Search results for: atomic orbitals

Authors: Shuwen Wu, Zhi LI

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Atomically dispersed Fe‒N₄ catalysts are proven as promising alternatives to commercial Pt/C for the oxygen reduction reaction. Most reported Fe‒N₄ catalysts suffer from inferior O‒O bond-breaking capability due to superoxo-like O₂ adsorption, though the isolated dual-atomic metal sites strategy is extensively adopted. Atomic Fe clusters hold greater promise for promoting O‒O bond cleavage by forming peroxo-like O₂ adsorption. However, the excessively strong binding strength between Fe clusters and oxygenated intermediates sacrifices the activity. Here, we first report a Fex/Cu‒N@CF catalyst with atomic Fe clusters functionalized by adjacent single Cu‒N₄ sites anchoring on a porous carbon nanofiber membrane. The theoretical calculation indicates that the single Cu‒N₄ sites can modulate the electronic configuration of Fe clusters to reduce O₂* protonation reaction free energy, which ultimately enhances the electrocatalytic performance. Particularly, the Cu‒N₄ sites can increase the overlaps between the d orbitals of Fe and p orbitals of O to accelerate O‒O cleavage in OOH*. As a result, this unique atomic catalyst exhibits a half potential (E1/2) of 0.944 V in an alkaline medium exceeding that of commercial Pt/C, whereas acidic performance E1/2 = 0.815 V is comparable to Pt/C. This work shows the great potential of single atoms for improvements in atomic cluster catalysts.

Keywords: Hierarchical porous fibers, atomic Fe clusters, Cu single atoms, oxygen reduction reaction; O-O bond cleavage

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Authors: Mebarek Boukelkoul, Abdelhalim Haroun

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By means of the first principle calculation, we have investigated the structural, magnetic and magneto-optical properties of the ultra-thin films of Fen/Cu(001) with (n=1, 2, 3). We adopted a relativistic approach using DFT theorem with local spin density approximation (LSDA). The electronic structure is performed within the framework of the Spin-Polarized Relativistic (SPR) Linear Muffin-Tin Orbitals (LMTO) with the Atomic Sphere Approximation (ASA) method. During the variational principle, the crystal wave function is expressed as a linear combination of the Bloch sums of the so-called relativistic muffin-tin orbitals centered on the atomic sites. The crystalline structure is calculated after an atomic relaxation process using the optimization of the total energy with respect to the atomic interplane distance. A body-centered tetragonal (BCT) pseudomorphic crystalline structure with a tetragonality ratio c/a larger than unity is found. The magnetic behaviour is characterized by an enhanced magnetic moment and a ferromagnetic interplane coupling. The polar magneto-optical Kerr effect spectra are given over a photon energy range extended to 15eV and the microscopic origin of the most interesting features are interpreted by interband transitions. Unlike thin layers, the anisotropy in the ultra-thin films is characterized by a perpendicular magnetization which is perpendicular to the film plane.

Keywords: ultrathin films, magnetism, magneto-optics, pseudomorphic structure

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Authors: Nishant Rodrigues, Nicole Spanedda, Chilukuri K. Mohan, Arindam Chakraborty

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A crucial objective in quantum chemistry is the computation of the energy levels of chemical systems. This task requires electron-repulsion integrals as inputs, and the steep computational cost of evaluating these integrals poses a major numerical challenge in efficient implementation of quantum chemical software. This work presents a moment-based machine-learning approach for the efficient evaluation of electron-repulsion integrals. These integrals were approximated using linear combinations of a small number of moments. Machine learning algorithms were applied to estimate the coefficients in the linear combination. A random forest approach was used to identify promising features using a recursive feature elimination approach, which performed best for learning the sign of each coefficient but not the magnitude. A neural network with two hidden layers were then used to learn the coefficient magnitudes along with an iterative feature masking approach to perform input vector compression, identifying a small subset of orbitals whose coefficients are sufficient for the quantum state energy computation. Finally, a small ensemble of neural networks (with a median rule for decision fusion) was shown to improve results when compared to a single network.

Keywords: quantum energy calculations, atomic orbitals, electron-repulsion integrals, ensemble machine learning, random forests, neural networks, feature extraction

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Authors: Ling Dai

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Surface-sensing devices such as atomic force microscope have been widely used to characterize the surface structure and properties of nanoscale polymer films. However, using molecular dynamics simulations, we show that there is intrinsic and unavoidable inelastic deformation at polymer surfaces induced by the sensing tip. For linear chain polymers like perfluoropolyether, such tip-induced deformation derives from the differences in the atomic interactions which are atomic specie-based Van der Waals interactions, and resulting in atomic shuffling and causing inelastic alternation in both molecular structures and mechanical properties at the regions of the polymer surface. For those aromatic chain polymers like epoxy, the intrinsic deformation is depicted as the intra-chain rotation of aromatic rings and kinking of linear atomic connections. The present work highlights the need to reinterpret the data obtained from surface-sensing tests by considering this intrinsic inelastic deformation occurring at polymer surfaces.

