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18th INDIAcom;11th international conference on computing for Sustainable Global Development, INDIACom 2024

作者： Bohra, Shresty Naik, Charmi Batra, Rashi Popat, Kinshu Kaur, Hargeet Pandit Deendayal Energy University Computer Science Engineering Gandhinagar India

ISBN: (纸本)9789380544519

Information security has become a major concern in today's digital world with the rapid growth of the internet. To confront this challenge, various techniques like cryptography and steganography have developed in the fields of computer security for protecting sensitive data from unauthorized access. the review paper explores modern steganography techniques, providing valuable information about their applications in data security. It analyzes the emerging field of dna-based steganography. the paper also examines the dynamic domain of audio steganography, focusing on the challenge of developing strong, high-capacity systems for secure communication. Additionally, it focuses on evaluation of digital image steganography methods. © 2024 Bharati Vidyapeeth, New Delhi.

关键词： Audio steganography Cracking probability Discrete Cosine Transform dna steganography Image steganography LSB Prisoners'problem RGB SNR Stego-Image Temporal Domain Transform Domain

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A geometric approach to gibbs energy landscapes and optimal dna codeword design

A geometric approach to gibbs energy landscapes and optimal ...

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18th international conference on dna computing and molecular programming, dna 18

作者： Garzon, Max H. Bobba, Kiran C. Computer Science University of Memphis TN 38152 United States

ISBN: (纸本)9783642322075

Finding a large set of single dna strands that do not crosshybridize to themselves or to their complements (so-called domains in the language of chemical reaction networks (CRNs)) is an important problem in dna computing, self-assembly, dna memories and phylogenetic analyses because of their error correction and prevention properties. In prior work, we have provided a theoretical framework to analyze this problem and showed that Codeword Design is NP-complete using any single reasonable metric that approximates the Gibbs energy, thus practically excluding the possibility of finding any procedure to find maximal sets exactly and efficiently. In this framework, codeword design is reduced to finding large sets of strands maximally separated in dna spaces and, therefore, the size of such sets depends on the geometry of these spaces. Here, we introduce a new general technique to embed them in Euclidean spaces in such a way that oligos with high/low hybridization affinity are mapped to neighboring/remote points in a geometric lattice, respectively. this embedding materializes long-held mataphors about codeword design in terms of sphere packing and leads to designs that are in some cases known to be provable nearly optimal for some oligo sizes. It also leads to upper and lower bounds on estimates of the size of optimal codes of size up to 32-mers, as well as to infinite families of dna strand lengths, based on estimates of the kissing (or contact) number for sphere packings in Euclidean spaces. Conversely, we show how solutions to dna codeword design obtained by experimental or other means can also provide solutions to difficult spherical packing geometric problems via this embedding. Finally, the reduction suggests an analytical tool to arrange the dynamics of strand displacement cascades in CRNs to effect the transformation through bounded Gibbs energy changes, and thus is potentially useful in compilers for wet tube implementation of biomolecular programs. © 2012 Spring

关键词： dna

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COMBINATION IS thE DOMINANT FREE-RADICAL PROCESS INITIATED IN dna BY IONIZING-RADIATION - AN OVERVIEW BASED ON SOLID-STATE EPR STUDIES

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international JOURNAL OF RADIATION BIOLOGY 1994年第5期66卷 491-497页

作者： BERNHARD, WA MROCZKA, N BARNES, J Department of Biophysics University of Rochester NY 14642.

An overview of the early processes initiated in dna by ionizing radiation is given from the perspective of studies done by solid-state EPR with the focus on radical combination. Comparisons with free radical formation and trapping in crystalline pyrimidines (1-methylcytosine, thymine, 1-methylthymine, 1-methyluracil, and cytosine monohydrate) provide insight into the processes occurring in dna. Between 25 and 50% of low LET ionizations in fully hydrated dna at 4K lead to trapped free radicals, the remaining unobserved radicals are assumed to have combined. the majority of the radicals trapped in dna at 4K (G similar to 0.3 mu mol/J) are believed to be in clusters. Based on the value of G, it is argued that the range of holes and bound electrons in dna at 4K are, in the main, limited to within the cluster diameter, similar to 4 nm. Proton transfer across hydrogen bonds promotes radical trapping and inhibits combination but is thermally reversible. Warming to room temperature mobilizes the reversibly trapped radicals and gives additional combination (50-80% of those trapped at 4K). the yield of free radicals, after anneal, is sufficient to account for the yield of single-strand breaks produced by direct effects.

