Search results for: time based DNA codes

Authors: L. K. Davis

Abstract:

The effects of the evolution force are observable in nature at all structural levels ranging from small molecular systems to conversely enormous biospheric systems. However, the evolution force and work associated with formation of biological structures has yet to be described mathematically or theoretically. In addressing the conundrum, we consider evolution from a unique perspective and in doing so we introduce the “Fundamental Theory of the Evolution Force: FTEF”. We utilized synthetic evolution artificial intelligence (SYN-AI) to identify genomic building blocks and to engineer 14-3-3 ζ docking proteins by transforming gene sequences into time-based DNA codes derived from protein hierarchical structural levels. The aforementioned served as templates for random DNA hybridizations and genetic assembly. The application of hierarchical DNA codes allowed us to fast forward evolution, while dampening the effect of point mutations. Natural selection was performed at each hierarchical structural level and mutations screened using Blosum 80 mutation frequency-based algorithms. Notably, SYN-AI engineered a set of three architecturally conserved docking proteins that retained motion and vibrational dynamics of native Bos taurus 14-3-3 ζ.

Keywords: 14-3-3 docking genes, synthetic protein design, time based DNA codes, writing DNA code from scratch.

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Authors: Shivaleela E. S., Shrikant S. Tangade

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In this paper optical code-division multiple-access (OCDMA) packet network is considered, which offers inherent security in the access networks. Two types of random access protocols are proposed for packet transmission. In protocol 1, all distinct codes and in protocol 2, distinct codes as well as shifted versions of all these codes are used. O-CDMA network performance using optical orthogonal codes (OOCs) 1-D and two-dimensional (2-D) wavelength/time single-pulse-per-row (W/T SPR) codes are analyzed. The main advantage of using 2-D codes instead of onedimensional (1-D) codes is to reduce the errors due to multiple access interference among different users. In this paper, correlation receiver is considered in the analysis. Using analytical model, we compute and compare packet-success probability for 1-D and 2-D codes in an O-CDMA network and the analysis shows improved performance with 2-D codes as compared to 1-D codes.

Keywords: Optical code-division multiple-access, optical CDMA correlation receiver, wavelength/time optical CDMA codes.

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Authors: J. S. Bhullar, Manish Gupta

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Classical Bose-Chaudhuri-Hocquenghem (BCH) codes C that contain their dual codes can be used to construct quantum stabilizer codes this chapter studies the properties of such codes. It had been shown that a BCH code of length n which contains its dual code satisfies the bound on weight of any non-zero codeword in C and converse is also true. One impressive difficulty in quantum communication and computation is to protect informationcarrying quantum states against undesired interactions with the environment. To address this difficulty, many good quantum errorcorrecting codes have been derived as binary stabilizer codes. We were able to shed more light on the structure of dual containing BCH codes. These results make it possible to determine the parameters of quantum BCH codes in terms of weight of non-zero dual codeword.

Keywords: Quantum Codes, BCH Codes, Dual BCH Codes, Designed Distance.

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Authors: Ashish Goswami, Rakesh Sharma

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In this paper, LDPC Codes based on defected fullerene graphs have been generated. And it is found that the codes generated are fast in encoding and better in terms of error performance on AWGN Channel.

Keywords: LDPC Codes, Fullerene Graphs, Defected Fullerene Graphs.

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Authors: O. P. Vinocha , J. S. Bhullar , Manish Gupta

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We considered repeated-root cyclic codes whose block length is divisible by the characteristic of the underlying field. Cyclic self dual codes are also the repeated root cyclic codes. It is known about the one-level squaring construction for binary repeated root cyclic codes. In this correspondence, we introduced of two level squaring construction for binary repeated root cyclic codes of length 2a b , a > 0, b is odd.

Keywords: Squaring Construction, generator matrix, selfdual codes, cyclic codes, coset codes, repeated root cycliccodes.

