| 689 | 210 |
|---|
| References | 690 |
| Ab Initio Molecular Dynamics Simulations of Aqueous Glycine Solutions: Solvation Structure and Vibrational Spectra | 692 |
| Introduction | 692 |
| Methods | 693 |
| Results and Discussion | 695 |
| Conclusions and Outlook | 699 |
| References | 699 |
| Cyclodimerization of DNA and RNA Bases: Ab Initio Study of the Cyclodimerization of the Uracil Dimer Through a Butane-Like Conical Intersection | 702 |
| Introduction | 702 |
| Computational Methods | 704 |
| Results and Discussion | 705 |
| Geometry Optimization | 705 |
| Vertical Excitation Energies | 706 |
| Reaction-Path Energy Profiles | 707 |
| Conclusions | 709 |
| Technical Support | 709 |
| References | 710 |
| Numerical Simulation of Electric Field Gradient Focusing and Separation of Analytes in Microchannels with Embedded Bipolar Electrode | 712 |
| Introduction | 712 |
| Experimental Section | 713 |
| Theoretical Background | 715 |
| Numerical Methods | 718 |
| Results and Discussion | 719 |
| Conclusion | 722 |
| References | 723 |
| Part VIII Bio Sciences | 724 |
|---|
| Annotation of Entirely Sequenced Genomes | 725 |
| Methods | 726 |
| Iterated Profile-Based Search (PSI-BLAST) | 726 |
| Functional Sequence Motifs (ProSite) | 726 |
| Low-Complexity Regions (SEG) | 726 |
| Domain Assignment (ProDom) | 727 |
| Secondary Structure (PHDsec) | 727 |
| Solvent Accessibility (PHDacc) | 727 |
| Globularity of Proteins (GLOBE) | 728 |
| Transmembrane Helices (PHDhtm) | 728 |
| Secondary Structure (PROFsec) and Solvent Accessibility (PROFacc) | 728 |
| Coiled-Coil Regions (COILS) | 729 |
| Disulphide Bridges (DISULFIND) | 729 |
| Structural Switches (ASP) | 729 |
| Localisation Classification (LOCtree) | 729 |
| Prediction of Nuclear Localisation Signal (PredictNLS) | 730 |
| Keyword Based Prediction of Cellular Localization (LOCkey) | 730 |
| Prediction of Unstructured Loops (NORSnet) | 730 |
| Prediction of Natively Unstructured Regions Through Contacts (Ucon) | 731 |
| Meta-Disorder Predictor (MD) | 731 |
| Prediction of Flexibility (PROFbval) | 731 |
| Reflect | 731 |
| Results and Discussion | 733 |
| Parallelization Techniques | 733 |
| Number of Processors Used/Degree of Parallelization | 734 |
| Job Run Times | 735 |
| Conclusion | 735 |
| References | 736 |
| Molecular Dynamics Simulation of the Nascent Peptide Chain in the Ribosomal Exit Tunnel | 738 |
| Introduction | 738 |
| Methods | 740 |
| Principles of Molecular Dynamics | 740 |
| Periodic Boundary Condition | 742 |
| Temperature and Pressure Coupling | 742 |
| Parallelisation Techniques | 743 |
| Preparation of Simulation System | 743 |
| Results | 744 |
| Achieved Performance on the HLRB system | 744 |
| Conformations of Polypeptides Inside the Tunnel | 744 |
| References | 746 |
| Preparing RAxML for the SPEC MPI Benchmark Suite | 747 |
| Introduction | 747 |
| The Phylogenetic Likelihood Kernel | 749 |
| Sources of Parallelism in Phylogenetic Analyses and Related Work | 750 |
| Efficient Parallelization of the Phylogenetic Likelihood Kernel | 751 |
| Master/Worker Scheme | 752 |
| Experimental Setup and Results | 754 |
| Conclusion | 756 |
| References | 757 |
| Parallel Computing with the R Language in a Supercomputing Environment | 759 |
| Introduction | 759 |
| R and Parallel Computing | 760 |
| R at the HLRB2 | 761 |
| Benchmark | 763 |
| Applications | 764 |
| Indirect Comparison of Interaction Graphs | 764 |
| Parallel Computing in Microarray Data | 766 |
| Conclusion | 768 |
| References | 769 |
