Search results for: Molecular biology
Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 365

Search results for: Molecular biology

365 Sorting Primitives and Genome Rearrangementin Bioinformatics: A Unified Perspective

Authors: Swapnoneel Roy, Minhazur Rahman, Ashok Kumar Thakur

Abstract:

Bioinformatics and computational biology involve the use of techniques including applied mathematics, informatics, statistics, computer science, artificial intelligence, chemistry, and biochemistry to solve biological problems usually on the molecular level. Research in computational biology often overlaps with systems biology. Major research efforts in the field include sequence alignment, gene finding, genome assembly, protein structure alignment, protein structure prediction, prediction of gene expression and proteinprotein interactions, and the modeling of evolution. Various global rearrangements of permutations, such as reversals and transpositions,have recently become of interest because of their applications in computational molecular biology. A reversal is an operation that reverses the order of a substring of a permutation. A transposition is an operation that swaps two adjacent substrings of a permutation. The problem of determining the smallest number of reversals required to transform a given permutation into the identity permutation is called sorting by reversals. Similar problems can be defined for transpositions and other global rearrangements. In this work we perform a study about some genome rearrangement primitives. We show how a genome is modelled by a permutation, introduce some of the existing primitives and the lower and upper bounds on them. We then provide a comparison of the introduced primitives.

Keywords: Sorting Primitives, Genome Rearrangements, Transpositions, Block Interchanges, Strip Exchanges.

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364 Differentiation between Common Tick Species Using Molecular Biology Techniques in Saudi Arabia

Authors: Kholoud A. Al-Shammery , Badr El-Sabah A. Fetoh, Ahmed M. Alshammari

Abstract:

Protein and Esterase electrophoresis were used to genetically identify two Saudi tick species. Engorged females of the camel tick Hyalomma dromedarii (Koch) (Acari: Ixodidae) and the cattle tick Boophilus annulatus (Say) (Acari: Ixodidae) ticks collected from infested camels and cattle in the animals resting house at Hail region in KSA were used. The results showed that there are a variation in both of protein and esterase activity levels and a high polymorphism within and between the genera and species of Hyalomma and Boophilus . In conclusion, the protein and esterase electrophoretic analysis used in the present study could successfully distinguish among tick species, commonly found in Saudi Arabia.

Keywords: Molecular biology, The camel tick Hyalomma dromedarii, The cattle tick Boophilus annulatus , Ticks.

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363 Structural Basis of Resistance of Helicobacterpylori DnaK to Antimicrobial Peptide Pyrrhocoricin

Authors: Musammat F. Nahar, Anna Roujeinikova

Abstract:

Bacterial molecular chaperone DnaK plays an essential role in protein folding, stress response and transmembrane targeting of proteins. DnaKs from many bacterial species, including Escherichia coli, Salmonella typhimurium and Haemophilus infleunzae are the molecular targets for the insect-derived antimicrobial peptide pyrrhocoricin. Pyrrhocoricin-like peptides bind in the substrate recognition tunnel. Despite the high degree of crossspecies sequence conservation in the substrate-binding tunnel, some bacteria are not sensitive to pyrrhocoricin. This work addresses the molecular mechanism of resistance of Helicobacter pylori DnaK to pyrrhocoricin. Homology modelling, structural and sequence analysis identify a single aminoacid substitution at the interface between the lid and the β-sandwich subdomains of the DnaK substrate-binding domain as the major determinant for its resistance.

Keywords: Helicobacter pylori, molecular chaperone DnaK, pyrrhocoricin, structural biology.

