RECENT ADVANCES in BIOLOGY, BIOPHYSICS, BIOENGINEERING and COMPUTATIONAL CHEMISTRY

Proceedings of the 5th WSEAS International Conference on CELLULAR and MOLECULAR BIOLOGY, BIOPHYSICS and BIOENGINEERING (BIO '09) Proceedings of the 3rd WSEAS International Conference on COMPUTATIONAL CHEMISTRY (COMPUCHEM '09)

Puerto De La Cruz, Tenerife, Canary Islands, Spain December 14-16, 2009

Recent Advances in Biology and Biomedicine A Series of Reference Books and Textbooks

Published by WSEAS Press ISSN: 1790-5125 www.wseas.org ISBN: 978-960-474-141-0 RECENT ADVANCES in BIOLOGY, BIOPHYSICS, BIOENGINEERING and COMPUTATIONAL CHEMISTRY

Puerto De La Cruz, Tenerife, Canary Islands, Spain December 14-16, 2009

Recent Advances in Biology and Biomedicine A Series of Reference Books and Textbooks

Published by WSEAS Press www.wseas.org

All the copyright of the present book belongs to the World Scientific and Engineering Academy and Society Press. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, or otherwise, without the prior written permission of the Editor of World Scientific and Engineering Academy and Society Press.

All papers of the present volume were peer reviewed by two independent reviewers. Acceptance was granted when both reviewers' recommendations were positive. See also: http://www.worldses.org/review/index.html

ISSN: 1790-5125 ISBN: 978-960-474-141-0

World Scientific and Engineering Academy and Society

RECENT ADVANCES in BIOLOGY, BIOPHYSICS, BIOENGINEERING and COMPUTATIONAL CHEMISTRY

Puerto De La Cruz, Tenerife, Canary Islands, Spain December 14-16, 2009

Editors: Prof. Cornelia A. Bulucea, University of Craiova, Romania Prof. Valeri Mladenov, Technical University of Sofia, Bulgaria Prof. Emil Pop, University of Petrosani, Romania Prof. Monica Leba, University of Petrosani, Romania Prof. Nikos Mastorakis, Technical University of Sofia, Bulgaria

International Program Committee Members: Jill Mesirov (MIT) Walter Thiel (Max Planck Institute) Thomas Lengauer (Saarbrucken) Wilfred van Gunsteren (ETH) Alfonso Valencia (CNB, Madrid) Alexander Lyubartsev (Stockholm University) Ceslovas Venclovas (Vilnius) Alexey Mazur (CNRS-UPR9080, IBPC) Martin Vingron (Max Planck Institute, Berlin) Alexey Onufiev (Virginia Tech) Shoshana Wodak (University of Toronto) Amedeo Palma (CNR-ISMN) Ralf Zimmer (Saarbrucken) Andriy Baumketner (UNC Charlotte) Haim Wolfson (Tel Aviv University) Dieter Hofmann (GKSS Research Centre) Alberto Apostolico (Padova University) George Shields (Hamilton College) Serafim Batzoglou (Stanford University) Hassan Safouhi (University of Alberta) Rita Casadio (Bologna University) Jaroslav Koca (Masaryk university, Fac Sci) Soren Brunak (Technical University Denmark) Jiri Vanicek (EPFL) Frank Eisenhaber (IMP, Vienna) Laurence Leherte (University of Namur) Marie- Nir Friedman (Hebrew University of Jerusalem) Pierre Gaigeot (Universite d'Evry val d'Essonne) Mikhail Gelfand (IITP, Moscow) Martin Parker (University of Leeds) Raffaele Giancarlo (Palermo University) Nick Quirke (Imperial College London) David Gilbert (University of Glasgow) Paul Smith (Kansas State University) Concettina Guerra (Padova University) Robert Woods (Carbohydrate Research Center) Roderic Guigo (IMIM, Barcelona) Roberto Lins (Pacific Northwest Laboratory) Sorin Istrail (Brown University) Roman Efremov (Shemyakin-Ovchinnikov) Simon Kasif (Boston University) Scott Brown (Abbott Laboratories) Andrzej Kolinski (Warsaw University) Shina Lynn Kamerlin (Southern California) Gregory Kucherov (LIFL, Lille) Tanja van Mourik (University of St Andrews) Giuseppe Lancia (Udine University) Yaoqi Zhou (Indiana University) Satoru Miyano (Tokyo University) Yingkai Zhang (New York University) Pavel Pevzner (San Diego) Ron Pinter (Technion, Haifa) Tal Pupko (Tel Aviv University) Aviv Regev (Harvard University) Isidore Rigoutsos (TJ Watson Research Center) Burkhardt Rost (Columbia University) Mikhail Roytberg (IMPB, Russia) Marie-France Sagot (Lyon) Eran Segal (Weizmann Institute of Science) Ron Shamir (Tel Aviv University) Roded Sharan (Tel Aviv University) Steve Skiena (SUNY Stony Brook) Jeff Skolnick (Georgia Institute of Technology) Wojciech Szpankowski (Purdue University) Anna Tramontano (University of Rome) Ron Unger (Bar Ilan University) Donald Truhlar (University of Minnesota) Graham Richards (University of Oxford) Minhaeng Cho (Korea University) Modesto Orozco (University of Barcelona) Pavel Hobza (Czech Republic) Rebecca Wade (EML Research) Richard Friesner (Columbia University) Todd Martinez (University of Illinois)

