[ { "id": "https://authors.library.caltech.edu/records/38h63-czk16", "eprint_id": 104900, "eprint_status": "archive", "datestamp": "2023-08-19 16:51:42", "lastmod": "2024-01-15 17:04:04", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" } ] }, "title": "Chemical Reaction Networks and Stochastic Local Search", "ispublished": "unpub", "full_text_status": "restricted", "note": "\u00a9 2019 Springer Nature Switzerland AG. \n\nFirst Online: 24 July 2019. \n\nThis work was supported in part by National Science Foundation (NSF) grant 1317694 \u2013 The Molecular Programming Project. Thanks to Matt Cook, David Soloveichik, Chris Thachuk, William Poole, Lulu Qian, Grzegorz Rozenberg, Moshe Vardi, Tony Rojko, and Henry Lester for stimulating questions, comments, and encouragement.", "abstract": "Stochastic local search can be an effective method for solving a wide variety of optimization and constraint satisfaction problems. Here I show that some stochastic local search algorithms map naturally to stochastic chemical reaction networks. This connection highlights new ways in which stochasticity in chemical reaction networks can be used for search and thus for finding solutions to problems. The central example is a chemical reaction network construction for solving Boolean formula satisfiability problems. Using an efficient general-purpose stochastic chemical reaction network simulator, I show that direct simulation of the networks proposed here can be more efficient, in wall-clock time, than a somewhat outdated but industrial-strength commercial satisfiability solver. While not of use for practical computing, the constructions emphasize that exploiting the stochasticity inherent in chemical reaction network dynamics is not inherently inefficient \u2013 and indeed I propose that stochastic local search could be an important aspect of biological computation and should be exploited when engineering future artificial cells.", "date": "2019-07-24", "date_type": "published", "publisher": "Springer", "place_of_pub": "Cham", "pagerange": "1-20", "id_number": "CaltechAUTHORS:20200810-152243847", "isbn": "978-3-030-26806-0", "book_title": "DNA Computing and Molecular Programming", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200810-152243847", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "CCF-1317694" } ] }, "contributors": { "items": [ { "id": "Thachuk-C", "name": { "family": "Thachuk", "given": "Chris" } }, { "id": "Liu-Yan", "name": { "family": "Liu", "given": "Yan" } } ] }, "doi": "10.1007/978-3-030-26807-7_1", "resource_type": "book_section", "pub_year": "2019", "author_list": "Winfree, Erik" }, { "id": "https://authors.library.caltech.edu/records/pfxa8-yma36", "eprint_id": 104916, "eprint_status": "archive", "datestamp": "2023-08-19 16:51:50", "lastmod": "2024-01-15 17:04:06", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Zolaktaf-S", "name": { "family": "Zolaktaf", "given": "Sedigheh" } }, { "id": "Dannenberg-F", "name": { "family": "Dannenberg", "given": "Frits" } }, { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" }, { "id": "Bouchard-C\u00f4t\u00e9-A", "name": { "family": "Bouchard-C\u00f4t\u00e9", "given": "Alexandre" } }, { "id": "Schmidt-Mark", "name": { "family": "Schmidt", "given": "Mark" } }, { "id": "Condon-A", "name": { "family": "Condon", "given": "Anne" } } ] }, "title": "Efficient Parameter Estimation for DNA Kinetics Modeled as Continuous-Time Markov Chains", "ispublished": "unpub", "full_text_status": "restricted", "note": "\u00a9 2019 Springer Nature Switzerland AG. \n\nFirst Online: 24 July 2019.", "abstract": "Nucleic acid kinetic simulators aim to predict the kinetics of interacting nucleic acid strands. Many simulators model the kinetics of interacting nucleic acid strands as continuous-time Markov chains (CTMCs). States of the CTMCs represent a collection of secondary structures, and transitions between the states correspond to the forming or breaking of base pairs and are determined by a nucleic acid kinetic model. The number of states these CTMCs can form may be exponentially large in the length of the strands, making two important tasks challenging, namely, mean first passage time (MFPT) estimation and parameter estimation for kinetic models based on MFPTs. Gillespie's stochastic simulation algorithm (SSA) is widely used to analyze nucleic acid folding kinetics, but could be computationally expensive for reactions whose CTMC has a large state space or for slow reactions. It could also be expensive for arbitrary parameter sets that occur in parameter estimation. Our work addresses these two challenging tasks, in the full state space of all non-pseudoknotted secondary structures of each reaction. In the first task, we show how to use a reduced variance stochastic simulation algorithm (RVSSA), which is adapted from SSA, to estimate the MFPT of a reaction's CTMC. In the second task, we estimate model parameters based on MFPTs. To this end, first, we show how to use a generalized method of moments (GMM) approach, where we minimize a squared norm of moment functions that we formulate based on experimental and estimated MFPTs. Second, to speed up parameter estimation, we introduce a fixed path ensemble inference (FPEI) approach, that we adapt from RVSSA. We implement and evaluate RVSSA and FPEI using the Multistrand kinetic simulator. In our experiments on a dataset of DNA reactions, FPEI speeds up parameter estimation compared to inference using SSA, by more than a factor of three for slow reactions. Also, for reactions with large state spaces, it speeds up parameter estimation by more than a factor of two.", "date": "2019-07-24", "date_type": "published", "publisher": "Springer", "place_of_pub": "Cham", "pagerange": "80-99", "id_number": "CaltechAUTHORS:20200811-134907797", "isbn": "978-3-030-26806-0", "book_title": "DNA Computing and Molecular Programming", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200811-134907797", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "contributors": { "items": [ { "id": "Thachuk-C", "name": { "family": "Thachuk", "given": "Chris" } }, { "id": "Liu-Yan", "name": { "family": "Liu", "given": "Yan" } } ] }, "doi": "10.1007/978-3-030-26807-7_5", "resource_type": "book_section", "pub_year": "2019", "author_list": "Zolaktaf, Sedigheh; Dannenberg, Frits; et el." }, { "id": "https://authors.library.caltech.edu/records/5bxzs-r2p68", "eprint_id": 97512, "eprint_status": "archive", "datestamp": "2023-08-19 16:51:35", "lastmod": "2024-01-14 21:51:24", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Brailovskaya-T", "name": { "family": "Brailovskaya", "given": "Tatiana" } }, { "id": "Gowri-G", "name": { "family": "Gowri", "given": "Gokul" } }, { "id": "Yu-Sean", "name": { "family": "Yu", "given": "Sean" } }, { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" } ] }, "title": "Reversible Computation Using Swap Reactions on a Surface", "ispublished": "unpub", "full_text_status": "restricted", "note": "\u00a9 2019 Springer Nature Switzerland AG. \n\nFirst Online: 24 July 2019. \n\nT. Brailovskaya, G. Gowri and S. Yu\u2014Equal contribution. \n\nSupport from National Science Foundation grant CCF-1317694 is gratefully acknowledged. We also thank Lulu Qian and Chris Thachuk for helpful discussion and comments.", "abstract": "Chemical reaction networks (CRNs) and DNA strand displacement systems have shown potential for implementing logically and physically reversible computation. It has been shown that CRNs on a surface allow highly scalable and parallelizable computation. In this paper, we demonstrate that simple rearrangement reactions on a surface, which we refer to as swaps, are capable of physically reversible Boolean computation. We present designs for elementary logic gates, a method for constructing arbitrary feedforward digital circuits, and a proof of their correctness.", "date": "2019-07-24", "date_type": "published", "publisher": "Springer", "place_of_pub": "Cham", "pagerange": "174-196", "id_number": "CaltechAUTHORS:20190730-094203386", "isbn": "978-3-030-26806-0", "book_title": "DNA Computing and Molecular Programming", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190730-094203386", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "CCF-1317694" } ] }, "contributors": { "items": [ { "id": "Thachuk-C", "name": { "family": "Thachuk", "given": "Chris" } }, { "id": "Liu-Yan", "name": { "family": "Liu", "given": "Yan" } } ] }, "doi": "10.1007/978-3-030-26807-7_10", "resource_type": "book_section", "pub_year": "2019", "author_list": "Brailovskaya, Tatiana; Gowri, Gokul; et el." }, { "id": "https://authors.library.caltech.edu/records/txa7d-9ka65", "eprint_id": 104917, "eprint_status": "archive", "datestamp": "2023-08-19 11:25:42", "lastmod": "2024-01-15 17:04:08", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Evans-C-G", "name": { "family": "Evans", "given": "Constantine G." }, "orcid": "0000-0002-7053-1670" }, { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" } ] }, "title": "Optimizing Tile Set Size While Preserving Proofreading with a DNA Self-assembly Compiler", "ispublished": "unpub", "full_text_status": "restricted", "note": "\u00a9 2018 Springer Nature Switzerland AG. \n\nFirst Online: 07 September 2018. \n\nWe thank Chigozie Nri, Philip Petersen, Lulu Qian, and Grigory Tikhomirov for discussions and collaboration on physical implementations and the Alhambra compiler, and Robert Johnson and William Poole for discussions on aTAM equivalence. This work was partially supported by the Evans Foundation and National Science Foundation award CCF-1317694.", "abstract": "Algorithmic DNA tile systems have the potential to allow the construction by self-assembly of large structures with complex nanometer-scale details out of relatively few monomer types, but are constrained by errors in growth and the limited sequence space of orthogonal DNA sticky ends that program tile interactions. We present a tile set optimization technique that, through analysis of algorithmic growth equivalence, potentially sensitive error pathways, and potential lattice defects, can significantly reduce the size of tile systems while preserving proofreading behavior that is essential for obtaining low error rates. Applied to systems implementing multiple algorithms that are far beyond the size of currently feasible implementations, the optimization technique results in systems that are comparable in size to already-implemented experimental systems.", "date": "2018-09-07", "date_type": "published", "publisher": "Springer", "place_of_pub": "Cham", "pagerange": "37-54", "id_number": "CaltechAUTHORS:20200811-140005797", "isbn": "978-3-030-00029-5", "book_title": "DNA Computing and Molecular Programming", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200811-140005797", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Evans Foundation" }, { "agency": "NSF", "grant_number": "CCF-1317694" } ] }, "contributors": { "items": [ { "id": "Doty-D", "name": { "family": "Doty", "given": "David" } }, { "id": "Dietz-H", "name": { "family": "Dietz", "given": "Hendrik" } } ] }, "doi": "10.1007/978-3-030-00030-1_3", "resource_type": "book_section", "pub_year": "2018", "author_list": "Evans, Constantine G. and Winfree, Erik" }, { "id": "https://authors.library.caltech.edu/records/1pfn7-t7n80", "eprint_id": 91151, "eprint_status": "archive", "datestamp": "2023-08-19 04:45:15", "lastmod": "2024-01-14 21:13:24", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Badelt-S", "name": { "family": "Badelt", "given": "Stefan" } }, { "id": "Shin-Seung-Woo", "name": { "family": "Shin", "given": "Seung Woo" } }, { "id": "Johnson-R-F", "name": { "family": "Johnson", "given": "Robert F." } }, { "id": "Dong-Qing", "name": { "family": "Dong", "given": "Qing" } }, { "id": "Thachuk-C", "name": { "family": "Thachuk", "given": "Chris" } }, { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" } ] }, "title": "A General-Purpose CRN-to-DSD Compiler with Formal Verification, Optimization, and Simulation Capabilities", "ispublished": "unpub", "full_text_status": "restricted", "note": "\u00a9 Springer International Publishing AG 2017. \n\nFirst Online: 24 August 2017. \n\nWe thank the U.S. National Science Foundation for support:\nNSF Grant CCF-1213127 and NSF Grant CCF-1317694 (\"The Molecular Programming Project\"). The Gordon and Betty Moore Foundation's Programmable Molecular Technology Initiative (PMTI). SB is funded by the Caltech Biology and Biological Engineering Division Fellowship.", "abstract": "The mathematical formalism of mass-action chemical reaction networks (CRNs) has been proposed as a mid-level programming language for dynamic molecular systems. Several systematic methods for translating CRNs into domain-level strand displacement (DSD) systems have been developed theoretically, and in some cases demonstrated experimentally. Software that facilitates the simulation of CRNs and DSDs, and that helps automate the construction of DSDs from CRNs, has been instrumental in advancing the field, but as yet has not incorporated the fundamental enabling concept for programming languages and compilers: a rigorous abstraction hierarchy with well-defined semantics at each level, and rigorous correctness proofs establishing the correctness of compilation from a higher level to a lower level. Here, we present a CRN-to-DSD compiler, Nuskell, that makes a first step in this direction. To support the wide range of translation schemes that have already been proposed in the literature, as well as potential new ones that are yet to be proposed, Nuskell provides a domain-specific programming language for translation schemes. A notion of correctness is established on a case-by-case basis using the rate-independent stochastic-level theories of pathway decomposition equivalence and/or CRN bisimulation. The \"best\" DSD implementation for a given CRN can be found by comparing the molecule size, network size, or simulation behavior for a variety of translation schemes. These