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DNA Computing in Microreactors [chapter]

Danny van Noort, Frank-Ulrich Gast, John S. McCaskill
2002 Lecture Notes in Computer Science  
The goal of this research is to improve the programmability of DNA-based computers.  ...  Novel clockable microreactors can be connected in various ways to solve combinatorial optimisation problems, such as Maximum Clique or 3-SAT.  ...  Acknowledgement The authors wish to acknowledge the support of the GMD for DNA computing and the German Ministry of Science (BMBF) for BioMIP's start-up grant (#01SF9952).  ... 
doi:10.1007/3-540-48017-x_4 fatcat:rvwodb3l6fft3on4wffjnl6m3u

DNA computing in microreactors

Patrick Wagler, Danny van Noort, John S. McCaskill, Laszlo B. Kish, Erol C. Harvey, William B. Spillman, Jr.
2001 BioMEMS and Smart Nanostructures  
The goal of this research is to improve the programmability of DNA-based computers.  ...  Novel clockable microreactors can be connected in various ways to solve combinatorial optimisation problems, such as Maximum Clique or 3-SAT.  ...  Acknowledgement The authors wish to acknowledge the support of the GMD for DNA computing and the German Ministry of Science (BMBF) for BioMIP's start-up grant (#01SF9952).  ... 
doi:10.1117/12.454623 fatcat:qwg7zryacfhexotsgnjjyu5or4

Simulation and Visualization of Flow Pattern in Microarrays for Liquid Phase Oligonucleotide and Peptide Synthesis

Sirimon O-Charoen, Onnop Srivannavit, Erdogan Gulari
2008 Biotechnology progress (Print)  
By proper design geometry, flow uniformity could be obtained in every microreactor in the microarrays.  ...  Computational fluid dynamics (CFD) is used to model and simulate the microfluidic microarrays to study geometrical effects on flow patterns.  ...  DNA Synthesis Chip Experiment DNA was synthesized in-situ on a microfluidic device in which the microreactor depth was intentionally increased.  ... 
doi:10.1021/bp060363o pmid:17480053 pmcid:PMC2531222 fatcat:xqq37ngz75dyzdy7qrdggookiy

Optically programming DNA computing in microflow reactors

John S. McCaskill
2001 Biosystems (Amsterdam. Print)  
The programmability and the integration of biochemical processing protocols are addressed for DNA computing using photochemical and microsystem techniques.  ...  The specific problem is encoded in an initial labeling pattern of each module with one of 2N DNA oligonucleotides, identical for all instances of maximal clique.  ...  beads in the microreactor.  ... 
doi:10.1016/s0303-2647(01)00099-5 pmid:11267740 fatcat:ewyjbpdzdjhlnfcmugk2rhsepy

Fluorogenic DNA sequencing in PDMS microreactors

Peter A Sims, William J Greenleaf, Haifeng Duan, X Sunney Xie
2011 Nature Methods  
We immobilized primed dnA templates in the microreactors, then sequentially introduced one of the four identically labeled tPlFns, sealed the microreactors and recorded a fluorescence image after template-directed  ...  phosphatase, primer extension by dnA polymerase using nonfluorescent tPlFns generates fluorophores, which are confined in the microreactors and detected.  ...  This work was performed in part at the Center for Nanoscale Systems, which is a part of Harvard University and a member of the National Nanotechnology Infrastructure Network, which is supported by the  ... 
doi:10.1038/nmeth.1629 pmid:21666670 pmcid:PMC3414871 fatcat:ji5qfkqitjffvm6gia5unzxcuq

Another expert system rule inference based on DNA molecule logic gates

Piotr Wąsiewicz, Ryszard S. Romaniuk
2013 Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2013  
It requires the unique representation of signals by DNA molecules. The main part of this work includes the concept of logic gates based on typical genetic engineering reactions.  ...  With the help of silicon industry microfluidic processors were invented utilizing nano membrane valves, pumps and microreactors.  ...  He used the miniaturization labon-a-chip methodology to solve in microreactors computational problems, which were previously computed in genetic engineering laboratory tubes [3] [4] [5] .  ... 
doi:10.1117/12.2032392 fatcat:ctao4i3dijcxdeooijxra7huaq

Microreactor Array Device

Peter Wiktor, Al Brunner, Peter Kahn, Ji Qiu, Mitch Magee, Xiaofang Bian, Kailash Karthikeyan, Joshua LaBaer
2015 Scientific Reports  
The device is validated by protein expressed in situ directly from DNA in a microarray of ,10,000 spots with no diffusion during three hours incubation.  ...  Proteins can also be expressed outside of living cells by subjecting gene DNA to 'cell-free' in vitro coupled transcription and translation (IVTT) reagent.  ...  Figure 6 | 6 Image rendered with proteins expressed from DNA in microreactors.  ... 
doi:10.1038/srep08736 pmid:25736721 pmcid:PMC4348619 fatcat:7w72qomdw5cs3awbfv7mqk7yyy

3D Printed Monolithic Microreactors for Real-Time Detection of Klebsiella pneumoniae and the Resistance Gene blaNDM-1 by Recombinase Polymerase Amplification

