Search results for: molecular mobility

Authors: R. Pilafkan, M. Kaffash Irzarahimi, S. F. Asbaghian Namin

Abstract:

The biaxial buckling behavior of single-layered graphene sheets (SLGSs) is studied in the present work. To consider the size-effects in the analysis, Eringen’s nonlocal elasticity equations are incorporated into classical plate theory (CLPT). A Generalized Differential Quadrature Method (GDQM) approach is utilized and numerical solutions for the critical buckling loads are obtained. Then, molecular dynamics (MD) simulations are performed for a series of zigzag SLGSs with different side-lengths and with various boundary conditions, the results of which are matched with those obtained by the nonlocal plate model to numerical the appropriate values of nonlocal parameter relevant to each type of boundary conditions.

Keywords: Biaxial buckling, single-layered graphene sheets, nonlocal elasticity, molecular dynamics simulation, classical plate theory.

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Authors: T.P. Sharma

Abstract:

Querying a data source and routing data towards sink becomes a serious challenge in static wireless sensor networks if sink and/or data source are mobile. Many a times the event to be observed either moves or spreads across wide area making maintenance of continuous path between source and sink a challenge. Also, sink can move while query is being issued or data is on its way towards sink. In this paper, we extend our already proposed Grid Based Data Dissemination (GBDD) scheme which is a virtual grid based topology management scheme restricting impact of movement of sink(s) and event(s) to some specific cells of a grid. This obviates the need for frequent path modifications and hence maintains continuous flow of data while minimizing the network energy consumptions. Simulation experiments show significant improvements in network energy savings and average packet delay for a packet to reach at sink.

Keywords: Mobility in WSNs, virtual grid, GBDD, clustering.

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Authors: D.Toghraie, A.R.Azimian

Abstract:

Molecular dynamics simulation of annular flow boiling in a nanochannel with 70000 particles is numerically investigated. In this research, an annular flow model is developed to predict the superheated flow boiling heat transfer characteristics in a nanochannel. To characterize the forced annular boiling flow in a nanochannel, an external driving force F ext ranging from 1to12PN (PN= Pico Newton) is applied along the flow direction to inlet fluid particles during the simulation. Based on an annular flow model analysis, it is found that saturation condition and superheat degree have great influences on the liquid-vapor interface. Also, the results show that due to the relatively strong influence of surface tension in small channel, the interface between the liquid film and vapor core is fairly smooth, and the mean velocity along the stream-wise direction does not change anymore.

Keywords: Lennard-Jones Potential, Molecular DynamicsSimulation, Periodic Boundary Conditions (PBC), Non-EquilibriumMolecular Dynamics (NEMD), Annular Flow Boiling

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Authors: Tithdanin Chav, Phichhang Ou

Abstract:

The study is about the e-banking consumer behavior of five major banks in Cambodia. This work aims to examine the relationships among job relevance, trust, mobility, perceived ease of use, perceived usefulness, attitude toward using, and intention to use of internet banking and apps. Also, the research develops and tests a conceptual model of intention to use internet banking by integrating the Technology Acceptance Model (TAM) and job relevance, trust, and mobility which were supported by Theory of Reasoned Action (TRA) and Theory of Planned Behavior (TPB). The proposed model was tested using Structural Equation Modeling (SEM), which was processed by using SPSS and AMOS with a sample size of 250 e-banking users. The results showed that there is a significant positive relationship among variables and attitudes toward using internet banking, and apps are the most factor influencing consumers’ intention to use internet banking and apps with the importance level in SEM 0.82 accounted by 82%. Significantly, all six hypotheses were accepted.

Keywords: Bank Apps, consumer intention, internet banking, technology acceptance model.