Keywords: polymer, surface, nano, molecular dynamics

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Authors: Majid Samavatian, Reza Gholamipour, Vahid Samavatian

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This study addresses the role of rejuvenation on the fluctuation of atomic-level stresses and nanoscale topological heterogeneity in ZrCuNiAl bulk metallic glass (BMG). Based on atomic force microscopy (AFM) results, the rejuvenation process leads to an increase in nanoscale spatial heterogeneity manifested by the intensification of the local viscoelastic response of the BMG nanostructure. It means that the rejuvenation process induces more loose-packing structures which behave towards an external load in a viscoelastic way. Hence, it is suggested that the alteration of such heterogeneity may be attributed to the variation of positional atomic rearrangement during the evolution of structural rejuvenation. On the other side, the synchrotron X-ray diffraction (XRD) results indicate that the rejuvenation intensifies the variation of internal stresses at the atomic level. This conclusion unfolds that the increase of atomic-level stresses during rejuvenation induces structural disordering and nanoscale heterogeneity in the amorphous material.

Keywords: bulk metallic glass, heterogeneity, rejuvenation, nanostructure

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Authors: Shivalinge Gowda

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The total mass attenuation coefficients m/r, of some halides such as, NaCl, KCl, CuCl, NaBr, KBr, RbCl, AgCl, NaI, KI, AgBr, CsI, HgCl₂, CdI₂ and HgI₂ were determined at photon energies 279.2, 320.07, 514.0, 661.6, 1115.5, 1173.2 and 1332.5 keV in a well-collimated narrow beam good geometry set-up using a high resolution, hyper pure germanium detector. The mass attenuation coefficients and the effective atomic cross sections are found to be in good agreement with the XCOM values. From these mass attenuation coefficients, the effective atomic cross sections s_a, of the compounds were determined. These effective atomic cross section s_a data so obtained are then used to compute the effective atomic numbers Z_eff. For this, the interpolation of total attenuation cross-sections of photons of energy E in elements of atomic number Z was performed by using the logarithmic regression analysis of the data measured by the authors and reported earlier for the above said energies along with XCOM data for standard energies. The best-fit coefficients in the photon energy range of 250 to 350 keV, 350 to 500 keV, 500 to 700 keV, 700 to 1000 keV and 1000 to 1500 keV by a piecewise interpolation method were then used to find the Z_eff of the compounds with respect to the effective atomic cross section s_a from the relation obtained by piece wise interpolation method. Using these Z_eff values, the electron densities N_el of halides were also determined. The present Z_eff and N_el values of halides are found to be in good agreement with the values calculated from XCOM data and other available published values.

Keywords: mass attenuation coefficient, atomic cross-section, effective atomic number, electron density

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Authors: Yuan Yan

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Interlayer interactions or hybridization in van der Waals (vdW) heterostructures of two-dimensional (2D) materials significantly influence their physical characteristics, including layer-dependent electronic and vibrational structures, magic-angle superconductivity, interlayer antiferromagnetism, and interlayer excitons. These interactions are sensitive to a set of interdependent and externally tunable parameters. To fully exploit the potential of these materials, it is crucial to understand the physical origins of interlayer interaction and hybridization. Traditional theories often attribute these interactions to the sharing of electrons via p orbital lone pairs or π electrons, based on the octet rule, which posits that p electrons are the primary occupants of the outermost atomic shells, except in hydrogen. However, our study challenges this prevailing belief. Through geometry-based analysis, we conducted a high-throughput screening of the Materials Project database and identified 1,623 layered materials. By examining the atomic structure and bonding characteristics of surface atoms, we demonstrate that s-orbital lone pairs can also drive interlayer interactions in two-dimensional materials. Using density functional theory, we further analyzed charge distribution and electronic localization. The crystal field and inert pair effect induce a Stark-like phenomenon, leading to energy level splitting and the formation of directional electron clouds. This allows these electrons to directly participate in the hybridization of interlayer wavefunctions without forming chemical bonds. it findings expand the understanding of interlayer interactions, revealing new mechanisms that govern these properties and providing a theoretical foundation for manipulating interlayer phenomena in 2D materials.

