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Local parallel biomolecular computing
 DNA Based Computers III, volume 48 of DIMACS
, 1999
"... Biomolecular Computation(BMC) is computation at the molecular scale, using biotechnology engineering techniques. Most proposed methods for BMC used distributed (molecular) parallelism (DP); where operations are executed in parallel on large numbers of distinct molecules. BMC done exclusively by DP r ..."
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Cited by 53 (16 self)
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Biomolecular Computation(BMC) is computation at the molecular scale, using biotechnology engineering techniques. Most proposed methods for BMC used distributed (molecular) parallelism (DP); where operations are executed in parallel on large numbers of distinct molecules. BMC done exclusively by DP requires that the computation execute sequentially within any given molecule (though done in parallel for multiple molecules). In contrast, local parallelism (LP) allows operations to be executed in parallel on each given molecule. Winfree, et al [W96, WYS96]) proposed an innovative method for LPBMC, that of computation by unmediated selfassembly of � arrays of DNA molecules, applying known domino tiling techniques (see Buchi [B62], Berger [B66], Robinson [R71], and Lewis and Papadimitriou [LP81]) in combination with the DNA selfassembly techniques of Seeman et al [SZC94]. The likelihood for successful unmediated selfassembly of computations has not been determined (we discuss a simple model of assembly where there may be blockages in selfassembly, but more sophisticated models may have a higher likelihood of success). We develop improved techniques to more fully exploit the potential power of LPBMC. To increase
Errorresistant Implementation of DNA Computations
 In Second Annual Meeting on DNA Based Computers
"... This paper introduces a new model of computation that employs the tools of molecular biology whose in vitro implementation is far more errorresistant than extant proposals. We describe an abstraction of the model which lends itself to natural algorithmic description, particularly for problems in ..."
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Cited by 30 (5 self)
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This paper introduces a new model of computation that employs the tools of molecular biology whose in vitro implementation is far more errorresistant than extant proposals. We describe an abstraction of the model which lends itself to natural algorithmic description, particularly for problems in the complexity class NP . In addition we describe a number of lineartime algorithms within our model, particularly for NP complete problems. We describe an in vitro realisation of the model and conclude with a discussion of future work. 1 Introduction The idea that living cells and molecular complexes can be viewed as potential machinic components dates back to the late 1950s, when Richard Feynman delivered his famous paper [4] describing "submicroscopic" computers. More recently, several papers [1, 10, 16] (also see [7, 13]) have advocated the realisation of massively parallel computation using the techniques and chemistry of molecular biology. Adleman describes how a computational...
Joining and Rotating Data with Molecules
 ICEC'97 Special Session on DNA Based Computation
, 1997
"... DNAbased computing is an attempt to solve computational problems with a large number of DNA molecules. Many theoretical results have been reported so far, but their conclusions are seldom supported in experiments. We suggest data encoded in the form of (tag data tag)+, and report our experimental ..."
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Cited by 18 (0 self)
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DNAbased computing is an attempt to solve computational problems with a large number of DNA molecules. Many theoretical results have been reported so far, but their conclusions are seldom supported in experiments. We suggest data encoded in the form of (tag data tag)+, and report our experimental results of performing concatenation and rotation of DNA. Our results also show the possibility of join and other operations in relational database with molecules. Keywords DNAcomputing, relational algebra, DNA, PCR I. Introduction DNAbased computing, a new attempt to solve computational problems in biological experiments, takes advantage of parallel reaction of a large number of DNA molecules. Each experimental step in molecular biology, such as restriction by enzyme, ligation, polymerase chain reaction (PCR), or gel electrophoresis (GE), is regarded as one step in computation, and many theoretical results have been derived ranging from solving NPcomplete problems [1], [2] to mode...
DNABased Cryptography
 5th DIMACS Workshop on DNA Based Computers, MIT
, 1999
"... Recent research has considered DNA as a medium for ultrascale computation and for ultracompact information storage. One potential key application is DNAbased, molecular cryptography systems. We present some procedures for DNAbased cryptography based on onetimepads that are in principle unbre ..."
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Cited by 17 (4 self)
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Recent research has considered DNA as a medium for ultrascale computation and for ultracompact information storage. One potential key application is DNAbased, molecular cryptography systems. We present some procedures for DNAbased cryptography based on onetimepads that are in principle unbreakable. Practical applications of cryptographic systems based on onetime pads are limited in conventional electronic media by the size of the onetimepad; however DNA provides a much more compact storage medium, and an extremely small amount of DNA su#ces even for huge onetimepads. We detail procedures for two DNA onetimepad encryption schemes: (i) a substitution method using libraries of distinct pads, each of which defines a specific, randomly generated, pairwise mapping; and (ii) an XOR scheme utilizing molecular computation and indexed, random key strings. These methods can be applied either for the encryption of natural DNA or for artificial DNA encoding binary data. In the latter case, we also present a novel use of chipbased DNA microarray technology for 2D data input and output.
