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

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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, Christian Gabriel Theiler, Joaquim Loizu Cisquella, Artur Perek, Guang-Yu Sun, Luke Simons, Olivier Claude Martin Février, Garance Hélène Salomé Durr-Legoupil-Nicoud, Davide Galassi

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

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

Matthieu Wyart, Carolina Brito Carvalho dos Santos

Amer Physical Soc2024

From Sequence to Dynamics to Function: Computational Design of Allostery and Ligand Selectivity in G-Protein Coupled Receptors

Mahdi Hijazi

EPFL2024

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

Zhidian Zhang

EPFL2024

Microsecond time-resolved cryo-electron microscopy

Ulrich Lorenz

2024