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Sample records for large basis ab

  1. Large basis ab initio shell model investigation of {sup 9}Be and {sup 11}Be

    SciTech Connect

    Forssen, C.; Navratil, P.; Ormand, W.E.; Caurier, E.

    2005-04-01

    We present the first ab initio structure investigation of the loosely bound {sup 11}Be nucleus, together with a study of the lighter isotope {sup 9}Be. The nuclear structure of these isotopes is particularly interesting because of the appearance of a parity-inverted ground state in {sup 11}Be. Our study is performed in the framework of the ab initio no-core shell model. Results obtained using four different, high-precision two-nucleon interactions, in model spaces up to 9({Dirac_h}/2{pi}){omega}, are shown. For both nuclei, and all potentials, we reach convergence in the level ordering of positive- and negative-parity spectra separately. Concerning their relative position, the positive-parity states are always too high in excitation energy, but a fast drop with respect to the negative-parity spectrum is observed when the model space is increased. This behavior is most dramatic for {sup 11}Be. In the largest model space we were able to reach, the 1/2{sup +} level has dropped down to become either the first or the second excited state, depending on which interaction we use. We also observe a contrasting behavior in the convergence patterns for different two-nucleon potentials and argue that a three-nucleon interaction is needed to explain the parity inversion. Furthermore, large-basis calculations of {sup 13}C and {sup 11}B are performed. This allows us to study the systematics of the position of the first unnatural-parity state in the N=7 isotone and the A=11 isobar. The {sup 11}B run in the 9({Dirac_h}/2{pi}){omega} model space involves a matrix with dimension exceeding 1.1x10{sup 9}, and is our largest calculation so far. We present results on binding energies, excitation spectra, level configurations, radii, electromagnetic observables, and {sup 10}Be+n overlap functions.

  2. Multiple-Timestep ab Initio Molecular Dynamics Using an Atomic Basis Set Partitioning.

    PubMed

    Steele, Ryan P

    2015-12-17

    This work describes an approach to accelerate ab initio Born-Oppenheimer molecular dynamics (MD) simulations by exploiting the inherent timescale separation between contributions from different atom-centered Gaussian basis sets. Several MD steps are propagated with a cost-efficient, low-level basis set, after which a dynamical correction accounts for large basis set relaxation effects in a time-reversible fashion. This multiple-timestep scheme is shown to generate valid MD trajectories, on the basis of rigorous testing for water clusters, the methanol dimer, an alanine polypeptide, protonated hydrazine, and the oxidized water dimer. This new approach generates observables that are consistent with those of target basis set trajectories, including MD-based vibrational spectra. This protocol is shown to be valid for Hartree-Fock, density functional theory, and second-order Møller-Plesset perturbation theory approaches. Recommended pairings include 6-31G as a low-level basis set for 6-31G** or 6-311G**, as well as cc-pVDZ as the subset for accurate dynamics with aug-cc-pVTZ. Demonstrated cost savings include factors of 2.6-7.3 on the systems tested and are expected to remain valid across system sizes.

  3. Vicinal proton—proton coupling constants. Basis set dependence in SCF ab initio calculations

    NASA Astrophysics Data System (ADS)

    San-Fabián, Jesús; Guilleme, Joaquín; Díez, Ernesto; Lazzeretti, Paolo; Malagoli, Massimo; Zanasi, Riccardo

    1993-04-01

    An SCF ab initio study of the angular dependence and substituent effects upon the vicinal coupling constants has been carried out for the molecules CH 3CH 3, CH 2FCH 3 and CHF 2CH 3. The four contributions to 3JHH ( JFC, JSD, JOD and JOP) have been computed using the STO-3G, 6-31G, 6-31G * and 6-31G ** basis sets. The major contributions arise from the FC term. The magnitude of the SD contributions is very small and near independent of the size of the basis set. The magnitude of the orbital contributions OR (=OD+OP) decreases as the size of the basis set increases. The FC term slightly overestimates both the individual and the interaction substituent effects for basis sets larger than the STO-3G one. For this basis such effects are underestimated.

  4. Challenges for large scale ab initio Quantum Monte Carlo

    NASA Astrophysics Data System (ADS)

    Kent, Paul

    2015-03-01

    Ab initio Quantum Monte Carlo is an electronic structure method that is highly accurate, well suited to large scale computation, and potentially systematically improvable in accuracy. Due to increases in computer power, the method has been applied to systems where established electronic structure methods have difficulty reaching the accuracies desired to inform experiment without empiricism, a necessary step in the design of materials and a helpful step in the improvement of cheaper and less accurate methods. Recent applications include accurate phase diagrams of simple materials through to phenomena in transition metal oxides. Nevertheless there remain significant challenges to achieving a methodology that is robust and systematically improvable in practice, as well as capable of exploiting the latest generation of high-performance computers. In this talk I will describe the current state of the art, recent applications, and several significant challenges for continued improvement. Supported through the Predictive Theory and Modeling for Materials and Chemical Science program by the Office of Basic Energy Sciences (BES), Department of Energy (DOE).

  5. Physical basis of large microtubule aster growth

    PubMed Central

    Ishihara, Keisuke; Korolev, Kirill S; Mitchison, Timothy J

    2016-01-01

    Microtubule asters - radial arrays of microtubules organized by centrosomes - play a fundamental role in the spatial coordination of animal cells. The standard model of aster growth assumes a fixed number of microtubules originating from the centrosomes. However, aster morphology in this model does not scale with cell size, and we recently found evidence for non-centrosomal microtubule nucleation. Here, we combine autocatalytic nucleation and polymerization dynamics to develop a biophysical model of aster growth. Our model predicts that asters expand as traveling waves and recapitulates all major aspects of aster growth. With increasing nucleation rate, the model predicts an explosive transition from stationary to growing asters with a discontinuous jump of the aster velocity to a nonzero value. Experiments in frog egg extract confirm the main theoretical predictions. Our results suggest that asters observed in large fish and amphibian eggs are a meshwork of short, unstable microtubules maintained by autocatalytic nucleation and provide a paradigm for the assembly of robust and evolvable polymer networks. DOI: http://dx.doi.org/10.7554/eLife.19145.001 PMID:27892852

  6. An ab initio investigation of disiloxane using extended basis sets and electron correlation

    SciTech Connect

    Nicholas, J.B.; Hopfinger, A.J.; Winans, R.E.

    1992-10-01

    The ab initio structure of disiloxane (H{sub 3}Si-O-SiH{sub 3}) is studied with a series of basis sets of increasing quality, including extended basis sets and explicit electron correlation at the single-reference single-and double-excitation configuration interaction (SDCI) level. The calculated molecular geometry and barrier to linearization of the Si-O-Si bond angle are compared to experimental and previous theoretical values. Results show that the rigorous expansion of the basis set leads to a good agreement with experimental data at the restricted Hartree-Fock (RHF) level. The potential energy curves and force constants for variation of the Si-O-Si angle and the Si-H and Si-O bond lengths are calculated and discussed in relationship to molecular modeling of zeolites and clays. The authors also investigated coupling between the Si-O bond and Si-O bond angle. They discuss the effects of temperature on the comparison between theoretical and experimental results. 46 refs., 4 figs., 4 tabs.

  7. Ab Initio Density Fitting: Accuracy Assessment of Auxiliary Basis Sets from Cholesky Decompositions.

    PubMed

    Boström, Jonas; Aquilante, Francesco; Pedersen, Thomas Bondo; Lindh, Roland

    2009-06-09

    The accuracy of auxiliary basis sets derived by Cholesky decompositions of the electron repulsion integrals is assessed in a series of benchmarks on total ground state energies and dipole moments of a large test set of molecules. The test set includes molecules composed of atoms from the first three rows of the periodic table as well as transition metals. The accuracy of the auxiliary basis sets are tested for the 6-31G**, correlation consistent, and atomic natural orbital basis sets at the Hartree-Fock, density functional theory, and second-order Møller-Plesset levels of theory. By decreasing the decomposition threshold, a hierarchy of auxiliary basis sets is obtained with accuracies ranging from that of standard auxiliary basis sets to that of conventional integral treatments.

  8. Structural basis for fragmenting the exopolysaccharide of Acinetobacter baumannii by bacteriophage ΦAB6 tailspike protein

    PubMed Central

    Lee, I-Ming; Tu, I-Fan; Yang, Feng-Ling; Ko, Tzu-Ping; Liao, Jiahn-Haur; Lin, Nien-Tsung; Wu, Chung-Yi; Ren, Chien-Tai; Wang, Andrew H.-J.; Chang, Ching-Ming; Huang, Kai-Fa; Wu, Shih-Hsiung

    2017-01-01

    With an increase in antibiotic-resistant strains, the nosocomial pathogen Acinetobacter baumannii has become a serious threat to global health. Glycoconjugate vaccines containing fragments of bacterial exopolysaccharide (EPS) are an emerging therapeutic to combat bacterial infection. Herein, we characterize the bacteriophage ΦAB6 tailspike protein (TSP), which specifically hydrolyzed the EPS of A. baumannii strain 54149 (Ab-54149). Ab-54149 EPS exhibited the same chemical structure as two antibiotic-resistant A. baumannii strains. The ΦAB6 TSP-digested products comprised oligosaccharides of two repeat units, typically with stoichiometric pseudaminic acid (Pse). The 1.48-1.89-Å resolution crystal structures of an N-terminally-truncated ΦAB6 TSP and its complexes with the semi-hydrolyzed products revealed a trimeric β-helix architecture that bears intersubunit carbohydrate-binding grooves, with some features unusual to the TSP family. The structures suggest that Pse in the substrate is an important recognition site for ΦAB6 TSP. A region in the carbohydrate-binding groove is identified as the determinant of product specificity. The structures also elucidated a retaining mechanism, for which the catalytic residues were verified by site-directed mutagenesis. Our findings provide a structural basis for engineering the enzyme to produce desired oligosaccharides, which is useful for the development of glycoconjugate vaccines against A. baumannii infection. PMID:28209973

  9. Structural basis for fragmenting the exopolysaccharide of Acinetobacter baumannii by bacteriophage ΦAB6 tailspike protein.

    PubMed

    Lee, I-Ming; Tu, I-Fan; Yang, Feng-Ling; Ko, Tzu-Ping; Liao, Jiahn-Haur; Lin, Nien-Tsung; Wu, Chung-Yi; Ren, Chien-Tai; Wang, Andrew H-J; Chang, Ching-Ming; Huang, Kai-Fa; Wu, Shih-Hsiung

    2017-02-17

    With an increase in antibiotic-resistant strains, the nosocomial pathogen Acinetobacter baumannii has become a serious threat to global health. Glycoconjugate vaccines containing fragments of bacterial exopolysaccharide (EPS) are an emerging therapeutic to combat bacterial infection. Herein, we characterize the bacteriophage ΦAB6 tailspike protein (TSP), which specifically hydrolyzed the EPS of A. baumannii strain 54149 (Ab-54149). Ab-54149 EPS exhibited the same chemical structure as two antibiotic-resistant A. baumannii strains. The ΦAB6 TSP-digested products comprised oligosaccharides of two repeat units, typically with stoichiometric pseudaminic acid (Pse). The 1.48-1.89-Å resolution crystal structures of an N-terminally-truncated ΦAB6 TSP and its complexes with the semi-hydrolyzed products revealed a trimeric β-helix architecture that bears intersubunit carbohydrate-binding grooves, with some features unusual to the TSP family. The structures suggest that Pse in the substrate is an important recognition site for ΦAB6 TSP. A region in the carbohydrate-binding groove is identified as the determinant of product specificity. The structures also elucidated a retaining mechanism, for which the catalytic residues were verified by site-directed mutagenesis. Our findings provide a structural basis for engineering the enzyme to produce desired oligosaccharides, which is useful for the development of glycoconjugate vaccines against A. baumannii infection.

  10. On the feasibility of ab initio electronic structure calculations for Cu using a single s orbital basis

    SciTech Connect

    Hegde, Ganesh Bowen, R. Chris

    2015-10-15

    The accuracy of a single s-orbital representation of Cu towards enabling multi-thousand atom ab initio calculations of electronic structure is evaluated in this work. If an electrostatic compensation charge of 0.3 electron per atom is used in this basis representation, the electronic transmission in bulk and nanocrystalline Cu can be made to compare accurately to that obtained with a Double Zeta Polarized basis set. The use of this representation is analogous to the use of single band effective mass representation for semiconductor electronic structure. With a basis of just one s-orbital per Cu atom, the representation is extremely computationally efficient and can be used to provide much needed ab initio insight into electronic transport in nanocrystalline Cu interconnects at realistic dimensions of several thousand atoms.

  11. Achieving the Complete-Basis Limit in Large Molecular Clusters: Computationally Efficient Procedures to Eliminate Basis-Set Superposition Error

    NASA Astrophysics Data System (ADS)

    Richard, Ryan M.; Herbert, John M.

    2013-06-01

    Previous electronic structure studies that have relied on fragmentation have been primarily interested in those methods' abilities to replicate the supersystem energy (or a related energy difference) without recourse to the ability of those supersystem results to replicate experiment or high accuracy benchmarks. Here we focus on replicating accurate ab initio benchmarks, that are suitable for comparison to experimental data. In doing this it becomes imperative that we correct our methods for basis-set superposition errors (BSSE) in a computationally feasible way. This criterion leads us to develop a new method for BSSE correction, which we term the many-body counterpoise correction, or MBn for short. MBn is truncated at order n, in much the same manner as a normal many-body expansion leading to a decrease in computational time. Furthermore, its formulation in terms of fragments makes it especially suitable for use with pre-existing fragment codes. A secondary focus of this study is directed at assessing fragment methods' abilities to extrapolate to the complete basis set (CBS) limit as well as compute approximate triples corrections. Ultimately, by analysis of (H_2O)_6 and (H_2O)_{10}F^- systems, it is concluded that with large enough basis-sets (triple or quad zeta) fragment based methods can replicate high level benchmarks in a fraction of the time.

  12. Efficacy of the SU(3) scheme for ab initio large-scale calculations beyond the lightest nuclei

    SciTech Connect

    Dytrych, T.; Maris, Pieter; Launey, K. D.; Draayer, J. P.; Vary, James; Langr, D.; Saule, E.; Caprio, M. A.; Catalyurek, U.; Sosonkina, M.

    2016-06-09

    We report on the computational characteristics of ab initio nuclear structure calculations in a symmetry-adapted no-core shell model (SA-NCSM) framework. We examine the computational complexity of the current implementation of the SA-NCSM approach, dubbed LSU3shell, by analyzing ab initio results for 6Li and 12C in large harmonic oscillator model spaces and SU(3)-selected subspaces. We demonstrate LSU3shell's strong-scaling properties achieved with highly-parallel methods for computing the many-body matrix elements. Results compare favorably with complete model space calculations and signi cant memory savings are achieved in physically important applications. In particular, a well-chosen symmetry-adapted basis a ords memory savings in calculations of states with a fixed total angular momentum in large model spaces while exactly preserving translational invariance.

  13. Molecular tailoring approach: a route for ab initio treatment of large clusters.

    PubMed

    Sahu, Nityananda; Gadre, Shridhar R

    2014-09-16

    system is broken down into two or more subsystems that can be readily treated computationally. Finally, the properties of the large system are obtained by patching the corresponding properties of all the subsystems. Due to these approximations, the resulting MTA-based energies carry some error in comparison with calculations based on the full system. An approach for correcting these errors has been attempted by grafting the error at a lower basis set onto a higher basis set. Furthermore, investigating the growth patterns and nucleation processes in clusters is necessary for understanding the structural transitions and the phenomena of magic numbers in cluster chemistry. Therefore, systematic building-up or the introduction of stochastics for generating molecular assemblies is the most crucial step for studying large clusters. In this Account, we discuss the working principle of MTA for probing molecular clusters at ab initio level followed by a brief summary of an automated and electrostatics-guided algorithm for building molecular assemblies. The molecular aggregates presented here as test cases are generated based on either an electrostatic criterion or the basin hopping method. At MP2 level computation, the errors in MTA-based grafted energies are typically reduced to a submillihartree level, reflecting the potential of finding accurate energies of molecular clusters much more quickly. In summary, MTA provides a platform for effectively studying large molecular clusters at ab initio level of theory using minimal computer hardware.

  14. High Yield Chemical Vapor Deposition Growth of High Quality Large-Area AB Stacked Bilayer Graphene

    PubMed Central

    Liu, Lixin; Zhou, Hailong; Cheng, Rui; Yu, Woo Jong; Liu, Yuan; Chen, Yu; Shaw, Jonathan; Zhong, Xing; Huang, Yu; Duan, Xiangfeng

    2012-01-01

    Bernal stacked (AB stacked) bilayer graphene is of significant interest for functional electronic and photonic devices due to the feasibility to continuously tune its band gap with a vertical electrical field. Mechanical exfoliation can be used to produce AB stacked bilayer graphene flakes but typically with the sizes limited to a few micrometers. Chemical vapor deposition (CVD) has been recently explored for the synthesis of bilayer graphene but usually with limited coverage and a mixture of AB and randomly stacked structures. Herein we report a rational approach to produce large-area high quality AB stacked bilayer graphene. We show that the self-limiting effect of graphene growth on Cu foil can be broken by using a high H2/CH4 ratio in a low pressure CVD process to enable the continued growth of bilayer graphene. A high temperature and low pressure nucleation step is found to be critical for the formation of bilayer graphene nuclei with high AB stacking ratio. A rational design of a two-step CVD process is developed for the growth of bilayer graphene with high AB stacking ratio (up to 90 %) and high coverage (up to 99 %). The electrical transport studies demonstrated that devices made of the as-grown bilayer graphene exhibit typical characteristics of AB stacked bilayer graphene with the highest carrier mobility exceeding 4,000 cm2/V·s at room temperature, comparable to that of the exfoliated bilayer graphene. PMID:22906199

  15. Importance of the ligand basis set in ab initio thermochemical calculations of transition metal species

    NASA Astrophysics Data System (ADS)

    Plascencia, Cesar; Wang, Jiaqi; Wilson, Angela K.

    2017-10-01

    The impact of basis set choice has been considered for a series of transition metal (TM) species. The need for higher level correlation consistent basis sets on both the metal and ligand has been investigated, and permutations in the pairings of basis set used for TM's and basis set used for ligands can lead to effective routes to complete basis set (CBS) limit extrapolations of thermochemical energetics with little change in thermochemical predictions as compared to those resulting from the use of traditional basis set pairings, while enabling computational cost savings. Basis set superposition errors (BSSE) that can arise have also been considered.

  16. Ab initio lifetime correction to scattering states for time-dependent electronic-structure calculations with incomplete basis sets

    NASA Astrophysics Data System (ADS)

    Coccia, Emanuele; Assaraf, Roland; Luppi, Eleonora; Toulouse, Julien

    2017-07-01

    We propose a method for obtaining effective lifetimes of scattering electronic states for avoiding the artificial confinement of the wave function due to the use of incomplete basis sets in time-dependent electronic-structure calculations of atoms and molecules. In this method, using a fitting procedure, the lifetimes are extracted from the spatial asymptotic decay of the approximate scattering wave functions obtained with a given basis set. The method is based on a rigorous analysis of the complex-energy solutions of the Schrödinger equation. It gives lifetimes adapted to any given basis set without using any empirical parameters. The method can be considered as an ab initio version of the heuristic lifetime model of Klinkusch et al. [J. Chem. Phys. 131, 114304 (2009)]. The method is validated on H and He atoms using Gaussian-type basis sets for the calculation of high-harmonic-generation spectra.

  17. Ab initio large unit cell calculations of the electronic structure of diamond nanocrystals

    NASA Astrophysics Data System (ADS)

    Abdulsattar, Mudar A.

    2011-05-01

    In order to reduce computational efforts, and separate surface and core properties, diamond nanocrystals in the present model is represented by a heterojunction between the surface and the core in which the surface represents the outer most four layers and the core by the rest of the internal region of nanocrystal. Ab initio restricted Hartree-Fock (RHF) method coupled with the large unit cell method (LUC) is used to determine the electronic structure and physical properties of diamond nanocrystals core part with different sizes. The use of STO-3G basis choice is made to be able to compare to semiempirical methods using the complete neglect of differential overlap (CNDO) that uses Slater type orbitals (STO). The oxygenated (001)-(1 × 1) facet that expands with larger sizes of nanocrystals is also investigated to determine the rule of the surface in nanocrystals electronic structure. The results show that the present method agrees with semiempirical method contraction of lattice constant with increasing nanocrystal size but disagrees with energy gap variation with nanocrystal size in some regions. After nearly 1.4 nm the energy gap which is controlled by surface states begins to rise. The lowest unoccupied molecular orbital (LUMO) is attributed to surface states that largely reduce the value of energy gap. The sources of disagreement between semiempirical and ab initio results are discussed. The present method shows a maximum increment of the lattice constant by 3.3% over the calculated bulk for the smallest diamond nanocrystals. The surface states are found mostly non-degenerated because of the effect of surface discontinuity and oxygen atoms. Valance and conduction bands are wider on the surface due to splitting and oxygen atoms. The method also shows fluctuations in the converged energy gap, valence band width and cohesive energy of the core part of nanocrystal. These fluctuations might partially explain the controversial experimental results for diamond

  18. Auxiliary basis expansions for large-scale electronic structure calculations.

    PubMed

    Jung, Yousung; Sodt, Alex; Gill, Peter M W; Head-Gordon, Martin

    2005-05-10

    One way to reduce the computational cost of electronic structure calculations is to use auxiliary basis expansions to approximate four-center integrals in terms of two- and three-center integrals, usually by using the variationally optimum Coulomb metric to determine the expansion coefficients. However, the long-range decay behavior of the auxiliary basis expansion coefficients has not been characterized. We find that this decay can be surprisingly slow. Numerical experiments on linear alkanes and a toy model both show that the decay can be as slow as 1/r in the distance between the auxiliary function and the fitted charge distribution. The Coulomb metric fitting equations also involve divergent matrix elements for extended systems treated with periodic boundary conditions. An attenuated Coulomb metric that is short-range can eliminate these oddities without substantially degrading calculated relative energies. The sparsity of the fit coefficients is assessed on simple hydrocarbon molecules and shows quite early onset of linear growth in the number of significant coefficients with system size using the attenuated Coulomb metric. Hence it is possible to design linear scaling auxiliary basis methods without additional approximations to treat large systems.

  19. Basis sets for ab initio periodic Hartree-Fock studies of zeolite/adsorbate interactions: He, Ne, and Ar in silica sodalite

    SciTech Connect

    Nada, R.; Nicholas, J.B.; McCarthy, M.I.; Hess, A.C.

    1996-11-15

    Silica sodalite is an ideal model system to establish base-line computer requirements of ab initio periodic Hartree-Fock (PHF) calculations of zeolites. In this article, the authors investigate the effect of various basis sets on the structural and electronic properties of bulk silica sodalite. They also study the interaction of He, Ne, and Ar with the sodalite cage. This work shows that basis-set superposition errors (BSSE) in calculations using STO-3G and 6-21G(*) basis sets are as large as the interaction energies, leading to poor confidence in the results. To cure this problem, the authors present high-quality basis sets for si, O, He, Ne, and Ar, optimized for use with PHF methods, and demonstrate that the new basis set greatly reduces BSSE. The theoretical barriers for transfer of the rare gases between sodalite cages are 5.6, 13.2, and 62.1 kcal/mol for He, Ne, and Ar. 27 refs., 6 figs., 8 tabs.

  20. Ab initio GW quasiparticle energies of small sodium clusters by an all-electron mixed-basis approach

    NASA Astrophysics Data System (ADS)

    Ishii, Soh; Ohno, Kaoru; Kawazoe, Yoshiyuki; Louie, Steven G.

    2001-04-01

    A state-of-the-art GW calculation is carried out for small sodium clusters, Na2, Na4, Na6, and Na8. The quasiparticle energies are evaluated by employing an ab initio GW code based on an all-electron mixed-basis approach, which uses both plane waves and atomic orbitals as basis functions. The calculated ionization potential and the electron affinity are in excellent agreement with available experimental data. The exchange and correlation parts to the electron self-energy within the GW approximation are presented from the viewpoint of their size dependence. In addition, the effect of the off-diagonal elements of the self-energy corrections to the local-density-approximation exchange-correlation potential is discussed. Na2 and Na8 have a larger energy gap than Na4 and Na6, consistent with the fact that they are magic number clusters.

  1. Ab initio large-amplitude quantum-tunneling dynamics in vinyl radical: a vibrationally adiabatic approach.

    PubMed

    Nesbitt, David J; Dong, Feng

    2008-04-21

    Large-amplitude tunneling in vinyl radical over a C2v planar transition state involves CCH bending excitation coupled to all other internal coordinates, resulting in a significant dependence of barrier height and shape on vibrational degrees of freedom at the zero-point level. An ab initio potential surface for vinyl radical has been calculated at the CCSD(T) level (AVnZ; n=2, 3, 4, 5) for vibrationally adiabatic 1D motion along the planar CCH bending tunneling coordinate, extrapolated to the complete basis set (CBS) limit and corrected for anharmonic zero-point effects. The polyatomic reduced moment of inertia is calculated explicitly as a function of tunneling coordinate, with eigenvalues and tunneling splittings obtained from numerical solution of the resulting 1D Schrödinger equation. Linear scaling of the CBS potential to match predicted and observed tunneling splittings empirically yields an adiabatic barrier height of DeltaEadiab=1696(20) cm(-1) which, when corrected for zero-point energy contributions, translates into an effective barrier of DeltaEeff=1602(20) cm(-1) consistent with estimates (DeltaE=1580(100) cm(-1)) by Tanaka and coworkers [J. Chem. Phys., 2004, 120, 3604-3618]. These zero-point-corrected potential surfaces are used to predict tunneling dynamics in vibrationally excited states of vinyl radical, providing strong support for previous jet-cooled high-resolution infrared studies [Dong et al., J. Phys. Chem. A, 2006, 110, 3059-3070] in the symmetric CH2 stretch mode.

  2. An extended basis set {ital ab} {ital initio} study of alkali metal cation--water clusters

    SciTech Connect

    Feller, D.; Glendening, E.D.; Woon, D.E.; Feyereisen, M.W.

    1995-09-01

    Ionic clusters comprised of a single alkali metal cation and up to eight water molecules were studied at the Hartree--Fock and correlated levels of theory using the correlation consistent sequence of basis sets. Estimates of the degree of convergence in the computed properties with respect to the complete basis set limit were facilitated by the underlying systematic manner in which the correlation consistent sets approach completeness. In favorable cases, improved property values could be obtained by fitting finite basis set results with a simple analytical expression in order to extrapolate to the complete basis set limit. The sensitivity of structures and binding energies were analyzed with regard to the inclusion of valence and core-valence correlation recovery at the MP2, MP4, and CCSD(T) levels of theory. The replacement of metal core electrons and the introduction of relativistic contributions via effective core potentials was compared to corresponding all-electron results. {copyright} {ital 1995} {ital American} {ital Institute} {ital of} {ital Physics}.

  3. Ab initio modeling of carbohydrates: on the proper selection of computational methods and basis sets

    USDA-ARS?s Scientific Manuscript database

    With the development of faster computer hardware and quantum mechanical software it has become more feasible to study large carbohydrate molecules via quantum mechanical methods. In the past, studies of carbohydrates were restricted to empirical/semiempirical methods and Hartree Fock. In the last ...

  4. Ab initio nuclear many-body perturbation calculations in the Hartree-Fock basis

    NASA Astrophysics Data System (ADS)

    Hu, B. S.; Xu, F. R.; Sun, Z. H.; Vary, J. P.; Li, T.

    2016-07-01

    Starting from realistic nuclear forces, the chiral N3LO and JISP16, we have applied many-body perturbation theory (MBPT) to the structure of closed-shell nuclei, 4He and 16O. The two-body N3LO interaction is softened by a similarity renormalization group transformation while JISP16 is adopted without renormalization. The MBPT calculations are performed within the Hartree-Fock (HF) bases. The angular momentum coupled scheme is used, which can reduce the computational task. Corrections up to the third order in energy and up to the second order in radius are evaluated. Higher-order corrections in the HF basis are small relative to the leading-order perturbative result. Using the antisymmetrized Goldstone diagram expansions of the wave function, we directly correct the one-body density for the calculation of the radius, rather than calculate corrections to the occupation probabilities of single-particle orbits as found in other treatments. We compare our results with other methods where available and find good agreement. This supports the conclusion that our methods produce reasonably converged results with these interactions. We also compare our results with experimental data.

  5. Dynamical properties of liquid water from ab initio molecular dynamics performed in the complete basis set limit

    NASA Astrophysics Data System (ADS)

    Lee, Hee-Seung; Tuckerman, Mark E.

    2007-04-01

    Dynamical properties of liquid water were studied using Car-Parrinello [Phys. Rev. Lett. 55, 2471 (1985)] ab initio molecular dynamics (AIMD) simulations within the Kohn-Sham (KS) density functional theory employing the Becke-Lee-Yang-Parr exchange-correlation functional for the electronic structure. The KS orbitals were expanded in a discrete variable representation basis set, wherein the complete basis set limit can be easily reached and which, therefore, provides complete convergence of ionic forces. In order to minimize possible nonergodic behavior of the simulated water system in a constant energy (NVE) ensemble, a long equilibration run (30ps) preceded a 60ps long production run. The temperature drift during the entire 60ps trajectory was found to be minimal. The diffusion coefficient [0.055Å2/ps] obtained from the present work for 32 D2O molecules is a factor of 4 smaller than the most up to date experimental value, but significantly larger than those of other recent AIMD studies. Adjusting the experimental result so as to match the finite-sized system used in the present study brings the comparison between theory and experiment to within a factor of 3. More importantly, the system is not observed to become "glassy" as has been reported in previous AIMD studies. The computed infrared spectrum is in good agreement with experimental data, especially in the low frequency regime where the translational and librational motions of water are manifested. The long simulation length also made it possible to perform detailed studies of hydrogen bond dynamics. The relaxation dynamics of hydrogen bonds observed in the present AIMD simulation is slower than those of popular force fields, such as the TIP4P potential, but comparable to that of the TIP5P potential.

  6. Accurate ab initio dipole moment surfaces of ozone: First principle intensity predictions for rotationally resolved spectra in a large range of overtone and combination bands

    NASA Astrophysics Data System (ADS)

    Tyuterev, Vladimir G.; Kochanov, Roman V.; Tashkun, Sergey A.

    2017-02-01

    Ab initio dipole moment surfaces (DMSs) of the ozone molecule are computed using the MRCI-SD method with AVQZ, AV5Z, and VQZ-F12 basis sets on a dense grid of about 1950 geometrical configurations. The analytical DMS representation used for the fit of ab initio points provides better behavior for large nuclear displacements than that of previous studies. Various DMS models were derived and tested. Vibration-rotation line intensities of 16O3 were calculated from these ab initio surfaces by the variational method using two different potential functions determined in our previous works. For the first time, a very good agreement of first principle calculations with the experiment was obtained for the line-by-line intensities in rotationally resolved ozone spectra in a large far- and mid-infrared range. This includes high overtone and combination bands up to Δ V = 6. A particular challenge was a correct description of the B-type bands (even Δ V3 values) that represented major difficulties for the previous ab initio investigations and for the empirical spectroscopic models. The major patterns of various B-type bands were correctly described without empirically adjusted dipole moment parameters. For the 10 μ m range, which is of key importance for the atmospheric ozone retrievals, our ab initio intensity results are within the experimental error margins. The theoretical values for the strongest lines of the ν3 band lie in general between two successive versions of HITRAN (HIgh-resolution molecular TRANsmission) empirical database that corresponded to most extended available sets of observations. The overall qualitative agreement in a large wavenumber range for rotationally resolved cold and hot ozone bands up to about 6000 cm-1 is achieved here for the first time. These calculations reveal that several weak bands are yet missing from available spectroscopic databases.

  7. Accurate ab initio dipole moment surfaces of ozone: First principle intensity predictions for rotationally resolved spectra in a large range of overtone and combination bands.

    PubMed

    Tyuterev, Vladimir G; Kochanov, Roman V; Tashkun, Sergey A

    2017-02-14

    Ab initio dipole moment surfaces (DMSs) of the ozone molecule are computed using the MRCI-SD method with AVQZ, AV5Z, and VQZ-F12 basis sets on a dense grid of about 1950 geometrical configurations. The analytical DMS representation used for the fit of ab initio points provides better behavior for large nuclear displacements than that of previous studies. Various DMS models were derived and tested. Vibration-rotation line intensities of (16)O3 were calculated from these ab initio surfaces by the variational method using two different potential functions determined in our previous works. For the first time, a very good agreement of first principle calculations with the experiment was obtained for the line-by-line intensities in rotationally resolved ozone spectra in a large far- and mid-infrared range. This includes high overtone and combination bands up to ΔV = 6. A particular challenge was a correct description of the B-type bands (even ΔV3 values) that represented major difficulties for the previous ab initio investigations and for the empirical spectroscopic models. The major patterns of various B-type bands were correctly described without empirically adjusted dipole moment parameters. For the 10 μm range, which is of key importance for the atmospheric ozone retrievals, our ab initio intensity results are within the experimental error margins. The theoretical values for the strongest lines of the ν3 band lie in general between two successive versions of HITRAN (HIgh-resolution molecular TRANsmission) empirical database that corresponded to most extended available sets of observations. The overall qualitative agreement in a large wavenumber range for rotationally resolved cold and hot ozone bands up to about 6000 cm(-1) is achieved here for the first time. These calculations reveal that several weak bands are yet missing from available spectroscopic databases.

  8. Large-scale ab initio investigation of lithium intercalation in single-walled nanotubes

    NASA Astrophysics Data System (ADS)

    Meunier, V.; Roland, Ch.; Bernholc, J.

    2001-03-01

    Both experiments and theory have shown that carbon nanotubes can take up more Li per carbon atom than graphite. There is therefore considerable interest in carbon nanotubes as a material for energy storage. To assess the usefulness of nanotubes as a battery material, we have carried out large-scale ab initio simulations of Li adsorption on both individual nanotubes and in nanotube ropes. Specific issues addressed include the effects of metallicity on Li adsorption, charge transfer effects, and the effects of topological defects (e.g., 5-7 pairs that form in highly strained nanotubes or during growth, larger 8-membered rings and open-ended nanotube fragments) in either localizing the Li ions, or in enhancing the permeability of the defective nanotubes. Furthermore, in order to understand the dynamics of Li motion, we have calculated activation energies for diffusive jumps of Li ions along and across nanotube walls both inside and outside nanotubes.

  9. High-yield chemical vapor deposition growth of high-quality large-area AB-stacked bilayer graphene.

    PubMed

    Liu, Lixin; Zhou, Hailong; Cheng, Rui; Yu, Woo Jong; Liu, Yuan; Chen, Yu; Shaw, Jonathan; Zhong, Xing; Huang, Yu; Duan, Xiangfeng

    2012-09-25

    Bernal-stacked (AB-stacked) bilayer graphene is of significant interest for functional electronic and photonic devices due to the feasibility to continuously tune its band gap with a vertical electric field. Mechanical exfoliation can be used to produce AB-stacked bilayer graphene flakes but typically with the sizes limited to a few micrometers. Chemical vapor deposition (CVD) has been recently explored for the synthesis of bilayer graphene but usually with limited coverage and a mixture of AB- and randomly stacked structures. Herein we report a rational approach to produce large-area high-quality AB-stacked bilayer graphene. We show that the self-limiting effect of graphene growth on Cu foil can be broken by using a high H(2)/CH(4) ratio in a low-pressure CVD process to enable the continued growth of bilayer graphene. A high-temperature and low-pressure nucleation step is found to be critical for the formation of bilayer graphene nuclei with high AB stacking ratio. A rational design of a two-step CVD process is developed for the growth of bilayer graphene with high AB stacking ratio (up to 90%) and high coverage (up to 99%). The electrical transport studies demonstrate that devices made of the as-grown bilayer graphene exhibit typical characteristics of AB-stacked bilayer graphene with the highest carrier mobility exceeding 4000 cm(2)/V · s at room temperature, comparable to that of the exfoliated bilayer graphene.

  10. Possibly similar genetic basis of resistance to Bacillus thuringiensis Cry1Ab protein in 3 resistant colonies of the sugarcane borer collected from Louisiana, USA.

    PubMed

    Yang, Fei; Chen, Mao; Gowda, Anilkumar; Kerns, David L; Huang, Fangneng

    2016-11-08

    The sugarcane borer, Diatraea saccharalis (F.), is a major maize borer pest and a target of transgenic maize expressing Bacillus thuringiensis (Bt) proteins in South America and the mid-southern region of the United States. Evolution of resistance in target pest populations is a great threat to the long-term efficacy of Bt crops. In this study, we compared the genetic basis of resistance to Cry1Ab protein in 3 resistant colonies of sugarcane borer established from field populations in Louisiana, USA. Responses of larvae to the Cry1Ab protein for the parental and 10 other cross colonies were assayed in a diet-incorporated bioassay. All 3 resistant colonies were highly resistant to the Cry1Ab protein with a resistance ratio of >555.6 fold. No maternal effect or sex linkage was evident for the resistance in the 3 colonies; and the resistance was functionally nonrecessive at the Cry1Ab concentrations of ≤ 3.16 μg/g, but it became recessive at ≥10 μg/g. In an interstrain complementation test for allelism, the F1 progeny from crosses between any 2 of the 3 resistant colonies exhibited the similar resistance levels as their parental colonies, indicating that the 3 colonies most likely shared a locus of Cry1Ab resistance. Results generated from this study should provide useful information in developing effective strategies for managing Bt resistance in the insect.

  11. Scalable fine-grained parallelization of plane-wave-based ab initio molecular dynamics for large supercomputers.

    PubMed

    Vadali, Ramkumar V; Shi, Yan; Kumar, Sameer; Kale, Laxmikant V; Tuckerman, Mark E; Martyna, Glenn J

    2004-12-01

    Many systems of great importance in material science, chemistry, solid-state physics, and biophysics require forces generated from an electronic structure calculation, as opposed to an empirically derived force law to describe their properties adequately. The use of such forces as input to Newton's equations of motion forms the basis of the ab initio molecular dynamics method, which is able to treat the dynamics of chemical bond-breaking and -forming events. However, a very large number of electronic structure calculations must be performed to compute an ab initio molecular dynamics trajectory, making the efficiency as well as the accuracy of the electronic structure representation critical issues. One efficient and accurate electronic structure method is the generalized gradient approximation to the Kohn-Sham density functional theory implemented using a plane-wave basis set and atomic pseudopotentials. The marriage of the gradient-corrected density functional approach with molecular dynamics, as pioneered by Car and Parrinello (R. Car and M. Parrinello, Phys Rev Lett 1985, 55, 2471), has been demonstrated to be capable of elucidating the atomic scale structure and dynamics underlying many complex systems at finite temperature. However, despite the relative efficiency of this approach, it has not been possible to obtain parallel scaling of the technique beyond several hundred processors on moderately sized systems using standard approaches. Consequently, the time scales that can be accessed and the degree of phase space sampling are severely limited. To take advantage of next generation computer platforms with thousands of processors such as IBM's BlueGene, a novel scalable parallelization strategy for Car-Parrinello molecular dynamics is developed using the concept of processor virtualization as embodied by the Charm++ parallel programming system. Charm++ allows the diverse elements of a Car-Parrinello molecular dynamics calculation to be interleaved with low

  12. WebMTA: a web-interface for ab initio geometry optimization of large molecules using molecular tailoring approach.

    PubMed

    Kavathekar, Ritwik; Khire, Subodh; Ganesh, V; Rahalkar, Anuja P; Gadre, Shridhar R

    2009-05-01

    A web-interface for geometry optimization of large molecules using a linear scaling method, i.e., cardinality guided molecular tailoring approach (CG-MTA), is presented. CG-MTA is a cut-and-stitch, fragmentation-based method developed in our laboratory, for linear scaling of conventional ab initio techniques. This interface provides limited access to CG-MTA-enabled GAMESS. It can be used to obtain fragmentation schemes for a given spatially extended molecule depending on the maximum allowed fragment size and minimum cut radius values provided by the user. Currently, we support submission of single point or geometry optimization jobs at Hartree-Fock and density functional theory levels of theory for systems containing between 80 to 200 first row atoms and comprising up to 1000 basis functions. The graphical user interface is built using HTML and Python at the back end. The back end farms out the jobs on an in-house Linux-based cluster running on Pentium-4 Class or higher machines using an @Home-based parallelization scheme (http://chem.unipune.ernet.in/ approximately tcg/mtaweb/).

  13. Systematic chemical variations in large 3AB iron meteorites: Clues to core crystallization

    NASA Technical Reports Server (NTRS)

    Haack, H.; Scott, E. R. D.; Rubio, G. S.; Gutierrez, D. F.; Lewis, C. F.; Wasson, J. T.; Brooks, R. R.; Guo, X.; Ryan, D. E.; Holzbecher, J.

    1993-01-01

    Analysis of numerous individual iron meteorites have shown that fractional crystallization of iron cores result in variations in chemical concentration of the solid core which span several orders of magnitude. The magnitude and direction of the resulting spatial gradients in the core can provide clues to the physical nature of the core crystallization process. We have analyzed suites of samples from three large 3AB irons (Cape York, 58t; Chupaderos, 24t; Morito, 10t) in order to estimate local chemical gradients. Initial results for the concentrations of Ge, Pd, Pt (Massey group), Ir, Au, As, Co, Os, and Rh (Dalhouse group), and P (Arizona group) show significant ranges among the Cape York and Chupaderos samples and marginally significant ranges among the Morito samples. Measurements of Au, Ir, Co, Ni, Cu, Ga, As, W, Re (from UCLA) and Ni and Co (Arizona group) are in progress. We find a spatial Ir gradient in Chupaderos with a magnitude similar to the one reported for Agpalilik (Cape York iron) by Esbensen et al.

  14. Accurate double many-body expansion potential energy surface for N3((4)A'') from correlation scaled ab initio energies with extrapolation to the complete basis set limit.

    PubMed

    Galvão, B R L; Varandas, A J C

    2009-12-31

    A new global potential energy surface is reported for the (4)A'' ground electronic state of the N(3) system from double many-body expansion theory and an extensive set of accurate ab initio energies extrapolated to the complete basis set limit. It shows three equivalent metastable potential wells for C(2v) geometries that are separated from the three N((4)S) + N(2) asymptotes by energy barriers as predicted from previous ab initio work. The potential well and barrier height now predicted lie 42.9 and 45.9 kcal mol(-1) above the atom-diatom dissociation limit, respectively, being about 1 kcal mol(-1) lower than previous theoretical estimates. The ab initio calculations here reported predict also a (4)B(1)/(4)A(2) conical intersection and reveal a new minimum with D(3h) symmetry that lies 147 kcal mol(-1) above the atom-diatom asymptote. All major topographical features of the potential energy surface are accurately described by the DMBE function, including the weakly bound van der Waals minima at large atom-diatom separations.

  15. Quantum wave packet ab initio molecular dynamics: an approach to study quantum dynamics in large systems.

    PubMed

    Iyengar, Srinivasan S; Jakowski, Jacek

    2005-03-15

    A methodology to efficiently conduct simultaneous dynamics of electrons and nuclei is presented. The approach involves quantum wave packet dynamics using an accurate banded, sparse and Toeplitz representation for the discrete free propagator, in conjunction with ab initio molecular dynamics treatment of the electronic and classical nuclear degree of freedom. The latter may be achieved either by using atom-centered density-matrix propagation or by using Born-Oppenheimer dynamics. The two components of the methodology, namely, quantum dynamics and ab initio molecular dynamics, are harnessed together using a time-dependent self-consistent field-like coupling procedure. The quantum wave packet dynamics is made computationally robust by using adaptive grids to achieve optimized sampling. One notable feature of the approach is that important quantum dynamical effects including zero-point effects, tunneling, as well as over-barrier reflections are treated accurately. The electronic degrees of freedom are simultaneously handled at accurate levels of density functional theory, including hybrid or gradient corrected approximations. Benchmark calculations are provided for proton transfer systems and the dynamics results are compared with exact calculations to determine the accuracy of the approach.

  16. Accurate ab initio calculations of the quadrupole moment of acetylene. A combined study of basis set, correlation, and vibrational effects

    NASA Astrophysics Data System (ADS)

    Lindh, R.; Liu, B.

    1991-03-01

    The quadrupole moment of acetylene has been studied at the multiconfiguration self-consistent field (MCSCF) and multireference single and double configuration interaction (MRSDCI) level of theory. At the MCSCF level the π-CI complete active space SCF (CASSCF) and the valence-CI CASSCF were employed. The subsequent MRSDCI calculations were continued until the reference space included all configuration state functions (CSFs) of the MCSCF wave function with a coefficient larger than 0.01 [MRSDCI(0.01)]. The higher level basis sets in this study were all based on van Duijneveldt's C(13s 8p) and H(6s) and extensions of that basis set. The study shows in a consistent way that both the one- and n-particle spaces are saturated at the highest level of theory. The study has revealed that in addition to the well known increase of the quadrupole moment due to the inclusion of polarizing functions in the basis (typically 0.20 a.u.), the inclusion of electronic correlation in the model wave function as well as vibrational corrections will decrease the quadrupole moment significantly more, -0.66, -0.49, and -0.36 a.u., for the correlation correction and zero-point correction for HCCH and DCCD, respectively. The most accurate computations predict the quadrupole moment of HCCH, including zero-point correction, to be 4.29±0.12 a.u., which discriminates the experimental estimates of 4.03±0.30, 4.28±0.30, and 4.57±0.30 a.u. (the first being the favored value). The quadrupole moment of DCCD is computed to 4.42±0.10 a.u. In the study it was observed that in contradiction to previous experiences the use of the model equilibrium geometries rather than the experimental geometry gives a smoother convergence as the level of theory is increased. The effects of basis set quality and electron correlation on the quadrupole moment are studied in detail. These effects are analyzed with reference to the redistribution of the electronic charge.

  17. Efficient formalism for large-scale ab initio molecular dynamics based on time-dependent density functional theory.

    PubMed

    Alonso, J L; Andrade, X; Echenique, P; Falceto, F; Prada-Gracia, D; Rubio, A

    2008-08-29

    A new "on the fly" method to perform Born-Oppenheimer ab initio molecular dynamics (AIMD) simulations is presented. Inspired by Ehrenfest dynamics in time-dependent density functional theory, the electronic orbitals are evolved by a Schrödinger-like equation, where the orbital time derivative is multiplied by a parameter. This parameter controls the time scale of the fictitious electronic motion and speeds up the calculations with respect to standard Ehrenfest dynamics. In contrast with other methods, wave function orthogonality needs not be imposed as it is automatically preserved, which is of paramount relevance for large-scale AIMD simulations.

  18. Identification of α-Fe in High-Silica Zeolites on the Basis of ab Initio Electronic Structure Calculations.

    PubMed

    Hallaert, Simon D; Bols, Max L; Vanelderen, Pieter; Schoonheydt, Robert A; Sels, Bert F; Pierloot, Kristine

    2017-09-05

    α-Fe is the precursor of the reactive Fe(IV)═O core responsible for methane oxidation in Fe-containing zeolites. To get more insight into the nature and stability of α-Fe in different zeolites, the binding of Fe(II) at six-membered-ring cation exchange sites (6MR) in ZSM-5, zeolite beta, and ferrierite was investigated using DFT and multireference ab initio methods (CASSCF/CASPT2). CASPT2 ligand field (LF) excitation energies of all sites were compared with the experimental DR-UV-vis spectra reported by Snyder et al. From this comparison it is concluded that the 16000 cm(-1) band of α-Fe, observed in all three zeolites, can uniquely be assigned to a high-spin square-planar (SP) Fe(II) located at a 6MR with an Al-Si-Si-Al sequence, where the Al atoms are positioned opposite in the ring and as close to each other as possible. The stability of such conformations is also confirmed by the binding energies obtained from DFT. The bands at 10000 cm(-1) in the experimental spectra, assigned to spectator Fe(II), are attributed to six-coordinated trigonal-prismatic Fe(II) species, as calculated for the γ-site in ZSM-5. The entatic effect of the zeolite lattice on the stability of the SP sites was investigated by making use of the unconstrained Fe(II) model complex FeL2 (with L = [Al(OH)4](-)). The SP conformer is approximately 2 kcal/mol more stable than the tetrahedral form, indicating that the SP coordination environment of α-Fe is not imposed by the zeolite lattice but rather electronically preferred by Fe(II) in the environment of four O ligands. A significant contribution to the stability of the SP conformer is provided by mixing of the doubly occupied 3dz(2) orbital with the higher lying 4s.

  19. Comparison of some dispersion-corrected and traditional functionals with CCSD(T) and MP2 ab initio methods: Dispersion, induction, and basis set superposition error

    PubMed Central

    Roy, Dipankar; Marianski, Mateusz; Maitra, Neepa T.; Dannenberg, J. J.

    2012-01-01

    We compare dispersion and induction interactions for noble gas dimers and for Ne, methane, and 2-butyne with HF and LiF using a variety of functionals (including some specifically parameterized to evaluate dispersion interactions) with ab initio methods including CCSD(T) and MP2. We see that inductive interactions tend to enhance dispersion and may be accompanied by charge-transfer. We show that the functionals do not generally follow the expected trends in interaction energies, basis set superposition errors (BSSE), and interaction distances as a function of basis set size. The functionals parameterized to treat dispersion interactions often overestimate these interactions, sometimes by quite a lot, when compared to higher level calculations. Which functionals work best depends upon the examples chosen. The B3LYP and X3LYP functionals, which do not describe pure dispersion interactions, appear to describe dispersion mixed with induction about as accurately as those parametrized to treat dispersion. We observed significant differences in high-level wavefunction calculations in a basis set larger than those used to generate the structures in many of the databases. We discuss the implications for highly parameterized functionals based on these databases, as well as the use of simple potential energy for fitting the parameters rather than experimentally determinable thermodynamic state functions that involve consideration of vibrational states. PMID:23039587

  20. Static second hyperpolarizability of diffuse electron compound M2X (M = Li, na; X = H, F): Ab-initio study of basis set effect and electron correlation

    NASA Astrophysics Data System (ADS)

    Hatua, Kaushik; Mondal, Avijit; Nandi, Prasanta K.

    2017-10-01

    Present investigation reveals that diffuse electron compounds M2X predict large (106 a.u.) γav value. The basis set dependence of γav showed that the quality of basis function rather than its size is more important. Sadlej's Pol basis set which is nearly four times less in size than aug-cc-pVQZ can give reliable estimate of γav. MP2 method in conjunction with large basis sets can give comparable results of γav that could be obtained from CCSD or CCSD(T). Higher order energy correction to MP2 leads to oscillatory behavior but inclusion of triple excitations to CCSD improves the magnitude of γav.

  1. Large scale ab initio calculations of extended defects in materials: screw dislocations in bcc metals

    NASA Astrophysics Data System (ADS)

    Dézerald, Lucile; Ventelon, Lisa; Willaime, François; Clouet, Emmanuel; Rodney, David

    2014-06-01

    Ab initio methods, based on the Density Functional Theory (DFT), have been extensively used to study point defects and defect clusters in materials. Present HPC resources and DFT codes now allow similar investigations to be performed on dislocations. The study of these extended defects requires not only larger simulation cells but also a higher accuracy because the energy differences, which are involved, are rather small, typically 50-to-100 meV for supercells containing 50-to-500 atoms. The topology of the Peierls potential of screw dislocations with 1/2 <111>Burgers vector, i.e. the 2D energy landscape seen by these dislocations, is being completely revisited by DFT calculations. From results obtained in all body-centered cubic (bcc) transition metals, except Cr (V, Nb, Ta, Mo, W and Fe), using the PWSCF code, which is part of the Quantum-Espresso package, we concluded that the 2D Peierls potentials have two common features: the single-hump shape of the barrier between two minima of the potential, and the presence of a maximum - and not a minimum as predicted by most empirical potentials - around the split core. In iron, the topology of the Peierls potential is reversed compared to the classical sinusoidal picture: the location of the saddle point and the maximum are indeed inverted with unexpected flat regions. The first results obtained within the framework of the PRACE project, DIMAIM (DIslocations in Metals using Ab Initio Methods), started at the beginning of 2013, will also be presented. In particular, in order to address the twinning-antitwinning asymmetry often observed in bcc metals and regarded as the major contribution to the breakdown of Schmid's law, we have determined the crystal orientation dependence of the Peierls stress, i.e. the critical stress required for dislocation motion. These computationally most expensive simulations were performed on the PRACE Tier-0 system at Barcelona Supercomputing Center (Marenostrum III). The scalability results

  2. Curvy-steps approach to constraint-free extended-Lagrangian ab initio molecular dynamics, using atom-centered basis functions: convergence toward Born-Oppenheimer trajectories.

    PubMed

    Herbert, John M; Head-Gordon, Martin

    2004-12-15

    A dynamical extension of the "curvy-steps" approach to linear-scaling self-consistent field calculations is presented, which yields an extended-Lagrangian formulation of ab initio molecular dynamics. An exponential parametrization of the one-electron density matrix, expressed in terms of atom-centered Gaussian basis functions, facilitates propagation along the manifold of density matrices in a geometrically correct fashion that automatically enforces idempotency constraints. The extended Lagrangian itself is constraint free, thus neither density matrix purification nor expensive, iterative solution for Lagrange multipliers is required. Propagation is highly efficient, and time steps compare favorably to those used in Car-Parrinello molecular dynamics simulations. The behavior of the method, especially with regard to the maintenance of adiabatic decoupling of nuclei and electrons, is examined for a sequence of diatomic molecules, and comparison is made to trajectories propagated on the converged Born-Oppenheimer surface. Certain claims to the contrary notwithstanding, our results demonstrate that vibrational frequencies may depend on the value of the fictitious mass parameter, even in an atom-centered basis. Light-atom stretching frequencies can be significantly redshifted, even when the nuclear and electronic energy scales are well separated. With a sufficiently small fictitious mass and a short time step, accurate frequencies can be obtained; we characterize appropriate values of these parameters for a wide range of vibrational frequencies.

  3. Large-Eddy Simulation using Orthogonal Projection onto Local Basis Functions

    NASA Astrophysics Data System (ADS)

    Pope, Stephen B.

    1999-11-01

    A new approach is described for the large-eddy simulation of inhomogeneous turbulent flows. The resolved velocity field is defined as a finite basis function representation in terms of local basis functions (e.g., B-splines or finite elements). The equations governing the resolved fields are therefore ordinary differential equations for the basis-function coefficients, rather than the partial differential equations that arise in the standard filtering approach (for inhomogeneous flows). As a consequence, issues of spatial numerical resolution and accuracy are avoided. The effects of the residual motions on the resolved fields are modelled directly in terms of the basis functions. In common with the MILES philosophy, the modelled term is significant only where the basis functions cannot accurately represent the non-linear terms; and its effect is to prevent oscillations in the fields. While the method is intended for the inhomogeneous turbulent flows governed by the Navier-Stokes equations, it is demonstrated in the simpler setting of Burgers' equation. The method is shown to perform well; and (for a given number of degrees of freedom) to be able to resolve a substantially greater range of lengthscales than the traditional methodology using the Smagorinsky model.

  4. Use of reduced basis technique in the inverse dynamics of large space cranes

    NASA Technical Reports Server (NTRS)

    Das, S. K.; Utku, S.; Wada, B. K.

    1990-01-01

    The inverse dynamics of adaptive structures used as space cranes can prove computationally expensive in the case of large structures, due to the large number of degrees of freedom involved. Consequently, reduced basis techniques (reduction techniques) are frequently used to reduce the problem size to a time manageable level (for possible use in real time control). A reduced basis technique is proposed which is different from, but related to, the path-derivatives reduction technique. A linearly independent set of deflection n-tuples is used, chosen at the beginning of the time range in which it is wished to reduce the equations, in whose subspace it is assumed that the deflection vectors of the unreduced problem will lie (approximately).

  5. Large Atomic Natural Orbital Basis Sets for the First Transition Row Atoms

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R. (Technical Monitor)

    1994-01-01

    Large atomic natural orbital (ANO) basis sets are tabulated for the Sc to Cu. The primitive sets are taken from the large sets optimized by Partridge, namely (21s 13p 8d) for Sc and Ti and (20s 12p 9d) for V to Cu. These primitive sets are supplemented with three p, one d, six f, and four g functions. The ANO sets are derived from configuration interaction density matrices constructed as the average of the lowest states derived from the 3d(sup n)4s(sup 2) and 3d(sup n+1)4s(sup 1) occupations. For Ni, the 1S(3d(sup 10)) state is included in the averaging. The choice of basis sets for molecular calculations is discussed.

  6. Comment on ``Accurate Hartree-Fock energy of extended systems using large Gaussian basis sets''

    NASA Astrophysics Data System (ADS)

    Civalleri, Bartolomeo; Orlando, Roberto; Zicovich-Wilson, Claudio M.; Roetti, Carla; Saunders, Victor R.; Pisani, Cesare; Dovesi, Roberto

    2010-03-01

    In a recent paper on Hartree-Fock (HF) calculations on solid LiH with large Gaussian-type basis sets, Paier [Phys. Rev. B 80, 174114 (2009)] report a comment that we dispute: that similar calculations appear unlikely to be feasible using the CRYSTAL code. Here we show that using a full HF approach within periodic boundary conditions as implemented in the CRYSTAL code the same total energy is obtained as from the schemes adopted by Paier

  7. Robust Periodic Hartree-Fock Exchange for Large-Scale Simulations Using Gaussian Basis Sets.

    PubMed

    Guidon, Manuel; Hutter, Jürg; VandeVondele, Joost

    2009-11-10

    Hartree-Fock exchange with a truncated Coulomb operator has recently been discussed in the context of periodic plane-waves calculations [Spencer, J.; Alavi, A. Phys. Rev. B: Solid State, 2008, 77, 193110]. In this work, this approach is extended to Gaussian basis sets, leading to a stable and accurate procedure for evaluating Hartree-Fock exchange at the Γ-point. Furthermore, it has been found that standard hybrid functionals can be transformed into short-range functionals without loss of accuracy. The well-defined short-range nature of the truncated exchange operator can naturally be exploited in integral screening procedures and makes this approach interesting for both condensed phase and gas phase systems. The presented Hartree-Fock implementation is massively parallel and scales up to ten thousands of cores. This makes it feasible to perform highly accurate calculations on systems containing thousands of atoms or ten thousands of basis functions. The applicability of this scheme is demonstrated by calculating the cohesive energy of a LiH crystal close to the Hartree-Fock basis set limit and by performing an electronic structure calculation of a complete protein (rubredoxin) in solution with a large and flexible basis set.

  8. Efficient solution of Poisson's equation using discrete variable representation basis sets for Car-Parrinello ab initio molecular dynamics simulations with cluster boundary conditions

    NASA Astrophysics Data System (ADS)

    Lee, Hee-Seung; Tuckerman, Mark E.

    2008-12-01

    An efficient computational approach to perform Car-Parrinello ab initio molecular dynamics (CPAIMD) simulations under cluster (free) boundary conditions is presented. The general approach builds upon a recent real-space CPAIMD formalism using discrete variable representation (DVR) basis sets [Y. Liu et al., Phys. Rev. B 12, 125110 (2003); H.-S. Lee and M. E. Tuckerman, J. Phys. Chem. A 110, 5549 (2006)]. In order to satisfy cluster boundary conditions, a DVR based on sinc functions is utilized to expand the Kohn-Sham orbitals and electron density. Poisson's equation is solved in order to calculate the Hartree potential via an integral representation of the 1/r singularity. Excellent convergence properties are achieved with respect to the number of grid points (or DVR functions) and the size of the simulation cell. A straightforward implementation of the present approach leads to near linear scaling [O(N4/3)] of the computational cost with respect to the system size (N) for the solution of Poisson's equation. The accuracy and stability of CPAIMD simulations based on sinc DVR are tested for a model problem as well as for N2 and a water dimer.

  9. Efficient solution of Poisson's equation using discrete variable representation basis sets for Car-Parrinello ab initio molecular dynamics simulations with cluster boundary conditions.

    PubMed

    Lee, Hee-Seung; Tuckerman, Mark E

    2008-12-14

    An efficient computational approach to perform Car-Parrinello ab initio molecular dynamics (CPAIMD) simulations under cluster (free) boundary conditions is presented. The general approach builds upon a recent real-space CPAIMD formalism using discrete variable representation (DVR) basis sets [Y. Liu et al., Phys. Rev. B 12, 125110 (2003); H.-S. Lee and M. E. Tuckerman, J. Phys. Chem. A 110, 5549 (2006)]. In order to satisfy cluster boundary conditions, a DVR based on sinc functions is utilized to expand the Kohn-Sham orbitals and electron density. Poisson's equation is solved in order to calculate the Hartree potential via an integral representation of the 1/r singularity. Excellent convergence properties are achieved with respect to the number of grid points (or DVR functions) and the size of the simulation cell. A straightforward implementation of the present approach leads to near linear scaling [O(N(4/3))] of the computational cost with respect to the system size (N) for the solution of Poisson's equation. The accuracy and stability of CPAIMD simulations based on sinc DVR are tested for a model problem as well as for N(2) and a water dimer.

  10. Efficient preconditioning of the electronic structure problem in large scale ab initio molecular dynamics simulations

    SciTech Connect

    Schiffmann, Florian; VandeVondele, Joost

    2015-06-28

    We present an improved preconditioning scheme for electronic structure calculations based on the orbital transformation method. First, a preconditioner is developed which includes information from the full Kohn-Sham matrix but avoids computationally demanding diagonalisation steps in its construction. This reduces the computational cost of its construction, eliminating a bottleneck in large scale simulations, while maintaining rapid convergence. In addition, a modified form of Hotelling’s iterative inversion is introduced to replace the exact inversion of the preconditioner matrix. This method is highly effective during molecular dynamics (MD), as the solution obtained in earlier MD steps is a suitable initial guess. Filtering small elements during sparse matrix multiplication leads to linear scaling inversion, while retaining robustness, already for relatively small systems. For system sizes ranging from a few hundred to a few thousand atoms, which are typical for many practical applications, the improvements to the algorithm lead to a 2-5 fold speedup per MD step.

  11. Efficient preconditioning of the electronic structure problem in large scale ab initio molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Schiffmann, Florian; VandeVondele, Joost

    2015-06-01

    We present an improved preconditioning scheme for electronic structure calculations based on the orbital transformation method. First, a preconditioner is developed which includes information from the full Kohn-Sham matrix but avoids computationally demanding diagonalisation steps in its construction. This reduces the computational cost of its construction, eliminating a bottleneck in large scale simulations, while maintaining rapid convergence. In addition, a modified form of Hotelling's iterative inversion is introduced to replace the exact inversion of the preconditioner matrix. This method is highly effective during molecular dynamics (MD), as the solution obtained in earlier MD steps is a suitable initial guess. Filtering small elements during sparse matrix multiplication leads to linear scaling inversion, while retaining robustness, already for relatively small systems. For system sizes ranging from a few hundred to a few thousand atoms, which are typical for many practical applications, the improvements to the algorithm lead to a 2-5 fold speedup per MD step.

  12. Ab initio phenomenological simulation of the growth of large tumor cell populations

    NASA Astrophysics Data System (ADS)

    Chignola, Roberto; DelFabbro, Alessio; Dalla Pellegrina, Chiara; Milotti, Edoardo

    2007-06-01

    In a previous paper we have introduced a phenomenological model of cell metabolism and of the cell cycle to simulate the behavior of large tumor cell populations (Chignola and Milotti 2005 Phys. Biol. 2 8). Here we describe a refined and extended version of the model that includes some of the complex interactions between cells and their surrounding environment. The present version takes into consideration several additional energy-consuming biochemical pathways such as protein and DNA synthesis, the tuning of extracellular pH and of the cell membrane potential. The control of the cell cycle, which was previously modeled by means of ad hoc thresholds, has been directly addressed here by considering checkpoints from proteins that act as targets for phosphorylation on multiple sites. As simulated cells grow, they can now modify the chemical composition of the surrounding environment which in turn acts as a feedback mechanism to tune cell metabolism and hence cell proliferation: in this way we obtain growth curves that match quite well those observed in vitro with human leukemia cell lines. The model is strongly constrained and returns results that can be directly compared with actual experiments, because it uses parameter values in narrow ranges estimated from experimental data, and in perspective we hope to utilize it to develop in silico studies of the growth of very large tumor cell populations (106 cells or more) and to support experimental research. In particular, the program is used here to make predictions on the behavior of cells grown in a glucose-poor medium: these predictions are confirmed by experimental observation.

  13. Ghost transmission: How large basis sets can make electron transport calculations worse

    SciTech Connect

    Herrmann, Carmen; Solomon, Gemma C.; Subotnik, Joseph E.; Mujica, Vladimiro; Ratner, Mark A.

    2010-01-01

    The Landauer approach has proven to be an invaluable tool for calculating the electron transport properties of single molecules, especially when combined with a nonequilibrium Green’s function approach and Kohn–Sham density functional theory. However, when using large nonorthogonal atom-centered basis sets, such as those common in quantum chemistry, one can find erroneous results if the Landauer approach is applied blindly. In fact, basis sets of triple-zeta quality or higher sometimes result in an artificially high transmission and possibly even qualitatively wrong conclusions regarding chemical trends. In these cases, transport persists when molecular atoms are replaced by basis functions alone (“ghost atoms”). The occurrence of such ghost transmission is correlated with low-energy virtual molecular orbitals of the central subsystem and may be interpreted as a biased and thus inaccurate description of vacuum transmission. An approximate practical correction scheme is to calculate the ghost transmission and subtract it from the full transmission. As a further consequence of this study, it is recommended that sensitive molecules be used for parameter studies, in particular those whose transmission functions show antiresonance features such as benzene-based systems connected to the electrodes in meta positions and other low-conducting systems such as alkanes and silanes.

  14. A hierarchical research by large-scale and ab initio electronic structure theories—Si and Ge cleavage and stepped (111)-2×1 surfaces

    NASA Astrophysics Data System (ADS)

    Hoshi, T.; Tanikawa, M.; Ishii, A.

    2010-09-01

    The ab initio calculation with the density functional theory and plane-wave bases is carried out for stepped Si(1 1 1)-2×1 surfaces that were predicted in a cleavage simulation by the large-scale (order- N) electronic structure theory (T. Hoshi, Y. Iguchi and T. Fujiwara, Phys. Rev. B 72 (2005) 075323). The present ab initio calculation confirms the predicted stepped structure and its bias-dependent STM image. Moreover, two (meta)stable step-edge structures are found and compared. The investigation is carried out also for Ge(1 1 1)-2×1 surfaces, so as to construct a common understanding among elements. The present study demonstrates the general importance of the hierarchical research between large-scale and ab initio electronic structure theories.

  15. Accurate Hartree-Fock energy of extended systems using large Gaussian basis sets

    NASA Astrophysics Data System (ADS)

    Paier, Joachim; Diaconu, Cristian V.; Scuseria, Gustavo E.; Guidon, Manuel; Vandevondele, Joost; Hutter, Jürg

    2009-11-01

    Calculating highly accurate thermochemical properties of condensed matter via wave-function-based approaches (such as, e.g., Hartree-Fock or hybrid functionals) has recently attracted much interest. We here present two strategies providing accurate Hartree-Fock energies for solid LiH in a large Gaussian basis set and applying periodic boundary conditions. The total energies were obtained using two different approaches, namely, a supercell evaluation of Hartree-Fock exchange using a truncated Coulomb operator and an extrapolation toward the full-range Hartree-Fock limit of a Padé fit to a series of short-range screened Hartree-Fock calculations. These two techniques agreed to significant precision. We also present the Hartree-Fock cohesive energy of LiH (converged to within sub-millielectron volt) at the experimental equilibrium volume as well as the Hartree-Fock equilibrium lattice constant and bulk modulus.

  16. The new allelic variant of the subtilase cytotoxin (subAB2) is common among Shiga toxin-producing Escherichia coli strains from large game animals and their meat and meat products.

    PubMed

    Sánchez, Sergio; Díaz-Sánchez, Sandra; Martínez, Remigio; Llorente, María Teresa; Herrera-León, Silvia; Vidal, Dolors

    2013-10-25

    Subtilase cytotoxin (SubAB) is an AB5 toxin produced by Shiga toxin (Stx)-producing Escherichia coli (STEC) strains usually lacking the eae gene product intimin. Two allelic variants of SubAB encoding genes have been described: subAB1, located on a plasmid, and subAB2, located on a pathogenicity island (PAI) together with tia gene. While subAB1 has been reported to be more frequent among bovine strains, subAB2 has been mainly associated with strains from small ruminants. We investigated the presence of the two variants of subAB among 59 eae-negative STEC from large game animals (deer and wild boar) and their meat and meat products in order to assess the role of other species in the epidemiology of subAB-positive, eae-negative STEC. For this approach, the strains were PCR-screened for the presence of subAB, including the specific detection of both allelic variants, for the presence of saa, tia and sab, and for stx subtyping. Overall, subAB genes were detected in 71.2% of the strains: 84.1% of the strains from deer and 33.3% of the strains from wild boar. Most of them (97.6%) possessed subAB2 and most of these subAB2-positive strains (92.7%) were also positive for tia and negative for saa, suggesting the presence of the subAB2-harbouring PAI. Subtype stx2b was present in most of the strains (67.8%) and a statistically significant association could be established between subAB2 and stx2b. Our results suggest that large game animals, mainly deer, may represent an important animal reservoir of subAB2-positive, eae-negative STEC, and also highlight the risk of human infection posed by the consumption of large game meat and meat products.

  17. Application of the MELCOR code to design basis PWR large dry containment analysis.

    SciTech Connect

    Phillips, Jesse; Notafrancesco, Allen; Tills, Jack Lee

    2009-05-01

    The MELCOR computer code has been developed by Sandia National Laboratories under USNRC sponsorship to provide capability for independently auditing analyses submitted by reactor manufactures and utilities. MELCOR is a fully integrated code (encompassing the reactor coolant system and the containment building) that models the progression of postulated accidents in light water reactor power plants. To assess the adequacy of containment thermal-hydraulic modeling incorporated in the MELCOR code for application to PWR large dry containments, several selected demonstration designs were analyzed. This report documents MELCOR code demonstration calculations performed for postulated design basis accident (DBA) analysis (LOCA and MSLB) inside containment, which are compared to other code results. The key processes when analyzing the containment loads inside PWR large dry containments are (1) expansion and transport of high mass/energy releases, (2) heat and mass transfer to structural passive heat sinks, and (3) containment pressure reduction due to engineered safety features. A code-to-code benchmarking for DBA events showed that MELCOR predictions of maximum containment loads were equivalent to similar predictions using a qualified containment code known as CONTAIN. This equivalency was found to apply for both single- and multi-cell containment models.

  18. Structural basis for the superior activity of the large isoform of snow flea antifreeze protein.

    PubMed

    Mok, Yee-Foong; Lin, Feng-Hsu; Graham, Laurie A; Celik, Yeliz; Braslavsky, Ido; Davies, Peter L

    2010-03-23

    The snow flea (Hypogastrum harveyi) is protected from freezing at sub-zero temperatures by a glycine-rich antifreeze protein (AFP) that binds to seed ice crystals and prevents them from growing larger. This AFP is hyperactive and comprises two isoforms [Graham, L. A., and Davies, P. L. (2005) Science 310, 461]. The larger isoform (15.7 kDa) exhibits several-fold higher activity than the smaller isoform (6.5 kDa), although it is considerably less abundant. To establish the molecular basis for this difference in activity, we determined the sequence of the large isoform. The primary sequences of these two isoforms are surprisingly divergent. However, both contain tripeptide repeats and turn motifs that enabled us to build a three-dimensional model of the large isoform based upon the six-polyproline helix structure of the small isoform. Our model contains 13 polyproline type II helices connected by proline-containing loops stacked into two flat sheets oriented antiparallel to one another. The structure is strictly amphipathic, with a hydrophilic surface on one side and a hydrophobic, putative ice-binding surface on the other. The putative ice-binding site is approximately twice as large in area as that of the small isoform, providing an explanation for the difference in activity that is consistent with other examples noted. By tagging the recombinant AFP with green fluorescent protein, we observed its binding to multiple planes of ice, especially the basal plane. This finding supports the correlation between AFP hyperactivity and basal plane binding first observed with spruce budworm AFP.

  19. Mechanical and hydrologic basis for the rapid motion of a large tidewater glacier. 1: Observations

    NASA Technical Reports Server (NTRS)

    Meier, Mark; Lundstrom, Scott; Stone, Dan; Kamb, Barclay; Engelhardt, Hermann; Humphrey, Neil; Dunlap, William W.; Fahnestock, Mark; Krimmel, Robert M.; Walters, Roy

    1994-01-01

    Measurements of glacier flow velocity and basal water pressure at two sites on Columbia Glacier, Alaska, are combined with meteorological and hydrologic data to provide an observational basis for assessing the role of water storage and basal water pressure in the rapid movement of this large glacier. During the period from July 5 to August 31, 1987, coordinated observations were made of glacier surface motion and of water level in five boreholes drilled to (or in one case near to) the glacier bed at two sites, 5 and 12 km from the terminus. Glacier velocities increased downglacier in this reach from about 4 m/d to about 7 m/d. Three types of time variation in velocity and other variables were revealed: (1) Diurnal fluctuation in water input/output, borehole water level, and ice velocity (fluctuation amplitude 5 to 8%); (2) Speed-up events in glacier motion (15-30% speed-up), lasting about three days, and ocurring at times of enhanced input of water, in some cases from rain and in others from ice ablation enhanced by strong, warm winds; (3) 'Extra-slowdown' events, in which, after a speed-up event, the ice velocity decreased in about 3 days to a level consistently lower than that prior to the speed-up event. All of the time variations were due, directly or indirectly, to variations in water input to the glacier.

