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16th international conference on dna computing and molecular programming

作者： Zhang, David Yu CALTECH Pasadena CA 91125 USA

ISBN: (纸本)9783642183041

dna strand displacement has been used to construct a variety of components, devices, and circuits. the sequences of involved nucleic acid molecules can greatly influence the kinetics and function of strand displacement reactions. To facilitate consideration of spurious reactions during the design process, one common strategy is to subdivide dna strands into domains, continuous nucleic acid bases that can be abstracted to act as a unit in hybridization and dissociation. Here, considerations for domain-based sequence design are discussed, and heuristics are presented for the sequence design of domains. Based on these heuristics, a randomized algorithm is implemented for sequence design.

关键词： dna

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dna computing and molecular programming 1

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丛书名： Lecture Notes in Computer Science

1000年

作者： Russell Deaton Akira Suyama

ISBN: (数字)9783642106040

ISBN: (纸本)9783642106033

this book constitutes the thoroughly refereed post-conference proceedings of the 15th international Meeting on dna computing, dna15, held in Fayetteville, AR, USA, in June 2009. the 16 revised full papers presented were carefully selected during two rounds of reviewing and improvement from 38 submissions. the papers feature current interdisciplinary research in molecular-scale manipulation of matter - in particular, implementation of nanoscale computation and programmed assembly of materials are of interest, thus reflecting a broader scope beyond dna-based nanotechnology and computation.

关键词： theory of Computation Biochemistry, general Nanotechnology and Microengineering Computation by Abstract Devices Algorithm Analysis and Problem Complexity Computational Biology/Bioinformatics

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A Formal Language Model of dna Polymerase Enzymatic Activity

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FUNDAMENTA INFORMATICAE 2015年第1-2期138卷 179-192页

作者： Enaganti, Srujan Kumar Kari, Lila Kopecki, Steffen Univ Western Ontario Dept Comp Sci London ON N6A 5B7 Canada

We propose and investigate a formal language operation inspired by the naturally occurring phenomenon of dna primer extension by a dna-template-directed dna Polymerase enzyme. Given two dna strings u and v, where the shorter string v (called primer) is Watson-Crick complementary and can thus bind to a substring of the longer string u (called template) the result of the primer extension is a dna string that is complementary to a suffix of the template which starts at the binding position of the primer. the operation of dna primer extension can be abstracted as a binary operation on two formal languages: a template language L-1 and a primer language L-2. We call this language operation L-1 - directed extension of L-2 and study the closure properties of various language classes, including the classes in the Chomsky hierarchy, under directed extension. Furthermore, we answer the question under what conditions can a given language of target strings be generated from a given template language when the primer language is unknown. We use the canonic inverse of directed extension in order to obtain the optimal solution (the minimal primer language) to this question.

关键词： FORMAL languages dna primers dna polymerases ENZYME kinetics BINARY system (Mathematics)

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Fabrication of a Carbon Chain Based Nanosensor for Maximizing Spatial Resolution in dna Sequencing 15

Fabrication of a Carbon Chain Based Nanosensor for Maximizin...

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IEEE 15th international conference on Nano/Micro Engineered and molecular System (NEMS)

作者： Ma, Bo Tung, Steve Univ Arkansas Dept Mech Engn Fayetteville AR 72701 USA

ISBN: (纸本)9781728172309

Using a carbon chain as the sensing element can significantly improve the spatial resolution in nanodevice based single molecule dna sequencing. In this report, we demonstrate a top-down approach to reduce a single monolayer graphene attached to a silicon microelectrode chip to a sub-nanometer wide carbon chain suitable for dna sequencing. this approach consists three major processing steps to first transfer the graphene to the chip, dice the attached graphene into graphene nanoribbons using Focused Ion Beam (FIB), and finally reduce the ribbon width by knocking off carbon atoms on the ribbon edge using Transmission Electron Microscopy (TEM). A final carbon chain of 0.8 nm wide and 5 nm long is accomplished. the measured electrical properties of the reduced graphene agree well with previous studies.

