New Strategies for Integrative Dynamic Modeling of Macromolecular Assembly

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Inferring free-energy barriers and kinetic rates from molecular dynamics via underdamped Langevin models

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Rare events include many of the most interesting transformation processes in condensed matter, from phase transitions to biomolecular conformational changes to chemical reactions. Access to the corresponding mechanisms, free-energy landscapes and kinetic r ...

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Advancing Computational Chemistry with Stochastic and Artificial Intelligence Approaches

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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 ...

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The role of Zn in C-S-H atomic structure, nucleation and growth

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The most promising solution towards cementitious materials with a lower carbon footprint is the partial substitution of the clinker by supplementary cementitious materials (SCMs) such as fly ash, blast furnace slag, limestone and calcined clays. The produc ...

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Universal machine learning for the response of atomistic systems to external fields

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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 ...

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Atomic-level structure determination of amorphous molecular solids by NMR

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Structure determination of amorphous materials remains challenging, owing to the disorder inherent to these materials. Nuclear magnetic resonance (NMR) powder crystallography is a powerful method to determine the structure of molecular solids, but disorder ...

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Computer-implemented design of peptide:receptor signaling complexes for enhanced chemotaxis

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The present invention relates to a computer-implemented method for engineering the interaction between a protein and a cognate peptide that are capable of forming a molecular complex, wherein the method comprises (a) preparing in silico a library of test p ...

2023

Coupled Rotary and Oscillatory Motion in a Second-Generation Molecular Motor Pd Complex

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Molecular machines offer many opportunities for the development of responsive materials and introduce autono-mous motion in molecular systems. While basic molecular switches and motors carry out one type of motion upon being exposed to an external stimulus ...

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Two antagonistic response regulators control Pseudomonas aeruginosa polarization during mechanotaxis

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The opportunistic pathogen Pseudomonas aeruginosa adapts to solid surfaces to enhance virulence and infect its host. Type IV pili (T4P), long and thin filaments that power surface-specific twitching motility, allow single cells to sense surfaces and contro ...

WILEY2023

Factorized structure of the long-range two-electron integrals tensor and its application in quantum chemistry

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We introduce two new approximation methods for the numerical evaluation of the long-range component of the range-separated Coulomb potential and the approximation of the resulting high dimensional Two-Electron Integrals tensor (TEI) with long-range interac ...

Academic Press Inc Elsevier Science2023

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

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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

Protein target highlights in CASP15: Analysis of models by structure providers

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We present an in-depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the su ...

WILEY2023