WorldWideScience

Sample records for orbital based molecular

  1. Molecular Orbital Based Design Guidelines for Hypergolic Energetic Ionic Liquids

    Science.gov (United States)

    2015-01-01

    should be synthesized to further validate our probabilistic approach for identifying EIL hypergols. DMP is one anion that has a lower “energy gap”, but...orbitals (HOMO) of the anions for a series of ionic liquids and the lowest occupied molecular orbital (LUMO) of HNO3, and variation in the computed...relative heats of formation, DHf, of these anions to develop correlations to predict hypergol activity between an ionic liquid fuel and nitric acid as

  2. Chaos Behaviour of Molecular Orbit

    Institute of Scientific and Technical Information of China (English)

    LIU Shu-Tang; SUN Fu-Yan; SHEN Shu-Lan

    2007-01-01

    Based on H(u)ckel's molecular orbit theory,the chaos and;bifurcation behaviour of a molecular orbit modelled by a nonlinear dynamic system is studied.The relationship between molecular orbit and its energy level in the nonlinear dynamic system is obtained.

  3. Ab initio Path Integral Molecular Dynamics Based on Fragment Molecular Orbital Method

    Science.gov (United States)

    Fujita, Takatoshi; Watanabe, Hirofumi; Tanaka, Shigenori

    2009-10-01

    We have developed an ab initio path integral molecular dynamics method based on the fragment molecular orbital method. This “FMO-PIMD” method can treat both nuclei and electrons quantum mechanically, and is useful to simulate large hydrogen-bonded systems with high accuracy. After a benchmark calculation for water monomer, water trimer and glycine pentamer have been studied using the FMO-PIMD method to investigate nuclear quantum effects on structure and molecular interactions. The applicability of the present approach is demonstrated through a number of test calculations.

  4. Graph of atomic orbitals and the molecular structure-descriptors based on it

    Directory of Open Access Journals (Sweden)

    ANDREY A. TOROPOV

    2005-04-01

    Full Text Available The graph of atomic orbitals (GAO is a novel type of molecular graph, recently proposed by one of the authors. Various molecular structure-descriptors computed for GAO are compared with their analogs computed for ordinary molecular graphs. The quality of these structure-descriptors was tested for correlation with the normal boiling points of alkanes and cycloalkanes. In all the studied cases, the results based on GAO are similar to, and usually slightly better than, those obtained by means of ordinary molecular graps.

  5. Diffractive molecular-orbital tomography

    Science.gov (United States)

    Zhai, Chunyang; Zhu, Xiaosong; Lan, Pengfei; Wang, Feng; He, Lixin; Shi, Wenjing; Li, Yang; Li, Min; Zhang, Qingbin; Lu, Peixiang

    2017-03-01

    High-order-harmonic generation in the interaction of femtosecond lasers with atoms and molecules opens the path to molecular-orbital tomography and to probe the electronic dynamics with attosecond-Ångström resolutions. Molecular-orbital tomography requires both the amplitude and phase of the high-order harmonics. Yet the measurement of phases requires sophisticated techniques and represents formidable challenges at present. Here we report a scheme, called diffractive molecular-orbital tomography, to retrieve the molecular orbital solely from the amplitude of high-order harmonics without measuring any phase information. We have applied this method to image the molecular orbitals of N2, CO2, and C2H2 . The retrieved orbital is further improved by taking account the correction of Coulomb potential. The diffractive molecular-orbital tomography scheme, removing the roadblock of phase measurement, significantly simplifies the molecular-orbital tomography procedure and paves an efficient and robust way to the imaging of more complex molecules.

  6. Molecular integrals for exponential-type orbitals using hyperspherical harmonics

    DEFF Research Database (Denmark)

    Avery, James Emil; Avery, John Scales

    2015-01-01

    Exponential-type orbitals are better suited to calculations of molecular electronic structure than are Gaussians, since ETO's can accurately represent the behavior of molecular orbitals near to atomic nuclei, as well as their long-distance exponential decay. Orbitals based on Gaussians fail in bo...

  7. A third-generation density-functional-theory-based method for calculating canonical molecular orbitals of large molecules.

    Science.gov (United States)

    Hirano, Toshiyuki; Sato, Fumitoshi

    2014-07-28

    We used grid-free modified Cholesky decomposition (CD) to develop a density-functional-theory (DFT)-based method for calculating the canonical molecular orbitals (CMOs) of large molecules. Our method can be used to calculate standard CMOs, analytically compute exchange-correlation terms, and maximise the capacity of next-generation supercomputers. Cholesky vectors were first analytically downscaled using low-rank pivoted CD and CD with adaptive metric (CDAM). The obtained Cholesky vectors were distributed and stored on each computer node in a parallel computer, and the Coulomb, Fock exchange, and pure exchange-correlation terms were calculated by multiplying the Cholesky vectors without evaluating molecular integrals in self-consistent field iterations. Our method enables DFT and massively distributed memory parallel computers to be used in order to very efficiently calculate the CMOs of large molecules.

  8. An energy decomposition analysis for second-order Møller–Plesset perturbation theory based on absolutely localized molecular orbitals

    Energy Technology Data Exchange (ETDEWEB)

    Thirman, Jonathan, E-mail: thirman@berkeley.edu; Head-Gordon, Martin, E-mail: mhg@cchem.berkeley.edu [Department of Chemistry, Kenneth S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, Berkeley, California 94720 (United States)

    2015-08-28

    An energy decomposition analysis (EDA) of intermolecular interactions is proposed for second-order Møller–Plesset perturbation theory (MP2) based on absolutely localized molecular orbitals (ALMOs), as an extension to a previous ALMO-based EDA for self-consistent field methods. It decomposes the canonical MP2 binding energy by dividing the double excitations that contribute to the MP2 wave function into classes based on how the excitations involve different molecules. The MP2 contribution to the binding energy is decomposed into four components: frozen interaction, polarization, charge transfer, and dispersion. Charge transfer is defined by excitations that change the number of electrons on a molecule, dispersion by intermolecular excitations that do not transfer charge, and polarization and frozen interactions by intra-molecular excitations. The final two are separated by evaluations of the frozen, isolated wave functions in the presence of the other molecules, with adjustments for orbital response. Unlike previous EDAs for electron correlation methods, this one includes components for the electrostatics, which is vital as adjustment to the electrostatic behavior of the system is in some cases the dominant effect of the treatment of electron correlation. The proposed EDA is then applied to a variety of different systems to demonstrate that all proposed components behave correctly. This includes systems with one molecule and an external electric perturbation to test the separation between polarization and frozen interactions and various bimolecular systems in the equilibrium range and beyond to test the rest of the EDA. We find that it performs well on these tests. We then apply the EDA to a halogen bonded system to investigate the nature of the halogen bond.

  9. Molecular diagnosis of orbital inflammatory disease.

    Science.gov (United States)

    Rosenbaum, James T; Choi, Dongseok; Wilson, David J; Grossniklaus, Hans E; Sibley, Cailin H; Harrington, Christina A; Planck, Stephen R

    2015-04-01

    Orbital inflammatory diseases include thyroid eye disease (TED), granulomatosis with polyangiitis (GPA), sarcoidosis, and nonspecific orbital inflammation (NSOI). Histopathological diagnosis usually relies on the clinical context and is not always definitive. Gene expression profiling provides diagnostic and therapeutic information in several malignancies, but its role in evaluating nonmalignant disease is relatively untested. We hypothesized that gene expression profiling could provide diagnostic information for NSOI. We collected formalin-fixed, paraffin-embedded orbital biopsies from 10 institutions and 83 subjects including 25 with thyroid eye disease, 25 nonspecific orbital inflammation, 20 healthy controls, 6 with granulomatosis with polyangiitis, and 7 with sarcoidosis. Tissues were divided into discovery and validation sets. Gene expression was quantified using Affymetrix U133 Plus 2.0 microarrays. A random forest statistical algorithm based on data from 39 probe sets identified controls, GPA, or TED with an average accuracy of 76% (p=0.02). Random forest analysis indicated that 52% of tissues from patients with nonspecific inflammation were consistent with a diagnosis of GPA. Molecular diagnosis by gene expression profiling will augment clinical data and histopathology in differentiating forms of orbital inflammatory disease.

  10. Molecular orbital imaging for partially aligned molecules

    Science.gov (United States)

    Qin, Meiyan; Zhu, Xiaosong

    2017-01-01

    We investigate molecular orbital reconstruction using high-order harmonic emissions from partially aligned molecular ensembles. By carrying out the reconstruction procedure using the harmonic sampling with or without the spectral minimum, the roles of the harmonic phase and amplitude modulation due to the partial alignment can be separately studied. It is found that with the prior knowledge of the orbital symmetry, the reconstructed result is very sensitive to the modulation of the harmonic phase for the πg orbital, while in the case of σg orbital, the reconstructed result is mainly determined by the harmonic amplitude. These results can provide an important reference for the future experiment of molecular orbital imaging.

  11. A Simple Huckel Molecular Orbital Plotter

    Science.gov (United States)

    Ramakrishnan, Raghunathan

    2013-01-01

    A program is described and presented to readily plot the molecular orbitals from a Huckel calculation. The main features of the program and the scope of its applicability are discussed through some example organic molecules. (Contains 2 figures.)

  12. Analytic second derivative of the energy for density functional theory based on the three-body fragment molecular orbital method

    Energy Technology Data Exchange (ETDEWEB)

    Nakata, Hiroya, E-mail: nakata.h.ab@m.titech.ac.jp [Center for Biological Resources and Informatics, Tokyo Institute of Technology, B-62 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501 (Japan); RIKEN, Research Cluster for Innovation, Nakamura Lab, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Japan Society for the Promotion of Science, Kojimachi Business Center Building, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083 (Japan); Fedorov, Dmitri G., E-mail: d.g.fedorov@aist.go.jp [NRI, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568 (Japan); Zahariev, Federico; Schmidt, Michael W.; Gordon, Mark S. [Department of Chemistry and Ames Laboratory, US-DOE, Iowa State University, Ames, Iowa 50011 (United States); Kitaura, Kazuo [Graduate School of System Informatics, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501 (Japan); Nakamura, Shinichiro [RIKEN, Research Cluster for Innovation, Nakamura Lab, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan)

    2015-03-28

    Analytic second derivatives of the energy with respect to nuclear coordinates have been developed for spin restricted density functional theory (DFT) based on the fragment molecular orbital method (FMO). The derivations were carried out for the three-body expansion (FMO3), and the two-body expressions can be obtained by neglecting the three-body corrections. Also, the restricted Hartree-Fock (RHF) Hessian for FMO3 can be obtained by neglecting the density-functional related terms. In both the FMO-RHF and FMO-DFT Hessians, certain terms with small magnitudes are neglected for computational efficiency. The accuracy of the FMO-DFT Hessian in terms of the Gibbs free energy is evaluated for a set of polypeptides and water clusters and found to be within 1 kcal/mol of the corresponding full (non-fragmented) ab initio calculation. The FMO-DFT method is also applied to transition states in S{sub N}2 reactions and for the computation of the IR and Raman spectra of a small Trp-cage protein (PDB: 1L2Y). Some computational timing analysis is also presented.

  13. Energy Decomposition Analysis Based on Absolutely Localized Molecular Orbitals for Large-Scale Density Functional Theory Calculations in Drug Design.

    Science.gov (United States)

    Phipps, M J S; Fox, T; Tautermann, C S; Skylaris, C-K

    2016-07-12

    We report the development and implementation of an energy decomposition analysis (EDA) scheme in the ONETEP linear-scaling electronic structure package. Our approach is hybrid as it combines the localized molecular orbital EDA (Su, P.; Li, H. J. Chem. Phys., 2009, 131, 014102) and the absolutely localized molecular orbital EDA (Khaliullin, R. Z.; et al. J. Phys. Chem. A, 2007, 111, 8753-8765) to partition the intermolecular interaction energy into chemically distinct components (electrostatic, exchange, correlation, Pauli repulsion, polarization, and charge transfer). Limitations shared in EDA approaches such as the issue of basis set dependence in polarization and charge transfer are discussed, and a remedy to this problem is proposed that exploits the strictly localized property of the ONETEP orbitals. Our method is validated on a range of complexes with interactions relevant to drug design. We demonstrate the capabilities for large-scale calculations with our approach on complexes of thrombin with an inhibitor comprised of up to 4975 atoms. Given the capability of ONETEP for large-scale calculations, such as on entire proteins, we expect that our EDA scheme can be applied in a large range of biomolecular problems, especially in the context of drug design.

  14. Apparent Reversal of Molecular Orbitals Reveals Entanglement

    Science.gov (United States)

    Yu, Ping; Kocić, Nemanja; Repp, Jascha; Siegert, Benjamin; Donarini, Andrea

    2017-08-01

    The frontier orbital sequence of individual dicyanovinyl-substituted oligothiophene molecules is studied by means of scanning tunneling microscopy. On NaCl /Cu (111 ) , the molecules are neutral, and the two lowest unoccupied molecular states are observed in the expected order of increasing energy. On NaCl /Cu (311 ) , where the molecules are negatively charged, the sequence of two observed molecular orbitals is reversed, such that the one with one more nodal plane appears lower in energy. These experimental results, in open contradiction with a single-particle interpretation, are explained by a many-body theory predicting a strongly entangled doubly charged ground state.

  15. Molecular orbital calculations using chemical graph theory

    CERN Document Server

    Dias, Jerry Ray

    1993-01-01

    Professor John D. Roberts published a highly readable book on Molecular Orbital Calculations directed toward chemists in 1962. That timely book is the model for this book. The audience this book is directed toward are senior undergraduate and beginning graduate students as well as practicing bench chemists who have a desire to develop conceptual tools for understanding chemical phenomena. Although, ab initio and more advanced semi-empirical MO methods are regarded as being more reliable than HMO in an absolute sense, there is good evidence that HMO provides reliable relative answers particularly when comparing related molecular species. Thus, HMO can be used to rationalize electronic structure in 1t-systems, aromaticity, and the shape use HMO to gain insight of simple molecular orbitals. Experimentalists still into subtle electronic interactions for interpretation of UV and photoelectron spectra. Herein, it will be shown that one can use graph theory to streamline their HMO computational efforts and to arrive...

  16. Molecular orbitals for properties and spectroscopies

    Energy Technology Data Exchange (ETDEWEB)

    Robert, Vincent [Laboratoire de Chimie Quantique, Institut de Chimie, Université de Strasbourg, 1 rue Blaise Pascal 67000 Strasbourg-France (France); Domingo, Alex [Quantum Chemistry and Physical Chemistry Celestijnenlaan 200f, 3001 Heverlee - Belgium (Belgium); Braunstein, Pierre; Danopoulos, Andreas; Monakhov, Kirill [Laboratoire de Chimie de Coordination, Institut de Chimie, Université de Strasbourg, 4 rue Blaise Pascal 67081 Strasbourg-France (France)

    2015-12-31

    The description and clarification of spectroscopies and properties goes through ab initio calculations. Wave function based calculations (CASSCF/CASPT2) are particularly appealing since they offer spectroscopic accuracy and means of interpretation. we performed such calculations to elucidate the origin of unusual structural changes and intramolecular electron transfer phenomenon. Based on optimized molecular orbitals and a reading of the multireference wave function, it is suggested that intimate interactions are likely to considerably modify the standard pictures. A so-called PIMA (polarization-induced metalâĹŠarene) interaction similar to the more familiar anion-π interaction is responsible for a significant deviation from sp{sup 3} geometry and an energetic stabilization of 50 kJ/mol in Cr(II) benzyl organometallic complexes. In a similar fashion, it is proposed that the energetic profile of the IVCT (inter valence charge transfer) exhibits strong similarities to the Marcus’ theory, suggesting a response behaviour of the ensemble of electrons as electron transfer occurs in Fe{sup 2+}/Fe{sup 3+} bimetallic compound. The electronic reorganization induced by the IVCT process accounts for 11.8 eV, a very large effect that reduces the transfer energy down to 0.89 eV, in very good agreement with experiments.

  17. Trimer effects in fragment molecular orbital-linear combination of molecular orbitals calculation of one-electron orbitals for biomolecules.

    Science.gov (United States)

    Kobori, Tomoki; Sodeyama, Keitaro; Otsuka, Takao; Tateyama, Yoshitaka; Tsuneyuki, Shinji

    2013-09-07

    The fragment molecular orbital (FMO)-linear combination of molecular orbitals (LCMO) method incorporates as an efficient post-process calculation of one-electron orbitals of the whole system after the FMO total energy calculation. A straightforward way to increase the accuracy is inclusion of the trimer effect. Here, we derive a comprehensive formulation called the FMO3-LCMO method. To keep the computational costs of the trimer term low enough, we use a matrix-size reduction technique. We evaluated the accuracy and efficiency of the FMO3-LCMO scheme in model biological systems (alanine oligomer and chignolin). The results show that delocalized electronic orbitals with covalent and hydrogen bonds are better described at the trimer level, and the FMO3-LCMO method is applicable to quantitative evaluations of a wide range of frontier orbitals in large biosystems.

  18. Alpha cluster states and molecular orbitals in sd-shell nuclei

    Energy Technology Data Exchange (ETDEWEB)

    Kimura, M. [Creative Research Institution Sousei Research Department, Hokkaido University, Sapporo 001-0021 (Japan); Furutachi, N. [Meme Media Laboratory, Hokkaido University, Sapporo 060-8628 (Japan); Kanada-En' yo, Y. [Yukawa Institute for Theoretical Physics, Kyoto University, Kyoto 606-8502 (Japan)

    2010-03-01

    The alpha-clustering and molecular-orbitals of {sup 22}Ne and F isotopes are investigated based on antisymmetrized molecular dynamics (AMD). The observed candidates for the alpha cluster state of {sup 22}Ne are understood as the molecular-orbital states and alpha+{sup 18}O di-nuclei states. The presence of the molecular-orbital states in the O and F isotopes and the drastic reduction of their excitation energy near the neutron-drip line are predicted.

  19. Unrestricted density functional theory based on the fragment molecular orbital method for the ground and excited state calculations of large systems

    Energy Technology Data Exchange (ETDEWEB)

    Nakata, Hiroya, E-mail: nakata.h.ab@m.titech.ac.jp [Center for Biological Resources and Informatics, Tokyo Institute of Technology, B-62 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501 (Japan); RIKEN, Research Cluster for Innovation, Nakamura Lab, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Fedorov, Dmitri G. [NRI, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568 (Japan); Yokojima, Satoshi [RIKEN, Research Cluster for Innovation, Nakamura Lab, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Tokyo University of Pharmacy and Life Sciences, 1423-1 Horinouchi, Hachioji-shi, Tokyo 192-0392 (Japan); Kitaura, Kazuo [Graduate School of System Informatics, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501 (Japan); Sakurai, Minoru [Center for Biological Resources and Informatics, Tokyo Institute of Technology, B-62 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501 (Japan); Nakamura, Shinichiro [RIKEN, Research Cluster for Innovation, Nakamura Lab, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan)

    2014-04-14

    We extended the fragment molecular orbital (FMO) method interfaced with density functional theory (DFT) into spin unrestricted formalism (UDFT) and developed energy gradients for the ground state and single point excited state energies based on time-dependent DFT. The accuracy of FMO is evaluated in comparison to the full calculations without fragmentation. Electronic excitations in solvated organic radicals and in the blue copper protein, plastocyanin (PDB code: 1BXV), are reported. The contributions of solvent molecules to the electronic excitations are analyzed in terms of the fragment polarization and quantum effects such as interfragment charge transfer.

  20. Dissipative particle dynamics (DPD) simulations with fragment molecular orbital (FMO) based effective parameters for 1-Palmitoyl-2-oleoyl phosphatidyl choline (POPC) membrane

    Science.gov (United States)

    Doi, Hideo; Okuwaki, Koji; Mochizuki, Yuji; Ozawa, Taku; Yasuoka, Kenji

    2017-09-01

    In dissipative particle dynamics (DPD) simulations, it is necessary to use the so-called χ parameter set that express the effective interactions between particles. Recently, we have developed a new scheme to evaluate the χ parameters in a non-empirical way through a series of fragment molecular orbital (FMO) calculations. As a challenging test, we have performed the DPD simulations using the FMO-based χ parameters for a mixture of 1-Palmitoyl-2-oleoyl phosphatidyl choline (POPC) and water. The structures of both membrane and vesicle were formed successfully. The calculated structural parameters of membrane were in good agreement with experimental results.

  1. Development of calculation and analysis methods for the dynamic first hyperpolarizability based on the ab initio molecular orbital-quantum master equation method.

    Science.gov (United States)

    Kishi, Ryohei; Fujii, Hiroaki; Kishimoto, Shingo; Murata, Yusuke; Ito, Soichi; Okuno, Katsuki; Shigeta, Yasuteru; Nakano, Masayoshi

    2012-05-03

    We develop novel calculation and analysis methods for the dynamic first hyperpolarizabilities β [the second-order nonlinear optical (NLO) properties at the molecular level] in the second-harmonic generation based on the quantum master equation method combined with the ab initio molecular orbital (MO) configuration interaction method. As examples, we have evaluated off-resonant dynamic β values of donor (NH(2))- and/or acceptor (NO(2))-substituted benzenes using these methods, which are shown to reproduce those by the conventional summation-over-states method well. The spatial contributions of electrons to the dynamic β of these systems are also analyzed using the dynamic β density and its partition into the MO contributions. The present results demonstrate the advantage of these methods in unraveling the mechanism of dynamic NLO properties and in building the structure-dynamic NLO property relationships of real molecules.

  2. Inversion of Strong Field Photoelectron Spectra for Molecular Orbital Imaging

    CERN Document Server

    Puthumpally-Joseph, R; Peters, M; Nguyen-Dang, T T; Atabek, O; Charron, E

    2016-01-01

    Imaging structures at the molecular level is a fast developing interdisciplinary research field that spans across the boundaries of physics and chemistry. High spatial resolution images of molecules can be obtained with photons or ultrafast electrons. In addition, images of valence molecular orbitals can be extracted via tomographic techniques based on the coherent XUV radiation emitted by a molecular gas exposed to an intense ultra-short infrared laser pulse. In this paper, we demonstrate that similar information can be obtained by inverting energy resolved photoelectron spectra using a simplified analytical model.

  3. Polarized Molecular Orbital Model Chemistry. II. The PMO Method.

    Science.gov (United States)

    Zhang, Peng; Fiedler, Luke; Leverentz, Hannah R; Truhlar, Donald G; Gao, Jiali

    2011-04-12

    We present a new semiempirical molecular orbital method based on neglect of diatomic differential overlap. This method differs from previous NDDO-based methods in that we include p orbitals on hydrogen atoms to provide a more realistic modeling of polarizability. As in AM1-D and PM3-D, we also include damped dispersion. The formalism is based on the original MNDO one, but in the process of parameterization we make some specific changes to some of the functional forms. The present article is a demonstration of the capability of the new approach, and it presents a successful parametrization for compounds composed only of hydrogen and oxygen atoms, including the important case of water clusters.

  4. Molecular orbital theory of ballistic electron transport through molecules

    Science.gov (United States)

    Ernzerhof, Matthias; Rocheleau, Philippe; Goyer, Francois

    2009-03-01

    Electron transport through molecules occurs, for instance, in STM imaging and in conductance measurements on molecular electronic devices (MEDs). To model these phenomena, we use a non-Hermitian model Hamiltonian [1] for the description of open systems that exchange current density with their environment. We derive qualitative, molecular-orbital-based rules relating molecular structure and conductance. We show how side groups attached to molecular conductors [2] can completely suppress the conductance. We discuss interference effects in aromatic molecules [3] that can also inhibit electron transport. Rules are developed [1] for the prediction of Fano resonances. All these phenomena are explained with a molecular orbital theory [1,4] for molecules attached to macroscopic reservoirs. [1] F. Goyer, M. Ernzerhof, and M. Zhuang, JCP 126, 144104 (2007); M. Ernzerhof, JCP 127, 204709 (2007). [2] M. Ernzerhof, M. Zhuang, and P. Rocheleau, JCP 123, 134704 (2005); G. C. Solomon, D Q. Andrews, R P. Van Duyne, and M A. Ratner, JACS 130, 7788 (2008). [3] M. Ernzerhof, H. Bahmann, F. Goyer, M. Zhuang, and P. Rocheleau, JCTC 2, 1291 (2006); G. C. Solomon, D. Q. Andrews, R. P. Van Duyne, and M. A. Ratner, JCP 129, 054701 (2008). [4] B.T. Pickup, P.W. Fowler, CPL 459, 198 (2008); P. Rocheleau and M. Ernzerhof, JCP, submitted.

  5. Three- and four-body corrected fragment molecular orbital calculations with a novel subdividing fragmentation method applicable to structure-based drug design.

    Science.gov (United States)

    Watanabe, Chiduru; Fukuzawa, Kaori; Okiyama, Yoshio; Tsukamoto, Takayuki; Kato, Akifumi; Tanaka, Shigenori; Mochizuki, Yuji; Nakano, Tatsuya

    2013-04-01

    We develop an inter-fragment interaction energy (IFIE) analysis based on the three- and four-body corrected fragment molecular orbital (FMO3 and FMO4) method to evaluate the interactions of functional group units in structure-based drug design context. The novel subdividing fragmentation method for a ligand (in units of their functional groups) and amino acid residues (in units of their main and side chains) enables us to understand the ligand-binding mechanism in more detail without sacrificing chemical accuracy of the total energy and IFIEs by using the FMO4 method. We perform FMO4 calculations with the second order Møller-Plesset perturbation theory for an estrogen receptor (ER) and the 17β-estradiol (EST) complex using the proposed fragmentation method and assess the interaction for each ligand-binding site by the FMO4-IFIE analysis. When the steroidal EST is divided into two functional units including "A ring" and "D ring", respectively, the FMO4-IFIE analysis reveals their binding affinity with surrounding fragments of the amino acid residues; the "A ring" of EST has polarization interaction with the main chain of Thr347 and two hydrogen bonds with the side chains of Glu353 and Arg394; the "D ring" of EST has a hydrogen bond with the side chain of His524. In particular, the CH/π interactions of the "A ring" of EST with the side chains of Leu387 and Phe404 are easily identified in cooperation with the CHPI program. The FMO4-IFIE analysis using our novel subdividing fragmentation method, which provides higher resolution than the conventional IFIE analysis in units of ligand and each amino acid reside in the framework of two-body approximation, is a useful tool for revealing ligand-binding mechanism and would be applicable to rational drug design such as structure-based drug design and fragment-based drug design.

  6. Orbital free molecular dynamics; Approche sans orbitale des plasmas denses

    Energy Technology Data Exchange (ETDEWEB)

    Lambert, F

    2007-08-15

    The microscopic properties of hot and dense plasmas stay a field essentially studied thanks to classical theories like the One Component Plasma, models which rely on free parameters, particularly ionization. In order to investigate these systems, we have used, in this PhD work, a semi-classical model, without free parameters, that is based on coupling consistently classical molecular dynamics for the nuclei and orbital free density functional theory for the electrons. The electronic fluid is represented by a free energy entirely determined by the local density. This approximation was validated by a comparison with an ab initio technique, quantum molecular dynamics. This one is identical to the previous except for the description of the free energy that depends on a quantum-independent-particle model. Orbital free molecular dynamics was then used to compute equation of state of boron and iron plasmas in the hot and dense regime. Furthermore, comparisons with classical theories were performed on structural and dynamical properties. Finally, equation of state and transport coefficients mixing laws were studied by direct simulation of a plasma composed of deuterium and copper. (author)

  7. Local Molecular Orbitals from a Projection onto Localized Centers.

    Science.gov (United States)

    Heßelmann, Andreas

    2016-06-14

    A localization method for molecular orbitals is presented which exploits the locality of the eigenfunctions associated with the largest eigenvalues of the matrix representation of spatially localized functions. Local molecular orbitals are obtained by a projection of the canonical orbitals onto the set of the eigenvectors which correspond to the largest eigenvalues of these matrices. Two different types of spatially localized functions were chosen in this work, a two-parameter smooth-step-type function and the weight functions determined by a Hirshfeld partitioning of the molecular volume. It is shown that the method can provide fairly local occupied molecular orbitals if the positions of the set of local functions are set to the molecular bond centers. The method can also yield reasonably well-localized virtual molecular orbitals, but here, a sensible choice of the positions of the functions are the atomic sites and the locality then depends more strongly on the shape of the set of local functions. The method is tested for a range of polypeptide molecules in two different conformations, namely, a helical and a β-sheet conformation. Futhermore, it is shown that an adequate locality of the occupied and virtual orbitals can also be obtained for highly delocalized systems.

  8. Conformation effects on the molecular orbitals of serine

    Institute of Scientific and Technical Information of China (English)

    Wang Ke-Dong; Ma Peng-Fei; Shan Xu

    2011-01-01

    This paper calculates the five most stable conformers of serine with Hartree-Fock theory, density functional theory (B3LYP), M0ller-Plesset perturbation theory (MP4(SDQ)) and electron propagation theory with the 6-311++G(2d,2p) basis set. The calculated vertical ionization energies for the valence molecular orbitals of each conformer are in agreement with the experimental data, indicating that a range of molecular conformations would coexist in an equilibrium sample. Information of the five outer valence molecular orbitals for each conformer is explored in coordinate and momentum spaces using dual space analysis to investigate the conformational processes, which are generated from the global minimum conformer Serl by rotation of C2-C3 (Ser4), C1-C2 (Ser5) and C1-O2 (Ser2 and Ser3). Orbitals 28a, 27a and 26a are identified as the fingerprint orbitals for all the conformational processes.

  9. Orbits

    CERN Document Server

    Xu, Guochang

    2008-01-01

    This is the first book of the satellite era which describes orbit theory with analytical solutions of the second order with respect to all possible disturbances. Based on such theory, the algorithms of orbits determination are completely revolutionized.

  10. Structural and electronic properties of Sin, Sin+, and AlSin-1 (n=2-13) clusters: Theoretical investigation based on ab initio molecular orbital theory

    Science.gov (United States)

    Nigam, Sandeep; Majumder, Chiranjib; Kulshreshtha, S. K.

    2004-10-01

    The geometric and electronic structures of Sin, Sin+, and AlSin-1 clusters (2⩽n⩽13) have been investigated using the ab initio molecular orbital theory under the density functional theory formalism. The hybrid exchange-correlation energy function (B3LYP) and a standard split-valence basis set with polarization functions [6-31G(d)] were employed for this purpose. Relative stabilities of these clusters have been analyzed based on their binding energies, second difference in energy (Δ 2E) and fragmentation behavior. The equilibrium geometry of the neutral and charged Sin clusters show similar structural growth. However, significant differences have been observed in the electronic structure leading to their different stability pattern. While for neutral clusters, the Si10 is magic, the extra stability of the Si11+ cluster over the Si10+ and Si12+ bears evidence for the magic behavior of the Si11+ cluster, which is in excellent agreement with the recent experimental observations. Similarly for AlSin-1 clusters, which is isoelectronic with Sin+ clusters show extra stability of the AlSi10 cluster suggesting the influence of the electronic structures for different stabilities between neutral and charged clusters. The ground state geometries of the AlSin-1 clusters show that the impurity Al atom prefers to substitute for the Si atom, that has the highest coordination number in the host Sin cluster. The fragmentation behavior of all these clusters show that while small clusters prefers to evaporate monomer, the larger ones dissociate into two stable clusters of smaller size.

  11. Molecular design of electron transport with orbital rule: toward conductance-decay free molecular junctions.

    Science.gov (United States)

    Tada, Tomofumi; Yoshizawa, Kazunari

    2015-12-28

    In this study, we report our viewpoint of single molecular conductance in terms of frontier orbitals. The orbital rule derived from orbital phase and amplitude is a powerful guideline for the qualitative understanding of molecular conductance in both theoretical and experimental studies. The essence of the orbital rule is the phase-related quantum interference, and on the basis of this rule a constructive or destructive pathway for electron transport is easily predicted. We have worked on the construction of the orbital rule for more than ten years and recently found from its application that π-stacked molecular junctions fabricated experimentally are in line with the concept for conductance-decay free junctions. We explain the orbital rule using benzene molecular junctions with the para-, meta- and ortho-connections and discuss linear π-conjugated chains and π-stacked molecular junctions with respect to their small decay factors in this manuscript.

  12. Imaging the Temporal Evolution of Molecular Orbitals during Ultrafast Dissociation

    Science.gov (United States)

    Sann, H.; Havermeier, T.; Müller, C.; Kim, H.-K.; Trinter, F.; Waitz, M.; Voigtsberger, J.; Sturm, F.; Bauer, T.; Wallauer, R.; Schneider, D.; Weller, M.; Goihl, C.; Tross, J.; Cole, K.; Wu, J.; Schöffler, M. S.; Schmidt-Böcking, H.; Jahnke, T.; Simon, M.; Dörner, R.

    2016-12-01

    We investigate the temporal evolution of molecular frame angular distributions of Auger electrons emitted during ultrafast dissociation of HCl following a resonant single-photon excitation. The electron emission pattern changes its shape from that of a molecular σ orbital to that of an atomic p state as the system evolves from a molecule into two separated atoms.

  13. Ab initio molecular orbital calculation considering the quantum mechanical effect of nuclei by path integral molecular dynamics

    Science.gov (United States)

    Shiga, Motoyuki; Tachikawa, Masanori; Miura, Shinichi

    2000-12-01

    We present an accurate calculational scheme for many-body systems composed of electrons and nuclei, by path integral molecular dynamics technique combined with the ab initio molecular orbital theory. Based upon the scheme, the simulation of a water molecule at room temperature is demonstrated, applying all-electron calculation at the Hartree-Fock level of theory.

  14. Analytic energy derivatives for the calculation of the first-order molecular properties using the domain-based local pair-natural orbital coupled-cluster theory

    Science.gov (United States)

    Datta, Dipayan; Kossmann, Simone; Neese, Frank

    2016-09-01

    The domain-based local pair-natural orbital coupled-cluster (DLPNO-CC) theory has recently emerged as an efficient and powerful quantum-chemical method for the calculation of energies of molecules comprised of several hundred atoms. It has been demonstrated that the DLPNO-CC approach attains the accuracy of a standard canonical coupled-cluster calculation to about 99.9% of the basis set correlation energy while realizing linear scaling of the computational cost with respect to system size. This is achieved by combining (a) localized occupied orbitals, (b) large virtual orbital correlation domains spanned by the projected atomic orbitals (PAOs), and (c) compaction of the virtual space through a truncated pair natural orbital (PNO) basis. In this paper, we report on the implementation of an analytic scheme for the calculation of the first derivatives of the DLPNO-CC energy for basis set independent perturbations within the singles and doubles approximation (DLPNO-CCSD) for closed-shell molecules. Perturbation-independent one-particle density matrices have been implemented in order to account for the response of the CC wave function to the external perturbation. Orbital-relaxation effects due to external perturbation are not taken into account in the current implementation. We investigate in detail the dependence of the computed first-order electrical properties (e.g., dipole moment) on the three major truncation parameters used in a DLPNO-CC calculation, namely, the natural orbital occupation number cutoff used for the construction of the PNOs, the weak electron-pair cutoff, and the domain size cutoff. No additional truncation parameter has been introduced for property calculation. We present benchmark calculations on dipole moments for a set of 10 molecules consisting of 20-40 atoms. We demonstrate that 98%-99% accuracy relative to the canonical CCSD results can be consistently achieved in these calculations. However, this comes with the price of tightening the

  15. Tomographic imaging of asymmetric molecular orbitals with a two-color multicycle laser field

    CERN Document Server

    Qin, Meiyan; Zhang, Qingbin; Lu, Peixiang

    2013-01-01

    We theoretically demonstrate a scheme for tomographic reconstruction of asymmetric molecular orbitals based on high-order harmonic generation with a two-color multicycle laser field. It is shown that by adjusting the relative phase of the two fields, the returning electrons can be forced to recollide from one direction for all the orientations of molecules. Thus the reconstruction of the asymmetric orbitals can be carried out with multicycle laser field. This releases the stringent requirement of a single-cycle pulse with a stabilized and controllable carrier-envelop phase for the tomographic imaging of asymmetric molecular orbitals.

  16. Conjugated polymers based on benzo[2,1-b:3,4-b']dithiophene with low-lying highest occupied molecular orbital energy levels for organic photovoltaics.

    Science.gov (United States)

    Xiao, Shengqiang; Stuart, Andrew C; Liu, Shubin; You, Wei

    2009-07-01

    Fusing bithiophene units with a benzo moiety, benzo[2,1-b:3,4-b']dithiophene (BDT), was projected by theoretical calculations to lower the highest occupied molecular orbital (HOMO) energy level of the resulting polymers compared with that of the bithiophene unit, which would enhance the open circuit voltage of bulk heterojunction photovoltaic cells fabricated from BDT-based polymers blended with PCBM. The homopolymer of BDT (HMPBDT) and alternating copolymer of BDT with 2,1,3-benzothiadiazole (PBDT-BT) were therefore synthesized and fully characterized. Both the homopolymer (HMPBDT) and the copolymer (PBDT-BT) were experimentally confirmed to have low HOMO energy levels (-5.70 eV for HMPBDT and -5.34 eV for PBDT-BT). Introducing the acceptor moiety (2,1,3-benzothiadiazole) successfully lowered the optical band gap of the copolymer from 2.31 eV (HMPBDT) to 1.78 eV (PBDT-BT). Bulk heterojunction photovoltaic devices were fabricated from blends of these structurally related polymers with PBCM to investigate the photovoltaic performances. The optimized device of HMPBDT:PCBM (1:3, 180 nm) exhibited an improved open circuit voltage (V(oc)) of 0.76 V, a short circuit current (J(sc)) of 0.34 mA/cm(2), and a fill factor (FF) of 0.40, offering an overall efficiency of 0.10%. The observed large phase separation of the thin film by AFM and the large band gap were accountable for the small current. The optimized device of PBDT-BT:PCBM (1:3, 55 nm) demonstrated a better efficiency of 0.6%, with V(oc) = 0.72 V, J(sc) = 2.06 mA/cm(2), and FF = 0.42. The much improved current was attributed to the lower bandgap and better film morphology. However, the low hole mobility limited the thickness of the PBDT-BT:PCBM film, making inaccessible the thicker film which would utilize more light and enhance the current. Further improvements are expected if the mobility and film morphology can be improved by the new materials design, together with low band gap and low HOMO energy level.

  17. Super-atom molecular orbital excited states of fullerenes.

    Science.gov (United States)

    Johansson, J Olof; Bohl, Elvira; Campbell, Eleanor E B

    2016-09-13

    Super-atom molecular orbitals are orbitals that form diffuse hydrogenic excited electronic states of fullerenes with their electron density centred at the centre of the hollow carbon cage and a significant electron density inside the cage. This is a consequence of the high symmetry and hollow structure of the molecules and distinguishes them from typical low-lying molecular Rydberg states. This review summarizes the current experimental and theoretical studies related to these exotic excited electronic states with emphasis on femtosecond photoelectron spectroscopy experiments on gas-phase fullerenes.This article is part of the themed issue 'Fullerenes: past, present and future, celebrating the 30th anniversary of Buckminster Fullerene'.

  18. Tailoring approach for obtaining molecular orbitals of large systems

    Indian Academy of Sciences (India)

    Anuja P Rahalkar; Shridhar R Gadre

    2012-01-01

    Molecular orbitals (MO’s) within Hartree-Fock (HF) theory are of vital importance as they provide preliminary information of bonding and features such as electron localization and chemical reactivity. The contemporary literature treats the Kohn-Sham orbitals within density functional theory (DFT) equivalently to the MO's obtained within HF framework. The high scaling order of ab initio methods is the main hurdle in obtaining the MO's for large molecular systems. With this view, an attempt is made in the present work to employ molecular tailoring approach (MTA) for obtaining the complete set of MO's including occupied and virtual orbitals, for large molecules at HF and B3LYP levels of theory. The energies of highest occupied and lowest unoccupied molecular orbitals, and hence the band gaps, are accurately estimated by MTA for most of the test cases benchmarked in this study, which include -conjugated molecules. Typically, the root mean square errors of valence MO's are in range of 0.001 to 0.010 a.u. for all the test cases examined. MTA shows a time advantage factor of 2 to 3 over the corresponding actual calculation, for many of the systems reported.

  19. Mapping enzymatic catalysis using the effective fragment molecular orbital method

    DEFF Research Database (Denmark)

    Svendsen, Casper Steinmann; Fedorov, Dmitri G.; Jensen, Jan Halborg

    2013-01-01

    We extend the Effective Fragment Molecular Orbital (EFMO) method to the frozen domain approach where only the geometry of an active part is optimized, while the many-body polarization effects are considered for the whole system. The new approach efficiently mapped out the entire reaction path of ...

  20. Destructive quantum interference in electron transport: A reconciliation of the molecular orbital and the atomic orbital perspective

    Science.gov (United States)

    Zhao, Xin; Geskin, Victor; Stadler, Robert

    2017-03-01

    Destructive quantum interference (DQI) in single molecule electronics is a purely quantum mechanical effect and is entirely defined by the inherent properties of the molecule in the junction such as its structure and symmetry. This definition of DQI by molecular properties alone suggests its relation to other more general concepts in chemistry as well as the possibility of deriving simple models for its understanding and molecular device design. Recently, two such models have gained a wide spread attention, where one was a graphical scheme based on visually inspecting the connectivity of the carbon sites in conjugated π systems in an atomic orbital (AO) basis and the other one puts the emphasis on the amplitudes and signs of the frontier molecular orbitals (MOs). There have been discussions on the range of applicability for these schemes, but ultimately conclusions from topological molecular Hamiltonians should not depend on whether they are drawn from an AO or a MO representation, as long as all the orbitals are taken into account. In this article, we clarify the relation between both models in terms of the zeroth order Green's function and compare their predictions for a variety of systems. From this comparison, we conclude that for a correct description of DQI from a MO perspective, it is necessary to include the contributions from all MOs rather than just those from the frontier orbitals. The cases where DQI effects can be successfully predicted within a frontier orbital approximation we show them to be limited to alternant even-membered hydrocarbons, as a direct consequence of the Coulson-Rushbrooke pairing theorem in quantum chemistry.

  1. On the physical interpretation of the nuclear molecular orbital energy.

    Science.gov (United States)

    Charry, Jorge; Pedraza-González, Laura; Reyes, Andrés

    2017-06-07

    Recently, several groups have extended and implemented molecular orbital (MO) schemes to simultaneously obtain wave functions for electrons and selected nuclei. Many of these schemes employ an extended Hartree-Fock approach as a first step to find approximate electron-nuclear wave functions and energies. Numerous studies conducted with these extended MO methodologies have explored various effects of quantum nuclei on physical and chemical properties. However, to the best of our knowledge no physical interpretation has been assigned to the nuclear molecular orbital energy (NMOE) resulting after solving extended Hartree-Fock equations. This study confirms that the NMOE is directly related to the molecular electrostatic potential at the position of the nucleus.

  2. Study on the construction of satisfactory nonorthogonal localized molecular orbitals

    Institute of Scientific and Technical Information of China (English)

    FENG; Huasheng; BIAN; Jiang; LI; Lemin

    2004-01-01

    Comparing to orthogonal localized molecular orbitals (OLMO), the nonorthogonal localized molecular orbitals (NOLMO) exhibit bonding pictures more accordant with those in the traditional chemistry. They are more contracted, so that they have a better transferability and better performances for the calculation of election correlation energies and for the linear scaling algorithms of large systems. The satisfactory NOLMOs should be as contracted as possible while their shapes and spatial distribution keep in accordance with the traditional chemical bonding picture. It is found that the spread of NOLMOs is a monotonic decreasing function of their orthogonality, and it may reduce to any extent as the orthogonality descends. However, when the orthogonality descends to some point, the shapes and spatial distribution of the NOLMOs deviate drastically from the traditional chemical bonding picture, and finally the NOLMOs tend to linear dependence. Without the requirement of orthogonalization, some other constraints have to be imposed for constructing satisfactory NOLMOs by minimizing their spread functional. It is shown that satisfactory results can be generated by coupling the minimization of orbital spread functionals with the maximization of the distances between orbital centroids.

  3. Laser induced electron diffraction: a tool for molecular orbital imaging

    CERN Document Server

    Peters, Michel; Charron, Eric; Keller, Arne; Atabek, Osman

    2012-01-01

    We explore the laser-induced ionization dynamics of N2 and CO2 molecules subjected to a few-cycle, linearly polarized, 800\\,nm laser pulse using effective two-dimensional single active electron time-dependent quantum simulations. We show that the electron recollision process taking place after an initial tunnel ionization stage results in quantum interference patterns in the energy resolved photo-electron signals. If the molecule is initially aligned perpendicular to the field polarization, the position and relative heights of the associated fringes can be related to the molecular geometrical and orbital structure, using a simple inversion algorithm which takes into account the symmetry of the initial molecular orbital from which the ionized electron is produced. We show that it is possible to extract inter-atomic distances in the molecule from an averaged photon-electron signal with an accuracy of a few percents.

  4. Intramolecular charge ordering in the multi molecular orbital system (TTM-TTP)I3

    Science.gov (United States)

    Bonnet, Marie-Laure; Robert, Vincent; Tsuchiizu, Masahisa; Omori, Yukiko; Suzumura, Yoshikazu

    2010-06-01

    Starting from the structure of the (TTM-TTP)I3 molecular-based material, we examine the characteristics of frontier molecular orbitals using ab initio (CASSCF/CASPT2) configurations interaction calculations. It is shown that the singly occupied and second-highest-occupied molecular orbitals are close to each other, i.e., this compound should be regarded as a two-orbital system. By dividing virtually the [TTM-TTP] molecule into three fragments, an effective model is constructed to rationalize the origin of this picture. In order to investigate the low-temperature, symmetry breaking experimentally observed in the crystal, the electronic distribution in a pair of [TTM-TTP] molecules is analyzed from CASPT2 calculations. Our inspection supports and explains the speculated intramolecular charge ordering which is likely to give rise to low-energy magnetic properties.

  5. GAUSSIAN 76: An ab initio Molecular Orbital Program

    Science.gov (United States)

    Binkley, J. S.; Whiteside, R.; Hariharan, P. C.; Seeger, R.; Hehre, W. J.; Lathan, W. A.; Newton, M. D.; Ditchfield, R.; Pople, J. A.

    1978-01-01

    Gaussian 76 is a general-purpose computer program for ab initio Hartree-Fock molecular orbital calculations. It can handle basis sets involving s, p and d-type Gaussian functions. Certain standard sets (STO-3G, 4-31G, 6-31G*, etc.) are stored internally for easy use. Closed shell (RHF) or unrestricted open shell (UHF) wave functions can be obtained. Facilities are provided for geometry optimization to potential minima and for limited potential surface scans.

  6. Efficient construction of nonorthogonal localized molecular orbitals in large systems.

    Science.gov (United States)

    Cui, Ganglong; Fang, Weihai; Yang, Weitao

    2010-08-26

    Localized molecular orbitals (LMOs) are much more compact representations of electronic degrees of freedom than canonical molecular orbitals (CMOs). The most compact representation is provided by nonorthogonal localized molecular orbitals (NOLMOs), which are linearly independent but are not orthogonal. Both LMOs and NOLMOs are thus useful for linear-scaling calculations of electronic structures for large systems. Recently, NOLMOs have been successfully applied to linear-scaling calculations with density functional theory (DFT) and to reformulating time-dependent density functional theory (TDDFT) for calculations of excited states and spectroscopy. However, a challenge remains as NOLMO construction from CMOs is still inefficient for large systems. In this work, we develop an efficient method to accelerate the NOLMO construction by using predefined centroids of the NOLMO and thereby removing the nonlinear equality constraints in the original method ( J. Chem. Phys. 2004 , 120 , 9458 and J. Chem. Phys. 2000 , 112 , 4 ). Thus, NOLMO construction becomes an unconstrained optimization. Its efficiency is demonstrated for the selected saturated and conjugated molecules. Our method for fast NOLMO construction should lead to efficient DFT and NOLMO-TDDFT applications to large systems.

  7. Graph-based Methods for Orbit Classification

    Energy Technology Data Exchange (ETDEWEB)

    Bagherjeiran, A; Kamath, C

    2005-09-29

    An important step in the quest for low-cost fusion power is the ability to perform and analyze experiments in prototype fusion reactors. One of the tasks in the analysis of experimental data is the classification of orbits in Poincare plots. These plots are generated by the particles in a fusion reactor as they move within the toroidal device. In this paper, we describe the use of graph-based methods to extract features from orbits. These features are then used to classify the orbits into several categories. Our results show that existing machine learning algorithms are successful in classifying orbits with few points, a situation which can arise in data from experiments.

  8. End-group Influence on the Frontier Molecular Orbital Reorganization in Molecular Junctions -- Effect on Thermopower

    Science.gov (United States)

    Balachandran, Janakiraman; Reddy, Pramod; Dunietz, Barry; Gavini, Vikram

    2014-03-01

    The frontier molecular orbital (FMO) reorganization and in turn on the thermopower of the aromatic molecules trapped between metal electrodes (aka molecular junctions) depends on two effects namely (1) the stabilization effect - due to the physical presence of the metal electrode atoms and (2) change in e-e interactions - due to end-group mediated charge transfer. The stabilization effect always reduces the FMO energies. The charge transfer effect increases the FMO energies in charge-gaining molecules, which in turn opposes the stabilization effect resulting in a small overall shift. However, the charge transfer effect decreases the FMO energies in charge-losing molecules, which in turn complements the stabilization effect resulting in a large overall downward shift. This hypothesis is validated by delineating the shifts due to stabilization and charge-transfer effects independently. Further we also demonstrate the generality of the hypothesis by applying it on a wide range of aromatic molecules with different length and end-groups. Finally, we also present computationally efficient strategies, based on the proposed mechanism, to quantitatively compute the FMO reorganization which in turn has potential for high throughput analysis of molecular junctions.

  9. Localization of molecular orbitals: from fragments to molecule.

    Science.gov (United States)

    Li, Zhendong; Li, Hongyang; Suo, Bingbing; Liu, Wenjian

    2014-09-16

    Conspectus Localized molecular orbitals (LMO) not only serve as an important bridge between chemical intuition and molecular wave functions but also can be employed to reduce the computational cost of many-body methods for electron correlation and excitation. Therefore, how to localize the usually completely delocalized canonical molecular orbitals (CMO) into confined physical spaces has long been an important topic: It has a long history but still remains active to date. While the known LMOs can be classified into (exact) orthonormal and nonorthogonal, as well as (approximate) absolutely localized MOs, the ways for achieving these can be classified into two categories, a posteriori top-down and a priori bottom-up, depending on whether they invoke the global CMOs (or equivalently the molecular density matrix). While the top-down approaches have to face heavy tasks of minimizing or maximizing a given localization functional typically of many adjacent local extrema, the bottom-up ones have to invoke some tedious procedures for first generating a local basis composed of well-defined occupied and unoccupied subsets and then maintaining or resuming the locality when solving the Hartree-Fock/Kohn-Sham (HF/KS) optimization condition. It is shown here that the good of these kinds of approaches can be combined together to form a very efficient hybrid approach that can generate the desired LMOs for any kind of gapped molecules. Specifically, a top-down localization functional, applied to individual small subsystems only, is minimized to generate an orthonormal local basis composed of functions centered on the preset chemical fragments. The familiar notion for atomic cores, lone pairs, and chemical bonds emerges here automatically. Such a local basis is then employed in the global HF/KS calculation, after which a least action is taken toward the final orthonormal localized molecular orbitals (LMO), both occupied and virtual. This last step is very cheap, implying that, after

  10. Mapping enzymatic catalysis using the effective fragment molecular orbital method

    DEFF Research Database (Denmark)

    Svendsen, Casper Steinmann; Fedorov, Dmitri G.; Jensen, Jan Halborg

    2013-01-01

    We extend the Effective Fragment Molecular Orbital (EFMO) method to the frozen domain approach where only the geometry of an active part is optimized, while the many-body polarization effects are considered for the whole system. The new approach efficiently mapped out the entire reaction path...... determine the reaction barrier of chorismate mutase to be [Formula: see text] kcal mol(-1) for MP2/cc-pVDZ and [Formula: see text] for MP2/cc-pVTZ in an ONIOM approach using EFMO-RHF/6-31G(d) for the high and low layers, respectively....

  11. In silico simulations of tunneling barrier measurements for molecular orbital-mediated junctions: A molecular orbital theory approach to scanning tunneling microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Terryn, Raymond J.; Sriraman, Krishnan; Olson, Joel A., E-mail: jolson@fit.edu; Baum, J. Clayton, E-mail: cbaum@fit.edu [Department of Chemistry, Florida Institute of Technology, 150 West University Boulevard, Melbourne, Florida 32901 (United States); Novak, Mark J. [Department of Chemistry and Applied Biological Sciences, South Dakota School of Mines and Technology, 501 E. Saint Joseph Street, Rapid City, South Dakota 57701 (United States)

    2016-09-15

    A new simulator for scanning tunneling microscopy (STM) is presented based on the linear combination of atomic orbitals molecular orbital (LCAO-MO) approximation for the effective tunneling Hamiltonian, which leads to the convolution integral when applied to the tip interaction with the sample. This approach intrinsically includes the structure of the STM tip. Through this mechanical emulation and the tip-inclusive convolution model, dI/dz images for molecular orbitals (which are closely associated with apparent barrier height, ϕ{sub ap}) are reported for the first time. For molecular adsorbates whose experimental topographic images correspond well to isolated-molecule quantum chemistry calculations, the simulator makes accurate predictions, as illustrated by various cases. Distortions in these images due to the tip are shown to be in accord with those observed experimentally and predicted by other ab initio considerations of tip structure. Simulations of the tunneling current dI/dz images are in strong agreement with experiment. The theoretical framework provides a solid foundation which may be applied to LCAO cluster models of adsorbate–substrate systems, and is extendable to emulate several aspects of functional STM operation.

  12. Tuning the effective spin-orbit coupling in molecular semiconductors

    KAUST Repository

    Schott, Sam

    2017-05-11

    The control of spins and spin to charge conversion in organics requires understanding the molecular spin-orbit coupling (SOC), and a means to tune its strength. However, quantifying SOC strengths indirectly through spin relaxation effects has proven difficult due to competing relaxation mechanisms. Here we present a systematic study of the g-tensor shift in molecular semiconductors and link it directly to the SOC strength in a series of high-mobility molecular semiconductors with strong potential for future devices. The results demonstrate a rich variability of the molecular g-shifts with the effective SOC, depending on subtle aspects of molecular composition and structure. We correlate the above g-shifts to spin-lattice relaxation times over four orders of magnitude, from 200 to 0.15 μs, for isolated molecules in solution and relate our findings for isolated molecules in solution to the spin relaxation mechanisms that are likely to be relevant in solid state systems.

  13. MISCONCEPTION REMEDIATION OF ATOMIC ORBITAL, MOLECULAR ORBITAL, AND HIBRIDIZIATION CONCEPTS BY COMPUTER ASISSTED INSTRUCTION WITH ANIMATION AND SIMULATION MODEL

    Directory of Open Access Journals (Sweden)

    Sri Mursiti

    2010-06-01

    Full Text Available The research of Computer Asissted Instruction with animation and simulation was used to misconception remediation of atomic orbital, molecular orbital, and hibridiziation concepts. The applicated instruction model was focused on concept approach with macromedia flash player and power point programme. The subject of this research were the 2nd semestre students of Chemistry Department. The data were collected by using of true-false pre-test and post- test followed by the reason of its. The analysis reveals that the Computer Asissted Instruction with animation and simulation model increased the understanding of atomic orbital, molecular orbital, and hibridiziation concepts or remediation of concepts missconception, shown by the significant score gained between before and after the implementation of Computer Asissted Instruction with animation and simulation model. The instruction model developed the students's generic skills too.   Keywords: animation simulation,misconception remediation, orbital, hibridization

  14. New hybrid method for reactive systems from integrating molecular orbital or molecular mechanics methods with analytical potential energy surfaces.

    Science.gov (United States)

    Espinosa-Garciá, Joaquín; Rangel, Cipriano; Navarrete, Marta; Corchado, José C

    2004-09-15

    A computational approach to calculating potential energy surfaces for reactive systems is presented and tested. This hybrid approach is based on integrated methods where calculations for a small model system are performed by using analytical potential energy surfaces, and for the real system by using molecular orbital or molecular mechanics methods. The method is tested on a hydrogen abstraction reaction by using the variational transition-state theory with multidimensional tunneling corrections. The agreement between the calculated and experimental information depends on the quality of the method chosen for the real system. When the real system is treated by accurate quantum mechanics methods, the rate constants are in excellent agreement with the experimental measurements over a wide temperature range. When the real system is treated by molecular mechanics methods, the results are still good, which is very encouraging since molecular mechanics itself is not at all capable of describing this reactive system. Since no experimental information or additional fits are required to apply this method, it can be used to improve the accuracy of molecular orbital methods or to extend the molecular mechanics method to treat any reactive system with the single constraint of the availability of an analytical potential energy surface that describes the model system.

  15. Molecular electric moments calculated by using natural orbital functional theory

    CERN Document Server

    Mitxelena, Ion

    2016-01-01

    The molecular electric dipole, quadrupole and octupole moments of a selected set of 21 spin-compensated molecules are determined employing the extended version of the Piris natural orbital functional 6 (PNOF6), using the triple-$\\zeta$ Gaussian basis set with polarization functions developed by Sadlej, at the experimental geometries. The performance of the PNOF6 is established by carrying out a statistical analysis of the mean absolute errors with respect to the experiment. The calculated PNOF6 electric moments agree satisfactorily with the corresponding experimental data, and are in good agreement with the values obtained by accurate ab initio methods, namely, the coupled-cluster single and doubles (CCSD) and multi-reference single and double excitation configuration interaction (MRSD-CI) methods.

  16. Sulfur at nickel-alumina interfaces - Molecular orbital theory

    Science.gov (United States)

    Hong, S. Y.; Anderson, Alfred B.; Smialek, James L.

    1990-01-01

    Previous studies on Al-Ni alloys containing sulfur as an impurity suggest that, when S is in the interface between a metal and an oxide scale, it weakens the chemical bonding between them. This paper investigates factors responsible for this effect, using a molecular orbital theory to predict sulfur structures and electronic properties on the Ni-Al2O3 interface. It is shown that, in absence of S, the basal plane of Al2O3 will bind strongly through the Al(3+) cation surface to Ni (111). When segregated S impurity is present on the Ni surface, there are too few interfacial AlS bonds to effect good adhesion, leading to an inhibition of the oxide scale adhesion in NiCrAl alloys.

  17. 'Orbital volume restoration rate after orbital fracture'; a CT-based orbital volume measurement for evaluation of orbital wall reconstructive effect.

    Science.gov (United States)

    Wi, J M; Sung, K H; Chi, M

    2017-01-13

    PurposeTo evaluate the effect of orbital reconstruction and factors related to the effect of orbital reconstruction by assessing of orbital volume using orbital computed tomography (CT) in cases of orbital wall fracture.MethodsIn this retrospective study, 68 patients with isolated blowout fractures were evaluated. The volumes of orbits and herniated orbital tissues were determined by CT scans using a three-dimensional reconstruction technique (the Eclipse Treatment Planning System). Orbital CT was performed preoperatively, immediately after surgery, and at final follow ups (minimum of 6 months). We evaluated the reconstructive effect of surgery making a new formula, 'orbital volume reconstruction rate' from orbital volume differences between fractured and contralateral orbits before surgery, immediately after surgery, and at final follow up.ResultsMean volume of fractured orbits before surgery was 23.01±2.60 cm(3) and that of contralateral orbits was 21.31±2.50 cm(3) (P=0.005). Mean volume of the fractured orbits immediately after surgery was 21.29±2.42 cm(3), and that of the contralateral orbits was 21.33±2.52 cm(3) (P=0.921). Mean volume of fractured orbits at final follow up was 21.50±2.44 cm(3), and that of contralateral orbits was 21.32±2.50 cm(3) (P=0.668). The mean orbital volume reconstruction rate was 100.47% immediately after surgery and 99.17% at final follow up. No significant difference in orbital volume reconstruction rate was observed with respect to fracture site or orbital implant type. Patients that underwent operation within 14 days of trauma had a better reconstruction rate at final follow up than patients who underwent operation over 14 days after trauma (P=0.039).ConclusionComputer-based measurements of orbital fracture volume can be used to evaluate the reconstructive effect of orbital implants and provide useful quantitative information. Significant reduction of orbital volume is observed immediately after orbital wall

  18. Ab initio derivation of multi-orbital extended Hubbard model for molecular crystals

    Science.gov (United States)

    Tsuchiizu, Masahisa; Omori, Yukiko; Suzumura, Yoshikazu; Bonnet, Marie-Laure; Robert, Vincent

    2012-01-01

    From configuration interaction (CI) ab initio calculations, we derive an effective two-orbital extended Hubbard model based on the gerade (g) and ungerade (u) molecular orbitals (MOs) of the charge-transfer molecular conductor (TTM-TTP)I3 and the single-component molecular conductor [Au(tmdt)2]. First, by focusing on the isolated molecule, we determine the parameters for the model Hamiltonian so as to reproduce the CI Hamiltonian matrix. Next, we extend the analysis to two neighboring molecule pairs in the crystal and we perform similar calculations to evaluate the inter-molecular interactions. From the resulting tight-binding parameters, we analyze the band structure to confirm that two bands overlap and mix in together, supporting the multi-band feature. Furthermore, using a fragment decomposition, we derive the effective model based on the fragment MOs and show that the staking TTM-TTP molecules can be described by the zig-zag two-leg ladder with the inter-molecular transfer integral being larger than the intra-fragment transfer integral within the molecule. The inter-site interactions between the fragments follow a Coulomb law, supporting the fragment decomposition strategy.

  19. Communication through molecular bridges: different bridge orbital trends result in common property trends.

    Science.gov (United States)

    Proppe, Jonny; Herrmann, Carmen

    2015-02-05

    Common trends in communication through molecular bridges are ubiquitous in chemistry, such as the frequently observed exponential decay of conductance/electron transport and of exchange spin coupling with increasing bridge length, or the increased communication through a bridge upon closing a diarylethene photoswitch. For antiferromagnetically coupled diradicals in which two equivalent spin centers are connected by a closed-shell bridge, the molecular orbitals (MOs) whose energy splitting dominates the coupling strength are similar in shape to the MOs of the dithiolated bridges, which in turn can be used to rationalize conductance. Therefore, it appears reasonable to expect the observed common property trends to result from common orbital trends. We illustrate based on a set of model compounds that this assumption is not true, and that common property trends result from either different pairs of orbitals being involved, or from orbital energies not being the dominant contribution to property trends. For substituent effects, an effective modification of the π system can make a comparison difficult.

  20. Electronic absorption spectra and geometry of organic molecules an application of molecular orbital theory

    CERN Document Server

    Suzuki, Hiroshi

    1967-01-01

    Electronic Absorption Spectra and Geometry of Organic Molecules: An Application of Molecular Orbital Theory focuses on electronic absorption spectra of organic compounds and molecules. The book begins with the discussions on molecular spectra, electronic absorption spectra of organic compounds, and practical measures of absorption intensity. The text also focuses on molecular orbital theory and group theory. Molecular state functions; fundamental postulates of quantum theory; representation of symmetry groups; and symmetry operations and symmetry groups are described. The book also dis

  1. Orbital-Free Molecular Dynamics Simulations at Extreme Conditions

    Science.gov (United States)

    Kress, J. D.; Collins, L. A.; Ticknor, C.

    2015-06-01

    Large-scale molecular dynamics (MD) simulations in an orbital-free (OF) density-functional theory (DFT) formulation have been performed for pure and mixed species over a broad range of temperatures (T) and densities (ρ) that includes the warm, dense matter and high-energy density physics regimes. A finite-temperature Thomas-Fermi-Dirac form with a local-density exchange-correlation potential and a regularized electron-ion interaction represents the quantum nature of the electrons. In particular, we examine the efficacy of the OFMD approach as an effective bridge between Kohn-Sham DFT MD at low temperatures and simple, fully-ionized plasma models at high temperatures. Comparisons against intermediate-range constructions such as the Yukawa and one-component plasmas are also made. We examine the mass transport (diffusion, viscosity) properties of various systems, ranging from light to heavy elements, including lithium hydride (LiH), mixtures of LiH with uranium, mixtures of deuterium-tritium (DT) with plutonium and mixtures of DT with plastic (CH). The OFMD mass transport results have been fitted to simple functions of ρ and T suitable for use in hydrodynamics simulation codes.

  2. Preparation and structure investigation of novel Schiff bases using spectroscopic, thermal analyses and molecular orbital calculations and studying their biological activities.

    Science.gov (United States)

    Zayed, Ehab M; Zayed, M A; El-Desawy, M

    2015-01-05

    Two novel Schiff's bases (EB1 and L1) as new macrocyclic compounds were prepared via condensation reactions between bisaldehyde (2,2'-(ethane-1,2-diylbis(oxy))dibenzaldehyde): firstly with hydrazine carbothioamide to give (EB1), secondly with 4,6-diaminopyrimidine-2-thiol to give (L1). EB1 has a general formula C₁₈H₂₀N₆O₂S₂ of mole mass=416.520, and IUPAC name ((N,N'Z,N,N'E)-N,N'-(((ethane1,2diylbis(oxy))bis(2,1phenylene))bis(methanylylidene))bis(1hydrazinylmethanethioamide). L1 has a general formula C₂₀H₁₆N₄O₂S of mole mass=376.10; and IUPAC name 1,2-bis(2-vinylphenoxy)ethane4,6-diaminopyrimidine-2-thiol). The structures of the compounds obtained were characterized based on elemental analysis, FT-IR and (1)H NMR spectra, mass, and thermogravimetric analysis (TG, DTG). The activation thermodynamic parameters, such as, ΔE(*), ΔH(*), ΔS(*) and ΔG(*) were calculated from the TG curves using Coats-Redfern method. It is important to investigate their structures to know the active groups and weak bond responsible for their biological activities. The obtained thermal (TA) and mass (MS) practical results are confirmed by semi-empirical MO-calculation using PM3 procedure, on the neutral and positively charged forms of these novel Schiff bases. Therefore, comparison between MS and TA helps in selection of the proper pathway representing the decomposition of these compounds to give indication about their structures and consequently their biological activities. Their biological activities have been tested in vitro against Escherichia coli, Proteus vulgaris, Bacillissubtilies and Staphylococcus aurous bacteria in order to assess their antimicrobial potential.

  3. Conformational analysis of methylphenidate: comparison of molecular orbital and molecular mechanics methods

    Science.gov (United States)

    Gilbert, Kathleen M.; Skawinski, William J.; Misra, Milind; Paris, Kristina A.; Naik, Neelam H.; Buono, Ronald A.; Deutsch, Howard M.; Venanzi, Carol A.

    2004-11-01

    Methylphenidate (MP) binds to the cocaine binding site on the dopamine transporter and inhibits reuptake of dopamine, but does not appear to have the same abuse potential as cocaine. This study, part of a comprehensive effort to identify a drug treatment for cocaine abuse, investigates the effect of choice of calculation technique and of solvent model on the conformational potential energy surface (PES) of MP and a rigid methylphenidate (RMP) analogue which exhibits the same dopamine transporter binding affinity as MP. Conformational analysis was carried out by the AM1 and AM1/SM5.4 semiempirical molecular orbital methods, a molecular mechanics method (Tripos force field with the dielectric set equal to that of vacuum or water) and the HF/6-31G* molecular orbital method in vacuum phase. Although all three methods differ somewhat in the local details of the PES, the general trends are the same for neutral and protonated MP. In vacuum phase, protonation has a distinctive effect in decreasing the regions of space available to the local conformational minima. Solvent has little effect on the PES of the neutral molecule and tends to stabilize the protonated species. The random search (RS) conformational analysis technique using the Tripos force field was found to be capable of locating the minima found by the molecular orbital methods using systematic grid search. This suggests that the RS/Tripos force field/vacuum phase protocol is a reasonable choice for locating the local minima of MP. However, the Tripos force field gave significantly larger phenyl ring rotational barriers than the molecular orbital methods for MP and RMP. For both the neutral and protonated cases, all three methods found the phenyl ring rotational barriers for the RMP conformers/invertamers (denoted as cte, tte, and cta) to be: cte, tte> MP > cta. Solvation has negligible effect on the phenyl ring rotational barrier of RMP. The B3LYP/6-31G* density functional method was used to calculate the phenyl

  4. Orbital Energy-Based Reaction Analysis of SN2 Reactions

    Directory of Open Access Journals (Sweden)

    Takao Tsuneda

    2016-07-01

    Full Text Available An orbital energy-based reaction analysis theory is presented as an extension of the orbital-based conceptual density functional theory. In the orbital energy-based theory, the orbitals contributing to reactions are interpreted to be valence orbitals giving the largest orbital energy variation from reactants to products. Reactions are taken to be electron transfer-driven when they provide small variations for the gaps between the contributing occupied and unoccupied orbital energies on the intrinsic reaction coordinates in the initial processes. The orbital energy-based theory is then applied to the calculations of several S N2 reactions. Using a reaction path search method, the Cl− + CH3I → ClCH3 + I− reaction, for which another reaction path called “roundabout path” is proposed, is found to have a precursor process similar to the roundabout path just before this SN2 reaction process. The orbital energy-based theory indicates that this precursor process is obviously driven by structural change, while the successor SN2 reaction proceeds through electron transfer between the contributing orbitals. Comparing the calculated results of the SN2 reactions in gas phase and in aqueous solution shows that the contributing orbitals significantly depend on solvent effects and these orbitals can be correctly determined by this theory.

