{"@context":"http://iiif.io/api/presentation/2/context.json","@id":"https://repo.library.stonybrook.edu/cantaloupe/iiif/2/manifest.json","@type":"sc:Manifest","label":"Probing DNA Dynamics with Fluorescence Cross-Correlation Spectroscopy","metadata":[{"label":"dc.description.sponsorship","value":"This work is sponsored by the Stony Brook University Graduate School in compliance with the requirements for completion of degree."},{"label":"dc.format","value":"Monograph"},{"label":"dc.format.medium","value":"Electronic Resource"},{"label":"dc.identifier.uri","value":"http://hdl.handle.net/11401/76986"},{"label":"dc.language.iso","value":"en_US"},{"label":"dc.publisher","value":"The Graduate School, Stony Brook University: Stony Brook, NY."},{"label":"dcterms.abstract","value":"DNA Polymer dynamics are fundamental to the function of biological systems. Examples include gene regulation, cell division, threading and transport through pores. We address the limitations of previous experimental studies of polymer dynamics by designing, building, and characterizing a novel, custom Fluorescence Cross-Correlation Spectroscopy (FCCS) system. We detail the optical considerations for quantitatively describing and shaping the confocal volume. The hardware is supplemented by a robust theoretical foundation of correlation analysis and how it applies to polymer dynamics. We carry this theory through in the design of novel fitting methods and software. We utilize our FCCS setup to quantitatively measure important polymer dynamics of DNA in solution, such as diffusion coefficients and relaxation time, both more carefully and at lower molecular weights than typically accessible by single color FCS or standard fluorescence microscopy. By establishing a well-characterized FCCS measurement platform and detailing its functionality and applicability to polymer dynamics, we lay the foundation to applying our system to further measurements within nano-confinement. A detailed nanofabrication approach is provided. Better understanding internal polymer dynamics under nano-confinement has significant potential applications in designing more robust molecular separations technologies as well as the ability to address fundamental research questions in biophysics and molecular biology."},{"label":"dcterms.available","value":"2017-09-20T16:51:36Z"},{"label":"dcterms.contributor","value":"Entcheva, Emilia"},{"label":"dcterms.creator","value":"Bakowski, Tomasz"},{"label":"dcterms.dateAccepted","value":"2017-09-20T16:51:36Z"},{"label":"dcterms.dateSubmitted","value":"2017-09-20T16:51:36Z"},{"label":"dcterms.description","value":"Department of Biomedical Engineering."},{"label":"dcterms.extent","value":"120 pg."},{"label":"dcterms.format","value":"Monograph"},{"label":"dcterms.identifier","value":"http://hdl.handle.net/11401/76986"},{"label":"dcterms.issued","value":"2015-12-01"},{"label":"dcterms.language","value":"en_US"},{"label":"dcterms.provenance","value":"Made available in DSpace on 2017-09-20T16:51:36Z (GMT). No. of bitstreams: 1\nBakowski_grad.sunysb_0771E_12557.pdf: 9899335 bytes, checksum: 23820c8335cb2bc522215cb53969959c (MD5)\n  Previous issue date:    1"},{"label":"dcterms.publisher","value":"The Graduate School, Stony Brook University: Stony Brook, NY."},{"label":"dcterms.subject","value":"Biomedical engineering"},{"label":"dcterms.title","value":"Probing DNA Dynamics with Fluorescence Cross-Correlation Spectroscopy"},{"label":"dcterms.type","value":"Dissertation"},{"label":"dc.type","value":"Dissertation"}],"description":"This manifest was generated dynamically","viewingDirection":"left-to-right","sequences":[{"@type":"sc:Sequence","canvases":[{"@id":"https://repo.library.stonybrook.edu/cantaloupe/iiif/2/canvas/page-1.json","@type":"sc:Canvas","label":"Page 1","height":1650,"width":1275,"images":[{"@type":"oa:Annotation","motivation":"sc:painting","resource":{"@id":"https://repo.library.stonybrook.edu/cantaloupe/iiif/2/26%2F96%2F77%2F26967780363234930542710982628913675964/full/full/0/default.jpg","@type":"dctypes:Image","format":"image/jpeg","height":1650,"width":1275,"service":{"@context":"http://iiif.io/api/image/2/context.json","@id":"https://repo.library.stonybrook.edu/cantaloupe/iiif/2/26%2F96%2F77%2F26967780363234930542710982628913675964","profile":"http://iiif.io/api/image/2/level2.json"}},"on":"https://repo.library.stonybrook.edu/cantaloupe/iiif/2/canvas/page-1.json"}]}]}]}