Search results for: Lattice Boltzmann method

Authors: Mansour Tarafdar, Mohammad Saniee Abade

Abstract:

This paper investigates the problem of sampling from transactional data streams. We introduce CFISDS as a content based sampling algorithm that works on a landmark window model of data streams and preserve more informed sample in sample space. This algorithm that work based on closed frequent itemset mining tasks, first initiate a concept lattice using initial data, then update lattice structure using an incremental mechanism.Incremental mechanism insert, update and delete nodes in/from concept lattice in batch manner. Presented algorithm extracts the final samples on demand of user. Experimental results show the accuracy of CFISDS on synthetic and real datasets, despite on CFISDS algorithm is not faster than exist sampling algorithms such as Z and DSS.

Keywords: Sampling, data streams, closed frequent item set mining.

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Authors: Juyoung Kim, Taegeun Park

Abstract:

In this paper, we propose a fully-utilized, block-based 2D DWT (discrete wavelet transform) architecture, which consists of four 1D DWT filters with two-channel QMF lattice structure. The proposed architecture requires about 2MN-3N registers to save the intermediate results for higher level decomposition, where M and N stand for the filter length and the row width of the image respectively. Furthermore, the proposed 2D DWT processes in horizontal and vertical directions simultaneously without an idle period, so that it computes the DWT for an N×N image in a period of N2(1-2-2J)/3. Compared to the existing approaches, the proposed architecture shows 100% of hardware utilization and high throughput rates. To mitigate the long critical path delay due to the cascaded lattices, we can apply the pipeline technique with four stages, while retaining 100% of hardware utilization. The proposed architecture can be applied in real-time video signal processing.

Keywords: discrete wavelet transform, VLSI architecture, QMF lattice filter, pipelining.

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Authors: Atul K. Desai, Hemal J. Shah

Abstract:

The tall windmill towers are designed as monopole tower or lattice tower. In the present research, a 125-meter high hybrid tower which is a combination of lattice and monopole type is proposed. The response of hybrid tower is compared with conventional monopole tower. The towers were analyzed in finite element method software considering nonlinear seismic time history load. The synthetic seismic time history for different soil is derived using the SeismoARTIF software. From the present research, it is concluded that, in the hybrid tower, we are not getting resonance condition. The base shear is less in hybrid tower compared to monopole tower for different soil conditions.

Keywords: Dynamic analysis, hybrid wind mill tower, resonance condition, synthetic time history.

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Authors: Shams-ul-Islam, Raheela Manzoor, Zhou Chao Ying

Abstract:

A two-dimensional numerical study for flow past a square cylinder in presence of flat plate both at upstream and downstream position is carried out using the single-relaxation-time lattice Boltzmann method for gap spacing 0.5 and 1. We select Reynolds numbers from 80 to 200. The wake structure mechanism within gap spacing and near wake region, vortex structures around and behind the main square cylinder in presence of flat plate are studied and compared with flow pattern around a single square cylinder. The results are obtained in form of vorticity contour, streamlines, power spectra analysis, time trace analysis of drag and lift coefficients. Four different types of flow patterns were observed in both configurations, named as (i) Quasi steady flow (QSF), (ii) steady flow (SF), (iii) shear layer reattachment (SLR), (iv) single bluff body (SBB). It is observed that upstream flat plate plays a vital role in significant drag reduction. On the other hand, rate of suppression of vortex shedding is high for downstream flat plate case at low Reynolds numbers. The reduction in mean drag force and root mean square value of drag force for upstream flat plate case are89.1% and 86.3% at (Re, g) = (80, 0.5d) and (120, 1d) and reduction for downstream flat plate case for mean drag force and root mean square value of drag force are 11.10% and 97.6% obtained at (180, 1d) and (180, 0.5d).

Keywords: Detached flat plates, drag and lift coefficients, Reynolds numbers, square cylinder, Strouhal number.