Preface This year the 5th WSEAS International Conference on CELLULAR and MOLECULAR BIOLOGY, BIOPHYSICS and BIOENGINEERING (BIO'09) and the 3rd WSEAS International Conference on COMPUTATIONAL CHEMISTRY (COMPUCHEM'09) were held at Puerto De La Cruz, Tenerife, Canary Islands, Spain, December 14-16, 2009. The conferences remain faithful to their original idea of providing a platform to discuss biology of cell, metabolism, molecular biology, neural modeling, biophysics, biochemistry, computer biology, genetics, theoretical chemistry, computational material science, numerical analysis for chemical engineering and chemistry, computational intelligence tools for chemistry and chemical engineering, computational molecular science and nanoscience, mathematical molecular medicine, chemical fluid mechanics, environmental chemical engineering etc. with participants from all over the world, both from academia and from industry.

Their success is reflected in the papers received, with participants coming from several countries, allowing a real multinational multicultural exchange of experiences and ideas.

The accepted papers of these conferences are published in this Book that will be indexed by ISI. Please, check it: www.worldses.org/indexes as well as in the CD-ROM Proceedings. They will be also available in the E-Library of the WSEAS. The best papers will be also promoted in many Journals for further evaluation.

Conferences such as these can only succeed as a team effort, so the Editors want to thank the International Scientific Committee and the Reviewers for their excellent work in reviewing the papers as well as their invaluable input and advice.

The Editors

RECENT ADVANCES in BIOLOGY, BIOPHYSICS, BIOENGINEERING and COMPUTATIONAL CHEMISTRY

Table of Contents

Plenary Lecture 1: Nanoparticles for the Transport of Antiretroviral Drugs across the Blood- 11 Brain Barrier: A Potential Therapy for the Acquired Immunodeficiency Syndrome Yung-Chih Kuo

Plenary Lecture 2: Creation of Electromagnetic Structure-Creating Spaces to Improve the 12 Growth of Some Types of Cells and Albumins Vladyslav Vlastopulo

Plenary Lecture 3: A New Way of Natural Oligopeptide Primary Structure Elucidation 13 Alexander A. Zamyatnin

Studies on a Promising Anticancer Molecule of Marine Origin. Results of an Interdisciplinary 15 Study A. Zovko, T. Turk, M. Faimali, F. Garaventa, E. Chelossi, C. Falugi, M. G. Aluigi, C. Angelini, S. Trombino, L. Gallus, S. Ferrando, P. Russo, L. Paleari, K. Sepcic

An Intelligent Controller of the Chemical Reactor 24 Jelenka Savkovic-Stevanovic

Evolution of Proliferating Cells under Different Decaying Behaviors of the Total Tumor Cells 30 During a Course of Treatment Mitra Shojania Feizabadi

A New Way of Natural Oligopeptide Primary Structure Elucidation 33 Alexander A. Zamyatnin

Nitrate Removal from the Cetina Surface Water by using Bacteria Attached to Lewatit M600 39 Lucija Foglar, Ana-Marija Babic, Mario Siljeg

Information Theory-Based Code Optimization of Matrix Elements for Overall Rotation 45 Angular Momenta Maria Eugenia Castro, Camelia Munoz-Caro, Alfonso Nino

Nanoaggregation and Solubility of Crude Oil Asphaltenes from Molecular Dynamics 51 Simulations Francesco Frigerio

Computational Study of Nodifloridin-A and Nodiflorifin-B, with Highlight on the Peculiarities 58 of Acylated Phloroglucinol Derivatives Liliana Mammino, Mwadham M. Kabanda

