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Modular Verification of dna Strand Displacement Networks via Serializability Analysis

19th international conference on dna computing and molecular programming

作者： Lakin, Matthew R. Phillips, Andrew Stefanovic, Darko Univ New Mexico Dept Comp Sci Albuquerque NM 87131 USA Microsoft Res Biol Computat Grp Cambridge CB1 2FB England Univ New Mexico Ctr Biomed Engn Albuquerque NM 87131 USA

ISBN: (纸本)9783319019284;9783319019277

dna strand displacement gates can be used to emulate arbitrary chemical reactions, and a number of different schemes have been proposed to achieve this. Here we develop modular correctness proofs for strand displacement encodings of chemical reaction networks and show how they may be applied to two-domain strand displacement systems. Our notion of correctness is serializability of interleaved reaction encodings, and we infer this global property from the properties of the gates that encode the individual chemical reactions. this allows correctness to be inferred for arbitrary systems constructed using these components, and we illustrate this by applying our results to a two-domain implementation of a well-known approximate majority voting system.

关键词： Encoding (symbols)

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dna Walker Circuits: Computational Potential, Design, and Verification

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19th international conference on dna computing and molecular programming

作者： Dannenberg, Fritsw Kwiatkowska, Marta thachuk, Chris Turberfield, Andrew J. Univ Oxford Dept Comp Sci Wolfson BldgPk Rd Oxford OX1 3QD England Univ Oxford Dept Phys Clarendon Lab Oxford OX1 2JD England

ISBN: (纸本)9783319019284;9783319019277

Unlike their traditional, silicon counterparts, dna computers have natural interfaces with both chemical and biological systems. these can be used for a number of applications, including the precise arrangement of matter at the nanoscale and the creation of smart biosensors. Like silicon circuits, dna strand displacement systems (DSD) can evaluate non-trivial functions. However, these systems can be slow and are susceptible to errors. It has been suggested that localised hybridization reactions could overcome some of these challenges. Localised reactions occur in dna 'walker' systems which were recently shown to be capable of navigating a programmable track tethered to an origami tile. We investigate the computational potential of these systems for evaluating Boolean functions. dna walkers, like DSDs, are also susceptible to errors. We develop a discrete stochastic model of dna walker 'circuits' based on experimental data, and demonstrate the merit of using probabilistic model checking techniques to analyse their reliability, performance and correctness.

关键词： dna

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Graph-theoretic formalization of hybridization in dna sticker complexes

Graph-theoretic formalization of hybridization in DNA sticke...

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17th international conference on dna computing and molecular programming

作者： Brijder, Robert Gillis, Joris J. M. Van den Bussche, Jan Hasselt Univ Diepenbeek Belgium Transnat Univ Limburg Diepenbeek Belgium

ISBN: (纸本)9783642236372

Sticker complexes are a formal graph-based data model for a restricted class of dna complexes, motivated by potential applications to databases. this data model allows for a purely declarative definition of hybridization. We introduce the notion of terminating hybridization, which intuitively means that only a finite number of different products can be generated. We characterize this notion in purely graph-theoretic terms. Under a finite alphabet, each product is shown to be of polynomial size. Yet, terminating hybridization can still produce results of exponential size, in that there may be exponentially many different (nonisomorphic) finished products. We indicate a class of complexes where hybridization is guaranteed to be polynomially bounded.

关键词： dna Hybridization Graph-theory Complexity

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Improved dna-sticker arithmetic: tube-encoded-carry, Logarithmic Number System and Monte-Carlo methods

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NATURAL computing 2013年第2期12卷 235-246页

作者： Arnold, Mark G. POB 605 Laramie WY 82070 USA

the sticker model of computation, implemented using robotic processing of dna, manipulates in parallel many bitstrings, called strands, that are contained in a limited number of tubes. Prior sticker arithmetic algorithms, patterned on digital-electronics, generate carry bits in the strand, either wasting bits or using a clear operation (with problematic biochemical implementation). the novel addition algorithm here does not need to record the carry. Instead, which tube holds a particular strand implicitly encodes the carry. the speed and number of tubes are half that of prior approaches. Further encoding data in the Logarithmic Number System (LNS) allows such integer operations to perform cost-effective real multiplications, divisions and roots. An example LNS Euclidian norm is more efficient than prior methods, assuming perfect operations. Unfortunately, dna-stickers are unreliable. this paper uses sticker unreliability as a source of randomness to implement Monte-Carlo (MC) arithmetic (previously fabricated in silicon at the cost of pseudo-random generators). With stickers, the randomness is free. MC engineering mimics natural systems using unreliable but redundant components. Here, MC randomness is only useful in low-order bits. Multiple re-testing of the same bit ("refinement") trades improved reliability for slower operation using more tubes. Simulations (with different sizes, probabilities and refinement) show that increasing refinement as a function of bit position allows imperfect implementations to achieve suitable MC strand-error distributions, predicting 1000x speed-mass advantage of sticker-MCLNS over conventional supercomputers.