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Authors: Alexandra Oliveros, Miguel Sotaquirá

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DNA microarray technology is widely used by geneticists to diagnose or treat diseases through gene expression. This technology is based on the hybridization of a tissue-s DNA sequence into a substrate and the further analysis of the image formed by the thousands of genes in the DNA as green, red or yellow spots. The process of DNA microarray image analysis involves finding the location of the spots and the quantification of the expression level of these. In this paper, a tool to perform DNA microarray image analysis is presented, including a spot addressing method based on the image projections, the spot segmentation through contour based segmentation and the extraction of relevant information due to gene expression.

Keywords: Contour segmentation, DNA microarrays, edge detection, image processing, segmentation, spot addressing.

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Authors: Raju Bhukya, DVLN Somayajulu

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Pattern matching is one of the fundamental applications in molecular biology. Searching DNA related data is a common activity for molecular biologists. In this paper we explore the applicability of a new pattern matching technique called Index based Forward Backward Multiple Pattern Matching algorithm(IFBMPM), for DNA Sequences. Our approach avoids unnecessary comparisons in the DNA Sequence due to this; the number of comparisons of the proposed algorithm is very less compared to other existing popular methods. The number of comparisons rapidly decreases and execution time decreases accordingly and shows better performance.

Keywords: Comparisons, DNA Sequence, Index.

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Authors: Nikolai Krainiukov, Boris Melnikov

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We study the properties of maximal prefix codes. The codes have many applications in computer science, theory of formal languages, data processing and data classification. Our approaches to study use finite state automata (so-called flower automata) for the representation of prefix codes. An important task is the decomposition of prefix codes into prime prefix codes (factors). We discuss properties of such prefix code decompositions. A linear time algorithm is designed to find the prime decomposition. We used the GAP computer algebra system, which allows us to perform algebraic operations for free semigroups, monoids and automata.

Keywords: Maximal prefix code, regular languages, flower automata, prefix code decomposing.

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Authors: Zuwairie Ibrahim, Yusei Tsuboi, Osamu Ono, Marzuki Khalid

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Deoxyribonucleic Acid or DNA computing has emerged as an interdisciplinary field that draws together chemistry, molecular biology, computer science and mathematics. Thus, in this paper, the possibility of DNA-based computing to solve an absolute 1-center problem by molecular manipulations is presented. This is truly the first attempt to solve such a problem by DNA-based computing approach. Since, part of the procedures involve with shortest path computation, research works on DNA computing for shortest path Traveling Salesman Problem, in short, TSP are reviewed. These approaches are studied and only the appropriate one is adapted in designing the computation procedures. This DNA-based computation is designed in such a way that every path is encoded by oligonucleotides and the path-s length is directly proportional to the length of oligonucleotides. Using these properties, gel electrophoresis is performed in order to separate the respective DNA molecules according to their length. One expectation arise from this paper is that it is possible to verify the instance absolute 1-center problem using DNA computing by laboratory experiments.

Keywords: DNA computing, operation research, 1-center problem.

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Authors: Gurjit Kaur, Neena Gupta

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In this paper, we have analyzed and compared the performance of various coding schemes. The basic ID prime sequence codes are unique in only dimension, i.e. time slots, whereas 2D coding techniques are not unique by their time slots but with their wavelengths also. In this research, we have evaluated and compared the performance of 1D and 2D coding techniques constructed using prime sequence coding pattern for Optical Code Division Multiple Access (OCDMA) system on a single platform. Analysis shows that 2D prime code supports lesser number of active users than 1D codes, but they are having large code family and are the most secure codes compared to other codes. The performance of all these codes is analyzed on basis of number of active users supported at a Bit Error Rate (BER) of 10-9.

Keywords: CDMA, OCDMA, BER, OOC, PC, EPC, MPC, 2-D PC/PC, λc, λa.

