2009
For availability of preprints see personal webpage of co-workers
09-001
Peter Schuster
Welche Voraussetzungen benötigt Spitzenforschung und woran kann man ihre Ergebnisse messen?
ÖAW Almanach, 158: 277-282, 2009
09-002
Paul E. Phillipson and Peter Schuster
Modeling by Nonlinear Differential Equations: Dissipative and Conservative Processes
World Scientific, Hackensack, NJ, 2009
09-003
Peter Schuster
Free will, information, quantum mechanics, and biology. It pays to distinguish different forms of free choice and information
Complexity, 15(1): 8–10, 2009
09-004
Peter Schuster
Genotypes and phenotypes in the evolution of molecules
European Review, 17: 281–319, 2009
09-005
Ivo L. Hofacker
RNA secondary structure analysis using the Vienna RNA Package
In A.D. Baxevanis and D.B. Davison, editors
Current Protocols in Bioinformatics, volume 1. John Wiley & Sons, 2009
09-006
German G. Leparc, Thomas Tuchler, Gerald Striedner, Karl Bayer, Peter Sykacek, Ivo L. Hofacker and David P. Kreil
Model-based probe set optimization for high-performance microarrays
Nucl.Acids Res., 37: e18, 2009
09-007
Ronny Lorenz, Christoph Flamm and Ivo L. Hofacker
2d projections of RNA folding landscapes
In I. Grosse, S. Neumann, S. Posch, F. Schreiber, and P.F. Stadler, editors, German Conference on Bioinformatics 2009
volume 157 of Lecture Notes in Informatics, pages 11–20, Bonn, Gesellschaft f. Informatik, 2009
09-008
Thomas A. Jones, Wolfgang Otto, Manja Marz, Sean R. Eddy and Peter F. Stadler
A survey of nematode SmY RNAs
RNA Biology, 6: 5-8, 2009
09-009
Frank Jühling, Mario Mörl, Roland K. Hartmann, Mathias Sprinzl, Peter F. Stadler and Joern Pütz
tRNAdb 2009: compilation of tRNA sequences and tRNA genes
Nucleic.Acids Research, 37: D159-D162, 2009
09-010
Gil Benkö, Florian Centler, Peter Dittrich, Christoph Flamm, Bärbel M. R. Stadler and Peter F. Stadler
A Topological Approach to Chemical Organization
Alife, 15: 71-88, 2009
09-011
Gavin C. Conant and Peter F. Stadler
Solvent exposure imparts similar selective pressures across a range of yeast proteins
Mol.Biol.Evol., 26: 1155-1161, 2009
09-012
Claudia S. Copeland, Manja Marz, Dominic Rose, Jana Hertel, Paul J. Brindley, Clara Bermudez Santana, Stephanie Kehr, Camille Stephan Otto-Attolini and Peter F. Stadler
Homology-Based Annotation of Non-coding RNAs in the Genomes of Schistosoma mansoni and Schistosoma japonicum
BMC Genomic, 10: 464, 2009
09-013
Karen E. Chambers, Ryan McDaniell, Jeremy F. Raincrow, Maya Deshmukh, Peter F Stadler and Chi-hua Chiu
Hox cluster duplications in the basal teleost Hiodon alosoides (Osteoglossomorpha)
Th.Biosci., :online first , 2009
09-014
Jana Hertel, Danielle de Jong, Manja Marz, Dominic Rose, Hakim Tafer, Andrea Tanzer, Bernd Schierwater and Peter F. Stadler
Non-Coding RNA Annotation of the Genome of Trichoplax adhaerens
Nucleic Acids Res., 37: 1602-1615, 2009
09-015
Michael Hiller, Sven Findeiss, Claudia Nickel, Sandro Lein, Manja Marz, Dominik Rose, Christine Schulz, Rolf Backofen, Sonja J. Prohaska, Gunter Reuter and Peter F. Stadler
Conserved Introns Reveal Novel Transcripts in Drosophila melanogaster
Genome Res., : 19(7) , 1289-1300, 2009
09-016
Markus Riester, Peter F. Stadler and Konstantin Klemm
FRANz: Fast reconstruction of wild pedigrees
Bioinformatics, 25: 2134-2139, 2009
09-017
Konstantin Klemm and Peter F. Stadler
A note on fundamental, non-fundamental, and robust cycle bases
Discrete Appl.Math., 157: 2432-2438 , 2009
09-018
Axel Mosig, Türker Biyikoglu, Sonja J. Prohaska and Peter F. Stadler
Discovering cis-regulatory modules by optimizing barbecues
Discr.Appl.Math., 157: 2458-2468, 2009
09-019
David Langenberger, Clara Bermudez-Santana, Jana Hertel, Philipp Khaitovich, Steve Hoffmann and Peter F. Stadler
Evidence for Human microRNA-Offset RNAs in Small RNA Sequencing Data
Bioinformatics, 25(18): 2298-301, 2009
09-020
W.N. Gansterer, A.R. Gruber and C. Pacher