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362 Implementation of an Undergraduate Integrated Biology and Chemistry Course

Authors: Jayson G. Balansag

Abstract:

An integrated biology and chemistry (iBC) course for freshmen college students was developed in University of Delaware. This course will prepare students to (1) become interdisciplinary thinkers in the field of biology and (2) collaboratively work with others from multiple disciplines in the future. This paper documents and describes the implementation of the course. The information gathered from reading literature, classroom observations, and interviews were used to carry out the purpose of this paper. The major goal of the iBC course is to align the concepts between Biology and Chemistry, so that students can draw science concepts from both disciplines which they can apply in their interdisciplinary researches. This course is offered every fall and spring semesters of each school year. Students enrolled in Biology are also enrolled in Chemistry during the same semester. The iBC is composed of lectures, laboratories, studio sessions, and workshops and is taught by the faculty from the biology and chemistry departments. In addition, the preceptors, graduate teaching assistants, and studio fellows facilitate the laboratory and studio sessions. These roles are interdependent with each other. The iBC can be used as a model for higher education institutions who wish to implement an integrated biology course.

Keywords: Integrated biology and chemistry, integration, interdisciplinary research, new biology, undergraduate science education.

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361 Gender Differences in Biology Academic Performances among Foundation Students of PERMATApintar® National Gifted Center

Authors: N. Nor Azman, M. F. Kamarudin, S. I. Ong, N. Maaulot

Abstract:

PERMATApintar® National Gifted Center is, to the author’s best of knowledge, the first center in Malaysia that provides a platform for Malaysian talented students with high ability in thinking. This center has built a teaching and learning biology curriculum that suits the ability of these gifted students. The level of PERMATApintar® biology curriculum is basically higher than the national biology curriculum. Here, the foundation students are exposed to the PERMATApintar® biology curriculum at the age of as early as 11 years old. This center practices a 4-time-a-year examination system to monitor the academic performances of the students. Generally, most of the time, male students show no or low interest towards biology subject compared to female students. This study is to investigate the association of students’ gender and their academic performances in biology examination. A total of 39 students’ scores in twelve sets of biology examinations in 3 years have been collected and analyzed by using the statistical analysis. Based on the analysis, there are no significant differences between male and female students against the biology academic performances with a significant level of p = 0.05. This indicates that gender is not associated with the scores of biology examinations among the students. Another result showed that the average score for male studenta was higher than the female students. Future research can be done by comparing the biology academic achievement in Malaysian National Examination (Sijil Pelajaran Malaysia, SPM) between the Foundation 3 students (Grade 9) and Level 2 students (Grade 11) with similar PERMATApintar® biology curriculum.

Keywords: Academic performances, biology, gender differences, gifted students.

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360 An Index based Forward Backward Multiple Pattern Matching Algorithm

Authors: Raju Bhukya, DVLN Somayajulu

Abstract:

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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359 Virtual Laboratory for Learning Biology – A Preliminary Investigation

Authors: Murniza Muhamad, Halimah Badioze Zaman, Azlina Ahmad

Abstract:

This study aims to conduct a preliminary investigation to determine the topic to be focused in developing Virtual Laboratory For Biology (VLab-Bio). Samples involved in answering the questionnaire are form five students (equivalent to A-Level) and biology teachers. Time and economical resources for the setting up and construction of scientific laboratories can be solved with the adaptation of virtual laboratories as an educational tool. Thus, it is hoped that the proposed virtual laboratory will help students to learn the abstract concepts in biology. Findings show that the difficult topic chosen is Cell Division and the learning objective to be focused in developing the virtual lab is “Describe the application of knowledge on mitosis in cloning".

Keywords: biology education, computer simulation, virtual laboratory, virtual reality

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358 The Meaning and Structure of Ecological Education of Biology Specialists in Kazakhstan

Authors: E. Tazabekova, B. Amirasheva, L. Amirasheva

Abstract:

This article examines the nature and structure of ecological education of biology specialists in Kazakhstan. Also characterizes the ecological education in high school and specific features in training of biology specialists.

Keywords: Ecological education, environment.