  20. The molecular basis for ANE syndrome revealed by the large ribosomal subunit processome interactome

    PubMed Central

    McCann, Kathleen L; Teramoto, Takamasa; Zhang, Jun; Tanaka Hall, Traci M; Baserga, Susan J

    2016-01-01

    ANE syndrome is a ribosomopathy caused by a mutation in an RNA recognition motif of RBM28, a nucleolar protein conserved to yeast (Nop4). While patients with ANE syndrome have fewer mature ribosomes, it is unclear how this mutation disrupts ribosome assembly. Here we use yeast as a model system and show that the mutation confers growth and pre-rRNA processing defects. Recently, we found that Nop4 is a hub protein in the nucleolar large subunit (LSU) processome interactome. Here we demonstrate that the ANE syndrome mutation disrupts Nop4’s hub function by abrogating several of Nop4’s protein-protein interactions. Circular dichroism and NMR demonstrate that the ANE syndrome mutation in RRM3 of human RBM28 disrupts domain folding. We conclude that the ANE syndrome mutation generates defective protein folding which abrogates protein-protein interactions and causes faulty pre-LSU rRNA processing, thus revealing one aspect of the molecular basis of this human disease. DOI: http://dx.doi.org/10.7554/eLife.16381.001 PMID:27077951

  1. High-performance ab initio density matrix renormalization group method: Applicability to large-scale multireference problems for metal compounds

    NASA Astrophysics Data System (ADS)

    Kurashige, Yuki; Yanai, Takeshi

    2009-06-01

    This article presents an efficient and parallelized implementation of the density matrix renormalization group (DMRG) algorithm for quantum chemistry calculations. The DMRG method as a large-scale multireference electronic structure model is by nature particularly efficient for one-dimensionally correlated systems, while the present development is oriented toward applications for polynuclear transition metal compounds, in which the macroscopic one-dimensional structure of electron correlation is absent. A straightforward extension of the DMRG algorithm is proposed with further improvements and aggressive optimizations to allow its application with large multireference active space, which is often demanded for metal compound calculations. Special efficiency is achieved by making better use of sparsity and symmetry in the operator and wave function representations. By accomplishing computationally intensive DMRG calculations, the authors have found that a large number of renormalized basis states are required to represent high entanglement of the electron correlation for metal compound applications, and it is crucial to adopt auxiliary perturbative correction to the projected density matrix during the DMRG sweep optimization in order to attain proper convergence to the solution. Potential energy curve calculations for the Cr2 molecule near the known equilibrium precisely predicted the full configuration interaction energies with a correlation space of 24 electrons in 30 orbitals [denoted by (24e,30o)]. The energies are demonstrated to be accurate to 0.6mEh (the error from the extrapolated best value) when as many as 10 000 renormalized basis states are employed for the left and right DMRG block representations. The relative energy curves for [Cu2O2]2+ along the isomerization coordinate were obtained from DMRG and other correlated calculations, for which a fairly large orbital space (32e,62o) is modeled as a full correlation space. The DMRG prediction nearly overlaps

  2. The composite regulatory basis of the large X-effect in mouse speciation.

    PubMed

    Larson, Erica L; Keeble, Sara; Vanderpool, Dan; Dean, Matthew D; Good, Jeffrey M

    2016-12-20

    The disruption of meiotic sex chromosome inactivation (MSCI) has been proposed to be a major developmental mechanism underlying the rapid evolution of hybrid male sterility. We tested this idea by analyzing cell-specific gene expression across spermatogenesis in two lineages of house mice and their sterile and fertile reciprocal hybrids. We found pervasive disruption of sex chromosome gene expression in sterile hybrids at every stage of spermatogenesis. Failure of MSCI was developmentally preceded by increased silencing of autosomal genes, supporting the hypothesis that divergence at the hybrid incompatibility gene, Prdm9, results in increased rates of autosomal asynapsis which in turn triggers widespread silencing of unsynapsed chromatin. We also detected opposite patterns of postmeiotic overexpression or hyper-repression of the sex chromosomes in reciprocal hybrids, supporting the hypothesis that genomic conflict has driven functional divergence that leads to deleterious X-Y dosage imbalances in hybrids. Our developmental timeline also exposed more subtle patterns of mitotic misregulation on the X chromosome, a previously undocumented stage of spermatogenic disruption in this cross. These results indicate that multiple hybrid incompatibilities have converged on a common regulatory phenotype, the disrupted expression of the sex chromosomes during spermatogenesis. Collectively, these data reveal a composite regulatory basis to hybrid male sterility in mice that helps resolve the mechanistic underpinnings of the well-documented large X-effect in mice speciation. We propose that the inherent sensitivity of spermatogenesis to X-linked regulatory disruption has the potential to be a major driver of reproductive isolation in species with chromosomal sex determination.

  3. Basis set convergence of CCSD(T) equilibrium geometries using a large and diverse set of molecular structures

    NASA Astrophysics Data System (ADS)

    Spackman, Peter R.; Jayatilaka, Dylan; Karton, Amir

    2016-09-01

    We examine the basis set convergence of the CCSD(T) method for obtaining the structures of the 108 neutral first- and second-row species in the W4-11 database (with up to five non-hydrogen atoms). This set includes a total of 181 unique bonds: 75 H—X, 49 X—Y, 43 X=Y, and 14 X≡Y bonds (where X and Y are first- and second-row atoms). As reference values, geometries optimized at the CCSD(T)/aug'-cc-pV(6+d)Z level of theory are used. We consider the basis set convergence of the CCSD(T) method with the correlation consistent basis sets cc-pV(n+d)Z and aug'-cc-pV(n+d)Z (n = D, T, Q, 5) and the Weigend-Ahlrichs def2-n ZVPP basis sets (n = T, Q). For each increase in the highest angular momentum present in the basis set, the root-mean-square deviation (RMSD) over the bond distances is decreased by a factor of ˜4. For example, the following RMSDs are obtained for the cc-pV(n+d)Z basis sets 0.0196 (D), 0.0050 (T), 0.0015 (Q), and 0.0004 (5) Å. Similar results are obtained for the aug'-cc-pV(n+d)Z and def2-n ZVPP basis sets. The double-zeta and triple-zeta quality basis sets systematically and significantly overestimate the bond distances. A simple and cost-effective way to improve the performance of these basis sets is to scale the bond distances by an empirical scaling factor of 0.9865 (cc-pV(D+d)Z) and 0.9969 (cc-pV(T+d)Z). This results in RMSDs of 0.0080 (scaled cc-pV(D+d)Z) and 0.0029 (scaled cc-pV(T+d)Z) Å. The basis set convergence of larger basis sets can be accelerated via standard basis-set extrapolations. In addition, the basis set convergence of explicitly correlated CCSD(T)-F12 calculations is investigated in conjunction with the cc-pVnZ-F12 basis sets (n = D, T). Typically, one "gains" two angular momenta in the explicitly correlated calculations. That is, the CCSD(T)-F12/cc-pVnZ-F12 level of theory shows similar performance to the CCSD(T)/cc-pV(n+2)Z level of theory. In particular, the following RMSDs are obtained for the cc-pVnZ-F12 basis sets 0

  4. Basis set convergence of CCSD(T) equilibrium geometries using a large and diverse set of molecular structures.

    PubMed

    Spackman, Peter R; Jayatilaka, Dylan; Karton, Amir

    2016-09-14

    We examine the basis set convergence of the CCSD(T) method for obtaining the structures of the 108 neutral first- and second-row species in the W4-11 database (with up to five non-hydrogen atoms). This set includes a total of 181 unique bonds: 75 H-X, 49 X-Y, 43 X=Y, and 14 X≡Y bonds (where X and Y are first- and second-row atoms). As reference values, geometries optimized at the CCSD(T)/aug'-cc-pV(6+d)Z level of theory are used. We consider the basis set convergence of the CCSD(T) method with the correlation consistent basis sets cc-pV(n+d)Z and aug'-cc-pV(n+d)Z (n = D, T, Q, 5) and the Weigend-Ahlrichs def2-n ZVPP basis sets (n = T, Q). For each increase in the highest angular momentum present in the basis set, the root-mean-square deviation (RMSD) over the bond distances is decreased by a factor of ∼4. For example, the following RMSDs are obtained for the cc-pV(n+d)Z basis sets 0.0196 (D), 0.0050 (T), 0.0015 (Q), and 0.0004 (5) Å. Similar results are obtained for the aug'-cc-pV(n+d)Z and def2-n ZVPP basis sets. The double-zeta and triple-zeta quality basis sets systematically and significantly overestimate the bond distances. A simple and cost-effective way to improve the performance of these basis sets is to scale the bond distances by an empirical scaling factor of 0.9865 (cc-pV(D+d)Z) and 0.9969 (cc-pV(T+d)Z). This results in RMSDs of 0.0080 (scaled cc-pV(D+d)Z) and 0.0029 (scaled cc-pV(T+d)Z) Å. The basis set convergence of larger basis sets can be accelerated via standard basis-set extrapolations. In addition, the basis set convergence of explicitly correlated CCSD(T)-F12 calculations is investigated in conjunction with the cc-pVnZ-F12 basis sets (n = D, T). Typically, one "gains" two angular momenta in the explicitly correlated calculations. That is, the CCSD(T)-F12/cc-pVnZ-F12 level of theory shows similar performance to the CCSD(T)/cc-pV(n+2)Z level of theory. In particular, the following RMSDs are obtained for the cc-pVnZ-F12 basis sets 0.0019 (D

  5. Complete Genome Sequence of the Multiresistant Acinetobacter baumannii Strain AbH12O-A2, Isolated during a Large Outbreak in Spain

    PubMed Central

    Merino, M.; Alvarez-Fraga, L.; Gómez, M. J.; Aransay, A. M.; Lavín, J. L.; Chaves, F.

    2014-01-01

    We report the complete genome sequence of Acinetobacter baumannii strain AbH12O-A2, isolated during a large outbreak in Spain. The genome has 3,875,775 bp and 3,526 coding sequences, with 39.4% G+C content. The availability of this genome will facilitate the study of the pathogenicity of the Acinetobacter species. PMID:25395646

  6. Ab initio molecular orbital study of the effects of basis set size on the calculated structure and acidity of hydroxyl groups in framework molecular sieves

    SciTech Connect

    Nicholas, J.B.; Hopfinger, A.J. ); Harrison, R.J.; Iton, L.E.; Curtiss, L.A.; Winans, R.E. )

    1992-12-10

    The structures, force constants, and relative acidities of a series of molecules that mimic the geometries of terminal and bridging hydroxyl groups in various substituted zeolites and clays are calculated by ab initio molecular orbital methods. The molecules are structural analogs of disiloxane H[sub 3]T-O-TH[sub 3], and the protonated form H[sub 3]T, Si, Al, B, and P. Also included are H[sub 3]/SiO[sup [minus

  7. On the performance of large Gaussian basis sets for the computation of total atomization energies

    NASA Technical Reports Server (NTRS)

    Martin, J. M. L.

    1992-01-01

    The total atomization energies of a number of molecules have been computed using an augmented coupled-cluster method and (5s4p3d2f1g) and 4s3p2d1f) atomic natural orbital (ANO) basis sets, as well as the correlation consistent valence triple zeta plus polarization (cc-pVTZ) correlation consistent valence quadrupole zeta plus polarization (cc-pVQZ) basis sets. The performance of ANO and correlation consistent basis sets is comparable throughout, although the latter can result in significant CPU time savings. Whereas the inclusion of g functions has significant effects on the computed Sigma D(e) values, chemical accuracy is still not reached for molecules involving multiple bonds. A Gaussian-1 (G) type correction lowers the error, but not much beyond the accuracy of the G1 model itself. Using separate corrections for sigma bonds, pi bonds, and valence pairs brings down the mean absolute error to less than 1 kcal/mol for the spdf basis sets, and about 0.5 kcal/mol for the spdfg basis sets. Some conclusions on the success of the Gaussian-1 and Gaussian-2 models are drawn.

  8. Ab Initio Calculations on Large Molecules Using Molecular Fragments. Evidence of Hydrogen Bonding in Polypeptides of Glycine

    PubMed Central

    Shipman, Lester L.; Christoffersen, Ralph E.

    1972-01-01

    Ab initio calculations on di-, tri-, tetra-, and pentapeptides of glycine in various conformations are reported. Hydrogen bonding is observed as an important stabilizing force in α-helical conformations. These studies on polypeptides of glycine of reasonable size show for the first time that the forces acting to stabilize polypeptide conformations can be extracted directly from theoretical studies, without prior postulation of their existence or need for concern that neglect or approximation of various integrals may have biased the results. PMID:4508323

  9. Hydrogen diffusion in bulk and nanoclusters of MgH2 and the role of catalysts on the basis of ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    Ramzan, M.; Hussain, T.; Ahuja, R.

    2009-06-01

    We present ab initio molecular dynamics calculations based on density functional theory to study the hydrogen-deuterium exchange in bulk and nanoclusters of MgH2. Our calculations reveal the important role of catalysts to diffuse the hydrogen at low temperatures and increase the diffusion rate. We determine the diffusion constants, ⟨D⟩ of deuterium, and show the single hydrogen-deuterium exchange in bulk and nanocluster of MgH2. Our calculated value of diffusion constant of deuterium in bulk MgH2 is in excellent agreement with the experimental value. Furthermore, we show the edge site importance of catalysts in the fast diffusion of hydrogen.

  10. Large-scale all-electron density functional theory calculations using an enriched finite-element basis

    NASA Astrophysics Data System (ADS)

    Kanungo, Bikash; Gavini, Vikram

    2017-01-01

    We present a computationally efficient approach to perform large-scale all-electron density functional theory calculations by enriching the classical finite element basis with compactly supported atom-centered numerical basis functions that are constructed from the solution of the Kohn-Sham (KS) problem for single atoms. We term these numerical basis functions as enrichment functions, and the resultant basis as the enriched finite element basis. The compact support for the enrichment functions is obtained by using smooth cutoff functions, which enhances the conditioning and maintains the locality of the enriched finite element basis. The integrals involved in the evaluation of the discrete KS Hamiltonian and overlap matrix in the enriched finite element basis are computed using an adaptive quadrature grid that is constructed based on the characteristics of enrichment functions. Further, we propose an efficient scheme to invert the overlap matrix by using a blockwise matrix inversion in conjunction with special reduced-order quadrature rules, which is required to transform the discrete Kohn-Sham problem to a standard eigenvalue problem. Finally, we solve the resulting standard eigenvalue problem, in each self-consistent field iteration, by using a Chebyshev polynomial based filtering technique to compute the relevant eigenspectrum. We demonstrate the accuracy, efficiency, and parallel scalability of the proposed method on semiconducting and heavy-metallic systems of various sizes, with the largest system containing 8694 electrons. We obtain accuracies in the ground-state energies that are ˜1 mHa with reference ground-state energies employing classical finite element as well as Gaussian basis sets. Using the proposed formulation based on enriched finite element basis, for accuracies commensurate with chemical accuracy, we observe a staggering 50 -300 -fold reduction in the overall computational time when compared to classical finite element basis. Further, we find a

  11. A Large Inversion Involving GNAS Exon A/B and All Exons Encoding Gsα Is Associated With Autosomal Dominant Pseudohypoparathyroidism Type Ib (PHP1B).

    PubMed

    Grigelioniene, Giedre; Nevalainen, Pasi I; Reyes, Monica; Thiele, Susanne; Tafaj, Olta; Molinaro, Angelo; Takatani, Rieko; Ala-Houhala, Marja; Nilsson, Daniel; Eisfeldt, Jesper; Lindstrand, Anna; Kottler, Marie-Laure; Mäkitie, Outi; Jüppner, Harald

    2017-04-01

    Pseudohypoparathyroidism type Ib (PHP1B) is characterized primarily by resistance to parathyroid hormone (PTH) and thus hypocalcemia and hyperphosphatemia, in most cases without evidence for Albright hereditary osteodystrophy (AHO). PHP1B is associated with epigenetic changes at one or several differentially-methylated regions (DMRs) within GNAS, which encodes the α-subunit of the stimulatory G protein (Gsα) and splice variants thereof. Heterozygous, maternally inherited STX16 or GNAS deletions leading to isolated loss-of-methylation (LOM) at exon A/B alone or at all maternal DMRs are the cause of autosomal dominant PHP1B (AD-PHP1B). In this study, we analyzed three affected individuals, the female proband and her two sons. All three revealed isolated LOM at GNAS exon A/B, whereas the proband's healthy maternal grandmother and uncle showed normal methylation at this locus. Haplotype analysis was consistent with linkage to the STX16/GNAS region, yet no deletion could be identified. Whole-genome sequencing of one of the patients revealed a large heterozygous inversion (1,882,433 bp). The centromeric breakpoint of the inversion is located 7,225 bp downstream of GNAS exon XL, but its DMR showed no methylation abnormality, raising the possibility that the inversion disrupts a regulatory element required only for establishing or maintaining exon A/B methylation. Because our three patients presented phenotypes consistent with PHP1B, and not with PHP1A, the Gsα promoter is probably unaffected by the inversion. Our findings expand the spectrum of genetic mutations that lead to LOM at exon A/B alone and thus biallelic expression of the transcript derived from this alternative first GNAS exon. © 2017 American Society for Bone and Mineral Research. © 2017 American Society for Bone and Mineral Research.

  12. Possible calcium centers for hydrogen storage applications: An accurate many-body study by AFQMC calculations with large basis sets

    NASA Astrophysics Data System (ADS)

    Purwanto, Wirawan; Krakauer, Henry; Zhang, Shiwei; Virgus, Yudistira

    2011-03-01

    Weak H2 physisorption energies present a significant challenge to first-principle theoretical modeling and prediction of materials for H storage. There has been controversy regarding the accuracy of DFT on systems involving Ca cations. We use the auxiliary-field quantum Monte Carlo (AFQMC) method to accurately predict the binding energy of Ca + , - 4{H}2 . AFQMC scales as Nbasis3and has demonstrated accuracy similar to or better than the gold-standard coupled cluster CCSD(T) method. We apply a modified Cholesky decomposition to achieve efficient Hubbard-Stratonovich transformation in AFQMC at large basis sizes. We employ the largest correlation consistent basis sets available, up to Ca/cc-pCV5Z, to extrapolate to the complete basis limit. The calculated potential energy curve exhibits binding with a double-well structure. Supported by DOE and NSF. Calculations were performed at OLCF Jaguar and CPD.

  13. Ab initio analytical Raman intensities for periodic systems through a coupled perturbed Hartree-Fock/Kohn-Sham method in an atomic orbital basis. I. Theory.

    PubMed

    Maschio, Lorenzo; Kirtman, Bernard; Rérat, Michel; Orlando, Roberto; Dovesi, Roberto

    2013-10-28

    We present a fully analytical formulation for calculating Raman intensities of crystalline periodic systems using a local basis set. Numerical differentiation with respect to atomic coordinates and with respect to wavevectors is entirely avoided as is the determination of crystal orbital coefficient derivatives with respect to nuclear displacements. Instead, our method utilizes the orbital energy-weighted density matrix and is based on the self-consistent solution of first- and second-order Coupled Perturbed Hartree-Fock/Kohn-Sham equations for the electronic response to external electric fields at the equilibrium geometry. This method has also been implemented in the Crystal program, which uses a Gaussian type basis set.

  14. An extended basis inexact shift-invert Lanczos for the efficient solution of large-scale generalized eigenproblems

    NASA Astrophysics Data System (ADS)

    Rewieński, M.; Lamecki, A.; Mrozowski, M.

    2013-09-01

    This paper proposes a technique, based on the Inexact Shift-Invert Lanczos (ISIL) method with Inexact Jacobi Orthogonal Component Correction (IJOCC) refinement, and a preconditioned conjugate-gradient (PCG) linear solver with multilevel preconditioner, for finding several eigenvalues for generalized symmetric eigenproblems. Several eigenvalues are found by constructing (with the ISIL process) an extended projection basis. Presented results of numerical experiments confirm the technique can be effectively applied to challenging, large-scale problems characterized by very dense spectra, such as resonant cavities with spatial dimensions which are large with respect to wavelengths of the resonating electromagnetic fields. It is also shown that the proposed scheme based on inexact linear solves delivers superior performance, as compared to methods which rely on exact linear solves, indicating tremendous potential of the 'inexact solve' concept. Finally, the scheme which generates an extended projection basis is found to provide a cost-efficient alternative to classical deflation schemes when several eigenvalues are computed.

  15. Structural basis for translational surveillance by the large ribosomal subunit-associated protein quality control complex

    PubMed Central

    Lyumkis, Dmitry; Oliveira dos Passos, Dario; Tahara, Erich B.; Webb, Kristofor; Bennett, Eric J.; Vinterbo, Staal; Potter, Clinton S.; Carragher, Bridget; Joazeiro, Claudio A. P.

    2014-01-01

    All organisms have evolved mechanisms to manage the stalling of ribosomes upon translation of aberrant mRNA. In eukaryotes, the large ribosomal subunit-associated quality control complex (RQC), composed of the listerin/Ltn1 E3 ubiquitin ligase and cofactors, mediates the ubiquitylation and extraction of ribosome-stalled nascent polypeptide chains for proteasomal degradation. How RQC recognizes stalled ribosomes and performs its functions has not been understood. Using single-particle cryoelectron microscopy, we have determined the structure of the RQC complex bound to stalled 60S ribosomal subunits. The structure establishes how Ltn1 associates with the large ribosomal subunit and properly positions its E3-catalytic RING domain to mediate nascent chain ubiquitylation. The structure also reveals that a distinguishing feature of stalled 60S particles is an exposed, nascent chain-conjugated tRNA, and that the Tae2 subunit of RQC, which facilitates Ltn1 binding, is responsible for selective recognition of stalled 60S subunits. RQC components are engaged in interactions across a large span of the 60S subunit surface, connecting the tRNA in the peptidyl transferase center to the distally located nascent chain tunnel exit. This work provides insights into a mechanism linking translation and protein degradation that targets defective proteins immediately after synthesis, while ignoring nascent chains in normally translating ribosomes. PMID:25349383

  16. Structural basis for translational surveillance by the large ribosomal subunit-associated protein quality control complex.

    PubMed

    Lyumkis, Dmitry; Oliveira dos Passos, Dario; Tahara, Erich B; Webb, Kristofor; Bennett, Eric J; Vinterbo, Staal; Potter, Clinton S; Carragher, Bridget; Joazeiro, Claudio A P

    2014-11-11

    All organisms have evolved mechanisms to manage the stalling of ribosomes upon translation of aberrant mRNA. In eukaryotes, the large ribosomal subunit-associated quality control complex (RQC), composed of the listerin/Ltn1 E3 ubiquitin ligase and cofactors, mediates the ubiquitylation and extraction of ribosome-stalled nascent polypeptide chains for proteasomal degradation. How RQC recognizes stalled ribosomes and performs its functions has not been understood. Using single-particle cryoelectron microscopy, we have determined the structure of the RQC complex bound to stalled 60S ribosomal subunits. The structure establishes how Ltn1 associates with the large ribosomal subunit and properly positions its E3-catalytic RING domain to mediate nascent chain ubiquitylation. The structure also reveals that a distinguishing feature of stalled 60S particles is an exposed, nascent chain-conjugated tRNA, and that the Tae2 subunit of RQC, which facilitates Ltn1 binding, is responsible for selective recognition of stalled 60S subunits. RQC components are engaged in interactions across a large span of the 60S subunit surface, connecting the tRNA in the peptidyl transferase center to the distally located nascent chain tunnel exit. This work provides insights into a mechanism linking translation and protein degradation that targets defective proteins immediately after synthesis, while ignoring nascent chains in normally translating ribosomes.

  17. Developing the Physics Basis of Fast Ignition Experiments at Future Large Fusion-class lasers

    SciTech Connect

    Mackinnon, A J; Key, M H; Hatchett, S; MacPhee, A G; Foord, M; Tabak, M; Town, R J; Patel, P K

    2008-02-08

    The Fast Ignition (FI) concept for Inertial Confinement Fusion (ICF) has the potential to provide a significant advance in the technical attractiveness of Inertial Fusion Energy (IFE) reactors. FI differs from conventional 'central hot spot' (CHS) target ignition by using one driver (laser, heavy ion beam or Z-pinch) to create a dense fuel and a separate ultra-short, ultra-intense laser beam to ignite the dense core. FI targets can burn with {approx} 3X lower density fuel than CHS targets, resulting in (all other things being equal) lower required compression energy, relaxed drive symmetry, relaxed target smoothness tolerances, and, importantly, higher gain. The short, intense ignition pulse that drives this process interacts with extremely high energy density plasmas; the physics that controls this interaction is only now becoming accessible in the lab, and is still not well understood. The attraction of obtaining higher gains in smaller facilities has led to a worldwide explosion of effort in the studies of FI. In particular, two new US facilities to be completed in 2009/2010, OMEGA/OMEGA EP and NIF-ARC (as well as others overseas) will include FI investigations as part of their program. These new facilities will be able to approach FI conditions much more closely than heretofore using direct drive (dd) for OMEGA/OMEGA EP and indirect drive (id) for NIF-ARC. This LDRD has provided the physics basis for the development of the detailed design for integrated Fast ignition experiments on these facilities on the 2010/2011 timescale. A strategic initiative LDRD has now been formed to carry out integrated experiments using NIF ARC beams to heat a full scale FI assembled core by the end of 2010.

  18. Large variation among photoreceptors as the basis of visual flexibility in the common backswimmer

    PubMed Central

    Immonen, Esa-Ville; Ignatova, Irina; Gislen, Anna; Warrant, Eric; Vähäsöyrinki, Mikko; Weckström, Matti; Frolov, Roman

    2014-01-01

    The common backswimmer, Notonecta glauca, uses vision by day and night for functions such as underwater prey animal capture and flight in search of new habitats. Although previous studies have identified some of the physiological mechanisms facilitating such flexibility in the animal's vision, neither the biophysics of Notonecta photoreceptors nor possible cellular adaptations are known. Here, we studied Notonecta photoreceptors using patch-clamp and intracellular recording methods. Photoreceptor size (approximated by capacitance) was positively correlated with absolute sensitivity and acceptance angles. Information rate measurements indicated that large and more sensitive photoreceptors performed better than small ones. Our results suggest that backswimmers are adapted for vision in both dim and well-illuminated environments by having open-rhabdom eyes with large intrinsic variation in absolute sensitivity among photoreceptors, exceeding those found in purely diurnal or nocturnal species. Both electrophysiology and microscopic analysis of retinal structure suggest two retinal subsystems: the largest peripheral photoreceptors provide vision in dim light and the smaller peripheral and central photoreceptors function primarily in sunlight, with light-dependent pigment screening further contributing to adaptation in this system by dynamically recruiting photoreceptors with varying sensitivity into the operational pool. PMID:25274359

  19. Large variation among photoreceptors as the basis of visual flexibility in the common backswimmer.

    PubMed

    Immonen, Esa-Ville; Ignatova, Irina; Gislen, Anna; Warrant, Eric; Vähäsöyrinki, Mikko; Weckström, Matti; Frolov, Roman

    2014-11-22

    The common backswimmer, Notonecta glauca, uses vision by day and night for functions such as underwater prey animal capture and flight in search of new habitats. Although previous studies have identified some of the physiological mechanisms facilitating such flexibility in the animal's vision, neither the biophysics of Notonecta photoreceptors nor possible cellular adaptations are known. Here, we studied Notonecta photoreceptors using patch-clamp and intracellular recording methods. Photoreceptor size (approximated by capacitance) was positively correlated with absolute sensitivity and acceptance angles. Information rate measurements indicated that large and more sensitive photoreceptors performed better than small ones. Our results suggest that backswimmers are adapted for vision in both dim and well-illuminated environments by having open-rhabdom eyes with large intrinsic variation in absolute sensitivity among photoreceptors, exceeding those found in purely diurnal or nocturnal species. Both electrophysiology and microscopic analysis of retinal structure suggest two retinal subsystems: the largest peripheral photoreceptors provide vision in dim light and the smaller peripheral and central photoreceptors function primarily in sunlight, with light-dependent pigment screening further contributing to adaptation in this system by dynamically recruiting photoreceptors with varying sensitivity into the operational pool.

  20. Structural basis of laminin binding to the LARGE glycans on dystroglycan

    PubMed Central

    Briggs, David C.; Yoshida-Moriguchi, Takako; Zheng, Tianqing; Venzke, David; Anderson, Mary; Strazzulli, Andrea; Moracci, Marco; Yu, Liping; Hohenester, Erhard; Campbell, Kevin P.

    2016-01-01

    Dystroglycan is a highly glycosylated extracellular matrix receptor with essential functions in skeletal muscle and the nervous system. Reduced matrix binding by α-dystroglycan (α-DG) due to perturbed glycosylation is a pathological feature of several forms of muscular dystrophy. Like-acetylglucosaminyltransferase (LARGE) synthesizes the matrix-binding heteropolysaccharide [-glucuronic acid-β1,3-xylose-α1,3-]n. Using a dual exoglycosidase digestion, we confirm that this polysaccharide is present on native α-DG from skeletal muscle. The atomic details of matrix binding were revealed by a high-resolution crystal structure of laminin G-like (LG) domains 4-5 of laminin α2 bound to a LARGE-synthesized oligosaccharide. A single glucuronic acid-β1,3-xylose disaccharide repeat straddles a Ca2+ ion in the LG4 domain, with oxygen atoms from both sugars replacing Ca2+-bound water molecules. The chelating binding mode accounts for the high affinity of this protein-carbohydrate interaction. These results reveal a novel mechanism of carbohydrate recognition and provide a structural framework for elucidating the mechanisms underlying muscular dystrophy. PMID:27526028

  1. A dynamical basis for the parameterization of organized deep convection in large-scale numerical models

    NASA Technical Reports Server (NTRS)

    Moncrieff, M. W.

    1984-01-01

    A hierarchy of steady, nonlinear, semianalytic models of different types of convection were produced. These provide a theoretical framework for determining cloud outflow fluxes of both dynamic and thermodynamic quantities, which can be used to formulate dynamical transports in parameterization schemes. This was achieved by exploiting certain Lagrangian conservation properties of steady flow, from which an equation for the vertical displacement of particles can be obtained and the outflow entropy, energy and momentum fluxes and the infow/outflow mass fluxes can be determined from solution to the equation. These fluxes are determined in terms of grid scale parameters such as convective available potential energy (CAPE), cloud layer shear, and horizontal pressure gradients. Five main types of system models are identified, respectively representing archtypes of convection in zero shear, large shear, midlatitude squall lines, tropical squall lines and cellular convection. The downdraught is an important aspect in the first four of these and the cloud scale transport of momentum is very distinctive.

  2. Rigorous Ab Initio Quantum Embedding for Quantum Chemistry Using Green's Function Theory: Screened Interaction, Nonlocal Self-Energy Relaxation, Orbital Basis, and Chemical Accuracy.

    PubMed

    Nguyen Lan, Tran; Kananenka, Alexei A; Zgid, Dominika

    2016-10-11

    We present a detailed discussion of the self-energy embedding theory (SEET), which is a quantum embedding scheme allowing us to describe a chosen subsystem very accurately while keeping the description of the environment at a lower level. We apply SEET to molecular examples where our chosen subsystem is made out of a set of strongly correlated orbitals while the weakly correlated orbitals constitute an environment. Consequently, a highly accurate method is used to calculate the self-energy for the system, while a lower-level method is employed to find the self-energy for the environment. Such a self-energy separation is very general, and to make the SEET procedure applicable to multiple systems, a detailed and practical procedure for the evaluation of the system and environment self-energy is necessary. We list all of the intricacies for one of the possible procedures while focusing our discussion on many practical implementation aspects such as the choice of best orbital basis, impurity solver, and many steps necessary to reach chemical accuracy. Finally, on a set of carefully chosen molecular examples, we demonstrate that SEET, which is a controlled, systematically improvable Green's function method, can be as accurate as established wave function quantum chemistry methods.

  3. New basis set superposition error free ab initio MO-VB interaction potential: Molecular-dynamics simulation of water at critical and supercritical conditions

    NASA Astrophysics Data System (ADS)

    Famulari, Antonino; Specchio, Roberto; Sironi, Maurizio; Raimondi, Mario

    1998-02-01

    Recently, a controversy has come to light in literature regarding the structure of water in nonambient conditions. Disagreement is evident between the site-site pair correlation functions of water derived from neutron diffraction and those obtained by computer simulations which employ effective pairwise potentials to express the intermolecular interactions. In this paper the SCFMI method (self-consistent field for molecular interaction) followed by nonorthogonal CI (configuration interaction) calculations was used to determine a new water-water interaction potential, which is BSSE (basis set superposition error) free in an a priori fashion. Extensive calculations were performed on water dimer and trimer and a new parametrization of a NCC-like (Niesar-Corongiu-Clementi) potential was accomplished. This was employed in the molecular-dynamics simulation of water. The effect of temperature and density variations was examined. Acceptable agreement between site-site correlation functions derived from neutron diffraction data and from computer simulation was reached. In particular, a weakening of the hydrogen bonded structure was observed on approaching the critical point, which reproduces the experimental behavior. The simulations were performed using the MOTECC (modern techniques in computational chemistry) suite of programs. The present results show the importance of BSSE-free nonorthogonal orbitals in an accurate description of the intermolecular potential of water.

  4. Euglena light-harvesting chlorophyll A/B binding protein (LHCP) synthesized as an unusually large precursor

    SciTech Connect

    Rikin, A.; Meyer, A.; Schwartzbach, S.

    1987-04-01

    Light increased the rate of LHCP synthesis as measured by pulse-labeling with /sup 35/SO/sub 4/ and immunoprecipitation with antibody specific for Euglena LHCP. In addition to the mature LHCP, 26,000 daltons, the LHCP specific antibody immunoprecipitated large amounts of several proteins having molecular weights of approximately 100,000. On immunoblots of immunoprecipitated unlabeled protein, the antibody only detected the mature LHCP suggesting that the high molecular weight proteins are not LHCP aggregates produced during immunoprecipitation. After a 10 min pulse with /sup 35/SO/sub 4/, the 100,000 dalton proteins constituted over 80% of the immunoprecipitated material. In a subsequent chase, the radioactivity in the 100,000 dalton proteins decreased and the radioactivity in the mature LHCP increased suggesting a precursor-product relationship. After a 35 minute chase, the mature LHCP was the major radioactive protein immunoprecipitated. Peptide mapping and in vitro translation are being used to clarify the structural and functional relationships, if any, between the 100,000 and 26,000 dalton immunoprecipitation products.

  5. Large-Scale Hybrid Density Functional Theory Calculations in the Condensed-Phase: Ab Initio Molecular Dynamics in the Isobaric-Isothermal Ensemble

    NASA Astrophysics Data System (ADS)

    Ko, Hsin-Yu; Santra, Biswajit; Distasio, Robert A., Jr.; Wu, Xifan; Car, Roberto

    Hybrid functionals are known to alleviate the self-interaction error in density functional theory (DFT) and provide a more accurate description of the electronic structure of molecules and materials. However, hybrid DFT in the condensed-phase has a prohibitively high associated computational cost which limits their applicability to large systems of interest. In this work, we present a general-purpose order(N) implementation of hybrid DFT in the condensed-phase using Maximally localized Wannier function; this implementation is optimized for massively parallel computing architectures. This algorithm is used to perform large-scale ab initio molecular dynamics simulations of liquid water, ice, and aqueous ionic solutions. We have performed simulations in the isothermal-isobaric ensemble to quantify the effects of exact exchange on the equilibrium density properties of water at different thermodynamic conditions. We find that the anomalous density difference between ice I h and liquid water at ambient conditions as well as the enthalpy differences between ice I h, II, and III phases at the experimental triple point (238 K and 20 Kbar) are significantly improved using hybrid DFT over previous estimates using the lower rungs of DFT This work has been supported by the Department of Energy under Grants No. DE-FG02-05ER46201 and DE-SC0008626.

  6. Accurate ab initio potential energy curves for the classic Li-F ionic-covalent interaction by extrapolation to the complete basis set limit and modeling of the radial nonadiabatic coupling.

    PubMed

    Varandas, A J C

    2009-09-28

    Multireference configuration interaction calculations using large correlation consistent basis sets and full configuration interaction calculations with the smallest of such basis are utilized to describe the ionic-neutral curve crossing for the title system. The results of the former calculations have then been extrapolated to the complete basis set limit using the uniform singlet- and triplet-pair extrapolation scheme. A recent suggestion for locating the nonadiabatic matrix terms at the point where the dynamical correlation split vanishes has also been tested. Additionally, a consistent formalism is suggested to model the radial dependence of the nonadiabatic matrix terms that warrants an overlap dependence away from the crossing. When applied to LiF, the overall approach yields results in excellent agreement with the commonly accepted values for the geometric and energetic attributes at both the equilibrium and diabatic crossing regions.

  7. Accurate ab initio-based adiabatic global potential energy surface for the 2{sup 2}A″ state of NH{sub 2} by extrapolation to the complete basis set limit

    SciTech Connect

    Li, Y. Q.; Ma, F. C.; Sun, M. T.

    2013-10-21

    A full three-dimensional global potential energy surface is reported first time for the title system, which is important for the photodissociation processes. It is obtained using double many-body expansion theory and an extensive set of accurate ab initio energies extrapolated to the complete basis set limit. Such a work can be recommended for dynamics studies of the N({sup 2}D) + H{sub 2} reaction, a reliable theoretical treatment of the photodissociation dynamics and as building blocks for constructing the double many-body expansion potential energy surface of larger nitrogen/hydrogen containing systems. In turn, a preliminary theoretical study of the reaction N({sup 2}D)+H{sub 2}(X{sup 1}Σ{sub g}{sup +})(ν=0,j=0)→NH(a{sup 1}Δ)+H({sup 2}S) has been carried out with the method of quasi-classical trajectory on the new potential energy surface. Integral cross sections and thermal rate constants have been calculated, providing perhaps the most reliable estimate of the integral cross sections and the rate constants known thus far for such a reaction.

  8. Remembering AB

    NASA Astrophysics Data System (ADS)

    Belyayev, S. T.

    2013-06-01

    In 1947 I became a second-year student at Moscow State University's Physics and Engineering Department, where a part of the week's classes were taught at base organizations. Our group's base was the future Kurchatov Institute, at that time known as the mysterious "Laboratory N^circ 2," and later as LIPAN. . Besides group lectures and practical work at the experimental laboratories, we also had access to the general seminars which Igor Vasilyevich Kurchatov tried to hold, with Leonid Vasilyevich Groshev filling in when he was absent. At the seminar, theorists spoke as welcome co-presenters and commentators. In 1949 I felt ready to approach A. B. Migdal to ask if I could transfer to his theoretical sector. In response, he suggested a number of simple qualitative problems, which I then successfully solved. (Incidentally, AB used the very same "introductory problems" for screening many generations of students.) So I wound up among AB's students. From 1952 on (for 10 years) I also served as an employee of the Migdal Sector. My memoirs here are mainly inspired by these years of constant communication with AB. After my departure for Novosibirsk in 1962, although our meetings still took place, they became occasional....

  9. Kitaev interactions between j = 1/2 moments in honeycomb Na2IrO3 are large and ferromagnetic: insights from ab initio quantum chemistry calculations

    NASA Astrophysics Data System (ADS)

    Katukuri, Vamshi M.; Nishimoto, S.; Yushankhai, V.; Stoyanova, A.; Kandpal, H.; Choi, Sungkyun; Coldea, R.; Rousochatzakis, I.; Hozoi, L.; van den Brink, Jeroen

    2014-01-01

    Na2IrO3, a honeycomb 5d5 oxide, has been recently identified as a potential realization of the Kitaev spin lattice. The basic feature of this spin model is that for each of the three metal-metal links emerging out of a metal site, the Kitaev interaction connects only spin components perpendicular to the plaquette defined by the magnetic ions and two bridging ligands. The fact that reciprocally orthogonal spin components are coupled along the three different links leads to strong frustration effects and nontrivial physics. While the experiments indicate zigzag antiferromagnetic order in Na2IrO3, the signs and relative strengths of the Kitaev and Heisenberg interactions are still under debate. Herein we report results of ab initio many-body electronic-structure calculations and establish that the nearest-neighbor exchange is strongly anisotropic with a dominant ferromagnetic Kitaev part, whereas the Heisenberg contribution is significantly weaker and antiferromagnetic. The calculations further reveal a strong sensitivity to tiny structural details such as the bond angles. In addition to the large spin-orbit interactions, this strong dependence on distortions of the Ir2O2 plaquettes singles out the honeycomb 5d5 oxides as a new playground for the realization of unconventional magnetic ground states and excitations in extended systems.

  10. Structural Basis for Calcium and Magnesium Regulation of a Large Conductance Calcium-activated Potassium Channel with β1 Subunits*

    PubMed Central

    Liu, Hao-Wen; Hou, Pan-Pan; Guo, Xi-Ying; Zhao, Zhi-Wen; Hu, Bin; Li, Xia; Wang, Lu-Yang; Ding, Jiu-Ping; Wang, Sheng

    2014-01-01

    Large conductance Ca2+- and voltage-activated potassium (BK) channels, composed of pore-forming α subunits and auxiliary β subunits, play important roles in diverse physiological activities. The β1 is predominately expressed in smooth muscle cells, where it greatly enhances the Ca2+ sensitivity of BK channels for proper regulation of smooth muscle tone. However, the structural basis underlying dynamic interaction between BK mSlo1 α and β1 remains elusive. Using macroscopic ionic current recordings in various Ca2+ and Mg2+ concentrations, we identified two binding sites on the cytosolic N terminus of β1, namely the electrostatic enhancing site (mSlo1(K392,R393)-β1(E13,T14)), increasing the calcium sensitivity of BK channels, and the hydrophobic site (mSlo1(L906,L908)-β1(L5,V6,M7)), passing the physical force from the Ca2+ bowl onto the enhancing site and S6 C-linker. Dynamic binding of these sites affects the interaction between the cytosolic domain and voltage-sensing domain, leading to the reduction of Mg2+ sensitivity. A comprehensive structural model of the BK(mSlo1 α-β1) complex was reconstructed based on these functional studies, which provides structural and mechanistic insights for understanding BK gating. PMID:24764303

  11. Wide-range photoabsorption cross-sections of simple metals: large basis-set OPW calculations for sodium

    NASA Astrophysics Data System (ADS)

    Kitamura, Hikaru

    2013-02-01

    Photoabsorption cross-sections of simple metals are formulated through a solid-state band theory based on the orthogonalized-plane-wave (OPW) method in Slater’s local-exchange approximation, where interband transitions of core and conduction electrons are evaluated up to the soft x-ray regime by using large basis sets. The photoabsorption cross-sections of a sodium crystal are computed for a wide photon energy range from 3 to 1800 eV. It is found that the numerical results reproduce the existing x-ray databases fairly well for energies above the L2,3-edge (31 eV), verifying a consistency between solid-state and atomic models for inner-shell photoabsorption; additional oscillatory structures in the present spectra manifest solid-state effects. Our computed results in the vacuum ultraviolet regime (6-30 eV) are also in better agreement with experimental data compared to earlier theories, although some discrepancies remain in the range of 20-30 eV. The influence of the core eigenvalues on the absorption spectra is examined.

  12. Authorization basis requirements comparison report

    SciTech Connect

    Brantley, W.M.

    1997-08-18

    The TWRS Authorization Basis (AB) consists of a set of documents identified by TWRS management with the concurrence of DOE-RL. Upon implementation of the TWRS Basis for Interim Operation (BIO) and Technical Safety Requirements (TSRs), the AB list will be revised to include the BIO and TSRs. Some documents that currently form part of the AB will be removed from the list. This SD identifies each - requirement from those documents, and recommends a disposition for each to ensure that necessary requirements are retained when the AB is revised to incorporate the BIO and TSRs. This SD also identifies documents that will remain part of the AB after the BIO and TSRs are implemented. This document does not change the AB, but provides guidance for the preparation of change documentation.

  13. Off-Center Gaussian Functions, an Alternative Atomic Orbital Basis Set for Accurate Noncovalent Interaction Calculations of Large Systems.

    PubMed

    Melicherčík, Miroslav; Pitoňák, Michal; Kellö, Vladimír; Hobza, Pavel; Neogrády, Pavel

    2013-12-10

    Proper description of noncovalent interactions requires, among other things, the use of diffuse atomic orbital (AO) basis sets. However, the presence of diffuse functions, especially in extended molecular systems, can lead to linear dependent AO basis sets. This in turn results, for example, in molecular orbital optimization problems or, when dependencies are removed in unpredictable and possibly geometry-dependent accuracy fluctuations. In this work, an alternative approach is proposed which suffers no linear dependence problems and delivers comparably accurate noncovalent interaction energies. An algorithm is proposed and implemented to construct a grid of off-center s-type Gaussian functions surrounding the molecule; substituting the presence of atom-centered diffuse basis functions. While the number of basis functions in the grid is comparable to the number of diffuse basis functions in aug-cc-pVXZ (for each cardinality number "X") basis sets for small molecular systems, the ratio becomes more favorable with increasing system size. The grid is constructed in a way that it is unique for a molecule (monomer) and, thus, independent of noncovalent complex/cluster geometry. The grid parameters, such as the density of grid points and s-function exponents, are obtained via optimization toward the S22 data set on the MP2 level. The quality, transferability, and versatility of the grid is tested on the S66 data set as well as on several cuts through the potential energy surface for noncovalent complexes, such as methyl-guanine···methyl-cytosine conversion from stacked to hydrogen-bonded structure.

  14. Spin-orbit decomposition of ab initio nuclear wave functions

    NASA Astrophysics Data System (ADS)

    Johnson, Calvin W.

    2015-03-01

    Although the modern shell-model picture of atomic nuclei is built from single-particle orbits with good total angular momentum j , leading to j -j coupling, decades ago phenomenological models suggested that a simpler picture for 0 p -shell nuclides can be realized via coupling of the total spin S and total orbital angular momentum L . I revisit this idea with large-basis, no-core shell-model calculations using modern ab initio two-body interactions and dissect the resulting wave functions into their component L - and S -components. Remarkably, there is broad agreement with calculations using the phenomenological Cohen-Kurath forces, despite a gap of nearly 50 years and six orders of magnitude in basis dimensions. I suggest that L -S decomposition may be a useful tool for analyzing ab initio wave functions of light nuclei, for example, in the case of rotational bands.

  15. Full CI calibration of model hamiltonian, large basis set studies of the H 2-H 2 van der Waals interaction.

    NASA Astrophysics Data System (ADS)

    Burton, P. G.

    1983-08-01

    The non-variational CEPA2 PNO ansatz, recently employed in detailed studies of the H 2-H 2 van der Waals interaction by Burton and Senff and the full CI extrapolation studies on the same system by Burton are discussed in relation to the explicit full CI study of Harrison and Handy for the planar T configuration of H 2-H 2 ( R = 6.5 ao) in a basis of 80 functions.

  16. Specific polyclonal F(ab')2 neutralize a large panel of highly pathogenic avian influenza A viruses (H5N1) and control infection in mice.

    PubMed

    Herbreteau, Cécile Hélène; Jacquot, Frédéric; Rith, Sareth; Vacher, Laurent; Nguyen, Ludovic; Carbonnelle, Caroline; Lotteau, Vincent; Jolivet, Michel; Raoul, Hervé; Buchy, Philippe; Saluzzo, Jean-François

    2014-01-01

    There is still no specific therapy for infection with the highly pathogenic avian influenza A virus (HPAI) H5N1, which caused 39 human cases with a 64% fatality rate in 2013. We prepared highly purified specific equine polyclonal immunoglobulin fragments (F(ab')2) against H5N1 and tested them for efficacy in vitro and with different administration schedules in H5N1-challenged BALB/c mice. in vitro, F(ab')2 neutralized 21 different H5N1 strains from different areas, representative of 11 different clades and sub-clades and 9 years of evolution of the virus. In vivo mouse experiments identified that the most efficient administration protocol consists of five consecutive daily injections after infection; 10 mg/kg giving a 60% increase in survival. These data demonstrate the ability of anti-H5N1 F(ab')2 to markedly reduce the mortality and morbidity associated with infection of mice with HPAI H5N1 virus, and their potential for human therapy.

  17. Single particle calculations for a Woods-Saxon potential with triaxial deformations, and large Cartesian oscillator basis

    NASA Astrophysics Data System (ADS)

    Mohammed-Azizi, B.; Medjadi, D. E.

    2004-01-01

    We present a computer program which solves the Schrodinger equation of the stationary states for an average nuclear potential of Woods-Saxon type. In this work, we take specifically into account triaxial (i.e. ellipsoidal) nuclear surfaces. The deformation is specified by the usual Bohr parameters. The calculations are carried out in two stages. In the first, one calculates the representative matrix of the Hamiltonian in the Cartesian oscillator basis. In the second stage one diagonalizes this matrix with the help of subroutines of the Eispack library. If it is wished, one can calculate all eigenvalues, or only the part of the eigenvalues that are contained in a fixed interval defined in advance. In this latter case the eigenvectors are given conjointly. The program is very rapid, and the run-time is mainly used for the diagonalization. Thus, it is possible to use a significant number of the basis states in order to insure a best convergence of the results. Program summaryProgram obtainable from:CPC Program Library, Queen's University of Belfast, N. Ireland Title of program:Triaxial Catalogue number:ADSK Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADSK Licensing provisions:None Computer:PC. AMD Athlon 1000 MHz Hard disk:40 Go Ram:256 Mo Swap file:4 Go Operating system:WINDOWS XP Software used:Microsoft Visual Fortran 5.0A (with full optimizations in the settings project options) Programming language:Fortran 77/90 (double precision) Number of bits in a word:32 Number of lines:7662 No. of bytes in distributed program, including test data, etc.:174 601 Distribution format:tar gzip file Nature of the problem: The single particle energies and the single particle wave functions are calculated from one-body Hamiltonian including a central field of Woods-Saxon type, a spin-orbit interaction, and the Coulomb potential for the protons. We consider only ellipsoidal (triaxial) shapes. The deformation of the nuclear shape is fixed by the usual Bohr parameters ( β,

  18. Single particle calculations for a Woods Saxon potential with triaxial deformations, and large Cartesian oscillator basis (new version code)

    NASA Astrophysics Data System (ADS)

    Mohammed-Azizi, B.; Medjadi, D. E.

    2007-05-01

    We present a new version of the computer program which solves the Schrödinger equation of the stationary states for an average nuclear potential of Woods-Saxon type. In this work, we take specifically into account triaxial (i.e. ellipsoidal) nuclear surfaces. The deformation is specified by the usual Bohr parameters. The calculations are carried out in two stages. In the first, one calculates the representative matrix of the Hamiltonian in the Cartesian oscillator basis. In the second stage one diagonalizes this matrix with the help of subroutines of the EISPACK library. This new version calculates all the eigenvalues up to a given cutoff energy, and gives the components of the corresponding eigenfunctions. For a more convenient handling, these results are stored simultaneously in the computer memory, and on a files. Program summaryTitle of program:Triaxial2007 Catalogue identifier:ADSK_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADSK_v2_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Summary of revision:One input file instead two. Reduced number of input parameters. Storage of eigenvalues and eigenvectors in memory in a very simple way which makes the code very convenient to the user. Reasons for the new version: More convenient handling of the eigenvectors Catalogue number old version: ADSK Catalogue number new version:ADSK_v2_0 Journal: Computer Physics Commun. 156 (2004) 241-282 Licensing provisions: none Computer: PC Pentium 4, 2600 MHz Hard disk: 40 Gb RAM: 256 Mb Swap file: 4 Gb Operating system: WINDOWS XP Software used: Compaq Visual FORTRAN (with full optimizations in the settings project options) Programming language used:Fortran 77/90 (double precision) Number of bits in a word: 32 No. of lines in distributed program, including test data, etc.:4058 No. of bytes in distributed program, including test data, etc.:75 590 Distribution format:tar.gz Nature of the problem: The single particle energies

  19. River systems as providers of goods and services: a basis for comparing desired and undesired effects of large dam projects.

    PubMed

    Brismar, Anna

    2002-05-01

    In developing countries, large dam projects continue to be launched, primarily to secure a time-stable fresh-water supply and to generate hydropower. Meanwhile, calls for environmentally sustainable development put pressure on the dam-building industry to integrate ecological concerns in project planning and decision-making. Such integration requires environmental impact statements (EISs) that can communicate the societal implications of the ecological effects in terms that are understandable and useful to planners and decision-makers. The purpose of this study is to develop a basic framework for assessing the societal implications of the river ecological effects expected of a proposed large dam project. The aim is to facilitate a comparison of desired and potential undesired effects on-site and downstream. The study involves two main tasks: to identify key river goods and services that a river system may provide, and to analyze how the implementation of a large dam project may alter the on-site capacity and downstream potentials to derive river goods and services from the river system. Three river goods and six river services are identified. River goods are defined as extractable partly man-made products and river services as naturally sustained processes. By four main types of flow manipulations, a large dam project improves the on-site capacity to derive desired river goods, but simultaneously threatens the provision of desirable river goods and services downstream. However, by adjusting the site, design, and operational schedule of the proposed dam project, undesirable effects on river goods and services can be minimized.

  20. Common, but complex, mode of resistance of Plutella xylostella to Bacillus thuringiensis toxins Cry1Ab and Cry1Ac.

    PubMed

    Sayyed, Ali H; Gatsi, Roxani; Ibiza-Palacios, M Sales; Escriche, Baltasar; Wright, Denis J; Crickmore, Neil

    2005-11-01

    A field collected population of Plutella xylostella (SERD4) was selected in the laboratory with Bacillus thuringiensis endotoxins Cry1Ac (Cry1Ac-SEL) and Cry1Ab (Cry1Ab-SEL). Both subpopulations showed similar phenotypes: high resistance to the Cry1A toxins and little cross-resistance to Cry1Ca or Cry1D. A previous analysis of the Cry1Ac-SEL showed incompletely dominant resistance to Cry1Ac with more than one factor, at least one of which was sex influenced. In the present study reciprocal mass crosses between Cry1Ab-SEL and a laboratory susceptible population (ROTH) provided evidence that Cry1Ab resistance was also inherited as incompletely dominant trait with more than one factor, and at least one of the factors was sex influenced. Analysis of single pair mating indicated that Cry1Ab-SEL was still heterogeneous for Cry1Ab resistance genes, showing genes with different degrees of dominance. Binding studies showed a large reduction of specific binding of Cry1Ab and Cry1Ac to midgut membrane vesicles of the Cry1Ab-SEL subpopulation. Cry1Ab-SEL was found to be more susceptible to trypsin-activated Cry1Ab toxin than protoxin, although no defect in toxin activation was found. Present and previous results indicate a common basis of resistance to both Cry1Ab and Cry1Ac in selected subpopulations and suggest that a similar set of resistance genes are responsible for resistance to Cry1Ab and Cry1Ac and are selected whichever toxin was used. The possibility of an incompletely dominant trait of resistant to these toxins should be taken into account when considering refuge resistance management strategies.

  1. Large-Scale Atmospheric Circulation Patterns Associated with Temperature Extremes as a Basis for Model Evaluation: Methodological Overview and Results

    NASA Astrophysics Data System (ADS)

    Loikith, P. C.; Broccoli, A. J.; Waliser, D. E.; Lintner, B. R.; Neelin, J. D.

    2015-12-01

    Anomalous large-scale circulation patterns often play a key role in the occurrence of temperature extremes. For example, large-scale circulation can drive horizontal temperature advection or influence local processes that lead to extreme temperatures, such as by inhibiting moderating sea breezes, promoting downslope adiabatic warming, and affecting the development of cloud cover. Additionally, large-scale circulation can influence the shape of temperature distribution tails, with important implications for the magnitude of future changes in extremes. As a result of the prominent role these patterns play in the occurrence and character of extremes, the way in which temperature extremes change in the future will be highly influenced by if and how these patterns change. It is therefore critical to identify and understand the key patterns associated with extremes at local to regional scales in the current climate and to use this foundation as a target for climate model validation. This presentation provides an overview of recent and ongoing work aimed at developing and applying novel approaches to identifying and describing the large-scale circulation patterns associated with temperature extremes in observations and using this foundation to evaluate state-of-the-art global and regional climate models. Emphasis is given to anomalies in sea level pressure and 500 hPa geopotential height over North America using several methods to identify circulation patterns, including self-organizing maps and composite analysis. Overall, evaluation results suggest that models are able to reproduce observed patterns associated with temperature extremes with reasonable fidelity in many cases. Model skill is often highest when and where synoptic-scale processes are the dominant mechanisms for extremes, and lower where sub-grid scale processes (such as those related to topography) are important. Where model skill in reproducing these patterns is high, it can be inferred that extremes are

  2. Bone Tissue Engineering Under Xenogeneic-Free Conditions in a Large Animal Model as a Basis for Early Clinical Applicability.

    PubMed

    Weigand, Annika; Beier, Justus P; Schmid, Rafael; Knorr, Tobias; Kilian, David; Götzl, Rebekka; Gerber, Thomas; Horch, Raymund E; Boos, Anja M

    2017-03-01

    For decades, researchers have been developing a range of promising strategies in bone tissue engineering with the aim of producing a significant clinical benefit over existing therapies. However, a major problem concerns the traditional use of xenogeneic substances for the expansion of cells, which complicates direct clinical transfer. The study's aim was to establish a totally autologous sheep model as a basis for further preclinical studies and future clinical application. Ovine mesenchymal stromal cells (MSC) were cultivated in different concentrations (0%, 2%, 5%, 10%, and 25%) of either autologous serum (AS) or fetal calf serum (FCS). With an increase of serum concentration, enhanced metabolic activity and proliferation could be observed. There were minor differences between MSC cultivated in AS or FCS, comparing gene and protein expression of osteogenic and stem cell markers, morphology, and osteogenic differentiation. MSC implanted subcutaneously in the sheep model, together with a nanostructured bone substitute, either in stable block or moldable putty form, induced similar vascularization and remodeling of the bone substitute irrespective of cultivation of MSC in AS or FCS and osteogenic differentiation. The bone substitute in block form together with MSC proved particularly advantageous in the induction of ectopic bone formation compared to the cell-free control and putty form. It could be demonstrated that AS is suitable for replacement of FCS for cultivation of ovine MSC for bone tissue engineering purposes. Substantial progress has been made in the development of a strictly xenogeneic-free preclinical animal model to bring future clinical application of bone tissue engineering strategies within reach.

  3. Large Density-Functional and Basis-Set Effects for the DMSO Reductase Catalyzed Oxo-Transfer Reaction.

    PubMed

    Li, Ji-Lai; Mata, Ricardo A; Ryde, Ulf

    2013-03-12

    The oxygen-atom transfer reaction catalyzed by the mononuclear molybdenum enzyme dimethyl sulfoxide reductase (DMSOR) has attracted considerable attention through both experimental and theoretical studies. We show here that this reaction is more sensitive to details of quantum mechanical calculations than what has previously been appreciated. Basis sets of at least triple-ζ quality are needed to obtain qualitatively correct results. Dispersion has an appreciable effect on the reaction, in particular the binding of the substrate or the dissociation of the product (up to 34 kJ/mol). Polar and nonpolar solvation effects are also significant, especially if the enzyme can avoid cavitation effects by using a preformed active-site cavity. Relativistic effects are considerable (up to 22 kJ/mol), but they are reasonably well treated by a relativistic effective core potential. Various density-functional methods give widely different results for the activation and reaction energy (differences of over 100 kJ/mol), mainly reflecting the amount of exact exchange in the functional, owing to the oxidation of Mo from +IV to +VI. By calibration toward local CCSD(T0) calculations, we show that none of eight tested functionals (TPSS, BP86, BLYP, B97-D, TPSSH, B3LYP, PBE0, and BHLYP) give accurate energies for all states in the reaction. Instead, B3LYP gives the best activation barrier, whereas pure functionals give more accurate energies for the other states. Our best results indicate that the enzyme follows a two-step associative reaction mechanism with an overall activation enthalpy of 63 kJ/mol, which is in excellent agreement with the experimental results.

  4. Exploring the cellular basis of human disease through a large-scale mapping of deleterious genes to cell types.

    PubMed

    Cornish, Alex J; Filippis, Ioannis; David, Alessia; Sternberg, Michael J E

    2015-09-01

    Each cell type found within the human body performs a diverse and unique set of functions, the disruption of which can lead to disease. However, there currently exists no systematic mapping between cell types and the diseases they can cause. In this study, we integrate protein-protein interaction data with high-quality cell-type-specific gene expression data from the FANTOM5 project to build the largest collection of cell-type-specific interactomes created to date. We develop a novel method, called gene set compactness (GSC), that contrasts the relative positions of disease-associated genes across 73 cell-type-specific interactomes to map genes associated with 196 diseases to the cell types they affect. We conduct text-mining of the PubMed database to produce an independent resource of disease-associated cell types, which we use to validate our method. The GSC method successfully identifies known disease-cell-type associations, as well as highlighting associations that warrant further study. This includes mast cells and multiple sclerosis, a cell population currently being targeted in a multiple sclerosis phase 2 clinical trial. Furthermore, we build a cell-type-based diseasome using the cell types identified as manifesting each disease, offering insight into diseases linked through etiology. The data set produced in this study represents the first large-scale mapping of diseases to the cell types in which they are manifested and will therefore be useful in the study of disease systems. Overall, we demonstrate that our approach links disease-associated genes to the phenotypes they produce, a key goal within systems medicine.

  5. Ab initio Potential Energy Surface for H-H2

    NASA Technical Reports Server (NTRS)

    Partridge, Harry; Bauschlicher, Charles W., Jr.; Stallcop, James R.; Levin, Eugene

    1993-01-01

    Ab initio calculations employing large basis sets are performed to determine an accurate potential energy surface for H-H2 interactions for a broad range of separation distances. At large distances, the spherically averaged potential determined from the calculated energies agrees well with the corresponding results determined from dispersion coefficients; the van der Waals well depth is predicted to be 75 +/- (mu)E(sub h). Large basis sets have also been applied to reexamine the accuracy of theoretical repulsive potential energy surfaces. Multipolar expansions of the computed H-H2 potential energy surface are reported for four internuclear separation distances (1.2, 1.401, 1.449, and 1.7a(sub 0) of the hydrogen molecule. The differential elastic scattering cross section calculated from the present results is compared with the measurements from a crossed beam experiment.

  6. Ab initio Potential Energy Surface for H-H2

    NASA Technical Reports Server (NTRS)

    Partridge, Harry; Bauschlicher, Charles W., Jr.; Stallcop, James R.; Levin, Eugene

    1993-01-01

    Ab initio calculations employing large basis sets are performed to determine an accurate potential energy surface for H-H2 interactions for a broad range of separation distances. At large distances, the spherically averaged potential determined from the calculated energies agrees well with the corresponding results determined from dispersion coefficients; the van der Waals well depth is predicted to be 75 +/- (mu)E(sub h). Large basis sets have also been applied to reexamine the accuracy of theoretical repulsive potential energy surfaces. Multipolar expansions of the computed H-H2 potential energy surface are reported for four internuclear separation distances (1.2, 1.401, 1.449, and 1.7a(sub 0) of the hydrogen molecule. The differential elastic scattering cross section calculated from the present results is compared with the measurements from a crossed beam experiment.

  7. Small Atomic Orbital Basis Set First‐Principles Quantum Chemical Methods for Large Molecular and Periodic Systems: A Critical Analysis of Error Sources

    PubMed Central

    Sure, Rebecca; Brandenburg, Jan Gerit

    2015-01-01

    Abstract 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. PMID:27308221

  8. Small Atomic Orbital Basis Set First-Principles Quantum Chemical Methods for Large Molecular and Periodic Systems: A Critical Analysis of Error Sources.

    PubMed

    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.

  9. A density functional and ab initio investigation of the p-aminobenzoic acid molecule

    NASA Astrophysics Data System (ADS)

    Lago, A. F.; Dávalos, J. Z.; de Brito, A. Naves

    2007-08-01

    The p-aminobenzoic acid (C 7H 7NO 2) molecule has been investigated at different levels of theory. DFT methods (B3LYP and PBE1PBE), second order Møller-Plesset perturbation theory (MP2) and composite ab initio methods (G3MP2 and CBS) have been employed, in conjunction with large basis sets. Important informations on the electronic structure and thermochemistry of this molecule have been extracted, and the performance of the density functional and ab initio methods has been evaluated, based on the comparison of the calculated and the available experimental data.

  10. Location of Si vacancies and [Ti(OSi)4] and [Ti(OSi)3OH] sites in the MFI framework: a large cluster and full ab initio study.

    PubMed

    Yuan, Shuping; Si, Hongzong; Fu, Aiping; Chu, Tianshu; Tian, Fenghui; Duan, Yun-Bo; Wang, Jianguo

    2011-02-10

    Titanium silicalite-1 (TS-1) is an important catalyst for selective oxidation reactions. However, the nature and structure of the active sites and the mechanistic details of the catalytic reactions over TS-1 have not been well-understood, leaving a continuous debate on the genesis of active sites on the TS-1 surface in the literature. In this work, the location of Si vacancies and [Ti(OSi)(4)] and [Ti(OSi)(3)OH] sites in the MFI (Framework Type Code of ZSM-5 (Zeolite Socony Mobile-Five)) framework has been studied using a full ab initio method with 40T clusters with a Si:Ti molar ratio of 39:1. It was shown that the former four energetically favorable sites for Si vacancies are T6, T12, T4, and T8 and for Ti centers of [Ti(OSi)(4)] are T10, T4, T8 and T11, being partially the same sites. Whether by replacing Si vacancies or substituting the fully coordinated Si sites, the most preferential site for Ti is T10, which indicates that the insertion mechanism does not affect the favorable sites of Ti in the MFI lattice. For the defective [Ti(OSi)(3)OH] sites, it was found that the Si vacancy at T6 with a Ti at its neighboring T9 site (T6-def-T9-Ti pair) is the most energetically favorable one, followed by a T6-def-T5-Ti pair with a small energy gap. These findings are significant to elucidate the nature of the active sites and the mechanism of reactions catalyzed by TS-1 and to design the TS-1 catalyst.

  11. Accurate prediction of the blood-brain partitioning of a large set of solutes using ab initio calculations and genetic neural network modeling.

    PubMed

    Hemmateenejad, Bahram; Miri, Ramin; Safarpour, Mohammad A; Mehdipour, Ahmad R

    2006-08-01

    A genetic algorithm-based artificial neural network model has been developed for the accurate prediction of the blood-brain barrier partitioning (in logBB scale) of chemicals. A data set of 123 logBB (115 old molecules and 8 new molecules) of a diverse set of chemicals was chosen in this study. The optimum 3D geometry of the molecules was estimated by the ab initio calculations at the level of RHF/STO-3G, and consequently, different electronic descriptors were calculated for each molecule. Indeed, logP as a measure of hydrophobicity and different topological indices were also calculated. A three-layered artificial neural network with backpropagation of an error-learning algorithm was employed to process the nonlinear relationship between the calculated descriptors and logBB data. Genetic algorithm was used as a feature selection method to select the most relevant set of descriptors as the input of the network. Modeling of the logBB data by the only quantum descriptors produced a 5:4:1 ANN structure with RMS error of validation and crossvalidation equal to 0.224 and 0.227, respectively. Better nonlinear model (RMS(V) and RMS(CV) equals to 0.097 and 0.099, respectively) was obtained by the incorporation of the logP and the principal components of the topological indices to electronic descriptors. The ultimate performances of the models were obtained by the application of the models to predict the logBB of 23 molecules that did not have contribution in the steps of model development. The best model produced RMS error of prediction 0.140, and could predict about 98% of variances in the logBB data. Copyright 2006 Wiley Periodicals, Inc.

  12. DCMB that combines divide-and-conquer and mixed-basis set methods for accurate geometry optimizations, total energies, and vibrational frequencies of large molecules.

    PubMed

    Wu, Anan; Xu, Xin

    2012-06-15

    We present a method, named DCMB, for the calculations of large molecules. It is a combination of a parallel divide-and-conquer (DC) method and a mixed-basis (MB) set scheme. In this approach, atomic forces, total energy and vibrational frequencies are obtained from a series of MB calculations, which are derived from the target system utilizing the DC concept. Unlike the fragmentation based methods, all DCMB calculations are performed over the whole target system and no artificial caps are introduced so that it is particularly useful for charged and/or delocalized systems. By comparing the DCMB results with those from the conventional method, we demonstrate that DCMB is capable of providing accurate prediction of molecular geometries, total energies, and vibrational frequencies of molecules of general interest. We also demonstrate that the high efficiency of the parallel DCMB code holds the promise for a routine geometry optimization of large complex systems.

  13. Structural elucidation of the mechanistic basis of degeneracy in the primary humoral response.

    PubMed

    Khan, Tarique; Salunke, Dinakar M

    2012-02-15

    The mechanistic basis for efficient combating of the infinite range of foreign Ags by the limited repertoire of naive Abs expressed on primary B cell surfaces during their first encounter was addressed through elegantly designed crystallographic analyses. Resolution of the discrepancy arising from the limited number of possible germline Ab receptors on primary B cells for recognizing the unlimited pool of possible Ags has been attempted by invoking the degenerate recognition potential of the germline Abs. Structural analyses of germline mAb BBE6.12H3 in an Ag-free state, as well as bound to four different peptide Ags, established the correlation of its degenerate specificity with conformational versatility of the paratope. Six distinct paratope topologies observed for a single germline mAb provided a quantitative description of the primary Ag recognition repertoire at the tertiary structural level. Each of the four different peptide Ags was bound specifically to a distinct conformation of the paratope, which was also different from that of the Ag-free states of the same germline mAb. A minimal conserved motif in the pristine Ag-combining site essential for multispecificity and Ag binding-mediated change in the elbow angle of Fab was also discernible. It is proposed that the generation of a primary Ab repertoire involves large, yet finite, germline Ab clones, each capable of adopting discrete conformations, which in turn exhibit diverse binding modes.

  14. Use of Two-Body Correlated Basis Functions with van der Waals Interaction to Study the Shape-Independent Approximation for a Large Number of Trapped Interacting Bosons

    NASA Astrophysics Data System (ADS)

    Lekala, M. L.; Chakrabarti, B.; Das, T. K.; Rampho, G. J.; Sofianos, S. A.; Adam, R. M.; Haldar, S. K.

    2017-01-01

    We study the ground-state and the low-lying excitations of a trapped Bose gas in an isotropic harmonic potential for very small (˜ 3) to very large (˜ 10^7 ) particle numbers. We use the two-body correlated basis functions and the shape-dependent van der Waals interaction in our many-body calculations. We present an exhaustive study of the effect of inter-atomic correlations and the accuracy of the mean-field equations considering a wide range of particle numbers. We calculate the ground-state energy and the one-body density for different values of the van der Waals parameter C6 . We compare our results with those of the modified Gross-Pitaevskii results, the correlated Hartree hypernetted-chain equations (which also utilize the two-body correlated basis functions), as well as of the diffusion Monte Carlo for hard sphere interactions. We observe the effect of the attractive tail of the van der Waals potential in the calculations of the one-body density over the truly repulsive zero-range potential as used in the Gross-Pitaevskii equation and discuss the finite-size effects. We also present the low-lying collective excitations which are well described by a hydrodynamic model in the large particle limit.

  15. Infinite-basis calculations of binding energies for the hydrogen bonded and stacked tetramers of formic acid and formamide and their use for validation of hybrid DFT and ab initio methods.

    PubMed

    Zhao, Yan; Truhlar, Donald G

    2005-08-04

    Benchmark stabilization energies for planar H-bonded and stacked structures of formic acid tetramers and formamide tetramers were determined as the sum of the infinite basis set limit of MP2 energies and a CCSD(T) correction term evaluated with the 6-31G*(0.25) basis set. The infinite basis (IB) set limit of MP2 energies was determined by two-point extrapolation using the aug-cc-pVXZ basis sets for X = D and T and separate extrapolation of the Hartree-Fock and correlation energies with new IB parameters for augmented basis sets determined here. Final stabilization energies (kcal/mol) for the tetramer studied are in the range of 4.6 to approximately 6.7 kcal/mol and they were used as reference data to test 14 density functionals. Among the tested DFT methods, PWB6K gives the best performance with an average error equal to only 30% of the average binding energy. In contrast, the popular B3LYP functional has an average error of 85%. We recommend the PWB6K method for exploring the potential energy surfaces of organic complexes and clusters and supramolecular assemblies.

  16. A geometrical correction for the inter- and intra-molecular basis set superposition error in Hartree-Fock and density functional theory calculations for large systems

    NASA Astrophysics Data System (ADS)

    Kruse, Holger; Grimme, Stefan

    2012-04-01

    chemistry yields MAD=0.68 kcal/mol, which represents a huge improvement over plain B3LYP/6-31G* (MAD=2.3 kcal/mol). Application of gCP-corrected B97-D3 and HF-D3 on a set of large protein-ligand complexes prove the robustness of the method. Analytical gCP gradients make optimizations of large systems feasible with small basis sets, as demonstrated for the inter-ring distances of 9-helicene and most of the complexes in Hobza's S22 test set. The method is implemented in a freely available FORTRAN program obtainable from the author's website.

  17. AB175. The first large-scale study of VHL gene mutation spectrum and genotype-phenotype correlationship of VHL disease in China

    PubMed Central

    Peng, Shuanghe; Gong, Kan

    2015-01-01

    Objective VHL disease is the most common hereditary renal cancer, and it is an autosomal-dominant inherited familial cancer syndrome caused by germline mutations of the VHL tumor suppressor gene. The golden standard for diagnosing VHL disease is to find the VHL gene mutation in patients’ genes. In the world, the United States had summarized 469 VHL families from the United States, Europe and Japan to summarize VHL gene mutation spectrum and the genotype-phenotype correlationship. However, no such large number of samples’ analysis had been done in China. The purpose of this study is to finish the first large-scale study of VHL gene mutation spectrum and genotype-phenotype correlationship of VHL disease in China. Methods We have gathered 172 Chinese VHL families including 89 families diagnosed in our hospital and 83 families from other domestic hospitals gathered by literature summary. Then we made statistical analysis of data from 172 Chinese VHL families. Results In the 172 Chinese VHL families, germline mutations were identified in 165 (96%) families. Point mutations were found in 103 (62%) families, large deletions were found in 32 (19%) families, micro-deletions or micro-insertions were found in 21 (13%) families, and splice mutations were found in 9 (6%) families. We found 9 hot mutation codons that affected more than 4 families each, and they were codon65, codon76, codon78, codon80, codon86, codon88, codon161, codon162 and codon167. The onset of pheochromocytoma in VHL patients was related to mutations in VHL gene locus 482, 482, 499, 499. Mutations in VHL gene locus 257, 257, 481 was negatively related to the onset of pheochromocytoma. The occurrence of retinal angioma associated with VHL gene large deletions. Mutations in VHL gene locus 226, 233, 239, 257, 263, 481, 486, 499, 500 was related to the onset of renal cell carcinoma. Conclusions We have finished the first large-scale study of VHL gene mutation spectrum and genotype-phenotype correlationship

  18. Optical and other material properties of SiO2 from ab initio studies

    NASA Astrophysics Data System (ADS)

    Warmbier, Robert; Mohammed, Faris; Quandt, Alexander

    2014-07-01

    The optical properties of photonic devices largely depend on the dielectric properties of the underlying materials. We apply modern ab initio methods to study crystalline SiO2 phases, which serve as toy models for amorphous glass. We discuss the dielectric response from the infrared to the VIS/UV, which is crucial for glass based photonic applications. Low density silica, like cristobalite, may provide a good basis for high transmission optical devices.

