Publications related to A Novel Hamiltonian Replica Exchange MD Protocol to Enhance Protein Conformational Space Sampling

Related publications (33)

Granular Avalanche Impact on a Structure using DEM and FEM

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

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

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

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

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

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

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

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

Synergetic Support of Cartilage Homeostasis via Coupled Thermal-Hydrostatic Pressure Stimuli

Yanheng Guo

Cartilage homeostasis, crucial for musculoskeletal function, is orchestrated by interconnected biophysical cues. In healthy cartilage, repetitive compressive loading not only elicits a range of mechanical stimuli but also induces a gradual transient temper ...

EPFL2024

Engineering novel protein interactions with therapeutic potential using deep learning-guided surface design

Anthony Marchand

Proteins are foundational biomolecules of life playing a crucial role in a myriad of biological processes. Their function often requires interplay with other biomolecules, including proteins themselves. Protein-protein interactions (PPIs) are essential for ...

EPFL2024

Thermal transport of glasses via machine learning driven simulations

Federico Grasselli, Paolo Pegolo

Accessing the thermal transport properties of glasses is a major issue for the design of production strategies of glass industry, as well as for the plethora of applications and devices where glasses are employed. From the computational standpoint, the che ...

Frontiers Media Sa2024

Pseudo-Three-Dimensional Analytical Model of Linear Induction Motors for High-Speed Applications

Mario Paolone, André Hodder, Simone Rametti, Lucien André Félicien Pierrejean

Literature on linear induction motors (LIMs) has proposed several approaches to model the behavior of such devices for different applications. In terms of accuracy and fidelity, field analysis-based models are the most relevant. Closed-form or numerical so ...

2024

Microsecond time-resolved cryo-electron microscopy

Ulrich Lorenz

Microsecond time-resolved cryo-electron microscopy has emerged as a novel approach for directly observing protein dynamics. By providing microsecond temporal and near-atomic spatial resolution, it has the potential to elucidate a wide range of dynamics tha ...

2024

Predictive power-sharing scaling law in double-null L-mode plasmas

Paolo Ricci, Christian Gabriel Theiler, Olivier Claude Martin Février, Garance Hélène Salomé Durr-Legoupil-Nicoud, Louis Nicolas Stenger, Brenno Jason Sanzio Peter De Lucca, Kyungtak Lim

The physical mechanisms regulating the power sharing at the outer targets of L-mode double-null (DN) configurations are investigated using nonlinear, flux-driven, three-dimensional two-fluid simulations. Scans of parameters that regulate the turbulent leve ...

IOP Publishing Ltd2024

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

The time-domain Cartesian multipole expansion of electromagnetic fields

Emanuela Radici, Farhad Rachidi-Haeri, Marcos Rubinstein, Nicolas Mora Parra, Elias Per Joachim Le Boudec

Time-domain solutions of Maxwell’s equations in homogeneous and isotropic media are paramount to studying transient or broadband phenomena. However, analytical solutions are generally unavailable for practical applications, while numerical solutions are co ...

Nature Publishing Group2024

Solvation Free Energies from Machine Learning Molecular Dynamics

Nicola Marzari, Nicéphore Arthur François Bonnet

The present work proposes an extension to the approach of [Xi, C; et al. J. Chem. Theory Comput. 2022, 18, 6878] to calculate ion solvation free energies from first-principles (FP) molecular dynamics (MD) simulations of a hybrid solvation model. The approa ...

Amer Chemical Soc2024

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

Simulation and Fabrication of Monolithic III-V Photodetectors on Si: The Role of Growth Facets and Localization of Heterojunctions

Kirsten Emilie Moselund, Simone Iadanza

In this work, we provide important parameters to take into account when fabricating in-plane III-V photodetectors (PDs) integrated on silicon (Si) using template-assisted selective epitaxy (TASE). Their performance has previously been demonstrated, and her ...

IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC2024

Efficient and insightful descriptors for representing molecular and material space

Alexander Jan Goscinski

Data-driven approaches have been applied to reduce the cost of accurate computational studies on materials, by using only a small number of expensive reference electronic structure calculations for a representative subset of the materials space, and using ...

EPFL2024