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357 Sorptive Storage of Natural Gas on Molecular Sieves: Dynamic Investigation

Authors: S. Al-Asheh, K. Al-Emadi

Abstract:

In recent years, there have been attempts to store natural gas in adsorptive form. This is called adsorptive natural gas, or ANG. The problem with this technology is the low sorption capacity. The purpose is to achieve compressed natural gas (CNG) capacity of 230 V/V. Further research is required to achieve such target. Several research studies have been performed with this target; through either the modification or development of new sorbents or the optimization of the operation sorption process itself. In this work, storage of methane on molecular sieves 5A and 13X was studied on dry basis, and on wet basis to certain extent. The temperature and the pressure dynamics were investigated. The results indicated that regardless of the charge pressure, the time for the peak temperature during the methane charge process is always the same. This can be used as a characteristic of the adsorbent. The total achieved deliveries using molecular sieves were much lower than that of activated carbons; 53.0 V/V for the case of 13X molecular sieves and 43 V/V for the case of 5A molecular sieves, both at 2oC and 4 MPa (580 psi). Investigation of charge pressure dynamic using wet molecular sieves at 2oC and a mass ratio of 0.5, revealed slowness of the process and unexpected behavior.

Keywords: Methane, Molecular sieves, Adsorption, Delivery, Storage.

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356 Effect of Plasticizer Additives on the Mechanical Properties of Cement Composite – A Molecular Dynamics Analysis

Authors: R. Mohan, V. Jadhav, A. Ahmed, J. Rivas, A. Kelkar

Abstract:

Cementitious materials are an excellent example of a composite material with complex hierarchical features and random features that range from nanometer (nm) to millimeter (mm) scale. Multi-scale modeling of complex material systems requires starting from fundamental building blocks to capture the scale relevant features through associated computational models. In this paper, molecular dynamics (MD) modeling is employed to predict the effect of plasticizer additive on the mechanical properties of key hydrated cement constituent calcium-silicate-hydrate (CSH) at the molecular, nanometer scale level. Due to complexity, still unknown molecular configuration of CSH, a representative configuration widely accepted in the field of mineral Jennite is employed. The effectiveness of the Molecular Dynamics modeling to understand the predictive influence of material chemistry changes based on molecular / nanoscale models is demonstrated.

Keywords: Cement composite, Mechanical Properties, Molecular Dynamics, Plasticizer additives.

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355 DNA Computing for an Absolute 1-Center Problem: An Evolutionary Approach

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

Abstract:

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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354 All Proteins Have a Basic Molecular Formula

Authors: Homa Torabizadeh

Abstract:

This study proposes a basic molecular formula for all proteins. A total of 10,739 proteins belonging to 9 different protein groups classified on the basis of their functions were selected randomly. They included enzymes, storage proteins, hormones, signalling proteins, structural proteins, transport proteins, immunoglobulins or antibodies, motor proteins and receptor proteins. After obtaining the protein molecular formula using the ProtParam tool, the H/C, N/C, O/C, and S/C ratios were determined for each randomly selected sample. In this case, H, N, O, and S coefficients were specified per carbon atom. Surprisingly, the results demonstrated that H, N, O, and S coefficients for all 10,739 proteins are similar and highly correlated. This study demonstrates that despite differences in the structure and function, all known proteins have a similar basic molecular formula CnH1.58 ± 0.015nN0.28 ± 0.005nO0.30 ± 0.007nS0.01 ± 0.002n. The total correlation between all coefficients was found to be 0.9999.

Keywords: Protein molecular formula, Basic unit formula, Protparam tool.

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353 Molecular Electronic Devices based on Carotenoid Derivatives

Authors: Vicente F. P. Aleixo, Augusto C. F. Saraiva, Jordan Del Nero

Abstract:

The production of devices in nanoscale with specific molecular rectifying function is one of the most significant goals in state-of-art technology. In this work we show by ab initio quantum mechanics calculations coupled with non-equilibrium Green function, the design of an organic two-terminal device. These molecular structures have molecular source and drain with several bridge length (from five up to 11 double bonds). Our results are consistent with significant features as a molecular rectifier and can be raised up as: (a) it can be used as bi-directional symmetrical rectifier; (b) two devices integrated in one (FET with one operational region, and Thyristor thiristor); (c) Inherent stability due small intrinsic capacitance under forward/reverse bias. We utilize a scheme for the transport mechanism based on previous properties of ¤Ç bonds type that can be successfully utilized to construct organic nanodevices.