features are illustrated with a 3-reaction oscillator CRN and a 32-reaction feedforward boolean circuit CRN.", "date": "2017-08-24", "date_type": "published", "publisher": "Springer", "place_of_pub": "Cham, Switzerland", "pagerange": "232-248", "id_number": "CaltechAUTHORS:20181126-085056720", "isbn": "978-3-319-66798-0", "book_title": "DNA Computing and Molecular Programming", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181126-085056720", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "CCF-1213127" }, { "agency": "NSF", "grant_number": "CCF-1317694" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Caltech Division of Biology and Biological Engineering" } ] }, "contributors": { "items": [ { "id": "Brijder-R", "name": { "family": "Brijder", "given": "Robert" } }, { "id": "Qian-Lulu", "name": { "family": "Qian", "given": "Lulu" } } ] }, "doi": "10.1007/978-3-319-66799-7_15", "resource_type": "book_section", "pub_year": "2017", "author_list": "Badelt, Stefan; Shin, Seung Woo; et el." }, { "id": "https://authors.library.caltech.edu/records/tgwe9-zwv34", "eprint_id": 91153, "eprint_status": "archive", "datestamp": "2023-08-21 21:37:24", "lastmod": "2024-01-14 21:13:26", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Poole-W", "name": { "family": "Poole", "given": "William" } }, { "id": "Ortiz-Mu\u00f1oz-A", "name": { "family": "Ortiz-Mu\u00f1oz", "given": "Andr\u00e9s" }, "orcid": "0000-0003-1824-3230" }, { "id": "Behera-A", "name": { "family": "Behera", "given": "Abhishek" } }, { "id": "Jones-N-S", "name": { "family": "Jones", "given": "Nick S." } }, { "id": "Ouldridge-T-E", "name": { "family": "Ouldridge", "given": "Thomas E." } }, { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" }, { "id": "Gopalkrishnan-M", "name": { "family": "Gopalkrishnan", "given": "Manoj" } } ] }, "title": "Chemical Boltzmann Machines", "ispublished": "unpub", "full_text_status": "restricted", "keywords": "DNA origami; Knot theory; Graph theory; Chinese postman problem", "note": "\u00a9 Springer International Publishing AG 2017. \n\nFirst Online: 24 August 2017. \n\nThis work was supported in part by U.S. National Science\nFoundation (NSF) graduate fellowships to WP and to AOM, by NSF grant CCF-1317694 to EW, and by the Gordon and Betty Moore Foundation through Grant GBMF2809 to the Caltech Programmable Molecular Technology Initiative (PMTI), by a Royal Society University Research Fellowship to TEO, and by a Bharti Centre for Communication in IIT Bombay award to AB.", "abstract": "How smart can a micron-sized bag of chemicals be? How can an artificial or real cell make inferences about its environment? From which kinds of probability distributions can chemical reaction networks sample? We begin tackling these questions by showing three ways in which a stochastic chemical reaction network can implement a Boltzmann machine, a stochastic neural network model that can generate a wide range of probability distributions and compute conditional probabilities. The resulting models, and the associated theorems, provide a road map for constructing chemical reaction networks that exploit their native stochasticity as a computational resource. Finally, to show the potential of our models, we simulate a chemical Boltzmann machine to classify and generate MNIST digits in-silico.", "date": "2017-08-24", "date_type": "published", "publisher": "Springer", "place_of_pub": "Cham, Switzerland", "pagerange": "210-231", "id_number": "CaltechAUTHORS:20181126-090207704", "isbn": "978-3-319-66798-0", "book_title": "DNA Computing and Molecular Programming", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181126-090207704", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF Graduate Research Fellowship" }, { "agency": "NSF", "grant_number": "CCF-1317694" }, { "agency": "Gordon and Betty Moore Foundation", "grant_number": "GBMF2809" }, { "agency": "Royal Society" }, { "agency": "India Institute of Technology" } ] }, "contributors": { "items": [ { "id": "Brijder-R", "name": { "family": "Brijder", "given": "Robert" } }, { "id": "Qian-Lulu", "name": { "family": "Qian", "given": "Lulu" } } ] }, "doi": "10.1007/978-3-319-66799-7_14", "resource_type": "book_section", "pub_year": "2017", "author_list": "Poole, William; Ortiz-Mu\u00f1oz, Andr\u00e9s; et el." }, { "id": "https://authors.library.caltech.edu/records/xp5nf-fxf94", "eprint_id": 91155, "eprint_status": "archive", "datestamp": "2023-08-19 04:45:31", "lastmod": "2024-01-14 21:13:30", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Zolaktaf-S", "name": { "family": "Zolaktaf", "given": "Sedigheh" } }, { "id": "Dannenberg-F", "name": { "family": "Dannenberg", "given": "Frits" } }, { "id": "Rudelis-X", "name": { "family": "Rudelis", "given": "Xander" } }, { "id": "Condon-A", "name": { "family": "Condon", "given": "Anne" } }, { "id": "Schaeffer-J-M", "name": { "family": "Schaeffer", "given": "Joseph M." } }, { "id": "Schmidt-Mark", "name": { "family": "Schmidt", "given": "Mark" } }, { "id": "Thachuk-C", "name": { "family": "Thachuk", "given": "Chris" } }, { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" } ] }, "title": "Inferring Parameters for an Elementary Step Model of DNA Structure Kinetics with Locally Context-Dependent Arrhenius Rates", "ispublished": "unpub", "full_text_status": "restricted", "note": "\u00a9 Springer International Publishing AG 2017. \n\nFirst Online: 24 August 2017. \n\nWe thank the U.S. National Science Foundation (awards 0832824, 1213127, 1317694, 1643606), the Gordon and Betty Moore Foundation's Programmable Molecular Technology Initiative, and the Natural Sciences and Engineering Research Council of Canada for support. We also thank the anonymous reviewers for their helpful comments and suggestions.", "abstract": "Models of nucleic acid thermal stability are calibrated to a wide range of experimental observations, and typically predict equilibrium probabilities of nucleic acid secondary structures with reasonable accuracy. By comparison, a similar calibration and evaluation of nucleic acid kinetic models to a broad range of measurements has not been attempted so far. We introduce an Arrhenius model of interacting nucleic acid kinetics that relates the activation energy of a state transition with the immediate local environment of the affected base pair. Our model can be used in stochastic simulations to estimate kinetic properties and is consistent with existing thermodynamic models. We infer parameters for our model using an ensemble Markov chain Monte Carlo (MCMC) approach on a training dataset with 320 kinetic measurements of hairpin closing and opening, helix association and dissociation, bubble closing and toehold-mediated strand exchange. Our new model surpasses the performance of the previously established Metropolis model both on the training set and on a testing set of size 56 composed of toehold-mediated 3-way strand displacement with mismatches and hairpin opening and closing rates: reaction rates are predicted to within a factor of three for 93.4% and 78.5% of reactions for the training and testing sets, respectively.", "date": "2017-08-24", "date_type": "published", "publisher": "Springer", "place_of_pub": "Cham, Switzerland", "pagerange": "172-187", "id_number": "CaltechAUTHORS:20181126-091545698", "isbn": "978-3-319-66798-0", "book_title": "DNA Computing and Molecular Programming", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20181126-091545698", "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": "IIS-1213127" }, { "agency": "NSF", "grant_number": "CCF-1317694" }, { "agency": "NSF", "grant_number": "CHE-1643606" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Natural Sciences and Engineering Research Council of Canada (NSERC)" } ] }, "contributors": { "items": [ { "id": "Brijder-R", "name": { "family": "Brijder", "given": "Robert" } }, { "id": "Qian-Lulu", "name": { "family": "Qian", "given": "Lulu" } } ] }, "doi": "10.1007/978-3-319-66799-7_12", "resource_type": "book_section", "pub_year": "2017", "author_list": "Zolaktaf, Sedigheh; Dannenberg, Frits; et el." }, { "id": "https://authors.library.caltech.edu/records/sm0c6-t7n21", "eprint_id": 79158, "eprint_status": "archive", "datestamp": "2023-08-20 13:23:50", "lastmod": "2024-01-13 20:35:50", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Schiefer-N", "name": { "family": "Schiefer", "given": "Nicholas" } }, { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" } ] }, "title": "Time Complexity of Computation and Construction in the Chemical Reaction Network-Controlled Tile Assembly Model", "ispublished": "unpub", "full_text_status": "restricted", "note": "\u00a9 2016 Springer International Publishing Switzerland. \n\nFirst Online: 14 August 2016.\n\nWe acknowledge financial support from National Science Foundation grant CCF-1317694 and the Soli Deo Gloria Summer Undergraduate Research Fellowship at the California Institute of Technology. We also thank Dave Doty and Damien Woods for their insights.", "abstract": "In isolation, chemical reaction networks and tile-based self-assembly are well-studied models of chemical computation. Previously, we introduced the chemical reaction network-controlled tile assembly model (CRN-TAM), in which a stochastic chemical reaction network can act as a non-local control and signalling system for tile-based assembly, and showed that the CRN-TAM can perform several tasks related to the simulation of Turing machines and construction of algorithmic shapes with lower space or program complexity than in either of its parent models. Here, we introduce a kinetic variant of the CRN-TAM and investigate the time complexity of computation and construction. We analyze the time complexity of decision problems in the CRN-TAM, and show that decidable languages can be decided as efficiently by CRN-TAM programs as by Turing machines. We also give a lower bound for the space-time complexity of CRN-TAM computation that rules out efficient parallel stack machines. We provide efficient parallel implementations of non-deterministic computations, showing among other things that CRN-TAM programs can decide languages in NTIME(f(n))\u2229coNTIME(f(n)) in O(f(n)+n+logc) time with 1\u2212exp(\u2212c) probability, using volume exponential in n. Lastly, we provide basic mechanisms for parallel computations that share information and illustrate the limits of parallel computation in the CRN-TAM.", "date": "2016-08-14", "date_type": "published", "publisher": "Springer", "place_of_pub": "Cham, Switzerland", "pagerange": "165-182", "id_number": "CaltechAUTHORS:20170718-122926337", "isbn": "978-3-319-43993-8", "book_title": "DNA Computing and Molecular Programming", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170718-122926337", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "CCF-1317694" }, { "agency": "Caltech Summer Undergraduate Research Fellowship (SURF)" } ] }, "contributors": { "items": [ { "id": "Rondelez-Y", "name": { "family": "Rondelez", "given": "Yannick" } }, { "id": "Woods-D", "name": { "family": "Woods", "given": "Damien" } } ] }, "doi": "10.1007/978-3-319-43994-5_11", "resource_type": "book_section", "pub_year": "2016", "author_list": "Schiefer, Nicholas and Winfree, Erik" }, { "id": "https://authors.library.caltech.edu/records/5a09z-v9n43", "eprint_id": 99129, "eprint_status": "archive", "datestamp": "2023-08-20 13:23:53", "lastmod": "2024-01-14 21:58:58", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Johnson-R-F", "name": { "family": "Johnson", "given": "Robert F." } }, { "id": "Dong-Qing", "name": { "family": "Dong", "given": "Qing" } }, { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" } ] }, "title": "Verifying Chemical Reaction Network Implementations: A Bisimulation Approach", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 2016 Springer International Publishing Switzerland. \n\nFirst Online 14 August 2016. \n\nThe authors would like to thank Chris Thachuk, Damien Woods, Dave Doty, and Seung Woo Shin for helpful discussions. RFJ and EW were supported by NSF grants 1317694, 1213127, and 0832824. RFJ was supported by Caltech's Summer Undergraduate Research Fellowship program and an NSF graduate fellowship. QD's current affiliation is Epic Systems, Madison, Wisconsin.", "abstract": "Efforts in programming DNA and other biological molecules have recently focused on general schemes to physically implement arbitrary Chemical Reaction Networks. Errors in some of the proposed schemes have driven a desire for formal verification methods. We show that by interpreting each implementation species as a set of formal species, the concept of weak bisimulation can be adapted to CRNs in a way that agrees with an intuitive notion of a correct implementation. We give examples of how to use bisimulation to prove the correctness of an implementation or detect subtle problems. We examine the complexity of finding a valid interpretation between two CRNs if one exists, and that of checking whether an interpretation is valid. We show that both are PSPACE-complete in the general case, but are NP-complete and polynomial-time respectively under an assumption that holds in many practical cases. We give algorithms for both of those problems.", "date": "2016-08-14", "date_type": "published", "publisher": "Springer", "place_of_pub": "Cham", "pagerange": "114-134", "id_number": "CaltechAUTHORS:20191007-155606936", "isbn": "9783319439938", "book_title": "DNA Computing and Molecular Programming", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20191007-155606936", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "CCF-1317694" }, { "agency": "NSF", "grant_number": "IIS-1213127" }, { "agency": "NSF", "grant_number": "CCF-0832824" }, { "agency": "Caltech Summer Undergraduate Research Fellowship (SURF)" }, { "agency": "NSF Graduate Research Fellowship" } ] }, "contributors": { "items": [ { "id": "Rondelez-Y", "name": { "family": "Rondelez", "given": "Yannick" } }, { "id": "Woods-D", "name": { "family": "Woods", "given": "Damien" } } ] }, "doi": "10.1007/978-3-319-43994-5_8", "resource_type": "book_section", "pub_year": "2016", "author_list": "Johnson, Robert