Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 7

Search results for: pseudopotential

7 Unsupervised Classification of DNA Barcodes Species Using Multi-Library Wavelet Networks

Authors: Abdesselem Dakhli, Wajdi Bellil, Chokri Ben Amar


DNA Barcode, a short mitochondrial DNA fragment, made up of three subunits; a phosphate group, sugar and nucleic bases (A, T, C, and G). They provide good sources of information needed to classify living species. Such intuition has been confirmed by many experimental results. Species classification with DNA Barcode sequences has been studied by several researchers. The classification problem assigns unknown species to known ones by analyzing their Barcode. This task has to be supported with reliable methods and algorithms. To analyze species regions or entire genomes, it becomes necessary to use similarity sequence methods. A large set of sequences can be simultaneously compared using Multiple Sequence Alignment which is known to be NP-complete. To make this type of analysis feasible, heuristics, like progressive alignment, have been developed. Another tool for similarity search against a database of sequences is BLAST, which outputs shorter regions of high similarity between a query sequence and matched sequences in the database. However, all these methods are still computationally very expensive and require significant computational infrastructure. Our goal is to build predictive models that are highly accurate and interpretable. This method permits to avoid the complex problem of form and structure in different classes of organisms. On empirical data and their classification performances are compared with other methods. Our system consists of three phases. The first is called transformation, which is composed of three steps; Electron-Ion Interaction Pseudopotential (EIIP) for the codification of DNA Barcodes, Fourier Transform and Power Spectrum Signal Processing. The second is called approximation, which is empowered by the use of Multi Llibrary Wavelet Neural Networks (MLWNN).The third is called the classification of DNA Barcodes, which is realized by applying the algorithm of hierarchical classification.

Keywords: DNA barcode, electron-ion interaction pseudopotential, Multi Library Wavelet Neural Networks (MLWNN)

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6 Study of the Energy Levels in the Structure of the Laser Diode GaInP

Authors: Abdelali Laid, Abid Hamza, Zeroukhi Houari, Sayah Naimi


This work relates to the study of the energy levels and the optimization of the Parameter intrinsic (a number of wells and their widths, width of barrier of potential, index of refraction etc.) and extrinsic (temperature, pressure) in the Structure laser diode containing the structure GaInP. The methods of calculation used; - method of the empirical pseudo potential to determine the electronic structures of bands, - graphic method for optimization. The found results are in concord with those of the experiment and the theory.

Keywords: semi-conductor, GaInP/AlGaInP, pseudopotential, energy, alliages

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5 First Principle study of Electronic Structure of Silicene Doped with Galium

Authors: Mauludi Ariesto Pamungkas, Wafa Maftuhin


Gallium with three outer electrons commonly are used as dopants of silicon to make it P type and N type semiconductor respectively. Silicene, one-atom-thick silicon layer is one of emerging two dimension materials after the success of graphene. The effects of Gallium doping on electronic structure of silicine are investigated by using first principle calculation based on Density Functional Theory (DFT) calculation and norm conserving pseudopotential method implemented in ABINIT code. Bandstructure of Pristine silicene is similar to that of graphene. Effect of Ga doping on bandstructure of silicene depend on the position of Ga adatom on silicene

Keywords: silicene, effects of Gallium doping, Density Functional Theory (DFT), graphene

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4 Theoretical Prediction of the Structural, Elastic, Electronic, Optical, and Thermal Properties of Cubic Perovskites CsXF3 (X = Ca, Sr, and Hg) under Pressure Effect

Authors: M. A. Ghebouli, A. Bouhemadou, H. Choutri, L. Louaila


Some physical properties of the cubic perovskites CsXF3 (X = Sr, Ca, and Hg) have been investigated using pseudopotential plane–wave (PP-PW) method based on the density functional theory (DFT). The calculated lattice constants within GGA (PBE) and LDA (CA-PZ) agree reasonably with the available experiment data. The elastic constants and their pressure derivatives are predicted using the static finite strain technique. We derived the bulk and shear moduli, Young’s modulus, Poisson’s ratio and Lamé’s constants for ideal polycrystalline aggregates. The analysis of B/G ratio indicates that CsXF3 (X = Ca, Sr, and Hg) are ductile materials. The thermal effect on the volume, bulk modulus, heat capacities CV, CP, and Debye temperature was predicted.

Keywords: perovskite, PP-PW method, elastic constants, electronic band structure

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3 Ab Initio Studies of Structural and Thermal Properties of Aluminum Alloys

Authors: M. Saadi, S. E. H. Abaidia, M. Y. Mokeddem.


