{"title":"Robust Signal Restoration in Chemical Reaction Networks","authors":"T. Klinge","doi":"10.1145/2967446.2967465","DOIUrl":"https://doi.org/10.1145/2967446.2967465","url":null,"abstract":"Molecular computing systems that are contained in well-mixed volumes are often modeled using chemical reaction networks. In these systems, concentrations of molecules are treated as signals and used for both communication and memory storage. A common design challenge for such a system is to avoid memory corruption caused by noise in the input signals. In this paper, we analyze two signal restoration algorithms for molecular systems modeled with chemical reaction networks. These algorithms are designed to prevent a memory signal from degrading over time, and we show that under modest conditions these algorithms will maintain the memory indefinitely. We also present an exact solution of the running time of the first algorithm which demonstrates that it converges in logarithmic time.","PeriodicalId":281609,"journal":{"name":"Proceedings of the 3rd ACM International Conference on Nanoscale Computing and Communication","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132959890","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}
A. Green, Jongmin Kim, D. Ma, P. Silver, J. Collins, Peng Yin
{"title":"Ribocomputing devices for sophisticated in vivo logic computation","authors":"A. Green, Jongmin Kim, D. Ma, P. Silver, J. Collins, Peng Yin","doi":"10.1145/2967446.2970373","DOIUrl":"https://doi.org/10.1145/2967446.2970373","url":null,"abstract":"Synthetic biology aims to create functional devices, systems, and organisms with novel and useful functions taking advantage of engineering principles applied to biology. Despite great progress over the last decade, an underlying problem in synthetic biology remains the limited number of high-performance, modular, composable parts. A potential route to solve parts bottleneck problem in synthetic biology utilizes the programmability of nucleic acids inspired by molecular programming approaches that have demonstrated complex biomolecular circuits evaluating logic expressions in test tubes. Using a library of de-novo-designed toehold switches with orthogonality and modular composability, we demonstrate how toehold switches can be incorporated into decision-making RNA networks termed ribocomputing devices to rapidly evaluate complex logic in living cells. We have successfully demonstrated a 4-input AND gate, a 6-input OR gate, and a 12-input expression in disjunctive normal form in E. coli. The compact encoding of ribocomputing system using a library of modular parts is amenable to aggressive scale-up towards complex control of in vivo circuitry towards autonomous behaviors and biomedical applications.","PeriodicalId":281609,"journal":{"name":"Proceedings of the 3rd ACM International Conference on Nanoscale Computing and Communication","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2016-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130858219","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}
{"title":"Proceedings of the 3rd ACM International Conference on Nanoscale Computing and Communication","authors":"W. Gerstacker, Y. Koucheryavy, G. Morabito","doi":"10.1145/2967446","DOIUrl":"https://doi.org/10.1145/2967446","url":null,"abstract":"","PeriodicalId":281609,"journal":{"name":"Proceedings of the 3rd ACM International Conference on Nanoscale Computing and Communication","volume":"51 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125703768","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}