  19. Ab Initio potential grid based docking: From High Performance Computing to In Silico Screening

    NASA Astrophysics Data System (ADS)

    de Jonge, Marc R.; Vinkers, H. Maarten; van Lenthe, Joop H.; Daeyaert, Frits; Bush, Ian J.; van Dam, Huub J. J.; Sherwood, Paul; Guest, Martyn F.

    2007-09-01

    We present a new and completely parallel method for protein ligand docking. The potential of the docking target structure is obtained directly from the electron density derived through an ab initio computation. A large subregion of the crystal structure of Isocitrate Lyase, was selected as docking target. To allow the full ab initio treatment of this region special care was taken to assign optimal basis functions. The electrostatic potential is tested by docking a small charged molecule (succinate) into the binding site. The ab initio grid yields a superior result by producing the best binding orientation and position, and by recognizing it as the best. In contrast the same docking procedure, but using a classical point-charge based potential, produces a number of additional incorrect binding poses, and does not recognize the correct pose as the best solution.

  20. Impact of incomplete metal coverage on the electrical properties of metal-CNT contacts: A large-scale ab initio study

    SciTech Connect

    Fediai, Artem Ryndyk, Dmitry A.; Seifert, Gotthard; Mothes, Sven; Schroter, Michael; Claus, Martin; Cuniberti, Gianaurelio

    2016-09-05

    Using a dedicated combination of the non-equilibrium Green function formalism and large-scale density functional theory calculations, we investigated how incomplete metal coverage influences two of the most important electrical properties of carbon nanotube (CNT)-based transistors: contact resistance and its scaling with contact length, and maximum current. These quantities have been derived from parameter-free simulations of atomic systems that are as close as possible to experimental geometries. Physical mechanisms that govern these dependences have been identified for various metals, representing different CNT-metal interaction strengths from chemisorption to physisorption. Our results pave the way for an application-oriented design of CNT-metal contacts.

  1. Third-Order Incremental Dual-Basis Set Zero-Buffer Approach for Large High-Spin Open-Shell Systems.

    PubMed

    Zhang, Jun; Dolg, Michael

    2015-03-10

    The third-order incremental dual-basis set zero-buffer approach (inc3-db-B0) is an efficient, accurate, and black-box quantum chemical method for obtaining correlation energies of large systems, and it has been successfully applied to many real chemical problems. In this work, we extend this approach to high-spin open-shell systems. In the open-shell approach, we will first decompose the occupied orbitals of a system into several domains by a K-means clustering algorithm. The essential part is that we preserve the active (singly occupied) orbitals in all the calculations of the domain correlation energies. The duplicated contributions of the active orbitals to the correlation energy are subtracted from the incremental expansion. All techniques of truncating the virtual space such as the B0 approximation can be applied. This open-shell inc3-db-B0 approach is combined with the CCSD and CCSD(T) methods and applied to the computations of a singlet-triplet gap and an electron detachment process. Our approach exhibits an accuracy better than 0.6 kcal/mol or 0.3 eV compared with the standard implementation, while it saves a large amount of the computational time and can be efficiently parallelized.

  2. Determination of waste decay rate for a large Finnish landfill by calibrating methane generation models on the basis of methane recovery and emissions.

    PubMed

    Sormunen, Kai; Laurila, Tuomas; Rintala, Jukka

    2013-10-01

    The aim of this study was to determine the methane (CH(4)) generation factor (k) and CH(4) generation potential (L) for bulk waste in order to calibrate a CH(4) generation model (USEPA Landgem 3.02) and provide information on the remaining CH(4) generation potential in a large (54 ha) municipal solid waste landfill located in a boreal climate. The CH(4) generation model was calibrated by actual CH(4) recovery and emission measurement data. Moreover, waste characterisation information from a previous study was considered.The appropriate k for bulk waste was 0.18 in the studied landfill, which indicated a higher rate of degradation than proposed by the Intergovernmental Panel on Climate Change as a default k value of 0.09 for wet conditions in boreal and temperate climes, whereas the calibrated L of 100 m(3)/t was lower than estimated on the basis of a previous waste characterisation study. The results demonstrate the importance of model calibration, as inappropriate model parameters may result in a large discrepancy (approximately 100 % or 119 million m(3) having an energy equivalent of nearly 1.2 TWh) in cumulative CH(4) generation estimates within a 18-year timescale (2012–30) at the studied landfill.

  3. Towards Accurate Ab Initio Predictions of the Spectrum of Methane

    NASA Technical Reports Server (NTRS)

    Schwenke, David W.; Kwak, Dochan (Technical Monitor)

    2001-01-01

    We have carried out extensive ab initio calculations of the electronic structure of methane, and these results are used to compute vibrational energy levels. We include basis set extrapolations, core-valence correlation, relativistic effects, and Born- Oppenheimer breakdown terms in our calculations. Our ab initio predictions of the lowest lying levels are superb.

  4. Ab initio analytical Raman intensities for periodic systems through a coupled perturbed Hartree-Fock/Kohn-Sham method in an atomic orbital basis. II. Validation and comparison with experiments

    NASA Astrophysics Data System (ADS)

    Maschio, Lorenzo; Kirtman, Bernard; Rérat, Michel; Orlando, Roberto; Dovesi, Roberto

    2013-10-01

    In this work, we validate a new, fully analytical method for calculating Raman intensities of periodic systems, developed and presented in Paper I [L. Maschio, B. Kirtman, M. Rérat, R. Orlando, and R. Dovesi, J. Chem. Phys. 139, 164101 (2013)]. Our validation of this method and its implementation in the CRYSTAL code is done through several internal checks as well as comparison with experiment. The internal checks include consistency of results when increasing the number of periodic directions (from 0D to 1D, 2D, 3D), comparison with numerical differentiation, and a test of the sum rule for derivatives of the polarizability tensor. The choice of basis set as well as the Hamiltonian is also studied. Simulated Raman spectra of α-quartz and of the UiO-66 Metal-Organic Framework are compared with the experimental data.

  5. Ab initio analytical Raman intensities for periodic systems through a coupled perturbed Hartree-Fock/Kohn-Sham method in an atomic orbital basis. II. Validation and comparison with experiments.

    PubMed

    Maschio, Lorenzo; Kirtman, Bernard; Rérat, Michel; Orlando, Roberto; Dovesi, Roberto

    2013-10-28

    In this work, we validate a new, fully analytical method for calculating Raman intensities of periodic systems, developed and presented in Paper I [L. Maschio, B. Kirtman, M. Rérat, R. Orlando, and R. Dovesi, J. Chem. Phys. 139, 164101 (2013)]. Our validation of this method and its implementation in the CRYSTAL code is done through several internal checks as well as comparison with experiment. The internal checks include consistency of results when increasing the number of periodic directions (from 0D to 1D, 2D, 3D), comparison with numerical differentiation, and a test of the sum rule for derivatives of the polarizability tensor. The choice of basis set as well as the Hamiltonian is also studied. Simulated Raman spectra of α-quartz and of the UiO-66 Metal-Organic Framework are compared with the experimental data.

  6. The association between pulmonary function impairment and colon inflammation in ulcerative colitis patients: A scientific basis for exterior-interior correlation between lung and large intestine.

    PubMed

    Wang, Jian-Yun; Wang, Xin-Yue; Wu, Hua-Yang; Sun, Hui-Yi; Liu, Da-Ming; Zhang, Wen; Jin, Chen-Xi; Wang, Shuo-Ren

    2016-12-01

    To investigated the involvement of pulmonary function impairment in ulcerative colitis (UC), to explore a scientific basis for the Chinese medicine (CM) theory of exterior-interior correlation between Lung (Fei) and Large intestine (Dachang). Totally 120 patients with a diagnosis of UC were recruited and the demographics, clinical data, and blood samples were collected. C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR) concentrations were measured. Every patient accepted pulmonary function test and took chest radiograph (CXR).> RESULTS: Pulmonary function abnormalities were present in 72 of 120 patients. The median (interquartile range) vital capacity (VC), forced vital capacity (FVC), forced expiratory volume in 1 s (FEV1), carbon monoxide diffusion capacity (DLCO) of lung, total lung capacity (TLC) and functional residual volume (FRV) were decreased in distal UC and pancolitis compared with ulcerative prochitis (P <0.0005). Male patients had increased VC, FEV1/FVC, and residual volume (RV)/TLC compared with female (P <0.0005), but decreased DLCO and carbon monoxide iffusion capacity (KCO) of lung/alveolar ventilation (P <0.0005). Age was strongly correlated with RV (Spearman rank correlation coefficient (rs)=-0.57,P <0.0001), and RV/TLC (rs=0.48,P<0.0001). Age was also correlated with FEV1/FVC (rs=-0.29, P=0.001), forced expiratory flow in 75% vital capacity (FEF75%, rs=-0.20, P=0.03), DLCO (rs=-0.21, P=0.02), TLC (rs=-0.25, P=0.006), and FRV (rs=-0.28, P=0.002). The course of disease was correlated with FEF75% (rs=-0.18, P=0.049) and KCO (rs=-0.19, P=0.036). Chest radiograph abnormalities were presented in 38 of 120. Pulmonary symptoms were presented in 10 of 120. Other extraintestinal complications were presented in 21 of 120. Pulmonary function impairment was more frequently than other extraintestinal complications in UC patients, which may be affected by sex, age, extent and course of disease. These results may be a scientific basis for the

  7. Comment on ``Curvy-steps approach to constraint-free extended-Lagrangian ab initio molecular dynamics, using atom-centered basis functions: Convergence toward Born-Oppenheimer trajectories'' [J. Chem. Phys. 121, 11542 (2004)

    NASA Astrophysics Data System (ADS)

    Iyengar, Srinivasan S.; Schlegel, H. Bernhard; Scuseria, Gustavo E.; Millam, John M.; Frisch, Michael J.

    2005-07-01

    The curvy-extended-Lagrangian molecular-dynamics (ELMD) approach [J. M. Herbert and M. Head-Gordon, J. Chem. Phys. 121, 11542 (2004)] is similar to atom-centered density-matrix propagation (ADMP) [H. B. Schlegel, J. M. Millam, S. S. Iyengar, G. A. Voth, A. D. Daniels, G. E. Scuseria, and M. J. Frisch, J. Chem. Phys. 114, 9758 (2001); S. S. Iyengar, H.B. Schlegel, J.M. Millam, G.A. Voth, G.E. Scuseria, and M.J. Frisch, ibid.115, 10291 (2001); H.B. Schlegel, S.S. Iyengar, X. Li, J.M. Millam, G.A. Voth, G.E. Scuseria, and M.J. Frisch, ibid. 117, 8694 (2002); S.S. Iyengar, H.B. Schlegel, G.A. Voth, J.M. Millam, G.E. Scuseria, and M.J. Frisch, Israel J. Chem. 42, 191 (2002)] and based on Car-Parrinello [Phys. Rev. Lett. 55, 2471 (1985)] extended-Lagrangian [H.C. Andersen, J. Chem. Phys. 72, 2384 (1980)] molecular dynamics. Similarities between curvy-ELMD and ADMP arise from using unconverged electronic single-particle density matrices within Gaussian basis functions as dynamical variables. Curvy-ELMD differs from ADMP in not requiring idempotency to be explicitly enforced. In this Comment, we address several misleading remarks in Refs. 1 [J.M. Herbert and M. Head-Gordon, J. Chem. Phys. 121, 11542 (2004)] and 8 [J.M. Herbert and M. Head-Gordon, J. Chem. Phys. (submitted)].

  8. mAbs

    PubMed Central

    2009-01-01

    The twenty two monoclonal antibodies (mAbs) currently marketed in the U.S. have captured almost half of the top-20 U.S. therapeutic biotechnology sales for 2007. Eight of these products have annual sales each of more than $1 B, were developed in the relatively short average period of six years, qualified for FDA programs designed to accelerate drug approval, and their cost has been reimbursed liberally by payers. With growth of the product class driven primarily by advancements in protein engineering and the low probability of generic threats, mAbs are now the largest class of biological therapies under development. The high cost of these drugs and the lack of generic competition conflict with a financially stressed health system, setting reimbursement by payers as the major limiting factor to growth. Advances in mAb engineering are likely to result in more effective mAb drugs and an expansion of the therapeutic indications covered by the class. The parallel development of biomarkers for identifying the patient subpopulations most likely to respond to treatment may lead to a more cost-effective use of these drugs. To achieve the success of the current top-tier mAbs, companies developing new mAb products must adapt to a significantly more challenging commercial environment. PMID:20061824

  9. An expanded calibration study of the explicitly correlated CCSD(T)-F12b method using large basis set standard CCSD(T) atomization energies

    NASA Astrophysics Data System (ADS)

    Feller, David; Peterson, Kirk A.

    2013-08-01

    The effectiveness of the recently developed, explicitly correlated coupled cluster method CCSD(T)-F12b is examined in terms of its ability to reproduce atomization energies derived from complete basis set extrapolations of standard CCSD(T). Most of the standard method findings were obtained with aug-cc-pV7Z or aug-cc-pV8Z basis sets. For a few homonuclear diatomic molecules it was possible to push the basis set to the aug-cc-pV9Z level. F12b calculations were performed with the cc-pVnZ-F12 (n = D, T, Q) basis set sequence and were also extrapolated to the basis set limit using a Schwenke-style, parameterized formula. A systematic bias was observed in the F12b method with the (VTZ-F12/VQZ-F12) basis set combination. This bias resulted in the underestimation of reference values associated with small molecules (valence correlation energies <0.5 Eh) and an even larger overestimation of atomization energies for bigger systems. Consequently, caution should be exercised in the use of F12b for high accuracy studies. Root mean square and mean absolute deviation error metrics for this basis set combination were comparable to complete basis set values obtained with standard CCSD(T) and the aug-cc-pVDZ through aug-cc-pVQZ basis set sequence. However, the mean signed deviation was an order of magnitude larger. Problems partially due to basis set superposition error were identified with second row compounds which resulted in a weak performance for the smaller VDZ-F12/VTZ-F12 combination of basis sets.

  10. An expanded calibration study of the explicitly correlated CCSD(T)-F12b method using large basis set standard CCSD(T) atomization energies.

    PubMed

    Feller, David; Peterson, Kirk A

    2013-08-28

    The effectiveness of the recently developed, explicitly correlated coupled cluster method CCSD(T)-F12b is examined in terms of its ability to reproduce atomization energies derived from complete basis set extrapolations of standard CCSD(T). Most of the standard method findings were obtained with aug-cc-pV7Z or aug-cc-pV8Z basis sets. For a few homonuclear diatomic molecules it was possible to push the basis set to the aug-cc-pV9Z level. F12b calculations were performed with the cc-pVnZ-F12 (n = D, T, Q) basis set sequence and were also extrapolated to the basis set limit using a Schwenke-style, parameterized formula. A systematic bias was observed in the F12b method with the (VTZ-F12/VQZ-F12) basis set combination. This bias resulted in the underestimation of reference values associated with small molecules (valence correlation energies <0.5 E(h)) and an even larger overestimation of atomization energies for bigger systems. Consequently, caution should be exercised in the use of F12b for high accuracy studies. Root mean square and mean absolute deviation error metrics for this basis set combination were comparable to complete basis set values obtained with standard CCSD(T) and the aug-cc-pVDZ through aug-cc-pVQZ basis set sequence. However, the mean signed deviation was an order of magnitude larger. Problems partially due to basis set superposition error were identified with second row compounds which resulted in a weak performance for the smaller VDZ-F12/VTZ-F12 combination of basis sets.

  11. Implementation of renormalized excitonic method at ab initio level.

    PubMed

    Zhang, Hongjiang; Malrieu, Jean-Paul; Ma, Haibo; Ma, Jing

    2012-01-05

    The renormalized excitonic method [Hajj et al., Phys Rev B 2005, 72, 224412], in which the excited state of the whole system may be described as a linear combination of local excitations, has been implemented at ab initio level. Its performance is tested on the ionization potential and the energy gap between singlet ground state and lowest triplet for linear molecular hydrogen chains and more realistic systems, such as polyenes and polysilenes, using full configuration interaction (FCI) wave functions with a minimal basis set. The influence of different block sizes and the extent of interblock interactions are investigated. It has been demonstrated that satisfactory results can be obtained if the near degeneracies between the model space and the outer space are avoided and if interactions between the next-nearest neighbor blocks are considered. The method can be used with larger basis sets and other accurate enough ab initio evaluations (instead of FCI) of local excited states, from blocks, or from dimers or trimers of blocks. It provides a new possibility to accurately and economically describe the low-lying delocalized excited states of large systems, even inhomogeneous ones.

  12. Multiwavelength Observations of AB Doradus

    NASA Astrophysics Data System (ADS)

    Slee, O. B.; Erkan, N.; Johnston-Hollitt, M.; Budding, E.

    2014-04-01

    We have observed the bright, magnetically active multiple star AB Doradus in a multiwavelength campaign centring around two large facility allocations in November 2006 and January, 2007. Our observations have covered at least three large flares. These flares were observed to produce significant hardening of the X-ray spectra during their very initial stages. We monitored flare-related effects using the Suzaku X-ray satellite and the Australia Telescope Compact Array (ATCA) at 3.6 and 6 cm. Observations at 11 and 21 cm were also included, but they were compromised by interference. Optical monitoring was also provided by broadband B and V photometry and some high-dispersion spectrograms. From this multiwavelength coverage we find that the observed flare effects can be mainly associated with a large active region near longitude zero. The second major X-ray and microwave flare of Jan 8, 2007 was observed with a favourable geometry that allowed its initial high-energy impulsive phase to be observed in the higher frequency range of Suzaku's XIS detectors. The fractional circular polarisation (Stokes V/I) was measured in the uv data for the complete runs, for 25 min integrations and, at 4.80 GHz, for 5 min integrations, using the radio data of Nov 21 2006 and Jan 08 2007. Most of the full data sets showed V/I fractions from AB Dor B that were significant at greater than the 3σ level. In several of the 5 min integrations at 4.80 and 8.64 GHz this fraction reached a significance level between 3 and 9σ. Lack of angular resolution prevented identification of these high V/I values with one or other of the two low-mass red-dwarf components of AB Dor B.

  13. The innovative use of a large-scale industry biomedical consortium to research the genetic basis of drug induced serious adverse events.

    PubMed

    Holden, Arthur L

    2007-01-01

    The International Serious Adverse Event Consortium (SAEC) is a pharmaceutical industry and FDA led international (501 c3 non-profit) consortium, focused on identifying and validating DNA-variants useful in predicting the risk of drug induced, rare serious adverse events (SAEs). As such, it functions with the explicit purpose of enhancing the 'public good'. Its members are (i) organizations engaged principally in the business of discovering, developing and marketing pharmaceutical products, or (ii) a charitable, governmental, or other non-profit organization with an interest in researching the molecular basis of drug response.Drug-induced, rare SAEs present significant health issues for patients; and pose challenges for the safe use of approved drugs and the development of new drugs. Examples of drug-induced, rare SAEs include hepatotoxicity, QT prolongation, rhabdomyolosis, serious skin rashes (e.g. SJS), edema, acute renal failure, acute hypersensitivity, anemias/neutropenias, excessive weigh gain, retinopathy, vasculitis, among others. The rarity of such drug induced SAEs and the absence of effective government surveillance/research networks, makes it extremely difficult for any one company or research entity to accrue enough SAE cases and controls to conduct effective whole genome studies. Central to the notion of the SAEC is industry, government and health care providers can join forces to make use of a variety of sample and data resources in researching the genetic basis of these events.The purpose of the SAEC is threefold:•To carry out research directed toward the discovery of DNA-variants clinically useful in understanding and predicting the risk of drug induced serious adverse events and similar scientific research.•To ensure the widespread availability of the results of such research to the scientific research community and the public at large for no charge through publication and web-based methods; and•To educate the scientific research and medical

  14. Erythema ab igne.

    PubMed

    Miller, Kristen; Hunt, Raegan; Chu, Julie; Meehan, Shane; Stein, Jennifer

    2011-10-15

    Erythema ab igne is a reticulated, erythematous or hyperpigmented dermatosis that results from chronic and repeated exposure to low levels of infrared radiation. Multiple heat sources have been reported to cause this condition, which include heated reclining chairs, heating pads, hot water bottles, car heaters, electric space heaters, and, more recently, laptop computers. Treatment consists of withdrawing the inciting heat source. Although erythema ab igne carries a good prognosis, it is not necessarily a self-limited diagnosis as patients are at long-term risk of developing subsequent cutaneous malignant conditions, which include squamous cell and merkel-cell carcinomas.

  15. The local electron affinity for non-minimal basis sets.

    PubMed

    Clark, Timothy

    2010-07-01

    A technique known as intensity filtering is introduced to select valence-like virtual orbitals for calculating the local electron affinity, EA(L). Intensity filtering allows EA(L) to be calculated using semiempirical molecular orbital techniques that include polarisation functions. Without intensity filtering, such techniques yield spurious EA(L) values that are dominated by the polarisation functions. As intensity filtering should also be applicable for ab initio or density functional theory calculations with large basis sets, it also makes EA(L) available for these techniques.

  16. Structure, Biological Functions and Applications of the AB5 Toxins

    PubMed Central

    Beddoe, Travis; Paton, Adrienne W.; Le Nours, Jérôme; Rossjohn, Jamie; Paton, James C.

    2010-01-01

    AB5 toxins are important virulence factors for several major bacterial pathogens, including Bordetella pertussis, Vibrio cholerae, Shigella dysenteriae and at least two distinct pathotypes of Escherichia coli. The AB5 toxins are so termed because they comprise a catalytic A-subunit, which is responsible for disruption of essential host functions, and a pentameric B-subunit that binds to specific glycan receptors on the target cell surface. The molecular mechanisms by which these AB5 toxins cause disease have been largely unraveled, including recent insights into a novel AB5 toxin family, subtilase cytotoxin (SubAB). Furthermore, AB5 toxins have become a valuable tool for studying fundamental cellular functions, and are now being investigated for potential applications in the clinical treatment of human diseases. PMID:20202851

  17. Structure, biological functions and applications of the AB5 toxins.

    PubMed

    Beddoe, Travis; Paton, Adrienne W; Le Nours, Jérôme; Rossjohn, Jamie; Paton, James C

    2010-07-01

    AB(5) toxins are important virulence factors for several major bacterial pathogens, including Bordetella pertussis, Vibrio cholerae, Shigella dysenteriae and at least two distinct pathotypes of Escherichia coli. The AB(5) toxins are so named because they comprise a catalytic A-subunit, which is responsible for disruption of essential host functions, and a pentameric B-subunit that binds to specific glycan receptors on the target cell surface. The molecular mechanisms by which the AB(5) toxins cause disease have been largely unravelled, including recent insights into a novel AB(5) toxin family, subtilase cytotoxin (SubAB). Furthermore, AB(5) toxins have become a valuable tool for studying fundamental cellular functions, and are now being investigated for potential applications in the clinical treatment of human diseases. Copyright 2010 Elsevier Ltd. All rights reserved.

  18. Ab Initio Potential Energy Surface for H-H2

    NASA Technical Reports Server (NTRS)

    Patridge, Harry; Bauschlicher, Charles W., Jr.; Stallcop, James R.; Levin, Eugene

    1993-01-01

    Ab initio calculations employing large basis sets are performed to determine an accurate potential energy surface for H-H2 interactions for a broad range of separation distances. At large distances, the spherically averaged potential determined from the calculated energies agrees well with the corresponding results determined from dispersion coefficients; the van der Waals well depth is predicted to be 75 +/- 3 micro E(h). Large basis sets have also been applied to reexamine the accuracy of theoretical repulsive potential energy surfaces (25-70 kcal/mol above the H-H2 asymptote) at small interatomic separations; the Boothroyd, Keogh, Martin, and Peterson (BKMP) potential energy surface is found to agree with results of the present calculations within the expected uncertainty (+/- 1 kcal/mol) of the fit. Multipolar expansions of the computed H-H2 potential energy surface are reported for four internuclear separation distances (1.2, 1.401, 1.449, and 1.7a(0)) of the hydrogen molecule. The differential elastic scattering cross section calculated from the present results is compared with the measurements from a crossed beam experiment.

  19. Ab Initio Potential Energy Surface for H-H2

    NASA Technical Reports Server (NTRS)

    Patridge, Harry; Bauschlicher, Charles W., Jr.; Stallcop, James R.; Levin, Eugene

    1993-01-01

    Ab initio calculations employing large basis sets are performed to determine an accurate potential energy surface for H-H2 interactions for a broad range of separation distances. At large distances, the spherically averaged potential determined from the calculated energies agrees well with the corresponding results determined from dispersion coefficients; the van der Waals well depth is predicted to be 75 +/- 3 micro E(h). Large basis sets have also been applied to reexamine the accuracy of theoretical repulsive potential energy surfaces (25-70 kcal/mol above the H-H2 asymptote) at small interatomic separations; the Boothroyd, Keogh, Martin, and Peterson (BKMP) potential energy surface is found to agree with results of the present calculations within the expected uncertainty (+/- 1 kcal/mol) of the fit. Multipolar expansions of the computed H-H2 potential energy surface are reported for four internuclear separation distances (1.2, 1.401, 1.449, and 1.7a(0)) of the hydrogen molecule. The differential elastic scattering cross section calculated from the present results is compared with the measurements from a crossed beam experiment.

  20. Ab initio studies of hydrocarbon peroxyl radicals

    SciTech Connect

    Besler, B.H.; Sevilla, M.D.; MacNeille, P.

    1986-11-20

    Extensive ab initio molecular orbital calculations have been performed for the importance series of peroxyl radicals (O/sub 2//sup .-/), HO/sub 2//sup ./, CH/sub 3/O/sub 2//sup ./, (CH/sub 3/)/sub 2/CHO/sub 2//sup ./, and (CH/sub 3/CH/sub 2/)/sub 2/CHO/sub 2//sup ./. Parameters calculated include equilibrium geometries, harmonic vibrational frequencies, dipole moments, and isotropic and anisotropic hyperfine couplings. Equilibrium geometries were of primary interest. In the two large hydrocarbon peroxyl radicals the carbon atoms and appropriate hydrogen atoms were constrained to be coplanar and the O-O group was forced to be perpendicular to the carbon chain in order to stimulate the presence of a peroxyl radical site in a polyethylene chain. Calculations were performed with large Gaussian basis sets (up to 6-311 ++G(d,p)). Calculations for HO/sub 2//sup ./ including electron correlation utilizing Moeller-Plesset perturbation theory were performed at the following levels: MP2(6-31G(d)) and 6-311G(d,p), MP3(6-311G(d,p)) and MP4SDTQ(6-311(d,p)). Calculated values are compared against the highly accurate experimental data for HO/sub 2//sup ./ known from microwave, laser magnetic resonance, and diode laser studies in order to determine the level of calculation necessary for accurate predictions. Comparison of the various calculations shows that MP2(6-31G(d)) compares favorably with MP4SDTQ(6-311G(d,p)) at a considerable savings in computation time.

  1. A global ab initio potential for HCN/HNC, exact vibrational energies, and comparison to experiment

    NASA Technical Reports Server (NTRS)

    Bentley, Joseph A.; Bowman, Joel M.; Gazdy, Bela; Lee, Timothy J.; Dateo, Christopher E.

    1992-01-01

    An ab initio (i.e., from first principles) calculation of vibrational energies of HCN and HNC is reported. The vibrational calculations were done with a new potential derived from a fit to 1124 ab initio electronic energies which were calculated using the highly accurate CCSD(T) coupled-cluster method in conjunction with a large atomic natural orbital basis set. The properties of this potential are presented, and the vibrational calculations are compared to experiment for 54 vibrational transitions, 39 of which are for zero total angular momentum, J = 0, and 15 of which are for J = 1. The level of agreement with experiment is unprecedented for a triatomic with two nonhydrogen atoms, and demonstrates the capability of the latest computational methods to give reliable predictions on a strongly bound triatomic molecule at very high levels of vibrational excitation.

  2. Ab initio ground-state potential energy function and vibration-rotation energy levels of imidogen, NH.

    PubMed

    Koput, Jacek

    2015-06-30

    The accurate ground-state potential energy function of imidogen, NH, has been determined from ab initio calculations using the multireference averaged coupled-pair functional (MR-ACPF) method in conjunction with the correlation-consistent core-valence basis sets up to octuple-zeta quality. The importance of several effects, including electron correlation beyond the MR-ACPF level of approximation, the scalar relativistic, adiabatic, and nonadiabatic corrections were discussed. Along with the large one-particle basis set, all of these effects were found to be crucial to attain "spectroscopic" accuracy of the theoretical predictions of vibration-rotation energy levels of NH.

  3. Theoretical ab initio study of Xenon pentafluoride anion. Mechanism of Xenon pseudorotation

    NASA Astrophysics Data System (ADS)

    Fleurat-Lessard, Paul; Durupthy, Olivier; Volatron, François

    2002-09-01

    Ab initio calculations have been performed on XeF 5- anion at the MP2 and CCSD(T) levels with a large basis set. Four extrema have been optimized and characterized by frequencies analysis. We find the absolute minimum to be of D 5h symmetry in accordance with the experimental data; the theoretical vibrational spectrum of this minimum is in good agreement with the experimental one. Three other extrema are found to be higher in energy depending on the angular separation of the Xenon lone pairs as predicted by the VSEPR theory. Finally the characterized transition state has been found to belong to the Xenon pseudorotation pathway.

  4. Iodine-131-labeled MAb F(ab')2 fragments are more efficient and less toxic than intact anti-CEA antibodies in radioimmunotherapy of large human colon carcinoma grafted in nude mice

    SciTech Connect

    Buchegger, F.; Pelegrin, A.; Delaloye, B.; Bischof-Delaloye, A.; Mach, J.P. )

    1990-06-01

    During one week, beginning 18 days after transplantation, nude mice bearing human colon carcinoma ranging from 115 to 943 mm3 (mean 335 mm3) were treated by repeated intravenous injections of either iodine-131-({sup 131}I) labeled intact antibodies or {sup 131}I-labeled corresponding F(ab')2 fragments of a pool of four monoclonal antibodies (MAbs) directed against distinct epitopes of carcinoembryonic antigen (CEA). Complete tumor remission was observed in 8 of 10 mice after therapy with F(ab')2 and 6 of the animals survived 10 mo in good health. In contrast, after treatment with intact MAbs, tumors relapsed in 7 of 8 mice after remission periods of 1 to 3.5 mo despite the fact that body weight loss and depression of peripheral white blood cells, symptoms of radiation toxicity, and the calculated radiation doses for liver, spleen, bone, and blood were increased or equal in these animals as compared to mice treated with F(ab')2.

  5. Fine-needle aspiration cytology yield as a basis for morphological, molecular, and cytogenetic diagnosis in alk-positive anaplastic large cell lymphoma with atypical clinical presentation.

    PubMed

    Bogdanic, Maja; Ostojic Kolonic, Slobodanka; Kaic, Gordana; Kardum Paro, Mirjana Mariana; Lasan Trcic, Ruzica; Kardum-Skelin, Ika

    2017-01-01

    ALK positive anaplastic large cell lymphoma is a T-cell lymphoma usually occurring in children and young adults. It frequently involves lymph nodes and extranodal sites and is associated with favorable prognosis. A 20-year old man was admitted for painful mass in the left axilla with overlying skin redness. Clinical presentation and US findings were highly suspicious for sarcoma. Definitive diagnosis was established cytolologically and using ancillary technologies from cytological samples. Fine needle aspiration cytology of tumor mass (lymph node conglomerate and surrounding tissue) show predominance of large, pleomorphic, atypical cells with large nuclei and vacuolised cytoplasm. Atypical cells immunocytochemically were positive for LCA, CD30, CD3, EMA, and ALK; negative for CD15 and CD56. NPM-ALK transcript was detected by reverse transcriptase-polymerase chain reaction (RT-PCT). Molecular analysis of TCRß and TCRγ genes demonstrated clonal TCR genes rearrangement. Complex karyotype with multiple numerical and structural changes was found on conventional cytogenetics. These findings excluded sarcoma and corroborated the diagnosis of ALK positive ALCL. Cutaneous involvement in ALCL can clinically mimic sarcoma, especially in cases with localized disease without B symptoms. In those cases, immunostaining, PCR, and conventional cytogenetics are helpful to exclude sarcoma. Diagn. Cytopathol. 2017;45:51-54. © 2016 Wiley Periodicals, Inc.

  6. Single particle calculations for a Woods-Saxon potential with triaxial deformations, and large Cartesian oscillator basis (TRIAXIAL 2014, Third version of the code Triaxial)

    NASA Astrophysics Data System (ADS)

    Mohammed-Azizi, B.; Medjadi, D. E.

    2014-11-01

    Theory and FORTRAN program of the first version of this code (TRIAXIAL) have already been described in detail in Computer Physics Comm. 156 (2004) 241-282. A second version of this code (TRIAXIAL 2007) has been given in CPC 176 (2007) 634-635. The present FORTRAN program is the third version (TRIAXIAL 2014) of the same code. Now, It is written in free format. As the former versions, this FORTRAN program solves the same Schrodinger equation of the independent particle model of the atomic nucleus with the same method. However, the present version is much more convenient. In effect, it is characterized by the fact that the eigenvalues and the eigenfunctions can be given by specific subroutines. The latters did not exist in the old versions (2004 and 2007). In addition, it is to be noted that in the previous versions, the eigenfunctions were only given by their coefficients of their expansion onto the harmonic oscillator basis. This method is needed in some cases. But in other cases, it is preferable to treat the eigenfunctions directly in configuration space. For this reason, we have implemented an additional subroutine for this task. Some other practical subroutines have also been implemented. Moreover, eigenvalues and eigenfunctions are recorded onto several files. All these new features of the code and some important aspects of its structure are explained in the document ‘Triaxial2014 use.pdf’. Catalogue identifier: ADSK_v3_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADSK_v3_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 13672 No. of bytes in distributed program, including test data, etc.: 217598 Distribution format: tar.gz Programming language: FORTRAN 77/90 (double precision). Computer: PC. Pentium 4, 2600MHz and beyond. Operating system: WINDOWS XP

  7. Solution of the Dirac equation using the Rayleigh-Ritz method: Flexible basis coupling large and small components. Results for one-electron systems

    NASA Astrophysics Data System (ADS)

    Baǧcı, A.; Hoggan, P. E.

    2016-07-01

    An algebraic solution of the Dirac equation is reinvestigated. Slater-type spinor orbitals and their corresponding system of differential equations are defined in two- and four-component formalism. They describe the radial function in components of the wave function of the Dirac equation solution to high accuracy. They constitute the matrix elements arising in a generalized eigenvalue equation. These terms are evaluated through prolate spheroidal coordinates. The corresponding integrals are calculated by the numerical global-adaptive method taking into account the Gauss-Kronrod numerical integration extension. Sample calculations are performed using flexible basis sets generated with both signs of the relativistic angular momentum quantum number κ . Applications to one-electron atoms and diatomics are detailed. Variationally optimum values for orbital parameters are obtained at given nuclear separation. Methods discussed in this work are capable of yielding highly accurate relativistic two-center integrals for all ranges of orbital parameters. This work provides an efficient way to overcome the problems that arise in relativistic calculations.

  8. Solution of the Dirac equation using the Rayleigh-Ritz method: Flexible basis coupling large and small components. Results for one-electron systems.

    PubMed

    Bağcı, A; Hoggan, P E

    2016-07-01

    An algebraic solution of the Dirac equation is reinvestigated. Slater-type spinor orbitals and their corresponding system of differential equations are defined in two- and four-component formalism. They describe the radial function in components of the wave function of the Dirac equation solution to high accuracy. They constitute the matrix elements arising in a generalized eigenvalue equation. These terms are evaluated through prolate spheroidal coordinates. The corresponding integrals are calculated by the numerical global-adaptive method taking into account the Gauss-Kronrod numerical integration extension. Sample calculations are performed using flexible basis sets generated with both signs of the relativistic angular momentum quantum number κ. Applications to one-electron atoms and diatomics are detailed. Variationally optimum values for orbital parameters are obtained at given nuclear separation. Methods discussed in this work are capable of yielding highly accurate relativistic two-center integrals for all ranges of orbital parameters. This work provides an efficient way to overcome the problems that arise in relativistic calculations.

  9. MELCOR 1.8.2 assessment: Aerosol experiments ABCOVE AB5, AB6, AB7, and LACE LA2

    SciTech Connect

    Souto, F.J.; Haskin, F.E.; Kmetyk, L.N.

    1994-10-01

    The MELCOR computer code has been used to model four of the large-scale aerosol behavior experiments conducted in the Containment System Test Facility (CSTF) vessel. Tests AB5, AB6 and AB7 of the ABCOVE program simulate the dry aerosol conditions during a hypothetical severe accident in an LMFBR. Test LA2 of the LACE program simulates aerosol behavior in a condensing steam environment during a postulated severe accident in an LWR with failure to isolate the containment. The comparison of code results to experimental data show that MELCOR is able to correctly predict most of the thermal-hydraulic results in the four tests. MELCOR predicts reasonably well the dry aerosol behavior of the ABCOVE tests, but significant disagreements are found in the aerosol behavior modelling for the LA2 experiment. These results tend to support some of the concerns about the MELCOR modelling of steam condensation onto aerosols expressed in previous works. During these analyses, a limitation in the MELCOR input was detected for the specification of the aerosol parameters for more than one component. A Latin Hypercube Sampling (LHS) sensitivity study of the aerosol dynamic constants is presented for test AB6. The study shows the importance of the aerosol shape factors in the aerosol deposition behavior, and reveals that MELCOR input/output processing is highly labor intensive for uncertainty and sensitivity analyses based on LHS.

  10. Evolutionary origins of retroposon lineages of Mhc class II Ab alleles.

    PubMed

    Lu, C C; Ye, Y; She, J X; Bonhomme, F; Wakeland, E K

    1996-01-01

    Major histocompatibility complex (Mhc) class II Ab genes have evolved into three distinct lineages. While lineage 2 alleles differ from lineage 1 alleles by the insertion of a retroposon in intron 2, the basis for the extremely large intron 2 in lineage 3 alleles has heretofore been undetermined. In this report, we demonstrate by nucleotide sequencing that the genomic sequences of prototypic alleles from all three lineages diverge significantly and that lineage 3 is derived from lineage 2 by two insertional events in intron 2. One insert, composed of a member of B1 short interspersed repetitive elements (SINEs), occurs 508 base pairs (bp) 3' of exon 2, and the other, 1141 bp 3' of exon 2 within the retroposon that distinguishes lineage 2 from lineage 1. To assess the evolutionary stability of these lineages and the extent of ancestral polymorphisms of Ab within Mus species, we extended our restriction site polymorphism analysis to include 86 alleles from 120 independently derived H2 haplotypes from 12 separate species and subspecies of Mus. A phylogenetic tree revealing the relationships of these Ab alleles with respect to restriction site polymorphisms, but excluding the retroposon insertions, demonstrated that these lineages have distinctive genomic structures beyond the retroposon polymorphisms. In summary, these mouse Ab genes were produced from successive retroposon insertion events. Lineage 1 and 2 were detected in a variety of Mus species, including Mus caroli, indicating that these lineages diverged more than 2 million years ago. Lineage 3 alleles were found only in the Mus musculus subspecies, suggesting that it diverged from lineage 2 more recently. These results indicate that all three lineages of Ab have persisted through several speciation events in the genus Mus.

  11. Laptop Induced Erythema Ab Igne

    PubMed Central

    Nayak, Sudhir U K; Shenoi, Shrutakirthi D; Prabhu, Smitha

    2012-01-01

    Erythema ab igne is a reticular, pigmented dermatosis caused by prolonged and repeated exposure to infrared radiation that is insufficient to produce a burn. The use of laptop computers has increased manifold in the recent past. Prolonged contact of the laptop with the skin can lead to the development of erythema ab igne. We present a case of erythema ab igne secondary to laptop use in an Indian student. PMID:22615512

  12. Laptop induced erythema ab igne.

    PubMed

    Nayak, Sudhir U K; Shenoi, Shrutakirthi D; Prabhu, Smitha

    2012-03-01

    Erythema ab igne is a reticular, pigmented dermatosis caused by prolonged and repeated exposure to infrared radiation that is insufficient to produce a burn. The use of laptop computers has increased manifold in the recent past. Prolonged contact of the laptop with the skin can lead to the development of erythema ab igne. We present a case of erythema ab igne secondary to laptop use in an Indian student.

  13. First fully ab initio potential energy surface of methane with a spectroscopic accuracy

    NASA Astrophysics Data System (ADS)

    Nikitin, A. V.; Rey, M.; Tyuterev, Vl. G.

    2016-09-01

    Full 9-dimensional ab initio potential energy surfaces for the methane molecule are constructed using extended electronic structure coupled-cluster calculations with various series of basis sets following increasing X cardinal numbers: cc-pVXZ (X = 3, 4, 5, 6), aug-cc-ACVXZ (X = 3, 4, 5), and cc-pCVXZ-F12 (X = 3, 4). High-order dynamic electron correlations including triple and quadrupole excitations as well as relativistic and diagonal Born-Oppenheimer breakdown corrections were accounted for. Analytical potential functions are parametrized as non-polynomial expansions in internal coordinates in irreducible tensor representation. Vibrational energy levels are reported using global variational nuclear motion calculations with exact kinetic energy operator and a full account of the tetrahedral symmetry of CH4. Our best ab initio surface including above-mentioned contributions provides the rms (obs.-calc.) errors of less than 0.11 cm-1 for vibrational band centers below 4700 cm-1, and ˜0.3 cm-1 for all 229 assigned experimentally determined vibrational levels up to the Icosad range <7900 cm-1 without empirically adjusted parameters. These results improve the accuracy of ab initio methane vibrational predictions by more than an order of magnitude with respect to previous works. This is an unprecedented accuracy of first-principles calculations of a five-atomic molecule for such a large data set. New ab initio potential results in significantly better band center predictions even in comparison with best available empirically corrected potential energy surfaces. The issues related to the basis set extrapolation and an additivity of various corrections at this level of accuracy are discussed.

  14. Polymorphism in self-assembled AB6 binary nanocrystal superlattices.

    PubMed

    Ye, Xingchen; Chen, Jun; Murray, Christopher B

    2011-03-02

    We report the formation and systematic struc-tural characterization of a new AB(6) polymorph with the body-centered cubic (bcc) symmetry in binary nanocrystal superlattices (BNSLs). The bcc-AB(6) phase, lacking any atomic analogue, is isomorphic to certain alkali-metal intercalation compounds of fullerene C(60) (e.g., K(6)C(60)). On the basis of the space-filling principle, we further tailor the relative phase stability of the two AB(6) polymorphs-CaB(6) and bcc-AB(6)-from coexistence to phase-pure bcc-AB(6), highlighting the entropic effect as the main driving-force of the self-organization of BNSLs. We also discuss the implication of surface topology studies and the observation of twinning and preferential orientation in bcc-AB(6) on the growth mechanism of BNSLs. Furthermore, the connection between the bcc-AB(6) phase and the (3(2).4.3.4) Archimedean tiling shows the promise of further exploration on the structural diversity (both periodic and aperiodic) in this emerging class of metamaterials. The identification and the ability to tune the relative phase stability of polymorphic structures provide a unique opportunity to engineer the interparticle coupling through controlled clustering and/or interconnectivity of sublattice in BNSLs with identical stoichiometry.

  15. The role of next-generation sequencing in understanding the genomic basis of diffuse large B cell lymphoma and advancing targeted therapies.

    PubMed

    Dubois, Sydney; Jardin, Fabrice

    2016-03-01

    Next Generation Sequencing (NGS) has redefined the genetic landscape of Diffuse Large B-Cell Lymphoma (DLBCL) by identifying recurrent somatic mutations. Importantly, in some cases these mutations impact potentially actionable targets, thus affording novel personalized therapy opportunities. At the forefront of today's precision therapy era, how to best incorporate NGS into daily clinical practice is of primordial concern, in order to tailor patient's treatment regimens according to their individual mutational profiles. With the advent of cell-free DNA sequencing, which provides a sensitive and less invasive means of monitoring DLBCL patients, the clinical feasibility of NGS has been greatly improved. This article reviews the current landscape of DLBCL mutations, as well as the targeted therapies developed to counter their effects, and discusses how best to utilize NGS data for treatment decision-making.

  16. Solid-State Structure of Abeta (Ab) in Alzheimer's Disease.

    PubMed

    Lu, Junxia; Dong, Xing-Qi; Zhang, Jian-Jun

    2017-02-08

    Alzheimer's disease (AD) has become the most common neurodegenerative disease. The deposition of amyloid fibrils in the brain is one of the characteristics of AD. The fibrils are composed of amyloid-b peptide (Ab). Ab is produced through a series event of protease cleavage of a transmembrane protein called β-amyloid precursor protein (APP) which is commonly expressed in the brain. The production of Ab and its propensity to aggregation to form oligomers and fibrils are believed to initiate a sequence of events that lead to AD dementia. The production of Ab is influenced by the transmembrane domain (TM) structure of APP. The structure variety of different Ab assemblies including oligomers and fibrils may result in different neurotoxicity to the brain. Therefore, enormous work has been carried out to study the structure of APP TM and various Ab assemblies. Solid-state NMR has advantages in studying immobile protein structures with large molecular weight. In this review, solid-state NMR structure of APP TM and different Ab assemblies will be discussed, especially various Ab amyloid fibril structures. This structural information greatly enhanced our understanding in AD, providing fundamental knowledge that will help in finding a treatment for AD.

  17. Terminal Forecast Reference Notebook, Osan AB, Korea.

    DTIC Science & Technology

    1981-06-30

    40 miles northeast through southeast of the base. Three seperate valleys merge in the vacinity of Osan AB to form a relatively large flat basin about...than those over the mountains, which at times may be completely obscured by clouds; this situation obviously can be dangerous for low-flying or...most frequently in late spring through early fall, these storms can usually be avoided by aircraft; a more dangerous situation may be encountered in

  18. The electronic character of PTCDA thin films in comparison to other perylene-based organic semi-conductors: ab initio-, TD-DFT and semi-empirical computations of the opto-electronic properties of large aggregates.

    PubMed

    Bellinger, Daniel; Pflaum, Jens; Brüning, Christoph; Engel, Volker; Engels, Bernd

    2017-01-18

    Perylene-based compounds are promising materials for opto-electronic thin film devices but despite intense investigations, important details of their electronic structure are still under debate. For perylene-3,4,9,10-tetracarboxylic dianhydrid (PTCDA), the theoretical models predict a different relative energetic order of Frenkel and Charge Transfer (CT) states. Additionally, while one model indicates strong differences between PTCDA on one hand and other perylene-based compounds on the other, recent ab initio computations indicate electronic properties of all perylene-based compounds to resemble each other. Finally, the models disagree about the amount of mixing between CT and Frenkel states. Definitive answers to these questions are difficult because the approaches use various approximations. Up to date, the ab initio based methods employ rather small model systems and neglect environmental effects. In the present work, we improve our former approach by analyzing the effects of the various simplifications. In more detail, we increase the size of the model systems, include environmental effects and investigate the influence of exciton-phonon couplings on the absorption spectrum. The computations for larger aggregates were performed with the ZINDO/S approach, because benchmark computations show that it provides accurate vertical excitation energies for Frenkel, as well as CT states.

  19. Comparative analysis of European wide marine ecosystem shifts: a large-scale approach for developing the basis for ecosystem-based management.

    PubMed

    Möllmann, Christian; Conversi, Alessandra; Edwards, Martin

    2011-08-23

    Abrupt and rapid ecosystem shifts (where major reorganizations of food-web and community structures occur), commonly termed regime shifts, are changes between contrasting and persisting states of ecosystem structure and function. These shifts have been increasingly reported for exploited marine ecosystems around the world from the North Pacific to the North Atlantic. Understanding the drivers and mechanisms leading to marine ecosystem shifts is crucial in developing adaptive management strategies to achieve sustainable exploitation of marine ecosystems. An international workshop on a comparative approach to analysing these marine ecosystem shifts was held at Hamburg University, Institute for Hydrobiology and Fisheries Science, Germany on 1-3 November 2010. Twenty-seven scientists from 14 countries attended the meeting, representing specialists from seven marine regions, including the Baltic Sea, the North Sea, the Barents Sea, the Black Sea, the Mediterranean Sea, the Bay of Biscay and the Scotian Shelf off the Canadian East coast. The goal of the workshop was to conduct the first large-scale comparison of marine ecosystem regime shifts across multiple regional areas, in order to support the development of ecosystem-based management strategies.

  20. Large deformation of uniaxially loaded slender microbeams on the basis of modified couple stress theory: Analytical solution and Galerkin-based method

    NASA Astrophysics Data System (ADS)

    Kiani, Keivan

    2017-09-01

    Large deformation regime of micro-scale slender beam-like structures subjected to axially pointed loads is of high interest to nanotechnologists and applied mechanics community. Herein, size-dependent nonlinear governing equations are derived by employing modified couple stress theory. Under various boundary conditions, analytical relations between axially applied loads and deformations are presented. Additionally, a novel Galerkin-based assumed mode method (AMM) is established to solve the highly nonlinear equations. In some particular cases, the predicted results by the analytical approach are also checked with those of AMM and a reasonably good agreement is reported. Subsequently, the key role of the material length scale on the load-deformation of microbeams is discussed and the deficiencies of the classical elasticity theory in predicting such a crucial mechanical behavior are explained in some detail. The influences of slenderness ratio and thickness of the microbeam on the obtained results are also examined. The present work could be considered as a pivotal step in better realizing the postbuckling behavior of nano-/micro- electro-mechanical systems consist of microbeams.

  1. Sensitivity of large-basin hydrological response to changes of climate parameters: an analysis on the basis of delta-change approach.

    NASA Astrophysics Data System (ADS)

    Gelfan, Alexander; Krylenko, Inna; Kalugin, Andrei; Lavrenov, Alexander; Merkulov, Nikita

    2017-04-01

    The fundamentally complex nature of hydrological systems limits our ability for accurate prediction of their responses to the inherently uncertain climate change. In this context, hydrological climate impact studies can be focused more on "what might change and why, rather than on the exact magnitude of any change" (Peel, Blöschl, 2011). Sensitivity analysis provides opportunities to offer explanation for physical mechanisms and indicate main drivers of possible changes of hydrological systems. Sensitivity analysis was performed through numerical experiments with the physically-based regional hydrological models developed on the ground of the ECOMAG (ECOlogical Model for Applied Geophysics) hydrological modeling platform for 4 large river basins located in the different physiographic and climatic zones: Lena, Mackenzie, Amur, and Selenga River basins. Being driven by the data of meteorological observations or reanalysis, the regional hydrological models demonstrated good performance in reproducing the long-term historical streamflow data recorded in the listed basins. A delta-change approach was used for construction from the observation data the synthetic series of meteorological data. The latter were transformed by small constant perturbations and, as a result, the constructed synthetic series were characterized by the changed multi-year mean of climatic variables (air temperature and precipitation) in comparison with historical data. The artificial series were used as the inputs into the hydrological model whose responses may be interpreted in terms of sensitivity of the basins' water regime to the pre-determined changes of climatic norms. The elasticity (sensitivity) indexes showing changes of water regime characteristics (mean and variances of annual and seasonal flow) to small changes in climatic norms were determined from the simulated responses. Physical mechanisms of influences of different physiographic conditions on hydrologic sensitivity indexes were

  2. WHO types A and AB thymomas: not always benign.

    PubMed

    Jain, Rohit K; Mehta, Rutika J; Henley, John D; Kesler, Kenneth A; Loehrer, Patrick J; Badve, Sunil

    2010-12-01

    The 2004 WHO classification of thymic tumors recognizes five major subtypes of thymomas and thymic carcinoma. Subtypes A and AB thymomas are purported to be benign neoplasms, although prior studies have suggested a potential for malignant behavior. The purpose of this study was to assess the clinical behavior of A and AB thymomas identified from a large institutional pathologic database. A retrospective slide review of 500 thymic epithelial tumors identified 71 (∼ 14%) cases of types A and AB thymomas. Clinical history and follow-up information were obtained through retrospective chart review. There were 38 and 33 cases of types A and AB thymomas, respectively. Complete follow-up data were available in 37 (52%) cases. Eighteen (49%) patients (type A, n=9 and type AB, n=9) had evidence of recurrent/metastatic disease at an average of 62 months (range from 6 to 244 months) after initial diagnosis. Survival curves for patients with types A and AB thymomas, with and without recurrences, show a statistically significant difference (P=0.001 and 0.005, respectively). Analysis of this large cohort confirms the potential for subtypes A and AB thymomas to show malignant behavior. Long-term clinical monitoring, therefore, appears to be justified in these cases. This study also shows the poor correlation between the WHO classification and tumor behavior.

  3. Ab initio Theory of Semiconductor Nanocrystals

    NASA Astrophysics Data System (ADS)

    Wang, Lin-Wang

    2007-03-01

    With blooming experimental synthesis of various nanostructures out of many semiconductor materials, there is an urgent need to calculate the electronic structures and optical properties of these nanosystems based on reliable ab initio methods. Unfortunately, due to the O(N^3) scaling of the conventional ab initio calculation methods based on the density functional theory (DFT), and the >1000 atom sizes of the most experimental nanosystems, the direct applications of these conventional ab intio methods are often difficult. Here we will present the calculated results using our O(N) scaling charge patching method (CPM) [1,2] to nanosystems up to 10,000 atoms. The CPM yields the charge density of a nanosystem by patching the charge motifs generated from small prototype systems. The CPM electron/hole eigen energies differ from the directly calculated results by only ˜10-20 meV. We will present the optical band gaps of quantum dots and wires, quantum rods, quantum dot/quantum well, and quantum dots doped with impurities. Besides good agreements with experimental measurements, we will demonstrate why it is important to perform ab initio calculations, in contrast with the continuum model k.p calculations. We will show the effects of surface polarization potentials and the internal electric fields. Finally, a linear scaling 3 dimensional fragment (LS3DF) method will be discussed. The LS3DF method can be used to calculate the total energy and atomic forces of a large nanosystem, with the results practically the same as the direct DFT method. Our work demonstrates that, with the help of supercomputers, it is now feasible to calculate the electronic structures and optical properties of >10,000 atom nanocrystals with ab initio accuracy. [1] L.W. Wang, Phys. Rev. Lett. 88, 256402 (2002). [2] J. Li, L.W. Wang, Phys. Rev. B 72, 125325 (2005).

  4. The application of ab initio calculations to molecular spectroscopy

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.

    1989-01-01

    The state of the art in ab initio molecular structure calculations is reviewed, with an emphasis on recent developments such as full configuration-interaction benchmark calculations and atomic natural orbital basis sets. It is shown that new developments in methodology combined with improvements in computer hardware are leading to unprecedented accuracy in solving problems in spectroscopy.

  5. The application of ab initio calculations to molecular spectroscopy

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.

    1989-01-01

    The state of the art in ab initio molecular structure calculations is reviewed with an emphasis on recent developments, such as full configuration-interaction benchmark calculations and atomic natural orbital basis sets. It is found that new developments in methodology, combined with improvements in computer hardware, are leading to unprecedented accuracy in solving problems in spectroscopy.

  6. Towards accurate ab initio predictions of the vibrational spectrum of methane

    NASA Technical Reports Server (NTRS)

    Schwenke, David W.

    2002-01-01

    We have carried out extensive ab initio calculations of the electronic structure of methane, and these results are used to compute vibrational energy levels. We include basis set extrapolations, core-valence correlation, relativistic effects, and Born-Oppenheimer breakdown terms in our calculations. Our ab initio predictions of the lowest lying levels are superb.

  7. Features of the application of the Monte Carlo method to calculations for large RBMK reactors and to model correction on the basis of data from in-core detectors

    SciTech Connect

    Ivanov, I. E. Schukin, N. V.; Bychkov, S. A.; Druzhinin, V. E.; Lysov, D. A.; Shmonin, Yu. V.; Gurevich, M. I.

    2014-12-15

    Statistical errors in sampling neutron fields in physically large systems like an RBMK are analyzed both qualitatively and quantitatively. Recommendations concerning the choice of parameters for calculations are given. A new procedure for Monte Carlo RBMK calculations with model corrections on the basis of data from in-core detectors is proposed. Dedicated software based on the CUDA software and hardware platform is developed for computational research. Results of testing the procedure and software in question via calculations for real RBMK reactors are discussed.

  8. Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics

    NASA Astrophysics Data System (ADS)

    Makhov, Dmitry V.; Glover, William J.; Martinez, Todd J.; Shalashilin, Dmitrii V.

    2014-08-01

    We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as "cloning," in analogy to the "spawning" procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, "trains," as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.

  9. Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics.

    PubMed

    Makhov, Dmitry V; Glover, William J; Martinez, Todd J; Shalashilin, Dmitrii V

    2014-08-07

    We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as "cloning," in analogy to the "spawning" procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, "trains," as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.

  10. Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics

    SciTech Connect

    Makhov, Dmitry V.; Shalashilin, Dmitrii V.; Glover, William J.; Martinez, Todd J.

    2014-08-07

    We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as “cloning,” in analogy to the “spawning” procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, “trains,” as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.

  11. Ab initio calculations in the symplectic no-core configuration interaction framework

    NASA Astrophysics Data System (ADS)

    McCoy, Anna; Caprio, Mark; Dytrych, Tomas

    2016-09-01

    A major challenge in quantitatively predicting nuclear structure directly from realistic nucleon-nucleon interactions, i.e., ab initio, arises due to an explosion in the dimension of the traditional Slater determinant basis as the number of nucleons and included shells increases. The need for including highly excited configurations arises, in large part, because the kinetic energy induces strong coupling across shells. However, the kinetic energy conserves symplectic symmetry. By combining this symplectic symmetry with the no-core configuration interaction (NCCI) framework, we reduce the size of basis necessary to obtain accurate results for p-shell nuclei. Supported by the US DOE under Grants DE-AC05-06OR23100 and DE-FG02-95ER-40934, and the Czech Science Foundation under Grant No. 16-16772S.

  12. Ab initio infrared and Raman spectra

    NASA Astrophysics Data System (ADS)

    Fredkin, Donald R.; Komornicki, Andrew; White, Steven R.; Wilson, Kent R.

    1983-06-01

    We discuss several ways in which molecular absorption and scattering spectra can be computed ab initio, from the fundamental constants of nature. These methods can be divided into two general categories. In the first, or sequential, type of approach, one first solves the electronic part of the Schrödinger equation in the Born-Oppenheimer approximation, mapping out the potential energy, dipole moment vector (for infrared absorption) and polarizability tensor (for Raman scattering) as functions of nuclear coordinates. Having completed the electronic part of the calculation, one then solves the nuclear part of the problem either classically or quantum mechanically. As an example of the sequential ab initio approach, the infrared and Raman rotational and vibrational-rotational spectral band contours for the water molecule are computed in the simplest rigid rotor, normal mode approximation. Quantum techniques are used to calculate the necessary potential energy, dipole moment, and polarizability information at the equilibrium geometry. A new quick, accurate, and easy to program classical technique involving no reference to Euler angles or special functions is developed to compute the infrared and Raman band contours for any rigid rotor, including asymmetric tops. A second, or simultaneous, type of ab initio approach is suggested for large systems, particularly those for which normal mode analysis is inappropriate, such as liquids, clusters, or floppy molecules. Then the curse of dimensionality prevents mapping out in advance the complete potential, dipole moment, and polarizability functions over the whole space of nuclear positions of all atoms, and a solution in which the electronic and nuclear parts of the Born-Oppenheimer approximation are simultaneously solved is needed. A quantum force classical trajectory (QFCT) molecular dynamic method, based on linear response theory, is described, in which the forces, dipole moment, and polarizability are computed quantum

  13. The computation of ionization potentials for second-row elements by ab initio and density functional theory methods

    SciTech Connect

    Jursic, B.S.

    1996-12-31

    Up to four ionization potentials of elements from the second-row of the periodic table were computed using the ab initio (HF, MP2, MP3, MP4, QCISD, GI, G2, and G2MP2) and DFT (B3LY, B3P86, B3PW91, XALPHA, HFS, HFB, BLYP, BP86, BPW91, BVWN, XAPLY, XAP86, XAPW91, XAVWN, SLYR SP86, SPW91 and SVWN) methods. In all of the calculations, the large 6-311++G(3df,3pd) gaussian type of basis set was used. The computed values were compared with the experimental results and suitability of the ab initio and DFF methods were discussed, in regard to reproducing the experimental data. From the computed ionization potentials of the second-row elements, it can be concluded that the HF ab initio computation is not capable of reproducing the experimental results. The computed ionization potentials are too low. However, by using the ab initio methods that include electron correlation, the computed IPs are becoming much closer to the experimental values. In all cases, with the exception of the first ionization potential for oxygen, the G2 computation result produces ionization potentials that are indistinguishable from the experimental results.

  14. An ab initio potential energy surface and dynamics of the Ar+H2+ → ArH + + H reaction

    NASA Astrophysics Data System (ADS)

    Liu, Xinguo; Liu, Huirong; Zhang, Qinggang

    2011-04-01

    An ab initio potential energy surface (PES) for the ground state (1 2A') of the chemical reaction Ar+H2+ → ArH + + H has been constructed from a set of accurate ab initio data, which we have computed using the coupled-cluster theory including all single and double excitations plus perturbative corrections for the triples UCCSD(T) with a large orbital basis set of aug-cc-pV5Z. The new PES has a root-mean-square (rms) error of 0.5341 kcal/mol. The total integral reaction cross-sections have been calculated at three collision energies by means of the quasi-classical trajectory (QCT) calculation based on the new PES and compared with previous TSH results.

  15. Ab Interno Trabeculectomy

    PubMed Central

    Pantcheva, Mina B.; Kahook, Malik Y.

    2010-01-01

    Anterior chamber drainage angle surgery, namely trabeculotomy and goniotomy, has been commonly utilized in children for many years. Its’ reported success has ranged between 68% and 100% in infants and young children with congenital glaucoma. However, the long-term success of these procedures has been limited in adults presumably due to the formation of anterior synechiae (AS) in the postoperative phase. Recently, ab interno trabeculectomy with the Trabectome™ has emerged as a novel surgical approach to effectively and selectively remove and ablate the trabecular meshwork and the inner wall of the Schlemm’s canal in an attempt to avoid AS formation or other forms of wound healing with resultant closure of the cleft. This procedure seems to have an appealing safety profile with respect to early hypotony or infection if compared to trabeculectomy or glaucoma drainage device implantation. This might be advantageous in some of the impoverish regions of the Middle East and Africa where patients experience difficulties keeping up with their postoperative visits. It is important to note that no randomized trial comparing the Trabectome to other glaucoma procedures appears to have been published to date. Trabectome surgery is not a panacea, however, and it is associated with early postoperative intraocular pressure spikes that may require additional glaucoma surgery as well as a high incidence of hyphema. Reported results show that postoperative intraocular pressure (IOP) remains, at best, in the mid-teen range making it undesirable in patients with low-target IOP goals. A major advantage of Trabectome surgery is that it does not preclude further glaucoma surgery involving the conjunctiva, such as a trabeculectomy or drainage device implantation. As prospective randomized long-term clinical data become available, we will be better positioned to elucidate the exact role of this technique in the glaucoma surgical armamentarium. PMID:21180426

  16. Autonomous Biological System (ABS) experiments.

    PubMed

    MacCallum, T K; Anderson, G A; Poynter, J E; Stodieck, L S; Klaus, D M

    1998-12-01

    Three space flight experiments have been conducted to test and demonstrate the use of a passively controlled, materially closed, bioregenerative life support system in space. The Autonomous Biological System (ABS) provides an experimental environment for long term growth and breeding of aquatic plants and animals. The ABS is completely materially closed, isolated from human life support systems and cabin atmosphere contaminants, and requires little need for astronaut intervention. Testing of the ABS marked several firsts: the first aquatic angiosperms to be grown in space; the first higher organisms (aquatic invertebrate animals) to complete their life cycles in space; the first completely bioregenerative life support system in space; and, among the first gravitational ecology experiments. As an introduction this paper describes the ABS, its flight performance, advantages and disadvantages.

  17. Ab Initio Crystal Field for Lanthanides.

    PubMed

    Ungur, Liviu; Chibotaru, Liviu F

    2017-03-13

    An ab initio methodology for the first-principle derivation of crystal-field (CF) parameters for lanthanides is described. The methodology is applied to the analysis of CF parameters in [Tb(Pc)2 ](-) (Pc=phthalocyanine) and Dy4 K2 ([Dy(4) K(2) O(OtBu)(12) ]) complexes, and compared with often used approximate and model descriptions. It is found that the application of geometry symmetrization, and the use of electrostatic point-charge and phenomenological CF models, lead to unacceptably large deviations from predictions based on ab initio calculations for experimental geometry. It is shown how the predictions of standard CASSCF (Complete Active Space Self-Consistent Field) calculations (with 4f orbitals in the active space) can be systematically improved by including effects of dynamical electronic correlation (CASPT2 step) and by admixing electronic configurations of the 5d shell. This is exemplified for the well-studied Er-trensal complex (H3 trensal=2,2',2"-tris(salicylideneimido)trimethylamine). The electrostatic contributions to CF parameters in this complex, calculated with true charge distributions in the ligands, yield less than half of the total CF splitting, thus pointing to the dominant role of covalent effects. This analysis allows the conclusion that ab initio crystal field is an essential tool for the decent description of lanthanides.

  18. AB initio infrared and Raman spectra

    NASA Astrophysics Data System (ADS)

    Fredkin, D. R.; Komornicki, A.; White, S. R.; Wilson, K. R.

    1982-08-01

    We discuss several ways in which molecular absorption and scattering spectra can be computed ab initio, from the fundamental constants of nature. These methods can be divided into two general categories. In the first, or sequential, type of approach, one first solves the electronic part of the Schroedinger equation in the Born-Oppenheimer approximation, mapping out the potential energy, dipole moment vector (for infrared absorption) and polarizability tensor (for Raman scattering) as functions of nuclear coordinates. Having completed the electronic part of the calculation, one then solves the nuclear part of the problem either classically or quantum mechanically. As an example of the sequential ab initio approach, the infrared and Raman rotational and vibrational-rotational spectral band contours for the water molecule are computed in the simplest rigid rotor, normal mode approximation. Quantum techniques, are used to calculate the necessary potential energy, dipole moment, and polarizability information at the equilibrium geometry. A new quick, accurate, and easy to program classical technique involving no reference to Euler angles or special functions is developed to compute the infrared and Raman angles or special functions is developed to compute the infrared and Raman band contours for any rigid rotor, including asymmetric tops. A second, or simultaneous, type of ab initio approach is suggested for large systems, particularly those for which normal mode analysis is inappropriate, such as liquids, clusters, or floppy molecules.

  19. Complete Basis Set Model Chemistries

    NASA Astrophysics Data System (ADS)

    Ochterski, Joseph Wallace

    1994-01-01

    The major source of error in most ab initio calculations of molecular energies is the truncation of the one-electron basis set. Extrapolation to the complete basis set second -order (CBS2) limit using the N^{-1 } asymptotic convergence of N-configuration pair natural orbital (PNO) expansions can be combined with the use of relatively small basis sets for the higher-order correlation energy to develop cost effective computational models. Following this strategy, four new computational models denoted CBS-4, CBS-q, CBS-Q, and CBS-QCI/APNO are introduced. The mean absolute deviations (MAD) from experiment for the 125 energies of the G2 test set are 2.0, 1.7, 1.0 and 0.5 kcal/mol, respectively. The error distributions for all six models are indistinguishable from Gaussian distribution functions. Calculations on the cyclopropenyl radical and cyclopropenylidene provide new dissociation energies which are in accord with an interpretation of the thermochemistry emphasizing aromaticity. Several levels of theory are examined as candidates for the routine calculation of molecular geometries. The very simple UHF/3-21G* model gives bond lengths to an accuracy of +/-0.027 A compared with experiment for a test set of 69 small molecules. The commonly used MP2/6-31G* model (RMS error 0.025 A) offers virtually no improvement and use of the considerably more expensive QCISD calculations with the same basis set provides only a modest reduction to 0.020 A. However, spin projected MP3 calculations with a modified basis set including f -functions on Si, P, S, and Cl, reduce the RMS error to 0.010 A. This PMP3/6-31Gdf* model is recommended as a general scheme of geometry optimization for small molecules. The equilibrium structure and binding energy of the water dimer have been determined for several levels of ab initio theory. The basis set convergence of the SCF energy, the intramolecular and intermolecular MP2 energy, and higher-order effects, are examined separately and realistic error

  20. Anharmonic effects in the infra-red spectrum of SiH 3Br — an ab initio study

    NASA Astrophysics Data System (ADS)

    Klatt, Günter; Willets, Andrew; Handy, Nicholas C.

    1996-02-01

    The potential energy surface of SiH 3Br was calculated up to quartic terms by ab initio quantum chemistry. To obtain the harmonic force field we performed a MP2 calculation with a large (TZ2P) basis set, while the cubic and quartic components have been evaluated both at SCF and MP2 levels. Second-order perturbation theory was then used to evaluate many of the constants describing anharmonicity of the molecular potential. The Coriolis resonance between the modes ν2 and ν5 was accounted for. A comparison with experimental data confirms ohe quality of our calculation.

  1. Ab initio quantum direct dynamics simulations of ultrafast photochemistry with Multiconfigurational Ehrenfest approach

    NASA Astrophysics Data System (ADS)

    Makhov, Dmitry V.; Symonds, Christopher; Fernandez-Alberti, Sebastian; Shalashilin, Dmitrii V.

    2017-08-01

    The Multiconfigurational Ehrenfest (MCE) method is a quantum dynamics technique which allows treatment of a large number of quantum nuclear degrees of freedom. This paper presents a review of MCE and its recent applications, providing a summary of the formalisms, including its ab initio direct dynamics versions and also giving a summary of recent results. Firstly, we describe the Multiconfigurational Ehrenfest version 2 (MCEv2) method and its applicability to direct dynamics and report new calculations which show that the approach converges to the exact result in model systems with tens of degrees of freedom. Secondly, we review previous ;on the fly; ab initio Multiple Cloning (AIMC-MCE) MCE dynamics results obtained for systems of a similar size, in which the calculations treat every electron and every nucleus of a polyatomic molecule on a fully quantum basis. We also review the Time Dependent Diabatic Basis (TDDB) version of the technique and give an example of its application. We summarise the details of the sampling techniques and interpolations used for calculation of the matrix elements, which make our approach efficient. Future directions of work are outlined.

  2. Real-world predictions from ab initio molecular dynamics simulations.

    PubMed

    Kirchner, Barbara; di Dio, Philipp J; Hutter, Jürg

    2012-01-01

    In this review we present the techniques of ab initio molecular dynamics simulation improved to its current stage where the analysis of existing processes and the prediction of further chemical features and real-world processes are feasible. For this reason we describe the relevant developments in ab initio molecular dynamics leading to this stage. Among them, parallel implementations, different basis set functions, density functionals, and van der Waals corrections are reported. The chemical features accessible through AIMD are discussed. These are IR, NMR, as well as EXAFS spectra, sampling methods like metadynamics and others, Wannier functions, dipole moments of molecules in condensed phase, and many other properties. Electrochemical reactions investigated by ab initio molecular dynamics methods in solution, on surfaces as well as complex interfaces, are also presented.

  3. Carbon dioxide hydrate phase equilibrium and cage occupancy calculations using ab initio intermolecular potentials.

    PubMed

    Velaga, Srinath C; Anderson, Brian J

    2014-01-16

    Gas hydrate deposits are receiving increased attention as potential locations for CO2 sequestration, with CO2 replacing the methane that is recovered as an energy source. In this scenario, it is very important to correctly characterize the cage occupancies of CO2 to correctly assess the sequestration potential as well as the methane recoverability. In order to predict accurate cage occupancies, the guest–host interaction potential must be represented properly. Earlier, these potential parameters were obtained by fitting to experimental equilibrium data and these fitted parameters do not match with those obtained by second virial coefficient or gas viscosity data. Ab initio quantum mechanical calculations provide an independent means to directly obtain accurate intermolecular potentials. A potential energy surface (PES) between H2O and CO2 was computed at the MP2/aug-cc-pVTZ level and corrected for basis set superposition error (BSSE), an error caused due to the lower basis set, by using the half counterpoise method. Intermolecular potentials were obtained by fitting Exponential-6 and Lennard-Jones 6-12 models to the ab initio PES, correcting for many-body interactions. We denoted this model as the “VAS” model. Reference parameters for structure I carbon dioxide hydrate were calculated using the VAS model (site–site ab initio intermolecular potentials) as Δμ(w)(0) = 1206 ± 2 J/mol and ΔH(w)(0) = 1260 ± 12 J/mol. With these reference parameters and the VAS model, pure CO2 hydrate equilibrium pressure was predicted with an average absolute deviation of less than 3.2% from the experimental data. Predictions of the small cage occupancy ranged from 32 to 51%, and the large cage is more than 98% occupied. The intermolecular potentials were also tested by calculating the pure CO2 density and diffusion of CO2 in water using molecular dynamics simulations.

  4. Hamiltonian Light-Front Ffield Theory in a Basis Function Approach

    SciTech Connect

    Vary, J.P.; Honkanen, H.; Li, Jun; Maris, P.; Brodsky, S.J.; Harindranath, A.; de Teramond, G.F.; Sternberg, P.; Ng, E.G.; Yang, C.

    2009-05-15

    Hamiltonian light-front quantum field theory constitutes a framework for the non-perturbative solution of invariant masses and correlated parton amplitudes of self-bound systems. By choosing the light-front gauge and adopting a basis function representation, we obtain a large, sparse, Hamiltonian matrix for mass eigenstates of gauge theories that is solvable by adapting the ab initio no-core methods of nuclear many-body theory. Full covariance is recovered in the continuum limit, the infinite matrix limit. There is considerable freedom in the choice of the orthonormal and complete set of basis functions with convenience and convergence rates providing key considerations. Here, we use a two-dimensional harmonic oscillator basis for transverse modes that corresponds with eigensolutions of the soft-wall AdS/QCD model obtained from light-front holography. We outline our approach, present illustrative features of some non-interacting systems in a cavity and discuss the computational challenges.

