Ausgewählte Publikationen


Determining factors for the unfolding pathway of peptides, peptoids, and peptidic foldamers.
L. Uribe, J. Gauss und G. Diezemann, J. Phys. Chem. B 120 10433 (2016)

A thermodynamic model of monovalent cation homeostasis in the yeast saccharomyces cerevisiae PLoS.
S. Gerber, M. Fröhlich, H. Lichtenberg-Fraté, S. Shabala, L. Shabala und E. Klipp, Comput. Biol. 12 (1), e1004703. doi: 10.1371/journal.pcbi.1004703, PMID: 26815455 (2016)

Constraining lithospheric flow.
J. P. Kaus (2016). Science. Vol. 353, Issue 6307, Sept. 30, 2016, doi:10.1126/science.aai8442

A multiscale approach to the migration of cancer stem cells: mathematical modelling and simulations.
N. Sfakianakis, N. Kolbe, N. Hellmann, M. Lukacova-Medvidova und B. Math. Biol., 79 (1), (2017), pp. 209–235, accepted 2016

Nucleon matrix elements from lattice QCD with all-mode-averaging and a domain-decomposed solver: an exploratory study.
G. von Hippel, T. D. Rae, E. Shintani und H. Wittig, Nucl. Phys. B914 (2017) 138

SNVSniffer: an integrated caller for germline and somatic single-nucleotide and indel mutations
Y. Liu, M. Loewer, S. Aluru, B. Schmidt, BMC Systems Biology 2016, 10(Suppl 2):47

Parallel and Space-Efficient Construction of Burrows-Wheeler Transform and Suffix Array for Big Genome Data
Y. Liu, T. Hankeln, B. Schmidt, IEEE/ACM Transactions on Computational Biology and Informatics Vol. 13, No. 3, May/June 2016


Origin and Flow History of Air Parcels in Orographic Banner Clouds
S. Schappert and V. Wirth, J. Atmos. Sci., 72, 3389-3403 (2015)

Geodynamic inversion to constrain the non-linear rheology of the lithosphere
T. Baumann, B. J. P. Kaus, Geophysical Journal International 202, 1289- 1316 (2015)

Cinema Data Mining: The Smell of Fear.
J. Wicker, N. Krauter, B. Derstorff, C. Stönner, E. Bourtsoukidis, T. Klüpfel, J. Williams,
S. Kramer, KDD 2015, 1295-1304

A study on time discretization and adaptive mesh refinement methods for the simulation of cancer invasion: the urokinase model
N. Kolbe, J. Katuchova, N. Sfakianakis, N. Hellmann, M. Lukacova-Medvidova,
Appl. Math. Comput. 273 (2016), 353–376

Anomaly Detection in Random Heterogeneous Media
(with a foreword by Prof. Dr. Lassi Päivärinta) M. Simon, Springer-Verlag, Berlin, 2015.

From Feynman-Kac formulae to numerical stochastic homogenization in electrical impedance tomography
M. Simon, accepted for publication in Annals of Applied Probability

A partially reflecting random walk on spheres algorithm for electrical impedance tomography
S. Maire, M. Simon, Journal of Computational Physics, 303 (2015), 413–430


A relation between screening masses and real-time rates
B. B. Brandt, A. Francis, M. Laine and H. B. Meyer, JHEP 1405, 117 (2014)

Redox Potentials and Acidity Constants from Density Functional Theory Based Molecular Dynamics
J. Cheng, X. Liu, J. VandeVondele, M. Sulpizi, and M. Sprik, Acc. Chem. Res. 47, (12): 3522-9, 2014

Quantification of the microstructural evolution of polycrystalline fabrics using FAME: Application to in situ deformation of ice
Peternell, M., Dierckx, M., Wilson, C.J.L., Piazolo, S., 2014. Journal of Structural Geology 61, 109-122.

All-Food-Seq (AFS): a quantifiable screen for species in biological samples by deep DNA sequencing
F. Ripp, C. Krombholz, Y. Liu, M. Weber, A. Schäfer, B. Schmidt, R. Köppel, T. Hankeln: BMC Genomics 15:639, 2014

Adaptive discontinuous evolution Galerkin method for dry atmospheric flow
L. Yelash, A. Müller, M. Lukacova-Medvidova, F. X. Giraldo, V. Wirth,, J. Comput.
Phys. 268 (2014), 106–133.