关键词： dna arithmetic Sticker system Addition Logarithmic Number System (LNS) Monte-Carlo Arithmetic

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One-dimensional staged self-assembly

One-dimensional staged self-assembly

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17th international conference on dna computing and molecular programming

作者： Demaine, Erik D. Eisenstat, Sarah Ishaque, Mashhood Winslow, Andrew MIT Comp Sci & Artificial Intelligence Lab Cambridge MA 02139 USA Tufts Univ Dept Comp Sci Medford MA 02155 USA

ISBN: (纸本)9783642236372

We introduce the problem of staged self-assembly of one-dimensional nanostructures, which becomes interesting when the elements are labeled (e.g., representing functional units that must be placed at specific locations). In a restricted model in which each operation has a single terminal assembly, we prove that assembling a given string of labels with the fewest steps is equivalent, up to constant factors, to compressing the string to be uniquely derived from the smallest possible context-free grammar (a well-studied O(log n)-approximable problem) and that the problem is NP-hard. Without this restriction, we show that the optimal assembly can be substantially smaller than the optimal context-free grammar, by a factor of even for binary strings of length n. Fortunately, we can bound this separation in model power by a quadratic function in the number of distinct glues or tiles allowed in the assembly, which is typically small in practice.

关键词： Context-free grammar Wang tile dna computing Complexity

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Improved dna-sticker arithmetic: tube-encoded-carry, Logarithmic Number System and Monte-Carlo methods

Improved DNA-sticker arithmetic: tube-encoded-carry, Logarit...

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17th international conference on dna computing and molecular programming

作者： Arnold, Mark G. POB 605 Laramie WY 82070 USA

关键词： dna arithmetic Sticker system Addition Logarithmic Number System (LNS) Monte-Carlo Arithmetic

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Genalign — A high performance implementation for aligning the compressed dna sequences

Genalign — A high performance implementation for aligning t...

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international conference on Advanced computing Technologies (ICACT)

作者： D Satyanvesh Kaliuday Balleda P K Baruah Sri Sathya Sai Institute of Higher Learning Prasanthi Nilayam India

In molecular biology, sequence alignment is a way of arranging dna, RNA or protein sequences to identify regions of similarity between the sequences. However, this is a challenging problem since the dna sequences are huge in size and the databases are growing at an exponential rate. It requires tremendous amount of memory and large computational power. For example, the human genome in raw format ranges from 2 to 30 Tera-bytes. the inherent property of dna is that it contains many repeats which makes it highly compressible. this paper presents a new approach of aligning the sequences after compressing them. the alignment consists of both ungapped and gapped alignment. Multi-cores and GPUs can be used to align these huge sequences quickly on the compressed sequences. the focus mainly is on aligning the huge sequences accurately. the ungapped alignment achieves a speedup of upto 56 on K20 Kepler GPUs and the gapped alignment achieves a speedup of upto 15 on multi-cores.

关键词： dna Graphics processing units Dynamic programming Heuristic algorithms Instruction sets Random access memory Bioinformatics

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PARP1 gene variation and microglial activity on [11C]PBR28 PET in older adults at risk for Alzheimer's disease

PARP1 gene variation and microglial activity on [11C]PBR28 P...

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3rd international Workshop on Multimodal Brain Image Analysis, MBIA 2013, Held in Conjunction with the 16th international conference on Medical Image computing and Computer Assisted Intervention, MICCAI 2013

作者： Kim, Sungeun Nho, Kwangsik Risacher, Shannon L. Inlow, Mark Swaminathan, Shanker Yoder, Karmen K. Shen, Li West, John D. McDonald, Brenna C. Tallman, Eileen F. Hutchins, Gary D. Fletcher, James W. Farlow, Martin R. Ghetti, Bernardino Saykin, Andrew J. Center for Neuroimaging Department of Radiology and Imaging Sciences Indiana University School of Medicine Indianapolis IN United States Center for Computational Biology and Bioinformatics Indiana University School of Medicine Indianapolis IN United States Indiana Alzheimer Disease Center Indiana University School of Medicine Indianapolis IN United States Department of Mathematics Rose-Hulman Institute of Technology Terre Haute IN United States Department of Neurology Indiana University School of Medicine Indianapolis IN United States Indiana Institute for Biomedical Imaging Sciences Indiana University School of Medicine Indianapolis IN United States Department of Pathology and Laboratory Medicine Indiana University School of Medicine Indianapolis IN United States Department of Medical and Molecular Genetics Indiana University School of Medicine Indianapolis IN United States