F.; Dong, Qing; et el." }, { "id": "https://authors.library.caltech.edu/records/b9keh-ytk18", "eprint_id": 104932, "eprint_status": "archive", "datestamp": "2023-08-22 16:01:35", "lastmod": "2024-01-15 17:04:14", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Thachuk-C", "name": { "family": "Thachuk", "given": "Chris" } }, { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" }, { "id": "Soloveichik-D", "name": { "family": "Soloveichik", "given": "David" }, "orcid": "0000-0002-2585-4120" } ] }, "title": "Leakless DNA Strand Displacement Systems", "ispublished": "unpub", "full_text_status": "restricted", "keywords": "Strand Displacement; Leak Pathway; Bottom Strand; Complementary Domain; Hypothetical Experiment", "note": "\u00a9 2015 Springer International Publishing Switzerland. \n\nFirst Online: 21 July 2015. \n\nThe authors are supported by a Banting Fellowship (CT), NSF CCF/HCC Grant No. 1213127, NSF CCF Grant No. 1317694, and NIGMS Systems Biology Center grant P50 GM081879 (DS). We thank Boya Wang and Robert Machinek for helpful discussions.", "abstract": "While current experimental demonstrations have been limited to small computational tasks, DNA strand displacement systems (DSD systems) [25] hold promise for sophisticated information processing within chemical or biological environments. A DSD system encodes designed reactions that are facilitated by three-way or four-way toehold-mediated strand displacement. However, such systems are capable of spurious displacement events that lead to leak: incorrect signal production. We have identified sources of leak pathways in typical existing DSD schemes that rely on toehold sequestration and are susceptible to toeless strand displacement (i.e. displacement reactions that occur despite the absence of a toehold). Based on this understanding, we propose a simple, domain-level motif for the design of leak-resistant DSD systems. This motif forms the basis of a number of DSD schemes that do not rely on toehold sequestration alone to prevent spurious displacements. Spurious displacements are still possible in our systems, but require multiple, low probability events to occur. Our schemes can implement combinatorial Boolean logic formulas and can be extended to implement arbitrary chemical reaction networks.", "date": "2015-07-21", "date_type": "published", "publisher": "Springer", "place_of_pub": "Cham", "pagerange": "133-153", "id_number": "CaltechAUTHORS:20200812-120743269", "isbn": "978-3-319-21998-1", "book_title": "DNA Computing and Molecular Programming", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200812-120743269", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Natural Sciences and Engineering Research Council of Canada (NSERC)" }, { "agency": "NSF", "grant_number": "CCF-1213127" }, { "agency": "NSF", "grant_number": "CCF-1317694" }, { "agency": "NIH", "grant_number": "P50 GM081879" } ] }, "contributors": { "items": [ { "id": "Phillips-A", "name": { "family": "Phillips", "given": "Andrew" } }, { "id": "Yin-Peng", "name": { "family": "Yin", "given": "Peng" } } ] }, "doi": "10.1007/978-3-319-21999-8_9", "resource_type": "book_section", "pub_year": "2015", "author_list": "Thachuk, Chris; Winfree, Erik; et el." }, { "id": "https://authors.library.caltech.edu/records/pvacj-t2m32", "eprint_id": 104920, "eprint_status": "archive", "datestamp": "2023-08-22 16:01:28", "lastmod": "2024-01-15 17:04:10", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Schaeffer-Joseph-Malcolm", "name": { "family": "Schaeffer", "given": "Joseph Malcolm" } }, { "id": "Thachuk-C", "name": { "family": "Thachuk", "given": "Chris" } }, { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" } ] }, "title": "Stochastic Simulation of the Kinetics of Multiple Interacting Nucleic Acid Strands", "ispublished": "unpub", "full_text_status": "restricted", "keywords": "Single Base Pair; Continuous Time Markov Process; Gillespie Algorithm; Loop Graph; Pseudoknotted Structure", "note": "\u00a9 2015 Springer International Publishing Switzerland. \n\nFirst Online: 21 July 2015. \n\nWe are greatly indebted to years of insights, suggestions, and feedback from Niles Pierce, Robert Dirks, Justin Bois, and Victor Beck, especially their contributions to the formulation of the energy model and the first step simulation mode. This work has been funded by National Science Foundation grants DMS-0506468, CCF-0832824, CCF-1213127, CCF-1317694, and the Gordon and Betty Moore Foundation through the Caltech Programmable Molecular Technology Initiative.", "abstract": "DNA nanotechnology is an emerging field which utilizes the unique structural properties of nucleic acids in order to build nanoscale devices, such as logic gates, motors, walkers, and algorithmic structures. Predicting the structure and interactions of a DNA device requires effective modeling of both the thermodynamics and the kinetics of the DNA strands within the system. The kinetics of a set of DNA strands can be modeled as a continuous time Markov process through the state space of all secondary structures. The primary means of exploring the kinetics of a DNA system is by simulating trajectories through the state space and aggregating data over many such trajectories. We expand on previous work by extending the thermodynamics and kinetics models to handle multiple strands in a fixed volume, in a way that is consistent with previous models. We developed data structures and algorithms that allow us to take advantage of local properties of secondary structure, improving the efficiency of the simulator so that we can handle reasonably large systems. Finally, we illustrate the simulator's analysis methods on a simple case study.", "date": "2015-07-21", "date_type": "published", "publisher": "Springer", "place_of_pub": "Cham", "pagerange": "194-211", "id_number": "CaltechAUTHORS:20200811-152309514", "isbn": "978-3-319-21998-1", "book_title": "DNA Computing and Molecular Programming", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200811-152309514", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "DMS-0506468" }, { "agency": "NSF", "grant_number": "CCF-0832824" }, { "agency": "NSF", "grant_number": "CCF-1213127" }, { "agency": "NSF", "grant_number": "CCF-1317694" }, { "agency": "Gordon and Betty Moore Foundation" }, { "agency": "Caltech Programmable Molecular Technology Initiative" } ] }, "contributors": { "items": [ { "id": "Phillips-Andrew", "name": { "family": "Phillips", "given": "Andrew" } }, { "id": "Yin-Peng", "name": { "family": "Yin", "given": "Peng" } } ] }, "doi": "10.1007/978-3-319-21999-8_13", "resource_type": "book_section", "pub_year": "2015", "author_list": "Schaeffer, Joseph Malcolm; Thachuk, Chris; et el." }, { "id": "https://authors.library.caltech.edu/records/0tq84-hgv56", "eprint_id": 60077, "eprint_status": "archive", "datestamp": "2023-08-20 04:10:26", "lastmod": "2024-01-13 16:24:42", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Schiefer-N", "name": { "family": "Schiefer", "given": "Nicholas" } }, { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" } ] }, "title": "Universal Computation and Optimal Construction in the Chemical Reaction Network-Controlled Tile Assembly Model", "ispublished": "unpub", "full_text_status": "restricted", "note": "\u00a9 2015 Springer. \n\nWe acknowledge financial support from National Science Foundation grant CCF-1317694. We also thank Dave Doty, for his helpful comments and suggestions, and Kevin Li, for his useful suggestions on an early draft of this paper.", "abstract": "Tile-based self-assembly and chemical reaction networks provide two well-studied models of scalable DNA-based computation. Although tile self-assembly provides a powerful framework for describing Turing-universal self-assembling systems, assembly logic in tile self-assembly is localized, so that only the nearby environment can affect the process of self-assembly. We introduce a new model of tile-based self-assembly in which a well-mixed chemical reaction network interacts with self-assembling tiles to exert non-local control on the self-assembly process. Through simulation of multi-stack machines, we demonstrate that this new model is efficiently Turing-universal, even when restricted to unbounded space in only one spatial dimension. Using a natural notion of program complexity, we also show that this new model can produce many complex shapes with programs of lower complexity. Most notably, we show that arbitrary connected shapes can be produced by a program with complexity bounded by the Kolmogorov complexity of the shape, without the large scale factor that is required for the analogous result in the abstract tile assembly model. These results suggest that controlled self-assembly provides additional algorithmic power over tile-only self-assembly, and that non-local control enhances our ability to perform computation and algorithmically self-assemble structures from small input programs.", "date": "2015", "date_type": "published", "publisher": "Springer", "place_of_pub": "Cham, Switzerland", "pagerange": "34-54", "id_number": "CaltechAUTHORS:20150904-111819530", "isbn": "978-3-319-21998-1", "book_title": "DNA Computing and Molecular Programming: 21st International Conference, DNA 21, Boston and Cambridge, MA, USA, August 17-21, 2015. Proceedings", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20150904-111819530", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "CCF-1317694" } ] }, "doi": "10.1007/978-3-319-21999-8_3", "resource_type": "book_section", "pub_year": "2015", "author_list": "Schiefer, Nicholas and Winfree, Erik" }, { "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/esd5f-zr675", "eprint_id": 36616, "eprint_status": "archive", "datestamp": "2023-08-19 14:08:32", "lastmod": "2023-10-20 23:24:08", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Woods-D", "name": { "family": "Woods", "given": "Damien" } }, { "id": "Chen-H-L", "name": { "family": "Chen", "given": "Ho-Lin" } }, { "id": "Goodfriend-S", "name": { "family": "Goodfriend", "given": "Scott" } }, { "id": "Dabby-N", "name": { "family": "Dabby", "given": "Nadine" } }, { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" }, { "id": "Yin-P", "name": { "family": "Yin", "given": "Peng" } } ] }, "title": "Active Self-Assembly of Algorithmic Shapes and Patterns in Polylogarithmic Time", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 2013 held by the author/owner(s). ITCS'13, January 9\u201312, 2013, Berkeley, California, USA. ACM 978-1-4503-1859-4/13/01. Supported by NSF grants CCF-1219274, CCF-1162589, and 0832824|the Molecular Programming Project, an NSF Graduate Fellowship, and The Caltech Center for Biological Circuit Design. Many thanks to Niles Pierce and Patrick Mullen for valuable discussions.\n\n
Submitted - 1301.2626v1.pdf
", "abstract": "We describe a computational model for studying the complexity of self-assembled structures with active molecular components. Our model captures notions of growth and movement ubiquitous in biological systems. The model is inspired by biology's fantastic ability to assemble biomolecules that form systems with complicated structure and dynamics, from molecular motors that walk on rigid tracks and proteins that dynamically alter the structure of the cell during mitosis, to embryonic development where large-scale complicated organisms efficiently grow from a single cell. Using this active self-assembly model, we show how to efficiently self-assemble shapes and patterns from simple monomers. For example, we show how to grow a line of monomers in time and number of monomer states that is merely logarithmic in the length of the line.\nOur main results show how to grow arbitrary connected two-dimensional geometric shapes and patterns in expected time that is polylogarithmic in the size of the shape, plus roughly the time required to run a Turing machine deciding whether or not a given pixel is in the shape. We do this while keeping the number of monomer types logarithmic in shape size, plus those monomers required by the Kolmogorov complexity of the shape or pattern. This work thus highlights the efficiency advantages of active self-assembly over passive self-assembly and motivates experimental effort to construct general-purpose active molecular self-assembly systems.", "date": "2013-01", "date_type": "published", "publisher": "ACM", "place_of_pub": "New York, NY", "pagerange": "353-354", "id_number": "CaltechAUTHORS:20130128-100842529", "isbn": "978-1-4503-1859-4", "book_title": "Proceedings of the 4th conference on Innovations in Theoretical Computer Science", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20130128-100842529", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "CCF-1219274" }, { "agency": "NSF", "grant_number": "CCF-1162589" }, { "agency": "NSF Molecular Programming Project", "grant_number": "0832824" }, { "agency": "NSF Graduate Fellowship" }, { "agency": "Caltech Center for Biological Circuit Design" } ] }, "doi": "10.1145/2422436.2422476", "primary_object": { "basename": "1301.2626v1.pdf", "url": "https://authors.library.caltech.edu/records/esd5f-zr675/files/1301.2626v1.pdf" }, "resource_type": "book_section", "pub_year": "2013", "author_list": "Woods, Damien; Chen, Ho-Lin; et el." }, { "id": "https://authors.library.caltech.edu/records/5mdh8-pp183", "eprint_id": 46019, "eprint_status": "archive", "datestamp": "2023-08-19 14:03:24", "lastmod": "2024-01-13 16:05:28", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Evans-C-G", "name": { "family": "Evans", "given": "Constantine G." }, "orcid": "0000-0002-7053-1670" }, { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" } ] }, "title": "DNA Sticky End Design and Assignment for Robust Algorithmic Self-assembly", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 2013 Springer International Publishing Switzerland.\n\nAccepted Version - StickyDesign2013.pdf
