Asynchronous and Infinite Replica Exchange Transition Interface Sampling
A possible alternative to running chemical experiments in the laboratory could be to conduct them digitally instead, by running computer simulations. One prominent simulation technique is Molecular Dynamics (MD), which simulates the dynamics of molecular systems at the atomic scale. With sufficientl...
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ftntnutrondheimi:oai:ntnuopen.ntnu.no:11250/3132608 2024-06-23T07:52:04+00:00 Asynchronous and Infinite Replica Exchange Transition Interface Sampling Zhang, Daniel Tianhou Erp, Titus van Koch, Henrik Høyvik, Ida-Marie Riccardi, Enrico 2024 application/pdf https://hdl.handle.net/11250/3132608 eng eng NTNU Doctoral theses at NTNU;2024:215 Paper A: Roet, Sander Johannes Simon; Zhang, Daniel Tianhou; van Erp, Titus Sebastiaan. Exchanging Replicas with Unequal Cost, Infinitely and Permanently. Journal of Physical Chemistry A 2022 https://doi.org/10.1021/acs.jpca.2c06004 Copyright © 2022 The Authors. Published by American Chemical Society. This publication is licensed under CC-BY 4.0. Paper B: Zhang, Daniel Tianhou; Riccardi, Enrico; van Erp, Titus Sebastiaan. Enhanced path sampling using subtrajectory Monte Carlo moves. Journal of Chemical Physics 2023 https://doi.org/10.1063/5.0127249 - Reproduced with the permission of AIP Publishing Paper C: Zhang, Daniel Tianhou; Baldauf, Lukas; Roet, Sander Johannes Simon; Lervik, Anders; van Erp, Titus Sebastiaan. Highly parallelizable path sampling with minimal rejections using asynchronous replica exchange and infinite swaps. Proceedings of the National Academy of Sciences of the United States of America 2024 ;Volum 121. https://doi.org/10.1073/pnas.2318731121 - Copyright © 2024 the Author(s). Published by PNAS. This article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND). urn:isbn:978-82-326-8021-4 urn:issn:2703-8084 https://hdl.handle.net/11250/3132608 VDP::Mathematics and natural science: 400::Chemistry: 440 Doctoral thesis 2024 ftntnutrondheimi https://doi.org/10.1021/acs.jpca.2c0600410.1063/5.012724910.1073/pnas.2318731121 2024-06-10T23:32:46Z A possible alternative to running chemical experiments in the laboratory could be to conduct them digitally instead, by running computer simulations. One prominent simulation technique is Molecular Dynamics (MD), which simulates the dynamics of molecular systems at the atomic scale. With sufficiently accurate molecular models and enough computational power, the underlying mechanisms for the initiation and occurrence of chemical phenomena could then possibly be understood, like for chemical reactions, phase transitions, permeation, protein folding, and membrane fusion. In combination with experiments, computer simulations can therefore help drive the development of new drug candidates, vaccines, catalysts, and technologies like energy storage and conversion materials. By running straightforward MD, however, observing one single dynamical event may require thousands of years in wall time, far too long to be of any practical use. By utilizing the Monte Carlo (MC) based Replica Exchange Transition Interface Sampling (RETIS) method instead, we reduce the required wall time converge to months or up to one year. While doable, reducing the required simulation time even more would be highly beneficial. The major work presented in this thesis has therefore been to improve the RETIS method by developing various smart MC-based enhancements, like introducing a new, fast decorrelating MC move called Wire Fencing, reducing MC move rejection by biasing the acceptance probability, enabling the calculation of infinite replica exchange swaps without the factorial cost, and deriving a parallel RE scheme with linear MD scaling. Connecting the various enhancements together forms the infinity RETIS protocol that enables rapid convergence and the calculation of rate constants within days or weeks instead. Together with method development, we have also applied infinity RETIS to study a number of rare events, like water autoionization, the formation of carbonic acid from solvated carbon dioxide, the electron transfer reaction between ... Doctoral or Postdoctoral Thesis Carbonic acid NTNU Open Archive (Norwegian University of Science and Technology) |
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NTNU Open Archive (Norwegian University of Science and Technology) |
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ftntnutrondheimi |
language |
English |
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VDP::Mathematics and natural science: 400::Chemistry: 440 |