  5. Design of GEO helix tourist orbit based on perturbation compensation

    Science.gov (United States)

    Xu, Yanli; Zhou, Haijun; Dai, Huayu

    2017-05-01

    Constrained by country area and technology level, GEO target and environment's detection become practical difficulty which restrict development of our country's space technology. Helix tourist orbit is introduced; orbit formation effect from perturbation of nonsphericfigure of the Earth, the solar and lunar attraction is analyzed; orbit design method based on perturbation compensation is put forward.

  6. Orbital-Free Density Functional Theory for Molecular Structure Calculations

    Institute of Scientific and Technical Information of China (English)

    Huajie Chen; Aihui Zhou

    2008-01-01

    We give here an overview of the orbital-free density functional theory that is used for modeling atoms and molecules. We review typical approximations to the kinetic energy, exchange-correlation corrections to the kinetic and Hartree energies, and constructions of the pseudopotentials. We discuss numerical discretizations for the orbital-free methods and include several numerical results for illustrations.

  7. Many-body expansion of the Fock matrix in the fragment molecular orbital method

    Science.gov (United States)

    Fedorov, Dmitri G.; Kitaura, Kazuo

    2017-09-01

    A many-body expansion of the Fock matrix in the fragment molecular orbital method is derived up to three-body terms for restricted Hartree-Fock and density functional theory in the atomic orbital basis and compared to the expansion in the basis of fragment molecular orbitals (MOs). The physical nature of many-body corrections is revealed in terms of charge transfer terms. An improvement of the fragment MO expansion is proposed by adding exchange to the embedding. The accuracy of all developed methods is demonstrated in comparison to unfragmented results for polyalanines, a water cluster, Trp-cage (PDB: 1L2Y) and crambin (PDB: 1CRN) proteins, a zeolite cluster, a Si nano-wire, and a boron nitride ribbon. The physical nature of metallicity is discussed, and it is shown what kinds of metallic systems can be treated by fragment-based methods. The density of states is calculated for a fully closed and a partially open nano-ring of boron nitride with a diameter of 105 nm.

  8. Empirical LCAO parameters for \\pi molecular orbitals in planar organic molecules

    CERN Document Server

    Hawke, Laurence; Simserides, Constantinos

    2008-01-01

    We present a simplified LCAO model for the description of \\pi molecular orbitals in organic molecules containing \\pi-bonds between carbon, nitrogen, or oxygen atoms with sp2 hybridization, which we show to be quite accurate in predicting the energy of the highest occupied \\pi orbital and the first \\pi-\\pi* transition energy of a large set of organic compounds. We provide four empirical parameter values for the diagonal matrix elements of the LCAO description, corresponding to atoms of carbon, nitrogen with one pz electron, nitrogen with two pz electrons, and oxygen. The bond-distance dependent formula (proportional to 1/d^2) of Harrison is used for the non-diagonal matrix elements between neighboring atoms. The predictions of our calculations have been tested against available experimental results in more than sixty organic molecules, including benzene and its derivatives, polyacenes, aromatic hydrocarbons of various geometries, polyenes, ketones, aldehydes, azabenzenes, nucleic acids bases and others. The co...

  9. Multi-Orbital Molecular Compound (TTM-TTP)I3: Effective Model and Fragment Decomposition

    Science.gov (United States)

    Tsuchiizu, Masahisa; Omori, Yukiko; Suzumura, Yoshikazu; Bonnet, Marie-Laure; Robert, Vincent; Ishibashi, Shoji; Seo, Hitoshi

    2011-01-01

    The electronic structure of the molecular compound (TTM-TTP)I3, which exhibits a peculiar intra-molecular charge ordering, has been studied using multi-configuration ab initio calculations. First we derive an effective Hubbard-type model based on the molecular orbitals (MOs) of TTM-TTP; we set up a two-orbital Hamiltonian for the two MOs near the Fermi energy and determine its full parameters: the transfer integrals, the Coulomb and exchange interactions. The tight-binding band structure obtained from these transfer integrals is consistent with the result of the direct band calculation based on density functional theory. Then, by decomposing the frontier MOs into two parts, i.e., fragments, we find that the stacked TTM-TTP molecules can be described by a two-leg ladder model, while the inter-fragment Coulomb energies are scaled to the inverse of their distances. This result indicates that the fragment picture that we proposed earlier [M.-L. Bonnet et al.: J. Chem. Phys. 132 (2010) 214705] successfully describes the low-energy properties of this compound.

  10. Polarized Molecular Orbital Model Chemistry 3. The PMO Method Extended to Organic Chemistry.

    Science.gov (United States)

    Isegawa, Miho; Fiedler, Luke; Leverentz, Hannah R; Wang, Yingjie; Nachimuthu, Santhanamoorthi; Gao, Jiali; Truhlar, Donald G

    2013-01-08

    The polarized molecular orbital (PMO) method, a neglect-of-diatomic-differential-overlap (NDDO) semiempirical molecular orbital method previously parameterized for systems composed of O and H, is here extended to carbon. We modified the formalism and optimized all the parameters in the PMO Hamiltonian by using a genetic algorithm and a database containing both electrostatic and energetic properties; the new parameter set is called PMO2. The quality of the resulting predictions is compared to results obtained by previous NDDO semiempirical molecular orbital methods, both including and excluding dispersion terms. We also compare the PMO2 properties to SCC-DFTB calculations. Within the class of semiempirical molecular orbital methods, the PMO2 method is found to be especially accurate for polarizabilities, atomization energies, proton transfer energies, noncovalent complexation energies, and chemical reaction barrier heights and to have good across-the-board accuracy for a range of other properties, including dipole moments, partial atomic charges, and molecular geometries.

  11. Polarized Molecular Orbital Model Chemistry 3. The PMO Method Extended to Organic Chemistry

    Science.gov (United States)

    Isegawa, Miho; Fiedler, Luke; Leverentz, Hannah R.; Wang, Yingjie; Nachimuthu, Santhanamoorthi; Gao, Jiali; Truhlar, Donald G.

    2013-01-01

    The polarized molecular orbital (PMO) method, a neglect-of-diatomic-differential-overlap (NDDO) semiempirical molecular orbital method previously parameterized for systems composed of O and H, is here extended to carbon. We modified the formalism and optimized all the parameters in the PMO Hamiltonian by using a genetic algorithm and a database containing both electrostatic and energetic properties; the new parameter set is called PMO2. The quality of the resulting predictions is compared to results obtained by previous NDDO semiempirical molecular orbital methods, both including and excluding dispersion terms. We also compare the PMO2 properties to SCC-DFTB calculations. Within the class of semiempirical molecular orbital methods, the PMO2 method is found to be especially accurate for polarizabilities, atomization energies, proton transfer energies, noncovalent complexation energies, and chemical reaction barrier heights and to have good across-the-board accuracy for a range of other properties, including dipole moments, partial atomic charges, and molecular geometries. PMID:23704835

  12. A unified scheme for ab initio molecular orbital theory and path integral molecular dynamics

    Science.gov (United States)

    Shiga, Motoyuki; Tachikawa, Masanori; Miura, Shinichi

    2001-11-01

    We present a general approach for accurate calculation of chemical substances which treats both nuclei and electrons quantum mechanically, adopting ab initio molecular orbital theory for the electronic structure and path integral molecular dynamics for the nuclei. The present approach enables the evaluation of physical quantities dependent on the nuclear configuration as well as the electronic structure, within the framework of Born-Oppenheimer adiabatic approximation. As an application, we give the path integral formulation of electric response properties—dipole moment and polarizability, which characterize the changes both in electronic structure and nuclear configuration at a given temperature when uniform electrostatic field is present. We also demonstrate the calculation of a water molecule using the present approach and the result of temperature and isotope effects is discussed.

  13. Spin orbit torque based electronic neuron

    Energy Technology Data Exchange (ETDEWEB)

    Sengupta, Abhronil, E-mail: asengup@purdue.edu; Choday, Sri Harsha; Kim, Yusung; Roy, Kaushik [School of Electrical and Computer Engineering, Purdue University, West Lafayette, Indiana 47907 (United States)

    2015-04-06

    A device based on current-induced spin-orbit torque (SOT) that functions as an electronic neuron is proposed in this work. The SOT device implements an artificial neuron's thresholding (transfer) function. In the first step of a two-step switching scheme, a charge current places the magnetization of a nano-magnet along the hard-axis, i.e., an unstable point for the magnet. In the second step, the SOT device (neuron) receives a current (from the synapses) which moves the magnetization from the unstable point to one of the two stable states. The polarity of the synaptic current encodes the excitatory and inhibitory nature of the neuron input and determines the final orientation of the magnetization. A resistive crossbar array, functioning as synapses, generates a bipolar current that is a weighted sum of the inputs. The simulation of a two layer feed-forward artificial neural network based on the SOT electronic neuron shows that it consumes ∼3× lower power than a 45 nm digital CMOS implementation, while reaching ∼80% accuracy in the classification of 100 images of handwritten digits from the MNIST dataset.

  14. NEW METHOD FOR CALCULATING MOLECULAR ORBITALS WITH APPLICATION TO CYCLIC SYSTEMS,

    Science.gov (United States)

    New method for calculating molecular orbitals with application to cyclic systems: Stud; of the quantum mechanical problem of an electron bound to a configuration of N overlapping potentials. Reprinted from ’The Physical Review ’.

  15. The Symmetry Properties of Linear Combination Coefficients for Molecular Orbitals of Diatomic Molecules

    Institute of Scientific and Technical Information of China (English)

    Metin Orbay; Telhat Ozdogan

    2003-01-01

    In this paper, the symmetry properties of linear combination coefficients for molecular orbitals of diatomicmolecules, using Slater type orbitals, are presented with the help of the symmetry operations in group theory. In order totest the presented symmetry properties, the linear combination coefficients of molecular orbitalsfor the ground electronicstate of pilot molecules F2 and CO are calculated using constructed computer programs for Hartree-Fock-Roothaanequation. It is seen that the obtained computing results satisfy the presented symmetry properties.

  16. Validity boundary of orbital-free molecular dynamics method corresponding to thermal ionization of shell structure

    Science.gov (United States)

    Gao, Chang; Zhang, Shen; Kang, Wei; Wang, Cong; Zhang, Ping; He, X. T.

    2016-11-01

    With 6LiD as an example, we show that the applicable region of the orbital-free molecular dynamics (OFMD) method in a large temperature range is determined by the thermal ionization process of bound electrons in shell structures. The validity boundary of the OFMD method is defined roughly by the balance point of the average thermal energy of an electron and the ionization energy of the lowest localized electronic state. This theoretical proposition is based on the observation that the deviation of the OFMD method originates from its less accurate description to the charge density in partially ionized shells, as compared with the results of the extended first-principles molecular dynamics method, which well reproduces the charge density of shell structures.

  17. The Importance of Three-Body Interactions in Molecular Dynamics Simulations of Water with the Fragment Molecular Orbital Method

    Energy Technology Data Exchange (ETDEWEB)

    Pruitt, Spencer R.; Nakata, Hiroya; Nagata, Takeshi; Mayes, Maricris; Alexeev, Yuri; Fletcher, Graham D.; Fedorov, Dmitri G; Kitaura, Kazuo; Gordon, M

    2016-04-12

    The analytic first derivative with respect to nuclear coordinates is formulated and implemented in the framework of the three-body fragment molecular orbital (FMO) method. The gradient has been derived and implemented for restricted Hartree-Fock, second-order Møller-Plesset perturbation, and density functional theories. The importance of the three-body fully analytic gradient is illustrated through the failure of the two-body FMO method during molecular dynamics simulations of a small water cluster. The parallel implementation of the fragment molecular orbital method, its parallel efficiency, and its scalability on the Blue Gene/Q architecture up to 262,144 CPU cores, are also discussed.

  18. Laser-Induced Electron Diffraction: Inversion of Photoelectron Spectra for Molecular Orbital Imaging

    CERN Document Server

    Puthumpally-Joseph, R; Peters, M; Nguyen-Dang, T T; Atabek, O; Charron, E

    2016-01-01

    In this paper, we discuss the possibility of imaging molecular orbitals from photoelectron spectra obtained via Laser Induced Electron Diffraction (LIED) in linear molecules. This is an extension of our work published recently in Physical Review A \\textbf{94}, 023421 (2016) to the case of the HOMO-1 orbital of the carbon dioxide molecule. We show that such an imaging technique has the potential to image molecular orbitals at different internuclear distances in a sub-femtosecond time scale and with a resolution of a fraction of an Angstr\\"om.

  19. Magnetic and orbital ordering in the iron-based superconductors. Role of spin-orbit coupling

    Energy Technology Data Exchange (ETDEWEB)

    Ahn, Felix; Eremin, Ilya [Institut fuer Theoretische Physik III, Ruhr-Universitaet Bochum (Germany); Knolle, Johannes [Max Planck Institute for the Physics of Complex Systems, Dresden (Germany); Fernandes, Rafael [School of Physics and Astronomy, University of Minnesota, Minneapolis, MN (United States)

    2015-07-01

    We analyze the magnetic ordering in the iron-based superconductors in presence of spin-orbit coupling. Based on several tight-binding parametrizations of the 3d electron states we show how the spin-orbit coupling introduces the anisotropy of the magnetization of the striped antiferromagnetic state by lifting the degeneracy of all three components of the magnetization m{sub x}, m{sub y} and m{sub z}. The orientation of the magnetic moment is determined by the contribution of the xy, xz, and yz orbitals to the electronic states near the Fermi level of the electron and hole bands and is determined by the electron filling. We find that within an itinerant approach the magnetic ordering is most favorable along the wavevector of the striped AF state. This appears to be a natural consequence of the spin-orbit coupling in the striped AF state where the ferro-orbital order of the xz and yz orbitals is only a consequence of the striped AF order. We further analyze the role of spin-orbit coupling for the C{sub 4} magnetic structure where SDW order parameters with both wavevectors, Q{sub x} = (π,0) and Q{sub y} = (0,π), coexist.

  20. Molecular orbital studies (hardness, chemical potential and electrophilicity), vibrational investigation and theoretical NBO analysis of 4-4'-(1H-1,2,4-triazol-1-yl methylene) dibenzonitrile based on abinitio and DFT methods.

    Science.gov (United States)

    Sheela, N R; Muthu, S; Sampathkrishnan, S

    2014-01-01

    The Fourier transform infrared (FTIR) and FT Raman (FTR) of 4-4'-(1H-1, 2, 4-triazol-1-yl methylene) dibenzonitrile (4-HTMDBN) have been recorded and analyzed. The equilibrium geometry harmonic vibrational frequencies have been investigated with the help of standard HF and DFT methods with 6-31G(d,p) as basis set. The assignments of the vibrational spectra have been carried out with the help of normal co-ordinate analysis (NCA) following the scaled quantum mechanical force field methodology (SQMFF). Theoretical simulations of the FTIR and FTR spectra of the title compound have been calculated. The (1)H and (13)C Nuclear Magnetic Resonance (NMR) chemical shifts of the molecule were calculated by the Gauge including atomic orbital (GIAO) method. The stability of the molecule has been analyzed using natural bond orbital (NBO) analysis. The linear polarizability (α) and the first order hyperpolarizability (β) values of the investigated molecule have been computed using HF/DFT/6-31G(d,p) methods on the finite field approach. UV-Vis spectrum of the compound is recorded and the electronic properties such as HOMO and LUMO energies, are performed. The directly calculated ionization potential (IP), electron affinity (EA), electronegativity (χ), electrophilicity index (ω), hardness (η) and chemical potential (ρ) are all correlated with the HOMO and LUMO energies with their molecular properties. Mulliken population analysis on atomic charges, molecular electrostatic potential maps (MEP) and thermodynamical properties of title compound at different temperature have been calculated.

  1. Carbon Nanotube Based Molecular Electronics

    Science.gov (United States)

    Srivastava, Deepak; Saini, Subhash; Menon, Madhu

    1998-01-01

    Carbon nanotubes and the nanotube heterojunctions have recently emerged as excellent candidates for nanoscale molecular electronic device components. Experimental measurements on the conductivity, rectifying behavior and conductivity-chirality correlation have also been made. While quasi-one dimensional simple heterojunctions between nanotubes with different electronic behavior can be generated by introduction of a pair of heptagon-pentagon defects in an otherwise all hexagon graphene sheet. Other complex 3- and 4-point junctions may require other mechanisms. Structural stability as well as local electronic density of states of various nanotube junctions are investigated using a generalized tight-binding molecular dynamics (GDBMD) scheme that incorporates non-orthogonality of the orbitals. The junctions investigated include straight and small angle heterojunctions of various chiralities and diameters; as well as more complex 'T' and 'Y' junctions which do not always obey the usual pentagon-heptagon pair rule. The study of local density of states (LDOS) reveal many interesting features, most prominent among them being the defect-induced states in the gap. The proposed three and four pointjunctions are one of the smallest possible tunnel junctions made entirely of carbon atoms. Furthermore the electronic behavior of the nanotube based device components can be taylored by doping with group III-V elements such as B and N, and BN nanotubes as a wide band gap semiconductor has also been realized in experiments. Structural properties of heteroatomic nanotubes comprising C, B and N will be discussed.

  2. Spin-orbit coupled molecular quantum magnetism realized in inorganic solid.

    Science.gov (United States)

    Park, Sang-Youn; Do, S-H; Choi, K-Y; Kang, J-H; Jang, Dongjin; Schmidt, B; Brando, Manuel; Kim, B-H; Kim, D-H; Butch, N P; Lee, Seongsu; Park, J-H; Ji, Sungdae

    2016-09-21

    Molecular quantum magnetism involving an isolated spin state is of particular interest due to the characteristic quantum phenomena underlying spin qubits or molecular spintronics for quantum information devices, as demonstrated in magnetic metal-organic molecular systems, the so-called molecular magnets. Here we report the molecular quantum magnetism realized in an inorganic solid Ba3Yb2Zn5O11 with spin-orbit coupled pseudospin-½ Yb(3+) ions. The magnetization represents the magnetic quantum values of an isolated Yb4 tetrahedron with a total (pseudo)spin 0, 1 and 2. Inelastic neutron scattering results reveal that a large Dzyaloshinsky-Moriya interaction originating from strong spin-orbit coupling of Yb 4f is a key ingredient to explain magnetic excitations of the molecular magnet states. The Dzyaloshinsky-Moriya interaction allows a non-adiabatic quantum transition between avoided crossing energy levels, and also results in unexpected magnetic behaviours in conventional molecular magnets.

  3. Spin–orbit coupled molecular quantum magnetism realized in inorganic solid

    Science.gov (United States)

    Park, Sang-Youn; Do, S.-H.; Choi, K.-Y.; Kang, J.-H.; Jang, Dongjin; Schmidt, B.; Brando, Manuel; Kim, B.-H.; Kim, D.-H.; Butch, N. P.; Lee, Seongsu; Park, J.-H.; Ji, Sungdae

    2016-01-01

    Molecular quantum magnetism involving an isolated spin state is of particular interest due to the characteristic quantum phenomena underlying spin qubits or molecular spintronics for quantum information devices, as demonstrated in magnetic metal–organic molecular systems, the so-called molecular magnets. Here we report the molecular quantum magnetism realized in an inorganic solid Ba3Yb2Zn5O11 with spin–orbit coupled pseudospin-½ Yb3+ ions. The magnetization represents the magnetic quantum values of an isolated Yb4 tetrahedron with a total (pseudo)spin 0, 1 and 2. Inelastic neutron scattering results reveal that a large Dzyaloshinsky–Moriya interaction originating from strong spin–orbit coupling of Yb 4f is a key ingredient to explain magnetic excitations of the molecular magnet states. The Dzyaloshinsky–Moriya interaction allows a non-adiabatic quantum transition between avoided crossing energy levels, and also results in unexpected magnetic behaviours in conventional molecular magnets. PMID:27650796

  4. Monitoring objects orbiting earth using satellite-based telescopes

    Energy Technology Data Exchange (ETDEWEB)

    Olivier, Scot S.; Pertica, Alexander J.; Riot, Vincent J.; De Vries, Willem H.; Bauman, Brian J.; Nikolaev, Sergei; Henderson, John R.; Phillion, Donald W.

    2015-06-30

    An ephemeris refinement system includes satellites with imaging devices in earth orbit to make observations of space-based objects ("target objects") and a ground-based controller that controls the scheduling of the satellites to make the observations of the target objects and refines orbital models of the target objects. The ground-based controller determines when the target objects of interest will be near enough to a satellite for that satellite to collect an image of the target object based on an initial orbital model for the target objects. The ground-based controller directs the schedules to be uploaded to the satellites, and the satellites make observations as scheduled and download the observations to the ground-based controller. The ground-based controller then refines the initial orbital models of the target objects based on the locations of the target objects that are derived from the observations.

  5. The dynamical evolution of molecular clouds near the Galactic Centre - I. Orbital structure and evolutionary timeline

    CERN Document Server

    Kruijssen, J M Diederik; Longmore, Steven N

    2014-01-01

    We recently proposed that the star-forming potential of dense molecular clouds in the Central Molecular Zone (CMZ, i.e. the central few 100 pc) of the Milky Way is linked to their orbital dynamics, potentially giving rise to an absolute-time sequence of star-forming clouds. In this paper, we present an orbital model for the gas stream(s) observed in the CMZ. The model is obtained by integrating orbits in the observed gravitational potential and represents a good fit to the distribution of dense gas, reproducing all of its key properties. The orbit is also consistent with observational constraints not included in the fitting process, such as the velocities of Sgr B2 and the Arches and Quintuplet clusters. It differs from previous models: (1) the orbit is open rather than closed due to the extended mass distribution in the CMZ, (2) its orbital velocity is twice as high as in previous models, and (3) Sgr A$^*$ coincides with the focus of the (eccentric) orbit rather than being offset. Our orbital solution suppor...

  6. Orbit Clustering Based on Transfer Cost

    Science.gov (United States)

    Gustafson, Eric D.; Arrieta-Camacho, Juan J.; Petropoulos, Anastassios E.

    2013-01-01

    We propose using cluster analysis to perform quick screening for combinatorial global optimization problems. The key missing component currently preventing cluster analysis from use in this context is the lack of a useable metric function that defines the cost to transfer between two orbits. We study several proposed metrics and clustering algorithms, including k-means and the expectation maximization algorithm. We also show that proven heuristic methods such as the Q-law can be modified to work with cluster analysis.

  7. Image-charge-induced localization of molecular orbitals at metal-molecule interfaces

    DEFF Research Database (Denmark)

    Strange, M.; Thygesen, K. S.

    2012-01-01

    -conjugated molecular wire in contact with a metal surface. We find that image charge effects pull the frontier molecular orbitals toward the metal surface, while orbitals with higher or lower energy are pushed away. This affects both the size of the energetic image charge shifts and the coupling of the individual......Quasiparticle (QP) wave functions, also known as Dyson orbitals, extend the concept of single-particle states to interacting electron systems. Here we employ many-body perturbation theory in the GW approximation to calculate the QP wave functions for a semiempirical model describing a pi...... orbitals to the metal substrate. Full diagonalization of the QP equation and, to some extent, self-consistency in the GW self-energy, is important to describe the effect, which is not captured by standard density functional theory or Hartree-Fock. These results should be important for the understanding...

  8. Diels−Alder Reactions of Acyclic 2-Azadienes: A Semiempirical Molecular Orbital Study

    OpenAIRE

    Teresa M. V. D. Pinho e Melo; Fausto, Rui; Gonsalves, António M. d'A. Rocha

    1998-01-01

    Molecular orbital calculations (AM1) have been performed to obtain the frontier orbitals' (HOMO and LUMO) energies and polarization of a series of acyclic 2-azadienes. The results are used to rationalize the reactivity of the compounds studied with both electron-rich and electron-deficient dienophiles as well as the observed regioselectivity of the corresponding Diels−Alder reactions. http://dx.doi.org/10.1021/jo980090e

  9. Solution of multi-center molecular integrals of Slater-type orbitals

    Science.gov (United States)

    Tai, H.

    1989-01-01

    The troublesome multi-center molecular integrals of Slater-type orbitals (STO) in molecular physics calculations can be evaluated by using the Fourier transform and proper coupling of the two center exchange integrals. A numerical integration procedure is then readily rendered to the final expression in which the integrand consists of well known special functions of arguments containing the geometrical arrangement of the nuclear centers and the exponents of the atomic orbitals. A practical procedure was devised for the calculation of a general multi-center molecular integrals coupling arbitrary Slater-type orbitals. Symmetry relations and asymptotic conditions are discussed. Explicit expressions of three-center one-electron nuclear-attraction integrals and four-center two-electron repulsion integrals for STO of principal quantum number n=2 are listed. A few numerical results are given for the purpose of comparison.

  10. Calculation of the paramagnetism of large carbon nanotubes, using a parameter-independent molecular orbital model

    Science.gov (United States)

    Collado, J. R. Alvarez

    A previous self-consistent field molecular orbital method, able to describe systems having a large number of unpaired electrons, n, is reviewed and improved. This method is applied to the study of paramagnetism in large (1,000-16,000 atoms) zigzag carbon nanotubes, represented by their n values. The computational scheme is based on the Hückel neglect differential overlap approach. It is shown that dependence of n on the semiempirical parameters is very small, and so they can be removed from the calculation. Enhancement of the paramagnetism (increase of n), by use of a strong external magnetic field, is also studied. Finally, the dependence of the Fermi one-electron potential energies and the spin atomic densities on both the parameters and the shape of the nanotubes is analyzed.0

  11. In-Orbit Lifetime Prediction for LEO and HEO Based on Orbit Determination from TLE Data

    Science.gov (United States)

    Agueda, A.; Aivar, L.; Tirado, J.; Dolado, J. C.

    2013-08-01

    Objects in Low-Earth Orbits (LEO) and Highly Elliptical Orbits (HEO) are subjected to decay and re-entry into the atmosphere due mainly to the drag force. While being this process the best solution to avoid the proliferation of debris in space and ensure the sustainability of future space activities, it implies a threat to the population on ground. Thus, the prediction of the in-orbit lifetime of an object and the evaluation of the risk on population and ground assets constitutes a crucial task. This paper will concentrate on the first of these tasks. Unfortunately the lifetime of an object in space is remarkably difficult to predict. This is mainly due to the dependence of the atmospheric drag on a number of uncertain elements such as the density profile and its dependence on the solar activity, the atmospheric conditions, the mass and surface area of the object (very difficult to evaluate), its uncontrolled attitude, etc. In this paper we will present a method for the prediction of this lifetime based on publicly available Two-Line Elements (TLEs) from the American USSTRATCOM's Joint Space Operations Center (JSpOC). TLEs constitute an excellent source to access routinely orbital information for thousands of objects even though of their reduced and unpredictable accuracy. Additionally, the implementation of the method on a CNES's Java-based tool will be presented. This tool (OPERA) is executed routinely at CNES to predict the orbital lifetime of a whole catalogue of objects.

  12. Diffusion energy profiles in silica mesoporous molecular sieves modelled with the fragment molecular orbital method

    Science.gov (United States)

    Roskop, Luke; Fedorov, Dmitri G.; Gordon, Mark S.

    2013-07-01

    The fragment molecular orbital (FMO) method is used to model truncated portions of mesoporous silica nanoparticle (MSN) pores. The application of the FMO/RHF (restricted Hartree-Fock) method to MCM-41 type MSNs is discussed and an error analysis is given. The FMO/RHF method is shown to reliably approximate the RHF energy (error ∼0.2 kcal/mol), dipole moment (error ∼0.2 debye) and energy gradient (root mean square [RMS] error ∼0.2 × 10-3 a.u./bohr). Several FMO fragmentation schemes are employed to provide guidance for future applications to MSN models. An MSN pore model is functionalised with (phenyl)propyl substituents and the diffusion barrier for benzene passing through the pore is computed by the FMO/RHF-D method with the Grimme dispersion correction (RHF-D). For the reaction coordinates examined here, the maximum FMO/RHF-D interaction energies range from -0.3 to -5.8 kcal/mol.

  13. O( N) tight-binding molecular dynamics on massively parallel computers: an orbital decomposition approach

    Science.gov (United States)

    Canning, A.; Galli, G.; Mauri, F.; De Vita, A.; Car, R.

    1996-04-01

    The implementation of an O( N) tight-binding molecular dynamics code on the Cray T3D parallel computer is discussed. The O( N) energy functional depends on non-orthogonal, localised orbitals and a chemical potential parameter which determines the number of electrons in the system. The localisation introduces a sparse nature to the orbital data and Hamiltonian matrix, greatly changing the coding on parallel machines compared to non-localised systems. The data distribution, communication routines and dynamic load-balancing scheme of the program are presented in detail together with the speed and scaling of the code on various homogeneous and inhomogeneous physical systems. Performance results will be presented for systems of 2048 to 32768 atoms on 32 to 512 processors. We discuss the relevance to quantum molecular dynamics simulations with localised orbitals, of techniques used for programming short-range classical molecular dynamics simulations on parallel machines. The absence of global communications and the localised nature of the orbitals makes these algorithms extremely scalable in terms of memory and speed on parallel systems with fast communications. The main aim of this article is to present in detail all the new concepts and programming techniques that localisation of the orbitals introduces which scientists, coming from a background in non-localised quantum molecular dynamics simulations, may be unfamiliar with.

  14. GPS Based Reduced-Dynamic Orbit Determination for Low Earth Orbiters with Ambiguity Fixing

    Directory of Open Access Journals (Sweden)

    Yang Yang

    2015-01-01

    Full Text Available With the ever-increasing number of satellites in Low Earth Orbit (LEO for scientific missions, the precise determination of the position and velocity of the satellite is a necessity. GPS (Global Positioning System based reduced-dynamic orbit determination (RPOD method is commonly used in the post processing with high precision. This paper presents a sequential RPOD strategy for LEO satellite in the framework of Extended Kalman Filter (EKF. Precise Point Positioning (PPP technique is used to process the GPS observations, with carrier phase ambiguity resolution using Integer Phase Clocks (IPCs products. A set of GRACE (Gravity Recovery And Climate Experiment mission data is used to test and validate the RPOD performance. Results indicate that orbit determination accuracy could be improved by 15% in terms of 3D RMS error in comparison with traditional RPOD method with float ambiguity solutions.

  15. Pyrite oxidation and reduction - Molecular orbital theory considerations. [for geochemical redox processes

    Science.gov (United States)

    Luther, George W., III

    1987-01-01

    In this paper, molecular orbital theory is used to explain a heterogeneous reaction mechanism for both pyrite oxidation and reduction. The mechanism demonstrates that the oxidation of FeS2 by Fe(3+) may occur as a result of three important criteria: (1) the presence of a suitable oxidant having a vacant orbital (in case of liquid phase) or site (solid phase) to bind to the FeS2 via sulfur; (2) the initial formation of a persulfido (disulfide) bridge between FeS2 and the oxidant, and (3) an electron transfer from a pi(asterisk) orbital in S2(2-) to a pi or pi(asterisk) orbital of the oxidant.

  16. Molecular Orbitals of NO, NO[superscript+], and NO[superscript-]: A Computational Quantum Chemistry Experiment

    Science.gov (United States)

    Orenha, Renato P.; Galembeck, Sérgio E.

    2014-01-01

    This computational experiment presents qualitative molecular orbital (QMO) and computational quantum chemistry exercises of NO, NO[superscript+], and NO[superscript-]. Initially students explore several properties of the target molecules by Lewis diagrams and the QMO theory. Then, they compare qualitative conclusions with EHT and DFT calculations…

  17. Electronic and Redox Properties of Stacked-Ring Silicon Phthalocyanines from Molecular Orbital Theory.

    Science.gov (United States)

    1984-10-19

    a molecular orbital approximation to the electron delocalization energy.1 8 The ASED theory is derived from the Hellmann- Feynman formula for...34 . . 4.•" " ., .7% . r .- - - . , .-. - . . _ .-.- :.- .- . v ._ . _ . " - . ’ " _ _ 12. Wheeler , B. L.; Nagasubramanian, G.; Bard, A. J

  18. Impact of Ionosphere on GPS-based Precise Orbit Determination of Low Earth Orbiters

    Science.gov (United States)

    Arnold, D.; Jaeggi, A.; Beutler, G.; Meyer, U.; Schaer, S.

    2015-12-01

    Deficiencies in geodetic products derived from the orbital trajectories of Low Earth Orbiting (LEO) satellites determined by GPS-based Precise Orbit Determination (POD) were identified in recent years. The precise orbits of the Gravity Field and Steady-State Ocean Circulation Explorer (GOCE) mission are, e.g., severely affected by an increased position noise level over the geomagnetic poles and spurious signatures along the Earth's geomagnetic equator (see Fig. 1, which shows the carrier phase residuals of a reduced-dynamic orbit determination for GOCE in m). Such degradations may directly map into the gravity fields recovered from the orbits. They are related to a disturbed GPS signal propagation through the Earth's ionosphere and indicate that the GPS observation model and/or the data pre-processing need to be improved. While GOCE was the first mission where severe ionosphere-related problems became obvious, the GPS-based LEO POD of satellites of the more recent missions Swarm and Sentinel-1A turn out to be affected, as well. We characterize the stochastic and systematic behavior of the ionosphere by analyzing GPS data collected by the POD antennas of various LEO satellites covering a broad altitude range (e.g., GRACE, GOCE and Swarm) and for periods covering significant parts of an entire solar cycle, which probe substantially different ionosphere conditions. The information may provide the basis for improvements of data pre-processing to cope with the ionosphere-induced problems of LEO POD. The performance of cycle slip detection can, e.g., be degraded by large changes of ionospheric refraction from one measurement epoch to the next. Geographically resolved information on the stochastic properties of the ionosphere above the LEOs provide more realistic threshold values for cycle slip detection algorithms. Removing GPS data showing large ionospheric variations is a crude method to mitigate the ionosphere-induced artifacts in orbit and gravity field products

  19. In orbit debris-detection based on solar panels

    Science.gov (United States)

    Bauer, Waldemar; Romberg, Oliver; Pissarskoi, Alexei; Wiedemann, Carsten; Vörsmann, Peter

    2013-09-01

    The solar generator-based space debris impact detector (SOLID), currently under development at DLR, has a large impact area and offers high orbital flexibility. Once placed in orbit, it will collect space debris and micro-meteoroids impact data for software validation (e.g. MASTER or ORDEM). The verification of SOLID itself will be based on hypervelocity-impact testing (HVI-testing), anticipated to be performed at the Fraunhofer EMI (Ernst-Mach-Institute for High-Speed Dynamics in Freiburg, Germany). This paper presents the current state of SOLID development. Furthermore, the setup of the engineering model as well as corresponding assumptions in the manufacturing process is presented.

  20. Thermal Analysis Investigation of Dapoxetine and Vardenafil Hydrochlorides using Molecular Orbital Calculations.

    Science.gov (United States)

    Attia, Ali Kamal; Souaya, Eglal R; Soliman, Ethar A

    2015-11-01

    Thermal analysis techniques have been used to study the thermal behavior of dapoxetine and vardenafil hydrochlorides and confirmed using semi-empirical molecular orbital calculations. Thermogravimetric analysis, derivative thermogravimetry, differential thermal analysis and differential scanning calorimetry were used to determine the thermal behavior and purity of the drugs under investigation. Thermodynamic parameters such as activation energy, enthalpy, entropy and Gibbs free energy were calculated. Thermal behavior of DAP and VAR were confirmed using by semi-empirical molecular orbital calculations. The purity values were found to be 99.97% and 99.95% for dapoxetine and vardenafil hydrochlorides, respectively. The purity of dapoxetine and vardenafil hydrochlorides is similar to that found by reported methods according to DSC data. Thermal analysis justifies its application in quality control of pharmaceutical compounds due to its simplicity, sensitivity and low operational costs.

  1. Liquid Water through Density-Functional Molecular Dynamics: Plane-Wave vs Atomic-Orbital Basis Sets

    CERN Document Server

    Miceli, Giacomo; Pasquarello, Alfredo

    2016-01-01

    We determine and compare structural, dynamical, and electronic properties of liquid water at near ambient conditions through density-functional molecular dynamics simulations, when using either plane-wave or atomic-orbital basis sets. In both frameworks, the electronic structure and the atomic forces are self-consistently determined within the same theoretical scheme based on a nonlocal density functional accounting for van der Waals interactions. The overall properties of liquid water achieved within the two frameworks are in excellent agreement with each other. Thus, our study supports that implementations with plane-wave or atomic-orbital basis sets yield equivalent results and can be used indiscriminately in study of liquid water or aqueous solutions.

  2. Mass transport properties of Pu/DT mixtures from orbital free molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Kress, Joel David [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Ticknor, Christopher [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Collins, Lee A. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-09-16

    Mass transport properties (shear viscosity and diffusion coefficients) for Pu/DT mixtures were calculated with Orbital Free Molecular Dynamics (OFMD). The results were fitted to simple functions of mass density (for ρ=10.4 to 62.4 g/cm3) and temperature (for T=100 up to 3,000 eV) for Pu/DT mixtures consisting of 100/0, 25/75, 50/50, and 75/25 by number.

  3. Real-space observation of spin-split molecular orbitals of adsorbed single-molecule magnets

    National Research Council Canada - National Science Library

    Schwöbel, Jörg; Fu, Yingshuang; Brede, Jens; Dilullo, Andrew; Hoffmann, Germar; Klyatskaya, Svetlana; Ruben, Mario; Wiesendanger, Roland

    2012-01-01

    A key challenge in the field of molecular spintronics, and for the design of single-molecule magnet-based devices in particular, is the understanding and control of the molecular coupling at the electrode interfaces...

  4. Pseudo-symmetry analysis of the d-block molecular orbitals in four-coordinate complexes.

    Science.gov (United States)

    Falceto, Andrés; Casanova, David; Alemany, Pere; Alvarez, Santiago

    2013-06-03

    A rigorous definition of the concept of pseudo-symmetry, which is as important to chemistry as the concepts of symmetry implemented through group theory, should allow us to apply those group theoretical tools to molecules that are significantly distorted from those ideal symmetries best known and understood by the chemical community. In this paper, we consider four-coordinate transition-metal complexes with geometries along the interconversion path between the square and the tetrahedron and show how their molecular orbitals can be expressed in terms of either the tetrahedral or tetragonal symmetry groups. Furthermore, we analyze how the intensity of a d-d absorption band can be related to the degree of symmetry loss of the d-block molecular orbitals by means of their decomposition in terms of contributions from different pseudo-symmetry representations. As a final example, we also show how the substitution of a single ligand in a square planar complex affects the symmetry of the molecular orbitals and the absorption intensity associated to an electronic transition.

  5. High-order harmonics generated from single and multiple molecular orbits in mid-infrared laser fields

    Directory of Open Access Journals (Sweden)

    ZHANG Jingtao

    2015-08-01

    Full Text Available High-order harmonics generated from aligned molecules are studied by a nonperturbative QED theory and the effect of the multiple molecular orbits is included.The harmonic spectra generated from single molecular orbit exhibit an interference minimum which is induced by the molecular structure.The location of the spectral minimum shifts with the laser intensity in long laser pulses,but is fixed in ultrashort laser pulses.This difference is owed to the quiver motion of the electron in the laser pulses.The maximal shift of the spectral minimum equals to the increment of the ponderomotive energy and depends linearly on the laser intensity.The interference between the harmonics generated from multiple molecular orbits has two principal effects:one is obscuring the deep minima in the overall harmonic spectrum,the other is manifesting the phase jump in the harmonics generated from single molecular orbit.

  6. Pharmacophore modeling for anti-Chagas drug design using the fragment molecular orbital method.

    Directory of Open Access Journals (Sweden)

    Ryunosuke Yoshino

    Full Text Available Chagas disease, caused by the parasite Trypanosoma cruzi, is a neglected tropical disease that causes severe human health problems. To develop a new chemotherapeutic agent for the treatment of Chagas disease, we predicted a pharmacophore model for T. cruzi dihydroorotate dehydrogenase (TcDHODH by fragment molecular orbital (FMO calculation for orotate, oxonate, and 43 orotate derivatives.Intermolecular interactions in the complexes of TcDHODH with orotate, oxonate, and 43 orotate derivatives were analyzed by FMO calculation at the MP2/6-31G level. The results indicated that the orotate moiety, which is the base fragment of these compounds, interacts with the Lys43, Asn67, and Asn194 residues of TcDHODH and the cofactor flavin mononucleotide (FMN, whereas functional groups introduced at the orotate 5-position strongly interact with the Lys214 residue.FMO-based interaction energy analyses revealed a pharmacophore model for TcDHODH inhibitor. Hydrogen bond acceptor pharmacophores correspond to Lys43 and Lys214, hydrogen bond donor and acceptor pharmacophores correspond to Asn67 and Asn194, and the aromatic ring pharmacophore corresponds to FMN, which shows important characteristics of compounds that inhibit TcDHODH. In addition, the Lys214 residue is not conserved between TcDHODH and human DHODH. Our analysis suggests that these orotate derivatives should preferentially bind to TcDHODH, increasing their selectivity. Our results obtained by pharmacophore modeling provides insight into the structural requirements for the design of TcDHODH inhibitors and their development as new anti-Chagas drugs.

  7. Electronic structures of TiN and TiC-Extension of Molecular Orbital Method into Crystals

    Institute of Scientific and Technical Information of China (English)

    Bin Song; Gaoling Zhao

    2000-01-01

    Density of states and theoretical X-ray emission spectra for the valence bands of TiN and TiC are obtained with a molecular orbital method. In order to describe electronic structures of crystals, local clusters for the molecular orbital calculations are extended, including the effects from the outside of the cluster in the crystal. The theoretical results are in good agreement with the experimental ones.

  8. Study on Electric Charge Trapping in Cross-linking Polyethylene and Byproducts by using Molecular Orbital Calculation

    Science.gov (United States)

    Takada, Tatsuo; Hayase, Yuji; Miyake, Hiroaki; Tanaka, Yasuhiro; Yoshida, Masafumi

    This paper reports an examination of hetero-space charge trapping site in cross linked polyethylene (XLPE) using Molecular Orbital calculation. We chose a simple model for polyethylene (C24H50) with one molecular of acetophenone (one of cross linking byproducts), for the examination of XLPE sample. Molecular Orbital calculation can give the microscopic information of electron energy levels, electron density distributions and electro-static potential maps for the simple molecular mode of XLPE. It is presumed that the negative hetero-space charge (electron) and positive hetero-space charge (hole) were trapped at the permanent dipole of acetophenone, and the hole carrier could move in the polyethylene chain.

  9. Highest Occupied Molecular Orbital of Cyclopentanone by Binary (e, 2e) Spectroscopy

    Institute of Scientific and Technical Information of China (English)

    ZHANG Shu-Feng; NING Chuan-Gang; DENG Jing-Kang; REN Xue-Guang; SU Guo-Lin; YANG Tie-Cheng; HUANG Yan-Ru

    2006-01-01

    @@ We report the first measurements of the momentum profiles of highest occupied molecular orbital (HOMO) and the complete valence shell binding energy spectra of cyclopentanone with impact energies of 600 and 1200 eV by a binary (e, 2e) spectrometer. The experimental momentum profiles of the HOMO orbital are compared with the theoretical momentum distribution calculated using the Hartree-Fock and density functional theory methods with various basis sets. However, none of these calculations gives a completely satisfactory description of the momentum distributions of the HOMO 7b2. The inadequacy of the calculations could result in the intensity difference of the second maximum at p ~l.2a.u. between the experiment and the theory. The discrepancy between experimental and theoretical data in the low-momentum region is explained with the distorted wave effect.

  10. Covalent features in the hydrogen bond of a water dimer: molecular orbital analysis

    CERN Document Server

    Wang, Bo; Dai, Xing; Gao, Yang; Wang, Zhigang; Zhang, Rui-Qin

    2015-01-01

    The covalent-like characteristics of hydrogen bonds offer a new perspective on intermolecular interactions. Here, using density functional theory and post-Hartree-Fock methods, we reveal that there are two bonding molecular orbitals (MOs) crossing the O and H atoms of the hydrogen-bond in water dimer. Energy decomposition analysis also shows a non-negligible contribution of the induction term. These results illustrate the covalent-like character of the hydrogen bond between water molecules, which contributes to the essential understanding of ice, liquid water, related materials, and life sciences.

  11. Path Integral Molecular Dynamics for Hydrogen with Orbital-Free Density Functional Theory

    Science.gov (United States)

    Runge, Keith; Karasiev, Valentin; Deymier, Pierre

    2014-03-01

    The computational bottleneck for performing path-integral molecular dynamics (PIMD) for nuclei on a first principles electronic potential energy surface has been the speed with which forces from the electrons can be generated. Recent advances in orbital-free density functional theory (OF-DFT) not only allow for faster generation of first principles forces but also include the effects of temperature on the electron density. We will present results of calculations on hydrogen in warm dense matter conditions where the protons are described by PIMD and the electrons by OF-DFT. Work supported by U.S. Dept. of Energy, grant DE-SC0002139.

  12. Hybrid RHF/MP2 geometry optimizations with the effective fragment molecular orbital method

    DEFF Research Database (Denmark)

    Christensen, Anders Steen; Svendsen, Casper Steinmann; Fedorov, Dmitri G

    2014-01-01

    The frozen domain effective fragment molecular orbital method is extended to allow for the treatment of a single fragment at the MP2 level of theory. The approach is applied to the conversion of chorismate to prephenate by Chorismate Mutase, where the substrate is treated at the MP2 level of theory...... while the rest of the system is treated at the RHF level. MP2 geometry optimization is found to lower the barrier by up to 3.5 kcal/mol compared to RHF optimzations and ONIOM energy refinement and leads to a smoother convergence with respect to the basis set for the reaction profile. For double zeta...

  13. Multicenter molecular integrals for Slater orbitals of higher principal quantum numbers

    Science.gov (United States)

    Tai, H.

    1989-01-01

    As was shown earlier by Tai (1979), by using the Fourier-transform technique and properly coupling a pair of two-center exchange integrals, the multicenter molecular integrals can be cast into a simple expression upon which numerical procedures can be directly applied. In this paper, the procedure of Tai is extended to integrals involving orbitals with arbitrarily higher principal quantum number. The derivation is outlined, and the explicit expressions are presented for a three-center nuclear attraction integral and a four-center two-electron Coulomb repulsion integral of arbitrary higher states.

  14. The role of the exchange in the embedding electrostatic potential for the fragment molecular orbital method.

    Science.gov (United States)

    Fedorov, Dmitri G; Kitaura, Kazuo

    2009-11-01

    We have examined the role of the exchange in describing the electrostatic potential in the fragment molecular orbital method and showed that it should be included in the total Fock matrix to obtain an accurate one-electron spectrum; however, adding it to the Fock matrices of individual fragments and pairs leads to very large errors. For the error analysis we have used the virial theorem; numerical tests have been performed for solvated phenol at the Hartree-Fock level with the 6-31G( *) and 6-311G( * *) basis sets.

  15. Molecular Orbital Rule for Quantum Interference in Weakly Coupled Dimers: Low-Energy Giant Conductivity Switching Induced by Orbital Level Crossing.

    Science.gov (United States)

    Nozaki, Daijiro; Lücke, Andreas; Schmidt, Wolf Gero

    2017-02-16

    Destructive quantum interference (QI) in molecular junctions has attracted much attention in recent years. It can tune the conductance of molecular devices dramatically, which implies numerous potential applications in thermoelectric and switching applications. There are several schemes that address and rationalize QI in single molecular devices. Dimers play a particular role in this respect because the QI signal may disappear, depending on the dislocation of monomers. We derive a simple rule that governs the occurrence of QI in weakly coupled dimer stacks of both alternant and nonalternant polyaromatic hydrocarbons (PAHs) and extends the Tada-Yoshizawa scheme. Starting from the Green's function formalism combined with the molecular orbital expansion approach, it is shown that QI-induced antiresonances and their energies can be predicted from the amplitudes of the respective monomer terminal molecular orbitals. The condition is illustrated for a toy model consisting of two hydrogen molecules and applied within density functional calculations to alternant dimers of oligo(phenylene-ethynylene) and nonalternant PAHs. Minimal dimer structure modifications that require only a few millielectronvolts and lead to an energy crossing of the essentially preserved monomer orbitals are shown to result in giant conductance switching ratios.

  16. Higher-dimensional orbital-angular-momentum-based quantum key distribution with mutually unbiased bases

    CSIR Research Space (South Africa)

    Mafu, M

    2013-09-01

    Full Text Available We present an experimental study of higher-dimensional quantum key distribution protocols based on mutually unbiased bases, implemented by means of photons carrying orbital angular momentum. We perform (d + 1) mutually unbiased measurements in a...

  17. A polarizable force-field model for quantum-mechanical-molecular-mechanical Hamiltonian using expansion of point charges into orbitals.

    Science.gov (United States)

    Biswas, P K; Gogonea, Valentin

    2008-10-21

    We present an ab initio polarizable representation of classical molecular mechanics (MM) atoms by employing an angular momentum-based expansion scheme of the point charges into partial wave orbitals. The charge density represented by these orbitals can be fully polarized, and for hybrid quantum-mechanical-molecular-mechanical (QM/MM) calculations, mutual polarization within the QM/MM Hamiltonian can be obtained. We present the mathematical formulation and the analytical expressions for the energy and forces pertaining to the method. We further develop a variational scheme to appropriately determine the expansion coefficients and then validate the method by considering polarizations of ions by the QM system employing the hybrid GROMACS-CPMD QM/MM program. Finally, we present a simpler prescription for adding isotropic polarizability to MM atoms in a QM/MM simulation. Employing this simpler scheme, we present QM/MM energy minimization results for the classic case of a water dimer and a hydrogen sulfide dimer. Also, we present single-point QM/MM results with and without the polarization to study the change in the ionization potential of tetrahydrobiopterin (BH(4)) in water and the change in the interaction energy of solvated BH(4) (described by MM) with the P(450) heme described by QM. The model can be employed for the development of an extensive classical polarizable force-field.

  18. a Moessbauer Effect and Fenske-Hall Molecular Orbital Study of the Electronic Properties of Organoiron Clusters.

    Science.gov (United States)

    Buhl, Margaret Linn

    The electronic properties of trinuclear iron, tetranuclear iron butterfly, iron-cobalt, and iron-copper clusters have been studied experimentally at 78K by the Mossbauer effect and theoretically by Fenske-Hall molecular orbital calculations. The Mossbauer effect isomer shift is very sensitive to the differences in the iron s-electron densities in these clusters and, as expected, decreases as the sum of the iron 4s Mulliken population and the Clementi and Raimondi effective nuclear charge increases. The molecular orbital wave functions and the Mulliken atomic charges are used to calculate the electric field gradient at the metal nuclei and the iron Mossbauer effect quadrupole splittings. The valence contribution was found to be the major component of the electric field gradient in all the clusters studied. In general the calculated value of Delta E_ {Q} is larger than the observed value, as a result of neglect of the valence Sternheimer factor, R. The metal charge depends upon its electronegativity and upon the nature of its Lewis base ligands. The carbonyl ligand carbon charge becomes more positive as the metal electronegativity increases. The oxygen charge becomes more negative as the anionic cluster charge increases, and in so doing, yields the maximum anionic charge separation. The electronic properties of the terminal carbonyl ligands are similar to those of carbon monoxide, whereas the electronic properties of the bridging carbonyl ligands are similar to those of the carbonyl group found in aldehydes and ketones.

  19. A Simple Molecular Orbital Treatment of the Barrier to Internal Rotation in the Ethane Molecule

    Science.gov (United States)

    Smith, Derek W.

    1998-07-01

    The origin of the barrier to internal rotation in the ethane molecule is explored in terms of elementary molecular orbital (MO) considerations. Emphasis is placed on the antibonding effect, i.e. the result that an antibonding MO is more destabilized than its bonding counterpart is stabilized, relative to the parent atomic orbitals (AOs). It is shown that, in the case of two equivalent AOs, this effect is approximately proportional to the square of the overlap integral. By constructing the ethane Mos from those of two methyl fragments, it is shown that the most important orbital energy changes consequent upon rotation about the C-C bond can be expressed in terms of the antibonding effect arising from the filled twofold-degenerate p-bonding and -antibonding MOs. This can be reduced to the dependence on the rotation angle of the vicinal H-H overlap integrals, which are calculated explicitly, showing that the antibonding effect is minimised in the staggered conformation. A letter from Lawrence J. Sacks in our April 2000 issue addresses the above.

  20. Orbital-selective single molecule excitation and spectroscopy based on plasmon-exciton coupling

    CERN Document Server

    Imada, Hiroshi; Imai-Imada, Miyabi; Kawahara, Shota; Kimura, Kensuke; Kim, Yousoo

    2016-01-01

    The electronic excitation of molecules triggers diverse phenomena such as luminescence and photovoltaic effects, which are the bases of various energy-converting devices. Understanding and control of the excitations at the single-molecule level are long standing targets, however, they have been hampered by the limited spatial resolution in optical probing techniques. Here we investigate the electronic excitation of a single molecule with sub-molecular precision using a localised plasmon at the tip apex of a scanning tunnelling microscope (STM) as an excitation probe. Coherent energy transfer between the plasmon and molecular excitons is discovered when the plasmon is located in the proximity of isolated molecules, which is corroborated by a theoretical analysis. The polarised plasmonic field enables selective excitation of an electronic transition between anisotropic frontier molecular orbitals. Our findings have established the foundation of a novel single-molecule spectroscopy with STM, providing an integra...

  1. Liquid Be, Ca and Ba. An orbital-free ab-initio molecular dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Rio, B. G. del; González, L. E. [Departamento de Física Teórica, Atómica y Óptica, Universidad de Valladolid, 47011 Valladolid (Spain)

    2015-08-17

    Several static and dynamic properties of liquid beryllium (l-Be), liquid calcium (l-Ca) and liquid barium (l-Ba) near their triple point have been evaluated by the orbital-free ab initio molecular dynamics method (OF-AIMD), where the interaction between valence electrons and ions is described by means of local pseudopotentials. These local pseudopotentials used were constructed through a force-matching process with those obtained from a Kohn-Sham ab initio molecular dynamics study (KS-AIMD) of a reduced system with non-local pseudopotentials. The calculated static structures show good agreement with the available experimental data, including an asymmetric second peak in the structure factor which has been linked to the existence of a marked icosahedral short-range order in the liquid. As for the dynamic properties, we obtain collective density excitations whose associated dispersion relations exhibit a positive dispersion.

  2. Spin-orbit force, recoil corrections, and possible BB¯* and DD¯* molecular states

    Science.gov (United States)

    Zhao, Lu; Ma, Li; Zhu, Shi-Lin

    2014-05-01

    In the framework of the one-boson exchange model, we have calculated the effective potentials between two heavy mesons BB¯* and DD¯* from the t- and u-channel π-, η-, ρ-, ω-, and σ-meson exchanges with four kinds of quantum number: I=0, JPC=1++; I =0, JPC=1+-; I =1, JPC=1++; I =1, JPC=1+-. We keep the recoil corrections to the BB¯* and DD¯* systems up to O(1/M2). The spin-orbit force appears at O(/1M), which turns out to be important for the very loosely bound molecular states. Our numerical results show that the momentum-related corrections are unfavorable to the formation of the molecular states in the I =0, JPC=1++ and I =1, JPC=1+- channels in the DD¯* system.

  3. Elliptical formation control based on relative orbit elements

    Institute of Scientific and Technical Information of China (English)

    Yin Jianfeng; Han Chao

    2013-01-01

    A new set of relative orbit elements (ROEs) is used to derive a new elliptical formation flying model. In-plane and out-of-plane motions can be completely decoupled, which benefits ellip-tical formation design. The inverse transformation of the state transition matrix is derived to study the relative orbit control strategy. Impulsive feedback control laws are developed for both in-plane and out-of-plane relative motions. Control of in-plane and out-of-plane relative motions can be completely decoupled using the ROE-based feedback control law. A tangential impulsive control method is proposed to study the relationship of fuel consumption and maneuvering positions. An optimal analytical along-track impulsive control strategy is then derived. Different typical orbit maneuvers, including formation establishment, reconfiguration, long-distance maneuvers, and for-mation keeping, are taken as examples to demonstrate the performance of the proposed control laws. The effects of relative measurement errors are also considered to validate the high accuracy of the proposed control method.

  4. Introductory Molecular Orbital Theory: An Honors General Chemistry Computational Lab as Implemented Using Three-Dimensional Modeling Software

    Science.gov (United States)

    Ruddick, Kristie R.; Parrill, Abby L.; Petersen, Richard L.

    2012-01-01

    In this study, a computational molecular orbital theory experiment was implemented in a first-semester honors general chemistry course. Students used the GAMESS (General Atomic and Molecular Electronic Structure System) quantum mechanical software (as implemented in ChemBio3D) to optimize the geometry for various small molecules. Extended Huckel…

  5. Molecular-orbital and structural descriptors in theoretical investigation of electroreduction of nitrodiazoles

    Directory of Open Access Journals (Sweden)

    BRANKO KOLARIC

    2005-07-01

    Full Text Available It is shown how a simple theoretical approach can be used for the investigation of electro-organic reactions.Mononitroimidazoles and mononitropyrazoles were studied by the semiempirical MNDO-PM3 molecular orbital method. The electrochemical reduction potentials of diazoles have been correlated with the energy of the lowest unoccupied molecular orbital (LUMO. It was found that an admirable correlation could be obtained by the introduction of simple structural descriptors as a correction to the energy of the LUMO. The interaction of a molecule with its surrounding depends on electrostatic potential and on steric hindrance. Most of these steric effects are taken into account using two parameters having a very limited set of integer values. The first (b is the position of a ring substituent regarding ring nitrogens, which accounts for the different orientations of dipole moments and for the different shape of the electrostatic potential. The second (structural parameter (t is the type of the ring, which accounts mostly for different modes of electrode approach, and for different charge polarization patterns in two diazole rings. The extended correlation with ELUMO, b and t, is very good, having a regression coefficient r = 0.991. The intrinsic importance of b and t is exemplified by their high statistical weight.

  6. Superconductivity, Mott-Hubbard states, and molecular orbital order in intercalated fullerides

    CERN Document Server

    Iwasa, Y

    2003-01-01

    This article reviews the current status of chemically doped fullerene superconductors and related compounds, with particular focus on Mott-Hubbard states and the role of molecular orbital degeneracy. Alkaline-earth metal fullerides produce superconductors of several kinds, all of which have states with higher valence than (C sub 6 sub 0) sup 6 sup - , where the second lowest unoccupied molecular orbital (the LUMO + 1 state) is filled. Alkali-metal-doped fullerides, on the other hand, afford superconductors only at the stoichiometry A sub 3 C sub 6 sub 0 (A denotes alkali metal) and in basically fcc structures. The metallicity and superconductivity of A sub 3 C sub 6 sub 0 compounds are destroyed either by reduction of the crystal symmetry or by change in the valence of C sub 6 sub 0. This difference is attributed to the narrower bandwidth in the A sub 3 C sub 6 sub 0 system, causing electronic instability in Jahn-Teller insulators and Mott-Hubbard insulators. The latter metal-insulator transition is driven by...

  7. Molecular orbital studies of gas-phase interactions between complex molecules.

    Science.gov (United States)

    Gaudreault, Roger; Whitehead, M A; van de Ven, Theo G M

    2006-03-16

    Describing interactions among large molecules theoretically is a challenging task. As an example, we investigated gas-phase interactions between a linear nonionic oligomer and various model compounds (cofactors), which have been reported to associate experimentally, using PM3 semiempirical molecular orbital theory. As oligomer, we studied the hexamer of poly(ethylene oxide) (PEO), and as cofactors, we studied corilagin and related compounds containing phenolic groups (R-OH). These systems are of interest because they are models for PEO/cofactor flocculation systems, used in industrial applications. The PM3 delocalized molecular orbitals (DLMO) describe the bonding between (PEO)6 and cofactors, and some of them cover the complete complex. The DLMOs which cover the traditionally considered hydrogen bonds R-OH...O or R-CH...O show a distinct "pinch", a decrease of the electron density, between the H...O atoms. Calculations of Gibbs free energy, entropy, and enthalpy show that the PEO/cofactor complexes do not form at room temperature, because the loss of entropy exceeds the increase in enthalpy. The change in enthalpy is linearly related to the change in entropy for the different complexes. Even though bond lengths, bond angles, DLMOs, and electron densities for the PEO/cofactor complexes are consistent with the definition of hydrogen bonds, the number of intermolecular R-OH...O and R-CH...O bonds does not correlate with the enthalpy of association, indicating that the bonding mechanism for these systems is the sum of many small contributions of many delocalized orbitals.

  8. Study of the Molecular Geometry, Electronic Structure, and Thermal Stability of Phosphazene and Heterophosphazene Rings with ab Initio Molecular Orbital Calculations

    NARCIS (Netherlands)

    Jaeger, C.R.; Debowski, M.A.; Manners, I.; Vancso, G.J.

    1999-01-01

    Ab initio molecular orbital calculations at the MP2/6-31G* level of theory have been used to study the molecular geometry, electronic structure, and the thermal stability of six-membered phosphazene and heterophosphazene rings. The studies included the phosphazene ring [NPCl2]3, the carbophosphazene

  9. Statins in therapy: understanding their hydrophilicity, lipophilicity, binding to 3-hydroxy-3-methylglutaryl-CoA reductase, ability to cross the blood brain barrier and metabolic stability based on electrostatic molecular orbital studies.

    Science.gov (United States)

    Fong, Clifford W

    2014-10-06

    The atomic electrostatic potentials calculated by the CHELPG method have been shown to be sensitive indicators of the gas phase and solution properties of the statins. Solvation free energies in water, n-octanol and n-octane have been determined using the SMD solvent model. The percentage hydrophilicity and hydrophobicity (or lipophilicity) of the statins in solution have been determined using (a) the differences in solvation free energies between n-octanol and n-octane as a measure of hydrophilicity, and the solvation energy in octane as a measure of hydrophobicity (b) the sum of the atomic electrostatic charges on the hydrogen bonding and polar bonding nuclei of the common pharmacophore combined with a solvent measure of hydrophobicity, and (c) using the buried surface areas after statin binding to HMGCR to calculate the hydrophobicity of the bound statins. The data suggests that clinical definitions of statins as either "hydrophilic" or "lipophilic" based on experimental partition coefficients are misleading. An estimate of the binding energy between rosuvastatin and HMGCR has been made using: (a) a coulombic electrostatic interaction model, (b) the calculated desolvation and resolvation of the statin in water, and (c) the first shell transfer solvation energy as a proxy for the restructuring of the water molecules immediately adjacent to the active binding site of HMGCR prior to binding. Desolvation and resolvation of the statins before and after binding to HMGCR are major determinants of the energetics of the binding process. An analysis of the amphiphilic nature of lovastatin anion, acid and lactone and fluvastatin anion and their abilities to cross the blood brain barrier has indicated that this process may be dominated by desolvation and resolvation effects, rather than the statin molecular size or statin-lipid interactions within the bilayer. The ionization energy and electron affinity of the statins are sensitive physical indicators of the ease that the

  10. X-ray Constrained Extremely Localized Molecular Orbitals: Theory and Critical Assessment of the New Technique.

    Science.gov (United States)

    Genoni, Alessandro

    2013-07-09

    Following the X-ray constrained wave function approach proposed by Jayatilaka, we have devised a new technique that allows to extract molecular orbitals strictly localized on small molecular fragments from sets of experimental X-ray structure factors amplitudes. Since the novel strategy enables to obtain electron distributions that have quantum mechanical features and that can be easily interpreted in terms of traditional chemical concepts, the method can be also considered as a new useful tool for the determination and the analysis of charge densities from high-resolution X-ray experiments. In this paper, we describe in detail the theory of the new technique, which, in comparison to our preliminary work, has been improved both treating the effects of isotropic secondary extinctions and introducing a new protocol to halt the fitting procedure against the experimental X-ray scattering data. The performances of the novel strategy have been studied both in function of the basis-sets flexibility and in function of the quality of the considered crystallographic data. The tests performed on four different systems (α-glycine, l-cysteine, (aminomethyl)phosphonic acid and N-(trifluoromethyl)formamide) have shown that the achievement of good statistical agreements with the experimental measures mainly depends on the quality of the crystal structures (i.e., geometry positions and thermal parameters) used in the X-ray constrained calculations. Finally, given the reliable transferability of the obtained Extremely Localized Molecular Orbitals (ELMOs), we envisage to exploit the novel approach to construct new ELMOs databases suited to the development of linear-scaling methods for the refinement of macromolecular crystal structures.

  11. Modeling Photodetachment from HO2- Using the pd Case of the Generalized Mixed Character Molecular Orbital Model

    Science.gov (United States)

    Blackstone, Christopher C.; Sanov, Andrei

    2016-06-01

    Using the generalized model for photodetachment of electrons from mixed-character molecular orbitals, we gain insight into the nature of the HOMO of HO2- by treating it as a coherent superpostion of one p- and one d-type atomic orbital. Fitting the pd model function to the ab initio calculated HOMO of HO2- yields a fractional d-character, γp, of 0.979. The modeled curve of the anisotropy parameter, β, as a function of electron kinetic energy for a pd-type mixed character orbital is matched to the experimental data.

  12. Analytic formulation of derivative coupling vectors for complete active space configuration interaction wavefunctions with floating occupation molecular orbitals

    Science.gov (United States)

    Hohenstein, Edward G.

    2016-11-01

    The floating occupation molecular orbital complete active space configuration interaction (FOMO-CASCI) method is quite promising for the study of nonadiabatic processes. Use of this method directly in nonadiabatic dynamics simulations has been limited by the lack of available first-order nonadiabatic coupling vectors. Here, an analytic formulation of these derivative coupling vectors is presented for FOMO-CASCI wavefunctions using a simple Lagrangian-based approach. The derivative coupling vectors are applied in the optimization of minimum energy conical intersections of an aqueously solvated model compound for the chromophore of the green fluorescent protein (including 100 water molecules). The computational cost of the FOMO-CASCI derivative coupling vector is shown to scale quadratically, O ( N 2 ) , with system size and is applied to systems with up to 1000 atoms.

  13. Tracking target objects orbiting earth using satellite-based telescopes

    Energy Technology Data Exchange (ETDEWEB)

    De Vries, Willem H; Olivier, Scot S; Pertica, Alexander J

    2014-10-14

    A system for tracking objects that are in earth orbit via a constellation or network of satellites having imaging devices is provided. An object tracking system includes a ground controller and, for each satellite in the constellation, an onboard controller. The ground controller receives ephemeris information for a target object and directs that ephemeris information be transmitted to the satellites. Each onboard controller receives ephemeris information for a target object, collects images of the target object based on the expected location of the target object at an expected time, identifies actual locations of the target object from the collected images, and identifies a next expected location at a next expected time based on the identified actual locations of the target object. The onboard controller processes the collected image to identify the actual location of the target object and transmits the actual location information to the ground controller.

  14. Fourier transform photoelectron diffraction and its application to molecular orbitals and surface structure

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Xin [Pennsylvania State Univ., University Park, PA (United States)

    1998-11-30

    Photoemission intensities from the molecular orbitals of c(2x2)CO/Pt(111) over a wide photon energy range were measured and analyzed by the same methods developed for structural studies using core levels. The 4{sigma} orbital center of gravity is found to be concentrated between the C and O atoms, while that of the 5{sigma} orbital lies between the C atom and the Pt surface. The C 1s photoelectron diffraction was used to determine the adsorption geometry. The earlier ambiguity that multiple scattering is needed to correctly model a {chi} curve while single scattering is sufficient for understanding major peaks in the ARPEFS-FTS is clarified by studying the clean Ni(111) surface. In the normal emission case, several different combinations of scattering events have similar path length differences (PLDs), and can either cancel each other or enhance the corresponding FT peak. In the off-normal case the degeneracy is greatly reduced due to the lower degree of symmetry. In normal emission AR PEFS, up to third order multiple scattering is needed to describe fully both the {chi} curve and its FT spectrum. To improve the spectral resolution in the ARPEFS-FT analysis, several new spectral analysis methods are introduced. With both autocorrelation autoregression (ACAR) and autocorrelation eigenvector (ACE), we can produce a reliable power spectrum by following the order-closing procedure. The best spectra are usually obtained when the autocorrelation sequence is computed with lags up to half the data range. A simple way of determining surface adsorption sites is proposed as follows: First use a single scattering cluster for possible adsorption sites to construct the geometrical PLDs from the strong backscattering events; then compare these PLDs with those obtained from the ARPEFS-FT analysis of the experimental data. After the preferred adsorption site is determined, fine tune the interlayer distances according to the positional R-factor.

