Search results for: Molecular Interaction
Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 1319

Search results for: Molecular Interaction

1259 Observation of the Correlations between Pair Wise Interaction and Functional Organization of the Proteins, in the Protein Interaction Network of Saccaromyces Cerevisiae

Authors: N. Tuncbag, T. Haliloglu, O. Keskin

Abstract:

Understanding the cell's large-scale organization is an interesting task in computational biology. Thus, protein-protein interactions can reveal important organization and function of the cell. Here, we investigated the correspondence between protein interactions and function for the yeast. We obtained the correlations among the set of proteins. Then these correlations are clustered using both the hierarchical and biclustering methods. The detailed analyses of proteins in each cluster were carried out by making use of their functional annotations. As a result, we found that some functional classes appear together in almost all biclusters. On the other hand, in hierarchical clustering, the dominancy of one functional class is observed. In brief, from interaction data to function, some correlated results are noticed about the relationship between interaction and function which might give clues about the organization of the proteins.

Keywords: Pair-wise protein interactions, DIP database, functional correlations, biclustering.

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1258 Numerical Simulation of Fluid Structure Interaction Using Two-Way Method

Authors: Samira Laidaoui, Mohammed Djermane, Nazihe Terfaya

Abstract:

The fluid-structure coupling is a natural phenomenon which reflects the effects of two continuums: fluid and structure of different types in the reciprocal action on each other, involving knowledge of elasticity and fluid mechanics. The solution for such problems is based on the relations of continuum mechanics and is mostly solved with numerical methods. It is a computational challenge to solve such problems because of the complex geometries, intricate physics of fluids, and complicated fluid-structure interactions. The way in which the interaction between fluid and solid is described gives the largest opportunity for reducing the computational effort. In this paper, a problem of fluid structure interaction is investigated with two-way coupling method. The formulation Arbitrary Lagrangian-Eulerian (ALE) was used, by considering a dynamic grid, where the solid is described by a Lagrangian formulation and the fluid by a Eulerian formulation. The simulation was made on the ANSYS software.

Keywords: ALE, coupling, FEM, fluid-structure interaction, one-way method, two-way method.

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1257 Experimental Study of Frequency Behavior for a Circular Cylinder behind an Airfoil

Authors: S. Bajalan, A. Shadaram, N. Hedayat, A. Shams Taleghani

Abstract:

The interaction between wakes of bluff body and airfoil have profound influences on system performance in many industrial applications, e.g., turbo-machinery and cooling fan. The present work investigates the effect of configuration include; airfoil-s angle of attack, transverse and inline spacing of the models, on frequency behavior of the cylinder-s near-wake. The experiments carried on under subcritical flow regime, using the hot-wire anemometry (HWA). The relationship between the Strouhal numbers and arrangements provide an insight into the global physical processes of wake interaction and vortex shedding.

Keywords: Airfoil, Cylinder, Strouhal, Wake interaction

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1256 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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1255 Dynamic Interaction Network to Model the Interactive Patterns of International Stock Markets

Authors: Laura Lukmanto, Harya Widiputra, Lukas

Abstract:

Studies in economics domain tried to reveal the correlation between stock markets. Since the globalization era, interdependence between stock markets becomes more obvious. The Dynamic Interaction Network (DIN) algorithm, which was inspired by a Gene Regulatory Network (GRN) extraction method in the bioinformatics field, is applied to reveal important and complex dynamic relationship between stock markets. We use the data of the stock market indices from eight countries around the world in this study. Our results conclude that DIN is able to reveal and model patterns of dynamic interaction from the observed variables (i.e. stock market indices). Furthermore, it is also found that the extracted network models can be utilized to predict movement of the stock market indices with a considerably good accuracy.

Keywords: complex dynamic relationship, dynamic interaction network, interactive stock markets, stock market interdependence.

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1254 Usability Evaluation Framework for Computer Vision Based Interfaces

Authors: Muhammad Raza Ali, Tim Morris

Abstract:

Human computer interaction has progressed considerably from the traditional modes of interaction. Vision based interfaces are a revolutionary technology, allowing interaction through human actions, gestures. Researchers have developed numerous accurate techniques, however, with an exception to few these techniques are not evaluated using standard HCI techniques. In this paper we present a comprehensive framework to address this issue. Our evaluation of a computer vision application shows that in addition to the accuracy, it is vital to address human factors

Keywords: Usability evaluation, cognitive walkthrough, think aloud, gesture recognition.