We present the results of a systematic and comparative study of the bulk, the structural properties, and phonon calculations of aluminum alloys using several exchange–correlations functional theory (DFT) with different plane-wave basis pseudo potential techniques. Density functional theory implemented by the Vienna Ab Initio Simulation Package (VASP) technique is applied to calculate the bulk and the structural properties of several structures. The calculations were performed for within several exchange–correlation functional and pseudo pententials available in this code (local density approximation (LDA), generalized gradient approximation (GGA), projector augmented wave (PAW)). The lattice dynamic code “PHON” developed by Dario Alfè was used to calculate some thermodynamics properties and phonon dispersion relation frequency distribution of Aluminium alloys using the VASP LDA PAW and GGA PAW results. The bulk and structural properties of the calculated structures were compared to different experimental and calculated works.

Keywords: DFT, exchange-correlation functional, LDA, GGA, pseudopotential, PAW, VASP, PHON, phonon dispersion

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2 First-Principles Calculations of Hydrogen Adsorbed in Multi-Layer Graphene

Authors: Mohammad Shafiul Alam, Mineo Saito


Graphene-based materials have attracted much attention because they are candidates for post silicon materials. Since controlling of impurities is necessary to achieve nano device, we study hydrogen impurity in multi-layer graphene. We perform local spin Density approximation (LSDA) in which the plane wave basis set and pseudopotential are used. Previously hydrogen monomer and dimer in graphene is well theoretically studied. However, hydrogen on multilayer graphene is still not clear. By using first-principles electronic structure calculations based on the LSDA within the density functional theory method, we studied hydrogen monomers and dimers in two-layer graphene. We found that the monomers are spin-polarized and have magnetic moment 1 µB. We also found that most stable dimer is much more stable than monomer. In the most stable structures of the dimers in two-layer graphene, the two hydrogen atoms are bonded to the host carbon atoms which are nearest-neighbors. In this case two hydrogen atoms are located on the opposite sides. Whereas, when the two hydrogen atoms are bonded to the same sublattice of the host materials, magnetic moments of 2 µB appear in two-layer graphene. We found that when the two hydrogen atoms are bonded to third-nearest-neighbor carbon atoms, the electronic structure is nonmagnetic. We also studied hydrogen monomers and dimers in three-layer graphene. The result is same as that of two-layer graphene. These results are very important in the field of carbon nanomaterials as it is experimentally difficult to show the magnetic state of those materials.

Keywords: first-principles calculations, LSDA, multi-layer gra-phene, nanomaterials

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1 A Study on ZnO Nanoparticles Properties: An Integration of Rietveld Method and First-Principles Calculation

Authors: Kausar Harun, Ahmad Azmin Mohamad


Zinc oxide (ZnO) has been extensively used in optoelectronic devices, with recent interest as photoanode material in dye-sensitize solar cell. Numerous methods employed to experimentally synthesized ZnO, while some are theoretically-modeled. Both approaches provide information on ZnO properties, but theoretical calculation proved to be more accurate and timely effective. Thus, integration between these two methods is essential to intimately resemble the properties of synthesized ZnO. In this study, experimentally-grown ZnO nanoparticles were prepared by sol-gel storage method with zinc acetate dihydrate and methanol as precursor and solvent. A 1 M sodium hydroxide (NaOH) solution was used as stabilizer. The optimum time to produce ZnO nanoparticles were recorded as 12 hours. Phase and structural analysis showed that single phase ZnO produced with wurtzite hexagonal structure. Further work on quantitative analysis was done via Rietveld-refinement method to obtain structural and crystallite parameter such as lattice dimensions, space group, and atomic coordination. The lattice dimensions were a=b=3.2498Å and c=5.2068Å which were later used as main input in first-principles calculations. By applying density-functional theory (DFT) embedded in CASTEP computer code, the structure of synthesized ZnO was built and optimized using several exchange-correlation functionals. The generalized-gradient approximation functional with Perdew-Burke-Ernzerhof and Hubbard U corrections (GGA-PBE+U) showed the structure with lowest energy and lattice deviations. In this study, emphasize also given to the modification of valence electron energy level to overcome the underestimation in DFT calculation. Both Zn and O valance energy were fixed at Ud=8.3 eV and Up=7.3 eV, respectively. Hence, the following electronic and optical properties of synthesized ZnO were calculated based on GGA-PBE+U functional within ultrasoft-pseudopotential method. In conclusion, the incorporation of Rietveld analysis into first-principles calculation was valid as the resulting properties were comparable with those reported in literature. The time taken to evaluate certain properties via physical testing was then eliminated as the simulation could be done through computational method.

Keywords: density functional theory, first-principles, Rietveld-refinement, ZnO nanoparticles

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