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Neudorfer J.,University of Stuttgart | Stock A.,University of Stuttgart | Schneider R.,Karlsruhe Institute of Technology | Roller S.,German Research School for Simulation science GmbH | And 2 more authors.
IEEE Transactions on Plasma Science | Year: 2013

We present the simulation of the transient excitation and evolution of a TE34, 19 mode in the resonant cavity of the 170 GHz gyrotron. This gyrotron is planned for electron cyclotron resonance heating in the ITER tokamak fusion reactor. The numerical computation of a state-of-the-art gyrotron resonant cavity with a transient 3-D full wave particle-in-cell (PIC) method is a computationally demanding task. It was enabled by a highly scalable PIC scheme. To allow the numerical simulation of the high-frequency electromagnetic waves, we use a high-order discontinuous Galerkin method. © 1973-2012 IEEE. Source


Olubiyi O.O.,Julich Research Center | Olubiyi O.O.,German Research School for Simulation science GmbH | Strodel B.,Julich Research Center | Strodel B.,Heinrich Heine University Dusseldorf
Journal of Physical Chemistry B | Year: 2012

In this simulation study, we present a comparison of the secondary structure of the two major alloforms of the Alzheimer's peptide (Aβ1-40 and Aβ1-42) on the basis of molecular dynamics (MD) simulations on thea microsecond time scale using the two GROMOS96 force fields ffG43a2 and ffG53a6. We observe peptide and force-field related differences in the sampled conformations of Aβ1-40 and Aβ1-42, which we characterize in terms of NMR chemical shifts calculated from the MD trajectories and validate against the corresponding experimental NMR results. From this analysis, we can conclude that ffG53a6 is better able to model the structural propensities of Aβ1-40 and Aβ1-42 than ffG43a2. Furthermore, we provide a description of the influences of pH and binding of D3, a 12-residue d-enantiomeric peptide with demonstrated antiamyloid effects, on the structure of Aβ1-42. We demonstrate that, under slightly acidic conditions, protonation of the three histidine residues in Aβ1-42 promotes the formation of β-sheets via a reduction in electrostatic repulsion between the two terminal regions. Our studies further reveal that the binding between D3 and Aβ1-42 is driven by electrostatic interactions between negatively charged Aβ1-42 residues and the five positively charged arginine residues of D3. The binding of D3 was found to induce large conformational changes in the amyloid peptide, with a reduction in β-sheet units being the most significant effect recorded, possibly explaining the observed amyloid-inhibiting properties of the d-peptide. © 2012 American Chemical Society. Source


Otte P.,RWTH Aachen | Otte P.,German Research School for Simulation science GmbH | Frank M.,RWTH Aachen
Computers and Mathematics with Applications | Year: 2015

We derive Lattice Boltzmann (LBM) schemes to solve the Linearized Euler Equations in 1D, 2D, and 3D with the future goal of coupling them to an LBM scheme for Navier Stokes Equations and a Finite Volume scheme for Linearized Euler Equations. The derivation uses the analytical Maxwellian in a BGK model. In this way, we are able to obtain second-order schemes. In addition, we perform an L2-stability analysis. Numerical results validate the approach. © 2015 Elsevier Ltd. Source


Kolar M.,Czech Institute of Organic Chemistry And Biochemistry | Kolar M.,German Research School for Simulation science GmbH | Kolar M.,Julich Research Center | Hostas J.,Czech Institute of Organic Chemistry And Biochemistry | And 2 more authors.
Physical Chemistry Chemical Physics | Year: 2014

The σ-holes of halogen atoms on various aromatic scaffolds were described in terms of their size and magnitude. The electrostatic potential maps at the CAM-B3LYP-D3(bj)/def2-QZVP level were calculated and the σ-holes of more than 100 aromatic analogues were thoroughly analysed to relate the σ-holes to the binding preferences of the halogenated compounds. Both the size and magnitude of the σ-hole increase when passing from chlorinated to iodinated analogues. Also, the σ-hole properties were studied upon chemical substitution of the aromatic ring as well as in the aromatic ring. Further, the angular variations of the interactions were investigated on a selected set of halogenbenzene complexes with argon and hydrogen fluoride (HF). In order to analyse interaction energy components, DFT-SAPT angular scans were performed. The interaction energies of bromobenzene complexes were evaluated at the CCSD(T)/complete basis set level providing the benchmark energetic data. The strength of the halogen bond between halogenbenzenes and Ar atoms and HF molecules increases while its directionality decreases when passing from chlorine to iodine. The decrease of the directionality of the halogen bond is larger for a HF-containing complex and is caused by electrostatic and exchange-repulsion energies. These findings are especially valuable for protein-halogenated ligand-binding studies, applied in the realm of rational drug development and lead optimisation. © the Partner Organisations 2014. Source


Assassa F.,RWTH Aachen | Assassa F.,German Research School for Simulation science GmbH | Marquardt W.,RWTH Aachen
Computers and Chemical Engineering | Year: 2014

We present a wavelet-based grid refinement approach for direct multiple shooting applied to dynamic optimization problems. The algorithm, named adaptive multiple shooting, automatically generates a problem-dependent parameterization of the control profiles: Starting from an initially coarse parameterization, the control grid is refined iteratively using a wavelet analysis of the previously obtained optimal solution. Additional grid points are only inserted where required and redundant grid points are eliminated. Hence, the algorithm minimizes the number of grid points required to obtain accurate optimal control trajectories.First, we demonstrate the superiority of adaptive grid refinement over an equidistant discretization for the Williams-Otto semi-batch reactor employing multiple and single shooting. Here, the accuracy is checked using an optimal solution obtained by an indirect optimization approach. Second, we successfully demonstrate the efficiency of adaptive grid refinement compared to an equidistant discretization employing multiple shooting to a dynamically unstable HIPS ( high impact poly. styrene) polymerization reactor. © 2013 . Source

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