Ole Behrmann, Matthias Hügle, Franz Eckardt, Iris Bachmann, Cecilia Heller, Marina Schramm, Carrie Turner, Frank T. Hufert, Gregory Dame
2020 Micromachines  
Singleplex assays for both khe and blaNDM-1 achieved a limit of detection of 2.5 × 101 DNA copies while the duplex assay achieved 2.5 × 101 DNA copies for khe and 2.5 × 102 DNA copies for blaNDM-1.  ...  We 3D printed monolithic rtRPA microreactors and subjected the devices to different post curing protocols.  ...  In addition, the authors would like to thank the National reference laboratory for multidrug-resistant Gram-negative bacteria at the Ruhr-University Bochum for providing Klebsiella pneumoniae strains.  ... 
doi:10.3390/mi11060595 pmid:32560308 fatcat:zgww65cfwfgdjbakrps7ooin7i

Handheld Continuous-flow Real-time Fluorescence qPCR System with PVC Microreactor

Bing Shi, Yuanming Li, Di Wu, Wenming Wu
2020 The Analyst  
The polymerase chain reaction (PCR) has unique advantages of sensitivity, specificity and rapidity in pathogen detection, which makes it at the forefront of academia and application in molecular biology  ...  in which the concentration of template DNA was 10 6 copies per μL in each set.  ...  The bar plots represent the fluorescence intensity of the DNA template amplified products in the PVC and PTFE microreactors, respectively.  ... 
doi:10.1039/c9an01894h pmid:32095799 fatcat:dviiiflvdfavdbsxxitsr6g5mm

Noise-Induced Stability Analysis of a Capillary Flow Microreactor with Mixing by Radial Diffusion of Laminar Flow Profiles

Pratap R. Patnaik
2015 International Journal of Chemoinformatics and Chemical Engineering  
Simulations showed that although the aim of RDLFP is to improve mixing, poorly mixed microreactors are more robust to the influx of noise than well-mixed tubes.  ...  Multi-component noise in multi-fluid systems can also induce stochastic resonance, which may either enhance or reduce stability.  ...  Mixing is an inherent problem because the flow in capillary microreactors is predominantly laminar (Wirth, 2008) .  ... 
doi:10.4018/ijcce.2015010101 fatcat:ysxf3pq2afdspnmtjx2zqshs2m

Microfluidic reactor array device for massively parallel in situ synthesis of oligonucleotides

Onnop Srivannavit, Mayurachat Gulari, Zhishan Hua, Xiaolian Gao, Xiaochuan Zhou, Ailing Hong, Tiecheng Zhou, Erdogan Gulari
2009 Sensors and actuators. B, Chemical  
Depending on the design parameters, it is possible to achieve uniform flow and synthesis reaction in all of the reactors by proper design of the microreactors and the microchannels.  ...  The device is made of glass anodically bonded to silicon consisting of three level features: microreactors, microchannels and through inlet/outlet holes.  ...  Computer software, written in C ++ , was developed in-house to generate light patterns based on predetermined oDNA chip layout.  ... 
doi:10.1016/j.snb.2009.04.071 pmid:20161215 pmcid:PMC2716077 fatcat:aet2wequn5gctlvdk7nvq5si6i

Automated Design and Programming of a Microfluidic DNA Computer

Michael S. Livstone, Ron Weiss, Laura F. Landweber
2006 Natural Computing  
Previously, we described ways to implement the functions AND and OR in a DNA computer consisting of microreactors with attached heating elements that control annealing of DNA.  ...  Reducing the number of reactors in a DNA computer reduces the loss of DNA through binding to the surfaces of the system.  ...  Introduction One of the primary goals in the field of DNA computing is to reduce the time and space necessary to perform a computation.  ... 
doi:10.1007/s11047-005-3803-3 fatcat:2uhugizejzbyzb52z3sbode7te

PDMS valves in DNA computers

Danny van Noort, Byoung-Tak Zhang, Dan V. Nicolau
2005 Biomedical Applications of Micro- and Nanoengineering II  
One form of DNA computing is performed in microfluidics. A network of microreactors decides the computational aspects and DNA is the tool for selection procedures.  ...  To control complex microflow systems like this, a series of pneumatic valves are used to control the flow direction, i.e. the information direction, and to contain DNA functionalised beads in the microreactors  ...  We have applied the field of microfluidics to biomolecular computing, or better known as DNA computing [1] .  ... 
doi:10.1117/12.582170 fatcat:7qhthpp7fra53gooxwgctz5hdq

Fluorogenic pyrosequencing in microreactors

Jason A Steen, Matthew A Cooper
2011 Nature Methods  
s clustering algorithm holds great promise as a game-changer in the field of computational proteomics.  ...  (a) Clonally amplified DNA beads are deposited into a microreactor, and dNTPs are sequentially washed over the wells.  ... 
doi:10.1038/nmeth.1634 pmid:21716283 fatcat:iym5w3isbnb5jg52bzsqmjkwda

Integrated microfluidic reactors

Wei-Yu Lin, Yanju Wang, Shutao Wang, Hsian-Rong Tseng
2009 Nano Today  
of radiolabeled imaging probes for positron emission tomography (PET), (iii) sequential preparation of individually addressable conducting polymer nanowire (CPNW), and (iv) solid-phase synthesis of DNA  ...  In this review, we summarize recent progresses on the development of integrated microfluidics-based chemical reactors for (i) parallel screening of in situ click chemistry libraries, (ii) multistep synthesis  ...  To fully utilize the automation performance of the integrated microfluidic system, a computer-controlled interface was employed to operate this screening microreactor for preparation of 32 reaction mixtures  ... 
doi:10.1016/j.nantod.2009.10.007 pmid:20209065 pmcid:PMC2832182 fatcat:5wo674py3rbajicne3no3aikmm
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