Keywords: interlayer interaction, nanomaterials, 2D materials, van der waals, heterostructures

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Authors: Setareh Shekarsaraei, Marjan Moridi, Nasser L. Hadipour

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In this study, nuclear magnetic resonance spectroscopy and nuclear quadrupole resonance spectroscopy parameters of 14N (Nitrogen in imidazole ring) in N–H…O hydrogen bonding for Histidine hydrochloride monohydrate were calculated via density functional theory. We considered a five-molecule model system of Histidine hydrochloride monohydrate. Also, we examined the trends of environmental effect on hydrogen bonds as well as cooperativity. The functional used in this research is M06-2X which is a good functional and the obtained results have shown good agreement with experimental data. This functional was applied to calculate the NMR and NQR parameters. Some correlations among NBO parameters, NMR, and NQR parameters have been studied which have shown the existence of strong correlations among them. Furthermore, the geometry optimization has been performed using M062X/6-31++G(d,p) method. In addition, in order to study cooperativity and changes in structural parameters, along with increase in cluster size, natural bond orbitals have been employed.

Keywords: hydrogen bonding, density functional theory (DFT), natural bond orbitals (NBO), cooperativity effect

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Authors: Meng-Fei Cheng, Wei Fneg

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New Taiwan high school standards emphasize employing scientific models and modeling practices in physics learning. However, to our knowledge. Few studies address how scientific models and modeling are approached in current science teaching, and they do not examine the views of scientific models portrayed in the textbooks. To explore the views of scientific models and modeling in textbooks, this study investigated the atomic unit in different textbook versions as an example and provided suggestions for modeling curriculum. This study adopted a quantitative analysis of qualitative data in the atomic units of four mainstream version of Taiwan high school physics textbooks. The models were further analyzed using five dimensions of the views of scientific models (nature of models, multiple models, purpose of the models, testing models, and changing models); each dimension had three levels (low, medium, high). Descriptive statistics were employed to compare the frequency of describing the five dimensions of the views of scientific models in the atomic unit to understand the emphasis of the views and to compare the frequency of the eight scientific models’ use to investigate the atomic model that was used most often in the textbooks. Descriptive statistics were further utilized to investigate the average levels of the five dimensions of the views of scientific models to examine whether the textbooks views were close to the scientific view. The average level of the five dimensions of the eight atomic models were also compared to examine whether the views of the eight atomic models were close to the scientific views. The results revealed the following three major findings from the atomic unit. (1) Among the five dimensions of the views of scientific models, the most portrayed dimension was the 'purpose of models,' and the least portrayed dimension was 'multiple models.' The most diverse view was the 'purpose of models,' and the most sophisticated scientific view was the 'nature of models.' The least sophisticated scientific view was 'multiple models.' (2) Among the eight atomic models, the most mentioned model was the atomic nucleus model, and the least mentioned model was the three states of matter. (3) Among the correlations between the five dimensions, the dimension of 'testing models' was highly related to the dimension of 'changing models.' In short, this study examined the views of scientific models based on the atomic units of physics textbooks to identify the emphasized and disregarded views in the textbooks. The findings suggest how future textbooks and curriculum can provide a thorough view of scientific models to enhance students' model-based learning.

Keywords: atomic models, textbooks, science education, scientific model

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Authors: B. K. Kanungo, Monika Thakur, Minati Baral

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8-hydroxyquinoline, (8HQ), experiences a renaissance due to its utility as a building block in metallosupramolecular chemistry and its versatile use of its derivatives in various fields of analytical chemistry, materials science, and pharmaceutics. It forms stable complexes with a variety of metal ions. Assembly of more than one such unit to form a polydentate chelator enhances its coordinating ability and the related properties due to the chelate effect resulting in high stability constant. Keeping in view the above, a nonadentate chelator N-[3,5-bis(8-hydroxyquinoline-2-amido)cyclohexyl]-8-hydroxyquinoline-2-carboxamide, (TACH2OX), containing a central cis,cis-1,3,5-triaminocyclohexane appended to three 8-hydroxyquinoline at 2-position through amide linkage is developed, and its solution thermodynamics, photophysical and Density Functional Theory (DFT) studies were undertaken. The synthesis of TACH2OX was carried out by condensation of cis,cis-1,3,5-triaminocyclohexane, (TACH) with 8‐hydroxyquinoline‐2‐carboxylic acid. The brown colored solid has been fully characterized through melting point, infrared, nuclear magnetic resonance, electrospray ionization mass and electronic spectroscopy. In solution, TACH2OX forms protonated complexes below pH 3.4, which consecutively deprotonates to generate trinegative ion with the rise of pH. Nine protonation constants for the ligand were obtained that ranges between 2.26 to 7.28. The interaction of the chelator with two trivalent metal ion Fe3+ and Al3+ were studied in aqueous solution at 298 K. The metal-ligand formation constants (ML) obtained by potentiometric and spectrophotometric method agree with each other. The protonated and hydrolyzed species were also detected in the system. The in-silico studies of the ligand, as well as the complexes including their protonated and deprotonated species assessed by density functional theory technique, gave an accurate correlation with each observed properties such as the protonation constants, stability constants, infra-red, nmr, electronic absorption and emission spectral bands. The nature of electronic and emission spectral bands in terms of number and type were ascertained from time-dependent density functional theory study and the natural transition orbitals (NTO). The global reactivity indices parameters were used for comparison of the reactivity of the ligand and the complex molecules. The natural bonding orbital (NBO) analysis could successfully describe the structure and bonding of the metal-ligand complexes specifying the percentage of contribution in atomic orbitals in the creation of molecular orbitals. The obtained high value of metal-ligand formation constants indicates that the newly synthesized chelator is a very powerful synthetic chelator. The minimum energy molecular modeling structure of the ligand suggests that the ligand, TACH2OX, in a tripodal fashion firmly coordinates to the metal ion as hexa-coordinated chelate displaying distorted octahedral geometry by binding through three sets of N, O- donor atoms, present in each pendant arm of the central tris-cyclohexaneamine tripod.

