native lignins, including milled-wood lignin, enzymatic lignin, cellulolytic enzyme lignin, and enzymatic mild-acidolysis lignin. Which one is the most representative of the native lignin? Herein, near-native ligni ...

Amer Chemical Soc2023

End-to-end kernel learning via generative random Fourier features

Fanghui Liu, Jie Yang

Random Fourier features (RFFs) provide a promising way for kernel learning in a spectral case. Current RFFs-based kernel learning methods usually work in a two-stage way. In the first-stage process, learn-ing an optimal feature map is often formulated as a ...

ELSEVIER SCI LTD2023

Protein language models trained on multiple sequence alignments learn phylogenetic relationships

Anne-Florence Raphaëlle Bitbol, Umberto Lupo, Damiano Sgarbossa

Self-supervised neural language models with attention have recently been applied to biological sequence data, advancing structure, function and mutational effect prediction. Some protein language models, including MSA Transformer and AlphaFold's EvoFormer, ...

Nature Portfolio2022

Vanadium complexes with N-heterocyclic vinylidene ligands

Rosario Scopelliti, Kay Severin, Farzaneh Fadaei Tirani, Laura Piveteau, Bastiaan Kooij, Zhaowen Dong, Paul Varava

The preparation and the structural characterization of vanadium complexes with terminal and bridging N-heterocyclic vinylidene ligands is reported. The synthesis of the complexes was enabled by utilization of diazoolefins as ligand precursors. Structural d ...

Royal Society of Chemistry2022

2.5 Hz sample rate time-domain near-infrared optical tomography based on SPAD-camera image tissue hemodynamics

Edoardo Charbon, Scott Anthony Lindner, Martin Wolf, Jingjing Jiang

Tim-domain near-infrared optical tomography (TD NIROT) techniques based on diffuse light were gaining performance over the last years. They are capable of imaging tissue at several centimeters depth and reveal clinically relevant information, such as tissu ...

OPTICAL SOC AMER2022