Publications associées à Interfacial Water Many-Body Effects Drive Structural Dynamics and Allosteric Interactions in SARS-CoV-2 Main Protease Dimerization Interface

Stability of a liquid layer draining around a horizontal cylinder: Interplay of capillary and gravity forces

François Gallaire, Shahab Eghbali, Simeon Vladimirov Djambov

We study the drainage of a viscous liquid film coating the outside of a solid horizontal cylinder, where gravity acts vertically. We focus on the limit of large Ohnesorge numbers Oh, where inertia is negligible compared to viscous effects. We first study t ...

Amer Physical Soc2024

Experimental and ab initio derivation of interface stress in nanomultilayered coatings: Application to immiscible Cu/W system with variable in-plane stress

Claudia Cancellieri, Pandula Manura Liyanage, Giacomo Lorenzin

Interface stress is a fundamental descriptor for interphase boundaries and is defined in strict relation to the interface energy. In nanomultilayers with their intrinsically high interface density, the functional properties are dictated by the interface st ...

Elsevier2024

Secure Interface Design Leveraging Hardware/Software Support

Atri Bhattacharyya

Computer systems rely heavily on abstraction to manage the exponential growth of complexity across hardware and software. Due to practical considerations of compatibility between components of these complex systems across generations, developers have favou ...

EPFL2024

The Current State of the OBI DICT Project: A Bilingual e-Dictionary of Oracle-Bone Inscriptions with AI Image Recognition

This article reports on the current state of the OBI DICT project, a bilingual e-dictionary of oracle-bone inscriptions (OBI), incorporating artificial intelligence (AI) image recognition technology. It first provides a brief overview of the development of ...

Buro Van Die Wat2024

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

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

A Reduced Order Model for Domain Decompositions with Non-conforming Interfaces

Alfio Quarteroni, Andrea Manzoni

In this paper, we propose a reduced-order modeling strategy for two-way Dirichlet-Neumann parametric coupled problems solved with domain-decomposition (DD) sub-structuring methods. We split the original coupled differential problem into two sub-problems wi ...

Springer/Plenum Publishers2024

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

Machine Learning for Screening Small Molecules as Passivation Materials for Enhanced Perovskite Solar Cells

Mohammad Khaja Nazeeruddin, Bo Chen, Bin Ding, Chaohui Li, Yan Liu, Xianfu Zhang

Utilization of small molecules as passivation materials for perovskite solar cells (PSCs) has gained significant attention recently, with hundreds of small molecules demonstrating passivation effects. In this study, a high-accuracy machine learning model i ...

Wiley-VCH Verlag Gmbh2024

Structure and dynamics of liquid water from ab initio simulations: adding Minnesota density functionals to Jacob's ladder

Ursula Röthlisberger, Justin Villard, Martin Peter Bircher

The accurate representation of the structural and dynamical properties of water is essential for simulating the unique behavior of this ubiquitous solvent. Here we assess the current status of describing liquid water using ab initio molecular dynamics, wit ...

Royal Soc Chemistry2024

Wetting Dynamics Beneath an Impacting Droplet

Ramin Kaviani

Many natural and industrial processes involve fluid flow at a three phase interface between liquid, solid and gas. When the liquid is forced to move rapidly over the solid surface, the physical mechanisms governing contact line motions are multi-phase and ...

EPFL2023

Columnlike free-interface flows: symmetry breaking and linear instability

Shahab Eghbali

This thesis is dedicated to the analysis of a subclass of interfacial flows, columnlike free-interface flows, from two view angles: (i) the symmetry breaking under geometry-induced or external forces, (ii) their stability against infinitesimal disturbances ...

EPFL2023

Universal machine learning for the response of atomistic systems to external fields

Yaolong Zhang

Machine learned interatomic interaction potentials have enabled efficient and accurate molecular simulations of closed systems. However, external fields, which can greatly change the chemical structure and/or reactivity, have been seldom included in curren ...

Nature Portfolio2023

Systems and methods for de novo design of protein interactions with learned surface fingerprints

Anthony Marchand, Zander Harteveld, Pablo Gainza Cirauqui, Freyr Sverrisson, Andreas Scheck, Sarah Wehrle, Alexandra Krina Van Hall-Beauvais, Michael Bronstein

The present application relates to a computer-implemented systems and methods for protein interaction design using surface fingerprints. The method comprises predicting at least one target interface site with high binding propensity, wherein, optionally, t ...

2023

impresso Text Reuse at Scale. An interface for the exploration of text reuse data in semantically enriched historical newspapers

Maud Ehrmann, Matteo Romanello

Text Reuse reveals meaningful reiterations of text in large corpora. Humanities researchers use text reuse to study, e.g., the posterior reception of influential texts or to reveal evolving publication practices of historical media. This research is often ...

2023

Automated neuron tracking inside moving and deforming C. elegans using deep learning and targeted augmentation

Sahand Jamal Rahi, Kseniia Korchagina

Reading out neuronal activity from three-dimensional (3D) functional imaging requires segmenting and tracking individual neurons. This is challenging in behaving animals if the brain moves and deforms. The traditional approach is to train a convolutional n ...

Nature Portfolio2023

Structural Basis of the Allosteric Inhibition of Human ABCG2 by Nanobodies

Henning Paul-Julius Stahlberg, Dongchun Ni

ABCG2 is an ATP-binding cassette transporter that exports a wide range of xenobiotic compounds and has been recognized as a contributing factor for multidrug resistance in cancer cells. Substrate and inhibitor interactions with ABCG2 have been extensively ...

Academic Press Ltd- Elsevier Science Ltd2023

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

Automated music composition and generation system and method

Florian François Colombo

An automated music composition and generation system for automatically harmonizing digital pieces of music using an automated music composition and generation engine for multi-voice music harmonization, including a system-user interface configured to input ...

2023

Advancing Computational Chemistry with Stochastic and Artificial Intelligence Approaches

Justin Villard

Computational chemistry aims to simulate reactions and molecular properties at the atomic scale, advancing the design of novel compounds and materials with economic, environmental, and societal implications. However, the field relies on approximate quantum ...

EPFL2023