Non-splitting Tridiagonalization of Complex Symmetric Matrices
ICCS 2009, Part I, LNCS 5544, Springer-Verlag Berlin, pp. 481-490, 2009
09-021
Konstantin S. Rutkowski, Alfred Karpfen, Sonia M. Melikova, Wouter A. Herrebout, Alexander Koll, Peter Wolschann and Benjamin J. van der Veken
Cryospectroscopic and ab initio studies of haloform-trimethylamine H-bonded complexes
Phys.Chem.Chem.Phys., 11: 1551-1563, 2009
09-022
Pornpan Pungpo, Auradee Punkvang, Patchreenart Saparpakorn, Peter Wolschann and Supa Hannongbua
Recent Advances in NNRTI Design: Computer-Aided Molecular Design Approaches
Curr.Comp.-Aided Drug Design, 5: 1-12, 2009
09-023
Chakguy Prakasvudhisarn, Peter Wolschann and Luckhana Lawtrakul
Predicting Complexation Thermodynamic Parameters of βCyclodextrin with Chiral Guests by Using Swarm Intelligence and Support Vector Machines
Int.J.Mol.Sci., 10: 2107-2121, 2009
09-024
Kirsten Knape, Anton Beyer, Anna Stary, Gerhard Buchbauer and Peter Wolschann
Evolutionary trace of human odorant receptors of chromosome 17
Flavour Fragr.J., 24: 192-197, 2009
09-025
Sharareh Salar Behzadi, Chakguy Prakasvudhisarn, Johanna Klocker,Peter Wolschann and Helmut Viernstein
Comparison between two types of Artificial Neural Networks used for validation of pharmaceutical processes
Powder Technology, 195: 150–157, 2009
09-026
Iris Stappen, Gerhard Buchbauer, Wolfgang Robien and Peter Wolschann
13C-NMR spectra of santalol derivatives: a comparison of DFT-based calculations and database-oriented prediction techniques
Magn.Reson.Chem., 47: 720–726, 2009
09-027
Walter Snorr, Elisabeth Liedl, Petra Weiss-Greiler, Helmut Viernstein, Peter Wolschann
Density functional calculations on meloxicam–β-cyclodextrin inclusion complexes
Int.J.Pharma., 381: 146-152, 2009
09-028
Piyarat Nimmanpipug, Vannajan S. Lee, Peter Wolschann and Supot Hannongbua
Litchi chinensis-derived terpenoid as anti-HIV-1 protease agent: structural design from molecular dynamics simukations
Mol.Sim., 35: 673-680, 2009
09-029
Alfred Karpfen, Elisabeth Liedl and Peter Wolschann
Diazene, a Potential New Hydrogen Bond Donor and Acceptor with Blue-Shifted N–H Stretching Modes: A Theoretical Study
Polish J.Chem., 83: 933-942, 2009
09-030
J.C. Sancho-García, Alfred Karpfen
Theoretical approach to the conformational analysis of heteroaromatic dimers: 2-(2-Thienyl)pyrrole, 2-(2-thienyl)furan, and 2-(2-furyl)pyrrole
Chem.Phys.Letters, 473: 49-56, 2009
09-031
Alfred Karpfen and Eugene S. Kryachko
On the Intramolecular Origin of the Blue Shift of A - H Stretching Frequencies: Triatomic Hydrides HAX
J.Phys.Chem.A, 113: 5217-5223, 2009
09-032
K.S. Rutkowski, Alfred Karpfen, S.M. Melikova and P. Rodziewicz
Blue and Red Frequency Shift Effects Related with XA–H···B–Y Complex Formation
Polish J.Chem., 83: 965-980, 2009
09-033
Mario Vazdara, Mirjana Eckert-Maksic, Mario Barbatti and Hans Lischka
Excited-state non-adiabatic dynamics simulations of pyrrole
Mol.Phys., 107: 845-854, 2009
09-034
Mario Barbatti, Adelia J. Aquino, Hans Lischka, Christian Schriever,Stefan Lochbrunner and Eberhard Riedle
Ultrafast internal conversion pathway and mechanism in 2-(2'-hydroxyphenyl)benzothiazole: a case study for excited-state intramolecular proton transfer systems
Phys.Chem.Chem.Phys., 11: 1406-1415, 2009
09-035
Mario Barbatti, Hans Lischka, Susanne Salzmann and Christel M. Marian
UV excitation and radiationless deactivation of imidazol
J.Chem.Phys., 130: 034305, 2009
09-036
Jiri Pittner , Hans Lischka and Mario Barbatt
Optimization of mixed quantum-classical dynamics: Time-derivative coupling terms and selected couplings
Chem.Phys., 356: 147-152, 2009
09-037
Bernhard Sellner, Mario Barbatti and Hans Lischka
Dynamics starting at a conical intersection: Application to the photochemistry of pyrrole
J.Chem.Phys., 131: 024312, 2009
09-038
Itamap Borges Jr., Adelia J.A. Aquino, Mario Barbatti and Hans Lischka
The Electronically Excited States of RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine): Vertical Excitations
