Pub Date : 2020-06-01DOI: 10.4230/LIPIcs.DNA.2020.5
James I. Lathrop, J. H. Lutz, R. Lutz, Hugh D. Potter, Matthew R. Riley
We show that very simple molecular systems, modeled as chemical reaction networks, can have behaviors that exhibit dramatic phase transitions at certain population thresholds. Moreover, the magnitudes of these thresholds can thwart attempts to use simulation, model checking, or approximation by differential equations to formally verify the behaviors of such systems at realistic populations. We show how formal theorem provers can successfully verify some such systems at populations where other verification methods fail.
{"title":"Population-Induced Phase Transitions and the Verification of Chemical Reaction Networks","authors":"James I. Lathrop, J. H. Lutz, R. Lutz, Hugh D. Potter, Matthew R. Riley","doi":"10.4230/LIPIcs.DNA.2020.5","DOIUrl":"https://doi.org/10.4230/LIPIcs.DNA.2020.5","url":null,"abstract":"We show that very simple molecular systems, modeled as chemical reaction networks, can have behaviors that exhibit dramatic phase transitions at certain population thresholds. Moreover, the magnitudes of these thresholds can thwart attempts to use simulation, model checking, or approximation by differential equations to formally verify the behaviors of such systems at realistic populations. We show how formal theorem provers can successfully verify some such systems at populations where other verification methods fail.","PeriodicalId":77708,"journal":{"name":"DNA (Mary Ann Liebert, Inc.)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2020-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47100195","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-05-23DOI: 10.4230/LIPIcs.DNA.2020.7
A. Lankinen, Ismael Mullor Ruiz, T. Ouldridge
DNA strand displacement (DSD) reactions have been used to construct chemical reaction networks in which species act catalytically at the level of the overall stoichiometry of reactions. These effective catalytic reactions are typically realised through one or more of the following: many-stranded gate complexes to coordinate the catalysis, indirect interaction between the catalyst and its substrate, and the recovery of a distinct ``catalyst'' strand from the one that triggered the reaction. These facts make emulation of the out-of-equilibrium catalytic circuitry of living cells more difficult. Here, we propose a new framework for constructing catalytic DSD networks: Active Circuits of Duplex Catalysts (ACDC). ACDC components are all double-stranded complexes, with reactions occurring through 4-way strand exchange. Catalysts directly bind to their substrates, and and the ``identity'' strand of the catalyst recovered at the end of a reaction is the same molecule as the one that initiated it. We analyse the capability of the framework to implement catalytic circuits analogous to phosphorylation networks in living cells. We also propose two methods of systematically introducing mismatches within DNA strands to avoid leak reactions and introduce driving through net base pair formation. We then combine these results into a compiler to automate the process of designing DNA strands that realise any catalytic network allowed by our framework.
{"title":"Implementing Non-Equilibrium Networks with Active Circuits of Duplex Catalysts","authors":"A. Lankinen, Ismael Mullor Ruiz, T. Ouldridge","doi":"10.4230/LIPIcs.DNA.2020.7","DOIUrl":"https://doi.org/10.4230/LIPIcs.DNA.2020.7","url":null,"abstract":"DNA strand displacement (DSD) reactions have been used to construct chemical reaction networks in which species act catalytically at the level of the overall stoichiometry of reactions. These effective catalytic reactions are typically realised through one or more of the following: many-stranded gate complexes to coordinate the catalysis, indirect interaction between the catalyst and its substrate, and the recovery of a distinct ``catalyst'' strand from the one that triggered the reaction. These facts make emulation of the out-of-equilibrium catalytic circuitry of living cells more difficult. Here, we propose a new framework for constructing catalytic DSD networks: Active Circuits of Duplex Catalysts (ACDC). ACDC components are all double-stranded complexes, with reactions occurring through 4-way strand exchange. Catalysts directly bind to their substrates, and and the ``identity'' strand of the catalyst recovered at the end of a reaction is the same molecule as the one that initiated it. We analyse the capability of the framework to implement catalytic circuits analogous to phosphorylation networks in living cells. We also propose two methods of systematically introducing mismatches within DNA strands to avoid leak reactions and introduce driving through net base pair formation. We then combine these results into a compiler to automate the process of designing DNA strands that realise any catalytic network allowed by our framework.","PeriodicalId":77708,"journal":{"name":"DNA (Mary Ann Liebert, Inc.)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2020-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43041586","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-05-01DOI: 10.4230/LIPIcs.DNA.2020.9
David Doty, Benjamin L. Lee, Tristan Stérin
We introduce $textit{scadnano}$ (this https URL) (short for "scriptable cadnano"), a computational tool for designing synthetic DNA structures. Its design is based heavily on cadnano, the most widely-used software for designing DNA origami, with three main differences: 1. scadnano runs entirely in the browser, with $textit{no software installation}$ required. 2. scadnano designs, while they can be edited manually, can also be created and edited by a $textit{well-documented Python scripting library}$, to help automate tedious tasks. 3. The scadnano file format is $textit{easily human-readable}$. This goal is closely aligned with the scripting library, intended to be helpful when debugging scripts or interfacing with other software. The format is also somewhat more expressive than that of cadnano, able to describe a broader range of DNA structures than just DNA origami.
{"title":"scadnano: A Browser-Based, Scriptable Tool for Designing DNA Nanostructures","authors":"David Doty, Benjamin L. Lee, Tristan Stérin","doi":"10.4230/LIPIcs.DNA.2020.9","DOIUrl":"https://doi.org/10.4230/LIPIcs.DNA.2020.9","url":null,"abstract":"We introduce $textit{scadnano}$ (this https URL) (short for \"scriptable cadnano\"), a computational tool for designing synthetic DNA structures. Its design is based heavily on cadnano, the most widely-used software for designing DNA origami, with three main differences: \u00001. scadnano runs entirely in the browser, with $textit{no software installation}$ required. \u00002. scadnano designs, while they can be edited manually, can also be created and edited by a $textit{well-documented Python scripting library}$, to help automate tedious tasks. \u00003. The scadnano file format is $textit{easily human-readable}$. This goal is closely aligned with the scripting library, intended to be helpful when debugging scripts or interfacing with other software. The format is also somewhat more expressive than that of cadnano, able to describe a broader range of DNA structures than just DNA origami.","PeriodicalId":77708,"journal":{"name":"DNA (Mary Ann Liebert, Inc.)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2020-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47644637","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2019-12-31DOI: 10.1525/9780520933934-010
{"title":"Chapter 8. When Genes Belong to Groups and Not Individuals","authors":"","doi":"10.1525/9780520933934-010","DOIUrl":"https://doi.org/10.1525/9780520933934-010","url":null,"abstract":"","PeriodicalId":77708,"journal":{"name":"DNA (Mary Ann Liebert, Inc.)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42967527","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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