Non-equilibrium Markov state modeling of periodically driven biomolecules
- Publication type:
- Journal article
- Metadata:
-
- Autoren
- Fabian Knoch
- Thomas Speck
- Autoren-URL
- https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000458109300004&DestLinkType=FullRecord&DestApp=WOS_CPL
- DOI
- 10.1063/1.5055818
- eISSN
- 1089-7690
- Externe Identifier
- Clarivate Analytics Document Solution ID: HK6QW
- PubMed Identifier: 30736700
- ISSN
- 0021-9606
- Ausgabe der Veröffentlichung
- 5
- Zeitschrift
- JOURNAL OF CHEMICAL PHYSICS
- Artikelnummer
- ARTN 054103
- Datum der Veröffentlichung
- 2019
- Status
- Published
- Titel
- Non-equilibrium Markov state modeling of periodically driven biomolecules
- Sub types
- Article
- Ausgabe der Zeitschrift
- 150
Data source: Web of Science (Lite)
- Other metadata sources:
-
- Abstract
- <jats:p>Molecular dynamics simulations allow us to study the structure and dynamics of single biomolecules in microscopic detail. However, many processes occur on time scales beyond the reach of fully atomistic simulations and require coarse-grained multiscale models. While systematic approaches to construct such models have become available, these typically rely on microscopic dynamics that obey detailed balance. In vivo, however, biomolecules are constantly driven away from equilibrium in order to perform specific functions and thus break detailed balance. Here we introduce a method to construct Markov state models for systems that are driven through periodically changing one (or several) external parameter. We illustrate the method for alanine dipeptide, a widely used benchmark molecule for computational methods, exposed to a time-dependent electric field.</jats:p>
- Autoren
- Fabian Knoch
- Thomas Speck
- DOI
- 10.1063/1.5055818
- eISSN
- 1089-7690
- ISSN
- 0021-9606
- Ausgabe der Veröffentlichung
- 5
- Zeitschrift
- The Journal of Chemical Physics
- Sprache
- en
- Online publication date
- 2019
- Datum der Veröffentlichung
- 2019
- Status
- Published
- Herausgeber
- AIP Publishing
- Herausgeber URL
- http://dx.doi.org/10.1063/1.5055818
- Datum der Datenerfassung
- 2023
- Titel
- Non-equilibrium Markov state modeling of periodically driven biomolecules
- Ausgabe der Zeitschrift
- 150
Data source: Crossref
- Abstract
- Molecular dynamics simulations allow us to study the structure and dynamics of single biomolecules in microscopic detail. However, many processes occur on time scales beyond the reach of fully atomistic simulations and require coarse-grained multiscale models. While systematic approaches to construct such models have become available, these typically rely on microscopic dynamics that obey detailed balance. In vivo, however, biomolecules are constantly driven away from equilibrium in order to perform specific functions and thus break detailed balance. Here we introduce a method to construct Markov state models for systems that are driven through periodically changing one (or several) external parameter. We illustrate the method for alanine dipeptide, a widely used benchmark molecule for computational methods, exposed to a time-dependent electric field.
- Addresses
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudingerweg 7-9, 55128 Mainz, Germany.
- Autoren
- Fabian Knoch
- Thomas Speck
- DOI
- 10.1063/1.5055818
- eISSN
- 1089-7690
- Externe Identifier
- PubMed Identifier: 30736700
- Funding acknowledgements
- Deutsche Forschungsgemeinschaft: TRR 146
- Open access
- false
- ISSN
- 0021-9606
- Ausgabe der Veröffentlichung
- 5
- Zeitschrift
- The Journal of chemical physics
- Schlüsselwörter
- Dipeptides
- Markov Chains
- Models, Chemical
- Molecular Dynamics Simulation
- Sprache
- eng
- Medium
- Paginierung
- 054103
- Datum der Veröffentlichung
- 2019
- Status
- Published
- Datum der Datenerfassung
- 2019
- Titel
- Non-equilibrium Markov state modeling of periodically driven biomolecules.
- Sub types
- Journal Article
- Ausgabe der Zeitschrift
- 150
Data source: Europe PubMed Central
- Abstract
- Molecular dynamics simulations allow us to study the structure and dynamics of single biomolecules in microscopic detail. However, many processes occur on time scales beyond the reach of fully atomistic simulations and require coarse-grained multiscale models. While systematic approaches to construct such models have become available, these typically rely on microscopic dynamics that obey detailed balance. In vivo, however, biomolecules are constantly driven away from equilibrium in order to perform specific functions and thus break detailed balance. Here we introduce a method to construct Markov state models for systems that are driven through periodically changing one (or several) external parameter. We illustrate the method for alanine dipeptide, a widely used benchmark molecule for computational methods, exposed to a time-dependent electric field.
- Autoren
- Fabian Knoch
- Thomas Speck
- Autoren-URL
- https://www.ncbi.nlm.nih.gov/pubmed/30736700
- DOI
- 10.1063/1.5055818
- eISSN
- 1089-7690
- Ausgabe der Veröffentlichung
- 5
- Zeitschrift
- J Chem Phys
- Schlüsselwörter
- Dipeptides
- Markov Chains
- Models, Chemical
- Molecular Dynamics Simulation
- Sprache
- eng
- Country
- United States
- Paginierung
- 054103
- Datum der Veröffentlichung
- 2019
- Status
- Published
- Datum, an dem der Datensatz öffentlich gemacht wurde
- 2019
- Titel
- Non-equilibrium Markov state modeling of periodically driven biomolecules.
- Sub types
- Journal Article
- Ausgabe der Zeitschrift
- 150
Data source: PubMed
- Abstract
- Molecular dynamics simulations allow to study the structure and dynamics of single biomolecules in microscopic detail. However, many processes occur on time scales beyond the reach of fully atomistic simulations and require coarse-grained multiscale models. While systematic approaches to construct such models have become available, these typically rely on microscopic dynamics that obey detailed balance. In vivo, however, biomolecules are constantly driven away from equilibrium in order to perform specific functions and thus break detailed balance. Here we introduce a method to construct Markov state models for systems that are driven through periodically changing one (or several) external parameter. We illustrate the method for alanine dipeptide, a widely used benchmark molecule for computational methods, exposed to a time-dependent electric field.
- Autoren
- Fabian Knoch
- Thomas Speck
- Autoren-URL
- http://arxiv.org/abs/1901.06511v1
- Zeitschrift
- J. Chem. Phys.
- Schlüsselwörter
- cond-mat.stat-mech
- cond-mat.stat-mech
- physics.bio-ph
- physics.comp-ph
- Notes
- To appear in JCP
- Paginierung
- 054103
- Datum der Veröffentlichung
- 2019
- Herausgeber URL
- http://dx.doi.org/10.1063/1.5055818
- Datum der Datenerfassung
- 2019
- Datum, an dem der Datensatz öffentlich gemacht wurde
- 2019
- Titel
- Non-equilibrium Markov state modeling of periodically driven biomolecules
- Ausgabe der Zeitschrift
- 150
Files
1901.06511v1.pdf
Data source: arXiv
- Beziehungen:
- Property of