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1253 Coupled Galerkin-DQ Approach for the Transient Analysis of Dam-Reservoir Interaction

Authors: S. A. Eftekhari

Abstract:

In this paper, a numerical algorithm using a coupled Galerkin-Differential Quadrature (DQ) method is proposed for the solution of dam-reservoir interaction problem. The governing differential equation of motion of the dam structure is discretized by the Galerkin method and the DQM is used to discretize the fluid domain. The resulting systems of ordinary differential equations are then solved by the Newmark time integration scheme. The mixed scheme combines the simplicity of the Galerkin method and high accuracy and efficiency of the DQ method. Its accuracy and efficiency are demonstrated by comparing the calculated results with those of the existing literature. It is shown that highly accurate results can be obtained using a small number of Galerkin terms and DQM sampling points. The technique presented in this investigation is general and can be used to solve various fluid-structure interaction problems.

Keywords: Dam-reservoir system, Differential quadrature method, Fluid-structure interaction, Galerkin method, Integral quadrature method.

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1252 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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1251 Engineering Topology of Photonic Systems for Sustainable Molecular Structure: Autopoiesis Systems

Authors: Moustafa Osman Mohammed

Abstract:

This paper introduces topological order in descried social systems starting with the original concept of autopoiesis by biologists and scientists, including the modification of general systems based on socialized medicine. Topological order is important in describing the physical systems for exploiting optical systems and improving photonic devices. The stats of topologically order have some interesting properties of topological degeneracy and fractional statistics that reveal the entanglement origin of topological order, etc. Topological ideas in photonics form exciting developments in solid-state materials, that being; insulating in the bulk, conducting electricity on their surface without dissipation or back-scattering, even in the presence of large impurities. A specific type of autopoiesis system is interrelated to the main categories amongst existing groups of the ecological phenomena interaction social and medical sciences. The hypothesis, nevertheless, has a nonlinear interaction with its natural environment ‘interactional cycle’ for exchange photon energy with molecules without changes in topology (i.e., chemical transformation into products do not propagate any changes or variation in the network topology of physical configuration). The engineering topology of a biosensor is based on the excitation boundary of surface electromagnetic waves in photonic band gap multilayer films. The device operation is similar to surface Plasmonic biosensors in which a photonic band gap film replaces metal film as the medium when surface electromagnetic waves are excited. The use of photonic band gap film offers sharper surface wave resonance leading to the potential of greatly enhanced sensitivity. So, the properties of the photonic band gap material are engineered to operate a sensor at any wavelength and conduct a surface wave resonance that ranges up to 470 nm. The wavelength is not generally accessible with surface Plasmon sensing. Lastly, the photonic band gap films have robust mechanical functions that offer new substrates for surface chemistry to understand the molecular design structure, and create sensing chips surface with different concentrations of DNA sequences in the solution to observe and track the surface mode resonance under the influences of processes that take place in the spectroscopic environment. These processes led to the development of several advanced analytical technologies, which are automated, real-time, reliable, reproducible and cost-effective. This results in faster and more accurate monitoring and detection of biomolecules on refractive index sensing, antibody–antigen reactions with a DNA or protein binding. Ultimately, the controversial aspect of molecular frictional properties is adjusted to each other in order to form unique spatial structure and dynamics of biological molecules for providing the environment mutual contribution in investigation of changes due the pathogenic archival architecture of cell clusters.