Keywords: complexes, DFT, formation constant, TACH2OX

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Authors: Jing Zhao, Yongqing Bai, Qiaofang Shi, Huaihao Zhang

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Advances in software technology enable computational chemistry to be commonly applied in various research fields, especially in pedagogy. Thus, in order to expand and improve experimental instructions of computational chemistry for undergraduates, we designed an introductory experiment—research on acrylamide molecular structure and physicochemical properties. Initially, students construct molecular models of acrylamide and polyacrylamide in Gaussian and Materials Studio software respectively. Then, the infrared spectral data, atomic charge and molecular orbitals of acrylamide as well as solvation effect of polyacrylamide are calculated to predict their physicochemical performance. At last, rheological experiments are used to validate these predictions. Through the combination of molecular simulation (performed on Gaussian, Materials Studio) with experimental verification (rheology experiment), learners have deeply comprehended the chemical nature of acrylamide and polyacrylamide, achieving good learning outcomes.

Keywords: upper-division undergraduate, computer-based learning, laboratory instruction, molecular modeling

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Authors: S. Zhuiykov, Zh. Hai, H. Xu, C. Xue

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Unique and distinctive properties could be obtained on such two-dimensional (2D) semiconductor as tungsten trioxide (WO₃) when the reduction from multi-layer to one fundamental layer thickness takes place. This transition without damaging single-layer on a large spatial resolution remained elusive until the atomic layer deposition (ALD) technique was utilized. Here we report the ALD-enabled atomic-layer-precision development of a single layer WO₃ with thickness of 0.77±0.07 nm on a large spatial resolution by using (^tBuN)₂W(NMe₂)₂ as tungsten precursor and H₂O as oxygen precursor, without affecting the underlying SiO₂/Si substrate. Versatility of ALD is in tuning recipe in order to achieve the complete WO₃ with desired number of WO₃ layers including monolayer. Governed by self-limiting surface reactions, the ALD-enabled approach is versatile, scalable and applicable for a broader range of 2D semiconductors and various device applications.

Keywords: Atomic Layer Deposition (ALD), tungsten oxide, WO₃, two-dimensional semiconductors, single fundamental layer

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Authors: Ali Moafi, Kourosh Kalantarzadeh, Richard Kaner, Parviz Parvin, Ebrahim Asl Soleimani, Dougal McCulloch

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In-situ Raman spectroscopy of flexible graphene-oxide films examined upon exposure to hydrogen gas, air, and synthetic air. The changes in D and G peaks are attributed to defects responding to atomic hydrogen spilled over from the catalytic behavior of Pt nanoparticles distributed all over the film. High-resolution transmission electron microscopy images (HRTEM) as well as electron energy loss spectroscopy (EELS) were carried out to define the density of the samples.

Keywords: in situ Raman Spectroscopy, EELS, TEM, graphene oxide, graphene, atomic hydrogen

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Authors: Jianshu Yang, Delphine Sordes, Marek Kolmer, Christian Joachim

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Nanoelectronics, for example the calculating circuits integrating at molecule scale logic gates, atomic scale circuits, has been constructed and investigated recently. A major challenge is their functional properties characterization because of the connecting problem from atomic scale to micrometer scale. New experimental instruments and new processes have been proposed therefore. To satisfy a precisely measurement at atomic scale and then connecting micrometer scale electrical integration controller, the technique improvement is kept on going. Our new machine, a low temperature high vacuum four scanning tunneling microscope, as a customer required instrument constructed by Omicron GmbH, is expected to be scaling down to atomic scale characterization. Here, we will present our first testified results about the performance of this new instrument. The sample we selected is Au(111) surface. The measurements have been taken at 4.2 K. The atomic resolution surface structure was observed with each of four scanners with noise level better than 3 pm. With a tip-sample distance calibration by I-z spectra, the sample conductance has been derived from its atomic locally I-V spectra. Furthermore, the surface conductance measurement has been performed using two methods, (1) by landing two STM tips on the surface with sample floating; and (2) by sample floating and one of the landed tips turned to be grounding. In addition, single atom manipulation has been achieved with a modified tip design, which is comparable to a conventional LT-STM.