Keywords: ab initio, Carotenoid, Charge Transfer, Nanodevice

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352 Molecular and Electronic Structure of Chromium (III) Cyclopentadienyl Complexes

Authors: Salem El-tohami Ashoor

Abstract:

Here, we have shown the reaction of [Cr(ArN(CH2)3NAr)2Cl2] (1) where (Ar = 2,6-Pri 2C6H3) and in presence of NaCp (2) (Cp= C5H5 = cyclopentadien), with a center coordination η5 interaction between Cp as co-ligand and chromium metal center, for optimization we used density functional theory (DFT), under methods, explicitly including electrons correlations, for the final calculations as MB3LYP (Becke) (Lee–Yang–Parr) level of theory we used to obtain more exact results. This complex was calculated as electronic energy for molecular system, because the calculation accounting all electrons correlations interactions. The optimised of [Cr(ArN(CH2)3NAr)2(η5-Cp)] (Ar = 2,6-Pri2C6H3 and Cp = C5H5) was found to be thermally stable. By using Dewar-Chatt-Duncanson model, as a basis of the molecular orbital (MO) analysis and showed the highest occupied molecular orbital (HOMO) and lowest occupied molecular orbital LUMO.

Keywords: Chromium (III) cyclopentadienyl complexes, DFT, MO, HOMO, LUMO.

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351 Efficiency of Floristic and Molecular Markers to Determine Diversity in Iranian Populations of T. boeoticum

Authors: M. R. Naghavi, M. Maleki, S. F. Tabatabaei

Abstract:

In order to study floristic and molecular classification of common wild wheat (Triticum boeoticum Boiss.), an analysis was conducted on populations of the Triticum boeoticum collected from different regions of Iran. Considering all floristic compositions of habitats, six floristic groups (syntaxa) within the populations were identified. A high level of variation of T. boeoticum also detected using SSR markers. Our results showed that molecular method confirmed the grouping of floristic method. In other word, the results from our study indicate that floristic classification are still useful, efficient, and economic tools for characterizing the amount and distribution of genetic variation in natural populations of T. boeoticum. Nevertheless, molecular markers appear as useful and complementary techniques for identification and for evaluation of genetic diversity in studied populations.

Keywords: T. boeoticum, diversity, floristic, SSRs.

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350 Identifying Network Subgraph-Associated Essential Genes in Molecular Networks

Authors: Efendi Zaenudin, Chien-Hung Huang, Ka-Lok Ng

Abstract:

Essential genes play an important role in the survival of an organism. It has been shown that cancer-associated essential genes are genes necessary for cancer cell proliferation, where these genes are potential therapeutic targets. Also, it was demonstrated that mutations of the cancer-associated essential genes give rise to the resistance of immunotherapy for patients with tumors. In the present study, we focus on studying the biological effects of the essential genes from a network perspective. We hypothesize that one can analyze a biological molecular network by decomposing it into both three-node and four-node digraphs (subgraphs). These network subgraphs encode the regulatory interaction information among the network’s genetic elements. In this study, the frequency of occurrence of the subgraph-associated essential genes in a molecular network was quantified by using the statistical parameter, odds ratio. Biological effects of subgraph-associated essential genes are discussed. In summary, the subgraph approach provides a systematic method for analyzing molecular networks and it can capture useful biological information for biomedical research.

Keywords: Biological molecular networks, essential genes, graph theory, network subgraphs.

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349 The Study on Mechanical Properties of Graphene Using Molecular Mechanics

Authors: I-Ling Chang, Jer-An Chen

Abstract:

The elastic properties and fracture of two-dimensional graphene were calculated purely from the atomic bonding (stretching and bending) based on molecular mechanics method. Considering the representative unit cell of graphene under various loading conditions, the deformations of carbon bonds and the variations of the interlayer distance could be realized numerically under the geometry constraints and minimum energy assumption. In elastic region, it was found that graphene was in-plane isotropic. Meanwhile, the in-plane deformation of the representative unit cell is not uniform along armchair direction due to the discrete and non-uniform distributions of the atoms. The fracture of graphene could be predicted using fracture criteria based on the critical bond length, over which the bond would break. It was noticed that the fracture behavior were directional dependent, which was consistent with molecular dynamics simulation results.