Keywords: autopoiesis, engineering topology, photonic system molecular structure, biosensor

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1250 Interaction Effect of DGAT1 and Composite Genotype of Beta-Kappa Casein on Economic Milk Production Traits in Crossbred Holstein

Authors: A. Molee, N. Duanghaklang, P. Mernkrathoke

Abstract:

The objective was to determine the single gene and interaction effect of composite genotype of beta-kappa casein and DGAT1 gene on milk yield (MY) and milk composition, content of milk fat (%FAT), milk protein (%PRO), solid not fat (%SNF), and total solid (%TS) in crossbred Holstein cows. Two hundred and thirty- one cows were genotyped with PCR-RFLP for DGAT1 and composite genotype data of beta-kappa casein from previous work were used. Two model, (1), and (2), was used to estimate single gene effect, and interaction effect on the traits, respectively. The significance of interaction effects on all traits were detected. Most traits have consistent pattern of significant when model (1), and (2) were compared, except the effect of composite genotype of betakappa casein on %FAT, and the effect of DGAT1 on MY, which the significant difference was detected in only model (1).The results suggested that when the optimum of all traits was necessary, interaction effect should be concerned.

Keywords: composite genotype of beta-kappa casein, DGAT1gene, Milk composition, Milk yield

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1249 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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1248 Predicting Protein-Protein Interactions from Protein Sequences Using Phylogenetic Profiles

Authors: Omer Nebil Yaveroglu, Tolga Can

Abstract:

In this study, a high accuracy protein-protein interaction prediction method is developed. The importance of the proposed method is that it only uses sequence information of proteins while predicting interaction. The method extracts phylogenetic profiles of proteins by using their sequence information. Combining the phylogenetic profiles of two proteins by checking existence of homologs in different species and fitting this combined profile into a statistical model, it is possible to make predictions about the interaction status of two proteins. For this purpose, we apply a collection of pattern recognition techniques on the dataset of combined phylogenetic profiles of protein pairs. Support Vector Machines, Feature Extraction using ReliefF, Naive Bayes Classification, K-Nearest Neighborhood Classification, Decision Trees, and Random Forest Classification are the methods we applied for finding the classification method that best predicts the interaction status of protein pairs. Random Forest Classification outperformed all other methods with a prediction accuracy of 76.93%

Keywords: Protein Interaction Prediction, Phylogenetic Profile, SVM , ReliefF, Decision Trees, Random Forest Classification

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1247 Investigating Breakdowns in Human Robot Interaction: A Conversation Analysis Guided Single Case Study of a Human-Robot Communication in a Museum Environment

Authors: B. Arend, P. Sunnen, P. Caire

Abstract:

In a single case study, we show how a conversation analysis (CA) approach can shed light onto the sequential unfolding of human-robot interaction. Relying on video data, we are able to show that CA allows us to investigate the respective turn-taking systems of humans and a NAO robot in their dialogical dynamics, thus pointing out relevant differences. Our fine grained video analysis points out occurring breakdowns and their overcoming, when humans and a NAO-robot engage in a multimodally uttered multi-party communication during a sports guessing game. Our findings suggest that interdisciplinary work opens up the opportunity to gain new insights into the challenging issues of human robot communication in order to provide resources for developing mechanisms that enable complex human-robot interaction (HRI).

Keywords: Human-robot interaction, conversation analysis, dialogism, museum, breakdown.

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1246 Molecular Dynamics Analysis onI mpact Behaviour of Carbon Nanotubes and Graphene Sheets

Authors: Sajjad Seifoori

Abstract:

Impact behavior of striker on graphene sheet and carbon nanotube is investigated based on molecular dynamics (MD) simulations. A MD simulation is conducted to obtain the maximum dynamic deflections of a square and rectangular single-layered graphene sheets (SLGSs) with various values of side-length and striker parameter. Effect of (i) chirality, (ii) graphene side-length and nanotube length, (iii) striker mass on the maximum dynamic deflections of graphene and nanotube are investigated. The effect of different types of boundary condition on the maximum dynamic deflections is studied for zigzag and armchair SWCNTs with various aspect ratios (Length/Diameter).

Keywords: Impact, molecular dynamic, graphene, nanotube.

