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% This file was created by the TYPO3 extension
% bib
% --- Timezone: CET
% Creation date: 2022-11-30
% Creation time: 00-38-56
% --- Number of references
% 169
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@Article { OlbrichRKLvBOS2022,
title = {Deep learning based liquid level extraction from video observations of gas-liquid flows},
journal = {International Journal of Multiphase Flow},
year = {2022},
month = {9},
day = {10},
tags = {8.4,8.41},
DOI = {https://doi.org/10.1016/j.ijmultiphaseflow.2022.104247},
author = {Olbrich, M. and Riazy, L. and Kretz, T. and Leonard, T. and van Putten, D.S. and B{\"a}r, M. and Oberleithner, K. and Schmelter, S.}
}
@Article { BuranNB2022,
title = {Suppression of fibrillatory dynamics consisting of stable rotors by periodic pacing},
journal = {New Journal of Physics},
year = {2022},
month = {8},
day = {23},
volume = {24},
number = {August 2022},
tags = {8.4,8.41},
DOI = {https://doi.org/10.1088/1367-2630/ac8571},
author = {Buran, P. and Niedermayer, T. and B{\"a}r, M.}
}
@Phdthesis { Worlitzer2022,
title = {Collective motion and clustering in active polar fluids},
year = {2022},
month = {8},
day = {10},
tags = {8.4,8.41,8.43},
url = {https://www.depositonce.tu-berlin.de/bitstream/11303/17276/4/worlitzer_vasco.pdf},
school = {TU Berlin},
type = {PhD Thesis},
DOI = {http://dx.doi.org/10.14279/depositonce-16056},
author = {Worlitzer, V. M.}
}
@Article { StrakaWKHS2022,
title = {Simulation Uncertainty for a Virtual Ultrasonic Flow Meter},
journal = {Metrology},
year = {2022},
month = {7},
day = {18},
volume = {2},
number = {3},
pages = {335-359},
tags = {8.41},
DOI = {https://doi.org/10.3390/metrology2030021},
author = {Straka, Martin and Weissenbrunner, Andreas and Koglin, Christian and H{\"o}hne, Christian and Schmelter, Sonja}
}
@Article { WorlitzerJGBHEAB2022,
title = {Biophysical aspects underlying the swarm to biofilm transition},
journal = {Science Advances},
year = {2022},
month = {6},
day = {15},
volume = {8},
number = {24},
tags = {8.4,8.41,8.43,ActFluid},
DOI = {DOI: 10.1126/sciadv.abn8152},
author = {Worlitzer, V. M. and Jose, A. and Grinberg, I. and B{\"a}r, M. and Heidenreich, S. and Eldar, A. and Ariel, G. and Be´er, A.}
}
@Article { HerrWZAFL2022,
title = {Spontaneous polarization and cell guidance on asymmetric nanotopography},
journal = {Communications Physics},
year = {2022},
month = {5},
day = {11},
volume = {5},
number = {114},
tags = {8.4,8.41,8.43},
DOI = {https://doi.org/10.1038/s42005-022-00889-0},
author = {Herr, C. and Winkler, B. and Ziebert, F. and Aranson, I. S. and Fourkas, J. T. and Losert, W.}
}
@Article { PolanskyS2022,
title = {Implementation of turbulence damping in the OpenFOAM multiphase flow solver interFoam},
journal = {Archives of Thermodynamics},
year = {2022},
month = {3},
day = {1},
volume = {43},
number = {1},
pages = {21-43},
keywords = {Multiphase flow, Stratified flow, Turbulence damping, Computational fluid dynamics, OpenFOAM, Reynolds-averaged Navier–Stokes, Detached eddy simulation, Delayed detached eddy simulation},
tags = {8.4,8.41},
url = {http://journals.pan.pl/Content/122890/PDF/art02_internet.pdf},
DOI = {10.24425/ather.2022.140923},
author = {Polansky, Jiri and Schmelter, Sonja}
}
@Article { ReinkenHBK2022,
title = {Ising-like critical behavior of vortex lattices in an active fluid},
journal = {Physical Review Letters},
year = {2022},
month = {1},
day = {27},
volume = {128},
number = {4},
pages = {048004},