  15. New orbits based on speckle interferometry at SOAR

    CERN Document Server

    Tokovinin, Andrei

    2016-01-01

    Orbits of 55 visual binary stars are computed using recent speckle interferometry data from the SOAR telescope: 33 first-time orbits and 22 revisions of previous orbit calculations. The orbital periods range from 1.4 to 370 years, the quality of orbits ranges from definitive to preliminary and tentative. Most binaries consist of low-mass dwarfs and have short periods (median period 31 years). The dynamical parallaxes and masses are evaluated and compared to the Hipparcos parallaxes. Using differential speckle photometry, binary components are placed on the color-magnitude diagram.

  16. Orbital-free molecular dynamics simulations of transport properties in dense-plasma uranium

    Science.gov (United States)

    Kress, J. D.; Cohen, James S.; Kilcrease, D. P.; Horner, D. A.; Collins, L. A.

    2011-09-01

    We have calculated the self-diffusion coefficients and shear viscosity of dense-plasma uranium using orbital-free molecular dynamics (OFMD) at the Thomas-Fermi-Dirac level. The transport properties of uranium in this regime have not previously been investigated experimentally or theoretically. The OFMD calculations were performed for temperatures from 50 to 5000 eV and densities from ambient to 10 times compressed. The results are compared with the one-component-plasma (OCP) model, using effective charges given by the average-atom code INFERNO and by the regularization procedure from the OFMD method. The latter generally showed better agreement with the OFMD for viscosity and the former for diffusion. A Stokes-Einstein relationship of the OFMD viscosities and diffusion coefficients is found to hold fairly well with a constant of 0.075 ± 0.10, while the OCP/INFERNO model yields 0.13 ± 0.10.

  17. Molecular orbital ab initio and density functional theoretical study on reaction between PH2 and NO

    Institute of Scientific and Technical Information of China (English)

    HU; Zhengfa(胡正发); WANG; Zhenya(王振亚); LI; Haiyang(李海洋); ZHOU; Shikang(周士康)

    2002-01-01

    The theoretical study of reaction between PH2 and NO on the ground state potential energy surface is reported by using molecular orbital ab initio calculation and density function theory (DFT). Equilibrium structural parameters, harmonic vibrational frequencies, total energies and zero point energies of all species during reaction are computed by HF, MP2 (full) and B3LYP theory levels with the medium basis set 6-31G*. Theoretical results indicate that intermediate IM1(H2PNO) is firstly formed by overcoming a small energy barrier TS1, and then two four-membered ring transient states TS2 and TS5, with energy barriers 103.3 and 102.6 kJ/mol respectively,then H-migration and isomerization are completed and the products PN and H2O are formed. The reaction is exothermic one with -189.6 k J/mol released.

  18. Oxygen evolution on a SrFeO3 anode - Mechanistic considerations from molecular orbital theory

    Science.gov (United States)

    Mehandru, S. P.; Anderson, Alfred B.

    1989-01-01

    Various pathways proposed in the literature for the evolution of O2 in electrochemical oxidations are explored using the atom superposition and electron delocalization molecular orbital (ASED-MO) theory and the cluster models of the SrFeO3 surface as a prototype material. Calculations indicate that oxygen atoms can be easily formed on the (100) surface as well as on the edge cation sites of a SrFeO3 anode by the discharge of OH(-), followed by its deprotonation and electron transfer to the electrode. The O atoms can form O2 on the edge and corner sites, where the Fe(4+) is coordinated to four and three bulk oxygen anions, respectively. The calculations strongly disfavor mechanisms involving coupling of oxygen atoms adsorbed on different cations as well as a mechanism featuring an ozone intermediate.

  19. Analytic second derivatives of the energy in the fragment molecular orbital method.

    Science.gov (United States)

    Nakata, Hiroya; Nagata, Takeshi; Fedorov, Dmitri G; Yokojima, Satoshi; Kitaura, Kazuo; Nakamura, Shinichiro

    2013-04-28

    We developed the analytic second derivatives of the energy for the fragment molecular orbital (FMO) method. First we derived the analytic expressions and then introduced some approximations related to the first and second order coupled perturbed Hartree-Fock equations. We developed a parallel program for the FMO Hessian with approximations in GAMESS and used it to calculate infrared (IR) spectra and Gibbs free energies and to locate the transition states in SN2 reactions. The accuracy of the Hessian is demonstrated in comparison to ab initio results for polypeptides and a water cluster. By using the two residues per fragment division, we achieved the accuracy of 3 cm(-1) in the reduced mean square deviation of vibrational frequencies from ab initio for all three polyalanine isomers, while the zero point energy had the error not exceeding 0.3 kcal/mol. The role of the secondary structure on IR spectra, zero point energies, and Gibbs free energies is discussed.

  20. Mapping enzymatic catalysis using the effective fragment molecular orbital method: towards all ab initio biochemistry.

    Science.gov (United States)

    Steinmann, Casper; Fedorov, Dmitri G; Jensen, Jan H

    2013-01-01

    We extend the Effective Fragment Molecular Orbital (EFMO) method to the frozen domain approach where only the geometry of an active part is optimized, while the many-body polarization effects are considered for the whole system. The new approach efficiently mapped out the entire reaction path of chorismate mutase in less than four days using 80 cores on 20 nodes, where the whole system containing 2398 atoms is treated in the ab initio fashion without using any force fields. The reaction path is constructed automatically with the only assumption of defining the reaction coordinate a priori. We determine the reaction barrier of chorismate mutase to be [Formula: see text] kcal mol(-1) for MP2/cc-pVDZ and [Formula: see text] for MP2/cc-pVTZ in an ONIOM approach using EFMO-RHF/6-31G(d) for the high and low layers, respectively.

  1. The Effective Fragment Molecular Orbital Method for Fragments Connected by Covalent Bonds

    Science.gov (United States)

    Steinmann, Casper; Fedorov, Dmitri G.; Jensen, Jan H.

    2012-01-01

    We extend the effective fragment molecular orbital method (EFMO) into treating fragments connected by covalent bonds. The accuracy of EFMO is compared to FMO and conventional ab initio electronic structure methods for polypeptides including proteins. Errors in energy for RHF and MP2 are within 2 kcal/mol for neutral polypeptides and 6 kcal/mol for charged polypeptides similar to FMO but obtained two to five times faster. For proteins, the errors are also within a few kcal/mol of the FMO results. We developed both the RHF and MP2 gradient for EFMO. Compared to ab initio, the EFMO optimized structures had an RMSD of 0.40 and 0.44 Å for RHF and MP2, respectively. PMID:22844433

  2. The McClelland approximation and the distribution of π-electron molecular orbital energy levels

    Directory of Open Access Journals (Sweden)

    IVAN GUTMAN

    2007-10-01

    Full Text Available The total π-electron energy E of a conjugated hydrocarbon with n carbon atoms and m carbon–carbon bonds can be approximately calculated by means of the McClelland formula E = g SQRT(2mr, where g is an empirical fitting constant, g ≈ 0.9. It was claimed that the good quality of the McClelland approximation is a consequence of the fact that the π-electron molecular orbital energy levels are distributed in a nearly uniform manner. It will now be shown that the McClelland approximation does not depend on the nature of the distribution of energy levels, i.e., that it is compatible with a large variety of such distributions.

  3. Molecular-orbital decomposition of the ionization continuum for a diatomic molecule by angle- and energy-resolved photoelectron spectroscopy. I. Formalism

    Science.gov (United States)

    Park, Hongkun; Zare, Richard N.

    1996-03-01

    A theoretical formalism is developed for the quantum-state-specific photoelectron angular distributions (PADs) from the direct photoionization of a diatomic molecule in which both the ionizing state and the state of the ion follow Hund's case (b) coupling. The formalism is based on the molecular-orbital decomposition of the ionization continuum and therefore fully incorporates the molecular nature of the photoelectron-ion scattering within the independent electron approximation. The resulting expression for the quantum-state-specific PADs is dependent on two distinct types of dynamical quantities, one that pertains only to the ionization continuum and the other that depends both on the ionizing state and the ionization continuum. Specifically, the electronic dipole-moment matrix element rlλ exp(iηlλ) for the ejection of a photoelectron with orbital angular momentum quantum number l making a projection λ on the internuclear axis is expressed as ΣαλŪlαλλ exp (iπτ¯αλλ) Mαλλ, where Ūλ is the electronic transformation matrix, τ¯αλλ is the scattering phase shift associated with the αλth continuum molecular orbital, and Mαλλ is the real electronic dipole-moment matrix element that connects the ionizing orbital to the αλth continuum molecular orbital. Because Ūλ and τ¯αλλ depend only on the dynamics in the ionization continuum, this formalism allows maximal exploitation of the commonality between photoionization processes from different ionizing states. It also makes possible the direct experimental investigation of scattering matrices for the photoelectron-ion scattering and thus the dynamics in the ionization continuum by studying the quantum-state-specific PADs, as illustrated in the companion article on the photoionization of NO.

  4. Equivalent-core calculation of core-level relaxation energies in photoelectron spectroscopy: A molecular-orbital approach

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Y. [Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States); Zhuang, G.; Ross, P.N. [Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States); Van Hove, M.A.; Fadley, C.S. [Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (United States)]|[Department of Physics, University of California at Davis, Davis, California 95616 (United States)

    1998-10-01

    The equivalent-core approximation is implemented in a novel way so as to calculate core-level relaxation energies in photoelectron spectroscopy. The method is based on self-consistent field (SCF) Hartree{endash}Fock molecular-orbital calculations via linear combinations of atomic orbitals, and involves evaluating the difference of sums of two-electron Coulomb and exchange integrals, for all electrons in an atom and in its equivalent-core ion. By thus avoiding SCF calculations with a core hole present (the true final state of photoemission), this procedure is shown to significantly save computing time in comparison with an exact SCF direct-hole calculation. Application of the method in single atoms and selected molecules shows about a 10{percent} difference with respect to direct-hole calculation results. The approximation introduces about 1{endash}6 eV errors compared to the experimental results of gas phase molecules. This method thus should be a generally useful procedure for estimating relaxation energies in core spectra. {copyright} {ital 1998 American Institute of Physics.}

  5. Atomic orbital-based SOS-MP2 with tensor hypercontraction. I. GPU-based tensor construction and exploiting sparsity

    Science.gov (United States)

    Song, Chenchen; Martínez, Todd J.

    2016-05-01

    We present a tensor hypercontracted (THC) scaled opposite spin second order Møller-Plesset perturbation theory (SOS-MP2) method. By using THC, we reduce the formal scaling of SOS-MP2 with respect to molecular size from quartic to cubic. We achieve further efficiency by exploiting sparsity in the atomic orbitals and using graphical processing units (GPUs) to accelerate integral construction and matrix multiplication. The practical scaling of GPU-accelerated atomic orbital-based THC-SOS-MP2 calculations is found to be N2.6 for reference data sets of water clusters and alanine polypeptides containing up to 1600 basis functions. The errors in correlation energy with respect to density-fitting-SOS-MP2 are less than 0.5 kcal/mol for all systems tested (up to 162 atoms).

  6. Urea's effect on the ribonuclease A catalytic efficiency: a kinetic, 1H NMR and molecular orbital study.

    Science.gov (United States)

    Almarza, Jorge; Rincón, Luis; Bahsas, Alí; Pinto, María Angela; Brito, Francisco

    2013-02-01

    Understanding of protein-urea interactions is one of the greatest challenges to modern structural protein chemistry. Based in enzyme kinetics experiments and (1)H NMR spectroscopic analysis we proposed that urea, at low concentrations, directly interacts with the protonated histidines of the active center of RNase A, following a simple model of competitive inhibition. These results were supported by theoretical analysis based on the frontier molecular orbital theory and suggest that urea might establish a favorable interaction with the cationic amino acids. Our experimental evidence and theoretical analysis indicate that the initials steps of the molecular mechanism of Urea-RNase A interaction passes through the establishment of a three center four electron adduct. Also, our results would explain the observed disruption of the (1)H NMR signals corresponding to H12 and H119 (involved in catalysis) of the RNase A studied in the presence of urea. Our interaction model of urea-amino acids (cationic) can be extended to explain the inactivation of other enzymes with cationic amino acids at the active site.

  7. Orbit determination of space objects based on sparse optical data

    CERN Document Server

    Milani, A; Farnocchia, D; Rossi, A; Schildknecht, T; Jehn, R

    2010-01-01

    While building up a catalog of Earth orbiting objects, if the available optical observations are sparse, not deliberate follow ups of specific objects, no orbit determination is possible without previous correlation of observations obtained at different times. This correlation step is the most computationally intensive, and becomes more and more difficult as the number of objects to be discovered increases. In this paper we tested two different algorithms (and the related prototype software) recently developed to solve the correlation problem for objects in geostationary orbit (GEO), including the accurate orbit determination by full least squares solutions with all six orbital elements. Because of the presence in the GEO region of a significant subpopulation of high area to mass objects, strongly affected by non-gravitational perturbations, it was actually necessary to solve also for dynamical parameters describing these effects, that is to fit between 6 and 8 free parameters for each orbit. The validation w...

  8. CaH Rydberg series, oscillator strengths and photoionization cross sections from Molecular Quantum Defect and Dyson Orbital theories

    Science.gov (United States)

    Velasco, A. M.; Lavín, C.; Díaz-Tinoco, Manuel; Ortiz, J. V.

    2017-01-01

    In this work, electron-propagator methods are applied to the calculation of the ionization potential and vertical excitation energies for several Rydberg series of the CaH molecule. The present calculations cover more highly excited states than those previously reported. In particular, excitation energies for ns (n>5), np (n>5), nd (n>4) and nf Rydberg states are given. Oscillator strengths for electronic transitions involving Rydberg states of CaH, as well as photoionization cross sections for Rydberg channels, also have been determined by using the Molecular Quantum Defect Orbital approach. Good agreement has been found with the scarce comparative data that are available for oscillator strengths. To our knowledge, predictions of photoionization cross sections from the outermost orbital of CaH are made here for the first time. A Cooper minimum and mixed atomic orbital character in some of the Dyson orbitals are among the novel features of these present calculations.

  9. Construction of Different Kinds of Atomic and Molecular Orbitals Using Complete Orthonormal Sets of -ETO in Single Exponent Approximation

    Institute of Scientific and Technical Information of China (English)

    Guseinov I. Israfil; Erturk Murat

    2008-01-01

    Using complete orthonormal sets of Ψα -exponential type orbitals in single exponent approximation the new approach has been suggested for construction of different kinds of functions which can be useful in the theory of linear combination of atomic orbitals. These functions can be chosen properly according to the nature of the problems under consideration. This is rather important because the choice of the basis set may be play a crucial role in applications to atomic and molecular problems. As an example of application, different atomic orbitals for the ground states of the neutral and the first ten cationic members of the isoelectronic series of He atom are constructed by the solution of Hartree-Fock Roothaan equations using Ψ1, Ψ0 and Ψ-1 basis sets. The calculated results are close to the numerical Hartree-Fock values. The total energy, expansion coefficients, orbital exponents and virial ratio for each atom are presented.

  10. Spectroscopic studies and molecular orbital calculations of charge transfer complexation between 3,5-dimethylpyrazole with DDQ in acetonitrile.

    Science.gov (United States)

    Habeeb, Moustafa M; Al-Attas, Amirah S; Al-Raimi, Doaa S

    2015-05-05

    Charge transfer (CT) interaction between 3,5-dimethylpyrazole (DMP) with the π-acceptor 2,3-dichloro-5,6-dicyano-p-benzoquinon (DDQ) has been investigated spectrophotometrically in acetonitrile (AN). Simultaneous reddish brown color has been observed upon mixing donor with acceptor solutions attributing to CT complex formation. The electronic spectra of the formed complex exhibited multi-charge transfer bands at 429, 447, 506, 542 and 589nm, respectively. Job(')s method of continuous variations and spectrophotometric titration methods confirmed the formation of the studied complex in 1:2 ratio between DMP and DDQ. Benesi-Hildebrand equation has been applied to calculate the stability constant of the formed complex where it recorded high value supporting formation of stable complex. Molecular orbital calculations using MM2 method and GAMESS (General Atomic and Molecular Electronic Structure System) interface computations as a package of ChemBio3D Ultra12 software were carried out for more analysis of the formed complex in the gas phase. The computational analysis included energy minimisation, stabilisation energy, molecular geometry, Mullikan charges, molecular electrostatic potential (MEP) surfaces of reactants and complex as well as characterization of the higher occupied molecular orbitals (HOMO) and lower unoccupied molecular orbitals (LUMO) surfaces of the complex. A good consistency between experimental and theoretical results has been recorded.

  11. Spectroscopic mapping and selective electronic tuning of molecular orbitals in phosphorescent organometallic complexes – a new strategy for OLED materials

    Directory of Open Access Journals (Sweden)

    Pascal R. Ewen

    2014-11-01

    Full Text Available The improvement of molecular electronic devices such as organic light-emitting diodes requires fundamental knowledge about the structural and electronic properties of the employed molecules as well as their interactions with neighboring molecules or interfaces. We show that highly resolved scanning tunneling microscopy (STM and spectroscopy (STS are powerful tools to correlate the electronic properties of phosphorescent complexes (i.e., triplet emitters with their molecular structure as well as the local environment around a single molecule. We used spectroscopic mapping to visualize several occupied and unoccupied molecular frontier orbitals of Pt(II complexes adsorbed on Au(111. The analysis showed that the molecules exhibit a peculiar localized strong hybridization that leads to partial depopulation of a dz² orbital, while the ligand orbitals are almost unchanged. We further found that substitution of functional groups at well-defined positions can alter specific molecular orbitals without influencing the others. The results open a path toward the tailored design of electronic and optical properties of triplet emitters by smart ligand substitution, which may improve the performance of future OLED devices.

  12. Introduction to Computational Chemistry: Teaching Hu¨ckel Molecular Orbital Theory Using an Excel Workbook for Matrix Diagonalization

    Science.gov (United States)

    Litofsky, Joshua; Viswanathan, Rama

    2015-01-01

    Matrix diagonalization, the key technique at the heart of modern computational chemistry for the numerical solution of the Schrödinger equation, can be easily introduced in the physical chemistry curriculum in a pedagogical context using simple Hückel molecular orbital theory for p bonding in molecules. We present details and results of…

  13. Orbital momentum profiles and binding energy spectra for the complete valence shell of molecular fluorine

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, Y.; Brion, C.E. [British Columbia Univ., Vancouver, BC (Canada). Dept. of Chemistry; Brunger, M.J.; Zhao, K.; Grisogono, A.M.; Braidwood, S.; Weigold, E. [Flinders Univ. of South Australia, Adelaide, SA (Australia). Electronic Structure of Materials Centre; Chakravorty, S.J.; Davidson, E.R. [Indiana Univ., Bloomington, IN (United States). Dept. of Chemistry; Sgamellotti, A. [Univ di Perugia (Italy). Dipartimento di Chimica; von Niessen, W. [Technische Univ. Braunschweig (Germany). Inst fuer Physikalische

    1996-01-01

    The first electronic structural study of the complete valence shell binding energy spectrum of molecular fluorine, encompassing both the outer and inner valence regions, is reported. These binding energy spectra as well as the individual orbital momentum profiles have been measured using an energy dispersive multichannel electron momentum spectrometer at a total energy of 1500 eV, with an energy resolution of 1.5 eV and a momentum resolution of 0.1 a.u. The measured binding energy spectra in the energy range of 14-60 eV are compared with the results of ADC(4) many-body Green`s function and also direct-Configuration Interaction (CI) and MRSD-CI calculations. The experimental orbital electron momentum profiles are compared with SCF theoretical profiles calculated using the target Hartree-Fock approximation with a range of basis sets and with Density Functional Theory predictions in the target Kohn-Sham approximation with non-local potentials. The truncated (aug-cc-pv5z) Dunning basis sets were used for the Density Functional Theory calculations which also include some treatment of correlation via the exchange and correlation potentials. Comparisons are also made with the full ion-neutral overlap amplitude calculated with MRSD-CI wave functions. Large, saturated basis sets (199-GTO) were employed for both the high level SCF near Hartree-Fock limit and MRSD-CI calculations to investigate the effects of electron correlation and relaxation. 66 refs., 9 tabs., 9 figs.

  14. Studies of the molecular geometry, vibrational spectra, frontier molecular orbital, nonlinear optical and thermodynamics properties of aceclofenac by quantum chemical calculations.

    Science.gov (United States)

    Suresh, S; Gunasekaran, S; Srinivasan, S

    2014-05-05

    The solid phase FT-IR and FT-Raman spectra of 2-[2-[2-[(2,6-dichlorophenyl)amino]phenyl]acetyl] oxyacetic acid (Aceclofenac) have been recorded in the region 4000-400 and 4000-100 cm(-1) respectively. The optimized molecular geometry and fundamental vibrational frequencies are interpreted with the aid of structure optimizations and normal coordinate force field calculations based on density functional theory (DFT) method and a comparative study between Hartree Fork (HF) method 6-311++G(d,p) level basis set. The calculated harmonic vibrational frequencies were scaled and have been compared with experimental by obtained FT-IR and FT-Raman spectra. A detailed interpretation of the vibrational spectra of this compound has been made on the basis of the calculated potential energy distribution (PED). The time dependent DFT method employed to study its absorption energy and oscillator strength. The linear polarizability (α) and the first order hyper polarizability (β) values of the investigated molecule have been computed. The electronic properties, such as HOMO and LUMO energies, molecular electrostatic potential (MESP) were also performed. Stability of the molecule arising from hyper conjugative interaction, charge delocalization has been analyzed using natural bond orbital (NBO) analysis.

  15. Molecular structure, vibrational spectra, natural bond orbital and thermodynamic analysis of 3,6-dichloro-4-methylpyridazine and 3,6-dichloropyridazine-4-carboxylic acid by dft approach.

    Science.gov (United States)

    Prabavathi, N; Senthil Nayaki, N; Venkatram Reddy, B

    2015-02-05

    Vibrational spectral analysis of the molecules 3,6-dichloro-4-methylpyridazine (DMP) and 3,6-dichloropyridazine-4-carboxylic acid (DPC) was carried out using FT-IR and FT-Raman spectroscopic techniques. The molecular structure and vibrational spectra of DMP and DPC were obtained by the density functional theory (DFT) method, using B3LYP functional, with 6-311++G(d,p) basis set. A detailed interpretation of the Infrared and Raman spectra of the two molecules were reported based on potential energy distribution (PED). The theoretically predicted FTIR and FT-Raman spectra of the titled molecules have been simulated and were compared with the experimental spectra. Determination of electric dipole moment (μ) and hyperpolarizability β0 helps to study the non-linear optical (NLO) behavior of DMP and DPC. Stability of the molecules arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. (13)C and (1)H NMR spectra were recorded and (13)C and (1)H NMR chemical shifts of the molecules were calculated using the gauge independent atomic orbital (GIAO) method. UV-visible spectrum of the compounds was also recorded in the region 200-1100 nm and electronic properties, HOMO (Highest Occupied Molecular Orbitals) and LUMO (Lowest Unoccupied Molecular Orbitals) energies were measured by time-dependent TD-DFT approach. Charge density distribution and site of chemical reactivity of the molecule have been studied by mapping electron density isosurface with molecular electrostatic potential (MESP). Copyright © 2014 Elsevier B.V. All rights reserved.

  16. Stimulated Radiative Molecular Association in the Early Solar System: Orbital Radii of Satellites of Uranus, Jupiter, Neptune, and Saturn

    CERN Document Server

    Lombardi, James C

    2015-01-01

    The present investigation relates the orbital radii of regular satellites of Uranus, Jupiter, Neptune, and Saturn to photon energies in the spectra of atomic and molecular hydrogen. To explain these observations a model is developed involving stimulated radiative molecular association (SRMA) reactions among the photons and atoms in the protosatellite disks of the planets. In this model thermal energy is extracted from each disk due to a resonance at radii where there is a match between the temperature in the disk and a photon energy. Matter accumulates at these radii, and satellites and rings are ultimately formed. Orbital radii of satellites of Uranus, Jupiter, and Neptune are related to photon energies ($E_{PM}$ values) in the spectrum of molecular hydrogen. Orbital radii of satellites of Saturn are related to photon energies ($E_{PA}$ values) in the spectrum of atomic hydrogen. The first hint that such relationships exist is found in the linearity of the graphs of orbital radii of uranian satellites vs. or...

  17. Chemical insight from density functional modeling of molecular adsorption: Tracking the bonding and diffusion of anthracene derivatives on Cu(111) with molecular orbitals

    Energy Technology Data Exchange (ETDEWEB)

    Wyrick, Jonathan; Bartels, Ludwig, E-mail: ludwig.bartels@ucr.edu [Pierce Hall, University of California-Riverside, Riverside, California 92521 (United States); Einstein, T. L. [Department of Physics and Condensed Matter Theory Center, University of Maryland, College Park, Maryland 20742-4111 (United States)

    2015-03-14

    We present a method of analyzing the results of density functional modeling of molecular adsorption in terms of an analogue of molecular orbitals. This approach permits intuitive chemical insight into the adsorption process. Applied to a set of anthracene derivates (anthracene, 9,10-anthraquinone, 9,10-dithioanthracene, and 9,10-diselenonanthracene), we follow the electronic states of the molecules that are involved in the bonding process and correlate them to both the molecular adsorption geometry and the species’ diffusive behavior. We additionally provide computational code to easily repeat this analysis on any system.

  18. Chemical insight from density functional modeling of molecular adsorption: Tracking the bonding and diffusion of anthracene derivatives on Cu(111) with molecular orbitals

    Science.gov (United States)

    Wyrick, Jonathan; Einstein, T. L.; Bartels, Ludwig

    2015-03-01

    We present a method of analyzing the results of density functional modeling of molecular adsorption in terms of an analogue of molecular orbitals. This approach permits intuitive chemical insight into the adsorption process. Applied to a set of anthracene derivates (anthracene, 9,10-anthraquinone, 9,10-dithioanthracene, and 9,10-diselenonanthracene), we follow the electronic states of the molecules that are involved in the bonding process and correlate them to both the molecular adsorption geometry and the species' diffusive behavior. We additionally provide computational code to easily repeat this analysis on any system.

  19. Beyond frontier molecular orbital theory: a systematic electron transfer model (ETM) for polar bimolecular organic reactions.

    Science.gov (United States)

    Cahill, Katharine J; Johnson, Richard P

    2013-03-01

    Polar bimolecular reactions often begin as charge-transfer complexes and may proceed with a high degree of electron transfer character. Frontier molecular orbital (FMO) theory is predicated in part on this concept. We have developed an electron transfer model (ETM) in which we systematically transfer one electron between reactants and then use density functional methods to model the resultant radical or radical ion intermediates. Sites of higher reactivity are revealed by a composite spin density map (SDM) of odd electron character on the electron density surface, assuming that a new two-electron bond would occur preferentially at these sites. ETM correctly predicts regio- and stereoselectivity for a broad array of reactions, including Diels-Alder, dipolar and ketene cycloadditions, Birch reduction, many types of nucleophilic additions, and electrophilic addition to aromatic rings and polyenes. Conformational analysis of radical ions is often necessary to predict reaction stereochemistry. The electronic and geometric changes due to one-electron oxidation or reduction parallel the reaction coordinate for electrophilic or nucleophilic addition, respectively. The effect is more dramatic for one-electron reduction.

  20. Exact density functional and wave function embedding schemes based on orbital localization

    Science.gov (United States)

    Hégely, Bence; Nagy, Péter R.; Ferenczy, György G.; Kállay, Mihály

    2016-08-01

    Exact schemes for the embedding of density functional theory (DFT) and wave function theory (WFT) methods into lower-level DFT or WFT approaches are introduced utilizing orbital localization. First, a simple modification of the projector-based embedding scheme of Manby and co-workers [J. Chem. Phys. 140, 18A507 (2014)] is proposed. We also use localized orbitals to partition the system, but instead of augmenting the Fock operator with a somewhat arbitrary level-shift projector we solve the Huzinaga-equation, which strictly enforces the Pauli exclusion principle. Second, the embedding of WFT methods in local correlation approaches is studied. Since the latter methods split up the system into local domains, very simple embedding theories can be defined if the domains of the active subsystem and the environment are treated at a different level. The considered embedding schemes are benchmarked for reaction energies and compared to quantum mechanics (QM)/molecular mechanics (MM) and vacuum embedding. We conclude that for DFT-in-DFT embedding, the Huzinaga-equation-based scheme is more efficient than the other approaches, but QM/MM or even simple vacuum embedding is still competitive in particular cases. Concerning the embedding of wave function methods, the clear winner is the embedding of WFT into low-level local correlation approaches, and WFT-in-DFT embedding can only be more advantageous if a non-hybrid density functional is employed.

  1. Optically induced transport through semiconductor-based molecular electronics

    Science.gov (United States)

    Li, Guangqi; Fainberg, Boris D.; Seideman, Tamar

    2015-04-01

    A tight binding model is used to investigate photoinduced tunneling current through a molecular bridge coupled to two semiconductor electrodes. A quantum master equation is developed within a non-Markovian theory based on second-order perturbation theory with respect to the molecule-semiconductor electrode coupling. The spectral functions are generated using a one dimensional alternating bond model, and the coupling between the molecule and the electrodes is expressed through a corresponding correlation function. Since the molecular bridge orbitals are inside the bandgap between the conduction and valence bands, charge carrier tunneling is inhibited in the dark. Subject to the dipole interaction with the laser field, virtual molecular states are generated via the absorption and emission of photons, and new tunneling channels open. Interesting phenomena arising from memory are noted. Such a phenomenon could serve as a switch.

  2. Construction of Ligand Group Orbitals for Polyatomics and Transition-Metal Complexes Using an Intuitive Symmetry-Based Approach

    Science.gov (United States)

    Johnson, Adam R.

    2013-01-01

    A molecular orbital (MO) diagram, especially its frontier orbitals, explains the bonding and reactivity for a chemical compound. It is therefore important for students to learn how to construct one. The traditional methods used to derive these diagrams rely on linear algebra techniques to combine ligand orbitals into symmetry-adapted linear…

  3. Combined fragment molecular orbital cluster in molecule approach to massively parallel electron correlation calculations for large systems.

    Science.gov (United States)

    Findlater, Alexander D; Zahariev, Federico; Gordon, Mark S

    2015-04-16

    The local correlation "cluster-in-molecule" (CIM) method is combined with the fragment molecular orbital (FMO) method, providing a flexible, massively parallel, and near-linear scaling approach to the calculation of electron correlation energies for large molecular systems. Although the computational scaling of the CIM algorithm is already formally linear, previous knowledge of the Hartree-Fock (HF) reference wave function and subsequent localized orbitals is required; therefore, extending the CIM method to arbitrarily large systems requires the aid of low-scaling/linear-scaling approaches to HF and orbital localization. Through fragmentation, the combined FMO-CIM method linearizes the scaling, with respect to system size, of the HF reference and orbital localization calculations, achieving near-linear scaling at both the reference and electron correlation levels. For the 20-residue alanine α helix, the preliminary implementation of the FMO-CIM method captures 99.6% of the MP2 correlation energy, requiring 21% of the MP2 wall time. The new method is also applied to solvated adamantine to illustrate the multilevel capability of the FMO-CIM method.

  4. A Monte-Carlo based extension of the Meteor Orbit and Trajectory Software (MOTS) for computations of orbital elements

    Science.gov (United States)

    Albin, T.; Koschny, D.; Soja, R.; Srama, R.; Poppe, B.

    2016-01-01

    The Canary Islands Long-Baseline Observatory (CILBO) is a double station meteor camera system (Koschny et al., 2013; Koschny et al., 2014) that consists of 5 cameras. The two cameras considered in this report are ICC7 and ICC9, and are installed on Tenerife and La Palma. They point to the same atmospheric volume between both islands allowing stereoscopic observation of meteors. Since its installation in 2011 and the start of operation in 2012 CILBO has detected over 15000 simultaneously observed meteors. Koschny and Diaz (2002) developed the Meteor Orbit and Trajectory Software (MOTS) to compute the trajectory of such meteors. The software uses the astrometric data from the detection software MetRec (Molau, 1998) and determines the trajectory in geodetic coordinates. This work presents a Monte-Carlo based extension of the MOTS code to compute the orbital elements of simultaneously detected meteors by CILBO.

  5. Natural atomic orbital based energy density analysis: Implementation and applications

    Science.gov (United States)

    Baba, Takeshi; Takeuchi, Mari; Nakai, Hiromi

    2006-06-01

    We present an improvement of energy density analysis (EDA), which partitions the total energy obtained by Hartree-Fock and/or density functional theory calculations, with the use of the natural atomic orbital (NAO) [A.E. Reed et al., J. Chem. Phys. 83 (1985) 735] and Löwdin's symmetric-orthogonal orbital (LSO). The present NAO- and LSO-EDA schemes are applied to analyses of CO 2 and Li9+ with various basis sets. Numerical results confirm that NAO-EDA exhibits less basis-set dependence, while the conventional results are very sensitive to the adopted basis sets.

  6. Investigation of naproxen drug using mass spectrometry, thermal analyses and semi-empirical molecular orbital calculation

    Directory of Open Access Journals (Sweden)

    M.A. Zayed

    2017-03-01

    Full Text Available Naproxen (C14H14O3 is a non-steroidal anti-inflammatory drug (NSAID. It is important to investigate its structure to know the active groups and weak bonds responsible for medical activity. In the present study, naproxen was investigated by mass spectrometry (MS, thermal analysis (TA measurements (TG/DTG and DTA and confirmed by semi empirical molecular orbital (MO calculation, using PM3 procedure. These calculations included, bond length, bond order, bond strain, partial charge distribution, ionization energy and heat of formation (ΔHf. The mass spectra and thermal analysis fragmentation pathways were proposed and compared to select the most suitable scheme representing the correct fragmentation pathway of the drug in both techniques. The PM3 procedure reveals that the primary cleavage site of the charged molecule is the rupture of the COOH group (lowest bond order and high strain which followed by CH3 loss of the methoxy group. Thermal analysis of the neutral drug reveals a high response to the temperature variation with very fast rate. It decomposed in several sequential steps in the temperature range 80–400 °C. These mass losses appear as two endothermic and one exothermic peaks which required energy values of 255.42, 10.67 and 371.49 J g−1 respectively. The initial thermal ruptures are similar to that obtained by mass spectral fragmentation (COOH rupture. It was followed by the loss of the methyl group and finally by ethylene loss. Therefore, comparison between MS and TA helps in selection of the proper pathway representing its fragmentation. This comparison is successfully confirmed by MO-calculation.

  7. Bases moleculares de las leucemias agudas

    Directory of Open Access Journals (Sweden)

    G. Martínez Antuña

    2006-04-01

    Full Text Available El gran desarrollo de la biología molecular en los últimos años ha contribuido a un importante avance en los conocimientos relacionados con las bases moleculares de las leucemias agudas (LA. Ademas de profundizar en la biología de estas enfermedades y conocer las bases moleculares, ha renido también gran impacto en mejorar el resultado de los tratamientos y disminuir la toxicidad de las terapias.

  8. Using Atomic Orbitals and Kinesthetic Learning to Authentically Derive Molecular Stretching Vibrations

    Science.gov (United States)

    Bridgeman, Adam J.; Schmidt, Timothy W.; Young, Nigel A.

    2013-01-01

    The stretching modes of ML[subscript "x"] complexes have the same symmetry as the atomic orbitals on M that are used to form its s bonds. In the exercise suggested here, the atomic orbitals are used to derive the form of the stretching modes without the need for formal group theory. The analogy allows students to help understand many…

  9. Using Atomic Orbitals and Kinesthetic Learning to Authentically Derive Molecular Stretching Vibrations

    Science.gov (United States)

    Bridgeman, Adam J.; Schmidt, Timothy W.; Young, Nigel A.

    2013-01-01

    The stretching modes of ML[subscript "x"] complexes have the same symmetry as the atomic orbitals on M that are used to form its s bonds. In the exercise suggested here, the atomic orbitals are used to derive the form of the stretching modes without the need for formal group theory. The analogy allows students to help understand many…

  10. [Molecular bases of prion diseases].

    Science.gov (United States)

    Pokrovskiĭ, V I; Kiselev, O I

    1998-01-01

    The paper briefly analyzes the origin of priones and their association with the cellular gene and homologous protein of diseases in man and animals. There is evidence for a direct relationship of the agents that cause spongious encephalitis in the cattle and a new type of Creutzfeldt-Jacob disease in man. The molecular organization of priones and the conformational cellular protein changes underlying the infectious activation of the cell homologue of priones. Emphasis is first laid on the capacity of the cell homologue of priones and their infectiously active derivative to bind to DNA or RNA. In the context of concepts of the priones yeasts an attempt was made to explain the reproduction through the altered control of translation of mRNA that encodes the cellular homologue of priones, which accounts for the duration of the incubation period of the disease. The infections caused by priones are referred to as the so-called slow infections. But in the context of the proposed hypothesis, an infective process in the tissues did not really have some typical signs of infection and resembles accumulation diseases more without the replicative burst typical of infectious processes. The paper gives data on the vital cycle of priones in infected animals and changes in the accumulation of an infective agent. This assesses the currently available diagnostic methods and gives preference to the methods which will be based on the use of monoclonal antibodies that specifically recognize the conformationally altered form of an infectious prione or on the identification of primary oligomeric forms which manifest the onset of amyloidization of the damaged tissues. The main conclusion of the paper is that protein prionization is a common biological phenomenon and the diseases caused by these processes will increase in number in the near future, which makes it necessary to develop diagnostic methods and universal treatments of diseases, such as bacterial infections by using antibiotics.

  11. Spin orbit coupling for molecular ab initio density matrix renormalization group calculations: Application to g-tensors

    Science.gov (United States)

    Roemelt, Michael

    2015-07-01

    Spin Orbit Coupling (SOC) is introduced to molecular ab initio density matrix renormalization group (DMRG) calculations. In the presented scheme, one first approximates the electronic ground state and a number of excited states of the Born-Oppenheimer (BO) Hamiltonian with the aid of the DMRG algorithm. Owing to the spin-adaptation of the algorithm, the total spin S is a good quantum number for these states. After the non-relativistic DMRG calculation is finished, all magnetic sublevels of the calculated states are constructed explicitly, and the SOC operator is expanded in the resulting basis. To this end, spin orbit coupled energies and wavefunctions are obtained as eigenvalues and eigenfunctions of the full Hamiltonian matrix which is composed of the SOC operator matrix and the BO Hamiltonian matrix. This treatment corresponds to a quasi-degenerate perturbation theory approach and can be regarded as the molecular equivalent to atomic Russell-Saunders coupling. For the evaluation of SOC matrix elements, the full Breit-Pauli SOC Hamiltonian is approximated by the widely used spin-orbit mean field operator. This operator allows for an efficient use of the second quantized triplet replacement operators that are readily generated during the non-relativistic DMRG algorithm, together with the Wigner-Eckart theorem. With a set of spin-orbit coupled wavefunctions at hand, the molecular g-tensors are calculated following the scheme proposed by Gerloch and McMeeking. It interprets the effective molecular g-values as the slope of the energy difference between the lowest Kramers pair with respect to the strength of the applied magnetic field. Test calculations on a chemically relevant Mo complex demonstrate the capabilities of the presented method.

  12. Scheduler for monitoring objects orbiting earth using satellite-based telescopes

    Energy Technology Data Exchange (ETDEWEB)

    Olivier, Scot S; Pertica, Alexander J; Riot, Vincent J; De Vries, Willem H; Bauman, Brian J; Nikolaev, Sergei; Henderson, John R; Phillion, Donald W

    2015-04-28

    An ephemeris refinement system includes satellites with imaging devices in earth orbit to make observations of space-based objects ("target objects") and a ground-based controller that controls the scheduling of the satellites to make the observations of the target objects and refines orbital models of the target objects. The ground-based controller determines when the target objects of interest will be near enough to a satellite for that satellite to collect an image of the target object based on an initial orbital model for the target objects. The ground-based controller directs the schedules to be uploaded to the satellites, and the satellites make observations as scheduled and download the observations to the ground-based controller. The ground-based controller then refines the initial orbital models of the target objects based on the locations of the target objects that are derived from the observations.

  13. Estimating spacecraft attitude based on in-orbit sensor measurements

    DEFF Research Database (Denmark)

    Jakobsen, Britt; Lyn-Knudsen, Kevin; Mølgaard, Mathias

    2014-01-01

    AAUSAT3 was launched February 2013 as a science experiment for the Danish Maritime Safety Administration, for monitoring ship traffic in arctic regions. This mission has been a large success. AAUSAT4 is an enhanced version of the former satellite, and is expected to be launched in the winter of 2...... Orbit (LEO). Tuning of the EKF in space will slightly improve the performance of the EKF but it is possible to determine the attitude of the satellite with a relatively low angular error without in-orbit tuning....... solely on Earth or whether an in-orbit tuning/update of the algorithm is needed. of the EKF. Generally, sensor noise variances are larger in the in-orbit measurements than in the measurements obtained on ground. From Monte Carlo simulations with varying settings of the satellite inertia and initial time......, attitude and rotational velocity, the EKF proves to be robust against noisy or lacking sensor data. It is apparent from the comparison of noise parameters from Earth and space, that an EKF tuned using Earth measurements of sensor variances will attain an acceptable performance when operated in Low Earth...

  14. Artificial frozen orbit control scheme based on J2 perturbation

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Since the inclination of frozen orbit with non-rotation of the perigee that occurs due to J2 perturbation must be equal to the critical inclination, this regulation has restricted the application of frozen orbit a lot. In this paper, we propose two control strategies to eliminate the secular growth of the argument of the perigee for orbits that are not at the critical inclination. One control strategy is using transverse continuous low-thrust, and the other is using both the transverse and the radial continuous low-thrusts. Fuel optimization in the second control strategy is addressed to make sure that the fuel consumption is the minimum. Both strategies have no effect on other orbital parameters’ secular motion. It is proved that the strategy with transverse control could save more energy than the one with radial control. Simulations show that the second control strategy could save 54.6% and 86% of energy, respectively, compared with the two methods presented in the references.

  15. Equation of state of a dense plasma by orbital-free and quantum molecular dynamics: examination of two isothermal-isobaric mixing rules.

    Science.gov (United States)

    Danel, J-F; Kazandjian, L

    2015-01-01

    We test two isothermal-isobaric mixing rules, respectively based on excess-pressure and total-pressure equilibration, applied to the equation of state of a dense plasma. While the equation of state is generally known for pure species, that of arbitrary mixtures is not available so that the validation of accurate mixing rules, that implies resorting to first-principles simulations, is very useful. Here we consider the case of a plastic with composition C(2)H(3) and we implement two complementary ab initio approaches adapted to the dense plasma domain: quantum molecular dynamics, limited to low temperature by its computational cost, and orbital-free molecular dynamics, that can be implemented at high temperature. The temperature and density range considered is 1-10 eV and 0.6-10 g/cm(3) for quantum molecular dynamics, and 5-1000 eV and 1-10 g/cm(3) for orbital-free molecular dynamics. Simulations for the full C(2)H(3) mixture are the benchmark against which to assess the mixing rules, and both pressure and internal energy are compared. We find that the mixing rule based on excess-pressure equilibration is overall more accurate than that based on total-pressure equilibration; except for quantum molecular dynamics and a thermodynamic domain characterized by very low or negative excess pressures, it gives pressures which are generally within statistical error or within 1% of the exact ones. Besides, its superiority is amplified in the calculation of a principal Hugoniot.

  16. Exciton analysis of many-body wave functions: Bridging the gap between the quasiparticle and molecular orbital pictures

    Science.gov (United States)

    Bäppler, Stefanie A.; Plasser, Felix; Wormit, Michael; Dreuw, Andreas

    2014-11-01

    Exciton sizes and electron-hole binding energies, which are central properties of excited states in extended systems and crucial to the design of modern electronic devices, are readily defined within a quasiparticle framework but are quite challenging to understand in the molecular-orbital picture. The intent of this work is to bridge this gap by providing a general way of extracting the exciton wave function out of a many-body wave function obtained by a quantum chemical excited-state computation. This methodology, which is based on the one-particle transition density matrix, is implemented within the ab initio algebraic diagrammatic construction scheme for the polarization propagator and specifically the evaluation of exciton sizes, i.e., dynamic charge separation distances, is considered. A number of examples are presented. For stacked dimers it is shown that the exciton size for charge separated states corresponds to the intermolecular separation, while it only depends on the monomer size for locally excited states or Frenkel excitons. In the case of conjugated organic polymers, the tool is applied to analyze exciton structure and dynamic charge separation. Furthermore, it is discussed how the methodology may be used for the construction of a charge-transfer diagnostic for time-dependent density-functional theory.

  17. Lewis Acid-Base, Molecular Modeling, and Isotopic Labeling in a Sophomore Inorganic Chemistry Laboratory

    Science.gov (United States)

    Nataro, Chip; Ferguson, Michelle A.; Bocage, Katherine M.; Hess, Brian J.; Ross, Vincent J.; Swarr, Daniel T.

    2004-01-01

    An experiment to prepare a deuterium labeled adduct of a Lewis acid and Lewis base, to use computational methods allowing students to visualize the LUMO of Lewis acids, the HOMO of Lewis bases and the molecular orbitals of the adduct that is formed is developed. This allows students to see the interplay between calculated and experimental results.

  18. Molecular Machine-Based Active Plasmonics

    Science.gov (United States)

    2011-07-21

    integrated multifunctional sensors and devices based on switchable molecules. This outcome is essential for the development of carbon nanotube...constitutes a seminal step towards functional nanoelectromechanical systems ( NEMS ) based on artificial molecular muscles. In addition, we have published a

  19. An Efficient Method to Evaluate Intermolecular Interaction Energies in Large Systems Using Overlapping Multicenter ONIOM and the Fragment Molecular Orbital Method

    Science.gov (United States)

    Asada, Naoya; Fedorov, Dmitri G.; Kitaura, Kazuo; Nakanishi, Isao; Merz, Kenneth M.

    2012-01-01

    We propose an approach based on the overlapping multicenter ONIOM to evaluate intermolecular interaction energies in large systems and demonstrate its accuracy on several representative systems in the complete basis set limit at the MP2 and CCSD(T) level of theory. In the application to the intermolecular interaction energy between insulin dimer and 4′-hydroxyacetanilide at the MP2/CBS level, we use the fragment molecular orbital method for the calculation of the entire complex assigned to the lowest layer in three-layer ONIOM. The developed method is shown to be efficient and accurate in the evaluation of the protein-ligand interaction energies. PMID:23050059

  20. Applications of the molecular orbital graph theory (XI)——The molecular moment’s method of evaluating π-bond grade and judging relative reactivity of even AH

    Institute of Scientific and Technical Information of China (English)

    胡式贤; 刘晓平; 赵洪刚; 曹阳

    2000-01-01

    The tree graph method of evaluating the local molecular moment is proposed. By applying this method and the molecular moment formula of π-electron energy in the molecular orbital graph theory, a topological method of using the molecular moment to judge the relatively reactive point of even AH is achieved.

  1. Analytic energy gradients with frozen molecular orbitals in coupled-cluster and many-body perturbation theory methods: Systematic study of the magnitude and trends of the effects of frozen molecular orbitals

    Science.gov (United States)

    Baeck, Kyoung K.; Watts, John D.; Bartlett, Rodney J.

    1997-09-01

    Analytic coupled-cluster (CC) and many-body perturbation theory (MBPT) energy gradient methods with restricted Hartree-Fock (RHF), unrestricted Hartree-Fock (UHF), restricted open-shell Hartree-Fock (ROHF), and quasi-RHF(QRHF) reference functions are extended to permit dopping core and excited orbitals. By using the canonical property of the semicanonical ROHF orbitals and the RHF orbitals from which the QRHF reference function is constructed, it is shown that a general procedure can be established not only for RHF and UHF, but also for ROHF and QRHF reference functions. The basic theory and implementation are reported. To provide a systematic study of the trends and magnitudes of the effects of dropped molecular orbitals (MOs) on the structures, harmonic frequencies, and ir intensities, we study HCN, C2H2, CO2, HO2, and C2H4 at increasing levels of correlation and basis sets. The effects of the dropped MOs with the largest basis sets are about 0.003 Å and 0.1° in structures and about 1% on harmonic frequencies and ir intensities. The magnitude and the direction of the drop-MO effect tend to be almost constant from MBPT(2) to CCSD(T) methods. The two isomers of S3 are studied by the drop-MO-method, yielding very accurate results.

  2. Template-Based Orbital Wall Fracture Treatment Using Statistical Shape Analysis.

    Science.gov (United States)

    Doerfler, Hans-Martin; Huempfner-Hierl, Heike; Kruber, Daniel; Schulze, Peter; Hierl, Thomas

    2017-07-01

    Aim of this study was to investigate whether a mold generated from a statistical shape model of the orbit could be generated to provide a cost-efficient means for the treatment of orbital fractures. A statistical shape model was created from 131 computed tomographic (CT) scans of unaffected adult middle European human orbits. To generate the model, CT scans were segmented in Brainlab software, preregistered using anatomic landmarks, trimmed to an identical size, and definitely registered. Then, the model was created using the global master algorithm. Based on this model, a mold consisting of a male part and a female part was constructed and printed using a rapid prototyping technique. A statistical shape model of the human orbit was generated from 125 CT scans. Six scans (4.5%) presented major anatomic deviations and were discarded. A solid mold based on this model was printed. Using this mold, flat titanium mesh could be successfully deformed to serve as an orbital implant. A mold based on the statistical orbital shape could serve as a cost-effective means for the treatment of orbital fractures. It allows the anatomic preformation of titanium or resorbable implant material for orbital reconstruction. Because these materials could be cut from larger sheets, the use of a mold would be a cost-effective treatment alternative. Copyright © 2017 American Association of Oral and Maxillofacial Surgeons. Published by Elsevier Inc. All rights reserved.

  3. Dynamic characteristic of amitriptyline in water by ultrasonic relaxation method and molecular orbital calculation.

    Science.gov (United States)

    Nishikawa, Sadakatsu; Kamimura, Eri

    2011-02-03

    Ultrasonic absorption coefficients in the frequency range of 0.8-220 MHz have been measured in aqueous solution of amitriptyline (3-(10,11-dihydro-5H-dibenzo[a,d]cycloheptene-5-ylidene)-N,N-dimethyl-1-propanamine) in the concentration range from 0.20 to 0.60 mol dm(-3) at 25 °C. A single relaxational phenomenon has been observed, and the relaxation frequency is independent of the concentration. It has been also observed that the amplitude of the relaxational absorption increases linearly with the analytical concentration. From these ultrasonic relaxation data, it has been concluded that the relaxation is associated with a unimolecular reaction due to a conformational change of the solute molecule, such as a structural change due to a rotational motion of a group in the solute molecule. Molecular orbital semiempirical methods using AM1 (Austin model 1) and PM3 (modified neglect of diatomic overlap parametric method 3) have been applied to obtain the standard enthalpy of formation for amitriptyline molecule at various dihedral angles around one of the bonds in alkylamine side chain. The results have shown the two clear minimum standard enthalpies of formation for amitriptyline. From the difference of the two values, the standard enthalpy change between the two stable conformers has been calculated be 2.9 kJ mol(-1). On a rough assumption that the standard enthalpy change reflects the standard free energy change, the equilibrium constant for the rotational isomers has been estimated to be 0.31. Combining this value with the experimental ultrasonic relaxation frequency, the backward and forward rate constants have been evaluated. The standard enthalpy change of the reaction has been also estimated from the concentration dependence of the maximum absorption per wavelength, and it has been close to that calculated by the semiempirical methods. The ultrasonic absorption measurements have been also carried out in amitriptyline solution in the presence of

  4. Calculation of wave-functions with frozen orbitals in mixed quantum mechanics/molecular mechanics methods. II. Application of the local basis equation.

    Science.gov (United States)

    Ferenczy, György G

    2013-04-05

    The application of the local basis equation (Ferenczy and Adams, J. Chem. Phys. 2009, 130, 134108) in mixed quantum mechanics/molecular mechanics (QM/MM) and quantum mechanics/quantum mechanics (QM/QM) methods is investigated. This equation is suitable to derive local basis nonorthogonal orbitals that minimize the energy of the system and it exhibits good convergence properties in a self-consistent field solution. These features make the equation appropriate to be used in mixed QM/MM and QM/QM methods to optimize orbitals in the field of frozen localized orbitals connecting the subsystems. Calculations performed for several properties in divers systems show that the method is robust with various choices of the frozen orbitals and frontier atom properties. With appropriate basis set assignment, it gives results equivalent with those of a related approach [G. G. Ferenczy previous paper in this issue] using the Huzinaga equation. Thus, the local basis equation can be used in mixed QM/MM methods with small size quantum subsystems to calculate properties in good agreement with reference Hartree-Fock-Roothaan results. It is shown that bond charges are not necessary when the local basis equation is applied, although they are required for the self-consistent field solution of the Huzinaga equation based method. Conversely, the deformation of the wave-function near to the boundary is observed without bond charges and this has a significant effect on deprotonation energies but a less pronounced effect when the total charge of the system is conserved. The local basis equation can also be used to define a two layer quantum system with nonorthogonal localized orbitals surrounding the central delocalized quantum subsystem.

  5. Niobate-based octahedral molecular sieves

    Science.gov (United States)

    Nenoff, Tina M.; Nyman, May D.

    2003-07-22

    Niobate-based octahedral molecular sieves having significant activity for multivalent cations and a method for synthesizing such sieves are disclosed. The sieves have a net negatively charged octahedral framework, comprising niobium, oxygen, and octahedrally coordinated lower valence transition metals. The framework can be charge balanced by the occluded alkali cation from the synthesis method. The alkali cation can be exchanged for other contaminant metal ions. The ion-exchanged niobate-based octahedral molecular sieve can be backexchanged in acidic solutions to yield a solution concentrated in the contaminant metal. Alternatively, the ion-exchanged niobate-based octahedral molecular sieve can be thermally converted to a durable perovskite phase waste form.

  6. [Molecular bases of cancer immunology].

    Science.gov (United States)

    Barrera-Rodríguez, R; Peralta-Zaragoza, O; Madrid-Marina, V

    1995-01-01

    The immune system is a tight network of different types of cells and molecules. The coordinated action of these elements mounts a precise immune response against tumor cells. However, these cells present several escape mechanisms, leading to tumor progression. This paper shows several cellular and molecular events involved in the regulation of the immune response against tumor cells. The interaction of several molecules such as MHC, TcR, adhesins, tumor antigens and cytokines are discussed, as well as the most recent knowledge about escape mechanisms and immunotherapy.

  7. Projector Augmented Wave Method Incorporated into Gauss-Type Atomic Orbital Based Density Functional Theory.

    Science.gov (United States)

    Xiong, Xiao-Gen; Yanai, Takeshi

    2017-07-11

    The Projector Augmented Wave (PAW) method developed by Blöchl is well recognized as an efficient, accurate pseudopotential approach in solid-state density functional theory (DFT) calculations with the plane-wave basis. Here we present an approach to incorporate the PAW method into the Gauss-type function (GTF) based DFT implementation, which is widely used for molecular quantum chemistry calculations. The nodal and high-exponent GTF components of valence molecular orbitals (MOs) are removed or pseudized by the ultrasoft PAW treatment, while there is elaborate transparency to construct an accurate and well-controlled pseudopotential from all-electron atomic description and to reconstruct an all-electron form of valence MOs from the pseudo MOs. The smoothness of the pseudo MOs should benefit the efficiency of GTF-based DFT calculations in terms of elimination of high-exponent primitive GTFs and reduction of grid points in the numerical quadrature. The processes of the PAW method are divided into basis-independent and -dependent parts. The former is carried out using the previously developed PAW libraries libpaw and atompaw. The present scheme is implemented by incorporating libpaw into the conventional GTF-based DFT solver. The details of the formulations and implementations of GTF-related PAW procedures are presented. The test calculations are shown for illustrating the performance. With the near-complete GTF basis at the cc-pVQZ level, the total energies obtained using our PAW method with suited frozen core treatments converge to those with the conventional all-electron GTF-based method with a rather small absolute error.

  8. Introducing PROFESS 3.0: An advanced program for orbital-free density functional theory molecular dynamics simulations

    Science.gov (United States)

    Chen, Mohan; Xia, Junchao; Huang, Chen; Dieterich, Johannes M.; Hung, Linda; Shin, Ilgyou; Carter, Emily A.

    2015-05-01

    Orbital-free density functional theory (OFDFT) is a linear-scaling first-principles quantum mechanics method used to calculate the ground-state energy of a given system. Here we present a new version of PRinceton Orbital-Free Electronic Structure Software (PROFESS) with new features. First, PROFESS 3.0 provides a set of new kinetic energy density functionals (KEDFs) which are designed to model semiconductors or transition metals. Specifically, PROFESS 3.0 includes the Huang-Carter (HC) KEDF [1], a density decomposition method with fixed localized electronic density [2], the Wang-Govind-Carter (WGC) decomposition KEDF [3], and the Enhanced von Weizsäcker (EvW)-WGC KEDF [4]. Other major new functions are included, such as molecular dynamics with different statistical mechanical ensembles and spin-polarized density optimizers.

  9. Secondary orbital effect in the electrocyclic ring closure of 7-Azahepta-1,2,4,6-tetraeneA CASSCF molecular orbital study.

    Science.gov (United States)

    Duncan, James A; Calkins, David E G; Chavarha, Mariya

    2008-05-28

    Results of (10,9)CASSCF/6-31G* and B3LYP/6-31G* level calculations on the potential surface for the electrocyclic ring closure of E-7-azahepta-1,2,4,6-tetraene 3 to 1-aza-6-methylidenecyclohexa-2,4-diene ( 4) are reported, as well as parallel calculations on the electrocyclizations of hepta-1,2,4,6-tetraene 5, hexa-1,3,5-triene 7, Z and E-1-aza-1,3,5-hexatrienes 9 and 10, and Z-7-azahepta-1,2,4,6-tetraene 12 for purposes of careful comparison. The 3 --> 4 rearrangement has been studied computationally with density functional theory (DFT) by others, leading to disagreement over whether it is pseudopericyclic (de Lera, A. R.; Alvarez, R.; Lecea, B.; Torrado, A.; Cossío, F. P. Angew. Chem., Int. Ed. 2001, 40, 557-561; de Lera, A. R.; Cossío, F. P. Angew. Chem., Int. Ed. 2002, 41, 1150-1152) or pericyclic (Rodríguez-Otero, J.; Cabaleiro-Lago, E. Angew. Chem., Int. Ed. 2002, 41, 1147-1150). In accordance with disrotatory motion, the normal mode vectors for TS 3-->4 calculated at the (10,9)CASSCF/6-31G* level show a greater magnitude of rotation of the N1-H group relative to the N1-C2 bond being formed than in TS 3-->4 calculated at the B3LYP/6-31G* level. Furthermore, comparison of orbital correlation diagrams constructed entirely from localized complete active space (CAS) molecular orbitals (MOs) for the electrocyclizations of 3, 5, 7, 9, and 10 suggest that it is the highest occupied delocalized pi-MO of 3 that is primarily responsible for sigma-bond formation in 4, not the terminal allenyl pi-bond MO. However, there does appear to be a special secondary orbital effect role for the nitrogen lone-pair and hence the process is likely neither purely pericyclic nor pseudopericyclic.

  10. Application of periodic orbit theory in chaos-based security analysis

    Institute of Scientific and Technical Information of China (English)

    Long Min; Qiu Shui-Sheng

    2007-01-01

    Chaos-based encryption schemes have been studied extensively, while the security analysis methods for them are still problems to be resolved. Based on the periodic orbit theory, this paper proposes a novel security analysis method. The periodic orbits theory indicates that the fundamental frequency of the spiraling orbits is the natural frequency of associated linearized system, which is decided by the parameters of the chaotic system. Thus, it is possible to recover the plaintext of secure communication systems based on chaotic shift keying by getting the average time on the spiraling orbits. Analysis and simulation results show that the security analysis method can break chaos shift keying secure communication systems, which use the parameters as keys.

  11. Comparing Rover and Orbiter based observations at Meridiani Planum, Mars

    Science.gov (United States)

    Gellert, R.; Arvidson, R. E.; Campbell, J. L.; Clark, B. C.; Squyres, S.; Yen, A. S.

    2011-12-01

    The Alpha Particle X-ray Spectrometer (APXS) on board the MER rover Opportunity has documented the chemical composition of the bedrock at Meridiani Planum over the traverse of ~33 km so far. The bedrock is very high in sulfate, up to ~ 25 weight percents SO3, interpreted as sedimentary sandstone. The high precision and consistency of the acquired APXS data, mainly of the abraded samples, allowed the characterization of the homogeneous bedrock over the traverse. Inside Victoria and Endurance Crater the abundance of magnesium and sulfur dropped in a 1:1 molar ratio by about 30 % in parallel with an increase of chlorine by a factor of 3. This inferred the presence of magnesium sulfate and an unknown chlorine-compound. Moreover the identical change in soluble minerals between Victoria and Endurance craters (~6 km apart) might indicate a large scale change in a subsurface water table in the past. Using the scatter peak method in the APXS spectra, the excess of oxygen was determined to be equivalent to ~ 14% bound water for the average Meridiani outcrop. Besides bedrock, basaltic soil and a lag of hematitic concretions, the rover encountered several erratic rocks sitting on the plains. Both, iron-nickel meteorites and cobbles with a basaltic mineralogy are suggestive of emplacement as meteorites. The basaltic rocks, Bounce Rock and Marquette, are ejecta from different regions on Mars. The APXS data of even unbrushed surfaces, typically a mixture or airborne dust, soil and alteration rinds, clearly indicated significant differences to the dominating bedrock. Opportunity is expected to reach the rim of the Noachian-aged Endurance Crater in August 2011, where orbital instruments detected evidence for polyhydrated sulfates, Fe-Mg Smectites, as well as basaltic materials. It is unprecedented for a rover to drive into an area with these significant alteration minerals predicted from orbit. While the mineral spectrometers on the rover are now significantly degraded, the APXS

  12. Calculation of Two-center Nuclear Attraction Integrals over Slater Type Orbitals in Molecular Coordinate System

    Institute of Scientific and Technical Information of China (English)

    MAMEDOV,B.A.

    2004-01-01

    A closed analytical relation is derived for the two-center nuclear attraction integrals over Slater type orbitals (STOs) in terms of binomial coefficients. This formula can be used in highly accurate calculations of the nuclear attraction integrals. The relationships obtained are valid for arbitrary values of quantum numbers and screening constants of STOs and location of nuclei.

  13. Orbital free ab initio molecular dynamics simulation study of some static and dynamic properties of liquid noble metals

    Directory of Open Access Journals (Sweden)

    G.M. Bhuiyan

    2012-10-01

    Full Text Available Several static and dynamic properties of liquid Cu, Ag and Au at thermodynamic states near their respective melting points, have been evaluated by means of the orbital free ab-initio molecular dynamics simulation method. The calculated static structure shows good agreement with the available X-ray and neutron diffraction data. As for the dynamic properties, the calculated dynamic structure factors point to the existence of collective density excitations along with a positive dispersion for l-Cu and l-Ag. Several transport coefficients have been obtained which show a reasonable agreement with the available experimental data.

  14. Orbital free ab initio molecular dynamics simulation study of some static and dynamic properties of liquid noble metals

    CERN Document Server

    Bhuiyan, G M; González, D J; 10.5488/CMP.15.33604

    2012-01-01

    Several static and dynamic properties of liquid Cu, Ag and Au at thermodynamic states near their respective melting points, have been evaluated by means of the orbital free ab-initio molecular dynamics simulation method. The calculated static structure shows good agreement with the available X-ray and neutron diffraction data. As for the dynamic properties, the calculated dynamic structure factors point to the existence of collective density excitations along with a positive dispersion for l-Cu and l-Ag. Several transport coefficients have been obtained which show a reasonable agreement with the available experimental data.

  15. Automatic Identification of Axis Orbit Based on Both Wavelet Moment Invariants and Neural Network

    Institute of Scientific and Technical Information of China (English)

    FuXiang-qian; LiuGuang-lin; JiangJing; LiYou-ping

    2003-01-01

    Axis orbit is an important characteristic to be used in the condition monitoring and diagnosis system of rotating machine. The wavelet moment has the invariant to the translation, scaling and rotation. A method, which uses a neural network based on Radial Basis Function (RBF) and wavelet moment invariants to identify the orbit of shaft centerline of rotating machine is discussed in this paper. The principle and its application procedure of the method are introduced in detail. It gives simulation results of automatic identification for three typical axis orbits. It is proved that the method is effective and practicable.

  16. Automatic Identification of Axis Orbit Based on Both Wavelet Moment Invariants and Neural Network

    Institute of Scientific and Technical Information of China (English)

    Fu Xiang-qian; Liu Guang-lin; Jiang Jing; Li You-ping

    2003-01-01

    Axis orbit is an important characteristic to be used in the condition monitoring and diagnosis system of rota-ting machine. The wavelet moment has the invariant to the translation, scaling and rotation. A method, which uses a neural network based on Radial Basis Function (RBF) and wavelet moment invariants to identify the orbit of shaft centerline of rotating machine is discussed in this paper. The principle and its application procedure of the method are intro-duced in detail. It gives simulation results of automatic identi-fication for three typical axis orbits. It is proved that the method is effective and practicable.

  17. A new method based on Markov chains for deriving SB2 orbits directly from their spectra

    CERN Document Server

    Salomon, J -B; Guillout, P; Halbwachs, J -L; Arenou, F; Famaey, B; Lebreton, Y; Mazeh, T; Pourbaix, D; Tal-Or, L

    2012-01-01

    We present a new method to derive orbital elements of double-lined spectroscopic binaries (SB2). The aim is to have accurate orbital parameters of a selection of SB2 in order to prepare the exploitation of astrometric Gaia observations. Combined with our results, they should allow one to measure the mass of each star with a precision of better than 1%. The new method presented here consists of using the spectra at all epochs simultaneously to derive the orbital elements without templates. It is based on a Markov chain including a new method for disentangling the spectra.

  18. 信息动态%Midcourse trajectory correction based on orbital motion equation linearization

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    Midcourse trajectory correction is an essential technique to ensure the completion of long-time midcourse coasting missions, such as deep space exploration, long-distance rendezvous, and approaching observation.Based on perturbation guidance theory, this paper presents a correction strategy by linearizing the orbital motion equations about the nominal orbit. Orbital perturbations have an obvious effect on the spacecraft undertaking mission near the earth space, especially the J2 perturbation. Therefore, a modified method is proposed by adding correction terms onto the two-body matrices to reduce errors caused by perturbations. Finally, numerical simulations are conducted to verify the validity of the methods addressed herein.

  19. Analysis of electron correlation effects and contributions of NMR J-couplings from occupied localized molecular orbitals.

    Science.gov (United States)

    Zarycz, Natalia; Aucar, Gustavo A

    2012-02-02

    NMR J-coupling calculations at the second-order of polarization propagator approach, SOPPA, are among the most reliable. They include a high percentage of the total electron correlation effects in saturated and unsaturated molecular systems. Furthermore, J-couplings are quite sensitive to the whole electronic molecular framework. We present in this article the first study of all three response mechanisms, Fermi contact, FC, spin-dipolar, SD and paramagnetic spin-orbital, PSO, for J-couplings with occupied localized molecular orbitals at the SOPPA level of approach. Even though SOPPA results are not invariant under unitary transformations, the difference between results obtained with canonical and localized molecular orbitals, LMOs, are small enough to permit its application with confidence. The following small-size saturated and unsaturated compounds were analyzed: CH(4), CH(3)F, C(2)H(6), NH(3), C(2)H(4), CH(2)NH, H(2)C═CHF, and FHC═CHF. The local character of the FC mechanism that appears in J-couplings of these molecular models is shown through the analysis of contributions from LMOs. The importance of including the electron correlation on the engaged bonding orbitals for one-bond couplings is emphasized. Almost all electron correlation effects are included in such orbitals. Interesting findings were the large contributions by s-type LMOs to the C-H and C-C J-couplings; they are responsible for the variation of (1)J(C-C) when going from ethane to ethene and to 1,2-difluoroethene. The previously proposed hyperconjugative transfer mechanism has been tested. Among other tests we found the difference anti-syn of one-bond (1)J(C-H) in imine as due to both the corresponding σ(C-H) and the lone-pair, LP, contribution. Geminal and vicinal J-couplings were also analyzed. Our findings are in accord with a previous work by Pople and Bothner-by, who considered results taken from calculations or empirical data. For all geminal couplings the pattern of J-couplings, like

  20. Carbon-based ion and molecular channels

    Science.gov (United States)

    Sint, Kyaw; Wang, Boyang; Kral, Petr

    2008-03-01

    We design ion and molecular channels based on layered carboneous materials, with chemically-functionalized pore entrances. Our molecular dynamics simulations demonstrate that these ultra-narrow pores, with diameters around 1 nm, are highly selective to the charges and sizes of the passing (Na^+ and Cl^-) ions and short alkanes. We demonstrate that the molecular flows through these pores can be easily controlled by electrical and mechanical means. These artificial pores could be integrated in fluidic nanodevices and lab-on-a-chip techniques with numerous potential applications. [1] Kyaw Sint, Boyang Wang and Petr Kral, submitted. [2] Boyang Wang and Petr Kral, JACS 128, 15984 (2006).