Keywords: low temperature ultra-high vacuum four scanning tunneling microscope, nanoelectronics, point contact, single atom manipulation, tunneling resistance

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Authors: Lukman Andi Priyatna, Vivi Fauzia, Ferry Anggoro Ardy Nugroho

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Zinc oxide (ZnO) based nanostructures are ubiquitous in applications due to their favourable physicochemical properties and ease of fabrication. One widely accessible route to synthesize ZnO nanorods, which show promising performance in e.g. photoelectrochemical water splitting, is hydrothermal growth of ZnO seeds, obtained via an atomic nebulizer. Despite its popularity, study on the impact of the synthesis parameters in atomic nebulizer on the performance of the synthesized ZnO nanostructures is lacking. This study presents an investigation on the impact of the distance between substrates and atomic nebulizer nozzle on the photoelectrochemical water splitting performance of ZnO nanorods. Adjusting such a distance reveals an optimum separation which results in nanostructures with highest absorbance. Such high absorbance translates into improved photoelectrochemistry, as evaluated by higher photocurrent density, from 0.11 mA/cm² to 0.14 mA/cm² and higher Applied Bias Photon-to-Current Efficiency (ABPE) from 0.12% to 0.14%. These results underscore the importance of understanding and optimizing the experimental parameters during ZnO nanostructure synthesis. In a broader context, it advertises the need to carefully assess the corresponding fabrication parameters to optimize the performance of the obtained nanostructures.

Keywords: atomic nebulizer, photocurrent density, photoelectrochemical water splitting, ZnO nanorods

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Authors: Mehdi Shekarzadeh, Pejman Taghipour Birgani

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In this paper, the effect of mass and height of tip on the flexural vibration modes of an atomic force microscope (AFM) rectangular cantilever is analyzed. A closed-form expression for the sensitivity of vibration modes is derived using the relationship between the resonant frequency and contact stiffness of cantilever and sample. Each mode has a different sensitivity to variations in surface stiffness. This sensitivity directly controls the image resolution. It is obtained an AFM cantilever is more sensitive when the mass of tip is lower and the first mode is the most sensitive mode. Also, the effect of changes of tip height on the flexural sensitivity is negligible.

Keywords: atomic force microscope, AFM, vibration analysis, flexural vibration, cantilever

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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 (CEF) spin-orbit coupling, localized states, electron subshell, fine electronic structure

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Authors: Shahin A. Abdel-Naby, Asad T. Hassan, Stuart Loch, Michael Fogle, Negil R. Badnell, Michael S. Pindzola

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Accurate and reliable laboratory astrophysical data for electron-ion recombination are needed for plasma modeling. Dielectronic recombination (DR) rate coefficients are calculated for boron-like nitrogen and oxygen ions using state-of-the-art multi-configuration Breit-Pauli atomic structure AUTOSTRUCTURE collisional package within the generalized collisional-radiative framework. The calculations are performed in intermediate coupling scheme associated with n = 0 (2  2) and n = 1 (2  3) core-excitations. Good agreements are found between the theoretically convoluted rate coefficients and the experimental measurements performed at CRYRING heavy-ion storage ring for both ions. Fitting coefficients for the rate coefficients are produced for these ions in the temperature range q2(102-107) K, where q is the ion charge before recombination.

Keywords: Atomic data, atomic processes, electron-ion collision, plasma

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Authors: Fakhrosadat Sajjadian, Ramin Ghasemi Shayan

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The tumor microenvironment plays an fundamental part in tumor start, movement, metastasis, and treatment resistance. It varies from ordinary tissue in terms of its extracellular network, vascular and lymphatic arrange, as well as physiological conditions. The clinical application of atomic cancer imaging is regularly prevented by the tall commercialization costs of focused on imaging operators as well as the constrained clinical applications and little showcase measure of a few operators. . Since numerous cancer types share comparable characteristics of the tumor microenvironment, the capacity to target these biomarkers has the potential to supply clinically translatable atomic imaging advances for numerous types encompassing cancer and broad clinical applications. Noteworthy advance has been made in focusing on the tumor microenvironment for atomic cancer imaging. In this survey, we summarize the standards and methodologies of later progresses in atomic imaging of the tumor microenvironment, utilizing distinctive imaging modalities for early discovery and conclusion of cancer. To conclude, The tumor microenvironment (TME) encompassing tumor cells could be a profoundly energetic and heterogeneous composition of safe cells, fibroblasts, forerunner cells, endothelial cells, flagging atoms and extracellular network (ECM) components.