tags = {8.4,8.41,8.43,ActFluid},
DOI = {10.1103/PhysRevLett.128.048004},
author = {Reinken, H and Heidenreich, S and B{\"a}r, M and Klapp, S.H.L}
}
@Article { MehariS2021,
title = {Self-supervised representation learning from 12-lead ECG data},
journal = {Computers in Biology and Medicine},
year = {2021},
month = {12},
day = {18},
volume = {141},
pages = {105114},
tags = {8.4,8.41},
DOI = {https://doi.org/10.1016/j.compbiomed.2021.105114},
author = {Mehari, T and Strodthoff, N}
}
@Article { WilczekHB2021,
title = {Die Physik aktiver Fluide},
journal = {Physik Journal},
year = {2021},
month = {12},
day = {1},
volume = {20},
number = {12},
pages = {35},
tags = {8.4,8.41,8.43},
author = {Wilczek, M and Heidenreich, S and B{\"a}r, M}
}
@Article { WorlitzerABSBH2021,
title = {Turbulence-induced clustering in compressible active fluids},
journal = {Soft Matter},
year = {2021},
month = {11},
day = {11},
volume = {2021},
number = {17},
pages = {10447-10457},
tags = {8.4,8.41,8.43,ActFluid},
DOI = {https://doi.org/10.1039/D1SM01276B},
author = {Worlitzer, V M and Ariel, G and Be'er, A and Stark, H and B{\"a}r, M and Heidenreich, S}
}
@Article { KhmelinskaiaFYPS2021,
title = {Membrane-Mediated Self-Organization of Rod-Like DNA Origami on Supported Lipid Bilayers},
journal = {Advanced Materials Interfaces},
year = {2021},
month = {10},
day = {18},
volume = {8},
number = {24},
pages = {2101094},
tags = {8.4, 8.41},
DOI = {https://doi.org/10.1002/admi.202101094},
author = {Khmelinskaia, A and Franquelim, H G and Yaadav, R and Petrov, E P and Schwille, P}
}
@Article { KnotekSO2021,
title = {Assessment of different parameters used in mesh independence studies in two-phase slug flow simulations},
journal = {Measurement: Sensors},
year = {2021},
month = {9},
day = {28},
volume = {18},
pages = {100317},
tags = {8.4,8.41,Flow},
ISSN = {2665-9174},
DOI = {10.1016/j.measen.2021.100317},
author = {Knotek, Stanislav and Schmelter, Sonja and Olbrich, Marc}
}
@Article { SchmelterOKB2021,
title = {Analysis of multiphase flow simulations and comparison with high-speed video observations},
journal = {Measurement: Sensors},
year = {2021},
month = {9},
day = {23},
volume = {18},
pages = {100154},
tags = {8.4,8.41,Flow},
ISSN = {2665-9174},
DOI = {10.1016/j.measen.2021.100154},
author = {Schmelter, Sonja and Olbrich, Marc and Knotek, Stanislav and B{\"a}r, Markus}
}
@Article { OlbrichHLSBOS2021,
title = {Comparing temporal characteristics of slug flow from tomography measurements and video observations},
journal = {Measurement: Sensors},
year = {2021},
month = {9},
day = {22},
volume = {18},
pages = {100222},
tags = {8.4,8.41,Flow},
ISSN = {2665-9174},
DOI = {10.1016/j.measen.2021.100222},
author = {Olbrich, Marc and Hunt, Andrew and Leonard, Terri and S. van Putten, Dennis and B{\"a}r, Markus and Oberleithner, Kilian and Schmelter, Sonja}
}
@Article { PeledRHBAB2021,
title = {Heterogeneous bacterial swarms with mixed lengths},
journal = {Physical Review E},
year = {2021},
month = {3},
day = {29},
volume = {103},
number = {3},
pages = {032413},
tags = {8.4,8.41,8.43,ActFluid},
DOI = {10.1103/PhysRevE.103.032413},
author = {Peled, S and Ryan, S D and Heidenreich, S and B{\"a}r, M and Ariel, G and Be'er, A}
}
@Article { WorlitzerABSB2021,
title = {Motility-induced clustering and meso-scale turbulence in active polar fluids},
journal = {New Journal of Physics},
year = {2021},
month = {3},
day = {10},
volume = {23},
pages = {033012},
tags = {8.4,8.41,ActFluid},
DOI = {10.1088/1367-2630/abe72d},
