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NATURAL computing 2011年第1期10卷 209-241页

作者： Bernardino, Heder S. Barbosa, Helio J. C. Lab Nacl Computacao Cient BR-25651075 Petropolis RJ Brazil

this paper describes Grammar-based Immune programming (GIP) for evolving programs in an arbitrary language by immunological inspiration. GIP is based on Grammatical Evolution (GE) in which a grammar is used to define a language and decode candidate solutions to a valid representation (program). However, by default, GE uses a Genetic Algorithm in the search process while GIP uses an artificial immune system. Some modifications are needed of an immune algorithm to use a grammar in order to efficiently decode antibodies into programs. Experiments are performed to analyze algorithm behavior over different aspects and compare it with GEVA, a well known GE implementation. the methods are applied to identify a causal model (an ordinary differential equation) from an observed data set, to symbolically regress an iterated function f(f(x)) = g(x), and to find a symbolic representation of a discontinuous function.

关键词： Artificial immune system Grammatical evolution Immune programming Symbolic regression Model inference

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Design of a Biomolecular Device that Executes Process Algebra

Design of a Biomolecular Device That Executes Process Algebr...

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15th international conference on dna computing and molecular programming

作者： Majumder, Urmi Reif, John H. Duke Univ Dept Comp Sci Durham NC 27706 USA

ISBN: (纸本)9783642106033

Process algebras are widely used to define the formal semantics of concurrent communicating processes. In this paper, we implement a particularly expressive form of process algebra, known as stochastic pi-calculus;at the molecular scale by providing a design for a dna-based biomolecular device that simulates a process algebraic machine. Our design of the molecular stochastic pi-calculus system makes use of a modified form of Whiplash-PCR (WPCR) machines. In this design, we connect (via a tethering dna nanostructure) a number of dna strands, each of which corresponds to a WPCR. machine. this collection of WPCR machines are used to execute distinct concurrent processes, each with its own distinct program. Furthermore, their close proximity enables computation to proceed via communication.

关键词： dna

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Time-Complexity of Multilayered dna Strand Displacement Circuits

Time-Complexity of Multilayered DNA Strand Displacement Circ...

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15th international conference on dna computing and molecular programming

作者： Seelig, Georg Soloveichik, David Univ Washington Seattle WA 98195 USA CALTECH Pasadena CA USA

ISBN: (纸本)9783642106033

Recently we have shown how molecular logic circuits with many components arranged in multiple layers can be built using dna strand displacement reactions. the potential applications of this and similar technologies inspire the study of the computation time of multilayered molecular circuits. Using mass action kinetics to model dna strand displacement-based circuits, we discuss how computation time scales with the number of layers. We show that depending on circuit architecture, the time-complexity does not necessarily scale linearly with the depth as is assumed in the usual study of circuit complexity. We compare circuits with catalytic and non-catalytic components, showing that catalysis fundamentally alters asymptotic time-complexity. Our results rely on simple asymptotic arguments that should be applicable to a wide class of chemical circuits. these results may help to improve circuit performance and may be useful for the construction of faster, larger and more reliable molecular circuitry.

关键词： dna

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A Domain-Specific Language for programming in the Tile Assembly Model

A Domain-Specific Language for Programming in the Tile Assem...

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15th international conference on dna computing and molecular programming

作者： Doty, David Patitz, Matthew J. Iowa State Univ Dept Comp Sci Ames IA 50011 USA

ISBN: (纸本)9783642106033

We introduce a domain-specific language (DSL) for creating sets of tile types for simulations of the abstract Tile Assembly Model. the language defines objects known as tile templates, which represent related groups of tiles, and a small number of basic operations on tile templates that help to eliminate the error-prone drudgery of enumerating such tile types manually or with low-level constructs of general-purpose programming languages. the language is implemented as a class library in Python (a so-called internal DSL), but is presented independently of Python or object-oriented programming, with emphasis on support for a visual editing tool for creating large sets of complex tile types.

关键词： Problem oriented languages

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Renewable, Time-Responsive dna Logic Gates for Scalable Digital Circuits

Renewable, Time-Responsive DNA Logic Gates for Scalable Digi...

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15th international conference on dna computing and molecular programming

作者： Goel, Ashish Ibrahimi, Morteza Stanford Univ Dept Management Sci & Engn Stanford CA 94305 USA Stanford Univ Dept Comp Sci Stanford CA USA Stanford Univ Dept Elect Engn Stanford CA USA

ISBN: (纸本)9783642106033

In this article, we introduce a design of dna logic gates based on enzymatic restriction of dna strands. We present a construction for a set of one and two-input logic gates and argue that our construction can be generalized to implement any Boolean operation. A key feature of our design is its time-responsiveness, in the presence of appropriate fuels these gates can operate continuously and generate a time-dependent output in response to a time-dependant input. they can be interconnected to form digital circuits. Moreover, modulo connectivity information, the strand design and circuit design phases are decoupled.