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Authors: Abhijit Mitra, C. Ardil

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We investigate efficient spreading codes for transmitter based techniques of code division multiple access (CDMA) systems. The channel is considered to be known at the transmitter which is usual in a time division duplex (TDD) system where the channel is assumed to be the same on uplink and downlink. For such a TDD/CDMA system, both bitwise and blockwise multiuser transmission schemes are taken up where complexity is transferred to the transmitter side so that the receiver has minimum complexity. Different spreading codes are considered at the transmitter to spread the signal efficiently over the entire spectrum. The bit error rate (BER) curves portray the efficiency of the codes in presence of multiple access interference (MAI) as well as inter symbol interference (ISI).

Keywords: Code division multiple access, time division duplex, transmitter technique, precoding, pre-rake, rake, spreading code.

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Authors: Othman O. Khalifa, Sheroz khan, Mohamad Zaid, Muhamad Nawawi

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This paper mainly about the study on one of the widely used error correcting codes that is Low parity check Codes (LDPC). In this paper, the Regular LDPC code has been discussed The LDPC codes explained in this paper is about the Regular Binary LDPC codes or the Gallager.

Keywords: LDPC, channel coding.

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Authors: Khalid Abdelmoumen, Mustapha Najmeddine, Hussain Ben-Azza

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We present linear codes over finite commutative rings which are not necessarily Frobenius. We treat the notion of syndrome decoding by using Pontrjagin duality. We also give a version of Delsarte-s theorem over rings relating trace codes and subring subcodes.

Keywords: Codes, Finite Rings, Pontrjagin Duality, Trace Codes.

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Authors: G. Tamilpavai, C. Vishnuppriya

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Studying DNA (deoxyribonucleic acid) sequence is useful in biological processes and it is applied in the fields such as diagnostic and forensic research. DNA is the hereditary information in human and almost all other organisms. It is passed to their generations. Earlier stage detection of defective DNA sequence may lead to many developments in the field of Bioinformatics. Nowadays various tedious techniques are used to identify defective DNA. The proposed work is to analyze and identify the cancer-causing DNA motif in a given sequence. Initially the human DNA sequence is separated as k-mers using k-mer separation rule. The separated k-mers are clustered using Self Organizing Map (SOM). Using Levenshtein distance measure, cancer associated DNA motif is identified from the k-mer clusters. Experimental results of this work indicate the presence or absence of cancer causing DNA motif. If the cancer associated DNA motif is found in DNA, it is declared as the cancer disease causing DNA sequence. Otherwise the input human DNA is declared as normal sequence. Finally, elapsed time is calculated for finding the presence of cancer causing DNA motif using clustering formation. It is compared with normal process of finding cancer causing DNA motif. Locating cancer associated motif is easier in cluster formation process than the other one. The proposed work will be an initiative aid for finding genetic disease related research.

Keywords: Bioinformatics, cancer motif, DNA, k-mers, Levenshtein distance, SOM.

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Authors: Insah Bhurtah, P. Clarel Catherine, K. M. Sunjiv Soyjaudah

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The decoding of Low-Density Parity-Check (LDPC) codes is operated over a redundant structure known as the bipartite graph, meaning that the full set of bit nodes is not absolutely necessary for decoder convergence. In 2008, Soyjaudah and Catherine designed a recovery algorithm for LDPC codes based on this assumption and showed that the error-correcting performance of their codes outperformed conventional LDPC Codes. In this work, the use of the recovery algorithm is further explored to test the performance of LDPC codes while the number of iterations is progressively increased. For experiments conducted with small blocklengths of up to 800 bits and number of iterations of up to 2000, the results interestingly demonstrate that contrary to conventional wisdom, the error-correcting performance keeps increasing with increasing number of iterations.

Keywords: Error-correcting codes, information theory, low-density parity-check codes, sum-product algorithm.

