Computer codes for designing proton linear accelerators

International Nuclear Information System (INIS)

Kato, Takao

1992-01-01

Computer codes for designing proton linear accelerators are discussed from the viewpoint of not only designing but also construction and operation of the linac. The codes are divided into three categories according to their purposes: 1) design code, 2) generation and simulation code, and 3) electric and magnetic fields calculation code. The role of each category is discussed on the basis of experience at KEK (the design of the 40-MeV proton linac and its construction and operation, and the design of the 1-GeV proton linac). We introduce our recent work relevant to three-dimensional calculation and supercomputer calculation: 1) tuning of MAFIA (three-dimensional electric and magnetic fields calculation code) for supercomputer, 2) examples of three-dimensional calculation of accelerating structures by MAFIA, 3) development of a beam transport code including space charge effects. (author)

Joint design of QC-LDPC codes for coded cooperation system with joint iterative decoding

Science.gov (United States)

Zhang, Shunwai; Yang, Fengfan; Tang, Lei; Ejaz, Saqib; Luo, Lin; Maharaj, B. T.

2016-03-01

In this paper, we investigate joint design of quasi-cyclic low-density-parity-check (QC-LDPC) codes for coded cooperation system with joint iterative decoding in the destination. First, QC-LDPC codes based on the base matrix and exponent matrix are introduced, and then we describe two types of girth-4 cycles in QC-LDPC codes employed by the source and relay. In the equivalent parity-check matrix corresponding to the jointly designed QC-LDPC codes employed by the source and relay, all girth-4 cycles including both type I and type II are cancelled. Theoretical analysis and numerical simulations show that the jointly designed QC-LDPC coded cooperation well combines cooperation gain and channel coding gain, and outperforms the coded non-cooperation under the same conditions. Furthermore, the bit error rate performance of the coded cooperation employing jointly designed QC-LDPC codes is better than those of random LDPC codes and separately designed QC-LDPC codes over AWGN channels.

RevTrans: multiple alignment of coding DNA from aligned amino acid sequences

DEFF Research Database (Denmark)

Wernersson, Rasmus; Pedersen, Anders Gorm

2003-01-01

The simple fact that proteins are built from 20 amino acids while DNA only contains four different bases, means that the 'signal-to-noise ratio' in protein sequence alignments is much better than in alignments of DNA. Besides this information-theoretical advantage, protein alignments also benefit...... proteins. It is therefore preferable to align coding DNA at the amino acid level and it is for this purpose we have constructed the program RevTrans. RevTrans constructs a multiple DNA alignment by: (i) translating the DNA; (ii) aligning the resulting peptide sequences; and (iii) building a multiple DNA...

LUCID - an optical design and raytrace code

International Nuclear Information System (INIS)

Nicholas, D.J.; Duffey, K.P.

1980-11-01

A 2D optical design and ray trace code is described. The code can operate either as a geometric optics propagation code or provide a scalar diffraction treatment. There are numerous non-standard options within the code including design and systems optimisation procedures. A number of illustrative problems relating to the design of optical components in the field of high power lasers is included. (author)

DNA methylation of miRNA coding sequences putatively associated with childhood obesity.

Science.gov (United States)

Mansego, M L; Garcia-Lacarte, M; Milagro, F I; Marti, A; Martinez, J A

2017-02-01

Epigenetic mechanisms may be involved in obesity onset and its consequences. The aim of the present study was to evaluate whether DNA methylation status in microRNA (miRNA) coding regions is associated with childhood obesity. DNA isolated from white blood cells of 24 children (identification sample: 12 obese and 12 non-obese) from the Grupo Navarro de Obesidad Infantil study was hybridized in a 450 K methylation microarray. Several CpGs whose DNA methylation levels were statistically different between obese and non-obese were validated by MassArray® in 95 children (validation sample) from the same study. Microarray analysis identified 16 differentially methylated CpGs between both groups (6 hypermethylated and 10 hypomethylated). DNA methylation levels in miR-1203, miR-412 and miR-216A coding regions significantly correlated with body mass index standard deviation score (BMI-SDS) and explained up to 40% of the variation of BMI-SDS. The network analysis identified 19 well-defined obesity-relevant biological pathways from the KEGG database. MassArray® validation identified three regions located in or near miR-1203, miR-412 and miR-216A coding regions differentially methylated between obese and non-obese children. The current work identified three CpG sites located in coding regions of three miRNAs (miR-1203, miR-412 and miR-216A) that were differentially methylated between obese and non-obese children, suggesting a role of miRNA epigenetic regulation in childhood obesity. © 2016 World Obesity Federation.

Signalign: An Ontology of DNA as Signal for Comparative Gene Structure Prediction Using Information-Coding-and-Processing Techniques.

Science.gov (United States)

Yu, Ning; Guo, Xuan; Gu, Feng; Pan, Yi

2016-03-01

Conventional character-analysis-based techniques in genome analysis manifest three main shortcomings-inefficiency, inflexibility, and incompatibility. In our previous research, a general framework, called DNA As X was proposed for character-analysis-free techniques to overcome these shortcomings, where X is the intermediates, such as digit, code, signal, vector, tree, graph network, and so on. In this paper, we further implement an ontology of DNA As Signal, by designing a tool named Signalign for comparative gene structure analysis, in which DNA sequences are converted into signal series, processed by modified method of dynamic time warping and measured by signal-to-noise ratio (SNR). The ontology of DNA As Signal integrates the principles and concepts of other disciplines including information coding theory and signal processing into sequence analysis and processing. Comparing with conventional character-analysis-based methods, Signalign can not only have the equivalent or superior performance, but also enrich the tools and the knowledge library of computational biology by extending the domain from character/string to diverse areas. The evaluation results validate the success of the character-analysis-free technique for improved performances in comparative gene structure prediction.

Systematic analysis of coding and noncoding DNA sequences using methods of statistical linguistics

Science.gov (United States)

Mantegna, R. N.; Buldyrev, S. V.; Goldberger, A. L.; Havlin, S.; Peng, C. K.; Simons, M.; Stanley, H. E.

1995-01-01

We compare the statistical properties of coding and noncoding regions in eukaryotic and viral DNA sequences by adapting two tests developed for the analysis of natural languages and symbolic sequences. The data set comprises all 30 sequences of length above 50 000 base pairs in GenBank Release No. 81.0, as well as the recently published sequences of C. elegans chromosome III (2.2 Mbp) and yeast chromosome XI (661 Kbp). We find that for the three chromosomes we studied the statistical properties of noncoding regions appear to be closer to those observed in natural languages than those of coding regions. In particular, (i) a n-tuple Zipf analysis of noncoding regions reveals a regime close to power-law behavior while the coding regions show logarithmic behavior over a wide interval, while (ii) an n-gram entropy measurement shows that the noncoding regions have a lower n-gram entropy (and hence a larger "n-gram redundancy") than the coding regions. In contrast to the three chromosomes, we find that for vertebrates such as primates and rodents and for viral DNA, the difference between the statistical properties of coding and noncoding regions is not pronounced and therefore the results of the analyses of the investigated sequences are less conclusive. After noting the intrinsic limitations of the n-gram redundancy analysis, we also briefly discuss the failure of the zeroth- and first-order Markovian models or simple nucleotide repeats to account fully for these "linguistic" features of DNA. Finally, we emphasize that our results by no means prove the existence of a "language" in noncoding DNA.

Junk DNA and the long non-coding RNA twist in cancer genetics

NARCIS (Netherlands)

H. Ling (Hui); K. Vincent; M. Pichler; R. Fodde (Riccardo); I. Berindan-Neagoe (Ioana); F.J. Slack (Frank); G.A. Calin (George)

2015-01-01

textabstractThe central dogma of molecular biology states that the flow of genetic information moves from DNA to RNA to protein. However, in the last decade this dogma has been challenged by new findings on non-coding RNAs (ncRNAs) such as microRNAs (miRNAs). More recently, long non-coding RNAs

Mechanical design of DNA nanostructures

Science.gov (United States)

Castro, Carlos E.; Su, Hai-Jun; Marras, Alexander E.; Zhou, Lifeng; Johnson, Joshua

2015-03-01

Structural DNA nanotechnology is a rapidly emerging field that has demonstrated great potential for applications such as single molecule sensing, drug delivery, and templating molecular components. As the applications of DNA nanotechnology expand, a consideration of their mechanical behavior is becoming essential to understand how these structures will respond to physical interactions. This review considers three major avenues of recent progress in this area: (1) measuring and designing mechanical properties of DNA nanostructures, (2) designing complex nanostructures based on imposed mechanical stresses, and (3) designing and controlling structurally dynamic nanostructures. This work has laid the foundation for mechanically active nanomachines that can generate, transmit, and respond to physical cues in molecular systems.Structural DNA nanotechnology is a rapidly emerging field that has demonstrated great potential for applications such as single molecule sensing, drug delivery, and templating molecular components. As the applications of DNA nanotechnology expand, a consideration of their mechanical behavior is becoming essential to understand how these structures will respond to physical interactions. This review considers three major avenues of recent progress in this area: (1) measuring and designing mechanical properties of DNA nanostructures, (2) designing complex nanostructures based on imposed mechanical stresses, and (3) designing and controlling structurally dynamic nanostructures. This work has laid the foundation for mechanically active nanomachines that can generate, transmit, and respond to physical cues in molecular systems. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr07153k

Functional intersection of ATM and DNA-dependent protein kinase catalytic subunit in coding end joining during V(D)J recombination

DEFF Research Database (Denmark)

Lee, Baeck-Seung; Gapud, Eric J; Zhang, Shichuan

2013-01-01

V(D)J recombination is initiated by the RAG endonuclease, which introduces DNA double-strand breaks (DSBs) at the border between two recombining gene segments, generating two hairpin-sealed coding ends and two blunt signal ends. ATM and DNA-dependent protein kinase catalytic subunit (DNA-PKcs) ar......V(D)J recombination is initiated by the RAG endonuclease, which introduces DNA double-strand breaks (DSBs) at the border between two recombining gene segments, generating two hairpin-sealed coding ends and two blunt signal ends. ATM and DNA-dependent protein kinase catalytic subunit (DNA......-PKcs) are serine-threonine kinases that orchestrate the cellular responses to DNA DSBs. During V(D)J recombination, ATM and DNA-PKcs have unique functions in the repair of coding DNA ends. ATM deficiency leads to instability of postcleavage complexes and the loss of coding ends from these complexes. DNA...... when ATM is present and its kinase activity is intact. The ability of ATM to compensate for DNA-PKcs kinase activity depends on the integrity of three threonines in DNA-PKcs that are phosphorylation targets of ATM, suggesting that ATM can modulate DNA-PKcs activity through direct phosphorylation of DNA...

DNA Barcoding through Quaternary LDPC Codes.

Science.gov (United States)

Tapia, Elizabeth; Spetale, Flavio; Krsticevic, Flavia; Angelone, Laura; Bulacio, Pilar

2015-01-01

For many parallel applications of Next-Generation Sequencing (NGS) technologies short barcodes able to accurately multiplex a large number of samples are demanded. To address these competitive requirements, the use of error-correcting codes is advised. Current barcoding systems are mostly built from short random error-correcting codes, a feature that strongly limits their multiplexing accuracy and experimental scalability. To overcome these problems on sequencing systems impaired by mismatch errors, the alternative use of binary BCH and pseudo-quaternary Hamming codes has been proposed. However, these codes either fail to provide a fine-scale with regard to size of barcodes (BCH) or have intrinsic poor error correcting abilities (Hamming). Here, the design of barcodes from shortened binary BCH codes and quaternary Low Density Parity Check (LDPC) codes is introduced. Simulation results show that although accurate barcoding systems of high multiplexing capacity can be obtained with any of these codes, using quaternary LDPC codes may be particularly advantageous due to the lower rates of read losses and undetected sample misidentification errors. Even at mismatch error rates of 10(-2) per base, 24-nt LDPC barcodes can be used to multiplex roughly 2000 samples with a sample misidentification error rate in the order of 10(-9) at the expense of a rate of read losses just in the order of 10(-6).

DNA Barcoding through Quaternary LDPC Codes.

Directory of Open Access Journals (Sweden)

Elizabeth Tapia

Full Text Available For many parallel applications of Next-Generation Sequencing (NGS technologies short barcodes able to accurately multiplex a large number of samples are demanded. To address these competitive requirements, the use of error-correcting codes is advised. Current barcoding systems are mostly built from short random error-correcting codes, a feature that strongly limits their multiplexing accuracy and experimental scalability. To overcome these problems on sequencing systems impaired by mismatch errors, the alternative use of binary BCH and pseudo-quaternary Hamming codes has been proposed. However, these codes either fail to provide a fine-scale with regard to size of barcodes (BCH or have intrinsic poor error correcting abilities (Hamming. Here, the design of barcodes from shortened binary BCH codes and quaternary Low Density Parity Check (LDPC codes is introduced. Simulation results show that although accurate barcoding systems of high multiplexing capacity can be obtained with any of these codes, using quaternary LDPC codes may be particularly advantageous due to the lower rates of read losses and undetected sample misidentification errors. Even at mismatch error rates of 10(-2 per base, 24-nt LDPC barcodes can be used to multiplex roughly 2000 samples with a sample misidentification error rate in the order of 10(-9 at the expense of a rate of read losses just in the order of 10(-6.

DNA origami design of 3D nanostructures

DEFF Research Database (Denmark)

Andersen, Ebbe Sloth; Nielsen, Morten Muhlig

2009-01-01

[8]. We have recently developed a semi-automated DNA origami software package [9] that uses a 2D sequence editor in conjunction with several automated tools to facilitate the design process. Here we extend the use of the program for designing DNA origami structures in 3D and show the application......Structural DNA nanotechnology has been heavily dependent on the development of dedicated software tools for the design of unique helical junctions, to define unique sticky-ends for tile assembly, and for predicting the products of the self-assembly reaction of multiple DNA strands [1-3]. Recently......, several dedicated 3D editors for computer-aided design of DNA structures have been developed [4-7]. However, many of these tools are not efficient for designing DNA origami structures that requires the design of more than 200 unique DNA strands to be folded along a scaffold strand into a defined 3D shape...

Non coding RNA: sequence-specific guide for chromatin modification and DNA damage signaling

Directory of Open Access Journals (Sweden)

Sofia eFrancia

2015-11-01

Full Text Available Chromatin conformation shapes the environment in which our genome is transcribed into RNA. Transcription is a source of DNA damage, thus it often occurs concomitantly to DNA damage signaling. Growing amounts of evidence suggest that different types of RNAs can, independently from their protein-coding properties, directly affect chromatin conformation, transcription and splicing, as well as promote the activation of the DNA damage response (DDR and DNA repair. Therefore, transcription paradoxically functions to both threaten and safeguard genome integrity. On the other hand, DNA damage signaling is known to modulate chromatin to suppress transcription of the surrounding genetic unit. It is thus intriguing to understand how transcription can modulate DDR signaling while, in turn, DDR signaling represses transcription of chromatin around the DNA lesion. An unexpected player in this field is the RNA interference (RNAi machinery, which play roles in transcription, splicing and chromatin modulation in several organisms. Non-coding RNAs (ncRNAs and several protein factors involved in the RNAi pathway are well known master regulators of chromatin while only recent reports suggest that ncRNAs are involved in DDR signaling and homology-mediated DNA repair. Here, we discuss the experimental evidence supporting the idea that ncRNAs act at the genomic loci from which they are transcribed to modulate chromatin, DDR signaling and DNA repair.

Status of reactor core design code system in COSINE code package

Energy Technology Data Exchange (ETDEWEB)

Chen, Y.; Yu, H.; Liu, Z., E-mail: yuhui@snptc.com.cn [State Nuclear Power Software Development Center, SNPTC, National Energy Key Laboratory of Nuclear Power Software (NEKLS), Beijiing (China)

2014-07-01

For self-reliance, COre and System INtegrated Engine for design and analysis (COSINE) code package is under development in China. In this paper, recent development status of the reactor core design code system (including the lattice physics code and the core simulator) is presented. The well-established theoretical models have been implemented. The preliminary verification results are illustrated. And some special efforts, such as updated theory models and direct data access application, are also made to achieve better software product. (author)

Status of reactor core design code system in COSINE code package

International Nuclear Information System (INIS)

Chen, Y.; Yu, H.; Liu, Z.

2014-01-01

For self-reliance, COre and System INtegrated Engine for design and analysis (COSINE) code package is under development in China. In this paper, recent development status of the reactor core design code system (including the lattice physics code and the core simulator) is presented. The well-established theoretical models have been implemented. The preliminary verification results are illustrated. And some special efforts, such as updated theory models and direct data access application, are also made to achieve better software product. (author)

Superimposed Code Theorectic Analysis of DNA Codes and DNA Computing

Science.gov (United States)

2010-03-01

that the hybridization that occurs between a DNA strand and its Watson - Crick complement can be used to perform mathematical computation. This research...ssDNA single stranded DNA WC Watson – Crick A Adenine C Cytosine G Guanine T Thymine ... Watson - Crick (WC) duplex, e.g., TCGCA TCGCA . Note that non-WC duplexes can form and such a formation is called a cross-hybridization. Cross

A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region.

Science.gov (United States)

Kress, W John; Erickson, David L

2007-06-06

A useful DNA barcode requires sufficient sequence variation to distinguish between species and ease of application across a broad range of taxa. Discovery of a DNA barcode for land plants has been limited by intrinsically lower rates of sequence evolution in plant genomes than that observed in animals. This low rate has complicated the trade-off in finding a locus that is universal and readily sequenced and has sufficiently high sequence divergence at the species-level. Here, a global plant DNA barcode system is evaluated by comparing universal application and degree of sequence divergence for nine putative barcode loci, including coding and non-coding regions, singly and in pairs across a phylogenetically diverse set of 48 genera (two species per genus). No single locus could discriminate among species in a pair in more than 79% of genera, whereas discrimination increased to nearly 88% when the non-coding trnH-psbA spacer was paired with one of three coding loci, including rbcL. In silico trials were conducted in which DNA sequences from GenBank were used to further evaluate the discriminatory power of a subset of these loci. These trials supported the earlier observation that trnH-psbA coupled with rbcL can correctly identify and discriminate among related species. A combination of the non-coding trnH-psbA spacer region and a portion of the coding rbcL gene is recommended as a two-locus global land plant barcode that provides the necessary universality and species discrimination.

Context influences on TALE-DNA binding revealed by quantitative profiling.

Science.gov (United States)

Rogers, Julia M; Barrera, Luis A; Reyon, Deepak; Sander, Jeffry D; Kellis, Manolis; Joung, J Keith; Bulyk, Martha L

2015-06-11

Transcription activator-like effector (TALE) proteins recognize DNA using a seemingly simple DNA-binding code, which makes them attractive for use in genome engineering technologies that require precise targeting. Although this code is used successfully to design TALEs to target specific sequences, off-target binding has been observed and is difficult to predict. Here we explore TALE-DNA interactions comprehensively by quantitatively assaying the DNA-binding specificities of 21 representative TALEs to ∼5,000-20,000 unique DNA sequences per protein using custom-designed protein-binding microarrays (PBMs). We find that protein context features exert significant influences on binding. Thus, the canonical recognition code does not fully capture the complexity of TALE-DNA binding. We used the PBM data to develop a computational model, Specificity Inference For TAL-Effector Design (SIFTED), to predict the DNA-binding specificity of any TALE. We provide SIFTED as a publicly available web tool that predicts potential genomic off-target sites for improved TALE design.

Context influences on TALE–DNA binding revealed by quantitative profiling

Science.gov (United States)

Rogers, Julia M.; Barrera, Luis A.; Reyon, Deepak; Sander, Jeffry D.; Kellis, Manolis; Joung, J Keith; Bulyk, Martha L.

2015-01-01

Transcription activator-like effector (TALE) proteins recognize DNA using a seemingly simple DNA-binding code, which makes them attractive for use in genome engineering technologies that require precise targeting. Although this code is used successfully to design TALEs to target specific sequences, off-target binding has been observed and is difficult to predict. Here we explore TALE–DNA interactions comprehensively by quantitatively assaying the DNA-binding specificities of 21 representative TALEs to ∼5,000–20,000 unique DNA sequences per protein using custom-designed protein-binding microarrays (PBMs). We find that protein context features exert significant influences on binding. Thus, the canonical recognition code does not fully capture the complexity of TALE–DNA binding. We used the PBM data to develop a computational model, Specificity Inference For TAL-Effector Design (SIFTED), to predict the DNA-binding specificity of any TALE. We provide SIFTED as a publicly available web tool that predicts potential genomic off-target sites for improved TALE design. PMID:26067805

Blahut-Arimoto algorithm and code design for action-dependent source coding problems

DEFF Research Database (Denmark)

Trillingsgaard, Kasper Fløe; Simeone, Osvaldo; Popovski, Petar

2013-01-01

The source coding problem with action-dependent side information at the decoder has recently been introduced to model data acquisition in resource-constrained systems. In this paper, an efficient Blahut-Arimoto-type algorithm for the numerical computation of the rate-distortion-cost function...... for this problem is proposed. Moreover, a simplified two-stage code structure based on multiplexing is put forth, whereby the first stage encodes the actions and the second stage is composed of an array of classical Wyner-Ziv codes, one for each action. Leveraging this structure, specific coding/decoding...... strategies are designed based on LDGM codes and message passing. Through numerical examples, the proposed code design is shown to achieve performance close to the rate-distortion-cost function....

DNA origami design of 3D nanostructures

DEFF Research Database (Denmark)

Andersen, Ebbe Sloth; Nielsen, Morten Muhlig

2009-01-01

, several dedicated 3D editors for computer-aided design of DNA structures have been developed [4-7]. However, many of these tools are not efficient for designing DNA origami structures that requires the design of more than 200 unique DNA strands to be folded along a scaffold strand into a defined 3D shape...... [8]. We have recently developed a semi-automated DNA origami software package [9] that uses a 2D sequence editor in conjunction with several automated tools to facilitate the design process. Here we extend the use of the program for designing DNA origami structures in 3D and show the application...... by the construction of a DNA box with dimensions of 42 × 36 × 36 nm3. The software is available at www.cdna.dk/origami/ ....

Superimposed Code Theoretic Analysis of Deoxyribonucleic Acid (DNA) Codes and DNA Computing

Science.gov (United States)

2010-01-01

DNA strand and its Watson - Crick complement can be used to perform mathematical computation. This research addresses how the...Acid dsDNA double stranded DNA MOSAIC Mobile Stream Processing Cluster PCR Polymerase Chain Reaction RAM Random Access Memory ssDNA single stranded DNA WC Watson – Crick A Adenine C Cytosine G Guanine T Thymine ...are 5′→3′ and strands with strikethrough are 3′→5′. A dsDNA duplex formed between a strand and its reverse complement is called a

Design evaluation on sodium piping system and comparison of the design codes

International Nuclear Information System (INIS)

Lee, Dong Won; Jeong, Ji Young; Lee, Yong Bum; Lee, Hyeong Yeon

2015-01-01

A large-scale sodium test loop of STELLA-1 (Sodium integral effect test loop for safety simulation and assessment) with two main piping systems has been installed at KAERI. In this study, design evaluations on the main sodium piping systems in STELLA-1 have been conducted according to the DBR (design by rule) codes of the ASME B31.1 and RCC-MRx RB-3600. In addition, design evaluations according to the DBA (design by analysis) code of the ASME Section III Subsection NB-3200 have been conducted. The evaluation results for the present piping systems showed that results from the DBR codes were more conservative than those from the DBA code, and among the DBR codes, the non-nuclear code of the ASME B31.1 was more conservative than the French nuclear DBR code of the RCC-MRx RB-3600. The conservatism on the DBR codes of the ASME B31.1 and RCC-MRx RB-3600 was quantified based on the present sodium piping analyses.

Design evaluation on sodium piping system and comparison of the design codes

Energy Technology Data Exchange (ETDEWEB)

Lee, Dong Won; Jeong, Ji Young; Lee, Yong Bum; Lee, Hyeong Yeon [KAERI, Daejeon (Korea, Republic of)

2015-03-15

A large-scale sodium test loop of STELLA-1 (Sodium integral effect test loop for safety simulation and assessment) with two main piping systems has been installed at KAERI. In this study, design evaluations on the main sodium piping systems in STELLA-1 have been conducted according to the DBR (design by rule) codes of the ASME B31.1 and RCC-MRx RB-3600. In addition, design evaluations according to the DBA (design by analysis) code of the ASME Section III Subsection NB-3200 have been conducted. The evaluation results for the present piping systems showed that results from the DBR codes were more conservative than those from the DBA code, and among the DBR codes, the non-nuclear code of the ASME B31.1 was more conservative than the French nuclear DBR code of the RCC-MRx RB-3600. The conservatism on the DBR codes of the ASME B31.1 and RCC-MRx RB-3600 was quantified based on the present sodium piping analyses.

Interleaver Design for Turbo Coding

DEFF Research Database (Denmark)

Andersen, Jakob Dahl; Zyablov, Viktor

1997-01-01

By a combination of construction and random search based on a careful analysis of the low weight words and the distance properties of the component codes, it is possible to find interleavers for turbo coding with a high minimum distance. We have designed a block interleaver with permutations...

76 FR 11432 - Coding of Design Marks in Registrations

Science.gov (United States)

2011-03-02

...] Coding of Design Marks in Registrations AGENCY: United States Patent and Trademark Office, Commerce... practice of coding newly registered trademarks that include a design element with design mark codes based... notice and request for comments at 75 FR 81587, proposing to discontinue a secondary system of coding...

75 FR 81587 - Coding of Design Marks in Registrations

Science.gov (United States)

2010-12-28

... DEPARTMENT OF COMMERCE Patent and Trademark Office [Docket No. PTO-T-2010-0090] Coding of Design... discontinue its secondary design coding, the practice of coding newly registered trademarks in its searchable... temporarily retain the paper collection of registrations with design coding, while improving the accuracy of...

Advanced thermionic reactor systems design code

International Nuclear Information System (INIS)

Lewis, B.R.; Pawlowski, R.A.; Greek, K.J.; Klein, A.C.

1991-01-01

An overall systems design code is under development to model an advanced in-core thermionic nuclear reactor system for space applications at power levels of 10 to 50 kWe. The design code is written in an object-oriented programming environment that allows the use of a series of design modules, each of which is responsible for the determination of specific system parameters. The code modules include a neutronics and core criticality module, a core thermal hydraulics module, a thermionic fuel element performance module, a radiation shielding module, a module for waste heat transfer and rejection, and modules for power conditioning and control. The neutronics and core criticality module determines critical core size, core lifetime, and shutdown margins using the criticality calculation capability of the Monte Carlo Neutron and Photon Transport Code System (MCNP). The remaining modules utilize results of the MCNP analysis along with FORTRAN programming to predict the overall system performance

Advanced hardware design for error correcting codes

CERN Document Server

Coussy, Philippe

2015-01-01

This book provides thorough coverage of error correcting techniques. It includes essential basic concepts and the latest advances on key topics in design, implementation, and optimization of hardware/software systems for error correction. The book’s chapters are written by internationally recognized experts in this field. Topics include evolution of error correction techniques, industrial user needs, architectures, and design approaches for the most advanced error correcting codes (Polar Codes, Non-Binary LDPC, Product Codes, etc). This book provides access to recent results, and is suitable for graduate students and researchers of mathematics, computer science, and engineering. • Examines how to optimize the architecture of hardware design for error correcting codes; • Presents error correction codes from theory to optimized architecture for the current and the next generation standards; • Provides coverage of industrial user needs advanced error correcting techniques.

Coding of DNA samples and data in the pharmaceutical industry: current practices and future directions--perspective of the I-PWG.

Science.gov (United States)

Franc, M A; Cohen, N; Warner, A W; Shaw, P M; Groenen, P; Snapir, A

2011-04-01

DNA samples collected in clinical trials and stored for future research are valuable to pharmaceutical drug development. Given the perceived higher risk associated with genetic research, industry has implemented complex coding methods for DNA. Following years of experience with these methods and with addressing questions from institutional review boards (IRBs), ethics committees (ECs) and health authorities, the industry has started reexamining the extent of the added value offered by these methods. With the goal of harmonization, the Industry Pharmacogenomics Working Group (I-PWG) conducted a survey to gain an understanding of company practices for DNA coding and to solicit opinions on their effectiveness at protecting privacy. The results of the survey and the limitations of the coding methods are described. The I-PWG recommends dialogue with key stakeholders regarding coding practices such that equal standards are applied to DNA and non-DNA samples. The I-PWG believes that industry standards for privacy protection should provide adequate safeguards for DNA and non-DNA samples/data and suggests a need for more universal standards for samples stored for future research.

Improved Design of Unequal Error Protection LDPC Codes

Directory of Open Access Journals (Sweden)

Sandberg Sara

2010-01-01

Full Text Available We propose an improved method for designing unequal error protection (UEP low-density parity-check (LDPC codes. The method is based on density evolution. The degree distribution with the best UEP properties is found, under the constraint that the threshold should not exceed the threshold of a non-UEP code plus some threshold offset. For different codeword lengths and different construction algorithms, we search for good threshold offsets for the UEP code design. The choice of the threshold offset is based on the average a posteriori variable node mutual information. Simulations reveal the counter intuitive result that the short-to-medium length codes designed with a suitable threshold offset all outperform the corresponding non-UEP codes in terms of average bit-error rate. The proposed codes are also compared to other UEP-LDPC codes found in the literature.

Genetic Constructor: An Online DNA Design Platform.

Science.gov (United States)

Bates, Maxwell; Lachoff, Joe; Meech, Duncan; Zulkower, Valentin; Moisy, Anaïs; Luo, Yisha; Tekotte, Hille; Franziska Scheitz, Cornelia Johanna; Khilari, Rupal; Mazzoldi, Florencio; Chandran, Deepak; Groban, Eli

2017-12-15

Genetic Constructor is a cloud Computer Aided Design (CAD) application developed to support synthetic biologists from design intent through DNA fabrication and experiment iteration. The platform allows users to design, manage, and navigate complex DNA constructs and libraries, using a new visual language that focuses on functional parts abstracted from sequence. Features like combinatorial libraries and automated primer design allow the user to separate design from construction by focusing on functional intent, and design constraints aid iterative refinement of designs. A plugin architecture enables contributions from scientists and coders to leverage existing powerful software and connect to DNA foundries. The software is easily accessible and platform agnostic, free for academics, and available in an open-source community edition. Genetic Constructor seeks to democratize DNA design, manufacture, and access to tools and services from the synthetic biology community.

Scar-less multi-part DNA assembly design automation

Science.gov (United States)

Hillson, Nathan J.

2016-06-07

The present invention provides a method of a method of designing an implementation of a DNA assembly. In an exemplary embodiment, the method includes (1) receiving a list of DNA sequence fragments to be assembled together and an order in which to assemble the DNA sequence fragments, (2) designing DNA oligonucleotides (oligos) for each of the DNA sequence fragments, and (3) creating a plan for adding flanking homology sequences to each of the DNA oligos. In an exemplary embodiment, the method includes (1) receiving a list of DNA sequence fragments to be assembled together and an order in which to assemble the DNA sequence fragments, (2) designing DNA oligonucleotides (oligos) for each of the DNA sequence fragments, and (3) creating a plan for adding optimized overhang sequences to each of the DNA oligos.

A novel constraint for thermodynamically designing DNA sequences.

Directory of Open Access Journals (Sweden)

Qiang Zhang

Full Text Available Biotechnological and biomolecular advances have introduced novel uses for DNA such as DNA computing, storage, and encryption. For these applications, DNA sequence design requires maximal desired (and minimal undesired hybridizations, which are the product of a single new DNA strand from 2 single DNA strands. Here, we propose a novel constraint to design DNA sequences based on thermodynamic properties. Existing constraints for DNA design are based on the Hamming distance, a constraint that does not address the thermodynamic properties of the DNA sequence. Using a unique, improved genetic algorithm, we designed DNA sequence sets which satisfy different distance constraints and employ a free energy gap based on a minimum free energy (MFE to gauge DNA sequences based on set thermodynamic properties. When compared to the best constraints of the Hamming distance, our method yielded better thermodynamic qualities. We then used our improved genetic algorithm to obtain lower-bound DNA sequence sets. Here, we discuss the effects of novel constraint parameters on the free energy gap.

System Design Description for the TMAD Code

International Nuclear Information System (INIS)

Finfrock, S.H.

1995-01-01

This document serves as the System Design Description (SDD) for the TMAD Code System, which includes the TMAD code and the LIBMAKR code. The SDD provides a detailed description of the theory behind the code, and the implementation of that theory. It is essential for anyone who is attempting to review or modify the code or who otherwise needs to understand the internal workings of the code. In addition, this document includes, in Appendix A, the System Requirements Specification for the TMAD System

New features in the design code TLIE

International Nuclear Information System (INIS)

van Zeijts, J.

1993-01-01

We present features recently installed in the arbitrary-order accelerator design code TLIE. The code uses the MAD input language, and implements programmable extensions modeled after the C language that make it a powerful tool in a wide range of applications: from basic beamline design to high precision-high order design and even control room applications. The basic quantities important in accelerator design are easily accessible from inside the control language. Entities like parameters in elements (strength, current), transfer maps (either in Taylor series or in Lie algebraic form), lines, and beams (either as sets of particles or as distributions) are among the type of variables available. These variables can be set, used as arguments in subroutines, or just typed out. The code is easily extensible with new datatypes

Two human cDNA molecules coding for the Duchenne muscular dystrophy (DMD) locus are highly homologous

Energy Technology Data Exchange (ETDEWEB)

Rosenthal, A.; Speer, A.; Billwitz, H. (Zentralinstitut fuer Molekularbiologie, Berlin-Buch (Germany Democratic Republic)); Cross, G.S.; Forrest, S.M.; Davies, K.E. (Univ. of Oxford (England))

1989-07-11

Recently the complete sequence of the human fetal cDNA coding for the Duchenne muscular dystrophy (DMD) locus was reported and a 3,685 amino acid long, rod-shaped cytoskeletal protein (dystrophin) was predicted as the protein product. Independently, the authors have isolated and sequenced different DMD cDNA molecules from human adult and fetal muscle. The complete 12.5 kb long sequence of all their cDNA clones has now been determined and they report here the nucleotide (nt) and amino acid (aa) differences between the sequences of both groups. The cDNA sequence comprises the whole coding region but lacks the first 110 nt from the 5{prime}-untranslated region and the last 1,417 nt of the 3{prime}-untranslated region. They have found 11 nt differences (approximately 99.9% homology) from which 7 occurred at the aa level.

Design and Assembly of DNA Nano-Objects and 2D DNA Origami Arrays

Science.gov (United States)

Liu, Wenyan

DNA, which plays a central role in biology as the carrier of genetic information, is also an excellent candidate for structural nanotechnology. Researches have proven that a variety of complicated DNA assemblies, such as objects, 2D & 3D crystals, and nanomechanical devices, can be fabricated through the combination of robust branched DNA motifs and sticky ends. This dissertation focuses on the design and construction of DNA nano--objects and 2D DNA origami arrays. In this dissertation, we first describe the formation of a triangular species that has four strands per edge, held together by PX interactions. We demonstrate by nondenaturing gel electrophoresis and by atomic force microscopy (AFM) that we can combine a partial triangle with other strands to form a robust four--stranded molecule. By combining them with a novel three--domain molecule, we also demonstrate by AFM that these triangles can be self--assembled into a linear array. Second, we demonstrate our attempts to design and self--assemble 2D DNA origami arrays using several different strategies. Specifically, we introduce the self--assembly of 2D DNA origami lattices using a symmetric cross--like design. This design strategy resulted in a well--ordered woven latticework array with edge dimensions of 2--3 mum. This size is likely to be large enough to connect bottom-up methods of patterning with top--down approaches. Third, we illustrate the design and construction of DNA nano--objects for exploring the substrate preferences of topoisomerase (topo) II. We designed and fabricated four double rhombus--like DNA molecules, each of which contains a different conformation of crossover in the middle, as possible substrates to establish the structural preferences for topo II. We characterized the formation of each substrate molecule by gel electrophoresis. Finally, we study the effect of M13 DNA knotting on the formation of the DNA origami tiles. We demonstrate by atomic force microscopy (AFM) that knotted M13

Fundamentals of information theory and coding design

CERN Document Server

Togneri, Roberto

2003-01-01

In a clear, concise, and modular format, this book introduces the fundamental concepts and mathematics of information and coding theory. The authors emphasize how a code is designed and discuss the main properties and characteristics of different coding algorithms along with strategies for selecting the appropriate codes to meet specific requirements. They provide comprehensive coverage of source and channel coding, address arithmetic, BCH, and Reed-Solomon codes and explore some more advanced topics such as PPM compression and turbo codes. Worked examples and sets of basic and advanced exercises in each chapter reinforce the text's clear explanations of all concepts and methodologies.

Space-Time Code Designs for Broadband Wireless Communications

National Research Council Canada - National Science Library

Xia, Xiang-Gen

2005-01-01

The goal of this research is to design new space AND time codes, such as complex orthogonal space AND time block codes with rate above 1/2 from complex orthogonal designs for QAM, PSK, and CPM signals...

DNA-based genetic markers for Rapid Cycling Brassica rapa (Fast Plants type designed for the teaching laboratory.

Directory of Open Access Journals (Sweden)

Eryn E. Slankster

2012-06-01

Full Text Available We have developed DNA-based genetic markers for rapid-cycling Brassica rapa (RCBr, also known as Fast Plants. Although markers for Brassica rapa already exist, ours were intentionally designed for use in a teaching laboratory environment. The qualities we selected for were robust amplification in PCR, polymorphism in RCBr strains, and alleles that can be easily resolved in simple agarose slab gels. We have developed two single nucleotide polymorphism (SNP based markers and 14 variable number tandem repeat (VNTR-type markers spread over four chromosomes. The DNA sequences of these markers represent variation in a wide range of genomic features. Among the VNTR-type markers, there are examples of variation in a nongenic region, variation within an intron, and variation in the coding sequence of a gene. Among the SNP-based markers there are examples of polymorphism in intronic DNA and synonymous substitution in a coding sequence. Thus these markers can serve laboratory exercises in both transmission genetics and molecular biology.

Computer-aided design of DNA origami structures.

Science.gov (United States)

Selnihhin, Denis; Andersen, Ebbe Sloth

2015-01-01

The DNA origami method enables the creation of complex nanoscale objects that can be used to organize molecular components and to function as reconfigurable mechanical devices. Of relevance to synthetic biology, DNA origami structures can be delivered to cells where they can perform complicated sense-and-act tasks, and can be used as scaffolds to organize enzymes for enhanced synthesis. The design of DNA origami structures is a complicated matter and is most efficiently done using dedicated software packages. This chapter describes a procedure for designing DNA origami structures using a combination of state-of-the-art software tools. First, we introduce the basic method for calculating crossover positions between DNA helices and the standard crossover patterns for flat, square, and honeycomb DNA origami lattices. Second, we provide a step-by-step tutorial for the design of a simple DNA origami biosensor device, from schematic idea to blueprint creation and to 3D modeling and animation, and explain how careful modeling can facilitate later experimentation in the laboratory.

Differential DNA methylation profiles of coding and non-coding genes define hippocampal sclerosis in human temporal lobe epilepsy

Science.gov (United States)

Miller-Delaney, Suzanne F.C.; Bryan, Kenneth; Das, Sudipto; McKiernan, Ross C.; Bray, Isabella M.; Reynolds, James P.; Gwinn, Ryder; Stallings, Raymond L.

2015-01-01

Temporal lobe epilepsy is associated with large-scale, wide-ranging changes in gene expression in the hippocampus. Epigenetic changes to DNA are attractive mechanisms to explain the sustained hyperexcitability of chronic epilepsy. Here, through methylation analysis of all annotated C-phosphate-G islands and promoter regions in the human genome, we report a pilot study of the methylation profiles of temporal lobe epilepsy with or without hippocampal sclerosis. Furthermore, by comparative analysis of expression and promoter methylation, we identify methylation sensitive non-coding RNA in human temporal lobe epilepsy. A total of 146 protein-coding genes exhibited altered DNA methylation in temporal lobe epilepsy hippocampus (n = 9) when compared to control (n = 5), with 81.5% of the promoters of these genes displaying hypermethylation. Unique methylation profiles were evident in temporal lobe epilepsy with or without hippocampal sclerosis, in addition to a common methylation profile regardless of pathology grade. Gene ontology terms associated with development, neuron remodelling and neuron maturation were over-represented in the methylation profile of Watson Grade 1 samples (mild hippocampal sclerosis). In addition to genes associated with neuronal, neurotransmitter/synaptic transmission and cell death functions, differential hypermethylation of genes associated with transcriptional regulation was evident in temporal lobe epilepsy, but overall few genes previously associated with epilepsy were among the differentially methylated. Finally, a panel of 13, methylation-sensitive microRNA were identified in temporal lobe epilepsy including MIR27A, miR-193a-5p (MIR193A) and miR-876-3p (MIR876), and the differential methylation of long non-coding RNA documented for the first time. The present study therefore reports select, genome-wide DNA methylation changes in human temporal lobe epilepsy that may contribute to the molecular architecture of the epileptic brain. PMID

The DIT nuclear fuel assembly physics design code

International Nuclear Information System (INIS)

Jonsson, A.

1988-01-01

The DIT code is the Combustion Engineering, Inc. (C-E) nuclear fuel assembly design code. It belongs to a class of codes, all similar in structure and strategy, that may be characterized by the spectrum and spatial calculations being performed in two dimensions and in a single job step for the entire assembly. The forerunner of this class of codes is the United Kingdom Atomic Energy Authority WIMS code, the first version of which was completed 25 yr ago. The structure and strategy of assembly spectrum codes have remained remarkably similar to the original concept thus proving its usefulness. As other organizations, including C-E, have developed their own versions of the concept, many important variations have been added that significantly influence the accuracy and performance of the resulting computational tool. Those features, which are unique to the DIT code and which might be of interest to the community of fuel assembly physics design code users and developers, are described and discussed

ICRPfinder: a fast pattern design algorithm for coding sequences and its application in finding potential restriction enzyme recognition sites

Directory of Open Access Journals (Sweden)

Stafford Phillip

2009-09-01

Full Text Available Abstract Background Restriction enzymes can produce easily definable segments from DNA sequences by using a variety of cut patterns. There are, however, no software tools that can aid in gene building -- that is, modifying wild-type DNA sequences to express the same wild-type amino acid sequences but with enhanced codons, specific cut sites, unique post-translational modifications, and other engineered-in components for recombinant applications. A fast DNA pattern design algorithm, ICRPfinder, is provided in this paper and applied to find or create potential recognition sites in target coding sequences. Results ICRPfinder is applied to find or create restriction enzyme recognition sites by introducing silent mutations. The algorithm is shown capable of mapping existing cut-sites but importantly it also can generate specified new unique cut-sites within a specified region that are guaranteed not to be present elsewhere in the DNA sequence. Conclusion ICRPfinder is a powerful tool for finding or creating specific DNA patterns in a given target coding sequence. ICRPfinder finds or creates patterns, which can include restriction enzyme recognition sites, without changing the translated protein sequence. ICRPfinder is a browser-based JavaScript application and it can run on any platform, in on-line or off-line mode.

The Influence of Building Codes on Recreation Facility Design.

Science.gov (United States)

Morrison, Thomas A.

1989-01-01

Implications of building codes upon design and construction of recreation facilities are investigated (national building codes, recreation facility standards, and misperceptions of design requirements). Recreation professionals can influence architectural designers to correct past deficiencies, but they must understand architectural and…

Design of Packet-Based Block Codes with Shift Operators

Directory of Open Access Journals (Sweden)

Ilow Jacek

2010-01-01

Full Text Available This paper introduces packet-oriented block codes for the recovery of lost packets and the correction of an erroneous single packet. Specifically, a family of systematic codes is proposed, based on a Vandermonde matrix applied to a group of information packets to construct redundant packets, where the elements of the Vandermonde matrix are bit-level right arithmetic shift operators. The code design is applicable to packets of any size, provided that the packets within a block of information packets are of uniform length. In order to decrease the overhead associated with packet padding using shift operators, non-Vandermonde matrices are also proposed for designing packet-oriented block codes. An efficient matrix inversion procedure for the off-line design of the decoding algorithm is presented to recover lost packets. The error correction capability of the design is investigated as well. The decoding algorithm, based on syndrome decoding, to correct a single erroneous packet in a group of received packets is presented. The paper is equipped with examples of codes using different parameters. The code designs and their performance are tested using Monte Carlo simulations; the results obtained exhibit good agreement with the corresponding theoretical results.

Computer codes for RF cavity design

International Nuclear Information System (INIS)

Ko, K.

1992-08-01

In RF cavity design, numerical modeling is assuming an increasingly important role with the help of sophisticated computer codes and powerful yet affordable computers. A description of the cavity codes in use in the accelerator community has been given previously. The present paper will address the latest developments and discuss their applications to cavity toning and matching problems

Preliminary design studies for the DESCARTES and CIDER codes

International Nuclear Information System (INIS)

Eslinger, P.W.; Miley, T.B.; Ouderkirk, S.J.; Nichols, W.E.

1992-12-01

The Hanford Environmental Dose Reconstruction (HEDR) project is developing several computer codes to model the release and transport of radionuclides into the environment. This preliminary design addresses two of these codes: Dynamic Estimates of Concentrations and Radionuclides in Terrestrial Environments (DESCARTES) and Calculation of Individual Doses from Environmental Radionuclides (CIDER). The DESCARTES code will be used to estimate the concentration of radionuclides in environmental pathways, given the output of the air transport code HATCHET. The CIDER code will use information provided by DESCARTES to estimate the dose received by an individual. This document reports on preliminary design work performed by the code development team to determine if the requirements could be met for Descartes and CIDER. The document contains three major sections: (i) a data flow diagram and discussion for DESCARTES, (ii) a data flow diagram and discussion for CIDER, and (iii) a series of brief statements regarding the design approach required to address each code requirement

The Dit nuclear fuel assembly physics design code

International Nuclear Information System (INIS)

Jonsson, A.