Keywords: molecular, imaging, TME, medicine

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Authors: Amna Abdalla Mohammed Khalid, Pietro Parisse, Silvia Onesti, Loredana Casalis

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Basic cellular processes as DNA replication are crucial to cell life. Understanding at the molecular level the mechanisms that govern DNA replication in proliferating cells is fundamental to understand disease connected to genomic instabilities, as a genetic disease and cancer. A key step for DNA replication to take place, is unwinding the DNA double helix and this carried out by proteins called helicases. The archaeal MCM (minichromosome maintenance) complex from Methanothermobacter thermautotrophicus have being studied using Atomic Force Microscopy (AFM), imaging in air and liquid (Physiological environment). The accurate analysis of AFM topographic images allowed to understand the static conformations as well the interaction dynamic of MCM and DNA double helix in the present of ATP.

Keywords: DNA, protein-DNA interaction, MCM (mini chromosome manteinance) complex, atomic force microscopy (AFM)

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Authors: Thomas Bryan, Veton Kepuska, Ivica Kostanic

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A simple adaptive voice activity detector (VAD) is implemented using Gabor and gammatone atomic decomposition of speech for high Gaussian noise environments. Matching pursuit is used for atomic decomposition, and is shown to achieve optimal speech detection capability at high data compression rates for low signal to noise ratios. The most active dictionary elements found by matching pursuit are used for the signal reconstruction so that the algorithm adapts to the individual speakers dominant time-frequency characteristics. Speech has a high peak to average ratio enabling matching pursuit greedy heuristic of highest inner products to isolate high energy speech components in high noise environments. Gabor and gammatone atoms are both investigated with identical logarithmically spaced center frequencies, and similar bandwidths. The algorithm performs equally well for both Gabor and gammatone atoms with no significant statistical differences. The algorithm achieves 70% accuracy at a 0 dB SNR, 90% accuracy at a 5 dB SNR and 98% accuracy at a 20dB SNR using 30dB SNR as a reference for voice activity.

Keywords: atomic decomposition, gabor, gammatone, matching pursuit, voice activity detection

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Authors: Ömer Tamer, Davut Avcı, Yusuf Atalay

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Novel picolinate complex of manganese(II) ion, [Mn(pic)2] [pic: picolinate or 2-pyridinecarboxylate], was prepared and fully characterized by single crystal X-ray structure determination. The manganese(II) complex was characterized by FT-IR, FT-Raman and UV–Vis spectroscopic techniques. The C=O, C=N and C=C stretching vibrations were found to be strong and simultaneously active in IR and spectra. In order to support these experimental techniques, density functional theory (DFT) calculations were performed at Gaussian 09W. Although the supramolecular interactions have some influences on the molecular geometry in solid state phase, the calculated data show that the predicted geometries can reproduce the structural parameters. The molecular modeling and calculations of IR, Raman and UV-vis spectra were performed by using DFT levels. Nonlinear optical (NLO) properties of synthesized complex were evaluated by the determining of dipole moment (µ), polarizability (α) and hyperpolarizability (β). Obtained results demonstrated that the manganese(II) complex is a good candidate for NLO material. Stability of the molecule arising from hyperconjugative interactions and charge delocalization was analyzed using natural bond orbital (NBO) analysis. The highest occupied and the lowest unoccupied molecular orbitals (HOMO and LUMO) which is also known the frontier molecular orbitals were simulated, and obtained energy gap confirmed that charge transfer occurs within manganese(II) complex. Molecular electrostatic potential (MEP) for synthesized manganese(II) complex displays the electrophilic and nucleophilic regions. From MEP, the the most negative region is located over carboxyl O atoms while positive region is located over H atoms.

Keywords: DFT, picolinate, IR, Raman, nonlinear optic

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Authors: Hatem Diaf, Patrice Melinon, Antonio Pereira, Bernard Moine, Nicholas Blanchard, Florent Bourquard, Florence Garrelie, Christophe Donnet

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Glassy carbon exhibits excellent biological compatibility with live tissues meaning it has high potential for applications in life science. Moreover, glassy carbon has interesting properties including 'high temperature resistance', hardness, low density, low electrical resistance, low friction, and low thermal resistance. The structure of glassy carbon has long been a subject of debate. It is now admitted that glassy carbon is 100% sp2. This term is a little bit confusing as long sp2 hybridization defined from quantum chemistry is related to both properties: threefold configuration and pi bonding (parallel pz orbitals). Using plasma laser deposition of carbon clusters combined with pulsed nano/femto laser annealing, we are able to synthesize thin films of glassy carbon of good quality (probed by G band/ D disorder band ratio in Raman spectroscopy) without thermal post annealing. A careful inspecting of Raman signal, plasmon losses and structure performed by HRTEM (High Resolution Transmission Electron Microscopy) reveals that both properties (threefold and pi orbitals) cannot coexist together. The structure of the films is compared to models including schwarzites based from negatively curved surfaces at the opposite of onions or fullerene-like structures with positively curved surfaces. This study shows that a huge collection of porous carbon named vitreous carbon with different structures can coexist.

