Search results for: electrostatic interaction

Authors: Moustafa Osman Mohammed

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This paper introduces Luhmann’s autopoietic social systems starting with the original concept of autopoiesis by biologists and scientists, including the modification of general systems based on socialized medicine. A specific type of autopoietic system is explained in the three existing groups of the ecological phenomena: interaction, social and medical sciences. This hypothesis model, nevertheless, has a nonlinear interaction with its natural environment ‘interactional cycle’ for the exchange of photon energy with molecular without any changes in topology. The external forces in the systems environment might be concomitant with the natural fluctuations’ influence (e.g. radioactive radiation, electromagnetic waves). The cantilever sensor deploys insights to the future chip processor for prevention of social metabolic systems. Thus, the circuits with resonant electric and optical properties are prototyped on board as an intra–chip inter–chip transmission for producing electromagnetic energy approximately ranges from 1.7 mA at 3.3 V to service the detection in locomotion with the least significant power losses. Nowadays, therapeutic systems are assimilated materials from embryonic stem cells to aggregate multiple functions of the vessels nature de-cellular structure for replenishment. While, the interior actuators deploy base-pair complementarity of nucleotides for the symmetric arrangement in particular bacterial nanonetworks of the sequence cycle creating double-stranded DNA strings. The DNA strands must be sequenced, assembled, and decoded in order to reconstruct the original source reliably. The design of exterior actuators have the ability in sensing different variations in the corresponding patterns regarding beat-to-beat heart rate variability (HRV) for spatial autocorrelation of molecular communication, which consists of human electromagnetic, piezoelectric, electrostatic and electrothermal energy to monitor and transfer the dynamic changes of all the cantilevers simultaneously in real-time workspace with high precision. A prototype-enabled dynamic energy sensor has been investigated in the laboratory for inclusion of nanoscale devices in the architecture with a fuzzy logic control for detection of thermal and electrostatic changes with optoelectronic devices to interpret uncertainty associated with signal interference. Ultimately, the controversial aspect of molecular frictional properties is adjusted to each other and forms its unique spatial structure modules for providing the environment mutual contribution in the investigation of mass temperature changes due to pathogenic archival architecture of clusters.

Keywords: Autopoiesis, quantum photonics, portable energy, photonic structure, photodynamic therapeutic system.

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Authors: R. K. Apalowo, D. Chronopoulos

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A Finite Element (FE) based scheme is presented for quantifying guided wave interaction with Localised Nonlinear Structural Damage (LNSD) within structures of arbitrary layering and geometric complexity. The through-thickness mode-shape of the structure is obtained through a wave and finite element method. This is applied in a time domain FE simulation in order to generate time harmonic excitation for a specific wave mode. Interaction of the wave with LNSD within the system is computed through an element activation and deactivation iteration. The scheme is validated against experimental measurements and a WFE-FE methodology for calculating wave interaction with damage. Case studies for guided wave interaction with crack and delamination are presented to verify the robustness of the proposed method in classifying and identifying damage.

Keywords: Layered Structures, nonlinear ultrasound, wave interaction with nonlinear damage, wave finite element, finite element.

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Authors: Kuan-Liang Liu, Eric Lee, Jung-Jyh Lee, Jyh-Ping Hsu

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The electrical interaction between two axisymmetric spheroidal particles in an electrolyte solution is examined numerically. A Galerkin finite element method combined with a Newton-Raphson iteration scheme is proposed to evaluate the spatial variation in the electrical potential, and the result obtained used to estimate the interaction energy between two particles. We show that if the surface charge density is fixed, the potential gradient is larger at a point, which has a larger curvature, and if surface potential is fixed, surface charge density is proportional to the curvature. Also, if the total interaction energy against closest surface-to-surface curve exhibits a primary maximum, the maximum follows the order (oblate-oblate) > (sphere-sphere)>(oblate-prolate)>(prolate-prolate), and if the curve has a secondary minimum, the absolute value of the minimum follows the same order.

Keywords: interaction energy, interaction force, Poisson-Boltzmann equation, spheroid.