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A High-Performance Sequence Analysis Engine for Shotgun Metagenomics through GPU Acceleration 18

A High-Performance Sequence Analysis Engine for Shotgun Meta...

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18th IEEE international conference on Bioinformatics and Bioengineering

作者： Hsu, Ying-Feng Matsuoka, Morito Jung, Nicolas Matsumoto, Yuki Motooka, Daisuke Nakamura, Shota Osaka Univ Cybermedia Ctr Osaka Japan Osaka Univ Res Inst Microbial Dis Genome Informat Res Ctr Osaka Japan

ISBN: (纸本)9781538662175

With the continual growth of low-cost and high-throughput dna sequence technology, the scale and amount of next-generation sequencing (NGS) datasets are continually increasing in many genomics research areas. Shotgun metagenomics sequencing provides comprehensive information on microorganisms, based on complex samples of the ecosystem. Due to challenges of its scale and computational complexity, efficient sequence processing and analyzing tools are needed. In this paper, we propose a novel high-performance shotgun metagenomics sequence analysis engine for the task of sequence comparison. It includes two major components. First, a customized shifting database, which is optimized from any existing dna sequence dataset. Second, a high-performance sequence computation algorithm that utilizes the customized shifting reference database and accelerates GPU parallel computing. We elaborated upon the efficiency and computational complexity of our proposed approach in an HPC server, which has eight Nvidia Tesla P100 GPUs. We also conducted a case study to detect viral sequences from patients' blood samples. Our experimental result shows that we obtain similar accuracy to the conventional BLAST method, but with a computational speed that is about twenty times faster.

关键词： component shotgun metagenomics sequencing sequence comparison GPU acceleration parallel computing

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dna/RNA computing with biological nanopore in droplets system: And operation using RNA polymerization 18

DNA/RNA computing with biological nanopore in droplets syste...

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18th international conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2014

作者： Ohara, M. Takinoue, M. Kawano, R. Tokyo University of Agriculture and Technology Japan Tokyo Institute of Technology Japan

ISBN: (纸本)9780979806476

this paper describes AND operation using RNA translocation through an alpha-hemolysin (αHL) nanopore in two droplets system. We define the output of the binary signals "1" or "0" as "RNA transfers droplet through the nanopore" or "no translocation". the phenomena can be electrically monitored as the channel currents at the single molecule level. Although we have already proposed logic operation using dna and the nanopore, the next calculation cannot work due to the low concentration of output molecule. In this study, we used RNA polymerization in order to increase the concentration of the output molecule. © 14CBMS.

关键词： Drops

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Real time mechanical characterization of dna in liquid during a radiotherapy treatment and its theoretical analysis 18

Real time mechanical characterization of DNA in liquid durin...

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18th international conference on Solid-State Sensors, Actuators and Microsystems, TRANSDUCERS 2015

作者： Perret, G. Lacornerie, T. Manca, F. Giordano, S. Kumemura, M. Lafitte, N. Jalabert, L. Lartigau, E. Fujii, T. Cleri, F. Fujita, H. Collard, D. LIMMS CNRS-IIS UMI2820 Japan Centre Oscar Lambret University of Lille 2 France IEMN UMR8520 CNRS University of Lille 1 France Institute of Industrial Science University of Tokyo Japan

ISBN: (纸本)9781479989553

We report the first real-time biomechanical measurement of dna bundle degradation in stable condition when exposed to a therapeutic radiation beam and a theoretical model to describe dna damages. the Silicon Nano Tweezers and their new microfluidic system endure the harsh environment of radiation beams and still retain molecular-level accuracy. this result paves the way for both fundamental and clinical studies of dna degradation under radiation for improved tumor treatment. © 2015 IEEE.

关键词： Silicon

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the anodic aluminum oxide (AAO) template fabricated Localized Surface Plasmon Resonance (LSPR) sensor for the plasmonic coupling effect study 18

The anodic aluminum oxide (AAO) template fabricated Localize...