Keywords: Energy minimization, fracture, graphene, molecular mechanics.

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348 The Extension of Monomeric Computational Results to Polymeric Measurable Properties: An Introductory Computational Chemistry Experiment

Authors: Zhao Jing, Bai Yongqing, Shi Qiaofang, Zang Yang, Zhang Huaihao

Abstract:

Advances in software technology enable the computational chemistry to be commonly applied in various research fields, especially in pedagogy. Thus, in order to expand and improve experimental instructions of computational chemistry for undergraduates, we designed an introductory experiment—research on acrylamide molecular structure and physicochemical properties. Initially, students construct molecular models of acrylamide and polyacrylamide in Gaussian and Materials Studio software respectively. Then, the infrared spectral data, atomic charge and molecular orbitals of acrylamide as well as solvation effect of polyacrylamide are calculated to predict their physicochemical performance. At last, rheological experiments are used to validate these predictions. Through the combination of molecular simulation (performed on Gaussian, Materials Studio) with experimental verification (rheology experiment), learners have deeply comprehended the chemical nature of acrylamide and polyacrylamide, achieving good learning outcomes.

Keywords: Upper-division undergraduate, computer-based learning, laboratory instruction, amides, molecular modeling, spectroscopy.

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347 Breeding Biology and Induced Breeding Status of Freshwater Mud Eel, Monopterus cuchia

Authors: M. F. Miah, H. Ali, E. Zannath, T. M. Shuvra, M. N. Naser, M. K. Ahmed

Abstract:

In this study, breeding biology and induced breeding of freshwater mud eel, Monopterus cuchia was observed during the experimental period from February to June, 2013. Breeding biology of freshwater mud eel, Monopterus cuchia was considered in terms of gonadosomatic index, length-weight relationship of gonad, ova diameter and fecundity. The ova diameter was recorded from 0.3 mm to 4.30 mm and the individual fecundity was recorded from 155 to 1495 while relative fecundity was found from 2.64 to 12.45. The fecundity related to body weight and length of fish was also discussed. A peak of GSI was observed 2.14±0.2 in male and 5.1 ±1.09 in female. Induced breeding of freshwater mud eel, Monopterus cuchia was also practiced with different doses of different inducing agents like pituitary gland (PG), human chorionic gonadotropin (HCG), Gonadotropin releasing hormone (GnRH) and Ovuline-a synthetic hormone in different environmental conditions. However, it was observed that the artificial breeding of freshwater mud eel, Monopterus cuchia was not yet succeeded through inducing agents in captive conditions, rather the inducing agent showed negative impacts on fecundity and ovarian tissues. It was seen that mature eggs in the oviduct were reduced, absorbed and some eggs were found in spoiled condition.

Keywords: Breeding biology, induced breeding, Monopterus cuchia.

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346 Using Molecular Dynamics to Assess Mechanical Properties of PAN-Based Carbon Fibers Comprising Imperfect Crystals with Amorphous Structures

Authors: A. Ito, S. Okamoto

Abstract:

We constructed an atomic structure model for a PAN-based carbon fiber containing amorphous structures using molecular dynamics methods. It was found that basic physical properties such as crystallinity, Young’s modulus, and thermal conductivity of our model were nearly identical to those of real carbon fibers. We then obtained the tensile strength of a carbon fiber, which has no macro defects. We finally determined that the limitation of the tensile strength was 19 GPa.

Keywords: Amorphous, carbon fiber, molecular dynamics, tensile strength.