1987-01-01

DIT is the Combustion Engineering, Inc. (C-E) nuclear fuel assembly design code. It belongs to a class of codes, all similar in structure and strategy, which may be characterized by the spectrum and spatial calculations being performed in 2D and in a single job step for the entire assembly. The forerunner of this class of codes is the U.K.A.E.A. WIMS code, the first version of which was completed 25 years ago. The structure and strategy of assembly spectrum codes have remained remarkably similar to the original concept thus proving its usefulness. As other organizations, including C-E, have developed their own versions of the concept, many important variations have been added which significantly influence the accuracy and performance of the resulting computational tool. This paper describes and discusses those features which are unique to the DIT code and which might be of interest to the community of fuel assembly physics design code users and developers

Structural reliability codes for probabilistic design

DEFF Research Database (Denmark)

Ditlevsen, Ove Dalager

1997-01-01

probabilistic code format has not only strong influence on the formal reliability measure, but also on the formal cost of failure to be associated if a design made to the target reliability level is considered to be optimal. In fact, the formal cost of failure can be different by several orders of size for two...... different, but by and large equally justifiable probabilistic code formats. Thus, the consequence is that a code format based on decision theoretical concepts and formulated as an extension of a probabilistic code format must specify formal values to be used as costs of failure. A principle of prudence...... is suggested for guiding the choice of the reference probabilistic code format for constant reliability. In the author's opinion there is an urgent need for establishing a standard probabilistic reliability code. This paper presents some considerations that may be debatable, but nevertheless point...

LEGO: A modular accelerator design code

International Nuclear Information System (INIS)

Cai, Y.; Donald, M.; Irwin, J.; Yan, Y.

1997-08-01

An object-oriented accelerator design code has been designed and implemented in a simple and modular fashion. It contains all major features of its predecessors: TRACY and DESPOT. All physics of single-particle dynamics is implemented based on the Hamiltonian in the local frame of the component. Components can be moved arbitrarily in the three dimensional space. Several symplectic integrators are used to approximate the integration of the Hamiltonian. A differential algebra class is introduced to extract a Taylor map up to arbitrary order. Analysis of optics is done in the same way both for the linear and nonlinear case. Currently, the code is used to design and simulate the lattices of the PEP-II. It will also be used for the commissioning

Computer codes for RF cavity design

International Nuclear Information System (INIS)

Ko, K.

1992-01-01

In RF cavity design, numerical modeling is assuming an increasingly important role with the help of sophisticated computer codes and powerful yet affordable computers. A description of the cavity codes in use in the accelerator community has been given previously. The present paper will address the latest developments and discuss their applications to cavity tuning and matching problems. (Author) 8 refs., 10 figs

Evaluation of the DRAGON code for VHTR design analysis.

Energy Technology Data Exchange (ETDEWEB)

Taiwo, T. A.; Kim, T. K.; Nuclear Engineering Division

2006-01-12

This letter report summarizes three activities that were undertaken in FY 2005 to gather information on the DRAGON code and to perform limited evaluations of the code performance when used in the analysis of the Very High Temperature Reactor (VHTR) designs. These activities include: (1) Use of the code to model the fuel elements of the helium-cooled and liquid-salt-cooled VHTR designs. Results were compared to those from another deterministic lattice code (WIMS8) and a Monte Carlo code (MCNP). (2) The preliminary assessment of the nuclear data library currently used with the code and libraries that have been provided by the IAEA WIMS-D4 Library Update Project (WLUP). (3) DRAGON workshop held to discuss the code capabilities for modeling the VHTR.

Evaluation of the DRAGON code for VHTR design analysis

International Nuclear Information System (INIS)

Taiwo, T. A.; Kim, T. K.; Nuclear Engineering Division

2006-01-01

This letter report summarizes three activities that were undertaken in FY 2005 to gather information on the DRAGON code and to perform limited evaluations of the code performance when used in the analysis of the Very High Temperature Reactor (VHTR) designs. These activities include: (1) Use of the code to model the fuel elements of the helium-cooled and liquid-salt-cooled VHTR designs. Results were compared to those from another deterministic lattice code (WIMS8) and a Monte Carlo code (MCNP). (2) The preliminary assessment of the nuclear data library currently used with the code and libraries that have been provided by the IAEA WIMS-D4 Library Update Project (WLUP). (3) DRAGON workshop held to discuss the code capabilities for modeling the VHTR

The arbitrary order design code Tlie 1.0

International Nuclear Information System (INIS)

Zeijts, J. van; Neri, Filippo

1993-01-01

We describe the arbitrary order charged particle transfer map code TLIE. This code is a general 6D relativistic design code with a MAD compatible input language and among others implements user defined functions and subroutines and nested fitting and optimization. First we describe the mathematics and physics in the code. Aside from generating maps for all the standard accelerator elements we describe an efficient method for generating nonlinear transfer maps for realistic magnet models. We have implemented the method to arbitrary order in our accelerator design code for cylindrical current sheet magnets. We also have implemented a self-consistent space-charge approach as in CHARLIE. Subsequently we give a description of the input language and finally, we give several examples from productions run, such as cases with stacked multipoles with overlapping fringe fields. (Author)

Design of Packet-Based Block Codes with Shift Operators

Directory of Open Access Journals (Sweden)

Jacek Ilow

2010-01-01

Full Text Available This paper introduces packet-oriented block codes for the recovery of lost packets and the correction of an erroneous single packet. Specifically, a family of systematic codes is proposed, based on a Vandermonde matrix applied to a group of k information packets to construct r redundant packets, where the elements of the Vandermonde matrix are bit-level right arithmetic shift operators. The code design is applicable to packets of any size, provided that the packets within a block of k information packets are of uniform length. In order to decrease the overhead associated with packet padding using shift operators, non-Vandermonde matrices are also proposed for designing packet-oriented block codes. An efficient matrix inversion procedure for the off-line design of the decoding algorithm is presented to recover lost packets. The error correction capability of the design is investigated as well. The decoding algorithm, based on syndrome decoding, to correct a single erroneous packet in a group of n=k+r received packets is presented. The paper is equipped with examples of codes using different parameters. The code designs and their performance are tested using Monte Carlo simulations; the results obtained exhibit good agreement with the corresponding theoretical results.

Adventure Code Camp: Library Mobile Design in the Backcountry

OpenAIRE

Ward, David; Hahn, James; Mestre, Lori

2014-01-01

This article presents a case study exploring the use of a student Coding Camp as a bottom-up mobile design process to generate library mobile apps. A code camp sources student programmer talent and ideas for designing software services and features.  This case study reviews process, outcomes, and next steps in mobile web app coding camps. It concludes by offering implications for services design beyond the local camp presented in this study. By understanding how patrons expect to integrate li...

Adventure Code Camp: Library Mobile Design in the Backcountry

Directory of Open Access Journals (Sweden)

David Ward

2014-09-01

Full Text Available This article presents a case study exploring the use of a student Coding Camp as a bottom-up mobile design process to generate library mobile apps. A code camp sources student programmer talent and ideas for designing software services and features.  This case study reviews process, outcomes, and next steps in mobile web app coding camps. It concludes by offering implications for services design beyond the local camp presented in this study. By understanding how patrons expect to integrate library services and resources into their use of mobile devices, librarians can better design the user experience for this environment.

Multilevel LDPC Codes Design for Multimedia Communication CDMA System

Directory of Open Access Journals (Sweden)

Hou Jia

2004-01-01

Full Text Available We design multilevel coding (MLC with a semi-bit interleaved coded modulation (BICM scheme based on low density parity check (LDPC codes. Different from the traditional designs, we joined the MLC and BICM together by using the Gray mapping, which is suitable to transmit the data over several equivalent channels with different code rates. To perform well at signal-to-noise ratio (SNR to be very close to the capacity of the additive white Gaussian noise (AWGN channel, random regular LDPC code and a simple semialgebra LDPC (SA-LDPC code are discussed in MLC with parallel independent decoding (PID. The numerical results demonstrate that the proposed scheme could achieve both power and bandwidth efficiency.

An integrated PCR colony hybridization approach to screen cDNA libraries for full-length coding sequences.

Science.gov (United States)

Pollier, Jacob; González-Guzmán, Miguel; Ardiles-Diaz, Wilson; Geelen, Danny; Goossens, Alain

2011-01-01

cDNA-Amplified Fragment Length Polymorphism (cDNA-AFLP) is a commonly used technique for genome-wide expression analysis that does not require prior sequence knowledge. Typically, quantitative expression data and sequence information are obtained for a large number of differentially expressed gene tags. However, most of the gene tags do not correspond to full-length (FL) coding sequences, which is a prerequisite for subsequent functional analysis. A medium-throughput screening strategy, based on integration of polymerase chain reaction (PCR) and colony hybridization, was developed that allows in parallel screening of a cDNA library for FL clones corresponding to incomplete cDNAs. The method was applied to screen for the FL open reading frames of a selection of 163 cDNA-AFLP tags from three different medicinal plants, leading to the identification of 109 (67%) FL clones. Furthermore, the protocol allows for the use of multiple probes in a single hybridization event, thus significantly increasing the throughput when screening for rare transcripts. The presented strategy offers an efficient method for the conversion of incomplete expressed sequence tags (ESTs), such as cDNA-AFLP tags, to FL-coding sequences.

Cloning and expression of a cDNA coding for a human monocyte-derived plasminogen activator inhibitor

International Nuclear Information System (INIS)

Antalis, T.M.; Clark, M.A.; Barnes, T.; Lehrbach, P.R.; Devine, P.L.; Schevzov, G.; Goss, N.H.; Stephens, R.W.; Tolstoshev, P.

1988-01-01

Human monocyte-derived plasminogen activator inhibitor (mPAI-2) was purified to homogeneity from the U937 cell line and partially sequenced. Oligonucleotide probes derived from this sequence were used to screen a cDNA library prepared from U937 cells. One positive clone was sequenced and contained most of the coding sequence as well as a long incomplete 3' untranslated region (1112 base pairs). This cDNA sequence was shown to encode mPAI-2 by hybrid-select translation. A cDNA clone encoding the remainder of the mPAI-2 mRNA was obtained by primer extension of U937 poly(A) + RNA using a probe complementary to the mPAI-2 coding region. The coding sequence for mPAI-2 was placed under the control of the λ P/sub L/ promoter, and the protein expressed in Escherichia coli formed a complex with urokinase that could be detected immunologically. By nucleotide sequence analysis, mPAI-2 cDNA encodes a protein containing 415 amino acids with a predicted unglycosylated M/sub r/ of 46,543. The predicted amino acid sequence of mPAI-2 is very similar to placental PAI-2 and shows extensive homology with members of the serine protease inhibitor (serpin) superfamily. mPAI-2 was found to be more homologous to ovalbumin (37%) than the endothelial plasminogen activator inhibitor, PAI-1 (26%). The 3' untranslated region of the mPAI-2 cDNA contains a putative regulatory sequence that has been associated with the inflammatory mediators

Isolation and characterization of full-length cDNA clones coding for cholinesterase from fetal human tissues

International Nuclear Information System (INIS)

Prody, C.A.; Zevin-Sonkin, D.; Gnatt, A.; Goldberg, O.; Soreq, H.

1987-01-01

To study the primary structure and regulation of human cholinesterases, oligodeoxynucleotide probes were prepared according to a consensus peptide sequence present in the active site of both human serum pseudocholinesterase and Torpedo electric organ true acetylcholinesterase. Using these probes, the authors isolated several cDNA clones from λgt10 libraries of fetal brain and liver origins. These include 2.4-kilobase cDNA clones that code for a polypeptide containing a putative signal peptide and the N-terminal, active site, and C-terminal peptides of human BtChoEase, suggesting that they code either for BtChoEase itself or for a very similar but distinct fetal form of cholinesterase. In RNA blots of poly(A) + RNA from the cholinesterase-producing fetal brain and liver, these cDNAs hybridized with a single 2.5-kilobase band. Blot hybridization to human genomic DNA revealed that these fetal BtChoEase cDNA clones hybridize with DNA fragments of the total length of 17.5 kilobases, and signal intensities indicated that these sequences are not present in many copies. Both the cDNA-encoded protein and its nucleotide sequence display striking homology to parallel sequences published for Torpedo AcChoEase. These finding demonstrate extensive homologies between the fetal BtChoEase encoded by these clones and other cholinesterases of various forms and species

Computer codes used in particle accelerator design: First edition

International Nuclear Information System (INIS)

1987-01-01

This paper contains a listing of more than 150 programs that have been used in the design and analysis of accelerators. Given on each citation are person to contact, classification of the computer code, publications describing the code, computer and language runned on, and a short description of the code. Codes are indexed by subject, person to contact, and code acronym

Cloning and expression of a cDNA coding for a human monocyte-derived plasminogen activator inhibitor.

Science.gov (United States)

Antalis, T M; Clark, M A; Barnes, T; Lehrbach, P R; Devine, P L; Schevzov, G; Goss, N H; Stephens, R W; Tolstoshev, P

1988-02-01

Human monocyte-derived plasminogen activator inhibitor (mPAI-2) was purified to homogeneity from the U937 cell line and partially sequenced. Oligonucleotide probes derived from this sequence were used to screen a cDNA library prepared from U937 cells. One positive clone was sequenced and contained most of the coding sequence as well as a long incomplete 3' untranslated region (1112 base pairs). This cDNA sequence was shown to encode mPAI-2 by hybrid-select translation. A cDNA clone encoding the remainder of the mPAI-2 mRNA was obtained by primer extension of U937 poly(A)+ RNA using a probe complementary to the mPAI-2 coding region. The coding sequence for mPAI-2 was placed under the control of the lambda PL promoter, and the protein expressed in Escherichia coli formed a complex with urokinase that could be detected immunologically. By nucleotide sequence analysis, mPAI-2 cDNA encodes a protein containing 415 amino acids with a predicted unglycosylated Mr of 46,543. The predicted amino acid sequence of mPAI-2 is very similar to placental PAI-2 (3 amino acid differences) and shows extensive homology with members of the serine protease inhibitor (serpin) superfamily. mPAI-2 was found to be more homologous to ovalbumin (37%) than the endothelial plasminogen activator inhibitor, PAI-1 (26%). Like ovalbumin, mPAI-2 appears to have no typical amino-terminal signal sequence. The 3' untranslated region of the mPAI-2 cDNA contains a putative regulatory sequence that has been associated with the inflammatory mediators.

ASME Code requirements for multi-canister overpack design and fabrication

International Nuclear Information System (INIS)

SMITH, K.E.

1998-01-01

The baseline requirements for the design and fabrication of the MCO include the application of the technical requirements of the ASME Code, Section III, Subsection NB for containment and Section III, Subsection NG for criticality control. ASME Code administrative requirements, which have not historically been applied at the Hanford site and which have not been required by the US Nuclear Regulatory Commission (NRC) for licensed spent fuel casks/canisters, were not invoked for the MCO. As a result of recommendations made from an ASME Code consultant in response to DNFSB staff concerns regarding ASME Code application, the SNF Project will be making the following modifications: issue an ASME Code Design Specification and Design Report, certified by a Registered Professional Engineer; Require the MCO fabricator to hold ASME Section III or Section VIII, Division 2 accreditation; and Use ASME Authorized Inspectors for MCO fabrication. Incorporation of these modifications will ensure that the MCO is designed and fabricated in accordance with the ASME Code. Code Stamping has not been a requirement at the Hanford site, nor for NRC licensed spent fuel casks/canisters, but will be considered if determined to be economically justified

Isolation and sequencing of a cDNA coding for the human DF3 breast carcinoma-associated antigen

International Nuclear Information System (INIS)

Siddiqui, J.; Abe, M.; Hayes, D.; Shani, E.; Yunis, E.; Kufe, D.

1988-01-01

The murine monoclonal antibody (mAb) DF3 reacts with a high molecular weight glycoprotein detectable in human breast carcinomas. DF3 antigen expression correlates with human breast tumor differentiation, and the detection of a cross-reactive species in human milk has suggested that this antigen might be useful as a marker of differentiated mammary epithelium. To further characterize DF3 antigen expression, the authors have isolated a cDNA clone from a λgt11 library by screening with mAb DF3. The results demonstrate that this 309-base-pair cDNA, designated pDF9.3, codes for the DF3 epitope. Southern blot analyses of EcoRI-digested DNAs from six human tumor cell lines with 32 P-labeled pDF9.3 have revealed a restriction fragment length polymorphism. Variations in size of the alleles detected by pDF9.3 were also identified in Pst I, but not in HindIII, DNA digests. Furthermore, hybridization of 32 P-labeled pDF9.3 with total cellular RNA from each of these cell lines demonstrated either one or two transcripts that varied from 4.1 to 7.1 kilobases in size. The presence of differently sized transcripts detected by pDF9.3 was also found to correspond with the polymorphic expression of DF3 glycoproteins. Nucleotide sequence analysis of pDF9.3 has revealed a highly conserved (G + C)-rich 60-base-pair tandem repeat. These findings suggest that the variation in size of alleles coding for the polymorphic DF3 glycoprotein may represent different numbers of repeats

Cloning and expression of a cDNA coding for a human monocyte-derived plasminogen activator inhibitor.

OpenAIRE

Antalis, T M; Clark, M A; Barnes, T; Lehrbach, P R; Devine, P L; Schevzov, G; Goss, N H; Stephens, R W; Tolstoshev, P

1988-01-01

Human monocyte-derived plasminogen activator inhibitor (mPAI-2) was purified to homogeneity from the U937 cell line and partially sequenced. Oligonucleotide probes derived from this sequence were used to screen a cDNA library prepared from U937 cells. One positive clone was sequenced and contained most of the coding sequence as well as a long incomplete 3' untranslated region (1112 base pairs). This cDNA sequence was shown to encode mPAI-2 by hybrid-select translation. A cDNA clone encoding t...

Evaluation of the analysis models in the ASTRA nuclear design code system

Energy Technology Data Exchange (ETDEWEB)

Cho, Nam Jin; Park, Chang Jea; Kim, Do Sam; Lee, Kyeong Taek; Kim, Jong Woon [Korea Advanced Institute of Science and Technology, Taejon (Korea, Republic of)

2000-11-15

In the field of nuclear reactor design, main practice was the application of the improved design code systems. During the process, a lot of basis and knowledge were accumulated in processing input data, nuclear fuel reload design, production and analysis of design data, et al. However less efforts were done in the analysis of the methodology and in the development or improvement of those code systems. Recently, KEPO Nuclear Fuel Company (KNFC) developed the ASTRA (Advanced Static and Transient Reactor Analyzer) code system for the purpose of nuclear reactor design and analysis. In the code system, two group constants were generated from the CASMO-3 code system. The objective of this research is to analyze the analysis models used in the ASTRA/CASMO-3 code system. This evaluation requires indepth comprehension of the models, which is important so much as the development of the code system itself. Currently, most of the code systems used in domestic Nuclear Power Plant were imported, so it is very difficult to maintain and treat the change of the situation in the system. Therefore, the evaluation of analysis models in the ASTRA nuclear reactor design code system in very important.

EGNAS: an exhaustive DNA sequence design algorithm

Directory of Open Access Journals (Sweden)

Kick Alfred

2012-06-01

Full Text Available Abstract Background The molecular recognition based on the complementary base pairing of deoxyribonucleic acid (DNA is the fundamental principle in the fields of genetics, DNA nanotechnology and DNA computing. We present an exhaustive DNA sequence design algorithm that allows to generate sets containing a maximum number of sequences with defined properties. EGNAS (Exhaustive Generation of Nucleic Acid Sequences offers the possibility of controlling both interstrand and intrastrand properties. The guanine-cytosine content can be adjusted. Sequences can be forced to start and end with guanine or cytosine. This option reduces the risk of “fraying” of DNA strands. It is possible to limit cross hybridizations of a defined length, and to adjust the uniqueness of sequences. Self-complementarity and hairpin structures of certain length can be avoided. Sequences and subsequences can optionally be forbidden. Furthermore, sequences can be designed to have minimum interactions with predefined strands and neighboring sequences. Results The algorithm is realized in a C++ program. TAG sequences can be generated and combined with primers for single-base extension reactions, which were described for multiplexed genotyping of single nucleotide polymorphisms. Thereby, possible foldback through intrastrand interaction of TAG-primer pairs can be limited. The design of sequences for specific attachment of molecular constructs to DNA origami is presented. Conclusions We developed a new software tool called EGNAS for the design of unique nucleic acid sequences. The presented exhaustive algorithm allows to generate greater sets of sequences than with previous software and equal constraints. EGNAS is freely available for noncommercial use at http://www.chm.tu-dresden.de/pc6/EGNAS.

SAFETY IN THE DESIGN OF SCIENCE LABORATORIES AND BUILDING CODES.

Science.gov (United States)

HOROWITZ, HAROLD

THE DESIGN OF COLLEGE AND UNIVERSITY BUILDINGS USED FOR SCIENTIFIC RESEARCH AND EDUCATION IS DISCUSSED IN TERMS OF LABORATORY SAFETY AND BUILDING CODES AND REGULATIONS. MAJOR TOPIC AREAS ARE--(1) SAFETY RELATED DESIGN FEATURES OF SCIENCE LABORATORIES, (2) LABORATORY SAFETY AND BUILDING CODES, AND (3) EVIDENCE OF UNSAFE DESIGN. EXAMPLES EMPHASIZE…

SWAAM code development, verification and application to steam generator design

International Nuclear Information System (INIS)

Shin, Y.W.; Valentin, R.A.

1990-01-01

This paper describes the family of SWAAM codes developed by Argonne National Laboratory to analyze the effects of sodium/water reactions on LMR steam generators. The SWAAM codes were developed as design tools for analyzing various phenomena related to steam generator leaks and to predict the resulting thermal and hydraulic effects on the steam generator and the intermediate heat transport system (IHTS). The theoretical foundations and numerical treatments on which the codes are based are discussed, followed by a description of code capabilities and limitations, verification of the codes by comparison with experiment, and applications to steam generator and IHTS design. (author). 25 refs, 14 figs

Establishment of computer code system for nuclear reactor design - analysis

International Nuclear Information System (INIS)

Subki, I.R.; Santoso, B.; Syaukat, A.; Lee, S.M.

1996-01-01

Establishment of computer code system for nuclear reactor design analysis is given in this paper. This establishment is an effort to provide the capability in running various codes from nuclear data to reactor design and promote the capability for nuclear reactor design analysis particularly from neutronics and safety points. This establishment is also an effort to enhance the coordination of nuclear codes application and development existing in various research centre in Indonesia. Very prospective results have been obtained with the help of IAEA technical assistance. (author). 6 refs, 1 fig., 1 tab

FLP: a field line plotting code for bundle divertor design

International Nuclear Information System (INIS)

Ruchti, C.

1981-01-01

A computer code was developed to aid in the design of bundle divertors. The code can handle discrete toroidal field coils and various divertor coil configurations. All coils must be composed of straight line segments. The code runs on the PDP-10 and displays plots of the configuration, field lines, and field ripple. It automatically chooses the coil currents to connect the separatrix produced by the divertor to the outer edge of the plasma and calculates the required coil cross sections. Several divertor designs are illustrated to show how the code works

A finite element code for electric motor design

Science.gov (United States)

Campbell, C. Warren

1994-01-01

FEMOT is a finite element program for solving the nonlinear magnetostatic problem. This version uses nonlinear, Newton first order elements. The code can be used for electric motor design and analysis. FEMOT can be embedded within an optimization code that will vary nodal coordinates to optimize the motor design. The output from FEMOT can be used to determine motor back EMF, torque, cogging, and magnet saturation. It will run on a PC and will be available to anyone who wants to use it.

Optimal patch code design via device characterization

Science.gov (United States)

Wu, Wencheng; Dalal, Edul N.

2012-01-01

In many color measurement applications, such as those for color calibration and profiling, "patch code" has been used successfully for job identification and automation to reduce operator errors. A patch code is similar to a barcode, but is intended primarily for use in measurement devices that cannot read barcodes due to limited spatial resolution, such as spectrophotometers. There is an inherent tradeoff between decoding robustness and the number of code levels available for encoding. Previous methods have attempted to address this tradeoff, but those solutions have been sub-optimal. In this paper, we propose a method to design optimal patch codes via device characterization. The tradeoff between decoding robustness and the number of available code levels is optimized in terms of printing and measurement efforts, and decoding robustness against noises from the printing and measurement devices. Effort is drastically reduced relative to previous methods because print-and-measure is minimized through modeling and the use of existing printer profiles. Decoding robustness is improved by distributing the code levels in CIE Lab space rather than in CMYK space.

Applications of American design codes for elevated temperature environment

International Nuclear Information System (INIS)

Severud, L.K.

1980-03-01

A brief summary of the ASME Code rules of Case N-47 is presented. An overview of the typical procedure used to demonstrate Code compliance is provided. Application experience and some examples of detailed inelastic analysis and simplified-approximate methods are given. Recent developments and future trends in design criteria and ASME Code rules are also presented

CALIOP: a multichannel design code for gas-cooled fast reactors. Code description and user's guide

International Nuclear Information System (INIS)

Thompson, W.I.

1980-10-01

CALIOP is a design code for fluid-cooled reactors composed of parallel fuel tubes in hexagonal or cylindrical ducts. It may be used with gaseous or liquid coolants. It has been used chiefly for design of a helium-cooled fast breeder reactor and has built-in cross section information to permit calculations of fuel loading, breeding ratio, and doubling time. Optional cross-section input allows the code to be used with moderated cores and with other fuels

Design and Analysis of LT Codes with Decreasing Ripple Size

DEFF Research Database (Denmark)

Sørensen, Jesper Hemming; Popovski, Petar; Østergaard, Jan

2012-01-01

In this paper we propose a new design of LT codes, which decreases the amount of necessary overhead in comparison to existing designs. The design focuses on a parameter of the LT decoding process called the ripple size. This parameter was also a key element in the design proposed in the original...... work by Luby. Specifically, Luby argued that an LT code should provide a constant ripple size during decoding. In this work we show that the ripple size should decrease during decoding, in order to reduce the necessary overhead. Initially we motivate this claim by analytical results related...... to the redundancy within an LT code. We then propose a new design procedure, which can provide any desired achievable decreasing ripple size. The new design procedure is evaluated and compared to the current state of the art through simulations. This reveals a significant increase in performance with respect...

Design Aspects of the Rayleigh Convection Code

Science.gov (United States)

Featherstone, N. A.

2017-12-01

Understanding the long-term generation of planetary or stellar magnetic field requires complementary knowledge of the large-scale fluid dynamics pervading large fractions of the object's interior. Such large-scale motions are sensitive to the system's geometry which, in planets and stars, is spherical to a good approximation. As a result, computational models designed to study such systems often solve the MHD equations in spherical geometry, frequently employing a spectral approach involving spherical harmonics. We present computational and user-interface design aspects of one such modeling tool, the Rayleigh convection code, which is suitable for deployment on desktop and petascale-hpc architectures alike. In this poster, we will present an overview of this code's parallel design and its built-in diagnostics-output package. Rayleigh has been developed with NSF support through the Computational Infrastructure for Geodynamics and is expected to be released as open-source software in winter 2017/2018.

DNA strand breaks induced by electrons simulated with nanodosimetry Monte Carlo simulation code: NASIC

International Nuclear Information System (INIS)

Li, Junli; Qiu, Rui; Yan, Congchong; Xie, Wenzhang; Zeng, Zhi; Li, Chunyan; Wu, Zhen; Tung, Chuanjong

2015-01-01

The method of Monte Carlo simulation is a powerful tool to investigate the details of radiation biological damage at the molecular level. In this paper, a Monte Carlo code called NASIC (Nanodosimetry Monte Carlo Simulation Code) was developed. It includes physical module, pre-chemical module, chemical module, geometric module and DNA damage module. The physical module can simulate physical tracks of low-energy electrons in the liquid water event-by-event. More than one set of inelastic cross sections were calculated by applying the dielectric function method of Emfietzoglou's optical-data treatments, with different optical data sets and dispersion models. In the pre-chemical module, the ionised and excited water molecules undergo dissociation processes. In the chemical module, the produced radiolytic chemical species diffuse and react. In the geometric module, an atomic model of 46 chromatin fibres in a spherical nucleus of human lymphocyte was established. In the DNA damage module, the direct damages induced by the energy depositions of the electrons and the indirect damages induced by the radiolytic chemical species were calculated. The parameters should be adjusted to make the simulation results be agreed with the experimental results. In this paper, the influence study of the inelastic cross sections and vibrational excitation reaction on the parameters and the DNA strand break yields were studied. Further work of NASIC is underway (authors)

Isolation and expression of a novel chick G-protein cDNA coding for a G alpha i3 protein with a G alpha 0 N-terminus.

OpenAIRE

Kilbourne, E J; Galper, J B

1994-01-01

We have cloned cDNAs coding for G-protein alpha subunits from a chick brain cDNA library. Based on sequence similarity to G-protein alpha subunits from other eukaryotes, one clone was designated G alpha i3. A second clone, G alpha i3-o, was identical to the G alpha i3 clone over 932 bases on the 3' end. The 5' end of G alpha i3-o, however, contained an alternative sequence in which the first 45 amino acids coded for are 100% identical to the conserved N-terminus of G alpha o from species such...

SWAAM-code development and verification and application to steam generator designs

International Nuclear Information System (INIS)

Shin, Y.W.; Valentin, R.A.

1990-01-01

This paper describes the family of SWAAM codes which were developed by Argonne National Laboratory to analyze the effects of sodium-water reactions on LMR steam generators. The SWAAM codes were developed as design tools for analyzing various phenomena related to steam generator leaks and the resulting thermal and hydraulic effects on the steam generator and the intermediate heat transport system (IHTS). The paper discusses the theoretical foundations and numerical treatments on which the codes are based, followed by a description of code capabilities and limitations, verification of the codes and applications to steam generator and IHTS designs. 25 refs., 14 figs

A computer code to design liquid containers for vehicles

International Nuclear Information System (INIS)

Parizi, H.B.; Fard, M.P.; Dolatabadi, A.

2003-01-01

We are presenting the development of a modular code for the simulation of the fluid sloshing that occurs in the liquid containers in vehicles. Sloshing occurs when a partially filled container of liquid goes through transient or steady external forces. Under such conditions, the free surface of the liquid may move and the liquid may impact on the walls of the container, exchanging forces. These forces may cause numerous harmful and undesirable consequences in the operation of the vehicle, such as vehicle turn over. The fluid mechanic equations that describe the fluid sloshing in the container and the dynamic equations that describe the movement of the container are solved separately in two different codes. The codes are coupled weekly, such that the output of one code will be used as the input to the other code in the same time step. The outputs of the fluid code are the forces and torques that are applied to the body of the container due to sloshing, whereas the output of the dynamic code are the translational and rotational velocities and accelerations of the container. The proposed software can be used to test the performance of the designed container under various operating condition and allow effective improvements to the container design. The proposed code is different than the presently available codes, in that it will provide a true simulation of the coupled fluid and structure interaction. (author)

DNA cards: determinants of DNA yield and quality in collecting genetic samples for pharmacogenetic studies.

Science.gov (United States)

Mas, Sergi; Crescenti, Anna; Gassó, Patricia; Vidal-Taboada, Jose M; Lafuente, Amalia

2007-08-01

As pharmacogenetic studies frequently require establishment of DNA banks containing large cohorts with multi-centric designs, inexpensive methods for collecting and storing high-quality DNA are needed. The aims of this study were two-fold: to compare the amount and quality of DNA obtained from two different DNA cards (IsoCode Cards or FTA Classic Cards, Whatman plc, Brentford, Middlesex, UK); and to evaluate the effects of time and storage temperature, as well as the influence of anticoagulant ethylenediaminetetraacetic acid on the DNA elution procedure. The samples were genotyped by several methods typically used in pharmacogenetic studies: multiplex PCR, PCR-restriction fragment length polymorphism, single nucleotide primer extension, and allelic discrimination assay. In addition, they were amplified by whole genome amplification to increase genomic DNA mass. Time, storage temperature and ethylenediaminetetraacetic acid had no significant effects on either DNA card. This study reveals the importance of drying blood spots prior to isolation to avoid haemoglobin interference. Moreover, our results demonstrate that re-isolation protocols could be applied to increase the amount of DNA recovered. The samples analysed were accurately genotyped with all the methods examined herein. In conclusion, our study shows that both DNA cards, IsoCode Cards and FTA Classic Cards, facilitate genetic and pharmacogenetic testing for routine clinical practice.

A new method for species identification via protein-coding and non-coding DNA barcodes by combining machine learning with bioinformatic methods.

Science.gov (United States)

Zhang, Ai-bing; Feng, Jie; Ward, Robert D; Wan, Ping; Gao, Qiang; Wu, Jun; Zhao, Wei-zhong

2012-01-01

Species identification via DNA barcodes is contributing greatly to current bioinventory efforts. The initial, and widely accepted, proposal was to use the protein-coding cytochrome c oxidase subunit I (COI) region as the standard barcode for animals, but recently non-coding internal transcribed spacer (ITS) genes have been proposed as candidate barcodes for both animals and plants. However, achieving a robust alignment for non-coding regions can be problematic. Here we propose two new methods (DV-RBF and FJ-RBF) to address this issue for species assignment by both coding and non-coding sequences that take advantage of the power of machine learning and bioinformatics. We demonstrate the value of the new methods with four empirical datasets, two representing typical protein-coding COI barcode datasets (neotropical bats and marine fish) and two representing non-coding ITS barcodes (rust fungi and brown algae). Using two random sub-sampling approaches, we demonstrate that the new methods significantly outperformed existing Neighbor-joining (NJ) and Maximum likelihood (ML) methods for both coding and non-coding barcodes when there was complete species coverage in the reference dataset. The new methods also out-performed NJ and ML methods for non-coding sequences in circumstances of potentially incomplete species coverage, although then the NJ and ML methods performed slightly better than the new methods for protein-coding barcodes. A 100% success rate of species identification was achieved with the two new methods for 4,122 bat queries and 5,134 fish queries using COI barcodes, with 95% confidence intervals (CI) of 99.75-100%. The new methods also obtained a 96.29% success rate (95%CI: 91.62-98.40%) for 484 rust fungi queries and a 98.50% success rate (95%CI: 96.60-99.37%) for 1094 brown algae queries, both using ITS barcodes.

A new method for species identification via protein-coding and non-coding DNA barcodes by combining machine learning with bioinformatic methods.

Directory of Open Access Journals (Sweden)

Ai-bing Zhang

Full Text Available Species identification via DNA barcodes is contributing greatly to current bioinventory efforts. The initial, and widely accepted, proposal was to use the protein-coding cytochrome c oxidase subunit I (COI region as the standard barcode for animals, but recently non-coding internal transcribed spacer (ITS genes have been proposed as candidate barcodes for both animals and plants. However, achieving a robust alignment for non-coding regions can be problematic. Here we propose two new methods (DV-RBF and FJ-RBF to address this issue for species assignment by both coding and non-coding sequences that take advantage of the power of machine learning and bioinformatics. We demonstrate the value of the new methods with four empirical datasets, two representing typical protein-coding COI barcode datasets (neotropical bats and marine fish and two representing non-coding ITS barcodes (rust fungi and brown algae. Using two random sub-sampling approaches, we demonstrate that the new methods significantly outperformed existing Neighbor-joining (NJ and Maximum likelihood (ML methods for both coding and non-coding barcodes when there was complete species coverage in the reference dataset. The new methods also out-performed NJ and ML methods for non-coding sequences in circumstances of potentially incomplete species coverage, although then the NJ and ML methods performed slightly better than the new methods for protein-coding barcodes. A 100% success rate of species identification was achieved with the two new methods for 4,122 bat queries and 5,134 fish queries using COI barcodes, with 95% confidence intervals (CI of 99.75-100%. The new methods also obtained a 96.29% success rate (95%CI: 91.62-98.40% for 484 rust fungi queries and a 98.50% success rate (95%CI: 96.60-99.37% for 1094 brown algae queries, both using ITS barcodes.

Non-Binary Protograph-Based LDPC Codes: Analysis,Enumerators and Designs

OpenAIRE

Sun, Yizeng

2013-01-01

Non-binary LDPC codes can outperform binary LDPC codes using sum-product algorithm with higher computation complexity. Non-binary LDPC codes based on protographs have the advantage of simple hardware architecture. In the first part of this thesis, we will use EXIT chart analysis to compute the thresholds of different protographs over GF(q). Based on threshold computation, some non-binary protograph-based LDPC codes are designed and their frame error rates are compared with binary LDPC codes. ...

LDPC Code Design for Nonuniform Power-Line Channels

Directory of Open Access Journals (Sweden)

Sanaei Ali

2007-01-01

Full Text Available We investigate low-density parity-check code design for discrete multitone channels over power lines. Discrete multitone channels are well modeled as nonuniform channels, that is, different bits experience various channel parameters. We propose a coding system for discrete multitone channels that allows for using a single code over a nonuniform channel. The number of code parameters for the proposed system is much greater than the number of code parameters in conventional channel. Therefore, search-based optimization methods are impractical. We first formulate the problem of optimizing the rate of an irregular low-density parity-check code, with guaranteed convergence over a general nonuniform channel, as an iterative linear programming which is significantly more efficient than search-based methods. Then we use this technique for a typical power-line channel. The methodology of this paper is directly applicable to all decoding algorithms for which a density evolution analysis is possible.

Nuclear-thermal-coupled optimization code for the fusion breeding blanket conceptual design

International Nuclear Information System (INIS)

Li, Jia; Jiang, Kecheng; Zhang, Xiaokang; Nie, Xingchen; Zhu, Qinjun; Liu, Songlin

2016-01-01

Highlights: • A nuclear-thermal-coupled predesign code has been developed for optimizing the radial build arrangement of fusion breeding blanket. • Coupling module aims at speeding up the efficiency of design progress by coupling the neutronics calculation code with the thermal-hydraulic analysis code. • Radial build optimization algorithm aims at optimal arrangement of breeding blanket considering one or multiple specified objectives subject to the design criteria such as material temperature limit and available TBR. - Abstract: Fusion breeding blanket as one of the key in-vessel components performs the functions of breeding the tritium, removing the nuclear heat and heat flux from plasma chamber as well as acting as part of shielding system. The radial build design which determines the arrangement of function zones and material properties on the radial direction is the basis of the detailed design of fusion breeding blanket. For facilitating the radial build design, this study aims for developing a pre-design code to optimize the radial build of blanket with considering the performance of nuclear and thermal-hydraulic simultaneously. Two main features of this code are: (1) Coupling of the neutronics analysis with the thermal-hydraulic analysis to speed up the analysis progress; (2) preliminary optimization algorithm using one or multiple specified objectives subject to the design criteria in the form of constrains imposed on design variables and performance parameters within the possible engineering ranges. This pre-design code has been applied to the conceptual design of water-cooled ceramic breeding blanket in project of China fusion engineering testing reactor (CFETR).

Nuclear-thermal-coupled optimization code for the fusion breeding blanket conceptual design

Energy Technology Data Exchange (ETDEWEB)

Li, Jia, E-mail: lijia@ustc.edu.cn [School of Nuclear Science and Technology, University of Science and Technology of China, Hefei 230027, Anhui (China); Jiang, Kecheng; Zhang, Xiaokang [Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031, Anhui (China); Nie, Xingchen [School of Nuclear Science and Technology, University of Science and Technology of China, Hefei 230027, Anhui (China); Zhu, Qinjun; Liu, Songlin [Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031, Anhui (China)

2016-12-15

Highlights: • A nuclear-thermal-coupled predesign code has been developed for optimizing the radial build arrangement of fusion breeding blanket. • Coupling module aims at speeding up the efficiency of design progress by coupling the neutronics calculation code with the thermal-hydraulic analysis code. • Radial build optimization algorithm aims at optimal arrangement of breeding blanket considering one or multiple specified objectives subject to the design criteria such as material temperature limit and available TBR. - Abstract: Fusion breeding blanket as one of the key in-vessel components performs the functions of breeding the tritium, removing the nuclear heat and heat flux from plasma chamber as well as acting as part of shielding system. The radial build design which determines the arrangement of function zones and material properties on the radial direction is the basis of the detailed design of fusion breeding blanket. For facilitating the radial build design, this study aims for developing a pre-design code to optimize the radial build of blanket with considering the performance of nuclear and thermal-hydraulic simultaneously. Two main features of this code are: (1) Coupling of the neutronics analysis with the thermal-hydraulic analysis to speed up the analysis progress; (2) preliminary optimization algorithm using one or multiple specified objectives subject to the design criteria in the form of constrains imposed on design variables and performance parameters within the possible engineering ranges. This pre-design code has been applied to the conceptual design of water-cooled ceramic breeding blanket in project of China fusion engineering testing reactor (CFETR).

DESIGN OF ELECTROPHORESIS DEVICE FOR OPTIMATION OF DNA VISUALIZATION AND DNA CONCENTRATION USING SOFTWARE

Directory of Open Access Journals (Sweden)

H.P. Kusumaningrum

2014-07-01

Full Text Available Molekul DNA menunjukkan polarisasi yang kuat sehingga memungkinkan baik gerak elektroforesis berdasarkan muatan negatifnya maupun gerak dielektroforesis berdasarkan induksi polarisasi. Perancangan alat menggunakan kombinasi prinsip elektroforesis dan dielektroforesis dilengkapi perangkat lunak untuk mengukur konsentrasinya sangat diperlukan. Utamanya mengingat uji kualitatif DNA berbasis visualisasi pada gel elektroforesis bersifat sangat subyektif dan kurang terukur. Pengukuran konsentrasi DNA menggunakan spektrofotometer UV/VIS sangat tergantung oleh ketersediaannya di laboratorium. Penelitian bertujuan untuk mendesain piranti untuk mengukur konsentrasi DNA berdasarkan visualisasinya pada gel elektroforesis menggunakan perangkat lunak berbasis MatLab. Pengukuran konsentrasi DNA didasarkan visualisasinya pada gel elektroforesis lalu dibandingkan dengan hasil penghitungan spektrofotometer UV/VIS. Hasil penelitian menggunakan piranti tersebut memperlihatkan visualisasi DNA yang lebih optimal. Hasil pengukuran jumlah DNA menggunakan spektrofotometer memiliki kecenderungan yang sama dengan hasil pengukuran menggunakan perangkat lunak berbasis MatLab meskipun terdapat perbedaan nilai kuantitatif.ABSTRACTMolecules of deoxyribo nucleic acid (DNA show a strong polarization allowing for both motions of the dielectrophoresis induced by polarization and electrophoresis based on its negative charge. Considering high subjective and less quantifiable result of the visualization based qualitative test of DNA on gel electrophoresis, designing the tool using a combination of the principles of electrophoresis and dielectrophoresis completed with a software for optimization of DNA visualization and to measure the concentration of small and large–sized DNA fragment is very needed. Accuracy of measurement of DNA concentration using a spectrophotometer UV /VIS is depend on its availability in the laboratory. The aim of this study was to design device for

The computer code system for reactor radiation shielding in design of nuclear power plant

International Nuclear Information System (INIS)

Li Chunhuai; Fu Shouxin; Liu Guilian

1995-01-01

The computer code system used in reactor radiation shielding design of nuclear power plant includes the source term codes, discrete ordinate transport codes, Monte Carlo and Albedo Monte Carlo codes, kernel integration codes, optimization code, temperature field code, skyshine code, coupling calculation codes and some processing codes for data libraries. This computer code system has more satisfactory variety of codes and complete sets of data library. It is widely used in reactor radiation shielding design and safety analysis of nuclear power plant and other nuclear facilities

Storage Tanks - Selection Of Type, Design Code And Tank Sizing

International Nuclear Information System (INIS)

Shatla, M.N; El Hady, M.

2004-01-01

The present work gives an insight into the proper selection of type, design code and sizing of storage tanks used in the Petroleum and Process industries. In this work, storage tanks are classified based on their design conditions. Suitable design codes and their limitations are discussed for each tank type. The option of storage under high pressure and ambient temperature, in spherical and cigar tanks, is compared to the option of storage under low temperature and slight pressure (close to ambient) in low temperature and cryogenic tanks. The discussion is extended to the types of low temperature and cryogenic tanks and recommendations are given to select their types. A study of pressurized tanks designed according to ASME code, conducted in the present work, reveals that tanks designed according to ASME Section VIII DIV 2 provides cost savings over tanks designed according to ASME Section VIII DlV 1. The present work is extended to discuss the parameters that affect sizing of flat bottom cylindrical tanks. The analysis shows the effect of height-to-diameter ratio on tank instability and foundation loads

DNA Bar-Coding for Phytoplasma Identification

DEFF Research Database (Denmark)

Makarova, Olga; Contaldo, Nicoletta; Paltrinieri, Samanta

2013-01-01

Phytoplasma identi fi cation has proved dif fi cult due to their inability to be maintained in vitro. DNA barcoding is an identi fi cation method based on comparison of a short DNA sequence with known sequences from a database. A DNA barcoding tool has been developed for phytoplasma identi fi cat...... genes, can be used to identify the following phytoplasma groups: 16SrI, 16SrII, 16SrIII, 16SrIV, 16SrV, 16SrVI, 16SrVII, 16SrIX, 16SrX, 16SrXI, 16SrXII, 16SrXV, 16SrXX, 16SrXXI....... cation. While other sequencebased methods may be well adapted to identification of particular strains of phytoplasmas, often they cannot be used for the simultaneous identification of phytoplasmas from different groups. The phytoplasma DNA barcoding protocol in this chapter, based on the tuf and 16SrRNA......Phytoplasma identi fi cation has proved dif fi cult due to their inability to be maintained in vitro. DNA barcoding is an identi fi cation method based on comparison of a short DNA sequence with known sequences from a database. A DNA barcoding tool has been developed for phytoplasma identi fi...

cDNA sequence of human transforming gene hst and identification of the coding sequence required for transforming activity

International Nuclear Information System (INIS)

Taira, M.; Yoshida, T.; Miyagawa, K.; Sakamoto, H.; Terada, M.; Sugimura, T.

1987-01-01

The hst gene was originally identified as a transforming gene in DNAs from human stomach cancers and from a noncancerous portion of stomach mucosa by DNA-mediated transfection assay using NIH3T3 cells. cDNA clones of hst were isolated from the cDNA library constructed from poly(A) + RNA of a secondary transformant induced by the DNA from a stomach cancer. The sequence analysis of the hst cDNA revealed the presence of two open reading frames. When this cDNA was inserted into an expression vector containing the simian virus 40 promoter, it efficiently induced the transformation of NIH3T3 cells upon transfection. It was found that one of the reading frames, which coded for 206 amino acids, was responsible for the transforming activity

Design of deterministic interleaver for turbo codes

International Nuclear Information System (INIS)

Arif, M.A.; Sheikh, N.M.; Sheikh, A.U.H.

