Publications associées à Phage display libraries of differently sized bicyclic peptides

Palladium-based supramolecular assemblies: from complex structures to water-soluble anion-receptors

The combination of palladium salts and bipyridyl ligands can lead to the formation of a large variety of coordination complexes, with different shapes and sizes, displaying a very versatile host-guest chemistry. Increasing their structural complexity remai ...

EPFL2024

Investigating the intra-molecular and inter-molecular effects of post-translational modifications on intrinsically disordered protein regions and structured protein regions

Zhidian Zhang

Post-translational modifications (PTMs) play a pivotal role in regulating protein structure, interaction, and function. Aberrant PTM patterns are associated with diseases. Moreover, individual PTMs have a complex interaction with each other, known as PTM c ...

EPFL2024

Development of tools and methods for protein identification: From single molecules to in vivo applications

Salome Riccarda Püntener

As the fundamental machinery orchestrating cellular functions, proteins influence the state of every cell profoundly. As cells exhibit significant variations from one to another, analyzing the proteome on a single-cell level is imperative to unravel their ...

EPFL2024

Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations

Felix Naef, Pierre Vandergheynst, Cédric Gobet, Mohan Vamsi Nallapareddy, Francesco Craighero

Translation elongation plays an important role in regulating protein concentrations in the cell, and dysregulation of this process has been linked to several human diseases. In this study, we use data from ribo-seq experiments to model ribosome densities, ...

PMLR2024

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

The multivariate Serre conjecture ring

Luc Guyot

It is well-known that for any integral domain R, the Serre conjecture ring R(X), i.e., the localization of the univariate polynomial ring R[X] at monic polynomials, is a Bezout domain of Krull dimension

Academic Press Inc Elsevier Science2023

Scalable angular spectrum propagation

Felix Wechsler

Coherent field propagation is an essential computational tool in optics with applications ranging from computational optics and optical design to iterative field reconstructions. An improvement in the computational speed of current propagation methods is t ...

Optica Publishing Group2023

GLOBALLY plus -REGULAR VARIETIES AND THE MINIMAL MODEL PROGRAM FOR THREEFOLDS IN MIXED CHARACTERISTIC

Zsolt Patakfalvi, Joseph Allen Waldron

We establish the Minimal Model Program for arithmetic threefolds whose residue characteristics are greater than five. In doing this, we generalize the theory of global F-regularity to mixed characteristic and identify certain stable sections of adjoint lin ...

SPRINGER HEIDELBERG2023

Predicting Transformation Products during Aqueous Oxidation Processes: Current State and Outlook

Urs von Gunten

Water quality and its impacts on human and ecosystem health presents tremendous global challenges. While oxidative water treatment can solve many of these problems related to hygiene and micropollutants, identifying and predicting transformation products f ...

2023

Impact of phylogeny on structural contact inference from protein sequence data

Nicola Dietler, Umberto Lupo, Anne-Florence Raphaëlle Bitbol

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

Spatiotemporal Metabolic Liver Zonation and Consequences on Pathophysiology

Felix Naef, Tomaz Martini

Hepatocytes are the main workers in the hepatic factory, managing metabolism of nutrients and xenobiotics, production and recycling of proteins, and glucose and lipid homeostasis. Division of labor between hepatocytes is critical to coordinate complex comp ...

ANNUAL REVIEWS2023

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

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

Liquid metal infiltration of silicon based alloys into porous carbonaceous materials. Part I: Modelling of channel filling and reaction phase formation

Ludger Weber, Alberto Ortona, Manoj Kondibhau Naikade

A relation for an adequate pore fraction needed to obtain residual Si and C free composites via reactive Si-X alloy infiltration is presented. The volume ratio of SiC and carbonaceous phase, the composition of the infiltrating liquid and the apparent densi ...

ELSEVIER SCI LTD2022

Anchorage of shear reinforcement in beams and slabs

Aurelio Muttoni, Miguel Fernández Ruiz, Frédéric Monney, Qianhui Yu

Anchorage of shear reinforcement, such as links or stirrups, can be performed by providing hooks, bends or heads at their ends, by welding transverse reinforcement or by closing open stirrups with pins. Hooks and bends, also used to enhance the anchorage o ...

2022

Latent Mechanisms of Polarization Switching from In Situ Electron Microscopy Observations

Vasiliki Tileli, Reinis Ignatans

In situ scanning transmission electron microscopy enables observation of the domain dynamics in ferroelectric materials as a function of externally applied bias and temperature. The resultant data sets contain a wealth of information on polarization switch ...

WILEY-V C H VERLAG GMBH2022

Integrated Model for Comprehensive Digital Education Platforms

Denis Gillet, Isabelle Barbara Marie-Hélène Cardia, Kim Lan Phan Hoang, Maria Jesus Rodriguez Triana, Juan Carlos Farah

The trend towards generalized blended and active learning approaches in engineering education is redefining the requirements and the deployment schemes for digital education platforms. This paper presents a quadriptych techno- pedagogical model highlightin ...

IEEE2022

Nanobridge Stencil Enabling High Resolution Arbitrarily Shaped Metallic Thin Films on Various Substrates

Giovanni Boero, Jürgen Brugger, Yi-Chiang Sun

Stencil lithography (SL), which uses a perforated membrane as a reusable shadow mask to locally add material patterns on substrates provides a simple but versatile approach for the fabrication of functional devices on a large variety of substrate materials ...

Wiley2022

Protein language models trained on multiple sequence alignments learn phylogenetic relationships

Umberto Lupo, Anne-Florence Raphaëlle Bitbol, 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

Towards automating de novo protein design for novel functionalities: controlling protein folds and protein-protein interactions

Zander Harteveld

The sheer size of the protein sequence space is massive: a protein of 100 residues can have 20^100 possible sequence combinations; and knowing that this exceeds the number of atoms in the universe, the chance of randomly discovering a stable new sequence w ...

EPFL2022