Publication

Anisotropic Local Motions and Location of Amide Protons in Proteins

Publications associées (31)

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

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

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

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

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

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

Two-Carbon Ring Expansion of Cyclobutanols to Cyclohexenones Enabled by Indole Radical Cation Intermediate: Development and Application to a Total Synthesis of Uleine

Qian Wang, Jieping Zhu, Alexandre Julien Florent Leclair

A single-electron transfer (SET) oxidation of indole or benzo[b]thiophene to a radical cation reverses the intrinsic polarity of these pi-excessive bicyclic heteroarenes. Here we report an oxidative two-carbon homologation of cyclobutanols to cyclohexenone ...

AMER CHEMICAL SOC2022

Targeting molecular surfaces to engineer novel protein-based immunogens and inhibitors

Sarah Wehrle

Proteins are the basic building blocks necessary for the operation and regulation of virtually all functions in living organisms. Over millions of years, evolution has created a vast repertoire of proteins finely tuned to execute their biological functions ...

EPFL2022

Evidence of a transient phase during the hydrolysis of calcium-deficient hydroxyapatite

Jacques Lemaître

In the present paper, calcium deficient hydroxyapatite (Ca-def OHAP) has been examined in a transmission electron microscope. During the observation, the initial Ca-def OHAP was seen to transform first into a transient intermediate phase, then to a final, ...

WALTER DE GRUYTER GMBH2022

Nonlinear Inverse Problems in Quantitative Phase Imaging

Thanh-An Michel Pham

The topic of this thesis is the development of new algorithmic reconstruction methods for quantitative phase imaging (QPI). In the past decade, advanced QPI has emerged as a valuable tool to study label-free biological samples and uncover their 3D structur ...

EPFL2022

A generic framework for hierarchical de novo protein design

Bruno Emanuel Ferreira De Sousa Correia, Zander Harteveld, Jaume Bonet Martinez, Fabian Sesterhenn, Che Yang, Stéphane Rosset

De novo protein design enables the exploration of novel sequences and structures absent from the natural protein universe. De novo design also stands as a stringent test for our understanding of the underlying physical principles of protein folding and may ...

National Academy of Sciences2022

Non-destructive Prediction of the Buckling Load of Cylindrical Shells

Emilio José Lozano Vazquez

The current research focuses on the prediction of the maximum axial compression load a cylindrical shell is able to bear. This maximum axial compression load is the value at which a cylindrical shell loses stability and abruptly buckles. After the buckling ...

EPFL2022

Phase Reconstruction of Low-Energy Electron Holograms of Individual Proteins

Klaus Kern, Stephan Rauschenbach, Sven Alexander Szilagyi, Hannah Julia Ochner

Low-energy electron holography (LEEH) is one of the few techniques capable of imaging large and complex three-dimensional molecules, such as proteins, on the single molecule level at subnanometer resolution. During the imaging process, the structural infor ...

AMER CHEMICAL SOC2022

Visualization, Interactive Handling and Simulation of Molecules in Commodity Augmented Reality in Web Browsers Using moleculARweb's Virtual Modeling Kits

Matteo Dal Peraro, Luciano Andres Abriata, Lucien Fabrice Krapp, Fabio Jose Cortes Rodriguez

moleculARweb (https://molecularweb.epfl.ch) began as a website for education and outreach in chemistry and structural biology through augmented reality (AR) content that runs in the web browsers of regular devices like smartphones, tablets, and computers. ...

SWISS CHEMICAL SOC2022

Impact of dipole-dipole interactions on motility-induced phase separation

Ignacio Pagonabarraga Mora, Elena Sesé Sansa

We present a hydrodynamic theory for systems of dipolar active Brownian particles which, in the regime of weak dipolar coupling, predicts the onset of motility-induced phase separation (MIPS), consistent with Brownian dynamics (BD) simulations. The hydrody ...

ROYAL SOC CHEMISTRY2022

Correlations from structure and phylogeny combine constructively in the inference of protein partners from sequences

Nicola Dietler, Anne-Florence Raphaëlle Bitbol, Andonis Samuel Rene Gerardos

Inferring protein-protein interactions from sequences is an important task in computational biology. Recent methods based on Direct Coupling Analysis (DCA) or Mutual Information (MI) allow to find interaction partners among paralogs of two protein families ...

Public Library Science2022

Fast end-to-end learning on protein surfaces

Bruno Emanuel Ferreira De Sousa Correia, Freyr Sverrisson

Proteins' biological functions are defined by the geometric and chemical structure of their 3D molecular surfaces. Recent works have shown that geometric deep learning can be used on mesh-based representations of proteins to identify potential functional s ...

IEEE COMPUTER SOC2021

Cyclic thermomechanical behaviour of pile-soil interface and design methods for energy pile foundations

Elena Ravera

Energy piles are shallow geothermal systems integrated into structures already required for structural functions of civil works that provide both geothermal energy supply and structural support to the built environments. This research work is driven by the ...

EPFL2021

Structural design methodology in Integrally-Attached Timber Plate structures

Aryan Rezaei Rad, Petras Vestartas

The immediate application of research discoveries requires a global and exact understanding of the structure under consideration. To gain insight into the complex behavior of structures, numerical simulations are carried out in parallel to physical experim ...

Routledge, Taylor & Francis Group2021

Structure-Property Relationships in Complex Materials by Combining Supervised and Unsupervised Machine Learning

Benjamin Aaron Helfrecht

The work presented in this thesis combines supervised and unsupervised machine learning to examine structure-property relationships in databases of materials. While either supervised learning or unsupervised learning alone can be a powerful tool for assess ...

EPFL2021

Optical diffraction tomography from single-molecule localization microscopy

Michaël Unser, Thanh-An Michel Pham, Ferréol Arnaud Marie Soulez, Emmanuel Emilien Louis Soubies

Single-molecule localization microscopy (SMLM) is a powerful method for the imaging of cellular structures. This modality delivers nanoscale resolution by sequentially activating a subset of fluorescent molecules and by extracting their super-resolved posi ...

2021

Reviewing Challenges of Predicting Protein Melting Temperature Change Upon Mutation Through the Full Analysis of a Highly Detailed Dataset with High-Resolution Structures

Luciano Andres Abriata

Predicting the effects of mutations on protein stability is a key problem in fundamental and applied biology, still unsolved even for the relatively simple case of small, soluble, globular, monomeric, two-state-folder proteins. Many articles discuss the li ...

2021