2008-01-01

The choice of suitable interleaver for turbo codes can improve the performance considerably. For long block lengths, random interleavers perform well, but for some applications it is desirable to keep the block length shorter to avoid latency. For such applications deterministic interleavers perform better. The performance and design of a deterministic interleaver for short frame turbo codes is considered in this paper. The main characteristic of this class of deterministic interleaver is that their algebraic design selects the best permutation generator such that the points in smaller subsets of the interleaved output are uniformly spread over the entire range of the information data frame. It is observed that the interleaver designed in this manner improves the minimum distance or reduces the multiplicity of first few spectral lines of minimum distance spectrum. Finally we introduce a circular shift in the permutation function to reduce the correlation between the parity bits corresponding to the original and interleaved data frames to improve the decoding capability of MAP (Maximum A Posteriori) probability decoder. Our solution to design a deterministic interleaver outperforms the semi-random interleavers and the deterministic interleavers reported in the literature. (author)

Developing a Coding Scheme to Analyse Creativity in Highly-constrained Design Activities

DEFF Research Database (Denmark)

Dekoninck, Elies; Yue, Huang; Howard, Thomas J.

2010-01-01

This work is part of a larger project which aims to investigate the nature of creativity and the effectiveness of creativity tools in highly-constrained design tasks. This paper presents the research where a coding scheme was developed and tested with a designer-researcher who conducted two rounds...... of design and analysis on a highly constrained design task. This paper shows how design changes can be coded using a scheme based on creative ‘modes of change’. The coding scheme can show the way a designer moves around the design space, and particularly the strategies that are used by a creative designer...... larger study with more designers working on different types of highly-constrained design task is needed, in order to draw conclusions on the modes of change and their relationship to creativity....

Design criteria and pressure vessel codes - an American view

International Nuclear Information System (INIS)

Tuppeny, W.H.

1975-01-01

To the pressure vessel designer, codes and criteria represent the common ground where the stress analyst and the metallurgist must interact and evolve rules and procedures which will ensure safety and open-ended responsiveness to technological, economic, and environmental change. The paper briefly discusses the evolution and rationale behind the current ASME code sections -emphasizing those portions applicable to designs operating in the creep range. The author then proposes a plan of action so that the analysts and materials people can make optimum use of time and resources, and evolve data and design criteria which will be responsive to changing technology and the economic and safety requirements of the future. (author)

Design and synthesis of DNA four-helix bundles

Energy Technology Data Exchange (ETDEWEB)

Rangnekar, Abhijit; Gothelf, Kurt V [Department of Chemistry, Centre for DNA Nanotechnology (CDNA) and Interdisciplinary Nanoscience Center (iNANO), Aarhus University, DK-8000 Aarhus C (Denmark); LaBean, Thomas H, E-mail: kvg@chem.au.dk, E-mail: thl@cs.duke.edu [Department of Chemistry, Duke University, Durham, NC 27708 (United States)

2011-06-10

The field of DNA nanotechnology has evolved significantly in the past decade. Researchers have succeeded in synthesizing tile-based structures and using them to form periodic lattices in one, two and three dimensions. Origami-based structures have also been used to create nanoscale structures in two and three dimensions. Design and construction of DNA bundles with fixed circumference has added a new dimension to the field. Here we report the design and synthesis of a DNA four-helix bundle. It was found to be extremely rigid and stable. When several such bundles were assembled using appropriate sticky-ends, they formed micrometre-long filaments. However, when creation of two-dimensional sheet-like arrays of the four-helix bundles was attempted, nanoscale rings were observed instead. The exact reason behind the nanoring formation is yet to be ascertained, but it provides an exciting prospect for making programmable circular nanostructures using DNA.

Design and synthesis of DNA four-helix bundles

International Nuclear Information System (INIS)

Rangnekar, Abhijit; Gothelf, Kurt V; LaBean, Thomas H

2011-01-01

The field of DNA nanotechnology has evolved significantly in the past decade. Researchers have succeeded in synthesizing tile-based structures and using them to form periodic lattices in one, two and three dimensions. Origami-based structures have also been used to create nanoscale structures in two and three dimensions. Design and construction of DNA bundles with fixed circumference has added a new dimension to the field. Here we report the design and synthesis of a DNA four-helix bundle. It was found to be extremely rigid and stable. When several such bundles were assembled using appropriate sticky-ends, they formed micrometre-long filaments. However, when creation of two-dimensional sheet-like arrays of the four-helix bundles was attempted, nanoscale rings were observed instead. The exact reason behind the nanoring formation is yet to be ascertained, but it provides an exciting prospect for making programmable circular nanostructures using DNA.

DNA-based watermarks using the DNA-Crypt algorithm

Directory of Open Access Journals (Sweden)

Barnekow Angelika

2007-05-01

Full Text Available Abstract Background The aim of this paper is to demonstrate the application of watermarks based on DNA sequences to identify the unauthorized use of genetically modified organisms (GMOs protected by patents. Predicted mutations in the genome can be corrected by the DNA-Crypt program leaving the encrypted information intact. Existing DNA cryptographic and steganographic algorithms use synthetic DNA sequences to store binary information however, although these sequences can be used for authentication, they may change the target DNA sequence when introduced into living organisms. Results The DNA-Crypt algorithm and image steganography are based on the same watermark-hiding principle, namely using the least significant base in case of DNA-Crypt and the least significant bit in case of the image steganography. It can be combined with binary encryption algorithms like AES, RSA or Blowfish. DNA-Crypt is able to correct mutations in the target DNA with several mutation correction codes such as the Hamming-code or the WDH-code. Mutations which can occur infrequently may destroy the encrypted information, however an integrated fuzzy controller decides on a set of heuristics based on three input dimensions, and recommends whether or not to use a correction code. These three input dimensions are the length of the sequence, the individual mutation rate and the stability over time, which is represented by the number of generations. In silico experiments using the Ypt7 in Saccharomyces cerevisiae shows that the DNA watermarks produced by DNA-Crypt do not alter the translation of mRNA into protein. Conclusion The program is able to store watermarks in living organisms and can maintain the original information by correcting mutations itself. Pairwise or multiple sequence alignments show that DNA-Crypt produces few mismatches between the sequences similar to all steganographic algorithms.

DNA-based watermarks using the DNA-Crypt algorithm.

Science.gov (United States)

Heider, Dominik; Barnekow, Angelika

2007-05-29

The aim of this paper is to demonstrate the application of watermarks based on DNA sequences to identify the unauthorized use of genetically modified organisms (GMOs) protected by patents. Predicted mutations in the genome can be corrected by the DNA-Crypt program leaving the encrypted information intact. Existing DNA cryptographic and steganographic algorithms use synthetic DNA sequences to store binary information however, although these sequences can be used for authentication, they may change the target DNA sequence when introduced into living organisms. The DNA-Crypt algorithm and image steganography are based on the same watermark-hiding principle, namely using the least significant base in case of DNA-Crypt and the least significant bit in case of the image steganography. It can be combined with binary encryption algorithms like AES, RSA or Blowfish. DNA-Crypt is able to correct mutations in the target DNA with several mutation correction codes such as the Hamming-code or the WDH-code. Mutations which can occur infrequently may destroy the encrypted information, however an integrated fuzzy controller decides on a set of heuristics based on three input dimensions, and recommends whether or not to use a correction code. These three input dimensions are the length of the sequence, the individual mutation rate and the stability over time, which is represented by the number of generations. In silico experiments using the Ypt7 in Saccharomyces cerevisiae shows that the DNA watermarks produced by DNA-Crypt do not alter the translation of mRNA into protein. The program is able to store watermarks in living organisms and can maintain the original information by correcting mutations itself. Pairwise or multiple sequence alignments show that DNA-Crypt produces few mismatches between the sequences similar to all steganographic algorithms.

DNA-based watermarks using the DNA-Crypt algorithm

Science.gov (United States)

Heider, Dominik; Barnekow, Angelika

2007-01-01

Background The aim of this paper is to demonstrate the application of watermarks based on DNA sequences to identify the unauthorized use of genetically modified organisms (GMOs) protected by patents. Predicted mutations in the genome can be corrected by the DNA-Crypt program leaving the encrypted information intact. Existing DNA cryptographic and steganographic algorithms use synthetic DNA sequences to store binary information however, although these sequences can be used for authentication, they may change the target DNA sequence when introduced into living organisms. Results The DNA-Crypt algorithm and image steganography are based on the same watermark-hiding principle, namely using the least significant base in case of DNA-Crypt and the least significant bit in case of the image steganography. It can be combined with binary encryption algorithms like AES, RSA or Blowfish. DNA-Crypt is able to correct mutations in the target DNA with several mutation correction codes such as the Hamming-code or the WDH-code. Mutations which can occur infrequently may destroy the encrypted information, however an integrated fuzzy controller decides on a set of heuristics based on three input dimensions, and recommends whether or not to use a correction code. These three input dimensions are the length of the sequence, the individual mutation rate and the stability over time, which is represented by the number of generations. In silico experiments using the Ypt7 in Saccharomyces cerevisiae shows that the DNA watermarks produced by DNA-Crypt do not alter the translation of mRNA into protein. Conclusion The program is able to store watermarks in living organisms and can maintain the original information by correcting mutations itself. Pairwise or multiple sequence alignments show that DNA-Crypt produces few mismatches between the sequences similar to all steganographic algorithms. PMID:17535434

Ripple design of LT codes for AWGN channel

DEFF Research Database (Denmark)

Sørensen, Jesper Hemming; Koike-Akino, Toshiaki; Orlik, Philip

2012-01-01

In this paper, we present an analytical framework for designing LT codes in additive white Gaussian noise (AWGN) channels. We show that some of analytical results from binary erasure channels (BEC) also hold in AWGN channels with slight modifications. This enables us to apply a ripple-based design...

Comparison of elevated temperature design codes of ASME Subsection NH and RCC-MRx

Energy Technology Data Exchange (ETDEWEB)

Lee, Hyeong-Yeon, E-mail: hylee@kaeri.re.kr

2016-11-15

Highlights: • Comparison of elevated temperature design (ETD) codes was made. • Material properties and evaluation procedures were compared. • Two heat-resistant materials of Grade 91 steel and austenitic stainless steel 316 are the target materials in the present study. • Application of the ETD codes to Generation IV reactor components and a comparison of the conservatism was conducted. - Abstract: The elevated temperature design (ETD) codes are used for the design evaluation of Generation IV (Gen IV) reactor systems such as sodium-cooled fast reactor (SFR), lead-cooled fast reactor (LFR), and very high temperature reactor (VHTR). In the present study, ETD code comparisons were made in terms of the material properties and design evaluation procedures for the recent versions of the two major ETD codes, ASME Section III Subsection NH and RCC-MRx. Conservatism in the design evaluation procedures was quantified and compared based on the evaluation results for SFR components as per the two ETD codes. The target materials are austenitic stainless steel 316 and Mod.9Cr-1Mo steel, which are the major two materials in a Gen IV SFR. The differences in the design evaluation procedures as well as the material properties in the two ETD codes are highlighted.

Evaluation of three coding schemes designed for improved data communication

Science.gov (United States)

Snelsire, R. W.

1974-01-01

Three coding schemes designed for improved data communication are evaluated. Four block codes are evaluated relative to a quality function, which is a function of both the amount of data rejected and the error rate. The Viterbi maximum likelihood decoding algorithm as a decoding procedure is reviewed. This evaluation is obtained by simulating the system on a digital computer. Short constraint length rate 1/2 quick-look codes are studied, and their performance is compared to general nonsystematic codes.

Design validation of the ITER EC upper launcher according to codes and standards

Energy Technology Data Exchange (ETDEWEB)

Spaeh, Peter, E-mail: peter.spaeh@kit.edu [Karlsruhe Institute of Technology, Institute for Applied Materials, Association KIT-EURATOM, P.O. Box 3640, D-76021 Karlsruhe (Germany); Aiello, Gaetano [Karlsruhe Institute of Technology, Institute for Applied Materials, Association KIT-EURATOM, P.O. Box 3640, D-76021 Karlsruhe (Germany); Gagliardi, Mario [Karlsruhe Institute of Technology, Association KIT-EURATOM, P.O. Box 3640, D-76021 Karlsruhe (Germany); F4E, Fusion for Energy, Joint Undertaking, Barcelona (Spain); Grossetti, Giovanni; Meier, Andreas; Scherer, Theo; Schreck, Sabine; Strauss, Dirk; Vaccaro, Alessandro [Karlsruhe Institute of Technology, Institute for Applied Materials, Association KIT-EURATOM, P.O. Box 3640, D-76021 Karlsruhe (Germany); Weinhorst, Bastian [Karlsruhe Institute of Technology, Institute for Neutron Physics and Reactor Technology, Association KIT-EURATOM, P.O. Box 3640, D-76021 Karlsruhe (Germany)

2015-10-15

Highlights: • A set of applicable codes and standards has been chosen for the ITER EC upper launcher. • For a particular component load combinations, failure modes and stress categorizations have been determined. • The design validation was performed in accordance with the “design by analysis”-approach of the ASME boiler and pressure vessel code section III. - Abstract: The ITER electron cyclotron (EC) upper launcher has passed the CDR (conceptual design review) in 2005 and the PDR (preliminary design review) in 2009 and is in its final design phase now. The final design will be elaborated by the European consortium ECHUL-CA with contributions from several research institutes in Germany, Italy, the Netherlands and Switzerland. Within this consortium KIT is responsible for the design of the structural components (the upper port plug, UPP) and also the design integration of the launcher. As the selection of applicable codes and standards was under discussion for the past decade, the conceptual and the preliminary design of the launcher structure were not elaborated in straight accordance with a particular code but with a variety of well-acknowledged engineering practices. For the final design it is compulsory to validate the design with respect to a typical engineering code in order to be compliant with the ITER quality and nuclear requirements and to get acceptance from the French regulator. This paper presents typical design validation of the closure plate, which is the vacuum and Tritium barrier and thus a safety relevant component of the upper port plug (UPP), performed with the ASME boiler and pressure vessel code. Rationales for choosing this code are given as well as a comparison between different design methods, like the “design by rule” and the “design by analysis” approach. Also the selections of proper load specifications and the identification of potential failure modes are covered. In addition to that stress categorizations, analyses

Design validation of the ITER EC upper launcher according to codes and standards

International Nuclear Information System (INIS)

Spaeh, Peter; Aiello, Gaetano; Gagliardi, Mario; Grossetti, Giovanni; Meier, Andreas; Scherer, Theo; Schreck, Sabine; Strauss, Dirk; Vaccaro, Alessandro; Weinhorst, Bastian

2015-01-01

Highlights: • A set of applicable codes and standards has been chosen for the ITER EC upper launcher. • For a particular component load combinations, failure modes and stress categorizations have been determined. • The design validation was performed in accordance with the “design by analysis”-approach of the ASME boiler and pressure vessel code section III. - Abstract: The ITER electron cyclotron (EC) upper launcher has passed the CDR (conceptual design review) in 2005 and the PDR (preliminary design review) in 2009 and is in its final design phase now. The final design will be elaborated by the European consortium ECHUL-CA with contributions from several research institutes in Germany, Italy, the Netherlands and Switzerland. Within this consortium KIT is responsible for the design of the structural components (the upper port plug, UPP) and also the design integration of the launcher. As the selection of applicable codes and standards was under discussion for the past decade, the conceptual and the preliminary design of the launcher structure were not elaborated in straight accordance with a particular code but with a variety of well-acknowledged engineering practices. For the final design it is compulsory to validate the design with respect to a typical engineering code in order to be compliant with the ITER quality and nuclear requirements and to get acceptance from the French regulator. This paper presents typical design validation of the closure plate, which is the vacuum and Tritium barrier and thus a safety relevant component of the upper port plug (UPP), performed with the ASME boiler and pressure vessel code. Rationales for choosing this code are given as well as a comparison between different design methods, like the “design by rule” and the “design by analysis” approach. Also the selections of proper load specifications and the identification of potential failure modes are covered. In addition to that stress categorizations, analyses

Design of a VLSI Decoder for Partially Structured LDPC Codes

Directory of Open Access Journals (Sweden)

Fabrizio Vacca

2008-01-01

of their parity matrix can be partitioned into two disjoint sets, namely, the structured and the random ones. For the proposed class of codes a constructive design method is provided. To assess the value of this method the constructed codes performance are presented. From these results, a novel decoding method called split decoding is introduced. Finally, to prove the effectiveness of the proposed approach a whole VLSI decoder is designed and characterized.

Direct design of an energy landscape with bistable DNA origami mechanisms.

Science.gov (United States)

Zhou, Lifeng; Marras, Alexander E; Su, Hai-Jun; Castro, Carlos E

2015-03-11

Structural DNA nanotechnology provides a feasible technique for the design and fabrication of complex geometries even exhibiting controllable dynamic behavior. Recently we have demonstrated the possibility of implementing macroscopic engineering design approaches to construct DNA origami mechanisms (DOM) with programmable motion and tunable flexibility. Here, we implement the design of compliant DNA origami mechanisms to extend from prescribing motion to prescribing an energy landscape. Compliant mechanisms facilitate motion via deformation of components with tunable stiffness resulting in well-defined mechanical energy stored in the structure. We design, fabricate, and characterize a DNA origami nanostructure with an energy landscape defined by two stable states (local energy minima) separated by a designed energy barrier. This nanostructure is a four-bar bistable mechanism with two undeformed states. Traversing between those states requires deformation, and hence mechanical energy storage, in a compliant arm of the linkage. The energy barrier for switching between two states was obtained from the conformational distribution based on a Boltzmann probability function and closely follows a predictive mechanical model. Furthermore, we demonstrated the ability to actuate the mechanism into one stable state via additional DNA inputs and then release the actuation via DNA strand displacement. This controllable multistate system establishes a foundation for direct design of energy landscapes that regulate conformational dynamics similar to biomolecular complexes.

Classifying Coding DNA with Nucleotide Statistics

Directory of Open Access Journals (Sweden)

Nicolas Carels

2009-10-01

Full Text Available In this report, we compared the success rate of classification of coding sequences (CDS vs. introns by Codon Structure Factor (CSF and by a method that we called Universal Feature Method (UFM. UFM is based on the scoring of purine bias (Rrr and stop codon frequency. We show that the success rate of CDS/intron classification by UFM is higher than by CSF. UFM classifies ORFs as coding or non-coding through a score based on (i the stop codon distribution, (ii the product of purine probabilities in the three positions of nucleotide triplets, (iii the product of Cytosine (C, Guanine (G, and Adenine (A probabilities in the 1st, 2nd, and 3rd positions of triplets, respectively, (iv the probabilities of G in 1st and 2nd position of triplets and (v the distance of their GC3 vs. GC2 levels to the regression line of the universal correlation. More than 80% of CDSs (true positives of Homo sapiens (>250 bp, Drosophila melanogaster (>250 bp and Arabidopsis thaliana (>200 bp are successfully classified with a false positive rate lower or equal to 5%. The method releases coding sequences in their coding strand and coding frame, which allows their automatic translation into protein sequences with 95% confidence. The method is a natural consequence of the compositional bias of nucleotides in coding sequences.

Codes, standards, and requirements for DOE facilities: natural phenomena design

International Nuclear Information System (INIS)

Webb, A.B.

1985-01-01

The basic requirements for codes, standards, and requirements are found in DOE Orders 5480.1A, 5480.4, and 6430.1. The type of DOE facility to be built and the hazards which it presents will determine the criteria to be applied for natural phenomena design. Mandatory criteria are established in the DOE orders for certain designs but more often recommended guidance is given. National codes and standards form a great body of experience from which the project engineer may draw. Examples of three kinds of facilities and the applicable codes and standards are discussed. The safety program planning approach to project management used at Westinghouse Hanford is outlined. 5 figures, 2 tables

The MCU-RFFI Monte Carlo code for reactor design applications

International Nuclear Information System (INIS)

Gomin, E.A.; Maiorov, L.V.

1995-01-01

MCU-RFFI is a general-purpose, continuous-energy, general geometry Monte Carlo code for solving external source or criticality problems for neutron transport in the energy range of 20 MeV to 10 -5 eV. The main fields of MCU-RFFI applications are as follows: (a) nuclear data validation; (b) design calculations (space reactors and other); (c) verification of design codes. MCU-RFFI is also supplied with tools to check the accuracy of design codes. These tools permit the user to calculate: the few group parameters of reactor cells, including the diffusion coefficients defined in a variety of ways, reaction rates for various nuclei, energy and space bins, and the kinetic parameters of systems, taking into account delayed neutrons. Boundary conditions include vacuum, white and specular reflection, and the condition of translational symmetry. The criticals with the neutron leakage given by the buckling vector may be calculated by solving Benoist's problem. The curve of criticality coefficient dependence on buckling may be determined during the single code run and critical buckling may be determined. Double heterogeneous systems with fuel elements containing many thousands of spherical microcells can be solved

Analytic transfer maps for Lie algebraic design codes

International Nuclear Information System (INIS)

van Zeijts, J.; Neri, F.; Dragt, A.J.

1990-01-01

Lie algebraic methods provide a powerful tool for modeling particle transport through Hamiltonian systems. Briefly summarized, Lie algebraic design codes work as follows: first the time t flow generated by a Hamiltonian system is represented by a Lie algebraic map acting on the initial conditions. Maps are generated for each element in the lattice or beamline under study. Next all these maps are concatenated into a one-turn or one-pass map that represents the complete dynamics of the system. Finally, the resulting map is analyzed and design decisions are made based on the linear and nonlinear entries in the map. The authors give a short description of how to find Lie algebraic transfer maps in analytic form, for inclusion in accelerator design codes. As an example they find the transfer map, through third order, for the combined-function quadrupole magnet, and use such magnets to correct detrimental third-order aberrations in a spot forming system

Avatar DNA Nanohybrid System in Chip-on-a-Phone

Science.gov (United States)

Park, Dae-Hwan; Han, Chang Jo; Shul, Yong-Gun; Choy, Jin-Ho

2014-05-01

Long admired for informational role and recognition function in multidisciplinary science, DNA nanohybrids have been emerging as ideal materials for molecular nanotechnology and genetic information code. Here, we designed an optical machine-readable DNA icon on microarray, Avatar DNA, for automatic identification and data capture such as Quick Response and ColorZip codes. Avatar icon is made of telepathic DNA-DNA hybrids inscribed on chips, which can be identified by camera of smartphone with application software. Information encoded in base-sequences can be accessed by connecting an off-line icon to an on-line web-server network to provide message, index, or URL from database library. Avatar DNA is then converged with nano-bio-info-cogno science: each building block stands for inorganic nanosheets, nucleotides, digits, and pixels. This convergence could address item-level identification that strengthens supply-chain security for drug counterfeits. It can, therefore, provide molecular-level vision through mobile network to coordinate and integrate data management channels for visual detection and recording.

Research and Design in Unified Coding Architecture for Smart Grids

Directory of Open Access Journals (Sweden)

Gang Han

2013-09-01

Full Text Available Standardized and sharing information platform is the foundation of the Smart Grids. In order to improve the dispatching center information integration of the power grids and achieve efficient data exchange, sharing and interoperability, a unified coding architecture is proposed. The architecture includes coding management layer, coding generation layer, information models layer and application system layer. Hierarchical design makes the whole coding architecture to adapt to different application environments, different interfaces, loosely coupled requirements, which can realize the integration model management function of the power grids. The life cycle and evaluation method of survival of unified coding architecture is proposed. It can ensure the stability and availability of the coding architecture. Finally, the development direction of coding technology of the Smart Grids in future is prospected.

Design LDPC Codes without Cycles of Length 4 and 6

Directory of Open Access Journals (Sweden)

Kiseon Kim

2008-04-01

Full Text Available We present an approach for constructing LDPC codes without cycles of length 4 and 6. Firstly, we design 3 submatrices with different shifting functions given by the proposed schemes, then combine them into the matrix specified by the proposed approach, and, finally, expand the matrix into a desired parity-check matrix using identity matrices and cyclic shift matrices of the identity matrices. The simulation result in AWGN channel verifies that the BER of the proposed code is close to those of Mackay's random codes and Tanner's QC codes, and the good BER performance of the proposed can remain at high code rates.

Design specifications for ASME B and PV Code Section III nuclear class 1 piping

International Nuclear Information System (INIS)

Richardson, J.A.

1978-01-01

ASME B and PV Code Section III code regulations for nuclear piping requires that a comprehensive Design Specification be developed for ensuring that the design and installation of the piping meets all code requirements. The intent of this paper is to describe the code requirements, discuss the implementation of these requirements in a typical Class 1 piping design specification, and to report on recent piping failures in operating light water nuclear power plants in the US. (author)

Comparative analysis of design codes for timber bridges in Canada, the United States, and Europe

Science.gov (United States)

James Wacker; James (Scott) Groenier

2010-01-01

The United States recently completed its transition from the allowable stress design code to the load and resistance factor design (LRFD) reliability-based code for the design of most highway bridges. For an international perspective on the LRFD-based bridge codes, a comparative analysis is presented: a study addressed national codes of the United States, Canada, and...

Compiler design handbook optimizations and machine code generation

CERN Document Server

Srikant, YN

2003-01-01

The widespread use of object-oriented languages and Internet security concerns are just the beginning. Add embedded systems, multiple memory banks, highly pipelined units operating in parallel, and a host of other advances and it becomes clear that current and future computer architectures pose immense challenges to compiler designers-challenges that already exceed the capabilities of traditional compilation techniques. The Compiler Design Handbook: Optimizations and Machine Code Generation is designed to help you meet those challenges. Written by top researchers and designers from around the

Molecular design of sequence specific DNA alkylating agents.

Science.gov (United States)

Minoshima, Masafumi; Bando, Toshikazu; Shinohara, Ken-ichi; Sugiyama, Hiroshi

2009-01-01

Sequence-specific DNA alkylating agents have great interest for novel approach to cancer chemotherapy. We designed the conjugates between pyrrole (Py)-imidazole (Im) polyamides and DNA alkylating chlorambucil moiety possessing at different positions. The sequence-specific DNA alkylation by conjugates was investigated by using high-resolution denaturing polyacrylamide gel electrophoresis (PAGE). The results showed that polyamide chlorambucil conjugates alkylate DNA at flanking adenines in recognition sequences of Py-Im polyamides, however, the reactivities and alkylation sites were influenced by the positions of conjugation. In addition, we synthesized conjugate between Py-Im polyamide and another alkylating agent, 1-(chloromethyl)-5-hydroxy-1,2-dihydro-3H-benz[e]indole (seco-CBI). DNA alkylation reactivies by both alkylating polyamides were almost comparable. In contrast, cytotoxicities against cell lines differed greatly. These comparative studies would promote development of appropriate sequence-specific DNA alkylating polyamides against specific cancer cells.

JAERI thermal reactor standard code system for reactor design and analysis SRAC

International Nuclear Information System (INIS)

Tsuchihashi, Keichiro

1985-01-01

SRAC, JAERI thermal reactor standard code system for reactor design and analysis, developed in Japan Atomic Energy Research Institute, is for all types of thermal neutron nuclear design and analysis. The code system has undergone extensive verifications to confirm its functions, and has been used in core modification of the research reactor, detailed design of the multi-purpose high temperature gas reactor and analysis of the experiment with a critical assembly. In nuclear calculation with the code system, multi-group lattice calculation is first made with the libraries. Then, with the resultant homogeneous equivalent group constants, reactor core calculation is made. Described are the following: purpose and development of the code system, functions of the SRAC system, bench mark tests and usage state and future development. (Mori, K.)

Design Procedure of Graphite Components by ASME HTR Codes

Energy Technology Data Exchange (ETDEWEB)

Kang, Ji-Ho; Jo, Chang Keun [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

2016-10-15

In this study, the ASME B and PV Code, Subsection HH, Subpart A, design procedure for graphite components of HTRs was reviewed and the differences from metal materials were remarked. The Korean VHTR has a prismatic core which is made of multiple graphite blocks, reflectors, and core supports. One of the design issues is the assessment of the structural integrity of the graphite components because the graphite is brittle and shows quite different behaviors from metals in high temperature environment. The American Society of Mechanical Engineers (ASME) issued the latest edition of the code for the high temperature reactors (HTR) in 2015. In this study, the ASME B and PV Code, Subsection HH, Subpart A, Graphite Materials was reviewed and the special features were remarked. Due the brittleness of graphites, the damage-tolerant design procedures different from the conventional metals were adopted based on semi-probabilistic approaches. The unique additional classification, SRC, is allotted to the graphite components and the full 3-D FEM or equivalent stress analysis method is required. In specific conditions, the oxidation and viscoelasticity analysis of material are required. The fatigue damage rule has not been established yet.

Design Procedure of Graphite Components by ASME HTR Codes

International Nuclear Information System (INIS)

Kang, Ji-Ho; Jo, Chang Keun

2016-01-01

In this study, the ASME B and PV Code, Subsection HH, Subpart A, design procedure for graphite components of HTRs was reviewed and the differences from metal materials were remarked. The Korean VHTR has a prismatic core which is made of multiple graphite blocks, reflectors, and core supports. One of the design issues is the assessment of the structural integrity of the graphite components because the graphite is brittle and shows quite different behaviors from metals in high temperature environment. The American Society of Mechanical Engineers (ASME) issued the latest edition of the code for the high temperature reactors (HTR) in 2015. In this study, the ASME B and PV Code, Subsection HH, Subpart A, Graphite Materials was reviewed and the special features were remarked. Due the brittleness of graphites, the damage-tolerant design procedures different from the conventional metals were adopted based on semi-probabilistic approaches. The unique additional classification, SRC, is allotted to the graphite components and the full 3-D FEM or equivalent stress analysis method is required. In specific conditions, the oxidation and viscoelasticity analysis of material are required. The fatigue damage rule has not been established yet

Researching on knowledge architecture of design by analysis based on ASME code

International Nuclear Information System (INIS)

Bao Shiyi; Zhou Yu; He Shuyan

2003-01-01

The quality of knowledge-based system's knowledge architecture is one of decisive factors of knowledge-based system's validity and rationality. For designing the ASME code knowledge based system, this paper presents a knowledge acquisition method which is extracting knowledge through document analysis consulted domain experts' knowledge. Then the paper describes knowledge architecture of design by analysis based on the related rules in ASME code. The knowledge of the knowledge architecture is divided into two categories: one is empirical knowledge, and another is ASME code knowledge. Applied as the basement of the knowledge architecture, a general procedural process of design by analysis that is met the engineering design requirements and designers' conventional mode is generalized and explained detailed in the paper. For the sake of improving inference efficiency and concurrent computation of KBS, a kind of knowledge Petri net (KPN) model is proposed and adopted in expressing the knowledge architecture. Furthermore, for validating and verifying of the empirical rules, five knowledge validation and verification theorems are given in the paper. Moreover the research production is applicable to design the knowledge architecture of ASME codes or other engineering standards. (author)

Design of ACM system based on non-greedy punctured LDPC codes

Science.gov (United States)

Lu, Zijun; Jiang, Zihong; Zhou, Lin; He, Yucheng

2017-08-01

In this paper, an adaptive coded modulation (ACM) scheme based on rate-compatible LDPC (RC-LDPC) codes was designed. The RC-LDPC codes were constructed by a non-greedy puncturing method which showed good performance in high code rate region. Moreover, the incremental redundancy scheme of LDPC-based ACM system over AWGN channel was proposed. By this scheme, code rates vary from 2/3 to 5/6 and the complication of the ACM system is lowered. Simulations show that more and more obvious coding gain can be obtained by the proposed ACM system with higher throughput.

DENV gene of bacteriophage T4 codes for both pyrimidine dimer-DNA glycosylase and apyrimidinic endonuclease activities

International Nuclear Information System (INIS)

McMillan, S.; Edenberg, H.J.; Radany, E.H.; Friedberg, R.C.; Friedberg, E.C.

1981-01-01

Recent studies have shown that purified preparations of phage T4 UV DNA-incising activity (T4 UV endonuclease or endonuclease V of phase T4) contain a pyrimidine dimer-DNA glycosylase activity that catalyzes hydrolysis of the 5' glycosyl bond of dimerized pyrimidines in UV-irradiated DNA. Such enzyme preparations have also been shown to catalyze the hydrolysis of phosphodiester bonds in UV-irradiated DNA at a neutral pH, presumably reflecting the action of an apurinic/apyrimidinic endonuclease at the apyrimidinic sites created by the pyrimidine dimer-DNA glycosylase. In this study we found that preparations of T4 UV DNA-incising activity contained apurinic/apyrimidinic endonuclease activity that nicked depurinated form I simian virus 40 DNA. Apurinic/apyrimidinic endonuclease activity was also found in extracts of Escherichia coli infected with T4 denV + phage. Extracts of cells infected with T4 denV mutants contained significantly lower levels of apurinic/apyrimidinic endonuclease activity; these levels were no greater than the levels present in extracts of uninfected cells. Furthermore, the addition of DNA containing UV-irradiated DNA and T4 enzyme resulted in competition for pyrimidine dimer-DNA glycosylase activity against the UV-irradiated DNA. On the basis of these results, we concluded that apurinic/apyrimidinic endonuclease activity is encoded by the denV gene of phage T4, the same gene that codes for pyrimidine dimer-DNA glycosylase activity

General features of the neutronics design code EQUICYCLE

International Nuclear Information System (INIS)

Jirlow, K.

1978-10-01

The neutronics code EQUICYCLE has been developed and improved over a long period of time. It is expecially adapted to survey type design calculations of large fast power reactors with particular emphasis on the nuclear parameters for a realistic equilibrium fuel cycle. Thus the code is used to evaluate the breeding performance, the power distributions and the uranium and plutonium mass balance for realistic refuelling schemes. In addition reactivity coefficients can be calculated and the influence of burnup could be assessed. The code is two-dimensional and treats the reactor core in R-Z geometry. The basic ideas of the calculating scheme are successive iterative improvement of cross-section sets and flux spectra and use of the mid-cycle flux for burning the fuel according to a specified refuelling scheme. Normally given peak burn-ups and maximum power densities are used as boundary conditions. The code is capable of handling the unconventional, so called heterogeneous cores. (author)

Jointly Decoded Raptor Codes: Analysis and Design for the BIAWGN Channel

Directory of Open Access Journals (Sweden)

Venkiah Auguste

2009-01-01

Full Text Available Abstract We are interested in the analysis and optimization of Raptor codes under a joint decoding framework, that is, when the precode and the fountain code exchange soft information iteratively. We develop an analytical asymptotic convergence analysis of the joint decoder, derive an optimization method for the design of efficient output degree distributions, and show that the new optimized distributions outperform the existing ones, both at long and moderate lengths. We also show that jointly decoded Raptor codes are robust to channel variation: they perform reasonably well over a wide range of channel capacities. This robustness property was already known for the erasure channel but not for the Gaussian channel. Finally, we discuss some finite length code design issues. Contrary to what is commonly believed, we show by simulations that using a relatively low rate for the precode , we can improve greatly the error floor performance of the Raptor code.

Core design calculations of IRIS reactor using modified CORD-2 code package

International Nuclear Information System (INIS)

Pevec, D.; Grgic, D.; Jecmenica, R.; Petrovic, B.

2002-01-01

Core design calculations, with thermal-hydraulic feedback, for the first cycle of the IRIS reactor were performed using the modified CORD-2 code package. WIMSD-5B code is applied for cell and cluster calculations with two different 69-group data libraries (ENDF/BVI rev. 5 and JEF-2.2), while the nodal code GNOMER is used for diffusion calculations. The objective of the calculation was to address basic core design problems for innovative reactors with long fuel cycle. The results were compared to our results obtained with CORD-2 before the modification and to preliminary results obtained with CASMO code for a similar problem without thermal-hydraulic feedback.(author)

Computer codes for particle accelerator design and analysis: A compendium. Second edition

International Nuclear Information System (INIS)

Deaven, H.S.; Chan, K.C.D.

1990-05-01

The design of the next generation of high-energy accelerators will probably be done as an international collaborative efforts and it would make sense to establish, either formally or informally, an international center for accelerator codes with branches for maintenance, distribution, and consultation at strategically located accelerator centers around the world. This arrangement could have at least three beneficial effects. It would cut down duplication of effort, provide long-term support for the best codes, and provide a stimulating atmosphere for the evolution of new codes. It does not take much foresight to see that the natural evolution of accelerator design codes is toward the development of so-called Expert Systems, systems capable of taking design specifications of future accelerators and producing specifications for optimized magnetic transport and acceleration components, making a layout, and giving a fairly impartial cost estimate. Such an expert program would use present-day programs such as TRANSPORT, POISSON, and SUPERFISH as tools in the optimization process. Such a program would also serve to codify the experience of two generations of accelerator designers before it is lost as these designers reach retirement age. This document describes 203 codes that originate from 10 countries and are currently in use. The authors feel that this compendium will contribute to the dialogue supporting the international collaborative effort that is taking place in the field of accelerator physics today

A Proposed Chaotic-Switched Turbo Coding Design and Its Application for Half-Duplex Relay Channel

Directory of Open Access Journals (Sweden)

Tamer H. M. Soliman

2015-01-01

Full Text Available Both reliability and security are two important subjects in modern digital communications, each with a variety of subdisciplines. In this paper we introduce a new proposed secure turbo coding system which combines chaotic dynamics and turbo coding reliability together. As we utilize the chaotic maps as a tool for hiding and securing the coding design in turbo coding system, this proposed system model can provide both data secrecy and data reliability in one process to combat problems in an insecure and unreliable data channel link. To support our research, we provide different schemes to design a chaotic secure reliable turbo coding system which we call chaotic-switched turbo coding schemes. In these schemes the design of turbo codes chaotically changed depending on one or more chaotic maps. Extensions of these chaotic-switched turbo coding schemes to half-duplex relay systems are also described. Results of simulations of these new secure turbo coding schemes are compared to classical turbo codes with the same coding parameters and the proposed system is able to achieve secured reasonable bit error rate performance when it is made to switch between different puncturing and design configuration parameters especially with low switching rates.

Objective Oriented Design of Architecture for TH System Safety Analysis Code and Verification

Energy Technology Data Exchange (ETDEWEB)

Chung, Bub Dong

2008-03-15

In this work, objective oriented design of generic system analysis code has been tried based on the previous works in KAERI for two phase three field Pilot code. It has been performed to implement of input and output design, TH solver, component model, special TH models, heat structure solver, general table, trip and control, and on-line graphics. All essential features for system analysis has been designed and implemented in the final product SYSTF code. The computer language C was used for implementation in the Visual studio 2008 IDE (Integrated Development Environment) since it has easier and lighter than C++ feature. The code has simple and essential features of models and correlation, special component, special TH model and heat structure model. However the input features is able to simulate the various scenarios, such as steady state, non LOCA transient and LOCA accident. The structure validity has been tested through the various verification tests and it has been shown that the developed code can treat the non LOCA and LOCA simulation. However more detailed design and implementation of models are required to get the physical validity of SYSTF code simulation.

Objective Oriented Design of Architecture for TH System Safety Analysis Code and Verification

International Nuclear Information System (INIS)

Chung, Bub Dong

2008-03-01

In this work, objective oriented design of generic system analysis code has been tried based on the previous works in KAERI for two phase three field Pilot code. It has been performed to implement of input and output design, TH solver, component model, special TH models, heat structure solver, general table, trip and control, and on-line graphics. All essential features for system analysis has been designed and implemented in the final product SYSTF code. The computer language C was used for implementation in the Visual studio 2008 IDE (Integrated Development Environment) since it has easier and lighter than C++ feature. The code has simple and essential features of models and correlation, special component, special TH model and heat structure model. However the input features is able to simulate the various scenarios, such as steady state, non LOCA transient and LOCA accident. The structure validity has been tested through the various verification tests and it has been shown that the developed code can treat the non LOCA and LOCA simulation. However more detailed design and implementation of models are required to get the physical validity of SYSTF code simulation

An Abundant Class of Non-coding DNA Can Prevent Stochastic Gene Silencing in the C. elegans Germline

DEFF Research Database (Denmark)

Frøkjær-Jensen, Christian; Jain, Nimit; Hansen, Loren

2016-01-01

/or structure. Here, we demonstrate that a pervasive non-coding DNA feature in Caenorhabditis elegans, characterized by 10-base pair periodic An/Tn-clusters (PATCs), can license transgenes for germline expression within repressive chromatin domains. Transgenes containing natural or synthetic PATCs are resistant...

Utilization of MCNP code in the research and design for China advanced research reactor

International Nuclear Information System (INIS)

Shen Feng

2006-01-01

MCNP, which is the internationalized neutronics code, is used for nuclear research and design in China Advanced Research Reactor (CARR). MCNP is an important neutronics code in the research and design for CARR since many calculation tasks could be undertaken by it. Many nuclear parameters on reactor core, the design and optimization research for many reactor utilizations, much verification for other nuclear calculation code and so on are conducted with help of MCNP. (author)

Design of convolutional tornado code

Science.gov (United States)

Zhou, Hui; Yang, Yao; Gao, Hongmin; Tan, Lu

2017-09-01

As a linear block code, the traditional tornado (tTN) code is inefficient in burst-erasure environment and its multi-level structure may lead to high encoding/decoding complexity. This paper presents a convolutional tornado (cTN) code which is able to improve the burst-erasure protection capability by applying the convolution property to the tTN code, and reduce computational complexity by abrogating the multi-level structure. The simulation results show that cTN code can provide a better packet loss protection performance with lower computation complexity than tTN code.

Materials and design bases issues in ASME Code Case N-47

International Nuclear Information System (INIS)

Huddleston, R.L.; Swindeman, R.W.

1993-04-01

A preliminary evaluation of the design bases (principally ASME Code Case N-47) was conducted for design and operation of reactors at elevated temperatures where the time-dependent effects of creep, creep-fatigue, and creep ratcheting are significant. Areas where Code rules or regulatory guides may be lacking or inadequate to ensure the operation over the expected life cycles for the next-generation advanced high-temperature reactor systems, with designs to be certified by the US Nuclear Regulatory Commission, have been identified as unresolved issues. Twenty-two unresolved issues were identified and brief scoping plans developed for resolving these issues

Design of 240,000 orthogonal 25mer DNA barcode probes.

Science.gov (United States)

Xu, Qikai; Schlabach, Michael R; Hannon, Gregory J; Elledge, Stephen J

2009-02-17

DNA barcodes linked to genetic features greatly facilitate screening these features in pooled formats using microarray hybridization, and new tools are needed to design large sets of barcodes to allow construction of large barcoded mammalian libraries such as shRNA libraries. Here we report a framework for designing large sets of orthogonal barcode probes. We demonstrate the utility of this framework by designing 240,000 barcode probes and testing their performance by hybridization. From the test hybridizations, we also discovered new probe design rules that significantly reduce cross-hybridization after their introduction into the framework of the algorithm. These rules should improve the performance of DNA microarray probe designs for many applications.

Code comparison for accelerator design and analysis

International Nuclear Information System (INIS)

Parsa, Z.

1988-01-01

We present a comparison between results obtained from standard accelerator physics codes used for the design and analysis of synchrotrons and storage rings, with programs SYNCH, MAD, HARMON, PATRICIA, PATPET, BETA, DIMAD, MARYLIE and RACE-TRACK. In our analysis we have considered 5 (various size) lattices with large and small angles including AGS Booster (10/degree/ bend), RHIC (2.24/degree/), SXLS, XLS (XUV ring with 45/degree/ bend) and X-RAY rings. The differences in the integration methods used and the treatment of the fringe fields in these codes could lead to different results. The inclusion of nonlinear (e.g., dipole) terms may be necessary in these calculations specially for a small ring. 12 refs., 6 figs., 10 tabs

Design of an Object-Oriented Turbomachinery Analysis Code: Initial Results

Science.gov (United States)

Jones, Scott M.

2015-01-01

Performance prediction of turbomachines is a significant part of aircraft propulsion design. In the conceptual design stage, there is an important need to quantify compressor and turbine aerodynamic performance and develop initial geometry parameters at the 2-D level prior to more extensive Computational Fluid Dynamics (CFD) analyses. The Object-oriented Turbomachinery Analysis Code (OTAC) is being developed to perform 2-D meridional flowthrough analysis of turbomachines using an implicit formulation of the governing equations to solve for the conditions at the exit of each blade row. OTAC is designed to perform meanline or streamline calculations; for streamline analyses simple radial equilibrium is used as a governing equation to solve for spanwise property variations. While the goal for OTAC is to allow simulation of physical effects and architectural features unavailable in other existing codes, it must first prove capable of performing calculations for conventional turbomachines. OTAC is being developed using the interpreted language features available in the Numerical Propulsion System Simulation (NPSS) code described by Claus et al (1991). Using the NPSS framework came with several distinct advantages, including access to the pre-existing NPSS thermodynamic property packages and the NPSS Newton-Raphson solver. The remaining objects necessary for OTAC were written in the NPSS framework interpreted language. These new objects form the core of OTAC and are the BladeRow, BladeSegment, TransitionSection, Expander, Reducer, and OTACstart Elements. The BladeRow and BladeSegment consumed the initial bulk of the development effort and required determining the equations applicable to flow through turbomachinery blade rows given specific assumptions about the nature of that flow. Once these objects were completed, OTAC was tested and found to agree with existing solutions from other codes; these tests included various meanline and streamline comparisons of axial

Unitals and ovals of symmetric block designs in LDPC and space-time coding

Science.gov (United States)

Andriamanalimanana, Bruno R.

2004-08-01

An approach to the design of LDPC (low density parity check) error-correction and space-time modulation codes involves starting with known mathematical and combinatorial structures, and deriving code properties from structure properties. This paper reports on an investigation of unital and oval configurations within generic symmetric combinatorial designs, not just classical projective planes, as the underlying structure for classes of space-time LDPC outer codes. Of particular interest are the encoding and iterative (sum-product) decoding gains that these codes may provide. Various small-length cases have been numerically implemented in Java and Matlab for a number of channel models.

DIANA Code: Design and implementation of an analytic core calculus code by two group, two zone diffusion

International Nuclear Information System (INIS)

Mochi, Ignacio

2005-01-01

The principal parameters of nuclear reactors are determined in the conceptual design stage.For that purpose, it is necessary to have flexible calculation tools that represent the principal dependencies of such parameters.This capability is of critical importance in the design of innovative nuclear reactors.In order to have a proper tool that could assist the conceptual design of innovative nuclear reactors, we developed and implemented a neutronic core calculus code: DIANA (Diffusion Integral Analytic Neutron Analysis).To calculate the required parameters, this code generates its own cross sections using an analytic two group, two zones diffusion scheme based only on a minimal set of data (i.e. 2200 m/s and fission averaged microscopic cross sections, Wescott factors and Effective Resonance Integrals).Both to calculate cross sections and core parameters, DIANA takes into account heterogeneity effects that are included when it evaluates each zone.Among them lays the disadvantage factor of each energy group.DIANA was totally implemented through Object Oriented Programming using C++ language. This eases source code understanding and would allow a quick expansion of its capabilities if needed.The final product is a versatile and easy-to-use code that allows core calculations with a minimal amount of data.It also contains the required tools needed to perform many variational calculations such as the parameterisation of effective multiplication factors for different radii of the core.The diffusion scheme s simplicity allows an easy following of the involved phenomena, making DIANA the most suitable tool to design reactors whose physics lays beyond the parameters of present reactors.All this reasons make DIANA a good candidate for future innovative reactor analysis

RCC-E a Design Code for I and C and Electrical Systems

International Nuclear Information System (INIS)

Haure, J.M.

