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Multiscale simulations of protein dynamics

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Publications associées (33)

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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

Atomic investigations of dislocation phenomena in HCP magnesium and BCC high entropy alloys

Xin Liu

Dislocation phenomena in crystal materials are fundamental to understanding mechanical behaviors such as plasticity and strengthening. This study investigates the atomistic mechanisms of dislocation phenomena in hexagonal close-packed (HCP) magnesium (Mg) ...

EPFL2024

Augmented Memory: Sample-Efficient Generative Molecular Design with Reinforcement Learning

Philippe Schwaller, Jeff Guo

Sample efficiency is a fundamental challenge in de novo molecular design. Ideally, molecular generative models should learn to satisfy a desired objective under minimal calls to oracles (computational property predictors). This problem becomes more apparen ...

Amer Chemical Soc2024

Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations

Mohan Vamsi Nallapareddy, Pierre Vandergheynst, Felix Naef, Cédric Gobet, Francesco Craighero

Translation elongation plays an important role in regulating protein concentrations in the cell, and dysregulation of this process has been linked to several human diseases. In this study, we use data from ribo-seq experiments to model ribosome densities, ...

PMLR2024

Recording physiological history of cells with chemical labeling

Kai Johnsson, Julien Hiblot

Recordings of the physiological history of cells provide insights into biological processes, yet obtaining such recordings is a challenge. To address this, we introduce a method to record transient cellular events for later analysis. We designed proteins t ...

American Association for the Advancement of Science2024

The CRL5-SPSB3 ubiquitin ligase targets nuclear cGAS for degradation

Pauline Ambre Melenec, Andrea Ablasser, Jonathan Jean-Pierre Ricci, Baptiste Claude André Guey, Chong Liu, Pengbiao Xu, Ying Liu, Lingyun Li

Cyclic GMP-AMP synthase (cGAS) senses aberrant DNA during infection, cancer and inflammatory disease, and initiates potent innate immune responses through the synthesis of 2 ' 3 '-cyclic GMP-AMP (cGAMP)1-7. The indiscriminate activity of cGAS towards DNA d ...

Nature Portfolio2024

Computational Inverse Design of Shape Morphing Structures

Yingying Ren

Shape-morphing structures can transform between multiple geometric configurations, enabling a wide range of applications in architecture, robotics, personalizable medical devices, emergency shelters, and space technology. This thesis presents computational ...

EPFL2024

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

A diversity-driven discovery of potential nanoporous materials for energy-related applications

Sauradeep Majumdar

The design and discovery of potential novel materials is critical for the advancement of climate change mitigation technologies. In this respect, metal-organic frameworks (MOFs) have received considerable attention over the last two decades. The combinatio ...

EPFL2024

Structure-function analysis of the cyclic β-1,2-glucan synthase from Agrobacterium tumefaciens

Henning Paul-Julius Stahlberg, Dongchun Ni

The synthesis of complex sugars is a key aspect of microbial biology. Cyclic beta-1,2-glucan (C beta G) is a circular polysaccharide critical for host interactions of many bacteria, including major pathogens of humans (Brucella) and plants (Agrobacterium). ...

Nature Portfolio2024

Roughness Evolution Induced by Third-Body Wear

Jean-François Molinari, Tobias Brink, Antonio Joaquin Garcia Suarez

Surface roughness is a key factor when it comes to friction and wear, as well as to other physical properties. These phenomena are controlled by mechanisms acting at small scales, in which the topography of apparently flat surfaces is revealed. Roughness i ...

2024

Exciton migration in two-dimensional materials

Giovanni Consalvo Cistaro

Excitons play an essential role in the optical response of two-dimensional materials. These are bound states showing up in the band gaps of many-body systems and are conceived as quasiparticles formed by an electron and a hole. By performing real-time simu ...

Nature Portfolio2024

Adaptive Finite Elements with Large Aspect Ratio. Application to Aluminium Electrolysis

Paride Passelli

The goal of this work is to use anisotropic adaptive finite elements for the numerical simulation of aluminium electrolysis. The anisotropic adaptive criteria are based on a posteriori error estimates derived for simplified problems. First, we consider an ...

EPFL2024