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1245 Low Molecular Weight Heparin during Pregnancy

Authors: Sihana Ahmeti Lika, Merita Dauti, Ledjan Malaj

Abstract:

The objective of this study is to analyze the prophylactic usage of low molecular weight heparin (LMWH) along pregnancy and the correlation between their usage and month/week of pregnancy, in the Department of Gynecology and Obstetrics, at Clinical Hospital in Tetovo. A retrospective study was undertaken during 01 January – 31 December 2012. Over of one year, the total number of patients was 4636. Among the 1447 (32.21%) pregnant women, 298 (20.59%) of them were prescribed LMWH. The majority of patients given LMWH, 119 (39.93%) were diagnosed hypercoagulable. The age group with the highest attendance was 25- 35, 141 patients (47.32%). For 195 (65.44%) patients, this was their first pregnancy. Earliest stage of using LMWH was the second month of pregnancy 4 (1.34%) cases. The most common patients were 70 women along the seventh month (23.49%), followed by 68 in the ninth month of pregnancy (22.81%). Women in the 28th gestational week, were found to be the most affected, a total of 55 (78.57%) were in that week. Clexane 2000 and Fraxiparine 0.3 were the most common for which low molecular weight heparin was prescribed. The number of patients which received Clexane 2000 was 84 (28.19%), followed by those with Fraxiparine 0.3 81 (27.18%). The administration of LMWH is associated with long hospitalization (median 14,6 days).

Keywords: Hypercoagulable state, low molecular weight heparin, month of pregnancy, pregnant women.

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1244 The Role of Ga(Gallium)-flux and AlN(Aluminum Nitride) as the Interface Materials, between (Ga-face)GaN and (Siface)4H-SiC, through Molecular Dynamics Simulation

Authors: Srikanta Bose, Sudip K. Mazumder

Abstract:

We report here, the results of molecular dynamics simulation of p-doped (Ga-face)GaN over n-doped (Siface)( 0001)4H-SiC hetero-epitaxial material system with one-layer each of Ga-flux and (Al-face)AlN, as the interface materials, in the form of, the total Density of States (DOS). It is found that the total DOS at the Fermi-level for the heavily p-doped (Ga-face)GaN and ndoped (Si-face)4H-SiC hetero-epitaxial system, with one layer of (Al-face)AlN as the interface material, is comparatively higher than that of the various cases studied, indicating that there could be good vertical conduction across the (Ga-face)GaN over (Si-face)(0001)4HSiC hetero-epitaxial material system.

Keywords: Molecular dynamics, GaN, 4H-SiC, hetero-epitaxy.

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1243 Ab Initio Molecular Dynamics Simulations of Furfural at the Liquid-Solid Interface

Authors: Sanwu Wang, Hongli Dang, Wenhua Xue, Darwin Shields, Xin Liu, Friederike C. Jentoft, Daniel E. Resasco

Abstract:

The bonding configuration and the heat of adsorption of a furfural molecule on the Pd(111) surface were determined by ab initio density-functional-theory calculations. The dynamics of pure liquid water, the liquid-solid interface formed by liquid water and the Pd(111) surface, as well as furfural at the water-Pd interface, were investigated by ab initio molecular dynamics simulations at finite temperatures. Calculations and simulations suggest that the bonding configurations at the water-Pd interface promote decarbonylation of furfural.

Keywords: Ab initio molecular dynamics simulations, bio-fuels, density functional theory, liquid-solid interfaces.

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1242 BECOME: Body Experience-Based Co-Operation between Juveniles through Mutually Excited Team Gameplay

Authors: Tsugunosuke Sakai, Haruya Tamaki, Ryuichi Yoshida, Ryohei Egusa, Etsuji Yamaguchi, Shigenori Inagaki, Fusako Kusunoki, Miki Namatame, Masanori Sugimoto, Hiroshi Mizoguchi

Abstract:

We aim to develop a full-body interaction game that could let children cooperate and interact with other children in small groups. As the first step for our aim, the objective of the full-body interaction game developed in this study is to make interaction between children. The game requires two children to jump together with the same timing. We let children experience the game and answer the questionnaires. The children using several strategies to coordinate the timing of their jumps were observed. These included shouting time, watching each other, and jumping in a constant rhythm as if they were skipping rope. In this manner, we observed the children playing the game while cooperating with each other. The results of a questionnaire to evaluate the proposed interactive game indicate that the jumping game was a very enjoyable experience in which the participants could immerse themselves. Therefore, the game enabled children to experience cooperation with others by using body movements.

