Publications associées à Statistical Study of the Unfolding of Multimodular Proteins and their Energy Landscape by Atomic Force Microscopy

Publications associées (31)

A phase transition between positional and semantic learning in a solvable model of dot-product attention

Lenka Zdeborová, Florent Gérard Krzakala, Hugo Chao Cui, Freya Behrens

Many empirical studies have provided evidence for the emergence of algorithmic mechanisms (abilities) in the learning of language models, that lead to qualitative improvements in the model capabilities. Yet, a theoretical characterization of how such mecha ...

2025

Probing the latent hierarchical structure of data via diffusion models

Noam Itzhak Levi, Alessandro Favero, Antonio Sclocchi

High-dimensional data must be highly structured to be learnable. Although the compositional and hierarchical nature of data is often put forward to explain learnability, quantitative measurements establishing these properties are scarce. Likewise, accessin ...

2025

Magnetism of Single Surface Adsorbed Atoms Studied with Radio-Frequency STM

Clément Marie Soulard

This thesis investigates the magnetic properties of single atoms and molecules adsorbed on thin magnesium oxide decoupling layers, grown on a silver single crystal. To address these systems experimentally, we use a low temperature scanning tunneling micros ...

EPFL2024

Global existence for perturbations of the 2D stochastic Navier-Stokes equations with space-time white noise

Martin Hairer

We prove global in time well-posedness for perturbations of the 2D stochastic Navier-Stokes equations partial derivative( t)u + u center dot del u = Delta u - del p + sigma + xi, u(0, center dot ) = u(0),div (u) = 0, driven by additive space-time white noi ...

Springernature2024

Ion Spectroscopy Reveals Structural Difference for Proteins Microhydrated by Retention and Condensation of Water

Oleg Boyarkine, Andrei Zviagin

Protein ubiquitin in its +7 charge state microhydrated by 5 and 10 water molecules has been interrogated in the gas phase by cold ion UV/IR spectroscopy. The complexes were formed either by condensing water onto the unfolded bare proteins in a temperature- ...

Amer Chemical Soc2024

Spectral Estimators for High-Dimensional Matrix Inference

Farzad Pourkamali

A key challenge across many disciplines is to extract meaningful information from data which is often obscured by noise. These datasets are typically represented as large matrices. Given the current trend of ever-increasing data volumes, with datasets grow ...

EPFL2024

A 0.14-nJ/b 200-Mb/s 2.7-3.5-GHz Quasi-Balanced FSK Transceiver With PLL-Based Modulation and Sideband Energy Detection

Cong Ding

This paper describes a balanced frequency shift keying (FSK) modulation, namely quasi-balanced FSK (QB-FSK), for energy-efficient high-data-rate communication. Not suffering from data-pattern dependency, the proposed modulation method enables frequency mod ...

2024

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

Non-contact sensing for anomaly detection in wind turbine blades: A focus-SVDD with complex-valued auto-encoder approach

Olga Fink, Gaëtan Michel Frusque

The occurrence of manufacturing defects in wind turbine blade (WTB) production can result in significant increases in operation and maintenance costs of WTBs, reduce capacity factors of wind farms, and occasionally lead to severe and disastrous consequence ...

2024

Label-Free Techniques for Probing Biomolecular Condensates

Akhil Sai Naidu, Aleksandra Radenovic, Wayne Yang Wen Wei, Helena Miljkovic, Khalid Ashraf Mohie Ibrahim

Biomolecular condensates play important roles in a wide array of fundamental biological processes, such as cellular compartmentalization, cellular regulation, and other biochemical reactions. Since their discovery and first observations, an extensive and e ...

Amer Chemical Soc2024

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

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

Exploiting the Signal-Leak Bias in Diffusion Models

Athanasios Fitsios, Sabine Süsstrunk, Radhakrishna Achanta, Mahmut Sami Arpa, Martin Nicolas Everaert

There is a bias in the inference pipeline of most diffusion models. This bias arises from a signal leak whose distribution deviates from the noise distribution, creating a discrepancy between training and inference processes. We demonstrate that this signa ...

2024

Controlling crystal cleavage in focused ion beam shaped specimens for surface spectroscopy

Philip Johannes Walter Moll, Matthias Carsten Putzke

Our understanding of quantum materials is commonly based on precise determinations of their electronic spectrum by spectroscopic means, most notably angle-resolved photoemission spectroscopy (ARPES) and scanning tunneling microscopy. Both require atomicall ...

Aip Publishing2024

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

Mechanisms and functions of protein S-acylation

Françoise Gisou van der Goot Grunberg, Laurence Gouzi Abrami, Francisco De Magalhães Sarmento Ribeiro De Mesquita

Over the past two decades, protein S-acylation (often referred to as S-palmitoylation) has emerged as an important regulator of vital signalling pathways. S-Acylation is a reversible post-translational modification that involves the attachment of a fatty a ...

Nature Portfolio2024

Green hydrogen production using Shewanella oneidensis MR-1 bioanode and cuprous oxide-based photocathode

Michele Morgante

In recent years, many efforts have been made to find alternative renewable energy sources that can ideally replace the use of fossil fuels in all aspects. One of the new emerging energy technologies is the bioelectrochemical system, of which two types are ...

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

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

Random matrix methods for high-dimensional machine learning models

Antoine Philippe Michel Bodin

In the rapidly evolving landscape of machine learning research, neural networks stand out with their ever-expanding number of parameters and reliance on increasingly large datasets. The financial cost and computational resources required for the training p ...

EPFL2024