  1. Calcareous microfossil-based orbital cyclostratigraphy in the Arctic Ocean

    Science.gov (United States)

    Marzen, Rachel; DeNinno, Lauren H.; Cronin, Thomas M.

    2016-01-01

    Microfaunal and geochemical proxies from marine sediment records from central Arctic Ocean (CAO) submarine ridges suggest a close relationship over the last 550 thousand years (kyr) between orbital-scale climatic oscillations, sea-ice cover, marine biological productivity and other parameters. Multiple paleoclimate proxies record glacial to interglacial cycles. To understand the climate-cryosphere-productivity relationship, we examined the cyclostratigraphy of calcareous microfossils and constructed a composite Arctic Paleoclimate Index (API) "stack" from benthic foraminiferal and ostracode density from 14 sediment cores. Following the hypothesis that API is driven mainly by changes in sea-ice related productivity, the API stack shows the Arctic experienced a series of highly productive interglacials and interstadials every ∼20 kyr. These periods signify minimal ice shelf and sea-ice cover and maximum marine productivity. Rapid transitions in productivity are seen during shifts from interglacial to glacial climate states. Discrepancies between the Arctic API curves and various global climatic, sea-level and ice-volume curves suggest abrupt growth and decay of Arctic ice shelves related to climatic and sea level oscillations.

  2. Calcareous microfossil-based orbital cyclostratigraphy in the Arctic Ocean

    Science.gov (United States)

    Marzen, Rachel E.; DeNinno, Lauren H.; Cronin, Thomas M.

    2016-10-01

    Microfaunal and geochemical proxies from marine sediment records from central Arctic Ocean (CAO) submarine ridges suggest a close relationship over the last 550 thousand years (kyr) between orbital-scale climatic oscillations, sea-ice cover, marine biological productivity and other parameters. Multiple paleoclimate proxies record glacial to interglacial cycles. To understand the climate-cryosphere-productivity relationship, we examined the cyclostratigraphy of calcareous microfossils and constructed a composite Arctic Paleoclimate Index (API) "stack" from benthic foraminiferal and ostracode density from 14 sediment cores. Following the hypothesis that API is driven mainly by changes in sea-ice related productivity, the API stack shows the Arctic experienced a series of highly productive interglacials and interstadials every ∼20 kyr. These periods signify minimal ice shelf and sea-ice cover and maximum marine productivity. Rapid transitions in productivity are seen during shifts from interglacial to glacial climate states. Discrepancies between the Arctic API curves and various global climatic, sea-level and ice-volume curves suggest abrupt growth and decay of Arctic ice shelves related to climatic and sea level oscillations.

  3. DNA Based Molecular Scale Nanofabrication

    Science.gov (United States)

    2015-12-04

    water adsorption on DNA origami template and its impact on DNA- mediated chemical reactions. We also extended the concept of DNA- mediated reaction to...addition, we have expanded our efforts to include DNA- mediated HF etching of SiÜ2, DNA- mediated nanoimprinting lithography, DNA-based patterning of self...detailed kinetics study of DNA- mediated chemical reactions. Examples of such reactions include chemical vapor deposition (CVD) of inorganic oxide and HF

  4. Bioassays Based on Molecular Nanomechanics

    Directory of Open Access Journals (Sweden)

    Arun Majumdar

    2002-01-01

    Full Text Available Recent experiments have shown that when specific biomolecular interactions are confined to one surface of a microcantilever beam, changes in intermolecular nanomechanical forces provide sufficient differential torque to bend the cantilever beam. This has been used to detect single base pair mismatches during DNA hybridization, as well as prostate specific antigen (PSA at concentrations and conditions that are clinically relevant for prostate cancer diagnosis. Since cantilever motion originates from free energy change induced by specific biomolecular binding, this technique is now offering a common platform for label-free quantitative analysis of protein-protein binding, DNA hybridization DNA-protein interactions, and in general receptor-ligand interactions. Current work is focused on developing “universal microarrays” of microcantilever beams for high-throughput multiplexed bioassays.

  5. Molecular quantum magnetism with strong spin-orbit coupling in inorganic solid Ba3Yb2Zn5O11

    Science.gov (United States)

    Park, Sang-Youn; Ji, Sungdae; Park, Jae-Hoon; Do, Seunghwan; Choi, Kwang-Yong; Jang, Dongjin; Schmidt, Burkhard; Brando, Manuel; Butch, Nicholas

    The molecular magnet, assembly of finite number of spins which are isolated from environment, is a model system to study the quantum information process such as the qubit or spintronic devices. In past decades, the molecular magnet has been mostly realized in organic material, however, it has difficulty synthesizing materials or controlling their properties, meanwhile tremendous endeavors to search inorganic molecular magnet are continuing. Here, we propose Ba3Yb2Zn5O11 as a candidate of inorganic molecular magnet. This material consists of an alternating 3D-array of small and large tetrahedron containing antiferromagnetically coupled four pseudospin-1/2 Yb ions, and magnetic properties are described by an isolated tetrahedron without long-range magnetic ordering. Inelastic neutron scattering measurement with external magnetic field reveals that extraordinarily huge Dzyaloshinsky-Moriya (DM) interaction originating from strong spin-orbit coupling in Yb isospin is the key to explain energy level of tetrahedron in addition to Heisenberg exchange interaction and Zeeman effect. Magnetization measurement shows the Landau-Zener transition between avoided crossing levels caused by DM interaction.

  6. Spin-orbit coupling manipulating composite topological spin textures in atomic-molecular Bose-Einstein condensates

    Science.gov (United States)

    Liu, Chao-Fei; Juzeliūnas, Gediminas; Liu, W. M.

    2017-02-01

    Atomic-molecular Bose-Einstein condensates (BECs) offer brand new opportunities to revolutionize quantum gases and probe the variation of fundamental constants with unprecedented sensitivity. The recent realization of spin-orbit coupling (SOC) in BECs provides a new platform for exploring completely new phenomena unrealizable elsewhere. In this study, we find a way of creating a Rashba-Dresselhaus SOC in atomic-molecular BECs by combining the spin-dependent photoassociation and Raman coupling, which can control the formation and distribution of a different type of topological excitation—carbon-dioxide-like skyrmion. This skyrmion is formed by two half-skyrmions of molecular BECs coupling with one skyrmion of atomic BECs, where the two half-skyrmions locate at both sides of one skyrmion. Carbon-dioxide-like skyrmion can be detected by measuring the vortices structures using the time-of-flight absorption imaging technique in real experiments. Furthermore, we find that SOC can effectively change the occurrence of the Chern number in k space, which causes the creation of topological spin textures from some separated carbon-dioxide-like monomers each with topological charge -2 to a polymer chain of the skyrmions. This work helps in creating dual SOC atomic-molecular BECs and opens avenues to manipulate topological excitations.

  7. Plasmons in molecules: Microscopic characterization based on orbital transitions and momentum conservation

    Energy Technology Data Exchange (ETDEWEB)

    Krauter, Caroline M., E-mail: Caroline.Krauter@pci.uni-heidelberg.de [Theoretical Chemistry, Heidelberg University, Im Neuenheimer Feld 229, D-69120 Heidelberg (Germany); Interdisciplinary Center for Scientific Computing, Heidelberg University, Im Neuenheimer Feld 368, 69120 Heidelberg (Germany); Schirmer, Jochen; Pernpointner, Markus [Theoretical Chemistry, Heidelberg University, Im Neuenheimer Feld 229, D-69120 Heidelberg (Germany); Jacob, Christoph R. [Center for Functional Nanostructures and Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Strasse 1a, 76131 Karlsruhe (Germany); Dreuw, Andreas [Interdisciplinary Center for Scientific Computing, Heidelberg University, Im Neuenheimer Feld 368, 69120 Heidelberg (Germany)

    2014-09-14

    In solid state physics, electronic excitations are often classified as plasmons or single-particle excitations. The former class of states refers to collective oscillations of the electron density. The random-phase approximation allows for a quantum-theoretical treatment and a characterization on a microscopic level as a coherent superposition of a large number of particle-hole transitions with the same momentum transfer. However, small systems such as molecules or small nanoclusters lack the basic properties (momentum conservation and uniform exchange interaction) responsible for the formation of plasmons in the solid-state case. Despite an enhanced interest in plasmon-based technologies and an increasing number of studies regarding plasmons in molecules and small nanoclusters, their definition on a microscopic level of theory remains ambiguous. In this work, we analyze the microscopic properties of molecular plasmons in comparison with the homogeneous electron gas as a model system. Subsequently, the applicability of the derived characteristics is validated by analyzing the electronic excitation vectors with respect to orbital transitions for two linear polyenes within second order versions of the algebraic diagrammatic construction scheme for the polarization propagator.

  8. Molecular docking, TG/DTA, molecular structure, harmonic vibrational frequencies, natural bond orbital and TD-DFT analysis of diphenyl carbonate by DFT approach

    Science.gov (United States)

    Xavier, S.; Periandy, S.; Carthigayan, K.; Sebastian, S.

    2016-12-01

    Vibrational spectral analysis of Diphenyl Carbonate (DPC) is carried out by using FT-IR and FT-Raman spectroscopic techniques. It is found that all vibrational modes are in the expected region. Gaussian computational calculations were performed using B3LYP method with 6-311++G (d, p) basis set. The computed geometric parameters are in good agreement with XRD data. The observation shows that the structure of the carbonate group is unsymmetrical by ∼5° due to the attachment of the two phenyl rings. The stability of the molecule arising from hyperconjugative interaction and charge delocalization are analyzed by Natural Bond Orbital (NBO) study and the results show the lone pair transition has higher stabilization energy compared to all other. The 1H and 13C NMR chemical shifts are calculated using the Gauge-Including Atomic Orbital (GIAO) method with B3LYP/6-311++G (d, p) method. The chemical shifts computed theoretically go very closer to the experimental results. A study on the electronic and optical properties; absorption wavelengths, excitation energy, dipole moment and frontier molecular orbital energies and Molecular electrostatic potential (MEP) exhibit the high reactivity nature of the molecule. The non-linear optical property of the DPC molecule predicted theoretically found to be good candidate for NLO material. TG/DTA analysis was made and decomposition of the molecule with respect to the temperature was studied. DPC having the anthelmintic activity is docked in the Hemoglobin of Fasciola hepatica protein. The DPC has been screened to antimicrobial activity and found to exhibit antibacterial effects.

  9. Distant Retrograde Orbits for space-based Near Earth Objects detection

    Science.gov (United States)

    Stramacchia, Michele; Colombo, Camilla; Bernelli-Zazzera, Franco

    2016-09-01

    We analyse a concept for the detection of Potentially Hazardous Asteroids (PHAs) from a space-based network of telescopes on retrograde Distant Periodic Orbits. Planar periodic orbits are designed in the Sun-Earth circular restricted three-body problem, starting from initial conditions in the Hill's problem available from the literature. A family of retrograde orbits centred at the Earth is selected as baseline, based on their maximum distance from Earth, larger than the Earth-L2 distance. Indeed, spacecraft on such orbits can detect PHAs incoming from the Sun direction, which could not otherwise be monitored from current Earth-based systems. A trade-off on the orbit amplitude, asteroid diameter to be detected, and the constellation size is performed considering current visible sensor telescope technology. The Chelyabinsk meteor scenario is studied and the potential warning time that could be gained with a space-based survey system with respect to an Earth based-survey system is shown.

  10. Magnetism, Superconductivity, and Spontaneous Orbital Order in Iron-Based Superconductors: Which Comes First and Why?

    Directory of Open Access Journals (Sweden)

    Andrey V. Chubukov

    2016-12-01

    Full Text Available Magnetism and nematic order are the two nonsuperconducting orders observed in iron-based superconductors. To elucidate the interplay between them and ultimately unveil the pairing mechanism, several models have been investigated. In models with quenched orbital degrees of freedom, magnetic fluctuations promote stripe magnetism, which induces orbital order. In models with quenched spin degrees of freedom, charge fluctuations promote spontaneous orbital order, which induces stripe magnetism. Here, we develop an unbiased approach, in which we treat magnetic and orbital fluctuations on equal footing. Key to our approach is the inclusion of the orbital character of the low-energy electronic states into renormalization group (RG analysis. We analyze the RG flow of the couplings and argue that the same magnetic fluctuations, which are known to promote s^{+-} superconductivity, also promote an attraction in the orbital channel, even if the bare orbital interaction is repulsive. We next analyze the RG flow of the susceptibilities and show that, if all Fermi pockets are small, the system first develops a spontaneous orbital order, then s^{+-} superconductivity, and magnetic order does not develop down to T=0. We argue that this scenario applies to FeSe. In systems with larger pockets, such as BaFe_{2}As_{2} and LaFeAsO, we find that the leading instability is either towards a spin-density wave or superconductivity. We argue that in this situation nematic order is caused by composite spin fluctuations and is vestigial to stripe magnetism. Our results provide a unifying description of different iron-based materials.

  11. Magnetism, Superconductivity, and Spontaneous Orbital Order in Iron-Based Superconductors: Which Comes First and Why?

    Science.gov (United States)

    Chubukov, Andrey V.; Khodas, M.; Fernandes, Rafael M.

    2016-10-01

    Magnetism and nematic order are the two nonsuperconducting orders observed in iron-based superconductors. To elucidate the interplay between them and ultimately unveil the pairing mechanism, several models have been investigated. In models with quenched orbital degrees of freedom, magnetic fluctuations promote stripe magnetism, which induces orbital order. In models with quenched spin degrees of freedom, charge fluctuations promote spontaneous orbital order, which induces stripe magnetism. Here, we develop an unbiased approach, in which we treat magnetic and orbital fluctuations on equal footing. Key to our approach is the inclusion of the orbital character of the low-energy electronic states into renormalization group (RG) analysis. We analyze the RG flow of the couplings and argue that the same magnetic fluctuations, which are known to promote s+- superconductivity, also promote an attraction in the orbital channel, even if the bare orbital interaction is repulsive. We next analyze the RG flow of the susceptibilities and show that, if all Fermi pockets are small, the system first develops a spontaneous orbital order, then s+- superconductivity, and magnetic order does not develop down to T =0 . We argue that this scenario applies to FeSe. In systems with larger pockets, such as BaFe2 As2 and LaFeAsO, we find that the leading instability is either towards a spin-density wave or superconductivity. We argue that in this situation nematic order is caused by composite spin fluctuations and is vestigial to stripe magnetism. Our results provide a unifying description of different iron-based materials.

  12. 基于Helmert变换的GPS动力学轨道平滑%Orbit Fitting Based on Helmert Transformation

    Institute of Scientific and Technical Information of China (English)

    CHEN Junping; 王解先

    2009-01-01

    Orbit fitting is used in many GPS applications. For example, in Precise Point Positioning (PPP), GPS orbits (SP3 orbits) are normally retrieved either from IGS or from one of its Analysis Centers (ACs) with 15 minutes' sampling, which is much bigger than the normal observation sampling. Therefore, algorithms should be derived to fit GPS orbits to the observation time. Many methods based on interpolation were developed. Using these methods the orbits fit well at the sampling points.However, these methods ignore the physical motion model of GPS satellites. Therefore, the trajectories may not fit the true orbits at the periods in between 2 sampling epochs. To solve this problem, we develop a dynamic approach, in which a model based on Helmert transformation is developed in GPS orbit fitting. In this orbit fitting approach, GPS orbits at sampling points are treated as pseudo-observations. Thereafter, Helmert transformation is built up between the pseudo-observations and dynamically integrated orbits at each epoch. A set of Helmert parameters together with corrections of GPS initial orbits are then modeled as unknown parameters. Results show that the final fit orbits have the same precision as the IGS final orbits.

  13. Does covalency really increase across the 5f series? A comparison of molecular orbital, natural population, spin and electron density analyses of AnCp3 (An = Th-Cm; Cp = η(5)-C5H5).

    Science.gov (United States)

    Kirker, Ian; Kaltsoyannis, Nikolas

    2011-01-07

    The title compounds are studied with scalar relativistic, gradient-corrected (PBE) and hybrid (PBE0) density functional theory. The metal-Cp centroid distances shorten from ThCp(3) to NpCp(3), but lengthen again from PuCp(3) to CmCp(3). Examination of the valence molecular orbital structures reveals that the highest-lying Cp π(2,3)-based orbitals transform as 1e + 2e + 1a(1) + 1a(2). Above these levels come the predominantly metal-based 5f orbitals, which stabilise across the actinide series such that in CmCp(3) the 5f manifold is at more negative energy than the Cp π(2,3)-based levels. Mulliken population analysis shows metal d orbital participation in the e symmetry Cp π(2,3)-based orbitals. Metal 5f character is found in the 1a(1) and 1a(2) levels, and this contribution increases significantly from ThCp(3) to AmCp(3). This is in agreement with the metal spin densities, which are enhanced above their formal value in NpCp(3), PuCp(3) and especially AmCp(3) with both PBE and PBE0. However, atoms-in-molecules analysis of the electron densities indicates that the An-Cp bonding is very ionic, increasingly so as the actinide becomes heavier. It is concluded that the large metal orbital contributions to the Cp π(2,3)-based levels, and enhanced metal spin densities toward the middle of the actinide series arise from a coincidental energy match of metal and ligand orbitals, and do not reflect genuinely increased covalency (in the sense of appreciable overlap between metal and ligand levels and a build up of electron density in the region between the actinide and carbon nuclei).

  14. Orbital circularization of a planet accreting disk gas: the formation of distant jupiters in circular orbits based on a core accretion model

    Energy Technology Data Exchange (ETDEWEB)

    Kikuchi, Akihiro; Higuchi, Arika [Department of Earth and Planetary Sciences, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8551 (Japan); Ida, Shigeru, E-mail: kikuchi.a@geo.titech.ac.jp, E-mail: higuchia@geo.titech.ac.jp, E-mail: ida@elsi.jp [Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550 (Japan)

    2014-12-10

    Recently, gas giant planets in nearly circular orbits with large semimajor axes (a ∼ 30-1000 AU) have been detected by direct imaging. We have investigated orbital evolution in a formation scenario for such planets, based on a core accretion model. (1) Icy cores accrete from planetesimals at ≲ 30 AU, (2) they are scattered outward by an emerging nearby gas giant to acquire highly eccentric orbits, and (3) their orbits are circularized through the accretion of disk gas in outer regions, where they spend most of their time. We analytically derived equations to describe the orbital circularization through gas accretion. Numerical integrations of these equations show that the eccentricity decreases by a factor of more than 5 while the planetary mass increases by a factor of 10. Because runaway gas accretion increases planetary mass by ∼10-300, the orbits are sufficiently circularized. On the other hand, a is reduced at most only by a factor of two, leaving the planets in the outer regions. If the relative velocity damping by shock is considered, the circularization slows down, but is still efficient enough. Therefore, this scenario potentially accounts for the formation of observed distant jupiters in nearly circular orbits. If the apocenter distances of the scattered cores are larger than the disk sizes, their a shrink to a quarter of the disk sizes; the a-distribution of distant giants could reflect the outer edges of the disks in a similar way that those of hot jupiters may reflect inner edges.

  15. The Dimensions of the Orbital Cavity Based on High-Resolution Computed Tomography of Human Cadavers.

    Science.gov (United States)

    Felding, Ulrik Ascanius; Bloch, Sune Land; Buchwald, Christian von

    2016-06-01

    Blow-out fractures affect the volume and surface area of the orbital cavity. Estimation of these values after the trauma may help in deciding whether or not a patient is a candidate for surgery. Recent studies have provided estimates of orbital volume and area of bone defect, and correlated them with the degree of enophthalmos. However, a large degree of biological variation between individuals may preclude such absolute values from being successful indicators for surgery.Stereological methods have been used to estimate orbital cavity volume in a few studies, but to date these have not been used for surface area. To authors' knowledge, this study is the first to have measured the entire surface area of the orbital cavity.The volume and surface area of the orbital cavity were estimated in computed tomography scans of 11 human cadavers using unbiased stereological sampling techniques. The mean (± SD) total volume and total surface area of the orbital cavities was 24.27 ± 3.88 cm and 32.47 ± 2.96 cm, respectively. There was no significant difference in volume (P = 0.315) or surface area (P = 0.566) between the 2 orbital cavities.The stereological technique proved to be a robust and unbiased method that may be used as a gold standard for comparison with automated computer software. Future imaging studies in blow-out fracture patients may be based on individual and relative calculation involving both herniated volume and fractured surface area in relation to the total volume and surface area of the uninjured orbital cavity.

  16. Specular Andreev reflection in graphene-based superconducting junction with substate-induced spin orbit interaction

    Energy Technology Data Exchange (ETDEWEB)

    Bai, Chunxu, E-mail: chunxu_bai@semi.ac.cn [School of Physics, Anyang Normal University, Anyang 455000 (China); Yang, Yanling [School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083 (China); School of Physics, Anyang Normal University, Anyang 455000 (China)

    2016-08-26

    Based on the Dirac–Bogoliubov–de Gennes equation, the chirality-resolved transport properties through a ballistic graphene-based superconducting heterojunction with both the Rashba and the Dresselhaus spin orbit interaction have been investigated. Our results show that, in contrast to the retro-Andreev reflection suppressed by the spin orbit interaction (SOI), the specular Andreev reflection (SAR) can be enhanced largely by the SOI. Moreover, the Fabry–Perot interferences in the barrier region lead to the oscillating feature of the tunneling conductance. It is anticipated to apply the qualitative different results to diagnose the SAR in single layer graphene in the presence of both kinds of the SOI. - Highlights: • The retro-Andreev reflection in graphene is suppressed by the spin orbit interaction. • The specular Andreev reflection in graphene can be enhanced largely by the spin orbit interaction. • The Fabry–Perot interferences in the graphene-based barrier lead to the oscillating feature of the tunneling conductance. • The spin orbit interaction is also vital in diagnosing the specular Andreev reflection in graphene.

  17. Orbital order switching in molecular calculations using GGA functionals: Qualitative errors in materials modeling for electrochemical power sources and how to fix them

    Science.gov (United States)

    Sk, Mahasin Alam; Chen, Yingqian; Manzhos, Sergei

    2016-08-01

    We report a qualitative difference in molecular band structures and frontier orbital nodal structures in DFT calculations using GGA vs. hybrid functionals and Hartree Fock in molecules used in electrochemical power sources. This can have a significant effect in applications sensitive to redox potentials and to orbital overlaps (excitations, electron transfer rates) but for which the use of hybrid functionals is impractical, such as solids or interfaces used in electrochemical energy conversion and storage technologies. We show that correct band structures and nodal structures (ordering) of frontier orbitals can be obtained by applying a Hubbard correction to selected atomic states.

  18. Bonding, Backbonding, and Spin-Polarized Molecular Orbitals:Basis for Magnetism and Semiconducting Transport in V[TCNE]x~;;2

    Energy Technology Data Exchange (ETDEWEB)

    Kortright, Jeffrey B; Kortright, Jeffrey B; Lincoln, Derek M; Edelstein, Ruth Shima; Epstein, Arthur J

    2008-05-20

    X-ray absorption spectroscopy (XAS) and magnetic circular dichroism (MCD) at the V L2,3 and C and N K edges reveal bonding/backbonding interactions in films of the 400 K magnetic semiconductor V[TCNE]x~;;2. In V spectra, dxy-like orbitals are modeled assuming V2+ in an octahedral ligand field, while dz2 and dx2-y2 orbitals involved in strong covalent bonding cannot be modeled by atomic calculations. C and N MCD, and differences in XAS from neutral TCNE molecules, reveal spin-polarized molecular orbitals in V[TCNE]x~;;2 associated with backbonding interactions that yield its novel properties.

  19. Specular Andreev reflection in graphene-based superconducting junction with substate-induced spin orbit interaction

    Science.gov (United States)

    Bai, Chunxu; Yang, Yanling

    2016-08-01

    Based on the Dirac-Bogoliubov-de Gennes equation, the chirality-resolved transport properties through a ballistic graphene-based superconducting heterojunction with both the Rashba and the Dresselhaus spin orbit interaction have been investigated. Our results show that, in contrast to the retro-Andreev reflection suppressed by the spin orbit interaction (SOI), the specular Andreev reflection (SAR) can be enhanced largely by the SOI. Moreover, the Fabry-Perot interferences in the barrier region lead to the oscillating feature of the tunneling conductance. It is anticipated to apply the qualitative different results to diagnose the SAR in single layer graphene in the presence of both kinds of the SOI.

  20. Analogue spin-orbit torque device for artificial-neural-network-based associative memory operation

    Science.gov (United States)

    Borders, William A.; Akima, Hisanao; Fukami, Shunsuke; Moriya, Satoshi; Kurihara, Shouta; Horio, Yoshihiko; Sato, Shigeo; Ohno, Hideo

    2017-01-01

    We demonstrate associative memory operations reminiscent of the brain using nonvolatile spintronics devices. Antiferromagnet-ferromagnet bilayer-based Hall devices, which show analogue-like spin-orbit torque switching under zero magnetic fields and behave as artificial synapses, are used. An artificial neural network is used to associate memorized patterns from their noisy versions. We develop a network consisting of a field-programmable gate array and 36 spin-orbit torque devices. An effect of learning on associative memory operations is successfully confirmed for several 3 × 3-block patterns. A discussion on the present approach for realizing spintronics-based artificial intelligence is given.

  1. Specific interactions between lactose repressor protein and DNA affected by ligand binding: ab initio molecular orbital calculations.

    Science.gov (United States)

    Ohyama, Tatsuya; Hayakawa, Masato; Nishikawa, Shin; Kurita, Noriyuki

    2011-06-01

    Transcription mechanisms of gene information from DNA to mRNA are essentially controlled by regulatory proteins such as a lactose repressor (LacR) protein and ligand molecules. Biochemical experiments elucidated that a ligand binding to LacR drastically changes the mechanism controlled by LacR, although the effect of ligand binding has not been clarified at atomic and electronic levels. We here investigated the effect of ligand binding on the specific interactions between LacR and operator DNA by the molecular simulations combined with classical molecular mechanics and ab initio fragment molecular orbital methods. The results indicate that the binding of anti-inducer ligand strengthens the interaction between LacR and DNA, which is consistent with the fact that the binding of anti-inducer enhances the repression of gene transcription by LacR. It was also elucidated that hydrating water molecules existing between LacR and DNA contribute to the specific interactions between LacR and DNA. Copyright © 2011 Wiley Periodicals, Inc.

  2. Rings of C2H in the Molecular Disks Orbiting TW Hya and V4046 Sgr

    CERN Document Server

    Kastner, J H; Gorti, U; Hily-Blant, P; Oberg, K; Forveille, T; Andrews, S; Wilner, D

    2015-01-01

    We have used the Submillimeter Array to image, at ~1" resolution, C2H(3-2) emission from the molecule-rich circumstellar disks orbiting the nearby, classical T Tauri star systems TW Hya and V4046 Sgr. The SMA imaging reveals that the C2H emission exhibits a ring-like morphology within each disk, the inner hole radius of the C2H ring within the V4046 Sgr disk (~70 AU) is somewhat larger than than of its counterpart within the TW Hya disk (~45 AU). We suggest that, in each case, the C2H emission likely traces irradiation of the tenuous surface layers of the outer disks by high-energy photons from the central stars.

  3. Ab initio molecular orbital calculations of electronic couplings in the LH2 bacterial light-harvesting complex of Rps. acidophila

    Energy Technology Data Exchange (ETDEWEB)

    Scholes, G.D.; Fleming, G.R. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry]|[Lawrence Berkeley National Lab., CA (United States). Physical Biosciences Div.; Gould, I.R. [Imperial Coll. of Science, Technology and Medicine, London (United Kingdom). Dept. of Chemistry; Cogdell, R.J. [Univ. of Glasgow (United Kingdom). Div. of Biochemistry and Molecular Biology

    1999-04-01

    The results of ab initio molecular orbital calculations of excited states and electronic couplings (for energy transfer) between the B800 and B850 bacteriochlorophyll a (Bchl) chromophores in the peripheral light-harvesting complex (LH2) of the purple photosynthetic bacterium Rhodopseudomonas acidophila are reported. Electronic couplings are estimated from supermolecule calculations of Bchl dimers using the Ci-singles methodology and 3-21G{sup *} or 6-31G{sup *} basis sets. A scheme for dissecting the coupling into contributions from the Coulombic coupling and the short-range coupling (i.e., dependent on interchromophore orbital overlap) is reported. B850 couplings are calculated to be [total (Coulombic + short)]: intrapolypeptide dimer 320 (265 + 55) cm{sup {minus}1} and interpolypeptide dimer 255 (195 + 60) cm{sup {minus}1} at the CIS/6-31G{sup *} level. These results differ significantly from those estimated using the point dipole approximation. The effect of including Mg ligands (His residues) and H-bonding residues (Trp and Tyr) is also investigated. The consequences for superradiance and energy transfer dynamics and mechanism are discussed.

  4. Lyapunov-based Low-thrust Optimal Orbit Transfer: An approach in Cartesian coordinates

    CERN Document Server

    Zhang, Hantian; Cao, Qingjie

    2014-01-01

    This paper presents a simple approach to low-thrust optimal-fuel and optimal-time transfer problems between two elliptic orbits using the Cartesian coordinates system. In this case, an orbit is described by its specific angular momentum and Laplace vectors with a free injection point. Trajectory optimization with the pseudospectral method and nonlinear programming are supported by the initial guess generated from the Chang-Chichka-Marsden Lyapunov-based transfer controller. This approach successfully solves several low-thrust optimal problems. Numerical results show that the Lyapunov-based initial guess overcomes the difficulty in optimization caused by the strong oscillation of variables in the Cartesian coordinates system. Furthermore, a comparison of the results shows that obtaining the optimal transfer solution through the polynomial approximation by utilizing Cartesian coordinates is easier than using orbital elements, which normally produce strongly nonlinear equations of motion. In this paper, the Eart...

  5. Ab initio molecular orbital and infrared spectroscopic study of the conformation of secondary amides: derivatives of formanilide, acetanilide and benzylamides

    Science.gov (United States)

    Ilieva, S.; Hadjieva, B.; Galabov, B.

    1999-09-01

    Ab initio molecular orbital calculations at HF/4-31G level and infrared spectroscopic data for the frequencies are applied to analyse the grouping in a series model aromatic secondary amides: formanilide; acetanilide; o-methylacetanilide; 2,6-dimethylformanilide, 2,6-dimethylacetanilide; N-benzylacetamide and N-benzylformamide. The theoretical and experimental data obtained show that the conformational state of the molecules studied is determined by the fine balance of several intramolecular factors: resonance effect between the amide group and the aromatic ring, steric interaction between various substituents around the -NH-CO- grouping in the aromatic ring, conjugation between the carbonyl bond and the nitrogen lone pair as well as direct field influences inside the amide group.

  6. Tailoring the highest occupied molecular orbital level of poly(N-vinylcarbazole) hole transport layers in organic multilayer heterojunctions

    Energy Technology Data Exchange (ETDEWEB)

    Park, Young Ran [Graphene Research Institute, Sejong University, Gwangjin-gu, Seoul 143-747 (Korea, Republic of); Kim, Hyeong Jin; Hong, Young Joon, E-mail: shink@sejong.ac.kr, E-mail: yjhong@sejong.ac.kr [Graphene Research Institute, Sejong University, Gwangjin-gu, Seoul 143-747 (Korea, Republic of); Faculty of Nanotechnology and Advanced Materials Engineering, Sejong University, Gwangjin-gu, Seoul 143-747 (Korea, Republic of); Hybrid Materials Research Center, Sejong University, Gwangjin-gu, Seoul 143-747 (Korea, Republic of); Im, Sungjin; Shin, Koo, E-mail: shink@sejong.ac.kr, E-mail: yjhong@sejong.ac.kr [Graphene Research Institute, Sejong University, Gwangjin-gu, Seoul 143-747 (Korea, Republic of); Department of Chemistry, Sejong University, Gwangjin-gu, Seoul 143-747 (Korea, Republic of); Seo, Sunae [Graphene Research Institute, Sejong University, Gwangjin-gu, Seoul 143-747 (Korea, Republic of); Department of Physics, Sejong University, Gwangjin-gu, Seoul 143-747 (Korea, Republic of); Choi, Won Kook [Materials and Life Science Research Division, Korea Institute of Science and Technology, Hwarang-ro 14-gil, Seoul 136-791 (Korea, Republic of)

    2016-01-11

    We report the tailoring of the electronic structure of poly(N-vinylcarbazole) (PVK) using a mixture layer of polyaniline:poly(p-styrenesulfonic acid) (PANI:PSS) in organic multilayer PVK/PANI:PSS/poly(3,4-ethylenedioxythiophene):PSS heterojunctions. The overall electronic structure of the PVK overlayer was systematically down-shifted while the work function of PANI:PSS increased as a function of the PSS-to-PANI weight ratio for the ratio range from 1 to 11 in the PANI:PSS film. The down-shift in the highest occupied molecular orbital of PVK markedly reduced the hole injection barrier from PVK to quantum-dot (QD) layers in QD-light emitting diode (QD-LED) structures, resulting in superior electrical and electroluminescent characteristics for QD-LEDs. The influences of PANI:PSS thickness on the electronic structure of PVK and the performance of QD-LEDs are also discussed.

  7. The Role of Super-Atom Molecular Orbitals in Doped Fullerenes in a Femtosecond Intense Laser Field.

    Science.gov (United States)

    Xiong, Hui; Mignolet, Benoit; Fang, Li; Osipov, Timur; Wolf, Thomas J A; Sistrunk, Emily; Gühr, Markus; Remacle, Francoise; Berrah, Nora

    2017-12-01

    The interaction of gas phase endohedral fullerene Ho3N@C80 with intense (0.1-5 × 10(14) W/cm(2)), short (30 fs), 800 nm laser pulses was investigated. The power law dependence of Ho3N@C80(q+), q = 1-2, was found to be different from that of C60. Time-dependent density functional theory computations revealed different light-induced ionization mechanisms. Unlike in C60, in doped fullerenes, the breaking of the cage spherical symmetry makes super atomic molecular orbital (SAMO) states optically active. Theoretical calculations suggest that the fast ionization of the SAMO states in Ho3N@C80 is responsible for the n = 3 power law for singly charged parent molecules at intensities lower than 1.2 × 10(14) W/cm(2).

  8. Orbital-free molecular dynamics simulations of melting in $Na_{8}$ and $Na_{20} melting in steps

    CERN Document Server

    Aguado, A; Alonso, J A; Stott, M J; Aguado, Andres; Lopez, Jose M.; Alonso, Julio A.; Stott, Malcolm J.

    1999-01-01

    The melting-like transitions of Na8 and Na20 are investigated by extensive ab initio constant energy molecular dynamics simulations, using a variant of the Car-Parrinello method which employs an explicit electronic kinetic energy functional of the density, thus avoiding the use of one-particle orbitals. Several melting indicators are evaluated in order to determine the nature of the different transitions, and comparison with other theoretical calculations is made. Both Na8 and Na20 melt over a wide range of temperature. For Na8, a first transition is observed at approx. 110 K, between a rigid phase and a phase involving isomerization between the different permutational isomers of the ground state structure. The ``liquid'' phase is completely established at approx. 220 K. For Na20, three successive transitions are observed: the first phase transition, at approx. 110 K, is associated with isomerization transitions between those permutational isomers of the ground state structure which are obtained by interchang...

  9. Orbital-selective Mott phase of Cu-substituted iron-based superconductors

    Science.gov (United States)

    Liu, Yang; Zhao, Yang-Yang; Song, Yun

    2016-07-01

    We study the phase transition in Cu-substituted iron-based superconductors with a new developed real-space Green’s function method. We find that Cu substitution has strong effect on the orbital-selective Mott transition introduced by the Hund’s rule coupling. The redistribution of the orbital occupancy which is caused by the increase of the Hund’s rule coupling, gives rise to the Mott-Hubbard metal-insulator transition in the half-filled d xy orbital. We also find that more and more electronic states appear inside that Mott gap of the d xy orbital with the increase of Cu substitution, and the in-gap states around the Fermi level are strongly localized at some specific lattice sites. Further, a distinctive phase diagram, obtained for the Cu-substituted Fe-based superconductors, displays an orbital-selective insulating phase, as a result of the cooperative effect of the Hund’s rule coupling and the impurity-induced disorder.

  10. A nanoplasmonic switch based on molecular machines

    KAUST Repository

    Zheng, Yue Bing

    2009-06-01

    We aim to develop a molecular-machine-driven nanoplasmonic switch for its use in future nanophotonic integrated circuits (ICs) that have applications in optical communication, information processing, biological and chemical sensing. Experimental data show that an Au nanodisk array, coated with rotaxane molecular machines, switches its localized surface plasmon resonances (LSPR) reversibly when it is exposed to chemical oxidants and reductants. Conversely, bare Au nanodisks and disks coated with mechanically inert control compounds, do not display the same switching behavior. Along with calculations based on time-dependent density functional theory (TDDFT), these observations suggest that the nanoscale movements within surface-bound "molecular machines" can be used as the active components in plasmonic devices. ©2009 IEEE.

  11. Electronic Transport Properties of a Naphthopyran-Based Optical Molecular Switch:an ab initio Study

    Institute of Scientific and Technical Information of China (English)

    XIA Cai-Juan; LIU De-Sheng; ZHANG Ying-Tang

    2011-01-01

    The electronic transport properties of a. Naphthopyran-based molecular optical switch are investigated by using the nonequilibrium Green's Function formalism combined with first-principles density functional theory. The molecule that comprises the switch can convert between its open and closed forms upon photoexcitation. Theoretical results show that the current through the open form is significantly larger than that through the closed form, which is different from other optical switches based on ring-opening reactions of the molecular bridge. The maximum on-off ratio (about 90) can be obtained at 1.4 V. The physical origin of the switching behavior is interpreted based on the spatial distributions of molecular orbitals and the HOMO-LUMO gap. Our result shows that the naphthopyran-based molecule is a good candidate for optical molecular switches and will be useful in the near future.%@@ ronic transport properties of a naphthopyran-based molecular optical switch are investigated by using the nonequilibrium Green's function formalism combined with first-principles density functional theory.The molecule that comprises the switch can convert between its open and closed forms upon photoexcitation.Theoretical results show that the current through the open form is significantly larger than that through the closed form,which is different from other optical switches based on ring-opening reactions of the molecular bridge.The maximum on-off ratio(about 90)can be obtained at 1.4 V.The physical origin of the switching behavior is interpreted based on the spatial distributions of molecular orbitals and the HOMO-LUMO gap.Our result shows that the naphthopyran-based molecule is a good candidate for optical molecular switches and will be useful in the near future.

  12. Development of a nanosatellite de-orbiting system by reliability based design optimization

    Science.gov (United States)

    Nikbay, Melike; Acar, Pınar; Aslan, Alim Rüstem

    2015-12-01

    This paper presents design approaches to develop a reliable and efficient de-orbiting system for the 3USAT nanosatellite to provide a beneficial orbital decay process at the end of a mission. A de-orbiting system is initially designed by employing the aerodynamic drag augmentation principle where the structural constraints of the overall satellite system and the aerodynamic forces are taken into account. Next, an alternative de-orbiting system is designed with new considerations and further optimized using deterministic and reliability based design techniques. For the multi-objective design, the objectives are chosen to maximize the aerodynamic drag force through the maximization of the Kapton surface area while minimizing the de-orbiting system mass. The constraints are related in a deterministic manner to the required deployment force, the height of the solar panel hole and the deployment angle. The length and the number of layers of the deployable Kapton structure are used as optimization variables. In the second stage of this study, uncertainties related to both manufacturing and operating conditions of the deployable structure in space environment are considered. These uncertainties are then incorporated into the design process by using different probabilistic approaches such as Monte Carlo Simulation, the First-Order Reliability Method and the Second-Order Reliability Method. The reliability based design optimization seeks optimal solutions using the former design objectives and constraints with the inclusion of a reliability index. Finally, the de-orbiting system design alternatives generated by different approaches are investigated and the reliability based optimum design is found to yield the best solution since it significantly improves both system reliability and performance requirements.

  13. Molecular structure, vibrational spectroscopic studies and natural bond orbital analysis of 7-amino-4-trifluoromethyl coumarin

    Indian Academy of Sciences (India)

    M K Subramanian; P M Anbarasan; S Manimegalai

    2010-05-01

    Quantum mechanical calculations of energies, geometries and vibrational wave numbers of 7-amino-4-trifluoromethyl coumarin (7A4TFMC) were carried out using Hartree–Fock (HF) and density functional theory (DFT) using hybrid functional BLYP and B3LYP with 6-31G(d,p) as basis set. The optimized geometrical parameters obtained by HF and DFT calculations are in good agreement with the experimental X-ray data. The best method to reproduce the experimental wave numbers is B3LYP method with the 6-31G(d,p) basis set. The difference between the observed and scaled wave number values of most of the fundamentals is very small. A detailed interpretation of the infrared spectra of 7A4TFMC was also reported. The entropy of the title compound was also performed at HF using the hybrid functional BLYP and B3LYP with 6-31 G(d,p) as basis set levels of theory. Natural bond orbital (NBO) analysis of the title molecule is also carried out. The theoretical spectrogram for FTIR spectra of the title molecule has been constructed.

  14. Infrared spectroscopy of molecular ions in selected rotational and spin-orbit states

    Science.gov (United States)

    Jacovella, U.; Agner, J. A.; Schmutz, H.; Deiglmayr, J.; Merkt, F.

    2016-07-01

    First results are presented obtained with an experimental setup developed to record IR spectra of rotationally state-selected ions. The method we use is a state-selective version of a method developed by Schlemmer et al. [Int. J. Mass Spectrom. 185, 589 (1999); J. Chem. Phys. 117, 2068 (2002)] to record IR spectra of ions. Ions are produced in specific rotational levels using mass-analyzed-threshold-ionization spectroscopy. The state-selected ions generated by pulsed-field ionization of Rydberg states of high principal quantum number (n ≈ 200) are extracted toward an octupole ion guide containing a neutral target gas. Prior to entering the octupole, the ions are excited by an IR laser. The target gas is chosen so that only excited ions react to form product ions. These product ions are detected mass selectively as a function of the IR laser wavenumber. To illustrate this method, we present IR spectra of C 2 H2 + in selected rotational levels of the 2Πu,3/2 and 2Πu,1/2 spin-orbit components of the vibronic ground state.

  15. Simultaneous wavelength and orbital angular momentum demultiplexing using tunable MEMS-based Fabry-Perot filter

    DEFF Research Database (Denmark)

    Lyubopytov, Vladimir; Porfirev, Alexey P.; Gurbatov, Stanislav O.

    2017-01-01

    In this paper, we experimentally demonstrate simultaneous wavelength and orbital angular momentum (OAM) multiplexing/demultiplexing of 10 Gbit/s data streams using a new on-chip micro-component-tunable MEMS-based Fabry-Perot filter integrated with a spiral phase plate. In the experiment, two...

  16. Preliminary Analysis of a Novel SAR Based Emergency System for Earth Orbit Satellites using Galileo

    NARCIS (Netherlands)

    Gill, E.K.A.; Helderweirt, A.

    2010-01-01

    This paper presents a preliminary analysis of a novel Search and Rescue (SAR) based emergency system for Low Earth Orbit (LEO) satellites using the Galileo Global Navigation Satellite System (GNSS). It starts with a description of the space user SAR system including a concept description, mission ar

  17. Localization of periodic orbits of autonomous systems based on high-order extremum conditions

    Directory of Open Access Journals (Sweden)

    Starkov Konstantin E.

    2004-01-01

    Full Text Available This paper gives localization and nonexistence conditions of periodic orbits in some subsets of the state space. Mainly, our approach is based on high-order extremum conditions, on high-order tangency conditions of a nonsingular solution of a polynomial system with an algebraic surface, and on some ideas related to algebraically-dependent polynomials. Examples of the localization analysis of periodic orbits are presented including the Blasius equations, the generalized mass action (GMA system, and the mathematical model of the chemical reaction with autocatalytic step.

  18. A Novel Image Encryption Scheme Based on Multi-orbit Hybrid of Discrete Dynamical System

    Directory of Open Access Journals (Sweden)

    Ruisong Ye

    2014-10-01

    Full Text Available A multi-orbit hybrid image encryption scheme based on discrete chaotic dynamical systems is proposed. One generalized Arnold map is adopted to generate three orbits for three initial conditions. Another chaotic dynamical system, tent map, is applied to generate one pseudo-random sequence to determine the hybrid orbit points from which one of the three orbits of generalized Arnold map. The hybrid orbit sequence is then utilized to shuffle the pixels' positions of plain-image so as to get one permuted image. To enhance the encryption security, two rounds of pixel gray values' diffusion is employed as well. The proposed encryption scheme is simple and easy to manipulate. The security and performance of the proposed image encryption have been analyzed, including histograms, correlation coefficients, information entropy, key sensitivity analysis, key space analysis, differential analysis, etc. All the experimental results suggest that the proposed image encryption scheme is robust and secure and can be used for secure image and video communication applications.

  19. Cavity modes with optical orbital angular momentum in a metamaterial ring based on transformation optics.

    Science.gov (United States)

    Wu, H W; Wang, F; Dong, Y Q; Shu, F Z; Zhang, K; Peng, R W; Xiong, X; Wang, Mu

    2015-12-14

    In this work, we theoretically study the cavity modes with transverse orbital angular momentum in metamaterial ring based on transformation optics. The metamaterial ring is designed to transform the straight trajectory of light into the circulating one by enlarging the azimuthal angle, effectively presenting the modes with transverse orbital angular momentum. The simulation results confirm the theoretical predictions, which state that the transverse orbital angular momentum of the mode not only depends on the frequency of the incident light, but also depends on the transformation scale of the azimuthal angle. Because energy dissipation inevitably reduces the field amplitude of the modes, the confined electromagnetic energy and the quality factor of the modes inside the ring are also studied in order to evaluate the stability of those cavity modes. The results show that the metamaterial ring can effectively confine light with a high quality factor and maintain steady modes with the orbital angular momentum, even if the dimension of the ring is much smaller than the wavelength of the incident light. This technique for exploiting the modes with optical transverse orbital angular momentum may provides a unique platform for applications related to micromanipulation.

  20. Periodic orbits for space-based reflectors in the circular restricted three-body problem

    Science.gov (United States)

    Salazar, F. J. T.; McInnes, C. R.; Winter, O. C.

    2017-05-01

    The use of space-based orbital reflectors to increase the total insolation of the Earth has been considered with potential applications in night-side illumination, electric power generation and climate engineering. Previous studies have demonstrated that families of displaced Earth-centered and artificial halo orbits may be generated using continuous propulsion, e.g. solar sails. In this work, a three-body analysis is performed by using the circular restricted three body problem, such that, the space mirror attitude reflects sunlight in the direction of Earth's center, increasing the total insolation. Using the Lindstedt-Poincaré and differential corrector methods, a family of halo orbits at artificial Sun-Earth L_2 points are found. It is shown that the third order approximation does not yield real solutions after the reflector acceleration exceeds 0.245 mm s^{-2}, i.e. the analytical expressions for the in- and out-of-plane amplitudes yield imaginary values. Thus, a larger solar reflector acceleration is required to obtain periodic orbits closer to the Earth. Derived using a two-body approach and applying the differential corrector method, a family of displaced periodic orbits close to the Earth are therefore found, with a solar reflector acceleration of 2.686 mm s^{-2}.

  1. Periodic orbits for space-based reflectors in the circular restricted three-body problem

    Science.gov (United States)

    Salazar, F. J. T.; McInnes, C. R.; Winter, O. C.

    2016-11-01

    The use of space-based orbital reflectors to increase the total insolation of the Earth has been considered with potential applications in night-side illumination, electric power generation and climate engineering. Previous studies have demonstrated that families of displaced Earth-centered and artificial halo orbits may be generated using continuous propulsion, e.g. solar sails. In this work, a three-body analysis is performed by using the circular restricted three body problem, such that, the space mirror attitude reflects sunlight in the direction of Earth's center, increasing the total insolation. Using the Lindstedt-Poincaré and differential corrector methods, a family of halo orbits at artificial Sun-Earth L_2 points are found. It is shown that the third order approximation does not yield real solutions after the reflector acceleration exceeds 0.245 mm s^{-2} , i.e. the analytical expressions for the in- and out-of-plane amplitudes yield imaginary values. Thus, a larger solar reflector acceleration is required to obtain periodic orbits closer to the Earth. Derived using a two-body approach and applying the differential corrector method, a family of displaced periodic orbits close to the Earth are therefore found, with a solar reflector acceleration of 2.686 mm s^{-2}.

  2. Orbital-Parity Selective Superconducting Pairing Structures of Fe-based Superconductors under Glide Symmetry

    Science.gov (United States)

    Lin, Chiahui; Chou, Chung-Pin; Yin, Wei-Guo; Ku, Wei

    2014-03-01

    We show that the superconductivity in Fe-based superconductors consists of zero and finite momentum (π , π , 0) Cooper pairs with the same and different parities of the Fe 3 d orbitals respectively. The former develops the distinct gap structures for each orbital parity, and the latter is characteristic of spin singlet, spacial oddness and time reversal symmetry breaking. This originates from the unit cell containing two Fe atoms and two anions of staggered positioning with respect to the Fe square lattice. The in-plane translation is turned into glide translation, which dictates orbital-parity selective quasiparticles. Such novel pairing structures explain the unusual gap angular modulation on the hole pockets in recent ARPES and STS experiments. Work supported by DOE DE-AC02-98CH10886 and Chinese Academy of Engineering Physics and Ministry of Science and Technology.

  3. Tip-induced gating of molecular levels in carbene-based junctions

    Science.gov (United States)

    Foti, Giuseppe; Vázquez, Héctor

    2016-03-01

    We study the conductance of N-heterocyclic carbene-based (NHC) molecules on gold by means of first-principles calculations based on density-functional theory and non-equilibrium Green’s functions. We consider several tip structures and find a strong dependence of the position of the NHC molecular levels with the atomistic structure of the tip. The position of the lowest unoccupied molecular orbital (LUMO) can change by almost 0.8 eV with tip shape. Through an analysis of the net charge transfer, electron redistribution and work function for each tip structure, we rationalize the LUMO shifts in terms of the sum of the work function and the maximum electrostatic potential arising from charge rearrangement. These differences in the LUMO position, effectively gating the molecular levels, result in large conductance variations. These findings open the way to modulating the conductance of NHC-based molecular circuits through the controlled design of the tip atomistic structure.

  4. The Spin-orbit force, recoil corrections and possible $B \\bar{B}^{*}$ and $D \\bar{D}^{*}$ molecular states

    CERN Document Server

    Zhao, Lu; Zhu, Shi-Lin

    2014-01-01

    In the framework of the one boson exchange model, we have calculated the effective potentials between two heavy mesons $B \\bar{B}^{*}$ and $D \\bar{D}^{*}$ from the t- and u-channel $\\pi$, $\\eta$, $\\rho$, $\\omega$ and $\\sigma$ meson exchange with four kinds of quantum number: $I=0$, $J^{PC}=1^{++}$; $I=0$, $J^{PC}=1^{+-}$; $I=1$, $J^{PC}=1^{++}$; $I=1$, $J^{PC}=1^{+-}$. We keep the recoil corrections to the $B \\bar{B}^{*}$ and $D \\bar{D}^{*}$ system up to $O(\\frac{1}{M^2})$. The spin orbit force appears at $O(\\frac{1}{M})$, which turns out to be important for the very loosely bound molecular states. Our numerical results show that the momentum-related corrections are unfavorable to the formation of the molecular states in the $I=0$, $J^{PC}=1^{++}$ and $I=1$, $J^{PC}=1^{+-}$ channels in the $D \\bar{D}^{*}$ systems.

  5. Intraparticle Molecular Orbital Engineering of Semiconducting Polymer Nanoparticles as Amplified Theranostics for in Vivo Photoacoustic Imaging and Photothermal Therapy.

    Science.gov (United States)

    Lyu, Yan; Fang, Yuan; Miao, Qingqing; Zhen, Xu; Ding, Dan; Pu, Kanyi

    2016-04-26

    Optical theranostic nanoagents that seamlessly and synergistically integrate light-generated signals with photothermal or photodynamic therapy can provide opportunities for cost-effective precision medicine, while the potential for clinical translation requires them to have good biocompatibility and high imaging/therapy performance. We herein report an intraparticle molecular orbital engineering approach to simultaneously enhance photoacoustic brightness and photothermal therapy efficacy of semiconducting polymer nanoparticles (SPNs) for in vivo imaging and treatment of cancer. The theranostic SPNs have a binary optical component nanostructure, wherein a near-infrared absorbing semiconducting polymer and an ultrasmall carbon dot (fullerene) interact with each other to induce photoinduced electron transfer upon light irradiation. Such an intraparticle optoelectronic interaction augments heat generation and consequently enhances the photoacoustic signal and maximum photothermal temperature of SPNs by 2.6- and 1.3-fold, respectively. With the use of the amplified SPN as the theranostic nanoagent, it permits enhanced photoacoustic imaging and photothermal ablation of tumor in living mice. Our study thus not only introduces a category of purely organic optical theranostics but also highlights a molecular guideline to amplify the effectiveness of light-intensive imaging and therapeutic nanosystems.

  6. Decimal Integer Multiplication based on Molecular Beacons

    Directory of Open Access Journals (Sweden)

    Jing Wang

    2013-12-01

    Full Text Available Due to the enhancement of circuit integration level, and the accelerating of working frequency of traditional computer, it requires components dimension must be constantly decreased. So encapsulation, etching and other problems of chip are becoming more and more difficult to solve, which causes its performance also become unstable. In order to overcome this problem, DNA computing as a new kind of molecular computing mode, with its high parallelism, huge amounts of storage capacity, low energy consumption advantages has received extensive attention. Being the same with traditional electronic computer, DNA computer is composed by arithmetic operations such as addition, subtraction, multiplication and dividing and basic logic units such as AND, OR, NON gate. This paper puts forward a new method to realize decimal integer multiplication based on molecular beacons. The algorithm firstly converts decimal integer to binary number, and then resolves the multiplication process into multiplication of current bit and addition of intermediate result after shifting two steps. Molecular beacon is used as multiplying unit, coding sequence is used as multiplier in this method. Based on the working principle of molecular beacon, multiplication operation of two one-bit binary is simulated. And by recording fluorescence status of molecular beacon to observe intermediate result and carry-bit situation, the final result can be obtained through addition after shifting. Examples prove that this method can realize decimal integer multiplication rapidly and accurately. This method is similar to multiplication system in traditional electronic computer, and it provides a simple, easier operation method for DNA computer to realize arithmetic operation.

  7. Communication: Localized molecular orbital analysis of the effect of electron correlation on the anomalous isotope effect in the NMR spin-spin coupling constant in methane

    Energy Technology Data Exchange (ETDEWEB)

    Zarycz, M. Natalia C., E-mail: mnzarycz@gmail.com; Provasi, Patricio F., E-mail: patricio@unne.edu.ar [Department of Physics, University of Northeastern - CONICET, Av. Libertad 5500, Corrientes W3404AAS (Argentina); Sauer, Stephan P. A., E-mail: sauer@kiku.dk [Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø (Denmark)

    2014-10-21

    We discuss the effect of electron correlation on the unexpected differential sensitivity (UDS) in the {sup 1}J(C–H) coupling constant of CH{sub 4} using a decomposition into contributions from localized molecular orbitals and compare with the {sup 1}J(N–H) coupling constant in NH{sub 3}. In particular, we discuss the well known fact that uncorrelated coupled Hartree-Fock (CHF) calculations are not able to reproduce the UDS in methane. For this purpose we have implemented for the first time a localized molecular orbital analysis for the second order polarization propagator approximation with coupled cluster singles and doubles amplitudes—SOPPA(CCSD) in the DALTON program. Comparing the changes in the localized orbital contributions at the correlated SOPPA and SOPPA(CCSD) levels and at the uncorrelated CHF level, we find that the latter overestimates the effect of stretching the bond between the coupled atoms on the contribution to the coupling from the localized bonding orbital between these atoms. This disturbs the subtle balance between the molecular orbital contributions, which lead to the UDS in methane.

  8. Nodular Fasciitis of the Orbit: A Case Report Confirmed by Molecular Cytogenetic Analysis.

    Science.gov (United States)

    Anzeljc, Andrew J; Oliveira, Andre M; Grossniklaus, Hans E; Kim, Hee Joon; Hayek, Brent

    2016-02-12

    Nodular fasciitis is a benign fibroblastic proliferation typically found in the subcutaneous tissue or superficial fascia of the extremities that is often confused for malignancy. These lesions rarely occur on the eyelids and ocular adnexa and are seldom analyzed by ophthalmic pathologists. USP6 gene rearrangement has been recently demonstrated in nodular fasciitis and this rearrangement may lead to the formation of a fusion gene MYH9-USP6 in some cases. Herein, the authors describe a 38-year-old woman with a 6-month history of a progressively enlarging mass beneath her right medial upper eyelid. Histopathologic analysis of the excisional biopsy confirmed classic features of nodular fasciitis. Molecular cytogenetic analysis revealed a rearrangement of the USP6 locus, confirming the diagnosis of benign nodular fasciitis.

  9. Failure of single electron descriptions of molecular orbital collision processes. [Electron promotion mechanism

    Energy Technology Data Exchange (ETDEWEB)

    Elston, S.B.

    1978-01-01

    Inner-shell excitation occurring in low and moderate (keV range) energy collisions between light atomic and ionic systems is frequently describable in terms of molecular promotion mechanisms, which were extensively explored both theoretically and experimentally. The bulk of such studies have concentrated on processes understandable through the use of single- and independent-electron models. Nonetheless, it is possible to find cases of inner-shell excitation in relatively simple collision systems which involve nearly simultaneous multiple-electron transitions and transitions induced by inherently two-electron interactions. Evidence for these many- and nonindependent-electron phenomena in inner-shell excitation processes and the importance of considering such effects in the interpretation of collisionally induced excitation spectra is discussed. 13 references.

  10. A new theory for symmetry orbital and tensor (Ⅱ)——Symmetric reduction of molecular integrals and self-consistent field calculations

    Institute of Scientific and Technical Information of China (English)

    周泰锦; 莫亦荣

    1999-01-01

    The symmetry orbital-symmetry orbital tensor method is applied to the evaluation of molecular integrals (one-electron and two-electron integrals) and the symmetry-orbital-tensor and self-consistent-field (SOT-SCF) calculations. A calculation scheme is proposed to simplify the evaluation of integrals and a key equation is derived to reduce the computation efforts in SCF iterations. According to the key equation, compared with the traditional SCF method, the computation efficiencies including CPU timing and external disk (or internal memory) requirement increase in the magnitude of the square of the order of a point group. The new SOT method is expected to be useful in the theoretical calculations of large molecular systems of high point group symmetries.

  11. Localized molecular orbital analysis of the effect of electron correlation on the anomalous isotope effect in the NMR spin-spin coupling constant in methane

    DEFF Research Database (Denmark)

    Zarycz, M. Natalia C.; Sauer, Stephan P. A.; Provasi, Patricio F.

    2014-01-01

    We discuss the effect of electron correlation on the unexpected differential sensitivity (UDS) in the 1J(C-H) coupling constant of CH4 using a decomposition into contributions from localized molecular orbitals and compare with the 1J(N-H) coupling constant in NH3. In particular we discuss the well...... known fact that uncorrelated coupled Hartree-Fock (CHF) calculations are not able to reproduce the UDS in methane. For this purpose we have implemented for the first time a localized molecular orbital analysis for the second order polarization propagator approximation with coupled cluster singles...... and doubles amplitudes - SOPPA(CCSD) in the DALTON program. Comparing the changes in the localized orbital contributions at the correlated SOPPA and SOPPA(CCSD) levels and at the uncorrelated CHF level, we find that the latter overestimates the effect of stretching the bond between the coupled atoms...

  12. Initial Orbit Determination Based on Propagation of Admissible Regions with Differential Algebra

    Science.gov (United States)

    2017-01-19

    order n with limited computational effort. In addition to basic algebraic operations, operations for differentiation and integration can be easily...AFRL-AFOSR-UK-TR-2017-0022 Initial Orbit Determination based on propagation of admissible regions with Differential Algebra Pierluigi Di Lizia...Determination based on propagation of admissible regions with Differential Algebra 5a.  CONTRACT NUMBER 5b.  GRANT NUMBER FA9550-15-1-0244 5c

  13. Conductance of three-terminal molecular bridge based on tight-binding theory

    Institute of Scientific and Technical Information of China (English)

    Wang Li-Guang; Li Yong; Yu Ding-Wen; Katsunori Tagami; Masaru Tsukada

    2005-01-01

    The quantum transmission characteristic of three-benzene ring nano-molecular bridge is investigated theoretically by using Green's function approach based on tight-binding theory with only aπ orbital per carbon atom at the site.The transmission probabilities that electrons transport through the molecular bridge from one terminal to the other two terminals are obtained. The electronic current distributions inside the molecular bridge are calculated and shown in graphical analogy by the current density method based on Fisher-Lee formula at the energy points E=±0.42,±1.06 and ±1.5, respectively, where the transmission spectra appear peaks. We find that the transmission spectra are related to the incident electronic energy and the molecular levels strongly, and the current distributions agree well with Kirchhoff quantum current momentum conservation law.

  14. Comparing orbiter and rover image-based mapping of an ancient sedimentary environment, Aeolis Palus, Gale crater, Mars

    Science.gov (United States)

    Stack, Kathryn M.; Edwards, Christopher; Grotzinger, J. P.; Gupta, S.; Sumner, D.; Edgar, Lauren; Fraeman, A.; Jacob, S.; LeDeit, L.; Lewis, K.W.; Rice, M.S.; Rubin, D.; Calef, F.; Edgett, K.; Williams, R.M.E.; Williford, K.H.

    2016-01-01

    This study provides the first systematic comparison of orbital facies maps with detailed ground-based geology observations from the Mars Science Laboratory (MSL) Curiosity rover to examine the validity of geologic interpretations derived from orbital image data. Orbital facies maps were constructed for the Darwin, Cooperstown, and Kimberley waypoints visited by the Curiosity rover using High Resolution Imaging Science Experiment (HiRISE) images. These maps, which represent the most detailed orbital analysis of these areas to date, were compared with rover image-based geologic maps and stratigraphic columns derived from Curiosity’s Mast Camera (Mastcam) and Mars Hand Lens Imager (MAHLI). Results show that bedrock outcrops can generally be distinguished from unconsolidated surficial deposits in high-resolution orbital images and that orbital facies mapping can be used to recognize geologic contacts between well-exposed bedrock units. However, process-based interpretations derived from orbital image mapping are difficult to infer without known regional context or observable paleogeomorphic indicators, and layer-cake models of stratigraphy derived from orbital maps oversimplify depositional relationships as revealed from a rover perspective. This study also shows that fine-scale orbital image-based mapping of current and future Mars landing sites is essential for optimizing the efficiency and science return of rover surface operations.

  15. Comparing orbiter and rover image-based mapping of an ancient sedimentary environment, Aeolis Palus, Gale crater, Mars

    Science.gov (United States)

    Stack, K. M.; Edwards, C. S.; Grotzinger, J. P.; Gupta, S.; Sumner, D. Y.; Calef, F. J.; Edgar, L. A.; Edgett, K. S.; Fraeman, A. A.; Jacob, S. R.; Le Deit, L.; Lewis, K. W.; Rice, M. S.; Rubin, D.; Williams, R. M. E.; Williford, K. H.

    2016-12-01

    This study provides the first systematic comparison of orbital facies maps with detailed ground-based geology observations from the Mars Science Laboratory (MSL) Curiosity rover to examine the validity of geologic interpretations derived from orbital image data. Orbital facies maps were constructed for the Darwin, Cooperstown, and Kimberley waypoints visited by the Curiosity rover using High Resolution Imaging Science Experiment (HiRISE) images. These maps, which represent the most detailed orbital analysis of these areas to date, were compared with rover image-based geologic maps and stratigraphic columns derived from Curiosity's Mast Camera (Mastcam) and Mars Hand Lens Imager (MAHLI). Results show that bedrock outcrops can generally be distinguished from unconsolidated surficial deposits in high-resolution orbital images and that orbital facies mapping can be used to recognize geologic contacts between well-exposed bedrock units. However, process-based interpretations derived from orbital image mapping are difficult to infer without known regional context or observable paleogeomorphic indicators, and layer-cake models of stratigraphy derived from orbital maps oversimplify depositional relationships as revealed from a rover perspective. This study also shows that fine-scale orbital image-based mapping of current and future Mars landing sites is essential for optimizing the efficiency and science return of rover surface operations.

  16. Imaging momentum orbital densities of conformationally versatile molecules: a benchmark theoretical study of the molecular and electronic structures of dimethoxymethane.

    Science.gov (United States)

    Huang, Y R; Knippenberg, S; Hajgató, B; François, J-P; Deng, J K; Deleuze, M S

    2007-07-05

    (e,2e) ionization spectra enables us to identify specific fingerprints of through-space orbital interactions associated with the anomeric effect. At last, based on our 1p-GF/ADC(3) assignment of spectral bands, accurate and spherically averaged (e,2e) electron momentum distributions at an electron impact energy of 1200 eV are computed from the related Dyson orbitals. Very significant discrepancies are observed with momentum distributions obtained for several outer-valence levels using standard Kohn-Sham orbitals.

  17. Compensator-based 6-DOF control for probe asteroid-orbital-frame hovering with actuator limitations

    Science.gov (United States)

    Liu, Xiaosong; Zhang, Peng; Liu, Keping; Li, Yuanchun

    2016-05-01

    This paper is concerned with 6-DOF control of a probe hovering in the orbital frame of an asteroid. Considering the requirements of the scientific instruments pointing direction and orbital position in practical missions, the coordinate control of relative attitude and orbit between the probe and target asteroid is imperative. A 6-DOF dynamic equation describing the relative translational and rotational motion of a probe in the asteroid's orbital frame is derived, taking the irregular gravitation, model and parameter uncertainties and external disturbances into account. An adaptive sliding mode controller is employed to guarantee the convergence of the state error, where the adaptation law is used to estimate the unknown upper bound of system uncertainty. Then the controller is improved to deal with the practical problem of actuator limitations by introducing a RBF neural network compensator, which is used to approximate the difference between the actual control with magnitude constraint and the designed nominal control law. The closed-loop system is proved to be asymptotically stable through the Lyapunov stability analysis. Numerical simulations are performed to compare the performances of the preceding designed control laws. Simulation results demonstrate the validity of the control scheme using the compensator-based adaptive sliding mode control law in the presence of actuator limitations, system uncertainty and external disturbance.

  18. Hückel and möbius boundary conditions for solids and orbital symmmetry correlation in the rotational phase transition of molecular crystals

    Science.gov (United States)

    Chiu, Ying-Nan

    1983-05-01

    A new cyclic boundary condition which corresponds to a Möbius strip representation of a one-dimensional crystal is introduced. It is compared with the usual Bloch and Born—von Karman boundary condition which is shown to be a Hückel condition in the sense of LCAO MO treatment of a ring structure. The potential relevance of this Möbius condition to one-dimensional molecular and liquid crystals in which the relative molecular orientation changes during phase transition is alluded to. A comparison of the energies for the twisted and non-twisted form of the linear crystal is derived in the LCAO approximation. The orbital symmetry correlation in the concerted twist of the atomic or molecular orbitals atom! the linear backbone during a rotational polymorphic structural transition is also derived.

  19. Laplace-transformed atomic orbital-based Møller-Plesset perturbation theory for relativistic two-component Hamiltonians.

