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

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Inverse Geometric Locomotion

Numerous tasks in robotics and character animation involve solving combinations of inverse kinematics and motion planning problems that require the precise design of pose sequences to achieve desired motion objectives. Accounting for the complex interplay ...

2025

Granular Avalanche Impact on a Structure using DEM and FEM

Malika Romane Jenni

Mountain regions face a variety of natural hazards that menace infrastructure and the people living in these areas. Human activity in these areas is intensifying, making hazard analysis and risk mitigation critical. Switzerland, with its densely populated ...

2025

Experimental Observation of the Motion of Ions in a Resonantly Driven Plasma Wakefield Accelerator

Ambrogio Fasoli, Ivo Furno, Patrick Blanchard, Yanis Andrebe, Riccardo Agnello, Christine Stollberg

We show experimentally that an effect of motion of ions, observed in a plasma-based accelerator, depends inversely on the plasma ion mass. The effect appears within a single wakefield event and manifests itself as a bunch tail, occurring only when sufficie ...

2025

One Code to Predict Them All: Universal Encoding for Inquiry Modeling

Valentine Marie Delevaux, Tanja Christina Käser Jacober, Jade Maï L Cock

Interactive simulations enhance science education and foster inquiry skills, but their open-ended nature can be cognitively overloading. While adaptive systems offer timely support, research on predicting conceptual understanding in these environments is l ...

Springer Science and Business Media Deutschland GmbH2025

Singularity with and without disorder at Affleck-Kennedy-Lieb-Tasaki points

Frédéric Mila

The Affleck-Kennedy-Lieb-Tasaki (AKLT) point of the bilinear-biquadratic spin-1 chain is a cornerstone example of a disorder point where short-range correlations become incommensurate, and correlation lengths and momenta are nonanalytic. While the presence ...

American Physical Society (APS)2025

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

Introduction and Overview: Chapter 1 of the Special Issue: on the Path to Tokamak Burning Plasma Operation

Ambrogio Fasoli

The International Tokamak Physics Activity (ITPA) has developed a comprehensive overview of the results of its coordinated R&D activities in fusion physics and diagnostics implemented during the past two decades with the aim of developing an improved physi ...

IOP Publishing Ltd2025

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

CementFF4: Formal atomic charge polarizable force field for cementitious systems – Bulk and surface

Tecla Bottinelli Montandon, Karen Scrivener, Paul Bowen, Manuel Cordova, Ziga Casar

A general-purpose formal charge polarizable force field for cementitious systems, CementFF4, is presented. The force field includes the following species: Ca, Si, O, H, Al, Zn, OH− and H2O. The force field is a significant extension of previous force field ...

Pergamon-Elsevier Science Ltd2025

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

GRADE: Generating Realistic and Dynamic Environments for robotics research with Isaac Sim

Chenghao Xu

Photorealistic synthetic data and novel rendering techniques significantly advanced computer vision research. However, datasets focused on computer vision applications cannot be easily applied to robotics because they typically lack physics-related informa ...

SAGE Publications2025

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

A Study on Quantum Graph Neural Networks Applied to Molecular Physics

Su Yeon Chang

This paper introduces a novel architecture for Quantum Graph Neural Networks, which is significantly different from previous approaches found in the literature. The proposed approach produces similar outcomes with respect to previous models but with fewer ...

IOP Publishing Ltd2025

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

Ursula Röthlisberger, Martin Peter Bircher, Justin Villard

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

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

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

Ariane Andrée Marie Delrocq, Sahand Jamal Rahi

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 Publishing Group2023