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"disk0/00/01/37/53", "datestamp": "2020-06-03 22:03:26", "lastmod": "2023-11-08 00:12:04", "status_changed": "2020-06-03 22:03:26", "type": "thesis", "metadata_visibility": "show", "creators": { "items": [ { "email": "amitskov@gmail.com", "id": "Mitskovets-Anna", "name": { "family": "Mitskovets", "given": "Anna" }, "orcid": "0000-0003-1967-5334", "show_email": "NO" } ] }, "title": "Using DNA Origami to Create Hybrid Nanophotonic Architectures for Single-Photon Emitters", "ispublished": "unpub", "full_text_status": "public", "keywords": "Quantum plasmonics, DNA origami", "abstract": "
The limitations in physical dimensions of silicon transistors give us a stimulus to explore alternative systems for better computational performance. The most promising system that received a lot of attention in the past few years is a quantum computer. Ideally, a nanophotonic quantum computer would consist of hundreds of single-photon emitters, optical or plasmonic resonators, optical waveguides and interconnects. The main difficulty in large-scale production of such quantum photonic networks is the integration and deterministic coupling of single-photon sources to photonic elements.
\r\n\r\nIn the first part of this thesis, we utilize spontaneous parametric down-conversion to create correlated pairs of indistinguishable photons. These photons are generated by bismuth borate nonlinear crystal and then are coupled to a photonic chip where they interfere at directional couplers to produce a path-entangled state. Our photonic chip consists of waveguides, directional couplers, and a single Mach-Zender interferometer with a thermo-optic phase shifter. When a part of the waveguide connecting directional couplers is replace with a plasmonic waveguide, quantum state of photons is converted to plasmonic state. Here we report a measurement of path entanglement between surface plasmons with 95% contrast, confirming that a path-entangled state can indeed survive without measurable decoherence. Our measurement suggests that elastic scattering mechanisms of the type that might cause pure dephasing in plasmonic systems must be weak enough not to significantly perturb the state of the metal under the experimental conditions we investigated.
\r\n\r\nThe second part of this work is dedicated to the study of a novel DNA origami self-assembly technique for creating hybrid nanophotonic architectures to create single-photon emitters. DNA origami is a modular platform for the combination of molecular and colloidal components to create optical, electronic, and biological devices. We present a DNA origami molecule that can be deterministically positioned on a silicon chip within 3.2\u00b0 alignment. Orientation is absolute (all degrees of freedom are speci\ufb01ed) and arbitrary (every molecule\u2019s orientation is independently speci\ufb01ed). The use of orientation to optimize device performance is shown by aligning \ufb02uorescent emission dipoles within microfabricated optical cavities. Large-scale integration is demonstrated via an array of 3,456 DNA origami with 12 distinct orientations, which indicates the polarization of the excitation light. Following this experiment, we explore how many molecular emitters can be coupled to this DNA origami shape and discover interesting interactions between ssDNA extensions that can cause origami to fold along its seam. Finally, we examine DNA origami self-assembly methods that can be used to deterministically couple single-photon emitters to resonators in order to decrease pure-dephasing rates and increase indistinguishability of emitted photons.
", "date": "2020", "date_type": "degree", "id_number": "CaltechTHESIS:05312020-234931669", "refereed": "FALSE", "official_url": "https://resolver.caltech.edu/CaltechTHESIS:05312020-234931669", "related_url": { "items": [ { "description": "Article adapted for Chapter 2.", "type": "doi", "url": "https://doi.org/10.1088/1367-2630/17/2/023002" }, { "description": "Article adapted for Chapter 3.", "type": "arxiv", "url": "https://arxiv.org/abs/1808.04544" } ] }, "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "collection": "CaltechTHESIS", "reviewer": "Melissa Ray", "deposited_by": "Anna Mitskovets", "deposited_on": "2020-06-03 22:03:26", "doi": "10.7907/kqaj-ex65", "divisions": { "items": [ "div_eng" ] }, "institution": "California Institute of Technology", "thesis_type": "phd", "thesis_advisor": { "items": [ { "email": "haa@caltech.edu", "id": "Atwater-H-A", "name": { "family": "Atwater", "given": "Harry