    Science.gov (United States)

    Helmich-Paris, Benjamin; Repisky, Michal; Visscher, Lucas

    2016-07-07

    We present a formulation of Laplace-transformed atomic orbital-based second-order Møller-Plesset perturbation theory (MP2) energies for two-component Hamiltonians in the Kramers-restricted formalism. This low-order scaling technique can be used to enable correlated relativistic calculations for large molecular systems. We show that the working equations to compute the relativistic MP2 energy differ by merely a change of algebra (quaternion instead of real) from their non-relativistic counterparts. With a proof-of-principle implementation we study the effect of the nuclear charge on the magnitude of half-transformed integrals and show that for light elements spin-free and spin-orbit MP2 energies are almost identical. Furthermore, we investigate the effect of separation of charge distributions on the Coulomb and exchange energy contributions, which show the same long-range decay with the inter-electronic/atomic distance as for non-relativistic MP2. A linearly scaling implementation is possible if the proper distance behavior is introduced to the quaternion Schwarz-type estimates as for non-relativistic MP2.

  20. Laplace-transformed atomic orbital-based M{\\o}ller-Plesset perturbation theory for relativistic two-component Hamiltonians

    CERN Document Server

    Helmich-Paris, Benjamin; Visscher, Lucas

    2016-01-01

    We present a formulation of Laplace-transformed atomic orbital-based second-order M{\\o}ller-Plesset perturbation theory (MP2) energies for two-component Hamiltonians in the Kramers-restricted formalism. This low-order scaling technique can be used to enable correlated relativistic calculations for large molecular systems. We show that the working equations to compute the relativistic MP2 energy differ by merely a change of algebra (quaternion instead of real) from their non-relativistic counterparts. With a proof-of-principle implementation we study the effect of the nuclear charge on the magnitude of half-transformed integrals and show that for light elements spin-free and spin-orbit MP2 energies are almost identical. Furthermore, we investigate the effect of separation of charge distributions on the Coulomb and exchange energy con- tributions, which show the same long-range decay with the inter-electronic / atomic distance as for non-relativistic MP2. A linearly scaling implementation is possible if the pro...

  1. A Novel Double Cluster and Principal Component Analysis-Based Optimization Method for the Orbit Design of Earth Observation Satellites

    Directory of Open Access Journals (Sweden)

    Yunfeng Dong

    2017-01-01

    Full Text Available The weighted sum and genetic algorithm-based hybrid method (WSGA-based HM, which has been applied to multiobjective orbit optimizations, is negatively influenced by human factors through the artificial choice of the weight coefficients in weighted sum method and the slow convergence of GA. To address these two problems, a cluster and principal component analysis-based optimization method (CPC-based OM is proposed, in which many candidate orbits are gradually randomly generated until the optimal orbit is obtained using a data mining method, that is, cluster analysis based on principal components. Then, the second cluster analysis of the orbital elements is introduced into CPC-based OM to improve the convergence, developing a novel double cluster and principal component analysis-based optimization method (DCPC-based OM. In DCPC-based OM, the cluster analysis based on principal components has the advantage of reducing the human influences, and the cluster analysis based on six orbital elements can reduce the search space to effectively accelerate convergence. The test results from a multiobjective numerical benchmark function and the orbit design results of an Earth observation satellite show that DCPC-based OM converges more efficiently than WSGA-based HM. And DCPC-based OM, to some degree, reduces the influence of human factors presented in WSGA-based HM.

  2. As bases moleculares da hemofilia A

    Directory of Open Access Journals (Sweden)

    Simone Ferreira Pio

    2009-01-01

    Full Text Available As hemofilias são doenças hemorrágicas resultantes da deficiência de fator VIII (hemofilia A ou de fator IX (hemofilia B da coagulação, decorrentes de mutações nos genes que codificam os fatores VIII ou IX, respectivamente. A hemofilia A é mais frequente que a hemofilia B e acomete aproximadamente 1:10.000 nascimentos masculinos. A gravidade e frequência dos episódios hemorrágicos está relacionado ao nível residual de atividade de fator VIII presente no plasma e este relaciona-se ao tipo de mutação associada à doença. A clonagem do gene do fator VIII tornou possível o conhecimento das bases moleculares da hemofilia A, sendo hoje conhecidas mais de 1.000 mutações associadas à doença. O conhecimento das bases moleculares da hemofilia A permite uma melhor compreensão da relação genótipo-fenótipo da doença, tomada de condutas clínicas diferenciadas em casos de mutações associadas a um maior risco de desenvolvimento de inibidor, determinação da condição de portadora de hemofilia em mulheres relacionadas aos pacientes, implementação de programa de aconselhamento genético/orientação familiar e melhor compreensão das relações estruturais-funcionais do gene-proteína. Este artigo propõe revisar as bases moleculares da hemofilia A, os métodos laboratoriais utilizados para a caracterização das mutações e as implicações clínicas envolvidas no diagnóstico molecular da hemofilia A.Hemophilias are bleeding disorders due to deficiency of the blood coagulation factor VIII (hemophilia A or factor IX (hemophilia B, resulting from mutation on the gene coding for factor VIII or factor IX. Hemophilia A is more frequent than hemophilia B and affects 1:10,000 male newborns. The severity and frequency of hemorrhagic episodes is related to residual activity of factor VIII present in the plasma and relates to the type of mutation associated with the disorder. Cloning of the factor VIII gene has enabled researchers to

  3. Design of Acceptors with Suitable Frontier Molecular Orbitals to Match Donors via Substitutions on Perylene Diimide for Organic Solar Cells.

    Science.gov (United States)

    Lv, Xiaoli; Li, Zhuoxin; Li, Songyang; Luan, Guoyou; Liang, Dadong; Tang, Shanshan; Jin, Ruifa

    2016-05-13

    A series of perylene diimide (PDI) derivatives have been investigated at the CAM-B3LYP/6-31G(d) and the TD-B3LYP/6-31+G(d,p) levels to design solar cell acceptors with high performance in areas such as suitable frontier molecular orbital (FMO) energies to match oligo(thienylenevinylene) derivatives and improved charge transfer properties. The calculated results reveal that the substituents slightly affect the distribution patterns of FMOs for PDI-BI. The electron withdrawing group substituents decrease the FMO energies of PDI-BI, and the electron donating group substituents slightly affect the FMO energies of PDI-BI. The di-electron withdrawing group substituents can tune the FMOs of PDI-BI to be more suitable for the oligo(thienylenevinylene) derivatives. The electron withdrawing group substituents result in red shifts of absorption spectra and electron donating group substituents result in blue shifts for PDI-BI. The -CN substituent can improve the electron transport properties of PDI-BI. The -CH₃ group in different positions slightly affects the electron transport properties of PDI-BI.

  4. Accelerating Atomic Orbital-based Electronic Structure Calculation via Pole Expansion plus Selected Inversion

    OpenAIRE

    Lin, Lin

    2012-01-01

    We describe how to apply the recently developed pole expansion plus selected inversion (PEpSI) technique to Kohn-Sham density function theory (DFT) electronic structure calculations that are based on atomic orbital discretization. We give analytic expressions for evaluating charge density, total energy, Helmholtz free energy and atomic forces without using the eigenvalues and eigenvectors of the Kohn-Sham Hamiltonian. We also show how to update the chemical potential without using Kohn-Sham...

  5. Communication: Systematic shifts of the lowest unoccupied molecular orbital peak in x-ray absorption for a series of 3d metal porphyrins

    DEFF Research Database (Denmark)

    García Lastra, Juan Maria; Cook, P. L.; Himpsel, F. J.

    2010-01-01

    Porphyrins are widely used as dye molecules in solar cells. Knowing the energies of their frontier orbitals is crucial for optimizing the energy level structure of solar cells. We use near edge x-ray absorption fine structure (NEXAFS) spectroscopy to obtain the energy of the lowest unoccupied...... molecular orbital (LUMO) with respect to the N-1s core level of the molecule. A systematic energy shift of the N-1s to LUMO transition is found along a series of 3d metal octaethylporphyrins and explained by density functional theory. It is mainly due to a shift of the N-1s level rather than a shift...

  6. The approximate state transition matrix based on non-orthogonal decomposition and its application in orbit determination

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The Unit Vector Method (UVM) is an orbit determination method extensively applied. In this paper, the UVM and classical Differential Orbit Improvement (DOI) are compared, and a fusion method is given for the orbit determination with different kind data. Based on non-orthogonal decomposition of position and velocity vectors, an approximation scheme is constructed to calculate the state transition matrix. This method simplifies the calculation of the approximate state transition matrix, analyzes the convergence mechanism of the UVM, and makes clear the defect of weight strategy in UVM. Results of orbit the determination with simulating and real data show that this method has good numerical stability and rational weight distribution.

  7. Characterization of Orbital Debris via Hyper-Velocity Laboratory-Based Tests

    Science.gov (United States)

    Cowardin, Heather; Liou, J.-C.; Anz-Meador, Phillip; Sorge, Marlon; Opiela, John; Fitz-Coy, Norman; Huynh, Tom; Krisko, Paula

    2017-01-01

    Existing DOD and NASA satellite breakup models are based on a key laboratory test, Satellite Orbital debris Characterization Impact Test (SOCIT), which has supported many applications and matched on-orbit events involving older satellite designs reasonably well over the years. In order to update and improve these models, the NASA Orbital Debris Program Office, in collaboration with the Air Force Space and Missile Systems Center, The Aerospace Corporation, and the University of Florida, replicated a hypervelocity impact using a mock-up satellite, DebriSat, in controlled laboratory conditions. DebriSat is representative of present-day LEO satellites, built with modern spacecraft materials and construction techniques. Fragments down to 2 mm in size will be characterized by their physical and derived properties. A subset of fragments will be further analyzed in laboratory radar and optical facilities to update the existing radar-based NASA Size Estimation Model (SEM) and develop a comparable optical-based SEM. A historical overview of the project, status of the characterization process, and plans for integrating the data into various models will be discussed herein.

  8. Characterization of Orbital Debris via Hyper-Velocity Laboratory-Based Tests

    Science.gov (United States)

    Cowardin, Heather; Liou, J.-C.; Krisko, Paula; Opiela, John; Fitz-Coy, Norman; Sorge, Marlon; Huynh, Tom

    2017-01-01

    Existing DoD and NASA satellite breakup models are based on a key laboratory test, Satellite Orbital debris Characterization Impact Test (SOCIT), which has supported many applications and matched on-orbit events involving older satellite designs reasonably well over the years. In order to update and improve these models, the NASA Orbital Debris Program Office, in collaboration with the Air Force Space and Missile Systems Center, The Aerospace Corporation, and the University of Florida, replicated a hypervelocity impact using a mock-up satellite, DebriSat, in controlled laboratory conditions. DebriSat is representative of present-day LEO satellites, built with modern spacecraft materials and construction techniques. Fragments down to 2 mm in size will be characterized by their physical and derived properties. A subset of fragments will be further analyzed in laboratory radar and optical facilities to update the existing radar-based NASA Size Estimation Model (SEM) and develop a comparable optical-based SEM. A historical overview of the project, status of the characterization process, and plans for integrating the data into various models will be discussed herein.

  9. Impact of Dynamic Orbital Correlations on Magnetic Excitations in the Normal State of Iron-Based Superconductors

    Science.gov (United States)

    Lee, Wei-Cheng; Lv, Weicheng; Tranquada, John; Phillips, Philip

    2013-03-01

    We show here that orbital degrees of freedom produce a distinct signature in the magnetic excitation spectrum of iron-based superconductors above the magnetic ordering temperature. Because dxz and dyz orbitals are strongly connected with Fermi surface topology, the nature of magnetic excitations can be modified significantly due to the presence of either static or fluctuating orbital correlations. Within a five-orbital itinerant model, we show that static orbital order generally leads to an enhancement of commensurate magnetic excitations even when the original Fermi surface lacks nesting at commensurate wavevectors. When long-range orbital order is absent, Gaussian fluctuations beyond the standard random-phase approximation capture the effects of fluctuating orbital correlations on the magnetic excitations. We find that commensurate magnetic excitations can also be enhanced if the orbital correlations are strong. We propose that this unusual incommensurate-to-commensurate transformation is an important signature to distinguish orbital from spin physics in the normal state of iron-based superconductors. This work is supported by the Center for Emergent Superconductivity, a DOE Energy Frontier Research Center, Grant No. DE-AC0298CH1088.

  10. The average acceleration approach applied to gravity coefficients recovery based on GOCE orbits

    Directory of Open Access Journals (Sweden)

    Huang Qiang

    2012-11-01

    Full Text Available The average acceleration approach was applied to recover a gravity field model Model_ACA from GOCE precise science orbits from September 2 to November 2, 2010, and furthermore a so called sequential least square adjustment was used. The model was compared with other gravity field models based on CHAMP, GRACE and GOCE. The result shows that the model is superior to gravity field based on CHAMP, and with higher accuracy than other international gravity field models based on only GOCE data before 80 degree. The degree geoid height of Model_ACA reaches 3 cm up to 90 degree and order.

  11. FOB-SH: Fragment orbital-based surface hopping for charge carrier transport in organic and biological molecules and materials

    Science.gov (United States)

    Spencer, J.; Gajdos, F.; Blumberger, J.

    2016-08-01

    We introduce a fragment orbital-based fewest switches surface hopping method, FOB-SH, designed to efficiently simulate charge carrier transport in strongly fluctuating condensed phase systems such as organic semiconductors and biomolecules. The charge carrier wavefunction is expanded and the electronic Hamiltonian constructed in a set of singly occupied molecular orbitals of the molecular sites that mediate the charge transfer. Diagonal elements of the electronic Hamiltonian (site energies) are obtained from a force field, whereas the off-diagonal or electronic coupling matrix elements are obtained using our recently developed analytic overlap method. We derive a general expression for the exact forces on the adiabatic ground and excited electronic state surfaces from the nuclear gradients of the charge localized electronic states. Applications to electron hole transfer in a model ethylene dimer and through a chain of ten model ethylenes validate our implementation and demonstrate its computational efficiency. On the larger system, we calculate the qualitative behaviour of charge mobility with change in temperature T for different regimes of the intermolecular electronic coupling. For small couplings, FOB-SH predicts a crossover from a thermally activated regime at low temperatures to a band-like transport regime at higher temperatures. For higher electronic couplings, the thermally activated regime disappears and the mobility decreases according to a power law. This is interpreted by a gradual loss in probability for resonance between the sites as the temperature increases. The polaron hopping model solved for the same system gives a qualitatively different result and underestimates the mobility decay at higher temperatures. Taken together, the FOB-SH methodology introduced here shows promise for a realistic investigation of charge carrier transport in complex organic, aqueous, and biological systems.

  12. A hybrid framework of first principles molecular orbital calculations and a three-dimensional integral equation theory for molecular liquids: Multi-center molecular Ornstein–Zernike self-consistent field approach

    Energy Technology Data Exchange (ETDEWEB)

    Kido, Kentaro, E-mail: kido.kentaro@jaea.go.jp [Nuclear Safety Research Center, Japan Atomic Energy Agency, 2-4 Shirane, Shirakata, Tokai-mura, Naka-gun, Ibaraki 319-1195 (Japan); Kasahara, Kento [Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510 (Japan); Yokogawa, Daisuke [Department of Chemistry, Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602 (Japan); Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8062 (Japan); Sato, Hirofumi [Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510 (Japan); Elements Strategy Institute for Catalysts and Batteries (ESICB), Kyoto University, Katsura, Kyoto 615-8520 (Japan)

    2015-07-07

    In this study, we reported the development of a new quantum mechanics/molecular mechanics (QM/MM)-type framework to describe chemical processes in solution by combining standard molecular-orbital calculations with a three-dimensional formalism of integral equation theory for molecular liquids (multi-center molecular Ornstein–Zernike (MC-MOZ) method). The theoretical procedure is very similar to the 3D-reference interaction site model self-consistent field (RISM-SCF) approach. Since the MC-MOZ method is highly parallelized for computation, the present approach has the potential to be one of the most efficient procedures to treat chemical processes in solution. Benchmark tests to check the validity of this approach were performed for two solute (solute water and formaldehyde) systems and a simple S{sub N}2 reaction (Cl{sup −} + CH{sub 3}Cl → ClCH{sub 3} + Cl{sup −}) in aqueous solution. The results for solute molecular properties and solvation structures obtained by the present approach were in reasonable agreement with those obtained by other hybrid frameworks and experiments. In particular, the results of the proposed approach are in excellent agreements with those of 3D-RISM-SCF.

  13. Bulk Density of Comet 9P/Tempel 1 Based on Orbital and Rotational Nongravitational Effects

    Science.gov (United States)

    Samarasinha, Nalin H.; Belton, M.; Farnham, T.; Gutierrez, P.; Mueller, B.; Chesley, S.

    2009-09-01

    The accurate determination of bulk densities of cometary nuclei provides a strong indicator of their interior structure and will furnish insights into the conditions in the early solar system. The primary technique to determine cometary bulk densities is by correlating the secular orbital changes of the comet with the corresponding forces due to outgassing. However, significant uncertainties persist in these determinations as the accurate assessment of forces due to outgassing is difficult. Davidsson et al. (2007) derived a bulk density of 200-700 kg m-3 for comet 9P/Tempel 1 based on the orbital nongravitational forces. Richardson and colleagues (e.g,, Richardson et al. 2007) independently determined a density of 200-1000 kg m-3 for comet 9P/Tempel 1 based on the analysis of the ejecta fallback caused by the impactor of the Deep Impact mission. These density determinations based on widely different techniques yield consistent results; however, the allowed density range is relatively large. A simultaneous modeling of orbital and rotational changes in 9P/Tempel 1 is expected to yield more constraining results for the bulk density. Accurate determinations of the rotational changes (Belton et al. 2009) and the localized activity (cf. Farnham et al. 2007, Feaga et al. 2007, Schleicher 2006) of comet 9P/Tempel 1 allow us to simultaneously model the orbital and rotational changes caused by outgassing in a self-consistent manner. Initial results from this study will be presented at the meeting. We thank NASA Outer Planets Research Program. References: Belton, M.J.S. et al. 2009. Icarus, in preparation. Davidsson, B.J.R. et al. 2007, Icarus, 187, 306-320. Farnham, T.L. et al. 2007. Icarus, 187, 26-40. Feaga, L.M. et al. 2007. Icarus, 190, 345-356. Richardson, J.E. et al. 2007. Icarus, 190, 357-390. Schleicher D.G. 2006. Icarus, 181, 442-457.

  14. An efficient and near linear scaling pair natural orbital based local coupled cluster method

    Science.gov (United States)

    Riplinger, Christoph; Neese, Frank

    2013-01-01

    In previous publications, it was shown that an efficient local coupled cluster method with single- and double excitations can be based on the concept of pair natural orbitals (PNOs) [F. Neese, A. Hansen, and D. G. Liakos, J. Chem. Phys. 131, 064103 (2009), 10.1063/1.3173827]. The resulting local pair natural orbital-coupled-cluster single double (LPNO-CCSD) method has since been proven to be highly reliable and efficient. For large molecules, the number of amplitudes to be determined is reduced by a factor of 105-106 relative to a canonical CCSD calculation on the same system with the same basis set. In the original method, the PNOs were expanded in the set of canonical virtual orbitals and single excitations were not truncated. This led to a number of fifth order scaling steps that eventually rendered the method computationally expensive for large molecules (e.g., >100 atoms). In the present work, these limitations are overcome by a complete redesign of the LPNO-CCSD method. The new method is based on the combination of the concepts of PNOs and projected atomic orbitals (PAOs). Thus, each PNO is expanded in a set of PAOs that in turn belong to a given electron pair specific domain. In this way, it is possible to fully exploit locality while maintaining the extremely high compactness of the original LPNO-CCSD wavefunction. No terms are dropped from the CCSD equations and domains are chosen conservatively. The correlation energy loss due to the domains remains below 8800 basis functions and >450 atoms. In all larger test calculations done so far, the LPNO-CCSD step took less time than the preceding Hartree-Fock calculation, provided no approximations have been introduced in the latter. Thus, based on the present development reliable CCSD calculations on large molecules with unprecedented efficiency and accuracy are realized.

  15. Advanced molecular devices based on light-driven molecular motors

    NARCIS (Netherlands)

    Chen, Jiawen

    2015-01-01

    Nature has provided a large collection of molecular machines and devices that are among the most amazing nanostructures on this planet. These machines are able to operate complex biological processes which are of great importance in our organisms. Inspired by these natural devices, artificial molecu

  16. Advanced molecular devices based on light-driven molecular motors

    NARCIS (Netherlands)

    Chen, Jiawen

    2015-01-01

    Nature has provided a large collection of molecular machines and devices that are among the most amazing nanostructures on this planet. These machines are able to operate complex biological processes which are of great importance in our organisms. Inspired by these natural devices, artificial

  17. Monte Carlo simulations on atropisomerism of thienotriazolodiazepines applicable to slow transition phenomena using potential energy surfaces by ab initio molecular orbital calculations.

    Science.gov (United States)

    Morikami, Kenji; Itezono, Yoshiko; Nishimoto, Masahiro; Ohta, Masateru

    2014-01-01

    Compounds with a medium-sized flexible ring often show atropisomerism that is caused by the high-energy barriers between long-lived conformers that can be isolated and often have different biological properties to each other. In this study, the frequency of the transition between the two stable conformers, aS and aR, of thienotriazolodiazepine compounds with flexible 7-membered rings was estimated computationally by Monte Carlo (MC) simulations and validated experimentally by NMR experiments. To estimate the energy barriers for transitions as precisely as possible, the potential energy (PE) surfaces used in the MC simulations were calculated by molecular orbital (MO) methods. To accomplish the MC simulations with the MO-based PE surfaces in a practical central processing unit (CPU) time, the MO-based PE of each conformer was pre-calculated and stored before the MC simulations, and then only referred to during the MC simulations. The activation energies for transitions calculated by the MC simulations agreed well with the experimental ΔG determined by the NMR experiments. The analysis of the transition trajectories of the MC simulations revealed that the transition occurred not only through the transition states, but also through many different transition paths. Our computational methods gave us quantitative estimates of atropisomerism of the thienotriazolodiazepine compounds in a practical period of time, and the method could be applicable for other slow-dynamics phenomena that cannot be investigated by other atomistic simulations.

  18. Toward a W4-F12 approach: Can explicitly correlated and orbital-based ab initio CCSD(T) limits be reconciled?

    CERN Document Server

    Sylvetsky, Nitai; Karton, Amir; Martin, Jan M L

    2016-01-01

    In the context of high-accuracy computational thermochemistry, the valence CCSD correlation component of molecular atomization energies present the most severe basis set convergence problem, followed by the (T) component. In the present paper, we make a detailed comparison, for an expanded version of the W4-11 thermochemistry benchmark, between on the one hand orbital-based CCSD/AV{5,6}Z+d and CCSD/ACV{5,6}Z extrapolation, and on the other hand CCSD-F12b calculations with cc-pVQZ-F12 and cc-pV5Z-F12 basis sets. This latter basis set, now available for H--He, B--Ne, and Al--Ar, is shown to be very close to the basis set limit. Apparent differences (which can reach 0.35 kcal/mol for systems like CCl4) between orbital-based and CCSD-F12b basis set limits disappear if basis sets with additional radial flexibility, such as ACV{5,6}Z, are used for the orbital calculation. Counterpoise calculations reveal that, while TAEs with V5Z-F12 basis sets are nearly free of BSSE, orbital calculations have significant BSSE eve...

  19. Rationally designed fluorescence turn-on sensors: a new design strategy based on orbital control.

    Science.gov (United States)

    Jung, Hyo Sung; Ko, Kyoung Chul; Lee, Jae Hong; Kim, Sang Hoon; Bhuniya, Sankarprasad; Lee, Jin Yong; Kim, Youngmee; Kim, Sung Jin; Kim, Jong Seung

    2010-09-20

    Herein, we explore a new strategy in the chemo-sensor field for fluorescence amplification upon binding with metal ions based on controlled participation of the nitrogen lone pair orbital. The basic architecture of the sensor entails a fluorophore, the sp(2) hybridized nitrogen lone pair (-C═N-), and a chelator site referred to as the control part. Though nonplanar and nonfluorescent, compound IC1 achieved pseudo planarity from binding with Zn(2+) as indicated by the increased fluorescence signal. Its other analogue (IC2) is also planar, and unlike IC1-Zn(2+) was fluorescent with a lack of binding affinity to metal ions. The time-dependent density functional theory (TDDFT) calculations revealed that the fluorescence amplification was due to the blocking of the nitrogen lone pair orbital; unlikely geometrical rearrangements were insignificant. This could indicate a breakthrough concept in the future design of fluorescent turn-on sensors.

  20. Dynamical study of low Earth orbit debris collision avoidance using ground based laser

    Directory of Open Access Journals (Sweden)

    N.S. Khalifa

    2015-06-01

    Full Text Available The objective of this paper was to investigate the orbital velocity changes due to the effect of ground based laser force. The resulting perturbations of semi-major axis, miss distance and collision probability of two approaching objects are studied. The analytical model is applied for low Earth orbit debris of different eccentricities and area to mass ratio and the numerical test shows that laser of medium power ∼5 kW can perform a small change ΔV‾ of an average magnitude of 0.2 cm/s which can be accumulated over time to be about 3 cm/day. Moreover, it is confirmed that applying laser ΔV‾ results in decreasing collision probability and increasing miss distance in order to avoid collision.

  1. Theoretical investigation on the non-linear optical properties, vibrational spectroscopy and frontier molecular orbital of (E)-2-cyano-3-(3-hydroxyphenyl)acrylamide molecule

    Science.gov (United States)

    Xiao-Hong, Li; Hong-Ling, Cui; Rui-Zhou, Zhang; Xian-Zhou, Zhang

    2015-02-01

    The vibrational frequencies of (E)-2-cyano-3-(3-hydroxyphenyl)acrylamide (HB-CA) in the ground state have been calculated using density functional method (B3LYP) with B3LYP/6-311++G(d,p) basis set. The analysis of natural bond orbital was also performed. The IR spectra were obtained and interpreted by means of potential energies distributions (PEDs) using MOLVIB program. In addition, the results show that there exists Csbnd H⋯O hydrogen bond in the title compound, which is confirmed by the natural bond orbital analysis. The predicted NLO properties show that the title compound is a good candidate as nonlinear optical material. The analysis of frontier molecular orbitals shows that HB-CA has high excitation energies, good stability and high chemical hardness. The analysis of MEP map shows the negative and the positive potential sites.

  2. Theoretical investigation on the non-linear optical properties, vibrational spectroscopy and frontier molecular orbital of (E)-2-cyano-3-(3-hydroxyphenyl)acrylamide molecule.

    Science.gov (United States)

    Xiao-Hong, Li; Hong-Ling, Cui; Rui-Zhou, Zhang; Xian-Zhou, Zhang

    2015-02-25

    The vibrational frequencies of (E)-2-cyano-3-(3-hydroxyphenyl)acrylamide (HB-CA) in the ground state have been calculated using density functional method (B3LYP) with B3LYP/6-311++G(d,p) basis set. The analysis of natural bond orbital was also performed. The IR spectra were obtained and interpreted by means of potential energies distributions (PEDs) using MOLVIB program. In addition, the results show that there exists C-H⋯O hydrogen bond in the title compound, which is confirmed by the natural bond orbital analysis. The predicted NLO properties show that the title compound is a good candidate as nonlinear optical material. The analysis of frontier molecular orbitals shows that HB-CA has high excitation energies, good stability and high chemical hardness. The analysis of MEP map shows the negative and the positive potential sites.

  3. Multicolor Electrochromic Devices Based on Molecular Plasmonics.

    Science.gov (United States)

    Stec, Grant J; Lauchner, Adam; Cui, Yao; Nordlander, Peter; Halas, Naomi J

    2017-03-28

    Polycyclic aromatic hydrocarbon (PAH) molecules, the hydrogen-terminated, sub-nanometer-scale version of graphene, support plasmon resonances with the addition or removal of a single electron. Typically colorless when neutral, they are transformed into vivid optical absorbers in either their positively or negatively charged states. Here, we demonstrate a low-voltage, multistate electrochromic device based on PAH plasmon resonances that can be reversibly switched between nearly colorless (0 V), olive (+4 V), and royal blue (-3.5 V). The device exhibits highly efficient color change compared to electrochromic polymers and metal oxides, lower power consumption than liquid crystals, and is shown to reversibly switch for at least 100 cycles. We also demonstrate the additive property of molecular plasmon resonances in a single-layer device to display a reversible, transmissive-to-black device. This work illuminates the potential of PAH molecular plasmonics for the development of color displays and large-area color-changing applications due to their processability and ultralow power consumption.

  4. Spectroscopic (FT-IR, FT-Raman, NMR and UV-Visible) and quantum chemical studies of molecular geometry, Frontier molecular orbital, NLO, NBO and thermodynamic properties of salicylic acid

    Science.gov (United States)

    Suresh, S.; Gunasekaran, S.; Srinivasan, S.

    2014-11-01

    The solid phase FT-IR and FT-Raman spectra of 2-hydroxybenzoic acid (salicylic acid) have been recorded in the region 4000-400 and 4000-100 cm-1 respectively. The optimized molecular geometry and fundamental vibrational frequencies are interpreted with the aid of structure optimizations and normal coordinate force field calculations based on density functional theory (DFT) method and a comparative study between Hartree Fork (HF) method at 6-311++G(d,p) level basis set. The calculated harmonic vibrational frequencies are scaled and they are compared with experimentally obtained FT-IR and FT-Raman spectra. A detailed interpretation of the vibrational spectra of this compound has been made on the basis of the calculated potential energy distribution (PED). The time dependent DFT method is employed to predict its absorption energy and oscillator strength. The linear polarizability (α) and the first order hyper polarizability (β) values of the investigated molecule have been computed. The electronic properties, such as HOMO and LUMO energies, molecular electrostatic potential (MEP) are also performed. Stability of the molecule arising from hyper conjugative interaction, charge delocalization has been analyzed using natural bond orbital (NBO) analysis.

  5. Spectroscopic (FT-IR, FT-Raman, NMR and UV-Visible) and quantum chemical studies of molecular geometry, Frontier molecular orbital, NLO, NBO and thermodynamic properties of salicylic acid.

    Science.gov (United States)

    Suresh, S; Gunasekaran, S; Srinivasan, S

    2014-11-11

    The solid phase FT-IR and FT-Raman spectra of 2-hydroxybenzoic acid (salicylic acid) have been recorded in the region 4000-400 and 4000-100 cm(-1) respectively. The optimized molecular geometry and fundamental vibrational frequencies are interpreted with the aid of structure optimizations and normal coordinate force field calculations based on density functional theory (DFT) method and a comparative study between Hartree Fork (HF) method at 6-311++G(d,p) level basis set. The calculated harmonic vibrational frequencies are scaled and they are compared with experimentally obtained FT-IR and FT-Raman spectra. A detailed interpretation of the vibrational spectra of this compound has been made on the basis of the calculated potential energy distribution (PED). The time dependent DFT method is employed to predict its absorption energy and oscillator strength. The linear polarizability (α) and the first order hyper polarizability (β) values of the investigated molecule have been computed. The electronic properties, such as HOMO and LUMO energies, molecular electrostatic potential (MEP) are also performed. Stability of the molecule arising from hyper conjugative interaction, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. Published by Elsevier B.V.

  6. NASA's Newest Orbital Debris Ground-based Telescope Assets: MCAT and UKIRT

    Science.gov (United States)

    Lederer, S. M.; Frith, J. M.; Pace, L. F.; Cowardin, H. M.; Cowardin, H. M.; Hickson, P.; Glesne, T.; Maeda, R.; Buckalew, B.; Nishimoto, D.; hide

    2014-01-01

    NASA's Orbital Debris Program Office (ODPO) will break ground on Ascension Island in 2014 to build the newest optical (0.30 - 1.06 micrometers) ground-based telescope asset dedicated to the study of orbital debris. The Meter Class Autonomous Telescope (MCAT) is a 1.3m optical telescope designed to track objects in orbits ranging from Low Earth Orbit (LEO) to Geosynchronous Earth Orbit (GEO). Ascension Island is located in the South Atlantic Ocean, offering longitudinal sky coverage not afforded by the Ground-based Electro-Optical Deep Space Surveillance (GEODSS) network. With a fast-tracking dome, a suite of visible wide-band filters, and a time-delay integration (TDI) capable camera, MCAT is capable of multiple observing modes ranging from tracking cataloged debris targets to surveying the overall debris environment. Access to the United Kingdom Infrared Telescope (UKIRT) will extend our spectral coverage into the near- (0.8-5 micrometers) and mid- to far-infrared (8-25 micrometers) regime. UKIRT is a 3.8m telescope located on Mauna Kea on the Big Island of Hawaii. At nearly 14,000-feet and above the atmospheric inversion layer, this is one of the premier astronomical sites in the world and is an ideal setting for an infrared telescope. An unprecedented one-third of this telescope's time has been allocated to collect orbital debris data for NASA's ODPO over a 2-year period. UKIRT has several instruments available to obtain low-resolution spectroscopy in both the near-IR and the mid/far-IR. Infrared spectroscopy is ideal for constraining the material types, albedos and sizes of debris targets, and potentially gaining insight into reddening effects caused by space weathering. In addition, UKIRT will be used to acquire broadband photometric imaging at GEO with the Wide Field Camera (WFCAM) for studying known objects of interest as well as collecting data in survey-mode to discover new targets. Results from the first stage of the debris campaign will be presented. The

  7. An optimum organizational structure for a large earth-orbiting multidisciplinary Space Base

    Science.gov (United States)

    Ragusa, J. M.

    1973-01-01

    The purpose of this exploratory study was to identify an optimum hypothetical organizational structure for a large earth-orbiting multidisciplinary research and applications (R&A) Space Base manned by a mixed crew of technologists. Since such a facility does not presently exist, in situ empirical testing was not possible. Study activity was, therefore, concerned with the identification of a desired organizational structural model rather than the empirical testing of it. The essential finding of this research was that a four-level project type 'total matrix' model will optimize the efficiency and effectiveness of Space Base technologists.

  8. Time-efficient computation of the electronic structure of the C60 super-atom molecular orbital (SAMO) states in TDDFT

    Science.gov (United States)

    Mignolet, B.; Remacle, F.

    2016-12-01

    Fullerenes have a dense manifold of excited states composed of valence excited states and Rydberg states. Among Rydberg states, one distinguishes Super Atom Molecular Orbitals (SAMO), excited states in which an electron is promoted to a diffuse nanometer size molecular orbital with a hydrogenic-like character. Unlike typical Rydberg states, the electronic density of the SAMO states is mainly localized inside and in the close vicinity of the fullerene cage. In this proceeding, we propose a time-saving way to compute the electronic structure of the SAMO and Rydberg states of fullerenes at the TDDFT level by limiting the number of excitations allowed to build the excited states. We investigate the effect of limiting the number of excitations in C60 and compare it to the experimental binding energies. We also investigate the effect of the functional and basis set on the binding energies of the SAMO states.

  9. Stimulated Radiative Molecular Association in the Early Solar System. II. Orbital Radii of the Planets and Other Satellites of the Sun

    CERN Document Server

    Lombardi, James C

    2015-01-01

    In a previous investigation, the orbital radii of regular satellites of Uranus, Jupiter, Neptune, and Saturn are shown to be directly related to photon energies in the spectra of atomic and molecular hydrogen. To explain these observations a model was developed involving stimulated radiative molecular association (SRMA) reactions among photons and atoms in the protosatellite disks of the planets. In the present investigation, the previously developed model is applied to the planets and important satellites of the Sun. A key component of the model involves resonance associated with SRMA. Through this resonance, thermal energy is extracted from the protosun's protoplanetary disk at specific distances from the protosun wherever there is a match between the local thermal energy of the disk and the energy of photons impinging on the disk. Orbital radii of the planets and satellites are related to photon energies ($E_P$ values) in the spectrum of atomic hydrogen. An expression determined previously is used to relat...

  10. 分子轨道方法在有机反应机理中的应用%Application of Molecular Orbital Method to Organic Reaction Mechanisms

    Institute of Scientific and Technical Information of China (English)

    唐敏

    2014-01-01

    利用分子轨道理论直观解释了有机反应机理中所涉及到的立体化学、区域选择性以及对称性选择规律等有机化学中不易解释清楚的问题。相较于传统的“电子推动”方法,分子轨道方法更加直观,并能为有机反应机理的学习提供更深的理解。%The stereochemistry, regioselectivity and symmetry selectivity rules in organic reaction mechanisms, which are difficult to be explained clearly, are illustrated explicitly through molecular orbital theory. Compared to tra-ditional “electron pushing” method, molecular orbital method can give a visual interpretation and provide a better un-derstanding of organic reaction mechanisms.

  11. H-- Filtering Algorithms Case Study GPS-Based Satellite Orbit Determination

    Science.gov (United States)

    Kuang, Jinlu; Tan, Soonhie

    In this paper the new Hfiltering algorithms for the design of navigation systems for autonomous LEO satellite is introduced. The nominal orbit (i.e., position and velocity) is computed by integrating the classical orbital differential equations of the LEO satellite by using the 7th-8th order Runge- Kutta algorithms. The perturbations due to the atmospheric drag force, the lunar-solar attraction and the solar radiation pressure are included together with the Earth gravity model (EGM-96). The spherical harmonic coefficients of the EGM-96 are considered up to 72 for the order and degree. By way of the MATLAB GPSoft software, the simulated pseudo ranges between the user LEO satellite and the visible GPS satellites are generated when given the appropriate angle of mask. The effects of the thermal noises, tropospheric refraction, ionospheric refraction, and multipath of the antenna are also compensated numerically in the simulated pseudo ranges. The dynamic Position-Velocity (PV) model is obtained by modeling the velocity as nearly constant being the white noise process. To further accommodate acceleration in the process model, the Position-Velocity-Acceleration (PVA) model is investigated by assuming the acceleration to be the Gaussian- Markov process. The state vector for the PV model becomes 8-dimensional (3-states for positions, 3-states for velocities, 1-state for range (clock) bias error, 1-state for range (clock) drift error). The state vector for the PV model becomes 11-dimensional with the addition of three more acceleration states. Three filtering approaches are used to smooth the orbit solution based upon the GPS pseudo range observables. The numerical simulation shows that the observed orbit root-mean-square errors of 60 meters by using the least squares adjustment method are improved to be less than 5 meters within 16 hours of tracking time by using the Hfiltering algorithms. The results are compared with the ones obtained by using the Extended Kalman

  12. A molecular orbital study of a model of the Mg2+ coordination complex of the self splicing reaction of ribosomal RNA

    Science.gov (United States)

    McCourt, M.; Shibata, M.; McIver, J. W.; Rein, R.

    1988-01-01

    Recent discoveries have established the fact that RNA is capable of acting as an enzyme. In this study two different types of molecular orbital calculations, INDO and ab initio, were used in an attempt to assess the structural/functional role of the Mg2+ hydrated complex in ribozyme reactions. Preliminary studies indicate that the reaction is multistep and that the Mg2+ complex exerts a stabilizing effect on the intermediate or midpoint of the reaction.

  13. Positron-attachment to small molecules: Vibrational enhancement of positron affinities with configuration interaction level of multi-component molecular orbital approach

    Energy Technology Data Exchange (ETDEWEB)

    Tachikawa, Masanori [Quantum Chemistry Division, Graduate School of NanoBioScience, Yokohama City University, 22-2 Seto, Kanazawa, Yokohama 236-0027 (Japan)

    2015-12-31

    To theoretically demonstrate the binding of a positron to small polarized molecules, we have calculated the vibrational averaged positron affinity (PA) values along the local vibrational contribution with the configuration interaction level of multi-component molecular orbital method. This method can take the electron-positron correlation contribution into account through single electronic - single positronic excitation configurations. The PA values are enhanced by including the local vibrational contribution from vertical PA values due to the anharmonicity of the potential.

  14. Local random phase approximation with projected oscillator orbitals

    CERN Document Server

    Mussard, Bastien

    2015-01-01

    An approximation to the many-body London dispersion energy in molecular systems is expressed as a functional of the occupied orbitals only. The method is based on the local-RPA theory. The occupied orbitals are localized molecular orbitals and the virtual space is described by projected oscillator orbitals, i.e. functions obtained by multiplying occupied localized orbitals with solid spherical harmonic polynomials having their origin at the orbital centroids. Since we are interested in the long-range part of the correlation energy, responsible for dispersion forces, the electron repulsion is approximated by its multipolar expansion. This procedure leads to a fully non-empirical long-range correlation energy expression. Molecular dispersion coefficients calculated from determinant wave functions obtained by a range-separated hybrid method reproduce experimental values with less than 15% error.

  15. Quaternary ammonium room-temperature ionic liquid including an oxygen atom in side chain/lithium salt binary electrolytes: ab initio molecular orbital calculations of interactions between ions.

    Science.gov (United States)

    Tsuzuki, Seiji; Hayamizu, Kikuko; Seki, Shiro; Ohno, Yasutaka; Kobayashi, Yo; Miyashiro, Hajime

    2008-08-14

    Interactions of the lithium bis(trifluoromethylsulfonyl)amide (LiTFSA) complex with N, N-diethyl-N-methyl-N-(2-methoxyethyl) ammonium (DEME), 1-ethyl-3-methylimidazolium (EMIM) cations, neutral diethylether (DEE), and the DEMETFSA complex were studied by ab initio molecular orbital calculations. An interaction energy potential calculated for the DEME cation with the LiTFSA complex has a minimum when the Li atom has contact with the oxygen atom of DEME cation, while potentials for the EMIM cation with the LiTFSA complex are always repulsive. The MP2/6-311G**//HF/6-311G** level interaction energy calculated for the DEME cation with the LiTFSA complex was -18.4 kcal/mol. The interaction energy for the neutral DEE with the LiTFSA complex was larger (-21.1 kcal/mol). The interaction energy for the DEMETFSA complex with LiTFSA complex is greater (-23.2 kcal/mol). The electrostatic and induction interactions are the major source of the attraction in the two systems. The substantial attraction between the DEME cation and the LiTFSA complex suggests that the interaction between the Li cation and the oxygen atom of DEME cation plays important roles in determining the mobility of the Li cation in DEME-based room temperature ionic liquids.

  16. Electrochemical control of quantum interference in anthraquinone-based molecular switches

    DEFF Research Database (Denmark)

    Markussen, Troels; Schiøtz, Jakob; Thygesen, Kristian Sommer

    2010-01-01

    Using first-principles calculations we analyze the electronic transport properties of a recently proposed anthraquinone-based electrochemical switch. Robust conductance on/off ratios of several orders of magnitude are observed due to destructive quantum interference present in the anthraquinone b...... of hopping via the localized orbitals. The topology of the tight-binding model, which is dictated by the symmetries of the molecular orbitals, determines the amount of quantum interference.......Using first-principles calculations we analyze the electronic transport properties of a recently proposed anthraquinone-based electrochemical switch. Robust conductance on/off ratios of several orders of magnitude are observed due to destructive quantum interference present in the anthraquinone...

  17. Analysis of plasma equilibrium based on orbit-driven current density profile in steady-state plasma on QUEST

    Energy Technology Data Exchange (ETDEWEB)

    Nakamura, K., E-mail: nakamura@triam.kyushu-u.ac.jp [RIAM, Kyushu University, Kasuga 816-8580 (Japan); Alam, M.M. [IGSES, Kyushu University, Kasuga 816-8580 (Japan); Jiang, Y.Z. [Tsinghua University, Beijing 100084 (China); Mitarai, O. [Tokai University, Kumamoto 862-8652 (Japan); Kurihara, K.; Kawamata, Y.; Sueoka, M.; Takechi, M. [Japan Atomic Energy Agency, Naka 311-0193 (Japan); Hasegawa, M.; Tokunaga, K.; Araki, K.; Zushi, H.; Hanada, K.; Fujisawa, A.; Idei, H.; Nagashima, Y.; Kawasaki, S.; Nakashima, H.; Higashijima, A.; Nagata, T. [RIAM, Kyushu University, Kasuga 816-8580 (Japan); and others

    2016-11-01

    Highlights: • High energy particle guiding center orbit is calculated as a contour plot of conserved variable. • Current density profile is analyzed based on the orbit-driven current. • Plasma equilibrium is reconstructed by considering the hollow current profile. - Abstract: In the present RF-driven (ECCD) steady-state plasma on QUEST (B{sub t} = 0.25 T, R = 0.68 m, a = 0.40 m), plasma current seems to flow in the open magnetic surface outside of the closed magnetic surface in the low-field region according to plasma current fitting (PCF) method. We consider that the current in the open magnetic surface is due to orbit-driven current by high-energy particles in RF-driven plasma. So based on the analysis of current density profile based on the orbit-driven current, plasma equilibrium is to be calculated. We calculated high energy particles guiding center orbits as a contour plot of conserved variable in Hamiltonian formulation and considered particles initial position with different levels of energy and pitch angles that satisfy resonance condition. Then the profile of orbit-driven current is estimated by multiplying the particle density on the resonance surface and the velocity on the orbits. This analysis shows negative current near the magnetic axis and hollow current profile is expected even if pressure driven current is considered. Considering the hollow current profile shifted toward the low-field region, the equilibrium is fitted by J-EFIT coded by MATLAB.

  18. Tunable orbital angular momentum mode filter based on optical geometric transformation.

    Science.gov (United States)

    Huang, Hao; Ren, Yongxiong; Xie, Guodong; Yan, Yan; Yue, Yang; Ahmed, Nisar; Lavery, Martin P J; Padgett, Miles J; Dolinar, Sam; Tur, Moshe; Willner, Alan E

    2014-03-15

    We present a tunable mode filter for spatially multiplexed laser beams carrying orbital angular momentum (OAM). The filter comprises an optical geometric transformation-based OAM mode sorter and a spatial light modulator (SLM). The programmable SLM can selectively control the passing/blocking of each input OAM beam. We experimentally demonstrate tunable filtering of one or multiple OAM modes from four multiplexed input OAM modes with vortex charge of ℓ=-9, -4, +4, and +9. The measured output power suppression ratio of the propagated modes to the blocked modes exceeds 14.5 dB.

  19. Manipulating effective spin orbit coupling based on proximity effect in magnetic bilayers

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Y. Q.; Sun, N. Y.; Che, W. R.; Zhang, J. W.; Shan, R., E-mail: shan.rong@hotmail.com [School of Physics Science and Engineering, Tongji University, Shanghai 200092 (China); Li, X. L. [Shanghai Synchrotron Radiation Facility (SSRF), Shanghai 201204 (China); Zhu, Z. G., E-mail: zgzhu@ucas.ac.cn; Su, G., E-mail: gsu@ucas.ac.cn [School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049 (China); Theoretical Condensed Matter Physics and Computational Materials Physics Laboratory, College of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049 (China)

    2015-08-24

    A proximity effect of spin orbit coupling (SOC) is proposed in nonmagnetic metal/ferromagnet (NM/FM) bilayers by extending the Crépieux-Bruno (CB) theory. We demonstrate that over 1000% enhancement of the SOC strength can be realized based on this effect (Pt/FM bilayers) and it brings greatly enhanced anomalous Hall effect and anomalous Nernst effect. This work could help maximize the performance of magnetic transport property for the spintronics device using NM/FM as the key structure.

  20. Molecularly Imprinted Polymer/Metal Organic Framework Based Chemical Sensors

    Directory of Open Access Journals (Sweden)

    Zhenzhong Guo

    2016-10-01

    Full Text Available The present review describes recent advances in the concept of molecular imprinting using metal organic frameworks (MOF for development of chemical sensors. Two main strategies regarding the fabrication, performance and applications of recent sensors based on molecularly imprinted polymers associated with MOF are presented: molecularly imprinted MOF films and molecularly imprinted core-shell nanoparticles using MOF as core. The associated transduction modes are also discussed. A brief conclusion and future expectations are described herein.

  1. Molecularly Imprinted Polymer/Metal Organic Framework Based Chemical Sensors

    OpenAIRE

    Zhenzhong Guo; Anca Florea; Mengjuan Jiang; Yong Mei; Weiying Zhang; Aidong Zhang; Robert Săndulescu; Nicole Jaffrezic-Renault

    2016-01-01

    The present review describes recent advances in the concept of molecular imprinting using metal organic frameworks (MOF) for development of chemical sensors. Two main strategies regarding the fabrication, performance and applications of recent sensors based on molecularly imprinted polymers associated with MOF are presented: molecularly imprinted MOF films and molecularly imprinted core-shell nanoparticles using MOF as core. The associated transduction modes are also discussed. A brief conclu...

  2. Performance Analyses of the Radio Orbital Angular Momentum Steering Technique Based on Ka-Band Antenna

    Directory of Open Access Journals (Sweden)

    Mingtuan Lin

    2017-01-01

    Full Text Available The misalignment in the orbital angular momentum- (OAM- based system would distort the radiation patterns of twisted beams carrying OAM, consequently making the OAM-based communication infeasible. To tackle the misalignment problem, a radio OAM steering technique based on a uniform circular array (UCA is illustrated. Subsequently, simulations are conducted to explore the influence of the OAM steering on the OAM mode quality and transmission performance. Furthermore, UCAs working at Ka-band with formulated feeding networks are designed and fabricated to analyze the performance of the OAM steering. The influences of OAM steering on mode quality and orthogonality are then evaluated in the experiment. Overall, the analyses of OAM steering technique are beneficial for the development of radio OAM study.

  3. Selection of the best initial orbital elements of satellite based on fuzzy integration evaluation method

    Institute of Scientific and Technical Information of China (English)

    Yang Yong'an; Zhang Hongwei; Feng Zuren; Luo Yongjin

    2006-01-01

    The fuzzy integration evaluation method (FIEM) is studied in order to select the best orbital elements from the multi-group initial orbits determined by a satellite TT&C (Tracking, Telemetry and Control) center with all kinds of data sources. By employing FIEM together with the experience of TT&C experts, the index system to evaluate the selection of the best initial orbits is established after the data sources and orbit determination theories are studied. Besides, the concrete steps in employing the method are presented. Moreover, by taking the objects to be evaluated as evaluation experts, the problem of how to generate evaluation matrices is solved. Through practical application, the method to select the best initial orbital elements has been proved to be flexible and effective. The originality of the method is to find a new evaluation criterion (comparing the actually tracked orbits) replacing the traditional one (comparing the nominal orbits) for selecting the best orbital elements.

  4. NIR- and SWIR-based on-orbit vicarious calibrations for satellite ocean color sensors.

    Science.gov (United States)

    Wang, Menghua; Shi, Wei; Jiang, Lide; Voss, Kenneth

    2016-09-05

    The near-infrared (NIR) and shortwave infrared (SWIR)-based atmospheric correction algorithms are used in satellite ocean color data processing, with the SWIR-based algorithm particularly useful for turbid coastal and inland waters. In this study, we describe the NIR- and two SWIR-based on-orbit vicarious calibration approaches for satellite ocean color sensors, and compare results from these three on-orbit vicarious calibrations using satellite measurements from the Visible Infrared Imaging Radiometer Suite (VIIRS) onboard the Suomi National Polar-orbiting Partnership (SNPP). Vicarious calibration gains for VIIRS spectral bands are derived using the in situ normalized water-leaving radiance nLw(λ) spectra from the Marine Optical Buoy (MOBY) in waters off Hawaii. The SWIR vicarious gains are determined using VIIRS measurements from the South Pacific Gyre region, where waters are the clearest and generally stable. Specifically, vicarious gain sets for VIIRS spectral bands of 410, 443, 486, 551, and 671 nm derived from the NIR method using the NIR 745 and 862 nm bands, the SWIR method using the SWIR 1238 and 1601 nm bands, and the SWIR method using the SWIR 1238 and 2257 nm bands are (0.979954, 0.974892, 0.974685, 0.965832, 0.979042), (0.980344, 0.975344, 0.975357, 0.965531, 0.979518), and (0.980820, 0.975609, 0.975761, 0.965888, 0.978576), respectively. Thus, the NIR-based vicarious calibration gains are consistent with those from the two SWIR-based approaches with discrepancies mostly within ~0.05% from three data processing methods. In addition, the NIR vicarious gains (745 and 862 nm) derived from the two SWIR methods are (0.982065, 1.00001) and (0.981811, 1.00000), respectively, with the difference ~0.03% at the NIR 745 nm band. This is the fundamental basis for the NIR-SWIR combined atmospheric correction algorithm, which has been used to derive improved satellite ocean color products over open oceans and turbid coastal/inland waters. Therefore, a unified

  5. Grid-based continual analysis of molecular interior for drug discovery, QSAR and QSPR.

    Science.gov (United States)

    Potemkin, A V; Grishina, M A; Potemkin, V A

    2017-02-07

    In 1979, R.D.Cramer and M.Milne made a first realization of the above mentioned principles attempting to compare molecules by aligning them in space and by mapping their molecular fields to a 3D grid. Further, this approach was developed as the DYLOMMS (DYnamic Lattice-Oriented Molecular Modelling System) approach. In 1984, H.Wold and S.Wold proposed the use of partial least squares (PLS) analysis, instead of principal component analysis, to correlate the field values with biological activities. Then, in 1988 the method which was called CoMFA (Comparative Molecular Field Analysis) was introduced and the appropriate software became commercially available. Since 1988, a lot of 3D QSAR methods, algorithms and their modifications are introduced for solving of virtual drug discovery problems (e.g., CoMSIA, CoMMA, HINT, HASL, GOLPE, GRID, PARM, Raptor, BiS, CiS, ConGO,). All the methods can be divided into two groups (classes):1. Methods studying the exterior of molecules; 2) Methods studying the interior of molecules. A series of grid-based computational technologies for Continual Molecular Interior analysis (CoMIn) is invented in the current paper. The grid-based analysis is fulfilled by means of a lattice construction analogously to many other grid-based methods. The further continual elucidation of molecular structure is performed in various ways. (i) In the terms of intermolecular interactions potentials. This can be represented as a superposition of Coulomb, Van der Waals interactions and hydrogen bonds. All the potentials are well known continual functions and their values can be determined in all lattice points for a molecule. (ii) In the terms of quantum functions such as electron density distribution, Laplacian and Hamiltonian of electron density distribution, potential energy distribution, the highest occupied and the lowest unoccupied molecular orbitals distribution and their superposition. To reduce time of calculations using quantum methods based on the

  6. Molecular phylogeny of Ranunculaceae based on internal ...

    African Journals Online (AJOL)

    STORAGESEVER

    2009-10-19

    Oct 19, 2009 ... phylogenetic analysis of 92 species of Ranunculaceae, Paeoniaceae and Berberidaceae ... Ranunculaceae have complex chemical compositions, ..... Ro KE, Keener CS, McPheron BA (1997) Molecular Phylogenetic Study.

  7. Frontier orbital engineering of photo-hydrogen-evolving molecular devices: a clear relationship between the H2-evolving activity and the energy level of the LUMO.

    Science.gov (United States)

    Masaoka, Shigeyuki; Mukawa, Yuichiro; Sakai, Ken

    2010-07-07

    Two new Ru(II)Pt(II) dimers, [Ru(bpy)(2)(mu-L2)PtCl(2)](2+) (5) and [Ru(bpy)(2)(mu-L3)PtCl(2)](2+) (6), were synthesized and characterized, and their electrochemical and spectroscopic properties together with their photo-hydrogen-evolving activities were evaluated (bpy = 2,2'-bypridine; L2 = 4'-[1,10]phenanthrolin-5-ylcarbamoyl)-[2,2']bipyridinyl-4-carboxylic acid ethyl ester; L3 = 4'-methyl-[2,2']bipyridinyl-4-carboxylic acid [1,10]phenanthrolin-5-ylamide). The structures of 5 and 6 are basically identical with that of the first active model of a photo-hydrogen-evolving molecular device developed in our group, [Ru(bpy)(2)(mu-L1)PtCl(2)](2+) (4) (L1 = 4'-([1,10]phenanthrolin-5-ylcarbamoyl)-[2,2']bipyridinyl-4-carboxylic acid), except for the difference in the substituent group at the 4-position of the bpy moiety bound to Pt(II) (-COOH for 4; -COOEt for 5; -CH(3) for 6). Electrochemical studies revealed that the first reduction potential of 5 (E(1/2) = -1.23 V) is nearly consistent with that of 4 (E(1/2) = -1.20 V) but is more positive than that of 6 (E(1/2) = -1.39 V), where the first reduction is associated with the reduction of the bpy moiety bound to Pt(II), consistent with a general tendency that the first reduction of bpy shows an anodic shift upon introduction of electron-withdrawing group. Density functional theory (DFT) calculations for 5 and 6 also show that the lowest unoccupied molecular orbital (LUMO) corresponds to the pi* orbital of the bpy moiety bound to Pt(II) for all the Ru(II)Pt(II) dimers, and the energy level of the LUMO of 6 is destabilized compared with those of 4 and 5, consistent with the results of the electrochemical studies. The photochemical hydrogen evolution from water driven by 4-6 in the presence a sacrificial electron donor (EDTA) was investigated. 5 was found to be active as an H(2)-evolving catalyst, while 6 shows no activity at all. However, 6 was found to drive photochemical H(2) evolution in the presence of both EDTA and

  8. QSPR Calculation of Normal Boiling Points of Organic Molecules Based on the Use of Correlation Weighting of Atomic Orbitals with Extended Connectivity of Zero- and First-Order Graphs of Atomic Orbitals

    Directory of Open Access Journals (Sweden)

    Eduardo A. Castro

    2004-12-01

    Full Text Available We report the results of a calculation of the normal boiling points of a representative set of 200 organic molecules through the application of QSPR theory. For this purpose we have used a particular set of flexible molecular descriptors, the so called Correlation Weighting of Atomic Orbitals with Extended Connectivity of Zero- and First-Order Graphs of Atomic Orbitals. Although in general the results show suitable behavior to predict this physical chemistry property, the existence of some deviant behaviors points to a need to complement this index with some other sort of molecular descriptors. Some possible extensions of this study are discussed.

  9. Topological invariants of band insulators derived from the local-orbital based embedding potential

    Science.gov (United States)

    Ishida, H.; Liebsch, A.; Wortmann, D.

    2017-09-01

    We demonstrate that topological invariants of band insulators can be derived efficiently from the eigenvalues of the local-orbital (LO) based embedding potential, called also the contact (lead) self-energy. The LO based embedding potential is a bulk quantity. Given the tight-binding Hamiltonian describing the bulk valence and conduction bands, it is constructed straightforwardly from the bulk wave functions satisfying the generalized Bloch condition. When the one-electron energy ɛ is located within a projected bulk band gap at a given planar wave vector k , the embedding potential becomes Hermitian. Its real eigenvalues exhibit distinctly different behavior depending on the topological properties of the valence bands, thus enabling unambiguous identification of bulk topological invariants. We consider the Bernevig-Hughes-Zhang model as an example of a time-reversal invariant topological insulator and tin telluride (SnTe) crystallized in a rock-salt structure as an example of a topological crystalline insulator.

  10. Electronic Absorption Spectra of Tetrapyrrole-Based Pigments via TD-DFT: A Reduced Orbital Space Study.

    Science.gov (United States)

    Shrestha, Kushal; Virgil, Kyle A; Jakubikova, Elena

    2016-07-28

    Tetrapyrrole-based pigments play a crucial role in photosynthesis as principal light absorbers in light-harvesting chemical systems. As such, accurate theoretical descriptions of the electronic absorption spectra of these pigments will aid in the proper description and understanding of the overall photophysics of photosynthesis. In this work, time-dependent density functional theory (TD-DFT) at the CAM-B3LYP/6-31G* level of theory is employed to produce the theoretical absorption spectra of several tetrapyrrole-based pigments. However, the application of TD-DFT to large systems with several hundreds of atoms can become computationally prohibitive. Therefore, in this study, TD-DFT calculations with reduced orbital spaces (ROSs) that exclude portions of occupied and virtual orbitals are pursued as a viable, computationally cost-effective alternative to conventional TD-DFT calculations. The effects of reducing orbital space size on theoretical spectra are qualitatively and quantitatively described, and both conventional and ROS results are benchmarked against experimental absorption spectra of various tetrapyrrole-based pigments. The orbital reduction approach is also applied to a large natural pigment assembly that comprises the principal light-absorbing component of the reaction center in purple bacteria. Overall, we find that TD-DFT calculations with proper and judicious orbital space reductions can adequately reproduce conventional, full orbital space, TD-DFT results of all pigments studied in this work.

  11. Effect of π Orbital on I/V Characteristics and Transmission in Molecular Diode Structures with Au Contacts

    Directory of Open Access Journals (Sweden)

    A. Mallaiah

    2017-02-01

    Full Text Available The electronic transport properties of electrons in a molecules are observed by using Non equilibrium Green’s function(NEGF. We present a extremely through and careful computational approach well ordered method to do a framework analysis of donor (CH3 and acceptor (CN molecules connected between the Au(111 contacts, and also observed current progress through molecular devices depends on number of bonds or not. Such observations implementation through not possible by standard quantum chemistry soft wares. The results shows I-V characteristics, Transport spectrum and Transport analysis can effectively tune the molecules works like a conventional semi-conductor based diodes, these results invoke to design the logic gates and logic circuits.

  12. Project ORION: Orbital Debris Removal Using Ground-Based Sensors and Lasers

    Science.gov (United States)

    Campbell, J. W.

    1996-01-01

    About 100,000 pieces of 1 to 10-cm debris in low-Earth orbit are too small to track reliably but large enough to cripple or destroy spacecraft. The ORION team studied the feasibility of removing the debris with ground-based laser impulses. Photoablation experiments were surveyed and applied to likely debris materials. Laser intensities needed for debris orbit modification call for pulses on the order of lOkJ or continuous wave lasers on the order of 1 MW. Adaptive optics are necessary to correct for atmospheric turbulence. Wavelength and pulse duration windows were found that limit beam degradation due to nonlinear atmospheric processes. Debris can be detected and located to within about 10 microrads with existing radar and passive optical technology. Fine targeting would be accomplished with laser illumination, which might also be used for detection. Bistatic detection with communications satellites may also be possible. We recommend that existing technology be used to demonstrate the concept at a loss of about $20 million. We calculate that an installation to clear altitudes up to 800 km of 1 to 10-cm debris over 2 years of operation would cost about $80 million. Clearing altitudes up to 1,500 km would take about 3 years and cost about $160 million.

  13. A Mach-Zehnder interferometer based on orbital angular momentum for improved vortex coronagraph efficiency

    CERN Document Server

    Piron, P; Huby, E; Mawet, D; Ruane, M Karlsson ad G; Habraken, S; Absil, O; Surdej, J

    2016-01-01

    The Annular Groove Phase Mask (AGPM) is a vectorial vortex phase mask. It acts as a half-wave plate with a radial fast axis orientation operating in the mid infrared domain. When placed at the focus of a telescope element provides a continuous helical phase ramp for an on axis sources, which creates the orbital angular momentum. Thanks to that phase, the intensity of the central source is canceled by a down-stream pupil stop, while the off axis sources are not affected. However due to experimental conditions the nulling is hardly perfect. To improve the null, a Mach-Zehnder interferometer containing Dove prisms differently oriented can be proposed to sort out light based on its orbital angular momentum (OAM). Thanks to the differential rotation of the beam, a {\\pi} phase shift is achieved for the on axis light affected by a non zero OAM. Therefore the contrast between the star and its faint companion is enhanced. Nevertheless, due the Dove prisms birefringence, the performance of the interferometer is relativ...

  14. Prospects for ultrahigh-energy particle observation based on the lunar orbital LORD space experiment

    Science.gov (United States)

    Ryabov, V. A.; Chechin, V. A.; Gusev, G. A.; Maung, K. T.

    2016-08-01

    The problem of searching for highest-energy cosmic rays and neutrinos in the Universe is reviewed. Possibilities for using the radio method for detecting particles of energies above the GZK cut-off are analyzed. The method is based on the registration of coherent radio emission produced by cascades of most energetic particles in radio-transparent lunar regolith. The Luna-Resurs Orbiter space mission to be launched in the near future (2020) involves the Lunar Orbital Radio Detector (LORD). The design of the LORD space instrument and its scientific potentialities for registration of low-intense cosmic ray particle fluxes of energies above the GZK cut-off up to 1024eV are discussed. The designed LORD module (including the antenna, amplification, and data-acquisition systems) now is under construction. Exposure and capabilities of the LORD space experiment for detection of ultrahigh-energy cosmic rays and neutrinos have been compared with those for well-known current and proposed experiments. The LORD space experiment will make it possible to obtain important information on the highest-energy particles in the Universe, to verify modern models for the origin and the propagation of ultrahigh-energy cosmic rays and neutrinos.

  15. Artificial Sun synchronous frozen orbit control scheme design based on J2 perturbation

    Institute of Scientific and Technical Information of China (English)

    Gong-Bo Wang; Yun-He Meng; Wei Zheng; Guo-Jian Tang

    2011-01-01

    Sun synchronous orbit and frozen orbit formed due to J2 perturbation have very strict constraints on orbital parameters,which have restricted the application a lot.In this paper,several control strategies were illustrated to realize Sun synchronous frozen orbit with arbitrary orbital elements using continuous low-thrust.Firstly,according to mean element method,the averaged rate of change of the orbital elements,originating from disturbing constant accelerations over one orbital period,was derived from Gauss' variation of parameters equations.Then,we proposed that binormal acceleration could be used to realize Sun synchronous orbit,and radial or transverse acceleration could be adopted to eliminate the rotation of the argument of the perigee.Finally,amending methods on the control strategies mentioned above were presented to eliminate the residual secular growth.Simulation results showed that the control strategies illustrated in this paper could realize Sun synchronous frozen orbit with arbitrary orbital elements,and can save much more energy than the schemes presented in previous studies,and have no side effect on other orbital parameters' secular motion.

  16. The Method for Calculating Atmospheric Drag Coefficient Based on the Characteristics of Along-track Error in LEO Orbit Prediction

    Science.gov (United States)

    Wang, H. B.; Zhao, C. Y.; Liu, Z. G.; Zhang, W.

    2016-07-01

    The errors of atmosphere density model and drag coefficient are the major factors to restrain the accuracy of orbit prediction for the LEO (Low Earth Orbit) objects, which would affect unfavorably the space missions that need a high-precision orbit. This paper brings out a new method for calculating the drag coefficient based on the divergence laws of prediction error's along-track component. Firstly, we deduce the expression of along-track error in LEO's orbit prediction, revealing the comprehensive effect of the initial orbit and model's errors in the along-track direction. According to this expression, we work out a suitable drag coefficient adopted in prediction step on the basis of some certain information from orbit determination step, which will limit the increasing rate of along-track error and reduce the largest error in this direction, then achieving the goal of improving the accuracy of orbit prediction. In order to verify the method's accuracy and successful rate in the practice of orbit prediction, we use the full-arcs high precision position data from the GPS receiver on GRACE-A. The result shows that this new method can significantly improve the accuracy of prediction by about 45%, achieving a successful rate of about 71% and an effective rate of about 86%, with respect to classical method which uses the fitted drag coefficient directly from orbit determination step. Furthermore, the new method shows a preferable application value, because it is effective for low, moderate, and high solar radiation levels, as well as some quiet and moderate geomagnetic activity condition.

  17. Calculation of wave-functions with frozen orbitals in mixed quantum mechanics/molecular mechanics methods. Part I. Application of the Huzinaga equation.

    Science.gov (United States)

    Ferenczy, György G

    2013-04-05

    Mixed quantum mechanics/quantum mechanics (QM/QM) and quantum mechanics/molecular mechanics (QM/MM) methods make computations feasible for extended chemical systems by separating them into subsystems that are treated at different level of sophistication. In many applications, the subsystems are covalently bound and the use of frozen localized orbitals at the boundary is a possible way to separate the subsystems and to ensure a sensible description of the electronic structure near to the boundary. A complication in these methods is that orthogonality between optimized and frozen orbitals has to be warranted and this is usually achieved by an explicit orthogonalization of the basis set to the frozen orbitals. An alternative to this approach is proposed by calculating the wave-function from the Huzinaga equation that guaranties orthogonality to the frozen orbitals without basis set orthogonalization. The theoretical background and the practical aspects of the application of the Huzinaga equation in mixed methods are discussed. Forces have been derived to perform geometry optimization with wave-functions from the Huzinaga equation. Various properties have been calculated by applying the Huzinaga equation for the central QM subsystem, representing the environment by point charges and using frozen strictly localized orbitals to connect the subsystems. It is shown that a two to three bond separation of the chemical or physical event from the frozen bonds allows a very good reproduction (typically around 1 kcal/mol) of standard Hartree-Fock-Roothaan results. The proposed scheme provides an appropriate framework for mixed QM/QM and QM/MM methods.