Mitochondrial DNA Copy Number and Citrate Synthase Activity in Nonalcoholic Fatty Liver 64 Disease Induced in Rats by a high-fat plus Fructose Diet Fortified or not with Dehydroepiandrosterone (DHEA) Angela Maria Lezza, Pierluigi Cassano, Raffaella Mastrocola, Pesce Vito, Manuela Aragno, Maria Nicola Gadaleta

DFT Study of Tautomeric Equilibria of 6-Hydroxy—Flourocytosine 68 Behzad Chahkandi, Sorour Hasani

ISSN: 1790-5125 9 ISBN: 978-960-474-141-0 RECENT ADVANCES in BIOLOGY, BIOPHYSICS, BIOENGINEERING and COMPUTATIONAL CHEMISTRY

Investigation of Various Conformations of HCO-Gly-L-Val-Gly-NH2 Tripeptide in Elastin: Ab 74 Initio and DFT Calculations Behzad Chahkandi, Badrosadat Seyed Hosseini

Nanochannel and its Application in Analytical Chemistry 80 Zenglian Yue, Guoqing Zhao, Bin Peng, Shasheng Huang

On the Numerical Solution of Mathematical Models of Cancer Growth and Optimal Cancer 94 Therapy Nikos E. Mastorakis

Development of Transgenic Cotton Expressing Modified Bt and CpTI Genes by Pollen Tube 105 Pathway Mediated-Transformation Jinying Guo, Tianzhen Zhang

High Pest Resistance Transgenic Cotton Transformed with Bt and Sck Gene 110 Guo Jinying, Chen Tao, Zhang Tianzhen

The Genetic Stability of Transgenic Bt and Sck Insect-Resistant Cotton 115 Guo Jinying, Chen Tao, Zhang Tianzhen

Qsar Study of Anthranilic Acid Sulfonamides as Inhibitors of Methionine Aminopeptidase-2 119 using Different Chemometrics Tools Razieh Sabet, Mohsen Shahlaei, Afshin Fassihi

Virtual Reality Applied to the Management, Planning and Optimization of Surgical 126 Interventions Cristina Suarez-Mejias, Armando Cabral-Camacho, Daniel Derlinchan-Gonzalez, Tomas Gomez- Cia, Purificacion Gacto-Sanchez, Manuel Perez-Lorente, Carlos Parra-Calderon, Jose Maria De La Higuera-Gonzalez

Characterization of Codon Usage Bias in the Newly Identified DEV UL10 Gene 132 Tao Zhou, An-Chun Cheng, Ming-Shu Wang, Dekang Zhu,Renyong Jia, Qihui Luo, Hengmin Cui, Yi Zhou, Yin Wang, Zhiwen Xu, Zhengli Chen, Xiaoyue Chen, Xiaoyu Wang

Numerical Simulation of Thermal Response of the Skin Tissues 143 Iulia Maria Carstea, Ion Carstea

Authors Index 149

ISSN: 1790-5125 10 ISBN: 978-960-474-141-0 RECENT ADVANCES in BIOLOGY, BIOPHYSICS, BIOENGINEERING and COMPUTATIONAL CHEMISTRY

Plenary Lecture 1

Nanoparticles for the Transport of Antiretroviral Drugs across the Blood-Brain Barrier: A Potential Therapy for the Acquired Immunodeficiency Syndrome

Professor Yung-Chih Kuo Department of Chemical Engineering National Chung Cheng University Chia-Yi, Taiwan 62102, Republic of China E-mail: [email protected]

Abstract: Transport of antiretroviral agents into the central nervous system is an important issue because human immunodeficiency viruses (HIV) have been found to reside and replicate themselves in the brain parenchyma. This yields a complicated treatment for the acquired immunodeficiency syndrome. Recently, novel nanoparticles (NPs) have been developed for carrying anti-HIV drugs across the blood-brain barrier (BBB). In this presentation, the anti- HIV drugs incorporated with NPs to circumvent the BBB included zidovudine, lamivudine, stavudine, didanosine, delavirdine, and saquinavir. These pharmaceuticals were loaded on the surfaces of polymeric NPs or entrapped in the matrix of solid lipid nanoparticles (SLNs). Polybutylcyanoacrylate, methylmethacrylate-co- sulfopropylmethacrylate, and poly(lactide-co-glycolide) were among the typical polymeric NPs, and various kinds of SLNs with lipid core of tripalmitin, cacao butter, docosanoic acid, stearic acid, and Compritol ATO 888 were also discussed. On the surfaces of the drug carriers, bioactive molecules including polysorbate 80, sorbitan monolaurate, phospatidylcholine, cholesteryl hemisuccinate, taurocholate, stearylamine, dioctadecyldimethyl ammonium bromide, heparin, L-arginine, and transferrin were applied to stabilization or modification. Effects of cold storage, pH value, synthesis duration, stirring speed, lyophilization, and composition on the drug delivery system, and physicochemical characteristics including particle size and shape, molecular weight, zeta potential, mobility, drug distribution, loading and entrapment efficiency, and release kinetics were shown. In addition, confluent monolayer of brain-microvascular endothelial cells (BMECs) from both bovine and human and an in vivo rat model were employed to the evaluation of permeability across the BBB. Presence of the medium chemicals including alcohol and glutamic acid was also considered. It was generally observed that cytotoxicity and transendothelial electrical resistance of BMECs cocultured with NPs were in reasonable range, and dramatic increase in the permeability of NPs-mediated system could be obtained. Moreover, impacts of the exposure to electromagnetic field (EMF) including power, wave type, frequency, modulation or depth of amplitude modulation, and modulation or deviation of frequency modulations were demonstrated. Finally, the evidence of vesicular endocytosis of drug-containing NPs by clathrin-coated endosome and the expression of tight junction and P-glycoprotein on the plasma membranes of BMECs were presented.