Paradigms for Biomolecular Computation
 UNCONVENTIONAL MODELS OF COMPUTATION
, 1998
"... Biomolecular Computation (BMC) is computation done at the molecular scale, using Biotechnological techniques. This paper discusses the underlying biotechnology that BMC may utilize, and surveys a number of distinct paradigms for doing BMC. We also identify a number of key future experimental mile ..."
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Cited by 15 (6 self)
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Biomolecular Computation (BMC) is computation done at the molecular scale, using Biotechnological techniques. This paper discusses the underlying biotechnology that BMC may utilize, and surveys a number of distinct paradigms for doing BMC. We also identify a number of key future experimental milestones for the field of BMC.
Computationally Inspired Biotechnologies: Improved DNA Synthesis and Associative Search Using ErrorCorrecting Codes and VectorQuantization
 Sixth International Meeting on DNA Based Computers (DNA6), DIMACS Series in Discrete Mathematics and Theoretical Computer Science
, 2000
"... . The main theme of this paper is to take inspiration from methods used in computer science and related disciplines, and to apply these to develop improved biotechnology. In particular, our proposed improvements are made by adapting various information theoretic coding techniques which originate ..."
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Cited by 15 (7 self)
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. The main theme of this paper is to take inspiration from methods used in computer science and related disciplines, and to apply these to develop improved biotechnology. In particular, our proposed improvements are made by adapting various information theoretic coding techniques which originate in computational and information processing disciplines, but which we retailor to work in the biotechnology context. (a) We apply ErrorCorrecting Codes, developed to correct transmission errors in electronic media, to decrease (in certain contexts, optimally) error rates in opticallyaddressed DNA synthesis (e.g., of DNA chips). (b) We apply VectorQuantization (VQ) Coding techniques (which were previously used to cluster, quantize, and compress data such as speech and images) to improve I/O rates (in certain contexts, optimally) for transformation of electronic data to and from DNA with bounded error. (c) We also apply VQ Coding techniques, some of which hierarchically cluster ...
The Complexity and Viability of DNA Computations
, 1997
"... In this paper we examine complexity issues in DNA computation. We believe that these issues are paramount in the search for socalled "killer applications", that is, applications of DNA computation that would establish the superiority of this paradigm over others in particular domains. An assured fu ..."
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Cited by 14 (4 self)
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In this paper we examine complexity issues in DNA computation. We believe that these issues are paramount in the search for socalled "killer applications", that is, applications of DNA computation that would establish the superiority of this paradigm over others in particular domains. An assured future for DNA computation can only be established through the discovery of such applications. We demonstrate that current measures of complexity fall short of reality. Consequently, we define a more realistic model, a socalled strong model of computation which provides better estimates of the resources required by DNA algorithms. We also compare the complexities of published algorithms within this new model and the weaker, extant model which is commonly (often implicitly) assumed. 1 Introduction Following the inital promise and enthusiastic response to Adleman's seminal work [1] in DNA computation, progress towards the realisation of worthwhile computations in the laboratory has become st...
Molecular Computing, Bounded Nondeterminism, and Efficient Recursion
 In Proceedings of the 24th International Colloquium on Automata, Languages, and Programming
, 1998
"... The maximum number of strands used is an important measure of a molecular algorithm's complexity. This measure is also called the volume used by the algorithm. Every problem that can be solved by an NP Turing machine with b(n) binary nondeterministic choices can be solved by molecular computation in ..."
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Cited by 14 (5 self)
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The maximum number of strands used is an important measure of a molecular algorithm's complexity. This measure is also called the volume used by the algorithm. Every problem that can be solved by an NP Turing machine with b(n) binary nondeterministic choices can be solved by molecular computation in a polynomial number of steps, with four test tubes, in volume 2 b(n) . We identify a large class of recursive algorithms that can be implemented using bounded nondeterminism. This yields improved molecular algorithms for important problems like 3SAT, independent set, and 3colorability. 1. A model of molecular computing Molecular computation was first studied in [1, 20]. The models we define were inspired as well by the work of [3, 28]. A molecular sequence is a string over an alphabet \Sigma (we can use any alphabet we like, encoding characters of \Sigma by finite sequences of base pairs). A test tube is a multiset of molecular sequences. We describe the allowable operations below. Whe...