Bayesian anomaly detection in heterogeneous media with applications to geophysical tomography
M. Simon, Inverse Problems, 30 (2014), 114013


Measurements of Higgs boson production and couplings in diboson final states with the ATLAS detector at the LHC ATLAS Collaboration, G. Aad et al., Phys.Lett. B726 (2013), 88-119
(Koautoren des Schwerpunkts: V. Büscher, L. Köpke und S. Tapprogge)

Efficient computation of root mean square deviations under rigid transformations
A. K. Hildebrandt, M. Dietzen, T. Lengauer, H. P. Lenhof, E. Althaus and A. Hildebrandt, Journal of Computational Chemistry (2013), DOI: 10.1002/jcc.23513

Delamination and recycling of Archean crust caused by gravitational instabilities
T. E. Johnson, M. Brown, B. J. P. Kaus and J. A. Van Tongeren, Nature Geoscience 7 (2014), p. 47-52, DOI: 10.1038/NGEO2019

Electronic signature of the instantaneous asymmetry in the first coordination shell in liquid water
T. D. Kühne and R. Z. Khaliullin, Nature Commun. 4, 1450 (2013)

Mechanisms of Banner Cloud Formation
M. Voigt and V. Wirth, J. Atmos. Sci. 70 (2013), 3631-3640

Comparison between adaptive and uniform discontinuous Galerkin simulations in dry 2D bubble experiments A. Mueller, J. Behrens, F. X. Giraldo, V. Wirth, J. Computational Physics 235, 371-393 (2013)


K. Binder, A. Milchev, Polymer-Brushes on Flat and Curved Surfaces - How Computer Simulations can Help to Test Theories and to Interpret Experiments (Invited Review), J. Polym. Sci. B50, pp. 1515-1555 (2012)

H.-P. Hsu, K. Binder, Stretching semiflexible polymer chains: Evidence for the importance of excluded volume effects from Monte Carlo simulation, J. Chem. Phys. 136, pp. 1-20 (2012)

E.V. Albano, K. Binder, Wetting transition in the Two-Dimensional Blume-Capel Model: A Monte Carlo Study. Physical Review E85, pp. 1-14 (2012)

E.V. Albano, K. Binder, Finite-Size Scaling Approach for Critical Wetting: Rationalization in Terms of a Bulk Transition with an Order Parameter Exponent Equal to Zero. Phys. Rev. Lett. 109, pp. 1-4 (2012)

D. Rost, E. V. Gorelik, F. Assaad, N. Blümer
, Momentum-dependent pseudogaps in the half-filled two-dimensional Hubbard model. Phys. Rev. B 86, 155109 (2012)

E. V. Gorelik, D. Rost, T. Paiva, R. Scalettar, A. Klümper, N. Blümer
, Universal probes for antiferromagnetic correlations and entropy in cold fermions on optical lattices. 
Phys. Rev. A 85, 061602(R) (2012)

E. Jaenicke, B. Pairet, H. Hartmann, H. Decker, Crystallization and preliminary analysis of crystals from the 24-meric hemocyanin of emperor scorpion (Pandinus imperator) PLoS ONE 7(3): e32548 (2012)

P. Wigand, M. Blettner, J. Saloga, H. Decker, Prevalence of wine intolerance: results of a survey from Mainz, Germany. Dtsches Ärztebl. Intl. 109:437-444 (2012)

A. Jain, B. Dünweg, J. Ravi Prakash, Dynamic crossover scaling in polymer solutions. Physical Review Letters 109, 088302 (2012)

R. Schmitz, B. Dünweg, Numerical electrokinetics. Journal of Physics: Condensed Matter 24, 464111 (2012).

F.A. Evangelista, M. Hanauer, A. Köhn, J. Gauss, A sequential transformation approach to the internally contracted multireference coupled cluster method, J. Chem. Phys. 136 (2012)

D. Hoogewijs, B. Ebner, F. Germani, F.G. Hoffmann, A. Fabrizius, L. Moens, T. Burmester, S. Dewilde, J.F. Storz, S.N. Vinogradov, T. Hankeln, Androglobin: a chimeric globin in metazoans that is preferentially expressed in Mammalian testes. Mol Biol Evol. 29(4):1105-14 (2012)

S. Schülke, D. Dreidax, A. Malik, T. Burmester, E. Nevo, M. Band, A. Avivi, T. Hankeln, Living with stress: regulation of antioxidant defense genes in the subterranean, hypoxia-tolerant mole rat, Spalax. Gene. 500(2):199-206 (2012)

A. Malik, A. Korol, M. Weber, T. Hankeln, A. Avivi, M. Band, Transcriptome analysis of the spalax hypoxia survival response includes suppression of apoptosis and tight control of angiogenesis. BMC Genomics, 13:615 (2012)