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Authors: K. Sudprasert, M. Precharattana, N. Nuttavut, D. Triampo, B. Pattanasiri, Y. Lenbury, W. Triampo

Abstract:

The study of non-equilibrium systems has attracted increasing interest in recent years, mainly due to the lack of theoretical frameworks, unlike their equilibrium counterparts. Studying the steady state and/or simple systems is thus one of the main interests. Hence in this work we have focused our attention on the driven lattice gas model (DLG model) consisting of interacting particles subject to an external field E. The dynamics of the system are given by hopping of particles to nearby empty sites with rates biased for jumps in the direction of E. Having used small two dimensional systems of DLG model, the stochastic properties at nonequilibrium steady state were analytically studied. To understand the non-equilibrium phenomena, we have applied the analytic approach via master equation to calculate probability function and analyze violation of detailed balance in term of the fluctuation-dissipation theorem. Monte Carlo simulations have been performed to validate the analytic results.

Keywords: Non-equilibrium, lattice gas, stochastic process

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Authors: Zelalem Teshome Wale

Abstract:

The notions of I-vague groups with membership and non-membership functions taking values in an involutary dually residuated lattice ordered semigroup are introduced which generalize the notions with truth values in a Boolean algebra as well as those usual vague sets whose membership and non-membership functions taking values in the unit interval [0, 1]. Moreover, various operations and properties are established.

Keywords: Involutary dually residuated lattice ordered semigroup, I-vague set and I-vague group.

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Authors: Samir Abdelhamid, Noureddine Bouguechal

Abstract:

We report in this paper the model adopted by our system of continuous speech recognition in Arab language SySRA and the results obtained until now. This system uses the database Arabdic-10 which is a corpus of word for the Arab language and which was manually segmented. Phonetic decoding is represented by an expert system where the knowledge base is translated in the form of production rules. This expert system transforms a vocal signal into a phonetic lattice. The higher level of the system takes care of the recognition of the lattice thus obtained by deferring it in the form of written sentences (orthographical Form). This level contains initially the lexical analyzer which is not other than the module of recognition. We subjected this analyzer to a set of spectrograms obtained by dictating a score of sentences in Arab language. The rate of recognition of these sentences is about 70% which is, to our knowledge, the best result for the recognition of the Arab language. The test set consists of twenty sentences from four speakers not having taken part in the training.

Keywords: Continuous speech recognition, lexical analyzer, phonetic decoding, phonetic lattice, vocal signal.

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Authors: Hamid Reza Pakzad

Abstract:

Dust acoustic solitary waves are studied in warm dusty plasma containing negatively charged dusts, nonthermal ions and Boltzmann distributed electrons. Sagdeev pseudopotential method is used in order to investigate solitary wave solutions in the plasmas. The existence of compressive and rarefractive solitons is studied.

Keywords: Nonthermal, Soliton, Dust, Sagdeev potential

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Authors: Yilun Shang

Abstract:

We study a long-range percolation model in the hierarchical lattice ΩN of order N where probability of connection between two nodes separated by distance k is of the form min{αβ−k, 1}, α ≥ 0 and β > 0. The parameter α is the percolation parameter, while β describes the long-range nature of the model. The ΩN is an example of so called ultrametric space, which has remarkable qualitative difference between Euclidean-type lattices. In this paper, we characterize the sizes of large clusters for this model along the line of some prior work. The proof involves a stationary embedding of ΩN into Z. The phase diagram of this long-range percolation is well understood.

Keywords: percolation, component, hierarchical lattice, phase transition.

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Authors: Mounira RouaÐùnia, Noureddine Doghmane

Abstract:

In this paper we consider the problem of change detection and non stationary signals tracking. Using parametric estimation of signals based on least square lattice adaptive filters we consider for change detection statistical parametric methods using likelihood ratio and hypothesis tests. In order to track signals dynamics, we introduce a compensation procedure in the adaptive estimation. This will improve the adaptive estimation performances and fasten it-s convergence after changes detection.

Keywords: Change detection, Hypothesis test, likelihood ratioleast square lattice adaptive filters.

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Authors: Zelalem Teshome Wale

Abstract:

The notions of I-vague normal groups with membership and non-membership functions taking values in an involutary dually residuated lattice ordered semigroup are introduced which generalize the notions with truth values in a Boolean algebra as well as those usual vague sets whose membership and non-membership functions taking values in the unit interval [0, 1]. Various operations and properties are established.