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Authors: Ali Hamadi Dicko, Nicolas Tong-Yette, Benjamin Gilles, François Faure, Olivier Palombi

Abstract:

A novel hybrid model of the lumbar spine, allowing fast static and dynamic simulations of the disc pressure and the spine mobility, is introduced in this work. Our contribution is to combine rigid bodies, deformable finite elements, articular constraints, and springs into a unique model of the spine. Each vertebra is represented by a rigid body controlling a surface mesh to model contacts on the facet joints and the spinous process. The discs are modeled using a heterogeneous tetrahedral finite element model. The facet joints are represented as elastic joints with six degrees of freedom, while the ligaments are modeled using non-linear one-dimensional elastic elements. The challenge we tackle is to make these different models efficiently interact while respecting the principles of Anatomy and Mechanics. The mobility, the intradiscal pressure, the facet joint force and the instantaneous center of rotation of the lumbar spine are validated against the experimental and theoretical results of the literature on flexion, extension, lateral bending as well as axial rotation. Our hybrid model greatly simplifies the modeling task and dramatically accelerates the simulation of pressure within the discs, as well as the evaluation of the range of motion and the instantaneous centers of rotation, without penalizing precision. These results suggest that for some types of biomechanical simulations, simplified models allow far easier modeling and faster simulations compared to usual full-FEM approaches without any loss of accuracy.

Keywords: Hybrid, modeling, fast simulation, lumbar spine.

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Authors: W. Kiamouche, S. Lasmari, M. Benslama

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In order to derive important parameters concerning mobile subscriber MS with ongoing calls in Low Earth Orbit Mobile Satellite Systems LEO MSSs, a positioning system had to be integrated into MSS in order to localize mobile subscribers MSs and track them during the connection. Such integration is regarded as a complex implementation. We propose in this paper a novel method based on advantages of mobility model of Low Earth Orbit Mobile Satellite System LEO MSS which allows the evaluation of instant of subsequent handover of a MS even if its location is unknown. This method is utilized to propose a Dynamic Channel Reservation DCRlike scheme based on the DCR scheme previously proposed in literature. Results presented show that DCR-like technique gives different QoS performance than DCR. Indeed, an improve in handover blocking probability and an increase in new call blocking probability are observed for the DCR-like technique.

Keywords: cellular layout, DCR, LEO mobile satellite system, mobility model, positioning system

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Authors: J. Tengrang, T. Rungrotmongkol, S. Hannongbua

Abstract:

Every 2-3 years the influenza B virus serves epidemics. Neuraminidase (NA) is an important target for influenza drug design. Although, oseltamivir, an oral neuraminidase drug, has been shown good inhibitory efficiency against wild-type of influenza B virus, the lower susceptibility to the R152K mutation has been reported. Better understanding of oseltamivir efficiency and resistance toward the influenza B NA wild-type and R152K mutant, respectively, could be useful for rational drug design. Here, two complex systems of wild-type and R152K NAs with oseltamivir bound were studied using molecular dynamics (MD) simulations. Based on 5-ns MD simulation, the loss of notable hydrogen bond and decrease in per-residue decomposition energy from the mutated residue K152 contributed to drug compared to those of R152 in wildtype were found to be a primary source of high-level of oseltamivir resistance due to the R152K mutation.

Keywords: Influenza B neuraminidase, Molecular dynamics simulation, Oseltamivir resistance, R152K mutant

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Authors: J. Samuel Jesudoss

Abstract:

The purpose of the study was to find out the efficacy of selected mobility exercises and participation in special games on psychomotor abilities, functional abilities and skill performance among intellectually disabled children of age group under 14. Thirty male students who were studying in Balar Kalvi Nilayam and YMCA College Special School, Chennai, acted as subjects for the study. They were only mild and moderate in intellectual disability. These students did not undergo any special training or coaching programme apart from their regular routine physical activity classes as a part of the curriculum in the school. They were attached at random, based on age in which 30 belonged to under 14 age group, which was divided into three equal group of ten for each experimental treatment. 10 students (Treatment group I) underwent calisthenics and special games participation, 10 students (Treatment group II) underwent aquatics and special games participation, 10 students (Treatment group III) underwent yoga and special games participation. The subjects were tested on selected criterion variables prior (pre test) and after twelve weeks of training (post test). The pre and post test data collected from three groups on functional abilities(self care, learning, capacity for independent living), psychomotor variables(static balance, eye hand coordination, simple reaction time test) and skill performance (bocce skill, badminton skill, table tennis skill) were statistically examined for significant difference, by applying the analysis ANACOVA. Whenever an 'F' ratio for adjusted test was found to be significant for adjusted post test means, Scheffe-s test was followed as a post-hoc test to determine which of the paired mean differences was significant. The result of the study showed that among under 14 age groups there was a significant improvement on selected criterion variables such as, Balance, Coordination, self-care and learning and also in Bocce, Badminton & Table Tennis skill performance, due to mobility exercises and participation in special games. However there were no significant differences among the groups.

Keywords: Functional ability, intellectually disabled, Mobility exercises, Psychomotor ability.

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Authors: D. Toghraie, A. R. Azimian

Abstract:

In this paper, the Lennard -Jones potential is applied to molecules of liquid argon as well as its vapor and platinum as solid surface in order to perform a non-equilibrium molecular dynamics simulation to study the microscopic aspects of liquid-vapor-solid interactions. The channel is periodic in x and y directions and along z direction it is bounded by atomic walls. It was found that density of the liquids near the solid walls fluctuated greatly and that the structure was more like a solid than a liquid. This indicates that the interactions of solid and liquid molecules are very strong. The resultant surface tension, liquid density and vapor density are found to be well predicted when compared with the experimental data for argon. Liquid and vapor densities were found to depend on the cutoff radius which induces the use of P3M (particle-particle particle-mesh) method which was implemented for evaluation of force and surface tension.

Keywords: Lennard-Jones Potential, Molecular DynamicsSimulation, Periodic Boundary Conditions (PBC), Non-EquilibriumMolecular Dynamics (NEMD).

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Authors: W. P. Hu, J. V. Kumar, Jeffrey J. P. Tsai

Abstract:

The inhibition of SH2 domain regulated protein-protein interactions is an attractive target for developing an effective chemotherapeutic approach in the treatment of disease. Molecular simulation is a useful tool for developing new drugs and for studying molecular recognition. In this study, we searched potential drug compounds for the inhibition of SH2 domain by performing structural similarity search in PubChem Compound Database. A total of 37 compounds were screened from the database, and then we used the LibDock docking program to evaluate the inhibition effect. The best three compounds (AP22408, CID 71463546 and CID 9917321) were chosen for MD simulations after the LibDock docking. Our results show that the compound CID 9917321 can produce a more stable protein-ligand complex compared to other two currently known inhibitors of Src SH2 domain. The compound CID 9917321 may be useful for the inhibition of SH2 domain based on these computational results. Subsequently experiments are needed to verify the effect of compound CID 9917321 on the SH2 domain in the future studies.

Keywords: Nonpeptide inhibitor, Src SH2 domain, LibDock, molecular dynamics simulation.

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Authors: Rozhgar A. Khailany, Mehri Igci, Emine Bayraktar, Sakip Erturhan, Metin Karakok, Ahmet Arslan

Abstract:

Kidney cancer is the most lethal urological cancer accounting for 3% of adult malignancies. VHL, a tumor-suppressor gene, is best known to be associated with renal cell carcinoma (RCC). The VHL functions as negative regulator of hypoxia inducible factors. Recent sequencing efforts have identified several novel frequent mutations of histone modifying and chromatin remodeling genes in ccRCC (clear cell RCC) including PBRM1 and SETD2. The PBRM1 gene encodes the BAF180 protein, which involved in transcriptional activation and repression of selected genes. SETD2 encodes a histone methyltransferase, which may play a role in suppressing tumor development. In this study, RNAs of 30 paired tumor and normal samples that were grouped according to the types of kidney cancer and clinical characteristics of patients, including gender and average age were examined by RT-PCR, SSCP and sequencing techniques. VHL, PBRM1 and SETD2 expressions were relatively down-regulated. However, statistically no significance was found (Wilcoxon signed rank test, p>0.05). Interestingly, no mutation was observed on the contrary of previous studies. Understanding the molecular mechanisms involved in the pathogenesis of RCC has aided the development of molecular-targeted drugs for kidney cancer. Further analysis is required to identify the responsible genes rather than VHL, PBRM1 and SETD2 in kidney cancer.