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Authors: A. Jawahar

Abstract:

In this paper, the dependence of soliton pulses with respect to phase in a 10Gbps, single channel, dispersion uncompensated telecommunication system was studied. The characteristic feature of periodic soliton interaction was noted at the Interaction point (I=6202.5Km) in one collision length of L=12405.1 Km. The interaction point is located for 10Gbps system with an initial relative spacing (qo) of soliton as 5.28 using Perturbation theory. It is shown that, when two in-phase solitons are launched, they interact at the point I=6202.5 Km, but the interaction could be restricted with introduction of different phase initially. When the phase of the input solitons increases, the deviation of soliton pulses at the ‘I’ also increases. We have successfully demonstrated this effect in a telecommunication set-up in terms of Quality factor (Q), where the Q=0 for in-phase soliton. The Q was noted to be 125.9, 38.63, 47.53, 59.60, 161.37, and 78.04 for different phases such as 10o, 20o, 30o, 45o, 60o and 90o degrees respectively at Interaction point (I).

Keywords: Soliton interaction, Initial relative spacing, phase, Perturbation theory and telecommunication system.

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Authors: Waleed Maqableh, Ahmad Al-Hamad, Manjit Sidhu

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Augmented reality (AR) technology has the capability to provide many benefits in the field of education as a modern technology which aided learning and improved the learning experience. This paper evaluates AR based application with multiple markers interaction technique (touch-to-print) which is designed for analyzing the kinematics of 4BL mechanism in mechanical engineering. The application is termed as AR-4BL-MAST and it allows the users to touch the symbols on a paper in natural way of interaction. The evaluation of this application was performed with mechanical engineering students and human–computer interaction (HCI) experts to test its effectiveness as a tangible user interface application where the statistical results show its ability as an interaction technique, and it gives the users more freedom in interaction with the virtual mechanical objects.

Keywords: Augmented reality, engineering, four-bar linkage, Multimedia, user interface, visualization.

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Authors: Vinicius Binotte, Guilherme Baldo, Christiane Goulart, Carlos Valadão, Eliete Caldeira, Teodiano Bastos

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Socially assistive robotic has become increasingly active and it is present in therapies of people affected for several neurobehavioral conditions, such as Autism Spectrum Disorder (ASD). In fact, robots have played a significant role for positive interaction with children with ASD, by stimulating their social and cognitive skills. This work introduces a mobile socially-assistive robot, which was built for interaction with children with ASD, using non-linear control techniques for this interaction.

Keywords: Socially assistive robotics, mobile robot, autonomous control, autism.

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Authors: Patiparn Punyapalakul, Thitikamon Sitthisorn

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Ciprofloxacin (CIP) and Carbamazepine (CBZ), nonbiodegradable pharmaceutical residues, were become emerging pollutants in several aquatic environments. The objectives of this research were to study the possibility to recover these pharmaceuticals residues from pharmaceutical wastewater by increasing the selective adsorption on synthesized functionalized porous silicate, comparing with powdered activated carbon (PAC). Hexagonal mesoporous silicate (HMS), functionalized HMSs (3- aminopropyltriethoxy, 3- mercaptopropyltrimethoxy and noctyldimethyl) were synthesized and characterized physico-chemical characteristics. Obtained adsorption kinetics and isotherms showed that 3-mercaptopropyltrimethoxy functional groups grafted on HMS provided highest CIP and CBZ adsorption capacities; however, it was still lower than that of PAC. The kinetic results were compatible with pseudo-second order. The hydrophobicity and hydrogen bonding might play a key role on the adsorption. Furthermore, the capacities were affected by varying pH values due to the strength of hydrogen bonding between targeted compounds and adsorbents. Electrostatic interaction might not affect the adsorption capacities.

Keywords: Adsorption, Carbamazepine, Ciprofloxazin, Mesoporous Silicates, Surface functional groups

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Authors: Paolo Pilloni, Fabrizio Mulas, Salvatore Carta

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Nowadays, several research studies point up that an active lifestyle is essential for physical and mental health benefits. Mobile phones have greatly influenced people’s habits and attitudes also in the way they exercise. Our research work is mainly focused on investigating how to exploit mobile technologies to favour people’s exertion experience. To this end, we developed an exertion framework users can exploit through a real world mobile application, called EverywhereSport Run (EWRun), designed to act as a virtual personal trainer to support runners during their trainings. In this work, inspired by both previous findings in the field of interaction design for people with visual impairments, feedback gathered from real users of our framework, and positive results obtained from two experimentations, we present some new interaction facilities we designed to enhance the interaction experience during a training. The positive obtained results helped us to derive some interaction design recommendations we believe will be a valid support for designers of future mobile systems conceived to be used in circumstances where there are limited possibilities of interaction.

