| 1. |
- Aidas, Kestutis, et al.
(författare)
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The Dalton quantum chemistry program system
- 2014
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Ingår i: Wiley Interdisciplinary Reviews. Computational Molecular Science. - : Wiley. - 1759-0876. ; 4:3, s. 269-284
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Tidskriftsartikel (refereegranskat)abstract
- Dalton is a powerful general-purpose program system for the study of molecular electronic structure at the Hartree-Fock, Kohn-Sham, multiconfigurational self-consistent-field, MOller-Plesset, configuration-interaction, and coupled-cluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronic-structure models. Molecular gradients and Hessians are available for geometry optimizations, molecular dynamics, and vibrational studies, whereas magnetic resonance and optical activity can be studied in a gauge-origin-invariant manner. Frequency-dependent molecular properties can be calculated using linear, quadratic, and cubic response theory. A large number of singlet and triplet perturbation operators are available for the study of one-, two-, and three-photon processes. Environmental effects may be included using various dielectric-medium and quantum-mechanics/molecular-mechanics models. Large molecules may be studied using linear-scaling and massively parallel algorithms. Dalton is distributed at no cost from for a number of UNIX platforms.
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| 2. |
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| 3. |
- Luhmann, J. G., et al.
(författare)
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Investigating magnetospheric interaction effects on Titan's ionosphere with the Cassini orbiter Ion Neutral Mass Spectrometer, Langmuir Probe and magnetometer observations during targeted flybys
- 2012
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Ingår i: Icarus. - : Elsevier BV. - 0019-1035 .- 1090-2643. ; 219:2, s. 534-555
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Tidskriftsartikel (refereegranskat)abstract
- In the similar to 6 years since the Cassini spacecraft went into orbit around Saturn in 2004, roughly a dozen Titan flybys have occurred for which the Ion Neutral Mass Spectrometer (INMS) measured that moon's ionospheric density and composition. For these, and for the majority of the similar to 60 close flybys probing to altitudes down to similar to 950 km, Langmuir Probe electron densities were also obtained. These were all complemented by Cassini magnetometer observations of the magnetic fields affected by the Titan plasma interaction. Titan's ionosphere was expected to differ from those of other unmagnetized planetary bodies because of significant contributions from particle impact due to its magnetospheric environment. However, previous analyses of these data clearly showed the dominance of the solar photon source, with the possible exception of the nightside. This paper describes the collected ionospheric data obtained in the period between Cassini's Saturn Orbit Insertion in 2004 and 2009, and examines some of their basic characteristics with the goal of searching for magnetospheric influences. These influences might include effects on the altitude profiles of impact ionization by magnetospheric particles at the Titan orbit location, or by locally produced pickup ions freshly created in Titan's upper atmosphere. The effects of forces on the ionosphere associated with both the draped and penetrating external magnetic fields might also be discernable. A number of challenges arise in such investigations given both the observed order of magnitude variations in the magnetospheric particle sources and the unsteadiness of the magnetospheric magnetic field and plasma flows at Titan's (similar to 20Rs (Saturn Radius)) orbit. Transterminator flow of ionospheric plasma from the dayside may also supply some of the nightside ionosphere, complicating determination of the magnetospheric contribution. Moreover, we are limited by the sparse sampling of the ionosphere during the mission as the Titan interaction also depends on Saturn Local Time as well as possible intrinsic asymmetries and variations of Titan's neutral atmosphere. We use organizations of the data by key coordinate systems of the plasma interaction with Titan's ionosphere to help interpret the observations. The present analysis does not find clear characteristics of the magnetosphere's role in defining Titan's ionosphere. The observations confirm the presence of an ionosphere produced mainly by sunlight, and an absence of expected ionospheric field signatures in the data. Further investigation of the latter, in particular, may benefit from numerical experiments on the inner boundary conditions of 3D models including the plasma interaction and features such as neutral winds.
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| 4. |
- Niskanen, Johannes, et al.