2015-01-01

The paper deals with the stakes and strength of the RCC-E code applicable to Electrical and Instrumentation and control systems and components as regards dealing with safety class functions. The document is interlacing specifications between Owners, safety authorities, designers, and suppliers IAEA safety guides and IEC standards. The code is periodically updated and published by French Society for Design and Construction rules for Nuclear Island Components (AFCEN). The code is compliant with third generation PWR nuclear islands and aims to suit with national regulations as needed in a companion document. The Feedback experience of Fukushima and the licensing of UKEPR in the framework of Generic Design Assessment are lessons learnt that should be considered in the upgrading of the code. The code gathers a set of requirements and relevant good practices of several PWR design and construction practices related to the electrical and I and C systems and components, and electrical engineering documents dealing with systems, equipment and layout designs. Comprehensive statement including some recent developments will be provided about: - Offsite and onsite sources requirements including sources dealing the total loss of off sites and main onsite sources. - Highlights of a relevant protection level against high frequencies disturbances emitted by lightning strokes, Interfaces data used by any supplier or designer such as site data, rooms temperature, equipment maximum design temperature, alternative current and direct current electrical network voltages and frequency variation ranges, environmental conditions decoupling data, - Environmental Qualification process including normal, mild (earthquake resistant), harsh and severe accident ambient conditions. A suit made approach based on families, which are defined as a combination of mission time, duration and abnormal conditions (pressure, temperature, radiation), enables to better cope with Environmental Qualifications

Impact of ACI-ASME code on design and construction of nuclear containment structures

International Nuclear Information System (INIS)

Reedy, R.F.

1978-01-01

The effect of the ACI-ASME code for design and construction of concrete containment structures on the nuclear and concrete industries is examined. Topics covered include purpose of the code, general requirements, responsibilities and duties, design and construction specifications, quality assurance, inspection, the liner, and stamping

Ripple Design of LT Codes for BIAWGN Channels

DEFF Research Database (Denmark)

Sørensen, Jesper Hemming; Koike-Akino, Toshiaki; Orlik, Philip

2014-01-01

This paper presents a novel framework, which enables a design of rateless codes for binary input additive white Gaussian noise (BIAWGN) channels, using the ripple-based approach known from the works for the binary erasure channel (BEC). We reveal that several aspects of the analytical results from...

A contribution to the design of fast code converters for position encoders

Science.gov (United States)

Denic, Dragan B.; Dincic, Milan R.; Miljkovic, Goran S.; Peric, Zoran H.

2016-10-01

Pseudorandom binary sequences (PRBS) are very useful in many areas of applications. Absolute position encoders based on PRBS have many advantages. However, the pseudorandom code is not directly applicable to the digital electronic systems, hence a converter from pseudorandom to natural binary code is needed. Recently, a fast pseudorandom/natural code converter based on Galois PRBS generator (much faster than previously used converter based on Fibonacci PRBS generator) was proposed. One of the main parts of the Galois code converter is an initial logic. The problem of the design of the initial logic has been solved only for some single values of resolution, but it is still not solved for any value of resolution, which significantly limits the applicability of the fast Galois code converter. This paper solves this problem presenting the solution for the design of the initial logic of the fast Galois pseudorandom/natural code converters used in the pseudorandom position encoders, in general manner, that is for any value of the resolution, allowing for a wide applicability of the fast Galois pseudorandom position encoders. Rigorous mathematical derivation of the formula for the designing of the initial logic is presented. Simulation of the proposed converter is performed in NI MultiSim software. The proposed solution, although developed for pseudorandom position encoders, can be used in many other fields where PRBS are used.

Current Status of the Elevated Temperature Structure Design Codes for VHTR

International Nuclear Information System (INIS)

Kim, Jong-Bum; Kim, Seok-Hoon; Park, Keun-Bae; Lee, Won-Jae

2006-01-01

An elevated temperature structure design and analysis is one of the key issues in the VHTR (Very High Temperature Reactor) project to achieve an economic production of hydrogen which will be an essential energy source for the near future. Since the operating temperature of a VHTR is above 850 .deg. C, the existing code and standards are insufficient for a high temperature structure design. Thus the issues concerning a material selection and behaviors are being studied for the main structural components of a VHTR in leading countries such as US, France, UK, and Japan. In this study, the current status of the ASME code, French RCC-MR, UK R5, and Japanese code were investigated and the necessary R and D items were discussed

Validations of BWR nuclear design code using ABWR MOX numerical benchmark problems

International Nuclear Information System (INIS)

Takano, Shou; Sasagawa, Masaru; Yamana, Teppei; Ikehara, Tadashi; Yanagisawa, Naoki

2017-01-01

BWR core design code package (the HINES assembly code and the PANACH core simulator), being used for full MOX-ABWR core design, has been benchmarked against the high-fidelity numerical solutions as references, for the purpose of validating its capability of predicting the BWR core design parameters systematically from UO 2 to 100% MOX cores. The reference solutions were created by whole core critical calculations using MCNPs with the precisely modeled ABWR cores both in hot and cold conditions at BOC and EOC of the equilibrium cycle. A Doppler-Broadening Rejection Correction (DCRB) implemented MCNP5-1.4 with ENDF/B-VII.0 was mainly used to evaluate the core design parameters, except for effective delayed neutron fraction (β eff ) and prompt neutron lifetime (l) with MCNP6.1. The discrepancies in the results between the design codes HINES-PANACH and MCNPs for the core design parameters such as the bundle powers, hot pin powers, control rod worth, boron worth, void reactivity, Doppler reactivity, β eff and l, are almost within target accuracy, leading to the conclusion that HINES-PANACH has sufficient fidelity for application to full MOX-ABWR core design. (author)

Tuning porosity and radial mechanical properties of DNA origami nanotubes via crossover design

Science.gov (United States)

Ma, Zhipeng; Kawai, Kentaro; Hirai, Yoshikazu; Tsuchiya, Toshiyuki; Tabata, Osamu

2017-06-01

DNA origami nanotubes are utilized as structural platforms for the fabrication of various micro/nanosystems for drug delivery, optical or biological sensing, and even nanoscale robots. Their radial structural and mechanical properties, which play a crucial role in the effective use of micro/nanosystems, have not been fully studied. In particular, the effects of crossovers, which are basic structures for rationally assembling double-stranded DNA (dsDNA) helices into a nanotube configuration, have not yet been characterized experimentally. To investigate the effects of crossovers on the porosity and the radial mechanical properties of DNA origami nanotubes, we fabricated a DNA origami nanotube with varied crossover designs along the nanotube axis. The radial geometry of the DNA origami nanotube is experimentally characterized by both atomic force microscopy (AFM) and electron cryomicroscopy (cryo-EM). Moreover, the radial mechanical properties of the DNA origami nanotube including the radial modulus are directly measured by force-distance-based AFM. These measurements reveal that the porosity and the radial modulus of DNA origami nanotubes can be tuned by adjusting the crossover design, which enables the optimal design and construction of DNA origami nanostructures for various applications.

Crafting qualities in designing QR-coded embroidery and bedtime stories

NARCIS (Netherlands)

Kuusk, K.; Wensveen, S.A.G.; Tomico, O.

2014-01-01

There is a renewed interest into crafts and what it can mean when integrating new technologies into textiles. This paper proposes to embed craft qualities and sustainable values into designing smart textile projects. Our design iterations QR-Coded Embroidery and Bedtime Stories combine textiles,

Uropathogenic Escherichia coli virulence genes: invaluable approaches for designing DNA microarray probes.

Science.gov (United States)

Jahandeh, Nadia; Ranjbar, Reza; Behzadi, Payam; Behzadi, Elham

2015-01-01

The pathotypes of uropathogenic Escherichia coli (UPEC) cause different types of urinary tract infections (UTIs). The presence of a wide range of virulence genes in UPEC enables us to design appropriate DNA microarray probes. These probes, which are used in DNA microarray technology, provide us with an accurate and rapid diagnosis and definitive treatment in association with UTIs caused by UPEC pathotypes. The main goal of this article is to introduce the UPEC virulence genes as invaluable approaches for designing DNA microarray probes. Main search engines such as Google Scholar and databases like NCBI were searched to find and study several original pieces of literature, review articles, and DNA gene sequences. In parallel with in silico studies, the experiences of the authors were helpful for selecting appropriate sources and writing this review article. There is a significant variety of virulence genes among UPEC strains. The DNA sequences of virulence genes are fabulous patterns for designing microarray probes. The location of virulence genes and their sequence lengths influence the quality of probes. The use of selected virulence genes for designing microarray probes gives us a wide range of choices from which the best probe candidates can be chosen. DNA microarray technology provides us with an accurate, rapid, cost-effective, sensitive, and specific molecular diagnostic method which is facilitated by designing microarray probes. Via these tools, we are able to have an accurate diagnosis and a definitive treatment regarding UTIs caused by UPEC pathotypes.

Code conversion for system design and safety analysis of NSSS

Energy Technology Data Exchange (ETDEWEB)

Lee, Hae Cho; Kim, Young Tae; Choi, Young Gil; Kim, Hee Kyung [Korea Atomic Energy Research Institute, Taejon (Korea, Republic of)

1996-01-01

This report describes overall project works related to conversion, installation and validation of computer codes which are used in NSSS design and safety analysis of nuclear power plants. Domain/os computer codes for system safety analysis are installed and validated on Apollo DN10000, and then Apollo version are converted and installed again on HP9000/700 series with appropriate validation. Also, COOLII and COAST which are cyber version computer codes are converted into versions of Apollo DN10000 and HP9000/700, and installed with validation. This report details whole processes of work involved in the computer code conversion and installation, as well as software verification and validation results which are attached to this report. 12 refs., 8 figs. (author)

Adaption of the PARCS Code for Core Design Audit Analyses

Energy Technology Data Exchange (ETDEWEB)

Kim, Hyong Chol; Lee, Young Jin; Uhm, Jae Beop; Kim, Hyunjik [Nuclear Safety Evaluation, Daejeon (Korea, Republic of); Jeong, Hun Young; Ahn, Seunghoon; Woo, Swengwoong [Korea Institute of Nuclear Safety, Daejeon (Korea, Republic of)

2013-05-15

The eigenvalue calculation also includes quasi-static core depletion analyses. PARCS has implemented variety of features and has been qualified as a regulatory audit code in conjunction with other NRC thermal-hydraulic codes such as TRACE or RELAP5. In this study, as an adaptation effort for audit applications, PARCS is applied for an audit analysis of a reload core design. The lattice physics code HELIOS is used for cross section generation. PARCS-HELIOS code system has been established as a core analysis tool. Calculation results have been compared on a wide spectrum of calculations such as power distribution, critical soluble boron concentration, and rod worth. A reasonable agreement between the audit calculation and the reference results has been found.

Detected-jump-error-correcting quantum codes, quantum error designs, and quantum computation

International Nuclear Information System (INIS)

Alber, G.; Mussinger, M.; Beth, Th.; Charnes, Ch.; Delgado, A.; Grassl, M.

2003-01-01

The recently introduced detected-jump-correcting quantum codes are capable of stabilizing qubit systems against spontaneous decay processes arising from couplings to statistically independent reservoirs. These embedded quantum codes exploit classical information about which qubit has emitted spontaneously and correspond to an active error-correcting code embedded in a passive error-correcting code. The construction of a family of one-detected-jump-error-correcting quantum codes is shown and the optimal redundancy, encoding, and recovery as well as general properties of detected-jump-error-correcting quantum codes are discussed. By the use of design theory, multiple-jump-error-correcting quantum codes can be constructed. The performance of one-jump-error-correcting quantum codes under nonideal conditions is studied numerically by simulating a quantum memory and Grover's algorithm

Divide and control: split design of multi-input DNA logic gates.

Science.gov (United States)

Gerasimova, Yulia V; Kolpashchikov, Dmitry M

2015-01-18

Logic gates made of DNA have received significant attention as biocompatible building blocks for molecular circuits. The majority of DNA logic gates, however, are controlled by the minimum number of inputs: one, two or three. Here we report a strategy to design a multi-input logic gate by splitting a DNA construct.

Comparison of the General Electric BWR/6 standard plant design to the IAEA NUSS codes and guides

International Nuclear Information System (INIS)

D'Ardenne, W.H.; Sherwood, G.G.

1985-01-01

The General Electric BWR/6 Mark III standard plant design meets or exceeds current requirements of published International Atomic Energy Agency (IAEA) Nuclear Safety Standards (NUSS) codes and guides. This conclusion is based on a review of the NUSS codes and guides by General Electric and by the co-ordinated US review of the NUSS codes and guides during their development. General Electric compared the published IAEA NUSS codes and guides with the General Electric design. The applicability of each code and guide to the BWR/6 Mark III standard plant design was determined. Each code or guide was reviewed by a General Electric engineer knowledgeable about the structures, systems and components addressed and the technical area covered by that code or guide. The results of this review show that the BWR/6 Mark III standard plant design meets or exceeds the applicable requirements of the published IAEA NUSS codes and guides. The co-ordinated US review of the IAEA NUSS codes and guides corroborates the General Electric review. In the co-ordinated US review, the USNRC and US industry organizations (including General Electric) review the NUSS codes and guides during their development. This review ensures that the NUSS codes and guides are consistent with the current US government regulations, guidance and regulatory practices, US voluntary industry codes and standards, and accepted US industry design, construction and operational practices. If any inconsistencies are identified, comments are submitted to the IAEA by the USNRC. All US concerns submitted to the IAEA have been resolved. General Electric design reviews and the Final Design Approval (FDA) issued by the USNRC have verified that the General Electric BWR/6 Mark III standard plant design meets or exceeds the current US requirements, guidance and practices. Since these requirements, guidance and practices meet or exceed those of the NUSS codes and guides, so does the General Electric design. (author)

Novel BCH Code Design for Mitigation of Phase Noise Induced Cycle Slips in DQPSK Systems

DEFF Research Database (Denmark)

Leong, M. Y.; Larsen, Knud J.; Jacobsen, G.

2014-01-01

We show that by proper code design, phase noise induced cycle slips causing an error floor can be mitigated for 28 Gbau d DQPSK systems. Performance of BCH codes are investigated in terms of required overhead......We show that by proper code design, phase noise induced cycle slips causing an error floor can be mitigated for 28 Gbau d DQPSK systems. Performance of BCH codes are investigated in terms of required overhead...

Application of the MELCOR code to design basis PWR large dry containment analysis.

Energy Technology Data Exchange (ETDEWEB)

Phillips, Jesse; Notafrancesco, Allen (USNRC, Office of Nuclear Regulatory Research, Rockville, MD); Tills, Jack Lee (Jack Tills & Associates, Inc., Sandia Park, NM)

2009-05-01

The MELCOR computer code has been developed by Sandia National Laboratories under USNRC sponsorship to provide capability for independently auditing analyses submitted by reactor manufactures and utilities. MELCOR is a fully integrated code (encompassing the reactor coolant system and the containment building) that models the progression of postulated accidents in light water reactor power plants. To assess the adequacy of containment thermal-hydraulic modeling incorporated in the MELCOR code for application to PWR large dry containments, several selected demonstration designs were analyzed. This report documents MELCOR code demonstration calculations performed for postulated design basis accident (DBA) analysis (LOCA and MSLB) inside containment, which are compared to other code results. The key processes when analyzing the containment loads inside PWR large dry containments are (1) expansion and transport of high mass/energy releases, (2) heat and mass transfer to structural passive heat sinks, and (3) containment pressure reduction due to engineered safety features. A code-to-code benchmarking for DBA events showed that MELCOR predictions of maximum containment loads were equivalent to similar predictions using a qualified containment code known as CONTAIN. This equivalency was found to apply for both single- and multi-cell containment models.

Lnc2Meth: a manually curated database of regulatory relationships between long non-coding RNAs and DNA methylation associated with human disease.

Science.gov (United States)

Zhi, Hui; Li, Xin; Wang, Peng; Gao, Yue; Gao, Baoqing; Zhou, Dianshuang; Zhang, Yan; Guo, Maoni; Yue, Ming; Shen, Weitao; Ning, Shangwei; Jin, Lianhong; Li, Xia

2018-01-04

Lnc2Meth (http://www.bio-bigdata.com/Lnc2Meth/), an interactive resource to identify regulatory relationships between human long non-coding RNAs (lncRNAs) and DNA methylation, is not only a manually curated collection and annotation of experimentally supported lncRNAs-DNA methylation associations but also a platform that effectively integrates tools for calculating and identifying the differentially methylated lncRNAs and protein-coding genes (PCGs) in diverse human diseases. The resource provides: (i) advanced search possibilities, e.g. retrieval of the database by searching the lncRNA symbol of interest, DNA methylation patterns, regulatory mechanisms and disease types; (ii) abundant computationally calculated DNA methylation array profiles for the lncRNAs and PCGs; (iii) the prognostic values for each hit transcript calculated from the patients clinical data; (iv) a genome browser to display the DNA methylation landscape of the lncRNA transcripts for a specific type of disease; (v) tools to re-annotate probes to lncRNA loci and identify the differential methylation patterns for lncRNAs and PCGs with user-supplied external datasets; (vi) an R package (LncDM) to complete the differentially methylated lncRNAs identification and visualization with local computers. Lnc2Meth provides a timely and valuable resource that can be applied to significantly expand our understanding of the regulatory relationships between lncRNAs and DNA methylation in various human diseases. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Manchester Coding Option for SpaceWire: Providing Choices for System Level Design

Science.gov (United States)

Rakow, Glenn; Kisin, Alex

2014-01-01

This paper proposes an optional coding scheme for SpaceWire in lieu of the current Data Strobe scheme for three reasons. First reason is to provide a straightforward method for electrical isolation of the interface; secondly to provide ability to reduce the mass and bend radius of the SpaceWire cable; and thirdly to provide a means for a common physical layer over which multiple spacecraft onboard data link protocols could operate for a wide range of data rates. The intent is to accomplish these goals without significant change to existing SpaceWire design investments. The ability to optionally use Manchester coding in place of the current Data Strobe coding provides the ability to DC balanced the signal transitions unlike the SpaceWire Data Strobe coding; and therefore the ability to isolate the electrical interface without concern. Additionally, because the Manchester code has the clock and data encoded on the same signal, the number of wires of the existing SpaceWire cable could be optionally reduced by 50. This reduction could be an important consideration for many users of SpaceWire as indicated by the already existing effort underway by the SpaceWire working group to reduce the cable mass and bend radius by elimination of shields. However, reducing the signal count by half would provide even greater gains. It is proposed to restrict the data rate for the optional Manchester coding to a fixed data rate of 10 Megabits per second (Mbps) in order to make the necessary changes simple and still able to run in current radiation tolerant Field Programmable Gate Arrays (FPGAs). Even with this constraint, 10 Mbps will meet many applications where SpaceWire is used. These include command and control applications and many instruments applications with have moderate data rate. For most NASA flight implementations, SpaceWire designs are in rad-tolerant FPGAs, and the desire to preserve the heritage design investment is important for cost and risk considerations. The

Sub-THz spectroscopic characterization of vibrational modes in artificially designed DNA monocrystal

International Nuclear Information System (INIS)

Sizov, Igor; Rahman, Masudur; Gelmont, Boris; Norton, Michael L.; Globus, Tatiana

2013-01-01

Highlights: • Sub-THz spectroscopy is used to characterize artificially designed DNA monocrystal. • Results are obtained using a novel near field, RT, frequency domain spectrometer. • Narrow resonances of 0.1 cm −1 width in absorption spectra of crystal are observed. • Signature measured between 310 and 490 GHz is reproducible and well resolved. • Absorption pattern is explained in part by simulation results from dsDNA fragment. - Abstract: Sub-terahertz (sub-THz) vibrational spectroscopy is a new spectroscopic branch for characterizing biological macromolecules. In this work, highly resolved sub-THz resonance spectroscopy is used for characterizing engineered molecular structures, an artificially designed DNA monocrystal, built from a short DNA sequence. Using a recently developed frequency domain spectroscopic instrument operating at room temperature with high spectral and spatial resolution, we demonstrated very intense and specific spectral lines from a DNA crystal in general agreement with a computational molecular dynamics (MD) simulation of a short double stranded DNA fragment. The spectroscopic signature measured in the frequency range between 310 and 490 GHz is rich in well resolved and reproducible spectral features thus demonstrating the capability of THz resonance spectroscopy to be used for characterizing custom macromolecules and structures designed and implemented via nanotechnology for a wide variety of application domains. Analysis of MD simulation indicates that intense and narrow vibrational modes with atomic movements perpendicular (transverse) and parallel (longitudinal) to the long DNA axis coexist in dsDNA, with much higher contribution from longitudinal vibrations

Long non-coding RNAs as novel expression signatures modulate DNA damage and repair in cadmium toxicology

Science.gov (United States)

Zhou, Zhiheng; Liu, Haibai; Wang, Caixia; Lu, Qian; Huang, Qinhai; Zheng, Chanjiao; Lei, Yixiong

2015-10-01

Increasing evidence suggests that long non-coding RNAs (lncRNAs) are involved in a variety of physiological and pathophysiological processes. Our study was to investigate whether lncRNAs as novel expression signatures are able to modulate DNA damage and repair in cadmium(Cd) toxicity. There were aberrant expression profiles of lncRNAs in 35th Cd-induced cells as compared to untreated 16HBE cells. siRNA-mediated knockdown of ENST00000414355 inhibited the growth of DNA-damaged cells and decreased the expressions of DNA-damage related genes (ATM, ATR and ATRIP), while increased the expressions of DNA-repair related genes (DDB1, DDB2, OGG1, ERCC1, MSH2, RAD50, XRCC1 and BARD1). Cadmium increased ENST00000414355 expression in the lung of Cd-exposed rats in a dose-dependent manner. A significant positive correlation was observed between blood ENST00000414355 expression and urinary/blood Cd concentrations, and there were significant correlations of lncRNA-ENST00000414355 expression with the expressions of target genes in the lung of Cd-exposed rats and the blood of Cd exposed workers. These results indicate that some lncRNAs are aberrantly expressed in Cd-treated 16HBE cells. lncRNA-ENST00000414355 may serve as a signature for DNA damage and repair related to the epigenetic mechanisms underlying the cadmium toxicity and become a novel biomarker of cadmium toxicity.

Rotorcraft Optimization Tools: Incorporating Rotorcraft Design Codes into Multi-Disciplinary Design, Analysis, and Optimization

Science.gov (United States)

Meyn, Larry A.

2018-01-01

One of the goals of NASA's Revolutionary Vertical Lift Technology Project (RVLT) is to provide validated tools for multidisciplinary design, analysis and optimization (MDAO) of vertical lift vehicles. As part of this effort, the software package, RotorCraft Optimization Tools (RCOTOOLS), is being developed to facilitate incorporating key rotorcraft conceptual design codes into optimizations using the OpenMDAO multi-disciplinary optimization framework written in Python. RCOTOOLS, also written in Python, currently supports the incorporation of the NASA Design and Analysis of RotorCraft (NDARC) vehicle sizing tool and the Comprehensive Analytical Model of Rotorcraft Aerodynamics and Dynamics II (CAMRAD II) analysis tool into OpenMDAO-driven optimizations. Both of these tools use detailed, file-based inputs and outputs, so RCOTOOLS provides software wrappers to update input files with new design variable values, execute these codes and then extract specific response variable values from the file outputs. These wrappers are designed to be flexible and easy to use. RCOTOOLS also provides several utilities to aid in optimization model development, including Graphical User Interface (GUI) tools for browsing input and output files in order to identify text strings that are used to identify specific variables as optimization input and response variables. This paper provides an overview of RCOTOOLS and its use

High Performance Systolic Array Core Architecture Design for DNA Sequencer

Directory of Open Access Journals (Sweden)

Saiful Nurdin Dayana

2018-01-01

Full Text Available This paper presents a high performance systolic array (SA core architecture design for Deoxyribonucleic Acid (DNA sequencer. The core implements the affine gap penalty score Smith-Waterman (SW algorithm. This time-consuming local alignment algorithm guarantees optimal alignment between DNA sequences, but it requires quadratic computation time when performed on standard desktop computers. The use of linear SA decreases the time complexity from quadratic to linear. In addition, with the exponential growth of DNA databases, the SA architecture is used to overcome the timing issue. In this work, the SW algorithm has been captured using Verilog Hardware Description Language (HDL and simulated using Xilinx ISIM simulator. The proposed design has been implemented in Xilinx Virtex -6 Field Programmable Gate Array (FPGA and improved in the core area by 90% reduction.

LAVENDER: A steady-state core analysis code for design studies of accelerator driven subcritical reactors

Energy Technology Data Exchange (ETDEWEB)

Zhou, Shengcheng; Wu, Hongchun; Cao, Liangzhi; Zheng, Youqi, E-mail: yqzheng@mail.xjtu.edu.cn; Huang, Kai; He, Mingtao; Li, Xunzhao

2014-10-15

Highlights: • A new code system for design studies of accelerator driven subcritical reactors (ADSRs) is developed. • S{sub N} transport solver in triangular-z meshes, fine deletion analysis and multi-channel thermal-hydraulics analysis are coupled in the code. • Numerical results indicate that the code is reliable and efficient for design studies of ADSRs. - Abstract: Accelerator driven subcritical reactors (ADSRs) have been proposed and widely investigated for the transmutation of transuranics (TRUs). ADSRs have several special characteristics, such as the subcritical core driven by spallation neutrons, anisotropic neutron flux distribution and complex geometry etc. These bring up requirements for development or extension of analysis codes to perform design studies. A code system named LAVENDER has been developed in this paper. It couples the modules for spallation target simulation and subcritical core analysis. The neutron transport-depletion calculation scheme is used based on the homogenized cross section from assembly calculations. A three-dimensional S{sub N} nodal transport code based on triangular-z meshes is employed and a multi-channel thermal-hydraulics analysis model is integrated. In the depletion calculation, the evolution of isotopic composition in the core is evaluated using the transmutation trajectory analysis algorithm (TTA) and fine depletion chains. The new code is verified by several benchmarks and code-to-code comparisons. Numerical results indicate that LAVENDER is reliable and efficient to be applied for the steady-state analysis and reactor core design of ADSRs.

Joint beam design and user selection over non-binary coded MIMO interference channel

Science.gov (United States)

Li, Haitao; Yuan, Haiying

2013-03-01

In this paper, we discuss the problem of sum rate improvement for coded MIMO interference system, and propose joint beam design and user selection over interference channel. Firstly, we have formulated non-binary LDPC coded MIMO interference networks model. Then, the least square beam design for MIMO interference system is derived, and the low complexity user selection is presented. Simulation results confirm that the sum rate can be improved by the joint user selection and beam design comparing with single interference aligning beamformer.

Altruistic functions for selfish DNA.

Science.gov (United States)

Faulkner, Geoffrey J; Carninci, Piero

2009-09-15

Mammalian genomes are comprised of 30-50% transposed elements (TEs). The vast majority of these TEs are truncated and mutated fragments of retrotransposons that are no longer capable of transposition. Although initially regarded as important factors in the evolution of gene regulatory networks, TEs are now commonly perceived as neutrally evolving and non-functional genomic elements. In a major development, recent works have strongly contradicted this "selfish DNA" or "junk DNA" dogma by demonstrating that TEs use a host of novel promoters to generate RNA on a massive scale across most eukaryotic cells. This transcription frequently functions to control the expression of protein-coding genes via alternative promoters, cis regulatory non protein-coding RNAs and the formation of double stranded short RNAs. If considered in sum, these findings challenge the designation of TEs as selfish and neutrally evolving genomic elements. Here, we will expand upon these themes and discuss challenges in establishing novel TE functions in vivo.

Free-space optical code-division multiple-access system design

Science.gov (United States)

Jeromin, Lori L.; Kaufmann, John E.; Bucher, Edward A.

1993-08-01

This paper describes an optical direct-detection multiple access communications system for free-space satellite networks utilizing code-division multiple-access (CDMA) and forward error correction (FEC) coding. System performance is characterized by how many simultaneous users operating at data rate R can be accommodated in a signaling bandwidth W. The performance of two CDMA schemes, optical orthogonal codes (OOC) with FEC and orthogonal convolutional codes (OCC), is calculated and compared to information-theoretic capacity bounds. The calculations include the effects of background and detector noise as well as nonzero transmitter extinction ratio and power imbalance among users. A system design for 10 kbps multiple-access communications between low-earth orbit satellites is given. With near- term receiver technology and representative system losses, a 15 W peak-power transmitter provides 10-6 BER performance with seven interfering users and full moon background in the receiver FOV. The receiver employs an array of discrete wide-area avalanche photodiodes (APD) for wide field of view coverage. Issues of user acquisition and synchronization, implementation technology, and system scalability are also discussed.

Ube2V2 Is a Rosetta Stone Bridging Redox and Ubiquitin Codes, Coordinating DNA Damage Responses.

Science.gov (United States)

Zhao, Yi; Long, Marcus J C; Wang, Yiran; Zhang, Sheng; Aye, Yimon

2018-02-28

Posttranslational modifications (PTMs) are the lingua franca of cellular communication. Most PTMs are enzyme-orchestrated. However, the reemergence of electrophilic drugs has ushered mining of unconventional/non-enzyme-catalyzed electrophile-signaling pathways. Despite the latest impetus toward harnessing kinetically and functionally privileged cysteines for electrophilic drug design, identifying these sensors remains challenging. Herein, we designed "G-REX"-a technique that allows controlled release of reactive electrophiles in vivo. Mitigating toxicity/off-target effects associated with uncontrolled bolus exposure, G-REX tagged first-responding innate cysteines that bind electrophiles under true k cat / K m conditions. G-REX identified two allosteric ubiquitin-conjugating proteins-Ube2V1/Ube2V2-sharing a novel privileged-sensor-cysteine. This non-enzyme-catalyzed-PTM triggered responses specific to each protein. Thus, G-REX is an unbiased method to identify novel functional cysteines. Contrasting conventional active-site/off-active-site cysteine-modifications that regulate target activity, modification of Ube2V2 allosterically hyperactivated its enzymatically active binding-partner Ube2N, promoting K63-linked client ubiquitination and stimulating H2AX-dependent DNA damage response. This work establishes Ube2V2 as a Rosetta-stone bridging redox and ubiquitin codes to guard genome integrity.

Wind-induced transmission tower foundation loads. A field study-design code comparison

Energy Technology Data Exchange (ETDEWEB)

Savory, E. [Department of Mechanical and Materials Engineering, University of Western Ontario, London, Ont. (Canada); Parke, G.A.R.; Disney, P.; Toy, N. [School of Engineering, University of Surrey, Guildford, Surrey GU2 7XH (United Kingdom)

2008-06-15

This paper presents a comparison between the wind-induced foundation loads measured on a type L6 transmission line tower during a field study in the UK and those computed using the UK Code of Practice for lattice tower and transmission line design (BS8100). In this work, the Code provisions have been generalised to give the wind-induced strain in each of the tower legs immediately above the foundation as a function of wind direction and wind speed at the top of the tower. The complete data set from the field monitoring has been decomposed to provide a similar formulation for comparison purposes. The analysis shows excellent agreement between the Code calculations and the measured results, within the overall accuracy of the field data. This indicates that, at least for the tower type examined here, the existing design Code provides a reliable transformation of the local wind speed at the top of the tower into tension and compression loads on the foundations. (author)

User's manual for the Heat Pipe Space Radiator design and analysis Code (HEPSPARC)

Science.gov (United States)

Hainley, Donald C.

1991-01-01

A heat pipe space radiatior code (HEPSPARC), was written for the NASA Lewis Research Center and is used for the design and analysis of a radiator that is constructed from a pumped fluid loop that transfers heat to the evaporative section of heat pipes. This manual is designed to familiarize the user with this new code and to serve as a reference for its use. This manual documents the completed work and is intended to be the first step towards verification of the HEPSPARC code. Details are furnished to provide a description of all the requirements and variables used in the design and analysis of a combined pumped loop/heat pipe radiator system. A description of the subroutines used in the program is furnished for those interested in understanding its detailed workings.

Analysis and Design of a Fiber-optic Probe for DNA Sensors Final Report CRADA No. TSB-1147-95

Energy Technology Data Exchange (ETDEWEB)

Molau, Nicole [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Vail, Curtis [Accu.Photonics, Inc., Ann Arbor, MI (United States)

2018-01-24

In 1995, a challenge in the field of genetics dealt with the acquisition of efficient DNA sequencing techniques for reading the 3 billion base-pairs that comprised the human genome. AccuPhotonics, Inc. proposed to develop and manufacture a state-of-the-art near-field scanning optical microscopy (NSOM) fiber-optic probe that was expected to increase probe efficiency by two orders of magnitude over the existing state-of-the-art and to improve resolution to 10Å. The detailed design calculation and optimization of electrical properties of the fiber-optic probe tip geometry would be performed at LLNL, using existing finite-difference time-domain (FDTD) electromagnetic (EM) codes.

Error floor behavior study of LDPC codes for concatenated codes design

Science.gov (United States)

Chen, Weigang; Yin, Liuguo; Lu, Jianhua

2007-11-01

Error floor behavior of low-density parity-check (LDPC) codes using quantized decoding algorithms is statistically studied with experimental results on a hardware evaluation platform. The results present the distribution of the residual errors after decoding failure and reveal that the number of residual error bits in a codeword is usually very small using quantized sum-product (SP) algorithm. Therefore, LDPC code may serve as the inner code in a concatenated coding system with a high code rate outer code and thus an ultra low error floor can be achieved. This conclusion is also verified by the experimental results.

Designing Uniquely Addressable Bio-orthogonal Synthetic Scaffolds for DNA and RNA Origami.

Science.gov (United States)

Kozyra, Jerzy; Ceccarelli, Alessandro; Torelli, Emanuela; Lopiccolo, Annunziata; Gu, Jing-Ying; Fellermann, Harold; Stimming, Ulrich; Krasnogor, Natalio

2017-07-21

Nanotechnology and synthetic biology are rapidly converging, with DNA origami being one of the leading bridging technologies. DNA origami was shown to work well in a wide array of biotic environments. However, the large majority of extant DNA origami scaffolds utilize bacteriophages or plasmid sequences thus severely limiting its future applicability as a bio-orthogonal nanotechnology platform. In this paper we present the design of biologically inert (i.e., "bio-orthogonal") origami scaffolds. The synthetic scaffolds have the additional advantage of being uniquely addressable (unlike biologically derived ones) and hence are better optimized for high-yield folding. We demonstrate our fully synthetic scaffold design with both DNA and RNA origamis and describe a protocol to produce these bio-orthogonal and uniquely addressable origami scaffolds.

Benchmarking of the PHOENIX-P/ANC [Advanced Nodal Code] advanced nuclear design system

International Nuclear Information System (INIS)

Nguyen, T.Q.; Liu, Y.S.; Durston, C.; Casadei, A.L.

1988-01-01

At Westinghouse, an advanced neutronic methods program was designed to improve the quality of the predictions, enhance flexibility in designing advanced fuel and related products, and improve design lead time. Extensive benchmarking data is presented to demonstrate the accuracy of the Advanced Nodal Code (ANC) and the PHOENIX-P advanced lattice code. Qualification data to demonstrate the accuracy of ANC include comparison of key physics parameters against a fine-mesh diffusion theory code, TORTISE. Benchmarking data to demonstrate the validity of the PHOENIX-P methodologies include comparison of physics predictions against critical experiments, isotopics measurements and measured power distributions from spatial criticals. The accuracy of the PHOENIX-P/ANC Advanced Design System is demonstrated by comparing predictions of hot zero power physics parameters and hot full power core follow against measured data from operating reactors. The excellent performance of this system for a broad range of comparisons establishes the basis for implementation of these tools for core design, licensing and operational follow of PWR [pressurized water reactor] cores at Westinghouse

Contributions of the ORNL piping program to nuclear piping design codes and standards

International Nuclear Information System (INIS)

Moore, S.E.

1975-11-01

The ORNL Piping Program was conceived and established to develop basic information on the structural behavior of nuclear power plant piping components and to prepare this information in forms suitable for use in design analysis and codes and standards. One of the objectives was to develop and qualify stress indices and flexibility factors for direct use in Code-prescribed design analysis methods. Progress in this area is described

Principles of DNA architectonics: design of DNA-based nanoobjects

International Nuclear Information System (INIS)

Vinogradova, O A; Pyshnyi, D V

2012-01-01

The methods of preparation of monomeric DNA blocks that serve as key building units for the construction of complex DNA objects are described. Examples are given of the formation of DNA blocks based on native and modified oligonucleotide components using hydrogen bonding and nucleic acid-specific types of bonding and also some affinity interactions with RNA, proteins, ligands. The static discrete and periodic two- and three-dimensional DNA objects reported to date are described systematically. Methods used to prove the structures of DNA objects and the prospects for practical application of nanostructures based on DNA and its analogues in biology, medicine and biophysics are considered. The bibliography includes 195 references.

The development, qualification and availability of AECL analytical, scientific and design codes

International Nuclear Information System (INIS)

Kupferschmidt, W.C.H.; Fehrenbach, P.J.; Wolgemuth, G.A.; McDonald, B.H.; Snell, V.G.

2001-01-01

Over the past several years, AECL has embarked on a comprehensive program to develop, qualify and support its key safety and licensing codes, and to make executable versions of these codes available to the international nuclear community. To this end, we have instituted a company-wide Software Quality Assurance (SQA) Program for Analytical, Scientific and Design Computer Programs to ensure that the design, development, maintenance, modification, procurement and use of computer codes within AECL is consistent with today's quality assurance standards. In addition, we have established a comprehensive Code Validation Project (CVP) with the goal of qualifying AECL's 'front-line' safety and licensing codes by 2001 December. The outcome of this initiative will be qualified codes, which are properly verified and validated for the expected range of applications, with associated statements of accuracy and uncertainty for each application. The code qualification program, based on the CSA N286.7 standard, is intended to ensure (1) that errors are not introduced into safety analyses because of deficiencies in the software, (2) that an auditable documentation base is assembled that demonstrates to the regulator that the codes are of acceptable quality, and (3) that these codes are formally qualified for their intended applications. Because AECL and the Canadian nuclear utilities (i.e., Ontario Power Generation, Bruce Power, Hydro Quebec and New Brunswick Power) generally use the same safety and licensing codes, the nuclear industry in Canada has agreed to work cooperatively together towards the development, qualification and maintenance of a common set of analysis tools, referred to as the Industry Standard Toolset (IST). This paper provides an overview of the AECL Software Quality Assurance Program and the Code Validation Project, and their associated linkages to the Canadian nuclear community's Industry Standard Toolset initiative to cooperatively qualify and support commonly

A coupled systems code-CFD MHD solver for fusion blanket design

Energy Technology Data Exchange (ETDEWEB)

Wolfendale, Michael J., E-mail: m.wolfendale11@imperial.ac.uk; Bluck, Michael J.

2015-10-15

Highlights: • A coupled systems code-CFD MHD solver for fusion blanket applications is proposed. • Development of a thermal hydraulic systems code with MHD capabilities is detailed. • A code coupling methodology based on the use of TCP socket communications is detailed. • Validation cases are briefly discussed for the systems code and coupled solver. - Abstract: The network of flow channels in a fusion blanket can be modelled using a 1D thermal hydraulic systems code. For more complex components such as junctions and manifolds, the simplifications employed in such codes can become invalid, requiring more detailed analyses. For magnetic confinement reactor blanket designs using a conducting fluid as coolant/breeder, the difficulties in flow modelling are particularly severe due to MHD effects. Blanket analysis is an ideal candidate for the application of a code coupling methodology, with a thermal hydraulic systems code modelling portions of the blanket amenable to 1D analysis, and CFD providing detail where necessary. A systems code, MHD-SYS, has been developed and validated against existing analyses. The code shows good agreement in the prediction of MHD pressure loss and the temperature profile in the fluid and wall regions of the blanket breeding zone. MHD-SYS has been coupled to an MHD solver developed in OpenFOAM and the coupled solver validated for test geometries in preparation for modelling blanket systems.

Sub-10 nm patterning with DNA nanostructures: a short perspective

Science.gov (United States)

Du, Ke; Park, Myeongkee; Ding, Junjun; Hu, Huan; Zhang, Zheng

2017-11-01

DNA is the hereditary material that contains our unique genetic code. Since the first demonstration of two-dimensional (2D) nanopatterns by using designed DNA origami ˜10 years ago, DNA has evolved into a novel technique for 2D and 3D nanopatterning. It is now being used as a template for the creation of sub-10 nm structures via either ‘top-down’ or ‘bottom-up’ approaches for various applications spanning from nanoelectronics, plasmonic sensing, and nanophotonics. This perspective starts with an histroric overview and discusses the current state-of-the-art in DNA nanolithography. Emphasis is put on the challenges and prospects of DNA nanolithography as the next generation nanomanufacturing technique.

Code on the safety of nuclear power plants: Design

International Nuclear Information System (INIS)

1988-01-01

This Code is a compilation of nuclear safety principles aimed at defining the essential requirements necessary to ensure nuclear safety. These requirements are applicable to structures, systems and components, and procedures important to safety in nuclear power plants embodying thermal neutron reactors, with emphasis on what safety requirements shall be met rather than on specifying how these requirements can be met. It forms part of the Agency's programme for establishing Codes and Safety Guides relating to land based stationary thermal neutron power plants. The document should be used by organizations designing, manufacturing, constructing and operating nuclear power plants as well as by regulatory bodies

Exploring the Feasibility of a DNA Computer: Design of an ALU Using Sticker-Based DNA Model.

Science.gov (United States)

Sarkar, Mayukh; Ghosal, Prasun; Mohanty, Saraju P

2017-09-01

Since its inception, DNA computing has advanced to offer an extremely powerful, energy-efficient emerging technology for solving hard computational problems with its inherent massive parallelism and extremely high data density. This would be much more powerful and general purpose when combined with other existing well-known algorithmic solutions that exist for conventional computing architectures using a suitable ALU. Thus, a specifically designed DNA Arithmetic and Logic Unit (ALU) that can address operations suitable for both domains can mitigate the gap between these two. An ALU must be able to perform all possible logic operations, including NOT, OR, AND, XOR, NOR, NAND, and XNOR; compare, shift etc., integer and floating point arithmetic operations (addition, subtraction, multiplication, and division). In this paper, design of an ALU has been proposed using sticker-based DNA model with experimental feasibility analysis. Novelties of this paper may be in manifold. First, the integer arithmetic operations performed here are 2s complement arithmetic, and the floating point operations follow the IEEE 754 floating point format, resembling closely to a conventional ALU. Also, the output of each operation can be reused for any next operation. So any algorithm or program logic that users can think of can be implemented directly on the DNA computer without any modification. Second, once the basic operations of sticker model can be automated, the implementations proposed in this paper become highly suitable to design a fully automated ALU. Third, proposed approaches are easy to implement. Finally, these approaches can work on sufficiently large binary numbers.

MASTER- an indigenous nuclear design code of KAERI

International Nuclear Information System (INIS)

Cho, Byung Oh; Lee, Chang Ho; Park, Chan Oh; Lee, Chong Chul

1996-01-01

KAERI has recently developed the nuclear design code MASTER for the application to reactor physics analyses for pressurized water reactors. Its neutronics model solves the space-time dependent neutron diffusion equations with the advanced nodal methods. The major calculation categories of MASTER consist of microscopic depletion, steady-state and transient solution, xenon dynamics, adjoint solution and pin power and burnup reconstruction. The MASTER validation analyses, which are in progress aiming to submit the Uncertainty Topical Report to KINS in the first half of 1996, include global reactivity calculations and detailed pin-by-pin power distributions as well as in-core detector reaction rate calculations. The objective of this paper is to give an overall description of the CASMO/MASTER code system whose verification results are in details presented in the separate papers

Second International Workshop on Software Engineering and Code Design in Parallel Meteorological and Oceanographic Applications

Science.gov (United States)

OKeefe, Matthew (Editor); Kerr, Christopher L. (Editor)

1998-01-01

This report contains the abstracts and technical papers from the Second International Workshop on Software Engineering and Code Design in Parallel Meteorological and Oceanographic Applications, held June 15-18, 1998, in Scottsdale, Arizona. The purpose of the workshop is to bring together software developers in meteorology and oceanography to discuss software engineering and code design issues for parallel architectures, including Massively Parallel Processors (MPP's), Parallel Vector Processors (PVP's), Symmetric Multi-Processors (SMP's), Distributed Shared Memory (DSM) multi-processors, and clusters. Issues to be discussed include: (1) code architectures for current parallel models, including basic data structures, storage allocation, variable naming conventions, coding rules and styles, i/o and pre/post-processing of data; (2) designing modular code; (3) load balancing and domain decomposition; (4) techniques that exploit parallelism efficiently yet hide the machine-related details from the programmer; (5) tools for making the programmer more productive; and (6) the proliferation of programming models (F--, OpenMP, MPI, and HPF).

Feasibility Study of Core Design with a Monte Carlo Code for APR1400 Initial core

Energy Technology Data Exchange (ETDEWEB)

Kim, Jinsun; Chang, Do Ik; Seong, Kibong [KEPCO NF, Daejeon (Korea, Republic of)

2014-10-15

The Monte Carlo calculation becomes more popular and useful nowadays due to the rapid progress in computing power and parallel calculation techniques. There have been many attempts to analyze a commercial core by Monte Carlo transport code using the enhanced computer capability, recently. In this paper, Monte Carlo calculation of APR1400 initial core has been performed and the results are compared with the calculation results of conventional deterministic code to find out the feasibility of core design using Monte Carlo code. SERPENT, a 3D continuous-energy Monte Carlo reactor physics burnup calculation code is used for this purpose and the KARMA-ASTRA code system, which is used for a deterministic code of comparison. The preliminary investigation for the feasibility of commercial core design with Monte Carlo code was performed in this study. Simplified core geometry modeling was performed for the reactor core surroundings and reactor coolant model is based on two region model. The reactivity difference at HZP ARO condition between Monte Carlo code and the deterministic code is consistent with each other and the reactivity difference during the depletion could be reduced by adopting the realistic moderator temperature. The reactivity difference calculated at HFP, BOC, ARO equilibrium condition was 180 ±9 pcm, with axial moderator temperature of a deterministic code. The computing time will be a significant burden at this time for the application of Monte Carlo code to the commercial core design even with the application of parallel computing because numerous core simulations are required for actual loading pattern search. One of the remedy will be a combination of Monte Carlo code and the deterministic code to generate the physics data. The comparison of physics parameters with sophisticated moderator temperature modeling and depletion will be performed for a further study.