Keywords: Children, cooperation, full-body interaction game, kinect sensor.

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1241 Design Systems and the Need for a Usability Method: Assessing the Fitness of Components and Interaction Patterns in Design Systems Using Atmosphere Methodology

Authors: P. Johansson, S. Mardh

Abstract:

The present study proposes a usability test method, Atmosphere, to assess the fitness of components and interaction patterns of design systems. The method covers the user’s perception of the components of the system, the efficiency of the logic of the interaction patterns, perceived ease of use as well as the user’s understanding of the intended outcome of interactions. These aspects are assessed by combining measures of first impression, visual affordance and expectancy. The method was applied to a design system developed for the design of an electronic health record system. The study was conducted involving 15 healthcare personnel. It could be concluded that the Atmosphere method provides tangible data that enable human-computer interaction practitioners to analyze and categorize components and patterns based on perceived usability, success rate of identifying interactive components and success rate of understanding components and interaction patterns intended outcome.

Keywords: atomic design, atmosphere methodology, design system, expectancy testing, first impression testing, usability testing, visual affordance testing

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1240 Molecular Dynamics Simulation of Thermal Properties of Au3Ni Nanowire

Authors: J. Davoodi, F. Katouzi

Abstract:

The aim of this research was to calculate the thermal properties of Au3Ni Nanowire. The molecular dynamics (MD) simulation technique was used to obtain the effect of radius size on the energy, the melting temperature and the latent heat of fusion at the isobaric-isothermal (NPT) ensemble. The Quantum Sutton-Chen (Q-SC) many body interatomic potentials energy have been used for Gold (Au) and Nickel (Ni) elements and a mixing rule has been devised to obtain the parameters of these potentials for nanowire stats. Our MD simulation results show the melting temperature and latent heat of fusion increase upon increasing diameter of nanowire. Moreover, the cohesive energy decreased with increasing diameter of nanowire.

Keywords: Au3Ni Nanowire, Thermal properties, Molecular dynamics simulation

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1239 Computational Design of Inhibitory Agents of BMP-Noggin Interaction to Promote Osteogenesis

Authors: Shaila Ahmed, Raghu Prasad Rao Metpally, Sreedhara Sangadala, Boojala Vijay B Reddy

Abstract:

Bone growth factors, such as Bone Morphogenic Protein-2 (BMP-2) have been approved by the FDA to replace grafting for some surgical interventions, but the high dose requirement limits its use in patients. Noggin, an extracellular protein, blocks the effect of BMP-2 by binding to BMP. Preventing the BMP-2/noggin interaction will help increase the free concentration of BMP-2 and therefore should enhance its efficacy to induce bone formation. The work presented here involves computational design of novel small molecule inhibitory agents of BMP-2/noggin interaction, based on our current understanding of BMP-2, and its known putative ligands (receptors and antagonists). A successful acquisition of such an inhibitory agent of BMP-2/noggin interaction would allow clinicians to reduce the dose required of BMP-2 protein in clinical applications to promote osteogenesis. The available crystal structures of the BMPs, its receptors, and the binding partner noggin were analyzed to identify the critical residues involved in their interaction. In presenting this study, LUDI de novo design method was utilized to perform virtual screening of a large number of compounds from a commercially available library against the binding sites of noggin to identify the lead chemical compounds that could potentially block BMP-noggin interaction with a high specificity.

Keywords: Transforming growth factor-beta, Bone morphogenic proteins, Noggin, LUDI de novo design method, CAP small molecules.

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1238 Coding Considerations for Standalone Molecular Dynamics Simulations of Atomistic Structures

Authors: R. O. Ocaya, J. J. Terblans

Abstract:

The laws of Newtonian mechanics allow ab-initio molecular dynamics to model and simulate particle trajectories in material science by defining a differentiable potential function. This paper discusses some considerations for the coding of ab-initio programs for simulation on a standalone computer and illustrates the approach by C language codes in the context of embedded metallic atoms in the face-centred cubic structure. The algorithms use velocity-time integration to determine particle parameter evolution for up to several thousands of particles in a thermodynamical ensemble. Such functions are reusable and can be placed in a redistributable header library file. While there are both commercial and free packages available, their heuristic nature prevents dissection. In addition, developing own codes has the obvious advantage of teaching techniques applicable to new problems.

