分子模糊锁与钥匙的形式化方法

IF 0.7 4区 计算机科学 Q3 COMPUTER SCIENCE, THEORY & METHODS International Journal of Unconventional Computing Pub Date : 2013-05-28 DOI:10.7287/PEERJ.PREPRINTS.20V2
R. Wallace
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引用次数: 0

摘要

模糊锁与钥匙(FLK)在细胞间和细胞内的水平上驱动着大量复杂的逻辑门。我们引用了类似于研究非刚性分子{或相关的模糊对称扩展{的群形平铺环产物的表示来构建一个莫尔斯函数,该函数可以描述由信息催化驱动的自发对称破缺相变。然而,该函数也可用于构造类onsager随机动力学,通过与随机微分方程相关的丰富稳定性准则将其与相变方法联系起来。这两种方法提供了观察FLK的互补方式。从随机动力学中出现的极限条件使我们深入了解细胞的“广义免疫”,这需要越来越高的代谢自由能来维持基本的FLK过程。这些结果表明,更系统的研究可能阐明与FLK失败相关的病理,FLK是一个至关重要但神秘的生物学过程。
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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.
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来源期刊
International Journal of Unconventional Computing
International Journal of Unconventional Computing 工程技术-计算机:理论方法
CiteScore
2.00
自引率
11.80%
发文量
0
审稿时长
>12 weeks
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).
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