Keywords: glassy carbon, cluster deposition, coating, electronic structure

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Authors: M. Kharazmi, M. Zakeri, M. Packirisamy, J. Faraji

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Micro/Nanorobotics or manipulation of nanoparticles by Atomic Force Microscopic (AFM) is one of the most important solutions for controlling the movement of atoms, particles and micro/nano metrics components and assembling of them to design micro/nano-meter tools. Accurate modelling of manipulation requires identification of forces and mechanical knowledge in the Nanoscale which are different from macro world. Due to the importance of the adhesion forces and the interaction of surfaces at the nanoscale several friction models were presented. In this research, friction and normal forces that are applied on the AFM by using of the dynamic bending-torsion model of AFM are obtained based on Hurtado-Kim friction model (HK), Johnson-Kendall-Robert contact model (JKR) and Greenwood-Williamson roughness model (GW). Finally, the effect of standard deviation of asperities height on the normal load, friction force and friction coefficient are studied.

Keywords: atomic force microscopy, contact model, friction coefficient, Greenwood-Williamson model

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Authors: Debesh R. Roy

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The fundamental issue in understanding the origin and growth mechanism of nanomaterials, from a fundamental unit is a big challenging problem to the scientists. Recently, an immense attention is generated to the researchers for prediction of exceptionally stable atomic cluster units as the building units for future smart materials. The present study is a systematic investigation on the stability and electronic properties of a series of bimetallic (semiconductor-alkaline earth) clusters, viz., BxMg3 (x=1-5) is performed, in search for exceptional and/ or unusual stable motifs. A very popular hybrid exchange-correlation functional, B3LYP as proposed by A. D. Becke along with a higher basis set, viz., 6-31+G[d,p] is employed for this purpose under the density functional formalism. The magic stability among the concerned clusters is explained using the jellium model. It is evident from the present study that the magic stability of B4Mg3 cluster arises due to the jellium shell closure.

Keywords: atomic clusters, density functional theory, jellium model, magic clusters, smart nanomaterials

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Authors: Thomas Bryan, Veton Kepuska, Ivica Kostanic

Abstract:

Speaker recognition is performed in high Additive White Gaussian Noise (AWGN) environments using principals of Computational Auditory Scene Analysis (CASA). CASA methods often classify sounds from images in the time-frequency (T-F) plane using spectrograms or cochleargrams as the image. In this paper atomic decomposition implemented by matching pursuit performs a transform from time series speech signals to the T-F plane. The atomic decomposition creates a sparsely populated T-F vector in “weight space” where each populated T-F position contains an amplitude weight. The weight space vector along with the atomic dictionary represents a denoised, compressed version of the original signal. The arraignment or of the atomic indices in the T-F vector are used for classification. Unsupervised feature learning implemented by a sparse autoencoder learns a single dictionary of basis features from a collection of envelope samples from all speakers. The approach is demonstrated using pairs of speakers from the TIMIT data set. Pairs of speakers are selected randomly from a single district. Each speak has 10 sentences. Two are used for training and 8 for testing. Atomic index probabilities are created for each training sentence and also for each test sentence. Classification is performed by finding the lowest Euclidean distance between then probabilities from the training sentences and the test sentences. Training is done at a 30dB Signal-to-Noise Ratio (SNR). Testing is performed at SNR’s of 0 dB, 5 dB, 10 dB and 30dB. The algorithm has a baseline classification accuracy of ~93% averaged over 10 pairs of speakers from the TIMIT data set. The baseline accuracy is attributable to short sequences of training and test data as well as the overall simplicity of the classification algorithm. The accuracy is not affected by AWGN and produces ~93% accuracy at 0dB SNR.