(författare)
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Experimental and theoretical study of core-valence double photoionization of OCS
- 2010
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Ingår i: Physical Review A. Atomic, Molecular, and Optical Physics. - 1050-2947 .- 1094-1622. ; 82:4, s. 043436-
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Tidskriftsartikel (refereegranskat)abstract
- O 1s, C 1s, and S 2p core-valence double ionization electron spectra of the OCS molecule have been obtained experimentally by a time-of-flight photoelectron-photoelectron coincidence spectroscopy technique. In order to analyze and assign the spectral features observed, we present a protocol for computing core-valence ionization energies of such systems. The protocol is based on a restricted active space multiconfigurational self-consistent field (MCSCF) methodology with a freeze-relax procedure to guarantee a correct core-valence state root index without variational collapse. Corrections for extended dynamical correlation and core-core correlation, respectively, are made by multiconfigurational perturbation theory and by uncontracted basis set Moller-Plesset theory. Envisioning applications to larger molecules, a spin-restricted open-shell density functional method is also applied for the lowest core-valence energies. Furthermore, cross sections through a scheme for computing multiatom Auger transitions generating core-valence holes are presented. We find that the procedure outlined is capable of deriving the energy onset of core-valence ionization within a fraction of an eV and that assignments can be made of the most salient spectral features.
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| 5. |
- Thiele, I., et al.
(författare)
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A community-driven global reconstruction of human metabolism
- 2013
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Ingår i: Nature Biotechnology. - : Springer Science and Business Media LLC. - 1087-0156 .- 1546-1696. ; 31:5, s. 419-
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Tidskriftsartikel (refereegranskat)abstract
- Multiple models of human metabolism have been reconstructed, but each represents only a subset of our knowledge. Here we describe Recon 2, a community-driven, consensus 'metabolic reconstruction', which is the most comprehensive representation of human metabolism that is applicable to computational modeling. Compared with its predecessors, the reconstruction has improved topological and functional features, including similar to 2x more reactions and similar to 1.7x more unique metabolites. Using Recon 2 we predicted changes in metabolite biomarkers for 49 inborn errors of metabolism with 77% accuracy when compared to experimental data. Mapping metabolomic data and drug information onto Recon 2 demonstrates its potential for integrating and analyzing diverse data types. Using protein expression data, we automatically generated a compendium of 65 cell type-specific models, providing a basis for manual curation or investigation of cell-specific metabolic properties. Recon 2 will facilitate many future biomedical studies and is freely available at http://humanmetabolism.org/.
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| 6. |
- Aidas, Kestutis, et al.
(författare)
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Photoabsorption of Acridine Yellow and Proflavin Bound to Human Serum Albumin Studied by Means of Quantum Mechanics/Molecular Dynamics
- 2013
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 117:7, s. 2069-2080
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Tidskriftsartikel (refereegranskat)abstract
- Attempting to unravel mechanisms in optical probing of proteins, we have performed pilot calculations of two cationic chromophores-acridine yellow and proflavin-located at different binding sites within human serum albumin, including the two primary drug binding sites as well as a heme binding site. The computational scheme adopted involves classical molecular dynamics simulations of the ligands bound to the protein and subsequent linear response polarizable embedding density functional theory calculations of the excitation energies. A polarizable embedding potential consisting of point charges fitted to reproduce the electrostatic potential and isotropic atomic polarizabilities computed individually for every residue of the protein was used in the linear response calculations. Comparing the calculated aqueous solution-to-protein shifts of maximum absorption energies to available experimental data, we concluded that the cationic proflavin chromophore is likely not to bind albumin at its drug binding site I nor at its heme binding site. Although agreement with experimental data could only be obtained in qualitative terms, our results clearly indicate that the difference in optical response of the two probes is due to deprotonation, and not, as earlier suggested, to different binding sites. The ramifications of this finding for design of molecular probes targeting albumin or other proteins is briefly discussed.
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| 7. |
- Andersson, Egil, 1981-, et al.
(författare)
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Core-valence double photoionization of the CS2 molecule
- 2010
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 133:9, s. 94305-
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Tidskriftsartikel (refereegranskat)abstract
- Double photoionization spectra of the CS2 molecule have been recorded using the TOF-PEPECO technique in combination with synchrotron radiation at the photon energies h nu=220, 230, 240, 243, and 362.7 eV. The spectra were recorded in the S 2p and C 1s inner-shell ionization regions and reflect dicationic states formed out of one inner-shell vacancy and one vacancy in the valence region. MCSCF calculations were performed to model the energies of the dicationic states. The spectra associated with a S 2p vacancy are well structured and have been interpreted in some detail by comparison to conventional S 2p and valence photoelectron spectra. The lowest inner-shell-valence dicationic state is observed at the vertical double ionization energy 188.45 eV and is associated with a (2p(3/2))(-1)(2 pi(g))(-1) double vacancy. The spectrum connected to the C 1s vacancy shows a distinct line at 310.8 eV, accompanied by additional broad features at higher double ionization energies. This line is associated with a (C 1s)(-1)(2 pi(g))(-1) double vacancy. (C-) 2010 American Institute of Physics. [doi: 10.1063/1.3469812]
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| 8. |
- Becker, Chandler A., et al.