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345 X-Ray Fluorescence Molecular Imaging with Improved Sensitivity for Biomedical Applications

Authors: Guohua Cao, Xu Dong

Abstract:

X-ray Fluorescence Molecular Imaging (XFMI) holds great promise as a low-cost molecular imaging modality for biomedical applications with high chemical sensitivity. However, for in vivo biomedical applications, a key technical bottleneck is the relatively low chemical sensitivity of XFMI, especially at a reasonably low radiation dose. In laboratory x-ray source based XFMI, one of the main factors that limits the chemical sensitivity of XFMI is the scattered x-rays. We will present our latest findings on improving the chemical sensitivity of XFMI using excitation beam spectrum optimization. XFMI imaging experiments on two mouse-sized phantoms were conducted at three different excitation beam spectra. Our results show that the minimum detectable concentration (MDC) of iodine can be readily increased by five times via excitation spectrum optimization. Findings from this investigation could find use for in vivo pre-clinical small-animal XFMI in the future.

Keywords: Molecular imaging, X-ray fluorescence, chemical sensitivity, X-ray scattering.

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344 Molecular Mechanism of Amino Acid Discrimination for the Editing Reaction of E.coli Leucyl-tRNA Synthetase

Authors: Keun Woo Lee, Minky Son, Chanin Park, Ayoung Baek

Abstract:

Certain tRNA synthetases have developed highly accurate molecular machinery to discriminate their cognate amino acids. Those aaRSs achieve their goal via editing reaction in the Connective Polypeptide 1 (CP1). Recently mutagenesis studies have revealed the critical importance of residues in the CP1 domain for editing activity and X-ray structures have shown binding mode of noncognate amino acids in the editing domain. To pursue molecular mechanism for amino acid discrimination, molecular modeling studies were performed. Our results suggest that aaRS bind the noncognate amino acid more tightly than the cognate one. Finally, by comparing binding conformations of the amino acids in three systems, the amino acid binding mode was elucidated and a discrimination mechanism proposed. The results strongly reveal that the conserved threonines are responsible for amino acid discrimination. This is achieved through side chain interactions between T252 and T247/T248 as well as between those threonines and the incoming amino acids.

Keywords: Amino acid discrimination, Binding free energy Leucyl-tRNAsynthetase, Molecular dynamics.

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343 DFT Study of Half Sandwich of Vanadium (IV) Cyclopentadienyl Complexes

Authors: Salem El-tohami Ashoor

Abstract:

A novel new vanadium (IV) complexes incorporating the chelating diamido cyclopentadienyl {ArN(CH2)3NAr)}2-((ηn-Cp)Cp)} (Ar = 2,6-Pri2C6H3)(Cp = C5H5 and n = 1,2,3,4 and 5) have been studied with calculation of the properties of species involved in various of cyclopentadienyl reaction. These were carried out under investigation of density functional theory (DFT) calculation, and comparing together. Other methods, explicitly including electron correlation, are necessary for more accurate calculations; MB3LYP (Becke) (Lee–Yang–Parr) level of theory often being used to obtain more exact results. These complexes were estimated of electronic energy for molecular system, because it accounts for all electron correlation interactions.

The optimised of [V(ArN(CH2)3NAr)2Cl(η5-Cp)] (Ar = 2,6-Pri2C6H3 and Cp= C5H5) was found to be thermally more stable than others of vanadium cyclopentadienyl. In the meantime the complex [V(ArN(CH2)3NAr)2Cl(η1-Cp)] (Ar = 2,6-Pri2C6H3 and Cp= C5H5) which is showed a low thermal stability in case of the just one carbon of cyclopentadienyl can be insertion with vanadium metal centre. By using Dewar-Chatt-Duncanson model, as a basis of the molecular orbital (MO) analysis and showed the highest occupied molecular orbital (HOMO) and lowest occupied molecular orbital LUMO.

Keywords: Vanadium(IV) cyclopentadienyl complexes, DFT, MO, HOMO, LUMO.