ISBN: (纸本)9783319021256

Increasing evidence suggests that inflammation is one pathophysiological mechanism in Alzheimer's disease (AD). Recent studies have identified an association between the poly (ADP-ribose) polymerase 1 (PARP1) gene and AD. this gene encodes a protein that is involved in many biological functions, including dna repair and chromatin remodeling, and is a mediator of inflammation. therefore, we performed a targeted genetic association analysis to investigate the relationship between the PARP1 polymorphisms and brain microglial activity as indexed by [11C]PBR28 positron emission tomography (PET). Participants were 26 non-Hispanic Caucasians in the Indiana Memory and Aging Study (IMAS). PET data were intensity-normalized by injected dose/total body weight. Average [11C]PBR28 standardized uptake values (SUV) from 6 bilateral regions of interest (thalamus, frontal, parietal, temporal, and cingulate cortices, and whole brain gray matter) were used as endophenotypes. Single nucleotide polymorphisms (SNPs) with 20% minor allele frequency that were within +/- 20 kb of the PARP1 gene were included in the analyses. Gene-level association analyses were performed using a dominant genetic model with translocator protein (18-kDa) (TSPO) genotype, age at PET scan, and gender as covariates. Analyses were performed with and without APOE Ε4 status as a covariate. Associations with [11C]PBR28 SUVs from thalamus and cingulate were significant at corrected p11C]PBR28 SUV showed that individuals with the "C" allele at rs6677172 and "A" allele at rs61835377 had higher [11C]PBR28 SUV than individuals without these alleles (corrected P11C]PBR28 SUV and brain atrophy at a follow-up visit, suggesting possible protective effect of microglial activity against cortical atrophy. Interestingly, all 6 AD and 2 of 3 LMCI participants in the current analysis had one or more copies of the "GG" allele combination, associated with lower cingulate [ 11C]PBR28 SUV, suggesting that this gene variant warrants fu

关键词： Positron emission tomography

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Using molecular computing for a data analysis prototype

Using molecular computing for a data analysis prototype

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16th international conference on Mechatronics Technology, ICMT 2012

作者： Wu, Kee-Rong Yeh, Chung-Wei Chu, Chih-Ping Department of Marine Engineering National Kaohsiung Marine University Kaohsiung Taiwan Department of Management Information System Kao Yuan University Kaohsiung Taiwan Department of Computer Science and Information Engineering National Cheng Kung University Tainan Taiwan

ISBN: (纸本)9787900769428

We present a promising development of a data analysis model, DAdna, with operational procedures by using deoxyribonucleic acid (dna) computing solution to exploit vast parallelism. the proposed solution is based mainly on the innovative bio-operations by Adleman and Amos to implement table design, simulate relational algebra, cluster and solve query problems. DAdna consists of three layers: (1) a Data definition layer, in which the records are represented by dna strands, (2) an Operational procedure layer, in which fundamental relational and extended operations are executed by dna-based procedures, and (3) a Query-analysis layer, in which the query is executed, involving the construction of relational tables and executing the operations in the Operational procedure layer. Hence, the dna based data cluster design proceeded with our well-organized scheme. Our proposed model can be used as an algorithmic basis for database operational procedures embedded in biomolecular computations for the further development and performing generalized data analysis with inherent molecular parallelism.

关键词： dna

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dna computing and molecular programming - 17th international conference, dna 17, Proceedings

DNA Computing and Molecular Programming - 17th International...

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17th international conference on dna computing and molecular programming, dna 17

ISBN: (纸本)9783642236372

the proceedings contain 14 papers. the topics discussed include: an autonomous dna nanodevice captures pH maps of living cells in culture and in vivo;the computer science of molecular programming;cooperation in an all-RNA network;designer dna architectures for bionanotechnology;an improved dna-sticker addition algorithm and its application to logarithmic arithmetic;graph-theoretic formalization of hybridization in dna sticker complexes;less haste, less waste: on recycling and its limits in strand displacement systems;computing maximal Kleene closures that are embeddable in a given constrained dna language;modelling, simulating and verifying Turing-powerful strand displacement systems;synthesizing small and reliable tile sets for patterned dna self-assembly;exact shapes and Turing universality at temperature 1 with a single negative glue;and multiple molecular spiders with a single localized source - the one-dimensional case.

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