Int.J.Quant.Chem., 109: 2348–2355, 2009
09-039
Daniel Tunega, Martin H. Gerzabek, Georg Haberhauer, Kai U. Totsched and Hans Lischka
Model study on sorption of polycyclic aromatic hydrocarbons to goethite
J.of Colloid and Interf.Sci., 330: 244–249, 2009
09-040
Felix Plasser, Mario Barbatti, Adelia J.A. Aquino and Hans Lischka
Excited-State Diproton Transfer in [2,2'-Bipyridyl]-3,3'-diol: the Mechanism Is Sequential, Not Concerted
J.Phys.Chem.A., 113: 8490–8499, 2009
09-041
Ivelina Georgieva, Lubomir Benco, Daniel Tunega, Natasha Trendafilova, Jürgen Hafner and Hans Lischka
Multiple adsorption of NO on cobalt-exchanged chabazite, mordenite, and ferrierite zeolites: A periodic density functional theory study
J.Chem.Phys., 131: 054101, 2009
09-042
Mirjana Eckert-Maksic, Hans Lischka, Zvonimir B. Maksic and Mario Vazdar
The Isomerization Barrier in Cyanocyclobutadienes: An ab Initio Multireference Average Quadratic Coupled Cluster Study
J.Phys.Chem.A, 113: 8351–8358, 2009
09-043
Adelia J.A. Aquino, Felix Plasser, Mario Barbatti, Hans Lischka
Ultrafast Excited-state Proton Transfer Processes: Energy Surfaces and On-the-fly Dynamics Simulations
Croat.Chem.Acta, 82: 105-114, 2009
09-044
Adelia J.A. Aquino, Daniel Tunega, Gabriele E. Schaumann, Georg Haberhauer, Martin H. Gerzabek and Hans Lischka
Stabilizing Capacity of Water Bridges in Nanopore Segments of Humic Substances: A Theoretical Investigation
J.Phys.Chem.C, 113: 16468–16475, 2009
09-045
Jaroslaw J. Szymczak, Mario Barbatti, Jason T. Soo Hoo, Jaclyn A. Adkins, Theresa L. Windus, Dana Nachtigallova, Hans Lischka
Photodynamics Simulations of Thymine: Relaxation into the First Excited Singlet State
J.Phys.Chem. A, 113: 12686–12693, 2009
09-046
Jaroslaw J. Szymczak, Mario Barbatti, Hans Lischka
Is the Photoinduced Isomerization in Retinal Protonated Schiff Bases a Single- or Double-Torsional Process?
J.Phys.Chem. A, 113: 11907–11918, 2009
09-047
Vladimir Lukes, Roland Solc, Hans Lischka and Harald Friedrich Kauffmann
Theoretical Study of the Relations between Structure and Photophysical Properties of Model Oligofluorenes with Central Keto Defect
J.Phys.Chem. A, 113: 14141–14149, 2009
09-048
Christoph Uiberacker and Werner Jakubetz
Strong-field dipole resonance: Limiting analytical cases
Phys.Rev.A, 80: 063406, 2009
09-049
Bernhard Helffer, Thomas Hoffmann-Ostenhof and S. Terracini
Nodal domains and spectral minimal partitions
Ann.I.H. Poincaré, 26: 101–138, 2009
09-050
Soren Fournais, Maria Hoffmann-Ostenhof, Thomas Hoffmann-Ostenhof and Thomas Ostergaard Sorensen
Analytic structure of solutions to multiconfiguration equations
J.Phys.A:Math.Theor., 42: 315208, 2009
09-051
Soren Fournais, Maria Hoffmann-Ostenhof, Thomas Hoffmann-Ostenhof and Thomas Ostergaard Sorensen
Analtic Structure of Mandy-Body Coulombic Wave Functions
Commun.Math.Phys., 289: 291-310, 2009
09-052
Virginie Bonnaillie-Noel, Bernhard Helffer and Thomas Hoffmann-Ostenhof
Aharonov-Bohm Hamiltonians, isospectrality and minimal partitions
J.Phys.A:Math.Theor., 42: 185203, 2009
09-053
Katharina F. Pirker, Christopher W.M. Kay, Klaus Stolze, Daniel Tunega, Thomas G. Reichenauer and Bernhard A. Goodman
Free radical generation in rosmarinic acid investigated by electron paramagnetic resonance spectroscopy
Free Radical Res., 43: 47-57, 2009
09-054
Joyce Ferreira Severino, Bernhard A. Goodman, Christopher W.M. Kay, Klaus Stolze, Daniel Tunega, Thomas G. Reichenauer and Katharina F. Pirker
Free radicals generated during oxidation of green tea polyphenols: Electron paramagnetic resonance spectroscopy combined with density functional theory calculations
Free Radical Biol.Med., 46: 1076-1088, 2009
09-055
Andreas Bernthaler, Irmgard Mühlberger, Raul Fechete, Paul Perco, Arno Lukas and Bernd Mayer
A dependency graph approach for the analysis of differential gene expression profiles
Mol.BioSyst., 5: 1720–1731, 2009