Keywords: Kidney cancer, molecular biomarker, expression analysis, mutation screening.

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Authors: Pooja, Megha Kulshrestha, V. K. Banga, Parvinder S. Sandhu

Abstract:

To support mobility in ATM networks, a number of technical challenges need to be resolved. The impact of handoff schemes in terms of service disruption, handoff latency, cost implications and excess resources required during handoffs needs to be addressed. In this paper, a one phase handoff and route optimization solution using reserved PVCs between adjacent ATM switches to reroute connections during inter-switch handoff is studied. In the second phase, a distributed optimization process is initiated to optimally reroute handoff connections. The main objective is to find the optimal operating point at which to perform optimization subject to cost constraint with the purpose of reducing blocking probability of inter-switch handoff calls for delay tolerant traffic. We examine the relation between the required bandwidth resources and optimization rate. Also we calculate and study the handoff blocking probability due to lack of bandwidth for resources reserved to facilitate the rapid rerouting.

Keywords: Wireless ATM, Mobility, Latency, Optimization rateand Blocking Probability.

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Authors: David Cobham

Abstract:

In higher education, a great degree of importance is placed on the internationalisation of the student experience. This is seen as a valuable contributor to elements such as building confidence, broadening knowledge, creating networks, and connections and enhancing employability for current students who will become the next generation of managers in technology and business. The COVID-19 pandemic has affected all areas of people’s lives. The limitations of travel coupled with the fears and concerns generated by the health risks have dramatically reduced the opportunity for students to engage with this agenda. Institutions of higher education have been required to rethink fundamental aspects of their business model from recruitment and enrolment, through learning approaches, assessment methods and the pathway to employment. This paper presents a case study which focuses on student mobility and how the physical experience of being in another country either to study, to work, to volunteer or to gain cultural and social enhancement has of necessity been replaced by alternative approaches. It considers trans-national education as an alternative to physical study overseas, virtual mobility and internships as an alternative to international work experience and adopting collaborative on-line projects as an alternative to in-person encounters. The paper concludes that although these elements have been adopted to address the current situation, the lessons learnt and the feedback gained suggests that they have contributed successfully in new and sometimes unexpected ways, and that they will persist beyond the present to become part of the "new normal" for the future. That being the case, senior leaders of institutions of higher education will be required to revisit their international plans and to rewrite their international strategies to take account of and build upon these changes.

Keywords: Trans-national education, internationalisation, higher education management, virtual mobility.

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Authors: Aline Fernandes Barata, Adriana Sansão Fontes

Abstract:

The overvaluation of the use of automobile has detrimentally affected the importance of pedestrians within the city and consequently its public spaces. As a way of treating contemporary urban paradigms, Tactical Urbanism aims to recover and activate spaces through fast and easily-applied actions that demonstrate the possibility of large-scale and long-term changes in cities. Tactical interventions have represented an important practice of redefining public spaces and urban mobility. The concept of Active Transportation coheres with the idea of sustainable urban mobility, characterizing the means of transportation through human propulsion, such as walking and cycling. This paper aims to debate the potential of Tactical Urbanism in promoting Active Transportation by revealing opportunities of transformation in the urban space of contemporary cities through initiatives that promote the protection and valorization of the presence of pedestrians and cyclists in cities, and that subvert the importance of motorized vehicles. In this paper, we present the character of these actions in two different ways: when they are used as tests for permanent interventions and when they have pre-defined start and end periods. Using recent initiatives to illustrate, we aim to discuss the role of small-scale actions in promoting and incentivizing a more active, healthy, sustainable and responsive urban way of life, presenting how some of them have developed through public policies. For that, we will present some examples of tactical actions that illustrate the encouragement of Active Transportation and trials to balance the urban opportunities for pedestrians and cyclists. These include temporary closure of streets, the creation of new alternatives and more comfortable areas for walking and cycling, and the subversion of uses in public spaces where the usage of cars are predominant.