关键词： Graphene

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Processing dna tokens in parallel computing 15

Processing DNA tokens in parallel computing

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15th international Parallel and Distributed Processing Symposium, IPDPS 2001

作者： Nowak, R. WĄsiewicz, P. Plucienniczak, A. Mulawka, J.J. Institute of Electronic Systems Warsaw University of Technology Nowowiejska 15/19 Warsaw00-665 Poland Institute of Biotechnology and Antibiotics Starościńska 5 Warsaw02-516 Poland

ISBN: (纸本)0769509908

In this paper a new technique of sending data between molecular processors is presented. the molecular processor is a processing data unit. Its computation results have to be sent to other units in the form of addressed messages - tokens. Necessary experiments were performed. All operations were implemented in dna. dna processors and tokens were specially designed dna strings. Results of experiments prove our assumptions. © 2001 IEEE.

关键词： dna

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Fast dna Sequencing via Transverse Differential Conductance

Fast DNA Sequencing via Transverse Differential Conductance

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15th international conference on Simulation of Semiconductor Processes and Devices (SISPAD 2010)

作者： He, Yuhui Scheicher, Ralph H. Grigoriev, Anton Ahuja, Rajeev Long, Shibing Ji, Zhuoyu Yu, Zhaoan Liu, Ming Chinese Acad Sci Inst Microelect Lab Nanofabricat & Novel Devices Integrated Techn Beijing Peoples R China Uppsala Univ Dept Phys & Astron Condensed Matter Theory Grp Uppsala Sweden Royal Inst Technol Dept Mat & Engn Appl Mat Phys SE-10044 Stockholm Sweden

ISBN: (纸本)9781424477012;9781424476992

We propose using characteristic transverse differential conductance for solid-state nanopore-based dna sequencing and have explored this idea by performing molecular dynamics simulations on the translocation progress of single-stranded dna molecule through the nanopore, and calculating the associated transverse differential conductance. Our results show that measurement of the transverse differential conductance is suitable to successfully discriminate between the four nucleotide types, and we show that this identification could even withstand electrical noise caused by fluctuations due to changes in the dna orientation. Our findings demonstrate several compelling advantages of the differential conductance approach, which may lead to important applications in rapid genome sequencing.

关键词： dna dna sequencing biological techniques electrical noise molecular biophysics molecular dynamics method molecular dynamics simulations nanobiotechnology nanopore rapid genome sequencing transverse differential conductance

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Investigating contributors of the mixed dna Samples by forensic Bioinformatics;Uncertainty to certainty for Crime Laboratories

Investigating contributors of the mixed DNA Samples by foren...

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15th international conference on Advanced computing Technologies (ICACT)

作者： Kumar, Amit Awadhanam, Sharda Kashyap, Amita Andhra Pradesh Police Academy Hyderabad|c|

ISBN: (纸本)9781467328166;9781467328180

Evidences from the crime scene inculcating mixed dna profiling data has always been a challenge to the forensic science laboratories and the crime investigation agencies. Not only it confuses the analysis but it may lead to serious fatal errors in analysis of final results which may result in convicting an innocent and quittance of a criminal free. 16 STR markers have become one of the most widely used genomic markers for identity testing and gene mapping due to their high degree of heterozygosity. We introduce forensic bioinformatics approach which proved to be very quick, precise and conclusive in assessment and analysis of the raw dna profiling data provided from the laboratory. In the present study, we have discussed the utility of forensic bioinformatics application to Short tandem repeat (STR) data in a theft and looting case which was used to evaluate specific regions (loci) within nuclear dna. the analysis was made through an "MS-Excel database management tool" where the dna Profiling data provided by the Forensic Laboratory was managed and analyzed on the grounds of the various loci present and their variability in different individuals. We have incorporated the same universal concept "Variability in STR regions can be used to distinguish one dna profile from another".

