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epresentation (CGR), a tool derived from the chaotic dynamical systems theory. If the DNA sequence is a random collection of bases, the CGR will be a uniformly filled square; on the other hand, any pattern visible in the CGR contains information on the DNA sequence. First we use the Markov Chain models proposed by Goldman (Nucleic Acids Research, 1993, Vol. 21, No. 10 2487-2491) to simulate the CGR of mitochondrial genomes. Then a simple correlation-related distance approach without sequence alignment based on the CGR of mitochondrial genomes is proposed to analyze the phylogeny of 64 selected vertebrates. Keywords: Mitochondrial genomes, chaos game representation, Markov Chain model simulation, vertebrate phylogeny OR-005 A New Approach for DNA Sequence Similarity Analysis based on Triplets of Nucleic Acid Bases Wei Dan1, Jiang Qingshan2,3 1. School of Information Science and Technology, Xiamen University, Xiamen, 361005, China 2. Chengdu University, Chengdu, 610106, China 3. Software School, Xiamen University, Xiamen, 361005, China Similarity analysis of DNA sequences is a basis in Bioinformatics. The characteristic distribution of L-tuple reflects the biological information involved in a biological sequence and thus may be used in DNA sequence similarity analysis. But similarity analysis based on characteristic distribution of L-tuple is not effective on very conservative sequence comparison. In this paper, a new similarity measurement approach based on TNAB (triplets of nucleic acid bases) is introduced for DNA sequence similarity analysis. The new approach can reflect the content feature and positional feature of a DNA sequence with the frequencies and position of occurrence of TNAB in the sequence. The experimental results show that the approach based on TNAB is effective on DNA sequence similarity analysis. Key Words: DNA sequences, Triplets of nucleotide bases, Similarity analysis, L-tuple; Frequency, Content feature, Positional feature, vector OR-006 A Proline-based Neuraminidase Inhibitor: DFT Studies on the Zwitterion Conformation, Stability and Formation Zhiwei Yang a, Gang Yang a, b, a. Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, P. R. China b. Institute of Theoretical Chemistry, Shandong University, Jinan 250100, P. R. China Corresponding author. Tel: +86-451-82192223; Fax: +86-451-82102082; E-mail: theobiochem@gmail.com The designs of potent neuraminidase (NA) inhibitors are an efficient way to deal with the recent “2009 H1N1” influenza epidemic. In this work, density functional calculations were employed to study the stability and formation of the zwitterions of 5-[(1R, 2S)-1-(acetylamino)-2methoxy-2-methylpentyl]-4-[(1Z)- 1-propenyl)-(4S, 5R)]-D-proline (BL), a proline-based NA inhibitor. Compared with proline, the zwitterion stability of BL is enhanced by 1.76 kcal mol-1 due to the introduction of functional groups. However, the zwitterion of BL will not represent a local minimum on the potential energy surface until the water molecules increase up to two (n = 2). With the addition of two and three water molecules, the energy differences between the zwitterions and corresponding canonical isomers were calculated at 3.13 and -1.54 kcal mol-1, respectively. The zwitterions of BL are
mainly stabilized by the H-bonds from water molecules, especially in the case of three water molecules where the carboxyl O atoms are largely coordination-saturated by three H-bonds of medium strengths and thus make the zwitterion stability even superior to the canonical isomer. With the presence of two and three water molecules, the energy barriers for the conversion processes from the canonical isomers to the zwitterions are equal to 4.96 and 3.13 kcal mol-1, respectively. It indicated that the zwitterion formation is facile to take place with the addition of two molecules and further facilitated by more water molecules. Besides, the zwitterion formation of BL is finished in a single step, unlike other NA inhibitors. Owing to the above advantages, BL is a good candidate of NA inhibitors and more attention should be paid in the explorations of BL-based drugs. OR-007 A strategy for parameter estimation for mRNA and protein dynamics Fortunato Bianconi , Mauro Boccadoro , Gabriele Lillacci , Paolo Valigi This paper proposes a methodology of parameter identification for nonlinear systems, in particular biochemical networks, based on a least squares procedure that treats the signals provided by a high gain observer. Prior to the estimation phase, identifiability and sensitivity analysis determine which parameters can and/or should be estimated. The procedure is tested on the data obtained by in silico experiments for a simple instance of a proposed general dynamic model of protein synthesis. Keywords: Biochemical Networks, Parameter, Identification, Identifiability , State OR-008 Mathematical Platform to Explore Comprehensive Effects of Different Drug Treatments in Patients with Multiple Myeloma Yan Wang1, David W. Smith2, Peter Pivonka2 1. Department of Civil & Environmental Engineering, University of Melbourne, Melbourne, VIC, Australia 2. Faculty of Engineering, Computing and Mathematics, University of Western Australia, Perth, WA, Australia Multiple Myeloma (MM) is an incurable but tractable blood cancer, in which over 70% of patients with MM are involved in bone disease such as bone pain, bone lesions and fracture. Besides widespread used Bisphosphonates (i.e. Pamidronate), published experimental data indicate that Denosumab, a fully human monoclonal antibody of RANKL, is very promising in terms of improving bone loss. Recently, Marathe et al. [1] coupled Denosumab pharmacokinetics in MM patients with bone homoestasishas to break through ‘black box’ limitations brought by using traditional approach of pharmacodynamics. However, impacts of MM on bone environment are ignored in the model. Hence, we aim to develop a MM disease model to be a mathematical platform, based on which comprehensive effects of different drug treatments in MM patients can be explored pre-clinically and a couple of regimes might be suggested for clinical trials. In this study, MM disease model focuses on examining the impacts of over-expressed RANKL and DKK1 by MM cells, which exerts their roles through increasing of ratio of RANKL to OPG and inhibiting activation of Wnt signaling respectively. On the other hand, counteractions of bone environment on MM cells are also examined in the model, which might be through bone resorption released TGF-β and over production of IL-6. Being a case study, we integrate the MM disease model with Denosumab and Pamidronate pharmacokinetics and then optimize the integrated model based on
Page 1 and 2: Abstracts Keynote & Plenary KN-001
Page 3 and 4: The nonlinear dynamical interaction
Page 5 and 6: Lim., Carmay Our research interests
Page 7 and 8: Email: jtus@phys.ualberta.caBackgro
Page 9 and 10: Formula drug or nutrient Any LMN is
Page 11 and 12: present study provide support to th
Page 13: Keywords: Amino acid index, non-cla
Page 17 and 18: generalized by Glazier and Graner [
Page 19 and 20: Profile-profile alignment may be th
Page 21 and 22: natural structure is coded in its a
Page 23 and 24: information will be presented. Assi
Page 25 and 26: Seasonal trade-off between water- a
Page 27 and 28: fluorescent protein ng, W.-D. Cheng
Page 29 and 30: 2. Email: xpgao@xtu.edu.cn Classifi
Page 31 and 32: * To whom correspondence should be
Page 33 and 34: analysis across different platforms
Page 35 and 36: 1.D. Q. Wei and G. N. Patey, Phys.
Page 37 and 38: 2. Göteborg University, Department
Page 39 and 40: Pushkal Samadhiya and S.K. Srivasta
Page 41 and 42: conformations may convert to each o
Page 43 and 44: and imidopropyl with 1,2,3-benzotri

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