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

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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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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, ...

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

Chattez avec Graph Search

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Microsecond Time-Resolved Cryo-Electron Microscopy

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Microsecond time-resolved cryo-electron microscopy

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

Mechanisms and functions of protein S-acylation

The time-domain Cartesian multipole expansion of electromagnetic fields

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