The fledgling field of DNA computers began in 1994 when Leonard Adleman surprised the scientific community by using DNA molecules, protein enzymes, and chemicals to solve an instance of a hard computational problem. This volume presents results from the second annual meeting on DNA computers held at Princeton only one and one-half years after Adleman's discovery. By drawing on the analogy between DNA computing and cutting-edge fields of biology (such as directed evolution), this volume highlights some of the exciting progress in the field and builds a strong foundation for the theory of molecular computation.

This proceedings volume presents the talks from the Fifth Annual Meeting on DNA Based Computers held at MIT. The conference brought together researchers and theorists from many disciplines who shared research results in biomolecular computation. Two styles of DNA computing were explored at the conference: 1) DNA computing based on combinatorial search, where randomly created DNA strands are used to encode potential solutions to a problem, and constraints induced by the problem are used to identify DNA strands that are solution witnesses; and 2) DNA computing based on finite-state machines, where the state of a computation is encoded in DNA, which controls the biochemical steps that advance the DNA-based machine from state to state. Featured articles include discussions on the formula satisfiability problem, self-assembly and nanomachines, simulation and design of molecular systems, and new theoretical approaches.

This book constitutes the thoroughly refereed post-proceedings of the 9th International Workshop on DNA Based Computers, DNA9, held in Madison, Wisconsin, USA in June 2003. The 22 revised full papers presented were carefully selected during two rounds of reviewing and improvement from initially 60 submissions. The papers are organized in topical sections on new experiments and tools, theory, computer simulation and sequence design, self-assembly and autonomous molecular computation, experimental solutions, and new computing models.

Molecular computing is a rapidly growing subarea of natural computing. On the one hand, molecular computing is concerned with the use of bio-molecules for the purpose of actual computations while, on the other hand, it attempts to understand the computational nature of molecular processes going on in living cells. The book presents a unique and authorative state-of-the-art survey on current research in molecular computing: 30 papers by leading researchers in the area are drawn together on the occasion of the 70th birthday of Tom Head, a pioneer in molecular computing. Among the topics addressed are molecular tiling, DNA self-assembly, splicing systems, DNA-based cryptography, DNA word design, gene assembly, and membrane computing.

Computers have become an essential component of modern biology. They help to manage the vast and increasing amount of biological data and continue to play an integral role in the discovery of new biological relationships. This in silico approach to biology has helped to reshape the modern biological sciences. With the biological revolution now among us, it is imperative that each scientist develop and hone today’s bioinformatics skills, if only at a rudimentary level. Bioinformatics Methods and Protocols was conceived as part of the Methods in Molecular Biology series to meet this challenge and to provide the experienced user with useful tips and an up-to-date overview of current developments. It builds upon the foundation that was provided in the two-volume set published in 1994 entitled Computer Analysis of Sequence Data. We divided Bioinformatics Methods and Protocols into five parts, including a thorough survey of the basic sequence analysis software packages that are available at most institutions, as well as the design and implemen- tion of an essential introductory Bioinformatics course. In addition, we included sections describing specialized noncommercial software, databases, and other resources available as part of the World Wide Web and a stimul- ing discussion of some of the computational challenges biologists now face and likely future solutions.

This book constitutes the thoroughly refereed post-proceedings of the 7th International Workshop on DNA-Based Computers, DNA7, held in Tampa, Florida, USA, in June 2001. The 26 revised full papers presented together with 9 poster papers were carefully reviewed and selected from 44 submissions. The papers are organized in topical sections on experimental tools, theoretical tools, probabilistic computational models, computer simulation and sequence design, algorithms, experimental solutions, nano-tech devices, biomimetic tools, new computing models, and splicing systems and membranes.

The papers in this volume were presented at the 6th International Meeting on DNA Based Computers, organized by the Leiden Center for Natural Computing and held from June 13 to June 17, 2000 at The Lorentz Center, University of Leiden, Leiden, The Netherlands. DNA Computing is a novel and fascinating development at the interface of computer science and molecular biology. It has emerged in recent years, not simply as an exciting technology for information processing, but also as a catalyst for knowledge transfer between information processing, nanotechnology, and biology. This area of research has the potential to change our understanding of the theory and practice of computing. The call for papers and poster presentations sought contributions of original research and technical expositions in all areas of bio-computation. A total of 33 abstracts were submitted of which 16 were accepted for presentation and included in the proceedings. The papers were selected by the program committee based on originality and quality of research and on relevance to the bio-computing eld. Invited talks were given by Masami Hagiya (Tokyo University), Laura La- weber (Princeton University), John Reif (Duke University), Thomas Schmidt (Leiden University), and Lloyd M. Smith (University of Wisconsin). Invited - pers based on the talks by Hagiya and Reif are included in this volume, along with the contributed papers. Additional tutorials were held on the rst and last days of the conference.

Biomolecular computing has emerged as an interdisciplinary ?eld that draws - gether chemistry, computer science, mathematics, molecular biology, and physics. Our knowledge on DNA nanotechnology and biomolecular computing increases exponentially with every passing year. The international meeting on DNA Based Computers has been a forum where scientists with di?erent backgrounds, yet sharing a common interest in biomolecular computing, meet and present their latest results. Continuing this tradition, the 8th International Meeting on DNA Based Computers (DNA8) focuses on the current theoretical and experimental results with the greatest impact. Papers and poster presentations were sought in all areas that relate to b- molecular computing, including (but not restricted to): algorithms and appli- tions, analysis of laboratory techniques/theoretical models, computational p- cesses in vitro and in vivo, DNA-computing-based biotechnological applications, DNA devices, error evaluation and correction, in vitro evolution, models of biomolecular computing (using DNA and/or other molecules), molecular - sign, nucleic acid chemistry, and simulation tools. Papers and posters with new experimental results were particularly encouraged. Authors who wished their work to be considered for either oral or poster presentation were asked to select from one of two submission “tracks”: – Track A - Full Paper – Track B - One-Page Abstract For authors with late-breaking results, or who were submitting their manuscript to a scienti?c journal, a one-page abstract, rather than a full paper, could be submitted in Track B. Authors could (optionally) include a preprint of their full paper, for consideration only by the program committee.

The contributors present the main results and techniques of their specialties in an easily accessible way accompanied with many references: historical, hints for complete proofs or solutions to exercises and directions for further research. This volume contains applications which have not appeared in any collection of this type. The book is a general source of information in computation theory, at the undergraduate and research level.

Natural computing brings together nature and computing to develop new computational tools for problem solving; to synthesize natural patterns and behaviors in computers; and to potentially design novel types of computers. Fundamentals of Natural Computing: Basic Concepts, Algorithms, and Applications presents a wide-ranging survey of novel techniqu