Brief Biography of the Speaker: Dr. Yung-Chih Kuo is a professor at the Department of Chemical Engineering, National Chung Cheng University. His research interests are related to biomaterials, drug delivery system, tissue engineering, blood-brain barrier, nervous regeneration, cancer therapy, biophysics, and colloid and interface science. In these fields, he has authored or coauthored over 100 reviewed journal papers, abstracts, book chapters, and technical reports. He is an honor member of Phi Tau Phi Society and an active life member of Biochemical Engineering Society of Taiwan and Taiwan Institute of Chemical Engineers. He was often invited as a manuscript reviewer for over 20 journals and an external reviewer for academic awards, research grants, faculty recruitments and promotions, and hosting international symposium subsidy.

ISSN: 1790-5125 11 ISBN: 978-960-474-141-0 RECENT ADVANCES in BIOLOGY, BIOPHYSICS, BIOENGINEERING and COMPUTATIONAL CHEMISTRY

Plenary Lecture 2

Creation of Electromagnetic Structure-Creating Spaces to Improve the Growth of Some Types of Cells and Albumins

Dr. Vladyslav Vlastopulo Research Laboratories VVL Chief of biophysical department Str. Gen. Petrova 9\2, app. 44 Odessa, 65065, Ukraine E-mail: [email protected]

Abstract: There are given some constructions of bio-field simulators for creating the electromagnetic structure- creating spaces and improving the growth of some types of cells and albumins. There are given investigations of such illnesses: outer covering wounds, anaemia, ligamentous disruption, neurology and diabetes mellitus, - with the help of different types of bio-field simulators..

Brief Biography of the Speaker: Dr. Vladyslav Vlastopulo is a scientifically-commercial director of biophysical department on creating of new biomedical methods and devices, bio-field simulators in "Research Laboratories VVL", Odessa, Ukraine, and professor of cathedra of ways and methods of struggling with marine corrosion and biological fouling in Odessa Marine University. His research interests are related to biomedical, tribologycal, biotribologycal and mechanical engineering and also biophysics, bio-field simulators, computer fragmentary treatment of diseases demanding the operations, drug abuse patients, obesity patients, the using in video, audio products for creating attracted bioenergetic advertisement, creation of joints on basis of hydrodynamical lubricant theory. He has more than 120 papers, abstracts, book chapters and technical reports in biomedical, tribologycal, biotribologycal and mechanical engineering, and 50 of them are inventions of Soviet Union, Russian Federation and Ukraine. He is a member of more than 20 international conferences on mechanical, biomedical, tribologycal engineering.

ISSN: 1790-5125 12 ISBN: 978-960-474-141-0 RECENT ADVANCES in BIOLOGY, BIOPHYSICS, BIOENGINEERING and COMPUTATIONAL CHEMISTRY

Plenary Lecture 3

A New Way of Natural Oligopeptide Primary Structure Elucidation

Professor Alexander A. Zamyatnin Departamento de Informatica Universidad Tecnica Federico Santa Maria 1680 av. Espana, Valparaiso V-110 CHILE also with Computer Biochemistry Group A. N. Bach Institute of Biochemistry Russian Academy of Sciences 33 Leninsky prosp., Moscow 119071 RUSSIAN FEDERATION E_mail: [email protected]