Keywords: Tactical urbanism, active transportation, sustainable mobility, non-motorized means.

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Authors: Jeffrey L. Duffany

Abstract:

Graph coloring is an important problem in computer science and many algorithms are known for obtaining reasonably good solutions in polynomial time. One method of comparing different algorithms is to test them on a set of standard graphs where the optimal solution is already known. This investigation analyzes a set of 50 well known graph coloring instances according to a set of complexity measures. These instances come from a variety of sources some representing actual applications of graph coloring (register allocation) and others (mycieleski and leighton graphs) that are theoretically designed to be difficult to solve. The size of the graphs ranged from ranged from a low of 11 variables to a high of 864 variables. The method used to solve the coloring problem was the square of the adjacency (i.e., correlation) matrix. The results show that the most difficult graphs to solve were the leighton and the queen graphs. Complexity measures such as density, mobility, deviation from uniform color class size and number of block diagonal zeros are calculated for each graph. The results showed that the most difficult problems have low mobility (in the range of .2-.5) and relatively little deviation from uniform color class size.

Keywords: graph coloring, complexity, algorithm.

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Authors: R. Manaffar, R. Maleki, S. Zare, N. Agh, S. Soltanian, B. Sehatnia, P. Sorgeloos, P. Bossier, G. Van Stappen

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Artemia is one of the most conspicuous invertebrates associated with aquaculture. It can be considered as a model organism, offering numerous advantages for comprehensive and multidisciplinary studies using morphologic or molecular methods. Since DNA extraction is an important step of any molecular experiment, a new and a rapid method of DNA extraction from adult Artemia was described in this study. Besides, the efficiency of this technique was compared with two widely used alternative techniques, namely Chelex® 100 resin and SDS-chloroform methods. Data analysis revealed that the new method is the easiest and the most cost effective method among the other methods which allows a quick and efficient extraction of DNA from the adult animal.

Keywords: APD, Artemia, DNA extraction, Molecularexperiments

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Authors: Shagufta Tabassum

Abstract:

The study of dielectric properties in a binary mixture of liquids is very useful to understand the liquid structure, molecular interaction, dynamics, and kinematics of the mixture. Time-domain reflectometry (TDR) is a powerful tool for studying the cooperation and molecular dynamics of the H-bonded system. Here we discuss the basic calibration and normalization procedure for TDR measurements. Our aim is to explain different types of error occur during TDR measurements and how to minimize it.

Keywords: time domain reflectometry measurement technique, cable and connector loss, oscilloscope loss, normalization technique

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Authors: A. Aljohani, M. Orif

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The concentration of polycyclic aromatic hydrocarbons (PAH) in clams (A. glabrata) was examined in samples collected from Alseef Beach, 30 km south of Jeddah city. Gas chromatography-mass spectrometry (GC-MS) was used to analyze the 14 PAHs. The concentration of total PAHs was found to range from 11.521 to 40.149 ng/gdw with a mean concentration of 21.857 ng/gdw, which is lower compared to similar studies. The lower molecular weight PAHs with three rings comprised 18.14% of the total PAH concentrations in the clams, while the high molecular weight PAHs with four rings, five rings, and six rings account for 81.86%. Diagnostic ratios for PAH source distinction suggested pyrogenic or anthropogenic sources.

Keywords: Bivalves, biomonitoring, hydrocarbons, PAHs.