Keywords: Human Computer Interaction, Interaction Design Guidelines, Persuasive Mobile Technologies for Sport and Health.

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Authors: Leandro Marcos Alves Vaz

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The teaching of physics in Brazilian public schools emphasizes strongly the theoretical aspects of this science, showing its philosophical and mathematical basis, but neglecting its experimental character. Perhaps the lack of science laboratories explains this practice. In this work, we present a method of teaching physics using the computer. As alternatives to real experiments, we have the trials through simulators, many of which are free software available on the internet. In order to develop a study on the use of simulators in teaching, knowing the impossibility of simulations on all topics in a given subject, we combined these programs with phenomenological and/or experimental texts in order to mitigate this limitation. This study proposes the use of simulators and the debate using phenomenological/experimental texts on electrostatic theme in groups of the 3rd year of EJA (Adult and Youth Education) in order to verify the advantages of this methodology. Some benefits of the hybridization of the traditional method with the tools used were: Greater motivation of the students in learning, development of experimental notions, proactive socialization to learning, greater easiness to understand some concepts and the creation of collaborative activities that can reduce timidity of part of the students.

Keywords: Physics teaching, simulators, youth and adult education, experimentation, electrostatic.

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Authors: Mella Ismelina Farma Rahayu

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Environmental problems could not be separated from unethical human perspectives and behaviors toward the environment. There is a fundamental error in the philosophy of people’s perspective about human and nature and their relationship with the environment, which in turn will create an inappropriate behavior in relation to the environment. The aim of this study is to investigate and to understand the ethics of the environment in the context of humans interacting with the environment by using the hermeneutic approach. The related theories and concepts collected from literature review are used as data, which were analyzed by using interpretation, critical evaluation, internal coherence, comparisons, and heuristic techniques. As a result of this study, there will be a picture related to the interaction of human and environment in the perspective of environmental ethics, as well as the problems of the value of ecological justice in the interaction of humans and environment. We suggest that the interaction between humans and environment need to be based on environmental ethics, in a spirit of mutual respect between humans and the natural world.

Keywords: The environment, environmental ethics, the interaction, value.

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Authors: Dowluru Ravi Kumar, Bhima Prabhakara Rao

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Propagation of solitons in single-mode birefringent fibers is considered under the presence of third-order dispersion (TOD). The behavior of two neighboring solitons and their interaction is investigated under the presence of third-order dispersion with different group velocity dispersion (GVD) parameters. It is found that third-order dispersion makes the resultant soliton to deviate from its ideal position and increases the interaction between adjacent soliton pulses. It is also observed that this deviation due to third-order dispersion is considerably small when the optical pulse propagates at wavelengths relatively far from the zerodispersion. Modified coupled nonlinear Schrödinger-s equations (CNLSE) representing the propagation of optical pulse in single mode fiber with TOD are solved using split-step Fourier algorithm. The results presented in this paper reveal that the third-order dispersion can substantially increase the interaction between the solitons, but large group velocity dispersion reduces the interaction between neighboring solitons.

Keywords: Birefringence, Group velocity dispersion, Polarization mode dispersion, Soliton interaction, Third order dispersion.

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Authors: Yuan-Hsiang Chang, Pin-Chi Lin, Li-Der Jeng

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Advance in techniques of image and video processing has enabled the development of intelligent video surveillance systems. This study was aimed to automatically detect moving human objects and to analyze events of dual human interaction in a surveillance scene. Our system was developed in four major steps: image preprocessing, human object detection, human object tracking, and motion trajectory analysis. The adaptive background subtraction and image processing techniques were used to detect and track moving human objects. To solve the occlusion problem during the interaction, the Kalman filter was used to retain a complete trajectory for each human object. Finally, the motion trajectory analysis was developed to distinguish between the interaction and non-interaction events based on derivatives of trajectories related to the speed of the moving objects. Using a database of 60 video sequences, our system could achieve the classification accuracy of 80% in interaction events and 95% in non-interaction events, respectively. In summary, we have explored the idea to investigate a system for the automatic classification of events for interaction and non-interaction events using surveillance cameras. Ultimately, this system could be incorporated in an intelligent surveillance system for the detection and/or classification of abnormal or criminal events (e.g., theft, snatch, fighting, etc.). 