Uncertainties in calculations of nuclear design code system for the high temperature engineering test reactor (HTTR)

International Nuclear Information System (INIS)

Shindo, R.; Yamashita, K.; Murata, I.

1991-01-01

The nuclear design code system for the HTTR consists of one dimensional cell burnup computer code, developed in JAERI and the TWOTRAN-2 transport code. In order to satisfy related design criteria, uncertainty of the calculation was investigated by comparing the calculated and experimental results. The experiments were performed with a graphite moderated critical assembly. It was confirmed that discrepancies between calculations and experiments were small enough to be allowed in the nuclear design of HTTR. 8 refs, 6 figs

Code Development for Control Design Applications: Phase I: Structural Modeling

International Nuclear Information System (INIS)

Bir, G. S.; Robinson, M.

1998-01-01

The design of integrated controls for a complex system like a wind turbine relies on a system model in an explicit format, e.g., state-space format. Current wind turbine codes focus on turbine simulation and not on system characterization, which is desired for controls design as well as applications like operating turbine model analysis, optimal design, and aeroelastic stability analysis. This paper reviews structural modeling that comprises three major steps: formation of component equations, assembly into system equations, and linearization

Designing thermal diode and heat pump based on DNA nanowire: Multifractal approach

Energy Technology Data Exchange (ETDEWEB)

Behnia, S., E-mail: s.behnia@iaurmia.ac.ir; Panahinia, R.

2017-07-12

The management of heat flow in DNA nano wire was considered. Thermal diode effect in DNA and the domain of its appearance dependent to system parameters have been detected. The appearance of directed thermal flow in thermodynamic sizes proposes the possibility of designing the macroscopic thermal rectifier. By applying driven force, pumping effect has been also observed. The resonance frequency of DNA and threshold amplitudes of driving force for attaining permanent pumping effect have been detected. Forasmuch as detecting negative differential thermal resistance (NDTR) phenomenon, DNA can act as a thermal transistor. By using an analytical parallel investigation based on Rényi spectrum analysis, threshold values to transition to NDTR and pumping regimes have been detected. - Highlights: • The control and management of heat current in DNA have been investigated. • Directed thermal flow and NDTR in DNA have been identified. • By increasing the system size, the reversed thermal rectification appeared. So, it is proposed the possibility of designing the macroscopic thermal rectifier. • Pumping effect accompanied with detection of resonance frequency of DNA has been observed. • To verify the results, we did a parallel analysis based on multifractal concept to detect threshold values for transition to pumping state and NDTR regime.

Effect of URM infills on seismic vulnerability of Indian code designed RC frame buildings

Science.gov (United States)

Haldar, Putul; Singh, Yogendra; Paul, D. K.

2012-03-01

Unreinforced Masonry (URM) is the most common partitioning material in framed buildings in India and many other countries. Although it is well-known that under lateral loading the behavior and modes of failure of the frame buildings change significantly due to infill-frame interaction, the general design practice is to treat infills as nonstructural elements and their stiffness, strength and interaction with the frame is often ignored, primarily because of difficulties in simulation and lack of modeling guidelines in design codes. The Indian Standard, like many other national codes, does not provide explicit insight into the anticipated performance and associated vulnerability of infilled frames. This paper presents an analytical study on the seismic performance and fragility analysis of Indian code-designed RC frame buildings with and without URM infills. Infills are modeled as diagonal struts as per ASCE 41 guidelines and various modes of failure are considered. HAZUS methodology along with nonlinear static analysis is used to compare the seismic vulnerability of bare and infilled frames. The comparative study suggests that URM infills result in a significant increase in the seismic vulnerability of RC frames and their effect needs to be properly incorporated in design codes.

The integrated code system CASCADE-3D for advanced core design and safety analysis

International Nuclear Information System (INIS)

Neufert, A.; Van de Velde, A.

1999-01-01

The new program system CASCADE-3D (Core Analysis and Safety Codes for Advanced Design Evaluation) links some of Siemens advanced code packages for in-core fuel management and accident analysis: SAV95, PANBOX/COBRA and RELAP5. Consequently by using CASCADE-3D the potential of modern fuel assemblies and in-core fuel management strategies can be much better utilized because safety margins which had been reduced due to conservative methods are now predicted more accurately. By this innovative code system the customers can now take full advantage of the recent progress in fuel assembly design and in-core fuel management.(author)

The applicability of ALPHA/PHOENIX/ANC nuclear design code system on Korean standard PWR's

International Nuclear Information System (INIS)

Lee, Kookjong; Choi, Kie-Yong; Lee, Hae-Chan; Roh, Eun-Rae

1996-01-01

For the Korean Standard Nuclear Power Plant (KSNPP) designed based on Combustion Engineering (CE) System 80, the Westinghouse nuclear design code system ALPHA/PHOENIX/ANC was applied to the follow-up design of initial and reload core of KSNPP. The follow-up design results of Yonggwang Unit 3 Cycle 1, 2 and Yonggwang Unit 4 Cycle 1 have shown good agreements with the measured data. The assemblywise power distributions have shown less than 2% average differences and critical boron concentrations have shown less than 20 ppm differences. All the low power physics test parameters are in good agreement. Consequently, APA design code system can be applied to KNSPP cores. (author)

Fuel management and core design code systems for pressurized water reactor neutronic calculations

International Nuclear Information System (INIS)

Ahnert, C.; Arayones, J.M.

1985-01-01

A package of connected code systems for the neutronic calculations relevant in fuel management and core design has been developed and applied for validation to the startup tests and first operating cycle of a 900MW (electric) PWR. The package includes the MARIA code system for the modeling of the different types of PWR fuel assemblies, the CARMEN code system for detailed few group diffusion calculations for PWR cores at operating and burnup conditions, and the LOLA code system for core simulation using onegroup nodal theory parameters explicitly calculated from the detailed solutions

MUP, CEC-DES, STRADE. Codes for uncertainty propagation, experimental design and stratified random sampling techniques

International Nuclear Information System (INIS)

Amendola, A.; Astolfi, M.; Lisanti, B.

1983-01-01

The report describes the how-to-use of the codes: MUP (Monte Carlo Uncertainty Propagation) for uncertainty analysis by Monte Carlo simulation, including correlation analysis, extreme value identification and study of selected ranges of the variable space; CEC-DES (Central Composite Design) for building experimental matrices according to the requirements of Central Composite and Factorial Experimental Designs; and, STRADE (Stratified Random Design) for experimental designs based on the Latin Hypercube Sampling Techniques. Application fields, of the codes are probabilistic risk assessment, experimental design, sensitivity analysis and system identification problems

Designing Optical Properties in DNA-Programmed Nanoparticle Superlattices

Science.gov (United States)

Ross, Michael Brendan

A grand challenge of modern science has been the ability to predict and design the properties of new materials. This approach to the a priori design of materials presents a number of challenges including: predictable properties of the material building blocks, a programmable means for arranging such building blocks into well understood architectures, and robust models that can predict the properties of these new materials. In this dissertation, we present a series of studies that describe how optical properties in DNA-programmed nanoparticle superlattices can be predicted prior to their synthesis. The first chapter provides a history and introduction to the study of metal nanoparticle arrays. Chapter 2 surveys and compares several geometric models and electrodynamics simulations with the measured optical properties of DNA-nanoparticle superlattices. Chapter 3 describes silver nanoparticle superlattices (rather than gold) and identifies their promise as plasmonic metamaterials. In chapter 4, the concept of plasmonic metallurgy is introduced, whereby it is demonstrated that concepts from materials science and metallurgy can be applied to the optical properties of mixed metallic plasmonic materials, unveiling rich and tunable optical properties such as color and asymmetric reflectivity. Chapter 5 presents a comprehensive theoretical exploration of anisotropy (non-spherical) in nanoparticle superlattice architectures. The role of anisotropy is discussed both on the nanoscale, where several desirable metamaterial properties can be tuned from the ultraviolet to near-infrared, and on the mesoscale, where the size and shape of a superlattice is demonstrated to have a pronounced effect on the observed far-field optical properties. Chapter 6 builds upon those theoretical data presented in chapter 5, including the experimental realization of size and shape dependent properties in DNA-programmed superlattices. Specifically, nanoparticle spacing is explored as a parameter that

An Examination of the Performance Based Building Code on the Design of a Commercial Building

Directory of Open Access Journals (Sweden)

John Greenwood

2012-11-01

Full Text Available The Building Code of Australia (BCA is the principal code under which building approvals in Australia are assessed. The BCA adopted performance-based solutions for building approvals in 1996. Performance-based codes are based upon a set of explicit objectives, stated in terms of a hierarchy of requirements beginning with key general objectives. With this in mind, the research presented in this paper aims to analyse the impact of the introduction of the performance-based code within Western Australia to gauge the effect and usefulness of alternative design solutions in commercial construction using a case study project. The research revealed that there are several advantages to the use of alternative designs and that all parties, in general, are in favour of the performance-based building code of Australia. It is suggested that change in the assessment process to streamline the alternative design path is needed for the greater use of the performance-based alternative. With appropriate quality control measures, minor variations to the deemed-to-satisfy provisions could easily be managed by the current and future building surveying profession.

Development of intelligent code system to support conceptual design of nuclear reactor core

International Nuclear Information System (INIS)

Kugo, Teruhiko; Nakagawa, Masayuki; Tsuchihashi, Keichiro

1997-01-01

An intelligent reactor design system IRDS has been developed to support conceptual design of new type reactor cores in the fields of neutronics, thermal-hydraulics and fuel behavior. The features of IRDS are summarized as follows: 1) a variety of computer codes to cover various design tasks relevant to 'static' and 'burnup' problems are implemented, 2) all the information necessary to the codes implemented is unified in a data base, 3) several data and knowledge bases are referred to in order to proceed design process efficiently for non-expert users, 4) advanced man-machine interface to communicate with the system through an interactive and graphical user interface is equipped and 5) a function to search automatically a design window, which is defined as a feasible parameter range to satisfy design requirement and criteria is employed to support the optimization or satisfication process. Applicability and productivity of the system are demonstrated by the design study of fuel pin for new type FBR cores. (author)

About the application of MCNP4 code in nuclear reactor core design calculations

International Nuclear Information System (INIS)

Svarny, J.

2000-01-01

This paper provides short review about application of MCNP code for reactor physics calculations performed in SKODA JS. Problems of criticality safety analysis of spent fuel systems for storage and transport of spent fuel are discussed and relevant applications are presented. Application of standard Monte Carlo code for accelerator driven system for LWR waste destruction is shown and conclusions are reviewed. Specific heterogeneous effects in neutron balance of WWER nuclear cores are solved for adjusting standard design codes. (Authors)

Dual-camera design for coded aperture snapshot spectral imaging.

Science.gov (United States)

Wang, Lizhi; Xiong, Zhiwei; Gao, Dahua; Shi, Guangming; Wu, Feng

2015-02-01

Coded aperture snapshot spectral imaging (CASSI) provides an efficient mechanism for recovering 3D spectral data from a single 2D measurement. However, since the reconstruction problem is severely underdetermined, the quality of recovered spectral data is usually limited. In this paper we propose a novel dual-camera design to improve the performance of CASSI while maintaining its snapshot advantage. Specifically, a beam splitter is placed in front of the objective lens of CASSI, which allows the same scene to be simultaneously captured by a grayscale camera. This uncoded grayscale measurement, in conjunction with the coded CASSI measurement, greatly eases the reconstruction problem and yields high-quality 3D spectral data. Both simulation and experimental results demonstrate the effectiveness of the proposed method.

Codon and amino-acid distribution in DNA

International Nuclear Information System (INIS)

Kim, J.K.; Yang, S.I.; Kwon, Y.H.; Lee, E.I.

2005-01-01

According to the Zipf's law, the distribution of rank-ordered frequency of words in the natural language can be modelled on the power law. In this paper, we examine the frequency distribution of 64 codons over the coding and non-coding regions of 88 DNA from EMBL and GenBank database, using exponential fitting. Also, we regard 20 amino-acids as vocabulary, perform the same frequency analysis to the same database and show that amino-acids can be used as biological meaningful words for Zipf's approach. Our analysis suggests that a natural language structure may exist not only in the coding region of DNA but in the non-coding one of DNA

Design codes for gas cooled reactor components

International Nuclear Information System (INIS)

1990-12-01

High-temperature gas-cooled reactor (HTGR) plants have been under development for about 30 years and experimental and prototype plants have been operated. The main line of development has been electricity generation based on the steam cycle. In addition the potential for high primary coolant temperature has resulted in research and development programmes for advanced applications including the direct cycle gas turbine and process heat applications. In order to compare results of the design techniques of various countries for high temperature reactor components, the IAEA established a Co-ordinated Research Programme (CRP) on Design Codes for Gas-Cooled Reactor Components. The Federal Republic of Germany, Japan, Switzerland and the USSR participated in this Co-ordinated Research Programme. Within the frame of this CRP a benchmark problem was established for the design of the hot steam header of the steam generator of an HTGR for electricity generation. This report presents the results of that effort. The publication also contains 5 reports presented by the participants. A separate abstract was prepared for each of these reports. Refs, figs and tabs

Analysis of the Current Technical Issues on ASME Code and Standard for Nuclear Mechanical Design(2009)

International Nuclear Information System (INIS)

Koo, Gyeong Hoi; Lee, B. S.; Yoo, S. H.

2009-11-01

This report describes the analysis on the current revision movement related to the mechanical design issues of the U.S ASME nuclear code and standard. ASME nuclear mechanical design in this report is composed of the nuclear material, primary system, secondary system and high temperature reactor. This report includes the countermeasures based on the ASME Code meeting for current issues of each major field. KAMC(ASME Mirror Committee) of this project is willing to reflect a standpoint of the domestic nuclear industry on ASME nuclear mechanical design and play a technical bridge role for the domestic nuclear industry in ASME Codes application

Analysis of the Current Technical Issues on ASME Code and Standard for Nuclear Mechanical Design(2009)

Energy Technology Data Exchange (ETDEWEB)

Koo, Gyeong Hoi; Lee, B. S.; Yoo, S. H.

2009-11-15

This report describes the analysis on the current revision movement related to the mechanical design issues of the U.S ASME nuclear code and standard. ASME nuclear mechanical design in this report is composed of the nuclear material, primary system, secondary system and high temperature reactor. This report includes the countermeasures based on the ASME Code meeting for current issues of each major field. KAMC(ASME Mirror Committee) of this project is willing to reflect a standpoint of the domestic nuclear industry on ASME nuclear mechanical design and play a technical bridge role for the domestic nuclear industry in ASME Codes application

Consideration of creep in design rules of AFCEN RCC-MRx 2012 code

International Nuclear Information System (INIS)

Lebarbe, T.; Petesch, C.; Lejeail, Y.; Lamagnere, P.; Dubiez-Le Goff, S.

2014-01-01

The 2012 edition of the RCC-MRx Code has been issued in French and English versions by AFCEN (Association Francaise pour les regles de Conception et de Construction des Materiels des Chaudieres Electro-nucleaires). This Code is the result of the merger of the RCC-MX 2008 developed in the context of the research reactor Jules Horowitz Reactor project, in the RCC-MR 2007 which set up rules applicable to the design of components operating at high temperature and to the Vacuum Vessel of ITER. This new edition is the opportunity to publish also the background of the rules. This paper is one illustration of what may be such a document, on a dedicated example, the creep rules. It contains an overview of the design rules associated to the creep damage and explains the purpose and the origins of these rules. This type of exercise is going to be generalized to all the parts of the code in AFCEN technical publications, the criteria. (authors)

Intricate and Cell Type-Specific Populations of Endogenous Circular DNA (eccDNA) in Caenorhabditis elegans and Homo sapiens.

Science.gov (United States)

Shoura, Massa J; Gabdank, Idan; Hansen, Loren; Merker, Jason; Gotlib, Jason; Levene, Stephen D; Fire, Andrew Z

2017-10-05

Investigations aimed at defining the 3D configuration of eukaryotic chromosomes have consistently encountered an endogenous population of chromosome-derived circular genomic DNA, referred to as extrachromosomal circular DNA (eccDNA). While the production, distribution, and activities of eccDNAs remain understudied, eccDNA formation from specific regions of the linear genome has profound consequences on the regulatory and coding capabilities for these regions. Here, we define eccDNA distributions in Caenorhabditis elegans and in three human cell types, utilizing a set of DNA topology-dependent approaches for enrichment and characterization. The use of parallel biophysical, enzymatic, and informatic approaches provides a comprehensive profiling of eccDNA robust to isolation and analysis methodology. Results in human and nematode systems provide quantitative analysis of the eccDNA loci at both unique and repetitive regions. Our studies converge on and support a consistent picture, in which endogenous genomic DNA circles are present in normal physiological states, and in which the circles come from both coding and noncoding genomic regions. Prominent among the coding regions generating DNA circles are several genes known to produce a diversity of protein isoforms, with mucin proteins and titin as specific examples. Copyright © 2017 Shoura et al.

Alterations in sperm DNA methylation, non-coding RNA expression, and histone retention mediate vinclozolin-induced epigenetic transgenerational inheritance of disease.

Science.gov (United States)

Ben Maamar, Millissia; Sadler-Riggleman, Ingrid; Beck, Daniel; McBirney, Margaux; Nilsson, Eric; Klukovich, Rachel; Xie, Yeming; Tang, Chong; Yan, Wei; Skinner, Michael K

2018-04-01

Epigenetic transgenerational inheritance of disease and phenotypic variation can be induced by several toxicants, such as vinclozolin. This phenomenon can involve DNA methylation, non-coding RNA (ncRNA) and histone retention, and/or modification in the germline (e.g. sperm). These different epigenetic marks are called epimutations and can transmit in part the transgenerational phenotypes. This study was designed to investigate the vinclozolin-induced concurrent alterations of a number of different epigenetic factors, including DNA methylation, ncRNA, and histone retention in rat sperm. Gestating females (F0 generation) were exposed transiently to vinclozolin during fetal gonadal development. The directly exposed F1 generation fetus, the directly exposed germline within the fetus that will generate the F2 generation, and the transgenerational F3 generation sperm were studied. DNA methylation and ncRNA were altered in each generation rat sperm with the direct exposure F1 and F2 generations being distinct from the F3 generation epimutations. Interestingly, an increased number of differential histone retention sites were found in the F3 generation vinclozolin sperm, but not in the F1 or F2 generations. All three different epimutation types were affected in the vinclozolin lineage transgenerational sperm (F3 generation). The direct exposure generations (F1 and F2) epigenetic alterations were distinct from the transgenerational sperm epimutations. The genomic features and gene pathways associated with the epimutations were investigated to help elucidate the integration of these different epigenetic processes. Our results show that the three different types of epimutations are involved and integrated in the mediation of the epigenetic transgenerational inheritance phenomenon.

Evaluation of the efficacy of twelve mitochondrial protein-coding genes as barcodes for mollusk DNA barcoding.

Science.gov (United States)

Yu, Hong; Kong, Lingfeng; Li, Qi

2016-01-01

In this study, we evaluated the efficacy of 12 mitochondrial protein-coding genes from 238 mitochondrial genomes of 140 molluscan species as potential DNA barcodes for mollusks. Three barcoding methods (distance, monophyly and character-based methods) were used in species identification. The species recovery rates based on genetic distances for the 12 genes ranged from 70.83 to 83.33%. There were no significant differences in intra- or interspecific variability among the 12 genes. The monophyly and character-based methods provided higher resolution than the distance-based method in species delimitation. Especially in closely related taxa, the character-based method showed some advantages. The results suggested that besides the standard COI barcode, other 11 mitochondrial protein-coding genes could also be potentially used as a molecular diagnostic for molluscan species discrimination. Our results also showed that the combination of mitochondrial genes did not enhance the efficacy for species identification and a single mitochondrial gene would be fully competent.

The histone codes for meiosis.

Science.gov (United States)

Wang, Lina; Xu, Zhiliang; Khawar, Muhammad Babar; Liu, Chao; Li, Wei

2017-09-01

Meiosis is a specialized process that produces haploid gametes from diploid cells by a single round of DNA replication followed by two successive cell divisions. It contains many special events, such as programmed DNA double-strand break (DSB) formation, homologous recombination, crossover formation and resolution. These events are associated with dynamically regulated chromosomal structures, the dynamic transcriptional regulation and chromatin remodeling are mainly modulated by histone modifications, termed 'histone codes'. The purpose of this review is to summarize the histone codes that are required for meiosis during spermatogenesis and oogenesis, involving meiosis resumption, meiotic asymmetric division and other cellular processes. We not only systematically review the functional roles of histone codes in meiosis but also discuss future trends and perspectives in this field. © 2017 Society for Reproduction and Fertility.

Is a genome a codeword of an error-correcting code?

Directory of Open Access Journals (Sweden)

Luzinete C B Faria

Full Text Available Since a genome is a discrete sequence, the elements of which belong to a set of four letters, the question as to whether or not there is an error-correcting code underlying DNA sequences is unavoidable. The most common approach to answering this question is to propose a methodology to verify the existence of such a code. However, none of the methodologies proposed so far, although quite clever, has achieved that goal. In a recent work, we showed that DNA sequences can be identified as codewords in a class of cyclic error-correcting codes known as Hamming codes. In this paper, we show that a complete intron-exon gene, and even a plasmid genome, can be identified as a Hamming code codeword as well. Although this does not constitute a definitive proof that there is an error-correcting code underlying DNA sequences, it is the first evidence in this direction.

Reactor physics computer code development for neutronic design, fuel-management, reactor operation and safety analysis of PHWRs

International Nuclear Information System (INIS)

Rastogi, B.P.

1989-01-01

This report discusses various reactor physics codes developed for neutronic design, fuel-management, reactor operation and safety analysis of PHWRs. These code packages have been utilized for nuclear design of 500 MWe and new 235 MWe PHWRs. (author)

An evaluation of ACI 349 code for design of the fastening system at nuclear power plant

International Nuclear Information System (INIS)

Jang, J.-B.; Suh, Y.-P.; Lee, J.-R.

2005-01-01

ACI 349 Code, revised on 2001, is only available for the anchor with diameter not exceeding 2 in. and tensile embedment not exceeding 25 in. in depth. So, ACI 349 Code can't be applied to the design of the large sized anchor with diameter exceeding 2 in. and tensile embedment exceeding 25 in. in depth which fastens the SG, RV, RCP, PZR, etc. at containment building. Therefore, an application of ACI 349 Code was investigated for the design of the small and large sized anchors under tensile load using the numerical analysis model which was developed on a basis of the various test data of cast-in-place anchor in this study. In conclusion, it is proved that ACI 349 Code is available for the design of the small and large sized cast-in-place anchor. (authors)

Comparison of Geant4-DNA simulation of S-values with other Monte Carlo codes

International Nuclear Information System (INIS)

André, T.; Morini, F.; Karamitros, M.; Delorme, R.; Le Loirec, C.; Campos, L.; Champion, C.; Groetz, J.-E.; Fromm, M.; Bordage, M.-C.; Perrot, Y.; Barberet, Ph.

2014-01-01

Monte Carlo simulations of S-values have been carried out with the Geant4-DNA extension of the Geant4 toolkit. The S-values have been simulated for monoenergetic electrons with energies ranging from 0.1 keV up to 20 keV, in liquid water spheres (for four radii, chosen between 10 nm and 1 μm), and for electrons emitted by five isotopes of iodine (131, 132, 133, 134 and 135), in liquid water spheres of varying radius (from 15 μm up to 250 μm). The results have been compared to those obtained from other Monte Carlo codes and from other published data. The use of the Kolmogorov–Smirnov test has allowed confirming the statistical compatibility of all simulation results

The Impact of Diagnostic Code Misclassification on Optimizing the Experimental Design of Genetic Association Studies

Directory of Open Access Journals (Sweden)

Steven J. Schrodi

2017-01-01

Full Text Available Diagnostic codes within electronic health record systems can vary widely in accuracy. It has been noted that the number of instances of a particular diagnostic code monotonically increases with the accuracy of disease phenotype classification. As a growing number of health system databases become linked with genomic data, it is critically important to understand the effect of this misclassification on the power of genetic association studies. Here, I investigate the impact of this diagnostic code misclassification on the power of genetic association studies with the aim to better inform experimental designs using health informatics data. The trade-off between (i reduced misclassification rates from utilizing additional instances of a diagnostic code per individual and (ii the resulting smaller sample size is explored, and general rules are presented to improve experimental designs.

Adaptation and implementation of the TRACE code for transient analysis in designs lead cooled fast reactors

International Nuclear Information System (INIS)

Lazaro, A.; Ammirabile, L.; Martorell, S.

2015-01-01

Lead-Cooled Fast Reactor (LFR) has been identified as one of promising future reactor concepts in the technology road map of the Generation IVC International Forum (GIF)as well as in the Deployment Strategy of the European Sustainable Nuclear Industrial Initiative (ESNII), both aiming at improved sustainability, enhanced safety, economic competitiveness, and proliferation resistance. This new nuclear reactor concept requires the development of computational tools to be applied in design and safety assessments to confirm improved inherent and passive safety features of this design. One approach to this issue is to modify the current computational codes developed for the simulation of Light Water Reactors towards their applicability for the new designs. This paper reports on the performed modifications of the TRACE system code to make it applicable to LFR safety assessments. The capabilities of the modified code are demonstrated on series of benchmark exercises performed versus other safety analysis codes. (Author)

Design of TIME2 code: time dependent effects on Land 2 type repositories for Department of the Environment

International Nuclear Information System (INIS)

1985-07-01

Design details for the proposed TIME2 computer code are presented for the purposes of information, planning and to serve as a guideline during code development. The TIME2 code will describe the long-term evolution of the environments of Land 2 type radioactive waste disposal sites (also known as 'time dependent effects'). Outlines are presented of code purpose and utilisation, specification and structure, input and output design, verification and validation, quality assurance and documentation. (author)

Theory and simulation of DNA-coated colloids: a guide for rational design.

Science.gov (United States)

Angioletti-Uberti, Stefano; Mognetti, Bortolo M; Frenkel, Daan

2016-03-07

By exploiting the exquisite selectivity of DNA hybridization, DNA-coated colloids (DNACCs) can be made to self-assemble in a wide variety of structures. The beauty of this system stems largely from its exceptional versatility and from the fact that a proper choice of the grafted DNA sequences yields fine control over the colloidal interactions. Theory and simulations have an important role to play in the optimal design of self assembling DNACCs. At present, the powerful model-based design tools are not widely used, because the theoretical literature is fragmented and the connection between different theories is often not evident. In this Perspective, we aim to discuss the similarities and differences between the different models that have been described in the literature, their underlying assumptions, their strengths and their weaknesses. Using the tools described in the present Review, it should be possible to move towards a more rational design of novel self-assembling structures of DNACCs and, more generally, of systems where ligand-receptor are used to control interactions.

Study of design parameters affecting the motion of DNA for nanoinjection

International Nuclear Information System (INIS)

David, Regis A; Jensen, Brian D; Howell, Larry L; Black, Justin L; Burnett, Sandra H

2012-01-01

This paper reports the effects of various parameters on the attraction and repulsion of DNA to and from a silicon lance. An understanding of DNA motion is crucial for a new approach to insert DNA, or other foreign microscopic matter, into a living cell. The approach, called nanoinjection, uses electrical forces to attract and repel the desired substance to a micromachined lance designed to pierce the cell membranes. We have developed mathematical models to predict the trajectory of DNA. The mathematical model allows investigation of the attraction/repulsion process by varying specific parameters. We find that the ground electrode placement, lance orientation and lance penetration significantly affect attraction or repulsion efficiency, while the gap, lance direction, lance tip width, lance tip half-angle and lance tip height do not. (paper)

The APR1400 Core Design by Using APA Code System

International Nuclear Information System (INIS)

Choi, Yu Sun; Koh, Byung Marn

2008-01-01

The nuclear design for APR1400 has been performed to prepare the core model for Automatic Load Follow Operation Simulation. APA (ALPHA/ PHOENIXP/ ANC) code system is a tool for the multi-cycle depletion calculations for APR1400. Its detail versions for ALPHA, PHOENIX-P and ANC are 8.9.3, 8.6.1 and 8.10.5, respectively. The first and equilibrium core depletion calculations for APR1400 have been performed to assure the target cycle length and confirm the safety parameters. The parameters are satisfied within limitation about nuclear design criteria. This APR1400 core models will be based on the design parameters for APR1400 Simulator

Transoptr-a second order beam transport design code with automatic internal optimization and general constraints

International Nuclear Information System (INIS)

Heighway, E.A.

1980-07-01

A second order beam transport design code with parametric optimization is described. The code analyzes the transport of charged particle beams through a user defined magnet system. The magnet system parameters are varied (within user defined limits) until the properties of the transported beam and/or the system transport matrix match those properties requested by the user. The code uses matrix formalism to represent the transport elements and optimization is achieved using the variable metric method. Any constraints that can be expressed algebraically may be included by the user as part of his design. Instruction in the use of the program is given. (auth)

The dnaN gene codes for the beta subunit of DNA polymerase III holoenzyme of escherichia coli.

Science.gov (United States)

Burgers, P M; Kornberg, A; Sakakibara, Y

1981-09-01

An Escherichia coli mutant, dnaN59, stops DNA synthesis promptly upon a shift to a high temperature; the wild-type dnaN gene carried in a transducing phage encodes a polypeptide of about 41,000 daltons [Sakakibara, Y. & Mizukami, T. (1980) Mol. Gen. Genet. 178, 541-553; Yuasa, S. & Sakakibara, Y. (1980) Mol. Gen. Genet. 180, 267-273]. We now find that the product of dnaN gene is the beta subunit of DNA polymerase III holoenzyme, the principal DNA synthetic multipolypeptide complex in E. coli. The conclusion is based on the following observations: (i) Extracts from dnaN59 cells were defective in phage phi X174 and G4 DNA synthesis after the mutant cells had been exposed to the increased temperature. (ii) The enzymatic defect was overcome by addition of purified beta subunit but not by other subunits of DNA polymerase III holoenzyme or by other replication proteins required for phi X174 DNA synthesis. (iii) Partially purified beta subunit from the dnaN mutant, unlike that from the wild type, was inactive in reconstituting the holoenzyme when mixed with the other purified subunits. (iv) Increased dosage of the dnaN gene provided by a plasmid carrying the gene raised cellular levels of the beta subunit 5- to 6-fold.

MVP utilization for PWR design code

International Nuclear Information System (INIS)

Matsumoto, Hideki; Tahara, Yoshihisa

2001-01-01

MHI studies the method of the spatially dependent resonance cross sections so as to predict the power distribution in a fuel pellet accurately. For this purpose, the multiband method and the Stoker/Weiss method were implemented to the 2 dimensional transport code PHOENIX-P, and the methods were validated by comparing them with MVP code. Although the appropriate reference was not obtain from the deterministic codes on the resonance cross section study, now the Monte Carlo code MVP result is available and useful as reference. It is shown here how MVP is used to develop the multiband method and the Stoker/Weiss method, and how effective the result of MVP is on the study of the resonance cross sections. (author)

Function and Application Areas in Medicine of Non-Coding RNA

Directory of Open Access Journals (Sweden)

Figen Guzelgul

2009-06-01

Full Text Available RNA is the genetic material converting the genetic code that it gets from DNA into protein. While less than 2 % of RNA is converted into protein , more than 98 % of it can not be converted into protein and named as non-coding RNAs. 70 % of noncoding RNAs consists of introns , however, the rest part of them consists of exons. Non-coding RNAs are examined in two classes according to their size and functions. Whereas they are classified as long non-coding and small non-coding RNAs according to their size , they are grouped as housekeeping non-coding RNAs and regulating non-coding RNAs according to their function. For long years ,these non-coding RNAs have been considered as non-functional. However, today, it has been proved that these non-coding RNAs play role in regulating genes and in structural, functional and catalitic roles of RNAs converted into protein. Due to its taking a role in gene silencing mechanism, particularly in medical world , non-coding RNAs have led to significant developments. RNAi technolgy , which is used in designing drugs to be used in treatment of various diseases , is a ray of hope for medical world. [Archives Medical Review Journal 2009; 18(3.000: 141-155

Software package for the design and analysis of DNA origami structures

DEFF Research Database (Denmark)

Andersen, Ebbe Sloth; Nielsen, Morten Muhlig; Dong, Mingdong

was observed on the mica surface with a fraction of the dolphin nanostructures showing extensive tail flexibility of approximately 90 degrees. The Java editor and tools are free software distributed under the GNU license. The open architecture of the editor makes it easy for the scientific community......A software package was developed for the semi-automated design of DNA origamis and further data analysis of Atomic Force Microscopy (AFM) images. As an example, we design the shape of a bottlenose dolphin and analyze it by means of high resolution AFM imaging. A high yield of DNA dolphins...... to contribute new tools and functionalities. Documentation, tutorials and software will be made available online....

Statistical core design methodology using the VIPRE thermal-hydraulics code

International Nuclear Information System (INIS)

Lloyd, M.W.; Feltus, M.A.

1995-01-01

An improved statistical core design methodology for developing a computational departure from nucleate boiling ratio (DNBR) correlation has been developed and applied in order to analyze the nominal 1.3 DNBR limit on Westinghouse Pressurized Water Reactor (PWR) cores. This analysis, although limited in scope, found that the DNBR limit can be reduced from 1.3 to some lower value and be accurate within an adequate confidence level of 95%, for three particular FSAR operational transients: turbine trip, complete loss of flow, and inadvertent opening of a pressurizer relief valve. The VIPRE-01 thermal-hydraulics code, the SAS/STAT statistical package, and the EPRI/Columbia University DNBR experimental data base were used in this research to develop the Pennsylvania State Statistical Core Design Methodology (PSSCDM). The VIPRE code was used to perform the necessary sensitivity studies and generate the EPRI correlation-calculated DNBR predictions. The SAS package used for these EPRI DNBR correlation predictions from VIPRE as a data set to determine the best fit for the empirical model and to perform the statistical analysis. (author)

Multi-line split DNA synthesis: a novel combinatorial method to make high quality peptide libraries

Directory of Open Access Journals (Sweden)

Ueno Shingo

2004-09-01

Full Text Available Abstract Background We developed a method to make a various high quality random peptide libraries for evolutionary protein engineering based on a combinatorial DNA synthesis. Results A split synthesis in codon units was performed with mixtures of bases optimally designed by using a Genetic Algorithm program. It required only standard DNA synthetic reagents and standard DNA synthesizers in three lines. This multi-line split DNA synthesis (MLSDS is simply realized by adding a mix-and-split process to normal DNA synthesis protocol. Superiority of MLSDS method over other methods was shown. We demonstrated the synthesis of oligonucleotide libraries with 1016 diversity, and the construction of a library with random sequence coding 120 amino acids containing few stop codons. Conclusions Owing to the flexibility of the MLSDS method, it will be able to design various "rational" libraries by using bioinformatics databases.

The Ductile Design Concept for Seismic Actions in Miscellaneous Design Codes

Directory of Open Access Journals (Sweden)

M. Budescu

2009-01-01

Full Text Available The concept of ductility estimates the capacity of the structural system and its components to deform prior to collapse, without a substantial loss of strength, but with an important energy amount dissipated. Consistent with the „Applied Technology Council” (ATC-34, from 1995, it was agreed that the reduction seismic response factor to decrease the design force. The purpose of this factor is to transpose the nonlinear behaviour of the structure and the energy dissipation capacity in a simplified form that can be used in the design stage. Depending on the particular structural model and the design standard the used values are different. The paper presents the characteristics of the ductility concept for the structural system. Along with this the general way of computing the reserve factor with the necessary explanations for the parameters that determine the behaviour factor are described. The purpose of this paper is to make a comparison between different international norms for the values and the distribution of the behaviour factor. The norms from the following countries are taken into consideration: the United States of America, New Zealand, Japan, Romania and the European general seismic code.

An explication of the Graphite Structural Design Code of core components for the High Temperature Engineering Test Reactor

International Nuclear Information System (INIS)

Iyoku, Tatsuo; Ishihara, Masahiro; Toyota, Junji; Shiozawa, Shusaku

1991-05-01

The integrity evaluation of the core graphite components for the High Temperature Engineering Test Reactor (HTTR) will be carried out based upon the Graphite Structural Design Code for core components. In the application of this design code, it is necessary to make clear the basic concept to evaluate the integrity of core components of HTTR. Therefore, considering the detailed design of core graphite structures such as fuel graphite blocks, etc. of HTTR, this report explicates the design code in detail about the concepts of stress and fatigue limits, integrity evaluation method of oxidized graphite components and thermal irradiation stress analysis method etc. (author)

Design of sampling tools for Monte Carlo particle transport code JMCT

International Nuclear Information System (INIS)

Shangguan Danhua; Li Gang; Zhang Baoyin; Deng Li

2012-01-01

A class of sampling tools for general Monte Carlo particle transport code JMCT is designed. Two ways are provided to sample from distributions. One is the utilization of special sampling methods for special distribution; the other is the utilization of general sampling methods for arbitrary discrete distribution and one-dimensional continuous distribution on a finite interval. Some open source codes are included in the general sampling method for the maximum convenience of users. The sampling results show sampling correctly from distribution which are popular in particle transport can be achieved with these tools, and the user's convenience can be assured. (authors)

The beta equilibrium, stability, and transport codes. Applications to the design of stellarators

International Nuclear Information System (INIS)

Bauer, F.; Garabedian, P.; Betancourt, O.; Wakatani, M.

1987-01-01

This book gives a detailed exposition of the available computational methods, documents the codes, and presents many examples showing how to run them and how to interpret the results. A listing of the recently completed BETA transport code is included. Current stellarator experiments are discussed, and the book contains significant applications to the design of major new stellarator experiments that are now in the planning stage

Comparative study of design of piping supports class 1, 2 and 3 considering german code KTA and ASME III - NF

International Nuclear Information System (INIS)

Faloppa, Altair A.; Fainer, Gerson; Mattar Neto, Miguel; Elias, Marcos V.

2013-01-01

The objective of this paper is developing a comparative study of the design criteria for class 1, 2, 3 piping supports considering the American Code ASME Section III - NF and the German Code KTA 3205.1 to the Primary Circuit, KTA 3205.2 to the others systems and KTA 3205.3 series-production standards supports of a PWR nuclear power plant. An additional purpose of the paper is a general analysis of the main design concepts of the American Code ASME Boiler and Pressure Vessel Code, Section III, Division 1 and German Nuclear Design Code KTA that was performed in order to aid the comparative study proposed. The relevance of this study is to show the differences between codes ASME and KTA since they were applied in the design of the Nuclear Power Plants Angra 1 and Angra 2, and to the design of Angra 3, which is at the moment under construction. It is also considered their use in the design of nuclear installations such as RMB - Reator MultiProposito Brasileiro and LABGENE - Laboratorio de Geracao Nucleoeletrica. (author)

Converting Panax ginseng DNA and chemical fingerprints into two-dimensional barcode.

Science.gov (United States)

Cai, Yong; Li, Peng; Li, Xi-Wen; Zhao, Jing; Chen, Hai; Yang, Qing; Hu, Hao

2017-07-01

In this study, we investigated how to convert the Panax ginseng DNA sequence code and chemical fingerprints into a two-dimensional code. In order to improve the compression efficiency, GATC2Bytes and digital merger compression algorithms are proposed. HPLC chemical fingerprint data of 10 groups of P. ginseng from Northeast China and the internal transcribed spacer 2 (ITS2) sequence code as the DNA sequence code were ready for conversion. In order to convert such data into a two-dimensional code, the following six steps were performed: First, the chemical fingerprint characteristic data sets were obtained through the inflection filtering algorithm. Second, precompression processing of such data sets is undertaken. Third, precompression processing was undertaken with the P. ginseng DNA (ITS2) sequence codes. Fourth, the precompressed chemical fingerprint data and the DNA (ITS2) sequence code were combined in accordance with the set data format. Such combined data can be compressed by Zlib, an open source data compression algorithm. Finally, the compressed data generated a two-dimensional code called a quick response code (QR code). Through the abovementioned converting process, it can be found that the number of bytes needed for storing P. ginseng chemical fingerprints and its DNA (ITS2) sequence code can be greatly reduced. After GTCA2Bytes algorithm processing, the ITS2 compression rate reaches 75% and the chemical fingerprint compression rate exceeds 99.65% via filtration and digital merger compression algorithm processing. Therefore, the overall compression ratio even exceeds 99.36%. The capacity of the formed QR code is around 0.5k, which can easily and successfully be read and identified by any smartphone. P. ginseng chemical fingerprints and its DNA (ITS2) sequence code can form a QR code after data processing, and therefore the QR code can be a perfect carrier of the authenticity and quality of P. ginseng information. This study provides a theoretical

Investigation of Navier-Stokes Code Verification and Design Optimization

Science.gov (United States)

Vaidyanathan, Rajkumar

2004-01-01

With rapid progress made in employing computational techniques for various complex Navier-Stokes fluid flow problems, design optimization problems traditionally based on empirical formulations and experiments are now being addressed with the aid of computational fluid dynamics (CFD). To be able to carry out an effective CFD-based optimization study, it is essential that the uncertainty and appropriate confidence limits of the CFD solutions be quantified over the chosen design space. The present dissertation investigates the issues related to code verification, surrogate model-based optimization and sensitivity evaluation. For Navier-Stokes (NS) CFD code verification a least square extrapolation (LSE) method is assessed. This method projects numerically computed NS solutions from multiple, coarser base grids onto a freer grid and improves solution accuracy by minimizing the residual of the discretized NS equations over the projected grid. In this dissertation, the finite volume (FV) formulation is focused on. The interplay between the xi concepts and the outcome of LSE, and the effects of solution gradients and singularities, nonlinear physics, and coupling of flow variables on the effectiveness of LSE are investigated. A CFD-based design optimization of a single element liquid rocket injector is conducted with surrogate models developed using response surface methodology (RSM) based on CFD solutions. The computational model consists of the NS equations, finite rate chemistry, and the k-6 turbulence closure. With the aid of these surrogate models, sensitivity and trade-off analyses are carried out for the injector design whose geometry (hydrogen flow angle, hydrogen and oxygen flow areas and oxygen post tip thickness) is optimized to attain desirable goals in performance (combustion length) and life/survivability (the maximum temperatures on the oxidizer post tip and injector face and a combustion chamber wall temperature). A preliminary multi-objective optimization

Brain cDNA clone for human cholinesterase

International Nuclear Information System (INIS)

McTiernan, C.; Adkins, S.; Chatonnet, A.; Vaughan, T.A.; Bartels, C.F.; Kott, M.; Rosenberry, T.L.; La Du, B.N.; Lockridge, O.

1987-01-01

A cDNA library from human basal ganglia was screened with oligonucleotide probes corresponding to portions of the amino acid sequence of human serum cholinesterase. Five overlapping clones, representing 2.4 kilobases, were isolated. The sequenced cDNA contained 207 base pairs of coding sequence 5' to the amino terminus of the mature protein in which there were four ATG translation start sites in the same reading frame as the protein. Only the ATG coding for Met-(-28) lay within a favorable consensus sequence for functional initiators. There were 1722 base pairs of coding sequence corresponding to the protein found circulating in human serum. The amino acid sequence deduced from the cDNA exactly matched the 574 amino acid sequence of human serum cholinesterase, as previously determined by Edman degradation. Therefore, our clones represented cholinesterase rather than acetylcholinesterase. It was concluded that the amino acid sequences of cholinesterase from two different tissues, human brain and human serum, were identical. Hybridization of genomic DNA blots suggested that a single gene, or very few genes coded for cholinesterase

Decoding DNA labels by melting curve analysis using real-time PCR.

Science.gov (United States)

Balog, József A; Fehér, Liliána Z; Puskás, László G

2017-12-01

Synthetic DNA has been used as an authentication code for a diverse number of applications. However, existing decoding approaches are based on either DNA sequencing or the determination of DNA length variations. Here, we present a simple alternative protocol for labeling different objects using a small number of short DNA sequences that differ in their melting points. Code amplification and decoding can be done in two steps using quantitative PCR (qPCR). To obtain a DNA barcode with high complexity, we defined 8 template groups, each having 4 different DNA templates, yielding 158 (>2.5 billion) combinations of different individual melting temperature (Tm) values and corresponding ID codes. The reproducibility and specificity of the decoding was confirmed by using the most complex template mixture, which had 32 different products in 8 groups with different Tm values. The industrial applicability of our protocol was also demonstrated by labeling a drone with an oil-based paint containing a predefined DNA code, which was then successfully decoded. The method presented here consists of a simple code system based on a small number of synthetic DNA sequences and a cost-effective, rapid decoding protocol using a few qPCR reactions, enabling a wide range of authentication applications.

A design of a wavelength-hopping time-spreading incoherent optical code division multiple access system

International Nuclear Information System (INIS)

Glesk, I.; Baby, V.

2005-01-01

We present the architecture and code design for a highly scalable, 2.5 Gb/s per user optical code division multiple access (OCDMA) system. The system is scalable to 100 potential and more than 10 simultaneous users, each with a bit error rate (BER) of less than 10 -9 . The system architecture uses a fast wavelength-hopping, time-spreading codes. Unlike frequency and phase sensitive coherent OCDMA systems, this architecture utilizes standard on off keyed optical pulses allocated in the time and wavelength dimensions. This incoherent OCDMA approach is compatible with existing WDM optical networks and utilizes off the shelf components. We discuss the novel optical subsystem design for encoders and decoders that enable the realization of a highly scalable incoherent OCDMA system with rapid reconfigurability. A detailed analysis of the scalability of the two dimensional code is presented and select network deployment architectures for OCDMA are discussed (Authors)

Nuclear component design ontology building based on ASME codes

International Nuclear Information System (INIS)

Bao Shiyi; Zhou Yu; He Shuyan

2005-01-01

The adoption of ontology analysis in the study of concept knowledge acquisition and representation for the nuclear component design process based on computer-supported cooperative work (CSCW) makes it possible to share and reuse numerous concept knowledge of multi-disciplinary domains. A practical ontology building method is accordingly proposed based on Protege knowledge model in combination with both top-down and bottom-up approaches together with Formal Concept Analysis (FCA). FCA exhibits its advantages in the way it helps establish and improve taxonomic hierarchy of concepts and resolve concept conflict occurred in modeling multi-disciplinary domains. With Protege-3.0 as the ontology building tool, a nuclear component design ontology based ASME codes is developed by utilizing the ontology building method. The ontology serves as the basis to realize concept knowledge sharing and reusing of nuclear component design. (authors)

Genetic Code Analysis Toolkit: A novel tool to explore the coding properties of the genetic code and DNA sequences

Science.gov (United States)

Kraljić, K.; Strüngmann, L.; Fimmel, E.; Gumbel, M.