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Authors: Manpreet Singh, Parvinder Singh Sandhu, Manjinder Singh Kahlon

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There are many classical algorithms for finding routing in FPGA. But Using DNA computing we can solve the routes efficiently and fast. The run time complexity of DNA algorithms is much less than other classical algorithms which are used for solving routing in FPGA. The research in DNA computing is in a primary level. High information density of DNA molecules and massive parallelism involved in the DNA reactions make DNA computing a powerful tool. It has been proved by many research accomplishments that any procedure that can be programmed in a silicon computer can be realized as a DNA computing procedure. In this paper we have proposed two tier approaches for the FPGA routing solution. First, geometric FPGA detailed routing task is solved by transforming it into a Boolean satisfiability equation with the property that any assignment of input variables that satisfies the equation specifies a valid routing. Satisfying assignment for particular route will result in a valid routing and absence of a satisfying assignment implies that the layout is un-routable. In second step, DNA search algorithm is applied on this Boolean equation for solving routing alternatives utilizing the properties of DNA computation. The simulated results are satisfactory and give the indication of applicability of DNA computing for solving the FPGA Routing problem.

Keywords: FPGA, Routing, DNA Computing.

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Authors: Ming-Chung Tsai, Kuan-Peng Chen, Zheng-Yao

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A systematic and exhaustive method based on the group structure of a unitary Lie algebra is proposed to generate an enormous number of quantum codes. With respect to the algebraic structure, the orthogonality condition, which is the central rule of generating quantum codes, is proved to be fully equivalent to the distinguishability of the elements in this structure. In addition, four types of quantum codes are classified according to the relation of the codeword operators and some initial quantum state. By linking the unitary Lie algebra with the additive group, the classical correspondences of some of these quantum codes can be rendered.

Keywords: Quotient-Algebra Partition, Codeword Spinors, Basis Codewords, Syndrome Spinors

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Authors: Jing Li, Xiuli Li

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This paper studies a special class of linear codes, called skew cyclic codes, over the ring R= F_q+uF_q+…+u^k-1F_q, where q is a prime power. A Gray map ɸ from R to F_q and a Gray map ɸ' from Rⁿ to Fⁿ_q are defined, as well as an automorphism Θ over R. It is proved that the images of skew cyclic codes over R under map ɸ' and Θ are cyclic codes over F_q, and they still keep the dual relation.

Keywords: Skew cyclic code, gray map, automophism, cyclic code.

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Authors: Gabofetswe Malema, Michael Liebelt

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LDPC codes could be used in magnetic storage devices because of their better decoding performance compared to other error correction codes. However, their hardware implementation results in large and complex decoders. This one of the main obstacles the decoders to be incorporated in magnetic storage devices. We construct small high girth and rate 2 columnweight codes from cage graphs. Though these codes have low performance compared to higher column weight codes, they are easier to implement. The ease of implementation makes them more suitable for applications such as magnetic recording. Cages are the smallest known regular distance graphs, which give us the smallest known column-weight 2 codes given the size, girth and rate of the code.

Keywords: Structured LDPC codes, cage graphs.

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Authors: S. Mawlood, L. Dennany, N. Watson, B. Pickard

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DNA analysis has been widely accepted as providing valuable evidence concerning the identity of the source of biological traces. Our work has showed that DNA samples can survive on cartridges even after firing. The study also raised the possibility of determining other information such as the age of the donor. Such information may be invaluable in certain cases where spent cartridges from automatic weapons are left behind at the scene of a crime. In spite of the nature of touch evidence and exposure to high chamber temperatures during shooting, we were still capable to retrieve enough DNA for profile typing. In order to estimate age of contributor, DNA methylation levels were analyzed using EpiTect system for retrieved DNA. However, results were not conclusive, due to low amount of input DNA.

Keywords: Age prediction, Fired cartridge, Trace DNA sample.

