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international conference on Artificial Reality and Telexistence (ICAT)

作者： Ping Zhu Xuqing Tang Zhenyuan Xu Weihong Guan School of Science Southern Yangtze University Wuxi China Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education Anhui University Hefei China

In this paper, we offers a new algebraic point of view for dna molecules and introduce the algebraic system by using the natural operation based on the Sigma = {A, C, G, T} . We characterize its structure by using the algebraic theory. We show that (L, oplus, otimes ) is the distribution lattice of rings with identical element. Furthermore,we generalize this result to the Wrho(V) , a set which elements simulates the dna molecules with sticky ends, the element is called an incomplete double stranded molecules consist of mixed dna molecules with double and single strands.

关键词： dna computing Lattices Laboratories Intelligent structures Signal processing Computational modeling Sequences Biochemistry Biological materials Genetics

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Physical properties of anticancer drug 6-thioguanine

Physical properties of anticancer drug 6-thioguanine

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16th international conference on Spectroscopy of Molecules and Crystals

作者： Rubin, YV Inst Low Temp Phys & Engn UA-61103 Kharkov Ukraine

ISBN: (纸本)0819454443

6-thioguanine has long been in use as an anticancer drug. In the recent years 6-thioguanine and its derivatives are coming into application as photosensibilizers, luminescence probes, targets for forming photo-crosslinks. To ascertain spectroscopic properties of 6-thioguanine, its UV absorption, low temperature (4.2K) luminescence and circular dichroism spectra were studied in solutions of different polarities. Spectrophotometric titration of 6-thioguanine was carried out in the pH 1-13 interval. the MP2 ab initio method was used to calculate the molecular structure, dipole moments, electronic density distribution, thermodynamic characteristics, UV and IR spectra of some 6-thioguanine tautomers. Based on theoretical calculations and experimental results, a diagram of electronic excited states of 6-thioguanine and a scheme of acid-base and tautomeric equilibrium of 6-thioguanine in the polar solvent were built. Migration of excitation in dna with incorporated 6-thioguanine was investigated. As well, we used 6-thioguanine as a luminescent probe to study structural changes in cryoprotector and dna solutions in the temperature range from 4.2 to 273K. In particular, glassification of the dna hydrate shell in the range of 200K was revealed.

关键词： absorption and luminescence electronic spectra IR-spectra ab initio calculations dna 6-thioguanine molecular and electronic structures

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K-group A* for multiple sequence alignment with quasi-natural gap costs

K-group A* for multiple sequence alignment with quasi-natura...

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Proceedings - 16th IEEE international conference on Tools with Artificial Intelligence, ICTAI 2004

作者： Zhou, Rong Hansen, Eric A. Dept. of Comp. Sci. and Engineering Mississippi State University Mississippi State MS 39762 United States

ISBN: (纸本)076952236X

Alignment of multiple protein or dna sequences is an important problem in Bioinformatics. Previous work has shown that the A* search algorithm can find optimal alignments for up to several sequences, and that a K-group generalization of A* can find approximate alignments for much larger numbers of sequences. In this paper, we describe the first implementation of K-group A* that uses quasinatural gap costs, the cost model used in practice by biologists. We also introduce a new method for computing gap-opening costs in profile alignment. Our results show that K-group A* can efficiently find optimal or close-to-optimal alignments for small groups of sequences, and, for large numbers of sequences, it can find higher-quality alignments than the widely-used CLUSTAL family of approximate alignment tools. this demonstrates the benefits of A* in aligning large numbers of sequences, as typically compared by biologists, and suggests that K-group A* could become a practical tool for multiple sequence alignment. © 2004 IEEE.

关键词： dna sequences

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Experimental and calculated enhancement factor in the SEIRA method

Experimental and calculated enhancement factor in the SEIRA ...

