Publikationen 2013



New phylogenomic data support the monophyly of Lophophorata and an Ectoproct-Phoronid clade and indicate that Polyzoa and Kryptrochozoa are caused by systematic bias
Nesnidal MP, Helmkampf M, Meyer A, Witek A, Bruchhaus I, Ebersberger I, Hankeln T, Lieb B, Struck TH, Hausdorf B.
BMC Evol Biol. 2013 Nov 17;13:253

Genomic basis of ecological niche divergence among cryptic sister species of non-biting midges.
Schmidt H, Greshake B, Feldmeyer B, Hankeln T, Pfenninger M.
BMC Genomics. 2013 Jun 10;14:384.

Platyzoan mitochondrial genomes
Wey-Fabrizius AR, Podsiadlowski L, Herlyn H, Hankeln T.
Mol Phylogenet Evol. 2013 Nov;69(2):365-75.

Phylogenetic analyses of endoparasitic Acanthocephala based on mitochondrial genomes suggest secondary loss of sensory organs
Weber M, Wey-Fabrizius AR, Podsiadlowski L, Witek A, Schill RO, Sugar L, Herlyn H, Hankeln T.
Mol Phylogenet Evol. 2013 Jan;66(1):182-9

Galaxy LIMS for next-generation sequencing.
Scholtalbers J, Rößler J, Sorn P, de Graaf J, Boisguérin V, Castle J, Sahin U.
Bioinformatics 2013 May 1;29(9):1233-4. doi: 10.1093/bioinformatics/btt115. Epub 2013 Mar 11. PubMed PMID: 23479349.

HLA typing from RNA-Seq sequence reads
Boegel S, Löwer M, Schäfer M, Bukur T, de Graaf J, Boisguérin V, Türeci O, Diken M, Castle JC, Sahin U.
Genome Med. 2013 Dec 22;4(12):102. [Epub ahead of print] PubMed PMID: 23259685.


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).

Liquid methane at extreme temperature and pressure: Implications for models of Uranus and Neptune
D. Richters and T. D. Kühne
JETP Lett. 97, 184 (2013).

Optimal calculation of the pair correlation function for an orthorombic system
K. Röhrig and T. D. Kühne
Phys. Rev. E 87, 045301 (2013).

First principles simulations of amorphous InSb
J. Los, T. D. Kühne, S. Gabardi and M. Bernasconi
Phys. Rev. B 87, 184201 (2013).

Inverse simulated annealing for the determination of amorphous structures
J. Los and T. D. Kühne
Phys. Rev. B 87, 214202 (2013).

Proton Transfer through the Water Gossamer
A. A. Hassanali, F. Giberti, J. Cuny, T. D. Kühne and M. Parrinello
Proc. Nat. Acad. Sci. USA 110, 13723 (2013).

Microscopic properties of liquid water from combined ab initio molecular dynamics and energy decomposition tudies

R. Z. Khaliullin and T. D. Kühne
Phys. Chem. Chem. Phys. 15, 15746 (2013).

Vibrational Signature of Water Molecules in Asymmetric Hydrogen Bonding Environments
C. Zhang, R. Z. Khaliullin, D. Bovi, L. Guidoni and T. D. Kühne
J. Phys. Chem. Lett. 4, 3245 (2013).

Quantum Monte Carlo Study of High Pressure Solid Molecular Hydrogen
S. Azadi, W. M. C. Foulkes and T. D. Kühne
New J. Phys. 15, 113005 (2013).

First principles study of the amorphous In3SbTe2 phase change compound
J. Los, T. D. Kühne, S. Gabardi and M. Bernasconi
Phys. Rev. B 88, 174203 (2013).

Einblicke in die Debatte zur lokalen Koordinationsstruktur in flüssigem Wasser
M. Dömer, T. Spura, R. Z. Khaliullin and T. D. Kühne
Nachr. Chemie 61, 1203 (2013)

Selenium adsorption on Mo(110): A first-principles investigation
G. Roma and L. Chiodo
Phys. Rev. B 87, 245420 (2013)

Adsorption of Se, Na, and O on the Mo(110) surface: modeling atomic mechanisms at the back contact of thin film chalcopyrite solar cells
G. Roma et al.


Online Estimation of Discrete Densities
Geilke, M, Karwath, A, Frank, E, and Kramer, S
Proceedings of the 13th IEEE International Conference on Data Mining, pp. 191-200. (2013)

A Large-Scale Empirical Evaluation of Cross-Validation and External Test Set Validation
Gütlein, M, Helma, C, Karwath, A, and Kramer, S
(Q)SAR Molecular Informatics, 32(5-6):516-528. (2013).