", "abstract": "A major challenge in practical DNA tile self-assembly is the minimization of errors. Using the kinetic Tile Assembly Model, a theoretical model of self-assembly, it has been shown that errors can be reduced through abstract tile set design. In this paper, we instead investigate the effects of \"sticky end\" sequence choices in systems using the kinetic model along with the nearest-neighbor model of DNA interactions. We show that both the sticky end sequences present in a system and their positions in the system can significantly affect error rates, and propose algorithms for sequence design and assignment.", "date": "2013", "date_type": "published", "publisher": "Springer", "place_of_pub": "Cham, Switzerland", "pagerange": "61-75", "id_number": "CaltechAUTHORS:20140530-150254025", "isbn": "978-3-319-01927-7", "book_title": "DNA Computing and Molecular Programming", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20140530-150254025", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "contributors": { "items": [ { "id": "Soloveichik-D", "name": { "family": "Soloveichik", "given": "David" } }, { "id": "Yurke-B", "name": { "family": "Yurke", "given": "Bernard" } } ] }, "doi": "10.1007/978-3-319-01928-4_5", "primary_object": { "basename": "StickyDesign2013.pdf", "url": "https://authors.library.caltech.edu/records/5mdh8-pp183/files/StickyDesign2013.pdf" }, "resource_type": "book_section", "pub_year": "2013", "author_list": "Evans, Constantine G. and Winfree, Erik" }, { "id": "https://authors.library.caltech.edu/records/jm59x-m4z18", "eprint_id": 31573, "eprint_status": "archive", "datestamp": "2023-08-19 06:57:53", "lastmod": "2023-10-17 18:41:04", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Densmore-D", "name": { "family": "Densmore", "given": "Douglas" } }, { "id": "Horowitz-M", "name": { "family": "Horowitz", "given": "Mark" } }, { "id": "Krishnaswamy-S", "name": { "family": "Krishnaswamy", "given": "Smita" } }, { "id": "Shen-X", "name": { "family": "Shen", "given": "Xiling" } }, { "id": "Arkin-A", "name": { "family": "Arkin", "given": "Adam" } }, { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" }, { "id": "Voigt-C", "name": { "family": "Voigt", "given": "Chris" } } ] }, "title": "Joint DAC/IWBDA special session design and synthesis of biological circuits", "ispublished": "unpub", "full_text_status": "restricted", "keywords": "bio-design automation, genetic compiler, chemical reaction\nnetworks, molecular computation, biological parts", "note": "\u00a9 2011 ACM.", "abstract": "With the growing complexity of synthetic biological circuits, robust and systematic methods are needed for design and test. Leveraging lessons learned from the semiconductor and design automation industries, synthetic biologists are starting to adopt computer-aided design and verification software with some success. However, due to the great challenges associated with designing synthetic biological circuits, this nascent approach has to address many problems not present in electronic circuits. In this session, three leading synthetic biologists will share how they have developed software tools to help design and verify their synthetic circuits, the unique challenges they face, and their insights into the next generation of tools for synthetic biology.", "date": "2011-06", "date_type": "published", "publisher": "Association for Computing Machinery (ACM)", "place_of_pub": "New York", "pagerange": "114-115", "id_number": "CaltechAUTHORS:20120521-113649301", "isbn": "978-1-4503-0636-2", "book_title": "Proceedings of the 48th Design Automation Conference", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20120521-113649301", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "doi": "10.1145/2024724.2024750", "resource_type": "book_section", "pub_year": "2011", "author_list": "Densmore, Douglas; Horowitz, Mark; et el." }, { "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\nSubmitted - 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/52pjb-zvg80", "eprint_id": 27411, "eprint_status": "archive", "datestamp": "2023-08-19 04:54:36", "lastmod": "2024-01-13 05:44:15", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Schulman-R", "name": { "family": "Schulman", "given": "Rebecca" }, "orcid": "0000-0003-4555-3162" }, { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" } ] }, "title": "Simple Evolution of Complex Crystal Species", "ispublished": "unpub", "full_text_status": "restricted", "note": "\u00a9 2011 Springer-Verlag Berlin Heidelberg.", "abstract": "Cairns-Smith has proposed that life began as structural patterns in clays that self-replicated during cycles of crystal growth and fragmentation. Complex, evolved crystal forms could then have catalyzed the formation of a more advanced genetic material. A crucial weakness of this theory is that it is unclear how complex crystals might arise through Darwinian selection. Here we investigate whether complex crystal patterns could evolve using a model system for crystal growth, DNA tile crystals, that is amenable to both theoretical and experimental inquiry. It was previously shown that in principle, the evolution of crystals assembled from a set of thousands of DNA tiles under very specific environmental conditions could produce arbitrarily complex patterns. Here we show that evolution driven only by the dearth of one monomer type could produce complex crystals from just 12 monomer types. The proposed mechanism of evolution is simple enough to test experimentally and is sufficiently general that it may apply to other DNA tile crystals or even to natural crystals, suggesting that complex crystals could evolve from simple starting materials because of relative differences in concentrations of the materials needed for growth.", "date": "2011", "date_type": "published", "publisher": "Springer", "place_of_pub": "Berlin", "pagerange": "147-161", "id_number": "CaltechAUTHORS:20111025-131913963", "isbn": "978-3-642-18304-1", "book_title": "DNA Computing and Molecular Programming", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111025-131913963", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "contributors": { "items": [ { "id": "Sakakibara-Y", "name": { "family": "Sakakibara", "given": "Yasubumi" } }, { "id": "Mi-Y-L", "name": { "family": "Mi", "given": "Yongli L." } } ] }, "doi": "10.1007/978-3-642-18305-8_14", "resource_type": "book_section", "pub_year": "2011", "author_list": "Schulman, Rebecca and Winfree, Erik" }, { "id": "https://authors.library.caltech.edu/records/pgm0a-wzh97", "eprint_id": 27327, "eprint_status": "archive", "datestamp": "2023-08-20 02:33:35", "lastmod": "2024-01-13 05:43:51", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cook-M", "name": { "family": "Cook", "given": "Matthew" } }, { "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" }, { "id": "Bruck-J", "name": { "family": "Bruck", "given": "Jehoshua" }, "orcid": "0000-0001-8474-0812" } ] }, "title": "Programmability of Chemical Reaction Networks", "ispublished": "unpub", "full_text_status": "restricted", "note": "\u00a9 2009 Springer-Verlag Berlin Heidelberg. \n\nThe research was supported in part by the \"Alpha Project\" at the Center for Genomic Experimentation and Computation, an NIH Center of Excellence (grant number P50 HG02370), as well as NSF Grants No. 0523761 and 0728703 to EW and NIMH Training Grant MH19138-15.", "abstract": "Motivated by the intriguing complexity of biochemical circuitry within individual cells we study Stochastic Chemical Reaction Networks (SCRNs), a formal model that considers a set of chemical reactions acting on a finite number of molecules in a well-stirred solution according to standard chemical kinetics equations. SCRNs have been widely used for describing naturally occurring (bio)chemical systems, and with the advent of synthetic biology they become a promising language for the design of artificial biochemical circuits. Our interest here is the computational power of SCRNs and how they relate to more conventional models of computation. We survey known connections and give new connections between SCRNs and Boolean Logic Circuits, Vector Addition Systems, Petri nets, Gate Implementability, Primitive Recursive Functions, Register Machines, Fractran, and Turing Machines. A theme to these investigations is the thin line between decidable and undecidable questions about SCRN behavior.", "date": "2009-08-13", "date_type": "published", "publisher": "Springer-Verlag", "place_of_pub": "Berlin", "pagerange": "543-584", "id_number": "CaltechAUTHORS:20111020-103016495", "isbn": "978-3-540-88868-0", "book_title": "Algorithmic Bioprocesses", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111020-103016495", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P50 HG02370" }, { "agency": "NSF", "grant_number": "CCF-0523761" }, { "agency": "NSF", "grant_number": "CCF-0728703" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "MH19138-15" } ] }, "contributors": { "items": [ { "id": "Condon-A", "name": { "family": "Condon", "given": "Anne" } }, { "id": "Salomaa-A", "name": { "family": "Salomaa", "given": "Arto" } }, { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" } }, { "id": "Harel-D", "name": { "family": "Harel", "given": "David" } }, { "id": "Kok-J-N", "name": { "family": "Kok", "given": "Joost N." } } ] }, "doi": "10.1007/978-3-540-88869-7_27", "resource_type": "book_section", "pub_year": "2009", "author_list": "Cook, Matthew; 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" }, { "id": "https://authors.library.caltech.edu/records/n9ee2-a1452", "eprint_id": 104933, "eprint_status": "archive", "datestamp": "2023-08-22 14:03:06", "lastmod": "2024-01-15 17:04:16", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Soloveichik-D", "name": { "family": "Soloveichik", "given": "David" }, "orcid": "0000-0002-2585-4120" }, { "id": "Seelig-G", "name": { "family": "Seelig", "given": "Georg" } }, { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" } ] }, "title": "DNA as a Universal Substrate for Chemical Kinetics", "ispublished": "unpub", "full_text_status": "restricted", "keywords": "Formal Species; Bimolecular Reaction; Strand Displacement; Unimolecular Reaction; Mass Action Kinetic", "note": "\u00a9 2009 Springer-Verlag Berlin Heidelberg. \n\nThis work was supported by NSF Grant 0728703. GS acknowledges support from the Swiss National Science Foundation and the Burroughs Wellcome Fund. We thank D. Zhang, J. Schaeffer, and M. Magnasco for useful discussions.", "abstract": "We show that a DNA-based chemical system can be constructed such that it closely approximates the dynamic behavior of an arbitrary system of coupled chemical reactions. Using strand displacement reactions as a primitive we explicitly construct reaction cascades with effectively unimolecular and bimolecular kinetics. Our construction allows for individual reactions to be coupled in arbitrary ways such that reactants can participate in multiple reactions simultaneously, correctly reproducing the desired dynamical properties. Thus arbitrary systems of chemical equations can be compiled into chemistry. We illustrate our method on a chaotic R\u00f6ssler attractor; simulations of the attractor and of our proposed DNA-based implementation show good agreement.", "date": "2009", "date_type": "published", "publisher": "Springer", "place_of_pub": "Berlin", "pagerange": "57-69", "id_number": "CaltechAUTHORS:20200812-121640271", "isbn": "978-3-642-03075-8", "book_title": "DNA Computing", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200812-121640271", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "CCF-0728703" }, { "agency": "Swiss National Science Foundation (SNSF)" }, { "agency": "Burroughs Wellcome Fund" } ] }, "contributors": { "items": [ { "id": "Goel-A", "name": { "family": "Goel", "given": "Ashish" } }, { "id": "Simmel-F-C", "name": { "family": "Simmel", "given": "Friedrich C." } }, { "id": "Sos\u00edk-P", "name": { "family": "Sos\u00edk", "given": "Petr" } } ] }, "doi": "10.1007/978-3-642-03076-5_6", "resource_type": "book_section", "pub_year": "2009", "author_list": "Soloveichik, David; Seelig, Georg; et el." }, { "id": "https://authors.library.caltech.edu/records/2n7w7-0kb24", "eprint_id": 73272, "eprint_status": "archive", "datestamp": "2023-08-19 22:17:53", "lastmod": "2023-10-24 15:11:07", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" } ] }, "title": "Toward molecular programming with DNA", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 2008 ACM.\n\nPresentation - 1346282.mp3
Presentation - 1346282.mp4
Presentation - p1-erik-slides.zip
