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   Articles with "path sampling" as a keyword



ATESA: An Automated Aimless Shooting Workflow.

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recommendations! Published in 2022 at "Journal of chemical theory and computation"

DOI: 10.1021/acs.jctc.2c00543

Abstract: Transition path sampling methods are powerful tools for studying the dynamics of rare events in molecular simulations. However, these methods are generally restricted to experts with the knowledge and resources to properly set up and… read more here.

Keywords: automated aimless; aimless shooting; atesa automated; transition path ... See more keywords

Competing Reaction Mechanisms of Peptide Bond Formation in Water Revealed by Deep Potential Molecular Dynamics and Path Sampling.

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recommendations! Published in 2024 at "Journal of the American Chemical Society"

DOI: 10.1021/jacs.4c03445

Abstract: The formation of an amide bond is an essential step in the synthesis of materials and drugs, and in the assembly of amino acids to form peptides. The mechanism of this reaction has been studied… read more here.

Keywords: reaction; path sampling; peptide bond; molecular dynamics ... See more keywords

Highly parallelizable path sampling with minimal rejections using asynchronous replica exchange and infinite swaps

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recommendations! Published in 2024 at "Proceedings of the National Academy of Sciences of the United States of America"

DOI: 10.1073/pnas.2318731121

Abstract: Significance Current molecular dynamics simulations have the capability to faithfully describe chemical reactions, nucleation, and protein folding events, providing essential information to drive the progress of technologies like catalysis and drug discovery. Nevertheless, even with… read more here.

Keywords: path sampling; highly parallelizable; replica exchange; parallelizable path ... See more keywords

STIM1 transmembrane helix dimerization captured by AI-guided transition path sampling

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recommendations! Published in 2025 at "Proceedings of the National Academy of Sciences of the United States of America"

DOI: 10.1101/2025.03.09.638703

Abstract: STIM1 is a Ca2+-sensing protein in the endoplasmic reticulum (ER) membrane. The depletion of ER Ca2+ stores induces a large conformational transition of the cytosolic STIM1 C-terminus, initiated by the dimerization of the transmembrane (TM)… read more here.

Keywords: path sampling; helix dimerization; ca2; transition ... See more keywords

Path sampling for lifetimes of metastable magnetic skyrmions and direct comparison with Kramers' method

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recommendations! Published in 2020 at "Physical Review B"

DOI: 10.1103/physrevb.101.060403

Abstract: We perform a direct comparison between transition state theory and forward flux sampling as a means to compute collapse rates of metastable magnetic skyrmions. We show that a good agreement is obtained between the two… read more here.

Keywords: sampling lifetimes; metastable magnetic; path sampling; direct comparison ... See more keywords