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2008 | Buch

Introduction Kapitel lesen Erstes Kapitel lesen

DNA Computing Models

verfasst von: Karl-Heinz Zimmermann, Israel Martínez-Pérez, Zoya Ignatova

Verlag: Springer US

Enthalten in: Springer Professional "Wirtschaft+Technik" , Springer Professional "Technik" , Springer Professional "Wirtschaft"

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Über dieses Buch

Sir Francis Crick would undoubtedly be at the front of the line ordering this fascinating book. Being one of the discoverers of DNA, he would be amazed at how his work has been applied to mankind's most important invention, the computer. DNA contains the genetic instructions for the biological development of cellular life forms or viruses. DNA computing uses DNA as a substrate for storing information, while molecular biological operations are used to manipulate this information.

DNA Computing Models begins with a comprehensive introduction to the field of DNA computing. This book emphasizes computational methods to tackle central problems of DNA computing, such as controlling living cells, building patterns, and generating nanomachines. DNA Computing Models presents laboratory-scale human-operated models of computation, including a description of the first experiment of DNA computation conducted by Adleman in 1994. It provides molecular-scale autonomous models of computation and addresses the design of computational devices working in living cells. It also addresses the important problem of proper word design for DNA computing.

DNA Computing Models is designed for researchers and advanced-level students in computers science, bioengineering and molecular biology as a reference or secondary text book. This book is also suitable for practitioners in industry.

Inhaltsverzeichnis

Frontmatter
Chapter 1. Introduction
Abstract
This introductory chapter envisions DNA computing from the perspective of molecular information technology, which is brought into focus by three confluent research directions. First, the size of semiconductor devices approaches the scale of large macromolecules. Second, the enviable computational capabilities of living organisms are increasingly traced to molecular mechanisms. Third, techniques for engineering molecular control structures into living cells start to emerge.
Zoya Ignatova, Karl-Heinz Zimmermann, Israel Martínez-Pérez
Chapter 2. Theoretical Computer Science
Abstract
This chapter provides a self-contained introduction to a collection of topics in computer science that focusses on the abstract, logical, and mathematical aspects of computing. First, mathematical structures called graphs are described that are used to model pairwise relations between objects from a certain collection. Second, abstract machines with a finite number of states called finite state automata are detailed. Third, mathematical models of computation are studied and their relationships to formal grammars are explained. Fourth, combinatorial logic is introduced, which describes logic circuits whose output is a pure function of the present input only. Finally, the degrees of complexity to solve a problem on a computer are outlined.
Zoya Ignatova, Karl-Heinz Zimmermann, Israel Martínez-Pérez
Chapter 3. Molecular Biology
Abstract
Genetic information is passed with high accuracy from the parental organism to the offspring and its expression governs the biochemical and physiological tasks of the cell. Although different types of cells exist and are shaped by development to fill different physiological niches, all cells have fundamental similarities and share common principles of organization and biochemical activities. This chapter gives an overview of general principles of the storage and flow of genetic information. It aims to summarize and describe in a broadly approachable way, from the point of view of molecular biology, some general terms, mechanisms and processes used as a base for the molecular computing in the subsequent chapters.
Zoya Ignatova, Karl-Heinz Zimmermann, Israel Martínez-Pérez
Chapter 4. Word Design for DNA Computing
Abstract
This chapter addresses the problem of negative word design negative word design: Construct a large set of oligonucleotides which selectively hybridize so that undesired molecules encoding false results or blocking the desired reactions are excluded. In practice, such a set of oligonucleotides is designed so that it simultaneously satisfies several thermodynamical and combinatorial constraints.
Zoya Ignatova, Karl-Heinz Zimmermann, Israel Martínez-Pérez
Chapter 5. Non-Autonomous DNA Models
Abstract
Early biomolecular computing research focussed on laboratoryscale human-operated DNA models of computation for solving complex computational problems. These models generate large combinatorial libraries of DNA to provide search spaces for parallel filtering algorithms. Many difierent methods for library generation, solution filtering, and output generation were experimentally studied. This chapter addresses the basic filtering models and describes two basic computationally complete and universal DNA models of computation, splicing model and sticker model.
Zoya Ignatova, Karl-Heinz Zimmermann, Israel Martínez-Pérez
Chapter 6. Autonomous DNA Models
Abstract
The second generation of DNA computing focusses on models that are molecular-scale, autonomous, and partially programmable. The computations are essentially driven by the self-assembly of DNA molecules and are modulated by DNA-manipulating enzymes. This chapter addresses basic autonomous DNA models emphasizing tile assembly, finite state automata, Turing machines, neural networks, and switching circuits.
Zoya Ignatova, Karl-Heinz Zimmermann, Israel Martínez-Pérez
Chapter 7. Cellular DNA Computing
Abstract
Cellular DNA computing investigates computational properties of DNA in its natural environment: the living cell. This chapter reviews some recent DNA computing models which are proposed to work at the cellular level. The first model describes gene synthesis during sexual reproduction in ciliates, while the other models focus on logical control or manipulation of cellular expression patterns.
Zoya Ignatova, Karl-Heinz Zimmermann, Israel Martínez-Pérez
Backmatter
Metadaten
Titel
DNA Computing Models
verfasst von
Karl-Heinz Zimmermann
Israel Martínez-Pérez
Zoya Ignatova
Copyright-Jahr
2008
Verlag
Springer US
Electronic ISBN
978-0-387-73637-2
Print ISBN
978-0-387-73635-8
DOI
https://doi.org/10.1007/978-0-387-73637-2