", "abstract": "Biological organisms are beautiful examples of programming. The program and data are stored in biological molecules such as DNA, RNA, and proteins; the algorithms are carried out by molecular and biochemical processes; and the end result is the creation and function of an organism. If we understood how to program molecular systems, what could we create? Lifelike technologies whose basic operations are chemical reactions? The fields of chemistry, physics, biology, and computer science are converging as we begin to synthesize molecules, molecular machines, and molecular systems of ever increasing complexity, leading to subdisciplines such as DNA nanotechnology, DNA computing, and synthetic biology. Having demonstrated simple devices and systems -- self-assembled structures, molecular motors, chemical logic gates -- researchers are now turning to the question of how to create large-scale integrated systems. To do so, we must learn how to manage complexity: how to efficiently specify the structure and behavior of intricate molecular systems, how to compile such specifications down to the design of molecules to be synthesized in the lab, and how to ensure that such systems function robustly. These issues will be illustrated for chemical logic circuits based on cascades of DNA hybridization reactions.", "date": "2008-03", "date_type": "published", "publisher": "ACM", "place_of_pub": "New York, NY", "id_number": "CaltechAUTHORS:20170105-124404623", "isbn": "978-1-59593-958-6", "book_title": "ASPLOS XIII Proceedings of the 13th international conference on Architectural support for programming languages and operating systems", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20170105-124404623", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "contributors": { "items": [ { "id": "Eggers-S", "name": { "family": "Eggers", "given": "Susan" } } ] }, "doi": "10.1145/1346281.1346282", "primary_object": { "basename": "1346282.mp3", "url": "https://authors.library.caltech.edu/records/2n7w7-0kb24/files/1346282.mp3" }, "related_objects": [ { "basename": "1346282.mp4", "url": "https://authors.library.caltech.edu/records/2n7w7-0kb24/files/1346282.mp4" }, { "basename": "p1-erik-slides.zip", "url": "https://authors.library.caltech.edu/records/2n7w7-0kb24/files/p1-erik-slides.zip" } ], "resource_type": "book_section", "pub_year": "2008", "author_list": "Winfree, Erik" }, { "id": "https://authors.library.caltech.edu/records/awcyr-76y79", "eprint_id": 24776, "eprint_status": "archive", "datestamp": "2023-08-19 17:01:57", "lastmod": "2023-10-24 14:55:21", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" } ] }, "title": "Algorithmic Self-Assembly of DNA", "ispublished": "unpub", "full_text_status": "restricted", "note": "\u00a9 2006 IEEE.\n\nIssue Date: 9-12 May 2006; Date of Current Version: 30 July 2007.", "abstract": "Nucleic acids have proven to be remarkably versatile as an engineering material for chemical tasks including the storage of information, catalyzing reactions creating and breaking bonds, mechanical manipulation using molecular motors, and constructing supramolecular structures. This talk will focus particularly on molecular self-assembly, giving examples of engineered DNA \"tiles\" that crystallize into two-dimensional sheets, one-dimensional tubes and ribbons, and information-guided patterns such as a Sierpinski triangle and a binary counter. A theme is how cooperative binding can be used to control nucleation and direct selective tile attachment. Such \"algorithmic\" self-assembly may provide a bottom-up fabrication method for creating complex, well-defined supramolecular structures that can be used as scaffolds or templates for applications such as arranging molecular electronic components into active circuits.", "date": "2006", "date_type": "published", "publisher": "IEEE", "place_of_pub": "Piscataway, NJ", "pagerange": "4-4", "id_number": "CaltechAUTHORS:20110810-095116353", "isbn": "978-1-4244-0337-0", "book_title": "Proceedings of the 2006 International Conference on Microtechnologies in Medicine and Biology", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110810-095116353", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "other_numbering_system": { "items": [ { "id": "9296580", "name": "INSPEC Accession Number" } ] }, "resource_type": "book_section", "pub_year": "2006", "author_list": "Winfree, Erik" }, { "id": "https://authors.library.caltech.edu/records/f3tmg-p8p50", "eprint_id": 22756, "eprint_status": "archive", "datestamp": "2023-08-19 16:55:57", "lastmod": "2024-01-13 00:10:53", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "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": "Complexity of compact proofreading for self-assembled patterns", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 2006 Springer-Verlag Berlin Heidelberg. \n\nWe thank Ho-Lin Chen, Ashish Goel, Paul Rothemund, Matthew Cook, and Nata\u0161a Jonoska for discussions that greatly contributed to this work. This work was supported by NSF NANO Grant No. 0432193.\n\nSubmitted - fragile_patterns_preprint_1_.pdf
", "abstract": "Fault-tolerance is a critical issue for biochemical computation. Recent theoretical work on algorithmic self-assembly has shown that error\n correcting tile sets are possible, and that they can achieve\n exponential decrease in error rates with a small increase in the number\n of tile types and the scale of the construction [24, 4]. Following\n [17], we consider the issue of applying similar schemes to achieve\n error correction without any increase in the scale of the assembled\n pattern. Using a new proofreading transformation, we show that compact\n proofreading can be performed for some patterns with a modest increase\n in the number of tile types. Other patterns appear to require an\n exponential number of tile types. A simple property of existing\n proofreading schemes - a strong kind of redundancy - is the culprit,\n suggesting that if general purpose compact proofreading schemes are to\n be found, this type of redundancy must be avoided.", "date": "2006", "date_type": "published", "publisher": "Springer", "place_of_pub": "Berlin", "pagerange": "305-324", "id_number": "CaltechAUTHORS:20110309-104201054", "isbn": "3-540-34161-7", "book_title": "DNA Computing", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110309-104201054", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "CCF-0432193" } ] }, "contributors": { "items": [ { "id": "Carbone-A", "name": { "family": "Carbone", "given": "Alessandra" } }, { "id": "Pierce-N-A", "name": { "family": "Pierce", "given": "Niles A." } } ] }, "doi": "10.1007/11753681_24", "primary_object": { "basename": "fragile_patterns_preprint_1_.pdf", "url": "https://authors.library.caltech.edu/records/f3tmg-p8p50/files/fragile_patterns_preprint_1_.pdf" }, "resource_type": "book_section", "pub_year": "2006", "author_list": "Soloveichik, David and Winfree, Erik" }, { "id": "https://authors.library.caltech.edu/records/e41xe-mmr22", "eprint_id": 98100, "eprint_status": "archive", "datestamp": "2023-08-19 17:08:15", "lastmod": "2024-01-14 21:52:55", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" } ] }, "title": "Fault-Tolerance in Biochemical Systems", "ispublished": "unpub", "full_text_status": "restricted", "note": "\u00a9 2006 Springer-Verlag Berlin Heidelberg.", "abstract": "Biochemistry is messy. It's a miracle any of it works. And yet it does. The wonderful diversity and amazing talents of living things derive from the biochemical processes that copy genetic information and use that information as a program to construct a sophisticated organization of matter and behaviour \u2013 reliably and robustly overcoming insult after insult from the environment. In this talk I will first discuss how known techniques for fault-tolerant computing, such as von Neumann's multiplexing technique for digital circuits, can be translated to the biochemical context. I will then discuss fault-tolerance in molecular self-assembly, which requires new techniques. Using a model of algorithmic self-assembly, a generalization of crystal growth processes, I will present techniques for controlling the nucleation of self-assembly, for reducing errors during growth, and for recovering after gross damage or fragmentation.", "date": "2006", "date_type": "published", "publisher": "Springer", "place_of_pub": "Berlin", "pagerange": "26", "id_number": "CaltechAUTHORS:20190822-092012516", "isbn": "978-3-540-38593-6", "book_title": "Unconventional Computation", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20190822-092012516", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "contributors": { "items": [ { "id": "Calude-C-S", "name": { "family": "Calude", "given": "Cristian S." } }, { "id": "Dinneen-M-J", "name": { "family": "Dinneen", "given": "Michael J." } }, { "id": "P\u0103un-G", "name": { "family": "P\u0103un", "given": "Gheorghe" } }, { "id": "Rozenberg-G", "name": { "family": "Rozenberg", "given": "Grzegorz" } }, { "id": "Stepney-S", "name": { "family": "Stepney", "given": "Susan" } } ] }, "doi": "10.1007/11839132_3", "resource_type": "book_section", "pub_year": "2006", "author_list": "Winfree, Erik" }, { "id": "https://authors.library.caltech.edu/records/cdegn-xhs37", "eprint_id": 27350, "eprint_status": "archive", "datestamp": "2023-08-19 17:04:09", "lastmod": "2024-01-13 05:43:58", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" } ] }, "title": "Self-Healing Tile Sets", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 2006 Springer. \n\nThe author is indebted to discussions with Ashish Goel, Ho-Lin Chen, Rebecca Schulman, David Soloveichik, Matthew Cook, and Paul Rothemund. This work was partially funded by NSF award #0523761.\n\nSubmitted - self_healing_paper_1_.pdf
", "abstract": "Biology provides the synthetic chemist with a tantalizing and frustrating challenge:\nto create complex objects, defined from the molecular scale up to meters,\nthat construct themselves from elementary components, and perhaps\neven reproduce themselves. This is the challenge of bottom-up fabrication.\nThe most compelling answer to this challenge was formulated in the early\n1980s by Ned Seeman, who realized that the information carried by DNA\nstrands provides a means to program molecular self-assembly, with potential\napplications including DNA scaffolds for crystallography [19] or for molecular\nelectronic circuits [15]. This insight opened the doors to engineering with the\nrich set of phenomena available in nucleic acid chemistry [20].", "date": "2006", "date_type": "published", "publisher": "Springer", "place_of_pub": "Berlin", "pagerange": "55-78", "id_number": "CaltechAUTHORS:20111021-093324589", "isbn": "9783540302964", "book_title": "Nanotechnology: Science and Computation", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111021-093324589", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "CCF-0523761" } ] }, "contributors": { "items": [ { "id": "Chen-Junghuei", "name": { "family": "Chen", "given": "Junghuei" } }, { "id": "Jonoska-N", "name": { "family": "Jonoska", "given": "Nata\u0161a" } }, { "id": "Rozenberg-G", "name": { "family": "Rozenberg", "given": "Grzegorz" } } ] }, "doi": "10.1007/3-540-30296-4_4", "primary_object": { "basename": "self_healing_paper_1_.pdf", "url": "https://authors.library.caltech.edu/records/cdegn-xhs37/files/self_healing_paper_1_.pdf" }, "resource_type": "book_section", "pub_year": "2006", "author_list": "Winfree, Erik" }, { "id": "https://authors.library.caltech.edu/records/4v9eb-j1b49", "eprint_id": 101452, "eprint_status": "archive", "datestamp": "2023-08-19 15:10:54", "lastmod": "2024-01-14 22:07:38", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Soloveichik-David", "name": { "family": "Soloveichik", "given": "David" }, "orcid": "0000-0002-2585-4120" }, { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" } ] }, "title": "Complexity of Self-assembled Shapes (Extended Abstract)", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 2005 Springer-Verlag Berlin Heidelberg. \n\nWe thank Len Adleman, members of his group, and Paul Rothemund for fruitful discussions and suggestions. We thank Rebecca Schulman and David Zhang for useful and entertaining conversations about descriptional complexity of tile systems. This work was supported by NSF CAREER Grant No. 0093486.\n\nSubmitted - 0412096.pdf
", "abstract": "The connection between self-assembly and computation suggests that a shape can be considered the output of a self-assembly \"program,\" a set of tiles that fit together to create a shape. It seems plausible that the size of the smallest self-assembly program that builds a shape and the shape's descriptional (Kolmogorov) complexity should be related. We show that under the notion of a shape that is independent of scale this is indeed so: in the Tile Assembly Model, the minimal number of distinct tile types necessary to self-assemble an arbitrarily scaled shape can be bounded both above and below in terms of the shape's Kolmogorov complexity. As part of the proof of the main result, we sketch a general method for converting a program outputting a shape as a list of locations into a set of tile types that self-assembles into a scaled up version of that shape. Our result implies, somewhat counter-intuitively, that self-assembly of a scaled up version of a shape often requires fewer tile types, and suggests that the independence of scale in self-assembly theory plays the same crucial role as the independence of running time in the theory of computability.", "date": "2005", "date_type": "published", "publisher": "Springer", "place_of_pub": "Berlin", "pagerange": "344-354", "id_number": "CaltechAUTHORS:20200221-095747956", "isbn": "978-3-540-26174-2", "book_title": "DNA Computing", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200221-095747956", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "CNS-0093486" } ] }, "contributors": { "items": [ { "id": "Ferretti-Claudio", "name": { "family": "Ferretti", "given": "Claudio" } }, { "id": "Mauri-Giancarlo", "name": { "family": "Mauri", "given": "Giancarlo" } }, { "id": "Zandron-Claudio", "name": { "family": "Zandron", "given": "Claudio" } } ] }, "doi": "10.1007/11493785_30", "primary_object": { "basename": "0412096.pdf", "url": "https://authors.library.caltech.edu/records/4v9eb-j1b49/files/0412096.pdf" }, "resource_type": "book_section", "pub_year": "2005", "author_list": "Soloveichik, David and Winfree, Erik" }, { "id": "https://authors.library.caltech.edu/records/yyhd4-hwj78", "eprint_id": 22761, "eprint_status": "archive", "datestamp": "2023-08-19 14:56:41", "lastmod": "2024-01-13 00:10:57", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Seelig-G", "name": { "family": "Seelig", "given": "Georg" } }, { "id": "Yurke-B", "name": { "family": "Yurke", "given": "Bernard" }, "orcid": "0000-0003-3913-2855" }, { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" } ] }, "title": "DNA hybridization catalysts and catalyst circuits", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 2005 Springer-Verlag Berlin Heidelberg. \n\nThanks to Ben Rahn, Jeremy Leibs, Joseph Schaeffer, Jongmin Kim, Dave Zhang, and especially Paul Rothemund for stimulating discussion and help preparing figures and simulations. GS was supported by the\nSwiss National Science Foundation, EW was supported by NSF CAREER Grant No. 0093486, NSF ITR Grant No. 0113443, and GenTel.\n\nSubmitted - catalysts_DNA10_preprint.pdf