关键词： Forensic Science Mix STR Forensic data management Crime scene data dna Profiling data management

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Improving precision in the study of indoor fungi: Recent changes and additions in the UNITE database for molecular identification of fungi 15

Improving precision in the study of indoor fungi: Recent cha...

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15th conference of the international Society of Indoor Air Quality and Climate, INDOOR AIR 2018

作者： Nilsson, R. Henrik Taylor, Andy F.S. Kõljalg, Urmas Abarenkov, Kessy University of Gothenburg Gothenburg Sweden The James Hutton Institute Criagiebuckler Aberdeen United Kingdom University of Tartu Tartu Estonia

ISBN: (纸本)9781713826514

Recent molecular ecology studies have found the built environment to contain a surprisingly large number of transient and resident fungi. Taxonomic identification of these fungi requires dna sequencing but even so remains error-prone. this presentation details the steps that the UNITE database for molecular identification of fungi (https://***/) has taken to facilitate molecular identification of the built mycobiome. the measures include organizing two sequence annotation workshops, sequencing >500 previously unsequenced fungal type specimens, implementing support for the MIxS-BE metadata standard, and devising several new software tools, including a search engine designed to find truly unknown fungi among public fungal dna sequences. this project resulted in more than 75,000 improvements (such as name changes and metadata additions) to public dna sequences relevant to the built mycobiome. these improvements were shared with a range of other databases and resources, including GenBank and the ISHAM database. © 2018 15th conference of the international Society of Indoor Air Quality and Climate, INDOOR AIR 2018. All rights reserved.

关键词： dna sequences

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Nanowall array chips for dna separation

Nanowall array chips for DNA separation

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15th international conference on Miniaturized Systems for Chemistry and Life Sciences 2011, MicroTAS 2011

作者： Yasui, Takao Kaji, Noritada Ogawa, Ryo Hashioka, Shingi Tokeshi, Manabu Horiike, Yasuhiro Baba, Yoshinobu Department of Applied Chemistry Graduate School of Engineering Nagoya University Japan FIRST Research Center for Innovative Nanobiodevices Nagoya University Japan Graduate School of Science ERATO Higashiyama Live-Holonics Project Nagoya University Japan National Institute for Materials Science Japan Japan

ISBN: (纸本)9781618395955

A 25 s separation of dna fragments (48.5 and 1 kbp fragments) was achieved by a nanowall array structure, although the separation of 1 kbp and 100 bp dna fragments was not. Direct observation of a single dna molecule indicates that it takes over 20 s for an elongated dna molecule to relax inside the nanowall array structure. Numerical fitting of dna molecular dynamics reveals that the balance between times for the transverse of an elongated dna molecule and the relaxation process of a dna molecule inside the nanowall array structure governs the separation of dna. Copyright © (2011) by the Chemical and Biological Microsystems Society.

关键词： molecular dynamics

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Microfluidic visualization of encounter complex in enzymatic digestion of single dna molecule by dual molecular tagging

Microfluidic visualization of encounter complex in enzymatic...

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15th international conference on Miniaturized Systems for Chemistry and Life Sciences 2011, MicroTAS 2011

作者： Onoshima, D. Kaji, N. Tokeshi, M. Baba, Y. FIRST Research Center for Innovative Nanobiodevices Nagoya University Japan Graduate School of Science ERATO Higashiyama Live-Holonics Project Nagoya University Japan Department of Applied Chemistry Graduate School of Engineering Nagoya University Japan Japan

ISBN: (纸本)9781618395955

We combined molecular tagging with microfluidics to study kinematics in a single dna molecular digestion. Moving tags of both dna ends revealed initial breakup of a single dna molecule into fragments induced by limited enzymatic digestion and subsequent rapid formation of transient structure in encounter complex. the method enables us to analyze rapid dissociation of weakly bound complexes derived from intramolecular transfer.

关键词： Kinematics

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