The UltraScan data analysis application is a software package that is able to take advantage of computational resources in order to support the interpretation of analytical ultracentrifugation (AUC) experiments. Since 2006, the UltraScan scientific gateway has been used with ordinary Web browsers in TeraGrid by scientists studying the solution properties of biological and synthetic molecules. Unlike other applications, UltraScan is implemented on a gateway architecture and leverages the power of supercomputing to extract very high resolution information from the experimental data. In this contribution, we will focus on several improvements of the UltraScan scientific gateway that enable a standardized job submission and management to computational resources while retaining its lightweight design in order to not disturb the established workflows of its end-users. This paper further presents a walkthrough of the architectural design including one real installation deployment of UltraScan in Europe. The aim is to provide evidence for the added value of open standards and resulting interoperability enabling not only UltraScan application submissions to resources offered in the US cyber infrastructure Extreme Science and Engineering Discovery Environment (XSEDE), but also submissions to similar infrastructures in Europe and around the world. The use of the Apache Airavata framework for scientific gateways within our approach bears the potential to have an impact on several other scientific gateways too.

A recently developed empirical dispersion correction (Grimme et al., J. Chem. Phys. 2010, 132, 154104) to standard density functional theory (DFT-D3) is implemented in the plane-wave program package VASP. The DFT-D3 implementation is compared with an implementation of the earlier DFT-D2 version (Grimme, J. Comput. Chem. 2004, 25, 1463; Grimme, J. Comput. Chem. 2006, 27, 1787). Summation of empirical pair potential terms is performed over all atom pairs in the reference cell and over atoms in shells of neighboring cells until convergence of the dispersion energy is obtained. For DFT-D3, the definition of coordination numbers has to be modified with respect to the molecular version to ensure convergence. The effect of three-center terms as implemented in the original molecular DFT-D3 version is investigated. The empirical parameters are taken from the original DFT-D3 version where they had been optimized for a reference set of small molecules. As the coordination numbers of atoms in bulk and surfaces are much larger than in the reference compounds, this effect has to be discussed. The results of test calculations for bulk properties of metals, metal oxides, benzene, and graphite indicate that the original parameters are also suitable for solid-state systems. In particular, the interlayer distance in bulk graphite and lattice constants of molecular crystals is considerably improved over standard functionals. With the molecular standard parameters (Grimme et al., J. Chem. Phys. 2010, 132, 154104; Grimme, J. Comput. Chem. 2006, 27, 1787) a slight overbinding is observed for ionic oxides where dispersion should not contribute to the bond. For simple adsorbate systems, such as Xe atoms and benzene on Ag(111), the DFT-D implementations reproduce experimental results with a similar accuracy as more sophisticated approaches based on perturbation theory (Rohlfing and Bredow, Phys. Rev. Lett. 2008, 101, 266106).

Extreme responses of a droplet ensemble during an entrainment and mixing process as present at the edge of a cloud are investigated by means of three-dimensional direct numerical simulations in the Euler-Lagrangian framework. We find that the Damkohler number Da, a dimensionless parameter which relates the fluid time scale to the typical evaporation time scale, can capture all aspects of the initial mixing process within the range of parameters accessible in this study. The mixing process is characterized by the limits of strongly homogeneous (Da << 1) and strongly inhomogeneous (Da >> 1) regimes. We explore these two extreme regimes and study the response of the droplet size distribution to the corresponding parameter settings through an enhancement and reduction of the response constant K in the droplet growth equation. Thus, Da is varied while Reynolds and Schmidt numbers are held fixed, and initial microphysical properties are held constant. In the homogeneous limit minimal broadening of the size distribution is observed as the new steady state is reached, whereas in the inhomogeneous limit the size distribution develops strong negative skewness, with the appearance of a pronounced exponential tail. The analysis in the Lagrangian framework allows us to relate the pronounced negative tail of the supersaturation distribution to that of the size distribution.