", "abstract": "Practically all of life's molecular processes, from chemical synthesis to replication, involve enzymes that carry out their functions through the catalysis of metastable fuels into waste products. Catalytic control of reaction rates will prove to be as useful and ubiquitous in\nDNA nanotechnology as it is in biology. Here we present experimental results on the control of the decay rates of a metastable DNA \"fuel\". We show that the fuel complex can be induced to decay with a rate about 1600 times faster than it would decay spontaneously. The original DNA hybridization catalyst [15] achieved a maximal speed-up of roughly 30. The fuel complex discussed here can therefore serve as the basic ingredient for an improved DNA hybridization catalyst. As an example application for DNA hybridization catalysts, we propose a method for implementing arbitrary digital logic circuits.", "date": "2005", "date_type": "published", "publisher": "Springer", "place_of_pub": "Berlin", "pagerange": "329-343", "id_number": "CaltechAUTHORS:20110309-104201845", "isbn": "3-540-26174-5", "book_title": "DNA Computing", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110309-104201845", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Swiss National Science Foundation (SNSF)" }, { "agency": "NSF", "grant_number": "CNS-0093486" }, { "agency": "NSF", "grant_number": "CCF-0113443" }, { "agency": "GenTel" } ] }, "contributors": { "items": [ { "id": "Ferretti-C", "name": { "family": "Ferretti", "given": "Claudio" } }, { "id": "Mauri-G", "name": { "family": "Mauri", "given": "Giancarlo" } }, { "id": "Zandron-C", "name": { "family": "Zandron", "given": "Claudio" } } ] }, "doi": "10.1007/11493785_29", "primary_object": { "basename": "catalysts_DNA10_preprint.pdf", "url": "https://authors.library.caltech.edu/records/yyhd4-hwj78/files/catalysts_DNA10_preprint.pdf" }, "resource_type": "book_section", "pub_year": "2005", "author_list": "Seelig, Georg; Yurke, Bernard; et el." }, { "id": "https://authors.library.caltech.edu/records/f428a-gx176", "eprint_id": 101473, "eprint_status": "archive", "datestamp": "2023-08-22 02:57:02", "lastmod": "2024-01-14 22:07:49", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Schulman-Rebecca", "name": { "family": "Schulman", "given": "Rebecca" }, "orcid": "0000-0003-4555-3162" }, { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" } ] }, "title": "Programmable Control of Nucleation for Algorithmic Self-assembly", "ispublished": "unpub", "full_text_status": "restricted", "keywords": "Critical Nucleus; Mismatch Error; Target Strand; Facet Error; Tile Assembly Model", "note": "\u00a9 2005 Springer-Verlag Berlin Heidelberg. \n\nThe authors are grateful to Ho-Lin Chen, Ashish Goel, Rizal Hariadi, Paul Rothemund, Bernie Yurke, and Dave Zhang for helpful advice and discussions. This work was supported by NSF CAREER Grant No. 0093486 to EW and an NSF Graduate Fellowship to RS.", "abstract": "Algorithmic self-assembly has been proposed as a mechanism for autonomous DNA computation and for bottom-up fabrication of complex nanodevices. Whereas much previous work has investigated self-assembly programs using an abstract model of irreversible, errorless assembly, experimental studies as well as more sophisticated reversible kinetic models indicate that algorithmic self-assembly is subject to several kinds of errors. Previously, it was shown that proofreading tile sets can reduce the occurrence of mismatch and facet errors. Here, we introduce the zig-zag tile set, which can reduce the occurrence of spurious nucleation errors. The zig-zag tile set takes advantage of the fact that assemblies must reach a critical size before their growth becomes favorable. By using a zig-zag tile set of greater width, we can increase the critical size of spurious assemblies without increasing the critical size of correctly seeded assemblies, exponentially reducing the spurious nucleation rate. In combination with proofreading results, this result indicates that algorithmic self-assembly can be performed with low error rates without a significant reduction in assembly speed. Furthermore, our zig-zag boundaries suggest methods for exquisite detection of DNA strands and for the replication of inheritable information without the use of enzymes.", "date": "2005", "date_type": "published", "publisher": "Springer", "place_of_pub": "Berlin", "pagerange": "319-328", "id_number": "CaltechAUTHORS:20200221-152848969", "isbn": "978-3-540-26174-2", "book_title": "DNA Computing", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200221-152848969", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "CNS-0093486" }, { "agency": "NSF Graduate Research Fellowship" } ] }, "contributors": { "items": [ { "id": "Ferretti-Claudio", "name": { "family": "Ferretti", "given": "Claudio" } }, { "id": "Mauri-Giancarlo", "name": { "family": "Mauri", "given": "Giancarlo" } }, { "id": "Zandron-Claudio", "name": { "family": "Zandron", "given": "Claudio" } } ] }, "doi": "10.1007/11493785_28", "resource_type": "book_section", "pub_year": "2005", "author_list": "Schulman, Rebecca and Winfree, Erik" }, { "id": "https://authors.library.caltech.edu/records/j4yzg-a7236", "eprint_id": 22758, "eprint_status": "archive", "datestamp": "2023-08-19 14:56:34", "lastmod": "2024-01-13 00:10:55", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Schulman-R", "name": { "family": "Schulman", "given": "Rebecca" }, "orcid": "0000-0003-4555-3162" }, { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" } ] }, "title": "Self-replication and evolution of DNA crystals", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 2005 Springer-Verlag Berlin Heidelberg.\n\nWe would like to thank Bernie Yurke, Gerald Joyce,\nAndy Ellington, Graham Cairns-Smith, Paul Rothemund, Dave Zhang and David\nSoloveichik for helpful discussion on sequence amplification and evolution. The\nAFM image in the inset of Figure 1c was taken by Ho-Lin Chen. This research\nwas partially supported by NSF awards #0093486 and #0432193.\n\nSubmitted - dna-crystal-evolution_preprint.pdf
", "abstract": "Is it possible to create a simple physical system that is capable of replicating itself? Can such a system evolve interesting behaviors, thus allowing it to adapt to a wide range of environments? This paper presents a design for such a replicator constructed exclusively from synthetic DNA. The basis for the replicator is crystal growth: information is stored in the spatial arrangement of monomers and copied from layer to layer by templating. Replication is achieved by fragmentation of crystals, which produces new crystals that carry the same information. Crystal replication avoids intrinsic problems associated with template-directed mechanisms for replication of one-dimensional polymers. A key innovation of our work is that by using programmable DNA tiles as the crystal monomers, we can design crystal growth processes that apply interesting selective pressures to the evolving sequences. While evolution requires that copying occur with high accuracy, we show how to adapt error-correction techniques from algorithmic self-assembly to lower the replication error rate as much as is required.", "date": "2005", "date_type": "published", "publisher": "Springer", "place_of_pub": "Berlin", "pagerange": "734-743", "id_number": "CaltechAUTHORS:20110309-104201367", "isbn": "3-540-28848-1", "book_title": "Advances in Artificial Life", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110309-104201367", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "CCF-0093486" }, { "agency": "NSF", "grant_number": "CCF-0432193" } ] }, "contributors": { "items": [ { "id": "Bentley-P-J", "name": { "family": "Bentley", "given": "Peter J." } }, { "id": "Capcarrere-M-S", "name": { "family": "Capcarrere", "given": "Mathieu S." } }, { "id": "Freitas-A-A", "name": { "family": "Freitas", "given": "Alex A." } }, { "id": "Johnson-C-G", "name": { "family": "Johnson", "given": "Colin G." } }, { "id": "Timmis-J", "name": { "family": "Timmis", "given": "Jon" } } ] }, "doi": "10.1007/11553090_74", "primary_object": { "basename": "dna-crystal-evolution_preprint.pdf", "url": "https://authors.library.caltech.edu/records/j4yzg-a7236/files/dna-crystal-evolution_preprint.pdf" }, "resource_type": "book_section", "pub_year": "2005", "author_list": "Schulman, Rebecca and Winfree, Erik" }, { "id": "https://authors.library.caltech.edu/records/1x89h-zdn73", "eprint_id": 22767, "eprint_status": "archive", "datestamp": "2023-08-19 12:43:07", "lastmod": "2024-01-13 00:11:01", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Schulman-R", "name": { "family": "Schulman", "given": "Rebecca" }, "orcid": "0000-0003-4555-3162" }, { "id": "Lee-Shaun", "name": { "family": "Lee", "given": "Shaun" } }, { "id": "Papadakis-N", "name": { "family": "Papadakis", "given": "Nick" } }, { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" } ] }, "title": "One dimensional boundaries for DNA tile self-assembly", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 2004 Springer-Verlag Berlin Heidelberg.\nWe would like to thank Bernie Yurke for pointing out the effects of slight differences\nin stoichiometry, and for his very descriptive term \"stoichiometry poisoning\".\nPaul Rnthemund, Rizal Hariadi, and other members of the DNA Lab\nprovided helpful hints and stimulating conversation. This work was supported by\nNSF CAREER Grant No. 0093486, DARPA BioComputation Contract F30602-01-2-0561, NASA NRA2-37143, and GenTel.\n\nSubmitted - OneDimBoundaries_DNA9_preprint.pdf
", "abstract": "In this paper we report the design and synthesis of DNA molecules (referred to as DNA tiles) with specific binding interactions that\n guide self-assembly to make one-dimensional assemblies shaped as lines,\n V's and X's. These DNA tile assemblies have been visualized by atomic\n force microscopy. The highly-variable distribution of shapes - e.g.,\n the length of the arms of X-shaped assemblies - gives us insight into\n how the assembly process is occurring. Using stochastic models that\n simulate addition and dissociation of each type of DNA tile, as well\n as simplified models that more cleanly examine the generic phenomena,\n we dissect the contribution of accretion vs aggregation, reversible vs\n irreversible and seeded vs unseeded assumptions for describing the\n growth processes. The results suggest strategies for controlling\n self-assembly to make more uniformly-shaped assemblies.", "date": "2004", "date_type": "published", "publisher": "Springer", "place_of_pub": "Berlin", "pagerange": "108-125", "id_number": "CaltechAUTHORS:20110309-104202835", "isbn": "3-540-20930-1", "book_title": "DNA Computing", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110309-104202835", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "CNS-0093486" }, { "agency": "Defense Advanced Research Projects Agency (DARPA)", "grant_number": "F30602-012-0561" }, { "agency": "NASA", "grant_number": "NRA2-37143" }, { "agency": "GenTel" } ] }, "contributors": { "items": [ { "id": "Chen-Junghei", "name": { "family": "Chen", "given": "Junghuei" } }, { "id": "Reif-J", "name": { "family": "Reif", "given": "John" } } ] }, "doi": "10.1007/978-3-540-24628-2_12", "primary_object": { "basename": "OneDimBoundaries_DNA9_preprint.pdf", "url": "https://authors.library.caltech.edu/records/1x89h-zdn73/files/OneDimBoundaries_DNA9_preprint.pdf" }, "resource_type": "book_section", "pub_year": "2004", "author_list": "Schulman, Rebecca; Lee, Shaun; et el." }, { "id": "https://authors.library.caltech.edu/records/jcvj4-7gn26", "eprint_id": 22768, "eprint_status": "archive", "datestamp": "2023-08-19 12:43:16", "lastmod": "2024-01-13 00:11:02", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" }, { "id": "Bekbolatov-R", "name": { "family": "Bekbolatov", "given": "Renat" } } ] }, "title": "Proofreading tile sets: Error correction for algorithmic self-assembly", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 2004 Springer-Verlag Berlin Heidelberg.\nThis work benefited from discussions with Leonard Adleman, Matthew Cook,\nAshish Gael, Paul Rothemund, Rebecca Schulman, Georg Seelig, David\nSoloveichik, and Chris Umans. Thanks to John Reif for encouraging me\nto write this up and for sharing his unpublished manuscript. EW and\nRB were supported by NSF CAREER Grant No. 0093486, DARPA BioComputation\nContract F30602-01-2-0561, NASA NRA2-37143, and GenTel.\nSimulation code and tile sets used in this paper, as well as MATLAB\nscripts for evaluating the kinetic trapping models, may be obtained from\nhttp://www .dna.caltech.edu/SupplementaryMaterial.\n\nSubmitted - proofreading_DNA9_preprint.pdf