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Authors: Sérgio F. Sousa, Nuno M. F. S. A. Cerqueira, Marta A. S. Perez, Irina S. Moreira, António J. M.Ribeiro, Ana R. A. P. Neves, Maria J. Ramos, Pedro A. Fernandes

Abstract:

In this work we report the recent progresses that have been achieved by our group in the last half decade on the field of computational proteomics. Specifically, we discuss the application of Molecular Dynamics Simulations and Electronic Structure Calculations in drug design, in the clarification of the structural and dynamic properties of proteins and enzymes and in the understanding of the catalytic and inhibition mechanism of cancer-related enzymes. A set of examples illustrate the concepts and help to introduce the reader into this important and fast moving field.

Keywords: Enzyme, Molecular Dynamics, Protein, Quantum Mechanics.

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Authors: Yen-Cheng Chen, Fu-Chen Yang

Abstract:

IETF defines mobility support in IPv6, i.e. MIPv6, to allow nodes to remain reachable while moving around in the IPv6 internet. When a node moves and visits a foreign network, it is still reachable through the indirect packet forwarding from its home network. This triangular routing feature provides node mobility but increases the communication latency between nodes. This deficiency can be overcome by using a Binding Update (BU) scheme, which let nodes keep up-to-date IP addresses and communicate with each other through direct IP routing. To further protect the security of BU, a Return Routability (RR) procedure was developed. However, it has been found that RR procedure is vulnerable to many attacks. In this paper, we will propose a lightweight RR procedure based on geometric computing. In consideration of the inherent limitation of computing resources in mobile node, the proposed scheme is developed to minimize the cost of computations and to eliminate the overhead of state maintenance during binding updates. Compared with other CGA-based BU schemes, our scheme is more efficient and doesn-t need nonce tables in nodes.

Keywords: Mobile IPv6, Binding update, Geometric computing.

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Authors: R. Haddad, K. Morris, V. Buchanan-Wollaston

Abstract:

Biochemical and molecular analysis of some antioxidant enzyme genes revealed different level of gene expression on oilseed (Brassica napus). For molecular and biochemical analysis, leaf tissues were harvested from plants at eight different developmental stages, from young to senescence. The levels of total protein and chlorophyll were increased during maturity stages of plant, while these were decreased during the last stages of plant growth. Structural analysis (nucleotide and deduced amino acid sequence, and phylogenic tree) of a complementary DNA revealed a high level of similarity for a family of Catalase genes. The expression of the gene encoded by different Catalase isoforms was assessed during different plant growth phase. No significant difference between samples was observed, when Catalase activity was statistically analyzed at different developmental stages. EST analysis exhibited different transcripts levels for a number of other relevant antioxidant genes (different isoforms of SOD and glutathione). The high level of transcription of these genes at senescence stages was indicated that these genes are senescenceinduced genes.

Keywords: Biochemical analysis, Oilseed, Expression pattern, Growth phases

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Authors: Jayant Sakhardande, Pratik Pattanayak, Mita Bhowmick

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An efficient reintegration of the disabled people in the family and society should be fulfilled; hence it is strongly needful to assist their diminished functions or to replace the totally lost functions. Assistive technology helps in neutralizing the impairment. Recent advancements in embedded systems have opened up a vast area of research and development for affordable and portable assistive devices for the visually impaired. Granted there are many assistive devices on the market that are able to detect obstacles, and numerous research and development currently in process to alleviate the cause, unfortunately the cost of devices, size of devices, intrusiveness and higher learning curve prevents the visually impaired from taking advantage of available devices. This project aims at the design and implementation of a detachable unit which is robust, low cost and user friendly, thus, trying to aggrandize the functionality of the existing white cane, to concede above-knee obstacle detection. The designed obstruction detector uses ultrasound sensors for detecting the obstructions before direct contact. It bestows haptic feedback to the user in accordance with the position of the obstacle.