Keywords: Motion detection, motion tracking, trajectory analysis, video surveillance.

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Authors: Hsuan-Chia Yang, Yan-Jhih Haung, Yu-Chuan Li

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Researchers of drug-drug interaction alert systems have often suggested that there were high overridden rate for alerts and also too false alerts. However, research about decreasing false alerts is scant. Therefore, the aim of this article attempts to proactive identification of false alert for drug-drug interaction and provide solution to decrease false alerts. This research involved retrospective analysis prescribing database and calculated false alert rate by using MYSQL and JAVA. Results of this study showed 17% of false alerts and the false alert rate in the hospitals (37%) was more than in the clinics. To conclude, this study described the importance that drug-drug interaction alert system should not only detect drug name but also detect frequency or route, as well as in providing solution to decrease false alerts.

Keywords: drug-drug interaction, proactive identification, false alert

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Authors: Hassen M. Ouakad

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In this paper, the influence of van der Waals, as well as electrostatic forces on the structural behavior of MEMS and NEMS actuators, has been investigated using of a Euler-Bernoulli beam continuous model. In the proposed nonlinear model, the electrostatic fringing-fields and the mid-plane stretching (geometric nonlinearity) effects have been considered. The nonlinear integro-differential equation governing the static structural behavior of the actuator has been derived. An original Galerkin-based reduced-order model has been developed to avoid problems arising from the nonlinearities in the differential equation. The obtained reduced-order model equations have been solved numerically using the Newton-Raphson method. The basic design parameters such as the pull-in parameters (voltage and deflection at pull-in), as well as the detachment length due to the van der Waals force of some investigated micro- and nano-actuators have been calculated. The obtained numerical results have been compared with some other existing methods (finite-elements method and finite-difference method) and the comparison showed good agreement among all assumed numerical techniques.

Keywords: MEMS, NEMS, fringing-fields, mid-plane stretching, Galerkin method.

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Authors: Ricardo A. Martins, Matheus S. da Silva, Gabriel H. F. Iarossi, Helen C. M. Senefonte, Cinthyan R. S. C. de Barbosa

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This paper is the development of a concept of the man/robot interaction. More accurately in developing of an autistic child that have more troubles with interaction, here offers an efficient solution, even though simple; however, less studied for this public. This concept is based on code applied thought out the Lego NXT kit, built for the interpretation of the robot, thereby can create this interaction in a constructive way for children suffering with Autism.

Keywords: Lego NXT, autism, ANN (Artificial Neural Network), Backpropagation.

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Authors: Ching-Wei Tsai, Chih-I Liu, Ruoh-Chyu Ruaana

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A new strategy for oriented immobilization of proteins was proposed. The strategy contains two steps. The first step is to search for a docking site away from the active site on the protein surface. The second step is trying to find a ligand that is able to grasp the targeted site of the protein. To avoid ligand binding to the active site of protein, the targeted docking site is selected to own opposite charges to those near the active site. To enhance the ligand-protein binding, both hydrophobic and electrostatic interactions need to be included. The targeted docking site should therefore contain hydrophobic amino acids. The ligand is then selected through the help of molecular docking simulations. The enzyme α-amylase derived from Aspergillus oryzae (TAKA) was taken as an example for oriented immobilization. The active site of TAKA is surrounded by negatively charged amino acids. All the possible hydrophobic sites on the surface of TAKA were evaluated by the free energy estimation through benzene docking. A hydrophobic site on the opposite side of TAKA-s active site was found to be positive in net charges. A possible ligand, 3,3-,4,4- – Biphenyltetra- carboxylic acid (BPTA), was found to catch TAKA by the designated docking site. Then, the BPTA molecules were grafted onto silica gels and measured the affinity of TAKA adsorption and the specific activity of thereby immobilized enzymes. It was found that TAKA had a dissociation constant as low as 7.0×10-6 M toward the ligand BPTA on silica gel. The increase in ionic strength has little effect on the adsorption of TAKA, which indicated the existence of hydrophobic interaction between ligands and proteins. The specific activity of the immobilized TAKA was compared with the randomly adsorbed TAKA on primary amine containing silica gel. It was found that the orderly immobilized TAKA owns a specific activity twice as high as the one randomly adsorbed by ionic interaction.