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16th international conference on Spectroscopy of Molecules and Crystals

作者： Dovbeshko, GI Shirshov, YM Chegel, VI Fesenko, OM Natl Acad Sci Ukraine Inst Phys UA-03039 Kiev Ukraine

ISBN: (纸本)0819454443

the use of the method of enhancement of infrared absorption by rough metallic surface (SEIRA) allows one to increase the probability of infrared transitions and to reveal a series of spectral manifestations of structural features of biological molecules. We analyzed various experimental techniques which gives a possibility to achieve enhancement in the infrared (IR) spectra. We studied the applicability of the SEIRA techniques for analysis of nucleic acids, lipids, and membranes. Under the conditions of our experiment and according to literature data, there was observed enhancement factor equal to 320 for vibrations of various molecular groups. Peculiarity of another optical amplifier, namely, colloidal gold that effectively used for enhancement of signal in IR absorption and Raman scattering, have been studied. We made an attempt to model the effect of enhancement of electrical field and their frequency dependence for different metal surfaces and obtained that silver, gold and copper are the best.

关键词： biological molecules dna Fourier transformed infrared (FTIR) spectroscopy surface enhanced infrared absorption (SEIRA) golden substrate gold-colloidal particles surface and local plasmon resonance (SPR)

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K-group A* for multiple sequence alignment with quasi-natural gap costs

K-group A* for multiple sequence alignment with quasi-natura...

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international conference on Tools for Artificial Intelligence (ICTAI)

作者： Rong Zhou E.A. Hansen Department of Computer Science and Engineering Mississippi State University MS USA

Alignment of multiple protein or dna sequences is an important problem in bioinformatics. Previous work has shown that the A* search algorithm can find optimal alignments for up to several sequences, and that a K-group generalization of A* can find approximate alignments for much larger numbers of sequences [T. Ikeda et al. (1999)]. In this paper, we describe the first implementation of K-group A* that uses quasinatural gap costs, the cost model used in practice by biologists. We also introduce a new method for computing gap-opening costs in profile alignment. Our results show that K-group A* can efficiently find optimal or close-to-optimal alignments for small groups of sequences, and, for large numbers of sequences, it can find higher-quality alignments than the widely-used CLUSTAL family of approximate alignment tools. this demonstrates the benefits of A* in aligning large numbers of sequences, as typically compared by biologists, and suggests that K-group A* could become a practical tool for multiple sequence alignment.

关键词： Costs Sequences Iterative algorithms dna Bioinformatics Dynamic programming State-space methods Computer science Protein engineering Biological system modeling

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'dna-proofing' for computer systems - a new approach to computer security?

'DNA-proofing' for computer systems - a new approach to comp...

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16th international-Federation-for-Information-Processing World Computer Congress (IFIP 2000)/Annual conference of TC11 (SEC 2000)

作者： Louwrens, CP Von Solms, SH Rand Afrikaans Univ Dept Comp Sci ZA-2006 Johannesburg South Africa

ISBN: (纸本)0792379144

Modern day network-centric computing can increasingly be viewed as a vast, extremely involved organism, of which the boundaries are not clear, and most of the constituent parts are unkown from any given viewpoint. It may even become impossible to ensure the security of computing systems in future with current approaches to computer security. On the other hand, nature has been successful in defending its complex biological systems from infection and damage for countless millennia by using highly specialized and evolved immune systems. It is therefore postulated that a highly effective defensive mechanism can be developed, to transparently enforce an acceptable level of security in very extensive and complex computer networks and systems, by building very basic, but specialized autonomous agents, that follow basic rules that can be deduced from biological immune systems. Key to this concept is the biological system's ability to distinguish what belongs to it and what is foreign and therefore needs to be destroyed. this is done, inter alia, via genetic information contained in the dna of each cell. Central to the proposed immune model is thus the concept of 'dna-proofing'.