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18th international conference on Nano/Micro Engineered and molecular Systems, NEMS 2023

作者： Hsieh, Chia-Chin Lee, Wang-Jiun Yeh, Kuan-Chun Huang, Nien-Tsu Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taipei10617 Taiwan

ISBN: (纸本)9798350333480

the localized surface plasmon resonance (LSPR) sensing has drawn significant attention in biosensing fields due to its label-free, dynamic, sensitive, and ease-of-operation sensing capability. In our study, we utilized an anodic aluminum oxide (AAO) template to fabricate a large-area LSPR sensor with adjustable nanostructure parameters such as period and diameter. By using different nanostructure patterns, we investigated the plasmonic coupling effect and optimized the nanostructure geometry. Our research demonstrates the real-time and multipoint detection of pathogen dna sequences. Based on the above features, we believe that this platform has the potential for point-of-care (POC) biosensing applications. © 2023 IEEE.

关键词： dna sequences

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Repeat analysis in dna sequences with parallel computing method on Grid

Repeat analysis in dna sequences with parallel computing met...

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18th IASTED international conference on Parallel and Distributed computing and Systems, PDCS 2006

作者： Arefin, Md. Ahsan Anwar, Abdullah Ibney Wasif, Abu Computer Science and Engineering Bangladesh University of Engineering and Technology Dhaka Bangladesh

the development of Grid environment provides an efficient way for implementing the parallel algorithm. Here we focus on the discovery of short recurring patterns in dna sequences that represent binding sites for certain proteins in the process of gene regulation. We develop parallel computing algorithm for solving this problem by partitioning the overall dna sequences. this provides us an option to implement the algorithm on Grid and to evaluate its performance. We use the open source software "Alchemi" for building the Grid environment. Also by using a merging repeat approach to find these patterns, we address other related problems, including finding of repetition with insertion and deletion.

关键词： dna sequences

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ON thE LINEARITY OF thE DOSE-EFFECT RELATIONSHIP OF dna DOUBLE-STRAND BREAKS

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international JOURNAL OF RADIATION BIOLOGY 1994年第5期66卷 549-552页

作者： CHADWICK, KH LEENHOUTS, HP RIVM LSO3720 BA BILTHOVENNETHERLANDS

Most radiation biologists believe that dna double-strand breaks are induced linearly with radiation dose for all. types of radiation. Since 1985, with the advent of elution and gel electrophoresis techniques which permit the measurement of dna double-strand breaks induced in mammalian cells at doses having radiobiological relevance, the true nature of the dose-effect relationship has been brought into some doubt. Many investigators measured curvilinear dose-effect relationships and a few found good correlations between the induction of the dna double-strand breaks and cell survival. We approach the problem pragmatically by assuming that the induction of dna double-strand breaks by I-125 Auger electron emitters incorporated into the dna of the cells is a linear function of the number of I-125 decays, and by comparing the dose-effect relationship for sparsely ionizing radiation against this standard. the conclusion drawn in that the curvilinear dose-effect relationships and the correlations with survival are real. the problem of why the dose-effect relationship is curvilinear when microdosimetric considerations predict that even for sparsely ionizing radiation energy deposition in and close to the Watson-Crick double helix should give a linear dose-effect relationship remains.

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dna computing Sequence Design Based on Bacterial Foraging Algorithm 18

DNA Computing Sequence Design Based on Bacterial Foraging Al...

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5th international conference on Bioinformatics Research and Applications (ICBRA)

作者： Ren, Jiankang Yao, Yao Dalian Univ Technol Sch Comp Sci & Technol Dalian Peoples R China

ISBN: (纸本)9781450366113

Since the quantity and quality of dna sequence directly affect the accuracy and efficiency of computation, the design of dna sequence is critical to dna computing. In order to improve the reliability of dna computing, there is a rich literature targeting at making dna sequences specifically hybridize at a lower melting temperature, no non-complementary bases pairs or mismatch hybridization in the reformed double helix. However, most of them are not good enough to control the melting temperature, because dna sequence design problem under the constraints of hamming distance, secondary structure, molecular thermodynamic is known to be NP-hard. For the sake of achieving the lower and similar melting temperature for each dna sequence, we proposed a dna sequence coding method based on Bacterial Foraging Algorithm (BFA). An evaluation criterion is particularly proposed to assess the quality of dna sequence in the optimization process. With BFA, high-quality dna strands are replicated to avoid the participation of inferior strands in the operation. Experiments show our proposed approach significantly outperforms existing methods in terms of continuity and melting temperature.

关键词： dna computing dna sequence design BFA

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