Reto Koradi's research while affiliated with Samsung and other places

A method and an apparatus provide a carousel interface for efficiently accessing data in a touchscreen enabled device. At least one previously navigated object is displayed in a reference region of the carousel interface. Objects associated with a last navigated object are displayed in a carousel belt region of the carousel interface such that the carousel belt region wraps around one end of the reference region. A user input for selecting an object in the carousel interface is received. In response to the user input for selecting an object, the carousel interface is navigated to the selected object, and the carousel interface is updated with the selected object as the last navigated object.

A new algorithm for molecular dynamics simulations of biological macromolecules on parallel computers, point-centered domain decomposition, is introduced. The molecular system is divided into clusters that are assigned to individual processors. Each cluster is characterized by a center point and comprises all atoms that are closer to its center point than to the center point of any other cluster. The point-centered domain decomposition algorithm is implemented in the new program OPALpusinga standard message passing library, so that it runs on both shared memory and massively parallel distributed memory computers. Benchmarks show that the program makes efficient use of up to 100 and more processors for realistic systems of a protein in water comprising 10000 to 20000 atoms. 2000 Elsevier Science B.V. All rights reserved. Keywords: Molecular dynamics; Parallel computing; Message passing; Domain decomposition; MPI; OPALp 1. Introduction Molecular dynamics (MD) simulations [1] have be...

A new approach for automated peak picking of multidimensional protein NMR spectra with strong overlap is introduced, which makes use of the program AUTOPSY (automatedpeak picking for NMRspectroscopy). The main elements of this program are a novel function for local noise level calculation, the use of symmetry considerations, and the use of lineshapes extracted from well-separated peaks for resolving groups of strongly overlapping peaks. The algorithm generates peak lists with precise chemical shift and integral intensities, and a reliability measure for the recognition of each peak. The results of automated peak picking of NOESY spectra with AUTOPSY were tested in combination with the combined automated NOESY cross peak assignment and structure calculation routine NOAH implemented in the program DYANA. The quality of the resulting structures was found to be comparable with those from corresponding data obtained with manual peak picking.

MOLMOL is a molecular graphics program for display, analysis, and manipulation of three-dimensional structures of biological macromolecules, with special emphasis on nuclear magnetic resonance (NMR) solution structures of proteins and nucleic acids. MOLMOL has a graphical user interface with menus, dialog boxes, and on-line help. The display possibilities include conventional presentation, as well as novel schematic drawings, with the option of combining different presentations in one view of a molecule. Covalent molecular structures can be modified by addition or removal of individual atoms and bonds, and three-dimensional structures can be manipulated by interactive rotation about individual bonds. Special efforts were made to allow for appropriate display and analysis of the sets of typically 20–40 conformers that are conventionally used to represent the result of an NMR structure determination, using functions for superimposing sets of conformers, calculation of root mean square distance (RMSD) values, identification of hydrogen bonds, checking and displaying violations of NMR constraints, and identification and listing of short distances between pairs of hydrogen atoms.

MOLMOL is a molecular graphics program for display, analysis, and manipulation of three-dimensional structures of biological macromolecules, with special emphasis on nuclear magnetic resonance (NMR) solution structures of proteins and nucleic acids. MOLMOL has a graphical user interface with menus, dialog boxes, and on-line help. The display possibilities include conventional presentation, as well as novel schematic drawings, with the option of combining different presentations in one view of a molecule. Covalent molecular structures can be modified by addition or removal of individual atoms and bonds, and three-dimensional structures can be manipulated by interactive rotation about individual bonds. Special efforts were made to allow for appropriate display and analysis of the sets of typically 20-40 conformers that are conventionally used to represent the result of an NMR structure determination, using functions for superimposing sets of conformers, calculation of root mean square distance (RMSD) values, identification of hydrogen bonds, checking and displaying violations of NMR constraints, and identification and listing of short distances between pairs of hydrogen atoms.

Mikrofiche-Ausg.: 2 Mikrofiches : 24x. Zürich, Eidgenössische Techn. Hochsch., Diss., 1996.

Diss. Nr. 11977 techn. Wiss. ETH Zürich. Literaturverz.