", "abstract": "For robust molecular implementation of tile-based algorithmic\nself-assembly, methods for reducing errors must be developed. Previous\nstudies suggested that by control of physical conditions, such as\ntemperature and the concentration of tiles, errors (\u03b5) can be reduced\nto an arbitrarily low rate - but at the cost of reduced speed (r) for\nthe self-assembly process. For tile sets directly implementing blocked\ncellular automata, it was shown that r \u2248 \u03b2\u03b5^2 was optimal. Here, we\nshow that an improved construction, which we refer to as proofreading\ntile sets, can in principle exploit the cooperativity of tile assembly reactions\nto dramatically improve the scaling behavior to r \u2248 \u03b2\u03b5 and better.\nThis suggests that existing DNA-based molecular tile approaches may be\nimproved to produce macroscopic algorithmic crystals with few errors.\nGeneralizations and limitations of the proofreading tile set construction\nare discussed.", "date": "2004", "date_type": "published", "publisher": "Springer", "place_of_pub": "Berlin", "pagerange": "126-144", "id_number": "CaltechAUTHORS:20110309-104203016", "isbn": "3-540-20930-1", "book_title": "DNA Computing", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110309-104203016", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "CNS-0093486" }, { "agency": "Defense Advanced Research Projects Agency (DARPA)", "grant_number": "F30602-01-2-0561" }, { "agency": "NASA", "grant_number": "NRA2-37143" }, { "agency": "GenTel" } ] }, "contributors": { "items": [ { "id": "Chen-Junghei", "name": { "family": "Chen", "given": "Junghuei" } }, { "id": "Reif-J", "name": { "family": "Reif", "given": "John" } } ] }, "doi": "10.1007/978-3-540-24628-2_13", "primary_object": { "basename": "proofreading_DNA9_preprint.pdf", "url": "https://authors.library.caltech.edu/records/jcvj4-7gn26/files/proofreading_DNA9_preprint.pdf" }, "resource_type": "book_section", "pub_year": "2004", "author_list": "Winfree, Erik and Bekbolatov, Renat" }, { "id": "https://authors.library.caltech.edu/records/fry6p-wqm45", "eprint_id": 22766, "eprint_status": "archive", "datestamp": "2023-08-19 12:42:58", "lastmod": "2024-01-13 00:10:59", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Cook-M", "name": { "family": "Cook", "given": "Matthew" } }, { "id": "Rothemund-P-W-K", "name": { "family": "Rothemund", "given": "Paul W. K." }, "orcid": "0000-0002-1653-3202" }, { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" } ] }, "title": "Self-assembled circuit patterns", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 2004 Springer-Verlag Berlin Heidelberg. \n\nM.C. is supported in part by the \"Alpha Project\" that is funded by a grant from the National Human Genome Research Institute (Grant No. P50 HG02370). P.W.K.R. is supported by a Beckman Postdoctoral Fellowship. E.W. is supported by NSF Career Grant No. 0093486, DARPA BIOCOMP Contract F30602-01-2-0561, and NASA NRA2-37143.\n\nSubmitted - SAcircuits_DNA9_preprint.pdf
", "abstract": "Self-assembly is a process in which basic units aggregate under attractive forces to form larger compound structures. Recent\n theoretical work has shown that pseudo-crystalline self-assembly can be\n algorithmic, in the sense that complex logic can be programmed into the\n growth process [26]. This theoretical work builds on the theory of\n two-dimensional tilings [8], using rigid square tiles called Wang\n tiles [24] for the basic units of self-assembly, and leads to\n Turing-universal models such as the Tile Assembly Model [28]. Using\n the Tile Assembly Model, we show how algorithmic self-assembly can be\n exploited for fabrication tasks such as constructing the patterns that\n define certain digital circuits, including demultiplexers, RAM arrays,\n pseudowavelet transforms, and Hadamard transforms. Since DNA\n self-assembly appears to be promising for implementing the arbitrary\n Wang tiles [30, 13] needed for programming in the Tile Assembly\n Model, algorithmic self-assembly methods such as those presented in\n this paper may eventually become a viable method of arranging molecular\n electronic components [18], such as carbon nanotubes [10, 1], into\n molecular-scale circuits.", "date": "2004", "date_type": "published", "publisher": "Springer", "place_of_pub": "Berlin", "pagerange": "91-107", "id_number": "CaltechAUTHORS:20110309-104202667", "isbn": "3-540-20930-1", "book_title": "DNA Computing", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110309-104202667", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH", "grant_number": "P50 HG02370" }, { "agency": "Arnold and Mabel Beckman Foundation" }, { "agency": "NSF", "grant_number": "CCF-0093486" }, { "agency": "Defense Advanced Research Projects Agency (DARPA)", "grant_number": "F30602-01-2-0561" }, { "agency": "NASA", "grant_number": "NRA2-37143" }, { "agency": "National Human Genome Research Institute" } ] }, "contributors": { "items": [ { "id": "Chen-J", "name": { "family": "Chen", "given": "Junghuei" } }, { "id": "Reif-J", "name": { "family": "Reif", "given": "John" } } ] }, "doi": "10.1007/978-3-540-24628-2_11", "primary_object": { "basename": "SAcircuits_DNA9_preprint.pdf", "url": "https://authors.library.caltech.edu/records/fry6p-wqm45/files/SAcircuits_DNA9_preprint.pdf" }, "resource_type": "book_section", "pub_year": "2004", "author_list": "Cook, Matthew; Rothemund, Paul W. K.; et el." }, { "id": "https://authors.library.caltech.edu/records/fkkm8-xz342", "eprint_id": 22770, "eprint_status": "archive", "datestamp": "2023-08-19 08:43:59", "lastmod": "2024-01-13 00:11:04", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" }, { "id": "Landweber-Laura-F", "name": { "family": "Landweber", "given": "Laura F." } } ] }, "title": "Introduction: Evolution and Computation: Where Do They Meet?", "ispublished": "unpub", "full_text_status": "public", "note": "[introduction included in front matter]", "abstract": "Evolutionary algorithms originated in the 1970s from the realization that computer programs can use the biologically inspired processes of genetic mutation, recombination, and selection to solve optimization problems that are analytically intractable. Successful applications to a wider gamut of problems became possible with the addition of new mechanisms such as generalized recombination, gene duplication, \"developmental\" evaluation of genomes, and unbounded genome size. Has this experience distilled concepts of importance for understanding biological evolution?", "date": "2002", "date_type": "published", "publisher": "Springer", "place_of_pub": "Berlin, Germany", "pagerange": "v-ix", "id_number": "CaltechAUTHORS:20110309-104203989", "isbn": "978-3-642-63081-1", "book_title": "Evolution as Computation: DIMACS Workshop, Princeton, January 1999", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20110309-104203989", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "contributors": { "items": [ { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" }, { "id": "Landweber-Laura-F", "name": { "family": "Landweber", "given": "Laura F." } } ] }, "resource_type": "book_section", "pub_year": "2002", "author_list": "Winfree, Erik and Landweber, Laura F." }, { "id": "https://authors.library.caltech.edu/records/cvc8r-5v978", "eprint_id": 104934, "eprint_status": "archive", "datestamp": "2023-08-21 21:53:36", "lastmod": "2024-01-15 17:04:18", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" } ] }, "title": "In Vitro Transcriptional Circuits", "ispublished": "unpub", "full_text_status": "restricted", "keywords": "Intelligent Machine; Recurrent Neural Network; Digital Circuit; Ring Oscillator; Drosophila Embryo", "note": "\u00a9 2001 Springer-Verlag London.", "abstract": "The structural similarity of neural networks and genetic regulatory networks to digital circuits, and hence to each other, was noted from the very beginning of their study [7,5]. Generic properties of both types of network have been analyzed using the same class of abstract models [3]. The same rate equations proposed for recurrent neural networks [4] have been used, with a few embellishments, to model genetic regulatory circuits controlling development of Drosophila embryos [6]. However, whereas research in neural networks has a long history of both analytic approaches, aimed at understanding the brain, and synthetic approaches, aimed at creating intelligent machines, research in genetic regulatory networks has been entirely analytic prior to very recent work implementing small synthetic genetic regulatory networks in E. Coli [8, 1, 2]. Although genetic regulatory systems are not fast, they are small; E. coli is one cubic micron yet it contains thousands of regulated genes.", "date": "2001", "date_type": "published", "publisher": "Springer", "place_of_pub": "London", "pagerange": "121-122", "id_number": "CaltechAUTHORS:20200812-123245128", "isbn": "978-1-85233-415-4", "book_title": "Unconventional Models of Computation, UMC'2K", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20200812-123245128", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "contributors": { "items": [ { "id": "Antoniou-I", "name": { "family": "Antoniou", "given": "I." } }, { "id": "Calude-C-S", "name": { "family": "Calude", "given": "C. S." } }, { "id": "Dinneen-M-J", "name": { "family": "Dinneen", "given": "M. J." } } ] }, "doi": "10.1007/978-1-4471-0313-4_10", "resource_type": "book_section", "pub_year": "2001", "author_list": "Winfree, Erik" }, { "id": "https://authors.library.caltech.edu/records/k0gxw-cqs09", "eprint_id": 27367, "eprint_status": "archive", "datestamp": "2023-08-21 21:48:37", "lastmod": "2024-01-13 05:44:00", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" }, { "id": "Eng-T", "name": { "family": "Eng", "given": "Tony" } }, { "id": "Rozenberg-G", "name": { "family": "Rozenberg", "given": "Grzegorz" } } ] }, "title": "String tile models for DNA computing by self-assembly", "ispublished": "unpub", "full_text_status": "public", "keywords": "Turing Machine; Maximal Assembly; Maximal Path; General Tile; Planar Tile", "note": "\u00a9 2001 Springer-Verlag Berlin Heidelberg. \n\nThe authors are indebted to Joost Engelfriet and Hendrik\nJan Hoogeboom for their guidance through the maze of results on the output languages of various sorts of \ntransducers, and to John Reif and Thorn LaBean\nfor their critical reading, discussion, and encouragement.\n\nSubmitted - stringtiles_preprint.pdf
", "abstract": "This paper investigates computation by linear assemblies of complex DNA tiles, which we call string tiles. By keeping track of the strands as they weave back and forth through the assembly, we show that surprisingly sophisticated calculations can be performed using linear self-assembly. Examples range from generating an addition table to providing O(1) solutions to CNF-SAT and DHPP. We classify the families of languages that can be generated by various types of DNA molecules, and establish a correspondence to the existing classes ET0L_(ml) and ET0L_(fin). Thus, linear self-assembly of string tiles can generate the output languages of finite-visit Turing Machines.", "date": "2001", "date_type": "published", "publisher": "Springer", "place_of_pub": "Berlin", "pagerange": "63-88", "id_number": "CaltechAUTHORS:20111024-092612665", "isbn": "978-3-540-42076-7", "book_title": "DNA Computing", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111024-092612665", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "contributors": { "items": [ { "id": "Condon-A", "name": { "family": "Condon", "given": "Anne" } } ] }, "doi": "10.1007/3-540-44992-2_6", "primary_object": { "basename": "stringtiles_preprint.pdf", "url": "https://authors.library.caltech.edu/records/k0gxw-cqs09/files/stringtiles_preprint.pdf" }, "resource_type": "book_section", "pub_year": "2001", "author_list": "Winfree, Erik; Eng, Tony; et el." }, { "id": "https://authors.library.caltech.edu/records/j28t5-3v273", "eprint_id": 72795, "eprint_status": "archive", "datestamp": "2023-08-19 05:43:01", "lastmod": "2023-10-23 22:57:24", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Rothemund-P-W-K", "name": { "family": "Rothemund", "given": "Paul W. K." }, "orcid": "0000-0002-1653-3202" }, { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" } ] }, "title": "The program-size complexity of self-assembled squares", "ispublished": "unpub", "full_text_status": "restricted", "note": "\u00a9 2000 ACM.", "abstract": "Molecular self-assembly gives rise to a great diversity of complex forms, from crystals and DNA helices to microtubules\nand holoenzymes. We study a formal model of pseudocrystalline self-assembly, called the Tile Assembly Model, in which a tile may be added to the growing object when the total interaction strength with its neighbors exceeds a parameter \u03a4. This model has been shown to be Turing-universal. Thus, self-assembled objects can be studied from the point of view of computational complexity. Here, we define the program size complexity of an NxN square to be the minimum number of distinct tiles required to self-assemble the square and no other objects. We study this complexity under the Tile Assembly Model and find a dramatic decrease in complexity, from N^2 tiles to O(log N) tiles, as \u03a4 is increased from 1 (where bonding is noncooperative) to 2 (allowing cooperative bonding). Further, we find that the size of the largest square uniquely produced by a set of n\ntiles grows faster than any computable function.", "date": "2000-05", "date_type": "published", "publisher": "ACM", "place_of_pub": "New York, NY", "pagerange": "459-468", "id_number": "CaltechAUTHORS:20161213-162052032", "isbn": "1-58113-184-4", "book_title": "STOC '00 Proceedings of the thirty-second annual ACM symposium on Theory of computing", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20161213-162052032", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "contributors": { "items": [ { "id": "Yao-Frances", "name": { "family": "Yao", "given": "Frances" } }, { "id": "Luks-E", "name": { "family": "Luks", "given": "Eugene" } } ] }, "doi": "10.1145/335305.335358", "resource_type": "book_section", "pub_year": "2000", "author_list": "Rothemund, Paul W. K. and Winfree, Erik" }, { "id": "https://authors.library.caltech.edu/records/1dgyt-fev23", "eprint_id": 27569, "eprint_status": "archive", "datestamp": "2023-08-19 05:03:20", "lastmod": "2024-01-13 05:45:34", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Chen-Kevin-Bio", "name": { "family": "Chen", "given": "Kevin" } }, { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" } ] }, "title": "Error Correction in DNA Computing: Misclassification and\n Strand Loss", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 2000 American Mathematical Society.\n\nPublished - Error_Correction.pdf