(författare)
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Thermodynamic modelling of liquids : CALPHAD approaches and contributions from statistical physics
- 2014
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Ingår i: Physica status solidi. B, Basic research. - : Wiley. - 0370-1972 .- 1521-3951. ; 251:1, s. 33-52
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Tidskriftsartikel (refereegranskat)abstract
- We describe current approaches to thermodynamic modelling of liquids for the CALPHAD method, the use of available experimental methods and results in this type of modelling, and considerations in the use of atomic-scale simulation methods to inform a CALPHAD approach. We begin with an overview of the formalism currently used in CALPHAD to describe the temperature dependence of the liquid Gibbs free energy and outline opportunities for improvement by reviewing the current physical understanding of the liquid. Brief descriptions of experimental methods for extracting high-temperature data on liquids and the preparation of undercooled liquid samples are presented. Properties of a well-determined substance, B-2 O-3, including the glass transition, are then discussed in detail to emphasize specific modelling requirements for the liquid. We then examine the two-state model proposed for CALPHAD in detail and compare results with experiment and theory, where available. We further examine the contributions of atomic-scale methods to the understanding of liquids and their potential for supplementing available data. We discuss molecular dynamics (MD) and Monte Carlo methods that employ atomic interactions from classical interatomic potentials, as well as contributions from ab initio MD. We conclude with a summary of our findings.
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| 9. |
- Cravens, T. E., et al.
(författare)
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Dynamical and magnetic field time constants for Titan's ionosphere : Empirical estimates and comparisons with Venus
- 2010
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Ingår i: Journal of Geophysical Research. - 0148-0227 .- 2156-2202. ; 115:8, s. A08319-
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Tidskriftsartikel (refereegranskat)abstract
- Plasma in Titan's ionosphere flows in response to forcing from thermal pressure gradients, magnetic forces, gravity, and ion-neutral collisions. This paper takes an empirical approach to the ionospheric dynamics by using data from Cassini instruments to estimate pressures, flow speeds, and time constants on the dayside and nightside. The plasma flow speed relative to the neutral gas speed is approximately 1 m s(-1) near an altitude of 1000 km and 200 m s(-1) at 1500 km. For comparison, the thermospheric neutral wind speed is about 100 m s(-1). The ionospheric plasma is strongly coupled to the neutrals below an altitude of about 1300 km. Transport, vertical or horizontal, becomes more important than chemistry in controlling ionospheric densities above about 1200-1500 km, depending on the ion species. Empirical estimates are used to demonstrate that the structure of the ionospheric magnetic field is determined by plasma transport (including neutral wind effects) for altitudes above about 1000 km and by magnetic diffusion at lower altitudes. The paper suggests that a velocity shear layer near 1300 km could exist at some locations and could affect the structure of the magnetic field. Both Hall and polarization electric field terms in the magnetic induction equation are shown to be locally important in controlling the structure of Titan's ionospheric magnetic field. Comparisons are made between the ionospheric dynamics at Titan and at Venus.
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| 10. |
- Cui, J., et al.
(författare)
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Ion transport in Titan's upper atmosphere
- 2010
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Ingår i: Journal of Geophysical Research. - 0148-0227 .- 2156-2202. ; 115, s. A06314-
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Tidskriftsartikel (refereegranskat)abstract
- Based on a combined Cassini data set including Ion Neutral Mass Spectrometer, Radio Plasma Wave Science, and Magnetometer measurements made during nine close encounters of the Cassini spacecraft with Titan, we investigate the electron ( or total ion) distribution in the upper ionosphere of the satellite between 1250 and 1600 km. A comparison of the measured electron distribution with that in diffusive equilibrium suggests global ion escape from Titan with a total ion loss rate of similar to(1.7 +/- 0.4) x 10(25) s(-1). Significant diurnal variation in ion transport is implied by the data, characterized by ion outflow at the dayside and ion inflow at the nightside, especially below similar to 1400 km. This is interpreted as a result of day-to-night ion transport, with a horizontal transport rate estimated to be similar to(1.4 +/- 0.5) x 10(24) s(-1). Such an ion flow is likely to be an important source for Titan's nightside ionosphere, as proposed in Cui et al. [2009a].
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