CUDASW++ 3.0: accelerating Smith-Waterman protein database search by coupling CPU and GPU SIMD instructions
Y. Liu, A. Wirawan, B. Schmidt
BMC Bioinformatics 14:117, 2013

Musket: amultistage k-mer spectrum based errorcorrector for Illumina sequence data
Y. Liu, J. Schroeder, B. Schmidt
Bioinformatics 29(3): 308-315, 2013

CUDA-enabled Sparse Matrix-Vector Multiplication on GPUs using atomic operations
H.V. Dang, B. Schmidt
Parallel Computing 39(11): 737-750, 2013

Iterative sparse matrix-vector multiplication for accelerating the block Wiedemann algorithm over GF(2) on multi-graphics processing unit systems
B. Schmidt, H. Aribowo, H.-V. Dang
Concurrency and Computation: Practice and Experience 25(4): 586-603,

Structural Difficulty in Grammatical Evolution versus Genetic Programming
Ann Thorhauer, Franz Rothlauf
Blum, C. et al. (Hrsg.): Proceedings of the ACM Genetic and Evolutionary Computation Conference (GECCO 2013), S. 997-1004. ACM Press

What is the right seeding strategy for your product?Results for the Bass-model
Jörn Grahl, Franz Rothlauf
2013, Business Research (BuR), second round


Contrast Agent Bolus Dispersion in a Realistic Coronary Artery Geometry: Influence of Outlet Boundary Conditions
K. Sommer, R. Schmidt, D. Graafen, H.-C. Breit, L. M. Schreiber., Ann.
Biomed. Eng., 42 (4), 787-796, 2014, doi: 10.1007/s10439-013-0950-z

Computational Fluid Dynamics Simulations of Contrast Agent Bolus Dispersion in a Coronary Bifurcation: Impact on MRI-based Quantification of Myocardial Perfusion
R. Schmidt, D. Graafen, S. Weber, L.M. Schreiber
Computational and Mathematical Methods in Medicine, Volume 2013 (2013), Article ID 513187,


Measurement of dijet cross sections in pp collisions at 7 TeV centre-of-mass energy using the ATLAS detector
G. Aad et al. [ATLAS Collaboration]
arXiv:1312.3524 [hep-ex], submitted to JHEP

Measurement of the high-mass Drell-Yan differential cross-section in pp collisions at ?s=7 TeV with the ATLAS detector
G. Aad et al. [ATLAS Collaboration]
Phys.Lett. B 725 (2013) 223-242 (2013), arXiv:1305.4192 [hep-ex]

Search for $t\bar t$ resonances in the lepton plus jets final state with ATLAS using 4.7 fb$^{-1}$ of $pp$ collisions at $\sqrt{s} = 7$ TeV
G. Aad et al. [ATLAS Collaboration],
arXiv:1305.2756 [hep-ex]

Evidence for the spin-0 nature of the Higgs boson using ATLAS data
G. Aad et al. [ATLAS Collaboration]
Phys. Lett. B 726 (2013), pp. 120-144, arXiv:1307.1432 [hep-ex]

Measurements of Higgs boson production and couplings in diboson final states with the ATLAS detector at the LHC
G. Aad et al. [ATLAS Collaboration]
Phys. Lett. B 726 (2013), pp. 88-119, arXiv:1307.1427 [hep-ex]

Next-to-leading order electroweak corrections to pp -> W+W- -> 4 leptons at the LHC in double-pole approximation
M. Billoni, S. Dittmaier, B. Jäger, C. Speckner
JHEP 1312 (2013) 043.

Monte Carlo tools for studies of non-standard electroweak gauge boson interactions in multi-boson processes: A Snowmass White Paper
C.Degrande et al.
arXiv:1309.7890 [hep-ph].

Electroweak W+W-jj prodution at NLO in QCD matched with parton shower in the POWHEG-BOX
B.Jäger, G.Zanderighi
JHEP 1304 (2013) 024.

Direct numerical integration for multi-loop integrals
S. Becker and S. Weinzierl
Eur. Phys. J. C 73, (2013), 2321,

Decomposition of one-loop QCD amplitudes into primitive amplitudes based on shuffle relations
Ch. Reuschle and S. Weinzierl
Phys. Rev. D 88, (2013), 105020,

Dipole subtraction with random polarisations
D. Götz, Ch. Schwan and S. Weinzierl
PoS (RADCOR 2013) 021,

Optimal persistent currents for interacting bosons on a 1D ring with a gauge field
M. Cominotti, D. Rossini, M. Rizzi, F. Hekking, and A. Minguzzi

Exploiting seeding of random number generators for efficient domain decomposition parallelization of dissipative particle dynamics
Y. Afshar, F. Schmid, A. Pishevar, S. Worley
Comp. Phys. Comm. 184, 1119 (2013).

The effective slip-length tensor for a flow over weakly stripping stripes
E.S. Asmolov, J. Zhou, F. Schmid, O.I. Vinogradova
Phys. Rev. E 88, 023004 (2013).

Effects of boundaries on structure formation in low-dimensional colloid model systems near the liquid-solid-transition in equilibrium and in external fields and under shear
S. Deutschländer, K. Franzrahe, B. Heinze et al
EPJ-ST 222, 2973 (2013).