  5. Germacrene D Cyclization: An Ab Initio Investigation

    PubMed Central

    Setzer, William N.

    2008-01-01

    Essential oils that contain large concentrations of germacrene D are typically accompanied by cadinane sesquiterpenoids. The acid-catalyzed cyclization of germacrene D to give cadinane and selinane sesquiterpenes has been computationally investigated using both density functional (B3LYP/6-31G*) and post Hartree-Fock (MP2/6-31G* *) ab initio methods. The calculated energies are in general agreement with experimentally observed product distributions, both from acid-catalyzed cyclizations as well as distribution of the compounds in essential oils. PMID:19325722

  6. Ab Initio and Ab Exitu No-Core Shell Model

    SciTech Connect

    Vary, J P; Navratil, P; Gueorguiev, V G; Ormand, W E; Nogga, A; Maris, P; Shirokov, A

    2007-10-02

    We outline two complementary approaches based on the no core shell model (NCSM) and present recent results. In the ab initio approach, nuclear properties are evaluated with two-nucleon (NN) and three-nucleon interactions (TNI) derived within effective field theory (EFT) based on chiral perturbation theory (ChPT). Fitting two available parameters of the TNI generates good descriptions of light nuclei. In a second effort, an ab exitu approach, results are obtained with a realistic NN interaction derived by inverse scattering theory with off-shell properties tuned to fit light nuclei. Both approaches produce good results for observables sensitive to spin-orbit properties.

  7. Clomethiazole (Astra Arcus AB).

    PubMed

    Mucke, H

    1999-02-01

    Clomethiazole has been marketed for several years as a sedative/antiepileptic. Astra is now developing it for the potential treatment of stroke. An NDA is expected to be filed in 1999/2000. A North American phase III trial for large stroke has commenced. This will include 1200 patients. Two other smaller scale phase III studies with clomethiazole have also commenced in North America for intracerebral hemorrhage (n=200) and safety in combination with TPA (n=100 to 200) (Genentech). A large-scale phase III trial has been completed in which clomethiazole was evaluated for its ability to reduce nerve damage in acute cerebrovascular ischemia. The multicenter, international trial, called CLASS (Clomethiazole Acute Stroke Study), analyzed 1360 patients and found no significant treatment effect. However, a subgroup of patients who presented with large stroke, experienced a significant benefit. Of these (n=545), 41% treated patients were functionally independent after 90 days, compared to 30% patients on placebo. Clomethiazole reduced functional disability and brain damage in the marmoset permanent MCAO model. Clomethiazole is thought to act through a GABAergic pathway, whereby it augments GABA's depressive effect on the CNS, giving the drug both hypnotic and neuroprotectant properties.

  8. Converging Nuclear Magnetic Shielding Calculations with Respect to Basis and System Size in Protein Systems

    PubMed Central

    Hartman, Joshua D.; Neubauer, Thomas J.; Caulkins, Bethany G.; Mueller, Leonard J.; Beran, Gregory J. O.

    2015-01-01

    Ab initio chemical shielding calculations greatly facilitate the interpretation of nuclear magnetic resonance (NMR) chemical shifts in biological systems, but the large sizes of these systems requires approximations in the chemical models used to represent them. Achieving good convergence in the predicted chemical shieldings is necessary before one can unravel how other complex structural and dynamical factors affect the NMR measurements. Here, we investigate how to balance trade-offs between using a better basis set or a larger cluster model for predicting the chemical shieldings of the substrates in two representative examples of protein-substrate systems involving different domains in tryptophan synthase: the N-(4′-trifluoromethoxybenzoyl)-2-aminoethyl phosphate (F9) ligand which binds in the α active site, and the 2-aminophenol (2AP) quinonoid intermediate formed in the β active site. We first demonstrate that a chemically intuitive three-layer, locally dense basis model that uses a large basis on the substrate, a medium triple-zeta basis to describe its hydrogen-bonding partners and/or surrounding van derWaals cavity, and a crude basis set for more distant atoms provides chemical shieldings in good agreement with much more expensive large basis calculations. Second, long-range quantum mechanical interactions are important, and one can accurately estimate them as a small-basis correction to larger-basis calculations on a smaller cluster. The combination of these approaches enables one to perform density functional theory NMR chemical shift calculations in protein systems that are well-converged with respect to both basis set and cluster size. PMID:25993979

  9. Integrated Design of Antibodies for Systems Biology Using Ab Designer.

    PubMed

    Pisitkun, Trairak; Dummer, Patrick; Somparn, Poorichaya; Hirankarn, Nattiya; Kopp, Jeffrey B; Knepper, Mark A

    2014-03-24

    In the current era of large-scale biology, systems biology has evolved as a powerful approach to identify complex interactions within biological systems. In addition to high throughput identification and quantification techniques, methods based on high-quality mono-specific antibodies remain an essential element of the approach. To assist the large-scale design and production of peptide-directed antibodies for systems biology studies, we developed a fully integrated online application, AbDesigner (http://helixweb.nih.gov/AbDesigner/), to help researchers select optimal peptide immunogens for antibody generation against relatively disordered regions of target proteins. Here we describe AbDesigner in terms of its features, comparing it to other software tools, and use it to design three antibodies against kidney disease-related proteins in human, viz. nephrin, podocin, and apolipoprotein L1.

  10. Ab Initio Potential Energy Surface and Internal Torsional-Wagging States of Hydroxylamine

    PubMed

    Makarewicz; Kreglewski; Senent

    1997-11-01

    The two-dimensional potential energy surface describing the interaction of the large-amplitude torsional and wagging motions in hydroxylamine has been determined from ab initio calculations. This surface has been sampled by a large set of grid points from a two-dimensional configuration space spanned by the torsional and wagging coordinates. At each grid point, the geometry optimization has been performed using the second-order Moller-Plesset perturbation theory with the basis set 6-311 + G(2d, p). At the optimized geometry, the single-point calculation of the electronic energy has been carried out using a larger basis set 6-311 + G(3df, 2p). This method was verified to yield the results comparable to those obtained by a direct optimization of the geometry with the basis set 6-311 + G(3df, 2p) which had been used by A. Chung-Phillips and K. A. Jebber (1995. J. Chem. Phys. 102, 7080-7087) to calculate the energies of only three points in the potential energy surface of hydroxylamine. The trans and cis local minima have been found on the determined potential energy surface. The localization features of the torsional-wagging states have been studied by solving the two-dimensional Schrodinger equation for the coupled torsional and wagging motions. Copyright 1997 Academic Press. Copyright 1997Academic Press

  11. AB 1725: A Comprehensive Analysis.

    ERIC Educational Resources Information Center

    California Community Colleges, Sacramento. Board of Governors.

    A summary and analysis is provided of California Assembly Bill (AB) 1725, a reform bill that provides new direction and support for the state's community colleges. The analysis addresses each of the eight sections of the bill: (1) mission, highlighting reforms related to mission statements, transfer core curriculum, remedial limits, articulation…

  12. Study of Nuclear Clustering from an Ab Initio Perspective

    NASA Astrophysics Data System (ADS)

    Kravvaris, Konstantinos; Volya, Alexander

    2017-08-01

    We put forward a new ab initio approach that seamlessly bridges the structure, clustering, and reactions aspects of the nuclear quantum many-body problem. The configuration interaction technique combined with the resonating group method based on a harmonic oscillator basis allows us to treat the reaction and multiclustering dynamics in a translationally invariant way and preserve the Pauli principle. Our presentation includes studies of Be,108 and an exploration of 3 α clustering in 12C.

  13. GAUSSIAN 76: An ab initio Molecular Orbital Program

    DOE R&D Accomplishments Database

    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.

  14. The study of molecular spectroscopy by ab initio methods

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.

    1991-01-01

    This review illustrates the potential of theory for solving spectroscopic problems. The accuracy of approximate techniques for including electron correlation have been calibrated by comparison with full configuration-interaction calculations. Examples of the application of ab initio calculations to vibrational, rotational, and electronic spectroscopy are given. It is shown that the state-averaged, complete active space self-consistent field, multireference configuration-interaction procedure provides a good approach for treating several electronic states accurately in a common molecular orbital basis.

  15. Properties of AdeABC and AdeIJK Efflux Systems of Acinetobacter baumannii Compared with Those of the AcrAB-TolC System of Escherichia coli

    PubMed Central

    Sugawara, Etsuko

    2014-01-01

    Acinetobacter baumannii contains RND-family efflux systems AdeABC and AdeIJK, which pump out a wide range of antimicrobial compounds, as judged from the MIC changes occurring upon deletion of the responsible genes. However, these studies may miss changes because of the high backgrounds generated by the remaining pumps and by β-lactamases, and it is unclear how the activities of these pumps compare quantitatively with those of the well-studied AcrAB-TolC system of Escherichia coli. We expressed adeABC and adeIJK of A. baumannii, as well as E. coli acrAB, in an E. coli host from which acrAB was deleted. The A. baumannii pumps were functional in E. coli, and the MIC changes that were observed largely confirmed the substrate range already reported, with important differences. Thus, the AdeABC system pumped out all β-lactams, an activity that was often missed in deletion studies. When the expression level of the pump genes was adjusted to a similar level for a comparison with AcrAB-TolC, we found that both A. baumannii efflux systems pumped out a wide range of compounds, but AdeABC was less effective than AcrAB-TolC in the extrusion of lipophilic β-lactams, novobiocin, and ethidium bromide, although it was more effective at tetracycline efflux. AdeIJK was remarkably more effective than a similar level of AcrAB-TolC in the efflux of β-lactams, novobiocin, and ethidium bromide, although it was less so in the efflux of erythromycin. These results thus allow us to compare these efflux systems on a quantitative basis, if we can assume that the heterologous systems are fully functional in the E. coli host. PMID:25246403

  16. Registration of nine sorghum seed parent (A/B) lines

    USDA-ARS?s Scientific Manuscript database

    Nine sorghum [Sorghum bicolor (L.) Moench] A1 cyto plasmic-genic male sterile seed parent (A) and their maintainer (B) lines [KS 133A/B, KS 134A/B, KS 135A/B, KS 136A/B, KS 137A/B, KS 138A/B, KS 139A/B, KS 140A/B and KS 141A/B] were released by the Kansas State University, Agricultural Research Cent...

  17. Zinc oxide nanotubes: An ab initio investigation of their structural, vibrational, elastic, and dielectric properties

    NASA Astrophysics Data System (ADS)

    Lacivita, V.; Erba, A.; Noël, Y.; Orlando, R.; D'Arco, Ph.; Dovesi, R.

    2013-06-01

    Structural, vibrational, elastic, and dielectric properties of ZnO single-walled nanotubes are investigated theoretically. Calculations are carried out by using a Gaussian basis set and the B3LYP hybrid functional as implemented in the periodic ab initio CRYSTAL code. Nanotubes with increasing radius display asymptotic limits to the infinite monolayer. One soft phonon mode is recognized, whose vibration frequency is shown to be connected to the elastic constant C11 of the monolayer as the 1D → 2D transition is approached. The value of Young's elastic modulus of the nanotubes denotes a remarkable flexibility. Electronic and ionic contributions to the polarizability turn out to be comparable in magnitude. In particular, geometry relaxations at increasing radii show large influence on the transverse vibrational polarizability.

  18. Ab initio MO calculation of force constants and dipole derivatives for formamide

    NASA Astrophysics Data System (ADS)

    Sugawara, Yoko; Hamada, Yoshiaki; Hirakawa, Akiko Y.; Tsuboi, Masamichi; Kato, Shigeki; Morokuma, Keiji

    1980-08-01

    Ab initio SCF MO calculations have been carried out for the equilibrium geometry, vibrational frequencies, force constants, dipole moment and its derivatives of formamide. The energy gradient method was employed and the 4-31G basis set was used. For in-plane vibrations: (1) Calculated normal frequencies were 10-20% greater than the observed fundamental frequencies. (2) Isotope shifts (- d0, - d1, - d2, and - d3 species) were well reproduced. (3) The calculated dipole moment derivatives showed a good correspondence with the infrared intensity pattern. (4) The NH 2 rocking—OCN bending cross term, which should be zero in the Urey—Bradley force field, came out to be as large as -0.18 mdyne A. For out-of-plane vibrations, especially for the NH 2 wagging, it was found to be essential to include polarization functions for N, C and O atoms.

  19. An ab initio potential energy surface and vibrational energy levels of ZnH2.

    PubMed

    Huang, Zheng Guo; Yu, Lei; Dai, Yu Mei

    2010-04-15

    A three-dimensional potential energy surface of the electronic ground state of ZnH(2) (X1 Sigma(g)+) molecule is constructed from more than 7500 ab initio points calculated at the internally contracted multireference configuration interaction with the Davidson correction (icMRCI+Q) level employing large basis sets. The calculated relative energies of various dissociation reactions are in good agreement with the previous theoretical/experimental values. Low-lying vibrational energy levels of ZnH(2), ZnD(2), and HZnD are calculated on the three-dimensional potential energy surface using the Lanczos algorithm, and found to be in good agreement with the available experimental band origins and the previous theoretical values. 2009 Wiley Periodicals, Inc.

  20. 12 CFR Appendixes A-B - [Reserved

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 12 Banks and Banking 6 2014-01-01 2012-01-01 true A Appendixes A-B Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY CAPITAL Regulatory Capital Requirements Appendixes A-B...

  1. 12 CFR Appendixes A-B - [Reserved

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 12 Banks and Banking 6 2013-01-01 2012-01-01 true A Appendixes A-B Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY CAPITAL Regulatory Capital Requirements Appendixes A-B...

  2. 12 CFR Appendixes A-B - [Reserved

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 5 2010-01-01 2010-01-01 false A Appendixes A-B Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY CAPITAL Regulatory Capital Requirements Appendixes A-B...

  3. 12 CFR Appendixes A-B - [Reserved

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 12 Banks and Banking 5 2011-01-01 2011-01-01 false A Appendixes A-B Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY CAPITAL Regulatory Capital Requirements Appendixes A-B...

  4. 12 CFR Appendixes A-B - [Reserved

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 12 Banks and Banking 6 2012-01-01 2012-01-01 false A Appendixes A-B Banks and Banking OFFICE OF THRIFT SUPERVISION, DEPARTMENT OF THE TREASURY CAPITAL Regulatory Capital Requirements Appendixes A-B...

  5. Time-dependent N-electron valence perturbation theory with matrix product state reference wavefunctions for large active spaces and basis sets: Applications to the chromium dimer and all-trans polyenes

    NASA Astrophysics Data System (ADS)

    Sokolov, Alexander Yu.; Guo, Sheng; Ronca, Enrico; Chan, Garnet Kin-Lic

    2017-06-01

    In earlier work [A. Y. Sokolov and G. K.-L. Chan, J. Chem. Phys. 144, 064102 (2016)], we introduced a time-dependent formulation of the second-order N-electron valence perturbation theory (t-NEVPT2) which (i) had a lower computational scaling than the usual internally contracted perturbation formulation and (ii) yielded the fully uncontracted NEVPT2 energy. Here, we present a combination of t-NEVPT2 with a matrix product state (MPS) reference wavefunction (t-MPS-NEVPT2) that allows us to compute uncontracted dynamic correlation energies for large active spaces and basis sets, using the time-dependent density matrix renormalization group algorithm. In addition, we report a low-scaling MPS-based implementation of strongly contracted NEVPT2 (sc-MPS-NEVPT2) that avoids computation of the four-particle reduced density matrix. We use these new methods to compute the dissociation energy of the chromium dimer and to study the low-lying excited states in all-trans polyenes (C4H6 to C24H26), incorporating dynamic correlation for reference wavefunctions with up to 24 active electrons and orbitals.

  6. On-the-fly ab intito calculations of anharmonic vibrational frequencies: Local-monomer theory and application to HCl clusters

    NASA Astrophysics Data System (ADS)

    Mancini, John S.; Bowman, Joel M.

    2013-10-01

    We present an on-the-fly quantum mechanical method to obtain anharmonic vibrational frequencies for molecular clusters. The basis for the method is the local-monomer model, a "divide and conquer" approach to theoretical spectroscopy, previously applied using full-dimensional surfaces [Y. Wang and J. M. Bowman, J. Chem. Phys. 134, 154510 (2011)]. The model consists of performing a local normal-mode analysis for each monomer in a cluster in the field of the surrounding monomers. Anharmonic vibrational frequencies are then determined for each monomer by numerically solving the Schrödinger equation in terms of the local coordinates using ab initio energies obtained directly. Residual monomer-monomer coupling is accounted for using the Hückel-coupling extension [Y. Wang and J. M. Bowman, J. Chem. Phys. 136, 144113 (2012)]. In addition to the direct local-monomer approach, we propose and demonstrate a composite ab initio technique to reduce computational costs for calculating the anharmonic frequencies of large clusters. This technique utilizes two ab initio methods, a lower level of theory to compute geometries and perform harmonic analyses and a subsequent higher level of theory to compute the energies used in the anharmonic frequency calculations. We demonstrate the on-the-fly approach on hydrogen chloride clusters ranging in size from the dimer to the hexamer. Comparisons of the theoretical frequencies are made to previous experiments. We find the method to be an effective and computationally efficient approach to compute anharmonic frequencies.

  7. Ab initio study of the molecular structure and vibrational spectrum of nitric acid and its protonated forms

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Rice, Julia E.

    1992-01-01

    The equilibrium structures, harmonic vibrational frequencies, IR intensities, and relative energetics of HNO3 and its protonated form H2NO3+ were investigated using double-zeta plus polarization and triple-zeta plus polarization basis sets in conjunction with high-level ab initio methods. The latter include second-order Moller-Plesset perturbation theory, the single and double excitation coupled cluster (CCSD) methods, a perturbational estimate of the effects of connected triple excitations (CCSD(T)), and the self-consistent field. To determine accurate energy differences CCSD(T) energies were computed using large atomic natural orbital basis sets. Four different isomers of H2NO3+ were considered. The lowest energy form of protonated nitric acid was found to correspond to a complex between H2O and NO2+, which is consistent with earlier theoretical and experimental studies.

  8. Ab initio study of the molecular structure and vibrational spectrum of nitric acid and its protonated forms

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Rice, Julia E.

    1992-01-01

    The equilibrium structures, harmonic vibrational frequencies, IR intensities, and relative energetics of HNO3 and its protonated form H2NO3+ were investigated using double-zeta plus polarization and triple-zeta plus polarization basis sets in conjunction with high-level ab initio methods. The latter include second-order Moller-Plesset perturbation theory, the single and double excitation coupled cluster (CCSD) methods, a perturbational estimate of the effects of connected triple excitations (CCSD(T)), and the self-consistent field. To determine accurate energy differences CCSD(T) energies were computed using large atomic natural orbital basis sets. Four different isomers of H2NO3+ were considered. The lowest energy form of protonated nitric acid was found to correspond to a complex between H2O and NO2+, which is consistent with earlier theoretical and experimental studies.

  9. Antigen identification and characterization of lung cancer specific monoclonal antibodies produced by mAb proteomics.

    PubMed

    Wang, Dongdong; Hincapie, Marina; Guergova-Kuras, Mariana; Kadas, Janos; Takacs, Laszlo; Karger, Barry L

    2010-04-05

    A mass spectrometric (MS)-based strategy for antigen (Ag) identification and characterization of globally produced monoclonal antibodies (mAbs) is described. Mice were immunized with a mixture of native glycoproteins, isolated from the pooled plasma of patients with nonsmall cell lung cancer (NSCLC), to generate a library of IgG-secreting hybridomas. Prior to immunization, the pooled NSCLC plasma was subjected to 3-sequential steps of affinity fractionation, including high abundant plasma protein depletion, glycoprotein enrichment, and polyclonal antibody affinity chromatography normalization. In this paper, to demonstrate the high quality of the globally produced mAbs, we selected 3 mAbs of high differentiating power against a matched, pooled normal plasma sample. After production of large quantities of the mAbs from ascites fluids, Ag identification was achieved by immunoaffinity purification, SDS-PAGE, Western blotting, and MS analysis of in-gel digest products. One antigen was found to be complement factor H, and the other two were mapped to different subunits of haptoglobin (Hpt). The 2 Hpt mAbs were characterized in detail to assess the quality of the mAbs produced by the global strategy. The affinity of one of the mAbs to the Hpt native tetramer form was found to have a K(D) of roughly 10(-9) M and to be 2 orders of magnitude lower than the reduced form, demonstrating the power of the mAb proteomics technology in generating mAbs to the natural form of the proteins in blood. The binding of this mAb to the beta-chain of haptoglobin was also dependent on glycosylation on this chain. The characterization of mAbs in this work reveals that the global mAb proteomics process can generate high-quality lung cancer specific mAbs capable of recognizing proteins in their native state.

  10. Ab Initio Calculation of NH_3 Spectrum

    NASA Astrophysics Data System (ADS)

    Polyansky, Oleg; Ovsyannikov, Roman I.; Kyuberis, Aleksandra; Lodi, Lorenzo; Tennyson, Jonathan; Yurchenko, Sergei N.; Yachmenev, Andrey; Zobov, Nikolay Fedorovich

    2016-06-01

    An ab initio potential energy surface (PES) for NH_3 is computed using the methodology pioneered for water (Polyansky et al. J. Phys. Chem. A, 117, 9633 (2013)). A multireference configuration calclulations are performed at 50000 points using quadruple and 5z basis sets to give a complete basis set (CBS) extrapolation. Relativistic and adiabatic surfaces are also computed. The points are fitted to an analytical PES. The rovibrational energy levels are computed using the program TROVE in both linearized and curvilinear coordinates. Better convergence is obtained for the higher energy levels using curvilinear coordinates: an accuracy of about 1 wn is achieved for the levels up to 12 000 wn. The levels up to 18 000 wn are reproduced with the accuracy of a few wn. These results are used to assign the visible spectrum of 14NH_3 recorded by Coy and Lehmann (J. Chem. Phys., 84, 5239 (1988)). Predicted rovibrational levels for NH_2D, NHD_2, ND_3 and 15NH_3 are given.

  11. AIDA: ab initio domain assembly server.

    PubMed

    Xu, Dong; Jaroszewski, Lukasz; Li, Zhanwen; Godzik, Adam

    2014-07-01

    AIDA: ab initio domain assembly server, available at http://ffas.burnham.org/AIDA/ is a tool that can identify domains in multi-domain proteins and then predict their 3D structures and relative spatial arrangements. The server is free and open to all users, and there is an option for a user to provide an e-mail to get the link to result page. Domains are evolutionary conserved and often functionally independent units in proteins. Most proteins, especially eukaryotic ones, consist of multiple domains while at the same time, most experimentally determined protein structures contain only one or two domains. As a result, often structures of individual domains in multi-domain proteins can be accurately predicted, but the mutual arrangement of different domains remains unknown. To address this issue we have developed AIDA program, which combines steps of identifying individual domains, predicting (separately) their structures and assembling them into multiple domain complexes using an ab initio folding potential to describe domain-domain interactions. AIDA server not only supports the assembly of a large number of continuous domains, but also allows the assembly of domains inserted into other domains. Users can also provide distance restraints to guide the AIDA energy minimization. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. Structural Basis for Antibody Recognition in the Receptor-binding Domains of Toxins A and B from Clostridium difficile*

    PubMed Central

    Murase, Tomohiko; Eugenio, Luiz; Schorr, Melissa; Hussack, Greg; Tanha, Jamshid; Kitova, Elena N.; Klassen, John S.; Ng, Kenneth K. S.

    2014-01-01

    Clostridium difficile infection is a serious and highly prevalent nosocomial disease in which the two large, Rho-glucosylating toxins TcdA and TcdB are the main virulence factors. We report for the first time crystal structures revealing how neutralizing and non-neutralizing single-domain antibodies (sdAbs) recognize the receptor-binding domains (RBDs) of TcdA and TcdB. Surprisingly, the complexes formed by two neutralizing antibodies recognizing TcdA do not show direct interference with the previously identified carbohydrate-binding sites, suggesting that neutralization of toxin activity may be mediated by mechanisms distinct from steric blockage of receptor binding. A camelid sdAb complex also reveals the molecular structure of the TcdB RBD for the first time, facilitating the crystallization of a strongly negatively charged protein fragment that has resisted previous attempts at crystallization and structure determination. Electrospray ionization mass spectrometry measurements confirm the stoichiometries of sdAbs observed in the crystal structures. These studies indicate how key epitopes in the RBDs from TcdA and TcdB are recognized by sdAbs, providing molecular insights into toxin structure and function and providing for the first time a basis for the design of highly specific toxin-specific therapeutic and diagnostic agents. PMID:24311789

  13. Structural basis for antibody recognition in the receptor-binding domains of toxins A and B from Clostridium difficile.

    PubMed

    Murase, Tomohiko; Eugenio, Luiz; Schorr, Melissa; Hussack, Greg; Tanha, Jamshid; Kitova, Elena N; Klassen, John S; Ng, Kenneth K S

    2014-01-24

    Clostridium difficile infection is a serious and highly prevalent nosocomial disease in which the two large, Rho-glucosylating toxins TcdA and TcdB are the main virulence factors. We report for the first time crystal structures revealing how neutralizing and non-neutralizing single-domain antibodies (sdAbs) recognize the receptor-binding domains (RBDs) of TcdA and TcdB. Surprisingly, the complexes formed by two neutralizing antibodies recognizing TcdA do not show direct interference with the previously identified carbohydrate-binding sites, suggesting that neutralization of toxin activity may be mediated by mechanisms distinct from steric blockage of receptor binding. A camelid sdAb complex also reveals the molecular structure of the TcdB RBD for the first time, facilitating the crystallization of a strongly negatively charged protein fragment that has resisted previous attempts at crystallization and structure determination. Electrospray ionization mass spectrometry measurements confirm the stoichiometries of sdAbs observed in the crystal structures. These studies indicate how key epitopes in the RBDs from TcdA and TcdB are recognized by sdAbs, providing molecular insights into toxin structure and function and providing for the first time a basis for the design of highly specific toxin-specific therapeutic and diagnostic agents.

  14. An operational multispectral scanner for bathymetric surveys - The ABS NORDA scanner

    NASA Technical Reports Server (NTRS)

    Haimbach, Stephen P.; Joy, Richard T.; Hickman, G. Daniel

    1987-01-01

    The Naval Ocean Research and Development Activity (NORDA) is developing the Airborne Bathymetric Survey (ABS) system, which will take shallow water depth soundings from a Navy P-3 aircraft. The system combines active and passive sensors to obtain optical measurements of water depth. The ABS NORDA Scanner is the systems passive multispectral scanner whose design goal is to provide 100 percent coverage of the seafloor, to depths of 20 m in average coastal waters. The ABS NORDA Scanner hardware and operational environment is discussed in detail. The optical model providing the basis for depth extraction is reviewed and the proposed data processing routine discussed.

  15. Ab initio study of MF2 (M=Mn, Fe, Co, Ni) rutile-type compounds using the periodic unrestricted Hartree-Fock approach

    NASA Astrophysics Data System (ADS)

    de P. R. Moreira, Ibério; Dovesi, Roberto; Roetti, Carla; Saunders, Victor R.; Orlando, Roberto

    2000-09-01

    The ab initio periodic unrestricted Hartree-Fock method has been applied in the investigation of the ground-state structural, electronic, and magnetic properties of the rutile-type compounds MF2 (M=Mn, Fe, Co, and Ni). All electron Gaussian basis sets have been used. The systems turn out to be large band-gap antiferromagnetic insulators; the optimized geometrical parameters are in good agreement with experiment. The calculated most stable electronic state shows an antiferromagnetic order in agreement with that resulting from neutron scattering experiments. The magnetic coupling constants between nearest-neighbor magnetic ions along the [001], [111], and [100] (or [010]) directions have been calculated using several supercells. The resulting ab initio magnetic coupling constants are reasonably satisfactory when compared with available experimental data. The importance of the Jahn-Teller effect in FeF2 and CoF2 is also discussed.

  16. Structural basis of aspartylglucosaminuria

    SciTech Connect

    Saito, Seiji; Ohno, Kazuki; Sugawara, Kanako; Suzuki, Toshihiro; Togawa, Tadayasu; Sakuraba, Hitoshi

    2008-12-26

    To elucidate the basis of aspartylglucosaminuria (AGU) from the viewpoint of enzyme structure, we constructed structural models of mutant aspartylglucosaminidase (AGA) proteins using molecular modeling software, TINKER. We classified the amino acid substitutions responsible for AGU and divided them into three groups based on the biochemical phenotype. Then, we examined the structural changes in the AGA protein for each group by calculating the solvent-accessible surface area (ASA), the number of atoms affected, and the root-mean-square deviation (RMSD). Our results revealed that the structural changes in group 1, which exhibits folding/transport defects and a complete deficiency of AGA activity, were generally large and located in the core region of the enzyme molecule. In group 2, exhibiting the mature AGA protein but no AGA activity, the functionally important region of the enzyme molecule was seriously affected. In group 3 exhibiting residual AGA activity, the structural changes in AGA were small and localized near the surface of the enzyme molecule. Coloring of affected atoms based on the distances between the wild-type and mutant ones revealed the characteristic structural changes in the AGA protein geographically and semi-quantitatively. Structural investigation provides us with a deeper insight into the basis of AGU.

  17. Ab initio calculations to support accurate modelling of the rovibronic spectroscopy calculations of vanadium monoxide (VO)

    NASA Astrophysics Data System (ADS)

    McKemmish, Laura K.; Yurchenko, Sergei N.; Tennyson, Jonathan

    2016-11-01

    Accurate knowledge of the rovibronic near-infrared and visible spectra of vanadium monoxide (VO) is very important for studies of cool stellar and hot planetary atmospheres. Here, the required ab initio dipole moment and spin-orbit coupling curves for VO are produced. This data forms the basis of a new VO line list considering 13 different electronic states and containing over 277 million transitions. Open shell transition, metal diatomics are challenging species to model through ab initio quantum mechanics due to the large number of low-lying electronic states, significant spin-orbit coupling and strong static and dynamic electron correlation. Multi-reference configuration interaction methodologies using orbitals from a complete active space self-consistent-field (CASSCF) calculation are the standard technique for these systems. We use different state-specific or minimal-state CASSCF orbitals for each electronic state to maximise the calculation accuracy. The off-diagonal dipole moment controls the intensity of electronic transitions. We test finite-field off-diagonal dipole moments, but found that (1) the accuracy of the excitation energies were not sufficient to allow accurate dipole moments to be evaluated and (2) computer time requirements for perpendicular transitions were prohibitive. The best off-diagonal dipole moments are calculated using wavefunctions with different CASSCF orbitals.

  18. AB219. Comparison of National Institutes of Health-Chronic Prostatitis Symptom Index with International Index of Erectile Function-5 in men with chronic prostatitis/chronic pelvic pain syndrome: a large cross-sectional study in China

    PubMed Central

    Gao, Jingjing; Gao, Pan; Zhang, Xiansheng

    2016-01-01

    Objective We evaluated the relationship between National Institutes of Health-Chronic Prostatitis Symptom Index (NIH-CPSI) and International Index of Erectile Function-5 (IIEF-5) in Chinese men with chronic prostatitis (CP)/chronic pelvic pain syndrome (CPPS). Methods A large cross-sectional and multicenter survey was conducted from July 2012 to January 2014. Male participants were recruited from urology clinics which were located at the five cities in China. All men participated the survey by completing a verbal questionnaire, which consisted of socio-demographics, past medical history, sexual history and self-estimated scales (e.g., the Chinese version of IIEF-5 and NIH-CPSI). Results Finally, 1,280 men completed the survey, with a response rate of 76.56%. Their mean age and BMI scores were 34.50±9.20 years and 24.36±1.70 kg/m2, respectively. Based on the CP/CPPS definition, a total of 801 men were diagnosed as CP/CPPS. Men with CP/CPPS reported higher scores of NIH-CPSI and lower scores of IIEF-5 than men without CP/CPPS (P<0.001 for all). Furthermore, NIH-CPSI scores were significantly negative correlated with IIEF-5 scores (P<0.001 for all). The total scores of NIH-CPSI were significantly stronger correlated with question 5 than other questions of IIEF-5 (adjusted r=−0.70, P<0.001). The total scores of IIEF-5 were significantly strongest correlated with pain symptoms scores of NIH-CPSI (adjusted r=−0.70, P<0.001). Strongest correlation was found between QoL impact and question 5 of IIEF-5 (adjusted r=−0.74, P<0.001). Conclusions NIH-CPSI scores were significantly negative correlated with IIEF-5 scores. Strongest correlation was found between QoL impact and question 5 of IIEF-5.

  19. Functional analysis of Vibrio vulnificus RND efflux pumps homologous to Vibrio cholerae VexAB and VexCD, and to Escherichia coli AcrAB.

    PubMed

    Lee, Seunghwa; Yeom, Ji-Hyun; Seo, Sojin; Lee, Minho; Kim, Sarang; Bae, Jeehyeon; Lee, Kangseok; Hwang, Jihwan

    2015-04-01

    Resistance-nodulation-division (RND) efflux pumps are associated with multidrug resistance in many gram-negative pathogens. The genome of Vibrio vulnificus encodes 11 putative RND pumps homologous to those of Vibrio cholerae and Escherichia coli. In this study, we analyzed three putative RND efflux pumps, showing homology to V. cholerae VexAB and VexCD and to E. coli AcrAB, for their functional roles in multidrug resistance of V. vulnificus. Deletion of the vexAB homolog resulted in increased susceptibility of V. vulnificus to bile acid, acriflavine, ethidium bromide, and erythromycin, whereas deletion of acrAB homologs rendered V. vulnificus more susceptible to acriflavine only. Deletion of vexCD had no effect on susceptibility of V. vulnificus to these chemicals. Upon exposure to these antibacterial chemicals, expression of tolCV1 and tolCV2, which are putative outer membrane factors of RND efflux pumps, was induced, whereas expression levels of vexAB, vexCD, and acrAB homologs were not significantly changed. Our results show that the V. vulnificus homologs of VexAB largely contributed to in vitro antimicrobial resistance with a broad substrate specificity that was partially redundant with the AcrAB pump homologs.

  20. Theoretical investigation of the He-I2(E3Πg) ion-pair state: Ab initio intermolecular potential and vibrational levels

    NASA Astrophysics Data System (ADS)

    Kalemos, Apostolos; Valdés, Álvaro; Prosmiti, Rita

    2012-07-01

    We present a theoretical study on the potential energy surface and vibrational bound states of the E electronic excited state of the HeI2 van der Waals system. The interaction energies are computed using accurate ab initio methods and large basis sets. Relativistic small-core effective core potentials in conjunction with a quintuple-zeta quality basis set are employed for the heavy iodine atoms in multireference configuration interaction calculations for the 3A' and 3A″ states. For the representation of the potential energy surface we used a general interpolation technique for constructing potential surfaces from ab initio data based on the reproducing kernel Hilbert space method. The surface presents global and local minima for T-shaped configurations with well-depths of 33.2 and 4.6 cm-1, respectively. Vibrational energies and states are computed through variational quantum mechanical calculations. We found that the binding energy of the HeI2(E) T-shaped isomer is 16.85 cm-1, in excellent agreement with recent experimental measurements. In lieu of more experimental data we also report our predictions on higher vibrational levels and we analyze the influence of the underlying surface on them. This is the first attempt to represent the potential surface of such a highly excited electronic state of a van der Waals complex, and it demonstrates the capability of the ab initio technology to provide accurate results for carrying out reliable studies to model experimental data.

  1. An Accurate ab initio Quartic Force Field and Vibrational Frequencies for CH4 and Isotopomers

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Martin, Jan M. L.; Taylor, Peter R.

    1995-01-01

    A very accurate ab initio quartic force field for CH4 and its isotopomers is presented. The quartic force field was determined with the singles and doubles coupled-cluster procedure that includes a quasiperturbative estimate of the effects of connected triple excitations, CCSD(T), using the correlation consistent polarized valence triple zeta, cc-pVTZ, basis set. Improved quadratic force constants were evaluated with the correlation consistent polarized valence quadruple zeta, cc-pVQZ, basis set. Fundamental vibrational frequencies are determined using second-order perturbation theory anharmonic analyses. All fundamentals of CH4 and isotopomers for which accurate experimental values exist and for which there is not a large Fermi resonance, are predicted to within +/- 6 cm(exp -1). It is thus concluded that our predictions for the harmonic frequencies and the anharmonic constants are the most accurate estimates available. It is also shown that using cubic and quartic force constants determined with the correlation consistent polarized double zeta, cc-pVDZ, basis set in conjunction with the cc-pVQZ quadratic force constants and equilibrium geometry leads to accurate predictions for the fundamental vibrational frequencies of methane, suggesting that this approach may be a viable alternative for larger molecules. Using CCSD(T), core correlation is found to reduce the CH4 r(e), by 0.0015 A. Our best estimate for r, is 1.0862 +/- 0.0005 A.

  2. An Accurate ab initio Quartic Force Field and Vibrational Frequencies for CH4 and Isotopomers

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Martin, Jan M. L.; Taylor, Peter R.

    1995-01-01

    A very accurate ab initio quartic force field for CH4 and its isotopomers is presented. The quartic force field was determined with the singles and doubles coupled-cluster procedure that includes a quasiperturbative estimate of the effects of connected triple excitations, CCSD(T), using the correlation consistent polarized valence triple zeta, cc-pVTZ, basis set. Improved quadratic force constants were evaluated with the correlation consistent polarized valence quadruple zeta, cc-pVQZ, basis set. Fundamental vibrational frequencies are determined using second-order perturbation theory anharmonic analyses. All fundamentals of CH4 and isotopomers for which accurate experimental values exist and for which there is not a large Fermi resonance, are predicted to within +/- 6 cm(exp -1). It is thus concluded that our predictions for the harmonic frequencies and the anharmonic constants are the most accurate estimates available. It is also shown that using cubic and quartic force constants determined with the correlation consistent polarized double zeta, cc-pVDZ, basis set in conjunction with the cc-pVQZ quadratic force constants and equilibrium geometry leads to accurate predictions for the fundamental vibrational frequencies of methane, suggesting that this approach may be a viable alternative for larger molecules. Using CCSD(T), core correlation is found to reduce the CH4 r(e), by 0.0015 A. Our best estimate for r, is 1.0862 +/- 0.0005 A.

  3. Guiding ab initio calculations by alchemical derivatives

    NASA Astrophysics Data System (ADS)

    to Baben, M.; Achenbach, J. O.; von Lilienfeld, O. A.

    2016-03-01

    We assess the concept of alchemical transformations for predicting how a further and not-tested change in composition would change materials properties. This might help to guide ab initio calculations through multidimensional property-composition spaces. Equilibrium volumes, bulk moduli, and relative lattice stability of fcc and bcc 4d transition metals Zr, Nb, Mo, Tc, Ru, Rh, Pd, and Ag are calculated using density functional theory. Alchemical derivatives predict qualitative trends in lattice stability while equilibrium volumes and bulk moduli are predicted with less than 9% and 28% deviation, respectively. Predicted changes in equilibrium volume and bulk moduli for binary and ternary mixtures of Rh-Pd-Ag are in qualitative agreement even for predicted bulk modulus changes as large as +100% or -50%. Based on these results, it is suggested that alchemical transformations could be meaningful for enhanced sampling in the context of virtual high-throughput materials screening projects.

  4. Ab initio molecular dynamics using hybrid density functionals.

    PubMed

    Guidon, Manuel; Schiffmann, Florian; Hutter, Jürg; VandeVondele, Joost

    2008-06-07

    Ab initio molecular dynamics simulations with hybrid density functionals have so far found little application due to their computational cost. In this work, an implementation of the Hartree-Fock exchange is presented that is specifically targeted at ab initio molecular dynamics simulations of medium sized systems. We demonstrate that our implementation, which is available as part of the CP2K/Quickstep program, is robust and efficient. Several prescreening techniques lead to a linear scaling cost for integral evaluation and storage. Integral compression techniques allow for in-core calculations on systems containing several thousand basis functions. The massively parallel implementation respects integral symmetry and scales up to hundreds of CPUs using a dynamic load balancing scheme. A time-reversible multiple time step scheme, exploiting the difference in computational efficiency between hybrid and local functionals, brings further time savings. With extensive simulations of liquid water, we demonstrate the ability to perform, for several tens of picoseconds, ab initio molecular dynamics based on hybrid functionals of systems in the condensed phase containing a few thousand Gaussian basis functions.

  5. Ab initio molecular dynamics using hybrid density functionals

    NASA Astrophysics Data System (ADS)

    Guidon, Manuel; Schiffmann, Florian; Hutter, Jürg; Vandevondele, Joost

    2008-06-01

    Ab initio molecular dynamics simulations with hybrid density functionals have so far found little application due to their computational cost. In this work, an implementation of the Hartree-Fock exchange is presented that is specifically targeted at ab initio molecular dynamics simulations of medium sized systems. We demonstrate that our implementation, which is available as part of the CP2K/Quickstep program, is robust and efficient. Several prescreening techniques lead to a linear scaling cost for integral evaluation and storage. Integral compression techniques allow for in-core calculations on systems containing several thousand basis functions. The massively parallel implementation respects integral symmetry and scales up to hundreds of CPUs using a dynamic load balancing scheme. A time-reversible multiple time step scheme, exploiting the difference in computational efficiency between hybrid and local functionals, brings further time savings. With extensive simulations of liquid water, we demonstrate the ability to perform, for several tens of picoseconds, ab initio molecular dynamics based on hybrid functionals of systems in the condensed phase containing a few thousand Gaussian basis functions.

  6. Systematic ab initio study of the electronic and magnetic properties of different pure and mixed iron systems

    SciTech Connect

    Izquierdo, J.; Vega, A.; Balbas, L. C.; Sanchez-Portal, Daniel; Junquera, Javier; Artacho, Emilio; Soler, Jose M.; Ordejon, Pablo

    2000-05-15

    We present a theoretical study of the electronic and magnetic properties of iron systems in different environments: pure iron systems [dimer, bcc bulk, (100) surface, and free-standing iron monolayer], and low-dimensional iron systems deposited on Ag (100) surface (monoatomic linear wires, iron monolayer, planar, and three-dimensional clusters). Electronic and magnetic properties have been calculated using a recently developed total-energy first-principles method based on density-functional theory with numerical atomic orbitals as a basis set for the description of valence electrons and nonlocal pseudopotentials for the atomic core. The Kohn-Sham equations are solved self-consistently within the generalized gradient approximation for the exchange-correlation potential. Tests on the pseudopotential, the basis set, grid spacing, and k sampling are carefully performed. This technique, which has been proved to be very efficient for large nonmagnetic systems, is applied in this paper to calculate electronic and magnetic properties of different iron nanostructures. The results compare well with previous ab initio all-electron calculations and with experimental data. The method predicts the correct trends in the magnetic moments of Fe systems for a great variety of environments and requires a smaller computational effort than other ab initio methods. (c) 2000 The American Physical Society.

  7. Applications of Basis Light-Front Quantization to QED

    NASA Astrophysics Data System (ADS)

    Vary, James P.; Zhao, Xingbo; Ilderton, Anton; Honkanen, Heli; Maris, Pieter; Brodsky, Stanley J.

    2014-06-01

    Hamiltonian light-front quantum field theory provides a framework for calculating both static and dynamic properties of strongly interacting relativistic systems. Invariant masses, correlated parton amplitudes and time-dependent scattering amplitudes, possibly with strong external time-dependent fields, represent a few of the important applications. By choosing the light-front gauge and adopting an orthonormal basis function representation, we obtain a large, sparse, Hamiltonian matrix eigenvalue problem for mass eigenstates that we solve by adapting ab initio no-core methods of nuclear many-body theory. In the continuum limit, the infinite matrix limit, we recover full covariance. Guided by the symmetries of light-front quantized theory, we adopt a two-dimensional harmonic oscillator basis for transverse modes that corresponds with eigensolutions of the soft-wall anti-de Sitter/quantum chromodynamics (AdS/QCD) model obtained from light-front holography. We outline our approach and present results for non-linear Compton scattering, evaluated non-perturbatively, where a strong and time-dependent laser field accelerates the electron and produces states of higher invariant mass i.e. final states with photon emission.

  8. Ab initio molecular simulations with numeric atom-centered orbitals

    NASA Astrophysics Data System (ADS)

    Blum, Volker; Gehrke, Ralf; Hanke, Felix; Havu, Paula; Havu, Ville; Ren, Xinguo; Reuter, Karsten; Scheffler, Matthias

    2009-11-01

    We describe a complete set of algorithms for ab initio molecular simulations based on numerically tabulated atom-centered orbitals (NAOs) to capture a wide range of molecular and materials properties from quantum-mechanical first principles. The full algorithmic framework described here is embodied in the Fritz Haber Institute "ab initio molecular simulations" (FHI-aims) computer program package. Its comprehensive description should be relevant to any other first-principles implementation based on NAOs. The focus here is on density-functional theory (DFT) in the local and semilocal (generalized gradient) approximations, but an extension to hybrid functionals, Hartree-Fock theory, and MP2/GW electron self-energies for total energies and excited states is possible within the same underlying algorithms. An all-electron/full-potential treatment that is both computationally efficient and accurate is achieved for periodic and cluster geometries on equal footing, including relaxation and ab initio molecular dynamics. We demonstrate the construction of transferable, hierarchical basis sets, allowing the calculation to range from qualitative tight-binding like accuracy to meV-level total energy convergence with the basis set. Since all basis functions are strictly localized, the otherwise computationally dominant grid-based operations scale as O(N) with system size N. Together with a scalar-relativistic treatment, the basis sets provide access to all elements from light to heavy. Both low-communication parallelization of all real-space grid based algorithms and a ScaLapack-based, customized handling of the linear algebra for all matrix operations are possible, guaranteeing efficient scaling (CPU time and memory) up to massively parallel computer systems with thousands of CPUs.

  9. Ab initio study of the diatomic fluorides FeF, CoF, NiF, and CuF.

    PubMed

    Koukounas, Constantine; Mavridis, Aristides

    2008-11-06

    The late-3d transition-metal diatomic fluorides MF = FeF, CoF, NiF, and CuF have been studied using variational multireference (MRCI) and coupled-cluster [RCCSD(T)] methods, combined with large to very large basis sets. We examined a total of 35 (2S+1)|Lambda| states, constructing as well 29 full potential energy curves through the MRCI method. All examined states are ionic, diabatically correlating to M(+)+F(-)((1)S). Notwithstanding the "eccentric" character of the 3d transition metals and the difficulties to accurately be described with all-electron ab initio methods, our results are, in general, in very good agreement with available experimental numbers.

  10. A new single-particle basis for nuclear many-body calculations

    NASA Astrophysics Data System (ADS)

    Puddu, G.

    2017-10-01

    Predominantly, harmonic oscillator single-particle wave functions are the preferred choice for a basis in ab initio nuclear many-body calculations. These wave-functions, although very convenient in order to evaluate the matrix elements of the interaction in the laboratory frame, have too fast a fall-off at large distances. In the past, as an alternative to the harmonic oscillator, other single-particle wave functions have been proposed. In this work, we propose a new single-particle basis, directly linked to nucleon–nucleon interaction. This new basis is orthonormal and complete, has the proper asymptotic behavior at large distances and does not contain the continuum which would pose severe convergence problems in nuclear many body calculations. We consider the newly proposed NNLO-opt nucleon–nucleon interaction, without any renormalization. We show that, unlike other bases, this single-particle representation has a computational cost similar to the harmonic oscillator basis with the same space truncation and it gives lower energies for 6He and 6Li.

  11. Phonocatalysis. An ab initio simulation experiment

    SciTech Connect

    Kim, Kwangnam; Kaviany, Massoud

    2016-06-15

    Using simulations, we postulate and show that heterocatalysis on large-bandgap semiconductors can be controlled by substrate phonons, i.e., phonocatalysis. With ab initio calculations, including molecular dynamic simulations, the chemisorbed dissociation of XeF{sub 6} on h-BN surface leads to formation of XeF{sub 4} and two surface F/h-BN bonds. The reaction pathway and energies are evaluated, and the sorption and reaction emitted/absorbed phonons are identified through spectral analysis of the surface atomic motion. Due to large bandgap, the atomic vibration (phonon) energy transfer channels dominate and among them is the match between the F/h-BN covalent bond stretching and the optical phonons. We show that the chemisorbed dissociation (the pathway activation ascent) requires absorption of large-energy optical phonons. Then using progressively heavier isotopes of B and N atoms, we show that limiting these high-energy optical phonons inhibits the chemisorbed dissociation, i.e., controllable phonocatalysis.

  12. Explicitly correlated atomic orbital basis second order Møller-Plesset theory.

    PubMed

    Hollman, David S; Wilke, Jeremiah J; Schaefer, Henry F

    2013-02-14

    The scope of problems treatable by ab initio wavefunction methods has expanded greatly through the application of local approximations. In particular, atomic orbital (AO) based wavefunction methods have emerged as powerful techniques for exploiting sparsity and have been applied to biomolecules as large as 1707 atoms [S. A. Maurer, D. S. Lambrecht, D. Flaig, and C. Ochsenfeld, J. Chem. Phys. 136, 144107 (2012)]. Correlated wavefunction methods, however, converge notoriously slowly to the basis set limit and, excepting the use of large basis sets, will suffer from a severe basis set incompleteness error (BSIE). The use of larger basis sets is prohibitively expensive for AO basis methods since, for example, second-order Møller-Plesset perturbation theory (MP2) scales linearly with the number of atoms, but still scales as O(N(5)) in the number of functions per atom. Explicitly correlated F12 methods have been shown to drastically reduce BSIE for even modestly sized basis sets. In this work, we therefore explore an atomic orbital based formulation of explicitly correlated MP2-F12 theory. We present working equations for the new method, which produce results identical to the widely used molecular orbital (MO) version of MP2-F12 without resorting to a delocalized MO basis. We conclude with a discussion of several possible approaches to a priori screening of contraction terms in our method and the prospects for a linear scaling implementation of AO-MP2-F12. The discussion includes concrete examples involving noble gas dimers and linear alkane chains.

  13. AB INITIO AND CALPHAD THERMODYNAMICS OF MATERIALS

    SciTech Connect

    Turchi, P A

    2004-04-14

    Ab initio electronic structure methods can supplement CALPHAD in two major ways for subsequent applications to stability in complex alloys. The first one is rather immediate and concerns the direct input of ab initio energetics in CALPHAD databases. The other way, more involved, is the assessment of ab initio thermodynamics {acute a} la CALPHAD. It will be shown how these results can be used within CALPHAD to predict the equilibrium properties of multi-component alloys.

  14. Five ab initio potential energy and dipole moment surfaces for hydrated NaCl and NaF. I. Two-body interactions.

    PubMed

    Wang, Yimin; Bowman, Joel M; Kamarchik, Eugene

    2016-03-21

    We report full-dimensional, ab initio-based potentials and dipole moment surfaces for NaCl, NaF, Na(+)H2O, F(-)H2O, and Cl(-)H2O. The NaCl and NaF potentials are diabatic ones that dissociate to ions. These are obtained using spline fits to CCSD(T)/aug-cc-pV5Z energies. In addition, non-linear least square fits using the Born-Mayer-Huggins potential are presented, providing accurate parameters based strictly on the current ab initio energies. The long-range behavior of the NaCl and NaF potentials is shown to go, as expected, accurately to the point-charge Coulomb interaction. The three ion-H2O potentials are permutationally invariant fits to roughly 20,000 coupled cluster CCSD(T) energies (awCVTZ basis for Na(+) and aVTZ basis for Cl(-) and F(-)), over a large range of distances and H2O intramolecular configurations. These potentials are switched accurately in the long range to the analytical ion-dipole interactions, to improve computational efficiency. Dipole moment surfaces are fits to MP2 data; for the ion-ion cases, these are well described in the intermediate- and long-range by the simple point-charge expression. The performance of these new fits is examined by direct comparison to additional ab initio energies and dipole moments along various cuts. Equilibrium structures, harmonic frequencies, and electronic dissociation energies are also reported and compared to direct ab initio results. These indicate the high fidelity of the new PESs.

  15. Five ab initio potential energy and dipole moment surfaces for hydrated NaCl and NaF. I. Two-body interactions

    NASA Astrophysics Data System (ADS)

    Wang, Yimin; Bowman, Joel M.; Kamarchik, Eugene

    2016-03-01

    We report full-dimensional, ab initio-based potentials and dipole moment surfaces for NaCl, NaF, Na+H2O, F-H2O, and Cl-H2O. The NaCl and NaF potentials are diabatic ones that dissociate to ions. These are obtained using spline fits to CCSD(T)/aug-cc-pV5Z energies. In addition, non-linear least square fits using the Born-Mayer-Huggins potential are presented, providing accurate parameters based strictly on the current ab initio energies. The long-range behavior of the NaCl and NaF potentials is shown to go, as expected, accurately to the point-charge Coulomb interaction. The three ion-H2O potentials are permutationally invariant fits to roughly 20 000 coupled cluster CCSD(T) energies (awCVTZ basis for Na+ and aVTZ basis for Cl- and F-), over a large range of distances and H2O intramolecular configurations. These potentials are switched accurately in the long range to the analytical ion-dipole interactions, to improve computational efficiency. Dipole moment surfaces are fits to MP2 data; for the ion-ion cases, these are well described in the intermediate- and long-range by the simple point-charge expression. The performance of these new fits is examined by direct comparison to additional ab initio energies and dipole moments along various cuts. Equilibrium structures, harmonic frequencies, and electronic dissociation energies are also reported and compared to direct ab initio results. These indicate the high fidelity of the new PESs.

  16. Interaction between haptoglobin subtypes and AB0 blood groups in a Bengalee population.

    PubMed

    Bandyopadhyay, Arup Ratan; Roy, Jayita Ghoshal

    2005-09-01

    Blood samples from 621 individuals of a Caste Hindu Population from West Bengal (India) were investigated in an attempt to find out an association between the AB0 blood groups and Haptoglobin (HP) subtypes. AB0 blood grouping was done on the basis of the agglutination test with standard anti-sera. Haptoglobin subtyping only for the HP*1 allele was done by Polyacrylamide Gel Electrophoresis (PAGE). A significant association was found with a significantly lower HP*1S allele frequency in blood group 0 versus other AB0 blood groups. A comparatively higher allele frequency of HP*1S was found in this population sample. An inverse relationship between HP*1S and HP*2 has been revealed in each blood group. It appears that the major portion of HP*1 alleles in the A, B, and AB blood groups belongs to the HP*1S allele compared to that of the 0 blood group.

  17. Multiple time step integrators in ab initio molecular dynamics

    SciTech Connect

    Luehr, Nathan; Martínez, Todd J.; Markland, Thomas E.

    2014-02-28

    Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy.

  18. Ab initio dynamical vertex approximation

    NASA Astrophysics Data System (ADS)

    Galler, Anna; Thunström, Patrik; Gunacker, Patrik; Tomczak, Jan M.; Held, Karsten

    2017-03-01

    Diagrammatic extensions of dynamical mean-field theory (DMFT) such as the dynamical vertex approximation (DΓ A) allow us to include nonlocal correlations beyond DMFT on all length scales and proved their worth for model calculations. Here, we develop and implement an Ab initio DΓ A approach (AbinitioDΓ A ) for electronic structure calculations of materials. The starting point is the two-particle irreducible vertex in the two particle-hole channels which is approximated by the bare nonlocal Coulomb interaction and all local vertex corrections. From this, we calculate the full nonlocal vertex and the nonlocal self-energy through the Bethe-Salpeter equation. The AbinitioDΓ A approach naturally generates all local DMFT correlations and all nonlocal G W contributions, but also further nonlocal correlations beyond: mixed terms of the former two and nonlocal spin fluctuations. We apply this new methodology to the prototypical correlated metal SrVO3.

  19. Ab initio Study of He Stability in hcp-Ti

    SciTech Connect

    Dai, Yunya; Yang, Li; Peng, SM; Long, XG; Gao, Fei; Zu, Xiaotao T.

    2010-12-20

    The stability of He in hcp-Ti was studied using ab initio method based on density functional theory. The results indicate that a single He atom prefers to occupy the tetrahedral site rather than the octahedral site. The interaction of He defects with Ti atoms has been used to explain the relative stabilities of He point defects in hcp-Ti. The relative stability of He defects in hcp-Ti is useful for He clustering and bubble nucleation in metal tritides, which provides the basis for development of improved atomistic models.

  20. Ab-Initio Shell Model with a Core

    SciTech Connect

    Lisetskiy, A F; Barrett, B R; Kruse, M; Navratil, P; Stetcu, I; Vary, J P

    2008-06-04

    We construct effective 2- and 3-body Hamiltonians for the p-shell by performing 12{h_bar}{Omega} ab initio no-core shell model (NCSM) calculations for A=6 and 7 nuclei and explicitly projecting the many-body Hamiltonians onto the 0{h_bar}{Omega} space. We then separate these effective Hamiltonians into 0-, 1- and 2-body contributions (also 3-body for A=7) and analyze the systematic behavior of these different parts as a function of the mass number A and size of the NCSM basis space. The role of effective 3- and higher-body interactions for A > 6 is investigated and discussed.

  1. Pseudorotation motion in tetrahydrofuran: an ab initio study.

    PubMed

    Rayón, Víctor M; Sordo, Jose A

    2005-05-22

    The use of different models based on experimental information about the observed level splitings, rotational constants, and far-infrared transition frequencies leads to different predictions on the equilibrium geometry for tetrahydrofuran. High-level ab initio calculations [coupled cluster singles, doubles (triples)/complete basis set (second order Moller-Plesset triple, quadrupole, quintuple)+zero-point energy(anharmonic)] suggest that the equilibrium conformation of tetrahydrofuran is an envelope C(s) structure. The theoretical geometrical parameters might be helpful to plan further microwave spectroscopic studies in order to get a physical interpretation of the measurements.

  2. Generation, characterization, and docking studies of DNA-hydrolyzing recombinant F(ab) antibodies.

    PubMed

    Zein, Haggag S; El-Sehemy, Ahmed A; Fares, Mohamed O; ElHefnawi, Mahmoud; da Silva, Jaime A Teixeira; Miyatake, Kazutaka

    2011-01-01

    Previously we established a series of catalytic antibodies (catAbs) capable of hydrolyzing DNA prepared by hybridoma technology. A group of these catAbs exhibited high reactivity and substrate specificity. To determine the molecular basis for these catAbs, we cloned, sequenced, and expressed the variable regions of this group of antibodies as functional F(ab) fragments. The nucleotide and deduced amino acid sequences of the expressed light chain (Vκ) germline gene assignments confidently belonged to germline family Vκ1A, gene bb1.1 and GenBank accession number EF672207 while heavy chain variable region V(H) genes belonged to V(H) 1/V(H) J558, gene V130.3 and GenBank accession number EF672221. A well-established expression system based on the pARA7 vector was examined for its ability to produce catalytically active antibodies. Recombinant F(ab) (rF(ab) ) fragments were purified and their hydrolyzing activity was analyzed against supercoiled pUC19 plasmid DNA (scDNA). The study of rF(ab) provides important information about the potential catalytic activities of antibodies whose structure allows us to understand their basis of catalysis. Molecular surface analysis and docking studies were performed on the molecular interactions between the antibodies and poly(dA9), poly(dG9), poly(dT9), and poly(dC9) oligomers. Surface analysis identified the important sequence motifs at the binding sites, and different effects exerted by arginine and tyrosine residues at different positions in the light and heavy chains. This study demonstrates the potential usefulness of the protein DNA surrogate in the investigation of the origin of anti-DNA antibodies. These studies may define important features of DNA catAbs.

  3. Ultrasound Biomicroscopy Comparison of Ab Interno and Ab Externo Intraocular Lens Scleral Fixation.

    PubMed

    Horiguchi, Lie; Garcia, Patricia Novita; Malavazzi, Gustavo Ricci; Allemann, Norma; Gomes, Rachel L R

    2016-01-01

    Purpose. To compare ab interno and ab externo scleral fixation of posterior chamber intraocular lenses (PCIOL) using ultrasound biomicroscopy (UBM). Methods. Randomized patients underwent ab externo or ab interno scleral fixation of a PCIOL. Ultrasound biomicroscopy was performed 3 to 6 months postoperatively, to determine PCIOL centration, IOL distance to the iris at 12, 3, 6, and 9 hours, and haptics placement in relation to the ciliary sulcus. Results. Fifteen patients were enrolled in the study. The ab externo technique was used in 7 eyes (46.6%) and the ab interno in 8 eyes (53.3%). In the ab externo technique, 14 haptics were located: 4 (28.57%) in the ciliary sulcus; 2 (14.28%) anterior to the sulcus; and 8 (57.14%) posterior to the sulcus, 6 in the ciliary body and 2 posterior to the ciliary body. In the ab interno group, 4 haptics (25.0%) were in the ciliary sulcus, 2 (12.50%) anterior to the sulcus, and 10 (75.0%) posterior to the sulcus, 4 in the ciliary body and 6 posterior to the ciliary body. Conclusions. Ab externo and ab interno scleral fixation techniques presented similar results in haptic placement. Ab externo technique presented higher vertical tilt when compared to the ab interno.

  4. A highly accurate ab initio potential energy surface for methane

    NASA Astrophysics Data System (ADS)

    Owens, Alec; Yurchenko, Sergei N.; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter

    2016-09-01

    A new nine-dimensional potential energy surface (PES) for methane has been generated using state-of-the-art ab initio theory. The PES is based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set limit and incorporates a range of higher-level additive energy corrections. These include core-valence electron correlation, higher-order coupled cluster terms beyond perturbative triples, scalar relativistic effects, and the diagonal Born-Oppenheimer correction. Sub-wavenumber accuracy is achieved for the majority of experimentally known vibrational energy levels with the four fundamentals of 12CH4 reproduced with a root-mean-square error of 0.70 cm-1. The computed ab initio equilibrium C-H bond length is in excellent agreement with previous values despite pure rotational energies displaying minor systematic errors as J (rotational excitation) increases. It is shown that these errors can be significantly reduced by adjusting the equilibrium geometry. The PES represents the most accurate ab initio surface to date and will serve as a good starting point for empirical refinement.

  5. Erythema ab igne: Usual site, unusual cause

    PubMed Central

    Manoharan, D.

    2015-01-01

    Erythema ab igne is reticular erythematous pigmented dermatoses seen in patients exposed to prolonged or repeated sub-threshold Infrared radiation inadequate to cause burns. Here, we report a case of erythema ab igne in a 40-year-old male patient seen over the abdomen due to prolonged laptop use. PMID:26015756

  6. Erythema ab igne: Usual site, unusual cause.

    PubMed

    Manoharan, D

    2015-04-01

    Erythema ab igne is reticular erythematous pigmented dermatoses seen in patients exposed to prolonged or repeated sub-threshold Infrared radiation inadequate to cause burns. Here, we report a case of erythema ab igne in a 40-year-old male patient seen over the abdomen due to prolonged laptop use.

  7. Three-dimensional ab initio potential energy surface for H-CO(X̃(2)A').

    PubMed

    Song, Lei; van der Avoird, Ad; Groenenboom, Gerrit C

    2013-08-15

    We present an ab initio potential for the H-CO(X̃(2)A') complex in which the CO bond length is varied and the long-range interactions between H and CO are accurately represented. It was computed using the spin-unrestricted open-shell single and double excitation coupled cluster method with perturbative triples [RHF-UCCSD(T)]. Three doubly augmented correlation-consistent basis sets were utilized to extrapolate the correlation energy to the complete basis set limit. More than 4400 data points were calculated and used for an analytic fit of the potential: long-range terms with inverse power dependence on the H-CO distance R were fit to the data points for large R, the reproducing kernel Hilbert space (RKHS) method was applied to the data at smaller distances. Our potential was compared with previous calculations and with some data extracted from spectroscopy. Furthermore, it was used in three-dimensional discrete variable representation (DVR) calculations of the vibrational frequencies and rotational constants of HCO, which agree very well with the most recently measured data. Also the dissociation energy D0 = 0.623 eV of HCO into H + CO obtained from these calculations agrees well with experimental values. Finally, we made preliminary two-dimensional (2D) calculations of the cross sections for rotationally inelastic H-CO collisions with the CO bond length fixed and obtained good agreement with recently published 2D results.

  8. High-level ab initio studies of hydrogen abstraction from prototype hydrocarbon systems.

    PubMed

    Temelso, Berhane; Sherrill, C David; Merkle, Ralph C; Freitas, Robert A

    2006-09-28

    Symmetric and nonsymmetric hydrogen abstraction reactions are studied using state-of-the-art ab initio electronic structure methods. Second-order Møller-Plesset perturbation theory (MP2) and the coupled-cluster singles, doubles, and perturbative triples [CCSD(T)] methods with large correlation consistent basis sets (cc-pVXZ, where X = D,T,Q) are used in determining the transition-state geometries, activation barriers, and thermodynamic properties of several representative hydrogen abstraction reactions. The importance of basis set, electron correlation, and choice of zeroth-order reference wave function in the accurate prediction of activation barriers and reaction enthalpies are also investigated. The ethynyl radical (*CCH), which has a very high affinity for hydrogen atoms, is studied as a prototype hydrogen abstraction agent. Our high-level quantum mechanical computations indicate that hydrogen abstraction using the ethynyl radical has an activation energy of less than 3 kcal mol(-1) for hydrogens bonded to an sp(2) or sp(3) carbon. These low activation barriers further corroborate previous studies suggesting that ethynyl-type radicals would make good tooltips for abstracting hydrogens from diamondoid surfaces during mechanosynthesis. Modeling the diamond C(111) surface with isobutane and treating the ethynyl radical as a tooltip, hydrogen abstraction in this reaction is predicted to be barrierless.

  9. An ab initio investigation of possible intermediates in the reaction of the hydroxyl and hydroperoxyl radicals

    NASA Technical Reports Server (NTRS)

    Jackels, C. F.

    1985-01-01

    Ab initio quantum chemical techniques are used to investigate covalently-bonded and hydrogen-bonded species that may be important intermediates in the reaction of hydroxyl and hydroperoxyl radicals. Stable structures of both types are identified. Basis sets of polarized double zeta quality and large scale configuration interaction wave functions are utilized. Based on electronic energies, the covalently bonded HOOOH species is 26.4 kcal/mol more stable than the OH and HO2 radicals. Similarly, the hydrogen bonded HO---HO2 species has an electronic energy 4.7 kcal/mol below that of the component radicals, after correction is made for the basis set superposition error. The hydrogen bonded form is planar, possesses one relatively normal hydrogen bond, and has the lowest energy 3A' and 1A' states that are essentially degenerate. The 1A" and 3A" excited states produced by rotation of the unpaired OH electron into the molecular plane are very slightly bound.

  10. Ab initio potential energy surface and microwave spectra for the H2—HCCCN complex

    NASA Astrophysics Data System (ADS)

    Qin, Miao; Zhu, Hua; Fan, Hongjun

    2017-08-01

    We present a four-dimensional ab initio potential energy surface of the H2—HCCCN complex at the coupled-cluster singles and doubles with noniterative inclusion of connected triples [CCSD(T)]-F12 level with a large basis set including an additional set of bond functions. The artificial neural networks method was extended to fit the intermolecular potential energy surface. The complex has a planar linear global minimum with the well depth of 199.366 cm-1 located at R = 5.09 Å, φ = 0°, θ1 = 0°, and θ2 = 180°. An additional planar local minimum is also found with a depth of 175.579 cm-1 that is located at R = 3.37 Å, φ = 0°, θ1 = 110°, and θ2 = 104°. The radial discrete variable representation/angular finite basis representation and the Lanczos algorithm were employed to calculate the rovibrational energy levels for four species of H2—HCCCN (pH2—HCCCN, oH2—HCCCN, pD2—HCCCN, and oD2—HCCCN). The rotational frequencies and spectroscopic parameters were also determined for four complexes, which agree well with the experimental values.

  11. Atomic Spectral Methods for Ab Initio Molecular Electronic Energy Surfaces: Transitioning From Small-Molecule to Biomolecular-Suitable Approaches.

    PubMed

    Mills, Jeffrey D; Ben-Nun, Michal; Rollin, Kyle; Bromley, Michael W J; Li, Jiabo; Hinde, Robert J; Winstead, Carl L; Sheehy, Jeffrey A; Boatz, Jerry A; Langhoff, Peter W

    2016-08-25

    Continuing attention has addressed incorportation of the electronically dynamical attributes of biomolecules in the largely static first-generation molecular-mechanical force fields commonly employed in molecular-dynamics simulations. We describe here a universal quantum-mechanical approach to calculations of the electronic energy surfaces of both small molecules and large aggregates on a common basis which can include such electronic attributes, and which also seems well-suited to adaptation in ab initio molecular-dynamics applications. In contrast to the more familiar orbital-product-based methodologies employed in traditional small-molecule computational quantum chemistry, the present approach is based on an "ex-post-facto" method in which Hamiltonian matrices are evaluated prior to wave function antisymmetrization, implemented here in the support of a Hilbert space of orthonormal products of many-electron atomic spectral eigenstates familiar from the van der Waals theory of long-range interactions. The general theory in its various forms incorporates the early semiempirical atoms- and diatomics-in-molecules approaches of Moffitt, Ellison, Tully, Kuntz, and others in a comprehensive mathematical setting, and generalizes the developments of Eisenschitz, London, Claverie, and others addressing electron permutation symmetry adaptation issues, completing these early attempts to treat van der Waals and chemical forces on a common basis. Exact expressions are obtained for molecular Hamiltonian matrices and for associated energy eigenvalues as sums of separate atomic and interaction-energy terms, similar in this respect to the forms of classical force fields. The latter representation is seen to also provide a long-missing general definition of the energies of individual atoms and of their interactions within molecules and matter free from subjective additional constraints. A computer code suite is described for calculations of the many-electron atomic eigenspectra and

  12. The Basis System

    SciTech Connect

    Dubois, P.F.

    1989-05-16

    This paper discusses the basis system. Basis is a program development system for scientific programs. It has been developed over the last five years at Lawrence Livermore National Laboratory (LLNL), where it is now used in about twenty major programming efforts. The Basis System includes two major components, a program development system and a run-time package. The run-time package provides the Basis Language interpreter, through which the user does input, output, plotting, and control of the program's subroutines and functions. Variables in the scientific packages are known to this interpreter, so that the user may arbitrarily print, plot, and calculate with, any major program variables. Also provided are facilities for dynamic memory management, terminal logs, error recovery, text-file i/o, and the attachment of non-Basis-developed packages.

  13. Hamiltonian light-front field theory in a basis function approach

    SciTech Connect

    Vary, J. P.; Honkanen, H.; Li Jun; Maris, P.; Brodsky, S. J.; Harindranath, A.; Sternberg, P.; Ng, E. G.; Yang, C.

    2010-03-15

    Hamiltonian light-front quantum field theory constitutes a framework for the nonperturbative solution of invariant masses and correlated parton amplitudes of self-bound systems. By choosing the light-front gauge and adopting a basis function representation, a large, sparse, Hamiltonian matrix for mass eigenstates of gauge theories is obtained that is solvable by adapting the ab initio no-core methods of nuclear many-body theory. Full covariance is recovered in the continuum limit, the infinite matrix limit. There is considerable freedom in the choice of the orthonormal and complete set of basis functions with convenience and convergence rates providing key considerations. Here we use a two-dimensional harmonic oscillator basis for transverse modes that corresponds with eigensolutions of the soft-wall anti-de Sitter/quantum chromodynamics (AdS/QCD) model obtained from light-front holography. We outline our approach and present illustrative features of some noninteracting systems in a cavity. We illustrate the first steps toward solving quantum electrodynamics (QED) by obtaining the mass eigenstates of an electron in a cavity in small basis spaces and discuss the computational challenges.

  14. Accelerating Convergence by Change of Basis for No-Core Configuration Interaction Calculations

    NASA Astrophysics Data System (ADS)

    Flores, Abraham R.; Caprio, Mark A.; Constantinou, Chrysovalantis

    2016-09-01

    Ab initio no-core configuration interaction (NCCI) calculations attempt to describe the structure of nuclei using realistic internucleon interactions. However, we can only describe these many-body systems within the limits of our computational power. As the number of nucleons increases, the calculations require more memory and processing power to reach convergence. Being able to accelerate convergence is crucial in extending the reach of NCCI calculations. Convergence can be obtained through a change of basis, for which we need to compute the overlaps of the radial functions for the new basis with those for the old basis. A large number of overlaps must be computed in order to accurately transform the many-body problem. Using alternative bases also requires the calculation of the one-body matrix elements for operators such as r2 and p2 in the new basis. We report a computer code that uses cubic spline interpolation to compute radial overlaps and radial integrals. This code facilitates using new bases to accelerate the convergence of NCCI calculations. Supported by the US NSF under Grant NSF-PHY05-52843 the US DOE under Grant DE-FG02-95ER-40934.

  15. Ab initio study of magnesium and magnesium hydride nanoclusters and nanocrystals: examining optimal structures and compositions for efficient hydrogen storage.

    PubMed

    Koukaras, Emmanuel N; Zdetsis, Aristides D; Sigalas, Michael M

    2012-09-26

    On the basis of the attractive possibility of efficient hydrogen storage in light metal hydrides, we have examined a large variety of Mg(n)H(m) nanoclusters and (MgH(2))(n) nanocrystals (n = 2-216, m = 2-436) using high level coupled cluster, CCSD(T), ab initio methods, and judicially chosen density functional calculations of comparable quality and (near chemical) accuracy. Our calculated desorption energies as a function of size and percentage of hydrogen have pinpointed optimal regions of sizes and concentrations of hydrogen which are in full agreement with recent experimental findings. Furthermore, our results reproduce the experimental desorption energy of 75.5 kJ/mol for the infinite system with remarkable accuracy (76.5 ± 1.5 kJ/mol).

  16. Ab initio investigations of A-site doping on the structure and electric polarization of HoMnO3

    NASA Astrophysics Data System (ADS)

    S, Sathya Sheela; C, Kanagaraj; Natesan, Baskaran

    2015-06-01

    We have investigated the effect of A-site doping on the structure and electric polarization of orthorhombic HoMnO3 using ab initio density functional theory calculations. We find that the substitution of rare earth ions, such as Lu, Y and La in place of Ho in orthorhombic HoMnO3 modifies the local structure around Mn ions drastically, and leads to the formation of two distinct Mn sites Mn(0) and Mn(1). As a result, large variance between Mn(0)O6 and Mn(1)O6 octahedral distortions arises. This variance in the octahedral distortions drives the disparate hopping of electrons between the eg orbitals enhancing the electronic polarization with increasing rare earth ion radius. The largest polarization of 7 µC/cm2 is obtained for La doped HoMnO3. This increase in polarization has been explained on the basis of radius mismatch induced local structural effects.