关键词： computer security dna-proofing anti-virus technology biological model immune system autonomous intelligent software agents

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A randomized, controlled, molecular study of condylomata acuminata clearance during treatment with imiquimod

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JOURNAL OF INFECTIOUS DISEASES 1998年第2期178卷 551-555页

作者： Tyring, SK Arany, I Stanley, MA Tomai, MA Miller, RL Smith, MH McDermott, DJ Slade, HB Univ Texas Med Branch Dept Microbiol & Immunol Galveston TX 77555 USA Univ Texas Med Branch Dept Dermatol Galveston TX 77555 USA Univ Cambridge Dept Pathol Cambridge CB2 1QP England 3M Pharmaceut Dept Pharmacol St Paul MN USA 3M Pharmaceut Dept Clin Res St Paul MN USA

Imiquimod, an immune response modifier, has been demonstrated to be safe and effective in the treatment of external genital and perianal warts caused by human papillomavirus (HPV), To identify the molecular mechanism(s) by which condylomata acuminata clear during topical treatment with imiquimod, wart skin biopsies were taken from patients before treatment, at treatment week 6, and at the end of treatment. Tissues were analyzed for HPV dna and for mRNA of several cytokines and HPV gene products. Wart clearance was associated with evidence of tissue production of interferon-alpha, -beta, and -gamma and tumor necrosis factor-cu, Regression of warts was strongly associated with a decrease in HPV dna and in mRNA expression for both early and late viral proteins. thus, topical imiquimod treatment of anogenital warts led to significant increases in local production of multiple interferon mRNAs and a significant reduction in virus load as measured by decreases in HPV dna and mRNA for early HPV proteins.

关键词： Warts Messenger RNA Cytokines Condylomata acuminata dna Biopsies Vehicles Erythema Viruses Genitalia

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Weak chirality in ordered dna phases

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molecular CRYSTALS AND LIQUID CRYSTALS SCIENCE AND TECHNOLOGY SECTION A-molecular CRYSTALS AND LIQUID CRYSTALS 1997年第1期299卷 265-275页

作者： Kamien, RD [a] Department of Physics and Astronomy University of Pennsylvania Philadelphia PA 19104 USA

Recent experiments(1) on aligned dna show hexatic order with no sign of macroscopic chirality. I make the analogy between smectic liquid crystals and chiral hexatics and show how the absence of chirality cannot occur in a thermodynamic phase of chiral molecules. In addition, I discuss the microscopic origin of chiral mesophases in liquid crystals and show that, within the context of central forces between ''atoms'' on ''molecules'', chiral interactions can occur only if there are biaxial correlations between the mesogens. Weak biaxial correlations can therefore lead to small cholesteric pitches.

关键词： dna

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Role of high performance parallel computing in biological research

Role of high performance parallel computing in biological re...

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Proceedings of the 16th Annual international conference of the IEEE Engineering in Medicine and Biology Society. Part 1 (of 2)

作者： Martino, Robert L. Johnson, Calvin A. Suh, Edward B. Trus, Benes L. Yap, Tieng K. Natl Inst of Health Bethesda United States

Scalable parallel computer architectures provide the computational performance demanded by advanced biological computing problems. NIH has developed a number of parallel algorithms and techniques useful in determining biological structure and function. these applications include processing electron micrographs to determine the three-dimensional structure of viruses, calculating the solvent accessible surface area of proteins to predict the three-dimensional conformation of these molecules from their primary structure, and searching for homologous dna sequences in large genetic databases. Timing results demonstrate substantial performance improvements with parallel implementations compared with conventional sequential systems.

关键词： Parallel processing systems

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the role of high performance parallel computing in biological research [molecular structure application]

The role of high performance parallel computing in biologica...

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Annual international conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

作者： R.L. Martino C.A. Johnson E.B. Suh B.L. Trus T.K. Yap Computational Bioscience and Engineering Laboratory Computer Research and Technology National Institutes of Health DHHS Bethesda MD USA

关键词： Parallel processing Biology computing Concurrent computing Computer architecture Parallel algorithms Application software Electrons Viruses (medical) Solvents Proteins

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