Keywords: Visually impaired, Ultrasonic sensors, Obstruction detector, Mobility aid

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Authors: Chanin Park, Sundarapandian Thangapandian, Yuno Lee, Minky Son, Shalini John, Young-sik Sohn, Keun Woo Lee

Abstract:

Hypertension is characterized with stress on the heart and blood vessels thus increasing the risk of heart attack and renal diseases. The Renin angiotensin system (RAS) plays a major role in blood pressure control. Renin is the enzyme that controls the RAS at the rate-limiting step. Our aim is to develop new drug-like leads which can inhibit renin and thereby emerge as therapeutics for hypertension. To achieve this, molecular dynamics (MD) simulation and receptor-based pharmacophore modeling were implemented, and three rennin-inhibitor complex structures were selected based on IC50 value and scaffolds of inhibitors. Three pharmacophore models were generated considering conformations induced by inhibitor. The compounds mapped to these models were selected and subjected to drug-like screening. The identified hits were docked into the active site of renin. Finally, hit1 satisfying the binding mode and interaction energy was selected as possible lead candidate to be used in novel renin inhibitors.

Keywords: Renin inhibitor, Molecular dynamics simulation, Structure-based pharmacophore modeling

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Authors: P. Sanzo

Abstract:

Increased physical fitness participation has been paralleled by increasedoveruse injuries such as insertional Achilles tendinosis (AT). Treatment has provided inconsistentresults. The use of extracorporeal shockwave therapy (ECSWT) offers a new treatment consideration.The purpose of this study was to assess the effects of ECSWTon pain, function, range of motion (ROM), joint mobility and strength in patients with AT. Thirty subjects were treated with ECSWT and measures were takenbefore and three months after treatment. There was significant differences in visual analog scale (VAS) scores for pain at rest (p=0.002); after activity (p= 0.0001); overall improvement(p=0.0001); Lower Extremity Functional Scale (LEFS) scores (p=0.002); dorsiflexion range of motion (ROM) (p=0.0001); plantarflexion strength (p=0.025); talocrural joint anterior glide (p=0.046); and subtalar joint medial and lateral glide (p=0.025).ECSWT offers a new intervention that may limit the progression of the disorder and the long term healthcare costs associated with AT.

Keywords: Extracorporeal shockwave therapy, shockwave therapy, Achilles tendinosis, range of motion, strength, joint mobility

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Authors: Jeong-Won Kang

Abstract:

Graphene, a single-atom sheet, has been considered as the most promising material for making future nanoelectromechanical systems as well as purely electrical switching with graphene transistors. Graphene-based devices have advantages in scaled-up device fabrication due to the recent progress in large area graphene growth and lithographic patterning of graphene nanostructures. Here we investigated its mechanical responses of circular graphene nanoflake under the nanoindentation using classical molecular dynamics simulations. A correlation between the load and the indentation depth was constructed. The nanoindented force in this work was applied to the center point of the circular graphene nanoflake and then, the resonance frequency could be tuned by a nanoindented depth. We found the hardening or the softening of the graphene nanoflake during its nanoindented-deflections, and such properties were recognized by the shift of the resonance frequency. The calculated mechanical parameters in the force-vs-deflection plot were in good agreement with previous experimental and theoretical works. This proposed schematics can detect the pressure via the deflection change or/and the resonance frequency shift, and also have great potential for versatile applications in nanoelectromechanical systems.

Keywords: Graphene, pressure sensor, circular graphene nanoflake, molecular dynamics.

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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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Authors: Jianwei Zhang, Dazhi Jiang, Huaxin Peng, Chunqi Wang

Abstract:

Stress-strain curve of inter-tube connected carbon nanotube (CNT) reinforced polymer composite under axial loading generated from molecular dynamics simulation is presented. Comparison of the response to axial mechanical loading between this composite system with composite systems reinforced by long, continuous CNTs (replicated via periodic boundary conditions) and short, discontinuous CNTs has been made. Simulation results showed that the inter-tube connection improved the mechanical properties of short discontinuous CNTs dramatically. Though still weaker than long CNT/polymer composite, more remarkable increase in the stiffness relative to the polymer was observed in the inter-tube connected CNT/polymer composite than in the discontinuous CNT/polymer composite. The manually introduced bridge break process resulted in a stress-strain curve of ductile fracture mode, which is consistent with the experimental result.