This paper introduces the new benchmarking environment JuBE. It is a stand-alone framework independent of the underlying benchmark applications and supports all steps of performing and analyzing benchmark runs on different computer systems. These steps are fully recorded to allow a consistent administration and analysis of the runs. JuBE is the benchmarking environment chosen by the European Projects DEISA and PRACE.

In this chapter, techniques and methods for the structure determination of clusters are reviewed with emphasis on how the combination of experimental data and the results of quantum chemical calculations can lead to a reliable and accurate description of the electronic and geometrical structure of clusters. After a review of density functional theory methods used for the calculation of molecular properties, the basic principles and features of current experimental techniques for the analysis of clusters are discussed in the first section. The next section describes in detail, on the basis of a variety of examples, the possibility of combining experimental and theoretical results in order to obtain structural information for clusters. Special attention is paid to the question of how experimental data and the results of quantum chemical calculations can be compared, how the information obtained via experiment and theory complement each other, and what degree of agreement between theory and experiment can be expected. This leads to the final section, where the necessary experimental conditions and improvements of theoretical models and methods are summarized with the aim to achieve a better match between experimental and theoretical results, and to thus gain a deeper insight into the structural properties of clusters.

A MinMax self-consistent-field (SCF) approach is derived in the framework of auxiliary density functional theory. It is shown that the SCF convergence can be guided by the fitting coefficients that arise from the variational fitting of the Coulomb potential. An in-core direct inversion of the iterative subspace (DIIS) algorithm is presented. Due to its reduced memory demand this new in-core DIIS method can be applied without overhead to very large systems with tens of thousands of basis and auxiliary functions. Due to the new DIIS error definition systems with fractional occupation numbers can be treated, too.

The cooperativity of intermolecular hydrogen bonds and adsorbate-surface interaction was studied theoretically for the prototype system formamide-silver. A dispersion-corrected density-functional method was employed for the study of the adsorption of hydrogen-bonded formamide networks on the Ag(111) surface, in order to account for weak van der Waals interaction. The dispersion correction considerably improved the calculated adsorption energy of formaldehyde with respect to experiment. We observed anticooperativity of formamide hydrogen bonds and molecule-surface interaction: at low coverage the formamide monomers adsorb vertically at the Ag(111) surface forming a weak O-Ag chemical bond. In contrast, formamide dimers, and also higher polymers formed by linear dimer chains, preferentially adsorb parallel to the surface. The surface-adsorbate interaction is rather weak, as demonstrated by small interaction energies, large vertical distances, and small perturbation of the molecular electronic structure. Consequently the adsorbate structures are very close to the corresponding gas-phase polymers. In this way, the reduction of adsorption energy per molecule in the parallel arrangement compared to the vertical adsorption is overcompensated.

Surface relaxation phenomena have been studied in an electrochemical environment using halide modified Cu(100) electrodes as model systems to unravel the impact of the chemical nature of the adsorbed halide, the applied potential, and the presence of solvent species on the surface interlayer spacings. Both, in situ STM and in situ x-ray scattering data point to lateral structures of the adsorbed halides on Cu(100) which are identical for both chloride and bromide. Under saturation conditions both halides form a p(1x1) adlayer on Cu(100) with reference to a conventional choice of the substrate fcc unit cell. The in situ x-ray scattering data clearly indicate that the copper-halide and the copper-copper interlayer spacings are much more affected by potential changes when bromide is adsorbed on the copper surface and are less affected when chloride is present. This difference in the potential dependence of both halides can be attributed to the larger polarizability of the bromide anion that is almost discharged on the copper surface at the highest applied potentials, while chloride remains largely ionic in the adsorbed state even at the highest applied potential. At the lowest applied potential of E-work=-150 mV [vs reversible hydrogen electrode (RHE)] the Br-Cu and the topmost Cu-Cu layer distances are expanded by 0.150 and 0.058 A, respectively, with reference to their bulk analogs CuBr and Cu. These spacings continuously contract by up to 0.075 and 0.038 A when the electrode potential is increased to E-work=+50 mV (RHE). Intriguingly, the second Cu layer experiences a potential-dependent buckling due to a different second-shell coordination of Cu by bromide while deeper Cu layers retain the bulk spacing at all potentials. Changes in the halide-copper and the copper-copper interlayer spacings are strongly correlated. An understanding of the in situ x-ray results is achieved by periodic quantum-chemical calculations at density-functional level that allow a modeling of the interfacial structure under consideration of potential and additional solvation effects. The latter originate from interaction of water molecules and counterions in the outer Helmholtz layer with the specifically adsorbed halides in the inner Helmholtz layer.