E. Gleixner, H. Herlyn, S. Zimmerling, T. Burmester, T. Hankeln, Testes-specific hemoglobins in Drosophila evolved by a combination of sub- and neofunctionalization after gene duplication. BMC Evol Biol. 12:34 (2012)

M. Schwiering, N. Hellmann, Validation of liposomal lipid composition by thin-layer chromatography. J. Liposome Res. 22, 279-84 (2012)

M. Dietzen, A. Hildebrandt, E. Zotenko, T. Lengauer, On the Applicability of Elastic Network Normal Modes in Small-Molecule Docking. J. Chem. Inf. Model., 52(3):844-56 (2012)

F. Benz, S. Hack, A. Hildebrandt, A Dynamic Program Analysis to find Floating-Point Accuracy Problems. Programming Language Design and Implementation (PLDI) 2012, Beijing, China (2012)

M. Thielmann, B.J.P. Kaus, Shear heating induced lithospheric localization: does it result in subduction? Earth and Planetary Science Letters. Vol. 359-360. pp. 1-13 (2012)

J. Ruh, B.J.P. Kaus, J.-P. Burg, Numerical investigation of deformation mechanics in fold-and-thrust belts: Influence of rheology of single and multiple decollements. Tectonics (2012)

B.J. Block, M. Lukacova-Medvidova, P. Virnau, L. Yelash, Accelerated GPU Simulation of Compressible Flow by the Discontinuous Evolution Galerkin Method. European Physical Journal Special Topics 210, 119-132 (2012)

B.B. Brandt, A. Francis, H.B. Meyer, H. Wittig, Thermal Correlators in the rho channel of two-flavor QCD. arXiv:1212.4200 (2012)

H.B. Meyer, Photodisintegration of a bound state on the torus. arXiv:1202.6675 (2012)

L. Giusti, H.B. Meyer, Implications of Poincare symmetry for thermal field theories in finite volume. arXiv:1211.6669 (2012)

S. Meinhardt, J. Smiatek, R. Eichhorn, F. Schmid, Separation of chiral particles in nanofluidic channels, Phys. Rev. Lett. 108 (2012)

J. Smiatek, F. Schmid, Mesoscopic simulation methods for studying flow and transport in electric fields in micro- and nanochannels, in „Advances in Microfluidics”, Chapter 5 (invited), pp. 97-126, InTech Open Access Publisher (2012)

Y. Liu, B. Schmidt, Long read alignment based on maximal exact match seeds. Bioinformatics, 28(18): i318-i324 (2012)

Y. Liu, B. Schmidt, D. Maskell, CUSHAW: a CUDA compatible short read aligner to large genomes based on the Burrows-Wheeler transform. Bioinformatics, 28(14): 1830-1837 (2012)

S. Limbach, E. Schömer, H. Wernli, Detection, tracking and event localization of jet stream features in 4-D atmospheric data, Geoscientific Model Development, 5(2) (2012)

M. Simon, Multilevel Bayesian reconstruction in impedance tomography, Oberwolfach Report No. 11/2012 (2012)

D. Reith, P. Cifra, A. Stasiak, P. Virnau, Effective stiffening of DNA due to nematic ordering causes DNA molecules packed in phage capsids to preferentially form torus knots. Nucl. Acids Res. 40, 5129 (2012)

M. Weigel, A. Arnold, P. Virnau (eds.), Computer Simulations on Graphics Processing Units. EPJ-ST 210, 1 (2012)

S. Becker, D. Götz, C. Reuschle, C. Schwan, S. Weinzierl, NLO results for five, six and seven jets in electron-positron annihilation. Phys. Rev. Lett. 108 (2012)

S. Becker, C. Reuschle, S. Weinzierl, Efficiency improvements for the numerical computation of NLO corrections, JHEP 1207 (2012)

D. Götz, C. Schwan, S. Weinzierl, Random polarisations of the dipoles, Phys. Rev. D85 (2012)

S. Becker, S. Weinzierl, Direct contour deformation with arbitrary masses in the loop, Phys. Rev. D86 (2012)

S. Becker, S. Weinzierl, Direct numerical integration for multi-loop integrals, arXiv:1211.0509 (2012)

V. Wirth, M. Kristen, M. Leschner, J. Reuder, J. H. Schween, Banner clouds observed at Mount Zugspitze. Atmos. Chem. Phys. 12, 3611-3625 (2012)