Keywords: Protein Oriented immobilization, Molecular docking, ligand design, surface modification.

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Authors: Chewa Thassana, Wicharn Techitdheera

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The spin (ms) and orbital (mo) magnetic moment of the antiferromagnetic NiO and MnO have been studied in the local spin density approximation (LSDA+U) within full potential linear muffin-tin orbital (FP-LMTO method with in the coulomb interaction U varying from 0 to 10eV, exchange interaction J, from 0 to 1.0eV, and volume compression VC in range of 0 to 80%. Our calculated results shown that the spin magnetic moments and the orbital magnetic moments increase linearly with increasing U and J. While the interesting behaviour appears when volume compression is greater than 70% for NiO and 50% for MnO at which ms collapses. Further increase of volume compression to be at 80% leads to the disappearance of both magnetic moments.

Keywords: spin-orbital magnetic moment, Coulomb interaction U and exchange interaction J, volume compression VC, LSDA+U.

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Authors: Manisha A. Hira, Arup Rakshit

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Textile substrates are endowed with flexibility and ease of making–up, but are non-conductors of electricity. Conductive materials like carbon can be incorporated into textile structures to make flexible conductive materials. Such conductive textiles find applications as electrostatic discharge materials, electromagnetic shielding materials and flexible materials to carry current or signals. This work focuses on use of carbon fiber as conductor of electricity. Carbon fibers in staple or tow form can be incorporated in textile yarn structure to conduct electricity. The paper highlights the process for development of these conductive yarns of polyester/carbon using Friction spinning (DREF) as well as ring spinning. The optimized process parameters for processing hybrid structure of polyester with carbon tow on DREF spinning and polyester with carbon staple fiber using ring spinning have been presented. The studies have been linked to highlight the electrical conductivity of the developed yarns. Further, the developed yarns have been incorporated as weft in fabric and their electrical conductivity has been evaluated. The paper demonstrates the structure and properties of fabrics developed from such polyester/carbon blend yarns and their suitability as electrically dissipative fabrics.

Keywords: Carbon fiber, hybrid yarns, electrostatic dissipative fabrics.

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Authors: J. Ruenin, S. Sukprasong, R. Phatthanakun, N. Chomnawang, P. Kuntanawat

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In this paper, a simple microfluidic device for monitoring algal cell behavior is proposed. An array of algal microwells is fabricated by PDMS soft-lithography using X-ray LIGA mold, placed on a glass substrate. Two layers of replicated PDMS and substrate are attached by oxygen plasma bonding, creating a microchannel for the microfluidic system. Algal cell are loaded into the microfluidic device, which provides positive charge on the bottom surface of wells. Algal cells, which are negative charged, can be attracted to the bottom of the wells via electrostatic interaction. By varying the concentration of algal cells in the loading suspension, it is possible to obtain wells with a single cell. Liquid medium for cells monitoring are flown continuously over the wells, providing nutrient and waste exchange between the well and the main flow. This device could lead to the uncovering of the quantitative biology of the algae, which is a key to effective and extensive algal utilizations in the field of biotechnology, food industry and bioenergy research and developments.

Keywords: Algal cells, microfluidic device, X-ray LIGA, X-ray lithography, metallic mold, synchrotron light, PDMS

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Authors: Omar Gaci, Stefan Balev

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In this paper we introduce the notion of protein interaction network. This is a graph whose vertices are the protein-s amino acids and whose edges are the interactions between them. Using a graph theory approach, we identify a number of properties of these networks. We compare them to the general small-world network model and we analyze their hierarchical structure.

Keywords: interaction network, protein structure, small-world network.

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Authors: Nazar Zaki, Safaai Deris, Hany Alashwal

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Detecting protein-protein interactions is a central problem in computational biology and aberrant such interactions may have implicated in a number of neurological disorders. As a result, the prediction of protein-protein interactions has recently received considerable attention from biologist around the globe. Computational tools that are capable of effectively identifying protein-protein interactions are much needed. In this paper, we propose a method to detect protein-protein interaction based on substring similarity measure. Two protein sequences may interact by the mean of the similarities of the substrings they contain. When applied on the currently available protein-protein interaction data for the yeast Saccharomyces cerevisiae, the proposed method delivered reasonable improvement over the existing ones.