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Authors: M. S. Muhammad, S. M. W. Masra, K. Kipli, N. Zamhari

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The capturing of gel electrophoresis image represents the output of a DNA computing algorithm. Before this image is being captured, DNA computing involves parallel overlap assembly (POA) and polymerase chain reaction (PCR) that is the main of this computing algorithm. However, the design of the DNA oligonucleotides to represent a problem is quite complicated and is prone to errors. In order to reduce these errors during the design stage before the actual in-vitro experiment is carried out; a simulation software capable of simulating the POA and PCR processes is developed. This simulation software capability is unlimited where problem of any size and complexity can be simulated, thus saving cost due to possible errors during the design process. Information regarding the DNA sequence during the computing process as well as the computing output can be extracted at the same time using the simulation software.

Keywords: DNA computing, PCR, POA, simulation software

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Authors: Hassan Berbia, Faissal Elbouanani, Rahal Romadi, Mostafa Belkasmi

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This paper introduces two decoders for binary linear codes based on Metaheuristics. The first one uses a genetic algorithm and the second is based on a combination genetic algorithm with a feed forward neural network. The decoder based on the genetic algorithms (DAG) applied to BCH and convolutional codes give good performances compared to Chase-2 and Viterbi algorithm respectively and reach the performances of the OSD-3 for some Residue Quadratic (RQ) codes. This algorithm is less complex for linear block codes of large block length; furthermore their performances can be improved by tuning the decoder-s parameters, in particular the number of individuals by population and the number of generations. In the second algorithm, the search space, in contrast to DAG which was limited to the code word space, now covers the whole binary vector space. It tries to elude a great number of coding operations by using a neural network. This reduces greatly the complexity of the decoder while maintaining comparable performances.

Keywords: Block code, decoding, methaheuristic, genetic algorithm, neural network

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Authors: Lilia M. Fernando, Matthew K. Vasher, Evangelyn C. Alocilja

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This paper describes the development of a DNA-based nanobiosensor to detect the dengue virus in mosquito using electrically active magnetic (EAM) nanoparticles as concentrator and electrochemical transducer. The biosensor detection encompasses two sets of oligonucleotide probes that are specific to the dengue virus: the detector probe labeled with the EAM nanoparticles and the biotinylated capture probe. The DNA targets are double hybridized to the detector and the capture probes and concentrated from nonspecific DNA fragments by applying a magnetic field. Subsequently, the DNA sandwiched targets (EAM-detector probe– DNA target–capture probe-biotin) are captured on streptavidin modified screen printed carbon electrodes through the biotinylated capture probes. Detection is achieved electrochemically by measuring the oxidation–reduction signal of the EAM nanoparticles. Results indicate that the biosensor is able to detect the redox signal of the EAM nanoparticles at dengue DNA concentrations as low as 10 ng/μl.

Keywords: Dengue, magnetic nanoparticles, mosquito, nanobiosensor.

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Authors: Seung-Jun Yu, Jang-Kyun Ahn, Eui-Young Lee, Hyoung-Kyu Song

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Space-time block codes (STBC) and spatial multiplexing (SM) are promising techniques that effectively exploit multipleinput multiple-output (MIMO) transmission to achieve more reliable communication and a higher multiplexing rate, respectively. In this paper, we study a practical design for hybrid scheme with multi-input multi-output orthogonal frequency division multiplexing (MIMOOFDM) systems to flexibly maximize the tradeoff between diversity and multiplexing gains. Unlike the existing STBC and SM designs which are suitable for the integer multiplexing rate, the proposed design can achieve arbitrary number of multiplexing rate.

Keywords: Space-Time Block Codes, Spatial Multiplexing, MIMO-OFDM.

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Authors: John Mark Lampos, Virgilio Sison

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Two constructions of unit-memory binary convolutional codes from linear block codes over the finite semi-local ring F2r +vF2r , where v2 = v, are presented. In both cases, if the linear block code is systematic, then the resulting convolutional encoder is systematic, minimal, basic and non-catastrophic. The Hamming free distance of the convolutional code is bounded below by the minimum Hamming distance of the block code. New examples of binary convolutional codes that meet the Heller upper bound for systematic codes are given.