Albert" }, "role": "advisor" }, { "email": "pwkr@dna.caltech.edu", "id": "Rothemund-P-W-K", "name": { "family": "Rothemund", "given": "Paul W. K." }, "role": "co-advisor" } ] }, "thesis_committee": { "items": [ { "email": "agopi@mit.edu", "id": "Gopinath-Ashwin", "name": { "family": "Gopinath", "given": "Ashwin" }, "role": "chair" }, { "email": "haa@caltech.edu", "id": "Atwater-H-A", "name": { "family": "Atwater", "given": "Harry Albert" }, "role": "member" }, { "email": "pwkr@dna.caltech.edu", "id": "Rothemund-P-W-K", "name": { "family": "Rothemund", "given": "Paul W. K." }, "role": "member" }, { "email": "vahala@caltech.edu", "id": "Vahala-K-J", "name": { "family": "Vahala", "given": "Kerry J." }, "role": "member" }, { "email": "faraon@caltech.edu", "id": "Faraon-A", "name": { "family": "Faraon", "given": "Andrei" }, "role": "member" } ] }, "thesis_degree": "PHD", "thesis_degree_grantor": "California Institute of Technology", "thesis_defense_date": "2020-05-29", "gradofc_approval_date": "2020-06-03", "review_status": "approved", "option_major": { "items": [ "appliedphys" ] }, "copyright_statement": "Author's Rights Authorization: I hereby certify that, if appropriate, I have obtained a written permission statement from the owner(s) of each third party copyrighted matter to be included in my thesis, dissertation, or project report, allowing distribution as specified below. I certify that the version I submitted here is the same as that approved by my advisory committee.\n\nI hereby grant to California Institute of Technology or its agents the non-exclusive license to archive and make accessible, under the conditions specified under \"Thesis Availability\" in this submission, my thesis, dissertation, or project report in whole or in part in all forms of media, now or hereafter known. I retain all other ownership rights to the copyright of the thesis, dissertation, or project report. I also retain the right to use in future works (such as articles or books) all or part of this thesis, dissertation, or project report.", "resource_type": "thesis", "pub_year": "2020", "author_list": "Mitskovets, Anna", "advisor_list": "Atwater, Harry Albert and Rothemund, Paul W. 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"media_duration": "0", "media_aspect_ratio": "0", "media_sample_start": "0", "media_sample_stop": "0", "relation": { "items": [ { "type": "http://eprints.org/relation/isVersionOf", "uri": "/id/document/41948" }, { "type": "http://eprints.org/relation/isVolatileVersionOf", "uri": "/id/document/41948" }, { "type": "http://eprints.org/relation/isIndexCodesVersionOf", "uri": "/id/document/41948" } ] } } ], "eprint_status": "archive", "userid": 1786, "dir": "disk0/00/00/77/72", "datestamp": "2013-06-03 22:26:44", "lastmod": "2019-10-04 00:01:20", "status_changed": "2013-06-03 22:26:44", "type": "thesis", "metadata_visibility": "show", "creators": { "items": [ { "email": "woocaltech@gmail.com", "id": "Woo-Sungwook", "name": { "family": "Woo", "given": "Sungwook" }, "show_email": "NO" } ] }, "title": "Beyond Watson and Crick: Programming the Self-Assembly and Reconfiguration of DNA Nanostructures Based on Stacking Interactions", "ispublished": "unpub", "full_text_status": "public", "keywords": "DNA Nanotechnology;self-assembly;base stacking;nano machines;ParMRC;plasmid segregation;crystallization;surface diffusion;binary coding;shape coding;molecular recognition;DNA nanostructures;DNA origami;stacking bonds;programmable self-assembly;DNA-protein hybrid nanostructures;ParM filaments;hierarchical self-assembly", "abstract": "Life is the result of the execution of molecular programs: like how an embryo is fated to become a human or a whale, or how a person\u2019s appearance is inherited from their parents, many biological phenomena are governed by genetic programs written in DNA molecules. At the core of such programs is the highly reliable base pairing interaction between nucleic acids. DNA nanotechnology exploits the programming power of DNA to build artificial nanostructures, molecular computers, and nanomachines. In particular, DNA origami\u2014which is a simple yet versatile technique that allows one to create various nanoscale shapes and patterns\u2014is at the heart of the technology. In this thesis, I describe the development of programmable self-assembly and reconfiguration of DNA origami nanostructures based on a unique strategy: rather than relying on Watson-Crick base pairing, we developed programmable bonds via the geometric arrangement of stacking interactions, which we termed stacking bonds. We further demonstrated that such bonds can be dynamically reconfigurable.