Keywords: Involutary dually residuated lattice ordered semigroup, I-vague set, I-vague group and I-vague normal group.

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Authors: B. J. C. Horsten, L. L. M. Veldhuis

Abstract:

Because support interference corrections are not properly understood, engineers mostly rely on expensive dummy measurements or CFD calculations. This paper presents a method based on uncorrected wind tunnel measurements and fast calculation techniques (it is a hybrid method) to calculate wall interference, support interference and residual interference (when e.g. a support member closely approaches the wind tunnel walls) for any type of wind tunnel and support configuration. The method provides with a simple formula for the calculation of the interference gradient. This gradient is based on the uncorrected measurements and a successive calculation of the slopes of the interference-free aerodynamic coefficients. For the latter purpose a new vortex-lattice routine is developed that corrects the slopes for viscous effects. A test case of a measurement on a wing proves the value of this hybrid method as trends and orders of magnitudes of the interference are correctly determined.

Keywords: Hybrid method, support interference, wall interference, wind tunnel corrections.

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Authors: M. Hanif, M. Salik

Abstract:

In the present research work we present the optical emission studies of the Indium (In) – Tin (Sn) plasma produced by the first (1064 nm) harmonic of an Nd: YAG nanosecond pulsed laser. The experimentally observed line profiles of neutral Indium (In I) and Tin (SnI) are used to extract the electron temperature (Te) using the Boltzmann plot method. Whereas, the electron number density (Ne) has been determined from the Stark broadening line profile method. The Te is calculated by varying the distance from the target surface along the line of propagation of plasma plume and also by varying the laser irradiance. Beside we have studied the variation of Ne as a function of laser irradiance as well as its variation with distance from the target surface.

Keywords: Indium – Tin plasma, laser ablation, optical emission spectroscopy, electron temperature, and electron number density.

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Authors: A. Faro, D. Giordano, F. Maiorana

Abstract:

Data mining uses a variety of techniques each of which is useful for some particular task. It is important to have a deep understanding of each technique and be able to perform sophisticated analysis. In this article we describe a tool built to simulate a variation of the Kohonen network to perform unsupervised clustering and support the entire data mining process up to results visualization. A graphical representation helps the user to find out a strategy to optimize classification by adding, moving or delete a neuron in order to change the number of classes. The tool is able to automatically suggest a strategy to optimize the number of classes optimization, but also support both tree classifications and semi-lattice organizations of the classes to give to the users the possibility of passing from one class to the ones with which it has some aspects in common. Examples of using tree and semi-lattice classifications are given to illustrate advantages and problems. The tool is applied to classify macroeconomic data that report the most developed countries- import and export. It is possible to classify the countries based on their economic behaviour and use the tool to characterize the commercial behaviour of a country in a selected class from the analysis of positive and negative features that contribute to classes formation. Possible interrelationships between the classes and their meaning are also discussed.

Keywords: Unsupervised classification, Kohonen networks, macroeconomics, Visual data mining, Cluster interpretation.

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Authors: Yanmin Zhao, Siu Ming Yiu

Abstract:

To claim the ownership for an executable program is a non-trivial task. An emerging direction is to add a watermark to the program such that the watermarked program preserves the original program’s functionality and removing the watermark would heavily destroy the functionality of the watermarked program. In this paper, the first watermarking signature scheme with the watermark and the constraint function hidden in the symmetric key setting is constructed. The scheme uses well-known techniques of lattice trapdoors and a lattice evaluation. The watermarking signature scheme is unforgeable under the Short Integer Solution (SIS) assumption and satisfies other security requirements such as the unremovability security property.

Keywords: Short integer solution problem, signatures, the symmetric-key setting, watermarking schemes.