Abstract: For more than a century, natural oligopeptides have attracted scientific attention as important biochemical regulators. Since that time, thousands natural oligopeptide regulators have been described, and now ~600 new natural oligopeptides emerge annually, out of a literature of >70 000 publications each year on oligopeptide chemistry and biology according to PubMed database. Their primary structure is determined either directly or by translation from nucleotide sequences. Both these ways are experimental and laborous. But there are a lot of unrecognized protein sequences in different public databases which can contain unknown oligopeptide structures. Thereupon we have carried out a theoretical structure–function analysis of known uncharacterized protein amino acid residue sequences in order to identify new oligopeptide primary structures. As an example, grape (Vitis vinifera) proteins were chosen. A special computer analysis was developed for such analysis. The data of GenBank and SwissProt databases containing primary structures of unrecognized grape proteins, EROP-Moscow database containing information on structure and functions of plant regulatory oligopeptides and specially created computer programs for the comparison of GenBank or SwissProt information with EROP-Moscow data were used. This method permitted to reveal new potentially active regulatory oligopeptide sequences after alignment procedure. It was been found 21 grape protein structure sites homologues to known regulatory oligopeptides elucidated from other plant species. Their similarity with other plant oligopeptide primary structures was from 54.4 to 95.7%. They can be characterized as putative antimicrobial oligopeptides and rapid alkalinization factors. The problem of existence of these oligopeptide structures in grape is discussed. It has been proposed that rapid alkalinization factors can also possess antimicrobial activity. This way of oligopeptide structure elucidation can be extended to oligopeptide structures of any functional class.

Brief Biography of the Speaker: Alexander A.Zamyatnin is scientist general of A.N.Bach Institute of Biochemistry, Russian Academy of Sciences, Moscow, Russian Federation and associated investigator of Santa Maria Technical University, Valparaiso, Chile. His area of expertise is endogenous oligopeptides (neuropeptides, hormones, toxins, antimicrobial), protein thermodynamics, structure-function relationship, ligand-receptor interaction, biosensors, computer biochemistry and biophysics, biological data bases, and drug design. He authored or co-authored over 200 scientific papers published in reviewed journals or presented at international conferences. He is the author of unique EROP-Moscow oligopeptide database (http://erop.inbi.ras.ru/; A.A.Zamyatnin et al. Nucleic Acids Research, 34, Database Issue, pp. D261-D266, 2006). He is a member of the European Peptide Society (from 1995).

ISSN: 1790-5125 13 ISBN: 978-960-474-141-0 RECENT ADVANCES in BIOLOGY, BIOPHYSICS, BIOENGINEERING and COMPUTATIONAL CHEMISTRY

Authors Index

Aluigi, M. G. 15 Gadaleta, M. N. 64 Savkovic-Stevanovic, J 24 Angelini, C. 15 Gallus, L. 15 Sepcic, K. 15 Aragno, M. 64 Garaventa, F. 15 Shahlaei, M. 119 Babic, A.-M. 39 Gomez-Cia, T. 126 Siljeg, M. 39 Cabral-Camacho, A. 126 Guo, J. 105, 110, 115 Suarez-Mejias, C. 126 Carstea, I. 143 Hasani, S. 68 Tao, C. 110, 115 Cassano, P. 64 Hosseini, B. S. 74 Tianzhen, Z. 110, 115 Castro, M. E. 45 Huang, S. 80 Trombino, S. 15 Chahkandi, B. 68, 74 Jia, R. 132 Turk, T. 15 Chelossi, E. 15 Kabanda, M. M. 58 Vito, P. 64 Chen, X. 132 Lezza, A. M. 64 Wang, M.-S. 132 Chen, Z. 132 Luo, Q. 132 Wang, X. 132 Cheng, A.-C. 132 Mammino, L. 58 Wang, Y. 132 Cui, H. 132 Maria Carstea, I. M. 143 Xu, Z. 132 De La Higuera-Gonzalez, J. M. 126 Mastorakis, N. E. 94 Yue, Z. 80 Derlinchan-Gonzalez, D. 126 Mastrocola, R. 64 Zamyatnin, A. A. 33 Faimali, M. 15 Munoz-Caro, C. 45 Zhang, T. 105 Falugi, C. 15 Nino, A. 45 Zhao, G. 80 Fassihi, A. 119 Paleari, L. 15 Zhou, T. 132 Feizabadi, M. S. 30 Parra-Calderon, C. 126 Zhou, Y. 132 Ferrando, S. 15 Peng, B. 80 Zhu, D. 132 Foglar, L. 39 Perez-Lorente, M. 126 Zovko, A. 15 Frigerio, F. 51 Russo, P. 15 Gacto-Sanchez, P. 126 Sabet, R. 119

ISSN: 1790-5125 149 ISBN: 978-960-474-141-0