", "abstract": "We present a method of transforming an extract-based DNA computation that is error-prone into one that is relatively error-free. These improvements in error rates are achieved without the supposition of any improvements in the reliability of the underlying laboratory techniques. We assume that only two types of errors are possible: a DNA strand may be incorrectly processed or it may be lost entirely. We show to deal with each of these\nerrors individually and then analyze the tradeoff when both must be optimized simultaneously.", "date": "2000", "date_type": "published", "publisher": "American Mathematical Society", "place_of_pub": "Providence, RI", "pagerange": "49-63", "id_number": "CaltechAUTHORS:20111102-073137217", "isbn": "9780821820537", "book_title": "DNA Based Computers V", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111102-073137217", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "contributors": { "items": [ { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" } }, { "id": "Gifford-D-K", "name": { "family": "Gifford", "given": "David K." } } ] }, "primary_object": { "basename": "Error_Correction.pdf", "url": "https://authors.library.caltech.edu/records/1dgyt-fev23/files/Error_Correction.pdf" }, "resource_type": "book_section", "pub_year": "2000", "author_list": "Chen, Kevin and Winfree, Erik" }, { "id": "https://authors.library.caltech.edu/records/pqzf3-d3r39", "eprint_id": 27564, "eprint_status": "archive", "datestamp": "2023-08-19 05:03:15", "lastmod": "2023-10-24 17:15:00", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "LaBean-T-H", "name": { "family": "LaBean", "given": "Thomas H." } }, { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" }, { "id": "Reif-J-H", "name": { "family": "Reif", "given": "John H." } } ] }, "title": "Experimental Progress in Computation by Self-Assembly of DNA Tilings", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 2000 American Mathematical Society.\nWe wish to sincerely thank: Ned Seeman and Hao Yan for their considerable\nand invaluable roles in construction and analysis of the TAO tile; Tony Eng\nand Grzegorz Rosenberg for development and enlightening discussion of string tile\nconcepts; and Wolfgang Frey and Ashutosh Chilkoti for assistance with atomic\nforce microscopy. This work was supported in part by Grants NSF/DARPA CCR-9725021, CCR-96-33567, NSF IRI-9619647, ARO contract DAAH-04-96-1-0448, and ONR contract N00014-99-1-0406.\n\nPublished - Experimental_Progress.pdf
", "abstract": "Approaches to DNA-based computing by self-assembly require the\nuse of D. T A nanostructures, called tiles, that have efficient chemistries, expressive\ncomputational power: and convenient input and output (I/O) mechanisms.\nWe have designed two new classes of DNA tiles: TAO and TAE, both\nof which contain three double-helices linked by strand exchange. Structural\nanalysis of a TAO molecule has shown that the molecule assembles efficiently\nfrom its four component strands. Here we demonstrate a novel method for\nI/O whereby multiple tiles assemble around a single-stranded (input) scaffold\nstrand. Computation by tiling theoretically results in the formation of structures\nthat contain single-stranded (output) reported strands, which can then\nbe isolated for subsequent steps of computation if necessary. We illustrate the\nadvantages of TAO and TAE designs by detailing two examples of massively\nparallel arithmetic: construction of complete XOR and addition tables by linear\nassemblies of DNA tiles. The three helix structures provide flexibility for\ntopological routing of strands in the computation: allowing the implementation\nof string tile models.", "date": "2000", "date_type": "published", "publisher": "American Mathematical Society", "place_of_pub": "Providence, RI", "pagerange": "123-40", "id_number": "CaltechAUTHORS:20111101-150157119", "isbn": "9780821820537", "book_title": "DNA Based Computers V", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111101-150157119", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF/Defense Advanced Research Projects Agency (DARPA)", "grant_number": "CCR-9725021" }, { "agency": "NSF/Defense Advanced Research Projects Agency (DARPA)", "grant_number": "CCR-96-33567" }, { "agency": "NSF", "grant_number": "IRI-9619647" }, { "agency": "Army Research Office (ARO)", "grant_number": "DAAH-04-96-1-0448" }, { "agency": "Office of Naval Research (ONR)", "grant_number": "N00014-99-1-0406" } ] }, "contributors": { "items": [ { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" } }, { "id": "Gifford-D-K", "name": { "family": "Gifford", "given": "David K." } } ] }, "primary_object": { "basename": "Experimental_Progress.pdf", "url": "https://authors.library.caltech.edu/records/pqzf3-d3r39/files/Experimental_Progress.pdf" }, "resource_type": "book_section", "pub_year": "2000", "author_list": "LaBean, Thomas H.; Winfree, Erik; et el." }, { "id": "https://authors.library.caltech.edu/records/v13f7-b7211", "eprint_id": 27378, "eprint_status": "archive", "datestamp": "2023-08-19 03:40:46", "lastmod": "2024-01-13 05:44:02", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" }, { "id": "Yang-Xiaoping", "name": { "family": "Yang", "given": "Xiaoping" } }, { "id": "Seeman-N-C", "name": { "family": "Seeman", "given": "Nadrian C." }, "orcid": "0000-0002-9680-4649" } ] }, "title": "Universal Computation via Self-assembly of DNA: Some Theory and Experiments", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 1999 American Mathematical Society.\nE. Winfree has been supported in part\nby National Institute for Mental Health (NIMH) Training Grant # 5 T32 MH 19138-06; also by\nGeneral Motors' Technology Research Partnerships program and by the Center for Neuromorphic\nSystems Engineering as a part of the National Science Foundation Engineering Research Center\nProgram under grant EEC-9402726. The experimental portion of this research has been partially\nsupported by grants N00014-89-J-3078 from the Office of Naval Research and GM-29554 from the\nNIH (to NCS).\n\nErik Winfree is grateful to the many people who have helped make his foray into\nthe world of molecules possible, enjoyable, and exciting; special thanks go to Len\nAdleman, Paul Rothemund, Sam Roweis, Dan Abrahams-Gessel, John Hopfield,\nand John Abelson who generously provided laboratory facilities at Caltech for some\nof the experiments reported here.\n\nPublished - Universal_Computation.pdf
Submitted - self-assem_preprint.pdf
", "abstract": "In this paper we examine the computational capabilities inherent in the hybridization of DNA molecules. First we consider theoretical models, and show that the self-assembly of oligonucleotides into linear duplex DNA can\nonly generate sets of sequences equivalent to regular languages. If branched DNA is used for self-assembly of dendrimer structures, only sets of sequences equivalent to context-free languages can be achieved. In contrast, the self-assembly of double crossover molecules into two dimensional sheets or three dimensional solids is theoretically capable of universal computation. The proof\nrelies on a very direct simulation of a universal class of cellular automata. In the second part of this paper, we present results from preliminary experiments which investigate the critical computational step in a two-dimensional self-assembly process.", "date": "1999", "date_type": "published", "publisher": "American Mathematical Society", "place_of_pub": "Providence, RI", "pagerange": "191-213", "id_number": "CaltechAUTHORS:20111024-101156919", "isbn": "0821807560", "book_title": "DNA Based Computers II", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111024-101156919", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NIH Predoctoral Fellowship", "grant_number": "5 T32 MH 19138-06" }, { "agency": "General Motors Technology Research Partnerships Program" }, { "agency": "NSF", "grant_number": "EEC-9402726" }, { "agency": "Office of Naval Research (ONR)", "grant_number": "N00014-89-J-3078" }, { "agency": "NIH", "grant_number": "GM-29554" } ] }, "contributors": { "items": [ { "id": "Landweber-L-F", "name": { "family": "Landweber", "given": "Laura F." } }, { "id": "Baum-E-B", "name": { "family": "Baum", "given": "Eric B." } } ] }, "primary_object": { "basename": "Universal_Computation.pdf", "url": "https://authors.library.caltech.edu/records/v13f7-b7211/files/Universal_Computation.pdf" }, "related_objects": [ { "basename": "self-assem_preprint.pdf", "url": "https://authors.library.caltech.edu/records/v13f7-b7211/files/self-assem_preprint.pdf" } ], "resource_type": "book_section", "pub_year": "1999", "author_list": "Winfree, Erik; Yang, Xiaoping; et el." }, { "id": "https://authors.library.caltech.edu/records/0z4ss-yr489", "eprint_id": 27383, "eprint_status": "archive", "datestamp": "2023-08-20 06:53:22", "lastmod": "2024-01-13 05:44:06", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" } ] }, "title": "Complexity of Restricted and Unrestricted Models of Molecular Computation", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 1996 American Mathematical Society. This work is supported in part by National Institute for Mental Health (NIMH) Training Grant # 5 T32 MH 19138-05; also by General Motors' Technology Research Partnerships program. The author would like to thank Paul W. K. Rothemund, Sam Roweis,\nand Matthew Cook for their stimulating discussion. Thanks especially to Jehoshua Bruck for pointing me to previous literature on branching programs. Thanks to my advisor John Hopfield for his support and encouragement.\n\nPublished - Complexity_Restricted.pdf
Submitted - models_preprint.pdf
", "abstract": "In [9] and [2] a formal model for molecular computing was\nproposed, which makes focused use of affinity purification.\nThe use of PCR was suggested to expand the range of\nfeasible computations, resulting in a second model. In this\nnote, we give a precise characterization of these two models\nin terms of recognized computational complexity classes,\nnamely branching programs (BP) and nondeterministic\nbranching programs (NBP) respectively. This allows us to\ngive upper and lower bounds on the complexity of desired\ncomputations. Examples are given of computable and\nuncomputable problems, given limited time.", "date": "1996", "date_type": "published", "publisher": "American Mathematical Society", "place_of_pub": "Providence, RI", "pagerange": "187-198", "id_number": "CaltechAUTHORS:20111024-134249923", "isbn": "0821805185", "book_title": "DNA based computers", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111024-134249923", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Institute for Mental Health (NIMH) Training Grant", "grant_number": "5 T32 MH 19138-05" }, { "agency": "General Motors Technology Research Partnerships Program" } ] }, "contributors": { "items": [ { "id": "Lipton-R-J", "name": { "family": "Lipton", "given": "Richard J." } }, { "id": "Baum-E-B", "name": { "family": "Baum", "given": "Eric B." } } ] }, "primary_object": { "basename": "Complexity_Restricted.pdf", "url": "https://authors.library.caltech.edu/records/0z4ss-yr489/files/Complexity_Restricted.pdf" }, "related_objects": [ { "basename": "models_preprint.pdf", "url": "https://authors.library.caltech.edu/records/0z4ss-yr489/files/models_preprint.pdf" } ], "resource_type": "book_section", "pub_year": "1996", "author_list": "Winfree, Erik" }, { "id": "https://authors.library.caltech.edu/records/0a55p-04j89", "eprint_id": 27382, "eprint_status": "archive", "datestamp": "2023-08-20 06:53:16", "lastmod": "2024-01-13 05:44:04", "type": "book_section", "metadata_visibility": "show", "creators": { "items": [ { "id": "Winfree-E", "name": { "family": "Winfree", "given": "Erik" }, "orcid": "0000-0002-5899-7523" } ] }, "title": "On the Computational Power of DNA Annealing and Ligation", "ispublished": "unpub", "full_text_status": "public", "note": "\u00a9 1996 American Mathematical Society.\nThis work is supported in part by National Institute for Mental Health (NIMH) Training Grant # 5 T32 MH 19138-05; also by General Motors' Technology Research Partnerships program.\n\nI would like to thank Paul W. K. Rothemund and Sam Roweis\nfor their stimulating discussion. I am indebted to Ned Seeman for\nmany excellent suggestions, as well as fundamental research on the\nbiochemistry this proposal hopes to exploit; and to Len Adleman\nfor inspiration and great discussions. John Baldeschwieler, Tom\nTheriault, Marc Unger, Sanjoy Mahajan, Carlos Brody, Dave Kewley,\nPam Reinagel, Al Barr, and Stuart Kauffman gave many useful\nsuggestions. Thanks to my advisor John Hopfield for his support and\nencouragement.\n\nPublished - Computational_Power.pdf
Submitted - ligation_preprint.pdf
", "abstract": "In [20] it was shown that the DNA primitives of Separate,\nMerge, and Amplify were not sufficiently powerful to invert\nfunctions defined by circuits in linear time. Dan Boneh et\nal [4] show that the addition of a ligation primitive, Append, provides the missing power. The question becomes, \"How powerful is ligation? Are Separate, Merge, and Amplify\nnecessary at all?\" This paper proposes to informally explore\nthe power of annealing and ligation for DNA computation.\nWe conclude, in fact, that annealing and ligation alone are\ntheoretically capable of universal computation.", "date": "1996", "date_type": "published", "publisher": "American Mathematical Society", "place_of_pub": "Providence, RI", "pagerange": "199-221", "id_number": "CaltechAUTHORS:20111024-133436564", "isbn": "0821805185", "book_title": "DNA Based Computers", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20111024-133436564", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "National Institute for Mental Health (NIMH) Training Grant", "grant_number": "5 T32 MH 19138-05" }, { "agency": "General Motors Technology Research Partnerships Program" } ] }, "contributors": { "items": [ { "id": "Lipton-R-J", "name": { "family": "Lipton", "given": "Richard J." } }, { "id": "Baum-E-B", "name": { "family": "Baum", "given": "Eric B." } } ] }, "primary_object": { "basename": "Computational_Power.pdf", "url": "https://authors.library.caltech.edu/records/0a55p-04j89/files/Computational_Power.pdf" }, "related_objects": [ { "basename": "ligation_preprint.pdf", "url": "https://authors.library.caltech.edu/records/0a55p-04j89/files/ligation_preprint.pdf" } ], "resource_type": "book_section", "pub_year": "1996", "author_list": "Winfree, Erik" } ]