Keywords: time-frequency plane, atomic decomposition, envelope sampling, Gabor atoms, matching pursuit, sparse dictionary learning, sparse autoencoder

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Authors: Ali A. Mutair

Abstract:

The concentration levels of iron (Fe), copper (Cu), zinc (Zn), cadmium (Cd) and lead (Pb) in different cigarette brands commonly produced and sold in Yemen were determined. Convenient sample treatment for cigarette tobacco of freshly opened packs was achieved by a sample preparation method based on dry digestion, and the concentrations of the analysed metals were measured by Flame Atomic Absorption Spectrometry (FAAS). The mean values obtained for Fe, Zn, Cu, Cd, and Pb in different Yemeni cigarette tobacco were 311, 52.2, 10.11, 1.71 and 4.06 µg/g dry weight, respectively. There is no more significant difference among cigarette brands tested. It was found that Fe was at the highest concentration, followed by Zn, Cu, Pb and Cd. The average relative standard deviation (RSD) ranged from 1.77% to 19.34%. The accuracy and precision of the results were checked by blank and recovery tests. The results show that Yemeni cigarettes contain heavy metal concentration levels that are similar to those in foreign cigarette brands reported by other studies in the worldwide.

Keywords: iron, zinc, copper, lead, cadmium, tobacco, Yemeni cigarette brands, atomic absorption spectrometry

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Authors: A. Kellou, L. Rouaiguia, L. Rabahi

Abstract:

In the present work, the atomic hydrogen absorption trend in the GdNi5 and GdNi4Cu rare earth compounds within the hexagonal CaCu5 type of crystal structure (space group P6/mmm) is investigated. The density functional theory (DFT) combined with the generalized gradient approximation (GGA) is used to study the site preference of atomic hydrogen at 0K. The octahedral and tetrahedral interstitial sites are considered. The formation energies and structural properties are determined in order to evaluate hydrogen effects on the stability of the studied compounds. The energetic diagram of hydrogen storage is established and compared in GdNi5 and GdNi4Cu. The magnetic properties of the selected compounds are determined using spin polarized calculations. The obtained results are discussed with and without hydrogen addition taking into account available theoretical and experimental results.

Keywords: density functional theory, hydrogen storage, rare earth compounds, structural and magnetic properties

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Authors: S. Krustev, V. Angelova, P. Zaprjanova

Abstract:

Selenium (Se) is an essential micro-nutrient for human and animals but it is highly toxic. Its organic compounds play an important role in biochemistry and nutrition of the cells. Concentration levels of this element in the different regions of the world vary considerably. This study aimed to compare the availability and levels of the Se in some rural areas of the Balkan Peninsula and relationship with the concentrations of other trace elements. For this purpose soil samples and wheat grains from different regions of Bulgaria, Serbia, Nord Macedonia, Romania, and Greece situated far from large industrial centers have been analyzed. The main methods for their determination were the atomic spectral techniques – atomic absorption and plasma atomic emission. As a result of this study, data on microelements levels from the main grain-producing regions of the Balkan Peninsula were determined and systematized. The presented results confirm the low levels of Se in this region: 0.222– 0.962 mg.kg^-1 in soils and 0.001 - 0.005 mg.kg^-1 in wheat grains and require measures to offset the effect of this deficiency.

Keywords: agricultural soils, balkan peninsula, rural areas, selenium

Procedia PDF Downloads 132

Authors: Yi Zhang, Yuan Tian, Jiehua Chen, Sihong Gu

Abstract:

Chip-scale spin-exchange relaxation free (SERF) atomic magnetometer makes use of millimeter-scale vapor cells micro-fabricated by Micro-electromechanical Systems (MEMS) technique and SERF mechanism, resulting in the characteristics of high spatial resolution and high sensitivity. It is useful for biomagnetic imaging including magnetoencephalography and magnetocardiography. In a prevailing scheme, circularly polarized on-resonance laser beam is adapted for both pumping and probing the atomic polarization. And the magnetic-field-sensitive signal is extracted by transmission laser intensity enhancement as a result of atomic polarization increase on zero field level crossing resonance. The scheme is very suitable for integration, however, the laser amplitude modulation (AM) noise and laser frequency modulation to amplitude modulation (FM-AM) noise is superimposed on the photon shot noise reducing the signal to noise ratio (SNR). To suppress AM and FM-AM noise the paper puts forward a novel scheme which adopts circularly polarized on-resonance light pumping and linearly polarized frequency-detuning laser probing. The transmission beam is divided into transmission and reflection beams by a polarization analyzer, the angle between the analyzer's transmission polarization axis and frequency-detuning laser polarization direction is set to 45°. The magnetic-field-sensitive signal is extracted by polarization rotation enhancement of frequency-detuning laser which induces two beams intensity difference increase as the atomic polarization increases. Therefore, AM and FM-AM noise in two beams are common-mode and can be almost entirely canceled by differential detection. We have carried out an experiment to study our scheme. The experiment reveals that the noise in the differential signal is obviously smaller than that in each beam. The scheme is promising to be applied for developing more sensitive chip-scale magnetometer.

Keywords: atomic magnetometer, chip scale, differential detection, spin-exchange relaxation free

Procedia PDF Downloads 170