author = {Worlitzer, V M and Ariel, G and Be'er, A and Stark, H and B{\"a}r, M and Heidenreich, S}
}
@Article { SmudaGHN2021,
title = {Function of Hemoglobin-Based Oxygen Carriers: Determination of Methemoglobin Content by Spectral Extinction Measurements},
journal = {Int J Mol Sci .},
year = {2021},
month = {2},
day = {10},
volume = {22},
number = {4},
pages = {1753},
tags = {8.4,8.41,Cyto},
DOI = {10.3390/ijms22041753},
author = {Smuda, K and Gienger, J and H{\"o}nicke, P and Neukammer, J}
}
@Article { SchmelterKOFB2021,
title = {On the influence of inlet perturbations on slug dynamics inhorizontal multiphase flow a computational study},
journal = {Metrologia},
year = {2021},
month = {1},
day = {21},
volume = {58},
number = {1},
pages = {014003},
tags = {8.4,8.41,Flow},
DOI = {10.1088/1681-7575/abd1c9},
author = {Schmelter, S and Knotek, S and Olbrich, M and Fiebach, A and B{\"a}r, M}
}
@Article { SchmidtFSSLS2021,
title = {The impact of 4D flow displacementartifacts on wall shear stress estimation},
journal = {Magnetic Resonance in Medicine},
year = {2021},
volume = {85},
number = {6},
pages = {3154-3168},
tags = {8.4,8.41,Flow},
DOI = {10.1002/mrm.28641},
author = {Schmidt, S and Flassbeck, S and Schmelter, S and Schmeyer, E and Ladd, M E and Schmitter, S}
}
@Article { OlbrichSBSOS2020,
title = {Identification of coherent structures in horizontal slug flow},
journal = {Flow Measurement and Instrumentation},
year = {2020},
month = {10},
day = {16},
volume = {76},
pages = {101814},
tags = {8.4,8.41,Flow},
DOI = {10.1016/j.flowmeasinst.2020.101814},
author = {Olbrich, M and Schmeyer, E and B{\"a}r, M and Sieber, M and Oberleithner, K and Schmelter, S}
}
@Article { OlbrichBOS2020,
title = {Statistical characterization of horizontal slug flow using snapshot proper orthogonal decomposition},
journal = {International Journal of Multiphase Flow},
year = {2020},
month = {9},
day = {6},
volume = {134},
pages = {103453},
tags = {8.4,8.41,Flow},
DOI = {10.1016/j.ijmultiphaseflow.2020.103453},
author = {Olbrich, M and B{\"a}r, M and Oberleithner, K and Schmelter, S}
}
@Article { ReinkenNHSBKA2020,
title = {Organizing bacterial vortex lattices by periodic obstacle arrays},
journal = {Commun Phys},
year = {2020},
month = {5},
day = {7},
volume = {3},
number = {76},
tags = {8.4,8.41,ActFluid},
DOI = {10.1038/s42005-020-0337-z},
author = {Reinken, H and Nishiguchi, D and Heidenreich, S and Sokolov, A and B{\"a}r, M and Klapp, S H L and Aranson, I S}
}
@Article { FarchminHSWBBH2020,
title = {Efficient Bayesian inversion for shape reconstruction of lithography masks},
journal = {Journal of Micro/Nanolithography, MEMS, and MOEMS},
year = {2020},
month = {5},
day = {5},
volume = {2},
number = {19},
pages = {1--11},
tags = {8.4,8.41,8.43,UQ,Scatter-Inv},
DOI = {10.1117/1.JMM.19.2.024001},
author = {Farchmin, N and Hammerschmidt, M and Schneider, P I and Wurm, M and Bodermann, B and B{\"a}r, M and Heidenreich, S}
}
@Article { BeaerIGKHBA2020,
title = {A phase diagram for bacterial swarming},
journal = {Commun Phys},
year = {2020},
month = {4},
day = {3},
volume = {3},
number = {66},
tags = {8.4,8.41,ActFluid},
DOI = {10.1038/s42005-020-0327-1},
author = {Be´er, A and Ilkanaiv, B and Gross, R and Kearns, D B and Heidenreich, S and B{\"a}r, M and Ariel, G}
}
@Article { SchmelterOSB2020,
title = {Numerical simulation, validation, and analysis of two-phase slug flow in large horizontal pipes},
journal = {Flow Measurement and Instrumentation},
year = {2020},