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Authors: Ashish R. Tanna, Hiren H. Joshi

Abstract:

The mineral having chemical compositional formula MgAl2O4 is called “spinel". The ferrites crystallize in spinel structure are known as spinel-ferrites or ferro-spinels. The spinel structure has a fcc cage of oxygen ions and the metallic cations are distributed among tetrahedral (A) and octahedral (B) interstitial voids (sites). The X-ray diffraction (XRD) intensity of each Bragg plane is sensitive to the distribution of cations in the interstitial voids of the spinel lattice. This leads to the method of determination of distribution of cations in the spinel oxides through XRD intensity analysis. The computer program for XRD intensity analysis has been developed in C language and also tested for the real experimental situation by synthesizing the spinel ferrite materials Mg0.6Zn0.4AlxFe2- xO4 and characterized them by X-ray diffractometry. The compositions of Mg0.6Zn0.4AlxFe2-xO4(x = 0.0 to 0.6) ferrites have been prepared by ceramic method and powder X-ray diffraction patterns were recorded. Thus, the authenticity of the program is checked by comparing the theoretically calculated data using computer simulation with the experimental ones. Further, the deduced cation distributions were used to fit the magnetization data using Localized canting of spins approach to explain the “recovery" of collinear spin structure due to Al3+ - substitution in Mg-Zn ferrites which is the case if A-site magnetic dilution and non-collinear spin structure. Since the distribution of cations in the spinel ferrites plays a very important role with regard to their electrical and magnetic properties, it is essential to determine the cation distribution in spinel lattice.

Keywords: Spinel ferrites, Localized canting of spins, X-ray diffraction, Programming in Borland C.

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Authors: S. Channgam, A. Sae-Tang, T. Termsaithong

Abstract:

In this research, the occurrences of large size events in various system sizes of the Bak-Tang-Wiesenfeld sandpile model are considered. The system sizes (square lattice) of model considered here are 25×25, 50×50, 75×75 and 100×100. The cross-correlation between the ratio of sites containing 3 grain time series and the large size event time series for these 4 system sizes are also analyzed. Moreover, a prediction method of the large-size event for the 50×50 system size is also introduced. Lastly, it can be shown that this prediction method provides a slightly higher efficiency than random predictions.

Keywords: Bak-Tang-Wiesenfeld sandpile model, avalanches, cross-correlation, prediction method.

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Authors: Na Cheng, Zi-li Chen

Abstract:

We investigate the sufficient condition under which each positive b-weakly compact operator is Dunford-Pettis. We also investigate the necessary condition on which each positive b-weakly compact operator is Dunford-Pettis. Necessary condition on which each positive b-weakly compact operator is weakly compact is also considered. We give the operator that is semi-compact, but it is not bweakly. We present a necessary and sufficient condition under which each positive semi-compact operator is b-weakly compact.

Keywords: b-weakly compact, Dunford-Pettis operator, M-weakly compact operator, L-weakly compact operator, semi-compact operator, weakly sequentially continuous lattice operations, order continuous norm, positive Schur property.

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Authors: B. Ghasemi, A. A. Najafzadeh Khoee

Abstract:

In this study, the effect of mechanical activation on the synthesis of Fe3Al/Al2O3 nanocomposite has been investigated by using mechanochemical method. For this purpose, Aluminum powder and hematite as precursors, with stoichiometric ratio, have been utilized and other effective parameters in milling process were kept constant. Phase formation analysis, crystallite size measurement and lattice strain were studied by X-ray diffraction (XRD) by using Williamson-Hall method as well as microstructure and morphology were explored by Scanning electron microscopy (SEM). Also, Energy-dispersive X-ray spectroscopy (EDX) analysis was used in order to probe the particle distribution. The results showed that after 30-hour milling, the reaction was started, combustibly done and completed.

Keywords: hematite, mechanochemical, milling, nanocomposite

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Authors: František Včelař, Zuzana Pátíková

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Recently a new type of very general relational structures, the so called (L-)complete propelattices, was introduced. These significantly generalize complete lattices and completely lattice L-ordered sets, because they do not assume the technically very strong property of transitivity. For these structures also the main part of the original Tarski’s fixed point theorem holds for (L-fuzzy) isotone maps, i.e., the part which concerns the existence of fixed points and the structure of their set. In this paper, fundamental properties of (L-)complete propelattices are recalled and the so called L-fuzzy relatively isotone maps are introduced. For these maps it is proved that they also have fixed points in L-complete propelattices, even if their set does not have to be of an awaited analogous structure of a complete propelattice.