2018-01-01

The genetic code is degenerated and it is assumed that redundancy provides error detection and correction mechanisms in the translation process. However, the biological meaning of the code's structure is still under current research. This paper presents a Genetic Code Analysis Toolkit (GCAT) which provides workflows and algorithms for the analysis of the structure of nucleotide sequences. In particular, sets or sequences of codons can be transformed and tested for circularity, comma-freeness, dichotomic partitions and others. GCAT comes with a fertile editor custom-built to work with the genetic code and a batch mode for multi-sequence processing. With the ability to read FASTA files or load sequences from GenBank, the tool can be used for the mathematical and statistical analysis of existing sequence data. GCAT is Java-based and provides a plug-in concept for extensibility. Availability: Open source Homepage:http://www.gcat.bio/

High-resolution coded-aperture design for compressive X-ray tomography using low resolution detectors

Science.gov (United States)

Mojica, Edson; Pertuz, Said; Arguello, Henry

2017-12-01

One of the main challenges in Computed Tomography (CT) is obtaining accurate reconstructions of the imaged object while keeping a low radiation dose in the acquisition process. In order to solve this problem, several researchers have proposed the use of compressed sensing for reducing the amount of measurements required to perform CT. This paper tackles the problem of designing high-resolution coded apertures for compressed sensing computed tomography. In contrast to previous approaches, we aim at designing apertures to be used with low-resolution detectors in order to achieve super-resolution. The proposed method iteratively improves random coded apertures using a gradient descent algorithm subject to constraints in the coherence and homogeneity of the compressive sensing matrix induced by the coded aperture. Experiments with different test sets show consistent results for different transmittances, number of shots and super-resolution factors.

Interface design of VSOP'94 computer code for safety analysis

International Nuclear Information System (INIS)

Natsir, Khairina; Andiwijayakusuma, D.; Wahanani, Nursinta Adi; Yazid, Putranto Ilham

2014-01-01

Today, most software applications, also in the nuclear field, come with a graphical user interface. VSOP'94 (Very Superior Old Program), was designed to simplify the process of performing reactor simulation. VSOP is a integrated code system to simulate the life history of a nuclear reactor that is devoted in education and research. One advantage of VSOP program is its ability to calculate the neutron spectrum estimation, fuel cycle, 2-D diffusion, resonance integral, estimation of reactors fuel costs, and integrated thermal hydraulics. VSOP also can be used to comparative studies and simulation of reactor safety. However, existing VSOP is a conventional program, which was developed using Fortran 65 and have several problems in using it, for example, it is only operated on Dec Alpha mainframe platforms and provide text-based output, difficult to use, especially in data preparation and interpretation of results. We develop a GUI-VSOP, which is an interface program to facilitate the preparation of data, run the VSOP code and read the results in a more user friendly way and useable on the Personal 'Computer (PC). Modifications include the development of interfaces on preprocessing, processing and postprocessing. GUI-based interface for preprocessing aims to provide a convenience way in preparing data. Processing interface is intended to provide convenience in configuring input files and libraries and do compiling VSOP code. Postprocessing interface designed to visualized the VSOP output in table and graphic forms. GUI-VSOP expected to be useful to simplify and speed up the process and analysis of safety aspects

Interface design of VSOP'94 computer code for safety analysis

Science.gov (United States)

Natsir, Khairina; Yazid, Putranto Ilham; Andiwijayakusuma, D.; Wahanani, Nursinta Adi

2014-09-01

Today, most software applications, also in the nuclear field, come with a graphical user interface. VSOP'94 (Very Superior Old Program), was designed to simplify the process of performing reactor simulation. VSOP is a integrated code system to simulate the life history of a nuclear reactor that is devoted in education and research. One advantage of VSOP program is its ability to calculate the neutron spectrum estimation, fuel cycle, 2-D diffusion, resonance integral, estimation of reactors fuel costs, and integrated thermal hydraulics. VSOP also can be used to comparative studies and simulation of reactor safety. However, existing VSOP is a conventional program, which was developed using Fortran 65 and have several problems in using it, for example, it is only operated on Dec Alpha mainframe platforms and provide text-based output, difficult to use, especially in data preparation and interpretation of results. We develop a GUI-VSOP, which is an interface program to facilitate the preparation of data, run the VSOP code and read the results in a more user friendly way and useable on the Personal 'Computer (PC). Modifications include the development of interfaces on preprocessing, processing and postprocessing. GUI-based interface for preprocessing aims to provide a convenience way in preparing data. Processing interface is intended to provide convenience in configuring input files and libraries and do compiling VSOP code. Postprocessing interface designed to visualized the VSOP output in table and graphic forms. GUI-VSOP expected to be useful to simplify and speed up the process and analysis of safety aspects.

Expression of protein-coding genes embedded in ribosomal DNA

DEFF Research Database (Denmark)

Johansen, Steinar D; Haugen, Peik; Nielsen, Henrik

2007-01-01

Ribosomal DNA (rDNA) is a specialised chromosomal location that is dedicated to high-level transcription of ribosomal RNA genes. Interestingly, rDNAs are frequently interrupted by parasitic elements, some of which carry protein genes. These are non-LTR retrotransposons and group II introns that e...... in the nucleolus....

Research on Image Encryption Based on DNA Sequence and Chaos Theory

Science.gov (United States)

Tian Zhang, Tian; Yan, Shan Jun; Gu, Cheng Yan; Ren, Ran; Liao, Kai Xin

2018-04-01

Nowadays encryption is a common technique to protect image data from unauthorized access. In recent years, many scientists have proposed various encryption algorithms based on DNA sequence to provide a new idea for the design of image encryption algorithm. Therefore, a new method of image encryption based on DNA computing technology is proposed in this paper, whose original image is encrypted by DNA coding and 1-D logistic chaotic mapping. First, the algorithm uses two modules as the encryption key. The first module uses the real DNA sequence, and the second module is made by one-dimensional logistic chaos mapping. Secondly, the algorithm uses DNA complementary rules to encode original image, and uses the key and DNA computing technology to compute each pixel value of the original image, so as to realize the encryption of the whole image. Simulation results show that the algorithm has good encryption effect and security.

The TALL-3D facility design and commissioning tests for validation of coupled STH and CFD codes

Energy Technology Data Exchange (ETDEWEB)

Grishchenko, Dmitry, E-mail: dmitry@safety.sci.kth.se; Jeltsov, Marti, E-mail: marti@safety.sci.kth.se; Kööp, Kaspar, E-mail: kaspar@safety.sci.kth.se; Karbojian, Aram, E-mail: karbojan@kth.se; Villanueva, Walter, E-mail: walter@safety.sci.kth.se; Kudinov, Pavel, E-mail: pavel@safety.sci.kth.se

2015-08-15

Highlights: • Design of a heavy liquid thermal-hydraulic loop for CFD/STH code validation. • Description of the loop instrumentation and assessment of measurement error. • Experimental data from forced to natural circulation transient. - Abstract: Application of coupled CFD (Computational Fluid Dynamics) and STH (System Thermal Hydraulics) codes is a prerequisite for computationally affordable and sufficiently accurate prediction of thermal-hydraulics of complex systems. Coupled STH and CFD codes require validation for understanding and quantification of the sources of uncertainties in the code prediction. TALL-3D is a liquid Lead Bismuth Eutectic (LBE) loop developed according to the requirements for the experimental data for validation of coupled STH and CFD codes. The goals of the facility design are to provide (i) mutual feedback between natural circulation in the loop and complex 3D mixing and stratification phenomena in the pool-type test section, (ii) a possibility to validate standalone STH and CFD codes for each subsection of the facility, and (iii) sufficient number of experimental data to separate the process of input model calibration and code validation. Description of the facility design and its main components, approach to estimation of experimental uncertainty and calibration of model input parameters that are not directly measured in the experiment are discussed in the paper. First experimental data from the forced to natural circulation transient is also provided in the paper.

An Investigation of the Methods of Logicalizing the Code-Checking System for Architectural Design Review in New Taipei City

Directory of Open Access Journals (Sweden)

Wei-I Lee

2016-12-01

Full Text Available The New Taipei City Government developed a Code-checking System (CCS using Building Information Modeling (BIM technology to facilitate an architectural design review in 2014. This system was intended to solve problems caused by cognitive gaps between designer and reviewer in the design review process. Along with considering information technology, the most important issue for the system’s development has been the logicalization of literal building codes. Therefore, to enhance the reliability and performance of the CCS, this study uses the Fuzzy Delphi Method (FDM on the basis of design thinking and communication theory to investigate the semantic difference and cognitive gaps among participants in the design review process and to propose the direction of system development. Our empirical results lead us to recommend grouping multi-stage screening and weighted assisted logicalization of non-quantitative building codes to improve the operability of CCS. Furthermore, CCS should integrate the Expert Evaluation System (EES to evaluate the design value under qualitative building codes.

State-of-the-art of wind turbine design codes: main features overview for cost-effective generation

Energy Technology Data Exchange (ETDEWEB)

Molenaar, D-P.; Dijkstra, S. [Delft University of Technology (Netherlands). Mechanical Engineering Systems and Control Group

1999-07-01

For successful large-scale application of wind energy, the price of electricity generated by wind turbines should decrease. Model-based control can be important since it has the potential to reduce fatigue loads, while simultaneously maintaining a desired amount of energy production. The controller synthesis, however, requires a mathematical model describing the most important dynamics of the complete wind turbine. In the wind energy community there is a wide variety in codes used to model a wind turbine's dynamic behaviour or to carry out design calculations. In this paper, the main features of the state-of-the-art wind turbine design codes have been investigated in order to judge the appropriateness of using one of these for the modeling, identification and control of flexible, variable speed wind turbines. It can be concluded that, although the sophistication of the design codes has increased enormously over the last two decades, they are, in general, not suitable for the design, and easy implementation of optimal operating strategies.

Decoding Non-Coding DNA: Trash or Treasure?

Indian Academy of Sciences (India)

that proteins, being the effector molecules of a cell, would determine ... value paradox states that the amount of cellular DNA is not ... They are also involved in nu- ... fold/matrix attachment regions (S/MARs). .... tumor suppressor gene PTEN.

Code assessment and modelling for Design Basis Accident Analysis of the European sodium fast reactor design. Part I: System description, modelling and benchmarking

International Nuclear Information System (INIS)

Lázaro, A.; Ammirabile, L.; Bandini, G.; Darmet, G.; Massara, S.; Dufour, Ph.; Tosello, A.; Gallego, E.; Jimenez, G.; Mikityuk, K.; Schikorr, M.; Bubelis, E.; Ponomarev, A.; Kruessmann, R.; Stempniewicz, M.

2014-01-01

Highlights: • Ten system-code models of the ESFR were developed in the frame of the CP-ESFR project. • Eight different thermohydraulic system codes adapted to sodium fast reactor's technology. • Benchmarking exercise settled to check the consistency of the calculations. • Upgraded system codes able to simulate the reactivity feedback and key safety parameters. -- Abstract: The new reactor concepts proposed in the Generation IV International Forum (GIF) are conceived to improve the use of natural resources, reduce the amount of high-level radioactive waste and excel in their reliability and safe operation. Among these novel designs sodium fast reactors (SFRs) stand out due to their technological feasibility as demonstrated in several countries during the last decades. As part of the contribution of EURATOM to GIF the CP-ESFR is a collaborative project with the objective, among others, to perform extensive analysis on safety issues involving renewed SFR demonstrator designs. The verification of computational tools able to simulate the plant behaviour under postulated accidental conditions by code-to-code comparison was identified as a key point to ensure reactor safety. In this line, several organizations employed coupled neutronic and thermal-hydraulic system codes able to simulate complex and specific phenomena involving multi-physics studies adapted to this particular fast reactor technology. In the “Introduction” of this paper the framework of this study is discussed, the second section describes the envisaged plant design and the commonly agreed upon modelling guidelines. The third section presents a comparative analysis of the calculations performed by each organisation applying their models and codes to a common agreed transient with the objective to harmonize the models as well as validating the implementation of all relevant physical phenomena in the different system codes

Code assessment and modelling for Design Basis Accident Analysis of the European sodium fast reactor design. Part I: System description, modelling and benchmarking

Energy Technology Data Exchange (ETDEWEB)

Lázaro, A., E-mail: aurelio.lazaro-chueca@ec.europa.eu [JRC-IET European Commission—Westerduinweg 3, PO Box-2, 1755 ZG Petten (Netherlands); UPV—Universidad Politecnica de Valencia, Cami de vera s/n-46002, Valencia (Spain); Ammirabile, L. [JRC-IET European Commission—Westerduinweg 3, PO Box-2, 1755 ZG Petten (Netherlands); Bandini, G. [ENEA, Via Martiri di Monte Sole 4, 40129 Bologna (Italy); Darmet, G.; Massara, S. [EDF, 1 avenue du Général de Gaulle, 92141 Clamart (France); Dufour, Ph.; Tosello, A. [CEA, St Paul lez Durance, 13108 Cadarache (France); Gallego, E.; Jimenez, G. [UPM, José Gutiérrez Abascal, 2-28006 Madrid (Spain); Mikityuk, K. [PSI—Paul Scherrer Institut, 5232 Villigen Switzerland (Switzerland); Schikorr, M.; Bubelis, E.; Ponomarev, A.; Kruessmann, R. [KIT—Institute for Neutron Physics and Reactor Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen Germany (Germany); Stempniewicz, M. [NRG, Utrechtseweg 310, PO Box 9034 6800 ES, Arnhem (Netherlands)

2014-01-15

Highlights: • Ten system-code models of the ESFR were developed in the frame of the CP-ESFR project. • Eight different thermohydraulic system codes adapted to sodium fast reactor's technology. • Benchmarking exercise settled to check the consistency of the calculations. • Upgraded system codes able to simulate the reactivity feedback and key safety parameters. -- Abstract: The new reactor concepts proposed in the Generation IV International Forum (GIF) are conceived to improve the use of natural resources, reduce the amount of high-level radioactive waste and excel in their reliability and safe operation. Among these novel designs sodium fast reactors (SFRs) stand out due to their technological feasibility as demonstrated in several countries during the last decades. As part of the contribution of EURATOM to GIF the CP-ESFR is a collaborative project with the objective, among others, to perform extensive analysis on safety issues involving renewed SFR demonstrator designs. The verification of computational tools able to simulate the plant behaviour under postulated accidental conditions by code-to-code comparison was identified as a key point to ensure reactor safety. In this line, several organizations employed coupled neutronic and thermal-hydraulic system codes able to simulate complex and specific phenomena involving multi-physics studies adapted to this particular fast reactor technology. In the “Introduction” of this paper the framework of this study is discussed, the second section describes the envisaged plant design and the commonly agreed upon modelling guidelines. The third section presents a comparative analysis of the calculations performed by each organisation applying their models and codes to a common agreed transient with the objective to harmonize the models as well as validating the implementation of all relevant physical phenomena in the different system codes.

Application of the ASME code in the design of the GA-4 and GA-9 casks

International Nuclear Information System (INIS)

Mings, W.J.; Koploy, M.A.

1992-01-01

General Atomics (GA) is developing two spent fuel shipping casks for transport by legal weight truck (LWT). The casks are designed to the loading, environmental conditions and safety requirements defined in Title 10 of the Code of Federal Regulations, Part 71 (10CFR71). To ensure that all components of the cask meet the 10CFR71 rules, GA established structural design criteria for each component based on NRC Regulatory Guides and the American Society of Mechanical Engineers Boiler and Pressure Vessel Code (ASME Code). This paper discusses the criteria used for different cask components, how they were applied and the conservatism and safety margins built into the criteria and assumption

Designing easy DNA extraction: Teaching creativity through laboratory practice.

Science.gov (United States)

Susantini, Endang; Lisdiana, Lisa; Isnawati; Tanzih Al Haq, Aushia; Trimulyono, Guntur

2017-05-01

Subject material concerning Deoxyribose Nucleic Acid (DNA) structure in the format of creativity-driven laboratory practice offers meaningful learning experience to the students. Therefore, a laboratory practice in which utilizes simple procedures and easy-safe-affordable household materials should be promoted to students to develop their creativity. This study aimed to examine whether designing and conducting DNA extraction with household materials could foster students' creative thinking. We also described how this laboratory practice affected students' knowledge and views. A total of 47 students participated in this study. These students were grouped and asked to utilize available household materials and modify procedures using hands-on worksheet. Result showed that this approach encouraged creative thinking as well as improved subject-related knowledge. Students also demonstrated positive views about content knowledge, social skills, and creative thinking skills. This study implies that extracting DNA with household materials is able to develop content knowledge, social skills, and creative thinking of the students. © 2016 by The International Union of Biochemistry and Molecular Biology, 45(3):216-225, 2017. © 2016 The International Union of Biochemistry and Molecular Biology.

Review of the margins for ASME code fatigue design curve - effects of surface roughness and material variability

International Nuclear Information System (INIS)

Chopra, O. K.; Shack, W. J.

2003-01-01

The ASME Boiler and Pressure Vessel Code provides rules for the construction of nuclear power plant components. The Code specifies fatigue design curves for structural materials. However, the effects of light water reactor (LWR) coolant environments are not explicitly addressed by the Code design curves. Existing fatigue strain-vs.-life ((var e psilon)-N) data illustrate potentially significant effects of LWR coolant environments on the fatigue resistance of pressure vessel and piping steels. This report provides an overview of the existing fatigue (var e psilon)-N data for carbon and low-alloy steels and wrought and cast austenitic SSs to define the effects of key material, loading, and environmental parameters on the fatigue lives of the steels. Experimental data are presented on the effects of surface roughness on the fatigue life of these steels in air and LWR environments. Statistical models are presented for estimating the fatigue (var e psilon)-N curves as a function of the material, loading, and environmental parameters. Two methods for incorporating environmental effects into the ASME Code fatigue evaluations are discussed. Data available in the literature have been reviewed to evaluate the conservatism in the existing ASME Code fatigue evaluations. A critical review of the margins for ASME Code fatigue design curves is presented

Review of the margins for ASME code fatigue design curve - effects of surface roughness and material variability.

Energy Technology Data Exchange (ETDEWEB)

Chopra, O. K.; Shack, W. J.; Energy Technology

2003-10-03

The ASME Boiler and Pressure Vessel Code provides rules for the construction of nuclear power plant components. The Code specifies fatigue design curves for structural materials. However, the effects of light water reactor (LWR) coolant environments are not explicitly addressed by the Code design curves. Existing fatigue strain-vs.-life ({var_epsilon}-N) data illustrate potentially significant effects of LWR coolant environments on the fatigue resistance of pressure vessel and piping steels. This report provides an overview of the existing fatigue {var_epsilon}-N data for carbon and low-alloy steels and wrought and cast austenitic SSs to define the effects of key material, loading, and environmental parameters on the fatigue lives of the steels. Experimental data are presented on the effects of surface roughness on the fatigue life of these steels in air and LWR environments. Statistical models are presented for estimating the fatigue {var_epsilon}-N curves as a function of the material, loading, and environmental parameters. Two methods for incorporating environmental effects into the ASME Code fatigue evaluations are discussed. Data available in the literature have been reviewed to evaluate the conservatism in the existing ASME Code fatigue evaluations. A critical review of the margins for ASME Code fatigue design curves is presented.

Noncoding DNA in lipofection of HeLa cells-a few insights.

Science.gov (United States)

Symens, Nathalie; Rejman, Joanna; Lucas, Bart; Demeester, Joseph; De Smedt, Stefaan C; Remaut, Katrien

2013-03-04

In cationic carrier-mediated gene delivery, the disproportional relationship between the quantity of delivered DNA and the amount of encoded protein produced is a well-known phenomenon. The numerous intracellular barriers which need to be overcome by pDNA to reach the nucleoplasm play a major role in it. In contrast to what one would expect, a partial replacement of coding pDNA by noncoding DNA does not lead to a decrease in transfection efficiency. The mechanism underlying this observation is still unclear. Therefore, we investigated which constituents of the transfection process might contribute to this phenomenon. Our data reveal that the topology of the noncoding plasmid DNA plays a major role. Noncoding pDNA can be used only in a supercoiled form to replace coding pDNA in Lipofectamine lipoplexes, without a loss in transfection levels. When noncoding pDNA is linearized or partly digested, it diminishes the transfection potential of coding pDNA, as does noncoding salmon DNA. The difference in transfection efficiencies could not be attributed to diverse physicochemical characteristics of the Lipofectamine lipoplexes containing different types of noncoding DNA or to the extent of their internalization. At the level of endosomal release, however, nucleic acid release from the endosomal compartment proceeds faster when lipoplexes contain noncoding salmon DNA. Since the half-life of pDNA in the cytosol hardly exceeds 90 min, it is conceivable that prolonged release of coding pDNA from complexes carrying supercoiled noncoding pDNA may explain its positive effect on transfection, while this depot effect does not exist when noncoding salmon DNA is used.

Rhombic-Shaped Nanostructures and Mechanical Properties of 2D DNA Origami Constructed with Different Crossover/Nick Designs.

Science.gov (United States)

Ma, Zhipeng; Huang, Yunfei; Park, Seongsu; Kawai, Kentaro; Kim, Do-Nyun; Hirai, Yoshikazu; Tsuchiya, Toshiyuki; Yamada, Hirofumi; Tabata, Osamu

2018-01-01

DNA origami methods enable the fabrication of various nanostructures and nanodevices, but their effective use depends on an understanding of their structural and mechanical properties and the effects of basic structural features. Frequency-modulation atomic force microscopy is introduced to directly characterize, in aqueous solution, the crossover regions of sets of 2D DNA origami based on different crossover/nick designs. Rhombic-shaped nanostructures formed under the influence of flexible crossovers placed between DNA helices are observed in DNA origami incorporating crossovers every 3, 4, or 6 DNA turns. The bending rigidity of crossovers is determined to be only one-third of that of the DNA helix, based on interhelical electrostatic forces reported elsewhere, and the measured pitches of the 3-turn crossover design rhombic-shaped nanostructures undergoing negligible bending. To evaluate the robustness of their structural integrity, they are intentionally and simultaneously stressed using force-controlled atomic force microscopy. DNA crossovers are verified to have a stabilizing effect on the structural robustness, while the nicks have an opposite effect. The structural and mechanical properties of DNA origami and the effects of crossovers and nicks revealed in this paper can provide information essential for the design of versatile DNA origami structures that exhibit specified and desirable properties. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mitochondrial DNA haplogroup phylogeny of the dog: Proposal for a cladistic nomenclature.

Science.gov (United States)

Fregel, Rosa; Suárez, Nicolás M; Betancor, Eva; González, Ana M; Cabrera, Vicente M; Pestano, José

2015-05-01

Canis lupus familiaris mitochondrial DNA analysis has increased in recent years, not only for the purpose of deciphering dog domestication but also for forensic genetic studies or breed characterization. The resultant accumulation of data has increased the need for a normalized and phylogenetic-based nomenclature like those provided for human maternal lineages. Although a standardized classification has been proposed, haplotype names within clades have been assigned gradually without considering the evolutionary history of dog mtDNA. Moreover, this classification is based only on the D-loop region, proven to be insufficient for phylogenetic purposes due to its high number of recurrent mutations and the lack of relevant information present in the coding region. In this study, we design 1) a refined mtDNA cladistic nomenclature from a phylogenetic tree based on complete sequences, classifying dog maternal lineages into haplogroups defined by specific diagnostic mutations, and 2) a coding region SNP analysis that allows a more accurate classification into haplogroups when combined with D-loop sequencing, thus improving the phylogenetic information obtained in dog mitochondrial DNA studies. Copyright © 2015 Elsevier B.V. All rights reserved.

Melt spreading code assessment, modifications, and initial application to the EPR core catcher design

International Nuclear Information System (INIS)

Farmer, M.T.; Basu, S.

2009-01-01

The Evolutionary Power Reactor (EPR) is a 1,600-MWe Pressurized Water Reactor (PWR) that is undergoing a design certification review by the U.S. Nuclear Regulatory Commission (NRC). The EPR severe accident design philosophy is predicated upon the fact that the projected power rating results in a narrow margin for in-vessel melt retention by external flooding. As a result, the design addresses ex-vessel core melt stabilization using a mitigation strategy that includes: 1) an external core melt retention system to temporarily hold core melt released from the vessel; 2) a layer of 'sacrificial' material that is admixed with the melt while in the core melt retention system; 3) a melt plug that, when failed, provides a pathway for the mixture to spread to a large core spreading chamber; and finally, 4) cooling and stabilization of the spread melt by controlled top and bottom flooding. The melt spreading process relies heavily on inertial flow of a low-viscosity admixed melt to a segmented spreading chamber, and assumes that the melt mass will be distributed to a uniform height in the chamber. The spreading phenomenon thus needs to be modeled properly in order to adequately assess the EPR design. The MELTSPREAD code, developed at Argonne National Laboratory, can model segmented, and both uniform and non-uniform spreading. The NRC is using MELTSPREAD to evaluate melt spreading in the EPR design. The development of MELTSPREAD ceased in the early 1990's, and so the code was first assessed against the more contemporary spreading database and code modifications, as warranted, were carried out before performing confirmatory plant calculations. This paper provides principle findings from the MELTSPREAD assessment activities and resulting code modifications, and also summarizes the results of initial scoping calculations for the EPR plant design and preliminary plant analyses, along with the plan for performing the final set of plant calculations including sensitivity studies

Restructuring of burnup sensitivity analysis code system by using an object-oriented design approach

International Nuclear Information System (INIS)

Kenji, Yokoyama; Makoto, Ishikawa; Masahiro, Tatsumi; Hideaki, Hyoudou

2005-01-01

A new burnup sensitivity analysis code system was developed with help from the object-oriented technique and written in Python language. It was confirmed that they are powerful to support complex numerical calculation procedure such as reactor burnup sensitivity analysis. The new burnup sensitivity analysis code system PSAGEP was restructured from a complicated old code system and reborn as a user-friendly code system which can calculate the sensitivity coefficients of the nuclear characteristics considering multicycle burnup effect based on the generalized perturbation theory (GPT). A new encapsulation framework for conventional codes written in Fortran was developed. This framework supported to restructure the software architecture of the old code system by hiding implementation details and allowed users of the new code system to easily calculate the burnup sensitivity coefficients. The framework can be applied to the other development projects since it is carefully designed to be independent from PSAGEP. Numerical results of the burnup sensitivity coefficient of a typical fast breeder reactor were given with components based on GPT and the multicycle burnup effects on the sensitivity coefficient were discussed. (authors)

Arabidopsis RNASE THREE LIKE2 Modulates the Expression of Protein-Coding Genes via 24-Nucleotide Small Interfering RNA-Directed DNA Methylation.

Science.gov (United States)

Elvira-Matelot, Emilie; Hachet, Mélanie; Shamandi, Nahid; Comella, Pascale; Sáez-Vásquez, Julio; Zytnicki, Matthias; Vaucheret, Hervé

2016-02-01

RNaseIII enzymes catalyze the cleavage of double-stranded RNA (dsRNA) and have diverse functions in RNA maturation. Arabidopsis thaliana RNASE THREE LIKE2 (RTL2), which carries one RNaseIII and two dsRNA binding (DRB) domains, is a unique Arabidopsis RNaseIII enzyme resembling the budding yeast small interfering RNA (siRNA)-producing Dcr1 enzyme. Here, we show that RTL2 modulates the production of a subset of small RNAs and that this activity depends on both its RNaseIII and DRB domains. However, the mode of action of RTL2 differs from that of Dcr1. Whereas Dcr1 directly cleaves dsRNAs into 23-nucleotide siRNAs, RTL2 likely cleaves dsRNAs into longer molecules, which are subsequently processed into small RNAs by the DICER-LIKE enzymes. Depending on the dsRNA considered, RTL2-mediated maturation either improves (RTL2-dependent loci) or reduces (RTL2-sensitive loci) the production of small RNAs. Because the vast majority of RTL2-regulated loci correspond to transposons and intergenic regions producing 24-nucleotide siRNAs that guide DNA methylation, RTL2 depletion modifies DNA methylation in these regions. Nevertheless, 13% of RTL2-regulated loci correspond to protein-coding genes. We show that changes in 24-nucleotide siRNA levels also affect DNA methylation levels at such loci and inversely correlate with mRNA steady state levels, thus implicating RTL2 in the regulation of protein-coding gene expression. © 2016 American Society of Plant Biologists. All rights reserved.

The artificial zinc finger coding gene 'Jazz' binds the utrophin promoter and activates transcription.

Science.gov (United States)

Corbi, N; Libri, V; Fanciulli, M; Tinsley, J M; Davies, K E; Passananti, C

2000-06-01

Up-regulation of utrophin gene expression is recognized as a plausible therapeutic approach in the treatment of Duchenne muscular dystrophy (DMD). We have designed and engineered new zinc finger-based transcription factors capable of binding and activating transcription from the promoter of the dystrophin-related gene, utrophin. Using the recognition 'code' that proposes specific rules between zinc finger primary structure and potential DNA binding sites, we engineered a new gene named 'Jazz' that encodes for a three-zinc finger peptide. Jazz belongs to the Cys2-His2 zinc finger type and was engineered to target the nine base pair DNA sequence: 5'-GCT-GCT-GCG-3', present in the promoter region of both the human and mouse utrophin gene. The entire zinc finger alpha-helix region, containing the amino acid positions that are crucial for DNA binding, was specifically chosen on the basis of the contacts more frequently represented in the available list of the 'code'. Here we demonstrate that Jazz protein binds specifically to the double-stranded DNA target, with a dissociation constant of about 32 nM. Band shift and super-shift experiments confirmed the high affinity and specificity of Jazz protein for its DNA target. Moreover, we show that chimeric proteins, named Gal4-Jazz and Sp1-Jazz, are able to drive the transcription of a test gene from the human utrophin promoter.

The PARTRAC code: Status and recent developments

Science.gov (United States)

Friedland, Werner; Kundrat, Pavel

Biophysical modeling is of particular value for predictions of radiation effects due to manned space missions. PARTRAC is an established tool for Monte Carlo-based simulations of radiation track structures, damage induction in cellular DNA and its repair [1]. Dedicated modules describe interactions of ionizing particles with the traversed medium, the production and reactions of reactive species, and score DNA damage determined by overlapping track structures with multi-scale chromatin models. The DNA repair module describes the repair of DNA double-strand breaks (DSB) via the non-homologous end-joining pathway; the code explicitly simulates the spatial mobility of individual DNA ends in parallel with their processing by major repair enzymes [2]. To simulate the yields and kinetics of radiation-induced chromosome aberrations, the repair module has been extended by tracking the information on the chromosome origin of ligated fragments as well as the presence of centromeres [3]. PARTRAC calculations have been benchmarked against experimental data on various biological endpoints induced by photon and ion irradiation. The calculated DNA fragment distributions after photon and ion irradiation reproduce corresponding experimental data and their dose- and LET-dependence. However, in particular for high-LET radiation many short DNA fragments are predicted below the detection limits of the measurements, so that the experiments significantly underestimate DSB yields by high-LET radiation [4]. The DNA repair module correctly describes the LET-dependent repair kinetics after (60) Co gamma-rays and different N-ion radiation qualities [2]. First calculations on the induction of chromosome aberrations have overestimated the absolute yields of dicentrics, but correctly reproduced their relative dose-dependence and the difference between gamma- and alpha particle irradiation [3]. Recent developments of the PARTRAC code include a model of hetero- vs euchromatin structures to enable

Conceptual OOP design of Pilot Code for Two-Fluid, Three-field Model with C++ 6.0

Energy Technology Data Exchange (ETDEWEB)

Chung, B. D.; Lee, Y. J

2006-09-15

To establish the concept of the objective oriented program (OOP) design for reactor safety analysis code, the preliminary OOP design for PILOT code, which based on one dimensional two fluid three filed model, has been attempted with C++ language feature. Microsoft C++ language has been used since it is available as groupware utilization in KAERI. The language has can be merged with Compac Visual Fortran 6.6 in Visual Studio platform. In the development platform, C++ has been used as main language and Fortran has been used as mixed language in connection with C++ main drive program. The mixed language environment is a specific feature provided in visual studio. Existing Fortran source was utilized for input routine of reading steam table from generated file and routine of steam property calculation. The calling convention and passing argument from C++ driver was corrected. The mathematical routine, such as inverse matrix conversion and tridiagonal matrix solver, has been used as PILOT Fortran routines. Simple volume and junction utilized in PILOT code can be treated as objects, since they are the basic construction elements of code system. Other routines for overall solution scheme have been realized as procedure C functions. The conceptual design which consists of hydraulic loop, component, volume, and junction class has been described in the appendix in order to give the essential OOP structure of system safety analysis code. The attempt shows that many part of system analysis code can be expressed as objects, although the overall structure should be maintained as procedure functions. The encapsulation of data and functions within an object can provide many beneficial aspects in programming of system code.

Conceptual OOP design of Pilot Code for Two-Fluid, Three-field Model with C++ 6.0

International Nuclear Information System (INIS)

Chung, B. D.; Lee, Y. J.

2006-09-01

To establish the concept of the objective oriented program (OOP) design for reactor safety analysis code, the preliminary OOP design for PILOT code, which based on one dimensional two fluid three filed model, has been attempted with C++ language feature. Microsoft C++ language has been used since it is available as groupware utilization in KAERI. The language has can be merged with Compac Visual Fortran 6.6 in Visual Studio platform. In the development platform, C++ has been used as main language and Fortran has been used as mixed language in connection with C++ main drive program. The mixed language environment is a specific feature provided in visual studio. Existing Fortran source was utilized for input routine of reading steam table from generated file and routine of steam property calculation. The calling convention and passing argument from C++ driver was corrected. The mathematical routine, such as inverse matrix conversion and tridiagonal matrix solver, has been used as PILOT Fortran routines. Simple volume and junction utilized in PILOT code can be treated as objects, since they are the basic construction elements of code system. Other routines for overall solution scheme have been realized as procedure C functions. The conceptual design which consists of hydraulic loop, component, volume, and junction class has been described in the appendix in order to give the essential OOP structure of system safety analysis code. The attempt shows that many part of system analysis code can be expressed as objects, although the overall structure should be maintained as procedure functions. The encapsulation of data and functions within an object can provide many beneficial aspects in programming of system code

Environmental construction of nano-material design codes. The example of simulation codes used in the CMD workshop

Energy Technology Data Exchange (ETDEWEB)

Miyazaki, Mikiya [Japan Atomic Energy Research Inst., Center for Promotion of Computational Science and Engineering, Kizu, Kyoto (Japan)

2003-05-01

Generally it is well known that the R and D works on new materials or devices will play a central role on the evolution of future society. But, the old ways based on the empirical and experimental approach have already reached the limit, especially for dealing with a strange substance and material. The structure of a substance and material is needed to be dealt with in detail by quantum mechanics, because the limit on accuracy has come in sight in the calculation using a classical theory. The research on the latest electronic state calculation technique founded on quantum mechanics made a great advance as the technique of solving these problems as well as the technique of a computational materials design. It enables the prediction of material properties because it is based on First Principles. Therefore, in the future it is expected to have a very high possibility of becoming a breakthrough in such a situation. In this article, the example calculation results by PC cluster on the codes (MACHIKANEYAMA-2000, OSAKA-2000) used in the CMD (Computational Materials Design) workshop, held on Sep. 19-21, at ITBL-Building and International Institute for Advanced Studies under the auspices of the University of Osaka, are described. Furthermore, the graphical user interfaces on the codes are examined. (author)

The RCC-MR design code for LMFBR components. A useful basis for fusion reactor design tools development

International Nuclear Information System (INIS)

Acker, D.; Chevereau, G.

1986-01-01

LMFBR and fusion reactors exhibit common features with regard to structural materials, temperature service level, loading types. So, design and construction rules used in France for LMFBR, that is to say RCC-MR Code, can constitute a good basis for fusion reactors design. Some original aspects of RCC-MR design rules are described, relating to unsignificant creep, ratchetting effect, fatigue and creep damage limits, creep damage evaluation, fatigue damage evaluation, buckling. The main originality of RCC-MR consists to propose comprehensive simplified rules based on elastic calculations and extended from classical cold temperatures to the elevated temperature domain. (author)

Tri-Lab Co-Design Milestone: In-Depth Performance Portability Analysis of Improved Integrated Codes on Advanced Architecture.

Energy Technology Data Exchange (ETDEWEB)

Hoekstra, Robert J. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Hammond, Simon David [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Richards, David [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Bergen, Ben [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2017-09-01

This milestone is a tri-lab deliverable supporting ongoing Co-Design efforts impacting applications in the Integrated Codes (IC) program element Advanced Technology Development and Mitigation (ATDM) program element. In FY14, the trilabs looked at porting proxy application to technologies of interest for ATS procurements. In FY15, a milestone was completed evaluating proxy applications in multiple programming models and in FY16, a milestone was completed focusing on the migration of lessons learned back into production code development. This year, the co-design milestone focuses on extracting the knowledge gained and/or code revisions back into production applications.

Hybrid real-code ant colony optimisation for constrained mechanical design

Science.gov (United States)

Pholdee, Nantiwat; Bureerat, Sujin

2016-01-01

This paper proposes a hybrid meta-heuristic based on integrating a local search simplex downhill (SDH) method into the search procedure of real-code ant colony optimisation (ACOR). This hybridisation leads to five hybrid algorithms where a Monte Carlo technique, a Latin hypercube sampling technique (LHS) and a translational propagation Latin hypercube design (TPLHD) algorithm are used to generate an initial population. Also, two numerical schemes for selecting an initial simplex are investigated. The original ACOR and its hybrid versions along with a variety of established meta-heuristics are implemented to solve 17 constrained test problems where a fuzzy set theory penalty function technique is used to handle design constraints. The comparative results show that the hybrid algorithms are the top performers. Using the TPLHD technique gives better results than the other sampling techniques. The hybrid optimisers are a powerful design tool for constrained mechanical design problems.

Characterization of the porcine carboxypeptidase E cDNA

DEFF Research Database (Denmark)

Hreidarsdôttir, G.E.; Cirera, Susanna; Fredholm, Merete

2007-01-01

the sequence of the cDNA for the porcine CPE gene including all the coding region and the 3'-UTR region was generated. Comparisons with bovine, human, mouse, and rat CPE cDNA sequences showed that the coding regions of the gene are highly conserved both at the nucleotide and at the amino acid level. A very low...

Realistic edge field model code REFC for designing and study of isochronous cyclotron

International Nuclear Information System (INIS)

Ismail, M.

1989-01-01

The focussing properties and the requirements for isochronism in cyclotron magnet configuration are well-known in hard edge field model. The fact that they quite often change considerably in realistic field can be attributed mainly to the influence of the edge field. A solution to this problem requires a field model which allows a simple construction of equilibrium orbit and yield simple formulae. This can be achieved by using a fitted realistic edge field (Hudson et al 1975) in the region of the pole edge and such a field model is therefore called a realistic edge field model. A code REFC based on realistic edge field model has been developed to design the cyclotron sectors and the code FIELDER has been used to study the beam properties. In this report REFC code has been described along with some relevant explaination of the FIELDER code. (author). 11 refs., 6 figs

The design of the CMOS wireless bar code scanner applying optical system based on ZigBee

Science.gov (United States)

Chen, Yuelin; Peng, Jian

2008-03-01

The traditional bar code scanner is influenced by the length of data line, but the farthest distance of the wireless bar code scanner of wireless communication is generally between 30m and 100m on the market. By rebuilding the traditional CCD optical bar code scanner, a CMOS code scanner is designed based on the ZigBee to meet the demands of market. The scan system consists of the CMOS image sensor and embedded chip S3C2401X, when the two dimensional bar code is read, the results show the inaccurate and wrong code bar, resulted from image defile, disturber, reads image condition badness, signal interference, unstable system voltage. So we put forward the method which uses the matrix evaluation and Read-Solomon arithmetic to solve them. In order to construct the whole wireless optics of bar code system and to ensure its ability of transmitting bar code image signals digitally with long distances, ZigBee is used to transmit data to the base station, and this module is designed based on image acquisition system, and at last the wireless transmitting/receiving CC2430 module circuit linking chart is established. And by transplanting the embedded RTOS system LINUX to the MCU, an applying wireless CMOS optics bar code scanner and multi-task system is constructed. Finally, performance of communication is tested by evaluation software Smart RF. In broad space, every ZIGBEE node can realize 50m transmission with high reliability. When adding more ZigBee nodes, the transmission distance can be several thousands of meters long.

French administrative practice and design codes for nuclear vessels

International Nuclear Information System (INIS)

Roche, R.L.

1987-07-01

French regulations on boilers and pressure vessels have prevailed for a very long time, the first measure having been promulgated on 29 October 1823. Restraining the attention to nuclear pressure vessels it must be pointed out regulations and enforcement by public authorities are more stringent than they are for conventional pressure vessels. The first part of this paper will be devoted to regulations with a special attention to the decree of 26 February 1974 and to the practice of public authorities in this field with special attention given to the Bureau de Controle de la Construction Nucleaire (BCCN = Bureau of Inspection of Nuclear Design and Manufacturing). The second part of this paper will deal with the French construction codes for nuclear components RCC-M (water reactors) and RCC-MR (elevated temperature design)

Software Design Document for the AMP Nuclear Fuel Performance Code

International Nuclear Information System (INIS)

Philip, Bobby; Clarno, Kevin T.; Cochran, Bill

2010-01-01

The purpose of this document is to describe the design of the AMP nuclear fuel performance code. It provides an overview of the decomposition into separable components, an overview of what those components will do, and the strategic basis for the design. The primary components of a computational physics code include a user interface, physics packages, material properties, mathematics solvers, and computational infrastructure. Some capability from established off-the-shelf (OTS) packages will be leveraged in the development of AMP, but the primary physics components will be entirely new. The material properties required by these physics operators include many highly non-linear properties, which will be replicated from FRAPCON and LIFE where applicable, as well as some computationally-intensive operations, such as gap conductance, which depends upon the plenum pressure. Because there is extensive capability in off-the-shelf leadership class computational solvers, AMP will leverage the Trilinos, PETSc, and SUNDIALS packages. The computational infrastructure includes a build system, mesh database, and other building blocks of a computational physics package. The user interface will be developed through a collaborative effort with the Nuclear Energy Advanced Modeling and Simulation (NEAMS) Capability Transfer program element as much as possible and will be discussed in detail in a future document.

Development and verifications of fast reactor fuel design code ''Ceptar''

International Nuclear Information System (INIS)

Ozawa, T.; Nakazawa, H.; Abe, T.

2001-01-01

The annular fuel is very beneficial for fast reactors, because it is available for both high power and high burn-up. Concerning the irradiation behavior of the annular fuel, most of annular pellets irradiated up to high burn-up showed shrinkage of the central hole due to deformation and restructuring of the pellets. It is needed to predict precisely the shrinkage of the central hole during irradiation, because it has a great influence on power-to-melt. In this paper, outline of CEPTAR code (Calculation code to Evaluate fuel pin stability for annular fuel design) developed to meet this need is presented. In this code, the radial profile of fuel density can be computed by using the void migration model, and law of conservation of mass defines the inner diameter. For the mechanical analysis, the fuel and cladding deformation caused by the thermal expansion, swelling and creep is computed by the stress-strain analysis using the approximation of plane-strain. In addition, CEPTAR can also take into account the effect of Joint-Oxide-Gain (JOG) which is observed in fuel-cladding gap of high burn-up fuel. JOG has an effect to decrease the fuel swelling and to improve the gap conductance due to deposition of solid fission product. Based on post-irradiation data on PFR annular fuel, we developed an empirical model for JOG. For code verifications, the thermal and mechanical data obtained from various irradiation tests and post-irradiation examinations were compared with the predictions of this code. In this study, INTA (instrumented test assembly) test in JOYO, PTM (power-to-melt) test in JOYO, EBR-II, FFTF and MTR in Harwell laboratory, and post-irradiation examinations on a number of PFR fuels, were used as verification data. (author)

miRNAting control of DNA methylation

Indian Academy of Sciences (India)

DNA methylation is a type of epigenetic modification where a methyl group is added to the cytosine or adenine residue of a given DNA sequence. It has been observed that DNA methylation is achieved by some collaborative agglomeration of certain proteins and non-coding RNAs. The assembly of IDN2 and its ...

Bioinformatics and multiepitope DNA immunization to design rational snake antivenom.

Directory of Open Access Journals (Sweden)

Simon C Wagstaff

2006-06-01

Full Text Available Snake venom is a potentially lethal and complex mixture of hundreds of functionally diverse proteins that are difficult to purify and hence difficult to characterize. These difficulties have inhibited the development of toxin-targeted therapy, and conventional antivenom is still generated from the sera of horses or sheep immunized with whole venom. Although life-saving, antivenoms contain an immunoglobulin pool of unknown antigen specificity and known redundancy, which necessitates the delivery of large volumes of heterologous immunoglobulin to the envenomed victim, thus increasing the risk of anaphylactoid and serum sickness adverse effects. Here we exploit recent molecular sequence analysis and DNA immunization tools to design more rational toxin-targeted antivenom.We developed a novel bioinformatic strategy that identified sequences encoding immunogenic and structurally significant epitopes from an expressed sequence tag database of a venom gland cDNA library of Echis ocellatus, the most medically important viper in Africa. Focusing upon snake venom metalloproteinases (SVMPs that are responsible for the severe and frequently lethal hemorrhage in envenomed victims, we identified seven epitopes that we predicted would be represented in all isomers of this multimeric toxin and that we engineered into a single synthetic multiepitope DNA immunogen (epitope string. We compared the specificity and toxin-neutralizing efficacy of antiserum raised against the string to antisera raised against a single SVMP toxin (or domains or antiserum raised by conventional (whole venom immunization protocols. The SVMP string antiserum, as predicted in silico, contained antibody specificities to numerous SVMPs in E. ocellatus venom and venoms of several other African vipers. More significantly, the antiserum cross-specifically neutralized hemorrhage induced by E. ocellatus and Cerastes cerastes cerastes venoms.These data provide valuable sequence and structure

Shader programming for computational arts and design: A comparison between creative coding frameworks

OpenAIRE

Gomez, Andres Felipe; Colubri, Andres; Charalambos, Jean Pierre

2016-01-01

We describe an Application Program Interface (API) that facilitates the use of GLSL shaders in computational design, interactive arts, and data visualization. This API was first introduced in the version 2.0 of Processing, a programming language and environment widely used for teaching and production in the context of media arts and design, and has been recently completed in the 3.0 release. It aims to incorporate low-level shading programming into code-based design, by int...