  17. Ab initio transition dipole moments and potential energy curves for the low-lying electronic states of CaH

    NASA Astrophysics Data System (ADS)

    Shayesteh, Alireza; Alavi, S. Fatemeh; Rahman, Moloud; Gharib-Nezhad, Ehsan

    2017-01-01

    Ab initio potential energy curves have been calculated for the X2Σ+, A2Π, B2Σ+, 12Δ, E2Π and D2Σ+ states of CaH using the multi-reference configuration interaction method with large active space and basis sets. Transition dipole moments were calculated at Ca-H distances from 2.0 a0 to 14.0 a0, and excited state lifetimes were obtained. Our theoretical transition dipole moments can be combined with the available experimental data on the X2Σ+, A2Π and B2Σ+ states to calculate Einstein A coefficients for all rovibronic transitions of CaH appearing in solar and stellar spectra.

  18. Safety Basis Report

    SciTech Connect

    R.J. Garrett

    2002-01-14

    As part of the internal Integrated Safety Management Assessment verification process, it was determined that there was a lack of documentation that summarizes the safety basis of the current Yucca Mountain Project (YMP) site characterization activities. It was noted that a safety basis would make it possible to establish a technically justifiable graded approach to the implementation of the requirements identified in the Standards/Requirements Identification Document. The Standards/Requirements Identification Documents commit a facility to compliance with specific requirements and, together with the hazard baseline documentation, provide a technical basis for ensuring that the public and workers are protected. This Safety Basis Report has been developed to establish and document the safety basis of the current site characterization activities, establish and document the hazard baseline, and provide the technical basis for identifying structures, systems, and components (SSCs) that perform functions necessary to protect the public, the worker, and the environment from hazards unique to the YMP site characterization activities. This technical basis for identifying SSCs serves as a grading process for the implementation of programs such as Conduct of Operations (DOE Order 5480.19) and the Suspect/Counterfeit Items Program. In addition, this report provides a consolidated summary of the hazards analyses processes developed to support the design, construction, and operation of the YMP site characterization facilities and, therefore, provides a tool for evaluating the safety impacts of changes to the design and operation of the YMP site characterization activities.

  19. The B AB AR detector

    NASA Astrophysics Data System (ADS)

    Aubert, B.; Bazan, A.; Boucham, A.; Boutigny, D.; De Bonis, I.; Favier, J.; Gaillard, J.-M.; Jeremie, A.; Karyotakis, Y.; Le Flour, T.; Lees, J. P.; Lieunard, S.; Petitpas, P.; Robbe, P.; Tisserand, V.; Zachariadou, K.; Palano, A.; Chen, G. P.; Chen, J. C.; Qi, N. D.; Rong, G.; Wang, P.; Zhu, Y. S.; Eigen, G.; Reinertsen, P. L.; Stugu, B.; Abbott, B.; Abrams, G. S.; Amerman, L.; Borgland, A. W.; Breon, A. B.; Brown, D. N.; Button-Shafer, J.; Clark, A. R.; Dardin, S.; Day, C.; Dow, S. F.; Fan, Q.; Gaponenko, I.; Gill, M. S.; Goozen, F. R.; Gowdy, S. J.; Gritsan, A.; Groysman, Y.; Hernikl, C.; Jacobsen, R. G.; Jared, R. C.; Kadel, R. W.; Kadyk, J.; Karcher, A.; Kerth, L. T.; Kipnis, I.; Kluth, S.; Kral, J. F.; Lafever, R.; LeClerc, C.; Levi, M. E.; Lewis, S. A.; Lionberger, C.; Liu, T.; Long, M.; Luo, L.; Lynch, G.; Luft, P.; Mandelli, E.; Marino, M.; Marks, K.; Matuk, C.; Meyer, A. B.; Minor, R.; Mokhtarani, A.; Momayezi, M.; Nyman, M.; Oddone, P. J.; Ohnemus, J.; Oshatz, D.; Patton, S.; Pedrali-Noy, M.; Perazzo, A.; Peters, C.; Pope, W.; Pripstein, M.; Quarrie, D. R.; Rasson, J. E.; Roe, N. A.; Romosan, A.; Ronan, M. T.; Shelkov, V. G.; Stone, R.; Strother, P. D.; Telnov, A. V.; von der Lippe, H.; Weber, T. F.; Wenzel, W. A.; Zizka, G.; Bright-Thomas, P. G.; Hawkes, C. M.; Kirk, A.; Knowles, D. J.; O'Neale, S. W.; Watson, A. T.; Watson, N. K.; Deppermann, T.; Koch, H.; Krug, J.; Kunze, M.; Lewandowski, B.; Peters, K.; Schmuecker, H.; Steinke, M.; Andress, J. C.; Barlow, N. R.; Bhimji, W.; Chevalier, N.; Clark, P. J.; Cottingham, W. N.; De Groot, N.; Dyce, N.; Foster, B.; Mass, A.; McFall, J. D.; Wallom, D.; Wilson, F. F.; Abe, K.; Hearty, C.; McKenna, J. A.; Thiessen, D.; Camanzi, B.; Harrison, T. J.; McKemey, A. K.; Tinslay, J.; Antohin, E. I.; Blinov, V. E.; Bukin, A. D.; Bukin, D. A.; Buzykaev, A. R.; Dubrovin, M. S.; Golubev, V. B.; Ivanchenko, V. N.; Kolachev, G. M.; Korol, A. A.; Kravchenko, E. A.; Mikhailov, S. F.; Onuchin, A. P.; Salnikov, A. A.; Serednyakov, S. I.; Skovpen, Yu. I.; Telnov, V. I.; Yushkov, A. N.; Booth, J.; Lankford, A. J.; Mandelkern, M.; Pier, S.; Stoker, D. P.; Zioulas, G.; Ahsan, A.; Arisaka, K.; Buchanan, C.; Chun, S.; Faccini, R.; MacFarlane, D. B.; Prell, S. A.; Rahatlou, Sh.; Raven, G.; Sharma, V.; Burke, S.; Callahan, D.; Campagnari, C.; Dahmes, B.; Hale, D.; Hart, P. A.; Kuznetsova, N.; Kyre, S.; Levy, S. L.; Long, O.; Lu, A.; May, J.; Richman, J. D.; Verkerke, W.; Witherell, M.; Yellin, S.; Beringer, J.; DeWitt, J.; Dorfan, D. E.; Eisner, A. M.; Frey, A.; Grillo, A. A.; Grothe, M.; Heusch, C. A.; Johnson, R. P.; Kroeger, W.; Lockman, W. S.; Pulliam, T.; Rowe, W.; Sadrozinski, H.; Schalk, T.; Schmitz, R. E.; Schumm, B. A.; Seiden, A.; Spencer, E. N.; Turri, M.; Walkowiak, W.; Wilder, M.; Williams, D. C.; Chen, E.; Dubois-Felsmann, G. P.; Dvoretskii, A.; Hanson, J. E.; Hitlin, D. G.; Kolomensky, Yu. G.; Metzler, S.; Oyang, J.; Porter, F. C.; Ryd, A.; Samuel, A.; Weaver, M.; Yang, S.; Zhu, R. Y.; Devmal, S.; Geld, T. L.; Jayatilleke, S.; Jayatilleke, S. M.; Mancinelli, G.; Meadows, B. T.; Sokoloff, M. D.; Bloom, P.; Broomer, B.; Erdos, E.; Fahey, S.; Ford, W. T.; Gaede, F.; van Hoek, W. C.; Johnson, D. R.; Michael, A. K.; Nauenberg, U.; Olivas, A.; Park, H.; Rankin, P.; Roy, J.; Sen, S.; Smith, J. G.; Wagner, D. L.; Blouw, J.; Harton, J. L.; Krishnamurthy, M.; Soffer, A.; Toki, W. H.; Warner, D. W.; Wilson, R. J.; Zhang, J.; Brandt, T.; Brose, J.; Dahlinger, G.; Dickopp, M.; Dubitzky, R. S.; Eckstein, P.; Futterschneider, H.; Kocian, M. L.; Krause, R.; Müller-Pfefferkorn, R.; Schubert, K. R.; Schwierz, R.; Spaan, B.; Wilden, L.; Behr, L.; Bernard, D.; Bonneaud, G. R.; Brochard, F.; Cohen-Tanugi, J.; Ferrag, S.; Fouque, G.; Gastaldi, F.; Matricon, P.; Mora de Freitas, P.; Renard, C.; Roussot, E.; T'Jampens, S.; Thiebaux, C.; Vasileiadis, G.; Verderi, M.; Anjomshoaa, A.; Bernet, R.; Di Lodovico, F.; Muheim, F.; Playfer, S.; Swain, J. E.; Falbo, M.; Bozzi, C.; Dittongo, S.; Folegani, M.; Piemontese, L.; Ramusino, A. C.; Treadwell, E.; Anulli, F.; Baldini-Ferroli, R.; Calcaterra, A.; de Sangro, R.; Falciai, D.; Finocchiaro, G.; Patteri, P.; Peruzzi, I. M.; Piccolo, M.; Xie, Y.; Zallo, A.; Bagnasco, S.; Buzzo, A.; Contri, R.; Crosetti, G.; Fabbricatore, P.; Farinon, S.; Lo Vetere, M.; Macri, M.; Minutoli, S.; Monge, M. R.; Musenich, R.; Pallavicini, M.; Parodi, R.; Passaggio, S.; Pastore, F. C.; Patrignani, C.; Pia, M. G.; Priano, C.; Robutti, E.; Santroni, A.; Bartoldus, R.; Dignan, T.; Hamilton, R.; Mallik, U.; Cochran, J.; Crawley, H. B.; Fischer, P. A.; Lamsa, J.; McKay, R.; Meyer, W. T.; Rosenberg, E. I.; Albert, J. N.; Beigbeder, C.; Benkebil, M.; Breton, D.; Cizeron, R.; Du, S.; Grosdidier, G.; Hast, C.; Höcker, A.; Lacker, H. M.; LePeltier, V.; Lutz, A. M.; Plaszczynski, S.; Schune, M. H.; Trincaz-Duvoid, S.; Truong, K.; Valassi, A.; Wormser, G.; Alford, O.; Behne, D.; Bionta, R. M.; Bowman, J.; Brigljević, V.; Brooks, A.; Dacosta, V. A.; Fackler, O.; Fujino, D.; Harper, M.; Lange, D. J.; Mugge, M.; O'Connor, T. G.; Olson, H.; Ott, L.; Parker, E.; Pedrotti, B.; Roeben, M.; Shi, X.; van Bibber, K.; Wenaus, T. J.; Wright, D. M.; Wuest, C. R.; Yamamoto, B.; Carroll, M.; Cooke, P.; Fry, J. R.; Gabathuler, E.; Gamet, R.; George, M.; Kay, M.; McMahon, S.; Muir, A.; Payne, D. J.; Sloane, R. J.; Sutcliffe, P.; Touramanis, C.; Aspinwall, M. L.; Bowerman, D. A.; Dauncey, P. D.; Eschrich, I.; Gunawardane, N. J. W.; Martin, R.; Nash, J. A.; Price, D. R.; Sanders, P.; Smith, D.; Azzopardi, D. E.; Back, J. J.; Dixon, P.; Harrison, P. F.; Newman-Coburn, D.; Potter, R. J. L.; Shorthouse, H. W.; Williams, M. I.; Vidal, P. B.; Cowan, G.; George, S.; Green, M. G.; Kurup, A.; Marker, C. E.; McGrath, P.; McMahon, T. R.; Salvatore, F.; Scott, I.; Vaitsas, G.; Brown, D.; Davis, C. L.; Li, Y.; Pavlovich, J.; Allison, J.; Barlow, R. J.; Boyd, J. T.; Fullwood, J.; Jackson, F.; Khan, A.; Lafferty, G. D.; Savvas, N.; Simopoulos, E. T.; Thompson, R. J.; Weatherall, J. H.; Bard, R.; Dallapiccola, C.; Farbin, A.; Jawahery, A.; Lillard, V.; Olsen, J.; Roberts, D. A.; Schieck, J. R.; Blaylock, G.; Flood, K. T.; Hertzbach, S. S.; Kofler, R.; Lin, C. S.; Willocq, S.; Wittlin, J.; Brau, B.; Cowan, R.; Taylor, F.; Yamamoto, R. K.; Britton, D. I.; Fernholz, R.; Houde, M.; Milek, M.; Patel, P. M.; Trischuk, J.; Lanni, F.; Palombo, F.; Bauer, J. M.; Booke, M.; Cremaldi, L.; Kroeger, R.; Reep, M.; Reidy, J.; Sanders, D. A.; Summers, D. J.; Arguin, J. F.; Beaulieu, M.; Martin, J. P.; Nief, J. Y.; Seitz, R.; Taras, P.; Woch, A.; Zacek, V.; Nicholson, H.; Sutton, C. S.; Cartaro, C.; Cavallo, N.; De Nardo, G.; Fabozzi, F.; Gatto, C.; Lista, L.; Piccolo, D.; Sciacca, C.; Cason, N. M.; LoSecco, J. M.; Alsmiller, J. R. G.; Gabriel, T. A.; Handler, T.; Heck, J.; Iwasaki, M.; Sinev, N. B.; Caracciolo, R.; Colecchia, F.; Dal Corso, F.; Galeazzi, F.; Marzolla, M.; Michelon, G.; Morandin, M.; Posocco, M.; Rotondo, M.; Santi, S.; Simonetto, F.; Stroili, R.; Torassa, E.; Voci, C.; Bailly, P.; Benayoun, M.; Briand, H.; Chauveau, J.; David, P.; De la Vaissière, C.; Del Buono, L.; Genat, J.-F.; Hamon, O.; Leruste, Ph.; Le Diberder, F.; Lebbolo, H.; Lory, J.; Martin, L.; Martinez-Vidal, F.; Roos, L.; Stark, J.; Versillé, S.; Zhang, B.; Manfredi, P. F.; Ratti, L.; Re, V.; Speziali, V.; Frank, E. D.; Gladney, L.; Guo, Q. H.; Panetta, J. H.; Angelini, C.; Batignani, G.; Bettarini, S.; Bondioli, M.; Bosi, F.; Carpinelli, M.; Forti, F.; Gaddi, A.; Gagliardi, D.; Giorgi, M. A.; Lusiani, A.; Mammini, P.; Morganti, M.; Morsani, F.; Neri, N.; Profeti, A.; Paoloni, E.; Raffaelli, F.; Rama, M.; Rizzo, G.; Sandrelli, F.; Simi, G.; Triggiani, G.; Haire, M.; Judd, D.; Paick, K.; Turnbull, L.; Wagoner, D. E.; Albert, J.; Bula, C.; Kelsey, M. H.; Lu, C.; McDonald, K. T.; Miftakov, V.; Sands, B.; Schaffner, S. F.; Smith, A. J. S.; Tumanov, A.; Varnes, E. W.; Bronzini, F.; Buccheri, A.; Bulfon, C.; Cavoto, G.; del Re, D.; Ferrarotto, F.; Ferroni, F.; Fratini, K.; Lamanna, E.; Leonardi, E.; Mazzoni, M. A.; Morganti, S.; Piredda, G.; Safai Tehrani, F.; Serra, M.; Voena, C.; Waldi, R.; Jacques, P. F.; Kalelkar, M.; Plano, R. J.; Adye, T.; Claxton, B.; Dowdell, J.; Egede, U.; Franek, B.; Galagedera, S.; Geddes, N. I.; Gopal, G. P.; Kay, J.; Lidbury, J.; Madani, S.; Metcalfe, S.; Metcalfe, S.; Markey, G.; Olley, P.; Watt, M.; Xella, S. M.; Aleksan, R.; Besson, P.; Bourgeois, P.; Convert, P.; De Domenico, G.; de Lesquen, A.; Emery, S.; Gaidot, A.; Ganzhur, S. F.; Georgette, Z.; Gosset, L.; Graffin, P.; Hamel de Monchenault, G.; Hervé, S.; Karolak, M.; Kozanecki, W.; Langer, M.; London, G. W.; Marques, V.; Mayer, B.; Micout, P.; Mols, J. P.; Mouly, J. P.; Penichot, Y.; Rolquin, J.; Serfass, B.; Toussaint, J. C.; Usseglio, M.; Vasseur, G.; Yeche, C.; Zito, M.; Copty, N.; Purohit, M. V.; Yumiceva, F. X.; Adam, I.; Adesanya, A.; Anthony, P. L.; Aston, D.; Bartelt, J.; Becla, J.; Bell, R.; Bloom, E.; Boeheim, C. T.; Boyarski, A. M.; Boyce, R. F.; Briggs, D.; Bulos, F.; Burgess, W.; Byers, B.; Calderini, G.; Chestnut, R.; Claus, R.; Convery, M. R.; Coombes, R.; Cottrell, L.; Coupal, D. P.; Coward, D. H.; Craddock, W. W.; DeBarger, S.; DeStaebler, H.; Dorfan, J.; Doser, M.; Dunwoodie, W.; Dusatko, J. E.; Ecklund, S.; Fieguth, T. H.; Freytag, D. R.; Glanzman, T.; Godfrey, G. L.; Haller, G.; Hanushevsky, A.; Harris, J.; Hasan, A.; Hee, C.; Himel, T.; Huffer, M. E.; Hung, T.; Innes, W. R.; Jessop, C. P.; Kawahara, H.; Keller, L.; King, M. E.; Klaisner, L.; Krebs, H. J.; Langenegger, U.; Langeveld, W.; Leith, D. W. G. S.; Louie, S. K.; Luitz, S.; Luth, V.; Lynch, H. L.; McDonald, J.; Manzin, G.; Marsiske, H.; Mattison, T.; McCulloch, M.; McDougald, M.; McShurley, D.; Menke, S.; Messner, R.; Metcalfe, S.; Morii, M.; Mount, R.; Muller, D. R.; Nelson, D.; Nordby, M.; O'Grady, C. P.; Olavson, L.; Olsen, J.; O'Neill, F. G.; Oxoby, G.; Paolucci, P.; Pavel, T.; Perl, J.; Pertsova, M.; Petrak, S.; Putallaz, G.; Raines, P. E.; Ratcliff, B. N.; Reif, R.; Robertson, S. H.; Rochester, L. S.; Roodman, A.; Russel, J. J.; Sapozhnikov, L.; Saxton, O. H.; Schietinger, T.; Schindler, R. H.; Schwiening, J.; Sciolla, G.; Seeman, J. T.; Serbo, V. V.; Shapiro, S.; Skarpass, K., Sr.; Snyder, A.; Soderstrom, E.; Soha, A.; Spanier, S. M.; Stahl, A.; Stiles, P.; Su, D.; Sullivan, M. K.; Talby, M.; Tanaka, H. A.; Va'vra, J.; Wagner, S. R.; Wang, R.; Weber, T.; Weinstein, A. J. R.; White, J. L.; Wienands, U.; Wisniewski, W. J.; Young, C. C.; Yu, N.; Burchat, P. R.; Cheng, C. H.; Kirkby, D.; Meyer, T. I.; Roat, C.; Henderson, R.; Khan, N.; Berridge, S.; Bugg, W.; Cohn, H.; Hart, E.; Weidemann, A. W.; Benninger, T.; Izen, J. M.; Kitayama, I.; Lou, X. C.; Turcotte, M.; Bianchi, F.; Bona, M.; Daudo, F.; Di Girolamo, B.; Gamba, D.; Grosso, P.; Smol, A.; Trapani, P. P.; Zanin, D.; Bosisio, L.; Della Ricca, G.; Lanceri, L.; Pompili, A.; Poropat, P.; Prest, M.; Rashevskaia, I.; Vallazza, E.; Vuagnin, G.; Panvini, R. S.; Brown, C.; De Silva, A.; Kowalewski, R.; Pitman, D.; Roney, J. M.; Band, H. R.; Charles, E.; Dasu, S.; Elmer, P.; Johnson, J. R.; Nielsen, J.; Orejudos, W.; Pan, Y.; Prepost, R.; Scott, I. J.; Walsh, J.; Wu, S. L.; Yu, Z.; Zobernig, H.; Moore, T. B.; Neal, H.

    2002-02-01

    B AB AR, the detector for the SLAC PEP-II asymmetric e +e - B Factory operating at the ϒ(4 S) resonance, was designed to allow comprehensive studies of CP-violation in B-meson decays. Charged particle tracks are measured in a multi-layer silicon vertex tracker surrounded by a cylindrical wire drift chamber. Electromagnetic showers from electrons and photons are detected in an array of CsI crystals located just inside the solenoidal coil of a superconducting magnet. Muons and neutral hadrons are identified by arrays of resistive plate chambers inserted into gaps in the steel flux return of the magnet. Charged hadrons are identified by d E/d x measurements in the tracking detectors and by a ring-imaging Cherenkov detector surrounding the drift chamber. The trigger, data acquisition and data-monitoring systems, VME- and network-based, are controlled by custom-designed online software. Details of the layout and performance of the detector components and their associated electronics and software are presented.

  20. Ab initio phonon limited transport

    NASA Astrophysics Data System (ADS)

    Verstraete, Matthieu

    We revisit the thermoelectric (TE) transport properties of two champion materials, PbTe and SnSe, using fully first principles methods. In both cases the performance of the material is due to subtle combinations of structural effects, scattering, and phase space reduction. In PbTe anharmonic effects are completely opposite to the predicted quasiharmonic evolution of phonon frequencies and to frequently (and incorrectly) cited extrapolations of experiments. This stabilizes the material at high T, but also tends to enhance its thermal conductivity, in a non linear manner, above 600 Kelvin. This explains why PbTe is in practice limited to room temperature applications. SnSe has recently been shown to be the most efficient TE material in bulk form. This is mainly due to a strongly enhanced carrier concentration and electrical conductivity, after going through a phase transition from 600 to 800 K. We calculate the transport coefficients as well as the defect concentrations ab initio, showing excellent agreement with experiment, and elucidating the origin of the double phase transition as well as the new charge carriers. AH Romero, EKU Gross, MJ Verstraete, and O Hellman PRB 91, 214310 (2015) O. Hellman, IA Abrikosov, and SI Simak, PRB 84 180301 (2011)

  1. Ab initio calculations for industrial materials engineering: successes and challenges.

    PubMed

    Wimmer, Erich; Najafabadi, Reza; Young, George A; Ballard, Jake D; Angeliu, Thomas M; Vollmer, James; Chambers, James J; Niimi, Hiroaki; Shaw, Judy B; Freeman, Clive; Christensen, Mikael; Wolf, Walter; Saxe, Paul

    2010-09-29

    Computational materials science based on ab initio calculations has become an important partner to experiment. This is demonstrated here for the effect of impurities and alloying elements on the strength of a Zr twist grain boundary, the dissociative adsorption and diffusion of iodine on a zirconium surface, the diffusion of oxygen atoms in a Ni twist grain boundary and in bulk Ni, and the dependence of the work function of a TiN-HfO(2) junction on the replacement of N by O atoms. In all of these cases, computations provide atomic-scale understanding as well as quantitative materials property data of value to industrial research and development. There are two key challenges in applying ab initio calculations, namely a higher accuracy in the electronic energy and the efficient exploration of large parts of the configurational space. While progress in these areas is fueled by advances in computer hardware, innovative theoretical concepts combined with systematic large-scale computations will be needed to realize the full potential of ab initio calculations for industrial applications.

  2. Characterization of X-ray flare properties of AB Dor

    NASA Astrophysics Data System (ADS)

    Lalitha, S.

    The strong similarities between the flares observed on the Sun and in low mass stars has raised question regarding dynamo in these stars. Using the Sun as a prototype, one may be able to address this. In this paper, we present an analysis of 30 intense X-ray flares observed from AB Dor. These flares detected in XMM-Newton data show a rapid rise (500-3000 s) and a slow decay (1000-6000 s). Our studies suggest that the scaling law between the flare peak emission measure and the flare peak temperature for all the flares observed on AB Dor is very similar to the relationship followed by solar flares. Furthermore, we obtain the frequency distribution of flare energies which is a crucial diagnostic to calculate the overall energy residing in a flare. Our results of this study indicate that the large flare (1033 <= E <= 1034 erg) may not contribute to the heating of the corona.

  3. Erythema ab igne: evolving technology, evolving presentation.

    PubMed

    Kesty, Katarina; Feldman, Steven R

    2014-11-15

    We present a case of a 49-year-old woman with erythema ab igne on her posterior thighs owing to 2-4 hours per day of seat heater use in her car. Erythema ab igne is caused by prolonged exposure to a heat source. It used to be caused mainly by wood stoves used to heat homes. Erythema ab igne is now more often related to other heat sources, including heating pads, laptop computers, and car seat heaters, as in our case. As technology changes, so does the presentation of skin conditions that are related to technology.

  4. Structural basis for the antibody neutralization of Herpes simplex virus

    SciTech Connect

    Lee, Cheng-Chung; Lin, Li-Ling; Chan, Woan-Eng; Ko, Tzu-Ping; Lai, Jiann-Shiun; Wang, Andrew H.-J.

    2013-10-01

    The gD–E317-Fab complex crystal revealed the conformational epitope of human mAb E317 on HSV gD, providing a molecular basis for understanding the viral neutralization mechanism. Glycoprotein D (gD) of Herpes simplex virus (HSV) binds to a host cell surface receptor, which is required to trigger membrane fusion for virion entry into the host cell. gD has become a validated anti-HSV target for therapeutic antibody development. The highly inhibitory human monoclonal antibody E317 (mAb E317) was previously raised against HSV gD for viral neutralization. To understand the structural basis of antibody neutralization, crystals of the gD ectodomain bound to the E317 Fab domain were obtained. The structure of the complex reveals that E317 interacts with gD mainly through the heavy chain, which covers a large area for epitope recognition on gD, with a flexible N-terminal and C-terminal conformation. The epitope core structure maps to the external surface of gD, corresponding to the binding sites of two receptors, herpesvirus entry mediator (HVEM) and nectin-1, which mediate HSV infection. E317 directly recognizes the gD–nectin-1 interface and occludes the HVEM contact site of gD to block its binding to either receptor. The binding of E317 to gD also prohibits the formation of the N-terminal hairpin of gD for HVEM recognition. The major E317-binding site on gD overlaps with either the nectin-1-binding residues or the neutralizing antigenic sites identified thus far (Tyr38, Asp215, Arg222 and Phe223). The epitopes of gD for E317 binding are highly conserved between two types of human herpesvirus (HSV-1 and HSV-2). This study enables the virus-neutralizing epitopes to be correlated with the receptor-binding regions. The results further strengthen the previously demonstrated therapeutic and diagnostic potential of the E317 antibody.

  5. Cationization increases brain distribution of an amyloid-beta protofibril selective F(ab')2 fragment.

    PubMed

    Syvänen, Stina; Edén, Desirée; Sehlin, Dag

    2017-11-04

    Antibodies and fragments thereof are, because of high selectivity for their targets, considered as potential therapeutics and biomarkers for several neurological disorders. However, due to their large molecular size, antibodies/fragments do not easily penetrate into the brain. The aim of the present study was to improve the brain distribution via adsorptive-mediated transcytosis of an amyloid-beta (Aβ) protofibril selective F(ab')2 fragment (F(ab')2-h158). F(ab')2-h158 was cationized to different extents and the specific and unspecific binding was studied in vitro. Next, cationized F(ab')2-h158 was labelled with iodine-125 and its brain distribution and pharmacokinetics was studied in mice. Cationization did not alter the in vitro affinity to Aβ protofibrils, but increased the unspecific binding somewhat. Ex vivo experiments revealed a doubling of brain concentrations compared with unmodified F(ab')2-h158 and in vivo imaging with single photon emission computed tomography (SPECT) showed that the cationized F(ab')2-h158, but not the unmodified F(ab')2-h158 could be visualized in the brain. To conclude, cationization is a means to increase brain concentrations of therapeutic antibodies or fragments and may facilitate the use of antibodies/fragments as imaging biomarkers in the brain. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  6. Ab initio study of phosphaalkenes

    SciTech Connect

    Liu, M.

    1992-01-01

    This dissertation presents the application of computational chemistry to investigate a new class of organic compound-phosphaalkenes. The history of room temperature stable phosphaalkenes is a matter of the last 20 years. The existence of the C[double bond]P [pi] bond has challenged the concept that the 2p-3p [pi] bond is supposed to be very unstable and weak. Theoretical study of this type of compound can clear up the unknown properties, reactivities and reaction mechanisms of phosphaalkenes. The aim of this research is to theoretically determine the electronic and molecular properties, the chemical properties, and predict synthetic candidates for this family. Employing ab initio quantum chemistry, the authors have completed 7 related projects. First, the authors examined the reaction mechanism in the general synthesis of 1,3-diphosphallene and located the step that controls the stereo-outcome of the final product. Second, the authors predicted 4-phosphamethylenecylopropene to be a stable compound, which has been successfully synthesized after this research appeared. Third, the rotational energy surface of the rotation from s-trans to s-cis for mon- and di-phospha-1,3-butadienes were examined and concluded that the rotation does not have a high barrier. Fourth, fifth, and sixth, the authors continued their interest in phospha-1,3-butadienes and investigated [2+2] and Diels-Alder reactions. The energetics and stereo consequences of these reactions have been explored in this research. Finally, they also systematically studied the bonding properties of phosphacumulenes and provided some structural insight for this unsettled area.

  7. Spectral monitoring of AB Aur

    NASA Astrophysics Data System (ADS)

    Rodríguez Díaz, L. F.; Oostra, B.

    2017-07-01

    The Astronomical Observatory of the Universidad de los Andes in Bogotá, Colombia, did a spectral monitoring during 2014 and 2015 to AB Aurigae, the brightest Herbig Ae/be star in the northern hemisphere. The aim of this project is applying spectral techniques, in order to identify specific features that could help us not only to understand how this star is forming, but also to establish a pattern to explain general star formation processes. We have recorded 19 legible spectra with a resolving power of R = 11,0000, using a 40 cm Meade telescope with an eShel spectrograph, coupled by a 50-micron optical fiber. We looked for the prominent absorption lines, the Sodium doublet at 5890Å and 5896Å, respectively and Magnesium II at 4481Å; to measure radial velocities of the star, but, we did not find a constant value. Instead, it ranges from 15 km/s to 32 km/s. This variability could be explained by means of an oscillation or pulsation of the external layers of the star. Other variabilities are observed in some emission lines: Hα, Hβ, He I at 5876Å and Fe II at 5018Å. It seems this phenomenon could be typical in stars that are forming and have a circumstellar disk around themselves. This variability is associated with the nonhomogeneous surface of the star and the interaction that it has with its disk. Results of this interaction could be seen also in the stellar wind ejected by the star. More data are required in order to look for a possible period in the changes of radial velocity of the star, the same for the variability of He I and Fe II, and phenomena present in Hα. We plan to take new data in January of 2017.

  8. Ab Initio Study of Polonium

    NASA Astrophysics Data System (ADS)

    Zabidi, Noriza Ahmad; Kassim, Hasan Abu; Shrivastava, Keshav N.

    2008-05-01

    Polonium is the only element with a simple cubic (sc) crystal structure. Atoms in solid polonium sit at the corners of a simple cubic unit cell and no where else. Polonium has a valence electron configuration 6s26p4 (Z = 84). The low temperature α-phase transforms into the rhombohedral (trigonal) β structure at ˜348 K. The sc α-Po unit cell constant is a = 3.345 Å. The beta form of polonium (β-Po) has the lattice parameters, aR = 3.359 Å and a rhombohedral angle 98°13'. We have performed an ab initio electronic structure calculation by using the density functional theory. We have performed the calculation with and without spin-orbit (SO) coupling by using both the LDA and the GGA for the exchange-correlations. The k-points in a simple cubic BZ are determined by R (0.5, 0.5, 0.5), Γ (0, 0, 0), X (0.5, 0, 0), M (0.5, 0.5, 0) and Γ (0, 0, 0). Other directions of k-points are Γ (0, 0, 0), X (0.5, 0, 0), R (0.5, 0.5, 0.5) and Γ (0, 0, 0). The SO splittings of p states at the Γ point in the GGA+SO scheme for α-Po are 0.04 eV and 0.02 eV while for the β-Po these are 0.03 eV and 0.97 eV. We have also calculated the vibrational spectra for the unit cells in both the structures. We find that exchanging of a Po atom by Pb atom produces several more bands and destabilizes the β phase.

  9. Ab Initio Study of Polonium

    SciTech Connect

    Zabidi, Noriza Ahmad; Kassim, Hasan Abu; Shrivastava, Keshav N.

    2008-05-20

    Polonium is the only element with a simple cubic (sc) crystal structure. Atoms in solid polonium sit at the corners of a simple cubic unit cell and no where else. Polonium has a valence electron configuration 6s{sup 2}6p{sup 4} (Z = 84). The low temperature {alpha}-phase transforms into the rhombohedral (trigonal) {beta} structure at {approx}348 K. The sc {alpha}-Po unit cell constant is a = 3.345 A. The beta form of polonium ({beta}-Po) has the lattice parameters, a{sub R} = 3.359 A and a rhombohedral angle 98 deg. 13'. We have performed an ab initio electronic structure calculation by using the density functional theory. We have performed the calculation with and without spin-orbit (SO) coupling by using both the LDA and the GGA for the exchange-correlations. The k-points in a simple cubic BZ are determined by R (0.5, 0.5, 0.5), {gamma} (0, 0, 0), X (0.5, 0, 0), M (0.5, 0.5, 0) and {gamma} (0, 0, 0). Other directions of k-points are {gamma} (0, 0, 0), X (0.5, 0, 0), R (0.5, 0.5, 0.5) and {gamma} (0, 0, 0). The SO splittings of p states at the {gamma} point in the GGA+SO scheme for {alpha}-Po are 0.04 eV and 0.02 eV while for the {beta}-Po these are 0.03 eV and 0.97 eV. We have also calculated the vibrational spectra for the unit cells in both the structures. We find that exchanging of a Po atom by Pb atom produces several more bands and destabilizes the {beta} phase.

  10. Ab Initio Infrared and Raman Spectra.

    DTIC Science & Technology

    1982-08-01

    tions. For parameters not depending on momenta, a parallel ab fhti Monte Carlo approach would use electronic energies and other parameters of... Monte Carlo approach. Specifically, as one of us has suggested,t I classical molecular dynamics may be integrated with ab iniHo quan- tum force...alternative approach, for phenomena which are not explicitly time dependent, is a Monte Carlo procedure in which at each trial nuclear configuration

  11. Accurate ab initio quartic force fields for borane and BeH2

    NASA Technical Reports Server (NTRS)

    Martin, J. M. L.; Lee, Timothy J.

    1992-01-01

    The quartic force fields of BH3 and BeH2 have been computed ab initio using an augmented coupled cluster (CCSD(T)) method and basis sets of spdf and spdfg quality. For BH3, the computed spectroscopic constants are in very good agreement with recent experimental data, and definitively confirm misassignments in some older work, in agreement with recent ab initio studies. Using the computed spectroscopic constants, the rovibrational partition function for both molecules has been constructed using a modified direct numerical summation algorithm, and JANAF-style thermochemical tables are presented.

  12. ABO-identical blood group matching has no survival benefit for AB heart transplant recipients.

    PubMed

    Bergenfeldt, Henrik; Höglund, Peter; Andersson, Bodil; Rådegran, Göran; Ohlsson, Mattias; Nilsson, Johan

    2015-03-01

    Although identical blood group matching is preferred, it is uncertain if this results in improved survival and, if so, how large the survival benefits are. Earlier studies have yielded conflicting results and are mostly based on single-center cohorts with few long-term results. Recipients with blood group AB are of particular interest regarding nonidentical blood group matching because they may receive organs from all blood groups. We wanted to test the hypothesis that ABO-identical matching results in superior survival in recipients with blood group AB. We used data from the International Society for Heart and Lung Transplantation registry to match a cohort of heart donors with transplant recipients with blood group AB. Cox regression analysis was used to assess the influence of blood group on outcome after heart transplantation. All-cause cumulative mortality during the study period was the primary end point. The study material consisted of 3,589 adult patients with blood group AB who had received heart transplants, representing 18,085 patient-years. No significant difference in survival after identical, as opposed to compatible, ABO matching was found for recipients with blood group AB. In subgroup analysis, we found improved survival for younger recipients (< 55 years) with blood group AB who underwent transplantation with organs from donor blood group O rather than AB (p = 0.02). We found no survival benefit for recipients with blood group AB transplanted with ABO-identical organs. In the subgroup of recipients younger than 55 years of age, our study suggests improved survival for recipients with blood group AB transplanted with an organ from a donor with blood group O. Copyright © 2015 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.

  13. Human malignant mesothelioma is recapitulated in immunocompetent BALB/c mice injected with murine AB cells

    PubMed Central

    Mezzapelle, Rosanna; Rrapaj, Eltjona; Gatti, Elena; Ceriotti, Chiara; Marchis, Francesco De; Preti, Alessandro; Spinelli, Antonello E.; Perani, Laura; Venturini, Massimo; Valtorta, Silvia; Moresco, Rosa Maria; Pecciarini, Lorenza; Doglioni, Claudio; Frenquelli, Michela; Crippa, Luca; Recordati, Camilla; Scanziani, Eugenio; de Vries, Hilda; Berns, Anton; Frapolli, Roberta; Boldorini, Renzo; D’Incalci, Maurizio; Bianchi, Marco E.; Crippa, Massimo P.

    2016-01-01

    Malignant Mesothelioma is a highly aggressive cancer, which is difficult to diagnose and treat. Here we describe the molecular, cellular and morphological characterization of a syngeneic system consisting of murine AB1, AB12 and AB22 mesothelioma cells injected in immunocompetent BALB/c mice, which allows the study of the interplay of tumor cells with the immune system. Murine mesothelioma cells, like human ones, respond to exogenous High Mobility Group Box 1 protein, a Damage-Associated Molecular Pattern that acts as a chemoattractant for leukocytes and as a proinflammatory mediator. The tumors derived from AB cells are morphologically and histologically similar to human MM tumors, and respond to treatments used for MM patients. Our system largely recapitulates human mesothelioma, and we advocate its use for the study of MM development and treatment. PMID:26961782

  14. Comprehensive screening for antigens overexpressed on carcinomas via isolation of human mAbs that may be therapeutic

    PubMed Central

    Kurosawa, Gene; Akahori, Yasushi; Morita, Miwa; Sumitomo, Mariko; Sato, Noriko; Muramatsu, Chiho; Eguchi, Keiko; Matsuda, Kazuki; Takasaki, Akihiko; Tanaka, Miho; Iba, Yoshitaka; Hamada-Tsutsumi, Susumu; Ukai, Yoshinori; Shiraishi, Mamoru; Suzuki, Kazuhiro; Kurosawa, Maiko; Fujiyama, Sally; Takahashi, Nobuhiro; Kato, Ryoichi; Mizoguchi, Yoshikazu; Shamoto, Mikihiro; Tsuda, Hiroyuki; Sugiura, Mototaka; Hattori, Yoshinobu; Miyakawa, Shuichi; Shiroki, Ryoichi; Hoshinaga, Kiyotaka; Hayashi, Nobuhiro; Sugioka, Atsushi; Kurosawa, Yoshikazu

    2008-01-01

    Although several murine mAbs that have been humanized became useful therapeutic agents against a few malignancies, therapeutic Abs are not yet available for the majority of the human cancers because of our lack of knowledge of which antigens (Ags) can become useful targets. In the present study we established a procedure for comprehensive identification of such Ags through the extensive isolation of human mAbs that may become therapeutic. Using the phage-display Ab library we isolated a large number of human mAbs that bind to the surface of tumor cells. They were individually screened by immunostaining, and clones that preferentially and strongly stained the malignant cells were chosen. The Ags recognized by those clones were isolated by immunoprecipitation and identified by MS. We isolated 2,114 mAbs with unique sequences and identified 21 distinct Ags highly expressed on several carcinomas. Of those 2,114 mAbs 356 bound specifically to one of the 21 Ags. After preparing complete IgG1 Abs the in vitro assay for Ab-dependent cell-mediated cytotoxicity (ADCC) and the in vivo assay in cancer-bearing athymic mice were performed to examine antitumor activity. The mAbs converted to IgG1 revealed effective ADCC as well as antitumor activity in vivo. Because half of the 21 Ags showed distinct tumor-specific expression pattern and the mAbs isolated showed various characteristics with strong affinity to the Ag, it is likely that some of the Ags detected will become useful targets for the corresponding carcinoma therapy and that several mAbs will become therapeutic agents. PMID:18474866

  15. Comprehensive screening for antigens overexpressed on carcinomas via isolation of human mAbs that may be therapeutic.

    PubMed

    Kurosawa, Gene; Akahori, Yasushi; Morita, Miwa; Sumitomo, Mariko; Sato, Noriko; Muramatsu, Chiho; Eguchi, Keiko; Matsuda, Kazuki; Takasaki, Akihiko; Tanaka, Miho; Iba, Yoshitaka; Hamada-Tsutsumi, Susumu; Ukai, Yoshinori; Shiraishi, Mamoru; Suzuki, Kazuhiro; Kurosawa, Maiko; Fujiyama, Sally; Takahashi, Nobuhiro; Kato, Ryoichi; Mizoguchi, Yoshikazu; Shamoto, Mikihiro; Tsuda, Hiroyuki; Sugiura, Mototaka; Hattori, Yoshinobu; Miyakawa, Shuichi; Shiroki, Ryoichi; Hoshinaga, Kiyotaka; Hayashi, Nobuhiro; Sugioka, Atsushi; Kurosawa, Yoshikazu

    2008-05-20

    Although several murine mAbs that have been humanized became useful therapeutic agents against a few malignancies, therapeutic Abs are not yet available for the majority of the human cancers because of our lack of knowledge of which antigens (Ags) can become useful targets. In the present study we established a procedure for comprehensive identification of such Ags through the extensive isolation of human mAbs that may become therapeutic. Using the phage-display Ab library we isolated a large number of human mAbs that bind to the surface of tumor cells. They were individually screened by immunostaining, and clones that preferentially and strongly stained the malignant cells were chosen. The Ags recognized by those clones were isolated by immunoprecipitation and identified by MS. We isolated 2,114 mAbs with unique sequences and identified 21 distinct Ags highly expressed on several carcinomas. Of those 2,114 mAbs 356 bound specifically to one of the 21 Ags. After preparing complete IgG(1) Abs the in vitro assay for Ab-dependent cell-mediated cytotoxicity (ADCC) and the in vivo assay in cancer-bearing athymic mice were performed to examine antitumor activity. The mAbs converted to IgG(1) revealed effective ADCC as well as antitumor activity in vivo. Because half of the 21 Ags showed distinct tumor-specific expression pattern and the mAbs isolated showed various characteristics with strong affinity to the Ag, it is likely that some of the Ags detected will become useful targets for the corresponding carcinoma therapy and that several mAbs will become therapeutic agents.

  16. Auxiliary Basis Sets for Density-Fitted MP2 Calculations: Correlation-Consistent Basis Sets for the 4d Elements.

    PubMed

    Hill, J Grant; Platts, James A

    2009-03-10

    Auxiliary basis sets for use in density fitting second-order Møller-Plesset perturbation theory and other correlated ab initio methods have been developed for the 4d transition metal elements Y-Tc and Rh-Pd (sets for Ru, Ag, and Cd are already available), to be used in conjunction with the correlation consistent basis sets with pseudopotentials cc-pVnZ-PP and aug-cc-pVnZ-PP. Correlation energy calculations for a test set of small- to medium-sized transition metal complexes encompassing a variety of oxidation states show that the error in using these auxiliary basis sets is around 3-4 orders of magnitude smaller than the error due to orbital basis set size. The effect of truncating the auxiliary basis sets to remove higher angular momentum functions is also considered.

  17. Ab initio molecular dynamics of liquid water using embedded-fragment second-order many-body perturbation theory towards its accurate property prediction

    PubMed Central

    Willow, Soohaeng Yoo; Salim, Michael A.; Kim, Kwang S.; Hirata, So

    2015-01-01

    A direct, simultaneous calculation of properties of a liquid using an ab initio electron-correlated theory has long been unthinkable. Here we present structural, dynamical, and response properties of liquid water calculated by ab initio molecular dynamics using the embedded-fragment spin-component-scaled second-order many-body perturbation method with the aug-cc-pVDZ basis set. This level of theory is chosen as it accurately and inexpensively reproduces the water dimer potential energy surface from the coupled-cluster singles, doubles, and noniterative triples with the aug-cc-pVQZ basis set, which is nearly exact. The calculated radial distribution function, self-diffusion coefficient, coordinate number, and dipole moment, as well as the infrared and Raman spectra are in excellent agreement with experimental results. The shapes and widths of the OH stretching bands in the infrared and Raman spectra and their isotropic-anisotropic Raman noncoincidence, which reflect the diverse local hydrogen-bond environment, are also reproduced computationally. The simulation also reveals intriguing dynamic features of the environment, which are difficult to probe experimentally, such as a surprisingly large fluctuation in the coordination number and the detailed mechanism by which the hydrogen donating water molecules move across the first and second shells, thereby causing this fluctuation. PMID:26400690

  18. Ab initio molecular dynamics of liquid water using embedded-fragment second-order many-body perturbation theory towards its accurate property prediction.

    PubMed

    Willow, Soohaeng Yoo; Salim, Michael A; Kim, Kwang S; Hirata, So

    2015-09-24

    A direct, simultaneous calculation of properties of a liquid using an ab initio electron-correlated theory has long been unthinkable. Here we present structural, dynamical, and response properties of liquid water calculated by ab initio molecular dynamics using the embedded-fragment spin-component-scaled second-order many-body perturbation method with the aug-cc-pVDZ basis set. This level of theory is chosen as it accurately and inexpensively reproduces the water dimer potential energy surface from the coupled-cluster singles, doubles, and noniterative triples with the aug-cc-pVQZ basis set, which is nearly exact. The calculated radial distribution function, self-diffusion coefficient, coordinate number, and dipole moment, as well as the infrared and Raman spectra are in excellent agreement with experimental results. The shapes and widths of the OH stretching bands in the infrared and Raman spectra and their isotropic-anisotropic Raman noncoincidence, which reflect the diverse local hydrogen-bond environment, are also reproduced computationally. The simulation also reveals intriguing dynamic features of the environment, which are difficult to probe experimentally, such as a surprisingly large fluctuation in the coordination number and the detailed mechanism by which the hydrogen donating water molecules move across the first and second shells, thereby causing this fluctuation.

  19. Probing the A-B interface of superfluid helium-3

    NASA Astrophysics Data System (ADS)

    Haley, Richard

    2015-03-01

    At temperatures around 1 mK helium-3 forms a BCS spin triplet condensate. The order parameter is sufficiently complex that more than one superfluid phase exists, each exhibiting a different broken symmetry, and there is a model first order transition between the two most stable phases, labeled A and B. The Lancaster Ultra-Low Temperature Group has developed techniques to probe the properties of the A-B interface in the deep sub-mK regime where the superfluid is in the pure condensate limit. Shaped and controllable magnetic fields are used to induce the transition, and to stabilize and move the A-B phase boundary inside the experimental volume. The latent heat of the transition has been measured, and the nucleation behavior shown to be incompatible with conventional thermodynamic models. Since superfluid helium-3 is inherently pure, and the order parameter transforms continuously across the A-B interface, it is the most coherent two-dimensional structure to which we have experimental access. It has been proposed that this 2D surface in the surrounding 3D bulk volume is a good analog of a cosmological brane separating two distinct quantum vacuum states; experiments that simulate brane annihilation and the creation of topological defects have been carried out at Lancaster. Other investigations have included measurements of the surface tension and wetting behavior of the interface. During these studies it was discovered that a large, unpredicted frictional force was acting on the interface even though it is moving through a pure superfluid. Recent breakthrough work on the dynamics of the A-B interface has finally solved this puzzle. Current experiments include a setup where the interface region is probed directly using quartz tuning fork resonators that couple to the local density of broken Cooper pair quasiparticle excitations and thus give insight into the order parameter energy gap structure as A transforms to B.

  20. The role of the basis set and the level of quantum mechanical theory in the prediction of the structure and reactivity of cisplatin.

    PubMed

    Paschoal, Diego; Marcial, Bruna L; Lopes, Juliana Fedoce; De Almeida, Wagner B; Dos Santos, Hélio F

    2012-11-05

    In this article, we conducted an extensive ab initio study on the importance of the level of theory and the basis set for theoretical predictions of the structure and reactivity of cisplatin [cis-diamminedichloroplatinum(II) (cDDP)]. Initially, the role of the basis set for the Pt atom was assessed using 24 different basis sets, including three all-electron basis sets (ABS). In addition, a modified all-electron double zeta polarized basis set (mDZP) was proposed by adding a set of diffuse d functions onto the existing DZP basis set. The energy barrier and the rate constant for the first chloride/water exchange ligand process, namely, the aquation reaction, were taken as benchmarks for which reliable experimental data are available. At the B3LYP/mDZP/6-31+G(d) level (the first basis set is for Pt and the last set is for all of the light atoms), the energy barrier was 22.8 kcal mol(-1), which is in agreement with the average experimental value, 22.9 ± 0.4 kcal mol(-1). For the other accessible ABS (DZP and ADZP), the corresponding values were 15.4 and 24.5 kcal mol(-1), respectively. The ADZP and mDZP are notably similar, raising the importance of diffuse d functions for the prediction of the kinetic properties of cDDP. In this article, we also analyze the ligand basis set and the level of theory effects by considering 36 basis sets at distinct levels of theory, namely, Hartree-Fock, MP2, and several DFT functionals. From a survey of the data, we recommend the mPW1PW91/mDZP/6-31+G(d) or B3PW91/mDZP/6-31+G(d) levels to describe the structure and reactivity of cDDP and its small derivatives. Conversely, for large molecules containing a cisplatin motif (for example, the cDDP-DNA complex), the lower levels B3LYP/LANL2DZ/6-31+G(d) and B3LYP/SBKJC-VDZ/6-31+G(d) are suggested. At these levels of theory, the predicted energy barrier was 26.0 and 25.9 kcal mol(-1), respectively, which is only 13% higher than the actual value.

  1. Neuromechanical Basis of Kinesiology.

    ERIC Educational Resources Information Center

    Enoka, Roger M.

    This textbook provides a scientific basis for the study of human motion. The eight chapters are organized under three major sections. Part One--The Force-Motion Relationship--contains chapters on (1) motion; (2) force; (3) types of movement analysis. In Part Two--The Simple Joint System--chapters concern (4) simple joint system components; (5)…

  2. Neuromechanical Basis of Kinesiology.

    ERIC Educational Resources Information Center

    Enoka, Roger M.

    This textbook provides a scientific basis for the study of human motion. The eight chapters are organized under three major sections. Part One--The Force-Motion Relationship--contains chapters on (1) motion; (2) force; (3) types of movement analysis. In Part Two--The Simple Joint System--chapters concern (4) simple joint system components; (5)…

  3. Ab initio and DFT study of the geometric structures and static dipole (hyper)polarizabilities of aromatic anions.

    PubMed

    Castellano, O; Bermúdez, Y; Giffard, M; Mabon, G; Cubillan, N; Sylla, M; Nguyen-Phu, X; Hinchliffe, A; Soscún, H

    2005-11-17

    The geometries and the static dipole (hyper)polarizabilities (alpha, beta, gamma) of a series of aromatic anions were investigated at the ab initio (HF, MP2, and MP4) and density functional theory DFT (B3LYP) levels of theory. The anions chosen for the present study are the benzenethiolate (Ph-S-), benzenecarboxylate (Ph-CO2-), benzenesulfinate (Ph-SO2-), benzenesulfonate (Ph-SO3-), and 1,3-benzenedicarboxylate (1,3-Ph-(CO2)2(2-)). For benzenethiolate anion, additional alpha, beta, and gamma calculations were performed at the coupled cluster CCSD level with MP2 optimized geometries. The standard diffuse and polarized 6-31+G(d,p) basis set was employed in conjunction to the ab initio and DFT methods. Additional HF calculations were performed with the 6-311++G(3d,3p) basis set for all the anions. The correlated electric properties were evaluated numerically within the formalism of finite field. The optimized geometries were analyzed in terms of the few reports about the phenolate and sulfonate ions. The results show that electron correlation effects on the polarizabilities are very important in all the anion series. Was found that Ph-SO2- is highly polarizable in terms of alpha and beta, and the Ph-S- is the highest second hyperpolarizable in the series. The results of alpha were rationalized in terms of the analysis of the polarization of charge based in Mulliken atomic population and the structural features of the optimized geometries of anions, whereas the large differences in the beta and gamma values in the series were respectively interpreted in terms of the bond length alternation BLA and the separation of charge in the aromatic ring by effects of the substitution. These results allowed us to suggest the benzenesulfinate and benzenethiolate anions as promising candidates that should be incorporated in ionic materials for second and third-order nonlinear optical devices.

  4. Evolution of AbGRI2-0, the Progenitor of the AbGRI2 Resistance Island in Global Clone 2 of Acinetobacter baumannii

    PubMed Central

    Blackwell, Grace A.; Nigro, Steven J.

    2015-01-01

    A320, isolated in the Netherlands in 1982 and also known as RUH134, is the earliest available multiply antibiotic-resistant (MAR) Acinetobacter baumannii isolate belonging to global clone 2 (GC2) and is the reference strain for this clone. The draft genome sequence of A320 was used to investigate the original location and configuration of the IS26-bounded AbGRI2 resistance island found in current GC2 isolates. PCR mapping and sequencing were used to order contigs composing the resistance islands. A320 contains two IS26-bounded resistance islands, AbGRI2-0a and AbGRI2-0b, of 7.8 kb and 25.4 kb, respectively. Together they contain blaTEM, aacC1, aadA1, sul1, catA1, and aphA1b genes, which confer resistance to antibiotics used clinically in the 1970s, as well as an incomplete mercury resistance module. Tracking the continuity of the chromosome and the target site duplications revealed that the two resistance islands were originally together as AbGRI2-0, an island of 32.4 kb, and were subsequently separated via an IS26-mediated intramolecular inversion that reversed the orientation of 1.54 Mb of the chromosome and duplicated an IS26. A320 contains an ancestral form of AbGRI2, and the original insertion site of the AbGRI2 island was identified. Many of the AbGRI2 versions present in the completed GC2 genomes can be derived from it via the variant AbGRI2-1. IS26-mediated inversions have also played a part in forming AbGRI2-0, and, upon reversal, large regions of AbGRI2-0 are identical to parts of AbaR0, the ancestral version of the AbaR islands present in GC1 isolates. This indicates a common source. PMID:26666934

  5. Cooperative effects in spherical spasers: Ab initio analytical model

    NASA Astrophysics Data System (ADS)

    Bordo, V. G.

    2017-06-01

    A fully analytical semiclassical theory of cooperative optical processes which occur in an ensemble of molecules embedded in a spherical core-shell nanoparticle is developed from first principles. Both the plasmonic Dicke effect and spaser generation are investigated for the designs in which a shell/core contains an arbitrarily large number of active molecules in the vicinity of a metallic core/shell. An essential aspect of the theory is an ab initio account of the feedback from the core/shell boundaries which significantly modifies the molecular dynamics. The theory provides rigorous, albeit simple and physically transparent, criteria for both plasmonic superradiance and surface plasmon generation.

  6. Carbonate-Bridged Lanthanoid Triangles: Single-Molecule Magnet Behavior, Inelastic Neutron Scattering, and Ab Initio Studies.

    PubMed

    Giansiracusa, Marcus J; Vonci, Michele; Van den Heuvel, Willem; Gable, Robert W; Moubaraki, Boujemaa; Murray, Keith S; Yu, Dehong; Mole, Richard A; Soncini, Alessandro; Boskovic, Colette

    2016-06-06

    comprised of contributions from large MJ, giving rise to slow magnetic relaxation. Although no direct evidence for intramolecular RE···RE magnetic coupling is observed in either magnetic or INS studies, on the basis of the ab initio calculations, we find noncollinear magnetic axes in 1-Er that are coplanar with the erbium triangle and radially arranged with respect to the triangle's centroid; thus, we argue that the absence of magnetic coupling in this system arises from dipolar and antiferromagnetic superexchange interactions that cancel each other out.

  7. Efficient Ab initio Modeling of Random Multicomponent Alloys

    DOE PAGES

    Jiang, Chao; Uberuaga, Blas P.

    2016-03-08

    Here, we present in this Letter a novel small set of ordered structures (SSOS) method that allows extremely efficient ab initio modeling of random multi-component alloys. Using inverse II-III spinel oxides and equiatomic quinary bcc (so-called high entropy) alloys as examples, we also demonstrate that a SSOS can achieve the same accuracy as a large supercell or a well-converged cluster expansion, but with significantly reduced computational cost. In particular, because of this efficiency, a large number of quinary alloy compositions can be quickly screened, leading to the identification of several new possible high entropy alloy chemistries. Furthermore, the SSOS methodmore » developed here can be broadly useful for the rapid computational design of multi-component materials, especially those with a large number of alloying elements, a challenging problem for other approaches.« less

  8. Efficient Ab initio Modeling of Random Multicomponent Alloys.

    PubMed

    Jiang, Chao; Uberuaga, Blas P

    2016-03-11

    We present in this Letter a novel small set of ordered structures (SSOS) method that allows extremely efficient ab initio modeling of random multicomponent alloys. Using inverse II-III spinel oxides and equiatomic quinary bcc (so-called high entropy) alloys as examples, we demonstrate that a SSOS can achieve the same accuracy as a large supercell or a well-converged cluster expansion, but with significantly reduced computational cost. In particular, because of this efficiency, a large number of quinary alloy compositions can be quickly screened, leading to the identification of several new possible high-entropy alloy chemistries. The SSOS method developed here can be broadly useful for the rapid computational design of multicomponent materials, especially those with a large number of alloying elements, a challenging problem for other approaches.

  9. Optimal immunization cocktails can promote induction of broadly neutralizing Abs against highly mutable pathogens.

    PubMed

    Shaffer, J Scott; Moore, Penny L; Kardar, Mehran; Chakraborty, Arup K

    2016-10-24

    Strategies to elicit Abs that can neutralize diverse strains of a highly mutable pathogen are likely to result in a potent vaccine. Broadly neutralizing Abs (bnAbs) against HIV have been isolated from patients, proving that the human immune system can evolve them. Using computer simulations and theory, we study immunization with diverse mixtures of variant antigens (Ags). Our results show that particular choices for the number of variant Ags and the mutational distances separating them maximize the probability of inducing bnAbs. The variant Ags represent potentially conflicting selection forces that can frustrate the Darwinian evolutionary process of affinity maturation. An intermediate level of frustration maximizes the chance of evolving bnAbs. A simple model makes vivid the origin of this principle of optimal frustration. Our results, combined with past studies, suggest that an appropriately chosen permutation of immunization with an optimally designed mixture (using the principles that we describe) and sequential immunization with variant Ags that are separated by relatively large mutational distances may best promote the evolution of bnAbs.

  10. Optimal immunization cocktails can promote induction of broadly neutralizing Abs against highly mutable pathogens

    PubMed Central

    Shaffer, J. Scott; Moore, Penny L.; Kardar, Mehran; Chakraborty, Arup K.

    2016-01-01

    Strategies to elicit Abs that can neutralize diverse strains of a highly mutable pathogen are likely to result in a potent vaccine. Broadly neutralizing Abs (bnAbs) against HIV have been isolated from patients, proving that the human immune system can evolve them. Using computer simulations and theory, we study immunization with diverse mixtures of variant antigens (Ags). Our results show that particular choices for the number of variant Ags and the mutational distances separating them maximize the probability of inducing bnAbs. The variant Ags represent potentially conflicting selection forces that can frustrate the Darwinian evolutionary process of affinity maturation. An intermediate level of frustration maximizes the chance of evolving bnAbs. A simple model makes vivid the origin of this principle of optimal frustration. Our results, combined with past studies, suggest that an appropriately chosen permutation of immunization with an optimally designed mixture (using the principles that we describe) and sequential immunization with variant Ags that are separated by relatively large mutational distances may best promote the evolution of bnAbs. PMID:27791170

  11. Determination of organic priority pollutants and emerging compounds in wastewater and snow samples using multiresidue protocols on the basis of microextraction by packed sorbents coupled to large volume injection gas chromatography-mass spectrometry analysis.

    PubMed

    Prieto, A; Schrader, S; Moeder, M

    2010-09-17

    This paper describes the development and validation of a new procedure for the simultaneous determination of 41 multi-class priority and emerging organic pollutants in water samples using microextraction by packed sorbent (MEPS) followed by large volume injection-gas chromatography-mass spectrometry (LVI-GC-MS). Apart from method parameter optimization the influence of humic acids as matrix components on the extraction efficiency of MEPS procedure was also evaluated. The list of target compounds includes polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), phthalate esters (PEs), nonylphenols (NPs), bisphenol A (BPA) and selected steroid hormones. The performance of the new at-line microextraction-LVI-GC-MS protocol was compared to standard solid-phase extraction (SPE) and LVI-GC-MS analysis. LODs for 100 mL samples (SPE) ranged from 0.2 to 736 ng L(-1) were obtained. LODs for 800 microL of sample (MEPS) were between 0.2 and 266 ng L(-1). In the case of MEPS methodology even a sample volume of only 800 microL allowed to detect the target compounds. These results demonstrate the high sensitivity of both procedures which permitted to obtain good recoveries (>75%) for all cases. The precision of the methods, calculated as relative standard deviation (RSD) was below 21% for all compounds and both methodologies. Finally, the developed methods were applied to the determination of target analytes in various samples, including snow and wastewater.

  12. Ab interno trabeculectomy: patient selection and perspectives.

    PubMed

    Vinod, Kateki; Gedde, Steven J

    2016-01-01

    Ab interno trabeculectomy is one among several recently introduced minimally invasive glaucoma surgeries that avoid a conjunctival incision and full-thickness sclerostomy involved in traditional glaucoma surgery. Ablation of the trabecular meshwork and inner wall of Schlemm's canal is performed in an arcuate fashion via a clear corneal incision, alone or in combination with phacoemulsification cataract surgery. Intraocular pressure reduction following ab interno trabeculectomy is limited by resistance in distal outflow pathways and generally stabilizes in the mid-to-high teens. Relief of medication burden has been demonstrated by some studies. A very low rate of complications, most commonly transient hyphema and intraocular pressure elevations in the immediate postoperative period, have been reported. However, available data are derived from small retrospective and prospective case series. Randomized, controlled trials are needed to better elucidate the potential merits of ab interno trabeculectomy in the combined setting versus phacoemulsification cataract surgery alone and to compare it with other minimally invasive glaucoma surgeries.

  13. Optimized energy landscape exploration using the ab initio based activation-relaxation technique.

    PubMed

    Machado-Charry, Eduardo; Béland, Laurent Karim; Caliste, Damien; Genovese, Luigi; Deutsch, Thierry; Mousseau, Normand; Pochet, Pascal

    2011-07-21

    Unbiased open-ended methods for finding transition states are powerful tools to understand diffusion and relaxation mechanisms associated with defect diffusion, growth processes, and catalysis. They have been little used, however, in conjunction with ab initio packages as these algorithms demanded large computational effort to generate even a single event. Here, we revisit the activation-relaxation technique (ART nouveau) and introduce a two-step convergence to the saddle point, combining the previously used Lanczós algorithm with the direct inversion in interactive subspace scheme. This combination makes it possible to generate events (from an initial minimum through a saddle point up to a final minimum) in a systematic fashion with a net 300-700 force evaluations per successful event. ART nouveau is coupled with BigDFT, a Kohn-Sham density functional theory (DFT) electronic structure code using a wavelet basis set with excellent efficiency on parallel computation, and applied to study the potential energy surface of C(20) clusters, vacancy diffusion in bulk silicon, and reconstruction of the 4H-SiC surface.

  14. Optimized energy landscape exploration using the ab initio based activation-relaxation technique

    NASA Astrophysics Data System (ADS)

    Machado-Charry, Eduardo; Béland, Laurent Karim; Caliste, Damien; Genovese, Luigi; Deutsch, Thierry; Mousseau, Normand; Pochet, Pascal

    2011-07-01

    Unbiased open-ended methods for finding transition states are powerful tools to understand diffusion and relaxation mechanisms associated with defect diffusion, growth processes, and catalysis. They have been little used, however, in conjunction with ab initio packages as these algorithms demanded large computational effort to generate even a single event. Here, we revisit the activation-relaxation technique (ART nouveau) and introduce a two-step convergence to the saddle point, combining the previously used Lanczós algorithm with the direct inversion in interactive subspace scheme. This combination makes it possible to generate events (from an initial minimum through a saddle point up to a final minimum) in a systematic fashion with a net 300-700 force evaluations per successful event. ART nouveau is coupled with BigDFT, a Kohn-Sham density functional theory (DFT) electronic structure code using a wavelet basis set with excellent efficiency on parallel computation, and applied to study the potential energy surface of C20 clusters, vacancy diffusion in bulk silicon, and reconstruction of the 4H-SiC surface.

  15. ``Phantom'' Modes in Ab Initio Tunneling Calculations: Implications for Theoretical Materials Optimization, Tunneling, and Transport

    NASA Astrophysics Data System (ADS)

    Barabash, Sergey V.; Pramanik, Dipankar

    2015-03-01

    Development of low-leakage dielectrics for semiconductor industry, together with many other areas of academic and industrial research, increasingly rely upon ab initio tunneling and transport calculations. Complex band structure (CBS) is a powerful formalism to establish the nature of tunneling modes, providing both a deeper understanding and a guided optimization of materials, with practical applications ranging from screening candidate dielectrics for lowest ``ultimate leakage'' to identifying charge-neutrality levels and Fermi level pinning. We demonstrate that CBS is prone to a particular type of spurious ``phantom'' solution, previously deemed true but irrelevant because of a very fast decay. We demonstrate that (i) in complex materials, phantom modes may exhibit very slow decay (appearing as leading tunneling terms implying qualitative and huge quantitative errors), (ii) the phantom modes are spurious, (iii) unlike the pseudopotential ``ghost'' states, phantoms are an apparently unavoidable artifact of large numerical basis sets, (iv) a presumed increase in computational accuracy increases the number of phantoms, effectively corrupting the CBS results despite the higher accuracy achieved in resolving the true CBS modes and the real band structure, and (v) the phantom modes cannot be easily separated from the true CBS modes. We discuss implications for direct transport calculations. The strategy for dealing with the phantom states is discussed in the context of optimizing high-quality high- κ dielectric materials for decreased tunneling leakage.

  16. Radiative lifetime of the a 3Σ+ state of HeH+ from ab initio calculations.

    PubMed

    Loreau, J; Liévin, J; Vaeck, N

    2010-09-21

    The first metastable triplet state of HeH(+) was found to be present in ion beam experiments, with its lifetime estimated to be between hundreds of milliseconds and thousand of seconds. In this work, we use ab initio methods to evaluate the radiative lifetimes of the six vibrational levels of the a (3)Σ(+) of HeH(+). The transition a (3)Σ(+)→X (1)Σ(+) is spin-forbidden, but acquires intensity through spin-orbit interaction with the singlet and triplet Π states. Large scale CASSCF/MRCI calculations using an adapted basis set were performed to determine the potential energy curves of the relevant states of HeH(+) as well as the matrix elements of the dipole and spin-orbit operators. The wave functions and energies of the vibrational levels of the a (3)Σ(+) and X (1)Σ(+) states are obtained using a B-spline method and compared to previous works. We find that the radiative lifetime of the vibrational levels increases strongly with v, the lifetime of the v=0 state being 150 s. We also analyze the contributions from discrete and continuum parts of the spectrum. With such a long lifetime, the a (3)Σ(+) state could have astrophysical implications.

  17. An ab initio investigation of possible intermediates in the reaction of the hydroxyl and hydroperoxyl radicals

    NASA Technical Reports Server (NTRS)

    Jackels, C. F.; Phillips, D. H.

    1986-01-01

    Ab initio quantum chemical techniques have been used to investigate covalently-bonded and hydrogen-bonded species that may be important intermediates in the reaction of hydroxyl and hydroperoxyl radicals. Stable structures of both types were identified. Basic sets of polarized double-zeta quality and large scale configuration interaction wave functions have been utilized. Based upon electronic energies, the covalently-bonded HOOOH species is found to be 26.4 kcal/mol more stable than the OH and HO2 radicals. Similarly, the hydrogen-bonded HO-HO2 species is found to have an electronic energy 4.7 kcal/mol below that of the component radicals, after correction is made for the basis set superposition error. The hydrogen-bonded form is found to be planar, to possess one relatively 'normal' hydrogen bond, and to have lowest energy 3A-prime and 1A-prime states that are essentially degenerate. The 1A-double prime and 3A-double prime excited states produced by rotation of the unpaired OH electron into the molecular plane are found to be very slightly bound.

  18. Ab initio investigation of the structure and alkali metal cation selectivity of 18-crown-6

    SciTech Connect

    Glendening, E.D.; Feller, D.; Thompson, M.A. )

    1994-11-16

    We present an ab inito, quantum mechanical study of 18-crown-6 (18c6) and its interaction with the alkali metal cations Li[sup +], Na[sup +], K[sup +], Rb[sup +], and Cs[sup +]. Geometries, binding energies, and binding enthalpies are evaluated at the restricted Hartree-Fock (RHF) level using standard basis sets (3-21G and 6-31 + G*) and relativistic effective core potentials. Electron correlation effects are determined at the MP2 level, and wave function analysis is performed by the natural bond orbital (NBO) and associated methods. The affinity of 18c6 for the alkali metal cations is quite strong (50-100 kcal mol[sup [minus]1], depending on cation type), arising largely from the electrostatic (ionic) interaction of the cation with the nucleophilic ether backbone. Charge transfer (covalent bonding) contributions are somewhat less important, only 20-50% as strong as the electrostatic interaction. Agreement of the calculated binding enthalpies and experimentally determined quantities is rather poor. For example, the binding energy for K[sup +]/18c6 (-71.5 kcal mol[sup [minus]1]) is about 30 kcal mol[sup [minus]1] stronger than that determined by experiment, and it is not clear how to reconcile this difference. Our calculations clearly show that solvation effects strongly influence cation selectivity. 48 refs., 12 figs., 5 tabs.

  19. Symmetry-guided large-scale shell-model theory

    NASA Astrophysics Data System (ADS)

    Launey, Kristina D.; Dytrych, Tomas; Draayer, Jerry P.

    2016-07-01

    In this review, we present a symmetry-guided strategy that utilizes exact as well as partial symmetries for enabling a deeper understanding of and advancing ab initio studies for determining the microscopic structure of atomic nuclei. These symmetries expose physically relevant degrees of freedom that, for large-scale calculations with QCD-inspired interactions, allow the model space size to be reduced through a very structured selection of the basis states to physically relevant subspaces. This can guide explorations of simple patterns in nuclei and how they emerge from first principles, as well as extensions of the theory beyond current limitations toward heavier nuclei and larger model spaces. This is illustrated for the ab initio symmetry-adapted no-core shell model (SA-NCSM) and two significant underlying symmetries, the symplectic Sp(3 , R) group and its deformation-related SU(3) subgroup. We review the broad scope of nuclei, where these symmetries have been found to play a key role-from the light p-shell systems, such as 6Li, 8B, 8Be, 12C, and 16O, and sd-shell nuclei exemplified by 20Ne, based on first-principle explorations; through the Hoyle state in 12C and enhanced collectivity in intermediate-mass nuclei, within a no-core shell-model perspective; up to strongly deformed species of the rare-earth and actinide regions, as investigated in earlier studies. A complementary picture, driven by symmetries dual to Sp(3 , R) , is also discussed. We briefly review symmetry-guided techniques that prove useful in various nuclear-theory models, such as Elliott model, ab initio SA-NCSM, symplectic model, pseudo- SU(3) and pseudo-symplectic models, ab initio hyperspherical harmonics method, ab initio lattice effective field theory, exact pairing-plus-shell model approaches, and cluster models, including the resonating-group method. Important implications of these approaches that have deepened our understanding of emergent phenomena in nuclei, such as enhanced

  20. Ab initio no-core solutions for 6Li

    NASA Astrophysics Data System (ADS)

    Shin, Ik Jae; Kim, Youngman; Maris, Pieter; Vary, James P.; Forssén, Christian; Rotureau, Jimmy; Michel, Nicolas

    2017-07-01

    We solve for properties of 6Li in the ab initio no-core full configuration (NCFC) approach and we separately solve for its ground state and {J}π ={2}2+ resonance with the Gamow shell model (GSM) in the Berggren basis. We employ both the JISP16 and chiral {{NNLO}}{opt} realistic nucleon-nucleon interactions and investigate the ground state energy, excitation energies, point proton root mean square (rms) radius and a suite of electroweak observables. We also extend and test methods to extrapolate the ground state energy, point proton rms radius, and electric quadrupole moment. We attain improved estimates of these observables in the NCFC approach by using basis spaces up through {N}\\max =18 that enable more definitive comparisons with experiment. Using the density matrix renormalization group approach with the JISP16 interaction, we find that we can significantly improve the convergence of the GSM treatment of the 6Li ground state and {J}π ={2}2+ resonance by adopting a natural orbital single-particle basis.

  1. Comparison of Property-Oriented Basis Sets for the Computation of Electronic and Nuclear Relaxation Hyperpolarizabilities.