关键词： Logic gates

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Survey on dna Encryption Techniques 15

Survey on DNA Encryption Techniques

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15th international conference on Advances in computing, Control, and Telecommunication Technologies, ACT 2024

作者： Sowmya, D. Manjula, G.R. Department of CS&E JNNCE Shivamogga India

ISBN: (纸本)9798331300579

the area of dna cryptography is an interdisciplinary field that has emerged recently, focusing on the possible applications of dna (deoxyribonucleic acid) molecules for secure encryption and data storage. It uses dna sequences to create methods for encoding, encrypting, and decoding data by fusing concepts from cryptography and molecular biology. this paper presents various works proposed in dna encoding. © Grenze Scientific Society, 2024.

关键词： Encoding (symbols)

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A Cellular Automaton Approach for Efficient computing on Surface Chemical Reaction Networks

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NEW GENERATION computing 2024年第2期42卷 217-235页

作者： Yu, Sihai Xu, Wenli Lee, Jia Isokawa, Teijiro Chongqing Univ Coll Comp Sci 174 Shazhengjie Chongqing 400044 Shapingba Peoples R China Univ Hyogo Grad Sch Engn 2167 Shosha Himeji Hyogo 6712280 Japan

A surface chemical reaction network (sCRN, Qian and Winfree in dna computing and molecular programming: 20th international conference, dna 20, Kyoto, Japan, September 22-26, 2014. Proceedings 20. Springer, 2014) is an emergent paradigm for molecular programming, in which a chemical molecule is placed at each site of a lattice, and each molecule may undergo either bi-molecular reactions associated with one of the nearest molecules or uni-molecular reactions autonomously. the lattice structure as well as the localized reactions between molecules facilitate an effective formalization of sCRNs in the framework of cellular automata. this formalism not only allows a systematic evaluation of the complexity of a sCRN, but also enables a formal approach to reduce the model's complexity for the sake of improving its effectiveness. To this end, this paper proposes a new sCRN model that has less complexity measured in terms of the numbers of both cell states and transition rules. Especially, universality of computations will be shown by implementing all asynchronous circuits, including the well-known full-adder, into the sCRN. the decreased complexity may enhance the feasibility of the proposed sCRN model for physical implementation.

关键词： molecular programming Surface CRN Cellular automata Universal computation Asynchronous circuit

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Automatic Design of dna Logic Gates Based on Kinetic Simulation

Automatic Design of DNA Logic Gates Based on Kinetic Simulat...

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15th international conference on dna computing and molecular programming

作者： Kawamata, Ibuki Tanaka, Fumiaki Hagiya, Masami Univ Tokyo Grad Sch Informat Sci & Technol Bunkyo Ku Tokyo 1138656 Japan

ISBN: (纸本)9783642106033

Recently, dna logic gates and dna machines have been developed using only a simple complementary base pairing of dna, that is, hybridization and branch migration. Because such reaction systems have been designed by trial and error, it has been difficult to design a complex system and to correctly verify the reaction. the purpose of this research is to develop a method for automatically searching and designing dna logic gates based on a kinetic simulation. Since the solution space that should be searched is quite large, a simulated-annealing method is used to search for a highly evaluated system from many candidates and find a semi-optimal one. A simulator based on a kinetic model is developed, which calculates the time change of concentrations of abstracted dna molecules. An evaluation function, in which the evaluation value rises when the logic gate works correctly, is also designed. the effectiveness of the proposed method is evaluated experimentally with an AND gate, which is designed automatically.

关键词： dna

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Construction of AND Gate for RTRACS with the Capacity of Extension to NAND Gate

Construction of AND Gate for RTRACS with the Capacity of Ext...

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15th international conference on dna computing and molecular programming

作者： Sakai, Yoko Mawatari, Yoriko Yamasaki, Kiyonari Shohda, Koh-ichiroh Suyama, Akira Univ Tokyo Grad Sch Arts & Sci Dept Life Sci Meguro Ku 3-8-1 Komaba Tokyo 1538902 Japan Univ Tokyo Grad Sch Arts & Sci Inst Phys Meguro Ku Tokyo 1538902 Japan

ISBN: (纸本)9783642106033

We have succeeded in construction of the AND gate using enzymatic reactions developed for modularized computation elements of the autonomous computing system RTRACS. Experimental results demonstrated that the molecular reaction for the AND gate generated the correct output RNA from input RNAs according to the truth table for the AND gate. the constructed molecular reaction for the AND gate can be extended to the NAND gate by small modifications, because not only a logical 1 but also a logical 0 for inputs and output was associated with the presence of RNA strands.

关键词： logic gate molecular computer

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molecular Beacon Based dna computing Model for 0-1 programming Problem

Molecular Beacon Based DNA Computing Model for 0-1 Programmi...

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4th international conference on Bio-Inspired computing

作者： Huang, Xiaohui Yin, Zhixiang Zhi, Lingying Hu, Juan Anhui Univ Sci & Technol Dept Math & Phys Huainan 232001 Anhui Peoples R China

ISBN: (纸本)9781424438655

molecular beacons have the advantages of simple structure, high sensitivity and quick response etc.. dna computing is a new method of simulating bio-molecular structure and computing using molecule biology technology, and creates a precedent in using bio-chemical reaction as the calculating tools. It is a novel way to solve a class of problems that are difficult to calculate NP-complete problem. In this paper the corresponding dna computing of implicit enumeration is given using the advantages of molecular beacons based on previous studies.

关键词： molecular Beacons dna computing Implicit Enumeration 0-1 programming problem

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