Keywords: Protein-Protein Interaction, support vector machine, feature extraction, pairwise alignment, Smith-Waterman score.

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Authors: Mohammad Shoyaib, M. Abdullah-Al-Wadud, Oksam Chae

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Proteomics is one of the largest areas of research for bioinformatics and medical science. An ambitious goal of proteomics is to elucidate the structure, interactions and functions of all proteins within cells and organisms. Predicting Protein-Protein Interaction (PPI) is one of the crucial and decisive problems in current research. Genomic data offer a great opportunity and at the same time a lot of challenges for the identification of these interactions. Many methods have already been proposed in this regard. In case of in-silico identification, most of the methods require both positive and negative examples of protein interaction and the perfection of these examples are very much crucial for the final prediction accuracy. Positive examples are relatively easy to obtain from well known databases. But the generation of negative examples is not a trivial task. Current PPI identification methods generate negative examples based on some assumptions, which are likely to affect their prediction accuracy. Hence, if more reliable negative examples are used, the PPI prediction methods may achieve even more accuracy. Focusing on this issue, a graph based negative example generation method is proposed, which is simple and more accurate than the existing approaches. An interaction graph of the protein sequences is created. The basic assumption is that the longer the shortest path between two protein-sequences in the interaction graph, the less is the possibility of their interaction. A well established PPI detection algorithm is employed with our negative examples and in most cases it increases the accuracy more than 10% in comparison with the negative pair selection method in that paper.

Keywords: Interaction graph, Negative training data, Protein-Protein interaction, Support vector machine.

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Authors: Rafal Michalski, Jakub Zygadlo

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We present the concept and scientific methods and algorithms of our computation system called ATOMIC MATTERS. This is the first presentation of the new computer package, that allows its user to describe physical properties of atomic localized electron systems subject to electromagnetic interactions. Our solution applies to situations where an unclosed electron 2p/3p/3d/4d/5d/4f/5f subshell interacts with an electrostatic potential of definable symmetry and external magnetic field. Our methods are based on Crystal Electric Field (CEF) approach, which takes into consideration the electrostatic ligands field as well as the magnetic Zeeman effect. The application allowed us to predict macroscopic properties of materials such as: Magnetic, spectral and calorimetric as a result of physical properties of their fine electronic structure. We emphasize the importance of symmetry of charge surroundings of atom/ion, spin-orbit interactions (spin-orbit coupling) and the use of complex number matrices in the definition of the Hamiltonian. Calculation methods, algorithms and convention recalculation tools collected in ATOMIC MATTERS were chosen to permit the prediction of magnetic and spectral properties of materials in isostructural series.

Keywords: Atomic matters, crystal electric field, spin-orbit coupling, localized states, electron subshell, fine electronic structure.

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Authors: S. Arun Prakash, V. Malathi, M. S. Mani Rajan

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The analytical bright two soliton solution of the 3- coupled nonlinear Schrödinger equations with variable coefficients in birefringent optical fiber is obtained by Darboux transformation method. To the design of ultra-speed optical devices, Soliton interaction and control in birefringence fiber is investigated. Lax pair is constructed for N coupled NLS system through AKNS method. Using two-soliton solution, we demonstrate different interaction behaviors of solitons in birefringent fiber depending on the choice of control parameters. Our results shows that interactions of optical solitons have some specific applications such as construction of logic gates, optical computing, soliton switching, and soliton amplification in wavelength division multiplexing (WDM) system.

Keywords: Optical soliton, soliton interaction, soliton switching, WDM.

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Authors: Eduardo Álvarez, Gerardo Quiroga, Jorge Orozco, Gabriel Chavira

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AmI proposes a new way of thinking about computers, which follows the ideas of the Ubiquitous Computing vision of Mark Weiser. In these, there is what is known as a Disappearing Computer Initiative, with users immersed in intelligent environments. Hence, technologies need to be adapted so that they are capable of replacing the traditional inputs to the system by embedding these in every-day artifacts. In this work, we present an approach, which uses Radiofrequency Identification (RFID) and Near Field Communication (NFC) technologies. In the latter, a new form of interaction appears by contact. We compare both technologies by analyzing their requirements and advantages. In addition, we propose using a combination of RFID and NFC.

Keywords: Touching interaction, ambient intelligence, NFC, RFID.