A model for rod-coil block copolymers
S. Dolezel, H. Behringer, F. Schmid
Polymer Science, Ser. C 55, 70 (2013).

Fibrinogen flexibility and implication for adsorption
S. Köhler, G. Settanni
Abs. of Papers of the American Chemical Society, 246, Meeting Abstract: 335-POLY (2013).

The flexibility of fibrinogen is important to understand its adsorption behavior
S. Köhler, G. Settanni
European Biophysics Journal with Biophysics Letters, 42, supplement: s92 (2013)

Elastic properties and line tension of self-assembled bilayer membranes
J. Li, K.A. Pastor, A.-C. Shi, F. Schmid, J. Zhou
Phys. Rev. E 88, 012718 (2013).

Understanding the microscopic origin of gold nanoparticles anisotropic growth from molecular dynamics simulations
S.K. Meena and M. Sulpizi
Langmuir, 2013, 29(48), 14954 DOI: 10.1021/la403843n

Monolayer curvature stabilizes nanoscale raft domains in mixed lipid bilayers
S. Meinhardt, R.L.C. Vink, F. Schmid
PNAS 110, 4476 (2013).

A hybrid particle-continuum model in soft-condensed matter simulations
S. Qi, H. Behringer, F. Schmid
NIC Series 46, 193 (2013).

Using field theory to construct hybrid particle-continuum simulation schemes with adaptive resolution for soft matter systems
S. Qi, H. Behringer, F. Schmid
New J. Physics 15, 125009 (2013).

Effects of ligand binding on the mechanical properties of ankyrin repeat protein gankyrin
G. Settanni, D. Serquera, P.E. Marszalek, E. Paci, L.S. Itzhaki,.
PLoS Comput Biol. 9(1):e1002864 (2013).

Fluctuations in lipid bilayers: Are they understood?
F. Schmid
Biophys. Rev. and Lett. 8, 1 (2013).

Self-consistent field approach for crosslinked copolymer materials
F. Schmid
Phys. Rev. Lett. 111, 028303 (2013).

Monte Carlo tests of nucleation concepts in the lattice gas model
F. Schmitz, P. Virnau, K. Binder
Phys. Rev. E 87, 053302 (2013).

Hyperbranched graft-copolymers by "Hypergrafting" of ABm monomers from polydisperse macroinitiator cores: Theory meets synthesis
C. Schüll, H. Rabbel, F. Schmid, H. Frey
Macromolecules 46, 5823 (2013).

Phase separation of colloid polymer mixtures under confinement
A.Statt, A. Winkler, P. Virnau, K. Binder, W.E. Nagel et al. (eds.)
High Peformance Computing in Science and Engineering ’13, 19, Springer-Verlag (2013).

Vibrational Sum Frequency Generation Spectroscopy of the Water Liquid-Vapor Interface from Density Functional Theory Based Molecular Dynamics Simulations
M. Sulpizi, M. Salanne, M. Sprik and M-P. Gaigeot
J. Phys. Chem. Lett., 4 (1), 83 (2013)

Influence of chain stiffness on knottedness in single polymers
P. Virnau, F. Rieger, D. Reith
Biochem. Soc. Trans. 41, 528 (2013).

Stick-slip motion and plastic flow of a two-dimensional colloidal crystal confined to moving corrugated rigid boundaries
D. Wilms, P. Virnau, K. Binder
Mol. Phys. 111, 22 (2013).

Computer simulations of structure, dynamics, and phase behaviour of colloidal fluids in confined geometry and under shear
A.Winkler, D. Winter, P. Chaudhuri et al
EPJ-ST 222, 2787 (2013).

Phase transitions and phase equilibria in spherical confinement
A.Winkler, A. Statt, P. Virnau, K. Binder
Phys. Rev. E 87, 032307 (2013).

Phase separation in colloidal suspensions by collective growth of domains
A.Winkler, P. Virnau, K. Binder, R.G. Winkler, G. Gompper,
Innovatives Supercomputing in Deutschland (inSiDE) 11, 30 (2013)

Hydrodynamic mechanisms of spinodal decomposition in confined colloid-polymer mixtures: A multiparticle collision dynamics study
Winkler, P. Virnau, K. Binder, R.G. Winkler, G. Gompper
J. Chem. Phys. 138, 054901 (2013).

AC-field induced polarization for uncharged colloids in salt solution: A Dissipative Particle Dynamics simulation
J. Zhou, F. Schmid
Eur. Phys. J. E 36, 33 (2013).

Computer simulations of charged colloids in alternating electric fields
J. Zhou, F. Schmid
Eur. Phys. J.: Special topics 222, 2911 (2013).

Dynamic and dielectric response of charged colloids in electrolyte solutions to external electric fields
J. Zhou, R. Schmitz, B. Dünweg, F. Schmid
J. Chem. Phys. 139, 024901 (2013).

Effective slippage on superhydrophobic trapezoidal grooves
J. Zhou, E.S. Asmolov, F. Schmid, O.I. Vinogradova
J. Chem. Phys. 139, 1748708 (2013).