    PubMed

    Zaleśny, Robert; Baranowska-Łączkowska, Angelika; Medveď, Miroslav; Luis, Josep M

    2015-09-08

    In the present work, we perform an assessment of several property-oriented atomic basis sets in computing (hyper)polarizabilities with a focus on the vibrational contributions. Our analysis encompasses the Pol and LPol-ds basis sets of Sadlej and co-workers, the def2-SVPD and def2-TZVPD basis sets of Rappoport and Furche, and the ORP basis set of Baranowska-Łączkowska and Łączkowski. Additionally, we use the d-aug-cc-pVQZ and aug-cc-pVTZ basis sets of Dunning and co-workers to determine the reference estimates of the investigated electric properties for small- and medium-sized molecules, respectively. We combine these basis sets with ab initio post-Hartree-Fock quantum-chemistry approaches (including the coupled cluster method) to calculate electronic and nuclear relaxation (hyper)polarizabilities of carbon dioxide, formaldehyde, cis-diazene, and a medium-sized Schiff base. The primary finding of our study is that, among all studied property-oriented basis sets, only the def2-TZVPD and ORP basis sets yield nuclear relaxation (hyper)polarizabilities of small molecules with average absolute errors less than 5.5%. A similar accuracy for the nuclear relaxation (hyper)polarizabilites of the studied systems can also be reached using the aug-cc-pVDZ basis set (5.3%), although for more accurate calculations of vibrational contributions, i.e., average absolute errors less than 1%, the aug-cc-pVTZ basis set is recommended. It was also demonstrated that anharmonic contributions to first and second hyperpolarizabilities of a medium-sized Schiff base are particularly difficult to accurately predict at the correlated level using property-oriented basis sets. For instance, the value of the nuclear relaxation first hyperpolarizability computed at the MP2/def2-TZVPD level of theory is roughly 3 times larger than that determined using the aug-cc-pVTZ basis set. We link the failure of the def2-TZVPD basis set with the difficulties in predicting the first-order field

  2. Ab initio modeling of TiO2 nanotubes

    NASA Astrophysics Data System (ADS)

    Szieberth, Dénes; Ferrari, Anna Maria; Noel, Yves; Ferrabone, Matteo

    2010-01-01

    TiO2 nanotubes constructed from a lepidocrocite-like TiO2 layer were investigated with ab initio methods employing the periodic CRYSTAL code. The dependence of strain energies, structural and electronic properties on the tube diameter was investigated in the 18-57 Å range. Nanotubes constructed by a (0,n) rollup proved to be the most stable at all diameters. All three types of rollup undergo significant reconstruction at diameters <25 Å. All investigated structures possess a high (~5.4 eV) band gap compared to bulk TiO2 phases (3.96 and 4.63 eV for rutile and anatase calculated with the same functional and basis set).

  3. Ab initio electronic and lattice dynamical properties of cerium dihydride

    NASA Astrophysics Data System (ADS)

    Gurel, Tanju; Eryigit, Resul

    2007-03-01

    The rare-earth metal hydrides are interesting systems because of the dramatic structural and electronic changes due to the hydrogen absorption and desorption. Among them, cerium dihydride (CeH2) is one of the less studied rare-earth metal-hydride. To have a better understanding, we have performed an ab initio study of electronic and lattice dynamical properties of CeH2 by using pseudopotential density functional theory within local density approximation (LDA) and a plane-wave basis. Electronic band structure of CeH2 have been obtained within LDA and as well as GW approximation. Lattice dynamical properties are calculated using density functional perturbation theory. The phonon spectrum is found to contain a set of high-frequency (˜ 850-1000 cm-1) optical bands, mostly hydrogen related, and low frequency cerium related acoustic modes climbing to 160 cm^ -1 at the zone boundary.

  4. Ab externo scleral fixation of intraocular lens.

    PubMed

    Slade, D Snow; Hater, Michael A; Cionni, Robert J; Crandall, Alan S

    2012-08-01

    We describe an ab externo technique that facilitates IOL scleral fixation and reduces the risk associated with previous ab externo scleral fixation techniques. This technique uses a microvitreoretinal blade and an internal limiting membrane forceps to create sclerotomies and retrieve the suture, respectively. Dr. Cionni is a consultant to Morcher GmbH, Stuttgart, Germany. Dr. Crandall is a consultant to Alcon Laboratories, Inc., Ft. Worth, Texas, USA. No other author has a financial or proprietary interest in any material or method mentioned. Copyright © 2012 ASCRS and ESCRS. Published by Elsevier Inc. All rights reserved.

  5. Laptop computer--associated erythema ab igne.

    PubMed

    Levinbook, Wendy Susser; Mallett, Janelle; Grant-Kels, Jane M

    2007-10-01

    A 40-year-old woman presented with an asymptomatic reticulated eruption on the thighs. After an extensive workup, she was diagnosed with erythema ab igne caused by laptop computer use. The eruption ultimately cleared several months after discontinuation of direct placement of the laptop computer on her thighs. Erythema ab igne is becoming increasingly associated with exposure to modern heat sources. A thorough history of patients with suspicious lesions should include questioning for contact with alternative heat sources to avoid an unnecessary workup for this condition.

  6. Reactive compatibilization of PBT/ABS blends by methyl methacrylate, glycidyl methacrylate, ethyl acrylate terpolymers

    NASA Astrophysics Data System (ADS)

    Hale, Wesley Raymond

    The impact resistance of poly(butylene terephthalate), PBT, has been improved by blending with acrylonitrile-butadiene-styrene terpolymers, ABS, as a minor dispersed phase; however, extensive coarsening of the dispersed phase in the blends occurs under certain heat fabrication conditions. The incorporation of certain reactive polymers (compatibilizers) that are miscible with the styrene/acrylonitrile (SAN) matrix of ABS should result in more stable morphologies. Terpolymers of methyl methacrylate, glycidyl methacrylate (GMA), ethyl acrylate, MGE, are effective as reactive compatibilizers for blends of PBT with SAN and ABS materials. The epoxide groups of MGE react with the carboxyl endgroups of PBT to form a MGE-g-PBT graft copolymer at the PBT/SAN interface to provide improved SAN or ABS dispersion, morphological stability, and a broadening of the melt processing window. Additionally, compatibilization produces large improvements in the low temperature fracture toughness of PBT/ABS blends; however, the toughness depends on the order of mixing blend components due to crosslinking reactions involving the epoxide groups of MGE catalyzed by residual acids present in some emulsion-made ABS materials. The PBT, ABS, and MGE type, content, and composition have been examined to evaluate their effects on the mechanical and morphological properties of PBT/ABS blends. Additionally, the effects of different processing conditions have been examined. High PBT melt viscosity is desirable for improving ABS dispersion and low temperature toughness of the blends. Generally, ABS materials with a high rubber content and low melt viscosity are desirable for toughening PBT. Moderate amounts of GMA in the blend were found to significantly improve blend properties. Melt blending can be performed using a variety of equipment; however, a co-rotating intermeshing twin screw extruder is the most effective for producing blends with excellent properties. The fracture properties of PBT/ABS

  7. Development of the ability to use recall to guide action, as indicated by infants' performance on AB.

    PubMed

    Diamond, A

    1985-08-01

    25 infants were tested every 2 weeks on the AB Object Permanence Task devised by Piaget, from the age when they first reached for a hidden object until they were 12 months. The delay between hiding and retrieval necessary to produce the AB error increased continuously throughout this period at an average rate of 2 sec/month, from under 2 sec at 7 1/2 months to over 10 sec by 12 months. All children displayed the AB error repeatedly over the months of testing. Large between-children differences in delay needed for the AB error were found at each age. Girls tolerated longer delays than boys. The characteristic pattern to the AB error did not vary over age or sex. Range of delay producing the AB error in any child was small. Errors disappeared when delays were reduced by 2-3 sec, and reaching became random or severely perseverative when delays were increased 2-3 sec above the level producing AB error. AB provides an index of the ability to carry out an intention based on stored information despite a conflicting habitual tendency.

  8. Radioactive Waste Management Basis

    SciTech Connect

    Perkins, B K

    2009-06-03

    The purpose of this Radioactive Waste Management Basis is to describe the systematic approach for planning, executing, and evaluating the management of radioactive waste at LLNL. The implementation of this document will ensure that waste management activities at LLNL are conducted in compliance with the requirements of DOE Order 435.1, Radioactive Waste Management, and the Implementation Guide for DOE Manual 435.1-1, Radioactive Waste Management Manual. Technical justification is provided where methods for meeting the requirements of DOE Order 435.1 deviate from the DOE Manual 435.1-1 and Implementation Guide.

  9. Characterization of mAb dimers reveals predominant dimer forms common in therapeutic mAbs

    PubMed Central

    Plath, Friederike; Ringler, Philippe; Graff-Meyer, Alexandra; Stahlberg, Henning; Lauer, Matthias E.; Rufer, Arne C.; Graewert, Melissa A.; Svergun, Dmitri; Gellermann, Gerald; Finkler, Christof; Stracke, Jan O.; Koulov, Atanas; Schnaible, Volker

    2016-01-01

    ABSTRACT The formation of undesired high molecular weight species such as dimers is an important quality attribute for therapeutic monoclonal antibody formulations. Therefore, the thorough understanding of mAb dimerization and the detailed characterization mAb dimers is of great interest for future pharmaceutical development of therapeutic antibodies. In this work, we focused on the analyses of different mAb dimers regarding size, surface properties, chemical identity, overall structure and localization of possible dimerization sites. Dimer fractions of different mAbs were isolated to a satisfactory purity from bulk material and revealed 2 predominant overall structures, namely elongated and compact dimer forms. The elongated dimers displayed one dimerization site involving the tip of the Fab domain. Depending on the stress applied, these elongated dimers are connected either covalently or non-covalently. In contrast, the compact dimers exhibited non-covalent association. Several interaction points were detected for the compact dimers involving the hinge region or the base of the Fab domain. These results indicate that mAb dimer fractions are rather complex and may contain more than one kind of dimer. Nevertheless, the overall appearance of mAb dimers suggests the existence of 2 predominant dimeric structures, elongated and compact, which are commonly present in preparations of therapeutic mAbs. PMID:27031922

  10. Diode laser surgery. Ab interno and ab externo versus conventional surgery in rabbits.

    PubMed

    Karp, C L; Higginbotham, E J; Edward, D P; Musch, D C

    1993-10-01

    Fibroblastic proliferation of subconjunctival tissues remains a primary mechanism of failure in filtration surgery. Minimizing the surgical manipulation of episcleral tissues may reduce scarring. Laser sclerostomy surgery involves minimal tissue dissection, and is gaining attention as a method of potentially improving filter duration in high-risk cases. Twenty-five New Zealand rabbits underwent filtration surgery in one eye, and the fellow eye remained as the unoperated control. Ten rabbits underwent ab externo diode laser sclerostomy surgery, ten underwent ab interno diode sclerostomy surgery, and five had posterior sclerostomy procedures. Filtration failure was defined as a less-than-4-mmHg intraocular pressure (IOP) difference between the operative and control eyes. The mean time to failure for the ab externo, ab interno, and conventional posterior sclerostomy techniques measured 17.4 +/- 11.5, 13.1 +/- 6.7, and 6.0 +/- 3.1 days, respectively. In a comparison of the laser-treated groups with the conventional procedure, the time to failure was significantly longer (P = 0.02) for the ab externo filter. The mean ab interno sclerostomy duration was longer than the posterior lip procedure, but this difference was not statistically significant (P = 0.15). The overall level of IOP reduction was similar in the three groups. These data suggest that diode laser sclerostomy is a feasible technique in rabbits, and the ab externo approach resulted in longer filter duration than the conventional posterior lip procedure in this model.

  11. Indium-111 labeled monoclonal antibodies (Ab): The effect of DTPA conjugation on the Ab activity and tissue distribution

    SciTech Connect

    Sakahara, H.; Endo, K.; Nakashima, T.; Ohta, H.; Okada, K.; Yoshida, O.; Ohmomo, Y.; Horiuchi, K.; Yokoyama, A.; Torizuka, K.

    1984-01-01

    Monoclonal antibodies (Ab) to human ..cap alpha..-fetoprotein (AFP) were conjugated with diethylenetriaminepentaacetic acid (DTPA) using cyclic DTPA anhydride and the obtained conjugates, DTPA-Ab, were labeled with In-111. The effect of DTPA conjugation on the affinity constant and the maximum binding capacity of Ab was evaluated by radioimmunoassay and Scatchard plot analysis and In-111 labeled DTPA-Ab were used for the radioimmunodetection of tumor. Ab containing 1.0 DTPA molecule per Ab showed almost full retention of both the affinity constant and the maximum binding capacity. Then, 40 ..mu..Ci of In-111 labeled DTPA-Ab were injected intravenously to nude mice bearing AFP-producing human testicular tumor and the resulted were compared with I-131 labeled Ab. Scintigraphy clearly revealed transplanted tumor. Localization of In-111 labeled DTPA-Ab was significantly higher than I-131 labeled Ab. Tumor to blood ratio obtained at 4 days after injection was 2.59 with In-111 labeled DTPA-Ab compared to 0.99 with I-131 labeled Ab. When more than 1.9 DTPA molecules were incorporated per Ab, the maximum binding capacity decreased, although the affinity constant was less affected. These In-111 labeled DTPA-Ab caused significantly higher liver accumulation. These results indicate that In-111 labeled DTPA-Ab at a cojugated DTPA to Ab molar ratio of 1.0 may be superior to I-131 labeled Ab for tumor imaging, but the maximum binding capacity and tissue distribution of In-111 labeled DTPA-AB are greatly dependent upon the number of DTPA molecules incorporated per Ab molecule.

  12. Rovibrational states of the H2O-H2 complex: An ab initio calculation

    NASA Astrophysics Data System (ADS)

    van der Avoird, Ad; Nesbitt, David J.

    2011-01-01

    All bound rovibrational levels of the H2O-H2 dimer are calculated for total angular momentum J = 0-5 on two recent intermolecular potential surfaces reported by Valiron et al. [J. Chem. Phys. 129, 134306 (2008)] and Hodges et al. [J. Chem. Phys. 120, 710 (2004)] obtained through ab initio calculations. The method used handles correctly the large amplitude internal motions in this complex; it involves a discrete variable representation of the intermolecular distance coordinate R and a basis of coupled free rotor wave functions for the hindered internal rotations and the overall rotation of the dimer. The basis is adapted to the permutation symmetry associated with the para/ortho (p/o) nature of both H2O and H2 as well as to inversion symmetry. Dimers containing oH2 are more strongly bound than dimers with pH2, as expected, with dissociation energies D_0 of 33.57, 36.63, 53.60, and 59.04 cm^{-1}for pH2O-pH2, oH2O-pH2, pH2O-oH2, and oH2O-oH2, respectively, on the potential of Valiron et al. that corresponds to a binding energy D_e of 235.14 cm^{-1}. Rovibrational wave functions are computed as well and the nature of the bound states in the four different dimer species is discussed. Converged rovibrational levels on both potentials agree well with the high-resolution spectrum reported by Weida and Nesbitt [J. Chem. Phys. 110, 156 (1999)]; the hindered internal rotor model that was used to interpret this spectrum is qualitatively correct.

  13. Thermophysical properties of krypton-helium gas mixtures from ab initio pair potentials

    NASA Astrophysics Data System (ADS)

    Jäger, Benjamin; Bich, Eckard

    2017-06-01

    A new potential energy curve for the krypton-helium atom pair was developed using supermolecular ab initio computations for 34 interatomic distances. Values for the interaction energies at the complete basis set limit were obtained from calculations with the coupled-cluster method with single, double, and perturbative triple excitations and correlation consistent basis sets up to sextuple-zeta quality augmented with mid-bond functions. Higher-order coupled-cluster excitations up to the full quadruple level were accounted for in a scheme of successive correction terms. Core-core and core-valence correlation effects were included. Relativistic corrections were considered not only at the scalar relativistic level but also using full four-component Dirac-Coulomb and Dirac-Coulomb-Gaunt calculations. The fitted analytical pair potential function is characterized by a well depth of 31.42 K with an estimated standard uncertainty of 0.08 K. Statistical thermodynamics was applied to compute the krypton-helium cross second virial coefficients. The results show a very good agreement with the best experimental data. Kinetic theory calculations based on classical and quantum-mechanical approaches for the underlying collision dynamics were utilized to compute the transport properties of krypton-helium mixtures in the dilute-gas limit for a large temperature range. The results were analyzed with respect to the orders of approximation of kinetic theory and compared with experimental data. Especially the data for the binary diffusion coefficient confirm the predictive quality of the new potential. Furthermore, inconsistencies between two empirical pair potential functions for the krypton-helium system from the literature could be resolved.

  14. Thermophysical properties of krypton-helium gas mixtures from ab initio pair potentials.

    PubMed

    Jäger, Benjamin; Bich, Eckard

    2017-06-07

    A new potential energy curve for the krypton-helium atom pair was developed using supermolecular ab initio computations for 34 interatomic distances. Values for the interaction energies at the complete basis set limit were obtained from calculations with the coupled-cluster method with single, double, and perturbative triple excitations and correlation consistent basis sets up to sextuple-zeta quality augmented with mid-bond functions. Higher-order coupled-cluster excitations up to the full quadruple level were accounted for in a scheme of successive correction terms. Core-core and core-valence correlation effects were included. Relativistic corrections were considered not only at the scalar relativistic level but also using full four-component Dirac-Coulomb and Dirac-Coulomb-Gaunt calculations. The fitted analytical pair potential function is characterized by a well depth of 31.42 K with an estimated standard uncertainty of 0.08 K. Statistical thermodynamics was applied to compute the krypton-helium cross second virial coefficients. The results show a very good agreement with the best experimental data. Kinetic theory calculations based on classical and quantum-mechanical approaches for the underlying collision dynamics were utilized to compute the transport properties of krypton-helium mixtures in the dilute-gas limit for a large temperature range. The results were analyzed with respect to the orders of approximation of kinetic theory and compared with experimental data. Especially the data for the binary diffusion coefficient confirm the predictive quality of the new potential. Furthermore, inconsistencies between two empirical pair potential functions for the krypton-helium system from the literature could be resolved.

  15. Rovibrational states of the H2O-H2 complex: an ab initio calculation.

    PubMed

    van der Avoird, Ad; Nesbitt, David J

    2011-01-28

    All bound rovibrational levels of the H(2)O-H(2) dimer are calculated for total angular momentum J = 0-5 on two recent intermolecular potential surfaces reported by Valiron et al. [J. Chem. Phys. 129, 134306 (2008)] and Hodges et al. [J. Chem. Phys. 120, 710 (2004)] obtained through ab initio calculations. The method used handles correctly the large amplitude internal motions in this complex; it involves a discrete variable representation of the intermolecular distance coordinate R and a basis of coupled free rotor wave functions for the hindered internal rotations and the overall rotation of the dimer. The basis is adapted to the permutation symmetry associated with the para/ortho (p/o) nature of both H(2)O and H(2) as well as to inversion symmetry. Dimers containing oH(2) are more strongly bound than dimers with pH(2), as expected, with dissociation energies D(0) of 33.57, 36.63, 53.60, and 59.04 cm(-1)for pH(2)O-pH(2), oH(2)O-pH(2), pH(2)O-oH(2), and oH(2)O-oH(2), respectively, on the potential of Valiron et al. that corresponds to a binding energy D(e) of 235.14 cm(-1). Rovibrational wave functions are computed as well and the nature of the bound states in the four different dimer species is discussed. Converged rovibrational levels on both potentials agree well with the high-resolution spectrum reported by Weida and Nesbitt [J. Chem. Phys. 110, 156 (1999)]; the hindered internal rotor model that was used to interpret this spectrum is qualitatively correct.

  16. yambo: An ab initio tool for excited state calculations

    NASA Astrophysics Data System (ADS)

    Marini, Andrea; Hogan, Conor; Grüning, Myrta; Varsano, Daniele

    2009-08-01

    yambo is an ab initio code for calculating quasiparticle energies and optical properties of electronic systems within the framework of many-body perturbation theory and time-dependent density functional theory. Quasiparticle energies are calculated within the GW approximation for the self-energy. Optical properties are evaluated either by solving the Bethe-Salpeter equation or by using the adiabatic local density approximation. yambo is a plane-wave code that, although particularly suited for calculations of periodic bulk systems, has been applied to a large variety of physical systems. yambo relies on efficient numerical techniques devised to treat systems with reduced dimensionality, or with a large number of degrees of freedom. The code has a user-friendly command-line based interface, flexible I/O procedures and is interfaced to several publicly available density functional ground-state codes. Program summaryProgram title:yambo Catalogue identifier: AEDH_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEDH_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public Licence v2.0 No. of lines in distributed program, including test data, etc.: 149 265 No. of bytes in distributed program, including test data, etc.: 2 848 169 Distribution format: tar.gz Programming language: Fortran 95, C Computer: any computer architecture, running any flavor of UNIX Operating system: GNU/Linux, AIX, Irix, OS/X Has the code been vectorised or parallelized?: Yes RAM: 10-1000 Mbytes Classification: 7.3, 4.4, 7.2 External routines:BLAS ( http://www.netlib.org/blas/) LAPACK ( http://www.netlib.org/lapack/) MPI ( http://www-unix.mcs.anl.gov/mpi/) is optional. BLACS ( http://www.netlib.org/scalapack/) is optional. SCALAPACK ( http://www.netlib.org/scalapack/) is optional. FFTW ( http://www.fftw.org/) is optional. netCDF ( http://www.unidata.ucar.edu/software/netcdf/) is optional. Nature of problem

  17. Accurate ab Initio Spin Densities.

    PubMed

    Boguslawski, Katharina; Marti, Konrad H; Legeza, Ors; Reiher, Markus

    2012-06-12

    We present an approach for the calculation of spin density distributions for molecules that require very large active spaces for a qualitatively correct description of their electronic structure. Our approach is based on the density-matrix renormalization group (DMRG) algorithm to calculate the spin density matrix elements as a basic quantity for the spatially resolved spin density distribution. The spin density matrix elements are directly determined from the second-quantized elementary operators optimized by the DMRG algorithm. As an analytic convergence criterion for the spin density distribution, we employ our recently developed sampling-reconstruction scheme [J. Chem. Phys.2011, 134, 224101] to build an accurate complete-active-space configuration-interaction (CASCI) wave function from the optimized matrix product states. The spin density matrix elements can then also be determined as an expectation value employing the reconstructed wave function expansion. Furthermore, the explicit reconstruction of a CASCI-type wave function provides insight into chemically interesting features of the molecule under study such as the distribution of α and β electrons in terms of Slater determinants, CI coefficients, and natural orbitals. The methodology is applied to an iron nitrosyl complex which we have identified as a challenging system for standard approaches [J. Chem. Theory Comput.2011, 7, 2740].

  18. Accurate ab Initio Spin Densities

    PubMed Central

    2012-01-01

    We present an approach for the calculation of spin density distributions for molecules that require very large active spaces for a qualitatively correct description of their electronic structure. Our approach is based on the density-matrix renormalization group (DMRG) algorithm to calculate the spin density matrix elements as a basic quantity for the spatially resolved spin density distribution. The spin density matrix elements are directly determined from the second-quantized elementary operators optimized by the DMRG algorithm. As an analytic convergence criterion for the spin density distribution, we employ our recently developed sampling-reconstruction scheme [J. Chem. Phys.2011, 134, 224101] to build an accurate complete-active-space configuration-interaction (CASCI) wave function from the optimized matrix product states. The spin density matrix elements can then also be determined as an expectation value employing the reconstructed wave function expansion. Furthermore, the explicit reconstruction of a CASCI-type wave function provides insight into chemically interesting features of the molecule under study such as the distribution of α and β electrons in terms of Slater determinants, CI coefficients, and natural orbitals. The methodology is applied to an iron nitrosyl complex which we have identified as a challenging system for standard approaches [J. Chem. Theory Comput.2011, 7, 2740]. PMID:22707921

  19. Efficient calculation of chiral three-nucleon forces up to N3LO for ab initio studies

    NASA Astrophysics Data System (ADS)

    Hebeler, K.; Krebs, H.; Epelbaum, E.; Golak, J.; Skibiński, R.

    2015-04-01

    We present a novel framework to decompose three-nucleon forces in a momentum-space partial-wave basis. The new approach is computationally much more efficient than previous methods and opens the way to ab initio studies of few-nucleon scattering processes, nuclei, and nuclear matter based on higher-order chiral three-nucleon forces. We use the new framework to calculate matrix elements of chiral three-nucleon forces at next-to-next-to-leading-order and next-to-next-to-next-to-leading-order in large basis spaces and carry out benchmark calculations for neutron matter and symmetric nuclear matter. We also study the size of the individual three-nucleon-force contributions for 3H . For nonlocal regulators, we find that the subleading terms, which have been neglected in most calculations so far, provide important contributions. All matrix elements are calculated and stored in a user-friendly way, such that values of low-energy constants as well as the form of regulator functions can be chosen freely.

  20. Intermolecular potential of the O2-O2 dimer. An ab initio study and comparison with experiment.

    PubMed

    Hernández-Lamoneda, Ramón; Bartolomei, Massimiliano; Hernández, Marta I; Campos-Martínez, José; Dayou, Fabrice

    2005-12-22

    Accurate intermolecular potentials for the lowest three multiplet states of O2-O2 dimer have been produced on the basis of ab initio calculations. The quintet potential was taken from previous highly correlated CCSD(T) calculations. In this work, we perform MRCI calculations, with large basis sets including bond functions, of the singlet and triplet states, which are of multireference character. As expected the size inconsistency and lack of higher order excitations limit the accuracy of the MRCI potentials specifically in describing the long range interactions. We show that the Heisenberg Hamiltonian provides an accurate representation of the exchange interactions in this system and this enables us to combine the accurate CCSD(T) potentials with the MRCI spin-exchange parameter to obtain accurate singlet and triplet potentials. The reliability of these potentials is tested by computing integral cross sections and comparing them with the detailed experimental study of the Perugia group, with excellent results. More interestingly, comparison with the experimentally derived potential shows important discrepancies for some angular orientations including that corresponding with the global minima, indicating the need for further work, both theoretical and experimental, to clarify their origin.

  1. High-level ab initio enthalpies of formation of 2,5-dimethylfuran, 2-methylfuran, and furan.

    PubMed

    Feller, David; Simmie, John M

    2012-11-29

    A high-level ab initio thermochemical technique, known as the Feller-Petersen-Dixon method, is used to calculate the total atomization energies and hence the enthalpies of formation of 2,5-dimethylfuran, 2-methylfuran, and furan itself as a means of rationalizing significant discrepancies in the literature. In order to avoid extremely large standard coupled cluster theory calculations, the explicitly correlated CCSD(T)-F12b variation was used with basis sets up to cc-pVQZ-F12. After extrapolating to the complete basis set limit and applying corrections for core/valence, scalar relativistic, and higher order effects, the final Δ(f)H° (298.15 K) values, with the available experimental values in parentheses are furan -34.8 ± 3 (-34.7 ± 0.8), 2-methylfuran -80.3 ± 5 (-76.4 ± 1.2), and 2,5-dimethylfuran -124.6 ± 6 (-128.1 ± 1.1) kJ mol(-1). The theoretical results exhibit a compelling internal consistency.

  2. Large haematoxylin-stainable keratohyaline granules in solar keratoses: immunohistochemical comparison using anti-Ted-H-1 antibody and antiloricrin antibody.

    PubMed

    Takahashi, M; Horiuchi, Y; Tezuka, T

    2005-11-01

    Our previous study showed that large keratohyaline granules (KHG) in molluscum contagiosum that stained with haematoxylin also reacted with anti-Ted-H-1 monoclonal antibody (mAb), but not with antifilaggrin mAb or antiloricrin polyclonal antibody (pAb). This finding indicated that the Ted-H-1 antigenic protein is a haematoxylin-stainable protein in KHG. To clarify the identity of the major component protein of the large KHG in solar keratosis, another disorder in which large KHG are observed. An enzyme immunohistochemical study was performed using antifilaggrin mAb, anti-Ted-H-1 mAb and antiloricrin pAb. Immunofluorescent double staining and immunoelectron microscopic analyses were performed using anti-Ted-H-1 mAb and antiloricrin pAb. Antifilaggrin mAb, anti-Ted-H-1 mAb and antiloricrin pAb reacted with normal KHG in nonlesional skin of solar keratosis, while only anti-Ted-H-1 mAb reacted with the large KHG in the lesions of solar keratosis. Antifilaggrin mAb did not react with large KHG. Antiloricrin pAb reacted with the cell membrane of the stratum granulosum, but not with large KHG. These findings suggest that the haematoxylin-stainable protein in the large KHG would be a Ted-H-1 antigen protein which was neither filaggrin nor loricrin.

  3. WEST Physics Basis

    NASA Astrophysics Data System (ADS)

    Bourdelle, C.; Artaud, J. F.; Basiuk, V.; Bécoulet, M.; Brémond, S.; Bucalossi, J.; Bufferand, H.; Ciraolo, G.; Colas, L.; Corre, Y.; Courtois, X.; Decker, J.; Delpech, L.; Devynck, P.; Dif-Pradalier, G.; Doerner, R. P.; Douai, D.; Dumont, R.; Ekedahl, A.; Fedorczak, N.; Fenzi, C.; Firdaouss, M.; Garcia, J.; Ghendrih, P.; Gil, C.; Giruzzi, G.; Goniche, M.; Grisolia, C.; Grosman, A.; Guilhem, D.; Guirlet, R.; Gunn, J.; Hennequin, P.; Hillairet, J.; Hoang, T.; Imbeaux, F.; Ivanova-Stanik, I.; Joffrin, E.; Kallenbach, A.; Linke, J.; Loarer, T.; Lotte, P.; Maget, P.; Marandet, Y.; Mayoral, M. L.; Meyer, O.; Missirlian, M.; Mollard, P.; Monier-Garbet, P.; Moreau, P.; Nardon, E.; Pégourié, B.; Peysson, Y.; Sabot, R.; Saint-Laurent, F.; Schneider, M.; Travère, J. M.; Tsitrone, E.; Vartanian, S.; Vermare, L.; Yoshida, M.; Zagorski, R.; Contributors, JET

    2015-06-01

    With WEST (Tungsten Environment in Steady State Tokamak) (Bucalossi et al 2014 Fusion Eng. Des. 89 907-12), the Tore Supra facility and team expertise (Dumont et al 2014 Plasma Phys. Control. Fusion 56 075020) is used to pave the way towards ITER divertor procurement and operation. It consists in implementing a divertor configuration and installing ITER-like actively cooled tungsten monoblocks in the Tore Supra tokamak, taking full benefit of its unique long-pulse capability. WEST is a user facility platform, open to all ITER partners. This paper describes the physics basis of WEST: the estimated heat flux on the divertor target, the planned heating schemes, the expected behaviour of the L-H threshold and of the pedestal and the potential W sources. A series of operating scenarios has been modelled, showing that ITER-relevant heat fluxes on the divertor can be achieved in WEST long pulse H-mode plasmas.

  4. Conformational stability, structural parameters and vibrational assignment from variable temperature infrared spectra of krypton solutions and ab initio calculations of ethylisothiocyanate.

    PubMed

    Durig, James R; Zheng, Chao

    2007-11-01

    Variable temperature (-105 to -150 degrees C) studies of the infrared spectra (3500-400 cm(-1)) of ethylisothiocyanate, CH(3)CH(2)NCS, dissolved in liquid krypton have been recorded. Additionally the infrared spectra of the gas and solid have been re-investigated. These spectroscopic data indicate a single conformer in all physical states with a large number of molecules in the gas phase at ambient temperature in excited states of the CN torsional mode which has a very low barrier to conformational interchange. To aid in the analyses of the vibrational and rotational spectra, ab initio calculations have been carried out by the perturbation method to the second order (MP2) with valence and core electron correlation using a variety of basis sets up to 6-311+G(2df,2pd). With the smaller basis sets up to 6-311+G(d,p) and cc-PVDZ, the cis conformer is indicated as a transition state with all larger basis sets the cis conformer is the only stable form. The predicted energy difference from these calculations between the cis form and the higher energy trans conformer is about 125 cm(-1) which represents essentially the barrier to internal rotation of the NCS group (rotation around NC axis). Density functional theory calculation by the B3LYP method with the same basis sets predicts this barrier to be about 25 cm(-1). By utilizing the previously reported microwave rotational constants with the structural parameters predicted by the ab initio MP2(full)/6-311+G(d,p) calculations, adjusted r(0) structural parameters have been obtained for the cis form. The determined heavy atom parameters are: r(NC)=1.196(5), r(CS)=1.579(5), r(CN)=1.439(5), r(CC)=1.519(5)A for the distances and angles of angleCCN=112.1(5), angleCNC=146.2(5), angleNCS=174.0(5) degrees . The centrifugal distortion constants, dipole moments, conformational stability, vibrational frequencies, infrared intensities and Raman activities have been predicted from ab initio calculations and compared to experimental

  5. Structural and Molecular Basis for Ebola Virus Neutralization by Protective Human Antibodies

    PubMed Central

    Misasi, John; Gilman, Morgan S.A.; Kanekiyo, Masaru; Gui, Miao; Cagigi, Alberto; Mulangu, Sabue; Corti, Davide; Ledgerwood, Julie E.; Lanzavecchia, Antonio; Cunningham, James; Muyembe-Tamfun, Jean Jacques; Baxa, Ulrich; Graham, Barney S.; Xiang, Ye; Sullivan, Nancy J.; McLellan, Jason S.

    2017-01-01

    Ebola virus causes hemorrhagic fever with a high mortality rate and for which there is no approved therapy. Two human monoclonal antibodies, mAb100 and mAb114, in combination protect non-human primates against all signs of Ebola virus disease, including viremia. Here, we demonstrate that mAb100 recognizes the base of the Ebola virus glycoprotein (GP) trimer, occludes access to the cathepsin-cleavage loop, and prevents the proteolytic cleavage of GP that is required for virus entry. We show that mAb114 interacts with the glycan cap and inner chalice of GP, remains associated following proteolytic removal of the glycan cap, and inhibits binding of cleaved GP to its receptor. These results define the basis of neutralization for two protective antibodies and may facilitate development of therapies and vaccines. PMID:26917592

  6. Approximate ab initio calculations of electronic structure of amorphous silicon

    NASA Astrophysics Data System (ADS)

    Durandurdu, M.; Drabold, D. A.; Mousseau, N.

    2000-12-01

    We report on ab initio calculations of electronic states of two large and realistic models of amorphous silicon generated using a modified version of the Wooten-Winer-Weaire algorithm and relaxed, in both cases, with a Keating and a modified Stillinger-Weber potentials. The models have no coordination defects and a very narrow bond-angle distribution. We compute the electronic density-of-states and pay particular attention to the nature of the band-tail states around the electronic gap. All models show a large and perfectly clean optical gap and realistic Urbach tails. Based on these results and the extended quasi-one-dimensional stringlike structures observed for certain eigenvalues in the band tails, we postulate that the generation of model a-Si without localized states might be achievable under certain circumstances.

  7. On the Strain Rate Sensitivity of Abs and Abs Plus Fused Deposition Modeling Parts

    NASA Astrophysics Data System (ADS)

    Vairis, A.; Petousis, M.; Vidakis, N.; Savvakis, K.

    2016-09-01

    In this work the effect of strain rate on the tensile strength of fused deposition modeling parts built with Acrylonitrile-butadiene-styrene (ABS) and ABS plus material is presented. ASTM D638-02a specimens were built with ABS and ABS plus and they were tested on a Schenck Trebel Co. tensile test machine at three different test speeds, equal, lower, and higher to the test speed required by the ASTM D638-02a standard. The experimental tensile strength results were compared and evaluated. The fracture surfaces of selected specimens were examined with a scanning electron microscope, to determine failure mode of the filament strands. It was found that, as the test speed increases, specimens develop higher tensile strength and have higher elastic modulus. Specimens tested in the highest speed of the experiment had on average about 10% higher elastic modulus and developed on average about 11% higher tensile strength.

  8. Molecular geometry and polarizability of small cadmium selenide clusters from all-electron ab initio and Density Functional Theory calculations.

    PubMed

    Karamanis, Panaghiotis; Maroulis, George; Pouchan, Claude

    2006-02-21

    We have calculated molecular geometries and electric polarizabilities for small cadmium selenide clusters. Our calculations were performed with conventional ab initio and density functional theory methods and Gaussian-type basis sets especially designed for (CdSe)(n). We find that the dipole polarizability per atom converges rapidly to the bulk value.

  9. Young, active radio stars in the AB Doradus moving group

    NASA Astrophysics Data System (ADS)

    Azulay, R.; Guirado, J. C.; Marcaide, J. M.; Martí-Vidal, I.; Ros, E.; Tognelli, E.; Hormuth, F.; Ortiz, J. L.

    2017-06-01

    Context. Precise determination of stellar masses is necessary to test the validity of pre-main-sequence (PMS) stellar evolutionary models, whose predictions are in disagreement with measurements for masses below 1.2 M⊙. To improve such a test, and based on our previous studies, we selected the AB Doradus moving group (AB Dor-MG) as the best-suited association on which to apply radio-based high-precision astrometric techniques to study binary systems. Aims: We seek to determine precise estimates of the masses of a set of stars belonging to the AB Dor-MG using radio and infrared observations. Methods: We observed in phase-reference mode with the Very Large Array (VLA) at 5 GHz and with the European VLBI Network (EVN) at 8.4 GHz the stars HD 160934, EK Dra, PW And, and LO Peg. We also observed some of these stars with the near-infrared CCD AstraLux camera at the Calar Alto observatory to complement the radio observations. Results: We determine model-independent dynamical masses of both components of the star HD 160934, A and c, which are 0.70 ± 0.07 M⊙ and 0.45 ± 0.04 M⊙, respectively. We revised the orbital parameters of EK Dra and we determine a sum of the masses of the system of 1.38 ± 0.08 M⊙. We also explored the binarity of the stars LO Peg and PW And. Conclusions: We found observational evidence that PMS evolutionary models underpredict the mass of PMS stars by 10%-40%, as previously reported by other authors. We also inferred that the origin of the radio emission must be similar in all observed stars, that is, extreme magnetic activity of the stellar corona that triggers gyrosynchrotron emission from non-thermal, accelerated electrons.

  10. Structural basis for nonneutralizing antibody competition at antigenic site II of the respiratory syncytial virus fusion protein

    PubMed Central

    Mousa, Jarrod J.; Sauer, Marion F.; Sevy, Alexander M.; Finn, Jessica A.; Alvarado, Gabriela; King, Hannah G.; Loerinc, Leah B.; Fong, Rachel H.; Doranz, Benjamin J.; Correia, Bruno E.; Kalyuzhniy, Oleksandr; Wen, Xiaolin; Jardetzky, Theodore S.; Schief, William R.; Ohi, Melanie D.; Meiler, Jens

    2016-01-01

    Palivizumab was the first antiviral monoclonal antibody (mAb) approved for therapeutic use in humans, and remains a prophylactic treatment for infants at risk for severe disease because of respiratory syncytial virus (RSV). Palivizumab is an engineered humanized version of a murine mAb targeting antigenic site II of the RSV fusion (F) protein, a key target in vaccine development. There are limited reported naturally occurring human mAbs to site II; therefore, the structural basis for human antibody recognition of this major antigenic site is poorly understood. Here, we describe a nonneutralizing class of site II-specific mAbs that competed for binding with palivizumab to postfusion RSV F protein. We also describe two classes of site II-specific neutralizing mAbs, one of which escaped competition with nonneutralizing mAbs. An X-ray crystal structure of the neutralizing mAb 14N4 in complex with F protein showed that the binding angle at which human neutralizing mAbs interact with antigenic site II determines whether or not nonneutralizing antibodies compete with their binding. Fine-mapping studies determined that nonneutralizing mAbs that interfere with binding of neutralizing mAbs recognize site II with a pose that facilitates binding to an epitope containing F surface residues on a neighboring protomer. Neutralizing antibodies, like motavizumab and a new mAb designated 3J20 that escape interference by the inhibiting mAbs, avoid such contact by binding at an angle that is shifted away from the nonneutralizing site. Furthermore, binding to rationally and computationally designed site II helix–loop–helix epitope-scaffold vaccines distinguished neutralizing from nonneutralizing site II antibodies. PMID:27791117

  11. Structural basis for nonneutralizing antibody competition at antigenic site II of the respiratory syncytial virus fusion protein.

    PubMed

    Mousa, Jarrod J; Sauer, Marion F; Sevy, Alexander M; Finn, Jessica A; Bates, John T; Alvarado, Gabriela; King, Hannah G; Loerinc, Leah B; Fong, Rachel H; Doranz, Benjamin J; Correia, Bruno E; Kalyuzhniy, Oleksandr; Wen, Xiaolin; Jardetzky, Theodore S; Schief, William R; Ohi, Melanie D; Meiler, Jens; Crowe, James E

    2016-11-01

    Palivizumab was the first antiviral monoclonal antibody (mAb) approved for therapeutic use in humans, and remains a prophylactic treatment for infants at risk for severe disease because of respiratory syncytial virus (RSV). Palivizumab is an engineered humanized version of a murine mAb targeting antigenic site II of the RSV fusion (F) protein, a key target in vaccine development. There are limited reported naturally occurring human mAbs to site II; therefore, the structural basis for human antibody recognition of this major antigenic site is poorly understood. Here, we describe a nonneutralizing class of site II-specific mAbs that competed for binding with palivizumab to postfusion RSV F protein. We also describe two classes of site II-specific neutralizing mAbs, one of which escaped competition with nonneutralizing mAbs. An X-ray crystal structure of the neutralizing mAb 14N4 in complex with F protein showed that the binding angle at which human neutralizing mAbs interact with antigenic site II determines whether or not nonneutralizing antibodies compete with their binding. Fine-mapping studies determined that nonneutralizing mAbs that interfere with binding of neutralizing mAbs recognize site II with a pose that facilitates binding to an epitope containing F surface residues on a neighboring protomer. Neutralizing antibodies, like motavizumab and a new mAb designated 3J20 that escape interference by the inhibiting mAbs, avoid such contact by binding at an angle that is shifted away from the nonneutralizing site. Furthermore, binding to rationally and computationally designed site II helix-loop-helix epitope-scaffold vaccines distinguished neutralizing from nonneutralizing site II antibodies.

  12. A potential energy surface for the process H2 + H2O yielding H + H + H2O - Ab initio calculations and analytical representation

    NASA Technical Reports Server (NTRS)

    Schwenke, David W.; Walch, Stephen P.; Taylor, Peter R.

    1991-01-01

    Extensive ab initio calculations on the ground state potential energy surface of H2 + H2O were performed using a large contracted Gaussian basis set and a high level of correlation treatment. An analytical representation of the potential energy surface was then obtained which reproduces the calculated energies with an overall root-mean-square error of only 0.64 mEh. The analytic representation explicitly includes all nine internal degrees of freedom and is also well behaved as the H2 dissociates; it thus can be used to study collision-induced dissociation or recombination of H2. The strategy used to minimize the number of energy calculations is discussed, as well as other advantages of the present method for determining the analytical representation.

  13. Ab initio quantum study of the photodynamics and absorption spectrum for the coupled 1(1)A2 and 1(1)B1 states of SO2.

    PubMed

    Lévêque, Camille; Komainda, Adrian; Taïeb, Richard; Köppel, Horst

    2013-01-28

    The nonadiabatic photoinduced dynamics occurring in the coupled 1(1)A(2) and 1(1)B(1) excited states of SO(2) is investigated using ab initio quantum dynamical methods. To this end, large scale calculations of the potential energy surfaces have been carried out at the multireference configuration interaction level. All vibrational degrees of freedom of the molecule are considered in the potential energy surface calculations and the quantum dynamical treatment. To deal with the symmetry-allowed conical intersection which occurs between the potential energy surfaces, we use the diabatic picture in the framework of regularized diabatic states. Wave-packet propagation on the coupled surfaces was performed and allowed to reproduce with good accuracy the complex absorption band observed experimentally in the 29,000-42,000 cm(-1) range. This provides a basis for a subsequent theoretical treatment of the high order harmonic spectra of SO(2).

  14. A potential energy surface for the process H2 + H2O yielding H + H + H2O - Ab initio calculations and analytical representation

    NASA Technical Reports Server (NTRS)

    Schwenke, David W.; Walch, Stephen P.; Taylor, Peter R.

    1991-01-01

    Extensive ab initio calculations on the ground state potential energy surface of H2 + H2O were performed using a large contracted Gaussian basis set and a high level of correlation treatment. An analytical representation of the potential energy surface was then obtained which reproduces the calculated energies with an overall root-mean-square error of only 0.64 mEh. The analytic representation explicitly includes all nine internal degrees of freedom and is also well behaved as the H2 dissociates; it thus can be used to study collision-induced dissociation or recombination of H2. The strategy used to minimize the number of energy calculations is discussed, as well as other advantages of the present method for determining the analytical representation.

  15. Laptop computer-induced erythema ab igne: a case report.

    PubMed

    Mohr, Melinda R; Scott, Kimberly A; Pariser, Robert M; Hood, Antoinette F

    2007-01-01

    Erythema ab igne is a condition characterized by reticulated telangiectasia and hyperpigmentation caused by repeated long-term exposure to infrared radiation insufficient to produce a burn. We report a case of laptop computer-induced erythema ab igne.

  16. Effectiveness of motorcycle antilock braking systems (ABS) in reducing crashes, the first cross-national study.

    PubMed

    Rizzi, Matteo; Strandroth, Johan; Kullgren, Anders; Tingvall, Claes; Fildes, Brian

    2015-01-01

    This study set out to evaluate the effectiveness of motorcycle antilock braking systems (ABS) in reducing real-life crashes. Since the European Parliament has voted on legislation making ABS mandatory on all new motorcycles over 125 cc from 2016, the fitment rate in Europe is likely to increase in the coming years. Though previous research has focused on mostly large displacement motorcycles, this study used police reports from Spain (2006-2009), Italy (2009), and Sweden (2003-2012) in order to analyze a wide range of motorcycles, including scooters, and compare countries with different motorcycling habits. The statistical analysis used odds ratio calculations with an induced exposure approach. Previous research found that head-on crashes were the least ABS-affected crash type and was therefore used as the nonsensitive crash type for ABS in these calculations. The same motorcycle models, with and without ABS, were compared and the calculations were carried out for each country separately. Crashes involving only scooters were further analyzed. The effectiveness of motorcycle ABS in reducing injury crashes ranged from 24% (95% confidence interval [CI], 12-36) in Italy to 29% (95% CI, 20-38) in Spain, and 34% (95% CI, 16-52) in Sweden. The reductions in severe and fatal crashes were even greater, at 34% (95% CI, 24-44) in Spain and 42% (95% CI, 23-61) in Sweden. The overall reductions of crashes involving ABS-equipped scooters (at least 250 cc) were 27% (95% CI, 12-42) in Italy and 22% (95% CI, 2-42) in Spain. ABS on scooters with at least a 250 cc engine reduced severe and fatal crashes by 31% (95% CI, 12-50), based on Spanish data alone. At this stage, there is more than sufficient scientific-based evidence to support the implementation of ABS on all motorcycles, even light ones. Further research should aim at understanding the injury mitigating effects of motorcycle ABS, possibly in combination with combined braking systems.

  17. The Epigenetic basis of diffuse large B-cell lymphoma

    PubMed Central

    Jiang, Yanwen; Melnick, Ari

    2015-01-01

    The pathogenesis of DLBCL is strongly linked to perturbation of epigenetic mechanisms. The germinal center (GC) B-cells from which DLBCLs arise are prone to instability in their cytosine methylation patterns. DLBCLs inherit this epigenetic instability and display variable degrees of epigenetic heterogeneity. Greater epigenetic heterogeneity is linked with poor clinical outcome. Somatic mutations of histone modifying proteins have also emerged as a hallmark of DLBCL. The effect of these somatic mutations may be to disrupt epigenetic switches that control the GC phenotype and “lock in” certain oncogenic features of GC B-cells resulting in malignant transformation. DNA methyltransferase and histone methyltransferase inhibitors are emerging as viable therapeutic approaches to erase aberrant epigenetic programming, suppress DLBCL growth and overcome chemotherapy resistance. This review will discuss these recent advances and their therapeutic implications. PMID:25805588

  18. A Basis for Secure Communication in Large Distributed Systems

    DTIC Science & Technology

    1987-01-01

    perhaps! access to remote resources requires no further authentication. Examples are V [11), Eden [3) and Cronus [ 4). The system is controlled...SE-11(1), January 1985. [ ·f R. Schantz et al. Cronus , A Distributed Operating System. BBN Lab: r-atories Report No. 5885 [5: Cheheyl et al

  19. Masses and activity of AB Doradus B a/b. The age of the AB Dor quadruple system revisited

    NASA Astrophysics Data System (ADS)

    Wolter, U.; Czesla, S.; Fuhrmeister, B.; Robrade, J.; Engels, D.; Wieringa, M.; Schmitt, J. H. M. M.

    2014-10-01

    We present a multiwavelength study of the close binary AB Dor Ba/b (Rst137B). Our study comprises astrometric orbit measurements, optical spectroscopy, X-ray and radio observations. Using all available adaptive optics images of AB Dor B taken with VLT/NACO from 2004 to 2009, we tightly constrain its orbital period to 360.6 ± 1.5 days. We present the first orbital solution of Rst 137B and estimate the combined mass of AB Dor Ba+b as 0.69+0.02-0.24 M⊙, slightly exceeding previous estimates based on IR photometry. Our determined orbital inclination of Rst 137B is close to the axial inclination of AB Dor A inferred from Doppler imaging. Our VLT/UVES spectra yield high rotational velocities of ≥30 km s-1 for both components Ba and Bb, in accord with previous measurements, which corresponds to rotation periods significantly shorter than one day. Our combined spectral model, using PHOENIX spectra, yields an effective temperature of 3310 ± 50 K for the primary and approximately 60 K less for the secondary. The optical spectra presumably cover a chromospheric flare and show that at least one component of Rst 137B is significantly active. Activity and weak variations are also found in our simultaneous XMM-Newton observations, while our ATCA radio data yield constant fluxes at the level of previous measurements. Using evolutionary models, our newly determined stellar parameters confirm that the age of Rst 137B is between 50 and 100 Myr. Based on observations collected at the European Southern Observatory, Paranal, Chile, 383.D-1002(A) and the ESO Science Archive Facility. Using data obtained with XMM-Newton, an ESA science mission with instruments and contributions directly funded by ESA Member states and NASA. Using data obtained with the Australia Telescope Compact Array (ATCA) operated by the Commonwealth Scientific and Industrial Research Organisation (CSIRO).

  20. Ab initio calculation of infrared intensities for hydrogen peroxide

    NASA Technical Reports Server (NTRS)

    Rogers, J. D.; Hillman, J. J.

    1982-01-01

    Results of an ab initio SCF quantum mechanical study are used to derive estimates for the infrared intensities of the fundamental vibrations of hydrogen peroxide. Atomic polar tensors (APTs) were calculated on the basis of a 4-31G basis set, and used to derive absolute intensities for the vibrational transitions. Comparison of the APTs calculated for H2O2 with those previously obtained for H2O and CH3OH, and of the absolute intensities derived from the H2O2 APTs with those derived from APTs transferred from H2O and CH3OH, reveals the sets of values to differ by no more than a factor of two, supporting the validity of the theoretical calculation. Values of the infrared intensities obtained correspond to A1 = 14.5 km/mol, A2 = 0.91 km/mol, A3 = 0.058 km/mol, A4 = 123 km/mol, A5 = 46.2 km/mol, and A6 = 101 km/mol. Charge, charge flux and overlap contributions to the dipole moment derivatives are also computed.

  1. Moderate-Cost Ab Initio Thermochemistry with Chemical Accuracy.

    PubMed

    Ganyecz, Ádám; Kállay, Mihály; Csontos, József

    2017-09-12

    A moderate-cost ab initio composite model chemistry including the explicitly correlated CCSD(T*)(F12) and conventional coupled-cluster methods up to perturbative quadruple excitations along with correlation consistent basis sets is developed. The model, named diet-HEAT-F12, is also augmented with diagonal Born-Oppenheimer and scalar relativistic corrections. The methods and basis sets used for the calculation of the individual components are selected to reproduce, as close as possible, without using any fitted parameters, the benchmark HEAT contributions. A well-defined recipe for calculating size-dependent 95% confidence intervals was also worked out for the model. The reliability of the protocol was checked using the W4-11 data set as well as a disjoint set of 23 accurate atomization energies collected from the literature and obtained by the procedure of Feller, Peterson, and Dixon. The best error statistics for the test set was yielded by the diet-HEAT-F12 protocol among the models W3X, W3X-L, and W3-F12 considered.

  2. Accurate ab initio vibrational energies of methyl chloride

    SciTech Connect

    Owens, Alec; Yurchenko, Sergei N.; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter

    2015-06-28

    Two new nine-dimensional potential energy surfaces (PESs) have been generated using high-level ab initio theory for the two main isotopologues of methyl chloride, CH{sub 3}{sup 35}Cl and CH{sub 3}{sup 37}Cl. The respective PESs, CBS-35{sup  HL}, and CBS-37{sup  HL}, are based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set (CBS) limit, and incorporate a range of higher-level (HL) additive energy corrections to account for core-valence electron correlation, higher-order coupled cluster terms, scalar relativistic effects, and diagonal Born-Oppenheimer corrections. Variational calculations of the vibrational energy levels were performed using the computer program TROVE, whose functionality has been extended to handle molecules of the form XY {sub 3}Z. Fully converged energies were obtained by means of a complete vibrational basis set extrapolation. The CBS-35{sup  HL} and CBS-37{sup  HL} PESs reproduce the fundamental term values with root-mean-square errors of 0.75 and 1.00 cm{sup −1}, respectively. An analysis of the combined effect of the HL corrections and CBS extrapolation on the vibrational wavenumbers indicates that both are needed to compute accurate theoretical results for methyl chloride. We believe that it would be extremely challenging to go beyond the accuracy currently achieved for CH{sub 3}Cl without empirical refinement of the respective PESs.

  3. Ab initio modeling of decomposition in iron based alloys

    NASA Astrophysics Data System (ADS)

    Gorbatov, O. I.; Gornostyrev, Yu. N.; Korzhavyi, P. A.; Ruban, A. V.

    2016-12-01

    This paper reviews recent progress in the field of ab initio based simulations of structure and properties of Fe-based alloys. We focus on thermodynamics of these alloys, their decomposition kinetics, and microstructure formation taking into account disorder of magnetic moments with temperature. We review modern theoretical tools which allow a consistent description of the electronic structure and energetics of random alloys with local magnetic moments that become totally or partially disordered when temperature increases. This approach gives a basis for an accurate finite-temperature description of alloys by calculating all the relevant contributions to the Gibbs energy from first-principles, including a configurational part as well as terms due to electronic, vibrational, and magnetic excitations. Applications of these theoretical approaches to the calculations of thermodynamics parameters at elevated temperatures (solution energies and effective interatomic interactions) are discussed including atomistic modeling of decomposition/clustering in Fe-based alloys. It provides a solid basis for understanding experimental data and for developing new steels for modern applications. The precipitation in Fe-Cu based alloys, the decomposition in Fe-Cr, and the short-range order formation in iron alloys with s-p elements are considered as examples.

  4. Structural basis for selectin mechanochemistry.

    PubMed

    Springer, Timothy A

    2009-01-06

    Selectins are adhesion molecules that resist large tensile forces applied by hydrodynamic forces to leukocytes binding to vessel walls. In crystals, the liganded (high-affinity) and unliganded (low-affinity) conformations differ in orientation between their tandem lectin and EGF domains. I examine how tensile force exerted on a selectin-ligand complex in vivo could favor the more extended, high-affinity conformation. Allostery is transmitted from the EGF-lectin domain interface to the ligand-binding interface on the lectin domain, 30 A away. Trp-1 of the lectin domain and the long axis of the EGF domain form an L-shaped prybar that is welded together by hydrogen bonds to the Trp-1 alpha-amino group. Pivoting of the prybar induced by force demolishes an interface between the Trp-1 side chain and the lectin domain at a switch1 region. These changes are transmitted by rigid body movement of the switch2 region to rearrangements in the switch3 region at the ligand binding site. Another switch region corresponds to a single residue in the EGF domain with large effects on ligand binding and rolling adhesion. Allostery in selectins, and the alignment of tensile force on a selectin-ligand complex with the transition pathway for conformational change, explain much of the structural basis for selectin mechanochemistry.

  5. 42 CFR 411.200 - Basis.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES MEDICARE PROGRAM EXCLUSIONS FROM MEDICARE AND LIMITATIONS ON MEDICARE PAYMENT Special Rules: Disabled Beneficiaries Who Are Also Covered Under Large Group Health Plans § 411.200 Basis. (a) This subpart is based on...

  6. 42 CFR 411.200 - Basis.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF HEALTH AND HUMAN SERVICES MEDICARE PROGRAM EXCLUSIONS FROM MEDICARE AND LIMITATIONS ON MEDICARE PAYMENT Special Rules: Disabled Beneficiaries Who Are Also Covered Under Large Group Health Plans § 411.200 Basis. (a) This subpart is based on...

  7. A "Traditional" Linguistic Basis for Language Teaching

    ERIC Educational Resources Information Center

    Anthony, Edward M.

    1970-01-01

    Presents an essentially Bloomfieldian approach to language and language teaching; sees the concept of language as interplay between stimuli and reactions as the basis of a wholly creditable system of teaching, a tremendous number of textbooks, and a large number of language courses." (FB)

  8. 77 FR 73279 - Airworthiness Directives; Saab AB, Saab Aerosystems Airplanes

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-10

    ...-261-AD; Amendment 39-17276; AD 2012-24-06] RIN 2120-AA64 Airworthiness Directives; Saab AB, Saab...). ACTION: Final rule. SUMMARY: We are adopting a new airworthiness directive (AD) for certain Saab AB, Saab..., 2012). Request To Revise Company Name and Email Address Saab AB (the commenter) requested that...

  9. Coupled-rearrangement-channel Gaussian-basis variational method for trinucleon bound states

    NASA Astrophysics Data System (ADS)

    Kameyama, H.; Kamimura, M.; Fukushima, Y.

    1989-08-01

    To the 3H and 3He ground states, we apply the coupled-rearrangement-channel variational method with Gaussian-basis functions which has successfully been used in precise calculations of muonic molecular ions, Coulomb-interacting three-body systems. The trinucleon wave function is decomposed into angular-momentum-projected three-body channels as done in the Faddeev equations method, but the interaction is fully incorporated with no partial-wave decomposition. The radial part of the channel amplitudes is expanded with a sufficient number of Gaussian-tail basis functions of the Jacobi coordinates. The Gaussian ranges are taken to be geometrical progressions which run from very short ranges through large enough ones. This ab initio variational approach is found to describe accurately both the short-range correlations and the asymptotic behavior. The Argonne V14 potential is used as an example of realistic two-nucleon interactions; for 3He, the Coulomb potential is included nonperturbatively. The calculation reproduces precisely the results of the Faddeev calculations for 3H and 3He for binding energy, probabilities of the S, S', P, and D states, and the S- and D-wave asymptotic normalization constants. Convergence of the present results is seen at a much smaller number of the three-body channels than in the Faddeev calculations. This is because the interaction is truncated in the angular momentum space in the Faddeev calculations but the full interaction is taken in the present method.

  10. Ab initio infrared and Raman spectra

    NASA Technical Reports Server (NTRS)

    Fredkin, D. R.; White, S. R.; Wilson, K. R.; Komornicki, A.

    1983-01-01

    It is pointed out that with increased computer power and improved computational techniques, such as the gradients developed in recent years, it is becoming practical to compute spectra ab initio, from the fundamental constants of nature, for systems of increasing complexity. The present investigation has the objective to explore several possible ab initio approaches to spectra, giving particular attention to infrared and nonresonance Raman. Two approaches are discussed. The sequential approach, in which first the electronic part and then later the nuclear part of the Born-Oppenheimer approximation is solved, is appropriate for small systems. The simultaneous approach, in which the electronic and nuclear parts are solved at the same time, is more appropriate for many-atom systems. A review of the newer quantum gradient techniques is provided, and the infrared and Raman spectral band contours for the water molecule are computed.

  11. Ab initio calculation of (hyper)polarizabilities using a sum-over-states formalism.

    NASA Astrophysics Data System (ADS)

    Taylor, Caroline M.; Chaudhuri, Rajat K.; Potts, Davin M.; Freed, Karl F.

    2001-03-01

    Hyperpolarizabilities are relevant to a wide range of non-linear optical properties. Ab initio computations often require a high level of correlation for accurate determination of β and γ , and especially of thier frequency dependence. While sum-over-states methods are widely used within semi-empirical frameworks, they have not been employed with high level ab initio methods because of the computational costs associated with calculating a sufficient number of states. The effective valence shell Hamiltonian method (H^v) is a highly correlated, size-extensive, ab initio, multireference, perturbative (``perturb-then-diagonalize'') method. A single H^v calculation yields a large number of states, making it ideal for use with the sum-over-states fomalism for determination of molecular properties. The method has been used to calculate the (hyper)polarizabilities of small polyene systems.

  12. Global exploration of the energy landscape of solids on the ab initio level.

    PubMed

    Doll, K; Schön, J C; Jansen, M

    2007-12-14

    Predicting which crystalline modifications can be present in a chemical system requires the global exploration of its energy landscape. Due to the large computational effort involved, in the past this search for sufficiently stable minima has been performed employing a variety of empirical potentials and cost functions followed by a local optimization on the ab initio level. However, this entails the risk of overlooking important modifications that are not modeled accurately using empirical potentials. In order to overcome this critical limitation, we develop an approach to employ ab initio energy functions during the global optimization phase of the structure prediction. As an example, we perform a global exploration of the landscape of LiF on the ab initio level and show that the relevant crystalline modifications are found during the search.

  13. Investigations for Thermal and Electrical Conductivity of ABS-Graphene Blended Prototypes.

    PubMed

    Singh, Rupinder; Sandhu, Gurleen S; Penna, Rosa; Farina, Ilenia

    2017-07-31

    The thermoplastic materials such as acrylonitrile-butadiene-styrene (ABS) and Nylon have large applications in three-dimensional printing of functional/non-functional prototypes. Usually these polymer-based prototypes are lacking in thermal and electrical conductivity. Graphene (Gr) has attracted impressive enthusiasm in the recent past due to its natural mechanical, thermal, and electrical properties. This paper presents the step by step procedure (as a case study) for development of an in-house ABS-Gr blended composite feedstock filament for fused deposition modelling (FDM) applications. The feedstock filament has been prepared by two different methods (mechanical and chemical mixing). For mechanical mixing, a twin screw extrusion (TSE) process has been used, and for chemical mixing, the composite of Gr in an ABS matrix has been set by chemical dissolution, followed by mechanical blending through TSE. Finally, the electrical and thermal conductivity of functional prototypes prepared from composite feedstock filaments have been optimized.

  14. Well-characterized sequence features of eukaryote genomes and implications for ab initio gene prediction.

    PubMed

    Huang, Ying; Chen, Shi-Yi; Deng, Feilong

    2016-01-01

    In silico analysis of DNA sequences is an important area of computational biology in the post-genomic era. Over the past two decades, computational approaches for ab initio prediction of gene structure from genome sequence alone have largely facilitated our understanding on a variety of biological questions. Although the computational prediction of protein-coding genes has already been well-established, we are also facing challenges to robustly find the non-coding RNA genes, such as miRNA and lncRNA. Two main aspects of ab initio gene prediction include the computed values for describing sequence features and used algorithm for training the discriminant function, and by which different combinations are employed into various bioinformatic tools. Herein, we briefly review these well-characterized sequence features in eukaryote genomes and applications to ab initio gene prediction. The main purpose of this article is to provide an overview to beginners who aim to develop the related bioinformatic tools.

  15. Investigations for Thermal and Electrical Conductivity of ABS-Graphene Blended Prototypes

    PubMed Central

    Singh, Rupinder; Sandhu, Gurleen S.; Penna, Rosa; Farina, Ilenia

    2017-01-01

    The thermoplastic materials such as acrylonitrile-butadiene-styrene (ABS) and Nylon have large applications in three-dimensional printing of functional/non-functional prototypes. Usually these polymer-based prototypes are lacking in thermal and electrical conductivity. Graphene (Gr) has attracted impressive enthusiasm in the recent past due to its natural mechanical, thermal, and electrical properties. This paper presents the step by step procedure (as a case study) for development of an in-house ABS-Gr blended composite feedstock filament for fused deposition modelling (FDM) applications. The feedstock filament has been prepared by two different methods (mechanical and chemical mixing). For mechanical mixing, a twin screw extrusion (TSE) process has been used, and for chemical mixing, the composite of Gr in an ABS matrix has been set by chemical dissolution, followed by mechanical blending through TSE. Finally, the electrical and thermal conductivity of functional prototypes prepared from composite feedstock filaments have been optimized. PMID:28773244

  16. Density-matrix based determination of low-energy model Hamiltonians from ab initio wavefunctions.

    PubMed

    Changlani, Hitesh J; Zheng, Huihuo; Wagner, Lucas K

    2015-09-14

    We propose a way of obtaining effective low energy Hubbard-like model Hamiltonians from ab initio quantum Monte Carlo calculations for molecular and extended systems. The Hamiltonian parameters are fit to best match the ab initio two-body density matrices and energies of the ground and excited states, and thus we refer to the method as ab initio density matrix based downfolding. For benzene (a finite system), we find good agreement with experimentally available energy gaps without using any experimental inputs. For graphene, a two dimensional solid (extended system) with periodic boundary conditions, we find the effective on-site Hubbard U(∗)/t to be 1.3 ± 0.2, comparable to a recent estimate based on the constrained random phase approximation. For molecules, such parameterizations enable calculation of excited states that are usually not accessible within ground state approaches. For solids, the effective Hamiltonian enables large-scale calculations using techniques designed for lattice models.

  17. Interaction of vermiculite with Katamin AB

    SciTech Connect

    Veksler, V.I.; Makashev, Yu.A.; Mikhailova, V.N.; Aleksandrova, E.M.; Vinogradova, I.A.

    1986-12-10

    Vermiculite can interact with quaternary ammonium salts to form organmineral compounds in the ion-exchange adsorption of these salts from waste water. This paper investigates this interaction between vermiculite and Katamin AB, a commercial cationic surfactant consisting of an aqueous solution of alkylbenyldimethylammonium chloride homologs. It is shown that ion exchange and molecular sorption occur simultaneously during the interaction and that vermiculite is a highly effective adsorbent in process water purification.

  18. Erythema Ab Igne Caused By Laptop Computer

    PubMed Central

    Guarneri, Claudio; Tchernev, Georgi; Wollina, Uwe; Lotti, Torello; Vaccaro, Mario

    2017-01-01

    Erythema ab igne (EAI) represents the stereotype of a modern technology induced disease. Originally produced by repeated exposure of the skin to a heat source, more often because of habits related to the job or personal activities, this condition now tends to occur more frequently, being associated with a variety of modern instruments. The aim of our report is to discuss this strange medical condition with a focus on clinical features, possible confounding differential diagnoses and recommendations for prevention. PMID:28785341

  19. Erythema Ab Igne Caused By Laptop Computer.

    PubMed

    Guarneri, Claudio; Tchernev, Georgi; Wollina, Uwe; Lotti, Torello; Vaccaro, Mario

    2017-07-25

    Erythema ab igne (EAI) represents the stereotype of a modern technology induced disease. Originally produced by repeated exposure of the skin to a heat source, more often because of habits related to the job or personal activities, this condition now tends to occur more frequently, being associated with a variety of modern instruments. The aim of our report is to discuss this strange medical condition with a focus on clinical features, possible confounding differential diagnoses and recommendations for prevention.

  20. Ab initio torsional potentials in silole dimers

    SciTech Connect

    Yamaguchi, Yoichi; Yamabe, Tokio

    1996-01-05

    The potential barriers for the internal rotation of silole dimers are studied theoretically using the ab initio molecular orbital method at the RHF/6-31G** level of calculations. In 2,2{prime}-bisilole, it is found that the anti-conformation is the most stable structure in the ground state and that the potential barrier height for rotation over the perpendicular conformation is 3.3 kcal/mol. 21 refs., 4 figs., 2 tabs.

  1. Crystal structure of the T315I mutant of AbI kinase.

    PubMed

    Zhou, Tianjun; Parillon, Lois; Li, Feng; Wang, Yihan; Keats, Jeff; Lamore, Sarah; Xu, Qihong; Shakespeare, William; Dalgarno, David; Zhu, Xiaotian

    2007-09-01

    Imatinib (Gleevec) is currently the frontline therapy for chronic myeloid leukemia (CML), a disease characterized by the presence of a constitutively activated chimeric tyrosine kinase protein Bcr-AbI. However, drug resistance often occurs at later stages of the disease, principally because of the occurrence of mutations in the kinase domain. Second generation Bcr-AbI inhibitors, such as dasatinib and nilotinib are capable of inhibiting many imatinib-resistant forms of the kinase but not the form in which threonine is mutated to isoleucine at the gatekeeper position (T315I). In this study, we present the crystal structure of the kinase domain of the c-AbI T315I mutant, as well as the wild-type form, in complex with a pyrrolopyridine inhibitor, PPY-A. The side chain of Ile315 is accommodated in the AbI T315I mutant structure without large conformational changes proximal to the site of mutation. In contrast to other inhibitors, such as imatinib and dasatinib, PPY-A does not occupy the hydrophobic pocket behind the gatekeeper residue. This binding mode, coupled with augmented contacts with the glycine-rich loop, appears to be critical for its ability to override the T315I mutation. The data presented here may provide structural guidance for the design of clinically useful inhibitors of Bcr-AbI T315I.

  2. Ab interno trabeculectomy: patient selection and perspectives

    PubMed Central

    Vinod, Kateki; Gedde, Steven J

    2016-01-01

    Ab interno trabeculectomy is one among several recently introduced minimally invasive glaucoma surgeries that avoid a conjunctival incision and full-thickness sclerostomy involved in traditional glaucoma surgery. Ablation of the trabecular meshwork and inner wall of Schlemm’s canal is performed in an arcuate fashion via a clear corneal incision, alone or in combination with phacoemulsification cataract surgery. Intraocular pressure reduction following ab interno trabeculectomy is limited by resistance in distal outflow pathways and generally stabilizes in the mid-to-high teens. Relief of medication burden has been demonstrated by some studies. A very low rate of complications, most commonly transient hyphema and intraocular pressure elevations in the immediate postoperative period, have been reported. However, available data are derived from small retrospective and prospective case series. Randomized, controlled trials are needed to better elucidate the potential merits of ab interno trabeculectomy in the combined setting versus phacoemulsification cataract surgery alone and to compare it with other minimally invasive glaucoma surgeries. PMID:27574396

  3. Basis set dependence using DFT/B3LYP calculations to model the Raman spectrum of thymine.

    PubMed

    Bielecki, Jakub; Lipiec, Ewelina

    2016-02-01

    Raman spectroscopy (including surface enhanced Raman spectroscopy (SERS) and tip enhanced Raman spectroscopy (TERS)) is a highly promising experimental method for investigations of biomolecule damage induced by ionizing radiation. However, proper interpretation of changes in experimental spectra for complex systems is often difficult or impossible, thus Raman spectra calculations based on density functional theory (DFT) provide an invaluable tool as an additional layer of understanding of underlying processes. There are many works that address the problem of basis set dependence for energy and bond length consideration, nevertheless there is still lack of consistent research on basis set influence on Raman spectra intensities for biomolecules. This study fills this gap by investigating of the influence of basis set choice for the interpretation of Raman spectra of the thymine molecule calculated using the DFT/B3LYP framework and comparing these results with experimental spectra. Among 19 selected Pople's basis sets, the best agreement was achieved using 6-31[Formula: see text](d,p), 6-31[Formula: see text](d,p) and 6-11[Formula: see text]G(d,p) sets. Adding diffuse functions or polarized functions for small basis set or use of a medium or large basis set without diffuse or polarized functions is not sufficient to reproduce Raman intensities correctly. The introduction of the diffuse functions ([Formula: see text]) on hydrogen atoms is not necessary for gas phase calculations. This work serves as a benchmark for further research on the interaction of ionizing radiation with DNA molecules by means of ab initio calculations and Raman spectroscopy. Moreover, this work provides a set of new scaling factors for Raman spectra calculation in the framework of DFT/B3LYP method.

  4. Transition state spectroscopy of the photoinduced Ca + CH3F reaction. 2. Experimental and ab initio studies of the free Ca...FCH3 complex.

    PubMed

    Mestdagh, J-M; Spiegelman, F; Gloaguen, E; Collier, M; Lepetit, F; Gaveau, M-A; Sanz, C Sanz; Soep, B

    2006-06-15

    The Ca* + CH3F --> CaF + CH3 reaction was photoinduced in 1:1 Ca...CH3F complexes formed in a supersonic expansion. The transition state of the reaction was explored by monitoring the electronically excited product, CaF, while scanning the laser that turns on the reaction. Moreover, the electronic structure of the Ca...FCH3 system was studied using ab initio methods by associating a pseudopotential description of the [Ca2+] and [F7+] cores, a core polarization operator on calcium, an extensive Gaussian basis and a treatment of the electronic problem at the CCSD(T) (ground state) and RSPT2 (excited states) level. In this contribution we present experimental results for the free complex and a comparison with the results of a previous experiment where the Ca...CH3F complexes are deposited at the surface of large argon clusters. The ab initio calculations allowed an interpretation of the experimental data in terms of two reaction mechanisms, one involving a partial charge transfer state, the other involving the excitation of the C-F stretch in the CH3F moiety prior to charge transfer.

  5. A global ab initio potential energy surface for the X 2A' ground state of the Si + OH → SiO + H reaction

    NASA Astrophysics Data System (ADS)

    Dayou, Fabrice; Duflot, Denis; Rivero-Santamaría, Alejandro; Monnerville, Maurice

    2013-11-01

    We report the first global potential energy surface (PES) for the X 2A' ground electronic state of the Si(3P) + OH(X2Π) → SiO(X^1Σ _g^+) + H(2S) reaction. The PES is based on a large number of ab initio energies obtained from multireference configuration interaction calculations plus Davidson correction (MRCI+Q) using basis sets of quadruple zeta quality. Corrections were applied to the ab initio energies in the reactant channel allowing a proper description of long-range interactions between Si(3P) and OH(X2Π). An analytical representation of the global PES has been developed by means of the reproducing kernel Hilbert space method. The reaction is found barrierless. Two minima, corresponding to the SiOH and HSiO isomers, and six saddle points, among which the isomerization transition state, have been characterized on the PES. The vibrational spectra of the SiOH/HSiO radicals have been computed from second-order perturbation theory and quantum dynamics methods. The structural, energetic, and spectroscopic properties of the two isomers are in good agreement with experimental data and previous high quality calculations.