Keywords: C-language, molecular dynamics, simulation, embedded atom method.

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1237 Visualized Characterization of Molecular Mobility for Water Species in Foods

Authors: Yasuyuki Konishi, Masayoshi Kobayashi

Abstract:

Six parameters, the effective diffusivity (De), activation energy of De, pre-exponential factor of De, amount (ASOW) of self-organized water species, and amplitude (α) of the forced oscillation of the molecular mobility (1/tC) derived from the forced cyclic temperature change operation, were characterized by using six typical foods, squid, sardines, scallops, salmon, beef, and pork, as a function of the correlation time (tC) of the water molecule-s proton retained in the foods. Each of the six parameters was clearly divided into the water species A1 and A2 at a specified value of tC =10-8s (=CtC), indicating an anomalous change in the physicochemical nature of the water species at the CtC. The forced oscillation of 1/tC clearly demonstrated a characteristic mode depending on the food shown as a three dimensional map associated with 1/tC, the amount of self-organized water, and tC.

Keywords: molecular mobility, self-organization, hysteresis, water species A1 and A2, forced cyclic temperature change operation (FCTCO)

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1236 Conformation Prediction of Human Plasmin and Docking on Gold Nanoparticle

Authors: Wen-Shyong Tzou, Chih-Ching Huang, Chin-Hwa Hu, Ying-Tsang Lo, Tun-Wen Pai, Chia-Yin Chiang, Chung-Hao Li, Hong-Jyuan Jian

Abstract:

Plasmin plays an important role in the human circulatory system owing to its catalytic ability of fibrinolysis. The immediate injection of plasmin in patients of strokes has intrigued many scientists to design vectors that can transport plasmin to the desired location in human body. Here we predict the structure of human plasmin and investigate the interaction of plasmin with the gold-nanoparticle. Because the crystal structure of plasminogen has been solved, we deleted N-terminal domain (Pan-apple domain) of plasminogen and generate a mimic of the active form of this enzyme (plasmin). We conducted a simulated annealing process on plasmin and discovered a very large conformation occurs. Kringle domains 1, 4 and 5 had been observed to leave its original location relative to the main body of the enzyme and the original doughnut shape of this enzyme has been transformed to a V-shaped by opening its two arms. This observation of conformational change is consistent with the experimental results of neutron scattering and centrifugation. We subsequently docked the plasmin on the simulated gold surface to predict their interaction. The V-shaped plasmin could utilize its Kringle domain and catalytic domain to contact the gold surface. Our findings not only reveal the flexibility of plasmin structure but also provide a guide for the design of a plasmin-gold nanoparticle.

Keywords: Docking, gold nanoparticle, molecular simulation, plasmin.

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1235 Molecular Analysis of Somaclonal Variation in Tissue Culture Derived Bananas Using MSAP and SSR Markers

Authors: Emma K. Sales, Nilda G. Butardo

Abstract:

The project was undertaken to determine the effects of modified tissue culture protocols e.g. age of culture and hormone levels (2,4-D) in generating somaclonal variation. Moreover, the utility of molecular markers (SSR and MSAP) in sorting off types/somaclones were investigated.

Results show that somaclonal variation is in effect due to prolonged subculture and high 2,4-D concentration. The resultant variation was observed to be due to high level of methylation events specifically cytosine methylation either at the internal or external cytosine and was identified by methylation sensitive amplification polymorphism (MSAP).Simple sequence repeats (SSR) on the other hand, was able to associate a marker to a trait of interest.

These therefore, show that molecular markers can be an important tool in sorting out variation/mutants at an early stage.

Keywords: Methylation, MSAP, somaclones, SSR, subculture, 2, 4-D.