Rational design of DNA sequences for nanotechnology, microarrays and molecular computers using Eulerian graphs.

Science.gov (United States)

Pancoska, Petr; Moravek, Zdenek; Moll, Ute M

2004-01-01

Nucleic acids are molecules of choice for both established and emerging nanoscale technologies. These technologies benefit from large functional densities of 'DNA processing elements' that can be readily manufactured. To achieve the desired functionality, polynucleotide sequences are currently designed by a process that involves tedious and laborious filtering of potential candidates against a series of requirements and parameters. Here, we present a complete novel methodology for the rapid rational design of large sets of DNA sequences. This method allows for the direct implementation of very complex and detailed requirements for the generated sequences, thus avoiding 'brute force' filtering. At the same time, these sequences have narrow distributions of melting temperatures. The molecular part of the design process can be done without computer assistance, using an efficient 'human engineering' approach by drawing a single blueprint graph that represents all generated sequences. Moreover, the method eliminates the necessity for extensive thermodynamic calculations. Melting temperature can be calculated only once (or not at all). In addition, the isostability of the sequences is independent of the selection of a particular set of thermodynamic parameters. Applications are presented for DNA sequence designs for microarrays, universal microarray zip sequences and electron transfer experiments.

HCPB TBM thermo mechanical design: Assessment with respect codes and standards and DEMO relevancy

International Nuclear Information System (INIS)

Cismondi, F.; Kecskes, S.; Aiello, G.

2011-01-01

In the frame of the activities of the European TBM Consortium of Associates the Helium Cooled Pebble Bed Test Blanket Module (HCPB-TBM) is developed in Karlsruhe Institute of Technology (KIT). After performing detailed thermal and fluid dynamic analyses of the preliminary HCPB TBM design, the thermo mechanical behaviour of the TBM under typical ITER loads has to be assessed. A synthesis of the different design options proposed has been realized building two different assemblies of the HCPB-TBM: these two assemblies and the analyses performed on them are presented in this paper. Finite Element thermo-mechanical analyses of two detailed 1/4 scaled models of the HCPB-TBM assemblies proposed have been performed, with the aim of verifying the accordance of the mechanical behaviour with the criteria of the design codes and standards. The structural design limits specified in the codes and standard are discussed in relation with the EUROFER available data and possible damage modes. Solutions to improve the weak structural points of the present design are identified and the DEMO relevancy of the present thermal and structural design parameters is discussed.

Detecting non-coding selective pressure in coding regions

Directory of Open Access Journals (Sweden)

Blanchette Mathieu

2007-02-01

Full Text Available Abstract Background Comparative genomics approaches, where orthologous DNA regions are compared and inter-species conserved regions are identified, have proven extremely powerful for identifying non-coding regulatory regions located in intergenic or intronic regions. However, non-coding functional elements can also be located within coding region, as is common for exonic splicing enhancers, some transcription factor binding sites, and RNA secondary structure elements affecting mRNA stability, localization, or translation. Since these functional elements are located in regions that are themselves highly conserved because they are coding for a protein, they generally escaped detection by comparative genomics approaches. Results We introduce a comparative genomics approach for detecting non-coding functional elements located within coding regions. Codon evolution is modeled as a mixture of codon substitution models, where each component of the mixture describes the evolution of codons under a specific type of coding selective pressure. We show how to compute the posterior distribution of the entropy and parsimony scores under this null model of codon evolution. The method is applied to a set of growth hormone 1 orthologous mRNA sequences and a known exonic splicing elements is detected. The analysis of a set of CORTBP2 orthologous genes reveals a region of several hundred base pairs under strong non-coding selective pressure whose function remains unknown. Conclusion Non-coding functional elements, in particular those involved in post-transcriptional regulation, are likely to be much more prevalent than is currently known. With the numerous genome sequencing projects underway, comparative genomics approaches like that proposed here are likely to become increasingly powerful at detecting such elements.

Optimum design of a coded mask X-ray telescope for rocket applications

International Nuclear Information System (INIS)

Gunson, J.; Polychronopulos, B.

1976-01-01

A review of the principles of current X-ray telescopes is made with particular emphasis on two-step imaging techniques involving coding masks. The merits and limitations of the various types of coding masks in use are examined in detail. The limitations are shown to arise from the finite nature of practical masks. By postulating periodicity, 'optimum masks' can be constructed with ideal imaging qualities. The theory for the design of such masks and the practical considerations involved in the design of a rocket-borne X-ray telescope system are discussed in full, with particular attention paid to resolution, field of view and image noise. The main emphasis throughout the paper is on one-dimensional masks but two-dimensional masks are also studied. It is concluded that optimum masks could prove very valuable in astronomical applications and also in other fields such as radiography, where high imaging quality coupled with high sensitivity and low cost are of utmost importance. (author)

Pressure vessel design codes: A review of their applicability to HTGR components at temperatures above 800 deg C

International Nuclear Information System (INIS)

Hughes, P.T.; Over, H.H.; Bieniussa, K.

1984-01-01

The governments of USA and Federal Republic of Germany have approved of cooperation between the two countries in an endeavour to establish structural design code for gas reactor components intended to operate at temperatures exceeding 800 deg C. The basis of existing codes and their applicability to gas reactor component design are reviewed in this paper. This review has raised a number of important questions as to the direct applicability of the present codes. The status of US and FRG cooperative efforts to obtain answers to these questions are presented

A study on technical issues of materials and design bases in ASME section III subsection NH code

International Nuclear Information System (INIS)

Lee, Hyeong Yeon; Kim, Jong Bum; Yoo, Bong

2000-12-01

In this study, an analysis of evaluation report by ORNL on the technical issues of elevated temperatures design guide line, ASME Code Section III Subsection NH was conducted and a brief evaluation procedure of the creep-fatigue damage was presented. ORNL published the report in 1993 and reviewed the issue areas where code rules or regulatory guides may be lacking or inadequate to ensure safe operation over the expected life cycles for liquid metal reactor systems. From historical viewpoint of the ASME NH code development, ASME Code Case 47 was changed much in 1989 edition, which includes the stress relaxation behavior in creep damage evaluation. Afterwards the 1992 version of CC N-47 was upgraded to Subsection NH in 1995 edition, which is the same with that of CC N-47 1992 edition except few material data. This report brings up the technical and regulatory issues that can not guarantee the safe and reliable operation of the ALMR which got the conceptual design certification from NRC. Twenty three technical issues were raised and settlement methodology were proposed. Additionally, the status of items approved by ASME code subgroup of elevated temperature design committee for the revision of the most recent 1998 edition of ASME NH was described

Programme DNA Lattices: Design, Synthesis and Applications

National Research Council Canada - National Science Library

Reif, John

2006-01-01

.... Self-assembled DNA nanostructures provide a methodology for bottom-up nanoscale construction of highly patterned systems, utilizing macromolecular DNA tiles" composed of branched DNA, self-assembled...

The RCC-MR design code for LMFBR components. A useful basic for fusion reactor design tools development

International Nuclear Information System (INIS)

Acker, D.; Chevereau, G.

1985-11-01

LMFBR and fusion reactors exhibit common features with regard to structural materials (Stainless steels), temperature service level (550-600 0 C), loading types. So, design and construction rules used in France for LMFBR, that is to say RCC-MR Code, can constitute a good basis for fusion reactors design. Some original aspects of RCC-MR design rules are described, relating to unsignificant creep, ratchetting effect, fatigue and creep damage limits, creep damage evaluation, fatigue damage evaluation, buckling. The main originality of RCC-MR consists to propose comprehensive simplified rules based on elastic calculations and extended from classical cold temperatures to the elevated temperature domain

Transcription and DNA Damage: Holding Hands or Crossing Swords?

Science.gov (United States)

D'Alessandro, Giuseppina; d'Adda di Fagagna, Fabrizio

2017-10-27

Transcription has classically been considered a potential threat to genome integrity. Collision between transcription and DNA replication machinery, and retention of DNA:RNA hybrids, may result in genome instability. On the other hand, it has been proposed that active genes repair faster and preferentially via homologous recombination. Moreover, while canonical transcription is inhibited in the proximity of DNA double-strand breaks, a growing body of evidence supports active non-canonical transcription at DNA damage sites. Small non-coding RNAs accumulate at DNA double-strand break sites in mammals and other organisms, and are involved in DNA damage signaling and repair. Furthermore, RNA binding proteins are recruited to DNA damage sites and participate in the DNA damage response. Here, we discuss the impact of transcription on genome stability, the role of RNA binding proteins at DNA damage sites, and the function of small non-coding RNAs generated upon damage in the signaling and repair of DNA lesions. Copyright © 2016 Elsevier Ltd. All rights reserved.

Development and application of methods and computer codes of fuel management and nuclear design of reload cycles in PWR

International Nuclear Information System (INIS)

Ahnert, C.; Aragones, J.M.; Corella, M.R.; Esteban, A.; Martinez-Val, J.M.; Minguez, E.; Perlado, J.M.; Pena, J.; Matias, E. de; Llorente, A.; Navascues, J.; Serrano, J.

1976-01-01

Description of methods and computer codes for Fuel Management and Nuclear Design of Reload Cycles in PWR, developed at JEN by adaptation of previous codes (LEOPARD, NUTRIX, CITATION, FUELCOST) and implementation of original codes (TEMP, SOTHIS, CICLON, NUDO, MELON, ROLLO, LIBRA, PENELOPE) and their application to the project of Management and Design of Reload Cycles of a 510 Mwt PWR, including comparison with results of experimental operation and other calculations for validation of methods. (author) [es

Interface design of VSOP'94 computer code for safety analysis

Energy Technology Data Exchange (ETDEWEB)

Natsir, Khairina, E-mail: yenny@batan.go.id; Andiwijayakusuma, D.; Wahanani, Nursinta Adi [Center for Development of Nuclear Informatics - National Nuclear Energy Agency, PUSPIPTEK, Serpong, Tangerang, Banten (Indonesia); Yazid, Putranto Ilham [Center for Nuclear Technology, Material and Radiometry- National Nuclear Energy Agency, Jl. Tamansari No.71, Bandung 40132 (Indonesia)

2014-09-30

Today, most software applications, also in the nuclear field, come with a graphical user interface. VSOP'94 (Very Superior Old Program), was designed to simplify the process of performing reactor simulation. VSOP is a integrated code system to simulate the life history of a nuclear reactor that is devoted in education and research. One advantage of VSOP program is its ability to calculate the neutron spectrum estimation, fuel cycle, 2-D diffusion, resonance integral, estimation of reactors fuel costs, and integrated thermal hydraulics. VSOP also can be used to comparative studies and simulation of reactor safety. However, existing VSOP is a conventional program, which was developed using Fortran 65 and have several problems in using it, for example, it is only operated on Dec Alpha mainframe platforms and provide text-based output, difficult to use, especially in data preparation and interpretation of results. We develop a GUI-VSOP, which is an interface program to facilitate the preparation of data, run the VSOP code and read the results in a more user friendly way and useable on the Personal 'Computer (PC). Modifications include the development of interfaces on preprocessing, processing and postprocessing. GUI-based interface for preprocessing aims to provide a convenience way in preparing data. Processing interface is intended to provide convenience in configuring input files and libraries and do compiling VSOP code. Postprocessing interface designed to visualized the VSOP output in table and graphic forms. GUI-VSOP expected to be useful to simplify and speed up the process and analysis of safety aspects.

Cloning and expression of cDNA coding for bouganin.

Science.gov (United States)

den Hartog, Marcel T; Lubelli, Chiara; Boon, Louis; Heerkens, Sijmie; Ortiz Buijsse, Antonio P; de Boer, Mark; Stirpe, Fiorenzo

2002-03-01

Bouganin is a ribosome-inactivating protein that recently was isolated from Bougainvillea spectabilis Willd. In this work, the cloning and expression of the cDNA encoding for bouganin is described. From the cDNA, the amino-acid sequence was deduced, which correlated with the primary sequence data obtained by amino-acid sequencing on the native protein. Bouganin is synthesized as a pro-peptide consisting of 305 amino acids, the first 26 of which act as a leader signal while the 29 C-terminal amino acids are cleaved during processing of the molecule. The mature protein consists of 250 amino acids. Using the cDNA sequence encoding the mature protein of 250 amino acids, a recombinant protein was expressed, purified and characterized. The recombinant molecule had similar activity in a cell-free protein synthesis assay and had comparable toxicity on living cells as compared to the isolated native bouganin.

Codes maintained by the LAACG [Los Alamos Accelerator Code Group] at the NMFECC

International Nuclear Information System (INIS)

Wallace, R.; Barts, T.

1990-01-01

The Los Alamos Accelerator Code Group (LAACG) maintains two groups of design codes at the National Magnetic Fusion Energy Computing Center (NMFECC). These codes, principally electromagnetic field solvers, are used for the analysis and design of electromagnetic components for accelerators, e.g., magnets, rf structures, pickups, etc. In this paper, the status and future of the installed codes will be discussed with emphasis on an experimental version of one set of codes, POISSON/SUPERFISH

Application of neutron/gamma transport codes for the design of explosive detection systems

International Nuclear Information System (INIS)

Elias, E.; Shayer, Z.

1994-01-01

Applications of neutron and gamma transport codes to the design of nuclear techniques for detecting concealed explosives material are discussed. The methodology of integrating radiation transport computations in the development, optimization and analysis phases of these new technologies is discussed. Transport and Monte Carlo codes are used for proof of concepts, guide the system integration, reduce the extend of experimental program and provide insight into the physical problem involved. The paper concentrates on detection techniques based on thermal and fast neutron interactions in the interrogated object. (authors). 6 refs., 1 tab., 5 figs

Lightning protection design of nuclear power plants. KTA safety code, version 6/99

International Nuclear Information System (INIS)

1999-06-01

This KTA safety code does not cover calculation methods for determination of lightning-induced voltage inputs to control room systems within the reactor building, as the literature presents a variety of applicable methods, which however cannot be directly applied to any power plant, due to the great diversity of geometries of the electrical systems and control room systems in nuclear power plants. Compliance with the design requirements of this safety code for shielding of buildings, and installation and shielding of cables, can be considered to offer the appropriate protection. (orig./CB) [de

Design and Characterization of DNA Strand-Displacement Circuits in Serum-Supplemented Cell Medium.

Science.gov (United States)

Fern, Joshua; Schulman, Rebecca

2017-09-15

The functional stability and lifetimes of synthetic molecular circuits in biological environments are important for long-term, stable sensors or controllers of cell or tissue behavior. DNA-based molecular circuits, in particular DNA strand-displacement circuits, provide simple and effective biocompatible control mechanisms and sensors, but are vulnerable to digestion by nucleases present in living tissues and serum-supplemented cell culture. The stability of double-stranded and single-stranded DNA circuit components in serum-supplemented cell medium and the corresponding effect of nuclease-mediated degradation on circuit performance were characterized to determine the major routes of degradation and DNA strand-displacement circuit failure. Simple circuit design choices, such as the use of 5' toeholds within the DNA complexes used as reactants in the strand-displacement reactions and the termination of single-stranded components with DNA hairpin domains at the 3' termini, significantly increase the functional lifetime of the circuit components in the presence of nucleases. Simulations of multireaction circuits, guided by the experimentally measured operation of single-reaction circuits, enable predictive realization of multilayer and competitive-reaction circuit behavior. Together, these results provide a basic route to increased DNA circuit stability in cell culture environments.

Computer-assisted design for scaling up systems based on DNA reaction networks.

Science.gov (United States)

Aubert, Nathanaël; Mosca, Clément; Fujii, Teruo; Hagiya, Masami; Rondelez, Yannick

2014-04-06

In the past few years, there have been many exciting advances in the field of molecular programming, reaching a point where implementation of non-trivial systems, such as neural networks or switchable bistable networks, is a reality. Such systems require nonlinearity, be it through signal amplification, digitalization or the generation of autonomous dynamics such as oscillations. The biochemistry of DNA systems provides such mechanisms, but assembling them in a constructive manner is still a difficult and sometimes counterintuitive process. Moreover, realistic prediction of the actual evolution of concentrations over time requires a number of side reactions, such as leaks, cross-talks or competitive interactions, to be taken into account. In this case, the design of a system targeting a given function takes much trial and error before the correct architecture can be found. To speed up this process, we have created DNA Artificial Circuits Computer-Assisted Design (DACCAD), a computer-assisted design software that supports the construction of systems for the DNA toolbox. DACCAD is ultimately aimed to design actual in vitro implementations, which is made possible by building on the experimental knowledge available on the DNA toolbox. We illustrate its effectiveness by designing various systems, from Montagne et al.'s Oligator or Padirac et al.'s bistable system to new and complex networks, including a two-bit counter or a frequency divider as well as an example of very large system encoding the game Mastermind. In the process, we highlight a variety of behaviours, such as enzymatic saturation and load effect, which would be hard to handle or even predict with a simpler model. We also show that those mechanisms, while generally seen as detrimental, can be used in a positive way, as functional part of a design. Additionally, the number of parameters included in these simulations can be large, especially in the case of complex systems. For this reason, we included the

Recommendations for codes and standards to be used for design and fabrication of high level waste canister

International Nuclear Information System (INIS)

Bermingham, A.J.; Booker, R.J.; Booth, H.R.; Ruehle, W.G.; Shevekov, S.; Silvester, A.G.; Tagart, S.W.; Thomas, J.A.; West, R.G.

1978-01-01

This study identifies codes, standards, and regulatory requirements for developing design criteria for high-level waste (HLW) canisters for commercial operation. It has been determined that the canister should be designed as a pressure vessel without provision for any overpressure protection type devices. It is recommended that the HLW canister be designed and fabricated to the requirements of the ASME Section III Code, Division 1 rules, for Code Class 3 components. Identification of other applicable industry and regulatory guides and standards are provided in this report. Requirements for the Design Specification are found in the ASME Section III Code. It is recommended that design verification be conducted principally with prototype testing which will encompass normal and accident service conditions during all phases of the canister life. Adequacy of existing quality assurance and licensing standards for the canister was investigated. One of the recommendations derived from this study is a requirement that the canister be N stamped. In addition, acceptance standards for the HLW waste should be established and the waste qualified to those standards before the canister is sealed. A preliminary investigation of use of an overpack for the canister has been made, and it is concluded that the use of an overpack, as an integral part of overall canister design, is undesirable, both from a design and economics standpoint. However, use of shipping cask liners and overpack type containers at the Federal repository may make the canister and HLW management safer and more cost effective. There are several possible concepts for canister closure design. These concepts can be adapted to the canister with or without an overpack. A remote seal weld closure is considered to be one of the most suitable closure methods; however, mechanical seals should also be investigated

A biological inspired fuzzy adaptive window median filter (FAWMF) for enhancing DNA signal processing.

Science.gov (United States)

Ahmad, Muneer; Jung, Low Tan; Bhuiyan, Al-Amin

2017-10-01

Digital signal processing techniques commonly employ fixed length window filters to process the signal contents. DNA signals differ in characteristics from common digital signals since they carry nucleotides as contents. The nucleotides own genetic code context and fuzzy behaviors due to their special structure and order in DNA strand. Employing conventional fixed length window filters for DNA signal processing produce spectral leakage and hence results in signal noise. A biological context aware adaptive window filter is required to process the DNA signals. This paper introduces a biological inspired fuzzy adaptive window median filter (FAWMF) which computes the fuzzy membership strength of nucleotides in each slide of window and filters nucleotides based on median filtering with a combination of s-shaped and z-shaped filters. Since coding regions cause 3-base periodicity by an unbalanced nucleotides' distribution producing a relatively high bias for nucleotides' usage, such fundamental characteristic of nucleotides has been exploited in FAWMF to suppress the signal noise. Along with adaptive response of FAWMF, a strong correlation between median nucleotides and the Π shaped filter was observed which produced enhanced discrimination between coding and non-coding regions contrary to fixed length conventional window filters. The proposed FAWMF attains a significant enhancement in coding regions identification i.e. 40% to 125% as compared to other conventional window filters tested over more than 250 benchmarked and randomly taken DNA datasets of different organisms. This study proves that conventional fixed length window filters applied to DNA signals do not achieve significant results since the nucleotides carry genetic code context. The proposed FAWMF algorithm is adaptive and outperforms significantly to process DNA signal contents. The algorithm applied to variety of DNA datasets produced noteworthy discrimination between coding and non-coding regions contrary

Verification of fire and explosion accident analysis codes (facility design and preliminary results)

International Nuclear Information System (INIS)

Gregory, W.S.; Nichols, B.D.; Talbott, D.V.; Smith, P.R.; Fenton, D.L.

1985-01-01

For several years, the US Nuclear Regulatory Commission has sponsored the development of methods for improving capabilities to analyze the effects of postulated accidents in nuclear facilities; the accidents of interest are those that could occur during nuclear materials handling. At the Los Alamos National Laboratory, this program has resulted in three computer codes: FIRAC, EXPAC, and TORAC. These codes are designed to predict the effects of fires, explosions, and tornadoes in nuclear facilities. Particular emphasis is placed on the movement of airborne radioactive material through the gaseous effluent treatment system of a nuclear installation. The design, construction, and calibration of an experimental ventilation system to verify the fire and explosion accident analysis codes are described. The facility features a large industrial heater and several aerosol smoke generators that are used to simulate fires. Both injected thermal energy and aerosol mass can be controlled using this equipment. Explosions are simulated with H 2 /O 2 balloons and small explosive charges. Experimental measurements of temperature, energy, aerosol release rates, smoke concentration, and mass accumulation on HEPA filters can be made. Volumetric flow rate and differential pressures also are monitored. The initial experiments involve varying parameters such as thermal and aerosol rate and ventilation flow rate. FIRAC prediction results are presented. 10 figs

Calibration Methods for Reliability-Based Design Codes

DEFF Research Database (Denmark)

Gayton, N.; Mohamed, A.; Sørensen, John Dalsgaard

2004-01-01

The calibration methods are applied to define the optimal code format according to some target safety levels. The calibration procedure can be seen as a specific optimization process where the control variables are the partial factors of the code. Different methods are available in the literature...

Characterization of non-coding DNA satellites associated with sweepoviruses (genus Begomovirus, Geminiviridae - definition of a distinct class of begomovirus-associated satellites

Directory of Open Access Journals (Sweden)

Gloria eLozano

2016-02-01

Full Text Available Begomoviruses (family Geminiviridae are whitefly-transmitted, plant-infecting single-stranded DNA viruses that cause crop losses throughout the warmer parts of the World. Sweepoviruses are a phylogenetically distinct group of begomoviruses that infect plants of the family Convolvulaceae, including sweet potato (Ipomoea batatas. Two classes of subviral molecules are often associated with begomoviruses, particularly in the Old World; the betasatellites and the alphasatellites. An analysis of sweet potato and Ipomoea indica samples from Spain and Merremia dissecta samples from Venezuela identified small non-coding subviral molecules in association with several distinct sweepoviruses. The sequences of 18 clones were obtained and found to be structurally similar to tomato leaf curl virus–satellite (ToLCV-sat, the first DNA satellite identified in association with a begomovirus, with a region with significant sequence identity to the conserved region of betasatellites, an A-rich sequence, a predicted stem-loop structure containing the nonanucleotide TAATATTAC, and a second predicted stem-loop. These sweepovirus-associated satellites join an increasing number of ToLCV-sat-like non-coding satellites identified recently. Although sharing some features with betasatellites, evidence is provided to suggest that the ToLCV-sat-like satellites are distinct from betasatellites and should be considered a separate class of satellites, for which the collective name deltasatellites is proposed.

Comparison benchmark between tokamak simulation code and TokSys for Chinese Fusion Engineering Test Reactor vertical displacement control design

International Nuclear Information System (INIS)

Qiu Qing-Lai; Xiao Bing-Jia; Guo Yong; Liu Lei; Wang Yue-Hang

2017-01-01

Vertical displacement event (VDE) is a big challenge to the existing tokamak equipment and that being designed. As a Chinese next-step tokamak, the Chinese Fusion Engineering Test Reactor (CFETR) has to pay attention to the VDE study with full-fledged numerical codes during its conceptual design. The tokamak simulation code (TSC) is a free boundary time-dependent axisymmetric tokamak simulation code developed in PPPL, which advances the MHD equations describing the evolution of the plasma in a rectangular domain. The electromagnetic interactions between the surrounding conductor circuits and the plasma are solved self-consistently. The TokSys code is a generic modeling and simulation environment developed in GA. Its RZIP model treats the plasma as a fixed spatial distribution of currents which couple with the surrounding conductors through circuit equations. Both codes have been individually used for the VDE study on many tokamak devices, such as JT-60U, EAST, NSTX, DIII-D, and ITER. Considering the model differences, benchmark work is needed to answer whether they reproduce each other’s results correctly. In this paper, the TSC and TokSys codes are used for analyzing the CFETR vertical instability passive and active controls design simultaneously. It is shown that with the same inputs, the results from these two codes conform with each other. (paper)

Analysis and application of ratcheting evaluation procedure of Japanese high temperature design code DDS

International Nuclear Information System (INIS)

Lee, H. Y.; Kim, J. B.; Lee, J. H.

2002-01-01

In this study, the evaluation procedure of Japanese DDS code which was recently developed to assess the progressive inelastic deformation occurring under repetition of secondary stresses was analyzed and the evaluation results according to DDS was compared those of the thermal ratchet structural test carried out by KAERI to analyze the conservativeness of the code. The existing high temperature codes of US ASME-NH and French RCC-MR suggest the limited ratcheting procedures for only the load cases of cyclic secondary stresses under primary stresses. So they are improper to apply to the actual ratcheting problem which can occur under cyclic secondary membrane stresses due to the movement of hot free surface for the pool type LMR. DDS provides explicitly an analysis procedure of ratcheting due to moving thermal gradients near hot free surface. A comparison study was carried out between the results by the design code of DDS and by the structural test to investigate the conservativeness of DDS code, which showed that the evaluation results by DDS were in good agreement with those of the structural test

Sequence analysis of mitochondrial DNA hypervariable region III of ...

African Journals Online (AJOL)

Aghomotsegin

2015-07-01

Jul 1, 2015 ... population genetics research, studies based on mitochondrial DNA (mtDNA) and Y-chromosome DNA are an excellent way of illustrating population structure .... avoid landing investigators into serious situations of medical genetic privacy and ethnics, especially for. mtDNA coding area whose mutation often ...

A mitochondrial DNA SNP multiplex assigning Caucasians into 36 haplo- and subhaplogroups

DEFF Research Database (Denmark)

Mikkelsen, Martin; Rockenbauer, Eszter; Sørensen, Erik

2008-01-01

Mitochondrial DNA (mtDNA) is maternally inherited without recombination events and has a high copy number, which makes mtDNA analysis feasible even when genomic DNA is sparse or degraded. Here, we present a SNP typing assay with 33 previously described mtDNA coding region SNPs for haplogroup...... previously typed by sequencing of the mitochondrial HV1 and HV2 regions. Haplogroup assignments based on mtDNA coding region SNPs and sequencing of HV1 and HV2 regions gave identical results for 27% of the samples, and except for one sample, differences in haplogroup assignments were at the subhaplogroup...

Melt spreading code assessment, modifications, and application to the EPR core catcher design

International Nuclear Information System (INIS)

Farmer, M.T.

2009-01-01

The Evolutionary Power Reactor (EPR) is under consideration by various utilities in the United States to provide base load electrical production, and as a result the design is undergoing a certification review by the U.S. Nuclear Regulatory Commission (NRC). The severe accident design philosophy for this reactor is based upon the fact that the projected power rating results in a narrow margin for in-vessel melt retention by external cooling of the reactor vessel. As a result, the design addresses ex-vessel core melt stabilization using a mitigation strategy that includes: (1) an external core melt retention system to temporarily hold core melt released from the vessel; (2) a layer of 'sacrificial' material that is admixed with the melt while in the core melt retention system; (3) a melt plug in the lower part of the retention system that, when failed, provides a pathway for the mixture to spread to a large core spreading chamber; and finally, (4) cooling and stabilization of the spread melt by controlled top and bottom flooding. The overall concept is illustrated in Figure 1.1. The melt spreading process relies heavily on inertial flow of a low-viscosity admixed melt to a segmented spreading chamber, and assumes that the melt mass will be distributed to a uniform height in the chamber. The spreading phenomenon thus needs to be modeled properly in order to adequately assess the EPR design. The MELTSPREAD code, developed at Argonne National Laboratory, can model segmented, and both uniform and nonuniform spreading. The NRC is thus utilizing MELTSPREAD to evaluate melt spreading in the EPR design. MELTSPREAD was originally developed to support resolution of the Mark I containment shell vulnerability issue. Following closure of this issue, development of MELTSPREAD ceased in the early 1990's, at which time the melt spreading database upon which the code had been validated was rather limited. In particular, the database that was utilized for initial validation consisted

Long Non-coding RNAs in Response to Genotoxic Stress

Institute of Scientific and Technical Information of China (English)

Xiaoman Li; Dong Pan; Baoquan Zhao; Burong Hu

2016-01-01

Long non-coding RNAs(lncRNAs) are increasingly involved in diverse biological processes.Upon DNA damage,the DNA damage response(DDR) elicits a complex signaling cascade,which includes the induction of lncRNAs.LncRNA-mediated DDR is involved in non-canonical and canonical manners.DNA-damage induced lncRNAs contribute to the regulation of cell cycle,apoptosis,and DNA repair,thereby playing a key role in maintaining genome stability.This review summarizes the emerging role of lncRNAs in DNA damage and repair.

SRAC: JAERI thermal reactor standard code system for reactor design and analysis

International Nuclear Information System (INIS)

Tsuchihashi, Keichiro; Takano, Hideki; Horikami, Kunihiko; Ishiguro, Yukio; Kaneko, Kunio; Hara, Toshiharu.

1983-01-01

The SRAC (Standard Reactor Analysis Code) is a code system for nuclear reactor analysis and design. It is composed of neutron cross section libraries and auxiliary processing codes, neutron spectrum routines, a variety of transport, 1-, 2- and 3-D diffusion routines, dynamic parameters and cell burn-up routines. By making the best use of the individual code function in the SRAC system, the user can select either the exact method for an accurate estimate of reactor characteristics or the economical method aiming at a shorter computer time, depending on the purpose of study. The user can select cell or core calculation; fixed source or eigenvalue problem; transport (collision probability or Sn) theory or diffusion theory. Moreover, smearing and collapsing of macroscopic cross sections are separately done by the user's selection. And a special attention is paid for double heterogeneity. Various techniques are employed to access the data storage and to optimize the internal data transfer. Benchmark calculations using the SRAC system have been made extensively for the Keff values of various types of critical assemblies (light water, heavy water and graphite moderated systems, and fast reactor systems). The calculated results show good prediction for the experimental Keff values. (author)

Stability analysis criteria in landfill design based on the Spanish code

International Nuclear Information System (INIS)

Estaire Gepp, J.; Pardo de Santayana, F.

2014-01-01

The design of a landfill requires performing stability analyses. To perform such analyses it is necessary to define different design situations and their corresponding safety factors. Geo synthetics are normally used to construct the lining system of the landfills, causing critical slip surfaces to pass along one of the different geosynthetic interfaces. Determination of the shear strength of such critical interfaces is, therefore, an extremely important issue. In this paper, these aspects are analysed based on what is set in the Spanish codes and in the technical literature. As a result of the study, some tables are presented which relate the different design situations (normal, accidental or extraordinary) to the shear strength of the lining system to be used (peak or residual) and define the minimum factor of safety to be accomplished. (Author)

Artificial Intelligence, DNA Mimicry, and Human Health.

Science.gov (United States)

Stefano, George B; Kream, Richard M

2017-08-14

The molecular evolution of genomic DNA across diverse plant and animal phyla involved dynamic registrations of sequence modifications to maintain existential homeostasis to increasingly complex patterns of environmental stressors. As an essential corollary, driver effects of positive evolutionary pressure are hypothesized to effect concerted modifications of genomic DNA sequences to meet expanded platforms of regulatory controls for successful implementation of advanced physiological requirements. It is also clearly apparent that preservation of updated registries of advantageous modifications of genomic DNA sequences requires coordinate expansion of convergent cellular proofreading/error correction mechanisms that are encoded by reciprocally modified genomic DNA. Computational expansion of operationally defined DNA memory extends to coordinate modification of coding and previously under-emphasized noncoding regions that now appear to represent essential reservoirs of untapped genetic information amenable to evolutionary driven recruitment into the realm of biologically active domains. Additionally, expansion of DNA memory potential via chemical modification and activation of noncoding sequences is targeted to vertical augmentation and integration of an expanded cadre of transcriptional and epigenetic regulatory factors affecting linear coding of protein amino acid sequences within open reading frames.

Discussion on LDPC Codes and Uplink Coding

Science.gov (United States)

Andrews, Ken; Divsalar, Dariush; Dolinar, Sam; Moision, Bruce; Hamkins, Jon; Pollara, Fabrizio

2007-01-01

This slide presentation reviews the progress that the workgroup on Low-Density Parity-Check (LDPC) for space link coding. The workgroup is tasked with developing and recommending new error correcting codes for near-Earth, Lunar, and deep space applications. Included in the presentation is a summary of the technical progress of the workgroup. Charts that show the LDPC decoder sensitivity to symbol scaling errors are reviewed, as well as a chart showing the performance of several frame synchronizer algorithms compared to that of some good codes and LDPC decoder tests at ESTL. Also reviewed is a study on Coding, Modulation, and Link Protocol (CMLP), and the recommended codes. A design for the Pseudo-Randomizer with LDPC Decoder and CRC is also reviewed. A chart that summarizes the three proposed coding systems is also presented.

Review of design codes of concrete encased steel short columns under axial compression

Directory of Open Access Journals (Sweden)

K.Z. Soliman

2013-08-01

Full Text Available In recent years, the use of encased steel concrete columns has been increased significantly in medium-rise or high-rise buildings. The aim of the present investigation is to assess experimentally the current methods and codes for evaluating the ultimate load behavior of concrete encased steel short columns. The current state of design provisions for composite columns from the Egyptian codes ECP203-2007 and ECP-SC-LRFD-2012, as well as, American Institute of Steel Construction, AISC-LRFD-2010, American Concrete Institute, ACI-318-2008, and British Standard BS-5400-5 was reviewed. The axial capacity portion of both the encased steel section and the concrete section was also studied according to the previously mentioned codes. Ten encased steel concrete columns have been investigated experimentally to study the effect of concrete confinement and different types of encased steel sections. The measured axial capacity of the tested ten composite columns was compared with the values calculated by the above mentioned codes. It is concluded that non-negligible discrepancies exist between codes and the experimental results as the confinement effect was not considered in predicting both the strength and ductility of concrete. The confining effect was obviously influenced by the shape of the encased steel section. The tube-shaped steel section leads to better confinement than the SIB section. Among the used codes, the ECP-SC-LRFD-2012 led to the most conservative results.

Designing an efficient LT-code with unequal error protection for image transmission

Science.gov (United States)

S. Marques, F.; Schwartz, C.; Pinho, M. S.; Finamore, W. A.

2015-10-01

The use of images from earth observation satellites is spread over different applications, such as a car navigation systems and a disaster monitoring. In general, those images are captured by on board imaging devices and must be transmitted to the Earth using a communication system. Even though a high resolution image can produce a better Quality of Service, it leads to transmitters with high bit rate which require a large bandwidth and expend a large amount of energy. Therefore, it is very important to design efficient communication systems. From communication theory, it is well known that a source encoder is crucial in an efficient system. In a remote sensing satellite image transmission, this efficiency is achieved by using an image compressor, to reduce the amount of data which must be transmitted. The Consultative Committee for Space Data Systems (CCSDS), a multinational forum for the development of communications and data system standards for space flight, establishes a recommended standard for a data compression algorithm for images from space systems. Unfortunately, in the satellite communication channel, the transmitted signal is corrupted by the presence of noise, interference signals, etc. Therefore, the receiver of a digital communication system may fail to recover the transmitted bit. Actually, a channel code can be used to reduce the effect of this failure. In 2002, the Luby Transform code (LT-code) was introduced and it was shown that it was very efficient when the binary erasure channel model was used. Since the effect of the bit recovery failure depends on the position of the bit in the compressed image stream, in the last decade many e orts have been made to develop LT-code with unequal error protection. In 2012, Arslan et al. showed improvements when LT-codes with unequal error protection were used in images compressed by SPIHT algorithm. The techniques presented by Arslan et al. can be adapted to work with the algorithm for image compression

Channel coding study for ultra-low power wireless design of autonomous sensor works

NARCIS (Netherlands)

Zhang, P.; Huang, Li; Willems, F.M.J.

2011-01-01

Ultra-low power wireless design is highly demanded for building up autonomous wireless sensor networks (WSNs) for many application areas. To keep certain quality of service with limited power budget, channel coding techniques can be applied to maintain the robustness and reliability of WSNs. In this

Production of DNA minicircles less than 250 base pairs through a novel concentrated DNA circularization assay enabling minicircle design with NF-κB inhibition activity

Science.gov (United States)

Thibault, Thomas; Degrouard, Jeril; Baril, Patrick; Pichon, Chantal; Midoux, Patrick

2017-01-01

Abstract Double-stranded DNA minicircles of less than 1000 bp in length have great interest in both fundamental research and therapeutic applications. Although minicircles have shown promising activity in gene therapy thanks to their good biostability and better intracellular trafficking, minicircles down to 250 bp in size have not yet been investigated from the test tube to the cell for lack of an efficient production method. Herein, we report a novel versatile plasmid-free method for the production of DNA minicircles comprising fewer than 250 bp. We designed a linear nicked DNA double-stranded oligonucleotide blunt-ended substrate for efficient minicircle production in a ligase-mediated and bending protein-assisted circularization reaction at high DNA concentration of 2 μM. This one pot multi-step reaction based-method yields hundreds of micrograms of minicircle with sequences of any base composition and position and containing or not a variety of site-specifically chemical modifications or physiological supercoiling. Biochemical and cellular studies were then conducted to design a 95 bp minicircle capable of binding in vitro two NF-κB transcription factors per minicircle and to efficiently inhibiting NF-κB-dependent transcriptional activity in human cells. Therefore, our production method could pave the way for the design of minicircles as new decoy nucleic acids. PMID:27899652

Tailoring DNA vaccines: designing strategies against HER2 positive cancers

Directory of Open Access Journals (Sweden)

Cristina eMarchini

2013-05-01

Full Text Available The crucial role of HER2 in epithelial transformation and its selective overexpression on cancer tissues makes it an ideal target for cancer immunotherapies such as passive immunotherapy with Trastuzumab. There are, however, a number of concerns regarding the use of monoclonal antibodies which include resistance, repeated treatments, considerable costs and side effects that make active immunotherapies against HER2 desirable alternative approaches. The efficacy of anti-HER2 DNA vaccination has been widely demonstrated in transgenic cancer-prone mice, which recapitulate several features of human breast cancers. Nonetheless, the rational design of a cancer vaccine able to trigger a long lasting immunity, and thus prevent tumor recurrence in patients, would require the understanding of how tolerance and immunosuppression regulate antitumor immune responses and, at the same time, the identification of the most immunogenic portions of the target protein. We herein retrace the findings that led to our most promising DNA vaccines that, by encoding human/rat chimeric forms of HER2, are able to circumvent peripheral tolerance. Preclinical data obtained with these chimeric DNA vaccines have provided the rationale for their use in an ongoing phase I clinical trial (EudraCT 2011-001104-34.

A new code for the design and analysis of the heliostat field layout for power tower system

Energy Technology Data Exchange (ETDEWEB)

Wei, Xiudong; Lu, Zhenwu; Yu, Weixing [Changchun Institute of Optics, Fine Mechanics and Physics of Chinese Academy of Sciences, Changchun 130033 (China); Wang, Zhifeng [The Key Laboratory of Solar Thermal Energy and Photovoltaic system, Institute of Electrical Engineering, Chinese Academy of Sciences, Beijing 100190 (China)

2010-04-15

A new code for the design and analysis of the heliostat field layout for power tower system is developed. In the new code, a new method for the heliostat field layout is proposed based on the edge ray principle of nonimaging optics. The heliostat field boundary is constrained by the tower height, the receiver tilt angle and size and the heliostat efficiency factor which is the product of the annual cosine efficiency and the annual atmospheric transmission efficiency. With the new method, the heliostat can be placed with a higher efficiency and a faster response speed of the design and optimization can be obtained. A new module for the analysis of the aspherical heliostat is created in the new code. A new toroidal heliostat field is designed and analyzed by using the new code. Compared with the spherical heliostat, the solar image radius of the field is reduced by about 30% by using the toroidal heliostat if the mirror shape and the tracking are ideal. In addition, to maximize the utilization of land, suitable crops can be considered to be planted under heliostats. To evaluate the feasibility of the crop growth, a method for calculating the annual distribution of sunshine duration on the land surface is developed as well. (author)

New quantum codes constructed from quaternary BCH codes

Science.gov (United States)

Xu, Gen; Li, Ruihu; Guo, Luobin; Ma, Yuena

2016-10-01

In this paper, we firstly study construction of new quantum error-correcting codes (QECCs) from three classes of quaternary imprimitive BCH codes. As a result, the improved maximal designed distance of these narrow-sense imprimitive Hermitian dual-containing quaternary BCH codes are determined to be much larger than the result given according to Aly et al. (IEEE Trans Inf Theory 53:1183-1188, 2007) for each different code length. Thus, families of new QECCs are newly obtained, and the constructed QECCs have larger distance than those in the previous literature. Secondly, we apply a combinatorial construction to the imprimitive BCH codes with their corresponding primitive counterpart and construct many new linear quantum codes with good parameters, some of which have parameters exceeding the finite Gilbert-Varshamov bound for linear quantum codes.

Overview of development and design of MPACT: Michigan parallel characteristics transport code

Energy Technology Data Exchange (ETDEWEB)

Kochunas, B.; Collins, B.; Jabaay, D.; Downar, T. J.; Martin, W. R. [Department of Nuclear Engineering and Radiological Sciences, University of Michigan, 2200 Bonisteel, Ann Arbor, MI 48109 (United States)

2013-07-01

MPACT (Michigan Parallel Characteristics Transport Code) is a new reactor analysis tool. It is being developed by students and research staff at the University of Michigan to be used for an advanced pin-resolved transport capability within VERA (Virtual Environment for Reactor Analysis). VERA is the end-user reactor simulation tool being produced by the Consortium for the Advanced Simulation of Light Water Reactors (CASL). The MPACT development project is itself unique for the way it is changing how students do research to achieve the instructional and research goals of an academic institution, while providing immediate value to industry. The MPACT code makes use of modern lean/agile software processes and extensive testing to maintain a level of productivity and quality required by CASL. MPACT's design relies heavily on object-oriented programming concepts and design patterns and is programmed in Fortran 2003. These designs are explained and illustrated as to how they can be readily extended to incorporate new capabilities and research ideas in support of academic research objectives. The transport methods currently implemented in MPACT include the 2-D and 3-D method of characteristics (MOC) and 2-D and 3-D method of collision direction probabilities (CDP). For the cross section resonance treatment, presently the subgroup method and the new embedded self-shielding method (ESSM) are implemented within MPACT. (authors)

A mutant Pfu DNA polymerase designed for advanced uracil-excision DNA engineering.

Science.gov (United States)

Nørholm, Morten H H

2010-03-16

The combined use of restriction enzymes with PCR has revolutionized molecular cloning, but is inherently restricted by the content of the manipulated DNA sequences. Uracil-excision based cloning is ligase and sequence independent and allows seamless fusion of multiple DNA sequences in simple one-tube reactions, with higher accuracy than overlapping PCR. Here, the addition of a highly efficient DNA polymerase and a low-background-, large-insertion- compatible site-directed mutagenesis protocol is described, largely expanding the versatility of uracil-excision DNA engineering. The different uracil-excision based molecular tools that have been developed in an open-source fashion, constitute a comprehensive, yet simple and inexpensive toolkit for any need in molecular cloning.

Extending the application range of a fuel performance code from normal operating to design basis accident conditions

International Nuclear Information System (INIS)

Van Uffelen, P.; Gyori, C.; Schubert, A.; Laar, J. van de; Hozer, Z.; Spykman, G.

2008-01-01

Two types of fuel performance codes are generally being applied, corresponding to the normal operating conditions and the design basis accident conditions, respectively. In order to simplify the code management and the interface between the codes, and to take advantage of the hardware progress it is favourable to generate a code that can cope with both conditions. In the first part of the present paper, we discuss the needs for creating such a code. The second part of the paper describes an example of model developments carried out by various members of the TRANSURANUS user group for coping with a loss of coolant accident (LOCA). In the third part, the validation of the extended fuel performance code is presented for LOCA conditions, whereas the last section summarises the present status and indicates needs for further developments to enable the code to deal with reactivity initiated accident (RIA) events

Haben repetitive DNA-Sequenzen biologische Funktionen?

Science.gov (United States)

John, Maliyakal E.; Knöchel, Walter

1983-05-01

By DNA reassociation kinetics it is known that the eucaryotic genome consists of non-repetitive DNA, middle-repetitive DNA and highly repetitive DNA. Whereas the majority of protein-coding genes is located on non-repetitive DNA, repetitive DNA forms a constitutive part of eucaryotic DNA and its amount in most cases equals or even substantially exceeds that of non-repetitive DNA. During the past years a large body of data on repetitive DNA has accumulated and these have prompted speculations ranging from specific roles in the regulation of gene expression to that of a selfish entity with inconsequential functions. The following article summarizes recent findings on structural, transcriptional and evolutionary aspects and, although by no means being proven, some possible biological functions are discussed.

