[ { "id": "https://authors.library.caltech.edu/records/zneh1-k5y76", "eprint_id": 79192, "eprint_status": "archive", "datestamp": "2023-08-20 02:48:39", "lastmod": "2024-01-13 20:35:57", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Qian-Lulu", "name": { "family": "Qian", "given": "Lulu" }, "orcid": "0000-0003-4115-2409" }, { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" } ] }, "title": "Parallel and Scalable Computation and Spatial Dynamics with DNA-Based Chemical Reaction Networks on a Surface", "ispublished": "unpub", "full_text_status": "restricted", "note": "\u00a9 2014 Springer International Publishing Switzerland. \n\nWe thank Ho-Lin Chen and David Yu Zhang for insightful\ndiscussions and suggestions. LQ and EW were supported by the Molecular Programming Project under NSF expedition in computing (0832824 and 1317694). LQ was supported by a Career Award at the Scientific Interface from the Burroughs Wellcome Fund (1010684), a Faculty Early Career Development Award from NSF (1351081), and a Okawa Foundation Research Grant (0656180).", "abstract": "We propose a theoretical framework that uses a novel DNA strand displacement mechanism to implement abstract chemical reaction networks (CRNs) on the surface of a DNA nanostructure, and show that surface CRNs can perform efficient algorithmic computation and create complex spatial dynamics. We argue that programming molecular behaviors with surface CRNs is systematic, parallel and scalable.", "date": "2014-09", "date_type": "published", "publisher": "Springer", "place_of_pub": "Cham, Switzerland", "pagerange": "114-131", "id_number": "CaltechAUTHORS:20170719-084200345", "isbn": "978-3-319-11294-7", "book_title": "DNA Computing and Molecular Programming", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170719-084200345", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "CCF-0832824" }, { "agency": "NSF", "grant_number": "CCF-1317694" }, { "agency": "Burroughs Wellcome Fund", "grant_number": "1010684" }, { "agency": "NSF", "grant_number": "CCF-1351081" }, { "agency": "Okawa Foundation", "grant_number": "0656180" } ] }, "contributors": { "items": [ { "id": "Murata-Satoshi", "name": { "family": "Murata", "given": "Satoshi" } }, { "id": "Kobayashi-Satoshi", "name": { "family": "Kobayashi", "given": "Satoshi" } } ] }, "doi": "10.1007/978-3-319-11295-4_8", "resource_type": "book_section", "pub_year": "2014", "author_list": "Qian, Lulu and Winfree, Erik" }, { "id": "https://authors.library.caltech.edu/records/dt6t7-c2710", "eprint_id": 27111, "eprint_status": "archive", "datestamp": "2023-08-19 04:54:02", "lastmod": "2024-01-13 05:42:34", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Qian-Lulu", "name": { "family": "Qian", "given": "Lulu" }, "orcid": "0000-0003-4115-2409" }, { "id": "Soloveichik-D", "name": { "family": "Soloveichik", "given": "David" }, "orcid": "0000-0002-2585-4120" }, { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" } ] }, "title": "Efficient Turing-Universal Computation with DNA Polymers", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 2011 Springer-Verlag Berlin Heidelberg. \n\nWe thank Ho-Lin Chen for insightful discussions and suggestions. Our development of the history-free CRN scheme grew out of extensive discussions with Luca Cardelli. We thank Anne Condon for clarifying discussions. This work was supported by the Molecular Programming Project under NSF grant 0832824 and an NSF CIFellows Award to DS.\n\n
Submitted - DNA_stack_machines2010_DNA16.pdf
", "abstract": "Bennett's proposed chemical Turing machine is one of the most important thought experiments in the study of the thermodynamics of computation. Yet the sophistication of molecular engineering required to physically construct Bennett's hypothetical polymer substrate and enzymes has deterred experimental implementations. Here we propose a chemical implementation of stack machines \u2014 a Turing-universal model of computation similar to Turing machines \u2014 using DNA strand displacement cascades as the underlying chemical primitive. More specifically, the mechanism described herein is the addition and removal of monomers from the end of a DNA polymer, controlled by strand displacement logic. We capture the motivating feature of Bennett's scheme: that physical reversibility corresponds to logically reversible computation, and arbitrarily little energy per computation step is required. Further, as a method of embedding logic control into chemical and biological systems, polymer-based chemical computation is significantly more efficient than geometry-free chemical reaction networks.", "date": "2011", "date_type": "published", "publisher": "Springer", "place_of_pub": "Berlin", "pagerange": "123-140", "id_number": "CaltechAUTHORS:20111006-081731222", "isbn": "978-3-642-18304-1", "book_title": "DNA computing and molecular programming", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111006-081731222", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "CCF-0832824" } ] }, "contributors": { "items": [ { "id": "Sakakibara-Y", "name": { "family": "Sakakibara", "given": "Yasubumi" } }, { "id": "Mi-Y", "name": { "family": "Mi", "given": "Y." } } ] }, "doi": "10.1007/978-3-642-18305-8_12", "primary_object": { "basename": "DNA_stack_machines2010_DNA16.pdf", "url": "https://authors.library.caltech.edu/records/dt6t7-c2710/files/DNA_stack_machines2010_DNA16.pdf" }, "resource_type": "book_section", "pub_year": "2011", "author_list": "Qian, Lulu; Soloveichik, David; et el." }, { "id": "https://authors.library.caltech.edu/records/6ktsa-7vy83", "eprint_id": 18924, "eprint_status": "archive", "datestamp": "2023-08-20 00:20:54", "lastmod": "2024-01-12 23:41:09", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Qian-Lulu", "name": { "family": "Qian", "given": "Lulu" }, "orcid": "0000-0003-4115-2409" }, { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" } ] }, "title": "A Simple DNA Gate Motif for Synthesizing Large-Scale Circuits", "ispublished": "unpub", "full_text_status": "restricted", "note": "\u00a9 2009 Springer-Verlag Berlin Heidelberg. \n\nThe authors thank Dave Zhang for discussion of the catalytic mechanism, Marc Riedel for providing example netlists from logic synthesis benchmarks, Virgil Griffith for suggesting useful techniques for DNA sequence design, Ho-Lin Chen and Shuki Bruck for suggesting the connection to relay circuits, David Soloveichik for Mathematica code for simulating chemical reaction networks, and Georg Seeling, Bernard Yurke, and everyone else for discussions and support. This work has been supported by NSF grant no. 0728703 and HFSP award no. RGY0074/2006-C.", "abstract": "The prospects of programming molecular systems to perform complex autonomous tasks has motivated research into the design of synthetic biochemical circuits. Of particular interest to us are cell-free nucleic acid systems that exploit non-covalent hybridization and strand displacement reactions to create cascades that implement digital and analog circuits. To date, circuits involving at most tens of gates have been demonstrated experimentally. Here, we propose a DNA catalytic gate architecture that appears suitable for practical synthesis of large-scale circuits involving possibly thousands of gates.", "date": "2009", "date_type": "published", "publisher": "Springer", "place_of_pub": "New York", "pagerange": "70-89", "id_number": "CaltechAUTHORS:20100707-102356969", "isbn": "978-3-642-03075-8", "book_title": "DNA computing : 14th International Meeting on DNA Computing, DNA 14, Prague, Czech Republic, June 2-9, 2008 : revised selected papers", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20100707-102356969", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "CCF-0728703" }, { "agency": "Human Frontier Science Program", "grant_number": "RGY0074/2006-C" } ] }, "doi": "10.1007/978-3-642-03076-5", "resource_type": "book_section", "pub_year": "2009", "author_list": "Qian, Lulu and Winfree, Erik" } ]