  18. Molecular and genetic bases of pancreatic cancer.

    Science.gov (United States)

    Vaccaro, Vanja; Gelibter, Alain; Bria, Emilio; Iapicca, Pierluigi; Cappello, Paola; Di Modugno, Francesca; Pino, Maria Simona; Nuzzo, Carmen; Cognetti, Francesco; Novelli, Francesco; Nistico, Paola; Milella, Michele

    2012-06-01

    Pancreatic cancer remains a formidable challenge for oncologists and patients alike. Despite intensive efforts, attempts at improving survival in the past 15 years, particularly in advanced disease, have failed. This is true even with the introduction of molecularly targeted agents, chosen on the basis of their action on pathways that were supposedly important in pancreatic cancer development and progression: indeed, with the notable exception of the epidermal growth factor receptor (EGFR) inhibitor erlotinib, that has provided a minimal survival improvement when added to gemcitabine, other agents targeting EGFR, matrix metallo-proteases, farnesyl transferase, or vascular endothelial growth factor have not succeeded in improving outcomes over standard gemcitabine monotherapy for a variety of different reasons. However, recent developments in the molecular epidemiology of pancreatic cancer and an ever evolving understanding of the molecular mechanisms underlying pancreatic cancer initiation and progression raise renewed hope to find novel, relevant therapeutic targets that could be pursued in the clinical setting. In this review we focus on molecular epidemiology of pancreatic cancer, epithelial-to-mesenchymal transition and its influence on sensitivity to EGFR-targeted approaches, apoptotic pathways, hypoxia-related pathways, developmental pathways (such as the hedgehog and Notch pathways), and proteomic analysis as keys to a better understanding of pancreatic cancer biology and, most importantly, as a source of novel molecular targets to be exploited therapeutically.

  19. Resection of giant ethmoid osteoma with orbital and skull base extension followed by duraplasty

    Directory of Open Access Journals (Sweden)

    Ferekidou Eliza

    2008-10-01

    Full Text Available Abstract Background Osteomas of ethmoid sinus are rare, especially when they involve anterior skull base and orbit, and lead to ophthalmologic and neurological symptoms. Case presentation The present case describes a giant ethmoid osteoma. Patient symptoms and signs were exophthalmos and proptosis of the left eye, with progressive visual acuity impairment and visual fields defects. CT/MRI scanning demonstrated a huge osseous lesion of the left ethmoid sinus (6.5 cm × 5 cm × 2.2 cm, extending laterally in to the orbit and cranially up to the anterior skull base. Bilateral extensive polyposis was also found. Endoscopic and external techniques were combined to remove the lesion. Bilateral endoscopic polypectomy, anterior and posterior ethmoidectomy and middle meatus antrostomy were performed. Finally, the remaining part of the tumor was reached and dissected from the surrounding tissue via a minimally invasive Lynch incision around the left middle canthus. During surgery, CSF rhinorrhea was observed and leakage was grafted with fascia lata and coated with bio-glu. Postoperatively, symptoms disappeared. Eighteen months after surgery, the patient is still free of symptoms. Conclusion Before management of ethmoid osteomas with intraorbital and skull base extension, a thorough neurological, ophthalmological and imaging evaluation is required, in order to define the bounders of the tumor, carefully survey the severity of symptoms and signs, and precisely plan the optimal treatment. The endoscopic procedure can constitute an important part of surgery undertaken for giant ethmoidal osteomas. In addition, surgeons always have to take into account a possible CSF leak and they have to be prepared to resolve it.

  20. A Census of Exoplanets in Orbits Beyond 0.5 AU via Space-based Microlensing

    CERN Document Server

    Bennett, David P; Beaulieu, J -P; Bond, I; Cheng, E; Cook, K; Friedman, S; Gaudi, B S; Gould, A; Jenkins, J; Kimble, R; Lin, D; Mather, J; Rich, M; Sahu, K; Sumi, T; Tenerelli, D; Udalski, A; Yock, P

    2009-01-01

    A space-based gravitational microlensing exoplanet survey will provide a statistical census of exoplanets with masses greater than 0.1 Earth-masses and orbital separations ranging from 0.5AU to infinity. This includes analogs to all the Solar System's planets except for Mercury, as well as most types of planets predicted by planet formation theories. Such a survey will provide results on the frequency of planets around all types of stars except those with short lifetimes. Close-in planets with separations < 0.5 AU are invisible to a space-based microlensing survey, but these can be found by Kepler. Other methods, including ground-based microlensing, cannot approach the comprehensive statistics on the mass and semi-major axis distribution of extrasolar planets that a space-based microlensing survey will provide. The terrestrial planet sensitivity of a ground-based microlensing survey is limited to the vicinity of the Einstein radius at 2-3 AU, and space-based imaging is needed to identify and determine the ...

  1. Logic circuits based on molecular spider systems.

    Science.gov (United States)

    Mo, Dandan; Lakin, Matthew R; Stefanovic, Darko

    2016-08-01

    Spatial locality brings the advantages of computation speed-up and sequence reuse to molecular computing. In particular, molecular walkers that undergo localized reactions are of interest for implementing logic computations at the nanoscale. We use molecular spider walkers to implement logic circuits. We develop an extended multi-spider model with a dynamic environment wherein signal transmission is triggered via localized reactions, and use this model to implement three basic gates (AND, OR, NOT) and a cascading mechanism. We develop an algorithm to automatically generate the layout of the circuit. We use a kinetic Monte Carlo algorithm to simulate circuit computations, and we analyze circuit complexity: our design scales linearly with formula size and has a logarithmic time complexity. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  2. A mission-oriented orbit design method of remote sensing satellite for region monitoring mission based on evolutionary algorithm

    Science.gov (United States)

    Shen, Xin; Zhang, Jing; Yao, Huang

    2015-12-01

    Remote sensing satellites play an increasingly prominent role in environmental monitoring and disaster rescue. Taking advantage of almost the same sunshine condition to same place and global coverage, most of these satellites are operated on the sun-synchronous orbit. However, it brings some problems inevitably, the most significant one is that the temporal resolution of sun-synchronous orbit satellite can't satisfy the demand of specific region monitoring mission. To overcome the disadvantages, two methods are exploited: the first one is to build satellite constellation which contains multiple sunsynchronous satellites, just like the CHARTER mechanism has done; the second is to design non-predetermined orbit based on the concrete mission demand. An effective method for remote sensing satellite orbit design based on multiobjective evolution algorithm is presented in this paper. Orbit design problem is converted into a multi-objective optimization problem, and a fast and elitist multi-objective genetic algorithm is utilized to solve this problem. Firstly, the demand of the mission is transformed into multiple objective functions, and the six orbit elements of the satellite are taken as genes in design space, then a simulate evolution process is performed. An optimal resolution can be obtained after specified generation via evolution operation (selection, crossover, and mutation). To examine validity of the proposed method, a case study is introduced: Orbit design of an optical satellite for regional disaster monitoring, the mission demand include both minimizing the average revisit time internal of two objectives. The simulation result shows that the solution for this mission obtained by our method meet the demand the users' demand. We can draw a conclusion that the method presented in this paper is efficient for remote sensing orbit design.

  3. Synthetic hydroxyapatite-based integrated orbital implants: A human pilot trial

    Directory of Open Access Journals (Sweden)

    Kundu Biswanath

    2005-01-01

    Full Text Available Purpose: Orbital implants are used as fillers following enucleation or evisceration surgeries to replace the lost volume for better cosmesis and motility of the artificial eye. Over the last decade porous hydroxyapatite (HAp implants derived from the naturally occurring corals, are increasingly used. Recently synthetic HAp-based implants have been introduced. After fibrovasculrisation they have the added advantage of being directly integrated with the artificial shell, thereby increasing the motility to a great extent. The current study, evaluated the efficacy of two different models of synthetic HAp with 75% porosity and pore sizes ranging from 100 to 300 mm. Methods: Synthetic HAp powders were prepared with a novel wet chemical route. Two models of porous orbital implants with the characteristic designs for both evisceration and enucleation surgery were developed, characterised and implanted to consecutive 25 human subjects, 17 following evisceration, and 8 following enucleation. The postoperative performances of these implants were evaluated in respect to the degree of volume replacement (implant + prosthesis, presence/absence of lagophthalmos and lower eye-lid laxity, status of socket and fornices. Magnetic resonance imaging assessed the stability of the implants within the socket and progressive fibro-vascularisation within the porous scaffold as a function of time. Finally, motility of the implants as well as the prostheses (horizontal movements by Lister Perimeter and subjective cosmetic results (qualitative were also evaluated. Results: During the 2.5 years of follow-up study, no significant postoperative complications were noticed. One case, showed an anterior implant exposure of 3-4 mm, and was managed with donor scleral patch graft and one case of conjunctival thinning was corrected by re-suturing the conjunctival dehiscence. Fourteen of the 25 patients had a very good movement of the prostheses (> 20° horizontal movement and the

  4. Ring-shaped Racetrack memory based on spin orbit torque driven chiral domain wall motions

    Science.gov (United States)

    Zhang, Yue; Zhang, Xueying; Hu, Jingtong; Nan, Jiang; Zheng, Zhenyi; Zhang, Zhizhong; Zhang, Youguang; Vernier, Nicolas; Ravelosona, Dafine; Zhao, Weisheng

    2016-10-01

    Racetrack memory (RM) has sparked enormous interest thanks to its outstanding potential for low-power, high-density and high-speed data storage. However, since it requires bi-directional domain wall (DW) shifting process for outputting data, the mainstream stripe-shaped concept certainly suffers from the data overflow issue. This geometrical restriction leads to increasing complexity of peripheral circuits or programming as well as undesirable reliability issue. In this work, we propose and study ring-shaped RM, which is based on an alternative mechanism, spin orbit torque (SOT) driven chiral DW motions. Micromagnetic simulations have been carried out to validate its functionality and exhibit its performance advantages. The current flowing through the heavy metal instead of ferromagnetic layer realizes the “end to end” circulation of storage data, which remains all the data in the device even if they are shifted. It blazes a promising path for application of RM in practical memory and logic.

  5. Synthetic-lattice enabled all-optical devices based on orbital angular momentum of light

    Science.gov (United States)

    Luo, Xi-Wang; Zhou, Xingxiang; Xu, Jin-Shi; Li, Chuan-Feng; Guo, Guang-Can; Zhang, Chuanwei; Zhou, Zheng-Wei

    2017-07-01

    All-optical photonic devices are crucial for many important photonic technologies and applications, ranging from optical communication to quantum information processing. Conventional design of all-optical devices is based on photon propagation and interference in real space, which may rely on large numbers of optical elements, and the requirement of precise control makes this approach challenging. Here we propose an unconventional route for engineering all-optical devices using the photon's internal degrees of freedom, which form photonic crystals in such synthetic dimensions for photon propagation and interference. We demonstrate this design concept by showing how important optical devices such as quantum memory and optical filters can be realized using synthetic orbital angular momentum (OAM) lattices in degenerate cavities. The design route utilizing synthetic photonic lattices may significantly reduce the requirement for numerous optical elements and their fine tuning in conventional design, paving the way for realistic all-optical photonic devices with novel functionalities.

  6. Quantum state tomography of orbital angular momentum photonics qubits via a projection-based technique

    CERN Document Server

    Nicolas, Adrien; Giacobino, Elisabeth; Maxein, Dominik; Laurat, Julien

    2014-01-01

    While measuring the orbital angular momentum state of bright light beams can be performed using imaging techniques, a full characterization at the single-photon level is challenging. For applications to quantum optics and quantum information science, such characterization is an essential capability. Here, we present a setup to perform the quantum state tomography of photonic qubits encoded in this degree of freedom. The method is based on a projective technique using spatial mode projection via fork holograms and single-mode fibers inserted into an interferometer. The alignment and calibration of the device is detailed as well as the measurement sequence to reconstruct the associated density matrix. Possible extensions to higher-dimensional spaces are discussed.

  7. RL-10 Based Combined Cycle For A Small Reusable Single-Stage-To-Orbit Launcher

    Science.gov (United States)

    Balepin, Vladimir; Price, John; Filipenco, Victor

    1999-01-01

    This paper discusses a new application of the combined propulsion known as the KLIN(TM) cycle, consisting of a thermally integrated deeply cooled turbojet (DCTJ) and liquid rocket engine (LRE). If based on the RL10 rocket engine family, the KLIN (TM) cycle makes a small single-stage-to-orbit (SSTO) reusable launcher feasible and economically very attractive. Considered in this paper are the concept and parameters of a small SSTO reusable launch vehicle (RLV) powered by the KLIN (TM) cycle (sSSTO(TM)) launcher. Also discussed are the benefits of the small launcher, the reusability, and the combined cycle application. This paper shows the significant reduction of the gross take off weight (GTOW) and dry weight of the KLIN(TM) cycle-powered launcher compared to an all-rocket launcher.

  8. Comment on Unified treatment for the evaluation of arbitrary multielectron multicenter molecular integrals over Slater-type orbitals with noninteger principal quantum numbers

    OpenAIRE

    Guseinov, I. I.

    2005-01-01

    Ozdogan (Int. J. Quantum Chem., 92 (2003) 419) published formulas for evaluating the multielectron multicenter molecular integrals over Slater-type orbitals (STOs). It is demonstrated that the formulas presented in this work are not original and they can easily be derived by means of a simple algebra from the relationship of our published papers (I.I.Guseinov, J.Mol.Struct.(Theochem), 417(1997)117; J.Mol.Struct.(Theochem), 593 (2002) 65; I.I.Guseinov,B.A.Mamedov,F.Oner,S.Huseyin, J.Mol.Struct...

  9. Functions of key residues in the ligand-binding pocket of vitamin D receptor: Fragment molecular orbital interfragment interaction energy analysis

    Science.gov (United States)

    Yamagishi, Kenji; Yamamoto, Keiko; Yamada, Sachiko; Tokiwa, Hiroaki

    2006-03-01

    Fragment molecular orbital-interfragment interaction energy calculations of the vitamin D receptor (VDR)/1α,25-dihydroxyvitamin D 3 complex were utilized to assign functions of key residues of the VDR. Only one residue forms a significant interaction with the corresponding hydroxy group of the ligand, although two residues are located around each hydroxy group. The degradation of binding affinity for derivatives upon removal of a hydroxy group is closely related to the trend in the strength of the hydrogen bonds. Type II hereditary rickets due to an Arg274 point mutation is caused by the lack of the strongest hydrogen bond.

  10. Nanoscale probe of magnetism, orbital occupation, and structural distortions in iron-based superconductors

    Science.gov (United States)

    Cantoni, Claudia

    2014-03-01

    Local probes of atomic and electronic structures with sub-nanometer spatial resolution can provide additional insights into the physics of iron-based superconductors (FBS) by resolving the influence of inhomogeneities that are typically averaged over by bulk-sensitive techniques. Here we apply aberration-corrected scanning transmission electron microscopy coupled with electron energy loss spectroscopy to a wide class of iron-based superconductors and parent compounds to decipher the interplay between crystal distortions, local magnetic moment, orbital occupancy, and charge doping in these complex materials. In addition to revealing universal trends for hole concentration and local magnetic moment across families of FBS, we directly observe the effects of magneto-elastic coupling in 122 arsenides at room temperature, well above the structural and antiferromagnetic transition. The presence of atomic displacements indicates that the C4 tetragonal symmetry is already broken at room temperature in unstrained crystals, lowering the symmetry to orthorhombic (I2mm), and that all of the crystals are twinned with domains the size of a few nanometers. By tracking these local atomic displacements as a function of doping level x, in Ba(Fe1-xCox)2 As2, we find that the domain size correlates with the magnitude of the dynamic Fe moment, and both are enhanced near optimal doping where the ordered moment is suppressed. The non-monotonic behavior of the local Fe magnetic moment is linked to the strong coupling between lattice, spin, and orbital degrees of freedom. Research supported by the Materials Sciences and Engineering Division Office of Basic Energy Sciences, U.S. Department of Energy.

  11. Bases moleculares de las lipodistrofias familiares

    OpenAIRE

    2013-01-01

    Con este estudio nos propusimos hacer un diagnóstico genético de pacientes fenotípicamente lipodistróficas y obtener evidencias que contribuyeran a esclarecer los mecanismos moleculares por los que se produce la pérdida de TA en pacientes con lipodistrofias familiares.

  12. Choice of high-apogee AES orbits on the basis of the qualitative methods of the theory of perturbations and situational analysis. Part I. Situational studies based on orbital tori

    Science.gov (United States)

    Prokhorenko, V. I.

    2016-03-01

    The paper discusses the problems of the choice of high-apogee orbits of artificial Earth satellites (AES), proceeding from the tasks of space experiments aimed at studying near-earth space and taking into account the features of the orbital evolution and ballistic lifetime. The suggested methods of the choice of orbits consist of two components. The first is based on the use of mathematical models of studied regions of near-earth space and various techniques of situation analysis, among which the annual and daily orbital tori developed by the author about 35 years ago are key. The second component is based on qualitative methods of the theory of perturbations of high-apogee AES orbits developed by M.L. Lidov more than 50 years ago.

  13. Spin-orbit coupling, spin-lattice relaxation and spin-memory studies of F center/molecular ion pairs in alkali halides

    Energy Technology Data Exchange (ETDEWEB)

    Baldacchini, G.; Botti, S.; Grassano, U.M.; Luty, F.

    1992-12-31

    The spin-orbit parameter, spin-lattice relaxation time, and spin-mixing parameter of F/sub H/(OH/sup -/) and F/sub H/(CN/sup -/) centers in several alkali halides were studied with magnetic circular dichroism at about 2 K. A close comparison of the experimental results before and after optically induced association of the F center with the molecular ion was made. In crystals of NaCl structure, the negative spin-orbit parameter changes little between F and F/sub H/ centers in the same host. For CsCl and CsBr two values of spin-orbit parameter were derived for F/sub H/(CN/sup -/) centers with axes parallel or perpendicular to the magnetic field. In all studied systems, the spin-lattice relaxation time was already shorter before aggregation as compared with F centers in pure crystals, and became further shortened by the F/sub H/ center formation. The spin-mixing parameter decreased slightly for F/sub H/(OH/sup -/) as compared with F centers, while it increased drastically for F/sub H/(CN/sup -/) defects and reaches its maximum possible value, 0.5 in cesium halides. First attempts to interpret these magneto-optical results are presented in this paper.

  14. Oligo Tröger's bases--new molecular scaffolds.

    Science.gov (United States)

    Dolenský, Bohumil; Havlík, Martin; Král, Vladimír

    2012-05-21

    Oligo Tröger's bases are compounds containing two or more Tröger's base subunits (1,5-methanodiareno[b,f][1,5]diazocines) sharing one or more arene parts. Due to their interesting molecular shapes, these compounds are studied as chiral molecular tweezers, clips, cavitands, clefts, calixes, etc. This review includes all available data on oligo Tröger's bases, and introduces their preparation and properties to a wide audience.

  15. Successive hydrogen-elimination reactions with low activation energies in the a-Si:H formation process: An ab initio molecular-orbital study

    Science.gov (United States)

    Sato, Kota; Sugiyama, Yoko; Uchiyama, Akihiko; Iwabuchi, Susumu; Hirano, Tsuneo; Koinuma, Hideomi

    1992-07-01

    Successive hydrogen elimination reactions with low activation energies during the formation of a-Si:H by silane plasma chemical vapor deposition are proposed on the basis of an ab initio molecular-orbital method. The activation energy of the first step, the reaction of a dangling-bond site with an adjacent tetrahedrally coordinated silicon atom, was found to be 25.2 kcal/mol at 0 K when the zero-point vibrational energy was taken into account. The subsequent step was an exothermic process with a lower activation energy. The total process was thermodynamically much more favorable than the molecular processes by which a hydrogen atom or molecule is eliminated.

  16. A linear- and sublinear-scaling method for calculating NMR shieldings in atomic orbital-based second-order Møller-Plesset perturbation theory.

    Science.gov (United States)

    Maurer, Marina; Ochsenfeld, Christian

    2013-05-07

    An atomic-orbital (AO) based formulation for calculating nuclear magnetic resonance chemical shieldings at the second-order Møller-Plesset perturbation theory level is introduced, which provides a basis for reducing the scaling of the computational effort with the molecular size from the fifth power to linear and for a specific nucleus to sublinear. The latter sublinear scaling in the rate-determining steps becomes possible by avoiding global perturbations with respect to the magnetic field and by solving for quantities that involve the local nuclear magnetic spin perturbation instead. For avoiding the calculation of the second-order perturbed density matrix, we extend our AO-based reformulation of the Z-vector method within a density matrix-based scheme. Our pilot implementation illustrates the fast convergence with respect to the required number of Laplace points and the asymptotic scaling behavior in the rate-determining steps.

  17. [Department of the molecular bases of semiotics].

    Science.gov (United States)

    Ternovyĭ, K S

    1995-01-01

    Department of molecular basis of semiotics was organized in 1986. The main task of the department was to work out new approaches in estimation of the state of immune and blood system at the tissue, cell and molecular levels, using biochemical, biophysical and molecular biology techniques. There are several main directions of scientific investigations at the department. Most informational methods were collected in "immunological portrait" for differential diagnostic and complex investigation of the immune system of autoimmune patients. This group of techniques was used to study changes in the immune system of Kievites after the Chernobyl disaster. A decrease of complement and thymic serum activity was detected. Antibodies against nuclear components appeared in 20% of donors. And a higher of circulating immune complex of low molecular weight was observed. Low level of thymic serum activity in blood of autoimmune patients with rheumatoid arthritis, lupus erythematosus, diabetes, herpes and other depends on the appearance of zinc-independent timuline inhibitor less then 2000 D. Another kind of thymic hormone inhibitors was detected in thymectomized adult mice. Its effect disappears when zinc added in blood rather due to competition for lymphocyte surface receptors timuline and its inactive analogue than other mechanism. Therapeutic effect of UV irradiation of patients' blood was shown to be closely connected with the changes in thymic serum activity in respect to stabilization of thymic hormone/inhibitor ratio. The immunochemical techniques were used to detect and investigate tumor-associated chromatin antigens in human and animal tumor cells. Antigens not found in normal tissues were detected when using rabbit antibodies against chromatin of rat hepatocarcinoma and human colon and carcinoma.(ABSTRACT TRUNCATED AT 250 WORDS)

  18. Molecular Bases of Cutaneous and Uveal Melanomas

    Directory of Open Access Journals (Sweden)

    Sudeep Gaudi

    2011-01-01

    Full Text Available Intensive research in recent years has begun to unlock the mysteries surrounding the molecular pathogenesis of melanoma, the deadliest of skin cancers. The high-penetrance, low-frequency susceptibility gene CDKN2A produces tumor suppressor proteins that function in concert with p53 and retinoblastoma protein to thwart melanomagenesis. Aberrant CDKN2A gene products have been implicated in a great many cases of familial cutaneous melanoma. Sporadic cases, on the other hand, often involve constitutive signal transduction along the mitogen-activated protein kinase (MAPK pathway, with particular focus falling upon mutated RAS and RAF protooncogenes. The proliferative effects of the MAPK pathway may be complemented by the antiapoptotic signals of the PI3K/AKT pathway. After skin, melanoma most commonly affects the eye. Data for the constitutive activation of the MAPK pathway in uveal melanoma exists as well, however, not through mutations of RAS and RAF. Rather, evidence implicates the proto-oncogene GNAQ. In the following discussion, we review the major molecular pathways implicated in both familial and sporadic cutaneous melanomagenesis, the former accounting for approximately 10% of cases. Additionally, we discuss the molecular pathways for which preliminary evidence suggests a role in uveal melanomagenesis.

  19. Investigation of the encapsulation of metal cations (Cu(2+), Zn(2+), Ca(2+) and Ba(2+)) by the dipeptide Phe-Phe using natural bond orbital theory and molecular dynamics simulation.

    Science.gov (United States)

    Bhunia, Snehasis; Singh, Ajeet; Ojha, Animesh K

    2017-03-01

    Complexes of the dipeptide phenylalanine-phenylalanine (Phe-Phe) with divalent metal cations (Cu(2+), Zn(2+), Ca(2+) and Ba(2+)) were studied at the B3LYP and MP2 levels of theory with the basis sets 6-311++G(d,p) and 6-31 + G(d) in the gas phase. The relative energies of these complexes indicated that cation-π bidentate/tridentate conformations are more favourable than other conformations with uncoordinated rings. These findings were confirmed by the calculated values of thermodynamic parameters such as the Gibbs free energy. Natural bond orbital (NBO) analysis was carried out to explore the metal-ligand coordination in Phe-Phe-Cu(2+)/Zn(2+) complexes. Possible orbital transitions, types of orbitals and their occupancies were determined for a range of Phe-Phe-Cu(2+)/Zn(2+) complexes. The charge transfer involved in various orbital transitions was explored by considering the second-order perturbation energy. NBO analysis revealed that the change transfer is stronger when the metal cation uses both the 4s + 4p subshells rather than just its 4p subshell. We also performed molecular dynamics (MD) simulations to check the stability and consistency of the most favourable binding motifs of Cu(2+), Zn(2+), Ca(2+) and Ba(2+) with Phe-Phe over time. The structures of the Phe-Phe-Cu(2+)/Zn(2+)/Ca(2+)/Ba(2+) complexes obtained using MD simulation were found to be in good agreement with those obtained in the DFT-based calculations. Graphical Abstract Conformational search on encapsulation of divalent metal cations (Ca(2+), Zn(2+), Ca(2+), Ba(2+)) by the Phe-Phe dipeptide.

  20. Orbital cellulitis

    Science.gov (United States)

    ... hemolytic streptococci may also cause orbital cellulitis. Orbital cellulitis infections in children may get worse very quickly and ... in the space around the eye. An orbital cellulitis infection can get worse very quickly. A person with ...

  1. Unidirectional light-driven molecular motors based on overcrowded alkenes.

    Science.gov (United States)

    Cnossen, Arjen; Browne, Wesley R; Feringa, Ben L

    2014-01-01

    Over the last two decades, interest in nanotechnology has led to the design and synthesis of a toolbox of nanoscale versions of macroscopic devices and components. In molecular nanotechnology, linear motors based on rotaxanes and rotary motors based on overcrowded alkenes are particularly promising for performing work at the nanoscale. In this chapter, progress on light-driven molecular motors based on overcrowded alkenes is reviewed. Both the so-called first and second generation molecular motors are discussed, as well as their potential applications.

  2. Automated global water mapping based on wide-swath orbital synthetic aperture radar

    Science.gov (United States)

    Westerhoff, R. S.; Kleuskens, M. P. H.; Winsemius, H. C.; Huizinga, H. J.; Brakenridge, G. R.

    2012-06-01

    This paper presents an automated technique, embedded in an online service, which ingests orbital synthetic aperture radar (SAR) imagery and outputs surface water maps in near real time and on a global scale. The service anticipates future open data dissemination of water extent information using the European Space Agency's Sentinel-1 data. The classification methods used are innovative but practical and different per 1 × 1 degree tile. For each tile, a probability distribution function of a pixel, being covered with water or being dry is established based on a long SAR training dataset. These probability distributions are conditional on the backscatter and the incidence angle. In classification mode the probability of water coverage is calculated, conditional on the current backscatter - incidence angle combination. The overlap between the probability distributions of a pixel being wet or dry is used as a proxy for the quality of our classification. The service has multiple uses, e.g. for water body dynamics in times of drought or for urgent inundation extent determination during floods. The service generates data systematically: it is not an on-demand service activated only for emergency response, but instead is always up-to-date and available. We demonstrate its use in flood situations using Envisat ASAR information during the 2011 Thailand floods. A first merge with a NASA near real time water product based on MODIS optical satellite imagery shows excellent agreement between these independent satellite-based water products.

  3. Self-consistent field theory based molecular dynamics with linear system-size scaling.

    Science.gov (United States)

    Richters, Dorothee; Kühne, Thomas D

    2014-04-01

    We present an improved field-theoretic approach to the grand-canonical potential suitable for linear scaling molecular dynamics simulations using forces from self-consistent electronic structure calculations. It is based on an exact decomposition of the grand canonical potential for independent fermions and does neither rely on the ability to localize the orbitals nor that the Hamilton operator is well-conditioned. Hence, this scheme enables highly accurate all-electron linear scaling calculations even for metallic systems. The inherent energy drift of Born-Oppenheimer molecular dynamics simulations, arising from an incomplete convergence of the self-consistent field cycle, is circumvented by means of a properly modified Langevin equation. The predictive power of the present approach is illustrated using the example of liquid methane under extreme conditions.

  4. Self-consistent field theory based molecular dynamics with linear system-size scaling

    Energy Technology Data Exchange (ETDEWEB)

    Richters, Dorothee [Institute of Mathematics and Center for Computational Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 9, D-55128 Mainz (Germany); Kühne, Thomas D., E-mail: kuehne@uni-mainz.de [Institute of Physical Chemistry and Center for Computational Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 7, D-55128 Mainz (Germany); Technical and Macromolecular Chemistry, University of Paderborn, Warburger Str. 100, D-33098 Paderborn (Germany)

    2014-04-07

    We present an improved field-theoretic approach to the grand-canonical potential suitable for linear scaling molecular dynamics simulations using forces from self-consistent electronic structure calculations. It is based on an exact decomposition of the grand canonical potential for independent fermions and does neither rely on the ability to localize the orbitals nor that the Hamilton operator is well-conditioned. Hence, this scheme enables highly accurate all-electron linear scaling calculations even for metallic systems. The inherent energy drift of Born-Oppenheimer molecular dynamics simulations, arising from an incomplete convergence of the self-consistent field cycle, is circumvented by means of a properly modified Langevin equation. The predictive power of the present approach is illustrated using the example of liquid methane under extreme conditions.

  5. Coal-based carbons with molecular sieve properties

    Energy Technology Data Exchange (ETDEWEB)

    El-Wakil, A.M.; Youssef, A.M.; Tollan, K.A. (Mansoura Univ. (Egypt))

    1991-01-01

    Carbon molecular sieves are used extensively in gas chromatography for the separation of permanent gases and light hydrocarbons. Carbon molecular sieves also find commercial application for the manufacture of pure hydrogen from hydrogen-rich gases such as coke-oven gas, and for the separation of air by the pressure-swing adsorption technique. The objective of this investigation was to prepare carbons from Maghara coal, recently available on the commercial market. Coal-based carbons, if they possess molecular sieve properties, are superior to molecular sieve carbons from agricultural by-products because they have more satisfactory mechanical properties.

  6. Charge-transfer mechanism for electrophilic aromatic nitration and nitrosation via the convergence of (ab initio) molecular-orbital and Marcus-Hush theories with experiments.

    Science.gov (United States)

    Gwaltney, Steven R; Rosokha, Sergiy V; Head-Gordon, Martin; Kochi, Jay K

    2003-03-19

    The highly disparate rates of aromatic nitrosation and nitration, despite the very similar (electrophilic) properties of the active species: NO(+) and NO(2)(+) in Chart 1, are quantitatively reconciled. First, the thorough mappings of the potential-energy surfaces by high level (ab initio) molecular-orbital methodologies involving extensive coupled-cluster CCSD(T)/6-31G optimizations establish the intervention of two reactive intermediates in nitration (Figure 8) but only one in nitrosation (Figure 7). Second, the same distinctive topologies involving double and single potential-energy minima (Figures 6 and 5) also emerge from the semiquantitative application of the Marcus-Hush theory to the transient spectral data. Such a striking convergence from quite different theoretical approaches indicates that the molecular-orbital and Marcus-Hush (potential-energy) surfaces are conceptually interchangeable. In the resultant charge-transfer mechanism, the bimolecular interactions of arene donors with both NO(+) and NO(2)(+) spontaneously lead (barrierless) to pi-complexes in which electron transfer is concurrent with complexation. Such a pi-complex in nitration is rapidly converted to the sigma-complex, whereas this Wheland adduct in nitrosation merely represents a high energy (transition-state) structure. Marcus-Hush analysis thus demonstrates how the strongly differentiated (arene) reactivities toward NO(+) and NO(2)(+) can actually be exploited in the quantitative development of a single coherent (electron-transfer) mechanism for both aromatic nitrosation and nitration.

  7. A Detailed Derivation of Gaussian Orbital-Based Matrix Elements in Electron Structure Calculations

    Science.gov (United States)

    Petersson, T.; Hellsing, B.

    2010-01-01

    A detailed derivation of analytic solutions is presented for overlap, kinetic, nuclear attraction and electron repulsion integrals involving Cartesian Gaussian-type orbitals. It is demonstrated how s-type orbitals can be used to evaluate integrals with higher angular momentum via the properties of Hermite polynomials and differentiation with…

  8. A Detailed Derivation of Gaussian Orbital-Based Matrix Elements in Electron Structure Calculations

    Science.gov (United States)

    Petersson, T.; Hellsing, B.

    2010-01-01

    A detailed derivation of analytic solutions is presented for overlap, kinetic, nuclear attraction and electron repulsion integrals involving Cartesian Gaussian-type orbitals. It is demonstrated how s-type orbitals can be used to evaluate integrals with higher angular momentum via the properties of Hermite polynomials and differentiation with…

  9. Orbit-based dynamical models of the Sculptor dSph galaxy

    NARCIS (Netherlands)

    Breddels, Maarten A.; Helmi, A.; van den Bosch, R.C.E.; van de Ven, G.; Battaglia, G.

    2013-01-01

    We have developed spherically symmetric dynamical models of dwarf spheroidal (dSph) galaxies using Schwarzschild's orbit superposition method. This type of modelling yields constraints both on the total mass distribution (e.g. enclosed mass and scale radius) and on the orbital structure of the syste

  10. GPS-based precise orbit determination and accelerometry for low flying satellites

    NARCIS (Netherlands)

    Van den IJssel, J.A.A.

    2014-01-01

    Atmospheric density models are currently the limiting factor in the accuracy of the dynamic orbit determination and prediction of satellites in a low Earth orbit. Any improvement in these models would greatly aid in applications such as re-entry prediction, ground-track maintenance of Earth observat

  11. Beyond Molecular Wires: Design Molecular Electronic Functions Based on Dipolar Effect.

    Science.gov (United States)

    Lo, Wai-Yip; Zhang, Na; Cai, Zhengxu; Li, Lianwei; Yu, Luping

    2016-09-20

    As the semiconductor companies officially abandoned the pursuit of Moore's law, the limitation of silicone-based semiconductor electronic devices is approaching. Single molecular devices are considered as a potential solution to overcome the physical barriers caused by quantum interferences because the intermolecular interactions are mainly through weak van der Waals force between molecular building blocks. In this bottom-up approach, components are built from atoms up, allowing great control over the molecular properties. Moreover, single molecular devices are powerful tools to understand quantum physics, reaction mechanism, and electron and charge transfer processes in organic semiconductors and molecules. So far, a great deal of effort is focused on understanding charge transport through organic single-molecular wires. However, to control charge transport, molecular diodes, switches, transistors, and memories are crucial. Significant progress in these topics has been achieved in the past years. The introduction and advances of scanning tunneling microscope break-junction (STM-BJ) techniques have led to more detailed characterization of new molecular structures. The modern organic chemistry provides an efficient access to a variety of functional moieties in single molecular device. These moieties have the potential to be incorporated in miniature circuits or incorporated as parts in molecular machines, bioelectronics devices, and bottom-up molecular devices. In this Account, we discuss progress mainly made in our lab in designing and characterizing organic single-molecular electronic components beyond molecular wires and with varied functions. We have synthesized and demonstrated molecular diodes with p-n junction structures through various scanning probe microscopy techniques. The assembly of the molecular diodes was achieved by using Langmuir-Blodgett technique or thiol/gold self-assembly chemistry with orthogonal protecting groups. We have thoroughly

  12. The Dimensions of the Orbital Cavity Based on High-Resolution Computed Tomography of Human Cadavers

    DEFF Research Database (Denmark)

    Felding, Ulrik Ascanius; Bloch, Sune Land; Buchwald, Christian von

    2016-01-01

    for surface area. To authors' knowledge, this study is the first to have measured the entire surface area of the orbital cavity.The volume and surface area of the orbital cavity were estimated in computed tomography scans of 11 human cadavers using unbiased stereological sampling techniques. The mean (± SD......Blow-out fractures affect the volume and surface area of the orbital cavity. Estimation of these values after the trauma may help in deciding whether or not a patient is a candidate for surgery. Recent studies have provided estimates of orbital volume and area of bone defect, and correlated them...... with the degree of enophthalmos. However, a large degree of biological variation between individuals may preclude such absolute values from being successful indicators for surgery.Stereological methods have been used to estimate orbital cavity volume in a few studies, but to date these have not been used...

  13. Antibody-controlled actuation of DNA-based molecular circuits

    Science.gov (United States)

    Engelen, Wouter; Meijer, Lenny H. H.; Somers, Bram; de Greef, Tom F. A.; Merkx, Maarten

    2017-02-01

    DNA-based molecular circuits allow autonomous signal processing, but their actuation has relied mostly on RNA/DNA-based inputs, limiting their application in synthetic biology, biomedicine and molecular diagnostics. Here we introduce a generic method to translate the presence of an antibody into a unique DNA strand, enabling the use of antibodies as specific inputs for DNA-based molecular computing. Our approach, antibody-templated strand exchange (ATSE), uses the characteristic bivalent architecture of antibodies to promote DNA-strand exchange reactions both thermodynamically and kinetically. Detailed characterization of the ATSE reaction allowed the establishment of a comprehensive model that describes the kinetics and thermodynamics of ATSE as a function of toehold length, antibody-epitope affinity and concentration. ATSE enables the introduction of complex signal processing in antibody-based diagnostics, as demonstrated here by constructing molecular circuits for multiplex antibody detection, integration of multiple antibody inputs using logic gates and actuation of enzymes and DNAzymes for signal amplification.

  14. Molecular bases of methamphetamine-induced neurodegeneration.

    Science.gov (United States)

    Cadet, Jean Lud; Krasnova, Irina N

    2009-01-01

    Methamphetamine (METH) is a highly addictive psychostimulant drug, whose abuse has reached epidemic proportions worldwide. The addiction to METH is a major public concern because its chronic abuse is associated with serious health complications including deficits in attention, memory, and executive functions in humans. These neuropsychiatric complications might, in part, be related to drug-induced neurotoxic effects, which include damage to dopaminergic and serotonergic terminals, neuronal apoptosis, as well as activated astroglial and microglial cells in the brain. Thus, the purpose of the present paper is to review cellular and molecular mechanisms that might be responsible for METH neurotoxicity. These include oxidative stress, activation of transcription factors, DNA damage, excitotoxicity, blood-brain barrier breakdown, microglial activation, and various apoptotic pathways. Several approaches that allow protection against METH-induced neurotoxic effects are also discussed. Better understanding of the cellular and molecular mechanisms involved in METH toxicity should help to generate modern therapeutic approaches to prevent or attenuate the long-term consequences of psychostimulant use disorders in humans.

  15. The Capacity Gain of Orbital Angular Momentum Based Multiple-Input-Multiple-Output System

    Science.gov (United States)

    Zhang, Zhuofan; Zheng, Shilie; Chen, Yiling; Jin, Xiaofeng; Chi, Hao; Zhang, Xianmin

    2016-05-01

    Wireless communication using electromagnetic wave carrying orbital angular momentum (OAM) has attracted increasing interest in recent years, and its potential to increase channel capacity has been explored widely. In this paper, we compare the technique of using uniform linear array consist of circular traveling-wave OAM antennas for multiplexing with the conventional multiple-in-multiple-out (MIMO) communication method, and numerical results show that the OAM based MIMO system can increase channel capacity while communication distance is long enough. An equivalent model is proposed to illustrate that the OAM multiplexing system is equivalent to a conventional MIMO system with a larger element spacing, which means OAM waves could decrease the spatial correlation of MIMO channel. In addition, the effects of some system parameters, such as OAM state interval and element spacing, on the capacity advantage of OAM based MIMO are also investigated. Our results reveal that OAM waves are complementary with MIMO method. OAM waves multiplexing is suitable for long-distance line-of-sight (LoS) communications or communications in open area where the multi-path effect is weak and can be used in massive MIMO systems as well.

  16. Antarctic Ice Sheet Slope and Aspect Based on Icesat's Repeat Orbit Measurement

    Science.gov (United States)

    Yuan, L.; Li, F.; Zhang, S.; Xie, S.; Xiao, F.; Zhu, T.; Zhang, Y.

    2017-09-01

    Accurate information of ice sheet surface slope is essential for estimating elevation change by satellite altimetry measurement. A study is carried out to recover surface slope of Antarctic ice sheet from Ice, Cloud and land Elevation Satellite (ICESat) elevation measurements based on repeat orbits. ICESat provides repeat ground tracks within 200 meters in cross-track direction and 170 meters in along-track direction for most areas of Antarctic ice sheet. Both cross-track and along-track surface slopes could be obtained by adjacent repeat ground tracks. Combining those measurements yields a surface slope model with resolution of approximately 200 meters. An algorithm considering elevation change is developed to estimate the surface slope of Antarctic ice sheet. Three Antarctic Digital Elevation Models (DEMs) were used to calculate surface slopes. The surface slopes from DEMs are compared with estimates by using in situ GPS data in Dome A, the summit of Antarctic ice sheet. Our results reveal an average surface slope difference of 0.02 degree in Dome A. High resolution remote sensing images are also used in comparing the results derived from other DEMs and this paper. The comparison implies that our results have a slightly better coherence with GPS observation than results from DEMs, but our results provide more details and perform higher accuracy in coastal areas because of the higher resolution for ICESat measurements. Ice divides are estimated based on the aspect, and are weakly consistent with ice divides from other method in coastal regions.

  17. The Capacity Gain of Orbital Angular Momentum Based Multiple-Input-Multiple-Output System.

    Science.gov (United States)

    Zhang, Zhuofan; Zheng, Shilie; Chen, Yiling; Jin, Xiaofeng; Chi, Hao; Zhang, Xianmin

    2016-01-01

    Wireless communication using electromagnetic wave carrying orbital angular momentum (OAM) has attracted increasing interest in recent years, and its potential to increase channel capacity has been explored widely. In this paper, we compare the technique of using uniform linear array consist of circular traveling-wave OAM antennas for multiplexing with the conventional multiple-in-multiple-out (MIMO) communication method, and numerical results show that the OAM based MIMO system can increase channel capacity while communication distance is long enough. An equivalent model is proposed to illustrate that the OAM multiplexing system is equivalent to a conventional MIMO system with a larger element spacing, which means OAM waves could decrease the spatial correlation of MIMO channel. In addition, the effects of some system parameters, such as OAM state interval and element spacing, on the capacity advantage of OAM based MIMO are also investigated. Our results reveal that OAM waves are complementary with MIMO method. OAM waves multiplexing is suitable for long-distance line-of-sight (LoS) communications or communications in open area where the multi-path effect is weak and can be used in massive MIMO systems as well.

  18. Roll coated large area ITO- and vacuum-free all organic solar cells from diketopyrrolopyrrole based non-fullerene acceptors with molecular geometry effects

    DEFF Research Database (Denmark)

    Brandt, Rasmus Guldbaek; Zhang, Fei; Andersen, Thomas Rieks

    2016-01-01

    In this paper, we investigate three diketopyrrolopyrrole (DPP) based small molecular non-fullerene acceptors, namely Ph(DPP)3, Ph(DPP)2, and PhDMe(DPP)2, focusing on molecular geometry effects on the frontier orbital level, light absorption, molecular configuration, electron mobility, thin film...... morphology, and photovoltaic performance of both spin-coated ITO based and roll coated large area, ITO- and vacuum-free organic solar cells (OSCs). For spin-coated devices based on P3HT as the donor polymer the solar cells gave power conversion efficiencies (PCEs) in the following order for (P3HT:PhDMe(DPP)2...

  19. Development of molecular resists based on Phenyl[4]calixarene derivatives.

    Science.gov (United States)

    Echigo, Masatoshi; Hayashi, Hiromi; Oizumi, Hiroaki; Matsumaro, Kazuyuki; Itani, Toshiro

    2010-04-01

    We have developed negative-tone molecular resist based on C-4-cyclohexylphenylcalix[4]resorcinarene(MGR108) and positive-tone molecular resist based on protected C-4-isopropylphenylcalix[4]resorcinarene (MGR104P). Both MGR108 and MGR104P showed high solubility in both conventional resist solvents such as propylene glycol monomethyl ether and conventional alkaline developer of 0.26N TMAHaq. In this paper, we show current performance of resists by EB lithography (EBL) and EUV lithography (EUVL).

  20. Controlling charge current through a DNA based molecular transistor

    Science.gov (United States)

    Behnia, S.; Fathizadeh, S.; Ziaei, J.

    2017-01-01

    Molecular electronics is complementary to silicon-based electronics and may induce electronic functions which are difficult to obtain with conventional technology. We have considered a DNA based molecular transistor and study its transport properties. The appropriate DNA sequence as a central chain in molecular transistor and the functional interval for applied voltages is obtained. I-V characteristic diagram shows the rectifier behavior as well as the negative differential resistance phenomenon of DNA transistor. We have observed the nearly periodic behavior in the current flowing through DNA. It is reported that there is a critical gate voltage for each applied bias which above it, the electrical current is always positive.

  1. DESCIFRANDO LAS BASES MOLECULARES DE LA RESISTENCIA CUANTITATIVA Deciphering the Molecular Bases of Quantitative Resistance

    Directory of Open Access Journals (Sweden)

    CAMILO LÓPEZ

    2011-08-01

    Full Text Available Uno de los factores que más afectan los cultivos son las enfermedades ocasionadas por patógenos. La resistencia vegetal ha sido clásicamente dividida en dos tipos: i completa, vertical o cualitativa que es gobernada por un solo gen e ii incompleta, horizontal o cuantitativa la cual es gobernada por varios genes. Aunque la resistencia cuantitativa provee resistencia de amplio espectro y es durable, los mecanismos moleculares subyacentes no han sido estudiados en detalle. En esta revisión se propone un modelo basado en co-localización de genes similares a los genes clásicos de resistencia cualitativa con QTLs (Quantitative Trait Loci para explicar el mecanismo involucrado en el reconocimiento del patógeno durante la resistencia cuantitativa. Además se presenta información acerca del progreso obtenido en los últimos tres años para entender este tipo de resistencia, lo que culminó con la clonación de varios genes asociados a resistencia cuantitativa. En conjunto, estos datos proveen nuevas luces sobre la naturaleza genética de este tipo de resistencia y de cómo puede ser empleada en programas de mejoramiento genético.Plant pathogens are some of the most important factors affecting crop production. Classically two general types of plant resistance to pathogens have been recognized: i complete, vertical or qualitative resistance governed by a single gene; and ii incomplete, horizontal or quantitative resistance, which is governed by several genes. Although quantitative resistance provides broad spectrum and more durable resistance, the underlying molecular mechanism involved in pathogen recognition has not been deeply studied. In this review, we proposed a model to explain the molecular mechanism involved in the pathogen recognition during the quantitative resistance. This is based on the co-localization of similar classical qualitative resistance genes with QTL (Quantitative Trait Loci. In addition, information is presented about the

  2. The molecular bases of the suicidal brain

    Science.gov (United States)

    Turecki, Gustavo

    2017-01-01

    Suicide ranks among the leading causes of death around the world, and takes a heavy emotional and public health toll on most societies. Both distal and proximal factors contribute to suicidal behaviour. Distal factors — such as familial and genetic predisposition, as well as early-life adversity — increase the lifetime risk of suicide. They alter responses to stress and other processes through epigenetic modification of genes and associated changes in gene expression, and through the regulation of emotional and behavioural traits. Proximal factors associate with the precipitation of a suicidal event and include alterations in key neurotransmitter systems, inflammatory changes and glial dysfunction in the brain. This Review explores the key molecular changes associated with suicidality, and presents some promising avenues for future research. PMID:25354482

  3. Molecular Transistor Based on the Biphenyl Substituents

    Directory of Open Access Journals (Sweden)

    A.G. Malashenko

    2016-11-01

    Full Text Available It was investigated the physical processes in the molecules, which have properties required in case of using as molecular switches, transistors, or other electronic elements of future computers. Studies show that in the molecules of biphenyl substituents the angle between the planes of the phenyl rings depends on the magnitude of the applied external electric field. So, the ratio of squares of cosines of the angles between the phenyl groups in the field 0.01 a.u. and without field reaches 18. It significantly changes the ability of electrons to move along the long axis of the molecule. By varying the nature of the substituents, we can obtain the molecule characteristics that make these molecules promising for future using. This effect provides the use of biphenyl substitutes as transistors in electrical circuits constructed on separate molecules.

  4. Local orbitals by minimizing powers of the orbital variance

    DEFF Research Database (Denmark)

    Jansik, Branislav; Høst, Stinne; Kristensen, Kasper;

    2011-01-01

    It is demonstrated that a set of local orthonormal Hartree–Fock (HF) molecular orbitals can be obtained for both the occupied and virtual orbital spaces by minimizing powers of the orbital variance using the trust-region algorithm. For a power exponent equal to one, the Boys localization function...... is obtained. For increasing power exponents, the penalty for delocalized orbitals is increased and smaller maximum orbital spreads are encountered. Calculations on superbenzene, C60, and a fragment of the titin protein show that for a power exponent equal to one, delocalized outlier orbitals may...

  5. The Distribution of the Orbits in the Geminid Meteoroid Stream Based on the Dispersion of their Periods

    Science.gov (United States)

    Hajdukova, M., Jr.

    2011-01-01

    Geminid meteoroids, selected from a large set of precisely-reduced meteor orbits from the photographic and radar catalogues of the IAU Meteor Data Center (Lindblad et al. 2003), and from the Japanese TV meteor shower catalogue (SonotaCo 2010), have been analyzed with the aim of determining the orbits distribution in the stream, based on the dispersion of their periods P . The values of the reciprocal semi-major axis 1/a in the stream showed small errors in the velocity measurements. Thus, it was statistically possible to also determine the relation between the observed and the real dispersion of the Geminids.

  6. Preliminary Analysis of Ground-based Orbit Determination Accuracy for the Wide Field Infrared Survey Telescope (WFIRST)

    Science.gov (United States)

    Sease, Brad

    2017-01-01

    The Wide Field Infrared Survey Telescope is a 2.4-meter telescope planned for launch to the Sun-Earth L2 point in 2026. This paper details a preliminary study of the achievable accuracy for WFIRST from ground-based orbit determination routines. The analysis here is divided into two segments. First, a linear covariance analysis of early mission and routine operations provides an estimate of the tracking schedule required to meet mission requirements. Second, a simulated operations scenario gives insight into the expected behavior of a daily Extended Kalman Filter orbit estimate over the first mission year given a variety of potential momentum unloading schemes.

  7. Research Update: Orbital polarization in LaNiO{sub 3}-based heterostructures

    Energy Technology Data Exchange (ETDEWEB)

    Disa, Ankit S., E-mail: ankit.disa@yale.edu; Walker, F. J. [Center for Research on Interface Structures and Phenomena and Department of Applied Physics, Yale University, New Haven, Connecticut 06511 (United States); Ismail-Beigi, Sohrab; Ahn, Charles H. [Center for Research on Interface Structures and Phenomena and Department of Applied Physics, Yale University, New Haven, Connecticut 06511 (United States); Department of Physics and Department of Mechanical Engineering and Materials Science, Yale University, New Haven, Connecticut 06511 (United States)

    2015-06-01

    The relative energies and occupancies of valence orbital states can dramatically influence collective electronic and magnetic phenomena in correlated transition metal oxide systems. We review the current state of research on the modification and control of these orbital properties in rare-earth nickelates, especially LaNiO{sub 3}, a model degenerate d orbital system where significant recent progress has been made. Theoretical and experimental results on thin films and heterostructures are described, including the influence of electronic correlation effects. We highlight the latest approaches to achieving non-degenerate bands and discuss the outlook and applicability of this body of knowledge to other correlated metal oxide systems.

  8. A Delphi-Based Framework for systems architecting of in-orbit exploration infrastructure for human exploration beyond Low Earth Orbit

    Science.gov (United States)

    Aliakbargolkar, Alessandro; Crawley, Edward F.

    2014-01-01

    The current debate in the U.S. Human Spaceflight Program focuses on the development of the next generation of man-rated heavy lift launch vehicles. While launch vehicle systems are of critical importance for future exploration, a comprehensive analysis of the entire exploration infrastructure is required to avoid costly pitfalls at early stages of the design process. This paper addresses this need by presenting a Delphi-Based Systems Architecting Framework for integrated architectural analysis of future in-orbit infrastructure for human space exploration beyond Low Earth Orbit. The paper is structured in two parts. The first part consists of an expert elicitation study to identify objectives for the in-space transportation infrastructure. The study was conducted between November 2011 and January 2012 with 15 senior experts involved in human spaceflight in the United States and Europe. The elicitation study included the formation of three expert panels representing exploration, science, and policy stakeholders engaged in a 3-round Delphi study. The rationale behind the Delphi approach, as imported from social science research, is discussed. Finally, a novel version of the Delphi method is presented and applied to technical decision-making and systems architecting in the context of human space exploration. The second part of the paper describes a tradespace exploration study of in-orbit infrastructure coupled with a requirements definition exercise informed by expert elicitation. The uncertainties associated with technical requirements and stakeholder goals are explicitly considered in the analysis. The outcome of the expert elicitation process portrays an integrated view of perceived stakeholder needs within the human spaceflight community. Needs are subsequently converted into requirements and coupled to the system architectures of interest to analyze the correlation between exploration, science, and policy goals. Pareto analysis is used to identify architectures

  9. Interplay between Magnetism, Superconductivity, and Orbital Order in 5-Pocket Model for Iron-Based Superconductors: Parquet Renormalization Group Study.

    Science.gov (United States)

    Classen, Laura; Xing, Rui-Qi; Khodas, Maxim; Chubukov, Andrey V

    2017-01-20

    We report the results of the parquet renormalization group (RG) analysis of the phase diagram of the most general 5-pocket model for Fe-based superconductors. We use as an input the orbital structure of excitations near the five pockets made out of d_{xz}, d_{yz}, and d_{xy} orbitals and argue that there are 40 different interactions between low-energy fermions in the orbital basis. All interactions flow under the RG, as one progressively integrates out fermions with higher energies. We find that the low-energy behavior is amazingly simple, despite the large number of interactions. Namely, at low energies the full 5-pocket model effectively reduces either to a 3-pocket model made of one d_{xy} hole pocket and two electron pockets or a 4-pocket model made of two d_{xz}/d_{yz} hole pockets and two electron pockets. The leading instability in the effective 4-pocket model is a spontaneous orbital (nematic) order, followed by s^{+-} superconductivity. In the effective 3-pocket model, orbital fluctuations are weaker, and the system develops either s^{+-} superconductivity or a stripe spin-density wave. In the latter case, nematicity is induced by composite spin fluctuations.

  10. Phase transitions in a frustrated biquadratic Heisenberg model with coupled orbital degrees of freedom for iron-based superconductors

    Science.gov (United States)

    Zhuo, W. Z.; Qin, M. H.; Dong, S.; Li, X. G.; Liu, J.-M.

    2016-03-01

    In this paper, we study a biquadratic Heisenberg model with coupled orbital degrees of freedom by using a Monte Carlo simulation to investigate the phase transitions in iron-based superconductors. The antiferroquadrupolar state, which may be related to the magnetism of FeSe [R. Yu and Q. Si, Phys. Rev. Lett. 115, 116401 (2015), 10.1103/PhysRevLett.115.116401], is stabilized by the anisotropic biquadratic interaction induced by a ferro-orbital-ordered state. It is revealed that the orbital and nematic transitions occur at the same temperature for all the cases, supporting the mechanism of the orbital-driven nematicity as revealed in most recent experiments [S. H. Baek, D. V. Efremov, J. M. Ok, J. S. Kim, J. van den Brink, and B. Büchner, Nat. Mater. 14, 210 (2015), 10.1038/nmat4138]. In addition, it is suggested that the orbital interaction may lead to the separation of the structural and magnetic phase transitions, as observed in many families of iron pnictides.

  11. Orbital structure of the GJ876 extrasolar planetary system, based on the latest Keck and HARPS radial velocity data

    CERN Document Server

    Baluev, Roman V

    2011-01-01

    We use full available array of radial velocity data, including recently published HARPS and Keck observatory sets, to characterize the orbital configuration of the planetary system orbiting GJ876. First, we propose and describe in detail a fast method to fit perturbed orbital configuration, based on the integration of the sensitivity equations inferred by the equations of the original $N$-body problem. Further, we find that it is unsatisfactory to treat the available radial velocity data for GJ876 in the traditional white noise model, because the actual noise appears autocorrelated (and demonstrates non-white frequency spectrum). The time scale of this correlation is about a few days, and the contribution of the correlated noise is about 2 m/s (i.e., similar to the level of internal errors in the Keck data). We propose a variation of the maximum-likelihood algorithm to estimate the orbital configuration of the system, taking into account the red noise effects. We show, in particular, that the non-zero orbital...

  12. Inquiry-Based Learning of Molecular Phylogenetics

    Science.gov (United States)

    Campo, Daniel; Garcia-Vazquez, Eva

    2008-01-01

    Reconstructing phylogenies from nucleotide sequences is a challenge for students because it strongly depends on evolutionary models and computer tools that are frequently updated. We present here an inquiry-based course aimed at learning how to trace a phylogeny based on sequences existing in public databases. Computer tools are freely available…

  13. The Galactic Center Molecular Cloud Survey. II. A Lack of Dense Gas & Cloud Evolution along Galactic Center Orbits

    CERN Document Server

    Kauffmann, Jens; Zhang, Qizhou; Menten, Karl M; Goldsmith, Paul F; Lu, Xing; Guzmán, Andrés E; Schmiedeke, Anika

    2016-01-01

    We present the first systematic study of the density structure of clouds found in a complete sample covering all major molecular clouds in the Central Molecular Zone (CMZ; inner $\\sim{}200~\\rm{}pc$) of the Milky Way. This is made possible by using data from the Galactic Center Molecular Cloud Survey (GCMS), the first study resolving all major molecular clouds in the CMZ at interferometer angular resolution. We find that many CMZ molecular clouds have unusually shallow density gradients compared to regions elsewhere in the Milky Way. This is possibly a consequence of weak gravitational binding of the clouds. The resulting relative absence of dense gas on spatial scales $\\sim{}0.1~\\rm{}pc$ is probably one of the reasons why star formation (SF) in dense gas of the CMZ is suppressed by a factor $\\sim{}10$, compared to solar neighborhood clouds. Another factor suppressing star formation are the high SF density thresholds that likely result from the observed gas kinematics. Further, it is possible but not certain t...

  14. Refining the Indications for the Addition of Orbital Osteotomy during Anterior Cranial Base Approaches: Morphometric and Radiologic Study of the Anterior Cranial Base Osteology.

    Science.gov (United States)

    DeBattista, Juan Carlos; Andaluz, Norberto; Zuccarello, Mario; Kerr, Robert G; Keller, Jeffrey T

    2014-08-01

    Objectives In anatomic and radiologic morphometric studies, we examine a predictive method, based on preoperative imaging of the anterior cranial base, to define when addition of orbital osteotomy is warranted. Design Anatomic and radiographic study. Setting In 100 dry skulls, measurements in the anterior cranial fossa included three lines and two angles based on computerized tomography (CT) scans taken in situ and validated using frameless stereotactic navigation. The medial angle (coronal plane) was the intersection between the highest point of both orbits and the midpoint between the two frontoethmoidal sutures to each orbital roof high point. The oblique angle (sagittal plane) was the intersection at the midpoint of the limbus sphenoidale. Results No identifiable morphometric patterns were found for our classification of anterior fossae; the two-tailed distribution pattern was similar for all skulls, disproving the hypothetical correlation between visual appearance and morphometry. Orbital heights (range: 6.6-18.7 mm) showed a linear relationship with medial and oblique angles, and they had a linear distribution relative to angular increments. Orbital heights > 11 mm were associated with angles ≥ 20 degrees and more likely to benefit from orbitotomy. Conclusion Preoperative CT measurement of orbital height appears feasible for predicting when orbitotomy is needed, and it warrants further testing.

  15. DataBus-based hybrid routing approach for orbit access networks in lunar exploration

    Science.gov (United States)

    Zeng, Hui; Meng, Ke; Deng, Julia

    2012-06-01

    One of the major challenges for lunar exploration missions is how to achieve dynamic and robust routing. To reduce the development cost, it is desirable to leverage existing technologies, such as routing in mobile ad hoc networks (MANETs) and delay tolerant networks (DTN). However, these technologies are developed for the Earth environment and hence need further investigation for the lunar environment. To support robust access and dynamic mission operations, we propose a DataBus-based Hybrid Routing (DBHR) approach that combines MANET reactive routing protocol (such as AODV) and DTN-based bundle delivery. Our DBHR approach is designed for a tiered architecture where remote nodes communicate with upper-tier gateways through data carriers (DataBus) using short-range radio interfaces. Our scheme explores the (non)availability of the end-to-end path between two peers using MANET routing and provides diverse route options based upon different parameters. This interaction between hop-by-hop DTN technologies and end-to-end MANET protocol will result in a reliable and robust routing protocol for orbit access and improve the overall communication capabilities. To evaluate its performance, we implemented our proposed scheme on commercial-off-theshelf (COTS) routers with the custom OpenWRT and tailored IBR-DTN bundle protocol distribution. The on-demand service request and grant mechanisms are also developed in our implementation to allow certain DTN nodes to reserve the future access opportunities. Finally, we demonstrate the achieved capabilities and performance gains through experiments on a hardware test bed that consists of several COTS routers with our implementation.

  16. Automated global water mapping based on wide-swath orbital synthetic-aperture radar

    Science.gov (United States)

    Westerhoff, R. S.; Kleuskens, M. P. H.; Winsemius, H. C.; Huizinga, H. J.; Brakenridge, G. R.; Bishop, C.

    2013-02-01

    This paper presents an automated technique which ingests orbital synthetic-aperture radar (SAR) imagery and outputs surface water maps in near real time and on a global scale. The service anticipates future open data dissemination of water extent information using the European Space Agency's Sentinel-1 data. The classification methods used are innovative and practical and automatically calibrated to local conditions per 1 × 1° tile. For each tile, a probability distribution function in the range between being covered with water or being dry is established based on a long-term SAR training dataset. These probability distributions are conditional on the backscatter and the incidence angle. In classification mode, the probability of water coverage per pixel of 1 km × 1 km is calculated with the input of the current backscatter - incidence angle combination. The overlap between the probability distributions of a pixel being wet or dry is used as a proxy for the quality of our classification. The service has multiple uses, e.g. for water body dynamics in times of drought or for urgent inundation extent determination during floods. The service generates data systematically: it is not an on-demand service activated only for emergency response, but instead is always up-to-date and available. We validate its use in flood situations using Envisat ASAR information during the 2011 Thailand floods and the Pakistan 2010 floods and perform a first merge with a NASA near real time water product based on MODIS optical satellite imagery. This merge shows good agreement between these independent satellite-based water products.

  17. Automated global water mapping based on wide-swath orbital synthetic-aperture radar

    Directory of Open Access Journals (Sweden)

    R. S. Westerhoff

    2013-02-01

    Full Text Available This paper presents an automated technique which ingests orbital synthetic-aperture radar (SAR imagery and outputs surface water maps in near real time and on a global scale. The service anticipates future open data dissemination of water extent information using the European Space Agency's Sentinel-1 data. The classification methods used are innovative and practical and automatically calibrated to local conditions per 1 × 1° tile. For each tile, a probability distribution function in the range between being covered with water or being dry is established based on a long-term SAR training dataset. These probability distributions are conditional on the backscatter and the incidence angle. In classification mode, the probability of water coverage per pixel of 1 km × 1 km is calculated with the input of the current backscatter – incidence angle combination. The overlap between the probability distributions of a pixel being wet or dry is used as a proxy for the quality of our classification. The service has multiple uses, e.g. for water body dynamics in times of drought or for urgent inundation extent determination during floods. The service generates data systematically: it is not an on-demand service activated only for emergency response, but instead is always up-to-date and available. We validate its use in flood situations using Envisat ASAR information during the 2011 Thailand floods and the Pakistan 2010 floods and perform a first merge with a NASA near real time water product based on MODIS optical satellite imagery. This merge shows good agreement between these independent satellite-based water products.

  18. Molecular-level architectural design using benzothiadiazole-based polymers for photovoltaic applications.

    Science.gov (United States)

    Viswanathan, Vinila N; Rao, Arun D; Pandey, Upendra K; Kesavan, Arul Varman; Ramamurthy, Praveen C

    2017-01-01

    A series of low band gap, planar conjugated polymers, P1 (PFDTBT), P2 (PFDTDFBT) and P3 (PFDTTBT), based on fluorene and benzothiadiazole, was synthesized. The effect of fluorine substitution and fused aromatic spacers on the optoelectronic and photovoltaic performance was studied. The polymer, derived from dithienylated benzothiodiazole and fluorene, P1, exhibited a highest occupied molecular orbital (HOMO) energy level at -5.48 eV. Density functional theory (DFT) studies as well as experimental measurements suggested that upon substitution of the acceptor with fluorine, both the HOMO and lowest unoccupied molecular orbital (LUMO) energy levels of the resulting polymer, P2, were lowered, leading to a higher open circuit voltage and short circuit current with an overall improvement of more than 110% for the photovoltaic devices. Moreover, a decrease in the torsion angle between the units was also observed for the fluorinated polymer P2 due to the enhanced electrostatic interaction between the fluorine substituents and sulfur atoms, leading to a high hole mobility. The use of a fused π-bridge in polymer P3 for the enhancement of the planarity as compared to the P1 backbone was also studied. This enhanced planarity led to the highest observed mobility among the reported three polymers as well as to an improvement in the device efficiency by more than 40% for P3.

  19. Accelerating Atomic Orbital-based Electronic Structure Calculation via Pole Expansion plus Selected Inversion

    CERN Document Server

    Lin, Lin; Yang, Chao; He, Lixin

    2012-01-01

    We describe how to apply the recently developed pole expansion plus selected inversion (PEpSI) technique to Kohn-Sham density function theory (DFT) electronic structure calculations that are based on atomic orbital discretization. We give analytic expressions for evaluating charge density, total energy, Helmholtz free energy and atomic forces without using the eigenvalues and eigenvectors of the Kohn-Sham Hamiltonian. We also show how to update the chemical potential without using Kohn-Sham eigenvalues. The advantage of using PEpSI is that it has a much lower computational complexity than that associated with the matrix diagonalization procedure. We demonstrate the performance gain by comparing the timing of PEpSI with that of diagonalization on insulating and metallic nanotubes. For these quasi-1D systems, the complexity of PEpSI is linear with respect to the number of atoms. This linear scaling can be observed in our computational experiments when the number of atoms in a nanotube is larger than a few hundr...

  20. Spin Filter Based on an Aharonov-Bohm Interferometer with Rashba Spin-Orbit Effect

    Institute of Scientific and Technical Information of China (English)

    FANG Ming; SUN Lian-Liang

    2008-01-01

    We propose a spin filter based on both the quantum interference and the Rashba spin-orbit (RSO) effects. This spin filter consists of a Aharonov-Bohm (AB) interferometer with two quantum dots (QDs) inserted in its arms.The influences of a magnetic flux ψ threading through the AB ring and the RSO interaction inside the two QDs are taken into account by using the nonequilibrium Green's function technique. Due to the existence of the RSO interaction, the electrons flowing through different arms of the ring will acquire a spin-dependent phase factor in the linewidth matrix elements. This phase factor, combined with the influence of the magnetic flux, will induce a spin-dependent electron transport through the device. Moreover, we show that by tuning the magnetic flux,the RSO strength and the inter-dot tunnelling coupling strength, a pure spin-up or spin-down conductance can be obtained when a spin-unpolarized current is injected from the external leads, which can be used to filter the electron spin.

  1. Three-Dimensional Simultaneous Arbitrary-Way Orbital Angular Momentum Generator Based on Transformation Optics

    Science.gov (United States)

    Zhang, Chen; Deng, Li; Hong, Wei Jun; Jiang, Wei Xiang; Zhu, Jian Feng; Zhou, Mi; Wang, Ling; Li, Shu Fang; Peng, Biao

    2016-12-01

    In wireless communications, people utilize the technology of diversity against multipath fading, so as to improve the reliability of communication equipment. One of the long-standing problems in diversity antennas is the limited number of diversity in a certain space. In this paper, we provide a solution to this issue by a three-dimensional (3D) simultaneous arbitrary-way orbital angular momentum (OAM) generator (3D SAWOG) based on transformation optics. The proposed 3D SAWOG consists of a metamaterial block and a group of transformation cylinders, by which arbitrary-way planar wavefronts can be converted to helical wavefronts with various topological charges simultaneously. The 2D four-way OAM generator and the 3D SAWOG are analyzed, designed, and simulated. The simulation results validate the performance of a 3D SAWOG successfully, indicating that the proposed model possess a high mode purity and expansibility. The SAWOG can be used as a novel diversity antenna array due to the orthogonal property among different modes, which could provide more degrees of freedom than traditional dual-polarization antennas, further improving the reliability of the communication systems.