  6. Torsion-wagging tunneling and vibrational states in hydrazine determined from its ab initio potential energy surface.

    PubMed

    Łodyga, Wiesław; Makarewicz, Jan

    2012-05-07

    Geometries, anharmonic vibrations, and torsion-wagging (TW) multiplets of hydrazine and its deuterated species are studied using high-level ab initio methods employing the second-order Mo̸ller-Plesset perturbation theory (MP2) as well as the coupled cluster singles and doubles model including connected triple corrections, CCSD(T), in conjunction with extended basis sets containing diffuse and core functions. To describe the splitting patterns caused by tunneling in TW states, the 3D potential energy surface (PES) for the large-amplitude TW modes is constructed. Stationary points in the 3D PES, including equivalent local minima and saddle points are characterized. Using this 3D PES, a flexible Hamiltonian is built numerically and then employed to solve the vibrational problem for TW coupled motion. The calculated ground state r(av) structure is expected to be more reliable than the experimental one that has been determined using a simplified structural model. The calculated fundamental frequencies allowed resolution of the assignment problems discussed earlier in the literature. The determined energy barriers, including the contributions from the small-amplitude vibrations, to the tunneling of the symmetric and antisymmetric wagging mode of 1997 cm(-1) and 3454 cm(-1), respectively, are in reasonable agreement with the empirical estimates of 2072 cm(-1) and 3312 cm(-1), respectively [W. Łodyga et al. J. Mol. Spectrosc. 183, 374 (1997)]. However, the empirical torsion barrier of 934 cm(-1) appears to be overestimated. The ab initio calculations yield two torsion barriers: cis and trans of 744 cm(-1) and 2706 cm(-1), respectively. The multiplets of the excited torsion states are predicted from the refined 3D PES.

  7. Torsion-wagging tunneling and vibrational states in hydrazine determined from its ab initio potential energy surface

    NASA Astrophysics Data System (ADS)

    Łodyga, Wiesław; Makarewicz, Jan

    2012-05-01

    Geometries, anharmonic vibrations, and torsion-wagging (TW) multiplets of hydrazine and its deuterated species are studied using high-level ab initio methods employing the second-order Møller-Plesset perturbation theory (MP2) as well as the coupled cluster singles and doubles model including connected triple corrections, CCSD(T), in conjunction with extended basis sets containing diffuse and core functions. To describe the splitting patterns caused by tunneling in TW states, the 3D potential energy surface (PES) for the large-amplitude TW modes is constructed. Stationary points in the 3D PES, including equivalent local minima and saddle points are characterized. Using this 3D PES, a flexible Hamiltonian is built numerically and then employed to solve the vibrational problem for TW coupled motion. The calculated ground state rav structure is expected to be more reliable than the experimental one that has been determined using a simplified structural model. The calculated fundamental frequencies allowed resolution of the assignment problems discussed earlier in the literature. The determined energy barriers, including the contributions from the small-amplitude vibrations, to the tunneling of the symmetric and antisymmetric wagging mode of 1997 cm-1 and 3454 cm-1, respectively, are in reasonable agreement with the empirical estimates of 2072 cm-1 and 3312 cm-1, respectively [W. Łodyga et al. J. Mol. Spectrosc. 183, 374 (1997), 10.1006/jmsp.1997.7271]. However, the empirical torsion barrier of 934 cm-1 appears to be overestimated. The ab initio calculations yield two torsion barriers: cis and trans of 744 cm-1 and 2706 cm-1, respectively. The multiplets of the excited torsion states are predicted from the refined 3D PES.

  8. Interaction-induced dipoles of hydrogen molecules colliding with helium atoms: a new ab initio dipole surface for high-temperature applications.

    PubMed

    Li, Xiaoping; Mandal, Anirban; Miliordos, Evangelos; Hunt, Katharine L C

    2012-01-28

    We report new ab initio results for the interaction-induced dipole moments Δμ of hydrogen molecules colliding with helium atoms. These results are needed in order to calculate collision-induced absorption spectra at high temperatures; applications include modeling the radiative profiles of very cool white dwarf stars, with temperatures from 3500 K to 9000 K. We have evaluated the dipoles based on finite-field calculations, with coupled cluster methods in MOLPRO 2006 and aug-cc-pV5Z (spdfg) basis sets for both the H and He centers. We have obtained values of Δμ for eight H(2) bond lengths ranging from 0.942 a.u. to 2.801 a.u., for 15 intermolecular separations R ranging from 2.0 a.u. to 10.0 a.u., and for 19 different relative orientations. In general, our values agree well with earlier ab initio results, for the geometrical configurations that are treated in common, but we have determined more points on the collision-induced dipole surface by an order of magnitude. These results make it possible to calculate transition probabilities for molecules in excited vibrational states, overtones, and rotational transitions with ΔJ > 4. We have cast our results in the symmetry-adapted form needed for absorption line shape calculations, by expressing Δμ as a series in the spherical harmonics of the orientation angles of the intermolecular vector and of a unit vector along the H(2) bond axis. The expansion coefficients depend on the H(2) bond length and the intermolecular distance R. For large separations R, we show that the ab initio values of the leading coefficients converge to the predictions from perturbation theory, including both classical multipole polarization and dispersion effects. © 2012 American Institute of Physics

  9. Ab initio calculation of bowl, cage, and ring isomers of C20 and C20-.

    PubMed

    An, Wei; Gao, Yi; Bulusu, Satya; Zeng, X C

    2005-05-22

    High-level ab initio calculations have been carried out to reexamine relative stability of bowl, cage, and ring isomers of C(20) and C(20)(-). The total electronic energies of the three isomers show different energy orderings, strongly depending on the hybrid functionals selected. It is found that among three popular hybrid density-functional (DF) methods B3LYP, B3PW91, PBE1PBE, and a new hybrid-meta-DF method TPSSKCIS, only the PBE1PBE method (with cc-pVTZ basis set) gives qualitatively correct energy ordering as that predicted from ab initio CCSD(T)/cc-pVDZ [CCSD(T)-coupled-cluster method including singles, doubles, and noniterative perturbative triples; cc-pVDZ-correlation consistent polarized valence double zeta] as well as from MP4(SDQ)/cc-pVTZ [MP4-fourth-order Moller-Plesset; cc-pVTZ-correlation consistent polarized valence triple zeta] calculations. Both CCSD(T) and MP4 calculations indicate that the bowl is most likely the global minimum of neutral C(20) isomers, followed by the fullerene cage and ring. For the anionic counterparts, the PBE1PBE calculation also agrees with MP4/cc-pVTZ calculation, both predicting that the bowl is still the lowest-energy structure of C(20)(-) at T=0 K, followed by the ring and the cage. In contrast, both B3LYP/cc-pVTZ and B3PW91/cc-pVTZ calculations predict that the ring is the lowest-energy structure of C(20)(-). Apparently, this good reliability in predicting the energy ordering renders the hybrid PBE method a leading choice for predicting relative stability among large-sized carbon clusters and other carbon nanostructures (e.g., finite-size carbon nanotubes, nano-onions, or nanohorns). The relative stabilities derived from total energy with Gibbs free-energy corrections demonstrate a changing ordering in which ring becomes more favorable for both C(20) and C(20)(-) at high temperatures. Finally, photoelectron spectra (PES) for the anionic C(20)(-) isomers have been computed. With binding energies up to 7 eV, the

  10. Detection and analysis of tupaia hepatocytes via mAbs against tupaia serum albumin

    PubMed Central

    Liu, Xuan; Yuan, Lunzhi; Yuan, Quan; Zhang, Yali; Wu, Kun; Zhang, Tianying; Wu, Yong; Hou, Wangheng; Wang, Tengyun; Liu, Pingguo; Shih, James Wai Kuo; Cheng, Tong; Xia, Ningshao

    2015-01-01

    On the basis of its close phylogenetic relationship with primates, the development of Tupaia belangeri as an infection animal model and drug metabolism model could provide a new option for preclinical studies, especially in hepatitis virus research. As a replacement for primary human hepatocytes (PHHs), primary tupaia hepatocytes (PTHs) have been widely used. Similar to human serum albumin, tupaia serum albumin (TSA) is the most common liver synthesis protein and is an important biomarker for PTHs and liver function. However, no detection or quantitative method for TSA has been reported. In this study, mouse monoclonal antibodies (mAbs) 4G5 and 9H3 against TSA were developed to recognize PTHs, and they did not show cross-reactivity with serum albumin from common experimental animals, such as the mouse, rat, cow, rabbit, goat, monkey, and chicken. The two mAbs also exhibited good performance in fluorescence activated cell sorting (FACS) analysis and immunofluorescence (IF) detection of PTHs. A chemiluminescent enzyme immune assay method using the two mAbs, with a linear range from 96.89 pg/ml to 49,609.38 pg/ml, was developed for the quantitative detection of TSA. The mAbs and the CLEIA method provide useful tools for research on TSA and PTHs. PMID:26597317

  11. Data and Analysis of the Double Stars STFA 10AB and STFA 1744AB

    NASA Astrophysics Data System (ADS)

    Arcilla, Marisa; Bowden, Sam; DeBlase, Jacqueline; Hall, Anthony; Hall, Corielyn; Hernandez, Alyssa; Renna, Danielle; Rodriguez, Fatima; Salazar, Cassandra; Sanchez, Andres; Teeter, Dayton; Brewer, Mark; Funk, Benjamin; Gillette, Travis; Sharpe, Scott

    2017-04-01

    Eighth grade students at Vanguard Preparatory School measured the double stars STFA 10AB and STFA 1744AB. A 22-inch Newtonian Alt/Az telescope and a 14-inch Celestron Schmidt Cassegrain telescope were used. The star Bellatrix was used as the calibration star to determine the scale constant of the 22-inch telescope to be 7.8 “/tick marks. The double star STFA 1744AB was used as the calibration star to determine the scale constant of the 14-inch telescope to be 5.1 “/tick marks. The separation and position angle of STFA 10AB was determined by the 22-inch telescope to be 347.9” and 339.3°. The separation and position angle of STFA 1744AB was determined by the 14-inch telescope to be 3.6” and 158.1°. The measurements that were calculated were compared to the most recent measurements listed in the Washington Double Star Catalog.

  12. Balanced Basis Sets in the Calculation of Potential Energy Curves for Diatomic Molecules.

    NASA Astrophysics Data System (ADS)

    Barclay, V. J.

    "Balanced" basis sets, which describe the internuclear region as well as the nuclear region, are examined in the context of an ab initio selection-extrapolation configuration -interaction method (MRD-CI). The sets are balanced by adding bond functions (BF's), which are s, p and d-type orbitals at the bond mid-point, to atomic-centred molecular basis sets, which have double and triple sets of valence -shell orbitals (DZ and TZ) and one or two sets of polarization functions (PF's). Potential energy curves and spectroscopic constants were calculated for the ground states of the hydrides H _2, OH, NaH, MgH, MH, SiH, PH, SH, HCl, and for the ionized species OH^+ and OH^{++}, and for the A^3Sigma_{u}, w^3Delta_{u} and B^3Pi_{g} excited states of N_2. The basis sets containing bond functions gave curves and constants superior to the DZP and (where calculated) TZPP results, and of quality similar to large basis set calculations in the literature. The single and double ionization potentials of OH, and the term energies of the N_2 excited states had error at the atomic asymptotes for all basis sets. The dissociation energies of the ground states of ten first-row diatomics (C_2, N_2, O_2, F_2, CN, CO, CF, NO, NF, and FO) were studied using balanced basis sets. A correlation was found to exist between the actual bond order of a species, and the number and kinds of orbitals which comprise the optimum BF. For MRD-CI diatomic calculations, the following BF's should be added to a DZP basis set (sp) (for a bond order of 1); 2(sp) (B. O. 1.5); (spd) (B. O. 2); 3(sp) (B. O. 2.5); 2(spd) (B. O. 3). The prescribed BF basis method was tested on the 26 second-row congeners Si _2, P_2, S _2, Cl_2, SiP, SiS, SiCl, PS, PCl, and ClS, and mixed-row congeners SiN, SiO, SiF, PO, PF, SF, SiC, PN, SO, ClF, CP, CS, CCl, NS, NCl, and ClO. An average error of 6% and a maximum error of 10% relative to known experimental D_{e }'s was found: compared to an average error of 18% for TZPP calculations

  13. AB initio calculations of the structure and stability of the non-rigid LiBF 4 molecule

    NASA Astrophysics Data System (ADS)

    Zakzhevzskii, V. G.; Boldyrev, A. I.; Charkin, O. P.

    1980-07-01

    Ab initio calculations of the potential energy surface, equilibrium geometry and energetic stability of the non-rigid LiBF4 molecule have been performed using the basis sets of Roos and Siegbahn, and Huzinaga and Dunning in a doublezeta contraction. The results are compared with similar ab initio data for LiBH 4, LiAlH 4, LiBeH -4, LiCH +4, Li 2 F 2, and LiBeF 3 ‡The geometry of the most disadvantageous configuration (m) was not optimized completely

  14. Liquid and solid phases of water: an extensive molecular dynamics simulation with an ab initio polarizable potential

    NASA Astrophysics Data System (ADS)

    Clementi, Enrico; Corongiu, Giorgina; Sciortino, Francesco

    1993-08-01

    Results are presented on the reliability of the ab initio, polarizable and flexible Nieser—Corongiu—Clementi potential at describing the structure and dynamics of the liquid and solid phases of water. For both structural and dynamic quantities the agreement between experimental and numerical results is good. A "substance" very similar to "real water" has indeed been created on the basis of ab initio quantum mechanical calculations. This gives confidence in the use of the simulations to examine features that are not directly measurable, but are of central importance in the understanding of water structure and dynamics.

  15. Ab Initio Finite-Temperature Electronic Absorption Spectrum of Formamide.

    PubMed

    Besley, Nicholas A; Doltsinis, Nikos L

    2006-11-01

    A combination of Car-Parrinello molecular dynamics (CP-MD) and high-level ab initio quantum chemical calculations has been used to calculate the electronic absorption spectrum of formamide at finite temperatures. Thermally broadened spectra have been obtained by averaging over a large number of single-point multireference configuration interaction excitation energies calculated for geometries sampled from a CP-MD simulation. Electronic excitation spectra of possible contaminants ammonia and formamidic acid have also been computed. Ammonia exhibits a strong peak in the shoulder region of the experimental formamide spectrum at 6.5 eV, and formamidic acid has a strong absorption above 7.5 eV. The calculations reproduce the shape of the experimental absorption spectrum, in particular, the low-energy shoulder of the main peak, and demonstrate how finite-temperature electronic absorption spectra can be computed from first principles.

  16. SEEDS Polarimetric Imagery of the AB Aur Protoplanetary Disk

    NASA Astrophysics Data System (ADS)

    Wisniewski, John P.; Fukagawa, M.; Grady, C.; Hashimoto, J.; Hodapp, K.; Kudo, T.; Munetake, M.; Okamoto, Y.; Tamura, M.; SEEDS Team

    2011-01-01

    The Strategic Exploration of Exoplanets and Disks with Subaru (SEEDS) is a large survey which will be observing roughly 200 protoplanetary and debris disk systems over the next five years using the HiCIAO coronagraph + AO188 system on the Subaru telescope. We present new J-band polarimetric differential imagery of the proto-type Herbig Ae star, AB Aurigae, which diagnoses scattered light from the system between 20 - 540 AU at a resolution of roughly 8 AU. We discuss the morphology we observe in the outer disk region in the context of previous observations of the system, and compare/contrast the morphology in the inner disk region with recent H-band imagery of the system made with HiCIAO (Hashimoto et al 2010). This work was supported in part by NSF grants AST 0802230 and AST 1009314 and the AAS' Chretien International Research Grant.

  17. The 2-alkyl-2H-indazole regioisomers of synthetic cannabinoids AB-CHMINACA, AB-FUBINACA, AB-PINACA, and 5F-AB-PINACA are possible manufacturing impurities with cannabimimetic activities.

    PubMed

    Longworth, Mitchell; Banister, Samuel D; Mack, James B C; Glass, Michelle; Connor, Mark; Kassiou, Michael

    2016-01-01

    Indazole-derived synthetic cannabinoids (SCs) featuring an alkyl substituent at the 1-position and l-valinamide at the 3-carboxamide position (e.g., AB-CHMINACA) have been identified by forensic chemists around the world, and are associated with serious adverse health effects. Regioisomerism is possible for indazole SCs, with the 2-alkyl-2H-indazole regioisomer of AB-CHMINACA recently identified in SC products in Japan. It is unknown whether this regiosiomer represents a manufacturing impurity arising as a synthetic byproduct, or was intentionally synthesized as a cannabimimetic agent. This study reports the synthesis, analytical characterization, and pharmacological evaluation of commonly encountered indazole SCs AB-CHMINACA, AB-FUBINACA, AB-PINACA, 5F-AB-PINACA and their corresponding 2-alkyl-2H-indazole regioisomers. Both regioisomers of each SC were prepared from a common precursor, and the physical properties, (1)H and (13)C nuclear magnetic resonance spectroscopy, gas chromatography-mass spectrometry, and ultraviolet-visible spectroscopy of all SC compounds are described. Additionally, AB-CHMINACA, AB-FUBINACA, AB-PINACA, and 5F-AB-PINACA were found to act as high potency agonists at CB1 (EC50 = 2.1-11.6 nM) and CB2 (EC50 = 5.6-21.1 nM) receptors in fluorometric assays, while the corresponding 2-alkyl-2H-indazole regioisomers demonstrated low potency (micromolar) agonist activities at both receptors. Taken together, these data suggest that 2-alkyl-2H-indazole regioisomers of AB-CHMINACA, AB-FUBINACA, AB-PINACA, and 5F-AB-PINACA are likely to be encountered by forensic chemists and toxicologists as the result of improper purification during the clandestine synthesis of 1-alkyl-1H-indazole regioisomers, and can be distinguished by differences in gas chromatography-mass spectrometry fragmentation pattern.

  18. Investigations of immunogenic, allergenic and adjuvant properties of Cry1Ab protein after intragastric exposure in a food allergy model in mice.

    PubMed

    Andreassen, Monica; Bøhn, Thomas; Wikmark, Odd-Gunnar; Bodin, Johanna; Traavik, Terje; Løvik, Martinus; Nygaard, Unni Cecilie

    2016-05-04

    In genetically modified (GM) crops there is a risk that the inserted genes may introduce new allergens and/or adjuvants into the food and feed chain. The MON810 maize, expressing the insecticidal Cry1Ab toxin, is grown in many countries worldwide. In animal models, intranasal and intraperitoneal immunisations with the purified Cry1Ab proteins have induced immune responses, and feeding trials with Cry1Ab-containing feed have revealed some altered immune responses. Previous investigations have primarily measured antibody responses to the protein, while investigations of clinical food allergy symptoms, or allergy promotion (adjuvant effect) associated with the Cry1Ab protein are largely missing. We aimed to investigate immunogenic, allergenic and adjuvant properties of purified Cry1Ab toxin (trypCry1Ab, i.e., trypsin activated Cry1Ab) in a mouse model of food allergy. Female C3H/HeJ mice were immunized by intragastric gavage of 10 μg purified, trypsin activated Cry1Ab toxin (trypCry1Ab) alone or together with the food allergen lupin. Cholera toxin was added as a positive control for adjuvant effect to break oral tolerance. Clinical symptoms (anaphylaxis) as well as humoral and cellular responses were assessed. In contrast to results from previous airway investigations, we observed no indication of immunogenic properties of trypCry1Ab protein after repeated intragastric exposures to one dose, with or without CT as adjuvant. Moreover, the results indicated that trypCry1Ab given by the intragastric route was not able to promote allergic responses or anaphylactic reactions against the co-administered allergen lupin at the given dose. The study suggests no immunogenic, allergenic or adjuvant capacity of the given dose of trypCry1Ab protein after intragastric exposure of prime aged mice.

  19. An ab initio study of the fcc and hcp structures of helium.

    PubMed

    Røeggen, I

    2006-05-14

    The hexagonal close packed (hcp) and face centered cubic (fcc) structures of helium are studied by using a new ab initio computational model for large complexes comprising small subsystems. The new model is formulated within the framework of the energy incremental scheme. In the calculation of intra- and intersystem energies, model systems are introduced. To each subsystem associated is a set of partner subsystems defined by a vicinity criterion. In the independent calculations of intra- and intersystem energies, the calculations are performed on model subsystems defined by the subsystems considered and their partner subsystems. A small and a large basis set are associated with each subsystem. For partner subsystems in a model system, the small basis set is adopted. By introducing a particular decomposition scheme, the intermolecular potential is written as a sum of effective one-body potentials. The binding energy per atom in an infinite crystal of atoms is the negative value of this one-body potential. The one-body potentials for hcp and fcc structures are calculated for the following nearest neighbor distances (d0): 4.6, 5.1, 5.4, 5.435, 5.5, 5.61, and 6.1 a.u. The equilibrium distance is 5.44 a.u. for both structures. The equilibrium dimer distance is 5.61 a.u. For the larger distances, i.e., d0 > 5.4 a.u., the difference of the effective one-body potentials for the two structures is less than 0.2 microE(h). However, the hcp structure has the lowest effective one-body potential for all the distances considered. For the smallest distance the difference in the effective one-body potential is 3.9 microE(h). Hence, for solid helium, i.e., helium under high pressure, the hcp structure is the preferred one. The error in the calculated effective one-body potential for the distance d0 = 5.61 a.u. is of the order of 1 microE(h) (approximately 0.5%).

  20. Undoing Gender Through Legislation and Schooling: the Case of AB 537 and AB 394 IN California, USA

    NASA Astrophysics Data System (ADS)

    Knotts, Greg

    2009-11-01

    This article investigates California laws AB 537: The Student Safety and Violence Prevention Act of 2000, and the recently enacted AB 394: Safe Place to Learn Act. Both demand that gender identity and sexual orientation be added to the lexicon of anti-harassment protection in public education. However, despite these progressive measures, schools have an unconscious acceptance of heteronormativity and gendered norms, which undermines both the spirit and language of these laws. This paper examines how California schools can both change standard practices and realise the transformative social change that laws like AB 537 and AB 394 can instigate. I assert that the systemic implementation of these laws, through the adoption, enforcement and evaluation of existing AB 537 Task Force Recommendations, is necessary for their success. My second assertion is that AB 537 and AB 394 have the potential to change and reconstitute gender-based and heteronormative standards at school sites.

  1. Anharmonic force field and vibrational dynamics of CH2F2 up to 5000 cm(-1) studied by Fourier transform infrared spectroscopy and state-of-the-art ab initio calculations.

    PubMed

    Tasinato, Nicola; Regini, Giorgia; Stoppa, Paolo; Pietropolli Charmet, Andrea; Gambi, Alberto

    2012-06-07

    Difluoromethane (CH(2)F(2), HFC-32) is a molecule used in refrigerant mixtures as a replacement of the more environmentally hazardous, ozone depleting, chlorofluorocarbons. On the other hand, presenting strong vibration-rotation bands in the 9 μm atmospheric window, it is a greenhouse gas which contributes to global warming. In the present work, the vibrational and ro-vibrational properties of CH(2)F(2), providing basic data for its atmospheric modeling, are studied in detail by coupling medium resolution Fourier transform infrared spectroscopy to high-level electronic structure ab initio calculations. Experimentally a full quantum assignment and accurate integrated absorption cross sections are obtained up to 5000 cm(-1). Ab initio calculations are carried out by using CCSD(T) theory and large basis sets of either the correlation consistent or atomic natural orbital hierarchies. By using vibrational perturbation theory to second order a complete set of vibrational and ro-vibrational parameters is derived from the ab initio quartic anharmonic force fields, which well compares with the spectroscopic constants retrieved experimentally. An excellent agreement between theory and experiment is achieved for vibrational energy levels and integrated absorption cross sections: transition frequencies up to four quanta of vibrational excitation are reproduced with a root mean square deviation (RMSD) of 7 cm(-1) while intensities are predicted within few km mol(-1) from the experiment. Basis set performances and core correlation effects are discussed throughout the paper. Particular attention is focused in the understanding of the anharmonic couplings which rule the vibrational dynamics of the |ν(1)>, |2ν(8)>, |2ν(2)> three levels interacting system. The reliability of the potential energy and dipole moment surfaces in reproducing the vibrational eigenvalues and intensities as well as in modeling the vibrational and ro-vibrational mixings over the whole 400-5000 cm(-1

  2. Ab initio charge-carrier mobility model for amorphous molecular semiconductors

    NASA Astrophysics Data System (ADS)

    Massé, Andrea; Friederich, Pascal; Symalla, Franz; Liu, Feilong; Nitsche, Robert; Coehoorn, Reinder; Wenzel, Wolfgang; Bobbert, Peter A.

    2016-05-01

    Accurate charge-carrier mobility models of amorphous organic molecular semiconductors are essential to describe the electrical properties of devices based on these materials. The disordered nature of these semiconductors leads to percolative charge transport with a large characteristic length scale, posing a challenge to the development of such models from ab initio simulations. Here, we develop an ab initio mobility model using a four-step procedure. First, the amorphous morphology together with its energy disorder and intermolecular charge-transfer integrals are obtained from ab initio simulations in a small box. Next, the ab initio information is used to set up a stochastic model for the morphology and transfer integrals. This stochastic model is then employed to generate a large simulation box with modeled morphology and transfer integrals, which can fully capture the percolative charge transport. Finally, the charge-carrier mobility in this simulation box is calculated by solving a master equation, yielding a mobility function depending on temperature, carrier concentration, and electric field. We demonstrate the procedure for hole transport in two important molecular semiconductors, α -NPD and TCTA. In contrast to a previous study, we conclude that spatial correlations in the energy disorder are unimportant for α -NPD. We apply our mobility model to two types of hole-only α -NPD devices and find that the experimental temperature-dependent current density-voltage characteristics of all devices can be well described by only slightly decreasing the simulated energy disorder strength.

  3. 40 CFR 174.506 - Bacillus thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn; exemption from the requirement of...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... Cry35Ab1 proteins in corn; exemption from the requirement of a tolerance. 174.506 Section 174.506... thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn; exemption from the requirement of a tolerance. Residues of Bacillus thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn are exempted from the requirement of a...

  4. 40 CFR 174.506 - Bacillus thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn; exemption from the requirement of...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... Cry35Ab1 proteins in corn; exemption from the requirement of a tolerance. 174.506 Section 174.506... thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn; exemption from the requirement of a tolerance. Residues of Bacillus thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn are exempted from the requirement of a...

  5. 40 CFR 174.506 - Bacillus thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn; exemption from the requirement of...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Cry35Ab1 proteins in corn; exemption from the requirement of a tolerance. 174.506 Section 174.506... thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn; exemption from the requirement of a tolerance. Residues of Bacillus thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn are exempted from the requirement of a...

  6. 40 CFR 174.506 - Bacillus thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn; exemption from the requirement of...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Cry35Ab1 proteins in corn; exemption from the requirement of a tolerance. 174.506 Section 174.506... thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn; exemption from the requirement of a tolerance. Residues of Bacillus thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn are exempted from the requirement of a...

  7. 40 CFR 174.506 - Bacillus thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn; exemption from the requirement of...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... Cry35Ab1 proteins in corn; exemption from the requirement of a tolerance. 174.506 Section 174.506... thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn; exemption from the requirement of a tolerance. Residues of Bacillus thuringiensis Cry34Ab1 and Cry35Ab1 proteins in corn are exempted from the requirement of a...

  8. Characterization of Large Water Clusters by Broadband Rotational Spectroscopy

    NASA Astrophysics Data System (ADS)

    Perez, Cristobal; Zaleski, Daniel P.; Seifert, Nathan A.; Pate, Brooks H.; Kisiel, Zbigniew; Temelso, Berhane; Shields, George C.; Shipman, Steven T.; Finnerman, Ian

    2013-06-01

    Most theoretical water models match with experimental result reasonably well up to n=10. For clusters larger than the decamer there is no clear consensus in the global minimum geometries, as the low-energy landscape for a given cluster size changes considerably depending on the model applied. However, there is agreement in considering the undecamer regime as one of the richer pure water cluster regimes, with a large number (>50) of isomers within 1 kcal/mol of the global minimum. Using broadband chirped-pulse Fourier transform microwave (CP-FTMW) spectroscopy operating in the 2-8 GHz frequency range, seven low-energy isomers of the water undecamer have been identified in a pulsed molecular beam. The observed water cluster structures have been identified as belonging to four families on basis to their rotational constants according to their different oxygen atom frameworks. These families can be explained by building up the structures from smaller water cluster subunits. Rotational spectra consistent with theoretical predictions for two isomers of (H_{2}O)_{13} and one of (H_{2}O)_{15} have also been identified. Due to the high density of lines observed in the broadband spectrum, the traditional method of pattern recognition using ab-initio calculations was replaced with a new approach combining high-level ab-initio calculations with automatic fitting tools. These autofitting routines were tested on these systems and are also briefly described.

  9. Ab-initio Studies Of Lithium Oxide

    NASA Astrophysics Data System (ADS)

    Gupta, M. K.; Goel, Prabhatasree; Mittal, R.; Chaplot, S. L.

    2010-12-01

    Lithium oxide is an important material because of its high thermal conductivity and superionic behavior at high temperature. It behaves like a superionic conductor above 1200 K. Phonon frequencies have been calculated using ab-initio method. The calculations of phonon dispersion relation near unit cell volume corresponding to the superionic transition indicate softening of zone boundary transverse acoustic phonon mode along (110). The instability of phonon mode could lead to the dynamical disorder of lithium sub lattice. Thermal expansion and equation of states are also computed. The results compare well with our previous semi-empirical potential calculations.

  10. Ab initio quantum chemistry: Methodology and applications

    PubMed Central

    Friesner, Richard A.

    2005-01-01

    This Perspective provides an overview of state-of-the-art ab initio quantum chemical methodology and applications. The methods that are discussed include coupled cluster theory, localized second-order Moller–Plesset perturbation theory, multireference perturbation approaches, and density functional theory. The accuracy of each approach for key chemical properties is summarized, and the computational performance is analyzed, emphasizing significant advances in algorithms and implementation over the past decade. Incorporation of a condensed-phase environment by means of mixed quantum mechanical/molecular mechanics or self-consistent reaction field techniques, is presented. A wide range of illustrative applications, focusing on materials science and biology, are discussed briefly. PMID:15870212

  11. Ab-initio phasing in protein crystallography

    NASA Astrophysics Data System (ADS)

    van der Plas, J. L.; Millane, Rick P.

    2000-11-01

    The central problem in the determination of protein structures form x-ray diffraction dada (x-ray crystallography) corresponds to a phase retrieval problem with undersampled amplitude data. Algorithms for this problem that have an increased radius of convergence have the potential for reducing the amount of experimental work, and cost, involved in determining protein structures. We describe such an algorithm. Application of the algorithm to a simulated crystallographic problem shows that it converges to the correct solution, with no initial phase information, where currently used algorithms fail. The results lend support to the possibility of ab initio phasing in protein crystallography.

  12. Molecular associations from ab initio pair potentials

    NASA Astrophysics Data System (ADS)

    Iglesias, E.; Sordo, T. L.; Sordo, J. A.

    1991-12-01

    A method of building up stable molecular associations by using pair potentials from ab initio calculations is presented. The Matsuoka-Clementi-Yoshimine potential has been chosen to emulate the water-water interactions while 1-6-12 potentials are used to compute both solute-solvent and solute-solute interactions. Parameters for neutral-amino-acid-water and neutral- amino-acid-neutral-amino-acid interactions are provided by the program. Supermolecules are constructed by minimization of the interaction energy of the molecules involved. Both steepest-decent and Fletcher-Powell algorithms are available to carry out such a minimization.

  13. An improved choice of oscillator basis for banana shaped nuclides

    SciTech Connect

    Chasman, R.R.

    1994-03-01

    The question of the appropriate choice of oscillator basis functions for studying exotic nuclear shapes is raised. Difficulties with the conventional choice of oscillator basis states are noted for shapes having a large banana component. A prescription for an improved oscillator basis to study these shapes is given. It can be applied in a more general context. New calculations with this improved basis are presented for the banana deformation mode. The change of basis gives results that improve the prospects of finding states in the banana minimum for many isotopes of Tl, Pb and Bi.

  14. Ab initio calculation of valley splitting in monolayer δ-doped phosphorus in silicon

    PubMed Central

    2013-01-01

    The differences in energy between electronic bands due to valley splitting are of paramount importance in interpreting transport spectroscopy experiments on state-of-the-art quantum devices defined by scanning tunnelling microscope lithography. Using vasp, we develop a plane-wave density functional theory description of systems which is size limited due to computational tractability. Nonetheless, we provide valuable data for the benchmarking of empirical modelling techniques more capable of extending this discussion to confined disordered systems or actual devices. We then develop a less resource-intensive alternative via localised basis functions in siesta, retaining the physics of the plane-wave description, and extend this model beyond the capability of plane-wave methods to determine the ab initio valley splitting of well-isolated δ-layers. In obtaining an agreement between plane-wave and localised methods, we show that valley splitting has been overestimated in previous ab initio calculations by more than 50%. PMID:23445785

  15. PPL2ab neurons restore sexual responses in aged Drosophila males through dopamine.

    PubMed

    Kuo, Shu-Yun; Wu, Chia-Lin; Hsieh, Min-Yen; Lin, Chen-Ta; Wen, Rong-Kun; Chen, Lien-Cheng; Chen, Yu-Hui; Yu, Yhu-Wei; Wang, Horng-Dar; Su, Yi-Ju; Lin, Chun-Ju; Yang, Cian-Yi; Guan, Hsien-Yu; Wang, Pei-Yu; Lan, Tsuo-Hung; Fu, Tsai-Feng

    2015-06-30

    Male sexual desire typically declines with ageing. However, our understanding of the neurobiological basis for this phenomenon is limited by our knowledge of the brain circuitry and neuronal pathways controlling male sexual desire. A number of studies across species suggest that dopamine (DA) affects sexual desire. Here we use genetic tools and behavioural assays to identify a novel subset of DA neurons that regulate age-associated male courtship activity in Drosophila. We find that increasing DA levels in a subset of cells in the PPL2ab neuronal cluster is necessary and sufficient for increased sustained courtship in both young and aged male flies. Our results indicate that preventing the age-related decline in DA levels in PPL2ab neurons alleviates diminished courtship behaviours in male Drosophila. These results may provide the foundation for deciphering the circuitry involved in sexual motivation in the male Drosophila brain.

  16. [Analysis on academic frame of A-B classic of acupuncture and moxibustion by Huang Fumi].

    PubMed

    Zhang, Jianbin

    2015-01-01

    The acupuncture-moxibustion academic frame system was firstly and systematically established in A-B Classic of Acupuncture and Moxibustion authored by HUANG Fu-mi, which explained the knowledge and logical relationship among different parts of acupuncture-moxibustion. The academic frame consisted of acupuncture-moxibustion basis and clinical application. In the basic theory, zang-fu, qi-blood, meridians, acupoint, pulse diagnosis, acupuncture manipulation, etiology and pathogenesis, etc. were included; in the clinical application, various kinds of clinical diseases and their acupuncture treatment were included. The academic frame established by A-B Classic of Acupuncture and Moxibustion is broader than the modern academic frame of acupuncture-moxibustion, in which the attribution and location of four-seas theory has certain differences from modern acupuncture-moxibustion theory.

  17. Ab Initio No-Core Shell Model Calculations Using Realistic Two- and Three-Body Interactions

    SciTech Connect

    Navratil, P; Ormand, W E; Forssen, C; Caurier, E

    2004-11-30

    There has been significant progress in the ab initio approaches to the structure of light nuclei. One such method is the ab initio no-core shell model (NCSM). Starting from realistic two- and three-nucleon interactions this method can predict low-lying levels in p-shell nuclei. In this contribution, we present a brief overview of the NCSM with examples of recent applications. We highlight our study of the parity inversion in {sup 11}Be, for which calculations were performed in basis spaces up to 9{Dirac_h}{Omega} (dimensions reaching 7 x 10{sup 8}). We also present our latest results for the p-shell nuclei using the Tucson-Melbourne TM three-nucleon interaction with several proposed parameter sets.

  18. Structural properties of liquid N-methylacetamide via ab initio, path integral, and classical molecular dynamics

    NASA Astrophysics Data System (ADS)

    Whitfield, T. W.; Crain, J.; Martyna, G. J.

    2006-03-01

    In order to better understand the physical interactions that stabilize protein secondary structure, the neat liquid state of a peptidic fragment, N-methylacetamide (NMA), was studied using computer simulation. Three different descriptions of the molecular liquid were examined: an empirical force field treatment with classical nuclei, an empirical force field treatment with quantum mechanical nuclei, and an ab initio density functional theory (DFT) treatment. The DFT electronic structure was evaluated using the BLYP approximate functional and a plane wave basis set. The different physical effects probed by the three models, such as quantum dispersion, many-body polarization, and nontrivial charge distributions on the liquid properties, were compared. Much of the structural ordering in the liquid is characterized by hydrogen bonded chains of NMA molecules. Modest structural differences are present among the three models of liquid NMA. The average molecular dipole in the liquid under the ab initio treatment, however, is enhanced by 60% over the gas phase value.

  19. CMAC with General Basis Functions.

    PubMed

    Chun-Shin, Lin; Ching-Tsan, Chiang

    1996-10-01

    The cerebellar model articulation controller (CMAC) is often used in learning control. It can be viewed as a basis function network (BFN). The conventional CMAC uses local constant basis functions. A disadvantage is that its output is constant within each quantized state and the derivative information is not preserved. If the constant basis functions are replaced by non-constant differentiable basis functions, the derivative information will be able to be stored into the structure as well. In this paper, the generalized scheme that uses general basis functions is investigated. The conventional CMAC is a special case of the generalized technique. The mathematical foundation for the modified scheme is derived and the convergence of learning is proved. Simulations for the CMAC with Gaussian basis functions (GBFs) are performed to demonstrate the improvement of accuracy in modeling, and the capability in providing derivative information. Copyright 1996 Elsevier Science Ltd

  20. Single-layered chrysotile nanotubes: A quantum mechanical ab initio simulation

    NASA Astrophysics Data System (ADS)

    D'Arco, Philippe; Noel, Yves; Demichelis, Raffaella; Dovesi, Roberto

    2009-11-01

    Chrysotile single-layered nanotubes, obtained by wrapping the Mg3Si2O5(OH)4 lizardite monolayer along the (n,-n) hexagonal lattice vector, are simulated at the ab initio level by using an all electron 6-31G∗ basis set and the B3LYP functional for n varying from 14 to 24 (the nanotube radius R referred to the oxygen connecting the Mg and Si layers increases from 20 to 35 Å). Because of the full exploitation of the helical symmetry, recently implemented in the CRYSTAL code, the computational cost for the full self-consistent field (SCF) and gradient calculation increases only by a factor of 2 and 1.2, respectively, when passing from the lizardite monolayer [18 atoms and 236 AOs (atomic orbitals) in the unit cell] to the (24, -24) tube (864 atoms and 11 328 AOs). The total energy of the tubes is always larger than that of the lizardite monolayer; the difference ΔE decreases very rapidly with n; for the largest tube here considered (n =24) ΔE is as small as 2.7 kJ/mol per formula unit (f.u.); extrapolating to larger n values, at about R =50 Å, ΔE becomes smaller than 1 kJ mol f.u. Very large energy gains are observed for small n values during optimization after rolling, mainly due to the rotation of the SiO4 tetrahedra that are in the inner part of the cylinder ("normal rolling"); such a rigid rotation accounts for about 85% of the overall relaxation energy. "Inverse rolling" tubes (SiO4 on the external wall of the tube) are shown to be less stable than the corresponding "normal" tubes.

  1. Structural Basis for Antibody Recognition of Lipid A

    PubMed Central

    Haji-Ghassemi, Omid; Müller-Loennies, Sven; Rodriguez, Teresa; Brade, Lore; Kosma, Paul; Brade, Helmut; Evans, Stephen V.

    2015-01-01

    Septic shock is a leading cause of death, and it results from an inflammatory cascade triggered by the presence of microbial products in the blood. Certain LPS from Gram-negative bacteria are very potent inducers and are responsible for a high percentage of septic shock cases. Despite decades of research, mAbs specific for lipid A (the endotoxic principle of LPS) have not been successfully developed into a clinical treatment for sepsis. To understand the molecular basis for the observed inability to translate in vitro specificity for lipid A into clinical potential, the structures of antigen-binding fragments of mAbs S1–15 and A6 have been determined both in complex with lipid A carbohydrate backbone and in the unliganded form. The two antibodies have separate germ line origins that generate two markedly different combining-site pockets that are complementary both in shape and charge to the antigen. mAb A6 binds lipid A through both variable light and heavy chain residues, whereas S1–15 utilizes exclusively the variable heavy chain. Both antibodies bind lipid A such that the GlcN-O6 attachment point for the core oligosaccharide is buried in the combining site, which explains the lack of LPS recognition. Longstanding reports of polyspecificity of anti-lipid A antibodies toward single-stranded DNA combined with observed homology of S1–15 and A6 and the reports of several single-stranded DNA-specific mAbs prompted the determination of the structure of S1–15 in complex with single-stranded DNA fragments, which may provide clues about the genesis of autoimmune diseases such as systemic lupus erythematosus, thyroiditis, and rheumatic autoimmune diseases. PMID:26085093

  2. In search of the X2BO and X2BS (X = H, F) free radicals: ab initio studies of their spectroscopic signatures.

    PubMed

    Clouthier, Dennis J

    2014-12-28

    The F2BO free radical is a known, although little studied, species but similar X2BY (X = H, D, F; Y = O, S) molecules are largely unknown. High level ab initio methods have been used to predict the molecular structures, vibrational frequencies (in cm(-1)), and relative energies of the ground and first two excited electronic states of these free radicals, as an aid to their eventual spectroscopic identification. The chosen theoretical methods and basis sets were tested on F2BO and found to give good agreement with the known experimental quantities. In particular, complete basis set extrapolations of coupled-cluster single and doubles with perturbative triple excitations/aug-cc-pVXZ (X = 3, 4, 5) energies gave excellent electronic term values, due to small changes in geometry between states and the lack of significant multireference character in the wavefunctions. The radicals are found to have planar C2v geometries in the X̃(2)B2 ground state, the low-lying Ã(2)B1 first excited state, and the higher B̃(2)A1 state. Some of these radicals have very small ground state dipole moments hindering microwave measurements. Infrared studies in matrices or in the gas phase may be possible although the fundamentals of H2BO and H2BS are quite weak. The most promising method of identifying these species in the gas phase appears to be absorption or laser-induced fluorescence spectroscopy through the allowed B̃-X̃ transitions which occur in the visible-near UV region of the electromagnetic spectrum. The ab initio results have been used to calculate the Franck-Condon profiles of the absorption and emission spectra, and the rotational structure of the B̃-X̃0(0)(0) bands has been simulated. The calculated single vibronic level emission spectra provide a unique, readily recognizable fingerprint of each particular radical, facilitating the experimental identification of new X2BY species in the gas phase.

  3. Competition between H-bonded and stacked dimers of pyrimidine: IR and theoretical ab-initio study

    NASA Astrophysics Data System (ADS)

    Carthy, W. M.; Smets, J.; Plokhotnichenko, C. A. M.; Radchenko, E. D.; Sheina, G. G.; Adamowicz, L.; Stepanian, S. G.

    A combined matrix isolation Fourier transform infrared experimental and ab-initio theoretical approach has been used to examine the vibrational spectra of pyrimidine dimers. It was found that the presence of pyrimidine dimers resulted in experimentally observed frequencies shifted relative to those of the pyrimidine monomer. Four stable pyrimidine dimer conformers were found via ab-initio calculations. Two of these conformers namely a stacked geometry and a Hbonded geometry in which pyrimidine monomer dipole moments orient antiparallel, had the lowest but very similar energies. Ab-initio harmonic frequencies of these two dimers and their shifts relative to the monomer's values were determined. The effect of Basis Set Superposition error on these calculated frequency shifts was also investigated. The comparison of the abinitio predicted and experimentally observed frequency shifts and an accompanying potential energy distribution analysis suggest that the lowest-energy H-bonded configuration is responsible for the experimentally observed phenomena.

  4. Molecular Basis of Differential B-Pentamer Stability of Shiga Toxins 1 and 2

    SciTech Connect

    Conrady, Deborah G.; Flagler, Michael J.; Friedmann, David R.; Vander Wielen, Bradley D.; Kovall, Rhett A.; Weiss, Alison A.; Herr, Andrew B.

    2012-06-27

    Escherichia coli strain O157:H7 is a major cause of food poisoning that can result in severe diarrhea and, in some cases, renal failure. The pathogenesis of E. coli O157:H7 is in large part due to the production of Shiga toxin (Stx), an AB{sub 5} toxin that consists of a ribosomal RNA-cleaving A-subunit surrounded by a pentamer of receptor-binding B subunits. There are two major isoforms, Stx1 and Stx2, which differ dramatically in potency despite having 57% sequence identity. Animal studies and epidemiological studies show Stx2 is associated with more severe disease. Although the molecular basis of this difference is unknown, data suggest it is associated with the B-subunit. Mass spectrometry studies have suggested differential B-pentamer stability between Stx1 and Stx2. We have examined the relative stability of the B-pentamers in solution. Analytical ultracentrifugation using purified B-subunits demonstrates that Stx2B, the more deadly isoform, shows decreased pentamer stability compared to Stx1B (EC{sub 50} = 2.3 {micro}M vs. EC{sub 50} = 0.043 {micro}M for Stx1B). X-ray crystal structures of Stx1B and Stx2B identified a glutamine in Stx2 (versus leucine in Stx1) within the otherwise strongly hydrophobic interface between B-subunits. Interchanging these residues switches the stability phenotype of the B-pentamers of Stx1 and Stx2, as demonstrated by analytical ultracentrifugation and circular dichroism. These studies demonstrate a profound difference in stability of the B-pentamers in Stx1 and Stx2, illustrate the mechanistic basis for this differential stability, and provide novel reagents to test the basis for differential pathogenicity of these toxins.

  5. Kinetics of Electrocatalytic Reactions from First-Principles: A Critical Comparison with the Ab Initio Thermodynamics Approach.

    PubMed

    Exner, Kai S; Over, Herbert

    2017-05-16

    Multielectron processes in electrochemistry require the stabilization of reaction intermediates (RI) at the electrode surface after every elementary reaction step. Accordingly, the bond strengths of these intermediates are important for assessing the catalytic performance of an electrode material. Current understanding of microscopic processes in modern electrocatalysis research is largely driven by theory, mostly based on ab initio thermodynamics considerations, where stable reaction intermediates at the electrode surface are identified, while the actual free energy barriers (or activation barriers) are ignored. This simple approach is popular in electrochemistry in that the researcher has a simple tool at hand in successfully searching for promising electrode materials. The ab initio TD approach allows for a rough but fast screening of the parameter space with low computational cost. However, ab initio thermodynamics is also frequently employed (often, even based on a single binding energy only) to comprehend on the activity and on the mechanism of an electrochemical reaction. The basic idea is that the activation barrier of an endergonic reaction step consists of a thermodynamic part and an additional kinetically determined barrier. Assuming that the activation barrier scales with thermodynamics (so-called Brønsted-Polanyi-Evans (BEP) relation) and the kinetic part of the barrier is small, ab initio thermodynamics may provide molecular insights into the electrochemical reaction kinetics. However, for many electrocatalytic reactions, these tacit assumptions are violated so that ab initio thermodynamics will lead to contradictions with both experimental data and ab initio kinetics. In this Account, we will discuss several electrochemical key reactions, including chlorine evolution (CER), oxygen evolution reaction (OER), and oxygen reduction (ORR), where ab initio kinetics data are available in order to critically compare the results with those derived from a

  6. Molecular Characterization of the Cytidine Monophosphate-N-Acetylneuraminic Acid Hydroxylase (CMAH) Gene Associated with the Feline AB Blood Group System.

    PubMed

    Omi, Toshinori; Nakazawa, Shota; Udagawa, Chihiro; Tada, Naomi; Ochiai, Kazuhiko; Chong, Yong Hwa; Kato, Yuiko; Mitsui, Hiroko; Gin, Azusa; Oda, Hitomi; Azakami, Daigo; Tamura, Kyoichi; Sako, Toshinori; Inagaki, Takeshi; Sakamoto, Atsushi; Tsutsui, Toshihiko; Bonkobara, Makoto; Tsuchida, Shuichi; Ikemoto, Shigenori

    2016-01-01

    Cat's AB blood group system (blood types A, B, and AB) is of major importance in feline transfusion medicine. Type A and type B antigens are Neu5Gc and Neu5Ac, respectively, and the enzyme CMAH participating in the synthesis of Neu5Gc from Neu5Ac is associated with this cat blood group system. Rare type AB erythrocytes express both Neu5Gc and Neu5Ac. Cat serum contains naturally occurring antibodies against antigens occurring in the other blood types. To understand the molecular genetic basis of this blood group system, we investigated the distribution of AB blood group antigens, CMAH gene structure, mutation, diplotypes, and haplotypes of the cat CMAH genes. Blood-typing revealed that 734 of the cats analyzed type A (95.1%), 38 cats were type B (4.9%), and none were type AB. A family of three Ragdoll cats including two type AB cats and one type A was also used in this study. CMAH sequence analyses showed that the CMAH protein was generated from two mRNA isoforms differing in exon 1. Analyses of the nucleotide sequences of the 16 exons including the coding region of CMAH examined in the 34 type B cats and in the family of type AB cats carried the CMAH variants, and revealed multiple novel diplotypes comprising several polymorphisms. Haplotype inference, which was focused on non-synonymous SNPs revealed that eight haplotypes carried one to four mutations in CMAH, and all cats with type B (n = 34) and AB (n = 2) blood carried two alleles derived from the mutated CMAH gene. These results suggested that double haploids selected from multiple recessive alleles in the cat CMAH loci were highly associated with the expression of the Neu5Ac on erythrocyte membrane in types B and AB of the feline AB blood group system.

  7. Molecular Characterization of the Cytidine Monophosphate-N-Acetylneuraminic Acid Hydroxylase (CMAH) Gene Associated with the Feline AB Blood Group System

    PubMed Central

    Tada, Naomi; Ochiai, Kazuhiko; Chong, Yong Hwa; Kato, Yuiko; Mitsui, Hiroko; Gin, Azusa; Oda, Hitomi; Azakami, Daigo; Tamura, Kyoichi; Sako, Toshinori; Inagaki, Takeshi; Sakamoto, Atsushi; Tsutsui, Toshihiko; Bonkobara, Makoto; Tsuchida, Shuichi; Ikemoto, Shigenori

    2016-01-01

    Cat’s AB blood group system (blood types A, B, and AB) is of major importance in feline transfusion medicine. Type A and type B antigens are Neu5Gc and Neu5Ac, respectively, and the enzyme CMAH participating in the synthesis of Neu5Gc from Neu5Ac is associated with this cat blood group system. Rare type AB erythrocytes express both Neu5Gc and Neu5Ac. Cat serum contains naturally occurring antibodies against antigens occurring in the other blood types. To understand the molecular genetic basis of this blood group system, we investigated the distribution of AB blood group antigens, CMAH gene structure, mutation, diplotypes, and haplotypes of the cat CMAH genes. Blood-typing revealed that 734 of the cats analyzed type A (95.1%), 38 cats were type B (4.9%), and none were type AB. A family of three Ragdoll cats including two type AB cats and one type A was also used in this study. CMAH sequence analyses showed that the CMAH protein was generated from two mRNA isoforms differing in exon 1. Analyses of the nucleotide sequences of the 16 exons including the coding region of CMAH examined in the 34 type B cats and in the family of type AB cats carried the CMAH variants, and revealed multiple novel diplotypes comprising several polymorphisms. Haplotype inference, which was focused on non-synonymous SNPs revealed that eight haplotypes carried one to four mutations in CMAH, and all cats with type B (n = 34) and AB (n = 2) blood carried two alleles derived from the mutated CMAH gene. These results suggested that double haploids selected from multiple recessive alleles in the cat CMAH loci were highly associated with the expression of the Neu5Ac on erythrocyte membrane in types B and AB of the feline AB blood group system. PMID:27755584

  8. Ab initio calculation of the potential bubble nucleus 34Si

    NASA Astrophysics Data System (ADS)

    Duguet, T.; Somà, V.; Lecluse, S.; Barbieri, C.; Navrátil, P.

    2017-03-01

    Background: The possibility that an unconventional depletion (referred to as a "bubble") occurs in the center of the charge density distribution of certain nuclei due to a purely quantum mechanical effect has attracted theoretical and experimental attention in recent years. Based on a mean-field rationale, a correlation between the occurrence of such a semibubble and an anomalously weak splitting between low angular-momentum spin-orbit partners has been further conjectured. Energy density functional and valence-space shell model calculations have been performed to identify and characterize the best candidates, among which 34Si appears as a particularly interesting case. While the experimental determination of the charge density distribution of the unstable 34Si is currently out of reach, (d ,p ) experiments on this nucleus have been performed recently to test the correlation between the presence of a bubble and an anomalously weak 1 /2--3 /2- splitting in the spectrum of 35Si as compared to 37S. Purpose: We study the potential bubble structure of 34Si on the basis of the state-of-the-art ab initio self-consistent Green's function many-body method. Methods: We perform the first ab initio calculations of 34Si and 36S. In addition to binding energies, the first observables of interest are the charge density distribution and the charge root-mean-square radius for which experimental data exist in 36S. The next observable of interest is the low-lying spectroscopy of 35Si and 37S obtained from (d ,p ) experiments along with the spectroscopy of 33Al and 35P obtained from knock-out experiments. The interpretation in terms of the evolution of the underlying shell structure is also provided. The study is repeated using several chiral effective field theory Hamiltonians as a way to test the robustness of the results with respect to input internucleon interactions. The convergence of the results with respect to the truncation of the many-body expansion, i.e., with respect to

  9. Longitudinal wheel slip during ABS braking

    NASA Astrophysics Data System (ADS)

    Hartikainen, Lassi; Petry, Frank; Westermann, Stephan

    2015-02-01

    Anti-lock braking system (ABS) braking tests with two subcompact passenger cars were performed on dry and wet asphalt, as well as on snow and ice surfaces. The operating conditions of the tyres in terms of wheel slip were evaluated using histograms of the wheel slip data. The results showed different average slip levels for different road surfaces. It was also found that changes in the tyre tread stiffness affected the slip operating range through a modification of the slip value at which the maximum longitudinal force is achieved. Variation of the tyre footprint length through modifications in the inflation pressure affected the slip operating range as well. Differences in the slip distribution between vehicles with different brake controllers were also observed. The changes in slip operating range in turn modified the relative local sliding speeds between the tyre and the road. The results highlight the importance of the ABS controller's ability to adapt to changing slip-force characteristics of tyres and provide estimates of the magnitude of the effects of different tyre and road operating conditions.

  10. Ab initio non-relativistic spin dynamics

    SciTech Connect

    Ding, Feizhi; Goings, Joshua J.; Li, Xiaosong; Frisch, Michael J.

    2014-12-07

    Many magnetic materials do not conform to the (anti-)ferromagnetic paradigm where all electronic spins are aligned to a global magnetization axis. Unfortunately, most electronic structure methods cannot describe such materials with noncollinear electron spin on account of formally requiring spin alignment. To overcome this limitation, it is necessary to generalize electronic structure methods and allow each electron spin to rotate freely. Here, we report the development of an ab initio time-dependent non-relativistic two-component spinor (TDN2C), which is a generalization of the time-dependent Hartree-Fock equations. Propagating the TDN2C equations in the time domain allows for the first-principles description of spin dynamics. A numerical tool based on the Hirshfeld partitioning scheme is developed to analyze the time-dependent spin magnetization. In this work, we also introduce the coupling between electron spin and a homogenous magnetic field into the TDN2C framework to simulate the response of the electronic spin degrees of freedom to an external magnetic field. This is illustrated for several model systems, including the spin-frustrated Li{sub 3} molecule. Exact agreement is found between numerical and analytic results for Larmor precession of hydrogen and lithium atoms. The TDN2C method paves the way for the ab initio description of molecular spin transport and spintronics in the time domain.

  11. Quantum phases of AB 2 fermionic chains

    NASA Astrophysics Data System (ADS)

    Murcia-Correa, L. S.; Franco, R.; Silva-Valencia, J.

    2016-02-01

    A fermionic chain is a one-dimensional system with fermions that interact locally and can jump between sites in the lattice, in particular an AB n chain type, where A and B are sites that exhibit a difference in energy level of Δ and site B is repeated n-times, such that the unit cell has n +1 sites. A limit case of this model, called the ionic Hubbard model (n = 1), has been widely studied due to its interesting physics and applications. In this paper, we study the ground state of an AB 2 chain, which describes the material R 4[Pt 2(P 2O5H2)4X] · nH 2 O. Specifically, we consider a filling with two electrons per unit cell, and using the density matrix renormalization group method we found that the system exhibits the band insulator and Mott correlated insulator phases, as well as an intermediate phase between them. For couplings of Δ = 2,10 and 20, we estimate the critical points that separate these phases through the structure factor and the energy gap in the sector of charge and spin, finding that the position of the critical point rises as a function of Δ.

  12. Ab initio based polarizable force field parametrization

    NASA Astrophysics Data System (ADS)

    Masia, Marco

    2008-05-01

    Experimental and simulation studies of anion-water systems have pointed out the importance of molecular polarization for many phenomena ranging from hydrogen-bond dynamics to water interfaces structure. The study of such systems at molecular level is usually made with classical molecular dynamics simulations. Structural and dynamical features are deeply influenced by molecular and ionic polarizability, which parametrization in classical force field has been an object of long-standing efforts. Although when classical models are compared to ab initio calculations at condensed phase, it is found that the water dipole moments are underestimated by ˜30%, while the anion shows an overpolarization at short distances. A model for chloride-water polarizable interaction is parametrized here, making use of Car-Parrinello simulations at condensed phase. The results hint to an innovative approach in polarizable force fields development, based on ab initio simulations, which do not suffer for the mentioned drawbacks. The method is general and can be applied to the modeling of different systems ranging from biomolecular to solid state simulations.

  13. Antibiotic stewardship through the EU project "ABS International".

    PubMed

    Allerberger, Franz; Frank, Annegret; Gareis, Roland

    2008-01-01

    The increasing problem of antimicrobial resistance requires implementation of antibiotic stewardship (ABS) programs. The project "ABS International--implementing antibiotic strategies for appropriate use of antibiotics in hospitals in member states of the European Union" was started in September 2006 in Austria, Belgium, the Czech Republic, Germany, Hungary, Italy, Poland, Slovenia and Slovakia. A training program for national ABS trainers was prepared and standard templates for ABS tools (antibiotic list, guides for antibiotic treatment and surgical prophylaxis, antibiotic-related organization) and valid process measures, as well as quality indicators for antibiotic use were developed. Specific ABS tools are being implemented in up to five healthcare facilities in each country. Although ABS International clearly focuses on healthcare institutions, future antimicrobial stewardship programs must also cover public education and antibiotic prescribing in primary care.

  14. Ab-Initio Molecular Dynamics Simulation of Graphene Sheet

    NASA Astrophysics Data System (ADS)

    Kolev, S.; Balchev, I.; Cvetkov, K.; Tinchev, S.; Milenov, T.

    2017-01-01

    The study of graphene is important because it is a promising material for a variety of applications in the electronic industry. In the present work, the properties of а 2D periodic graphene sheet are studied with the use of ab initio molecular dynamics. DFT in the generalized gradient approximation is used in order to carry out the dynamical simulations. The PBE functional and DZVP-MOLOPT basis set are implemented in the CP2K/Quickstep package. A periodic box, consisting of 288 carbon atoms is chosen for the simulations. After geometry optimization it has dimensions 2964 x 2964 x 1500 pm and form angles of 90, 90, 60 degrees. The dynamical simulation is run for 1 ps in the NPT ensemble, at temperature T = 298.15 K. The radial distribution function shows a first peak at 142 pm, marking the bond length between carbon atoms. The density of states for the periodic systems is simulated as occupied orbitals represent the valence band and unoccupied ones the conduction band. The calculated bandgap, as expected is close to 0 eV.

  15. Soyasaponin Ab ameliorates colitis by inhibiting the binding of lipopolysaccharide (LPS) to Toll-like receptor (TLR)4 on macrophages.

    PubMed

    Lee, In-Ah; Park, Young-Jun; Joh, Eun-Ha; Kim, Dong-Hyun

    2011-12-28

    Many clinical studies have shown that daily intake of soybean [ Glycine max (L.) Merr., Fabacease] or its foods may reduce the risk of osteoporosis, heart attack, hyperlipidemia, coronary heart disease, cardiovascular and chronic renal diseases, and cancers, including prostate, colon, and breast cancers. Of the soy constituents, soyasaponins exhibit anti-aging, antioxidant, apoptotic, and anti-inflammatory effects. However, the anti-inflammatory effect of soyasaponin Ab has not been thoroughly studied. Therefore, we investigated its anti-inflammatory effects in 2,4,6-trinitrobenzene sulfonic acid (TNBS)-induced colitic mice and lipopolysaccharide (LPS)-stimulated peritoneal macrophages. Soyasaponin Ab inhibited colon shortening, myeloperoxidase activity, the expression of cyclooxygenase-2 (COX-2) and inducible nitric oxide synthase (iNOS), and activation of the transcription factor nuclear factor-κB (NF-κB). Soyasaponin Ab (1, 2, 5, and 10 μM) inhibited the production of NO (IC(50) = 1.6 ± 0.1 μM) and prostaglandin E(2) (IC(50) = 2.0 ± 0.1 ng/mL), the expression of tumor necrosis factor (TNF)-α (IC(50) = 1.3 ± 0.1 ng/mL), interleukin (IL)-1β (IC(50) = 1.5 ± 0.1 pg/mL), and toll-like receptor (TLR)4, and the phosphorylation of interleukin-1 receptor-associated kinase (IRAK)-1 in LPS-stimulated peritoneal macrophages. Soyasaponin Ab weakly inhibited the phosphorylation of ERK, JNK, and p38. Soyasaponin Ab significantly reduced the binding of Alexa-Fluor-594-conjugated LPS to peritoneal macrophages. Soyasaponin Ab did not affect TLR4 expression or LPS-induced NF-κB activation in TLR4 siRNA-treated peritoneal macrophages (knockdown efficiency of TLR4 > 94%). On the basis of these findings, soyasaponin Ab may ameliorate colitis by inhibiting the binding of LPS to TLR4 on macrophages.

  16. Surface Observation Climatic Summaries (SOCS) for Yokota AB, Japan

    DTIC Science & Technology

    1988-11-01

    0*tSAFETAC/DS-88/202A OIC FILE COPY 0 00 N1 SURFACE OBSERVATION CLIMATIC SUMMARIES 0 FOR YOKOTA AB, JAPAN h F~ E TAC Prepared by 01-A, USAFETAC...62225-5438 REVIEW AND APPROVAL STATEMENT USAFETAC/DS-88/202, SURFACE OBSERVATION CLIMATIC SUMMARIES FOR YOKOTA AB JAPAN , NOVEMBER 1988, HAS BEEN REVIEWED...AB JAPAN 7. PERFORMING ORGANIZATION NAME AND ADDRESS: OPERATING LOCATION A, USAFETAC, FEDERAL BUILDING, ASHEVILLE, NC 28801-2723 8. PERFORMING

  17. Ab initio calculations of ten carbon/nitrogen cubanoids

    SciTech Connect

    Engelke, R. )

    1993-04-07

    The results of a uniform set of ab initio quantum-chemical calculations for 10 carbon/nitrogen cubanoids are presented. There are 22 possible C/N cubanoids with formulas (CH)[sub 8[minus]n]N[sub n], where 0 [le] n [le] 8. We give results for one cubanoid for each value of n; for n = 4 both the T[sub d] and C[sub 4v] structures are discussed. The geometries were optimized on the RHF/6-31G*//RHF/6-31G* energy hypersurfaces, and the stationary points so obtained were characterized by vibrational analyses. The effect of electron correlation on the energies of these structures is examined via MP2/6-31G*//RHF/6-31G* theory. All 10 structures are predicted to be stable molecules, and the vibrational analyses indicate that their geometries are well-defined by the RHF/6-31G*//energy hypersurfaces. Heats of formation are predicted via appropriate isodesmic reactions. All the structures are found to have large positive [delta]H[sub f]'s. Perhaps the most interesting result obtained is that the high-energy content of the nitrogen-rich cubanoids is not primarily due to bond strain, but rather to the high-energy content of the NN single bond. Comparisons of the ab initio [delta]H[sub f] values with semiempirical AM1, PM3, and MNDO predictions are made. If they can be synthesized and have reasonable kinetic stability, the C/N cubanoids containing four or more nitrogen atoms are likely to be important energetic materials. A brief discussion is given of the potential of these materials as propellants and explosives. 22 refs., 5 figs., 4 tabs.

  18. Molecular basis for erythrocyte shape

    NASA Astrophysics Data System (ADS)

    Elgsaeter, A.; Mikkelsen, A.

    1991-05-01

    The isolated plasma membrane of the human erythrocytes displays the same shape and shape transformations as the intact cells. It is therefore generally believed that the plasma membrane plays a dominant role in determining erythrocyte shape. The plasma membrane consists of a fluid lipid bilayer to the surface of which is attached a protein skeleton. The two halves of the lipid bilayer and the protein network (gel) are tighly coupled, but at the same time elastically deformable and can slide relative to one another in the plane of the cell membrane. The equilibrium shape of such a structure is determined by the combined mechano-chemical properties of the individual layers and equals the cell shape that for the given cell volume corresponds to the lowest total elastic free energy. The elastic free energy of the lipid bilayer is mainly associated with bending and change in surface area for each of the two lipid monolayer. For the protein membrane skeleton the elastic free energy mainly equals the sum of the local contributions due to shear deformation and surface change. When the mechano-chemical properties of each of the layers are known, calculation of the equilibrium shape is in principle just an exercise in standard continuum mechanics. The elastic properties of pure lipid monolayers have long been qualitatively fairly well known. The changes in lipid bilayer elastic properties resulting from the presence of integral membrane proteins have just recently become better understood. The detailed molecular basis for the elastic properties of the protein membrane skeleton remains unresolved despite many attempts to elucidate the problem. It is widely agreed that the elastic properties are largely accounted for by the highly elongated spectrin molecules, but whether the membrane skelton elasticity is mainly of entropic or entalphic origin is still unsettled.

  19. A novel gene amplification causes upregulation of the PatAB ABC transporter and fluoroquinolone resistance in Streptococcus pneumoniae.

    PubMed

    Baylay, Alison J; Ivens, Alasdair; Piddock, Laura J V

    2015-01-01

    Overexpression of the ABC transporter genes patA and patB confers efflux-mediated fluoroquinolone resistance in Streptococcus pneumoniae and is also linked to pneumococcal stress responses. Although upregulation of patAB has been observed in many laboratory mutants and clinical isolates, the regulatory mechanisms controlling expression of these genes are unknown. In this study, we aimed to identify the cause of high-level constitutive overexpression of patAB in M184, a multidrug-resistant mutant of S. pneumoniae R6. Using a whole-genome transformation and sequencing approach, we identified a novel duplication of a 9.2-kb region of the M184 genome which included the patAB genes. This duplication did not affect growth and was semistable with a low segregation rate. The expression levels of patAB in M184 were much higher than those that could be fully explained by doubling of the gene dosage alone, and inactivation of the first copy of patA had no effect on multidrug resistance. Using a green fluorescent protein reporter system, increased patAB expression was ascribed to transcriptional read-through from a tRNA gene upstream of the second copy of patAB. This is the first report of a large genomic duplication causing antibiotic resistance in S. pneumoniae and also of a genomic duplication causing antibiotic resistance by a promoter switching mechanism.

  20. Evaluation of a fully automated treponemal test and comparison with conventional VDRL and FTA-ABS tests.

    PubMed

    Park, Yongjung; Park, Younhee; Joo, Shin Young; Park, Myoung Hee; Kim, Hyon-Suk

    2011-11-01

    We evaluated analytic performances of an automated treponemal test and compared this test with the Venereal Disease Research Laboratory test (VDRL) and fluorescent treponemal antibody absorption test (FTA-ABS). Precision performance of the Architect Syphilis TP assay (TP; Abbott Japan, Tokyo, Japan) was assessed, and 150 serum samples were assayed with the TP before and after heat inactivation to estimate the effect of heat inactivation. A total of 616 specimens were tested with the FTA-ABS and TP, and 400 were examined with the VDRL. The TP showed good precision performance with total imprecision of less than a 10% coefficient of variation. An excellent linear relationship between results before and after heat inactivation was observed (R(2) = 0.9961). The FTA-ABS and TP agreed well with a κ coefficient of 0.981. The concordance rate between the FTA-ABS and TP was the highest (99.0%), followed by the rates between FTA-ABS and VDRL (85.0%) and between TP and VDRL (83.8%). The automated TP assay may be adequate for screening for syphilis in a large volume of samples and can be an alternative to FTA-ABS.

  1. Bacillus thuringiensis Cry34Ab1/Cry35Ab1 Interactions with Western Corn Rootworm Midgut Membrane Binding Sites

    PubMed Central

    Li, Huarong; Olson, Monica; Lin, Gaofeng; Hey, Timothy; Tan, Sek Yee; Narva, Kenneth E.

    2013-01-01

    Background Bacillus thuringiensis (Bt) Cry34Ab1/Cry35Ab1 are binary insecticidal proteins that are co-expressed in transgenic corn hybrids for control of western corn rootworm, Diabrotica virgifera virgifera LeConte. Bt crystal (Cry) proteins with limited potential for field-relevant cross-resistance are used in combination, along with non-transgenic corn refuges, as a strategy to delay development of resistant rootworm populations. Differences in insect midgut membrane binding site interactions are one line of evidence that Bt protein mechanisms of action differ and that the probability of receptor-mediated cross-resistance is low. Methodology/Principal Findings Binding site interactions were investigated between Cry34Ab1/Cry35Ab1 and coleopteran active insecticidal proteins Cry3Aa, Cry6Aa, and Cry8Ba on western corn rootworm midgut brush border membrane vesicles (BBMV). Competitive binding of radio-labeled proteins to western corn rootworm BBMV was used as a measure of shared binding sites. Our work shows that 125I-Cry35Ab1 binds to rootworm BBMV, Cry34Ab1 enhances 125I-Cry35Ab1 specific binding, and that 125I-Cry35Ab1 with or without unlabeled Cry34Ab1 does not share binding sites with Cry3Aa, Cry6Aa, or Cry8Ba. Two primary lines of evidence presented here support the lack of shared binding sites between Cry34Ab1/Cry35Ab1 and the aforementioned proteins: 1) No competitive binding to rootworm BBMV was observed for competitor proteins when used in excess with 125I-Cry35Ab1 alone or combined with unlabeled Cry34Ab1, and 2) No competitive binding to rootworm BBMV was observed for unlabeled Cry34Ab1 and Cry35Ab1, or a combination of the two, when used in excess with 125I-Cry3Aa, or 125I-Cry8Ba. Conclusions/Significance Combining two or more insecticidal proteins active against the same target pest is one tactic to delay the onset of resistance to either protein. We conclude that Cry34Ab1/Cry35Ab1 are compatible with Cry3Aa, Cry6Aa, or Cry8Ba for deployment as insect

  2. Surface Observation Climatic Summaries (SOCS) for Kadena AB, Japan.

    DTIC Science & Technology

    Ceiling; Cloud cover; Snow depth; Humidity; Barometric pressure; Atmospheric precipitation; Snow; Atmospheric temperature; Visibility; Wind; Kadena AB Japan; Military facilities; Computer printouts. (EDC)

  3. Ab initio no-core configuration interaction calculations of electromagnetic observables for p-shell nuclei using natural orbitals

    NASA Astrophysics Data System (ADS)

    Constantinou, Chrysovalantis; Caprio, Mark A.; Vary, James P.; Maris, Pieter

    2016-09-01

    The goal of ab initio nuclear theory is to provide quantitative predictions of nuclear observables, by solving the many-body problem starting from the internucleon interaction. The solution of the many-body problem involves large spaces with dimensions that grow fast with the number of nucleons and single-particle states included in the space. Convergence of nuclear observables in the employed space using an adequate set of single-particle orbitals is essential for making quantitative predictions. Long-range nuclear observables, such as the matrix elements of the E 2 operator, converge slowly when conventional oscillator single-particle orbitals are used for no-core configuration interaction (NCCI) calculations. Natural orbitals, obtained by diagonalizing the one-body density matrix from an initial NCCI calculation in the harmonic oscillator basis, provide accelerated convergence since they are adapted to the properties of the many-body wave function of the nucleus under study. We explore the convergence of electromagnetic observables of p-shell nuclei obtained using natural orbitals for NCCI calculations. Supported by the US DOE under Grants DE-FG02-95ER-40934, DESC0008485 (SciDAC/NUCLEI), and DE-FG02-87ER40371. Computational resources provided by NERSC (supported by US DOE Contract DE-AC02-05CH11231) and the Notre Dame Center for Research Computing.

  4. Ab initio Potential-Energy Surfaces and Electron-Spin-Exchange Cross Sections for H-O2 Interactions

    NASA Technical Reports Server (NTRS)

    Stallcop, James R.; Partridge, Harry; Levin, Eugene

    1996-01-01

    Accurate quartet- and doublet-state potential-energy surfaces for the interaction of a hydrogen atom and an oxygen molecule in their ground states have been determined from an ab initio calculation using large-basis sets and the internally contracted multireference configuration interaction method. These potential surfaces have been used to calculate the H-O2 electron-spin-exchange cross section; the square root of the cross section (in a(sub 0)), not taking into account inelastic effects, can be obtained approximately from the expressions 2.390E(sup -1/6) and 5.266-0.708 log10(E) at low and high collision energies E (in E(sub h)), respectively. These functional forms, as well as the oscillatory structure of the cross section found at high energies, are expected from the nature of the interaction energy. The mean cross section (the cross section averaged over a Maxwellian velocity distribution) agrees reasonably well with the results of measurements.

  5. Quantum calculations of vibrational energies of H3O2(-) and H5O2(+) with new ab initio potentials

    NASA Astrophysics Data System (ADS)

    Huang, Xinchuan; Braams, Bastiaan J.; Carter, Stuart; Bowman, Joel M.

    2004-03-01

    We have performed quantum mechanical studies of the vibrations of H3O2(-) and H5O2(+) in full dimensionality and with sufficient accuracy to resolve important features of the measured spectra. The computational procedure starts with extensive electronic structure calculations (several 10K configurations) at the CCSD(T) level of theory with augmented VTZ basis set using MOLPRO 2002. Then a global fit to the potential energy surface is constructed, based on a functional form that respects the spatial and permutational symmetries of the system. This PES fit is employed in a "Reaction Path Hamiltonian" MULTIMODE [1] calculation to obtain the vibrational spectrum. We provide comparisons with experimental data [2]. [1] MULTIMODE: A code to calculate rovibrational energies of polyatomic molecules, J. M. Bowman, S. Carter, and X.-C. Huang, Int. Rev. Phys. Chem. 22, 533 (2003). [2] Quantum calculations of vibrational energies of H3O2(-) with a new ab initio potential reveal large tunneling splittings. Manuscript in preparation, Dec 2003.

