{"title":"分子模糊锁与钥匙的形式化方法","authors":"R. Wallace","doi":"10.7287/PEERJ.PREPRINTS.20V2","DOIUrl":null,"url":null,"abstract":"The fuzzy lock-and-key (FLK) powers a vast array of sophisticated logic gates at inter- and intra-cellular levels. We invoke representations of groupoid tiling wreath products analogous to the study of nonrigid molecules { or of related fuzzy symmetry extensions { to build a Morse Function that can describe spontaneous symmetry breaking phase transitions driven by information catalysis. The Function can, however, also be used to construct an Onsager-like stochastic dynamics, linked to the phase transition approach by the rich stability criteria associated with stochastic dierential equations. The two methods provide complementary ways of looking at the FLK. A limit condition emerging from the stochastic dynamics gives insight into a cellular ‘generalized inammation’ requiring progressively higher commitment of metabolic free energy for maintenance of basic FLK processes. These results suggest that more systematic study may illuminate pathologies associated with the failure of the FLK, a centrally-important but enigmatic biological process.","PeriodicalId":54937,"journal":{"name":"International Journal of Unconventional Computing","volume":"71 1","pages":"93-110"},"PeriodicalIF":0.7000,"publicationDate":"2013-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"A Formal Approach to the Molecular Fuzzy Lock-and-Key\",\"authors\":\"R. Wallace\",\"doi\":\"10.7287/PEERJ.PREPRINTS.20V2\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"The fuzzy lock-and-key (FLK) powers a vast array of sophisticated logic gates at inter- and intra-cellular levels. We invoke representations of groupoid tiling wreath products analogous to the study of nonrigid molecules { or of related fuzzy symmetry extensions { to build a Morse Function that can describe spontaneous symmetry breaking phase transitions driven by information catalysis. The Function can, however, also be used to construct an Onsager-like stochastic dynamics, linked to the phase transition approach by the rich stability criteria associated with stochastic dierential equations. The two methods provide complementary ways of looking at the FLK. A limit condition emerging from the stochastic dynamics gives insight into a cellular ‘generalized inammation’ requiring progressively higher commitment of metabolic free energy for maintenance of basic FLK processes. These results suggest that more systematic study may illuminate pathologies associated with the failure of the FLK, a centrally-important but enigmatic biological process.\",\"PeriodicalId\":54937,\"journal\":{\"name\":\"International Journal of Unconventional Computing\",\"volume\":\"71 1\",\"pages\":\"93-110\"},\"PeriodicalIF\":0.7000,\"publicationDate\":\"2013-05-28\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"International Journal of Unconventional Computing\",\"FirstCategoryId\":\"94\",\"ListUrlMain\":\"https://doi.org/10.7287/PEERJ.PREPRINTS.20V2\",\"RegionNum\":4,\"RegionCategory\":\"计算机科学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"COMPUTER SCIENCE, THEORY & METHODS\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"International Journal of Unconventional Computing","FirstCategoryId":"94","ListUrlMain":"https://doi.org/10.7287/PEERJ.PREPRINTS.20V2","RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"COMPUTER SCIENCE, THEORY & METHODS","Score":null,"Total":0}
A Formal Approach to the Molecular Fuzzy Lock-and-Key
The fuzzy lock-and-key (FLK) powers a vast array of sophisticated logic gates at inter- and intra-cellular levels. We invoke representations of groupoid tiling wreath products analogous to the study of nonrigid molecules { or of related fuzzy symmetry extensions { to build a Morse Function that can describe spontaneous symmetry breaking phase transitions driven by information catalysis. The Function can, however, also be used to construct an Onsager-like stochastic dynamics, linked to the phase transition approach by the rich stability criteria associated with stochastic dierential equations. The two methods provide complementary ways of looking at the FLK. A limit condition emerging from the stochastic dynamics gives insight into a cellular ‘generalized inammation’ requiring progressively higher commitment of metabolic free energy for maintenance of basic FLK processes. These results suggest that more systematic study may illuminate pathologies associated with the failure of the FLK, a centrally-important but enigmatic biological process.
期刊介绍:
The International Journal of Unconventional Computing offers the opportunity for rapid publication of theoretical and experimental results in non-classical computing. Specific topics include but are not limited to:
physics of computation (e.g. conservative logic, thermodynamics of computation, reversible computing, quantum computing, collision-based computing with solitons, optical logic)
chemical computing (e.g. implementation of logical functions in chemical systems, image processing and pattern recognition in reaction-diffusion chemical systems and networks of chemical reactors)
bio-molecular computing (e.g. conformation based, information processing in molecular arrays, molecular memory)
cellular automata as models of massively parallel computing
complexity (e.g. computational complexity of non-standard computer architectures; theory of amorphous computing; artificial chemistry)
logics of unconventional computing (e.g. logical systems derived from space-time behavior of natural systems; non-classical logics; logical reasoning in physical, chemical and biological systems)
smart actuators (e.g. molecular machines incorporating information processing, intelligent arrays of actuators)
novel hardware systems (e.g. cellular automata VLSIs, functional neural chips)
mechanical computing (e.g. micromechanical encryption, computing in nanomachines, physical limits to mechanical computation).