\r\n\r\nThe first part of this thesis describes the design and implementation of stacking bonds. Our work addresses the fundamental question of whether one can create diverse bond types out of a single kind of attractive interaction\u2014a question first posed implicitly by Francis Crick while seeking a deeper understanding of the origin of life and primitive genetic code. For the creation of multiple specific bonds, we used two different approaches: binary coding and shape coding of geometric arrangement of stacking interaction units, which are called blunt ends. To construct a bond space for each approach, we performed a systematic search using a computer algorithm. We used orthogonal bonds to experimentally implement the connection of five distinct DNA origami nanostructures. We also programmed the bonds to control cis/trans configuration between asymmetric nanostructures.
\r\n\r\nThe second part of this thesis describes the large-scale self-assembly of DNA origami into two-dimensional checkerboard-pattern crystals via surface diffusion. We developed a protocol where the diffusion of DNA origami occurs on a substrate and is dynamically controlled by changing the cationic condition of the system. We used stacking interactions to mediate connections between the origami, because of their potential for reconfiguring during the assembly process. Assembling DNA nanostructures directly on substrate surfaces can benefit nano/microfabrication processes by eliminating a pattern transfer step. At the same time, the use of DNA origami allows high complexity and unique addressability with six-nanometer resolution within each structural unit.
\r\n\r\nThe third part of this thesis describes the use of stacking bonds as dynamically breakable bonds. To break the bonds, we used biological machinery called the ParMRC system extracted from bacteria. The system ensures that, when a cell divides, each daughter cell gets one copy of the cell\u2019s DNA by actively pushing each copy to the opposite poles of the cell. We demonstrate dynamically expandable nanostructures, which makes stacking bonds a promising candidate for reconfigurable connectors for nanoscale machine parts.
", "date": "2013", "date_type": "degree", "id_number": "CaltechTHESIS:05302013-123041371", "refereed": "FALSE", "official_url": "https://resolver.caltech.edu/CaltechTHESIS:05302013-123041371", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "collection": "CaltechTHESIS", "reviewer": "Kathy Johnson", "deposited_by": "Sungwook Woo", "deposited_on": "2013-06-03 22:26:44", "doi": "10.7907/4NZK-XK58", "divisions": { "items": [ "div_eng" ] }, "institution": "California Institute of Technology", "thesis_type": "phd", "thesis_advisor": { "items": [ { "email": "pwkr@dna.caltech.edu", "id": "Rothemund-P-W-K", "name": { "family": "Rothemund", "given": "Paul W. K." }, "role": "advisor" } ] }, "thesis_committee": { "items": [ { "email": "winfree@caltech.edu", "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "role": "chair" }, { "email": "pwkr@dna.caltech.edu", "id": "Rothemund-P-W-K", "name": { "family": "Rothemund", "given": "Paul W. K." }, "role": "member" }, { "email": "niles@caltech.edu", "id": "Pierce-N-A", "name": { "family": "Pierce", "given": "Niles A." }, "role": "member" }, { "email": "tirrell@caltech.edu", "id": "Tirrell-D-A", "name": { "family": "Tirrell", "given": "David A." }, "role": "member" }, { "email": "deborah@physics.ucsb.edu", "id": "Fygenson-D-K", "name": { "family": "Fygenson", "given": "Deborah K." }, "role": "member" }, { "email": "esa@mb.au.dk", "id": "Andersen-E-S", "name": { "family": "Andersen", "given": "Ebbe S." }, "role": "member" } ] }, "thesis_degree": "PHD", "thesis_degree_grantor": "California Institute of Technology", "thesis_defense_date": "2013-05-23", "gradofc_approval_date": "2013-05-03", "review_status": "approved", "option_major": { "items": [ "bioeng" ] }, "copyright_statement": "Author's Rights Authorization: I hereby certify that, if appropriate, I have obtained a written permission statement from the owner(s) of each third party copyrighted matter to be included in my thesis, dissertation, or project report, allowing distribution as specified below. I certify that the version I submitted here is the same as that approved by my advisory committee.\n\nI hereby grant to California Institute of Technology or its agents the non-exclusive license to archive and make accessible, under the conditions specified under \"Thesis Availability\" in this submission, my thesis, dissertation, or project report in whole or in part in all forms of media, now or hereafter known. I retain all other ownership rights to the copyright of the thesis, dissertation, or project report. I also retain the right to use in future works (such as articles or books) all or part of this thesis, dissertation, or project report.", "resource_type": "thesis", "pub_year": "2013", "author_list": "Woo, Sungwook", "advisor_list": "Rothemund, Paul W. K.", "comittee_list": "Winfree, Erik; Rothemund, Paul W. K.; et el." } ]