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1234 Eigenwave Analysis and Simulation of Disc Loaded Interaction Structure for Wideband Gyro-TWT Amplifier

Authors: R. K. Singh, P. K. Jain

Abstract:

In the present paper, disc loaded interaction structure for potential application in wideband Gyro-TWT amplifier has been analyzed, taking all the space and modal harmonics into consideration, for the eigenwave solutions. The analysis has been restricted to azimuthally symmetric TE0,n mode. Dispersion characteristics have been plotted by varying the structure parameters and have been validated against HFSS simulation results. The variation of eigenvalue with respect to different structure parameters has also been presented. It has been observed that disc periodicity plays very important role for wideband operation of disc-loaded Gyro-TWT.

Keywords: Broadbanding, Disc-loaded interaction structure, Eigenvalue, Gyro-TWT, HFSS.

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1233 An Expectation of the Rate of Inflation According to Inflation-Unemployment Interaction in Croatia

Authors: Zdravka Aljinović, Snježana Pivac, Boško Šego

Abstract:

According to the interaction of inflation and unemployment, expectation of the rate of inflation in Croatia is estimated. The interaction between inflation and unemployment is shown by model based on three first-order differential i.e. difference equations: Phillips relation, adaptive expectations equation and monetary-policy equation. The resulting equation is second order differential i.e. difference equation which describes the time path of inflation. The data of the rate of inflation and the rate of unemployment are used for parameters estimation. On the basis of the estimated time paths, the stability and convergence analysis is done for the rate of inflation.

Keywords: Differencing, inflation, time path, unemployment.

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1232 Structural and Electronic Characterization of Supported Ni and Au Catalysts used in Environment Protection Determined by XRD,XAS and XPS methods

Authors: N. Aldea, V. Rednic, F. Matei, Tiandou Hu, M. Neumann

Abstract:

The nickel and gold nanoclusters as supported catalysts were analyzed by XAS, XRD and XPS in order to determine their local, global and electronic structure. The present study has pointed out a strong deformation of the local structure of the metal, due to its interaction with oxide supports. The average particle size, the mean squares of the microstrain, the particle size distribution and microstrain functions of the supported Ni and Au catalysts were determined by XRD method using Generalized Fermi Function for the X-ray line profiles approximation. Based on EXAFS analysis we consider that the local structure of the investigated systems is strongly distorted concerning the atomic number pairs. Metal-support interaction is confirmed by the shape changes of the probability densities of electron transitions: Ni K edge (1s → continuum and 2p), Au LIII-edge (2p3/2 → continuum, 6s, 6d5/2 and 6d3/2). XPS investigations confirm the metal-support interaction at their interface.

Keywords: local and global structure, metal-support interaction, supported metal catalysts, synchrotron radiation, X-ray absorptionspectroscopy, X-ray diffraction, X-ray photoelectron spectroscopy.

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1231 Numerical Investigations on Group Piles’ Lateral Bearing Capacity Considering Interaction of Soil and Structure

Authors: Mahdi Sadeghian, Mahmoud Hassanlourad, Alireza Ardakani, Reza Dinarvand

Abstract:

In this research, the behavior of monopiles, under lateral loads, was investigated with vertical and oblique piles by Finite Element Method. In engineering practice when soil-pile interaction comes to the picture some simplifications are applied to reduce the design time. As a simplified replacement of soil and pile interaction analysis, pile could be replaced by a column. The height of the column would be equal to the free length of the pile plus a portion of the embedded length of it. One of the important factors studied in this study was that columns with an equivalent length (free length plus a part of buried depth) could be used instead of soil and pile modeling. The results of the analysis show that the more internal friction angle of the soil increases, the more the bearing capacity of the soil is achieved. This additional length is 6 to 11 times of the pile diameter in dense soil although in loose sandy soil this range might increase.

Keywords: Lateral bearing capacity, pile group, oblique pile, soil-structure interaction, depth of fixity.

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1230 Human Interactive E-learning Systems using Head Posture Images

Authors: Yucel Ugurlu

Abstract:

This paper explains a novel approach to human interactive e-learning systems using head posture images. Students- face and hair information are used to identify a human presence and estimate the gaze direction. We then define the human-computer interaction level and test the definition using ten students and seventy different posture images. The experimental results show that head posture images provide adequate information for increasing human-computer interaction in e-learning systems.

Keywords: E-learning, image segmentation, human-presence, gaze-direction, human-computer interaction, LabVIEW

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