Keywords: Fixed point, L-complete propelattice, L-fuzzy (relatively) isotone map, residuated lattice, transitivity.

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Authors: Samir Osman M., Mohammed Hassan S.

Abstract:

Sample of CsAg2I3 was prepared by solid state reaction. Then, microstructure parameters of this sample have been determined using wide angle X-ray scattering WAXS method. As well as, Cell parameters of crystal structure have been refined using CHEKCELL program. This analysis states that the lattice intrinsic strainof the sample is so small and the crystal size is on the order of 559Å.

Keywords: WAXS, Microstructure parameters, super-ionic conductor.

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Authors: Noor Ul Ain Bhatti, M. Junaid Khan, Javed Ahmad, Murtaza Saleem, Shahid M. Ramay, Saadat A. Siddiqi

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Manganese oxide is being recently used as electrode material for rechargeable batteries. In this study, Al incorporated Mn₂O₃ compositions were synthesized to study the effect of Al doping on electrochemical performance of host material. Structural studies were carried out using X-ray diffraction analysis to confirm the phase stability and explore the lattice parameters, crystallite size, lattice strain, density and cell volume. Morphology and composition were analyzed using field emission scanning electron microscope and energy dispersive X-ray spectroscopy, respectively. Dynamic light scattering analysis was performed to observe the average particle size of the compositions. FTIR measurements exhibit the O-Al-O and O-Mn-O and Al-O bonding and with increasing the concentration of Al, the vibrational peaks of Mn-O become sharper. An enhanced electrochemical performance was observed in compositions with higher Al content.

Keywords: Mn2O3, electrode materials, energy storage and conversion, electrochemical performance.

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Authors: Hong Seung Kim, Chang Hoi Kim, Lili Yue

Abstract:

Single-phase, high band gap energy Zn_0.5Mg_0.5O films were grown under oxygen pressure, using pulse laser deposition with a Zn_0.5Mg_0.5O target. Structural characterization studies revealed that the crystal structures of the Zn_X-1Mg_XO films could be controlled via changes in the oxygen pressure. TEM analysis showed that the thickness of the deposited Zn_1-xMg_xO thin films was 50–75 nm. As the oxygen pressure increased, we found that one axis of the crystals did not show a very significant increase in the crystallization compared with that observed at low oxygen pressure. The X-ray diffraction peak intensity for the hexagonal-ZnMgO (002) plane increased relative to that for the cubic-ZnMgO (111) plane. The corresponding c-axis of the h-ZnMgO lattice constant increased from 5.141 to 5.148 Å, and the a-axis of the c-ZnMgO lattice constant decreased from 4.255 to 4.250 Å. EDX analysis showed that the Mg content in the mixed-phase ZnMgO films decreased significantly, from 54.25 to 46.96 at.%. As the oxygen pressure was increased from 100 to 150 mTorr, the absorption edge red-shifted from 3.96 to 3.81 eV; however, a film grown at the highest oxygen pressure tested here (200 mTorr).

Keywords: MgO, UV LED, ZnMgO, ZnO.

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Authors: Nikhil Jain, Yang Xu, Bin Yu

Abstract:

The material behavior of graphene, a single layer of carbon lattice, is extremely sensitive to its dielectric environment. We demonstrate improvement in electronic performance of graphene nanowire interconnects with full encapsulation by lattice-matching, chemically inert, 2D layered insulator hexagonal boron nitride (h- BN). A novel layer-based transfer technique is developed to construct the h-BN/MLG/h-BN heterostructures. The encapsulated graphene wires are characterized and compared with that on SiO2 or h-BN substrate without passivating h-BN layer. Significant improvements in maximum current-carrying density, breakdown threshold, and power density in encapsulated graphene wires are observed. These critical improvements are achieved without compromising the carrier transport characteristics in graphene. Furthermore, graphene wires exhibit electrical behavior less insensitive to ambient conditions, as compared with the non-passivated ones. Overall, h-BN/graphene/h- BN heterostructure presents a robust material platform towards the implementation of high-speed carbon-based interconnects.