S. Capitani, M. Della Morte, G. von Hippel, B. Jäger, A. Jüttner, B. Knippschild, H.B. Meyer, H. Wittig, The Nucleon Axial Charge from Lattice QCD with Controlled Errors, Phys. Rev. D86 (2012)

M. Della Morte, B. Jäger, T. Rae, H. Wittig, Improved Interpolating Fields for Hadrons at non-zero Momentum, Eur. Phys. J. A48 139 (2012)

D. Rosenkranz, H. Zischler, proTRAC - a software for probabilistic piRNA clus
ter detection, visualization and analysis. BMC Bioinformatics, 13(1):5 (2012)

D. Rosenkranz, easyPAC: A Tool for fast Prediction, Testing and Reference Mapping of Degenerate PCR Primers from Alignments or Consensus Sequences. Evolutionary Bioinformatics, 8:151-159 (2012)


L. Pang, D. P. Landau, K. Binder „Phase transitions in thin films with competing surface fields and gradients” Phys. Rev. E84, 041602 (2011), p. 1-8

L. Pang, D. P. Landau, K. Binder „Simulation evidence for nonlocal interface models: Two correlation lengths describe critical wetting” Phys. Rev. Lett. 106, 236102 (2011)

E. V. Gorelik, N. Blümer, Antiferromagnetism of Lattice Fermions in an Optical Trap: the Dynamical Mean-Field Perspective, 
J. Low Temp. Phys. 165, 195 (2011)

C. Schmitt, Track finding in ATLAS using GPUs, Proceedings of ”Advanced Computingand Analysis Techniques in Physics Research (ACAT)”, September 5-9, 2011,Uxbridge, London; to be published in Journal of Physics

D. Hoogewijs, B. Ebner, F. Germani, F. G. Hoffmann, A. Fabrizius, L. Moens, T. Burmester, S. Dewilde, J. F. Storz, S.N. Vinogradov, T. Hankeln, Androglobin: a Chimeric Globin in Metazoans that is Preferentially Expressed in Mammalian Testes. Mol Biol Evol. 2011 Nov 24. [Epub ahead of print]

L. A. Guillermo, T. D. Kühne, D. Sebastiani, Mixed Grotthus and Vehicle Mechanism in Proton Conducting Polymers from Ab-Initio Molecular Dynamics Simulations, Chem. Mater. 23, 1424 (2011)

T. D. Kühne, T. A. Pascal, E. Kaxiras, Y. Jung, New Insights into the Structure of the Vapor/Water Interface from Large-Scale First-Principles Simulations, J. Phys. Chem. Lett. 2, 105 (2011)

S. Caravati, D. Colleoni, R. Mazzarello, T. D. Kühne, M. Krack, M. Bernasconi, M. Parrinello, First principles study of nitrogen doping in cubic and amorphous Ge2Sb2Te5, J. Phys.: Condens. Matter 23, 265801 (2011)

U. Kolb, M. Mugnaioli, Complementarities between precession electron and X-ray powder diffraction Z. Krist. Proc., 1, 1-13 (2011)

D. Denysenko, M. Grzywa, M. Tonigold, B. Schmitz, I. Krkljus, M. Hirscher, E. Mugnaioli, U. Kolb, J. Hanns, D. Volkmer, Elucidating Gating Effects for Hydrogen Sorption in MFU-4 Type Triazolate-based MOFs Featuring Different Pore Sizes, Chem. Eur. J. 17, 1837 - 1848 (2011)

U. Kolb, E. Mugnaioli, T.E. Gorelik, Automated electron diffraction tomography - a new tool for nano crystal structure analysis, Cryst. Res. Technology, Special issue 46, 542-554 (2011)

I. Andrusenko, E. Mugnaioli, T. E. Gorelik, D. Koll, M. Panthöfer, W. Tremel, U. Kolb, Structure Analysis of Titanate Nanorods by Automated Electron Diffraction Tomography, Acta Cryst. B67, 218-225 (2011)

E. Mugnaioli, T. Gorelik, A. Stewart, U. Kolb, In Krivovichev S.V., Ab-initio structure solution of nano-crystalline minerals and synthetic materials by automated electron tomography, ”Minerals as Advanced Materials II”, Springer, Berlin Heidelberg (2011)

Jiang J., Jorda J.L., Yu J., Baumes L.A., Mugnaioli E., Diaz-Cabanas M.J., Kolb U., Corma A., Synthesis and Structure Determination of the Hierarchical MESO-Microporous Zeolite ITQ-43, Science 333(6046), 1131-1134 (2011)