  6. Ab Initio Quantum Mechanical Description of Noncovalent Interactions at Its Limits: Approaching the Experimental Dissociation Energy of the HF Dimer.

    PubMed

    Řezáč, Jan; Hobza, Pavel

    2014-08-12

    Hydrogen fluoride dimer is a perfect model system for studying hydrogen bonding. Its size makes it possible to apply the most advanced theoretical methods available, yet it is a full-featured complex of molecules with nontrivial electronic structure and dynamic properties. Moreover, the dissociation energy of the HF dimer has been measured experimentally with an unparalleled accuracy of ±1 cm(-1)(Bohac et al. J. Chem. Phys. 1992, 9, 6681). In this work, we attempt to reproduce it by purely ab initio means, using advanced quantum-mechanical computational methods free of any empiricism. The purpose of this study is to demonstrate the capabilities of today's computational chemistry and to point out its limitations by identifying the contributions that introduce the largest uncertainty into the result. The dissociation energy is calculated using a composite scheme including large basis set CCSD(T) calculations, contributions of higher excitations up to CCSDTQ, relativistic and diagonal Born-Oppenheimer corrections and anharmonic vibrational calculations. The error of the calculated dissociation energy is 0.07 kcal/mol (25 cm(-1), 2.5%) when compared to the experiment. The major part of this error can be attributed to the inaccuracy of the calculations of the zero-point vibrational energy.

  7. The fate and transport of the Cry1Ab protein in an agricultural field and laboratory aquatic microcosms.

    PubMed

    Strain, Katherine E; Lydy, Michael J

    2015-08-01

    Genetically engineered crops expressing insecticidal crystalline proteins derived from Bacillus thuringiensis (Bt), were commercialized almost two decades ago as a means to manage agricultural pests. The Bt proteins are highly specific and only lethal upon ingestion, limiting the scope of toxicity to target insects. However, concern of exposure to non-target organisms and negative public perceptions regarding Bt crops has caused controversy surrounding their use. The objective of this research was to monitor the fate and transport of a Bt protein, Cry1Ab, in a large-scale agricultural field containing maize expressing the Cry1Ab protein and a non-Bt near isoline, and in aquatic microcosms. The highest environmental concentrations of the Cry1Ab protein were found in runoff water and sediment, up to 130ngL(-1) and 143ngg(-1) dry weight, respectively, with the Cry1Ab protein detected in both Bt and non-Bt maize fields. As surface runoff and residual crop debris can transport Bt proteins to waterways adjacent to agricultural fields, a series of laboratory experiments were conducted to determine the potential fate of the Cry1Ab protein under different conditions. The results showed that sediment type and temperature can influence the degradation of the Cry1Ab protein in an aquatic system and that the Cry1Ab protein can persist for up to two months. Although Cry1Ab protein concentrations measured in the field soil indicate little exposure to terrestrial organisms, the consistent input of Bt-contaminated runoff and crop debris into agricultural waterways is relevant to understanding potential consequences to aquatic species. Copyright © 2015 Elsevier Ltd. All rights reserved.

  8. Gangliosides, Ab1 and Ab2 antibodies II. Light versus heavy chain: An idiotype-anti-idiotype case study.

    PubMed

    López-Requena, Alejandro; Rodríguez, Mabel; de Acosta, Cristina Mateo; Moreno, Ernesto; Puchades, Yaquelin; González, Majela; Talavera, Ariel; Valle, Aisel; Hernández, Tays; Vázquez, Ana María; Pérez, Rolando

    2007-02-01

    The antibody heavy chain is generally more important than the light chain for the interaction with the antigen, although many reports demonstrate the influence of the light chain in the antibody binding properties. The heavy chains of anti-N-glycolyl-ganglioside P3 mAb and anti-idiotypic 1E10 mAb display complementary charged residues in their H-CDRs, particularly in H-CDR3. A basic residue in P3 mAb H-CDR1 was shown to be crucial for the interaction with the antigen and 1E10 mAb. The immunogenetic features of three other P3 mAb anti-idiotypic mAbs are now analyzed. One of them bears the same heavy chain as 1E10 mAb and a different light chain, but differs in its binding to P3 mAb mutants where H-CDR basic residues were replaced and in the binding to 1E10-specific phagotopes. Chimeric hybrid antibodies with P3 and 1E10 mAb heavy chains and unrelated light chains were obtained to further determine the importance of heavy chains in P3 and 1E10 mAb binding properties. One of the P3 heavy chain hybrid antibodies retained the specificity of P3 mAb with slight affinity differences. The heavy chains appear to play the main role in these mAb interactions, with the light chains modulating the affinity to their ligands.

  9. Calculation of second virial coefficients using ab initio intermolecular pair potentials for F2-F2 and H2-F2 dimers

    NASA Astrophysics Data System (ADS)

    Van, Tat Pham; Deiters, Ulrich K.

    2017-03-01

    The ab initio intermolecular pair potentials of dimers F2-F2 and H2-F2 were calculated from all constructed orientations, using the level of theory CCSD(T) and basis sets aug-cc-pVmZ (m = 2, 3, 23). The complete basis set limit aug-cc-pV23Z was extrapolated by ab initio interaction energies at the level of theory CCSD(T) with two basis sets aug-cc-pVmZ (m = 2, 3). Then the quantum mechanical results were used for constructing two new 5-site potential functions by fitting ab initio energies of dimers F2-F2 and H2-F2. The correlation between ab initio and the fitted ab initio energies of 5-site pair potentials for dimers F2-F2 and H2-F2 is appeared by fitness values R2 in range 0.99749-0.99997. The fitted potentials were used in standard thermodynamic relations to obtain the second virial coefficients and the results were compared to experimental data.

  10. [Gene frequencies and heterozygosity of the AB0 and RH blood group alleles in the populations of two cities of the Donetsk region, Ukraine].

    PubMed

    Mukhin, V N; Chinakh, D G; Avdeev, A V; Kuleba, V V; Afanas'ev, M V

    2003-04-01

    The frequencies of the AB0 and RH blood group alleles and heterozygosity indices were determined for the populations of two large industrial cities of Gorlovka and Mariupol. In the population of Gorlovka the gene frequencies were as follows: AB0*0 = 0.576, AB0*A = 0.266, AB0*B = 0.158, and RH*D = 0.592, in Mariupol the frequencies were AB0*0 = 0.584, AB0*A = 0.265, AB0*B = 0.151, and RH*D = 0.604. In Gorlovka the heterozygosity indices in respect to the AB0 and RH alleles were 0.572 and 0.483, respectively; in Mariupol, 0.566 and 0.478, respectively. There were no statistically significant differences between the two populations in respect to the genetic markers analyzed. However, the heterozygosity values obtained were more similar to the corresponding estimates for some populations of Russia, than for the total population of the Ukraine.

  11. Discovering chemistry with an ab initio nanoreactor

    SciTech Connect

    Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S.; Martínez, Todd J.

    2014-11-02

    Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. Ultimately, these results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings.

  12. Ab Initio Calculation of the Hoyle State

    SciTech Connect

    Epelbaum, Evgeny; Krebs, Hermann; Lee, Dean; Meissner, Ulf-G.

    2011-05-13

    The Hoyle state plays a crucial role in the helium burning of stars heavier than our Sun and in the production of carbon and other elements necessary for life. This excited state of the carbon-12 nucleus was postulated by Hoyle as a necessary ingredient for the fusion of three alpha particles to produce carbon at stellar temperatures. Although the Hoyle state was seen experimentally more than a half century ago nuclear theorists have not yet uncovered the nature of this state from first principles. In this Letter we report the first ab initio calculation of the low-lying states of carbon-12 using supercomputer lattice simulations and a theoretical framework known as effective field theory. In addition to the ground state and excited spin-2 state, we find a resonance at -85(3) MeV with all of the properties of the Hoyle state and in agreement with the experimentally observed energy.

  13. Ab Initio Reactive Computer Aided Molecular Design.

    PubMed

    Martínez, Todd J

    2017-03-21

    Few would dispute that theoretical chemistry tools can now provide keen insights into chemical phenomena. Yet the holy grail of efficient and reliable prediction of complex reactivity has remained elusive. Fortunately, recent advances in electronic structure theory based on the concepts of both element- and rank-sparsity, coupled with the emergence of new highly parallel computer architectures, have led to a significant increase in the time and length scales which can be simulated using first principles molecular dynamics. This opens the possibility of new discovery-based approaches to chemical reactivity, such as the recently proposed ab initio nanoreactor. We argue that due to these and other recent advances, the holy grail of computational discovery for complex chemical reactivity is rapidly coming within our reach.

  14. An ab initio study of hydroxylated graphane.

    PubMed

    Buonocore, Francesco; Capasso, Andrea; Lisi, Nicola

    2017-09-14

    Graphene-based derivatives with covalent functionalization and well-defined stoichiometry are highly desirable in view of their application as functional surfaces. Here, we have evaluated by ab initio calculations the energy of formation and the phase diagram of hydroxylated graphane structures, i.e., fully functionalized graphene derivatives coordinated with -H and -OH groups. We compared these structures to different hydrogenated and non-hydrogenated graphene oxide derivatives, with high level of epoxide and hydroxyl groups functionalization. Based on our calculations, stable phases of hydroxylated graphane with low and high contents of hydrogen are demonstrated for high oxygen and hydrogen partial pressure, respectively. Stable phases of graphene oxide with a mixed carbon hybridization are also found. Notably, the synthesis of hydroxylated graphane has been recently reported in the literature.

  15. An ab initio study of hydroxylated graphane

    NASA Astrophysics Data System (ADS)

    Buonocore, Francesco; Capasso, Andrea; Lisi, Nicola

    2017-09-01

    Graphene-based derivatives with covalent functionalization and well-defined stoichiometry are highly desirable in view of their application as functional surfaces. Here, we have evaluated by ab initio calculations the energy of formation and the phase diagram of hydroxylated graphane structures, i.e., fully functionalized graphene derivatives coordinated with -H and -OH groups. We compared these structures to different hydrogenated and non-hydrogenated graphene oxide derivatives, with high level of epoxide and hydroxyl groups functionalization. Based on our calculations, stable phases of hydroxylated graphane with low and high contents of hydrogen are demonstrated for high oxygen and hydrogen partial pressure, respectively. Stable phases of graphene oxide with a mixed carbon hybridization are also found. Notably, the synthesis of hydroxylated graphane has been recently reported in the literature.

  16. Discovering chemistry with an ab initio nanoreactor

    DOE PAGES

    Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; ...

    2014-11-02

    Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis frommore » primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. Ultimately, these results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings.« less

  17. Ab Initio Modeling of Molecular Radiation

    NASA Technical Reports Server (NTRS)

    Jaffe, Richard; Schwenke, David

    2014-01-01

    Radiative emission from excited states of atoms and molecules can comprise a significant fraction of the total heat flux experienced by spacecraft during atmospheric entry at hypersonic speeds. For spacecraft with ablating heat shields, some of this radiative flux can be absorbed by molecular constituents in the boundary layer that are formed by the ablation process. Ab initio quantum mechanical calculations are carried out to predict the strengths of these emission and absorption processes. This talk will describe the methods used in these calculations using, as examples, the 4th positive emission bands of CO and the 1g+ 1u+ absorption in C3. The results of these calculations are being used as input to NASA radiation modeling codes like NeqAir, HARA and HyperRad.

  18. Discovering chemistry with an ab initio nanoreactor

    NASA Astrophysics Data System (ADS)

    Martinez, Todd

    Traditional approaches for modeling chemical reaction networks such as those involved in combustion have focused on identifying individual reactions and using theoretical approaches to explore the underlying mechanisms. Recent advances involving graphical processing units (GPUs), commodity products developed for the videogaming industry, have made it possible to consider a distinct approach wherein one attempts to discover chemical reactions and mechanisms. We provide a brief summary of these developments and then discuss the concept behind the ``ab initio nanoreactor'' which explores the space of possible chemical reactions and molecular species for a given stoichiometry. The nanoreactor concept is exemplified with an example to the Urey-Miller reaction network which has been previously advanced as a potential model for prebiotic chemistry. We briefly discuss some of the future directions envisioned for the development of this nanoreactor concept.

  19. Discovering chemistry with an ab initio nanoreactor

    NASA Astrophysics Data System (ADS)

    Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S.; Martínez, Todd J.

    2014-12-01

    Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provide detailed physical insight. Although theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor—a highly accelerated first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor, we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, which provide new insight into the classic Urey-Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery, in addition to its traditional role of interpreting experimental findings.

  20. Discovering chemistry with an ab initio nanoreactor.

    PubMed

    Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S; Martínez, Todd J

    2014-12-01

    Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provide detailed physical insight. Although theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor--a highly accelerated first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor, we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, which provide new insight into the classic Urey-Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery, in addition to its traditional role of interpreting experimental findings.

  1. Discovering chemistry with an ab initio nanoreactor

    PubMed Central

    Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; Liu, Fang; Pande, Vijay S.; Martínez, Todd J.

    2014-01-01

    Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings. PMID:25411881

  2. Ab initio calculations of the H centers in MgF2 crystals

    NASA Astrophysics Data System (ADS)

    Abuova, F. U.; Akilbekov, A. T.; Kotomin, E. A.

    2012-08-01

    MgF2 with rutile structure is important wide-gap optical material with numerous applications. We present and discuss the results of calculations for basic hole defects - interstitial F atoms (called also the colour H centres). This study is based on the large scale ab initio DFT calculations using hybrid B3PW exchange-correlation functional as implemented into CRYSTAL computer code. The electronic structure, atomic geometry, charge density distribution are calculated and discussed.

  3. Visual Measurements of the Multiple Star STT 269 AB-C and ARN 8 AB-D

    NASA Astrophysics Data System (ADS)

    Frey, Thomas; Achildiyev, Irina; Alduenda, Chandra; Bridgeman, Reid; Chamberlain, Rebecca; Hendrix, Alex

    2011-01-01

    This astrometry project was performed by a member of the faculty and students from The Evergreen State College at the 2010 Pine Mountain Observatory Summer Science Research Workshop. This study involved measuring and analyzing the separation and position angles of the multiple star system STT 269 AB-C and ARN 8 AB-D. The astrometric binary AB was treated as a single star. Separation and position angles of the C and D components relative to AB were made. Percent differences between observed and literature values were all less than 1 percent.

  4. Ab initio alpha-alpha scattering

    NASA Astrophysics Data System (ADS)

    Elhatisari, Serdar; Lee, Dean; Rupak, Gautam; Epelbaum, Evgeny; Krebs, Hermann; Lähde, Timo A.; Luu, Thomas; Meißner, Ulf-G.

    2015-12-01

    Processes such as the scattering of alpha particles (4He), the triple-alpha reaction, and alpha capture play a major role in stellar nucleosynthesis. In particular, alpha capture on carbon determines the ratio of carbon to oxygen during helium burning, and affects subsequent carbon, neon, oxygen, and silicon burning stages. It also substantially affects models of thermonuclear type Ia supernovae, owing to carbon detonation in accreting carbon-oxygen white-dwarf stars. In these reactions, the accurate calculation of the elastic scattering of alpha particles and alpha-like nuclei—nuclei with even and equal numbers of protons and neutrons—is important for understanding background and resonant scattering contributions. First-principles calculations of processes involving alpha particles and alpha-like nuclei have so far been impractical, owing to the exponential growth of the number of computational operations with the number of particles. Here we describe an ab initio calculation of alpha-alpha scattering that uses lattice Monte Carlo simulations. We use lattice effective field theory to describe the low-energy interactions of protons and neutrons, and apply a technique called the ‘adiabatic projection method’ to reduce the eight-body system to a two-cluster system. We take advantage of the computational efficiency and the more favourable scaling with system size of auxiliary-field Monte Carlo simulations to compute an ab initio effective Hamiltonian for the two clusters. We find promising agreement between lattice results and experimental phase shifts for s-wave and d-wave scattering. The approximately quadratic scaling of computational operations with particle number suggests that it should be possible to compute alpha scattering and capture on carbon and oxygen in the near future. The methods described here can be applied to ultracold atomic few-body systems as well as to hadronic systems using lattice quantum chromodynamics to describe the interactions of

  5. Ablation dynamics in laser sclerotomy ab externo

    NASA Astrophysics Data System (ADS)

    Brinkmann, Ralf; Droege, Gerit; Mohrenstecher, Dirk; Scheu, M.; Birngruber, Reginald

    1996-01-01

    Laser sclerostomy ab externo with flashlamp excited mid-IR laser systems emitting in the 2-3 micrometer spectral range is in phase II clinical trials. Although acutely high success rates were achieved, the restenosis rate after several months is about 40%. Laser pulses of several hundreds of microseconds, known to induce thermo-mechanical explosive evaporation were used for this procedure. We investigated the ablation dynamics in tissue and the cavitation bubble dynamics in water by means of an Er:YAG laser system to estimate the extent of mechanical damage zones in the sclera and in the anterior chamber, which may contribute to the clinical failure. We found substantial mechanical tissue deformation during the ablation process caused by the cavitation effects. Stress waves up to several bar generated by explosive evaporization were measured. The fast mechanical stretching and collapsing of the scleral tissue induced by cavitation resulted in tissue dissection as could be proved by flash photography and histology. The observed high restenosis might be a result of a subsequent enhanced wound healing process. Early fistula occlusions due to iris adherences, observed in about 20% of the clinical cases may be attributed to intraocular trauma induced by vapor bubble expansion through the anterior chamber after scleral perforation. An automatic feedback system minimizing adverse effects by steering and terminating the laser process during scleral fistulization is demonstrated. Moreover, a new approach in laser sclerostomy ab externo is presented using a cw-IR laser diode system emitting at the 1.94 micrometer mid-IR water absorption peak. This system was used in vitro and showed smaller damage zones compared to the pulsed laser radiation.

  6. Ab initio alpha-alpha scattering.

    PubMed

    Elhatisari, Serdar; Lee, Dean; Rupak, Gautam; Epelbaum, Evgeny; Krebs, Hermann; Lähde, Timo A; Luu, Thomas; Meißner, Ulf-G

    2015-12-03

    Processes such as the scattering of alpha particles ((4)He), the triple-alpha reaction, and alpha capture play a major role in stellar nucleosynthesis. In particular, alpha capture on carbon determines the ratio of carbon to oxygen during helium burning, and affects subsequent carbon, neon, oxygen, and silicon burning stages. It also substantially affects models of thermonuclear type Ia supernovae, owing to carbon detonation in accreting carbon-oxygen white-dwarf stars. In these reactions, the accurate calculation of the elastic scattering of alpha particles and alpha-like nuclei--nuclei with even and equal numbers of protons and neutrons--is important for understanding background and resonant scattering contributions. First-principles calculations of processes involving alpha particles and alpha-like nuclei have so far been impractical, owing to the exponential growth of the number of computational operations with the number of particles. Here we describe an ab initio calculation of alpha-alpha scattering that uses lattice Monte Carlo simulations. We use lattice effective field theory to describe the low-energy interactions of protons and neutrons, and apply a technique called the 'adiabatic projection method' to reduce the eight-body system to a two-cluster system. We take advantage of the computational efficiency and the more favourable scaling with system size of auxiliary-field Monte Carlo simulations to compute an ab initio effective Hamiltonian for the two clusters. We find promising agreement between lattice results and experimental phase shifts for s-wave and d-wave scattering. The approximately quadratic scaling of computational operations with particle number suggests that it should be possible to compute alpha scattering and capture on carbon and oxygen in the near future. The methods described here can be applied to ultracold atomic few-body systems as well as to hadronic systems using lattice quantum chromodynamics to describe the interactions of

  7. The Orbit of 16 Cygni AB

    NASA Astrophysics Data System (ADS)

    Hauser, Heather M.; Marcy, Geoffrey W.

    1999-03-01

    The high orbital eccentricity of the planet around 16 Cygni B may have been induced by the companion star, 16 Cygni A, but only if the stellar binary has sufficiently small periastron distance. The long period of the stellar binary, ~3x10^4 yr, implies that less than 1% of the orbit has transpired since its first astrometric measurements in 1830. Therefore, we compute the orbit from the measured instantaneous velocity and position vectors, based on new precise Doppler and astrometric data, along with the Hipparcos parallax. The only unknown parameter is the separation between AB along the line of sight, constrained by the demand that the orbit be bound, which leads to a family of possible orbits for 16 Cygni AB. The physically plausible orbits have 18,200 yr

  8. Accurate calculation of the p Ka of trifluoroacetic acid using high-level ab initio calculations

    NASA Astrophysics Data System (ADS)

    Namazian, Mansoor; Zakery, Maryam; Noorbala, Mohammad R.; Coote, Michelle L.

    2008-01-01

    The p Ka value of trifluoroacetic acid has been successfully calculated using high-level ab initio methods such as G3 and CBS-QB3. Solvation energies have been calculated using CPCM continuum model of solvation at the HF and B3-LYP levels of theory with various basis sets. Excellent agreement with experiment (to within 0.4 p Ka units) was obtained using CPCM solvation energies at the B3-LYP/6-31+G(d) level (or larger) in conjunction with CBS-QB3 or G3 gas-phase energies of trifluoroacetic acid and its anion.

  9. The (100), (111) and (110) surfaces of diamond: an ab initio B3LYP study

    NASA Astrophysics Data System (ADS)

    De La Pierre, Marco; Bruno, Marco; Manfredotti, Chiara; Nestola, Fabrizio; Prencipe, Mauro; Manfredotti, Claudio

    2014-04-01

    We present an accurate ab initio study of the structure and surface energy of the low-index (100), (111) and (110) diamond faces, by using the hybrid Hartree-Fock/density functional B3LYP Hamiltonian and a localised all-electron Gaussian-type basis set. A two-dimensional periodic slab model has been adopted, for which convergence on both structural and energetic parameters has been thoroughly investigated. For all the three surfaces, possible relaxations and reconstructions have been considered; a detailed geometrical characterisation is provided for the most stable structure of each orientation. Surface energy is discussed for all the investigated faces.

  10. Ab initio molecular dynamics simulation study of successive hydrogenation reactions of carbon monoxide producing methanol

    NASA Astrophysics Data System (ADS)

    Pham, Thi Nu; Ono, Shota; Ohno, Kaoru

    2016-04-01

    Doing ab initio molecular dynamics simulations, we demonstrate a possibility of hydrogenation of carbon monoxide producing methanol step by step. At first, the hydrogen atom reacts with the carbon monoxide molecule at the excited state forming the formyl radical. Formaldehyde was formed after adding one more hydrogen atom to the system. Finally, absorption of two hydrogen atoms to formaldehyde produces methanol molecule. This study is performed by using the all-electron mixed basis approach based on the time dependent density functional theory within the adiabatic local density approximation for an electronic ground-state configuration and the one-shot GW approximation for an electronic excited state configuration.

  11. A high-precision ab initio determination of the equilibrium geometry and force field of HOC(+)

    NASA Technical Reports Server (NTRS)

    Defrees, D. J.; Bunker, P. R.; Binkley, J. S.; Mclean, A. D.

    1987-01-01

    The results of an ab initio molecular orbital investigation of the isoformyl cation, HOC(+), shape are reported. The effects of expanding the basis set to near the Hartree-Fock limit and of electron correlation were examined, and the results indicate that near the Hartree-Fock limit the HOC(+) is linear. An analytic potential function is presented, from which the calculated rotational energies are only 0.03 percent different from the experimental values. This represents a nearly two orders of magnitude reduction in error from earlier work.

  12. Ramsdellite-structured LiTiO 2: A new phase predicted from ab initio calculations

    NASA Astrophysics Data System (ADS)

    Koudriachova, M. V.

    2008-06-01

    A new phase of highly lithiated titania with potential application as an anode in Li-rechargeable batteries is predicted on the basis of ab initio calculations. This phase has a composition LiTiO2 and may be accessed through electrochemical lithiation of ramsdellite-structured TiO2 at the lowest potential reported for titanium dioxide based materials. The potential remains constant over a wide range of Li-concentrations. The new phase is metastable with respect to a tetragonally distorted rock salt structure, which hitherto has been the only known polymorph of LiTiO2.

  13. Ab initio study on electronically excited states of lithium isocyanide, LiNC

    NASA Astrophysics Data System (ADS)

    Yasumatsu, Hisato; Jeung, Gwang-Hi

    2014-01-01

    The electronically excited states of the lithium isocyanide molecule, LiNC, were studied by means of ab initio calculations. The bonding nature of LiNC up to ∼10 eV is discussed on the basis of the potential energy surfaces according to the interaction between the ion-pair and covalent states. The ion-pair states are described by Coulomb attractive interaction in the long distance range, while the covalent ones are almost repulsive or bound with a very shallow potential dent. These two states interact each other to form adiabatic potential energy surfaces with non-monotonic change in the potential energy with the internuclear distance.

  14. A high-precision ab initio determination of the equilibrium geometry and force field of HOC(+)

    NASA Technical Reports Server (NTRS)

    Defrees, D. J.; Bunker, P. R.; Binkley, J. S.; Mclean, A. D.

    1987-01-01

    The results of an ab initio molecular orbital investigation of the isoformyl cation, HOC(+), shape are reported. The effects of expanding the basis set to near the Hartree-Fock limit and of electron correlation were examined, and the results indicate that near the Hartree-Fock limit the HOC(+) is linear. An analytic potential function is presented, from which the calculated rotational energies are only 0.03 percent different from the experimental values. This represents a nearly two orders of magnitude reduction in error from earlier work.

  15. Ab Initio Electronic Structure Calculations of Cytochrome P450 -- Ligand Interactions

    NASA Astrophysics Data System (ADS)

    Segall, M. D.; Payne, M. C.; Ellis, S. W.; Tucker, G. T.

    1997-03-01

    The Cytochrome P450 superfamily of enzymes are of great interest in pharmacology as they participate in an enormous range of physiological processes including drug deactivation and xenobiotic detoxification. We apply ab initio electronic structure calculations to model the interactions of the haem molecule at the P450 active site with substrate and inhibitor ligands. These calculations, based on density function theory, were performed with the CETEP code which uses a plane wave basis set and pseudopotentials to perform efficient LDA, GGA and spin dependent calculations. A change in the spin state of the haem iron atom is observed on binding of a substrate molecule, consistent with the accepted reaction mechanism.

  16. Synthesis and Ab Initio/DFT Studies on 2-(4-methoxyphenyl)benzo[d]thiazole

    PubMed Central

    Arslan, Hakan; Algül, Öztekin

    2007-01-01

    2-aminothiophenol and 4-methoxybenzaldehyde were cyclized under microwave irridation and solvent free conditions to synthesize 2-(4-methoxyphenyl)benzo[d]thiazole. The molecular structure and vibrational frequencies of the title compound in the ground state have been investigated with ab initio (HF) and density functional theory methods (BLYP, B3LYP, B3PW91 and mPW1PW91) implementing the standard 6–311G(d,p) basis set. Comparison of the observed fundamental vibrational frequencies of title compound and calculated results by HF and DFT methods indicate that B3LYP is superior to the scaled HF approach for molecular problems.

  17. Low frequency of broadly neutralizing HIV antibodies during chronic infection even in quaternary epitope targeting antibodies containing large numbers of somatic mutations.

    PubMed

    Hicar, Mark D; Chen, Xuemin; Kalams, Spyros A; Sojar, Hakimuddin; Landucci, Gary; Forthal, Donald N; Spearman, Paul; Crowe, James E

    2016-02-01

    Neutralizing antibodies (Abs) are thought to be a critical component of an appropriate HIV vaccine response. It has been proposed that Abs recognizing conformationally dependent quaternary epitopes on the HIV envelope (Env) trimer may be necessary to neutralize diverse HIV strains. A number of recently described broadly neutralizing monoclonal Abs (mAbs) recognize complex and quaternary epitopes. Generally, many such Abs exhibit extensive numbers of somatic mutations and unique structural characteristics. We sought to characterize the native antibody (Ab) response against circulating HIV focusing on such conformational responses, without a prior selection based on neutralization. Using a capture system based on VLPs incorporating cleaved envelope protein, we identified a selection of B cells that produce quaternary epitope targeting Abs (QtAbs). Similar to a number of broadly neutralizing Abs, the Ab genes encoding these QtAbs showed extensive numbers of somatic mutations. However, when expressed as recombinant molecules, these Abs failed to neutralize virus or mediate ADCVI activity. Molecular analysis showed unusually high numbers of mutations in the Ab heavy chain framework 3 region of the variable genes. The analysis suggests that large numbers of somatic mutations occur in Ab genes encoding HIV Abs in chronically infected individuals in a non-directed, stochastic, manner.

  18. Low frequency of broadly neutralizing HIV antibodies during chronic infection even in quaternary epitope targeting antibodies containing large numbers of somatic mutations

    PubMed Central

    Hicar, Mark D.; Chen, Xuemin; Kalams, Spyros A.; Sojar, Hakimuddin; Landucci, Gary; Forthal, Donald N.; Spearman, Paul; Crowe, James E.

    2016-01-01

    Neutralizing antibodies (Abs) are thought to be a critical component of an appropriate HIV vaccine response. It has been proposed that Abs recognizing conformationally dependent quaternary epitopes on the HIV envelope (Env) trimer may be necessary to neutralize diverse HIV strains. A number of recently described broadly neutralizing monoclonal Abs (mAbs) recognize complex and quaternary epitopes. Generally, many such Abs exhibit extensive numbers of somatic mutations and unique structural characteristics. We sought to characterize the native antibody (Ab) response against circulating HIV focusing on such conformational responses, without a prior selection based on neutralization. Using a capture system based on VLPs incorporating cleaved envelope protein, we identified a selection of B cells that produce quaternary epitope targeting Abs (QtAbs). Similar to a number of broadly neutralizing Abs, the Ab genes encoding these QtAbs showed extensive numbers of somatic mutations. However, when expressed as recombinant molecules, these Abs failed to neutralize virus or mediate ADCVI activity. Molecular analysis showed unusually high numbers of mutations in the Ab heavy chain framework 3 region of the variable genes. The analysis suggests that large numbers of somatic mutations occur in Ab genes encoding HIV Abs in chronically infected individuals in a non-directed, stochastic, manner. PMID:26748387

  19. Analysis of radial basis function interpolation approach

    NASA Astrophysics Data System (ADS)

    Zou, You-Long; Hu, Fa-Long; Zhou, Can-Can; Li, Chao-Liu; Dunn, Keh-Jim

    2013-12-01

    The radial basis function (RBF) interpolation approach proposed by Freedman is used to solve inverse problems encountered in well-logging and other petrophysical issues. The approach is to predict petrophysical properties in the laboratory on the basis of physical rock datasets, which include the formation factor, viscosity, permeability, and molecular composition. However, this approach does not consider the effect of spatial distribution of the calibration data on the interpolation result. This study proposes a new RBF interpolation approach based on the Freedman's RBF interpolation approach, by which the unit basis functions are uniformly populated in the space domain. The inverse results of the two approaches are comparatively analyzed by using our datasets. We determine that although the interpolation effects of the two approaches are equivalent, the new approach is more flexible and beneficial for reducing the number of basis functions when the database is large, resulting in simplification of the interpolation function expression. However, the predicted results of the central data are not sufficiently satisfied when the data clusters are far apart.

  20. Combined ab externo and ab interno revision of failed filtering blebs with adjunctive mitomycin C.

    PubMed

    Magacho, Leopoldo; Shetty, Rajesh K

    2014-01-01

    To report the results of combined ab externo and ab interno revision with mitomycin C (MMC) of failed filtering blebs in glaucoma patients. Glaucoma patients with a failed trabeculectomy who had undergone internal and external revision with MMC in the last 6 years with at least 12 months of follow-up were considered. All study patients followed the same protocol in the operating room: injection of 0.2 mL of MMC (0.4 mg/mL) 2 cm lateral from the bleb followed by internal revision with an iris spatula and external revision with a 26-G × ½" needle. Success was defined as an intraocular pressure (IOP) ≥6 mm Hg and ≤18 mm Hg with (qualified) or without (absolute) any ocular hypotensive drugs. The study included 25 eyes of 22 glaucoma patients. Mean age was 65.2 ± 10.5 years. Mean follow-up was 26.9 ± 10.3 months. The IOP was reduced from 24.5 ± 6.0 mm Hg preoperatively to 10.0 ± 3.3 mm Hg at the last visit (p<0.001). The number of ocular hypotensive medications was reduced from 1.8 ± 1.0 to 0.2 ± 0.6 (p<0.001). There was no change in visual acuity (0.83 ± 0.75 vs 0.83 ± 0.74, p = 0.7). Three patients developed choroidal detachment, another eye had a transient hypotony with maculopathy, and 2 patients developed cataract. Absolute success was achieved in 80% of eyes, and qualified success in 16% of eyes. Combined ab externo and ab interno revision with MMC can be an effective technique to revitalize failed filtering blebs in glaucoma patients with minimal complications.

  1. A molecular mechanics valence force field for sulfonamides derived by ab initio methods

    SciTech Connect

    Nicholas, J.B.; Burke, B.J.; Hopfinger, A.J. ); Vance, R.; Martin, E. )

    1991-11-28

    Molecular mechanics valence force field parameters for the sulfonamide group, SO[sub 2]NH, have been derived from ab initio calculations at the RHF/6-31G* level of theory. The force field parameters were designed to be used in conjunction with existing parameters from the MM2/MMP2 force field. The new parameters are demonstrated to accurately reproduce the ab initio optimized geometries of four molecules that contain the sulfonamide group. The strategy used in force field parametrization is discussed. The conformational flexibility of the sulfonamide group has been investigated. Calculations at the RHF/6-31G* level reveal the existence of two stable conformers and that interconversion is achieved by nitrogen inversion rather than rotation about the S-N bond. The energetic effects of expanding the basis set to 6-31G** and of including MP2 and MP3 corrections for electron correlation are discussed. The geometries and Mulliken charges for the ab initio optimized structures are also reported.

  2. Theoretical study on isotope and temperature effect in hydronium ion using ab initio path integral simulation

    NASA Astrophysics Data System (ADS)

    Tachikawa, Masanori; Shiga, Motoyuki

    2004-09-01

    We have applied the ab initio path integral molecular dynamics simulation to study hydronium ion and its isotopes, which are the simplest systems for hydrated proton and deuteron. In this simulation, all the rotational and vibrational degrees of freedom are treated fully quantum mechanically, while the potential energies of the respective atomic configurations are calculated "on the fly" using ab initio quantum chemical approach. With the careful treatment of the ab initio electronic structure calculation by relevant choices in electron correlation level and basis set, this scheme is theoretically quite rigorous except for Born-Oppenheimer approximation. This accurate calculation allows a close insight into the structural shifts for the isotopes of hydronium ion by taking account of both quantum mechanical and thermal effects. In fact, the calculation is shown to be successful to quantitatively extract the geometrical isotope effect with respect to the Walden inversion. It is also shown that this leads to the isotope effect on the electronic structure as well as the thermochemical properties.

  3. 34 CFR Appendixes A-B to Part 682 - [Reserved

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 34 Education 3 2010-07-01 2010-07-01 false A Appendixes A-B to Part 682 Education Regulations of the Offices of the Department of Education (Continued) OFFICE OF POSTSECONDARY EDUCATION, DEPARTMENT OF EDUCATION FEDERAL FAMILY EDUCATION LOAN (FFEL) PROGRAM Appendixes A-B to Part...

  4. 12 CFR Appendices A-B to Part 717 - [Reserved

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 12 Banks and Banking 7 2014-01-01 2014-01-01 false A Appendices A-B to Part 717 Banks and Banking NATIONAL CREDIT UNION ADMINISTRATION REGULATIONS AFFECTING CREDIT UNIONS FAIR CREDIT REPORTING Appendices A-B to Part 717 ...

  5. 77 FR 19565 - Airworthiness Directives; Saab AB, Saab Aerosystems Airplanes

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-02

    ... Federal Aviation Administration 14 CFR Part 39 RIN 2120-AA64 Airworthiness Directives; Saab AB, Saab... rulemaking (NPRM). SUMMARY: We propose to adopt a new airworthiness directive (AD) for all Saab AB, Saab Aerosystems Model 340A (SAAB/SF340A) and SAAB 340B Airplanes. This proposed AD was prompted by reports...

  6. 77 FR 38470 - Airworthiness Directives; Saab AB, Saab Aerosystems Airplanes

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-06-28

    ...-116-AD; Amendment 39-17103; AD 2012-13-01] RIN 2120-AA64 Airworthiness Directives; Saab AB, Saab...). ACTION: Final rule. SUMMARY: We are adopting a new airworthiness directive (AD) for all Saab AB, Saab Aerosystems Model 340A (SAAB/SF340A) and SAAB 340B airplanes. This AD was prompted by reports indicating that...

  7. 78 FR 1731 - Airworthiness Directives; Saab AB, Saab Aerosystems Airplanes

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-01-09

    ...-079-AD; Amendment 39-17296; AD 2012-26-01] RIN 2120-AA64 Airworthiness Directives; Saab AB, Saab...). ACTION: Final rule. ] SUMMARY: We are adopting a new airworthiness directive (AD) for all Saab AB, Saab Aerosystems Model SAAB 2000 airplanes. This AD was prompted by reports of chafing on the bottom panel of the...

  8. 77 FR 38224 - Airworthiness Directives; Saab AB, Saab Aerosystems Airplanes

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-06-27

    ... Federal Aviation Administration 14 CFR Part 39 RIN 2120-AA64 Airworthiness Directives; Saab AB, Saab... rulemaking (NPRM). SUMMARY: We propose to adopt a new airworthiness directive (AD) for certain Saab AB, Saab Aerosystems Model 340A (SAAB/SF340A) and SAAB 340B airplanes. This proposed AD was prompted by reports of...

  9. 77 FR 60073 - Airworthiness Directives; Saab AB, Saab Aerosystems Airplanes

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-02

    ... TRANSPORTATION Federal Aviation Administration 14 CFR Part 39 RIN 2120-AA64 Airworthiness Directives; Saab AB, Saab Aerosystems Airplanes AGENCY: Federal Aviation Administration (FAA), DOT. ACTION: Notice of proposed rulemaking (NPRM). SUMMARY: We propose to adopt a new airworthiness directive (AD) for all Saab AB...

  10. 34 CFR Appendices A-B to Part 682 - [Reserved

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 34 Education 4 2011-07-01 2011-07-01 false A Appendices A-B to Part 682 Education Regulations of the Offices of the Department of Education (Continued) OFFICE OF POSTSECONDARY EDUCATION, DEPARTMENT OF EDUCATION (CONTINUED) FEDERAL FAMILY EDUCATION LOAN (FFEL) PROGRAM Appendices A-B to Part 682...

  11. 34 CFR Appendices A-B to Part 682 - [Reserved

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 34 Education 4 2013-07-01 2013-07-01 false A Appendices A-B to Part 682 Education Regulations of the Offices of the Department of Education (Continued) OFFICE OF POSTSECONDARY EDUCATION, DEPARTMENT OF EDUCATION (CONTINUED) FEDERAL FAMILY EDUCATION LOAN (FFEL) PROGRAM Appendices A-B to Part 682...

  12. 34 CFR Appendices A-B to Part 682 - [Reserved

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 34 Education 4 2012-07-01 2012-07-01 false A Appendices A-B to Part 682 Education Regulations of the Offices of the Department of Education (Continued) OFFICE OF POSTSECONDARY EDUCATION, DEPARTMENT OF EDUCATION (CONTINUED) FEDERAL FAMILY EDUCATION LOAN (FFEL) PROGRAM Appendices A-B to Part 682...

  13. 10 CFR Appendices A-B to Subpart F... - [Reserved

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 10 Energy 3 2013-01-01 2013-01-01 false A Appendices A-B to Subpart F of Part 430 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CONSERVATION PROGRAM FOR CONSUMER PRODUCTS Reserved Appendices A-B to Subpart F of Part 430...

  14. 10 CFR Appendices A-B to Subpart F... - [Reserved

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 10 Energy 3 2012-01-01 2012-01-01 false A Appendices A-B to Subpart F of Part 430 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CONSERVATION PROGRAM FOR CONSUMER PRODUCTS Reserved Appendices A-B to Subpart F of Part 430...

  15. 10 CFR Appendices A-B to Subpart F... - [Reserved

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 10 Energy 3 2014-01-01 2014-01-01 false A Appendices A-B to Subpart F of Part 430 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION ENERGY CONSERVATION PROGRAM FOR CONSUMER PRODUCTS Reserved Appendices A-B to Subpart F of Part 430...

  16. Ab initio calculations on peptide-derived oxazoles and thiazoles: Improved molecular mechanics parameters for the AMBER* force field

    NASA Astrophysics Data System (ADS)

    Boden, Christopher D. J.; Pattenden, Gerald

    1999-03-01

    Ab initio calculations at the RHF/6-31G* and MP2/6- 31G*//RHF/6-31G* levels of theory are performed for 2-methyl-4-carboxamido-oxazoles and -thiazoles, including rotational profiles for the ring-carboxamide bond, which showed the expected conjugation and hydrogen bonding effects. On the basis of these data, newly optimised stretch, bend and torsional parameters for the AMBER* force field are derived, along with CHELPG-fitted partial atomic charges.

  17. Ab initio potential energy surface and predicted microwave spectra for Ar--OCS dimer and structures of Arn--OCS (n = 2-14) clusters.

    PubMed

    Zhu, Hua; Guo, Yong; Xue, Ying; Xie, Daiqian

    2006-07-15

    An ab initio potential energy surface for the Ar--OCS dimer was calculated using the coupled-cluster singles and doubles with noniterative inclusion of connected triples [CCSD(T)] with a large basis set containing bond functions. The interaction energies were obtained by the supermolecular approach with the full counterpoise correction for the basis set superposition error. The CCSD(T) potential was found to have two minima corresponding to the T-shaped and the collinear Ar--SCO structures. The two-dimensional discrete variable representation method was employed to calculate the rovibrational energy levels for five isotopomers Ar--OCS, Ar--OC34S, Ar--O13CS, Ar--18OCS, and Ar--17OCS. The calculated pure rotational transition frequencies for the vibrational ground state of the five isotopomers are in good agreement with the observed values. The corresponding microwave spectra show that the b-type transitions (Delta Ka = +/-1) are significantly stronger than the a-type transitions (Delta Ka = 0). Minimum-energy structures of the Ar2--OCS trimer were been determined with MP2 optimization, whereas the minimum-energy structures of the Arn--OCS clusters with n = 3-14 were obtained with the pairwise additive potentials. It was found that there are two minima corresponding to one distorted tetrahedral structure and one planar structure for the ternary complex. The 14 nearest neighbor Ar atoms form the first solvation shell around the OCS molecule.

  18. Ab initio structural and spectroscopic study of HPS{sup x} and HSP{sup x} (x = 0,+1,−1) in the gas phase

    SciTech Connect

    Yaghlane, Saida Ben; Cotton, C. Eric; Francisco, Joseph S. E-mail: hochlaf@univ-mlv.fr; Linguerri, Roberto; Hochlaf, Majdi E-mail: hochlaf@univ-mlv.fr

    2013-11-07

    Accurate ab initio computations of structural and spectroscopic parameters for the HPS/HSP molecules and corresponding cations and anions have been performed. For the electronic structure computations, standard and explicitly correlated coupled cluster techniques in conjunction with large basis sets have been adopted. In particular, we present equilibrium geometries, rotational constants, harmonic vibrational frequencies, adiabatic ionization energies, electron affinities, and, for the neutral species, singlet-triplet relative energies. Besides, the full-dimensional potential energy surfaces (PESs) for HPS{sup x} and HSP{sup x} (x = −1,0,1) systems have been generated at the standard coupled cluster level with a basis set of augmented quintuple-zeta quality. By applying perturbation theory to the calculated PESs, an extended set of spectroscopic constants, including τ, first-order centrifugal distortion and anharmonic vibrational constants has been obtained. In addition, the potentials have been used in a variational approach to deduce the whole pattern of vibrational levels up to 4000 cm{sup −1} above the minima of the corresponding PESs.

  19. Interaction energies for the purine inhibitor roscovitine with cyclin-dependent kinase 2: correlated ab initio quantum-chemical, DFT and empirical calculations.

    PubMed

    Dobes, Petr; Otyepka, Michal; Strnad, Miroslav; Hobza, Pavel

    2006-05-24

    The interaction between roscovitine and cyclin-dependent kinase 2 (cdk2) was investigated by performing correlated ab initio quantum-chemical calculations. The whole protein was fragmented into smaller systems consisting of one or a few amino acids, and the interaction energies of these fragments with roscovitine were determined by using the MP2 method with the extended aug-cc-pVDZ basis set. For selected complexes, the complete basis set limit MP2 interaction energies, as well as the coupled-cluster corrections with inclusion of single, double and noninteractive triples contributions [CCSD(T)], were also evaluated. The energies of interaction between roscovitine and small fragments and between roscovitine and substantial sections of protein (722 atoms) were also computed by using density-functional tight-binding methods covering dispersion energy (DFTB-D) and the Cornell empirical potential. Total stabilisation energy originates predominantly from dispersion energy and methods that do not account for the dispersion energy cannot, therefore, be recommended for the study of protein-inhibitor interactions. The Cornell empirical potential describes reasonably well the interaction between roscovitine and protein; therefore, this method can be applied in future thermodynamic calculations. A limited number of amino acid residues contribute significantly to the binding of roscovitine and cdk2, whereas a rather large number of amino acids make a negligible contribution.

  20. Serious Gaming for Test & Evaluation of Clean-Slate (Ab Initio) National Airspace System (NAS) Designs

    NASA Technical Reports Server (NTRS)

    Allen, B. Danette; Alexandrov, Natalia

    2016-01-01

    Incremental approaches to air transportation system development inherit current architectural constraints, which, in turn, place hard bounds on system capacity, efficiency of performance, and complexity. To enable airspace operations of the future, a clean-slate (ab initio) airspace design(s) must be considered. This ab initio National Airspace System (NAS) must be capable of accommodating increased traffic density, a broader diversity of aircraft, and on-demand mobility. System and subsystem designs should scale to accommodate the inevitable demand for airspace services that include large numbers of autonomous Unmanned Aerial Vehicles and a paradigm shift in general aviation (e.g., personal air vehicles) in addition to more traditional aerial vehicles such as commercial jetliners and weather balloons. The complex and adaptive nature of ab initio designs for the future NAS requires new approaches to validation, adding a significant physical experimentation component to analytical and simulation tools. In addition to software modeling and simulation, the ability to exercise system solutions in a flight environment will be an essential aspect of validation. The NASA Langley Research Center (LaRC) Autonomy Incubator seeks to develop a flight simulation infrastructure for ab initio modeling and simulation that assumes no specific NAS architecture and models vehicle-to-vehicle behavior to examine interactions and emergent behaviors among hundreds of intelligent aerial agents exhibiting collaborative, cooperative, coordinative, selfish, and malicious behaviors. The air transportation system of the future will be a complex adaptive system (CAS) characterized by complex and sometimes unpredictable (or unpredicted) behaviors that result from temporal and spatial interactions among large numbers of participants. A CAS not only evolves with a changing environment and adapts to it, it is closely coupled to all systems that constitute the environment. Thus, the ecosystem that

  1. Cosmic microwave background polarimetry with ABS and ACT: Instrumental design, characterization, and analysis

    NASA Astrophysics Data System (ADS)

    Simon, Sara Michelle

    The LCDM model of the universe is supported by an abundance of astronomical observations, but it does not confirm a period of inflation in the early universe or explain the nature of dark energy and dark matter. The polarization of the cosmic microwave background (CMB) may hold the key to addressing these profound questions. If a period of inflation occurred in the early universe, it could have left a detectable odd-parity pattern called B-modes in the polarization of the CMB on large angular scales. Additionally, the CMB can be used to probe the structure of the universe on small angular scales through lensing and the detection of galaxy clusters and their motions via the Sunyaev-Zel'dovich effect, which can improve our understanding of neutrinos, dark matter, and dark energy. The Atacama B-mode Search (ABS) instrument was a cryogenic crossed-Dragone telescope located at an elevation of 5190m in the Atacama Desert in Chile that observed from February 2012 until October 2014. ABS searched on degree-angular scales for inflationary B-modes in the CMB and pioneered the use of a rapidly-rotating half-wave plate (HWP), which modulates the polarization of incoming light to permit the measurement of celestial polarization on large angular scales that would otherwise be obscured by 1/f noise from the atmosphere. Located next to ABS in the Atacama is the Atacama Cosmology Telescope (ACT), which is an off-axis Gregorian telescope. Its large 6m primary mirror facilitates measurements of the CMB on small angular scales. HWPs are baselined for use with the upgraded polarization-sensitive camera for ACT, called Advanced ACTPol, to extend observations of the polarized CMB to larger angular scales while also retaining sensitivity to small angular scales. The B-mode signal is extremely faint, and measuring it poses an instrumental challenge that requires the development of new technologies and well-characterized instruments. I will discuss the use of novel instrumentation and

  2. Modeling Central American Volcanic Front Primitive Lavas with the Arc Basalt Simulator (abs 4.0)

    NASA Astrophysics Data System (ADS)

    Feigenson, M.; Carr, M. J.; Gazel, E.

    2012-12-01

    We have used the Arc Basalt Simulator (ABS), developed by J-I Kimura, to explore the conditions and components of melting beneath the Central American volcanic front. ABS is a comprehensive forward model that incorporates slab dehydration and melting and mantle wedge fluxing and melting using realistic P-T conditions and experimentally determined phase relations and partition coefficients. We have applied ABS version 4.00, which includes melting/dehydration relations in eight distinct subducting layers, to model representative magma types along the Central American volcanic front. These magmas are first projected to primary melt compositions by the addition of olivine until they reach Fo90. Then, using a wide range of input parameters including variations in slab components, extent of peridotite depletion, depth of slab dehydration and wedge fluxing and degree of peridotite melting, successful model fits are generated (based on trace element and isotope matching). The solution space is probed using a Monte Carlo technique to cover the enormous range of parameter values. Nicaragua and Costa Rica represent geochemical and geophysical end members of the volcanic front, differing greatly in volcano volume, slab dip beneath the volcano, isotopic composition and incompatible element enrichment. Using appropriate input compositions for ABS 4.0, we find through millions of simulations that the Cerro Negro primary magma (Nicaragua) requires high degrees of source melting (22-27%) and large amounts of slab-derived water (3-5%). In contrast, the Irazu primary magma (central Costa Rica) is generated from more enriched sources with only a small amount of water (less than 0.5%) and at low degrees of partial melting (less than 5%). Other Central American lavas with intermediate geochemical characteristics are produced from conditions within the Nicaragua-Costa Rica range. By reproducing the lava geochemistry with ABS 4.0, it becomes possible to extract constraints on source input

  3. The Use of Solitaire AB Stents in Coil Embolization of Wide-Necked Cerebral Aneurysms.

    PubMed

    Li, Teng-Fei; Shui, Shao-Feng; Han, Xin-Wei; Yan, Lei; Ma, Ji; Guo, Dong; Zhu, Hong-Can; Wang, Shu-Kai; He, Yuan-Hong; Chen, Wen-Wu; Wei, Li-Ping; Wang, Ming-Ke; Song, Tai-Min

    2015-01-01

    The Solitaire AB stent is one of many assistant stents used for treating wide-necked cerebral aneurysm, and has been used since 2003. However, large sample studies on its safety and effectiveness are lacking. The objective of this study was to evaluate the effectiveness and safety of the Solitaire AB stent in the coil embolization of wide-necked cerebral aneurysms. Retrospective review of the clinical and image data of 116 patients with wide-necked cerebral aneurysms who had been enrolled at six interventional neuroradiology centers from February 2010 to February 2014 and had been treated by coil embolization; in total, 120 Solitaire AB stents were used. The degree of aneurysm occlusion was examined using digital subtraction angiography (DSA) immediately after the procedure and during follow-up, and was graded using the modified Raymond classification. We also observed complications to evaluate the safety and effectiveness of this therapy. The 120 Solitaire AB stents (4 mm × 15 mm, four stents; 4 mm × 20 mm, 16 stents; 6 mm × 20 mm, 36 stents; 6 mm × 30 mm, 64 stents) were inserted to treat 120 wide-necked cerebral aneurysms. All stents were inserted successfully. DSA immediately post-surgery revealed 55 cases of complete occlusion, 59 cases of neck remnant, and six cases of aneurysm remnant. Perioperatively, there were four cases of hemorrhage and four cases of stent thrombosis. The follow-up spanned 3-37 months; of 92 patients examined by DSA at the 6-month follow up, 12 had disease recurrence. The Solitaire AB stent is effective with a good technical success rate and short-term effect for assisting coil embolization of wide-necked cerebral aneurysms.

  4. Evidence for Radiogenic Sulfur-32 in Type AB Presolar Silicon Carbide Grains?

    NASA Astrophysics Data System (ADS)

    Fujiya, Wataru; Hoppe, Peter; Zinner, Ernst; Pignatari, Marco; Herwig, Falk

    2013-10-01

    We report C, Si, and S isotope measurements on 34 presolar silicon carbide grains of Type AB, characterized by 12C/13C < 10. Nitrogen, Mg-Al-, and Ca-Ti-isotopic compositions were measured on a subset of these grains. Three grains show large 32S excesses, a signature that has been previously observed for grains from supernovae (SNe). Enrichments in 32S may be due to contributions from the Si/S zone and the result of S molecule chemistry in still unmixed SN ejecta or due to incorporation of radioactive 32Si from C-rich explosive He shell ejecta. However, a SN origin remains unlikely for the three AB grains considered here, because of missing evidence for 44Ti, relatively low 26Al/27Al ratios (a few times 10-3), and radiogenic 32S along with low 12C/13C ratios. Instead, we show that born-again asymptotic giant branch (AGB) stars that have undergone a very-late thermal pulse (VLTP), known to have low 12C/13C ratios and enhanced abundances of the light s-process elements, can produce 32Si, which makes such stars attractive sources for AB grains with 32S excesses. This lends support to the proposal that at least some AB grains originate from born-again AGB stars, although uncertainties in the born-again AGB star models and possible variations of initial S-isotopic compositions in the parent stars of AB grains make it difficult to draw a definitive conclusion.

  5. ESR studies and dating of Egyptian gypsum at Ras Mala'ab, Sinai, Egypt

    NASA Astrophysics Data System (ADS)

    Abdel-Monem, A. A.; Abdel-Razek, Y. A.; Hassan, G. M.; Eissa, H. M.; Rasheed, N. M.; Morsy, M.

    2010-01-01

    A gypsum sample from the famous gypsum-anhydrite evaporitic deposit composing the Ras Mala'ab Formation, Upper Miocene, occurring at Ras Mala'ab, on the east coast of the Gulf of Suez, was subjected to electron spin resonance (ESR) dosimetric studies. ESR was further used to date the formation or most recent recrystallization of the gypsum. The gypsum derivative ESR spectrum is characterized by the large broad Fe2+ signal (g=2.50) and hf-sixtet Mn2+ signals. Only the characteristic gypsum signal (G1, g=2.0040) was detected between the third and fourth lines of the hf-Mn2+ which is attributed to the electron-center SO ? . This signal was sensitive to artificial γ-irradiation and showed significant enhancement using a γ-dose of 550 Gy. Additionally, the signal was very stable up to 400 °C. The gypsum sample with a total dose of 1500 Gy, determined graphically by extrapolating the linear relationship between defect concentration and the artificial γ-doses for (G1, g=2.0040) and an annual dose (D) due to cosmic rays (0.3 mGy), yielded an age of 5.00 Ma. This could mean the age of formation or latest recrystallization of this gypsum deposit. The geological age assignment of the Ras Mala'ab Group, including the evaporitic gypsum unit, is Middle to Late Miocene. It is directly overlain by the Pliocene clastics at the locality of Ras Mala'ab. This might suggest that these evaporitic gypsum facies represent the top of the Serravallian (mid-late) Miocene in the Gulf of Suez area. Since the Serravallian period was between 14.8 and 11.2 Ma ago; therefore, the ESR age of the Ras Mala'ab gypsum represents the latest recrystallization event of these gypsum deposits.

  6. EVIDENCE FOR RADIOGENIC SULFUR-32 IN TYPE AB PRESOLAR SILICON CARBIDE GRAINS?

    SciTech Connect

    Fujiya, Wataru; Hoppe, Peter; Zinner, Ernst; Pignatari, Marco; Herwig, Falk E-mail: peter.hoppe@mpic.de E-mail: mpignatari@gmail.com

    2013-10-20

    We report C, Si, and S isotope measurements on 34 presolar silicon carbide grains of Type AB, characterized by {sup 12}C/{sup 13}C < 10. Nitrogen, Mg-Al-, and Ca-Ti-isotopic compositions were measured on a subset of these grains. Three grains show large {sup 32}S excesses, a signature that has been previously observed for grains from supernovae (SNe). Enrichments in {sup 32}S may be due to contributions from the Si/S zone and the result of S molecule chemistry in still unmixed SN ejecta or due to incorporation of radioactive {sup 32}Si from C-rich explosive He shell ejecta. However, a SN origin remains unlikely for the three AB grains considered here, because of missing evidence for {sup 44}Ti, relatively low {sup 26}Al/{sup 27}Al ratios (a few times 10{sup –3}), and radiogenic {sup 32}S along with low {sup 12}C/{sup 13}C ratios. Instead, we show that born-again asymptotic giant branch (AGB) stars that have undergone a very-late thermal pulse (VLTP), known to have low {sup 12}C/{sup 13}C ratios and enhanced abundances of the light s-process elements, can produce {sup 32}Si, which makes such stars attractive sources for AB grains with {sup 32}S excesses. This lends support to the proposal that at least some AB grains originate from born-again AGB stars, although uncertainties in the born-again AGB star models and possible variations of initial S-isotopic compositions in the parent stars of AB grains make it difficult to draw a definitive conclusion.

  7. The Use of Solitaire AB Stents in Coil Embolization of Wide-Necked Cerebral Aneurysms

    PubMed Central

    Han, Xin-Wei; Yan, Lei; Ma, Ji; Guo, Dong; Zhu, Hong-Can; Wang, Shu-Kai; He, Yuan-Hong; Chen, Wen-Wu; Wei, Li-Ping; Wang, Ming-Ke; Song, Tai-Min

    2015-01-01

    Background The Solitaire AB stent is one of many assistant stents used for treating wide-necked cerebral aneurysm, and has been used since 2003. However, large sample studies on its safety and effectiveness are lacking. The objective of this study was to evaluate the effectiveness and safety of the Solitaire AB stent in the coil embolization of wide-necked cerebral aneurysms. Methods Retrospective review of the clinical and image data of 116 patients with wide-necked cerebral aneurysms who had been enrolled at six interventional neuroradiology centers from February 2010 to February 2014 and had been treated by coil embolization; in total, 120 Solitaire AB stents were used. The degree of aneurysm occlusion was examined using digital subtraction angiography (DSA) immediately after the procedure and during follow-up, and was graded using the modified Raymond classification. We also observed complications to evaluate the safety and effectiveness of this therapy. Results The 120 Solitaire AB stents (4 mm × 15 mm, four stents; 4 mm × 20 mm, 16 stents; 6 mm × 20 mm, 36 stents; 6 mm × 30 mm, 64 stents) were inserted to treat 120 wide-necked cerebral aneurysms. All stents were inserted successfully. DSA immediately post-surgery revealed 55 cases of complete occlusion, 59 cases of neck remnant, and six cases of aneurysm remnant. Perioperatively, there were four cases of hemorrhage and four cases of stent thrombosis. The follow-up spanned 3–37 months; of 92 patients examined by DSA at the 6-month follow up, 12 had disease recurrence. Conclusions The Solitaire AB stent is effective with a good technical success rate and short-term effect for assisting coil embolization of wide-necked cerebral aneurysms. PMID:26426804

  8. Authorization Basis Safety Classification of Transfer Bay Bridge Crane at the 105-K Basins

    SciTech Connect

    CHAFFEE, G.A.

    2000-04-06

    This supporting document provides the bases for the safety classification for the K Basin transfer bay bridge crane and the bases for the Structures, Systems, and Components (SSC) safety classification. A table is presented that delineates the safety significant components. This safety classification is based on a review of the Authorization Basis (AB). This Authorization Basis review was performed regarding AB and design baseline issues. The primary issues are: (1) What is the AB for the safety classification of the transfer bay bridge crane? (2) What does the SSC safety classification ''Safety Significant'' or ''Safety Significant for Design Only'' mean for design requirements and quality requirements for procurement, installation and maintenance (including replacement of parts) activities for the crane during its expected life time? The AB information on the crane was identified based on review of Department of Energy--Richland Office (RL) and Spent Nuclear Fuel (SNF) Project correspondence, K Basin Safety Analysis Report (SAR) and RL Safety Evaluation Reports (SERs) of SNF Project SAR submittals. The relevant correspondence, actions and activities taken and substantive directions or conclusions of these documents are provided in Appendix A.

  9. A genetic basis for the inviability of hybrids between sibling species of Drosophila

    SciTech Connect

    Hutter, P. ); Roote, J.; Ashburner, M. )

    1990-04-01

    An X-ray induced mutation of Drosophila melanogaster whose only known effect is the rescue of otherwise lethal interspecific hybrids has been characterized. This mutation, Hmr, maps to 1-31.84 (9D1-9E4). Hmr may be the consequence of a P element insertion. It rescues hybrid males from the cross of D. melanogaster females to males of its three sibling species, D. simulans, D. mauritiana and D. sechellia. This rescue is recessive, since hybrid males that carry both Hmr and a duplication expected to be Hmr{sup +} are not rescued. Hmr also rescues the otherwise inviable female hybrids from the cross of compound-X D. melanogaster females to males of its sibling species. This rescue is also recessive, since a compound-X heterozygous for Hmr does not rescue. Another mutation, discovered on the In(1)AB chromosome of D. melanogaster, is also found to rescue normally inviable species hybrids: unlike Hmr, however, In(1)AB rescues hybrid females from the cross of In(1)AB/Y males to sibling females, as well as hybrid males from the cross of In(1)AB females to sibling males. These data are interpreted on the basis of a model for the genetic basis of hybrid inviability of complementary genes.

  10. The molecular basis of human keratin disorders.

    PubMed

    Arin, Meral Julia

    2009-05-01

    Keratins are cytoskeletal proteins that provide structural support to epithelial cells and tissues. Perturbation causes cell and tissue fragility and accounts for a large number of genetic disorders in humans. In humans, 54 functional keratin genes exist and 21 different keratin genes including hair keratins and hair follicle-specific epithelial keratins have been associated with hereditary disorders. Moreover, keratins have been implicated in more complex traits such as liver disease and inflammatory bowel disease. Understanding the molecular basis of keratin disorders has been the basis for improved diagnosis with prognostic implications, genetic counseling and prenatal testing for severe disorders. Besides their mechanical role, keratins have newly identified functions in apoptosis, cell growth, tissue polarity, wound healing and tissue remodeling. Improved understanding of the regulatory functions of keratins may offer novel approaches to overcome current treatment limitations.

  11. Optimized Basis Sets for the Environment in the Domain-Specific Basis Set Approach of the Incremental Scheme.

    PubMed

    Anacker, Tony; Hill, J Grant; Friedrich, Joachim

    2016-04-21

    Minimal basis sets, denoted DSBSenv, based on the segmented basis sets of Ahlrichs and co-workers have been developed for use as environmental basis sets for the domain-specific basis set (DSBS) incremental scheme with the aim of decreasing the CPU requirements of the incremental scheme. The use of these minimal basis sets within explicitly correlated (F12) methods has been enabled by the optimization of matching auxiliary basis sets for use in density fitting of two-electron integrals and resolution of the identity. The accuracy of these auxiliary sets has been validated by calculations on a test set containing small- to medium-sized molecules. The errors due to density fitting are about 2-4 orders of magnitude smaller than the basis set incompleteness error of the DSBSenv orbital basis sets. Additional reductions in computational cost have been tested with the reduced DSBSenv basis sets, in which the highest angular momentum functions of the DSBSenv auxiliary basis sets have been removed. The optimized and reduced basis sets are used in the framework of the domain-specific basis set of the incremental scheme to decrease the computation time without significant loss of accuracy. The computation times and accuracy of the previously used environmental basis and that optimized in this work have been validated with a test set of medium- to large-sized systems. The optimized and reduced DSBSenv basis sets decrease the CPU time by about 15.4% and 19.4% compared with the old environmental basis and retain the accuracy in the absolute energy with standard deviations of 0.99 and 1.06 kJ/mol, respectively.

  12. Using Academic Behavior Index (AB-Index) to Develop a Learner Typology for Managing Enrollment and Course Offerings--A Data Mining Approach. IR Applications. Volume 10

    ERIC Educational Resources Information Center

    Luan, Jing

    2006-01-01

    This exploratory data mining project used distance-based clustering algorithms to study three indicators of student behavioral data collectively called AB-Index, and established a typology of six types of learners for a suburban community college. The study is based on the notion that student behavioral data are a good basis for new ways of doing…

  13. Undoing Gender through Legislation and Schooling: The Case of AB 537 and AB 394 in California, USA

    ERIC Educational Resources Information Center

    Knotts, Greg

    2009-01-01

    This article investigates California laws AB 537: The Student Safety and Violence Prevention Act of 2000, and the recently enacted AB 394: Safe Place to Learn Act. Both demand that gender identity and sexual orientation be added to the lexicon of anti-harassment protection in public education. However, despite these progressive measures, schools…

  14. Undoing Gender through Legislation and Schooling: The Case of AB 537 and AB 394 in California, USA

    ERIC Educational Resources Information Center

    Knotts, Greg

    2009-01-01

    This article investigates California laws AB 537: The Student Safety and Violence Prevention Act of 2000, and the recently enacted AB 394: Safe Place to Learn Act. Both demand that gender identity and sexual orientation be added to the lexicon of anti-harassment protection in public education. However, despite these progressive measures, schools…

  15. Enthalpy difference between conformations of normal alkanes: effects of basis set and chain length on intramolecular basis set superposition error

    NASA Astrophysics Data System (ADS)

    Balabin, Roman M.

    2011-03-01

    The quantum chemistry of conformation equilibrium is a field where great accuracy (better than 100 cal mol-1) is needed because the energy difference between molecular conformers rarely exceeds 1000-3000 cal mol-1. The conformation equilibrium of straight-chain (normal) alkanes is of particular interest and importance for modern chemistry. In this paper, an extra error source for high-quality ab initio (first principles) and DFT calculations of the conformation equilibrium of normal alkanes, namely the intramolecular basis set superposition error (BSSE), is discussed. In contrast to out-of-plane vibrations in benzene molecules, diffuse functions on carbon and hydrogen atoms were found to greatly reduce the relative BSSE of n-alkanes. The corrections due to the intramolecular BSSE were found to be almost identical for the MP2, MP4, and CCSD(T) levels of theory. Their cancelation is expected when CCSD(T)/CBS (CBS, complete basis set) energies are evaluated by addition schemes. For larger normal alkanes (N > 12), the magnitude of the BSSE correction was found to be up to three times larger than the relative stability of the conformer; in this case, the basis set superposition error led to a two orders of magnitude difference in conformer abundance. No error cancelation due to the basis set superposition was found. A comparison with amino acid, peptide, and protein data was provided.

  16. Computer-algebra calculations and measurements on AB spin systems for double-spin-echo sequences.

    PubMed

    Straubinger, K; Schick, F; Lutz, O

    1995-07-01

    The time evolution of the density operator of an AB spin system during a double-spin-echo pulse sequence is evaluated analytically by a computer-algebra system. The computer-algebra system allows one to generate the extensive formulas describing the density operator and yields an expression for the integral of the spectral signals. The simulation of spectra for arbitrary sequence timings can be easily performed by this new tool without risking errors that might occur in conventional calculations. The computer-algebra method can be extended straightforward to other pulse angles and types of sequences. The double-spin-echo pulse sequence is used in the point-resolved spectroscopy (PRESS) method which is often applied for volume selective examinations in vivo. For verification of the results generated by the computer-algebra system, 1H spectra from a half-liter spherical sample with an aqueous solution that was 0.1 M in sodium citrate and 0.1 M in sodium acetate were recorded after 90 degrees-180 degrees-180 degrees double-spin-echo pulse sequences on a 1.5-T whole-body unit. The measured behavior of the citrate AB spin system corresponds very well with the theoretical predictions. Thus, the theory provides the basis for optimization of sequence timings for double-spin-echo measurements with high signal gain from AB systems as, for example, citrate. In addition, the theoretically predicted signal modulations could be fitted to the experimental data, providing the transverse relaxation time of the AB-coupled protons.

  17. Kaiser-Bessel basis for particle-mesh interpolation

    NASA Astrophysics Data System (ADS)

    Gao, Xingyu; Fang, Jun; Wang, Han

    2017-06-01

    In this work, we introduce the Kaiser-Bessel interpolation basis for the particle-mesh interpolation in the fast Ewald method. A reliable a priori error estimate is developed to measure the accuracy of the force computation in correlated charge systems, and is shown to be effective in optimizing the shape parameter of the Kaiser-Bessel basis in terms of accuracy. By comparing the optimized Kaiser-Bessel basis with the traditional B -spline basis, we demonstrate that the former is more accurate than the latter in part of the working parameter space, say, a relatively small real-space cutoff, a relatively small reciprocal space mesh, and a relatively large truncation of basis. In some cases, the Kaiser-Bessel basis is found to be more than one order of magnitude more accurate.

  18. Kaiser-Bessel basis for particle-mesh interpolation.

    PubMed

    Gao, Xingyu; Fang, Jun; Wang, Han

    2017-06-01

    In this work, we introduce the Kaiser-Bessel interpolation basis for the particle-mesh interpolation in the fast Ewald method. A reliable a priori error estimate is developed to measure the accuracy of the force computation in correlated charge systems, and is shown to be effective in optimizing the shape parameter of the Kaiser-Bessel basis in terms of accuracy. By comparing the optimized Kaiser-Bessel basis with the traditional B-spline basis, we demonstrate that the former is more accurate than the latter in part of the working parameter space, say, a relatively small real-space cutoff, a relatively small reciprocal space mesh, and a relatively large truncation of basis. In some cases, the Kaiser-Bessel basis is found to be more than one order of magnitude more accurate.

  19. Structural and biochemical characterization of the wild type PCSK9-EGF(AB) complex and natural familial hypercholesterolemia mutants.

    PubMed

    Bottomley, Matthew J; Cirillo, Agostino; Orsatti, Laura; Ruggeri, Lionello; Fisher, Timothy S; Santoro, Joseph C; Cummings, Richard T; Cubbon, Rose M; Lo Surdo, Paola; Calzetta, Alessandra; Noto, Alessia; Baysarowich, Jennifer; Mattu, Marco; Talamo, Fabio; De Francesco, Raffaele; Sparrow, Carl P; Sitlani, Ayesha; Carfí, Andrea

    2009-01-09

    PCSK9 regulates low density lipoprotein receptor (LDLR) levels and consequently is a target for the prevention of atherosclerosis and coronary heart disease. Here we studied the interaction, of LDLR EGF(A/AB) repeats with PCSK9. We show that PCSK9 binds the EGF(AB) repeats in a pH-dependent manner. Although the PCSK9 C-terminal domain is not involved in LDLR binding, PCSK9 autocleavage is required. Moreover, we report the x-ray structure of the PCSK9DeltaC-EGF(AB) complex at neutral pH. Compared with the low pH PCSK9-EGF(A) structure, the new structure revealed rearrangement of the EGF(A) His-306 side chain and disruption of the salt bridge with PCSK9 Asp-374, thus suggesting the basis for enhanced interaction at low pH. In addition, the structure of PCSK9DeltaC bound to EGF(AB)(H306Y), a mutant associated with familial hypercholesterolemia (FH), reveals that the Tyr-306 side chain forms a hydrogen bond with PCSK9 Asp-374, thus mimicking His-306 in the low pH conformation. Consistently, Tyr-306 confers increased affinity for PCSK9. Importantly, we found that although the EGF(AB)(H306Y)-PCSK9 interaction is pH-independent, LDLR(H306Y) binds PCSK9 50-fold better at low pH, suggesting that factors other than His-306 contribute to the pH dependence of PCSK9-LDLR binding. Further, we determined the structures of EGF(AB) bound to PCSK9DeltaC containing the FH-associated D374Y and D374H mutations, revealing additional interactions with EGF(A) mediated by Tyr-374/His-374 and providing a rationale for their disease phenotypes. Finally, we report the inhibitory properties of EGF repeats in a cellular assay measuring LDL uptake.

  20. Structural and Biophysical Characterization of Bacillus thuringiensis Insecticidal Proteins Cry34Ab1 and Cry35Ab1

    PubMed Central

    Kelker, Matthew S.; Berry, Colin; Evans, Steven L.; Pai, Reetal; McCaskill, David G.; Wang, Nick X.; Russell, Joshua C.; Baker, Matthew D.; Yang, Cheng; Pflugrath, J. W.; Wade, Matthew; Wess, Tim J.; Narva, Kenneth E.

    2014-01-01

    Bacillus thuringiensis strains are well known for the production of insecticidal proteins upon sporulation and these proteins are deposited in parasporal crystalline inclusions. The majority of these insect-specific toxins exhibit three domains in the mature toxin sequence. However, other Cry toxins are structurally and evolutionarily unrelated to this three-domain family and little is known of their three dimensional structures, limiting our understanding of their mechanisms of action and our ability to engineer the proteins to enhance their function. Among the non-three domain Cry toxins, the Cry34Ab1 and Cry35Ab1 proteins from B. thuringiensis strain PS149B1 are required to act together to produce toxicity to the western corn rootworm (WCR) Diabrotica virgifera virgifera Le Conte via a pore forming mechanism of action. Cry34Ab1 is a protein of ∼14 kDa with features of the aegerolysin family (Pfam06355) of proteins that have known membrane disrupting activity, while Cry35Ab1 is a ∼44 kDa member of the toxin_10 family (Pfam05431) that includes other insecticidal proteins such as the binary toxin BinA/BinB. The Cry34Ab1/Cry35Ab1 proteins represent an important seed trait technology having been developed as insect resistance traits in commercialized corn hybrids for control of WCR. The structures of Cry34Ab1 and Cry35Ab1 have been elucidated to 2.15 Å and 1.80 Å resolution, respectively. The solution structures of the toxins were further studied by small angle X-ray scattering and native electrospray ion mobility mass spectrometry. We present here the first published structure from the aegerolysin protein domain family and the structural comparisons of Cry34Ab1 and Cry35Ab1 with other pore forming toxins. PMID:25390338