Publications associées à Cross-correlated relaxation measurements under adiabatic sweeps: determination of local order in proteins

Testing Theories of the Glass Transition with the Same Liquid but Many Kinetic Rules

Matthieu Wyart, Carolina Brito Carvalho dos Santos

We study the glass transition by exploring a broad class of kinetic rules that can significantly modify the normal dynamics of supercooled liquids while maintaining thermal equilibrium. Beyond the usual dynamics of liquids, this class includes dynamics in ...

Amer Physical 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

Frustrated magnets in the limit of infinite dimensions: Dynamics and disorder-free glass transition

Achille Mauri

We study the statistical mechanics and the equilibrium dynamics of a system of classical Heisenberg spins with frustrated interactions on a d -dimensional simple hypercubic lattice, in the limit of infinite dimensionality d -> infinity . In the analysis we ...

Amer Physical Soc2024

Microsecond Time-Resolved Cryo-Electron Microscopy

Oliver Florian Harder

Recently, single-particle cryo-electron microscopy emerged as a technique capable of determining protein structures at near-atomic resolution and resolving protein dynamics with a temporal resolution ranging from second to milliseconds. This thesis describ ...

EPFL2024

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

Microsecond time-resolved cryo-electron microscopy

Ulrich Lorenz

Microsecond time-resolved cryo-electron microscopy has emerged as a novel approach for directly observing protein dynamics. By providing microsecond temporal and near-atomic spatial resolution, it has the potential to elucidate a wide range of dynamics tha ...

2024

Predicting protein interactions using geometric deep learning on protein surfaces

Freyr Sverrisson

In the domain of computational structural biology, predicting protein interactions based on molecular structure remains a pivotal challenge. This thesis delves into this challenge through a series of interconnected studies. The first chapter introduces th ...

EPFL2024

Parallel flows as a key component to interpret Super-X divertor experiments

Basil Duval, Holger Reimerdes, Joaquim Loizu Cisquella, Christian Gabriel Theiler, Curdin Tobias Wüthrich, Olivier Claude Martin Février, Garance Hélène Salomé Durr-Legoupil-Nicoud, Davide Galassi, Lorenzo Martinelli, Sophie Danielle Angelica Gorno, Claudia Colandrea, Guang-Yu Sun, Luke Simons, Artur Perek

The Super-X Divertor (SXD) is an alternative divertor configuration leveraging total flux expansion at the Outer Strike Point (OSP). While the extended 2-Point Model (2PM) predicts facilitated detachment access and control in the SXD configuration, these a ...

IOP Publishing Ltd2024

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

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

Euclid: The search for primordial features

Georges Meylan, Frédéric Courbin, Fabio Finelli, Richard Massey, Marcello Farina, Yiming Li, Yi Wang

Primordial features, in particular oscillatory signals, imprinted in the primordial power spectrum of density perturbations represent a clear window of opportunity for detecting new physics at high-energy scales. Future spectroscopic and photometric measur ...

Edp Sciences S A2024

Climbing into their Skin to Understand Contextual Protein-Protein Associations and Localizations: Functional Investigations in Transgenic Live Model Organisms

Yimon Aye

Borrowing some quotes from Harper Lee's novel "To Kill A Mockingbird" to help frame our manuscript, we discuss methods to profile local proteomes. We initially focus on chemical biology regimens that function in live organisms and use reactive biotin speci ...

Wiley-V C H Verlag Gmbh2024

Dynamical Low-Rank Approximation for Stochastic Differential Equations

Fabio Nobile, Yoshihito Kazashi, Fabio Zoccolan

In this paper, we set the mathematical foundations of the Dynamical Low-Rank Approximation (DLRA) method for stochastic differential equations (SDEs). DLRA aims at approximating the solution as a linear combination of a small number of basis vectors with r ...

American Mathematical Society (AMS)2024

Fast viral dynamics revealed by microsecond time-resolved cryo-EM

Marcel Drabbels, Ulrich Lorenz, Oliver Florian Harder, Sarah Victoria Barrass

Observing proteins as they perform their tasks has largely remained elusive, which has left our understanding of protein function fundamentally incom- plete. To enable such observations, we have recently proposed a technique that improves the time resoluti ...

Nature Research2023

Density estimation in RKHS with application to Korobov spaces in high dimensions

Fabio Nobile, Yoshihito Kazashi

A kernel method for estimating a probability density function from an independent and identically distributed sample drawn from such density is presented. Our estimator is a linear combination of kernel functions, the coefficients of which are determined b ...

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

Protein target highlights in CASP15: Analysis of models by structure providers

Bruno Lemaitre, Luciano Andres Abriata, Kuan-Lin Wu, Samuel Rommelaere, Han Xiao

We present an in-depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the su ...

WILEY2023

A multi-reservoir extruder for time-resolved serial protein crystallography and compound screening at X-ray free-electron lasers

Camila Bacellar Cases Da Silveira, Christoph Bostedt

Serial crystallography at X-ray free-electron lasers (XFELs) permits the determination of radiation-damage free static as well as time-resolved protein structures at room temperature. Efficient sample delivery is a key factor for such experiments. Here, we ...

Nature Portfolio2023

Hierarchy of the Components in Spray-Dried, Protein-Excipient Particles Using DNP-Enhanced NMR Spectroscopy

David Lyndon Emsley, Baptiste Busi, Pierrick Berruyer, Andrea Bertarello

Protein-based drugs are becoming increasingly important, but there are challenges associated with their formulation (for example, formulating stable inhalable aerosols while maintaining the proper long-term stability of the protein). Determining the morpho ...

Amer Chemical Soc2023

Non-intrusive data-driven reduced-order modeling for time-dependent parametrized problems

Jan Sickmann Hesthaven, Junming Duan

Reduced-order models are indispensable for multi-query or real-time problems. However, there are still many challenges to constructing efficient ROMs for time-dependent parametrized problems. Using a linear reduced space is inefficient for time-dependent n ...

Academic Press Inc Elsevier Science2023