Keywords: Convolutional codes, semi-local ring, free distance, Heller bound.

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Authors: Hao Wang, Yanming Zou

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Two-dimensional (2D) bar codes were designed to carry significantly more data with higher information density and robustness than its 1D counterpart. Thanks to the popular combination of cameras and mobile phones, it will naturally bring great commercial value to use the camera phone for 2D bar code reading. This paper addresses the problem of specific 2D bar code design for mobile phones and introduces a low-level encoding method of matrix codes. At the same time, we propose an efficient scheme for 2D bar codes decoding, of which the effort is put on solutions of the difficulties introduced by low image quality that is very common in bar code images taken by a phone camera.

Keywords: 2D bar code reading, camera phone, low-level encoding, mixed model

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Authors: Rabiˆı DARITI, El Mamoun SOUIDI

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Linear error-block codes are a natural generalization of linear error correcting codes. The purpose of this paper is to generalize some results on the packing and the covering radii to the error-block case. We study their properties when a code undergoes some specific modifications and combinations with another code. We give a few bounds on the packing and the covering radii of these codes.

Keywords: Linear error-block codes, π-distance, Correction capacity, Packing radius, Covering radius.

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Authors: Zuzana Poborilova, Anna B. Ohlsson, Torkel Berglund, Anna Vildova, Petr Babula

Abstract:

Lawsone is a pigment that occurs naturally in plants. It has been used as a skin and hair dye for a long time. Moreover, its different biological activities have been reported. The present study focused on the effect of lawsone on a plant cell model represented by tobacco BY-2 cell suspension culture, which is used as a model comparable with the HeLa cells. It has been shown that lawsone inhibits the cell growth in the concentration-dependent manner. In addition, changes in DNA methylation level have been determined. We observed decreasing level of DNA methylation in the presence of increasing concentrations of lawsone. These results were accompanied with overproduction of reactive oxygen species (ROS). Since epigenetic modifications can be caused by different stress factors, there could be a connection between the changes in the level of DNA methylation and ROS production caused by lawsone.

Keywords: DNA methylation, Lawsone, Naphthoquinone, Reactive Oxygen Species.

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Authors: Seung Pil Pack

Abstract:

Deaminated lesions were produced via nitrosative oxidation of natural nucleobases; uracul (Ura, U) from cytosine (Cyt, C), hypoxanthine (Hyp, H) from adenine (Ade, A), and xanthine (Xan, X) and oxanine (Oxa, O) from guanine (Gua, G). Such damaged nucleobases may induce mutagenic problems, so that much attentions and efforts have been poured on the revealing of their mechanisms in vivo or in vitro. In this study, we employed these deaminated lesions as useful probes for analysis of DNA-binding/recognizing proteins or enzymes. Since the pyrimidine lesions such as Hyp, Oxa and Xan are employed as analogues of guanine, their comparative uses are informative for analyzing the role of Gua in DNA sequence in DNA-protein interaction. Several DNA oligomers containing such Hyp, Oxa or Xan substituted for Gua were designed to reveal the molecular interaction between DNA and protein. From this approach, we have got useful information to understand the molecular mechanisms of the DNA-recognizing enzymes, which have not ever been observed using conventional DNA oligomer composed of just natural nucleobases.

Keywords: Deaminated lesion, DNA-protein interaction, DNA-recognizing enzymes

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Authors: A. S. Poornima, R. Aparna, B. B. Amberker, Prashant Koulgi

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In this paper, we propose use of convolutional codes for file dispersal. The proposed method is comparable in complexity to the information Dispersal Algorithm proposed by M.Rabin and for particular choices of (non-binary) convolutional codes, is almost as efficient as that algorithm in terms of controlling expansion in the total storage. Further, our proposed dispersal method allows string search.

Keywords: Convolutional codes, File dispersal, Filereconstruction, Information Dispersal Algorithm, String search.

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