Publication

Phonon Lifetimes Throughout the Brillouin Zone at Elevated Temperatures from Experiment and ab initio

Publications associées (31)

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

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

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

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

Nanomechanical Modeling of the Bending Response of Silicon Nanowires

Yusuf Leblebici, Zuhal Tasdemir, Mustafa Yilmaz, Mohammad Nasr Esfahani

Understanding the mechanical behavior of silicon nanowiresis essentialfor the implementation of advanced nanoscale devices. Although bendingtests are predominantly used for this purpose, their findings shouldbe properly interpreted through modeling. Variou ...

AMER CHEMICAL SOC2023

Imaging and controlling coherent phonon wave packets in single graphene nanoribbons

Klaus Kern, Yang Luo

The motion of atoms is at the heart of any chemical or structural transformation in molecules and materials. Upon activation of this motion by an external source, several (usually many) vibrational modes can be coherently coupled, thus facilitating the che ...

Nature Portfolio2023

De novo designed proteins: a study in engineering novel folds and functions

Alexandra Krina Van Hall-Beauvais

Proteins control nearly every facet of life on a molecular level. Proteins are formed from linear strings of amino acids, which fold into three-dimensional structures that can enact functions. Evolution has created highly efficient proteins in diverse fold ...

EPFL2023

Many-body screening effects in liquid water

Alfredo Pasquarello, Igor Reshetnyak, Arnaud Guillaume Lorin

The screening arising from many-body excitations is a crucial quantity for describing absorption and inelastic X-ray scattering (IXS) of materials. Similarly, the electron screening plays a critical role in state-of-the-art approaches for determining the f ...

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

Optical manipulation of plasmonic nanoparticles: Applications in surface chemistry and nano-optics

Jeonghyeon Kim

Optical tweezers are devices that can manipulate nano- and microparticles using a laser. The principle of optical tweezers is to apply a force to an object using the momentum of light. This force is very small, but it is sufficient to move things in the mi ...

EPFL2023

Confirming the high pressure phase diagram of the Shastry-Sutherland model

Henrik Moodysson Rønnow, Martin Mansson

A Muon Spin Rotation (mu+SR) study was conducted to investigate the magnetic properties of SrCu2(BO3)(2) (SCBO) as a function of temperature/pressure. Measurements in zero field and transverse field confirm the absence of long range magnetic order at high ...

IOP PUBLISHING LTD2023

Computational Studies for the Design of Metalloenzyme Mimics

Guido Frisari

At present, there is no general standard automated method for engineering metalloenzymes, industrially-relevant systems able to catalyze environmentally friendly reactions. One of the most studied natural metalloenzymes is the second isoform of human carbo ...

EPFL2023

Spin wave spectra of single crystal CoPS3

Henrik Moodysson Rønnow, Mechthild Enderle, Luc Testa, Ursula Bengaard Hansen

The spin waves in single crystals of the layered van der Waals antiferromagnet CoPS3 have been measured using inelastic neutron scattering. The data show four distinct spin wave branches with large (>14 meV) energy gaps at the Brillouin zone center indicat ...

2023

Wigner Gaussian dynamics: Simulating the anharmonic and quantum ionic motion

Lorenzo Monacelli

The atomic motion controls important properties of materials, such as thermal transport, phase transitions, and vibrational spectra. However, simulating the ionic dynamics is exceptionally challenging when quantum fluctuations are relevant (e.g., at low te ...

AMER PHYSICAL SOC2023

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

Exploring the interplay of molecular pattern and valency for selective interactions at the bio-interface

Kaltrina Paloja

Cell-cell communication is fundamental for immune balance. Multivalent interactions of surface receptors at immune interfaces drive specific communication, with stimulatory and inhibitory signals guiding the immune outcome. Notably, the valency, affinity, ...

EPFL2023

Modeling non-covalent interactions in condensed phase

Veronika Juraskova

The modeling of non-covalent interactions, solvation effects, and chemical reactions in complex molecular environment is a challenging task. Current state-of-the-art approaches often rely on static computations using implicit solvent models and harmonic ap ...

EPFL2022

Real space and reciprocal space investigations of the spin dynamics in skyrmion-hosting materials

Le Yu

Magnetic skyrmions are whirl-like spin configurations with particle-like properties protected by non-trivial topology. Due to their unique spin structures and dynamical properties, they have attracted tremendous interests over the past decade, from fundame ...

EPFL2022

Effect of Co-Substitution on Hydrogen Absorption and Desorption Reactions of YMgNi4-Based Alloys

Loris Giovanni Lombardo, Andreas Züttel, Wen Luo, Heena Yang

YMgNi4-based alloys exhibit reversible hydrogen absorption and desorption reactions at near room temperature. Here, we report that Co-substituted YMgNi4-based alloys exhibited higher hydrogen contents and lower hydrogen absorption and desorption reaction p ...

AMER CHEMICAL SOC2022

Assessing the persistence of chalcogen bonds in solution with neural network potentials

Anne-Clémence Corminboeuf, Veronika Juraskova, Rubén Laplaza Solanas, Frédéric Célerse

Non-covalent bonding patterns are commonly harvested as a design principle in the field of catalysis, supramolecular chemistry, and functional materials to name a few. Yet, their computational description generally neglects finite temperature and environme ...

2022