Keywords: Carbon nanotube, inter-tube connection, molecular dynamics, stress-strain curve

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Authors: Mohsen A. M. El-Bendary, Mostafa A. R. El-Tokhy

Abstract:

This paper presents an efficient burst error spreading tool. Also, it studies a vital issue in wireless communications, which is the transmission of images over wireless networks. IEEE ZigBee 802.15.4 is a short-range communication standard that could be used for small distance multimedia transmissions. In fact, the ZigBee network is a Wireless Personal Area Network (WPAN), which needs a strong interleaving mechanism for protection against error bursts. Also, it is low power technology and utilized in the Wireless Sensor Networks (WSN) implementation. This paper presents the chaotic interleaving scheme as a data randomization tool for this purpose. This scheme depends on the chaotic Baker map. The mobility effects on the image transmission are studied with different velocity through utilizing the Jakes’ model. A comparison study between the proposed chaotic interleaving scheme and the traditional block and convolutional interleaving schemes for image transmission over a correlated fading channel is presented. The simulation results show the superiority of the proposed chaotic interleaving scheme over the traditional schemes.

Keywords: WPANs, Burst Errors, Mobility, Interleaving Techniques, Fading channels.

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Authors: Siddhartha Chauhan, Kumar S. Pandey, Prateek Chandra

Abstract:

One of the key research issues in wireless sensor networks (WSNs) is how to efficiently deploy sensors to cover an area. In this paper, we present a Fishnet Based Dispatch Scheme (FiBDS) with energy aware mobility and interest based sensing angle. We propose two algorithms, one is FiBDS centralized algorithm and another is FiBDS distributed algorithm. The centralized algorithm is designed specifically for the non-time critical applications, commonly known as non real-time applications while the distributed algorithm is designed specifically for the time critical applications, commonly known as real-time applications. The proposed dispatch scheme works in a phase-selection manner. In this in each phase a specific constraint is dealt with according to the specified priority and then moved onto the next phase and at the end of each only the best suited nodes for the phase are chosen. Simulation results are presented to verify their effectiveness. 

Keywords: Dispatch Scheme, Energy Aware Mobility, Interest based Sensing, Wireless Sensor Networks (WSNs).

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Authors: Nurul Bahiyah Ahmad Khairudin, Habibah A Wahab

Abstract:

A new approach to predict the 3D structures of proteins by combining the knowledge-based method and Molecular Dynamics Simulation is presented on the chicken villin headpiece subdomain (HP-36). Comparative modeling is employed as the knowledge-based method to predict the core region (Ala9-Asn28) of the protein while the remaining residues are built as extended regions (Met1-Lys8; Leu29-Phe36) which then further refined using Molecular Dynamics Simulation for 120 ns. Since the core region is built based on a high sequence identity to the template (65%) resulting in RMSD of 1.39 Å from the native, it is believed that this well-developed core region can act as a 'nucleation center' for subsequent rapid downhill folding. Results also demonstrate that the formation of the non-native contact which tends to hamper folding rate can be avoided. The best 3D model that exhibits most of the native characteristics is identified using clustering method which then further ranked based on the conformational free energies. It is found that the backbone RMSD of the best model compared to the NMR-MDavg is 1.01 Å and 3.53 Å, for the core region and the complete protein, respectively. In addition to this, the conformational free energy of the best model is lower by 5.85 kcal/mol as compared to the NMR-MDavg. This structure prediction protocol is shown to be effective in predicting the 3D structure of small globular protein with a considerable accuracy in much shorter time compared to the conventional Molecular Dynamics simulation alone.

Keywords: 3D model, Chicken villin headpiece subdomain, Molecular dynamic simulation NMR-MDavg, RMSD.

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