T. Klinge, James I. Lathrop, Sonia Moreno, Hugh D. Potter, Narun K. Raman, Matthew R. Riley
{"title":"ALCH:一种用于化学反应网络控制瓦片组装的命令式语言","authors":"T. Klinge, James I. Lathrop, Sonia Moreno, Hugh D. Potter, Narun K. Raman, Matthew R. Riley","doi":"10.4230/LIPIcs.DNA.2020.6","DOIUrl":null,"url":null,"abstract":"Schiefer and Winfree recently introduced the chemical reaction network-controlled tile assembly model (CRN-TAM), a variant of the abstract tile assembly model (aTAM). In the CRN-TAM, tile reactions are mediated via non-local chemical signals controlled by a chemical reaction network. This paper introduces ALCH, an imperative programming language for specifying CRN-TAM programs that can be compiled and simulated. ALCH includes standard language features such as Boolean variables, conditionals, loops, and CRN-TAM-specific constructs such as adding and removing tiles. ALCH also includes the branch and parallel structures which harness the nondeterministic and parallel nature of the CRN-TAM. ALCH also supports functional tileset specification. Using ALCH, we show that the discrete Sierpinski triangle and the discrete Sierpinski carpet can be strictly self-assembled in the CRN-TAM, which shows the CRN-TAM can self-assemble infinite shapes at scale 1 that the aTAM cannot. ALCH allows us to present these constructions at a high level, abstracting species and reactions into C-like code that is simpler to understand. We employ two new CRN-TAM techniques in our constructions. First, we use ALCH’s nondeterministic branching feature to probe previously placed tiles of the assembly and detect the presence and absence of tiles. Second, we use scaffolding tiles to precisely control tile placement by occluding any undesired binding sites. This paper is an extension of our previous work, updated to include a Sierpinski carpet construction and the parallel command.","PeriodicalId":49783,"journal":{"name":"Natural Computing","volume":"1 1","pages":"1-21"},"PeriodicalIF":1.7000,"publicationDate":"2022-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"3","resultStr":"{\"title\":\"ALCH: An imperative language for chemical reaction network-controlled tile assembly\",\"authors\":\"T. Klinge, James I. Lathrop, Sonia Moreno, Hugh D. Potter, Narun K. Raman, Matthew R. Riley\",\"doi\":\"10.4230/LIPIcs.DNA.2020.6\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Schiefer and Winfree recently introduced the chemical reaction network-controlled tile assembly model (CRN-TAM), a variant of the abstract tile assembly model (aTAM). In the CRN-TAM, tile reactions are mediated via non-local chemical signals controlled by a chemical reaction network. This paper introduces ALCH, an imperative programming language for specifying CRN-TAM programs that can be compiled and simulated. ALCH includes standard language features such as Boolean variables, conditionals, loops, and CRN-TAM-specific constructs such as adding and removing tiles. ALCH also includes the branch and parallel structures which harness the nondeterministic and parallel nature of the CRN-TAM. ALCH also supports functional tileset specification. Using ALCH, we show that the discrete Sierpinski triangle and the discrete Sierpinski carpet can be strictly self-assembled in the CRN-TAM, which shows the CRN-TAM can self-assemble infinite shapes at scale 1 that the aTAM cannot. ALCH allows us to present these constructions at a high level, abstracting species and reactions into C-like code that is simpler to understand. We employ two new CRN-TAM techniques in our constructions. First, we use ALCH’s nondeterministic branching feature to probe previously placed tiles of the assembly and detect the presence and absence of tiles. Second, we use scaffolding tiles to precisely control tile placement by occluding any undesired binding sites. This paper is an extension of our previous work, updated to include a Sierpinski carpet construction and the parallel command.\",\"PeriodicalId\":49783,\"journal\":{\"name\":\"Natural Computing\",\"volume\":\"1 1\",\"pages\":\"1-21\"},\"PeriodicalIF\":1.7000,\"publicationDate\":\"2022-01-21\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"3\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Natural Computing\",\"FirstCategoryId\":\"94\",\"ListUrlMain\":\"https://doi.org/10.4230/LIPIcs.DNA.2020.6\",\"RegionNum\":4,\"RegionCategory\":\"计算机科学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Natural Computing","FirstCategoryId":"94","ListUrlMain":"https://doi.org/10.4230/LIPIcs.DNA.2020.6","RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"COMPUTER SCIENCE, ARTIFICIAL INTELLIGENCE","Score":null,"Total":0}
ALCH: An imperative language for chemical reaction network-controlled tile assembly
Schiefer and Winfree recently introduced the chemical reaction network-controlled tile assembly model (CRN-TAM), a variant of the abstract tile assembly model (aTAM). In the CRN-TAM, tile reactions are mediated via non-local chemical signals controlled by a chemical reaction network. This paper introduces ALCH, an imperative programming language for specifying CRN-TAM programs that can be compiled and simulated. ALCH includes standard language features such as Boolean variables, conditionals, loops, and CRN-TAM-specific constructs such as adding and removing tiles. ALCH also includes the branch and parallel structures which harness the nondeterministic and parallel nature of the CRN-TAM. ALCH also supports functional tileset specification. Using ALCH, we show that the discrete Sierpinski triangle and the discrete Sierpinski carpet can be strictly self-assembled in the CRN-TAM, which shows the CRN-TAM can self-assemble infinite shapes at scale 1 that the aTAM cannot. ALCH allows us to present these constructions at a high level, abstracting species and reactions into C-like code that is simpler to understand. We employ two new CRN-TAM techniques in our constructions. First, we use ALCH’s nondeterministic branching feature to probe previously placed tiles of the assembly and detect the presence and absence of tiles. Second, we use scaffolding tiles to precisely control tile placement by occluding any undesired binding sites. This paper is an extension of our previous work, updated to include a Sierpinski carpet construction and the parallel command.
期刊介绍:
The journal is soliciting papers on all aspects of natural computing. Because of the interdisciplinary character of the journal a special effort will be made to solicit survey, review, and tutorial papers which would make research trends in a given subarea more accessible to the broad audience of the journal.