Keywords: Two-dimensional nanosheet, graphene, hexagonal boron nitride, heterostructure, interconnects.

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Authors: Tomio Iwasaki, Yosuke Kawahito

Abstract:

The adhesion strength and wettability at the interfaces between a polyetheretherketone (PEEK) resin and titanium dioxide (TiO2) have become more important because direct joining of PEEK resin and titanium (Ti), whose surface has usually the oxide (TiO2), is needed not only in vehicles such as airplanes, automobiles, and space vehicles, but also in medical devices such as implants. To realize strong joint between the PEEK resin and TiO2, the dependence of the adhesion strength and wettability on crystal orientations of rutile TiO2 were investigated by using molecular simulations. Molecular dynamics simulations were conducted by combining quantum-mechanics equation of electrons with Newton’s equation of motion of nuclear coordinates (atomic coordinates). By putting a PEEK-resin sphere on a rutile TiO2 surface and by heating the system to 650 K, the contact angles at the interfaces were calculated to evaluate the wettability. After the system is cooled to 300 K from 650 K, to evaluate the adhesin strength, the adhesive fracture energy is calculated as the difference between the energy of the PEEK-TiO2 attached state and that of the PEEK-TiO2 detached state. The results of the contact angles showed that PEEK resin on the TiO2(100) and that on the TiO2(001) surface has low wettability with large contact angles. On the other hand, PEEK resin on the TiO2(110) surface has high wettability with a small contact angle. The results of the adhesive fracture energies showed that the adhesion at the PEEK-resin/TiO2(100) and PEEK-resin/TiO2(001) interfaces are weak. On the other hand, the adhesion at the PEEK-resin/TiO2(110) interface is strong. To clarify the reason that the higher wettability and stronger adhesion are obtained at the PEEK/TiO2(110) interface than at the at the PEEK/TiO2(100) and PEEK/TiO2(001) interfaces, atomic configurations at the interfaces were visualized. The atomic configuration at the PEEK/TiO2(110) interface showed that the lattice-matched coherent interface is realized, and the atomic density is high. On the other hand, the atomic configuration at the PEEK/TiO2(001) interface showed the lattice-unmatched incoherent interface. The atomic configuration at the PEEK/TiO2(100) interface showed that the atomic density is very low although the lattice-matched interface is realized. Therefore, the lattice matching and the high atomic density at the PEEK/TiO2(001) interface are considered to be dominant factors in the high wettability and strong adhesion.

Keywords: Adhesion, direct joining, PEEK, TiO2, wettability.

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Authors: Basudev Ghosh, Sreyasi Banerjee

Abstract:

Using pseudo potential method arbitrary amplitude ion-acoustic solitary waves have been theoretically studied in a collisionless plasma consisting of warm drifting positive ions, Boltzmann positrons and nonthermal electrons. Ion-acoustic solitary wave solutions have been obtained and the dependence of the solitary wave profile on different plasma parameters has been studied numerically. Lower and higher order compressive and rarefactive solitary waves are observed in presence of positrons, nonthermal electrons, ion drift velocity and finite ion temperature. Inclusion of higher order nonlinearity is shown to have significant correction to the solitary wave profile for the same values of plasma parameters.

Keywords: Ion-acoustic waves, Nonthermal electrons, Sagdeev potential, Solitary waves.

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Authors: Hani Baek, Gwang Min Sun, Chansun Shin, Sung Ho Ahn

Abstract:

Fast neutron irradiation using nuclear reactors is an effective method to improve switching loss and short circuit durability of power semiconductor (insulated gate bipolar transistors (IGBT) and insulated gate transistors (IGT), etc.). However, not only fast neutrons but also thermal neutrons, epithermal neutrons and gamma exist in the nuclear reactor. And the electrical properties of the IGBT may be deteriorated by the irradiation of gamma. Gamma irradiation damages are known to be caused by Total Ionizing Dose (TID) effect and Single Event Effect (SEE), Displacement Damage. Especially, the TID effect deteriorated the electrical properties such as leakage current and threshold voltage of a power semiconductor. This work can confirm the effect of the gamma irradiation on the electrical properties of 600 V NPT-IGBT. Irradiation of gamma forms lattice defects in the gate oxide and Si-SiO₂ interface of the IGBT. It was confirmed that this lattice defect acts on the center of the trap and affects the threshold voltage, thereby negatively shifted the threshold voltage according to TID. In addition to the change in the carrier mobility, the conductivity modulation decreases in the n-drift region, indicating a negative influence that the forward voltage drop decreases. The turn-off delay time of the device before irradiation was 212 ns. Those of 2.5, 10, 30, 70 and 100 kRad(Si) were 225, 258, 311, 328, and 350 ns, respectively. The gamma irradiation increased the turn-off delay time of the IGBT by approximately 65%, and the switching characteristics deteriorated.

Keywords: NPT-IGBT, gamma irradiation, switching, turn-off delay time, recombination, trap center.

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Authors: Andreas Körtge, Susanne Stählke, Regina Lange, Mario Birkholz, Mirko Fraschke, Katrin Schulz, Barbara Nebe, Patrick Elter

Abstract:

A major challenge in biomaterials research is the regulation of protein adsorption which is a key factor for controlling the subsequent cell adhesion at implant surfaces. The aim of the present study was to control the adsorption of fibronectin (FN) and the attachment of MG-63 osteoblasts with an electronic nanostructure. Shallow doping line lattices with a period of 260 nm were produced for this purpose by implantation of phosphorous in silicon wafers. Protein coverage was determined after incubating the substrate with FN by means of an immunostaining procedure and the measurement of the fluorescence intensity with a TECAN analyzer. We observed an increased amount of adsorbed FN on the nanostructure compared to control substrates. MG-63 osteoblasts were cultivated for 24h on FN-incubated substrates and their morphology was assessed by SEM. Preferred orientation and elongation of the cells in direction of the doping lattice lines was observed on FN-coated nanostructures.

Keywords: Cell adhesion, electronic nanostructures, doping lattice, fibronectin, MG-63 osteoblasts, protein adsorption.

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Authors: Dhananjay C. Joshi, Jung-Hsin Lin

Abstract:

Protein-protein interactions (PPI) play a crucial role in many biological processes such as cell signalling, transcription, translation, replication, signal transduction, and drug targeting, etc. Structural information about protein-protein interaction is essential for understanding the molecular mechanisms of these processes. Structures of protein-protein complexes are still difficult to obtain by biophysical methods such as NMR and X-ray crystallography, and therefore protein-protein docking computation is considered an important approach for understanding protein-protein interactions. However, reliable prediction of the protein-protein complexes is still under way. In the past decades, several grid-based docking algorithms based on the Katchalski-Katzir scoring scheme were developed, e.g., FTDock, ZDOCK, HADDOCK, RosettaDock, HEX, etc. However, the success rate of protein-protein docking prediction is still far from ideal. In this work, we first propose a more practical measure for evaluating the success of protein-protein docking predictions,the rate of first success (RFS), which is similar to the concept of mean first passage time (MFPT). Accordingly, we have assessed the ZDOCK bound and unbound benchmarks 2.0 and 3.0. We also createda new benchmark set for protein-protein docking predictions, in which the complexes have experimentally determined binding affinity data. We performed free energy calculation based on the solution of non-linear Poisson-Boltzmann equation (nlPBE) to improve the binding mode prediction. We used the well-studied thebarnase-barstarsystem to validate the parameters for free energy calculations. Besides,thenlPBE-based free energy calculations were conducted for the badly predicted cases by ZDOCK and ZRANK. We found that direct molecular mechanics energetics cannot be used to discriminate the native binding pose from the decoys.Our results indicate that nlPBE-based calculations appeared to be one of the promising approaches for improving the success rate of binding pose predictions.

Keywords: protein-protein docking, protein-protein interaction, molecular mechanics energetics, Poisson-Boltzmann calculations

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

Abstract:

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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