Rozhdestvenskaya I., Mugnaioli E., Czank M., Depmeier W., Kolb U., Charoite, as an example of a structure with natural nanotubes , In Krivovichev S.V.: ”Minerals as Advanced Materials II”, Springer, Berlin Heidelberg, (2011)

Sedlmaier S.J., Mugnaioli E., Oeckler O., Kolb U., Schnick W., SrP3N5O - A Highly Condensed Layer Phosphate Structure Solved from a Nanocrystal by Automated Electron Diffraction Tomography, Chemistry - A European Journal , 17, 11258-11265 (2011)

Gemmi M., Fischer J., Merlini M., Poli S., Fumagalli P., Mugnaioli E., Kolb U., A new hydrous Al-bearing pyroxene as a water carrier in subduction zones, Earth and Planetary Science Letters 310 422-428 (2011)

Rozhdestvenskaya I., Mugnaioli E., Czank M., Depmeier W., Kolb U., Merlino S., Essential features of the polytypic charoite-96 structure compared to charoite-90, Mineral. Magazine, 75(6) 2833-2846 (2011)

Bellussi G., Montanari E., Di Paola E., Millini R., Carati A., Rizzo C., Parker W.O.J., Gemmi M., Mugnaioli E., Kolb U., Zanardi S., ECS-3: The First Crystalline Hybrid Organic-Inorganic Aluminosilicate with Open Porosity, Angew. Chem. Int Ed., 50 in print (2011)

T. E. Gorelik, J. van de Streek, A. F. M. Kilbinger, G. Brunklaus, U. Kolb, Ab-initio structure solution and refinement approaches based on electron diffraction data from oligo p-benzamides, Acta Cryst B, accepted (2011)

E. Mugnaioli, S. J. Sedlmaier, O. Oeckler, U. Kolb, W. Schnick, Ba6P12N17O9Br3 - A Column Phosphate Structure Solved from a Single Nanocrystal by Automated Electron Diffraction Tomography, European Journal of Inorganic Chemistry, accepted (2011)

U. Kolb T. Gorelik, Small organic molecules and higher homologues, in: Handbook of Nanoscopy, S. van Tendeloo and D. van Dyck (eds.), Wiley, Heidelberg in print (2011)

U. Kolb, Automated Diffraction Tomography ADT, in: Electron Crystallography, Kolb et al. (eds.), Kluwer Academic Publishers, Netherlands, NATO ASI Series E: Applied Sciences. in print (2011).

T. E. Gorelik, A. A. Stewart, U. Kolb, Structure solution with automated electron diffraction tomography data: different instrumental approaches, Journal of Microscopy, 244(3), 325-331 (2011)

E. Mugnaioli, U. Kolb, Applications of Automated Diffraction Tomography (ADT) on nanocrystalline porous materials, Microporous and Mesoporous Materials, accepted (2011)

H. Eshet, R. Z. Khaliullin, T. D. Kühne, J. Behler, M. Parrinello, Nucleation mechanism for direct graphite-to-diamond phase transition, Nature Mater. 10, 693-697 (2011)

A. Bollermann, S. Noelle, M. Lukacova-Medvidova, Finite Volume Evolution Galerkin Methods for Shallow Water Equations with Dry Beds, Comm. Comput. Physics 10(2),371-404 (2011)

A. Hundertmark-Zauskova, M. Lukacova-Medvidova, F. Prill, Large time step finite volumeevolution Galerkin methods, J. Sci. Comp., 48, 227-240 (2011)

L. Giusti, H.B. Meyer, Thermodynamic potentials from shifted boundary conditions: the scalar- field theory case, JHEP 1111 (2011) 087

D. Bernecker, H. B. Meyer, Vector Correlators in Lattice QCD: Methods and applications, Eur. Phys. J. A47 (2011) 148

S. Limbach, E. Schömer, H. Wernli, Detection, tracking and event localization of jet stream features in 4-D atmospheric data, Geoscientific Model Development, 5(2):457-470 (2012)

I. H. Radford, A. R. Fersht, G. Settanni, Combination of Markov state models and kinetic networks for the analysis of molecular dynamics simulations of peptide folding, J Phys Chem B. (2011) 115(22):7459-71

H. C. M. Fernandes, M. Weigel, Non-reversible Monte Carlo simulations of spin models, Comput. Phys. Commun. 182, 1856 (2011)

M. Weigel, T. Yavors'kii, GPU accelerated Monte Carlo simulations of lattice spin models, Physics Procedia 15, 92 (2011)