  2. Accelerating Atomic Orbital-based Electronic Structure Calculation via Pole Expansion plus Selected Inversion

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Lin; Chen, Mohan; Yang, Chao; He, Lixin

    2012-02-10

    We describe how to apply the recently developed pole expansion plus selected inversion (PEpSI) technique to Kohn-Sham density function theory (DFT) electronic structure calculations that are based on atomic orbital discretization. We give analytic expressions for evaluating charge density, total energy, Helmholtz free energy and atomic forces without using the eigenvalues and eigenvectors of the Kohn-Sham Hamiltonian. We also show how to update the chemical potential without using Kohn-Sham eigenvalues. The advantage of using PEpSI is that it has a much lower computational complexity than that associated with the matrix diagonalization procedure. We demonstrate the performance gain by comparing the timing of PEpSI with that of diagonalization on insulating and metallic nanotubes. For these quasi-1D systems, the complexity of PEpSI is linear with respect to the number of atoms. This linear scaling can be observed in our computational experiments when the number of atoms in a nanotube is larger than a few hundreds. Both the wall clock time and the memory requirement of PEpSI is modest. This makes it even possible to perform Kohn-Sham DFT calculations for 10,000-atom nanotubes on a single processor. We also show that the use of PEpSI does not lead to loss of accuracy required in a practical DFT calculation.

  3. Disorder and the extent of polymerization in calcium silicate and aluminosilicate glasses: O-17 NMR results and quantum chemical molecular orbital calculations

    Science.gov (United States)

    Lee, Sung Keun; Stebbins, Jonathan F.

    2006-08-01

    Estimation of the framework connectivity and the atomic structure of depolymerized silicate melts and glasses (NBO/T > 0) remains a difficult question in high-temperature geochemistry relevant to magmatic processes and glass science. Here, we explore the extent of disorder and the nature of polymerization in binary Ca-silicate and ternary Ca-aluminosilicate glasses with varying NBO/T (from 0 to 2.67) using O-17 NMR at two different magnetic fields of 9.4 and 14.1 T in conjunction with quantum chemical calculations. Non-random distributions among framework cations (Si and Al) are demonstrated in the variation of relative populations of oxygen sites with NBO/T. The proportion of non-bridging oxygen (NBO, Ca-O-Si) in the binary and ternary aluminosilicate glasses increases with NBO/T. While the trend is consistent with predictions from composition, the detailed fractions apparently deviate from the predicted values, suggesting further complications in the nature of polymerization. The proportion of each bridging oxygen in the glasses also varies with NBO/T. The fractions of Al-O-Si and Al-O-Al increase with increasing polymerization as CaO is replaced with Al 2O 3, while that of Si-O-Si seems to decrease, implying that activity of silica may decrease from calcium silicate to polymerized aluminosilicates (X=constant). Quantum chemical molecular orbital calculations based on density functional theory show that a silicate chain with Al-NBO (Ca-O-Al) has an energy penalty (calculated cluster energy difference) of about 108 kJ/mol compared with the cluster with Ca-O-Si, consistent with preferential depolymerization of Si-networks, reported in an earlier O-17 NMR study [Allwardt, J., Lee, S.K., Stebbins, J.F., 2003. Bonding preferences of non-bridging oxygens in calcium aluminosilicate glass: Evidence from O-17 MAS and 3QMAS NMR on calcium aluminate glass. Am. Mineral.88, 949-954]. These prominent types of non-randomness in the distributions suggest significant chemical

  4. Optimal separable bases and molecular collisions

    Energy Technology Data Exchange (ETDEWEB)

    Poirier, L W [Univ. of California, Berkeley, CA (United States)

    1997-12-01

    A new methodology is proposed for the efficient determination of Green`s functions and eigenstates for quantum systems of two or more dimensions. For a given Hamiltonian, the best possible separable approximation is obtained from the set of all Hilbert space operators. It is shown that this determination itself, as well as the solution of the resultant approximation, are problems of reduced dimensionality for most systems of physical interest. Moreover, the approximate eigenstates constitute the optimal separable basis, in the sense of self-consistent field theory. These distorted waves give rise to a Born series with optimized convergence properties. Analytical results are presented for an application of the method to the two-dimensional shifted harmonic oscillator system. The primary interest however, is quantum reactive scattering in molecular systems. For numerical calculations, the use of distorted waves corresponds to numerical preconditioning. The new methodology therefore gives rise to an optimized preconditioning scheme for the efficient calculation of reactive and inelastic scattering amplitudes, especially at intermediate energies. This scheme is particularly suited to discrete variable representations (DVR`s) and iterative sparse matrix methods commonly employed in such calculations. State to state and cumulative reactive scattering results obtained via the optimized preconditioner are presented for the two-dimensional collinear H + H{sub 2} {yields} H{sub 2} + H system. Computational time and memory requirements for this system are drastically reduced in comparison with other methods, and results are obtained for previously prohibitive energy regimes.

  5. Optimal separable bases and molecular collisions

    Energy Technology Data Exchange (ETDEWEB)

    Poirier, Lionel W. [Univ. of California, Berkeley, CA (United States)

    1997-12-01

    A new methodology is proposed for the efficient determination of Green`s functions and eigenstates for quantum systems of two or more dimensions. For a given Hamiltonian, the best possible separable approximation is obtained from the set of all Hilbert space operators. It is shown that this determination itself, as well as the solution of the resultant approximation, are problems of reduced dimensionality for most systems of physical interest. Moreover, the approximate eigenstates constitute the optimal separable basis, in the sense of self-consistent field theory. These distorted waves give rise to a Born series with optimized convergence properties. Analytical results are presented for an application of the method to the two-dimensional shifted harmonic oscillator system. The primary interest however, is quantum reactive scattering in molecular systems. For numerical calculations, the use of distorted waves corresponds to numerical preconditioning. The new methodology therefore gives rise to an optimized preconditioning scheme for the efficient calculation of reactive and inelastic scattering amplitudes, especially at intermediate energies. This scheme is particularly suited to discrete variable representations (DVR`s) and iterative sparse matrix methods commonly employed in such calculations. State to state and cumulative reactive scattering results obtained via the optimized preconditioner are presented for the two-dimensional collinear H + H2 → H2 + H system. Computational time and memory requirements for this system are drastically reduced in comparison with other methods, and results are obtained for previously prohibitive energy regimes.

  6. Molecular and Clinical Based Cardiovascular Care Program

    Science.gov (United States)

    2010-11-01

    vegetarian diet, exercise, stress management, group support), 186 subjects enrolled and 144 participated for 1 year. ■ RESULTS: At 3 months and 1...scoring system based on essential elements of the lacto-ovo vegetarian dietary pattern. Exercise and stress management adherence were not capped at...base- line low-fat diet and further decreased their dietary fat intake to 8.8% of total energy with adherence to a lacto-ovo vegetarian diet. The

  7. Comparison of Orbit-Based and Time-Offset-Based Geometric Correction Models for SAR Satellite Imagery Based on Error Simulation.

    Science.gov (United States)

    Hong, Seunghwan; Choi, Yoonjo; Park, Ilsuk; Sohn, Hong-Gyoo

    2017-01-17

    Geometric correction of SAR satellite imagery is the process to adjust the model parameters that define the relationship between ground and image coordinates. To achieve sub-pixel geolocation accuracy, the adoption of the appropriate geometric correction model and parameters is important. Until now, various geometric correction models have been developed and applied. However, it is still difficult for general users to adopt a suitable geometric correction models having sufficient precision. In this regard, this paper evaluated the orbit-based and time-offset-based models with an error simulation. To evaluate the geometric correction models, Radarsat-1 images that have large errors in satellite orbit information and TerraSAR-X images that have a reportedly high accuracy in satellite orbit and sensor information were utilized. For Radarsat-1 imagery, the geometric correction model based on the satellite position parameters has a better performance than the model based on time-offset parameters. In the case of the TerraSAR-X imagery, two geometric correction models had similar performance and could ensure sub-pixel geolocation accuracy.

  8. Comparison of Orbit-Based and Time-Offset-Based Geometric Correction Models for SAR Satellite Imagery Based on Error Simulation

    Science.gov (United States)

    Hong, Seunghwan; Choi, Yoonjo; Park, Ilsuk; Sohn, Hong-Gyoo

    2017-01-01

    Geometric correction of SAR satellite imagery is the process to adjust the model parameters that define the relationship between ground and image coordinates. To achieve sub-pixel geolocation accuracy, the adoption of the appropriate geometric correction model and parameters is important. Until now, various geometric correction models have been developed and applied. However, it is still difficult for general users to adopt a suitable geometric correction models having sufficient precision. In this regard, this paper evaluated the orbit-based and time-offset-based models with an error simulation. To evaluate the geometric correction models, Radarsat-1 images that have large errors in satellite orbit information and TerraSAR-X images that have a reportedly high accuracy in satellite orbit and sensor information were utilized. For Radarsat-1 imagery, the geometric correction model based on the satellite position parameters has a better performance than the model based on time-offset parameters. In the case of the TerraSAR-X imagery, two geometric correction models had similar performance and could ensure sub-pixel geolocation accuracy. PMID:28106729

  9. Comparison of Orbit-Based and Time-Offset-Based Geometric Correction Models for SAR Satellite Imagery Based on Error Simulation

    Directory of Open Access Journals (Sweden)

    Seunghwan Hong

    2017-01-01

    Full Text Available Geometric correction of SAR satellite imagery is the process to adjust the model parameters that define the relationship between ground and image coordinates. To achieve sub-pixel geolocation accuracy, the adoption of the appropriate geometric correction model and parameters is important. Until now, various geometric correction models have been developed and applied. However, it is still difficult for general users to adopt a suitable geometric correction models having sufficient precision. In this regard, this paper evaluated the orbit-based and time-offset-based models with an error simulation. To evaluate the geometric correction models, Radarsat-1 images that have large errors in satellite orbit information and TerraSAR-X images that have a reportedly high accuracy in satellite orbit and sensor information were utilized. For Radarsat-1 imagery, the geometric correction model based on the satellite position parameters has a better performance than the model based on time-offset parameters. In the case of the TerraSAR-X imagery, two geometric correction models had similar performance and could ensure sub-pixel geolocation accuracy.

  10. Vibrational spectra (FT-IR, FT-Raman), frontier molecular orbital, first hyperpolarizability, NBO analysis and thermodynamics properties of Piroxicam by HF and DFT methods.

    Science.gov (United States)

    Suresh, S; Gunasekaran, S; Srinivasan, S

    2015-03-05

    The solid phase FT-IR and FT-Raman spectra of 4-Hydroxy-2-methyl-N-(2-pyridinyl)-2H-1,2-benzothiazine-3-carboxamide-1,1-dioxide (Piroxicam) have been recorded in the region 4000-400 and 4000-100cm(-1) respectively. The molecular geometry, harmonic vibrational frequencies and bonding features of piroxicam in the ground state have been calculated by Hartree-Fock (HF) and density functional theory (DFT) methods using 6-311++G(d,p) basis set. The calculated harmonic vibrational frequencies are scaled and they are compared with experimental obtained by FT-IR and FT-Raman spectra. A detailed interpretation of the vibrational spectra of the title compound has been made on the basis of the calculated potential energy distribution (PED). The electronic properties, such as HOMO and LUMO energies, molecular electrostatic potential (MESP) are also performed. The linear polarizability (α) and the first order hyper polarizability (β) values of the title compound have been computed. The molecular stability arising from hyper conjugative interaction, charge delocalization has been analyzed using natural bond orbital (NBO) analysis.

  11. Vibrational spectra (FT-IR, FT-Raman), frontier molecular orbital, first hyperpolarizability, NBO analysis and thermodynamics properties of Piroxicam by HF and DFT methods

    Science.gov (United States)

    Suresh, S.; Gunasekaran, S.; Srinivasan, S.

    2015-03-01

    The solid phase FT-IR and FT-Raman spectra of 4-Hydroxy-2-methyl-N-(2-pyridinyl)-2H-1,2-benzothiazine-3-carboxamide-1,1-dioxide (Piroxicam) have been recorded in the region 4000-400 and 4000-100 cm-1 respectively. The molecular geometry, harmonic vibrational frequencies and bonding features of piroxicam in the ground state have been calculated by Hartree-Fock (HF) and density functional theory (DFT) methods using 6-311++G(d,p) basis set. The calculated harmonic vibrational frequencies are scaled and they are compared with experimental obtained by FT-IR and FT-Raman spectra. A detailed interpretation of the vibrational spectra of the title compound has been made on the basis of the calculated potential energy distribution (PED). The electronic properties, such as HOMO and LUMO energies, molecular electrostatic potential (MESP) are also performed. The linear polarizability (α) and the first order hyper polarizability (β) values of the title compound have been computed. The molecular stability arising from hyper conjugative interaction, charge delocalization has been analyzed using natural bond orbital (NBO) analysis.

  12. Vibrational spectra and ab initio molecular orbital calculations of the novel anti-cancer drug combretastatin A-4 prodrug

    Science.gov (United States)

    James, C.; Pettit, G. R.; Nielsen, O. F.; Jayakumar, V. S.; Joe, I. Hubert

    2008-10-01

    The NIR-FT Raman and FT-IR spectral studies of the novel antineoplastic and antiangiogenesis substance comprestatin A-4 prodrug (CA4P) were carried out. The equilibrium geometry, various bonding features and harmonic vibrational frequencies of CA4P have been investigated with the help of B3LYP density functional theory (DFT) method. The most preferred cis-configuration for its bioactivity has been demonstrated on the basis of torsional potential energy surface (PES) scan studies. Stability of the molecule arising from hyperconjugative interactions leading to its bioactivity, charge delocalization and mesomeric effects have been analyzed using natural bond orbital (NBO) analysis. Detailed assignments of the vibrational spectra have been made with the aid of theoretically predicted vibrational frequencies. The optimized geometry shows near-planarity of phenyl rings and perpendicular conformation of meta substituted methoxy group. The vibrational analysis confirms the differently acting ring modes, steric repulsion, π conjugation and back-donation.

  13. Molecular calculations of excitation energies and (hyper)polarizabilities with a statistical average of orbital model exchange-correlation potentials

    Science.gov (United States)

    Schipper, P. R. T.; Gritsenko, O. V.; van Gisbergen, S. J. A.; Baerends, E. J.

    2000-01-01

    An approximate Kohn-Sham exchange-correlation potential νxcSAOP is developed with the method of statistical averaging of (model) orbital potentials (SAOP) and is applied to the calculation of excitation energies as well as of static and frequency-dependent multipole polarizabilities and hyperpolarizabilities within time-dependent density functional theory (TDDFT). νxcSAOP provides high quality results for all calculated response properties and a substantial improvement upon the local density approximation (LDA) and the van Leeuwen-Baerends (LB) potentials for the prototype molecules CO, N2, CH2O, and C2H4. For the first three molecules and the lower excitations of the C2H4 the average error of the vertical excitation energies calculated with νxcSAOP approaches the benchmark accuracy of 0.1 eV for the electronic spectra.

  14. Molecular orbital imaging of the acetone S2 excited state using time-resolved (e, 2e) electron momentum spectroscopy.

    Science.gov (United States)

    Yamazaki, Masakazu; Oishi, Keiya; Nakazawa, Hiroyuki; Zhu, Chaoyuan; Takahashi, Masahiko

    2015-03-13

    We report a time-resolved (e, 2e) experiment on the deuterated acetone molecule in the S2 Rydberg state with a lifetime of 13.5 ps. The acetone S2 state was prepared by a 195 nm pump laser and probed with electron momentum spectroscopy using a 1.2 keV incident electron beam of 1 ps temporal width. In spite of the low data statistics as well as of the limited time resolution (±35  ps) due to velocity mismatch, the experimental results clearly demonstrate that electron momentum spectroscopy measurements of short-lived transient species are feasible, opening the door to time-resolved orbital imaging in momentum space.

  15. Real-Time PPP Based on the Coupling Estimation of Clock Bias and Orbit Error with Broadcast Ephemeris

    Directory of Open Access Journals (Sweden)

    Shuguo Pan

    2015-07-01

    Full Text Available Satellite orbit error and clock bias are the keys to precise point positioning (PPP. The traditional PPP algorithm requires precise satellite products based on worldwide permanent reference stations. Such an algorithm requires considerable work and hardly achieves real-time performance. However, real-time positioning service will be the dominant mode in the future. IGS is providing such an operational service (RTS and there are also commercial systems like Trimble RTX in operation. On the basis of the regional Continuous Operational Reference System (CORS, a real-time PPP algorithm is proposed to apply the coupling estimation of clock bias and orbit error. The projection of orbit error onto the satellite-receiver range has the same effects on positioning accuracy with clock bias. Therefore, in satellite clock estimation, part of the orbit error can be absorbed by the clock bias and the effects of residual orbit error on positioning accuracy can be weakened by the evenly distributed satellite geometry. In consideration of the simple structure of pseudorange equations and the high precision of carrier-phase equations, the clock bias estimation method coupled with orbit error is also improved. Rovers obtain PPP results by receiving broadcast ephemeris and real-time satellite clock bias coupled with orbit error. By applying the proposed algorithm, the precise orbit products provided by GNSS analysis centers are rendered no longer necessary. On the basis of previous theoretical analysis, a real-time PPP system was developed. Some experiments were then designed to verify this algorithm. Experimental results show that the newly proposed approach performs better than the traditional PPP based on International GNSS Service (IGS real-time products. The positioning accuracies of the rovers inside and outside the network are improved by 38.8% and 36.1%, respectively. The PPP convergence speeds are improved by up to 61.4% and 65.9%. The new approach can

  16. Real-Time PPP Based on the Coupling Estimation of Clock Bias and Orbit Error with Broadcast Ephemeris.

    Science.gov (United States)

    Pan, Shuguo; Chen, Weirong; Jin, Xiaodong; Shi, Xiaofei; He, Fan

    2015-07-22

    Satellite orbit error and clock bias are the keys to precise point positioning (PPP). The traditional PPP algorithm requires precise satellite products based on worldwide permanent reference stations. Such an algorithm requires considerable work and hardly achieves real-time performance. However, real-time positioning service will be the dominant mode in the future. IGS is providing such an operational service (RTS) and there are also commercial systems like Trimble RTX in operation. On the basis of the regional Continuous Operational Reference System (CORS), a real-time PPP algorithm is proposed to apply the coupling estimation of clock bias and orbit error. The projection of orbit error onto the satellite-receiver range has the same effects on positioning accuracy with clock bias. Therefore, in satellite clock estimation, part of the orbit error can be absorbed by the clock bias and the effects of residual orbit error on positioning accuracy can be weakened by the evenly distributed satellite geometry. In consideration of the simple structure of pseudorange equations and the high precision of carrier-phase equations, the clock bias estimation method coupled with orbit error is also improved. Rovers obtain PPP results by receiving broadcast ephemeris and real-time satellite clock bias coupled with orbit error. By applying the proposed algorithm, the precise orbit products provided by GNSS analysis centers are rendered no longer necessary. On the basis of previous theoretical analysis, a real-time PPP system was developed. Some experiments were then designed to verify this algorithm. Experimental results show that the newly proposed approach performs better than the traditional PPP based on International GNSS Service (IGS) real-time products. The positioning accuracies of the rovers inside and outside the network are improved by 38.8% and 36.1%, respectively. The PPP convergence speeds are improved by up to 61.4% and 65.9%. The new approach can change the

  17. Vision-based localization for on-orbit servicing of a partially cooperative satellite

    Science.gov (United States)

    Oumer, Nassir W.; Panin, Giorgio; Mülbauer, Quirin; Tseneklidou, Anastasia

    2015-12-01

    This paper proposes ground-in-the-loop, model-based visual localization system based on transmitted images to ground, to aid rendezvous and docking maneuvers between a servicer and a target satellite. In particular, we assume to deal with a partially cooperative target, i.e. passive and without fiducial markers, but supposed at least to keep a controlled attitude, up to small fluctuations, so that the approach mainly involves translational motion. For the purpose of localization, video cameras provide an effective and relatively inexpensive solution, working at a wide range of distances with an increasing accuracy and robustness during the approach. However, illumination conditions in space are especially challenging, due to the direct sunlight exposure and to the glossy surface of a satellite, that creates strong reflections and saturations and therefore a high level of background clutter and missing detections. We employ a monocular camera for mid-range tracking (20 - 5 m) and stereo camera at close-range (5 - 0.5 m), with the respective detection and tracking methods, both using intensity edges and robustly dealing with the above issues. Our tracking system has been extensively verified at the facility of the European Proximity Operations Simulator (EPOS) of DLR, which is a very realistic ground simulation able to reproduce sunlight conditions through a high power floodlight source, satellite surface properties using multilayer insulation foils, as well as orbital motion trajectories with ground-truth data, by means of two 6 DOF industrial robots. Results from this large dataset show the effectiveness and robustness of our method against the above difficulties.

  18. Influence of electron correlation and degeneracy on the Fukui matrix and extension of frontier molecular orbital theory to correlated quantum chemical methods.

    Science.gov (United States)

    Bultinck, Patrick; Van Neck, Dimitri; Acke, Guillaume; Ayers, Paul W

    2012-02-21

    The Fukui function is considered as the diagonal element of the Fukui matrix in position space, where the Fukui matrix is the derivative of the one particle density matrix (1DM) with respect to the number of electrons. Diagonalization of the Fukui matrix, expressed in an orthogonal orbital basis, explains why regions in space with negative Fukui functions exist. Using a test set of molecules, electron correlation is found to have a remarkable effect on the eigenvalues of the Fukui matrix. The Fukui matrices at the independent electron model level are mathematically proven to always have an eigenvalue equal to exactly unity while the rest of the eigenvalues possibly differ from zero but sum to zero. The loss of idempotency of the 1DM at correlated levels of theory causes the loss of these properties. The influence of electron correlation is examined in detail and the frontier molecular orbital concept is extended to correlated levels of theory by defining it as the eigenvector of the Fukui matrix with the largest eigenvalue. The effect of degeneracy on the Fukui matrix is examined in detail, revealing that this is another way by which the unity eigenvalue and perfect pairing of eigenvalues can disappear.

  19. Molecular structure, Normal Coordinate Analysis, harmonic vibrational frequencies, Natural Bond Orbital, TD-DFT calculations and biological activity analysis of antioxidant drug 7-hydroxycoumarin

    Science.gov (United States)

    Sebastian, S.; Sylvestre, S.; Jayarajan, D.; Amalanathan, M.; Oudayakumar, K.; Gnanapoongothai, T.; Jayavarthanan, T.

    2013-01-01

    In this work, we report harmonic vibrational frequencies, molecular structure, NBO and HOMO, LUMO analysis of Umbelliferone also known as 7-hydroxycoumarin (7HC). The optimized geometric bond lengths and bond angles obtained by computation (monomer and dimmer) shows good agreement with experimental XRD data. Harmonic frequencies of 7HC were determined and analyzed by DFT utilizing 6-311+G(d,p) as basis set. The assignments of the vibrational spectra have been carried out with the help of Normal Coordinate Analysis (NCA) following the Scaled Quantum Mechanical Force Field Methodology (SQMFF). The change in electron density (ED) in the σ* and π* antibonding orbitals and stabilization energies E(2) have been calculated by Natural Bond Orbital (NBO) analysis to give clear evidence of stabilization originating in the hyperconjugation of hydrogen-bonded interaction. The energy and oscillator strength calculated by Time-Dependent Density Functional Theory (TD-DFT) complements with the experimental findings. The simulated spectra satisfactorily coincides with the experimental spectra. Microbial activity of studied compounds was tested against Staphylococcus aureus, Streptococcus pyogenes, Bacillus subtilis, Escherichia coli, Psuedomonas aeruginosa, Klebsiella pneumoniae, Proteus mirabilis, Shigella flexneri, Salmonella typhi and Enterococcus faecalis.

  20. Orbital-free ab initio molecular dynamics study of the static structure and dynamic properties of the free liquid surface of Sn

    Directory of Open Access Journals (Sweden)

    del Rio B. G.

    2017-01-01

    Full Text Available We report results of an orbital-free ab initio molecular dynamics (OF-AIMD study of the free liquid surface (FLS of Sn at 1000 K and 600 K. A key ingredient in the OF-AIMD method is the local pseudopotential describing the ions-valence electrons interaction. We have used a force-matching method to derive a local pseudopotential suitable to account for the variation of the forces from the bulk to the FLS. We obtain very good results for structural properties, such as the reflectivity, including the characteristic shoulder it presents in x-ray experiments. Moreover we have been able to study ab initio for the first time the evolution in some dynamical properties as we move from the central region, where the system behaves like the bulk liquid, to the FLS.

  1. Orbital-free ab initio molecular dynamics study of the static structure and dynamic properties of the free liquid surface of Sn

    Science.gov (United States)

    del Rio, B. G.; González, L. E.

    2017-08-01

    We report results of an orbital-free ab initio molecular dynamics (OF-AIMD) study of the free liquid surface (FLS) of Sn at 1000 K and 600 K. A key ingredient in the OF-AIMD method is the local pseudopotential describing the ions-valence electrons interaction. We have used a force-matching method to derive a local pseudopotential suitable to account for the variation of the forces from the bulk to the FLS. We obtain very good results for structural properties, such as the reflectivity, including the characteristic shoulder it presents in x-ray experiments. Moreover we have been able to study ab initio for the first time the evolution in some dynamical properties as we move from the central region, where the system behaves like the bulk liquid, to the FLS.

  2. Small Atomic Orbital Basis Set First-Principles Quantum Chemical Methods for Large Molecular and Periodic Systems: A Critical Analysis of Error Sources.

    Science.gov (United States)

    Sure, Rebecca; Brandenburg, Jan Gerit; Grimme, Stefan

    2016-04-01

    In quantum chemical computations the combination of Hartree-Fock or a density functional theory (DFT) approximation with relatively small atomic orbital basis sets of double-zeta quality is still widely used, for example, in the popular B3LYP/6-31G* approach. In this Review, we critically analyze the two main sources of error in such computations, that is, the basis set superposition error on the one hand and the missing London dispersion interactions on the other. We review various strategies to correct those errors and present exemplary calculations on mainly noncovalently bound systems of widely varying size. Energies and geometries of small dimers, large supramolecular complexes, and molecular crystals are covered. We conclude that it is not justified to rely on fortunate error compensation, as the main inconsistencies can be cured by modern correction schemes which clearly outperform the plain mean-field methods.

  3. Using simple molecular orbital calculations to predict disease: fast DFT methods applied to enzymes implicated in PKU, Parkinson's disease and Obsessive Compulsive Disorder

    Science.gov (United States)

    Hofto, Laura; Hofto, Meghan; Cross, Jessica; Cafiero, Mauricio

    2007-09-01

    Many diseases can be traced to point mutations in the DNA coding for specific enzymes. These point mutations result in the change of one amino acid residue in the enzyme. We have developed a model using simple molecular orbital calculations which can be used to quantitatively determine the change in interaction between the enzyme's active site and necessary ligands upon mutation. We have applied this model to three hydroxylase proteins: phenylalanine hydroxylase, tyrosine hydroxylase, and tryptophan hydroxylase, and we have obtained excellent correlation between our results and observed disease symptoms. Furthermore, we are able to use this agreement as a baseline to screen other mutations which may also cause onset of disease symptoms. Our focus is on systems where the binding is due largely to dispersion, which is much more difficult to model inexpensively than pure electrostatic interactions. Our calculations are run in parallel on a sixteen processor cluster of 64-bit Athlon processors.

  4. CNDO/SCF molecular orbital structural studies and charge transfer complex formation between 4,4’-dimethoxydiquinone and uracil

    Directory of Open Access Journals (Sweden)

    Anwar S. El-Shahawy

    2004-12-01

    Full Text Available Through CNDO/SCF molecular orbital calculations, the structure of 4,4’-dimethoxy- diquinone (DQ has been discussed and compared with some related compounds. The electron transfer between DQ and uracil was studied in ethanol as an interaction medium. The ionization potentials and the electron affinities of the studied molecules have been calculated in addition to their charge densities giving the columbic potential energy of the donor and acceptor. The experimental charge transfer band lies at 500 nm. The electronic transitions have been calculated for the singlet and triplet transitions in uracil and DQ molecules using the SCF eigenvectors of the two HOMO’s, ψn-1 and ψ n, and the two LUMO’s, ψ n+1 and ψ n+2, using CI theory. The calculated electronic transitions are compared with those of the experimental data to verify the non-planar structure of the DQ molecule.

  5. Ion-molecule interactions in solutions of lithium perchlorate in propylene carbonate + diethyl carbonate mixtures: an IR and molecular orbital study.

    Science.gov (United States)

    Wang, Jianji; Wu, Yanping; Xuan, Xiaopeng; Wang, Hanqing

    2002-08-01

    FTIR spectra have been recorded and analyzed for solutions of lithium perchlorate in propylene carbonate (PC), diethyl carbonate (DEC), and PC + DEC mixtures. It has been shown that the carbonyl stretch bands for PC and DEC are very sensitive to the interaction between Li+ and the solvent molecules. They split with addition of LiClO4, indicating a strong interaction of Li+ with PC and DEC through the oxygen group of PC and both oxygen and ether oxygen atoms of DEC. In conjunction with molecular orbital calculation, the optimized geometries of solvation are given. In addition, solvent separated ion pairs and contact ion pairs were observed in LiClO4/DEC solutions, and no preferential solvation of Li+ in LiClO4/PC + DEC solutions were detected.

  6. Unidirectional Light-Driven Molecular Motors Based on Overcrowded Alkenes

    NARCIS (Netherlands)

    Cnossen, Arjen; Browne, Wesley R.; Feringa, Ben L.; Credi, Alberto; Silvi, Serena; Venturi, Margherita

    2014-01-01

    Over the last two decades, interest in nanotechnology has led to the design and synthesis of a toolbox of nanoscale versions of macroscopic devices and components. In molecular nanotechnology, linear motors based on rotaxanes and rotary motors based on overcrowded alkenes are particularly promising

  7. Self-Propagating Assembly of a Molecular-Based Multilayer

    Energy Technology Data Exchange (ETDEWEB)

    Motiei,L.; Altman, M.; Gupta, T.; Lupo, F.; Gulino, A.; Evmenenko, G.; Dutta, P.; van der Boom, M.

    2008-01-01

    Accelerated growth of a molecular-based material that is an active participant in its continuing self-propagated assembly has been demonstrated. This nonlinear growth process involves diffusion of palladium into a network consisting of metal-based chromophores linked via palladium.

  8. Development of a Silicon Carbide Molecular Beam Nozzle for Simulation Planetary Flybys and Low-Earth Orbit

    Science.gov (United States)

    Patrick, E. L.; Earle, G. D.; Kasprzak, W. T.; Mahaffy, Paul R.

    2008-01-01

    From commercial origins as a molybdenum molecular beam nozzle, a ceramic nozzle of silicon carbide (SiC) was developed for space environment simulation. The nozzle is mechanically stable under extreme conditions of temperature and pressure. A heated, continuous, supersonically-expanded hydrogen beam with a 1% argon seed produced an argon beam component of nearly 4 km/s, with an argon flux exceeding 1x1014 /cm2.s. This nozzle was part of a molecular beam machine used in the Atmospheric Experiments Branch at NASA Goddard Space Flight Center to characterize the performance of the University of Texas at Dallas Ram Wind Sensor (RWS) aboard the Air Force Communications/Navigation Outage Forecasting System (C/NOFS) launched in the Spring of 2008.

  9. PITCH ANGLE RESTRICTIONS IN LATE-TYPE SPIRAL GALAXIES BASED ON CHAOTIC AND ORDERED ORBITAL BEHAVIOR

    Energy Technology Data Exchange (ETDEWEB)

    Perez-Villegas, A.; Pichardo, B.; Moreno, E.; Peimbert, A. [Instituto de Astronomia, Universidad Nacional Autonoma de Mexico, A.P. 70-264, 04510 Mexico D.F. (Mexico); Velazquez, H. M., E-mail: barbara@astroscu.unam.mx [Observatorio Astronomico Nacional, Universidad Nacional Autonoma de Mexico, Apdo. Postal 877, 22800 Ensenada (Mexico)

    2012-01-20

    We built models for low bulge mass spiral galaxies (late type as defined by the Hubble classification) using a three-dimensional self-gravitating model for spiral arms, and analyzed the orbital dynamics as a function of pitch angle, ranging from 10 Degree-Sign to 60 Degree-Sign . Indirectly testing orbital self-consistency, we search for the main periodic orbits and studied the density response. For pitch angles up to approximately {approx}20 Degree-Sign , the response closely supports the potential readily permitting the presence of long-lasting spiral structures. The density response tends to 'avoid' larger pitch angles in the potential by keeping smaller pitch angles in the corresponding response. Spiral arms with pitch angles larger than {approx}20 Degree-Sign would not be long-lasting structures but would rather be transient. On the other hand, from an extensive orbital study in phase space, we also find that for late-type galaxies with pitch angles larger than {approx}50 Degree-Sign , chaos becomes pervasive, destroying the ordered phase space surrounding the main stable periodic orbits and even destroying them. This result is in good agreement with observations of late-type galaxies, where the maximum observed pitch angle is {approx}50 Degree-Sign .

  10. Environmental Phosphorus Recovery Based on Molecular Bioscavengers

    DEFF Research Database (Denmark)

    Gruber, Mathias Felix

    Phosphorus is a ubiquitous element of all known life and as such it is found throughout numerous key molecules related to various cellular functions. The supply of phosphorus is tightly linked to global food security, since phosphorus is used to produce agricultural fertilizers, without which...... it would not be possible to feed the world population. Sadly, the current supply of phosphorus is based on the gradual depletion of limited fossil reserves, and some estimates predict that within 15-25 years we will consume more phosphorus than we can produce. There is therefore a strong international...

  11. Molecular spintronics based on single-molecule magnets composed of multiple-decker phthalocyaninato terbium(III) complex.

    Science.gov (United States)

    Katoh, Keiichi; Isshiki, Hironari; Komeda, Tadahiro; Yamashita, Masahiro

    2012-06-01

    Unlike electronics, which is based on the freedom of the charge of an electron whose memory is volatile, spintronics is based on the freedom of the charge, spin, and orbital of an electron whose memory is non-volatile. Although in most GMR, TMR, and CMR systems, bulk or classical magnets that are composed of transition metals are used, this Focus Review considers the growing use of single-molecule magnets (SMMs) that are composed of multinuclear metal complexes and nanosized magnets, which exhibit slow magnetic-relaxation processes and quantum tunneling. Molecular spintronics, which combines spintronics and molecular electronics, is an emerging field of research. Using molecules is advantageous because their electronic and magnetic properties can be manipulated under specific conditions. Herein, recent developments in [LnPc]-based multiple-decker SMMs on surfaces for molecular spintronic devices are presented. First, we discuss the strategies for preparing single-molecular-memory devices by using SMMs. Next, we focus on the switching of the Kondo signal of [LnPc]-based multiple-decker SMMs that are adsorbed onto surfaces, their characterization by using STM and STS, and the relationship between the molecular structure, the electronic structure, and the Kondo resonance of [TbPc(2)]. Finally, the field-effect-transistor (FET) properties of surface-adsorbed [LnPc(2)] and [Ln(2)Pc(3)] cast films are reported, which is the first step towards controlling SMMs through their spins for applications in single-molecular memory and spintronics devices.

  12. Molecular orbital studies (hardness, chemical potential, electronegativity and electrophilicity), vibrational spectroscopic investigation and normal coordinate analysis of 5-{1-hydroxy-2-[(propan-2-yl)amino]ethyl}benzene-1,3-diol.

    Science.gov (United States)

    Muthu, S; Renuga, S

    2014-01-24

    FT-IR and FT-Raman spectra of 5-{1-hydroxy-2-[(propan-2-yl) amino] ethyl} benzene-1,3-diol (abbrevi- 54 ated as HPAEBD) were recorded in the region 4000-450 cm(-1) and 4000-100 cm(-1) respectively. The structure of the molecule was optimized and the structural characteristics were determined by density functional theory (B3LYP) and HF method with 6-31 G(d,p) as basis set. The theoretical wave numbers were scaled and compared with experimental FT-IR and FT-Raman spectra. A detailed interpretation of the vibrational spectra of this compound has been made on the basis of the calculated Potential energy distribution (PED). Stability of the molecule arising from hyperconjugation and charge delocalization is confirmed by the natural bond orbital analysis (NBO). The results show that electron density (ED) in the σ antibonding orbitals and E (2) energies confirm the occurrence of intra molecular charge transfer (ICT) within the molecule. The molecule orbital contributions were studied by using the total (TDOS), sum of α and β electron (αβDOS) density of States. Mulliken population analysis of atomic charges is also calculated. The calculated HOMO and LUMO energy gap shows that charge transfer occurs within the molecule. The electron density-based local reactivity descriptors such as Fukui functions were calculated to explain the chemical selectivity or reactivity site in this compound. On the basis of vibrational analyses, the thermodynamic properties of title compound at different temperatures have been calculated.

  13. I. Interaction of ammonia with single crystal rhodium catalysts. II. Hydrogen and nitrogen adsorption on a W(111) surface: a theoretical molecular orbital approach

    Energy Technology Data Exchange (ETDEWEB)

    Vavere, A.

    1979-01-01

    Rates of ammonia decomposition on (110), (100), and (111) single crystal faces of rhodium were measured at 580 to 725/sup 0/K and 10/sup -3/ to 500 x 10/sup -3/ torr. The decomposition rates were proportional to P/sub NH/sub 3//sup/1/2/ and P/sub NH/sub 3// at low and high hydrogen pressures, respectively. The H/sub 2/ kinetic order varied from 0 (low P/sub H/sub 2//) to -1.0 (high P/sub H/). The rate was independent of N/sub 2/ pressure. NH/sub 3/ decomposes about 1.5 times faster than ND/sub 3/ on the (110) and (111) faces. Rates on the (110) surface are over 10 times as rapid as on the (111). LEED, Auger, and flash desorption experiments indicated that boron was a significant surface poison and that the Rh(110) surface was essentially nitrogen-free. A rate expression is derived from a model involving surface species Rh/sub 2/NH, RhH, and RhN on a nearly bare RH surface. The rate limiting process involves the concurrent dehydrogenation of Rh/sub 2/NH and desorption of N/sub 2/. A decreasing NH/sub 3/ order (< 1/2) at high P/sub NH/sub 3// and low T is due to buildup of surface intermediates. The relative bonding energies of hydrogen and nitrogen chemisorbed at three sites on a W(111) surface were obtained via the extended Hueckel molecular orbital theory. The preferred site for both H and N chemisorption was determined as the TOP position, i.e., a single coordination site on top of a protruding W atom. The W(111) surface was simulated by truncated arrays of seven tungsten atoms. The basis set for the calculations included the tungsten valence orbitals plus the filled 5p orbitals needed for repulsion at small internuclear distances. N adsorption in the three-fold holes available on the W(111) lattices used disrupted the W--W bonds sufficiently to cause the overall bond energy to be less than for the single coordination site. The dissymmetry between the three-fold lattices and the four-fold W d orbitals may also be a contributing factor.

  14. Orbital interactions in chemistry

    CERN Document Server

    Albright, Thomas A; Whangbo, Myung-Hwan

    2013-01-01

    Explains the underlying structure that unites all disciplines in chemistry Now in its second edition, this book explores organic, organometallic, inorganic, solid state, and materials chemistry, demonstrating how common molecular orbital situations arise throughout the whole chemical spectrum. The authors explore the relationships that enable readers to grasp the theory that underlies and connects traditional fields of study within chemistry, thereby providing a conceptual framework with which to think about chemical structure and reactivity problems. Orbital Interactions

  15. [Bases for the formation of an ultrasound diagnostic image of orbital tissue].

    Science.gov (United States)

    Kharlap, S I; Vashkulatova, E A; Safonova, T N; Skvortsova, N V

    2010-01-01

    The paper touches upon the specific features of the structure of orbital formations, by considering their anatomic topography and biophysical properties. By studying the results of investigations of the morphological and biophysical studies of orbital tissues, the authors analyze their features and compare their relationships. These results unraveling each of the considered orbital anatomic elements from the acoustic profile ranges may be useful in understanding the nature of clinical changes, which will be able to interpret these or those diagnostic signs--guides and to trace their evolution. In addition, this approach can help interpret the texture of an ultrasound digital image of eye socket soft tissue and permit one to look at pathological clinical manifestations from the so-called biophysical essence. This will allow additional information to be gleaned, by analyzing the usual signs.

  16. Electronic transport properties of a quinone-based molecular switch

    Science.gov (United States)

    Zheng, Ya-Peng; Bian, Bao-An; Yuan, Pei-Pei

    2016-09-01

    In this paper, we carried out first-principles calculations based on density functional theory and non-equilibrium Green's function to investigate the electronic transport properties of a quinone-based molecule sandwiched between two Au electrodes. The molecular switch can be reversibly switched between the reduced hydroquinone (HQ) and oxidized quinone (Q) states via redox reactions. The switching behavior of two forms is analyzed through their I- V curves, transmission spectra and molecular projected self-consistent Hamiltonian at zero bias. Then we discuss the transmission spectra of the HQ and Q forms at different bias, and explain the oscillation of current according to the transmission eigenstates of LUMO energy level for Q form. The results suggest that this kind of a quinone-based molecule is usable as one of the good candidates for redox-controlled molecular switches.

  17. Hole states based on the {11}/{2}-[505] neutron orbital within the pairing gap

    Science.gov (United States)

    Peterson, R. J.; Garrett, J. D.

    1984-02-01

    Coupled-channel calculations have been performed for (d, p) and (d, t) reactions on the stable doubly even isotopes of Gd, Dy and Er for {11}/{2}- neutron transfer to the [505] band heads. Comparison to published data permitted reliable extraction of the occupation numbers for this orbital. The occupation numbers V2 were found to be much greater than the emptiness numbers U2, even for very low-lying excitations. These results can only be obtained for a very small pairing parameter, Δ, consistent with other less direct determinations. These results are as expected for a diminution of the pairing interaction for this oblate [505] orbital.

  18. Conformational and Molecular Structures of α,β-Unsaturated Acrylonitrile Derivatives: Photophysical Properties and Their Frontier Orbitals.

    Science.gov (United States)

    Percino, María Judith; Cerón, Margarita; Rodríguez, Oscar; Soriano-Moro, Guillermo; Castro, María Eugenia; Chapela, Víctor M; Siegler, Maxime A; Pérez-Gutiérrez, Enrique

    2016-03-28

    We report single crystal X-ray diffraction (hereafter, SCXRD) analyses of derivatives featuring the electron-donor N-ethylcarbazole or the (4-diphenylamino)phenyl moieties associated with a -CN group attached to a double bond. The compounds are (2Z)-3-(4-(diphenylamino)-phenyl)-2-(pyridin-3-yl)prop-2-enenitrile (I), (2Z)-3-(4-(diphenylamino)phenyl)-2-(pyridin-4-yl)-prop-2-enenitrile (II) and (2Z)-3-(9-ethyl-9H-carbazol-3-yl)-2-(pyridin-2-yl)enenitrile (III). SCXRD analyses reveal that I and III crystallize in the monoclinic space groups P2/c with Z' = 2 and C2/c with Z' = 1, respectively. Compound II crystallized in the orthorhombic space group Pbcn with Z' = 1. The molecular packing analysis was conducted to examine the pyridine core effect, depending on the ortho, meta- and para-positions of the nitrogen atom, with respect to the optical properties and number of independent molecules (Z'). It is found that the double bond bearing a diphenylamino moiety introduced properties to exhibit a strong π-π-interaction in the solid state. The compounds were examined to evaluate the effects of solvent polarity, the role of the molecular structure, and the molecular interactions on their self-assembly behaviors. Compound I crystallized with a cell with two conformers, anti and syn, due to interaction with solvent. DFT calculations indicated the anti and syn structures of I are energetically stable (less than 1 eV). Also electrochemical and photophysical properties of the compounds were investigated, as well as the determination of optimization calculations in gas and different solvent (chloroform, cyclohexane, methanol, ethanol, tetrahydrofuran, dichloromethane and dimethyl sulfoxide) in the Gaussian09 program. The effect of solvent by PCM method was also investigated. The frontier HOMO and LUMO energies and gap energies are reported.

  19. Conformational and Molecular Structures of α,β-Unsaturated Acrylonitrile Derivatives: Photophysical Properties and Their Frontier Orbitals

    Directory of Open Access Journals (Sweden)

    María Judith Percino

    2016-03-01

    Full Text Available We report single crystal X-ray diffraction (hereafter, SCXRD analyses of derivatives featuring the electron-donor N-ethylcarbazole or the (4-diphenylaminophenyl moieties associated with a -CN group attached to a double bond. The compounds are (2Z-3-(4-(diphenylamino-phenyl-2-(pyridin-3-ylprop-2-enenitrile (I, (2Z-3-(4-(diphenylaminophenyl-2-(pyridin-4-yl-prop-2-enenitrile (II and (2Z-3-(9-ethyl-9H-carbazol-3-yl-2-(pyridin-2-ylenenitrile (III. SCXRD analyses reveal that I and III crystallize in the monoclinic space groups P2/c with Z’ = 2 and C2/c with Z’ = 1, respectively. Compound II crystallized in the orthorhombic space group Pbcn with Z’ = 1. The molecular packing analysis was conducted to examine the pyridine core effect, depending on the ortho, meta- and para-positions of the nitrogen atom, with respect to the optical properties and number of independent molecules (Z’. It is found that the double bond bearing a diphenylamino moiety introduced properties to exhibit a strong π-π-interaction in the solid state. The compounds were examined to evaluate the effects of solvent polarity, the role of the molecular structure, and the molecular interactions on their self-assembly behaviors. Compound I crystallized with a cell with two conformers, anti and syn, due to interaction with solvent. DFT calculations indicated the anti and syn structures of I are energetically stable (less than 1 eV. Also electrochemical and photophysical properties of the compounds were investigated, as well as the determination of optimization calculations in gas and different solvent (chloroform, cyclohexane, methanol, ethanol, tetrahydrofuran, dichloromethane and dimethyl sulfoxide in the Gaussian09 program. The effect of solvent by PCM method was also investigated. The frontier HOMO and LUMO energies and gap energies are reported.

  20. Molecular partitioning based on the kinetic energy density

    Science.gov (United States)

    Noorizadeh, Siamak

    2016-05-01

    Molecular partitioning based on the kinetic energy density is performed to a number of chemical species, which show non-nuclear attractors (NNA) in their gradient maps of the electron density. It is found that NNAs are removed using this molecular partitioning and although the virial theorem is not valid for all of the basins obtained in the being used AIM, all of the atoms obtained using the new approach obey this theorem. A comparison is also made between some atomic topological parameters which are obtained from the new partitioning approach and those calculated based on the electron density partitioning.

  1. Understanding field variation, quantum chemical modeling and molecular orbital analyses of trans-3-(trans-4-imidazolyl) acrylic acid

    Science.gov (United States)

    Gayathri, R.; Arivazhagan, M.

    2017-02-01

    In this work, a joint experimental (FTIR and FT-Raman) and theoretical (DFT and ab-initio) study on the structure and the vibrations of Trans-3-(trans-4-imidazolyl) acrylic acid (TTIAA) are compared and analyzed. The assignment of each normal mode has been made using the observed and calculated frequencies. The optimized geometries, harmonic vibrational wavenumbers and intensities of vibrational bands of trans-3-(trans-4-imidazolyl) acrylic acid (TTIAA) have been carried out using the HF/B3LYP method using the standard 6311++G(d,p) basis set calculations in this investigation. The result describes the variation in electrostatic and transport properties for zero and various external applied field. The variation in MPA charges are small due to the application of EFs: however, in most cases it is found to be systematic and almost uniform. When the field increases from 0.00 to 0.02 VÅ-1, the hybridization of molecular levels broadens the DOS and decreases the HLG from 3.6609 to 1.2325 eV; the decrease of band gap at the high field indicates that this molecule exhibit considerable electrical conductivity. Fukui indices to determine the local reactive site for the molecular systems during electrophilic, nucleophilic, radical and dual descriptor attacks. The results clearly show the superiority of MPA scheme. This study may be useful to design new molecules with more electrical conductivity.

  2. Photo-induced reactions from efficient molecular dynamics with electronic transitions using the FIREBALL local-orbital density functional theory formalism.

    Science.gov (United States)

    Zobač, Vladimír; Lewis, James P; Abad, Enrique; Mendieta-Moreno, Jesús I; Hapala, Prokop; Jelínek, Pavel; Ortega, José

    2015-05-08

    The computational simulation of photo-induced processes in large molecular systems is a very challenging problem. Firstly, to properly simulate photo-induced reactions the potential energy surfaces corresponding to excited states must be appropriately accessed; secondly, understanding the mechanisms of these processes requires the exploration of complex configurational spaces and the localization of conical intersections; finally, photo-induced reactions are probability events, that require the simulation of hundreds of trajectories to obtain the statistical information for the analysis of the reaction profiles. Here, we present a detailed description of our implementation of a molecular dynamics with electronic transitions algorithm within the local-orbital density functional theory code FIREBALL, suitable for the computational study of these problems. As an example of the application of this approach, we also report results on the [2 + 2] cycloaddition of ethylene with maleic anhydride and on the [2 + 2] photo-induced polymerization reaction of two C60 molecules. We identify different deactivation channels of the initial electron excitation, depending on the time of the electronic transition from LUMO to HOMO, and the character of the HOMO after the transition.

  3. Conformational stability, molecular orbital studies (chemical hardness and potential), vibrational investigation and theoretical NBO analysis of 4-tert-butyl-3-methoxy-2,6-dinitrotoluene.

    Science.gov (United States)

    Saravanan, S; Balachandran, V; Vishwanathan, K

    2014-04-24

    The FT-IR and FT-Raman spectra of 4-tert-butyl-3-methoxy-2,6-dinitrotoluene (musk ambrette) have been recorded in the regions 4000-400 cm(-1) and 3500-100 cm(-1), respectively. The total energy calculations of musk ambrette were tried for the possible conformers. The molecular structure, geometry optimization, vibrational frequencies were obtained by the density functional theory (DFT) using B3LYP and LSDA method with 6-311G(d,p) basis set for the most stable conformer "C1". The complete assignments were performed on the basis of the potential energy distribution (PED) of the vibrational modes, calculated and the scaled values were compared with experimental FT-IR and FT-Raman spectra. The observed and the calculated frequencies are found to be in good agreement. The stability of the molecule arising from hyper conjugate interactions and the charge delocalization has been analyzed using bond orbital (NBO) analysis. The HOMO and LUMO energy gap reveals that the energy gap reflects the chemical activity of the molecule. The dipole moment (μ), polarizability (α), anisotropy polarizability (Δα) and first hyperpolarizability (βtot) of the molecule have been reported. The thermodynamic functions (heat capacity, entropy and enthalpy) were obtained for the range of temperature 100-1000 K. Information about the size, shape, charge density distribution and site of chemical reactivity of the molecule has been obtained by mapping electron density isosurface with molecular electrostatic potential (MEP).

  4. Action-angle formulation of generalized, orbit-based, fast-ion diagnostic weight functions

    Science.gov (United States)

    Stagner, L.; Heidbrink, W. W.

    2017-09-01

    Due to the usually complicated and anisotropic nature of the fast-ion distribution function, diagnostic velocity-space weight functions, which indicate the sensitivity of a diagnostic to different fast-ion velocities, are used to facilitate the analysis of experimental data. Additionally, when velocity-space weight functions are discretized, a linear equation relating the fast-ion density and the expected diagnostic signal is formed. In a technique known as velocity-space tomography, many measurements can be combined to create an ill-conditioned system of linear equations that can be solved using various computational methods. However, when velocity-space weight functions (which by definition ignore spatial dependencies) are used, velocity-space tomography is restricted, both by the accuracy of its forward model and also by the availability of spatially overlapping diagnostic measurements. In this work, we extend velocity-space weight functions to a full 6D generalized coordinate system and then show how to reduce them to a 3D orbit-space without loss of generality using an action-angle formulation. Furthermore, we show how diagnostic orbit-weight functions can be used to infer the full fast-ion distribution function, i.e., orbit tomography. In depth derivations of orbit weight functions for the neutron, neutral particle analyzer, and fast-ion D-α diagnostics are also shown.

  5. Correction of harmonic motion and Kepler orbit based on the minimal momentum uncertainty

    Science.gov (United States)

    Chung, Won Sang; Hassanabadi, Hassan

    2017-03-01

    In this paper we consider the deformed Heisenberg uncertainty principle with the minimal uncertainty in momentum which is called a minimal momentum uncertainty principle (MMUP). We consider MMUP in D-dimension and its classical analogue. Using these we investigate the MMUP effect for the harmonic motion and Kepler orbit.

  6. The Equation Based on the Rotational and Orbital Motion of the Planets

    Directory of Open Access Journals (Sweden)

    G.A. Korablev

    2017-03-01

    Full Text Available Equations of dependence of rotational and orbital motions of planets are given, their rotation angles are calculated. Wave principles of direct and reverse rotation of planets are established. The established dependencies are demonstrated at different scale levels of structural interactions, in biosystems as well. The accuracy of calculations corresponds to the accuracy of experimental data.

  7. Pitch Angle Restrictions in Late Type Spiral Galaxies Based on Chaotic and Ordered Orbital Behavior

    CERN Document Server

    Perez-Villegas, Angeles; Moreno, Edmundo; Peimbert, Antonio; Velazquez, Hector M

    2011-01-01

    We built models for low bulge mass spiral galaxies (late type as defined by the Hubble classification) using a 3-D self-gravitating model for spiral arms, and analyzed the orbital dynamics as a function of pitch angle, going from 10$\\deg$ to 60$\\deg$. Testing undirectly orbital self-consistency, we search for the main periodic orbits and studied the density response. For pitch angles up to approximately $\\sim 20\\deg$, the response supports closely the potential permitting readily the presence of long lasting spiral structures. The density response tends to "avoid" larger pitch angles in the potential, by keeping smaller pitch angles in the corresponding response. Spiral arms with pitch angles larger than $\\sim 20\\deg$, would not be long-lasting structures but rather transient. On the other hand, from an extensive orbital study in phase space, we also find that for late type galaxies with pitch angles larger than $\\sim 50\\deg$, chaos becomes pervasive destroying the ordered phase space surrounding the main sta...

  8. Molecular determinants for drug-receptor interactions. Part 2. An ab initio molecular orbital and dipole moment study of the novel nootropic agent piracetam (2-oxopyrrolidin-1-ylacetamide)

    Science.gov (United States)

    Lumbroso, H.; Liégeois, C.; Pappalardo, G. C.; Grassi, A.

    From the ab initio molecular energies of the possible conformers and from a classical dipole moment analysis of 2-oxopyrrolidin-l-ylacetamide (μ = 4.02 D in dioxan at 30.0°C), the preferred conformation in solution of this novel nootropic agent has been determined. The exocyclic N-CH 2 bond is rotated in one sense by 90° and the exocyclic CH 2-C bond rotated in the same sense by 120° from the "planar" ( OO)- cis conformation. The structures of the two enantiomers in solution differ from that of the crystalline molecule.

  9. Protein analysis based on molecular beacon probes and biofunctionalized nanoparticles

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    With the completion of the human genome-sequencing project, there has been a resulting change in the focus of studies from genomics to proteomics. By utilizing the inherent advantages of molecular beacon probes and biofunctionalized nanoparticles, a series of novel principles, methods and techniques have been exploited for bioanalytical and biomedical studies. This review mainly discusses the applications of molecular beacon probes and biofunctionalized nanoparticles-based technologies for realtime, in-situ, highly sensitive and highly selective protein analysis, including the nonspecific or specific protein detection and separation, protein/DNA interaction studies, cell surface protein recognition, and antigen-antibody binding process-based bacteria assays. The introduction of molecular beacon probes and biofunctionalized nanoparticles into the protein analysis area would necessarily advance the proteomics research.

  10. Plasmonic-Based Electrochemical Impedance Spectroscopy: Application to Molecular Binding

    Science.gov (United States)

    Lu, Jin; Wang, Wei; Wang, Shaopeng; Shan, Xiaonan; Li, Jinghong; Tao, Nongjian

    2012-01-01

    Plasmonic-based electrochemical impedance spectroscopy (P-EIS) is developed to investigate molecular binding on surfaces. Its basic principle relies on the sensitive dependence of surface plasmon resonance (SPR) signal on surface charge density, which is modulated by applying an AC potential to a SPR chip surface. The AC component of the SPR response gives the electrochemical impedance, and the DC component provides the conventional SPR detection. The plasmonic-based impedance measured over a range of frequency is in quantitative agreement with the conventional electrochemical impedance. Compared to the conventional SPR detection, P-EIS is sensitive to molecular binding taking place on the chip surface, and less sensitive to bulk refractive index changes or non-specific binding. Moreover, this new approach allows for simultaneous SPR and surface impedance analysis of molecular binding processes. PMID:22122514

  11. A vibrational circular dichroism implementation within a Slater-type-orbital based density functional framework and its application to hexa- and hepta-helicenes

    NARCIS (Netherlands)

    Baerends, Evert; Neugebauer, Johannes; Nicu, Valentin; Wolff, Stephen

    2008-01-01

    We describe the implementation of the rotational strengths for vibrational circular dichroism (VCD) in the Slater-type orbital based Amsterdam Density Functional (ADF) package. We show that our implementation, which makes use of analytical derivative techniques and London atomic orbitals, yields o

  12. Fullerene-based Anchoring Groups for Molecular Electronics

    DEFF Research Database (Denmark)

    Martin, Christian A.; Ding, Dapeng; Sørensen, Jakob Kryger

    2008-01-01

    We present results on a new fullerene-based anchoring group for molecular electronics. Using lithographic mechanically controllable break junctions in vacuum we have determined the conductance and stability of single-molecule junctions of 1,4-bis(fullero[c]pyrrolidin-1-yl)benzene. The compound can...

  13. Spaceborne Autonomous and Ground Based Relative Orbit Control for the TerraSAR-X/TanDEM-X Formation

    Science.gov (United States)

    Ardaens, J. S.; D'Amico, S.; Kazeminejad, B.; Montenbruck, O.; Gill, E.

    2007-01-01

    TerraSAR-X (TSX) and TanDEM-X (TDX) are two advanced synthetic aperture radar (SAR) satellites flying in formation. SAR interferometry allows a high resolution imaging of the Earth by processing SAR images obtained from two slightly different orbits. TSX operates as a repeat-pass interferometer in the first phase of its lifetime and will be supplemented after two years by TDX in order to produce digital elevation models (DEM) with unprecedented accuracy. Such a flying formation makes indeed possible a simultaneous interferometric data acquisition characterized by highly flexible baselines with range of variations between a few hundreds meters and several kilometers [1]. TSX has been successfully launched on the 15th of June, 2007. TDX is expected to be launched on the 31st of May, 2009. A safe and robust maintenance of the formation is based on the concept of relative eccentricity/inclination (e/i) vector separation whose efficiency has already been demonstrated during the Gravity Recovery and Climate Experiment (GRACE) [2]. Here, the satellite relative motion is parameterized by mean of relative orbit elements and the key idea is to align the relative eccentricity and inclination vectors to minimize the hazard of a collision. Previous studies have already shown the pertinence of this concept and have described the way of controlling the formation using an impulsive deterministic control law [3]. Despite the completely different relative orbit control requirements, the same approach can be applied to the TSX/TDX formation. The task of TDX is to maintain the close formation configuration by actively controlling its relative motion with respect to TSX, the leader of the formation. TDX must replicate the absolute orbit keeping maneuvers executed by TSX and also compensate the natural deviation of the relative e/i vectors. In fact the relative orbital elements of the formation tend to drift because of the secular non-keplerian perturbations acting on both satellites

  14. Identifying a descriptor for d-orbital delocalization in cathodes of Li batteries based on x-ray Compton scattering

    Energy Technology Data Exchange (ETDEWEB)

    Barbiellini, B., E-mail: B.Amidei@neu.edu; Wang, Yung Jui; Hafiz, H.; Bansil, A. [Department of Physics, Northeastern University, Boston, Massachusetts 02115 (United States); Suzuki, K.; Yamada, R.; Sakurai, H. [Faculty of Science and Technology, Gunma University, Kiryu, Gunma 376-8515 (Japan); Orikasa, Y.; Yamamoto, K.; Uchimoto, Y. [Guraduate School of Human and Environmental Studies, Kyoto University, Sakyo-ku, Kyoto 606-8501 (Japan); Kaprzyk, S. [Department of Physics, Northeastern University, Boston, Massachusetts 02115 (United States); Faculty of Physics and Applied Computer Science, AGH University of Science and Technology, aleja Mickiewicza 30, Krakow 30-059 (Poland); Itou, M.; Sakurai, Y. [Japan Synchrotron Radiation Research Institute (JASRI), SPring-8, Sayo, Hyogo 679-5198 (Japan)

    2016-08-15

    We discuss how x-ray Compton scattering spectra can be used for investigating the evolution of electronic states in cathode materials of Li batteries under the lithiation/delithiation process. In particular, our analysis of the Compton spectra taken from polycrystalline Li{sub x}CoO{sub 2} samples shows that the spectra are dominated by the contribution of the O-2p redox orbital. We identify a distinct signature of d-orbital delocalization, which is tied directly to the conductivity of the material, providing a descriptor based on Compton spectra for monitoring the lithiation range with improved conductivity and kinetics for electrochemical operation. Our study demonstrates that Compton scattering spectroscopy can provide a window for probing complex electronic mechanisms underlying the charging and discharging processes in Li-battery materials.

  15. The analysis of single-electron orbits in a free electron laser based upon a rectangular hybrid wiggler

    Science.gov (United States)

    Kordbacheh, A.; Ghahremaninezhad, Roghayeh; Maraghechi, B.

    2012-09-01

    A three-dimensional analysis of a novel free-electron laser (FEL) based upon a rectangular hybrid wiggler (RHW) is presented. This RHW is designed in a configuration composed of rectangular rings with alternating ferrite and dielectric spacers immersed in a solenoidal magnetic field. An analytic model of RHW is introduced by solution of Laplace's equation for the magnetostatic fields under the appropriate boundary conditions. The single-electron orbits in combined RHW and axial guide magnetic fields are studied when only the first and the third spatial harmonic components of the RHW field are taken into account and the higher order terms are ignored. The results indicate that the third spatial harmonic leads to group III orbits with a strong negative mass regime particularly in large solenoidal magnetic fields. RHW is found to be a promising candidate with favorable characteristics to be used in microwave FEL.

  16. Intelligent DNA-based molecular diagnostics using linked genetic markers

    Energy Technology Data Exchange (ETDEWEB)

    Pathak, D.K.; Perlin, M.W.; Hoffman, E.P.

    1994-12-31

    This paper describes a knowledge-based system for molecular diagnostics, and its application to fully automated diagnosis of X-linked genetic disorders. Molecular diagnostic information is used in clinical practice for determining genetic risks, such as carrier determination and prenatal diagnosis. Initially, blood samples are obtained from related individuals, and PCR amplification is performed. Linkage-based molecular diagnosis then entails three data analysis steps. First, for every individual, the alleles (i.e., DNA composition) are determined at specified chromosomal locations. Second, the flow of genetic material among the individuals is established. Third, the probability that a given individual is either a carrier of the disease or affected by the disease is determined. The current practice is to perform each of these three steps manually, which is costly, time consuming, labor-intensive, and error-prone. As such, the knowledge-intensive data analysis and interpretation supersede the actual experimentation effort as the major bottleneck in molecular diagnostics. By examining the human problem solving for the task, we have designed and implemented a prototype knowledge-based system capable of fully automating linkage-based molecular diagnostics in X-linked genetic disorders, including Duchenne Muscular Dystrophy (DMD). Our system uses knowledge-based interpretation of gel electrophoresis images to determine individual DNA marker labels, a constraint satisfaction search for consistent genetic flow among individuals, and a blackboard-style problem solver for risk assessment. We describe the system`s successful diagnosis of DMD carrier and affected individuals from raw clinical data.

  17. Effects of Rashba spin-orbit coupling on the conductance of graphene-based nanoribbons

    Science.gov (United States)

    Rashidian, Zeinab; Bayati, Parvin; Lorestaniwiess, Zeinab

    2017-03-01

    The transmission properties of armchair- and zigzag-edged graphene nanoribbon junctions between graphene electrodes are examined by means of the standard nonequilibrium Green’s function (NEGF) technique. The quantum transport of electrons is studied through a monolayer graphene strip in the presence of Rashba spin-orbit coupling that acts as a barrier between the two normal leads. The present work compares the conductances of nanoribbons with zigzag and armchair edges. Since the nature of induced gap for zigzag edge is different from armchair, it is expected to give rise to different types of conductance for each edge. Findings indicate that the Rashba strength has more pronounced influence on armchair ribbons than on zigzag ribbons, and the minimum conductance of 2G0 for nanoribbon remains intact even in the presence of the Rashba spin-orbit coupling. It is predicted that controllability of spin transport in the monolayer graphene may contribute to the development of well-known spintronics.

  18. A molecular shift register based on electron transfer

    Science.gov (United States)

    Hopfield, J. J.; Onuchic, Josenelson; Beratan, David N.

    1988-01-01

    An electronic shift-register memory at the molecular level is described. The memory elements are based on a chain of electron-transfer molecules and the information is shifted by photoinduced electron-transfer reactions. This device integrates designed electronic molecules onto a very large scale integrated (silicon microelectronic) substrate, providing an example of a 'molecular electronic device' that could actually be made. The design requirements for such a device and possible synthetic strategies are discussed. Devices along these lines should have lower energy usage and enhanced storage density.

  19. [Morphofunctional and molecular bases of pineal gland aging].

    Science.gov (United States)

    Khavinson, V Kh; Lin'kova, N S

    2012-01-01

    The review analyzed morphology, molecular and functional aspects of pineal gland aging and methods of it correction. The pineal gland is central organ, which regulates activity of neuroimmunoendocrine, antioxidant and other organisms systems. Functional activity of pineal gland is discreased at aging, which is the reason of melatonin level changing. The molecular and morphology research demonstrated, that pineal gland hadn't strongly pronounced atrophy at aging. Long-term experience showed, that peptides extract of pineal gland epithalamin and synthetic tetrapeptide on it base epithalon restored melatonin secretion in pineal gland and had strong regulatory activity at neuroimmunoendocrine and antioxidant organism systems.

  20. Chemical sensors based on molecularly modified metallic nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Haick, Hossam [Department of Chemical Engineering and Russell Berrie Nanotechnology Institute, Technion - Israel Institute of Technology, Haifa 32000 (Israel)

    2007-12-07

    This paper presents a concise, although admittedly non-exhaustive, didactic review of some of the main concepts and approaches related to the use of molecularly modified metal nanoparticles in or as chemical sensors. This paper attempts to pull together different views and terminologies used in sensors based on molecularly modified metal nanoparticles, including those established upon electrochemical, optical, surface Plasmon resonance, piezoelectric and electrical transduction approaches. Finally, this paper discusses briefly the main advantages and disadvantages of each of the presented class of sensors. (review article)

  1. Accelerating convergence of molecular dynamics-based structural relaxation

    DEFF Research Database (Denmark)

    Christensen, Asbjørn

    2005-01-01

    We describe strategies to accelerate the terminal stage of molecular dynamics (MD)based relaxation algorithms, where a large fraction of the computational resources are used. First, we analyze the qualitative and quantitative behavior of the QuickMin family of MD relaxation algorithms and explore...... the influence of spectral properties and dimensionality of the molecular system on the algorithm efficiency. We test two algorithms, the MinMax and Lanczos, for spectral estimation from an MD trajectory, and use this to derive a practical scheme of time step adaptation in MD relaxation algorithms to improve...

  2. Spin Interference in Rectangle Loop Based on Rashba and Dresselhaus Spin-Orbit Interactions

    Institute of Scientific and Technical Information of China (English)

    NI Jia-Ting; LIANG Xiao-Wan; CHEN Bin; T.Koga

    2009-01-01

    We demonstrate the amplitude and spin polarization of AAS oscillation changing with Rashba spin-orbit interaction(SOI)and Dresselhaus SOI.The amplitude and spin polarization of AB oscillation changing with Rashba SOI and Dresselhaus SOI are demonstrated as well.The ideal quasi-one-dimensional square loop does not exist in reality,therefore to match the experiment better we should consider the shape of the rectangle loop in theory.

  3. Coexistence of orbital degeneracy lifting and superconductivity in iron-based superconductors

    Science.gov (United States)

    Miao, H.; Wang, L.-M.; Richard, P.; Wu, S.-F.; Ma, J.; Qian, T.; Xing, L.-Y.; Wang, X.-C.; Jin, C.-Q.; Chou, C.-P.; Wang, Z.; Ku, W.; Ding, H.

    2014-06-01

    We report the angle-resolved photoemission spectroscopy observation of the lifting of symmetry-protected band degeneracy, and consequently the breakdown of local tetragonal symmetry in the superconducting state of Li(Fe1-xCox)As. Supported by theoretical simulations, we analyze the doping and temperature dependences of this band splitting and demonstrate an intimate connection between ferro-orbital correlations and superconductivity.