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Authors: Seung Pil Pack

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Deaminated lesions were produced via nitrosative oxidation of natural nucleobases; uracul (Ura, U) from cytosine (Cyt, C), hypoxanthine (Hyp, H) from adenine (Ade, A), and xanthine (Xan, X) and oxanine (Oxa, O) from guanine (Gua, G). Such damaged nucleobases may induce mutagenic problems, so that much attentions and efforts have been poured on the revealing of their mechanisms in vivo or in vitro. In this study, we employed these deaminated lesions as useful probes for analysis of DNA-binding/recognizing proteins or enzymes. Since the pyrimidine lesions such as Hyp, Oxa and Xan are employed as analogues of guanine, their comparative uses are informative for analyzing the role of Gua in DNA sequence in DNA-protein interaction. Several DNA oligomers containing such Hyp, Oxa or Xan substituted for Gua were designed to reveal the molecular interaction between DNA and protein. From this approach, we have got useful information to understand the molecular mechanisms of the DNA-recognizing enzymes, which have not ever been observed using conventional DNA oligomer composed of just natural nucleobases.

Keywords: Deaminated lesion, DNA-protein interaction, DNA-recognizing enzymes

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Authors: Ratchada Sopakayang, Gerhard A. Holzapfel

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In this study, a new constitutive model is developed to describe the hyperelastic behavior of collagenous tissues with a parallel arrangement of collagen fibers such as ligaments and tendons. The model is formulated using a continuum approach incorporating the structural changes of the main tissue components: collagen fibers, proteoglycan-rich matrix and fiber-matrix interaction. The mechanical contribution of the interaction between the fibers and the matrix is simply expressed by a coupling term. The structural change of the collagen fibers is incorporated in the constitutive model to describe the activation of the fibers under tissue straining. Finally, the constitutive model can easily describe the stress-stretch nonlinearity which occurs when a ligament/tendon is axially stretched. This study shows that the interaction between the fibers and the matrix contributes to the mechanical tissue response. Therefore, the model may lead to a better understanding of the physiological mechanisms of ligaments and tendons under axial loading.

Keywords: Hyperelasticity, constitutive model, fiber-matrix interaction, ligament, tendon.

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Authors: Rania A. Abul Seoud, Nahed H. Solouma, Abou-Baker M. Youssef, Yasser M. Kadah

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Due to the ever growing amount of publications about protein-protein interactions, information extraction from text is increasingly recognized as one of crucial technologies in bioinformatics. This paper presents a Protein Interaction Extraction System using a Link Grammar Parser from biomedical abstracts (PIELG). PIELG uses linkage given by the Link Grammar Parser to start a case based analysis of contents of various syntactic roles as well as their linguistically significant and meaningful combinations. The system uses phrasal-prepositional verbs patterns to overcome preposition combinations problems. The recall and precision are 74.4% and 62.65%, respectively. Experimental evaluations with two other state-of-the-art extraction systems indicate that PIELG system achieves better performance. For further evaluation, the system is augmented with a graphical package (Cytoscape) for extracting protein interaction information from sequence databases. The result shows that the performance is remarkably promising.

Keywords: Link Grammar Parser, Interaction extraction, protein-protein interaction, Natural language processing.

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Authors: Nurcan Tuncbag, Turkan Haliloglu, Ozlem Keskin

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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 the light of the clustering data, we have verified some interactions which were not identified as core interactions in DIP and also, we have characterized some functionally unknown proteins according to the interaction data and functional correlation. 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, also to predict new interactions and to characterize functions of unknown proteins.

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

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Authors: Pedro Campos, Miguel Campos, Carlos Ferreira

Abstract:

Interactive installations for public spaces are a particular kind of interactive systems, the design of which has been the subject of several research studies. Sensor-based applications are becoming increasingly popular, but the human-computer interaction community is still far from reaching sound, effective large-scale interactive installations for public spaces. The 6DSpaces project is described in this paper as a research approach based on studying the role of multisensory interactivity and how it can be effectively used to approach people to digital, scientific contents. The design of an entire scientific exhibition is described and the result was evaluated in the real world context of a Science Centre. Conclusions bring insight into how the human-computer interaction should be designed in order to maximize the overall experience.

Keywords: interaction design, human-computer interaction, multimedia, multisensory installations

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