Transcription of repetitive DNA in Neurospora crassa

Energy Technology Data Exchange (ETDEWEB)

Dutta, S K; Chaudhuri, R K

1975-01-01

Repeated DNA sequences of Neurospora crassa were isolated and characterized. Approximately 10 to 12 percent of N. crassa DNA sequence were repeated, of which 7.3 percent were found to be transcribed in mid-log phase of mycelial growth as measured by DNA:RNA hybridization. It is suggested that part of repetitive DNA transcripts in N. crassa were mitochondrial and part were nuclear DNA. Most of the nuclear repeated DNAs, however, code for rRNA and tRNA in N. crassa. (auth)

Designing universal primers for the isolation of DNA sequences encoding Proanthocyanidins biosynthetic enzymes in Crataegus aronia

Directory of Open Access Journals (Sweden)

Zuiter Afnan

2012-08-01

Full Text Available Abstract Background Hawthorn is the common name of all plant species in the genus Crataegus, which belongs to the Rosaceae family. Crataegus are considered useful medicinal plants because of their high content of proanthocyanidins (PAs and other related compounds. To improve PAs production in Crataegus tissues, the sequences of genes encoding PAs biosynthetic enzymes are required. Findings Different bioinformatics tools, including BLAST, multiple sequence alignment and alignment PCR analysis were used to design primers suitable for the amplification of DNA fragments from 10 candidate genes encoding enzymes involved in PAs biosynthesis in C. aronia. DNA sequencing results proved the utility of the designed primers. The primers were used successfully to amplify DNA fragments of different PAs biosynthesis genes in different Rosaceae plants. Conclusion To the best of our knowledge, this is the first use of the alignment PCR approach to isolate DNA sequences encoding PAs biosynthetic enzymes in Rosaceae plants.

Advanced Design of Dumbbell-shaped Genetic Minimal Vectors Improves Non-coding and Coding RNA Expression.

Science.gov (United States)

Jiang, Xiaoou; Yu, Han; Teo, Cui Rong; Tan, Genim Siu Xian; Goh, Sok Chin; Patel, Parasvi; Chua, Yiqiang Kevin; Hameed, Nasirah Banu Sahul; Bertoletti, Antonio; Patzel, Volker

2016-09-01

Dumbbell-shaped DNA minimal vectors lacking nontherapeutic genes and bacterial sequences are considered a stable, safe alternative to viral, nonviral, and naked plasmid-based gene-transfer systems. We investigated novel molecular features of dumbbell vectors aiming to reduce vector size and to improve the expression of noncoding or coding RNA. We minimized small hairpin RNA (shRNA) or microRNA (miRNA) expressing dumbbell vectors in size down to 130 bp generating the smallest genetic expression vectors reported. This was achieved by using a minimal H1 promoter with integrated transcriptional terminator transcribing the RNA hairpin structure around the dumbbell loop. Such vectors were generated with high conversion yields using a novel protocol. Minimized shRNA-expressing dumbbells showed accelerated kinetics of delivery and transcription leading to enhanced gene silencing in human tissue culture cells. In primary human T cells, minimized miRNA-expressing dumbbells revealed higher stability and triggered stronger target gene suppression as compared with plasmids and miRNA mimics. Dumbbell-driven gene expression was enhanced up to 56- or 160-fold by implementation of an intron and the SV40 enhancer compared with control dumbbells or plasmids. Advanced dumbbell vectors may represent one option to close the gap between durable expression that is achievable with integrating viral vectors and short-term effects triggered by naked RNA.

Aminotryptophan-containing barstar: structure--function tradeoff in protein design and engineering with an expanded genetic code.

Science.gov (United States)

Rubini, Marina; Lepthien, Sandra; Golbik, Ralph; Budisa, Nediljko

2006-07-01

The indole ring of the canonical amino acid tryptophan (Trp) possesses distinguished features, such as sterical bulk, hydrophobicity and the nitrogen atom which is capable of acting as a hydrogen bond donor. The introduction of an amino group into the indole moiety of Trp yields the structural analogs 4-aminotryptophan ((4-NH(2))Trp) and 5-aminotryptophan ((5-NH(2))Trp). Their hydrophobicity and spectral properties are substantially different when compared to those of Trp. They resemble the purine bases of DNA and share their capacity for pH-sensitive intramolecular charge transfer. The Trp --> aminotryptophan substitution in proteins during ribosomal translation is expected to result in related protein variants that acquire these features. These expectations have been fulfilled by incorporating (4-NH(2))Trp and (5-NH(2))Trp into barstar, an intracellular inhibitor of the ribonuclease barnase from Bacillus amyloliquefaciens. The crystal structure of (4-NH(2))Trp-barstar is similar to that of the parent protein, whereas its spectral and thermodynamic behavior is found to be remarkably different. The T(m) value of (4-NH(2))Trp- and (5-NH(2))Trp-barstar is lowered by about 20 degrees Celsius, and they exhibit a strongly reduced unfolding cooperativity and substantial loss of free energy in folding. Furthermore, folding kinetic study of (4-NH(2))Trp-barstar revealed that the denatured state is even preferred over native one. The combination of structural and thermodynamic analyses clearly shows how structures of substituted barstar display a typical structure-function tradeoff: the acquirement of unique pH-sensitive charge transfer as a novel function is achieved at the expense of protein stability. These findings provide a new insight into the evolution of the amino acid repertoire of the universal genetic code and highlight possible problems regarding protein engineering and design by using an expanded genetic code.

The Intertwined Roles of DNA Damage and Transcription

OpenAIRE

Di Palo, Giacomo

2016-01-01

DNA damage and transcription are two interconnected events. Transcription can induce damage and scheduled DNA damage can be required for transcription. Here, we analyzed genome-wide distribution of 8oxodG-marked oxidative DNA damage obtained by OxiDIP-Seq, and we found a correlation with transcription of protein coding genes.

Review of application code and standards for mechanical and piping design of HANARO fuel test loop

Energy Technology Data Exchange (ETDEWEB)

Kim, J. Y.

1998-02-01

The design and installation of the irradiation test facility for verification test of the fuel performance are very important in connection with maximization of the utilization of HANARO. HANARO fuel test loop was designed in accordance with the same code and standards of nuclear power plant because HANARO FTL will be operated the high pressure and temperature same as nuclear power plant operation conditions. The objective of this study is to confirm the propriety of application code and standards for mechanical and piping of HANARO fuel test loop and to decide the technical specification of FTL systems. (author). 18 refs., 8 tabs., 6 figs.

Physical association of pyrimidine dimer DNA glycosylase and apurinic/apyrimidinic DNA endonuclease essential for repair of ultraviolet-damaged DNA

International Nuclear Information System (INIS)

Nakabeppu, Y.; Sekiguchi, M.

1981-01-01

T4 endonuclease, which is involved in repair of uv-damaged DNA, has been purified to apparent physical homogeneity. Incubation of uv-irradiated poly(dA).poly(dT) with the purified enzyme preparations resulted in production of alkali-labile apyrimidinic sites, followed by formation of nicks in the polymer. By performing a limited reaction with T4 endonuclease V at pH 8.5, irradiated polymer was converted to an intermediate form that carried a large number of alkali-labile sites but only a few nicks. The intermediate was used as substrate for the assay of apurinic/apyrimidinic DNA endonuclease activity. The two activities, a pyrimidine dimer DNA glycosylase and an apurinic/apyrimidinic DNA endonuclease, were copurified and found in enzyme preparations that contained only a 16,000-dalton polypeptide. These results strongly suggested that a DNA glycosylase specific for pyrimidine dimers and an apurinic/apyrimidinic DNA endonuclease reside in a single polypeptide chain coded by the denV gene of bacteriophage T4

DLLExternalCode

Energy Technology Data Exchange (ETDEWEB)

2014-05-14

DLLExternalCode is the a general dynamic-link library (DLL) interface for linking GoldSim (www.goldsim.com) with external codes. The overall concept is to use GoldSim as top level modeling software with interfaces to external codes for specific calculations. The DLLExternalCode DLL that performs the linking function is designed to take a list of code inputs from GoldSim, create an input file for the external application, run the external code, and return a list of outputs, read from files created by the external application, back to GoldSim. Instructions for creating the input file, running the external code, and reading the output are contained in an instructions file that is read and interpreted by the DLL.

Design of variable-weight quadratic congruence code for optical CDMA

Science.gov (United States)

Feng, Gang; Cheng, Wen-Qing; Chen, Fu-Jun

2015-09-01

A variable-weight code family referred to as variable-weight quadratic congruence code (VWQCC) is constructed by algebraic transformation for incoherent synchronous optical code division multiple access (OCDMA) systems. Compared with quadratic congruence code (QCC), VWQCC doubles the code cardinality and provides the multiple code-sets with variable code-weight. Moreover, the bit-error rate (BER) performance of VWQCC is superior to those of conventional variable-weight codes by removing or padding pulses under the same chip power assumption. The experiment results show that VWQCC can be well applied to the OCDMA with quality of service (QoS) requirements.

Scrum Code Camps

DEFF Research Database (Denmark)

Pries-Heje, Lene; Pries-Heje, Jan; Dalgaard, Bente

2013-01-01

is required. In this paper we present the design of such a new approach, the Scrum Code Camp, which can be used to assess agile team capability in a transparent and consistent way. A design science research approach is used to analyze properties of two instances of the Scrum Code Camp where seven agile teams...

MSP-HTPrimer: a high-throughput primer design tool to improve assay design for DNA methylation analysis in epigenetics.

Science.gov (United States)

Pandey, Ram Vinay; Pulverer, Walter; Kallmeyer, Rainer; Beikircher, Gabriel; Pabinger, Stephan; Kriegner, Albert; Weinhäusel, Andreas

2016-01-01

Bisulfite (BS) conversion-based and methylation-sensitive restriction enzyme (MSRE)-based PCR methods have been the most commonly used techniques for locus-specific DNA methylation analysis. However, both methods have advantages and limitations. Thus, an integrated approach would be extremely useful to quantify the DNA methylation status successfully with great sensitivity and specificity. Designing specific and optimized primers for target regions is the most critical and challenging step in obtaining the adequate DNA methylation results using PCR-based methods. Currently, no integrated, optimized, and high-throughput methylation-specific primer design software methods are available for both BS- and MSRE-based methods. Therefore an integrated, powerful, and easy-to-use methylation-specific primer design pipeline with great accuracy and success rate will be very useful. We have developed a new web-based pipeline, called MSP-HTPrimer, to design primers pairs for MSP, BSP, pyrosequencing, COBRA, and MSRE assays on both genomic strands. First, our pipeline converts all target sequences into bisulfite-treated templates for both forward and reverse strand and designs all possible primer pairs, followed by filtering for single nucleotide polymorphisms (SNPs) and known repeat regions. Next, each primer pairs are annotated with the upstream and downstream RefSeq genes, CpG island, and cut sites (for COBRA and MSRE). Finally, MSP-HTPrimer selects specific primers from both strands based on custom and user-defined hierarchical selection criteria. MSP-HTPrimer produces a primer pair summary output table in TXT and HTML format for display and UCSC custom tracks for resulting primer pairs in GTF format. MSP-HTPrimer is an integrated, web-based, and high-throughput pipeline and has no limitation on the number and size of target sequences and designs MSP, BSP, pyrosequencing, COBRA, and MSRE assays. It is the only pipeline, which automatically designs primers on both genomic

RNA-DNA sequence differences spell genetic code ambiguities

DEFF Research Database (Denmark)

Bentin, Thomas; Nielsen, Michael L

2013-01-01

A recent paper in Science by Li et al. 2011(1) reports widespread sequence differences in the human transcriptome between RNAs and their encoding genes termed RNA-DNA differences (RDDs). The findings could add a new layer of complexity to gene expression but the study has been criticized. ...

Induction technology optimization code

International Nuclear Information System (INIS)

Caporaso, G.J.; Brooks, A.L.; Kirbie, H.C.

1992-01-01

A code has been developed to evaluate relative costs of induction accelerator driver systems for relativistic klystrons. The code incorporates beam generation, transport and pulsed power system constraints to provide an integrated design tool. The code generates an injector/accelerator combination which satisfies the top level requirements and all system constraints once a small number of design choices have been specified (rise time of the injector voltage and aspect ratio of the ferrite induction cores, for example). The code calculates dimensions of accelerator mechanical assemblies and values of all electrical components. Cost factors for machined parts, raw materials and components are applied to yield a total system cost. These costs are then plotted as a function of the two design choices to enable selection of an optimum design based on various criteria. (Author) 11 refs., 3 figs

DNA damage-inducible transcripts in mammalian cells

International Nuclear Information System (INIS)

Fornace, A.J. Jr.; Alamo, I. Jr.; Hollander, M.C.

1988-01-01

Hybridization subtraction at low ratios of RNA to cDNA was used to enrich for the cDNA of transcripts increased in Chinese hamster cells after UV irradiation. Forty-nine different cDNA clones were isolated. Most coded for nonabundant transcripts rapidly induced 2- to 10-fold after UV irradiation. Only 2 of the 20 cDNA clones sequenced matched known sequences (metallothionein I and II). The predicted amino acid sequence of one cDNA had two localized areas of homology with the rat helix-destabilizing protein. These areas of homology were at the two DNA-binding sites of this nucleic acid single-strand-binding protein. The induced transcripts were separated into two general classes. Class I transcripts were induced by UV radiation and not by the alkylating agent methyl methanesulfonate. Class II transcripts were induced by UV radiation and by methyl methanesulfonate. Many class II transcripts were induced also by H2O2 and various alkylating agents but not by heat shock, phorbol 12-tetradecanoate 13-acetate, or DNA-damaging agents which do not produce high levels of base damage. Since many of the cDNA clones coded for transcripts which were induced rapidly and only by certain types of DNA-damaging agents, their induction is likely a specific response to such damage rather than a general response to cell injury

On the Combination of Multi-Layer Source Coding and Network Coding for Wireless Networks

DEFF Research Database (Denmark)

Krigslund, Jeppe; Fitzek, Frank; Pedersen, Morten Videbæk

2013-01-01

quality is developed. A linear coding structure designed to gracefully encapsulate layered source coding provides both low complexity of the utilised linear coding while enabling robust erasure correction in the form of fountain coding capabilities. The proposed linear coding structure advocates efficient...

Teacher Candidates Implementing Universal Design for Learning: Enhancing Picture Books with QR Codes

Science.gov (United States)

Grande, Marya; Pontrello, Camille

2016-01-01

The purpose of this study was to investigate if teacher candidates could gain knowledge of the principles of Universal Design for Learning by enhancing traditional picture books with Quick Response (QR) codes and to determine if the process of making these enhancements would impact teacher candidates' comfort levels with using technology on both…

Production of DNA minicircles less than 250 base pairs through a novel concentrated DNA circularization assay enabling minicircle design with NF-κB inhibition activity.

Science.gov (United States)

Thibault, Thomas; Degrouard, Jeril; Baril, Patrick; Pichon, Chantal; Midoux, Patrick; Malinge, Jean-Marc

2017-03-17

Double-stranded DNA minicircles of less than 1000 bp in length have great interest in both fundamental research and therapeutic applications. Although minicircles have shown promising activity in gene therapy thanks to their good biostability and better intracellular trafficking, minicircles down to 250 bp in size have not yet been investigated from the test tube to the cell for lack of an efficient production method. Herein, we report a novel versatile plasmid-free method for the production of DNA minicircles comprising fewer than 250 bp. We designed a linear nicked DNA double-stranded oligonucleotide blunt-ended substrate for efficient minicircle production in a ligase-mediated and bending protein-assisted circularization reaction at high DNA concentration of 2 μM. This one pot multi-step reaction based-method yields hundreds of micrograms of minicircle with sequences of any base composition and position and containing or not a variety of site-specifically chemical modifications or physiological supercoiling. Biochemical and cellular studies were then conducted to design a 95 bp minicircle capable of binding in vitro two NF-κB transcription factors per minicircle and to efficiently inhibiting NF-κB-dependent transcriptional activity in human cells. Therefore, our production method could pave the way for the design of minicircles as new decoy nucleic acids. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

The nucleotide sequence of human transition protein 1 cDNA

Energy Technology Data Exchange (ETDEWEB)

Luerssen, H; Hoyer-Fender, S; Engel, W [Universitaet Goettingen (West Germany)

1988-08-11

The authors have screened a human testis cDNA library with an oligonucleotide of 81 mer prepared according to a part of the published nucleotide sequence of the rat transition protein TP 1. They have isolated a cDNA clone with the length of 441 bp containing the coding region of 162 bp for human transition protein 1. There is about 84% homology in the coding region of the sequence compared to rat. The human cDNA-clone encodes a polypeptide of 54 amino acids of which 7 are different to that of rat.

Coding Class

DEFF Research Database (Denmark)

Ejsing-Duun, Stine; Hansbøl, Mikala

Denne rapport rummer evaluering og dokumentation af Coding Class projektet1. Coding Class projektet blev igangsat i skoleåret 2016/2017 af IT-Branchen i samarbejde med en række medlemsvirksomheder, Københavns kommune, Vejle Kommune, Styrelsen for IT- og Læring (STIL) og den frivillige forening...... Coding Pirates2. Rapporten er forfattet af Docent i digitale læringsressourcer og forskningskoordinator for forsknings- og udviklingsmiljøet Digitalisering i Skolen (DiS), Mikala Hansbøl, fra Institut for Skole og Læring ved Professionshøjskolen Metropol; og Lektor i læringsteknologi, interaktionsdesign......, design tænkning og design-pædagogik, Stine Ejsing-Duun fra Forskningslab: It og Læringsdesign (ILD-LAB) ved Institut for kommunikation og psykologi, Aalborg Universitet i København. Vi har fulgt og gennemført evaluering og dokumentation af Coding Class projektet i perioden november 2016 til maj 2017...

Designer DNA Architectures: Applications in Nanomedicine

Directory of Open Access Journals (Sweden)

Arun Richard Chandrasekaran

2016-04-01

Full Text Available DNA has been used as a material for the construction of nanoscale objects. These nanostructures are programmable and allow the conjugation of biomolecular guests to improve their functionality. DNA nanostructures display a wide variety of characteristics, such as cellular permeabil‐ ity, biocompatibility and stability, and responsiveness to external stimuli, making them excellent candidates for applications in nanomedicine.

Design of Spreading-Codes-Assisted Active Imaging System

Directory of Open Access Journals (Sweden)

Alexey Volkov

2015-07-01

Full Text Available This work discusses an innovative approach to imaging which can improve the robustness of existing active-range measurement methods and potentially enhance their use in a variety of outdoor applications. By merging a proven modulation technique from the domain of spread-spectrum communications with the bleeding-edge CMOS sensor technology, the prototype of the modulated range sensor is designed and evaluated. A suitable set of application-specific spreading codes is proposed, evaluated and tested on the prototype. Experimental results show that the introduced modulation technique significantly reduces the impacts of environmental factors such as sunlight and external light sources, as well as mutual interference of identical devices. The proposed approach can be considered as a promising basis for a new generation of robust and cost-efficient range-sensing solutions for automotive applications, autonomous vehicles or robots.

Evaluation of Advanced Thermohydraulic System Codes for Design and Safety Analysis of Integral Type Reactors

International Nuclear Information System (INIS)

2014-02-01

The integral pressurized water reactor (PWR) concept, which incorporates the nuclear steam supply systems within the reactor vessel, is one of the innovative reactor types with high potential for near term deployment. An International Collaborative Standard Problem (ICSP) on Integral PWR Design, Natural Circulation Flow Stability and Thermohydraulic Coupling of Primary System and Containment during Accidents was established in 2010. Oregon State University, which made available the use of its experimental facility built to demonstrate the feasibility of the Multi-application Small Light Water Reactor (MASLWR) design, and sixteen institutes from seven Member States participated in this ICSP. The objective of the ICSP is to assess computer codes for reactor system design and safety analysis. This objective is achieved through the production of experimental data and computer code simulation of experiments. A loss of feedwater transient with subsequent automatic depressurization system blowdown and long term cooling was selected as the reference event since many different modes of natural circulation phenomena, including the coupling of primary system, high pressure containment and cooling pool are expected to occur during this transient. The power maneuvering transient is also tested to examine the stability of natural circulation during the single and two phase conditions. The ICSP was conducted in three phases: pre-test (with designed initial and boundary conditions established before the experiment was conducted), blind (with real initial and boundary conditions after the experiment was conducted) and open simulation (after the observation of real experimental data). Most advanced thermohydraulic system analysis codes such as TRACE, RELAPS and MARS have been assessed against experiments conducted at the MASLWR test facility. The ICSP has provided all participants with the opportunity to evaluate the strengths and weaknesses of their system codes in the transient

The Purine Bias of Coding Sequences is Determined by Physicochemical Constraints on Proteins.

Science.gov (United States)

Ponce de Leon, Miguel; de Miranda, Antonio Basilio; Alvarez-Valin, Fernando; Carels, Nicolas

2014-01-01

For this report, we analyzed protein secondary structures in relation to the statistics of three nucleotide codon positions. The purpose of this investigation was to find which properties of the ribosome, tRNA or protein level, could explain the purine bias (Rrr) as it is observed in coding DNA. We found that the Rrr pattern is the consequence of a regularity (the codon structure) resulting from physicochemical constraints on proteins and thermodynamic constraints on ribosomal machinery. The physicochemical constraints on proteins mainly come from the hydropathy and molecular weight (MW) of secondary structures as well as the energy cost of amino acid synthesis. These constraints appear through a network of statistical correlations, such as (i) the cost of amino acid synthesis, which is in favor of a higher level of guanine in the first codon position, (ii) the constructive contribution of hydropathy alternation in proteins, (iii) the spatial organization of secondary structure in proteins according to solvent accessibility, (iv) the spatial organization of secondary structure according to amino acid hydropathy, (v) the statistical correlation of MW with protein secondary structures and their overall hydropathy, (vi) the statistical correlation of thymine in the second codon position with hydropathy and the energy cost of amino acid synthesis, and (vii) the statistical correlation of adenine in the second codon position with amino acid complexity and the MW of secondary protein structures. Amino acid physicochemical properties and functional constraints on proteins constitute a code that is translated into a purine bias within the coding DNA via tRNAs. In that sense, the Rrr pattern within coding DNA is the effect of information transfer on nucleotide composition from protein to DNA by selection according to the codon positions. Thus, coding DNA structure and ribosomal machinery co-evolved to minimize the energy cost of protein coding given the functional

DNA immunisation. New histochemical and morphometric data

Directory of Open Access Journals (Sweden)

D Ehirchiou

2010-01-01

Full Text Available Splenic germinal center reactions were measured during primary response to a plasmidic DNA intramuscular injection. Cardiotoxin-pretreated Balb/c mice were immunized with DNA plasmids encoding or not the SAG1 protein, a membrane antigen of Toxoplasma gondii. Specific anti-SAG1 antibodies were detected on days 16 and 36 after injection of coding plasmids. The results of ELISAs showed that the SAG1-specific antibodies are of the IgG2a class. Morphometric analyses were done on serial immunostained cryosections of spleen and draining or non-draining lymph nodes. This new approach made it possible to evaluate the chronological changes induced by DNA immunisation in the germinal centres (in number and in size. Significant increases in the number of germinal centres were measured in the spleen and only in draining lymph nodes after plasmid injection. the measured changes of the germinal centers appeared to result from the adjuvant stimulatory effect of the plasmidic DNA since both the coding and the noncoding plasmid DNA induced them. No measurable changes were recorded in the Tdependent zone of lymph organs.

Design and construction of a DNA origami drug delivery system based on MPT64 antibody aptamer for tuberculosis treatment.

Science.gov (United States)

Ranjbar, Reza; Hafezi-Moghadam, Mohammad Sadegh

2016-02-01

With all of the developments on infectious diseases, tuberculosis (TB) remains a cause of death among people. One of the most promising assembly techniques in nano-technology is "scaffolded DNA origami" to design and construct a nano-scale drug delivery system. Because of the global health problems of tuberculosis, the development of potent new anti-tuberculosis drug delivery system without cross-resistance with known anti-mycobacterial agents is urgently needed. The aim of this study was to design a nano-scale drug delivery system for TB treatment using the DNA origami method. In this study, we presented an experimental research on a DNA drug delivery system for treating Tuberculosis. TEM images were visualized with an FEI Tecnai T12 BioTWIN at 120 kV. The model was designed by caDNAno software and computational prediction of the 3D solution shape and its flexibility was calculated with a CanDo server. Synthesizing the product was imaged using transmission electron microscopy after negative-staining by uranyl formate. We constructed a multilayer 3D DNA nanostructure system by designing square lattice geometry with the scaffolded-DNA-origami method. With changes in the lock and key sequences, we recommend that this system be used for other infectious diseases to target the pathogenic bacteria.

Cloning and expression of a cDNA coding for the human platelet-derived growth factor receptor: Evidence for more than one receptor class

International Nuclear Information System (INIS)

Gronwald, R.G.K.; Grant, F.J.; Haldeman, B.A.; Hart, C.E.; O'Hara, P.J.; Hagen, F.S.; Ross, R.; Bowen-Pope, D.F.; Murray, M.J.

1988-01-01

The complete nucleotide sequence of a cDNA encoding the human platelet-derived growth factor (PDGF) receptor is presented. The cDNA contains an open reading frame that codes for a protein of 1106 amino acids. Comparison to the mouse PDGF receptor reveals an overall amino acid sequence identity of 86%. This sequence identity rises to 98% in the cytoplasmic split tyrosine kinase domain. RNA blot hybridization analysis of poly(A) + RNA from human dermal fibroblasts detects a major and a minor transcript using the cDNA as a probe. Baby hamster kidney cells, transfected with an expression vector containing the receptor cDNA, express an ∼ 190-kDa cell surface protein that is recognized by an anti-human PDGF receptor antibody. The recombinant PDGF receptor is functional in the transfected baby hamster kidney cells as demonstrated by ligand-induced phosphorylation of the receptor. Binding properties of the recombinant PDGF receptor were also assessed with pure preparations of BB and AB isoforms of PDGF. Unlike human dermal fibroblasts, which bind both isoforms with high affinity, the transfected baby hamster kidney cells bind only the BB isoform of PDGF with high affinity. This observation is consistent with the existence of more than one PDGF receptor class

Validation of Printed Circuit Heat Exchanger Design Code KAIST{sub H}XD

Energy Technology Data Exchange (ETDEWEB)

Baik, Seungjoon; Kim, Seong Gu; Lee, Jekyoung; Lee, Jeong Ik [KAIST, Daejeon (Korea, Republic of)

2015-05-15

Supercritical carbon dioxide (S-CO{sub 2}) Brayton cycle has been suggested for the SFR due to the relatively mild sodium-CO{sub 2} interaction. The S-CO{sub 2} power conversion cycle can achieve not only high safety but also high efficiency with SFR core thermal condition. However, due to the dramatic property change near the critical point, the inlet pressure and temperature conditions of compressor can have significant effect on the overall cycle efficiency. To maintain the inlet condition of compressor, a sensitive precooler control system is required for stable operation. Therefore understanding the precooler performance is essential for the S-CO{sub 2} power conversion system. According to experimental result, designed PCHE showed high effectiveness in various operating regions. Comparing the experimental and the design data, heat transfer performance estimation showed less than 6% error. On the other hand, the pressure drop estimation showed large gap. The water side pressure drop showed 50-70% under estimation. Because the form losses were not included in the design code, water side pressure drop estimation result seems reliable. However, the CO{sub 2} side showed more than 70% over estimation in the pressure drop from the code. The authors suspect that the differences may have occurred by the channel corner shape. The real channel has round corners and smooth edge, but the correlation is based on the sharp edged zig-zag channel. Further studies are required to understand and interpret the results correctly in the future.

Lectin cDNA and transgenic plants derived therefrom

Science.gov (United States)

Raikhel, Natasha V.

2000-10-03

Transgenic plants containing cDNA encoding Gramineae lectin are described. The plants preferably contain cDNA coding for barley lectin and store the lectin in the leaves. The transgenic plants, particularly the leaves exhibit insecticidal and fungicidal properties.

Computational design and multiscale modeling of a nanoactuator using DNA actuation

International Nuclear Information System (INIS)

Hamdi, Mustapha

2009-01-01

Developments in the field of nano-biodevices coupling nanostructures and biological components are of great interest in medical nanorobotics. As the fundamentals of bio/non-bio interaction processes are still poorly understood in the design of these devices, design tools and multiscale dynamics modeling approaches are necessary at the fabrication pre-project stage. This paper proposes a new concept of optimized carbon nanotube based servomotor design for drug delivery and biomolecular transport applications. The design of an encapsulated DNA-multi-walled carbon nanotube actuator is prototyped using multiscale modeling. The system is parametrized by using a quantum level approach and characterized by using a molecular dynamics simulation. Based on the analysis of the simulation results, a servo nanoactuator using ionic current feedback is simulated and analyzed for application as a drug delivery carrier.

Mobius Assembly: A versatile Golden-Gate framework towards universal DNA assembly.

Directory of Open Access Journals (Sweden)

Andreas I Andreou

Full Text Available Synthetic biology builds upon the foundation of engineering principles, prompting innovation and improvement in biotechnology via a design-build-test-learn cycle. A community-wide standard in DNA assembly would enable bio-molecular engineering at the levels of predictivity and universality in design and construction that are comparable to other engineering fields. Golden Gate Assembly technology, with its robust capability to unidirectionally assemble numerous DNA fragments in a one-tube reaction, has the potential to deliver a universal standard framework for DNA assembly. While current Golden Gate Assembly frameworks (e.g. MoClo and Golden Braid render either high cloning capacity or vector toolkit simplicity, the technology can be made more versatile-simple, streamlined, and cost/labor-efficient, without compromising capacity. Here we report the development of a new Golden Gate Assembly framework named Mobius Assembly, which combines vector toolkit simplicity with high cloning capacity. It is based on a two-level, hierarchical approach and utilizes a low-frequency cutter to reduce domestication requirements. Mobius Assembly embraces the standard overhang designs designated by MoClo, Golden Braid, and Phytobricks and is largely compatible with already available Golden Gate part libraries. In addition, dropout cassettes encoding chromogenic proteins were implemented for cost-free visible cloning screening that color-code different cloning levels. As proofs of concept, we have successfully assembled up to 16 transcriptional units of various pigmentation genes in both operon and multigene arrangements. Taken together, Mobius Assembly delivers enhanced versatility and efficiency in DNA assembly, facilitating improved standardization and automation.

When Content Matters: The Role of Processing Code in Tactile Display Design.

Science.gov (United States)

Ferris, Thomas K; Sarter, Nadine

2010-01-01

The distribution of tasks and stimuli across multiple modalities has been proposed as a means to support multitasking in data-rich environments. Recently, the tactile channel and, more specifically, communication via the use of tactile/haptic icons have received considerable interest. Past research has examined primarily the impact of concurrent task modality on the effectiveness of tactile information presentation. However, it is not well known to what extent the interpretation of iconic tactile patterns is affected by another attribute of information: the information processing codes of concurrent tasks. In two driving simulation studies (n = 25 for each), participants decoded icons composed of either spatial or nonspatial patterns of vibrations (engaging spatial and nonspatial processing code resources, respectively) while concurrently interpreting spatial or nonspatial visual task stimuli. As predicted by Multiple Resource Theory, performance was significantly worse (approximately 5-10 percent worse) when the tactile icons and visual tasks engaged the same processing code, with the overall worst performance in the spatial-spatial task pairing. The findings from these studies contribute to an improved understanding of information processing and can serve as input to multidimensional quantitative models of timesharing performance. From an applied perspective, the results suggest that competition for processing code resources warrants consideration, alongside other factors such as the naturalness of signal-message mapping, when designing iconic tactile displays. Nonspatially encoded tactile icons may be preferable in environments which already rely heavily on spatial processing, such as car cockpits.

Code of practice and design principles for portable and transportable radiological protection systems

International Nuclear Information System (INIS)

Wells, F.H.; Powell, R.G.

1980-10-01

The Code of Practice and design principles for portable and transportable radiological protection systems are presented in three parts. Part 1 specifies the requirement for Radiological Protection Instrumentation (RPI) including operational characteristics and the effects of both a radiation and non-radiation environment. Part 2 satisfies the requirement for RPI equipment as regards the overall design, the availability, the reliability, the information display, the human factors, the power supplies, the manufacture and quality assurance, the testing and the cost. Part 3 deals with the supply, location and operation of the RPI equipment. (U.K.)

Comparative study of codes for the seismic design of structures

Directory of Open Access Journals (Sweden)

S. H. C. Santos

Full Text Available A general evaluation of some points of the South American seismic codes is presented herein, comparing them among themselves and with the American Standard ASCE/SEI 7/10 and with the European Standard Eurocode 8. The study is focused in design criteria for buildings. The Western border of South America is one of the most seismically active regions of the World. It corresponds to the confluence of the South American and Nazca plates. This region corresponds roughly to the vicinity of the Andes Mountains. This seismicity diminishes in the direction of the comparatively seismically quieter Eastern South American areas. The South American countries located in its Western Border possess standards for seismic design since some decades ago, being the Brazilian Standard for seismic design only recently published. This study is focused in some critical topics: definition of the recurrence periods for establishing the seismic input; definition of the seismic zonation and design ground motion values; definition of the shape of the design response spectra; consideration of soil amplification, soil liquefaction and soil-structure interaction; classification of the structures in different importance levels; definition of the seismic force-resisting systems and respective response modification coefficients; consideration of structural irregularities and definition of the allowable procedures for the seismic analyses. A simple building structure is analyzed considering the criteria of the several standards and obtained results are compared.

Data processing with microcode designed with source coding

Science.gov (United States)

McCoy, James A; Morrison, Steven E

2013-05-07

Programming for a data processor to execute a data processing application is provided using microcode source code. The microcode source code is assembled to produce microcode that includes digital microcode instructions with which to signal the data processor to execute the data processing application.

Effective coding with VHDL principles and best practice

CERN Document Server

Jasinski, Ricardo

2016-01-01

A guide to applying software design principles and coding practices to VHDL to improve the readability, maintainability, and quality of VHDL code. This book addresses an often-neglected aspect of the creation of VHDL designs. A VHDL description is also source code, and VHDL designers can use the best practices of software development to write high-quality code and to organize it in a design. This book presents this unique set of skills, teaching VHDL designers of all experience levels how to apply the best design principles and coding practices from the software world to the world of hardware. The concepts introduced here will help readers write code that is easier to understand and more likely to be correct, with improved readability, maintainability, and overall quality. After a brief review of VHDL, the book presents fundamental design principles for writing code, discussing such topics as design, quality, architecture, modularity, abstraction, and hierarchy. Building on these concepts, the book then int...

Design, synthesis and DNA-binding study of some novel morpholine linked thiazolidinone derivatives

Science.gov (United States)

War, Javeed Ahmad; Srivastava, Santosh Kumar; Srivastava, Savitri Devi

2017-02-01

The emergence of multiple drug resistance amongst bacterial strains resulted in many clinical drugs to be ineffective. Being vulnerable to bacterial infections any lack in the development of new antimicrobial drugs could pose a serious threat to public health. Here we report design and synthesis of a novel class of morpholine linked thiazolidinone hybrid molecules. The compounds were characterized by FT-IR, NMR and HRMS techniques. Susceptibility tests showed that most of the synthesized molecules were highly active against multiple bacterial strains. Compound 3f displayed MIC values which were better than the standard drug for most of the tested strains. DNA being a well defined target for many antimicrobial drugs was probed as possible target for these synthetic molecules. DNA-binding study of 3f with sm-DNA was probed through UV-vis absorption, fluorescence quenching, gel electrophoresis and molecular docking techniques. The studies revealed that compound 3f has strong affinity towards DNA and binds at the minor groove. The docking studies revealed that the compound 3f shows preferential binding towards A/T residues.

Design and Analysis of Compact DNA Strand Displacement Circuits for Analog Computation Using Autocatalytic Amplifiers.

Science.gov (United States)

Song, Tianqi; Garg, Sudhanshu; Mokhtar, Reem; Bui, Hieu; Reif, John

2018-01-19

A main goal in DNA computing is to build DNA circuits to compute designated functions using a minimal number of DNA strands. Here, we propose a novel architecture to build compact DNA strand displacement circuits to compute a broad scope of functions in an analog fashion. A circuit by this architecture is composed of three autocatalytic amplifiers, and the amplifiers interact to perform computation. We show DNA circuits to compute functions sqrt(x), ln(x) and exp(x) for x in tunable ranges with simulation results. A key innovation in our architecture, inspired by Napier's use of logarithm transforms to compute square roots on a slide rule, is to make use of autocatalytic amplifiers to do logarithmic and exponential transforms in concentration and time. In particular, we convert from the input that is encoded by the initial concentration of the input DNA strand, to time, and then back again to the output encoded by the concentration of the output DNA strand at equilibrium. This combined use of strand-concentration and time encoding of computational values may have impact on other forms of molecular computation.

Replicating animal mitochondrial DNA

Directory of Open Access Journals (Sweden)

Emily A. McKinney

2013-01-01

Full Text Available The field of mitochondrial DNA (mtDNA replication has been experiencing incredible progress in recent years, and yet little is certain about the mechanism(s used by animal cells to replicate this plasmid-like genome. The long-standing strand-displacement model of mammalian mtDNA replication (for which single-stranded DNA intermediates are a hallmark has been intensively challenged by a new set of data, which suggests that replication proceeds via coupled leading-and lagging-strand synthesis (resembling bacterial genome replication and/or via long stretches of RNA intermediates laid on the mtDNA lagging-strand (the so called RITOLS. The set of proteins required for mtDNA replication is small and includes the catalytic and accessory subunits of DNA polymerase y, the mtDNA helicase Twinkle, the mitochondrial single-stranded DNA-binding protein, and the mitochondrial RNA polymerase (which most likely functions as the mtDNA primase. Mutations in the genes coding for the first three proteins are associated with human diseases and premature aging, justifying the research interest in the genetic, biochemical and structural properties of the mtDNA replication machinery. Here we summarize these properties and discuss the current models of mtDNA replication in animal cells.

ETR/ITER systems code

Energy Technology Data Exchange (ETDEWEB)

Barr, W.L.; Bathke, C.G.; Brooks, J.N.; Bulmer, R.H.; Busigin, A.; DuBois, P.F.; Fenstermacher, M.E.; Fink, J.; Finn, P.A.; Galambos, J.D.; Gohar, Y.; Gorker, G.E.; Haines, J.R.; Hassanein, A.M.; Hicks, D.R.; Ho, S.K.; Kalsi, S.S.; Kalyanam, K.M.; Kerns, J.A.; Lee, J.D.; Miller, J.R.; Miller, R.L.; Myall, J.O.; Peng, Y-K.M.; Perkins, L.J.; Spampinato, P.T.; Strickler, D.J.; Thomson, S.L.; Wagner, C.E.; Willms, R.S.; Reid, R.L. (ed.)

1988-04-01

A tokamak systems code capable of modeling experimental test reactors has been developed and is described in this document. The code, named TETRA (for Tokamak Engineering Test Reactor Analysis), consists of a series of modules, each describing a tokamak system or component, controlled by an optimizer/driver. This code development was a national effort in that the modules were contributed by members of the fusion community and integrated into a code by the Fusion Engineering Design Center. The code has been checked out on the Cray computers at the National Magnetic Fusion Energy Computing Center and has satisfactorily simulated the Tokamak Ignition/Burn Experimental Reactor II (TIBER) design. A feature of this code is the ability to perform optimization studies through the use of a numerical software package, which iterates prescribed variables to satisfy a set of prescribed equations or constraints. This code will be used to perform sensitivity studies for the proposed International Thermonuclear Experimental Reactor (ITER). 22 figs., 29 tabs.

ETR/ITER systems code

International Nuclear Information System (INIS)

Barr, W.L.; Bathke, C.G.; Brooks, J.N.

1988-04-01

A tokamak systems code capable of modeling experimental test reactors has been developed and is described in this document. The code, named TETRA (for Tokamak Engineering Test Reactor Analysis), consists of a series of modules, each describing a tokamak system or component, controlled by an optimizer/driver. This code development was a national effort in that the modules were contributed by members of the fusion community and integrated into a code by the Fusion Engineering Design Center. The code has been checked out on the Cray computers at the National Magnetic Fusion Energy Computing Center and has satisfactorily simulated the Tokamak Ignition/Burn Experimental Reactor II (TIBER) design. A feature of this code is the ability to perform optimization studies through the use of a numerical software package, which iterates prescribed variables to satisfy a set of prescribed equations or constraints. This code will be used to perform sensitivity studies for the proposed International Thermonuclear Experimental Reactor (ITER). 22 figs., 29 tabs

Aspects of the design of the automated system for code generation of electrical items of technological equipment

Directory of Open Access Journals (Sweden)

Erokhin V.V.

2017-09-01

Full Text Available The article presents the aspects of designing an automated system for generating codes for electrical elements of process equipment using CASE-means. We propose our own technology of iterative development of such systems. The proposed methodology uses the tool to develop the ERwin Data Modeler databases of Computer Associates and the author's tool for the automatic generation of ERwin Class Builder code. The implemented design tool is a superstructure over the ERwin Data Modeler from Computer Associates, which extends its functionality. ERwin Data Modeler works with logical and physical data models and allows you to generate a description of the database and ddl-scripts.

Sequence of a cloned cDNA encoding human ribosomal protein S11

Energy Technology Data Exchange (ETDEWEB)

Lott, J B; Mackie, G A

1988-02-11

The authors have isolated a cloned cDNA that encodes human ribosomal protein (rp) S11 by screening a human fibroblast cDNA library with a labelled 204 bp DNA fragment encompassing residues 212-416 of pRS11, a rat rp Sll cDNA clone. The human rp S11 cloned cDNA consists of 15 residues of the 5' leader, the entire coding sequence and all 51 residues of the 3' untranslated region. The predicted amino acid sequence of 158 residues is identical to rat rpS11. The nucleotide sequence in the coding region differs, however, from that in rat in the first position in two codons and in the third position in 44 codons.

Code of practice and design principles, for installed radiological protection systems

International Nuclear Information System (INIS)

Powell, R.G.

1980-09-01

The main points on which a guide for designers and installers of radiological protection instrumentation (RPI) should be based have been examined by a small group of instrumentation engineers. The purpose of this document is to present a comprehensive and detailed review of these points. It is intended to give an overall coverage and serve as a reference document for specific points; it should also be of value to newcomers to the RPI field. The code presents a standard of good practice and takes the form of recommendations only. The contents cover: the requirement for RPI; design, availability and reliability, information displays, human factors, power supplies, manufacture, quality assurance, testing, cost, installation, operation, maintenance and documentation. Appendices include: Radon and thoron decay series, air sampling, reliability of component combinations and redundancy. (28 references). (author)

Applications of statistical physics and information theory to the analysis of DNA sequences

Science.gov (United States)

Grosse, Ivo

2000-10-01

DNA carries the genetic information of most living organisms, and the of genome projects is to uncover that genetic information. One basic task in the analysis of DNA sequences is the recognition of protein coding genes. Powerful computer programs for gene recognition have been developed, but most of them are based on statistical patterns that vary from species to species. In this thesis I address the question if there exist universal statistical patterns that are different in coding and noncoding DNA of all living species, regardless of their phylogenetic origin. In search for such species-independent patterns I study the mutual information function of genomic DNA sequences, and find that it shows persistent period-three oscillations. To understand the biological origin of the observed period-three oscillations, I compare the mutual information function of genomic DNA sequences to the mutual information function of stochastic model sequences. I find that the pseudo-exon model is able to reproduce the mutual information function of genomic DNA sequences. Moreover, I find that a generalization of the pseudo-exon model can connect the existence and the functional form of long-range correlations to the presence and the length distributions of coding and noncoding regions. Based on these theoretical studies I am able to find an information-theoretical quantity, the average mutual information (AMI), whose probability distributions are significantly different in coding and noncoding DNA, while they are almost identical in all studied species. These findings show that there exist universal statistical patterns that are different in coding and noncoding DNA of all studied species, and they suggest that the AMI may be used to identify genes in different living species, irrespective of their taxonomic origin.

A set of 100 chloroplast DNA primer pairs to study population genetics and phylogeny in monocotylenons

DEFF Research Database (Denmark)

Scarcelli, Nora; Bernaud, Adeline; Eiserhardt, Wolf L.

2011-01-01

Chloroplast DNA sequences are of great interest for population genetics and phylogenetic studies. However, only a small set of markers are commonly used. Most of them have been designed for amplification in a large range of Angiosperms and are located in the Large Single Copy (LSC). Here we...... anticipate that it will also be useful for phylogeny and bar-coding studies....

Protograph LDPC Codes Over Burst Erasure Channels

Science.gov (United States)

Divsalar, Dariush; Dolinar, Sam; Jones, Christopher

2006-01-01

In this paper we design high rate protograph based LDPC codes suitable for binary erasure channels. To simplify the encoder and decoder implementation for high data rate transmission, the structure of codes are based on protographs and circulants. These LDPC codes can improve data link and network layer protocols in support of communication networks. Two classes of codes were designed. One class is designed for large block sizes with an iterative decoding threshold that approaches capacity of binary erasure channels. The other class is designed for short block sizes based on maximizing minimum stopping set size. For high code rates and short blocks the second class outperforms the first class.

Programmable DNA-binding proteins from Burkholderia provide a fresh perspective on the TALE-like repeat domain.

Science.gov (United States)

de Lange, Orlando; Wolf, Christina; Dietze, Jörn; Elsaesser, Janett; Morbitzer, Robert; Lahaye, Thomas

2014-06-01

The tandem repeats of transcription activator like effectors (TALEs) mediate sequence-specific DNA binding using a simple code. Naturally, TALEs are injected by Xanthomonas bacteria into plant cells to manipulate the host transcriptome. In the laboratory TALE DNA binding domains are reprogrammed and used to target a fused functional domain to a genomic locus of choice. Research into the natural diversity of TALE-like proteins may provide resources for the further improvement of current TALE technology. Here we describe TALE-like proteins from the endosymbiotic bacterium Burkholderia rhizoxinica, termed Bat proteins. Bat repeat domains mediate sequence-specific DNA binding with the same code as TALEs, despite less than 40% sequence identity. We show that Bat proteins can be adapted for use as transcription factors and nucleases and that sequence preferences can be reprogrammed. Unlike TALEs, the core repeats of each Bat protein are highly polymorphic. This feature allowed us to explore alternative strategies for the design of custom Bat repeat arrays, providing novel insights into the functional relevance of non-RVD residues. The Bat proteins offer fertile grounds for research into the creation of improved programmable DNA-binding proteins and comparative insights into TALE-like evolution. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.