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342 On the Mathematical Structure and Algorithmic Implementation of Biochemical Network Models

Authors: Paola Lecca

Abstract:

Modeling and simulation of biochemical reactions is of great interest in the context of system biology. The central dogma of this re-emerging area states that it is system dynamics and organizing principles of complex biological phenomena that give rise to functioning and function of cells. Cell functions, such as growth, division, differentiation and apoptosis are temporal processes, that can be understood if they are treated as dynamic systems. System biology focuses on an understanding of functional activity from a system-wide perspective and, consequently, it is defined by two hey questions: (i) how do the components within a cell interact, so as to bring about its structure and functioning? (ii) How do cells interact, so as to develop and maintain higher levels of organization and functions? In recent years, wet-lab biologists embraced mathematical modeling and simulation as two essential means toward answering the above questions. The credo of dynamics system theory is that the behavior of a biological system is given by the temporal evolution of its state. Our understanding of the time behavior of a biological system can be measured by the extent to which a simulation mimics the real behavior of that system. Deviations of a simulation indicate either limitations or errors in our knowledge. The aim of this paper is to summarize and review the main conceptual frameworks in which models of biochemical networks can be developed. In particular, we review the stochastic molecular modelling approaches, by reporting the principal conceptualizations suggested by A. A. Markov, P. Langevin, A. Fokker, M. Planck, D. T. Gillespie, N. G. van Kampfen, and recently by D. Wilkinson, O. Wolkenhauer, P. S. Jöberg and by the author.

Keywords: Mathematical structure, algorithmic implementation, biochemical network models.

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341 Simulation of Water Droplet on Horizontally Smooth and Rough Surfaces Using Quasi-Molecular Modelling

Authors: S. Kulsri, M. Jaroensutasinee, K. Jaroensutasinee

Abstract:

We developed a method based on quasi-molecular modelling to simulate the fall of water drops on horizontally smooth and rough surfaces. Each quasi-molecule was a group of particles that interacted in a fashion entirely analogous to classical Newtonian molecular interactions. When a falling water droplet was simulated at low impact velocity on both smooth and rough surfaces, the droplets moved periodically (i.e. the droplets moved up and down for a certain period, finally they stopped moving and reached a steady state), spreading and recoiling without splash or break-up. Spreading rates of falling water droplets increased rapidly as time increased until the spreading rate reached its steady state at time t ~ 0.25 s for rough surface and t ~ 0.40 s for smooth surface. The droplet height above both surfaces decreased as time increased, remained constant after the droplet diameter attained a maximum value and reached its steady state at time t ~ 0.4 s. However, rough surface had higher spreading rates of falling water droplets and lower height on the surface than smooth one.

Keywords: Quasi-molecular modelling, particle modelling, molecular aggregate approach.

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340 Modeling Biology Inspired Reactive Agents Using X-machines

Authors: George Eleftherakis, Petros Kefalas, Anna Sotiriadou, Evangelos Kehris

Abstract:

Recent advances in both the testing and verification of software based on formal specifications of the system to be built have reached a point where the ideas can be applied in a powerful way in the design of agent-based systems. The software engineering research has highlighted a number of important issues: the importance of the type of modeling technique used; the careful design of the model to enable powerful testing techniques to be used; the automated verification of the behavioural properties of the system; the need to provide a mechanism for translating the formal models into executable software in a simple and transparent way. This paper introduces the use of the X-machine formalism as a tool for modeling biology inspired agents proposing the use of the techniques built around X-machine models for the construction of effective, and reliable agent-based software systems.

Keywords: Biology inspired agent, formal methods, x-machines.

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339 Categorization and Estimation of Relative Connectivity of Genes from Meta-OFTEN Network

Authors: U. Kairov, T. Karpenyuk, E. Ramanculov, A. Zinovyev

Abstract:

The most common result of analysis of highthroughput data in molecular biology represents a global list of genes, ranked accordingly to a certain score. The score can be a measure of differential expression. Recent work proposed a new method for selecting a number of genes in a ranked gene list from microarray gene expression data such that this set forms the Optimally Functionally Enriched Network (OFTEN), formed by known physical interactions between genes or their products. Here we present calculation results of relative connectivity of genes from META-OFTEN network and tentative biological interpretation of the most reproducible signal. The relative connectivity and inbetweenness values of genes from META-OFTEN network were estimated.