The development of the cyclic cluster model (CCM) formalism for Kohn-Sham auxiliary density functional theory (KS-ADFT) methods is presented. The CCM is a direct space approach for the calculation of perfect and defective systems under periodic boundary conditions. Translational symmetry is introduced in the CCM by integral weighting. A consistent weighting scheme for all two-center and three-center interactions appearing in the KS-ADFT method is presented. For the first time, an approach for the numerical integration of the exchange-correlation potential within the cyclic cluster formalism is derived. The presented KS-ADFT CCM implementation was applied to covalent periodic systems. The results of cyclic and molecular cluster model (MCM) calculations for trans-polyacetylene, graphene, and diamond are discussed as examples for systems periodic in one, two, and three dimensions, respectively. All structures were optimized. It is shown that the CCM results represent the results of MCM calculations in the limit of infinite molecular clusters. By analyzing the electronic structure, we demonstrate that the symmetry of the corresponding periodic systems is retained in CCM calculations. The obtained geometric and electronic structures are compared with available data from the literature.

Boron-doped bulk diamond and the boron-doped hydrogen terminated (001) surface of diamond were investigated using the cyclic cluster model. Structure and stability of the hydrogen-terminated (001) surface were calculated and compared with experimental and other theoretical results from the literature. Boron-doping was modeled by substitution of a carbon atom by a boron atom in different positions with increasing distance from the surface up to boron-doped bulk diamond. In agreement with experiments on nanoclusters, boron is most stable in the first surface layers. (c) 2008 Wiley Periodicals, Inc. J Comput Chem, 2008.

Most known DNA-dependent RNA polymerases (RNAPs) share a universal heptapeptide, called the NADFDGD motif. The crystal structures of RNAPs indicate that in all cases this motif forms a loop with an embedded triad of aspartic acid residues. This conserved loop is the key part of the active site. Based on the crystal structures of the yeast RNAP II, we have studied this common active site for three cases: (1) single RNAP, (2) pre-translocation elongation complex, and (3) post-translocation elongation complex. Here we have applied two different modeling methods, the GGA density functional theory method (PBE) of quantum mechanics (QM) and the ReaxFF reactive force field. The QM calculations indicate that the loop shrinks from pre- to post-translocation and expands from post- to pre- translocation. In addition, PBE MD simulations in the gas phase at 310 K shows that the loop in the single-RNAP case is tightly connected to a catalytic Mg(2+) ion and that there is an ordered hydrogen bond network in the loop. The corresponding ReaxFF MD simulation presents a less stable loop structure, suggesting that ReaxFF may underestimate the coordinating interactions between carbonyl oxygen and magnesium ion compared to the gas phase QM. However, with ReaxFF it was practical to study the dynamics for a much more detailed model for the post-translocational case, including the complete loop and solvent. This leads to a plausible reactant-side model that may explain the large difference in efficiency of NTP polymerization between RNA and DNA polymerases.

Density functional theory optimized basis sets for gradient corrected functionals for 3d transition metal atoms are presented. Double zeta valence polarization and triple zeta valence polarization basis sets are optimized with the PW86 functional. The performance of the newly optimized basis sets is tested in atomic and molecular calculations. Excitation energies of 3d transition metal atoms, as well as electronic configurations, structural parameters, dissociation energies, and harmonic vibrational frequencies of a large number of molecules containing 3d transition metal elements, are presented. The obtained results are compared with available experimental data as well as with other theoretical data from the literature.