Computed Three-Dimensional Atomic Force Microscopy Images of Biopolymers Using the Jarzynski Equality

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dc.contributorAalto-yliopistofi
dc.contributorAalto Universityen
dc.contributor.authorSumikama, Takashi
dc.contributor.authorCanova, Filippo Federici
dc.contributor.authorGao, David Z.
dc.contributor.authorPenedo, Marcos
dc.contributor.authorMiyazawa, Keisuke
dc.contributor.authorFoster, Adam S.
dc.contributor.authorFukuma, Takeshi
dc.contributor.departmentJapan Science and Technology Agency
dc.contributor.departmentSurfaces and Interfaces at the Nanoscale
dc.contributor.departmentNorwegian University of Science and Technology
dc.contributor.departmentSwiss Federal Institute of Technology Lausanne
dc.contributor.departmentKanazawa University
dc.contributor.departmentDepartment of Applied Physicsen
dc.date.accessioned2022-10-19T06:47:05Z
dc.date.available2022-10-19T06:47:05Z
dc.date.issued2022-06-16
dc.description.abstractThree-dimensional atomic force microscopy (3D-AFM) has resolved three-dimensional distributions of solvent molecules at solid-liquid interfaces at the subnanometer scale. This method is now being extended to the imaging of biopolymer assemblies such as chromosomes or proteins in cells, with the expectation of being able to resolve their three-dimensional structures. Here, we have developed a computational method to simulate 3D-AFM images of biopolymers by using the Jarzynski equality. It is found that some parts of the fiber structure of biopolymers are indeed resolved in the 3D-AFM image. The dependency of 3D-AFM images on the vertical scanning velocity is investigated, and optimum scanning velocities are found. It is also clarified that forces in nonequilibrium processes are measured in 3D-AFM measurements when the dynamics of polymers are slower than the scanning of the probe.en
dc.description.versionPeer revieweden
dc.format.extent7
dc.format.extent5365-5371
dc.format.mimetypeapplication/pdf
dc.identifier.citationSumikama , T , Canova , F F , Gao , D Z , Penedo , M , Miyazawa , K , Foster , A S & Fukuma , T 2022 , ' Computed Three-Dimensional Atomic Force Microscopy Images of Biopolymers Using the Jarzynski Equality ' , Journal of Physical Chemistry Letters , vol. 13 , no. 23 , pp. 5365-5371 . https://doi.org/10.1021/acs.jpclett.2c01093en
dc.identifier.doi10.1021/acs.jpclett.2c01093
dc.identifier.issn1948-7185
dc.identifier.otherPURE UUID: d320641b-1877-4456-9ddb-8094f38154cb
dc.identifier.otherPURE ITEMURL: https://research.aalto.fi/en/publications/d320641b-1877-4456-9ddb-8094f38154cb
dc.identifier.otherPURE FILEURL: https://research.aalto.fi/files/89094563/Computed_Three_Dimensional_Atomic_Force_Microscopy_Images_of_Biopolymers_Using_the_Jarzynski_Equality.pdf
dc.identifier.urihttps://aaltodoc.aalto.fi/handle/123456789/117284
dc.identifier.urnURN:NBN:fi:aalto-202210196072
dc.language.isoenen
dc.publisherAMERICAN CHEMICAL SOCIETY
dc.relation.ispartofseriesJournal of Physical Chemistry Lettersen
dc.relation.ispartofseriesVolume 13, issue 23en
dc.rightsopenAccessen
dc.titleComputed Three-Dimensional Atomic Force Microscopy Images of Biopolymers Using the Jarzynski Equalityen
dc.typeA1 Alkuperäisartikkeli tieteellisessä aikakauslehdessäfi
dc.type.versionpublishedVersion
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