spellingShingle |
VDP::Mathematics and natural science: 400::Chemistry: 440 Zhang, Daniel Tianhou Asynchronous and Infinite Replica Exchange Transition Interface Sampling |
topic_facet |
VDP::Mathematics and natural science: 400::Chemistry: 440 |
description |
A possible alternative to running chemical experiments in the laboratory could be to conduct them digitally instead, by running computer simulations. One prominent simulation technique is Molecular Dynamics (MD), which simulates the dynamics of molecular systems at the atomic scale. With sufficiently accurate molecular models and enough computational power, the underlying mechanisms for the initiation and occurrence of chemical phenomena could then possibly be understood, like for chemical reactions, phase transitions, permeation, protein folding, and membrane fusion. In combination with experiments, computer simulations can therefore help drive the development of new drug candidates, vaccines, catalysts, and technologies like energy storage and conversion materials. By running straightforward MD, however, observing one single dynamical event may require thousands of years in wall time, far too long to be of any practical use. By utilizing the Monte Carlo (MC) based Replica Exchange Transition Interface Sampling (RETIS) method instead, we reduce the required wall time converge to months or up to one year. While doable, reducing the required simulation time even more would be highly beneficial. The major work presented in this thesis has therefore been to improve the RETIS method by developing various smart MC-based enhancements, like introducing a new, fast decorrelating MC move called Wire Fencing, reducing MC move rejection by biasing the acceptance probability, enabling the calculation of infinite replica exchange swaps without the factorial cost, and deriving a parallel RE scheme with linear MD scaling. Connecting the various enhancements together forms the infinity RETIS protocol that enables rapid convergence and the calculation of rate constants within days or weeks instead. Together with method development, we have also applied infinity RETIS to study a number of rare events, like water autoionization, the formation of carbonic acid from solvated carbon dioxide, the electron transfer reaction between ... |
author2 |
Erp, Titus van Koch, Henrik Høyvik, Ida-Marie Riccardi, Enrico |
format |
Doctoral or Postdoctoral Thesis |
author |
Zhang, Daniel Tianhou |
author_facet |
Zhang, Daniel Tianhou |
author_sort |
Zhang, Daniel Tianhou |
title |
Asynchronous and Infinite Replica Exchange Transition Interface Sampling |
title_short |
Asynchronous and Infinite Replica Exchange Transition Interface Sampling |
title_full |
Asynchronous and Infinite Replica Exchange Transition Interface Sampling |
title_fullStr |
Asynchronous and Infinite Replica Exchange Transition Interface Sampling |
title_full_unstemmed |
Asynchronous and Infinite Replica Exchange Transition Interface Sampling |
title_sort |
asynchronous and infinite replica exchange transition interface sampling |
publisher |
NTNU |
publishDate |
2024 |
url |
https://hdl.handle.net/11250/3132608 |
genre |
Carbonic acid |
genre_facet |
Carbonic acid |
op_relation |
Doctoral theses at NTNU;2024:215 Paper A: Roet, Sander Johannes Simon; Zhang, Daniel Tianhou; van Erp, Titus Sebastiaan. Exchanging Replicas with Unequal Cost, Infinitely and Permanently. Journal of Physical Chemistry A 2022 https://doi.org/10.1021/acs.jpca.2c06004 Copyright © 2022 The Authors. Published by American Chemical Society. This publication is licensed under CC-BY 4.0. Paper B: Zhang, Daniel Tianhou; Riccardi, Enrico; van Erp, Titus Sebastiaan. Enhanced path sampling using subtrajectory Monte Carlo moves. Journal of Chemical Physics 2023 https://doi.org/10.1063/5.0127249 - Reproduced with the permission of AIP Publishing Paper C: Zhang, Daniel Tianhou; Baldauf, Lukas; Roet, Sander Johannes Simon; Lervik, Anders; van Erp, Titus Sebastiaan. Highly parallelizable path sampling with minimal rejections using asynchronous replica exchange and infinite swaps. Proceedings of the National Academy of Sciences of the United States of America 2024 ;Volum 121. https://doi.org/10.1073/pnas.2318731121 - Copyright © 2024 the Author(s). Published by PNAS. This article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND). urn:isbn:978-82-326-8021-4 urn:issn:2703-8084 https://hdl.handle.net/11250/3132608 |
op_doi |
https://doi.org/10.1021/acs.jpca.2c0600410.1063/5.012724910.1073/pnas.2318731121 |
_version_ |
1802643264195526656 |