  4. Simultaneous Laser Ranging and Communication from an Earth-Based Satellite Laser Ranging Station to the Lunar Reconnaissance Orbiter in Lunar Orbit

    Science.gov (United States)

    Sun, Xiaoli; Skillman, David R.; Hoffman, Evan D.; Mao, Dandan; McGarry, Jan F.; Neumann, Gregory A.; McIntire, Leva; Zellar, Ronald S.; Davidson, Frederic M.; Fong, Wai H.; Krainak, Michael A.; Zuber, Maria T.; Smith, David E.

    2013-01-01

    We report a free space laser communication experiment from the satellite laser ranging (SLR) station at NASA Goddard Space Flight Center (GSFC) to the Lunar Reconnaissance Orbiter (LRO) in lunar orbit through the on board one-way Laser Ranging (LR) receiver. Pseudo random data and sample image files were transmitted to LRO using a 4096-ary pulse position modulation (PPM) signal format. Reed-Solomon forward error correction codes were used to achieve error free data transmission at a moderate coding overhead rate. The signal fading due to the atmosphere effect was measured and the coding gain could be estimated.

  5. Orbital angular momentum of helical necklace beams in colloid-based nonlinear optical metamaterials (Conference Presentation)

    Science.gov (United States)

    Walasik, Wiktor T.; Silahli, Salih Z.; Litchinitser, Natalia M.

    2016-09-01

    Colloidal metamaterials are a robust and flexible platform for engineering of optical nonlinearities and studies of light filamentation. To date, nonlinear propagation and modulation instability of Gaussian beams and optical vortices carrying orbital angular momentum were studied in such media. Here, we investigate the propagation of necklace beams and the conservation of the orbital angular momentum in colloidal media with saturable nonlinearity. We study various scenarios leading to generation of helical necklace beams or twisted beams, depending on the radius, power, and charge of the input vortex beam. Helical beams are build of two separate solitary beams with circular cross-sections that spiral around their center of mass as a result of the equilibrium between the attraction force of in-phase solitons and the centrifugal force associated with the rotational movement. A twisted beam is a single beam with an elliptical cross-section that rotates around it's own axis. We show that the orbital angular momentum is converted into the rotational motion at different rates for helical and twisted beams. While earlier studies reported that solitary beams are expelled form the initial vortex ring along straight trajectories tangent to the vortex ring, we show that depending on the charge and the power of the initial beam, these trajectories can diverge from the tangential direction and may be curvilinear. These results provide a detailed description of necklace beam dynamics in saturable nonlinear media and may be useful in studies of light filamentation in liquids and light propagation in highly scattering colloids and biological samples.

  6. Supramolecular assemblies and molecular recognition of amphiphilic schiff bases with barbituric acid in organized molecular films.

    Science.gov (United States)

    Jiao, Tifeng; Liu, Minghua

    2005-02-24

    A bolaform Schiff base, N,N'-bis(salicylidene)-1,10-decanediamine (BSC10), has been synthesized and its interfacial hydrogen bond formation or molecular recognition with barbituric acid was investigated in comparison with that of a single chain Schiff base, 2-hydroxybenzaldehyde-octadecylamine (HBOA). It has been found that while HBOA formed a monolayer at the air/water interface, the bolaform Schiff base formed a multilayer film with ordered layer structure on water surface. When the Schiff bases were spread on the subphase containing barbituric acid, both of the Schiff bases could form hydrogen bonds with barbituric acid in situ in the spreading films. As a result, an increase of the molecular areas in the isotherms was observed. The in situ H-bonded films could be transferred onto solid substrates, and the transferred multilayer films were characterized by various methods such as UV-vis and FT-IR spectrosopies. Spectral changes were observed for the films deposited from the barbituric acid subphase, which supported the hydrogen bond formation between the Schiff bases and barbituric acid. By measuring the MS-TOF of the deposited films dissolved in CHCl3 solution, it was concluded that a 2:1 complex of HBOA with barbituric acid and a 1:2 complex of BSC10 with barbituric acid were formed. On the other hand, when the multilayer films of both Schiff bases were immersed in an aqueous solution of barbituric acid, a similar molecular recognition through the hydrogen bond occurred. A clear conformational change of the alkyl spacer in the bolaform Schiff base was observed during the complex formation with the barbituric acid.

  7. Graph-based interpretation of the Molecular Interstellar Medium Segmentation

    CERN Document Server

    Colombo, Dario; Ginsburg, Adam; Duarte-Cabral, Ana; Hughes, Annie

    2015-01-01

    We present a generalization of the Giant Molecular Cloud (GMC) identification problem based on cluster analysis. The method we designed, SCIMES (Spectral Clustering for Interstellar Molecular Emission Segmentation) considers the dendrogram of emission in the broader framework of graph theory and utilizes spectral clustering to find discrete regions with similar emission properties. For Galactic molecular cloud structures, we show that the characteristic volume and/or integrated CO luminosity are useful criteria to define the clustering, yielding emission structures that closely reproduce "by-eye" identification results. SCIMES performs best on well-resolved, high-resolution data, making it complementary to other available algorithms. Using 12CO(1-0) data for the Orion-Monoceros complex, we demonstrate that SCIMES provides robust results against changes of the dendrogram-construction parameters, noise realizations and degraded resolution. By comparing SCIMES with other cloud decomposition approaches, we show t...

  8. Gesture Interaction Browser-Based 3D Molecular Viewer.

    Science.gov (United States)

    Virag, Ioan; Stoicu-Tivadar, Lăcrămioara; Crişan-Vida, Mihaela

    2016-01-01

    The paper presents an open source system that allows the user to interact with a 3D molecular viewer using associated hand gestures for rotating, scaling and panning the rendered model. The novelty of this approach is that the entire application is browser-based and doesn't require installation of third party plug-ins or additional software components in order to visualize the supported chemical file formats. This kind of solution is suitable for instruction of users in less IT oriented environments, like medicine or chemistry. For rendering various molecular geometries our team used GLmol (a molecular viewer written in JavaScript). The interaction with the 3D models is made with Leap Motion controller that allows real-time tracking of the user's hand gestures. The first results confirmed that the resulting application leads to a better way of understanding various types of translational bioinformatics related problems in both biomedical research and education.

  9. Molecular docking and structure-based drug design strategies.

    Science.gov (United States)

    Ferreira, Leonardo G; Dos Santos, Ricardo N; Oliva, Glaucius; Andricopulo, Adriano D

    2015-07-22

    Pharmaceutical research has successfully incorporated a wealth of molecular modeling methods, within a variety of drug discovery programs, to study complex biological and chemical systems. The integration of computational and experimental strategies has been of great value in the identification and development of novel promising compounds. Broadly used in modern drug design, molecular docking methods explore the ligand conformations adopted within the binding sites of macromolecular targets. This approach also estimates the ligand-receptor binding free energy by evaluating critical phenomena involved in the intermolecular recognition process. Today, as a variety of docking algorithms are available, an understanding of the advantages and limitations of each method is of fundamental importance in the development of effective strategies and the generation of relevant results. The purpose of this review is to examine current molecular docking strategies used in drug discovery and medicinal chemistry, exploring the advances in the field and the role played by the integration of structure- and ligand-based methods.

  10. Orbital fluctuation theory in iron-based superconductors: s-wave superconductivity, structure transition, and impurity-induced nematic order

    OpenAIRE

    Kontani, H.; Inoue, Y.; Saito, T.; Yamakawa, Y.; Onari, S.

    2012-01-01

    The main features in iron-based superconductors would be (i) the orthorhombic transition accompanied by remarkable softening of shear modulus, (ii) high-Tc superconductivity close to the orthorhombic phase, and (iii) nematic transition in the tetragonal phase. In this paper, we present a unified explanation for them, based on the orbital fluctuation theory, considering both the e-ph and the Coulomb interaction. It is found that a small e-ph coupling constant ($\\lambda ~ 0.2$) is enough to pro...

  11. Virtual Screening and Molecular Design Based on Hierarchical Qsar Technology

    Science.gov (United States)

    Kuz'min, Victor E.; Artemenko, A. G.; Muratov, Eugene N.; Polischuk, P. G.; Ognichenko, L. N.; Liahovsky, A. V.; Hromov, A. I.; Varlamova, E. V.

    This chapter is devoted to the hierarchical QSAR technology (HiT QSAR) based on simplex representation of molecular structure (SiRMS) and its application to different QSAR/QSPR tasks. The essence of this technology is a sequential solution (with the use of the information obtained on the previous steps) of the QSAR paradigm by a series of enhanced models based on molecular structure description (in a specific order from 1D to 4D). Actually, it's a system of permanently improved solutions. Different approaches for domain applicability estimation are implemented in HiT QSAR. In the SiRMS approach every molecule is represented as a system of different simplexes (tetratomic fragments with fixed composition, structure, chirality, and symmetry). The level of simplex descriptors detailed increases consecutively from the 1D to 4D representation of the molecular structure. The advantages of the approach presented are an ability to solve QSAR/QSPR tasks for mixtures of compounds, the absence of the "molecular alignment" problem, consideration of different physical-chemical properties of atoms (e.g., charge, lipophilicity), and the high adequacy and good interpretability of obtained models and clear ways for molecular design. The efficiency of HiT QSAR was demonstrated by its comparison with the most popular modern QSAR approaches on two representative examination sets. The examples of successful application of the HiT QSAR for various QSAR/QSPR investigations on the different levels (1D-4D) of the molecular structure description are also highlighted. The reliability of developed QSAR models as the predictive virtual screening tools and their ability to serve as the basis of directed drug design was validated by subsequent synthetic, biological, etc. experiments. The HiT QSAR is realized as the suite of computer programs termed the "HiT QSAR" software that so includes powerful statistical capabilities and a number of useful utilities.

  12. Bio-Mimetic Sensors Based on Molecularly Imprinted Membranes

    Directory of Open Access Journals (Sweden)

    Catia Algieri

    2014-07-01

    Full Text Available An important challenge for scientific research is the production of artificial systems able to mimic the recognition mechanisms occurring at the molecular level in living systems. A valid contribution in this direction resulted from the development of molecular imprinting. By means of this technology, selective molecular recognition sites are introduced in a polymer, thus conferring it bio-mimetic properties. The potential applications of these systems include affinity separations, medical diagnostics, drug delivery, catalysis, etc. Recently, bio-sensing systems using molecularly imprinted membranes, a special form of imprinted polymers, have received the attention of scientists in various fields. In these systems imprinted membranes are used as bio-mimetic recognition elements which are integrated with a transducer component. The direct and rapid determination of an interaction between the recognition element and the target analyte (template was an encouraging factor for the development of such systems as alternatives to traditional bio-assay methods. Due to their high stability, sensitivity and specificity, bio-mimetic sensors-based membranes are used for environmental, food, and clinical uses. This review deals with the development of molecularly imprinted polymers and their different preparation methods. Referring to the last decades, the application of these membranes as bio-mimetic sensor devices will be also reported.

  13. A DFT study on structures, frontier molecular orbitals and UV-vis spectra of RuX(PPh3)(NHCPh2)L (X=Tp and Cp; L=Cl and N3).

    Science.gov (United States)

    Wang, Tsang-Hsiu; Wang, I-Teng; Huang, Wen-Lin; Huang, Li-Yu

    2014-01-01

    Geometry optimization for RuX(PPh3)(NHCPh2)(L) (X=hydridotris(pyrazolyl)borate (Tp) and cyclopentadiene (Cp); L=Cl and N3) are investigated by using density functional theory (DFT) with DZVP2/DZVP all-electron mixed basis sets and compared with available experimental values, and the calculated structures are in very good agreement with experimental data. The frontier molecular orbitals (FMOs) and electronic transitions have been investigated as well. Our calculations show that the π electron-rich ligand (N3) may increase the energies of occupied orbitals and reduce the energy gap of the HOMO-LUMO (ΔEL-H) in these ruthenium based complexes. The simulated UV-vis spectra of these complexes in methanol have been studied with time-dependent density functional theory (TD-DFT), and conductor-like polarizable continuum model (CPCM) was employed to account for the solvent effects. Our results show that a number of absorption peaks are found in the visible region (400-800 nm) with non-zero oscillator strengths. The strongest adsorption feature is associated to a transition from HOMO-2 to LUMO, which is assigned to metal-to-ligand charge transfer (MLCT) or metal/ligand-to-ligand charge transfer (MLCT/LLCT) depending on co-ligands. In addition, the Cp group increases electron-accept ability and results in red shift due to its π electron-rich and π donor characters. According to our results, these ruthenium based complexes are good candidates for dye-sensitized solar cell owing to their absorption intensities and rich absorption bands in the visible region. Copyright © 2013 Elsevier B.V. All rights reserved.

  14. Linear-scaling atomic orbital-based second-order Møller-Plesset perturbation theory by rigorous integral screening criteria.

    Science.gov (United States)

    Doser, Bernd; Lambrecht, Daniel S; Kussmann, Jörg; Ochsenfeld, Christian

    2009-02-14

    A Laplace-transformed second-order Moller-Plesset perturbation theory (MP2) method is presented, which allows to achieve linear scaling of the computational effort with molecular size for electronically local structures. Also for systems with a delocalized electronic structure, a cubic or even quadratic scaling behavior is achieved. Numerically significant contributions to the atomic orbital (AO)-MP2 energy are preselected using the so-called multipole-based integral estimates (MBIE) introduced earlier by us [J. Chem. Phys. 123, 184102 (2005)]. Since MBIE provides rigorous upper bounds, numerical accuracy is fully controlled and the exact MP2 result is attained. While the choice of thresholds for a specific accuracy is only weakly dependent upon the molecular system, our AO-MP2 scheme offers the possibility for incremental thresholding: for only little additional computational expense, the numerical accuracy can be systematically converged. We illustrate this dependence upon numerical thresholds for the calculation of intermolecular interaction energies for the S22 test set. The efficiency and accuracy of our AO-MP2 method is demonstrated for linear alkanes, stacked DNA base pairs, and carbon nanotubes: e.g., for DNA systems the crossover toward conventional MP2 schemes occurs between one and two base pairs. In this way, it is for the first time possible to compute wave function-based correlation energies for systems containing more than 1000 atoms with 10 000 basis functions as illustrated for a 16 base pair DNA system on a single-core computer, where no empirical restrictions are introduced and numerical accuracy is fully preserved.

  15. The Molecule Calculator: A web-server for fast quantum mechanics-based estimation of molecular properties

    CERN Document Server

    Jensen, Jan H

    2013-01-01

    A new web-server called The Molecule Calculator (MolCalc) is presented. The entry page is a molecular editor (JSmol) for interactive molecule building. The resulting structure can then be used to estimate molecular properties such as heats of formation and other thermodynamic properties, vibrational frequencies and vibrational modes, and molecular orbitals and orbital energies. These properties are computed using the GAMESS program at either the RHF/STO-3G (orbitals and orbital energies) or PM3 level of theory (all other properties) in a matter of seconds or minutes depending on the size of the molecule. The results, though approximate, can help students develop a "chemical intuition" about how molecular structure affects molecular properties, without performing the underlying calculations by hand, a near impossible task for all but the simplest chemical systems.

  16. IPv6 and IPsec Tests of a Space-Based Asset, the Cisco Router in Low Earth Orbit (CLEO)

    Science.gov (United States)

    Ivancic, William; Stewart, David; Wood, Lloyd; Jackson, Chris; Northam, James; Wilhelm, James

    2008-01-01

    This report documents the design of network infrastructure to support testing and demonstrating network-centric operations and command and control of space-based assets, using IPv6 and IPsec. These tests were performed using the Cisco router in Low Earth Orbit (CLEO), an experimental payload onboard the United Kingdom--Disaster Monitoring Constellation (UK-DMC) satellite built and operated by Surrey Satellite Technology Ltd (SSTL). On Thursday, 29 March 2007, NASA Glenn Research Center, Cisco Systems and SSTL performed the first configuration and demonstration of IPsec and IPv6 onboard a satellite in low Earth orbit. IPv6 is the next generation of the Internet Protocol (IP), designed to improve on the popular IPv4 that built the Internet, while IPsec is the protocol used to secure communication across IP networks. This demonstration was made possible in part by NASA s Earth Science Technology Office (ESTO) and shows that new commercial technologies such as mobile networking, IPv6 and IPsec can be used for commercial, military and government space applications. This has direct application to NASA s Vision for Space Exploration. The success of CLEO has paved the way for new spacebased Internet technologies, such as the planned Internet Routing In Space (IRIS) payload at geostationary orbit, which will be a U.S. Department of Defense Joint Capability Technology Demonstration. This is a sanitized report for public distribution. All real addressing has been changed to psueco addressing.

  17. Preliminary Scientific Results of Chang'E-1 Lunar Orbiter: Based on Payloads Detection Data in the First Phase

    Institute of Scientific and Technical Information of China (English)

    OUYANG Ziyuan; YANG Jianfeng; ZHANG Wenxi; WANG Jianyu; MOU Lingli; CHANG Jin; ZHANG Liyan; WANG Huanyu; LI Yongquan; ZHANG Xiaohui; ZHENG Yongchun; JIANG Jingshan; WANG Shijin; BIAN Wei; LI Chunlai; SUN Huixian; ZOU Yongliao; LIU Jianzhong; LIU Jianjun; ZHAO Baochang; REN Xin

    2008-01-01

    Chang'E-1 lunar Orbiter was launched by Long March 3A rocket from Xichang Satellite Launch Center at 18:05 BT (Beijing Time) Oct. 24, 2007. It is the first step of its ambitious three-stage moon program, a new milestone in the Chinese space exploration history. The primary science objectives of Chang'E-1 lunar orbiter are to obtain three-Dimension (3D) stereo images of the lunar surface, to analyze the distribution and abundance of elements on the surface, to investigate the thickness of lunar soil, evaluate helium-3 resources and other characteristics, and to detect the space environment around the moon. To achieve the above four mission objectives, eight sets of scientific instruments are chosen as the payloads of the lunar orbiter, including a CCD stereo camera (CCD), a Sagnac-based interferometer spectrometer (IIM), a Laser Altimeter (LAM), a Microwave Radiometer (MRM), a Gamma-Ray Spectrometer (GRS), an X-ray spectrometer (XRS), a High-Energy Particle Detector (HPD), and two Solar Wind Ion Detectors (SWID). The detected data of the payloads show that all payloads work well. This paper introduces the status of payloads in the first phase and preliminary scientific results.

  18. Graph-based interpretation of the molecular interstellar medium segmentation

    Science.gov (United States)

    Colombo, D.; Rosolowsky, E.; Ginsburg, A.; Duarte-Cabral, A.; Hughes, A.

    2015-12-01

    We present a generalization of the giant molecular cloud identification problem based on cluster analysis. The method we designed, SCIMES (Spectral Clustering for Interstellar Molecular Emission Segmentation) considers the dendrogram of emission in the broader framework of graph theory and utilizes spectral clustering to find discrete regions with similar emission properties. For Galactic molecular cloud structures, we show that the characteristic volume and/or integrated CO luminosity are useful criteria to define the clustering, yielding emission structures that closely reproduce `by-eye' identification results. SCIMES performs best on well-resolved, high-resolution data, making it complementary to other available algorithms. Using 12CO(1-0) data for the Orion-Monoceros complex, we demonstrate that SCIMES provides robust results against changes of the dendrogram-construction parameters, noise realizations and degraded resolution. By comparing SCIMES with other cloud decomposition approaches, we show that our method is able to identify all canonical clouds of the Orion-Monoceros region, avoiding the overdivision within high-resolution survey data that represents a common limitation of several decomposition algorithms. The Orion-Monoceros objects exhibit hierarchies and size-line width relationships typical to the turbulent gas in molecular clouds, although `the Scissors' region deviates from this common description. SCIMES represents a significant step forward in moving away from pixel-based cloud segmentation towards a more physical-oriented approach, where virtually all properties of the ISM can be used for the segmentation of discrete objects.

  19. Optimizing legacy molecular dynamics software with directive-based offload

    Science.gov (United States)

    Michael Brown, W.; Carrillo, Jan-Michael Y.; Gavhane, Nitin; Thakkar, Foram M.; Plimpton, Steven J.

    2015-10-01

    Directive-based programming models are one solution for exploiting many-core coprocessors to increase simulation rates in molecular dynamics. They offer the potential to reduce code complexity with offload models that can selectively target computations to run on the CPU, the coprocessor, or both. In this paper, we describe modifications to the LAMMPS molecular dynamics code to enable concurrent calculations on a CPU and coprocessor. We demonstrate that standard molecular dynamics algorithms can run efficiently on both the CPU and an x86-based coprocessor using the same subroutines. As a consequence, we demonstrate that code optimizations for the coprocessor also result in speedups on the CPU; in extreme cases up to 4.7X. We provide results for LAMMPS benchmarks and for production molecular dynamics simulations using the Stampede hybrid supercomputer with both Intel® Xeon Phi™ coprocessors and NVIDIA GPUs. The optimizations presented have increased simulation rates by over 2X for organic molecules and over 7X for liquid crystals on Stampede. The optimizations are available as part of the "Intel package" supplied with LAMMPS.

  20. Arthropod phylogeny based on eight molecular loci and morphology

    Science.gov (United States)

    Giribet, G.; Edgecombe, G. D.; Wheeler, W. C.

    2001-01-01

    The interrelationships of major clades within the Arthropoda remain one of the most contentious issues in systematics, which has traditionally been the domain of morphologists. A growing body of DNA sequences and other types of molecular data has revitalized study of arthropod phylogeny and has inspired new considerations of character evolution. Novel hypotheses such as a crustacean-hexapod affinity were based on analyses of single or few genes and limited taxon sampling, but have received recent support from mitochondrial gene order, and eye and brain ultrastructure and neurogenesis. Here we assess relationships within Arthropoda based on a synthesis of all well sampled molecular loci together with a comprehensive data set of morphological, developmental, ultrastructural and gene-order characters. The molecular data include sequences of three nuclear ribosomal genes, three nuclear protein-coding genes, and two mitochondrial genes (one protein coding, one ribosomal). We devised new optimization procedures and constructed a parallel computer cluster with 256 central processing units to analyse molecular data on a scale not previously possible. The optimal 'total evidence' cladogram supports the crustacean-hexapod clade, recognizes pycnogonids as sister to other euarthropods, and indicates monophyly of Myriapoda and Mandibulata.

  1. Spin filtering effect in colorimetric chemosensor L-based molecular devices modulated with different transition metal ions

    Energy Technology Data Exchange (ETDEWEB)

    Shi, F.V.; Lv, Y.Z. [School of Physics and Technology, University of Jinan, Jinan 250022 (China); Zhao, P., E-mail: ss_zhaop@ujn.edu.cn [School of Physics and Technology, University of Jinan, Jinan 250022 (China); Liu, D.S. [School of Physics, State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100 (China); Department of Physics, Jining University, Jining 273155 (China)

    2017-05-15

    Based on the density functional theory in conjunction with the non-equilibrium Green's function formalism, we explore the effect of transition metal (Mn, Fe, Co, Ni) ions on the magnetic transport properties of a new synthesized colorimetric chemosensor L. The calculated results show that only Mn-L can present high-efficiency spin filtering effect, even at room temperature. The underlying mechanism is explained by the spin-resolved electron occupation number, transmission spectra, molecular projected self-consistent Hamiltonian orbitals and their spatial distribution.

  2. Localized orbital corrections applied to thermochemical errors in density functional theory: The role of basis set and application to molecular reactions.

    Science.gov (United States)

    Goldfeld, Dahlia A; Bochevarov, Arteum D; Friesner, Richard A

    2008-12-07

    This paper is a logical continuation of the 22 parameter, localized orbital correction (LOC) methodology that we developed in previous papers [R. A. Friesner et al., J. Chem. Phys. 125, 124107 (2006); E. H. Knoll and R. A. Friesner, J. Phys. Chem. B 110, 18787 (2006).] This methodology allows one to redress systematic density functional theory (DFT) errors, rooted in DFT's inherent inability to accurately describe nondynamical correlation. Variants of the LOC scheme, in conjunction with B3LYP (denoted as B3LYP-LOC), were previously applied to enthalpies of formation, ionization potentials, and electron affinities and showed impressive reduction in the errors. In this paper, we demonstrate for the first time that the B3LYP-LOC scheme is robust across different basis sets [6-31G( *), 6-311++G(3df,3pd), cc-pVTZ, and aug-cc-pVTZ] and reaction types (atomization reactions and molecular reactions). For example, for a test set of 70 molecular reactions, the LOC scheme reduces their mean unsigned error from 4.7 kcal/mol [obtained with B3LYP/6-311++G(3df,3pd)] to 0.8 kcal/mol. We also verified whether the LOC methodology would be equally successful if applied to the promising M05-2X functional. We conclude that although M05-2X produces better reaction enthalpies than B3LYP, the LOC scheme does not combine nearly as successfully with M05-2X than with B3LYP. A brief analysis of another functional, M06-2X, reveals that it is more accurate than M05-2X but its combination with LOC still cannot compete in accuracy with B3LYP-LOC. Indeed, B3LYP-LOC remains the best method of computing reaction enthalpies.

  3. Molecular orbital study of coordinated dioxygen. I. Structure and bonding of model monomeric Co(II) complexes

    Science.gov (United States)

    Boča, R.

    1980-08-01

    The CNDO—UHF type of MO—LCAO—SCP calculation is carried out for model systems of dioxygen fixation: O 2 CoCl 4L 2- complexes in which L = none and L = NH 3. A geometry variation is performed with respect to 5 internal coordinates describing the degrees of freedom of the Co—O 2 group. The calculated geometry, spin densities and atomic charges agree with available data based on X-ray and ESR measurements of real dioxygen carriers. Structure and bonding of complexes are discussed in more detail.

  4. Standardised PCR-based molecular epidemiology of tuberculosis.

    Science.gov (United States)

    Allix-Béguec, C; Supply, P; Wanlin, M; Bifani, P; Fauville-Dufaux, M

    2008-05-01

    A population-based molecular epidemiology investigation has been undertaken to evaluate tuberculosis transmission and control in the Brussels-Capital Region (Belgium). All tuberculosis cases reported from January 2003 to December 2004 were investigated. In total, 536 Mycobacterium tuberculosis isolates (89% of culture-positive samples) were genotyped by the newly standardised 24 loci-based mycobacterial interspersed repetitive unit-variable number tandem-repeat typing, spoligotyping and IS6110 fingerprinting. Of all the patients, 30% were grouped based on strain clusters, suggesting a transmission index of 20%. An unsuspected outbreak entailing > or = 23 patients was evidenced by molecular typing analysis and confirmed by contact tracing. Foreign-born status accounted for 79% of the studied patients, including 37.9% illegal immigrants and asylum seekers. Among foreign-born patients, asylum seekers and illegal immigrants were significantly less abundant in strain clusters than settled residents. Tuberculosis in the Brussels-Capital Region is a bi-faceted problem, comprising both persisting recent transmission and "imported diseases". Molecular epidemiology based on real-time genotyping techniques has proven invaluable in better understanding tuberculosis transmission. However, it will most efficiently contribute to tuberculosis control when implemented in an integrated public health system.

  5. A Localized Molecular Orbital Study of the Halogen Substitution Effect on (103)Rh NMR Shielding in [Cp*RhX2]2, Where X = Cl, Br, or I.

    Science.gov (United States)

    Mirzaeva, Irina V; Mainichev, Dmitry A; Kozlova, Svetlana G

    2016-03-24

    (103)Rh NMR parameters and the bonding structure of three complexes of [Cp*RhX2]2, where X = Cl, Br, or I, have been studied with the help of natural bond orbitals (NBOs) and natural localized molecular orbitals (NLMOs). The complexes of [Cp*RhX2]2, where X = Cl, Br, or I, have similar bonding structures, with the major difference being in the degree of covalency of the Rh-X bonds. The decomposition of (103)Rh NMR shielding into diamagnetic, paramagnetic, and spin-orbit terms shows that normal halogen dependence (NHD) of the (103)Rh NMR shift is defined mostly by the paramagnetic term, with the spin-orbit term being significantly smaller. The decomposition of (103)Rh shielding into spin-free NBO and NLMO contributions shows that (103)Rh shielding is dominated by Rh d-orbital deshielding contributions. We explain the NHD of the (103)Rh NMR shift with the increase in the energies of the virtual antibonding Rh-X orbitals along the X = Cl, Br, and I series.

  6. OVERFLOW Simulations of Space Shuttle Orbiter Reentry Based on As-Built Geometry

    Science.gov (United States)

    Ma, Edward C.; Vicker, Darby J.; Campbell, Charles H.; Wilson, Brad; Pavek, Mike; Berger, Karen

    2012-01-01

    The Space Shuttle Orbiters Discovery and Endeavor have been digitally scanned to obtain outer mold line surfaces. Using these scans, the existing overset computational fluid dynamics (CFD) grid system will be modified by projecting the grid points to the scanned geometry. Simulations will be performed using the OVERFLOW solver and the results compared to previous OVERFLOW results on the theoretical geometry and the aerodynamic databook. The "bent airframe" term will be compared between the aerodynamic databook and the computations over a range of reentry conditions.

  7. Wavelength-selective orbital angular momentum generation based on a plasmonic metasurface

    Science.gov (United States)

    Yang, Kunpeng; Pu, Mingbo; Li, Xiong; Ma, Xiaoliang; Luo, Jun; Gao, Hui; Luo, Xiangang

    2016-06-01

    Nanoapertures with space-variant geometries are designed in a gold thin film to construct an ultrathin plasmonic metasurface, which has been demonstrated both numerically and experimentally to selectively generate and focus orbital angular momentum (OAM) beams with different topological charges at the wavelengths of 930 nm and 766 nm, respectively. Moreover, the interference patterns between the different circularly polarized transmission light were used to confirm the topological charges unambiguously. The agreement between the simulated and measured results suggests that the metasurface of wavelength-selective OAM modes may have potential applications in future optical communication systems.

  8. Constructing Periodic Phase Space Orbits from ab Initio Molecular Dynamics Trajectories to Analyze Vibrational Spectra: Case Study of the Zundel (H5O2(+)) Cation.

    Science.gov (United States)

    Dietrick, Scott M; Iyengar, Srinivasan S

    2012-12-11

    A method of analysis is introduced to probe the spectral features obtained from ab initio molecular dynamics simulations. Here, the instantaneous mass-weighted velocities are projected onto irreducible representations constructed from discrete time translation groups comprising operations that invoke the time-domain symmetries (or periodic phase space orbits) reflected in the spectra. The projected velocities are decomposed using singular value decomposition (SVD) to construct a set of "modes" pertaining to a given frequency domain. These modes now include all anharmonicities, as sampled during the dynamics simulations. In this approach, the underlying motions are probed in a manner invariant with respect to coordinate transformations, operations being performed along the time axis rather than coordinate axes, making the analysis independent of choice of reference frame. The method is used to probe the underlying motions responsible for the doublet at ∼1000 cm(-1) in the vibrational spectrum of the H5O2(+), Zundel cation. The associated analysis results are confirmed by projecting the Fourier transformed velocities onto the harmonic normal mode coordinates and a set of mass-weighted, symmetrized Jacobi coordinates. It is found that the two peaks of the doublet are described and differentiated by their respective contributions from the proton transfer, water-water stretch, and water wag coordinates, as these are defined. Temperature dependent effects are also briefly noted.

  9. NMR J-Coupling Constants of Tl-Pt Bonded Metal Complexes in Aqueous Solution: Ab Initio Molecular Dynamics and Localized Orbital Analysis.

    Science.gov (United States)

    Ducati, Lucas C; Marchenko, Alex; Autschbach, Jochen

    2016-11-21

    The influence of solvent (water) coordination and dynamics on the electronic structure and nuclear magnetic resonance (NMR) indirect spin-spin coupling (J-coupling) constants in a series of Tl-Pt bonded complexes is investigated using Kohn-Sham (KS) Car-Parrinello molecular dynamics (CPMD) and relativistic hybrid KS NMR calculations with and without coordination to water. Coordination of the Tl center by water molecules has a dramatic impact on (1)J(Tl-Pt) and other J-coupling constants. It is shown that a previous computational study of the same complexes using static optimized structures and nonhybrid functionals was correct about the important role of the solvent but obtained reasonable agreement with experimental NMR data because of a cancellation of substantial errors. For example, the CPMD trajectories show that on average the inner coordination shell of Tl is not saturated, as previously assumed, which leads to poor agreement with experiment when the J-coupling constants are averaged over the CPMD trajectories using NMR calculations with nonhybrid functionals. The combination of CPMD with hybrid KS NMR calculations provides a much more realistic computational model that reproduces the large magnitudes of (1)J(Tl-Pt) and the correct trends for other coupling constants. An analysis of (1)J(Tl-Pt) in terms of localized orbitals shows that the presence of coordinating water molecules increases the capacity for covalent interactions between Tl and Pt. There is pronounced multicenter bonding along the metal-metal axis of the complexes.

  10. An orbital-free molecular dynamics study of melting in $K_{20}, K_{55}, K_{92}, K_{142}, Rb_{55}$ and $Cs_{55}$ clusters

    CERN Document Server

    Aguado, A

    2001-01-01

    The melting-like transition in potasium clusters K_N, with N=20, 55, 92 and 142, is studied by using an orbital-free density-functional constant-energy molecular dynamics simulation method, and compared to previous theoretical results on the melting-like transition in sodium clusters of the same sizes. Melting in potasium and sodium clusters proceeds in a similar way: a surface melting stage develops upon heating before the homogeneous melting temperature is reached. Premelting effects are nevertheless more important and more easily established in potasium clusters, and the transition regions spread over temperature intervals which are wider than in the case of sodium. For all the sizes considered, the percentage melting temperature reduction when passing from Na to K clusters is substantially larger than in the bulk. Once those two materials have been compared for a number of different cluster sizes, we study the melting-like transition in Rb_55 and Cs_55 clusters and make a comparison with the melting behav...

  11. 推/拉型螺烯的前线分子轨道和电子光谱研究%Study on the Frontier Molecular Orbits and the Electronic Spectras of a Series of Push-Pull Helicenes

    Institute of Scientific and Technical Information of China (English)

    张新伟; 杨旭; 韩冰; 宋宣玉; 许军旗

    2014-01-01

    采用密度泛函理论B3LYP方法在6-31G( d, p)水平对一类推/拉型螺烯分子进行了几何结构优化,在得到稳定的分子构型后,用ZINDO/SCI方法计算了它们的前线分子轨道和电子光谱。结果表明,不同取代基和取代基的不同位置对分子的空间几何构型有一定的影响,HOMOs和LUMOs的分布特点说明该类分子有明显的电荷转移特征,通过优化设计不但可以提高非线性光学系数还可以增强这类分子的透明性。%The geometries of a series of push-pull helicenes were optimized by using density functional theory B3LYP method at the 6-31G (d, p) basis set level. Based on the obtained stable molecular configuration, the frontier molecular orbits and electronic spectras of these molecules were calculated by using the ZINDO/SCI method. The re-sults showed that the spatial molecular structures were different when the substituents or their positions were different. Through optimizing design, the distributions of HOMOs and LUMOs showed that these molecules have obviously charge transfer properties. Not only the nonlinear coefficients of this series of helicenes can be increased,but also the transpar-ences of such molecules can be enhanced.

  12. On Orbit Immuno-Based, Label-Free, White Blood Cell Counting System with MicroElectroMechanical Sensor (MEMS) Technology (OILWBCS-MEMS) Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Aurora Flight Sciences Corporation and partner, Draper Laboratory, propose to develop an on-orbit immuno-based label-free white blood cell counting system using MEMS...

  13. On Orbit Immuno-Based, Label-Free, White Blood Cell Counting System with MicroElectroMechanical Sensor (MEMS) Technology (OILWBCS-MEMS) Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Aurora Flight Sciences Corporation and our partner, Draper Laboratory, propose to develop an on orbit immuno-based, label-free, white blood cell counting system for...

  14. Modeling and prediction of daily gas concentration variation at a mining face based on the elliptic orbit model:A case study

    Institute of Scientific and Technical Information of China (English)

    Yang Zongchang; Zhou Shaowu

    2015-01-01

    Monitoring and analysis of daily gas concentrations at a mining face is a vital task on safety production and security management in the coal-mining industry. This study addresses modeling and prediction of daily gas concentration variations based on the elliptic orbit model. The model describes the hourly variation in daily gas concentration by mapping its time-series into the polar coordinates to create its elliptic orbit trace for further analysis. Experiments show workability of the proposed method that daily gas concentration variation at a mining face of one coal mine in China is well described by the elliptic orbit model. Result analysis and performance comparison of the proposed elliptic orbit model with the classical AR model on the same prediction tasks indicate potentiality of the proposed elliptic orbit model, which presents a vivid approach for modeling and forecasting daily gas concentration variations in an intuitive and concise way.

  15. Ground Tests and In-Orbit Performance of Variable Emittance Device Based on Manganese Oxide

    Science.gov (United States)

    Tachikawa, Sumitaka; Ohnishi, Akira; Nakamura, Yasuyuki; Okamoto, Akira

    A new thermal control material named the Smart Radiation Device (SRD) has shown improvement in development. The SRD can be used as a variable emittance radiator that controls the heat radiated into deep space without assistances of any electrical instruments or mechanical parts. Its total hemispherical emittance changes from low to high as the temperature increases. This new device reduces the energy consumption of the on-board heater, and decreases the weight and the cost of the thermal control system (TCS). Space environmental simulation tests on the ground were performed, and the first generation of the SRD has been demonstrating success on the MUSES-C ‘HAYABUSA’ spacecraft that was launched in May 2003. During its cruise on the orbit, the distance from the spacecraft to the sun varied from 0.86AU to 1.70AU. As the spacecraft experienced solar intensity variation by a factor 4, it was effective to use the variable emittance radiator for decreasing the heater power. In-orbit temperature indicated that the SRD had successfully minimized component temperature variation and saved heater power, as expected. With the opportunity to validate the SRD in space, this lightweight and low cost thermal control device offers a possibility for flexible thermal control on future spacecrafts.

  16. Rotating Space Debris Tracking Based on The Orbit-Attitude Coordinated Control

    Science.gov (United States)

    Wang, Shuquan; Zhu, Lingchao

    2016-07-01

    This paper investigates the rotating space debris tracking problem. Active capturing and removal of space debris are challenging because the space debris is noncoorperating. The scenario considered is that a rotating space debris is the target to be captured by a spacecraft with a robotic arm. One rough approach is to capture the space debris with a strong arm then detumble the rotation of the whole system using the attitude control system on board. In this way the arm and the spacecraft have to be strong enough to withstand the impact caused by the relative orbital and attitude motions. Another way is to at first track the motion of the characterized surface, which should be easier to capture, of the debris. Then the robotic arm is engaged to capture the debris. In this way, the impact applied on the robotic arm is greatly reduced such that the possibility of causing new debris is also reduced. The orbit-attitude coordinated controller is developed to track the motion of the space debris. The controller is assymptotically stable without considering the boundness of the control efforts. The stability in the situation of bounded control inputs is analyzed. Analytical criterion for a successful tracking is obtained in the situation that rotational motion of the space debris is percession.

  17. Reliability of unstable periodic orbit based control strategies in biological systems

    Energy Technology Data Exchange (ETDEWEB)

    Mishra, Nagender; Singh, Harinder P. [Department of Physics and Astrophysics, University of Delhi, Delhi 110007 (India); Hasse, Maria [Institut für Höchstleistungsrechnen, Universität Stuttgart, D-70569 Stuttgart (Germany); Biswal, B. [Cluster Innovation Center, University of Delhi, Delhi 110007 (India); Sri Venkateswara College, University of Delhi, Delhi 110021 (India)

    2015-04-15

    Presence of recurrent and statistically significant unstable periodic orbits (UPOs) in time series obtained from biological systems is now routinely used as evidence for low dimensional chaos. Extracting accurate dynamical information from the detected UPO trajectories is vital for successful control strategies that either aim to stabilize the system near the fixed point or steer the system away from the periodic orbits. A hybrid UPO detection method from return maps that combines topological recurrence criterion, matrix fit algorithm, and stringent criterion for fixed point location gives accurate and statistically significant UPOs even in the presence of significant noise. Geometry of the return map, frequency of UPOs visiting the same trajectory, length of the data set, strength of the noise, and degree of nonstationarity affect the efficacy of the proposed method. Results suggest that establishing determinism from unambiguous UPO detection is often possible in short data sets with significant noise, but derived dynamical properties are rarely accurate and adequate for controlling the dynamics around these UPOs. A repeat chaos control experiment on epileptic hippocampal slices through more stringent control strategy and adaptive UPO tracking is reinterpreted in this context through simulation of similar control experiments on an analogous but stochastic computer model of epileptic brain slices. Reproduction of equivalent results suggests that far more stringent criteria are needed for linking apparent success of control in such experiments with possible determinism in the underlying dynamics.

  18. Reliability of unstable periodic orbit based control strategies in biological systems

    Science.gov (United States)

    Mishra, Nagender; Hasse, Maria; Biswal, B.; Singh, Harinder P.

    2015-04-01

    Presence of recurrent and statistically significant unstable periodic orbits (UPOs) in time series obtained from biological systems is now routinely used as evidence for low dimensional chaos. Extracting accurate dynamical information from the detected UPO trajectories is vital for successful control strategies that either aim to stabilize the system near the fixed point or steer the system away from the periodic orbits. A hybrid UPO detection method from return maps that combines topological recurrence criterion, matrix fit algorithm, and stringent criterion for fixed point location gives accurate and statistically significant UPOs even in the presence of significant noise. Geometry of the return map, frequency of UPOs visiting the same trajectory, length of the data set, strength of the noise, and degree of nonstationarity affect the efficacy of the proposed method. Results suggest that establishing determinism from unambiguous UPO detection is often possible in short data sets with significant noise, but derived dynamical properties are rarely accurate and adequate for controlling the dynamics around these UPOs. A repeat chaos control experiment on epileptic hippocampal slices through more stringent control strategy and adaptive UPO tracking is reinterpreted in this context through simulation of similar control experiments on an analogous but stochastic computer model of epileptic brain slices. Reproduction of equivalent results suggests that far more stringent criteria are needed for linking apparent success of control in such experiments with possible determinism in the underlying dynamics.

  19. Envisioning the molecular choreography of DNA base excision repair.

    Science.gov (United States)

    Parikh, S S; Mol, C D; Hosfield, D J; Tainer, J A

    1999-02-01

    Recent breakthroughs integrate individual DNA repair enzyme structures, biochemistry and biology to outline the structural cell biology of the DNA base excision repair pathways that are essential to genome integrity. Thus, we are starting to envision how the actions, movements, steps, partners and timing of DNA repair enzymes, which together define their molecular choreography, are elegantly controlled by both the nature of the DNA damage and the structural chemistry of the participating enzymes and the DNA double helix.

  20. Design Concepts for a Small Space-Based GEO Relay Satellite for Missions Between Low Earth and near Earth Orbits

    Science.gov (United States)

    Bhasin, Kul B.; Warner, Joseph D.; Oleson, Steven; Schier, James

    2014-01-01

    The main purpose of the Small Space-Based Geosynchronous Earth orbiting (GEO) satellite is to provide a space link to the user mission spacecraft for relaying data through ground networks to user Mission Control Centers. The Small Space Based Satellite (SSBS) will provide services comparable to those of a NASA Tracking Data Relay Satellite (TDRS) for the same type of links. The SSBS services will keep the user burden the same or lower than for TDRS and will support the same or higher data rates than those currently supported by TDRS. At present, TDRSS provides links and coverage below GEO; however, SSBS links and coverage capability to above GEO missions are being considered for the future, especially for Human Space Flight Missions (HSF). There is also a rising need for the capability to support high data rate links (exceeding 1 Gbps) for imaging applications. The communication payload on the SSBS will provide S/Ka-band single access links to the mission and a Ku-band link to the ground, with an optical communication payload as an option. To design the communication payload, various link budgets were analyzed and many possible operational scenarios examined. To reduce user burden, using a larger-sized antenna than is currently in use by TDRS was considered. Because of the SSBS design size, it was found that a SpaceX Falcon 9 rocket could deliver three SSBSs to GEO. This will greatly reduce the launch costs per satellite. Using electric propulsion was also evaluated versus using chemical propulsion; the power system size and time to orbit for various power systems were also considered. This paper will describe how the SSBS will meet future service requirements, concept of operations, and the design to meet NASA users' needs for below and above GEO missions. These users' needs not only address the observational mission requirements but also possible HSF missions to the year 2030. We will provide the trade-off analysis of the communication payload design in terms of

  1. A CubeSat for Calibrating Ground-Based and Sub-Orbital Millimeter-Wave Polarimeters (CalSat)

    Science.gov (United States)

    Johnson, Bradley R.; Vourch, Clement J.; Drysdale, Timothy D.; Kalman, Andrew; Fujikawa, Steve; Keating, Brian; Kaufman, Jon

    2015-10-01

    We describe a low-cost, open-access, CubeSat-based calibration instrument that is designed to support ground-based and sub-orbital experiments searching for various polarization signals in the cosmic microwave background (CMB). All modern CMB polarization experiments require a robust calibration program that will allow the effects of instrument-induced signals to be mitigated during data analysis. A bright, compact and linearly polarized astrophysical source with polarization properties known to adequate precision does not exist. Therefore, we designed a space-based millimeter-wave calibration instrument, called CalSat, to serve as an open-access calibrator, and this paper describes the results of our design study. The calibration source on board CalSat is composed of five “tones” with one each at 47.1, 80.0, 140, 249 and 309GHz. The five tones we chose are well matched to (i) the observation windows in the atmospheric transmittance spectra, (ii) the spectral bands commonly used in polarimeters by the CMB community and (iii) the Amateur Satellite Service bands in the Table of Frequency Allocations used by the Federal Communications Commission. CalSat would be placed in a polar orbit allowing visibility from observatories in the Northern Hemisphere, such as Mauna Kea in Hawaii and Summit Station in Greenland, and the Southern Hemisphere, such as the Atacama Desert in Chile and the South Pole. CalSat also would be observable by balloon-borne instruments launched from a range of locations around the world. This global visibility makes CalSat the only source that can be observed by all terrestrial and sub-orbital observatories, thereby providing a universal standard that permits comparison between experiments using appreciably different measurement approaches.

  2. A CubeSat for Calibrating Ground-Based and Sub-Orbital Millimeter-Wave Polarimeters

    Science.gov (United States)

    Johnson, Bradley

    2016-06-01

    We describe a low-cost, open-access, CubeSat-based calibration instrument that is designed to support ground-based and sub-orbital experiments searching for various polarization signals in the cosmic microwave background (CMB). All modern CMB polarization experiments require a robust calibration program that will allow the effects of instrument-induced signals to be mitigated during data analysis. A bright, compact, and linearly polarized astrophysical source with polarization properties known to adequate precision does not exist. Therefore, we designed a space-based millimeter-wave calibration instrument, called CalSat, to serve as an open-access calibrator, and this paper describes the results of our design study. The calibration source on board CalSat is composed of five "tones'" with one each at 47.1, 80.0, 140, 249 and 309 GHz. The five tones we chose are well matched to (i) the observation windows in the atmospheric transmittance spectra, (ii) the spectral bands commonly used in polarimeters by the CMB community, and (iii) The Amateur Satellite Service bands in the Table of Frequency Allocations used by the Federal Communications Commission. CalSat will be placed in a polar orbit allowing visibility from observatories in the Northern Hemisphere, such as Mauna~Kea in Hawaii and Summit Station in Greenland, and the Southern Hemisphere, such as the Atacama Desert in Chile and the South Pole. CalSat also will be observable by balloon-borne instruments launched from a range of locations around the world. This global visibility makes CalSat the only source that can be observed by all terrestrial and sub-orbital observatories, thereby providing a universal standard that permits comparison between experiments using appreciably different measurement approaches.

  3. A Molecular Selection Index Method Based on Eigenanalysis

    Science.gov (United States)

    Cerón-Rojas, J. Jesús; Castillo-González, Fernando; Sahagún-Castellanos, Jaime; Santacruz-Varela, Amalio; Benítez-Riquelme, Ignacio; Crossa, José

    2008-01-01

    The traditional molecular selection index (MSI) employed in marker-assisted selection maximizes the selection response by combining information on molecular markers linked to quantitative trait loci (QTL) and phenotypic values of the traits of the individuals of interest. This study proposes an MSI based on an eigenanalysis method (molecular eigen selection index method, MESIM), where the first eigenvector is used as a selection index criterion, and its elements determine the proportion of the trait's contribution to the selection index. This article develops the theoretical framework of MESIM. Simulation results show that the genotypic means and the expected selection response from MESIM for each trait are equal to or greater than those from the traditional MSI. When several traits are simultaneously selected, MESIM performs well for traits with relatively low heritability. The main advantages of MESIM over the traditional molecular selection index are that its statistical sampling properties are known and that it does not require economic weights and thus can be used in practical applications when all or some of the traits need to be improved simultaneously. PMID:18716338

  4. A versatile platform for manipulating photonic spin and orbital states based on liquid crystal microstructures (Conference Presentation)

    Science.gov (United States)

    Lu, Yan-Qing; Hu, Wei; Ming, Yang

    2016-09-01

    Utilizing the spin degree of freedom breaks new ground for designing photonic devices. Seeking out a suitable platform for flexible steering of photonic spin states is a critical task. In this work, we demonstrate a versatile Liquid crystal (LC) based platform for manipulating photonic spin and orbital states. Owing to the photoalignment technique, the local and fine tuning of the LC medium is effectively implemented to form various anisotropic microstructures. The light-matter interaction in the corresponding medium is tailored to control the evolution of photonic spin states. The physical mechanism of such a system is investigated, and the corresponding dynamical equation is obtained. The high flexibility endows the LC-based photonic system with great value to be used for Hamiltonian engineering. As an illustration, the optical analogue of intrinsic spin Hall effect (SHE) in electronic systems is presented. The pseudospins of photons are driven to split by the anisotropic effective magnetic field arising from the inhomogeneous spin-orbit interaction (SOI) in the twisting microstructures. In virtue of the designability of the LC-based platform, the form of the interaction Hamiltonian is regulated to present diverse PSHE phenomena, which is hard to be realized in the solid electronic systems. Some representative samples are prepared for experimental observation, and the results are in good agreement with theoretical predictions. We believe the tunable LC system may shed new light on future photonic quantum applications.

  5. Molecular Beacon CNT-based Detection of SNPs

    Science.gov (United States)

    Egorova, V. P.; Krylova, H. V.; Lipnevich, I. V.; Veligura, A. A.; Shulitsky, B. G.; Y Fedotenkova, L.

    2015-11-01

    An fluorescence quenching effect due to few-walled carbon nanotubes chemically modified by carboxyl groups has been utilized to discriminate Single Nucleotide Polymorphism (SNP). It was shown that the complex obtained from these nanotube and singlestranded primer DNA is formed due to stacking interactions between the hexagons of the nanotubes and aromatic rings of nucleotide bases as well as due to establishing of hydrogen bonds between acceptor amine groups of nucleotide bases and donor carboxyl groups of the nanotubes. It has been demonstrated that these complexes may be used to make highly effective DNA biosensors detecting SNPs which operate as molecular beacons.

  6. Troger's base molecular scaffolds in dicarboxylic acid recognition.

    Science.gov (United States)

    Goswami, S; Ghosh, K; Dasgupta, S

    2000-04-07

    Artificial receptors (1-5) have been designed and synthesized from simple precursors. The chain length selectivity studies of dicarboxylic acids within the cavities of new fluorescent Troger's base molecular frameworks (1-3) have been carried out with a critical examination of their role of rigidity as well as flexibility in selective binding in comparison to receptor 5. The chiral resolution of the racemic Troger's base receptors (1 and 2) by chiral recognition with (+)- camphoric acid using hydrogen-bonding interactions has been studied.

  7. High-temperature molecular magnets based on cyanovanadate building blocks: spontaneous magnetization at 230 k.

    Science.gov (United States)

    Entley, W R; Girolami, G S

    1995-04-21

    The molecular-based magnetic materials Cs(2)Mn(||)[V(||)(CN)(6)] (1) and (Et(4)N)(0.5)Mn(l.25)- [V(CN)(5)].2H(2)O (2) (where Et is ethyl) were prepared by the addition of manganese(II) triflate to aqueous solutions of the hexacyanovanadate(II) ion at 0 degrees C. Whereas 1 crystallizes in a face-centered cubic lattice, 2 crystallizes in a noncubic space group. The cesium salt (1) has features characteristic of a three-dimensional ferrimagnet with a Néel transition at 125 kelvin. The tetraethylammonium salt (2) also behaves as a three-dimensional ferrimagnet with a Néel temperature of 230 kelvin; only two other molecular magnets have higher magnetic ordering temperatures. Saturation magnetization measurements indicate that in both compounds the V(II) and high-spin Mn(II) centers are antiferromagnetically coupled. Both 1 and 2 exhibit hysteresis loops characteristic of soft magnets below their magnetic phase-transition temperatures. The high magnetic ordering temperatures of these cyano-bridged solids confirm that the incorporation of early transition elements into the lattice promotes stronger magnetic coupling by enhancing the backbonding into the cyanide pi* orbitals.

  8. Toward a W4-F12 approach: Can explicitly correlated and orbital-based ab initio CCSD(T) limits be reconciled?

    Science.gov (United States)

    Sylvetsky, Nitai; Peterson, Kirk A.; Karton, Amir; Martin, Jan M. L.

    2016-06-01

    In the context of high-accuracy computational thermochemistry, the valence coupled cluster with all singles and doubles (CCSD) correlation component of molecular atomization energies presents the most severe basis set convergence problem, followed by the (T) component. In the present paper, we make a detailed comparison, for an expanded version of the W4-11 thermochemistry benchmark, between, on the one hand, orbital-based CCSD/AV{5,6}Z + d and CCSD/ACV{5,6}Z extrapolation, and on the other hand CCSD-F12b calculations with cc-pVQZ-F12 and cc-pV5Z-F12 basis sets. This latter basis set, now available for H-He, B-Ne, and Al-Ar, is shown to be very close to the basis set limit. Apparent differences (which can reach 0.35 kcal/mol for systems like CCl4) between orbital-based and CCSD-F12b basis set limits disappear if basis sets with additional radial flexibility, such as ACV{5,6}Z, are used for the orbital calculation. Counterpoise calculations reveal that, while total atomization energies with V5Z-F12 basis sets are nearly free of BSSE, orbital calculations have significant BSSE even with AV(6 + d)Z basis sets, leading to non-negligible differences between raw and counterpoise-corrected extrapolated limits. This latter problem is greatly reduced by switching to ACV{5,6}Z core-valence basis sets, or simply adding an additional zeta to just the valence orbitals. Previous reports that all-electron approaches like HEAT (high-accuracy extrapolated ab-initio thermochemistry) lead to different CCSD(T) limits than "valence limit + CV correction" approaches like Feller-Peterson-Dixon and Weizmann-4 (W4) theory can be rationalized in terms of the greater radial flexibility of core-valence basis sets. For (T) corrections, conventional CCSD(T)/AV{Q,5}Z + d calculations are found to be superior to scaled or extrapolated CCSD(T)-F12b calculations of similar cost. For a W4-F12 protocol, we recommend obtaining the Hartree-Fock and valence CCSD components from CCSD-F12b/cc-pV{Q,5}Z-F12

  9. Orbital angular momentum complex spectrum analyzer for vortex light based on rotational Doppler Effect

    CERN Document Server

    Zhou, Hailong; Dong, Jianji; Zhang, Pei; Chen, Dongxu; Cai, Xinlun; Li, Fuli; Zhang, Xinliang

    2016-01-01

    The function to measure orbital angular momentum (OAM) distribution of vortex light is essential for OAM applications. Although there are lots of works to measure OAM modes, it is difficult to measure the power distribution of different OAM modes quantitatively and instantaneously, let alone measure the phase distribution among them. In this work, we demonstrate an OAM complex spectrum analyzer, which enables to measure the power and phase distribution of OAM modes simultaneously by employing rotational Doppler Effect. The original OAM mode distribution is mapped to electrical spectrum of beating signals with a photodetector. The power distribution and phase distribution of superimposed OAM beams are successfully retrieved by analyzing the electrical spectrum. We also extend the measurement to other spatial modes, such as linear polarization modes. These results represent a new landmark of spatial mode analysis and show great potentials in optical communication and OAM quantum state tomography.

  10. An Advanced Orbiting Systems Approach to Quality of Service in Space-Based Intelligent Communication Networks

    Science.gov (United States)

    Riha, Andrew P.

    2005-01-01

    As humans and robotic technologies are deployed in future constellation systems, differing traffic services will arise, e.g., realtime and non-realtime. In order to provide a quality of service framework that would allow humans and robotic technologies to interoperate over a wide and dynamic range of interactions, a method of classifying data as realtime or non-realtime is needed. In our paper, we present an approach that leverages the Consultative Committee for Space Data Systems (CCSDS) Advanced Orbiting Systems (AOS) data link protocol. Specifically, we redefine the AOS Transfer Frame Replay Flag in order to provide an automated store-and-forward approach on a per-service basis for use in the next-generation Interplanetary Network. In addition to addressing the problem of intermittent connectivity and associated services, we propose a follow-on methodology for prioritizing data through further modification of the AOS Transfer Frame.

  11. Ballistic spin interferometer based on the Rashba and Dresselhaus spin orbit interactions

    Science.gov (United States)

    Ni, Jiating; Chen, Bin; Koga, T.

    2008-09-01

    By using the Al'tshuler-Aronov-Spivak (AAS) model, we give the amplitude changing with Rashba spin-orbit interaction (SOI) and Dresselhaus SOI strength. In the first idea 1D square loop (SL), Rashba SOI acts on two sides while Dresselhaus SOI acts on the other two sides. In the second SL, we consume Rashba SOI and Dresselhaus SOI act on four sides simultaneously. This model can be replaced by another one that Rashba SOI and Dresselhaus SOI act on every side independently, and each side is twice long. We theoretically illustrate the influence of the Dresselhaus SOI on node position and number. To explain the “half oscillation” phenomenon found in experiment, we apply Dresselhaus SOI to the ideal 1D SL. The conclusion is that the Dresselhaus SOI has a strong effect on the emergence of “half oscillation”.

  12. Ballistic spin interferometer based on the Rashba and Dresselhaus spin-orbit interactions

    Energy Technology Data Exchange (ETDEWEB)

    Ni Jiating [Department of Physics, Hangzhou Normal University, Hangzhou 310018 (China)], E-mail: jtni112@hotmail.com; Chen Bin [Department of Physics, Hangzhou Normal University, Hangzhou 310018 (China); Koga, T. [Division of Electronics for Informatics, Graduate School of Information Science and Technology, Hokkaido University, N-14, W-9, Kita-ku, Sapporo, Hokkaido 060-0814 (Japan); CREST, Japan Science and Technology Agency, 4-1-8, Honchou, Kawaguchi, Saitama 332-0012 (Japan)

    2008-09-15

    By using the Al'tshuler-Aronov-Spivak (AAS) model, we give the amplitude changing with Rashba spin-orbit interaction (SOI) and Dresselhaus SOI strength. In the first idea 1D square loop (SL), Rashba SOI acts on two sides while Dresselhaus SOI acts on the other two sides. In the second SL, we consume Rashba SOI and Dresselhaus SOI act on four sides simultaneously. This model can be replaced by another one that Rashba SOI and Dresselhaus SOI act on every side independently, and each side is twice long. We theoretically illustrate the influence of the Dresselhaus SOI on node position and number. To explain the 'half oscillation' phenomenon found in experiment, we apply Dresselhaus SOI to the ideal 1D SL. The conclusion is that the Dresselhaus SOI has a strong effect on the emergence of 'half oscillation'.

  13. International Space Station as a Base Camp for Exploration Beyond Low Earth Orbit

    Science.gov (United States)

    Raftery, Michael; Hoffman, Jeffrey

    2011-01-01

    The idea for using the International Space Station (ISS) as platform for exploration has matured in the past year and the concept continues to gain momentum. ISS provides a robust infrastructure which can be used to test systems and capabilities needed for missions to the Moon, Mars, asteroids and other potential destinations. International cooperation is a critical enabler and ISS has already demonstrated successful management of a large multi-national technical endeavor. Systems and resources needed for expeditions can be aggregated and thoroughly tested at ISS before departure thus providing wide operational flexibility and the best assurance of mission success. A small part of ISS called an Exploration Platform (ISS-EP) can be placed at Earth-Moon Libration point 1 (EML1) providing immediate benefits and flexibility for future exploration missions. We will show how ISS and the ISS-EP can be used to reduce risk and improve the operational flexibility for missions beyond low earth orbit. Life support systems and other technology developed for ISS can be evolved and adapted to the ISS-EP and other exploration spacecraft. New technology, such as electric propulsion and advanced life support systems can be tested and proven at ISS as part of an incremental development program. Commercial companies who are introducing transportation and other services will benefit with opportunities to contribute to the mission since ISS will serve as a focal point for the commercialization of low earth orbit services. Finally, we will show how use of ISS provides immediate benefits to the scientific community because its capabilities are available today and certain critical aspects of exploration missions can be simulated.

  14. Photomechanical Bending of Azobenzene-Based Photochromic Molecular Fibers

    Directory of Open Access Journals (Sweden)

    Riku Matsui

    2013-03-01

    Full Text Available Microfibers composed of azobenzene-based photochromic amorphous molecular materials, namely low molecular-mass photochromic materials with a glass-forming property, could be fabricated. These fibers were found to exhibit mechanical bending motion upon irradiation with a laser beam. In addition, the bending direction could be controlled by altering the polarization direction of the irradiated light without changing the position of the light source or the wavelength of the light. In-situ fluorescence observation of mass transport induced at the surface of the fiber doped with CdSe quantum dots suggested that the bending motions were related with the photoinduced mass transport taking place near the irradiated surface of the fiber.

  15. Affinity sensor based on immobilized molecular imprinted synthetic recognition elements.

    Science.gov (United States)

    Lenain, Pieterjan; De Saeger, Sarah; Mattiasson, Bo; Hedström, Martin

    2015-07-15

    An affinity sensor based on capacitive transduction was developed to detect a model compound, metergoline, in a continuous flow system. This system simulates the monitoring of low-molecular weight organic compounds in natural flowing waters, i.e. rivers and streams. During operation in such scenarios, control of the experimental parameters is not possible, which poses a true analytical challenge. A two-step approach was used to produce a sensor for metergoline. Submicron spherical molecularly imprinted polymers, used as recognition elements, were obtained through emulsion polymerization and subsequently coupled to the sensor surface by electropolymerization. This way, a robust and reusable sensor was obtained that regenerated spontaneously under the natural conditions in a river. Small organic compounds could be analyzed in water without manipulating the binding or regeneration conditions, thereby offering a viable tool for on-site application.

  16. Accelerating convergence of molecular dynamics-based structural relaxation

    DEFF Research Database (Denmark)

    Christensen, Asbjørn

    2005-01-01

    We describe strategies to accelerate the terminal stage of molecular dynamics (MD)based relaxation algorithms, where a large fraction of the computational resources are used. First, we analyze the qualitative and quantitative behavior of the QuickMin family of MD relaxation algorithms and explore...... the influence of spectral properties and dimensionality of the molecular system on the algorithm efficiency. We test two algorithms, the MinMax and Lanczos, for spectral estimation from an MD trajectory, and use this to derive a practical scheme of time step adaptation in MD relaxation algorithms to improve...... efficiency. We also discuss the implementation aspects. Secondly, we explore the final state refinement acceleration by a combination with the conjugate gradient technique, where the key ingredient is an implicit corrector step. Finally, we test the feasibility of passive Hessian matrix accumulation from...

  17. Study of the molecular structure, ionization spectrum, and electronic wave function of 1,3-butadiene using electron momentum spectroscopy and benchmark Dyson orbital theories

    Science.gov (United States)

    Deleuze, M. S.; Knippenberg, S.

    2006-09-01

    The scope of the present work is to reconcile electron momentum spectroscopy with elementary thermodynamics, and refute conclusions drawn by Saha et al. in J. Chem. Phys. 123, 124315 (2005) regarding fingerprints of the gauche conformational isomer of 1,3-butadiene in electron momentum distributions that were experimentally inferred from gas phase (e,2e) measurements on this compound [M. J. Brunger et al., J. Chem. Phys. 108, 1859 (1998)]. Our analysis is based on thorough calculations of one-electron and shake-up ionization spectra employing one-particle Green's function theory along with the benchmark third-order algebraic diagrammatic construction [ADC(3)] scheme. Accurate spherically averaged electron momentum distributions are correspondingly computed from the related Dyson orbitals. The ionization spectra and Dyson orbital momentum distributions that were computed for the trans-conformer of 1,3-butadiene alone are amply sufficient to quantitatively unravel the shape of all available experimental (e,2e) electron momentum distributions. A comparison of theoretical ADC(3) spectra for the s-trans and gauche energy minima with inner- and outer-valence high-resolution photoelectron measurements employing a synchrotron radiation beam [D. M. P. Holland et al., J. Phys. B 29, 3091 (1996)] demonstrates that the gauche structure is incompatible with ionization experiments in high-vacuum conditions and at standard temperatures. On the other hand, outer-valence Green's function calculations on the s-trans energy minimum form and approaching basis set completeness provide highly quantitative insights, within ˜0.2eV accuracy, into the available experimental one-electron ionization energies. At last, analysis of the angular dependence of relative (e,2e) ionization intensities nicely confirms the presence of one rather intense π-2 π*+1 satellite at ˜13.1eV in the ionization spectrum of the s-trans conformer.

  18. The Calculation of NMR Chemical Shifts in Periodic Systems Based on Gauge Including Atomic Orbitals and Density Functional Theory.

    Science.gov (United States)

    Skachkov, Dmitry; Krykunov, Mykhaylo; Kadantsev, Eugene; Ziegler, Tom

    2010-05-11

    We present here a method that can calculate NMR shielding tensors from first principles for systems with translational invariance. Our approach is based on Kohn-Sham density functional theory and gauge-including atomic orbitals. Our scheme determines the shielding tensor as the second derivative of the total electronic energy with respect to an external magnetic field and a nuclear magnetic moment. The induced current density due to a periodic perturbation from nuclear magnetic moments is obtained through numerical differentiation, whereas the influence of the responding perturbation in terms of the external magnetic field is evaluated analytically. The method is implemented into the periodic program BAND. It employs a Bloch basis set made up of Slater-type or numeric atomic orbitals and represents the Kohn-Sham potential fully without the use of effective core potentials. Results from calculations of NMR shielding constants based on the present approach are presented for isolated molecules as well as systems with one-, two- and three-dimensional periodicity. The reported values are compared to experiment and results from calculations on cluster models.

  19. Vortex Laser based on III-V semiconductor metasurface: direct generation of coherent Laguerre-Gauss modes carrying controlled orbital angular momentum.

    Science.gov (United States)

    Seghilani, Mohamed S; Myara, Mikhael; Sellahi, Mohamed; Legratiet, Luc; Sagnes, Isabelle; Beaudoin, Grégoire; Lalanne, Philippe; Garnache, Arnaud

    2016-12-05

    The generation of a coherent state, supporting a large photon number, with controlled orbital-angular-momentum L = ħl (of charge l per photon) presents both fundamental and technological challenges: we demonstrate a surface-emitting laser, based on III-V semiconductor technology with an integrated metasurface, generating vortex-like coherent state in the Laguerre-Gauss basis. We use a first order phase perturbation to lift orbital degeneracy of wavefunctions, by introducing a weak anisotropy called here "orbital birefringence", based on a dielectric metasurface. The azimuthal symmetry breakdown and non-linear laser dynamics create "orbital gain dichroism" allowing selecting vortex handedness. This coherent photonic device was characterized and studied, experimentally and theoretically. It exhibits a low divergence (50 dB vortex purity), and single frequency operation in a stable low noise regime (0.1% rms). Such high performance laser opens the path to widespread new photonic applications.

  20. Experimental investigation of the EPR parameters and molecular orbital bonding coefficients for VO2+ ion in NaH2PO4·2H2O single crystals

    Science.gov (United States)

    Kalfaoğlu, Emel; Karabulut, Bünyamin

    2016-09-01

    Electron paramagnetic resonance (EPR) spectra of VO2+ ions in NaH2PO4·2H2O single crystal have been studied. The spin-Hamiltonian parameters and molecular orbital bonding coefficients were calculated. The angular variation of the EPR spectra shows two different VO2+ complexes. These are located in different chemical environment and each environment contains four magnetically inequivalent VO2+ sites. The crystal field around VO2+ ion is approximately axially symmetric since a strong V=O bond distorts the crystal lattice. Spin Hamiltonian parameters and molecular orbital bonding coefficients were calculated from the EPR data and the nature of bonding in the complex was discussed together.