Keywords: Microarray, META-OFTEN, gene network.

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338 Structure Based Computational Analysis and Molecular Phylogeny of C- Phycocyanin Gene from the Selected Cyanobacteria

Authors: N. Reehana, A. Parveez Ahamed, D. Mubarak Ali, A. Suresh, R. Arvind Kumar, N. Thajuddin

Abstract:

Cyanobacteria play a vital role in the production of phycobiliproteins that includes phycocyanin and phycoerythrin pigments. Phycocyanin and related phycobiliproteins have wide variety of application that is used in the food, biotechnology and cosmetic industry because of their color, fluorescent and antioxidant properties. The present study is focused to understand the pigment at molecular level in the Cyanobacteria Oscillatoria terebriformis NTRI05 and Oscillatoria foreaui NTRI06. After extraction of genomic DNA, the amplification of C-Phycocyanin gene was done with the suitable primer PCβF and PCαR and the sequencing was performed. Structural and Phylogenetic analysis was attained using the sequence to develop a molecular model.

Keywords: Cyanobacteria, C-Phycocyanin gene, Phylogenetic analysis, Structural analysis.

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337 Probability-Based Damage Detection of Structures Using Model Updating with Enhanced Ideal Gas Molecular Movement Algorithm

Authors: M. R. Ghasemi, R. Ghiasi, H. Varaee

Abstract:

Model updating method has received increasing attention in damage detection structures based on measured modal parameters. Therefore, a probability-based damage detection (PBDD) procedure based on a model updating procedure is presented in this paper, in which a one-stage model-based damage identification technique based on the dynamic features of a structure is investigated. The presented framework uses a finite element updating method with a Monte Carlo simulation that considers the uncertainty caused by measurement noise. Enhanced ideal gas molecular movement (EIGMM) is used as the main algorithm for model updating. Ideal gas molecular movement (IGMM) is a multiagent algorithm based on the ideal gas molecular movement. Ideal gas molecules disperse rapidly in different directions and cover all the space inside. This is embedded in the high speed of molecules, collisions between them and with the surrounding barriers. In IGMM algorithm to accomplish the optimal solutions, the initial population of gas molecules is randomly generated and the governing equations related to the velocity of gas molecules and collisions between those are utilized. In this paper, an enhanced version of IGMM, which removes unchanged variables after specified iterations, is developed. The proposed method is implemented on two numerical examples in the field of structural damage detection. The results show that the proposed method can perform well and competitive in PBDD of structures.

Keywords: Enhanced ideal gas molecular movement, ideal gas molecular movement, model updating method, probability-based damage detection, uncertainty quantification.

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336 Molecular Dynamics of Fatty Acid Interacting with Carbon Nanotube as Selective Device

Authors: David L. Azevedo, Jordan Del Nero

Abstract:

In this paper we study a system composed by carbon nanotube (CNT) and bundle of carbon nanotube (BuCNT) interacting with a specific fatty acid as molecular probe. Full system is represented by open nanotube (or nanotubes) and the linoleic acid (LA) relaxing due the interaction with CNT and BuCNT. The LA has in his form an asymmetric shape with COOH termination provoking a close BuCNT interaction mainly by van der Waals force field. The simulations were performed by classical molecular dynamics with standard parameterizations. Our results show that these BuCNT and CNT are dynamically stable and it shows a preferential interaction position with LA resulting in three features: (i) when the LA is interacting with CNT and BuCNT (including both termination, CH2 or COOH), the LA is repelled; (ii) when the LA terminated with CH2 is closer to open extremity of BuCNT, the LA is also repelled by the interaction between them; and (iii) when the LA terminated with COOH is closer to open extremity of BuCNT, the LA is encapsulated by the BuCNT. These simulations are part of a more extensive work on searching efficient selective molecular devices and could be useful to reach this goal.

Keywords: Carbon Nanotube, Linoleic Acid, MolecularDynamics.

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