month = {3},
day = {10},
volume = {73},
pages = {101722},
tags = {8.4,8.41,Flow},
DOI = {10.1016/j.flowmeasinst.2020.101722},
author = {Schmelter, S and Olbrich, M and Schmeyer, E and B{\"a}r, M}
}
@Article { BarGHP2020,
title = {Self-Propelled Rods: Insights and Perspectives for Active Matter},
journal = {Annual Review of Condensed Matter Physics},
year = {2020},
month = {3},
day = {1},
volume = {11},
pages = {441--466},
tags = {8.4,8.41,ActFluid},
DOI = {10.1146/annurev-conmatphys-031119-050611},
author = {B{\"a}r, M and Gro{\ss}mann, R and Heidenreich, S and Peruani, F}
}
@Article { GiengerGOBN2019,
title = {Assessment of deformation of human red blood cells in flow cytometry: measurement and simulation of bimodal forward scatter distributions},
journal = {Biomedical Optics Express},
year = {2019},
month = {9},
day = {1},
volume = {10},
number = {9},
pages = {4531 -- 4550},
tags = {8.4,8.41,Cyto},
DOI = {10.1364/BOE.10.004531},
author = {Gienger, J and Gross, H and Ost, V and B{\"a}r, M and Neukammer, J}
}
@Article { SchmelterOSB2019,
title = {Numerical simulation, validation, and analysis of two-phase slug flow in large horizontal pipes},
journal = {Proceedings of the 18th International Flow Measurement Conference FLOMEKO 2019},
year = {2019},
month = {7},
day = {1},
tags = {8.4,8.41,Flow},
author = {Schmelter, S and Olbrich, M and Schmeyer, E and B{\"a}r, M}
}
@Article { OlbrichSBSOS2019,
title = {Identification of coherent structures in horizontal slug flow},
journal = {Proceedings of the 18th International Flow Measurement Conference FLOMEKO 2019},
year = {2019},
month = {7},
day = {1},
tags = {8.4,8.41,Flow},
author = {Olbrich, M and Schmeyer, E and B{\"a}r, M and Sieber, M and Oberleithner, K and Schmelter, S}
}
@Article { KulawiakLBE2019,
title = {Active poroelastic two-phase model for the motion of Physarum microplasmodia},
journal = {PLoS One},
year = {2019},
month = {5},
day = {14},
volume = {14},
number = {8},
tags = {8.4,8.41},
DOI = {10.1101/638312},
author = {Kulawiak, D A and L{\"o}ber, J and B{\"a}r, M and Engel, H}
}
@Article { RiazySOAvNS2019,
title = {Porous medium 3D flow simulation of contrast media washout in cardiac MRI reflects myocardial injury},
journal = {Magnetic Resonance in Medicine},
year = {2019},
month = {4},
day = {16},
note = {advance online publication},
tags = {8.4,8.41, flow},
DOI = {10.1002/mrm.27756},
author = {Riazy, L and Sch{\"a}ffter, T and Olbrich, M and Schueler, J A and v. Knobelsdorff-Brenkenhoff, F and Niendorf, T and Schulz-Menger, J}
}
@Article { GiengerSMBN2019,
title = {Refractive index of human red blood cells between 290 nm and 1100 nm determined by optical extinction measurements},
journal = {Scientific Reports},
year = {2019},
month = {3},
day = {15},
volume = {9},
tags = {8.4,8.41,Cyto},
DOI = {10.1038/s41598-019-38767-5},
author = {Gienger, J and Smuda, K and M{\"u}ller, R and B{\"a}r, M and Neukammer, J}
}
@Article { AlvesdBd2019,
title = {Simulation of the Perfusion of Contrast Agent Used in Cardiac Magnetic Resonance: A Step Toward Non-invasive Cardiac Perfusion Quantification},
journal = {Front. Physiol.},
year = {2019},
month = {3},
day = {14},
volume = {10},
number = {177},
tags = {8.4,8.41},
DOI = {10.3389/fphys.2019.00177},
author = {Alves, J. R and de Queiroz, R. A. B and B{\"a}r, M and dos Santos, R. W}
}
@Article { ReinkenHBK2019,
title = {Anisotropic mesoscale turbulence and pattern formation in microswimmer suspensions induced by orienting external fields},
journal = {New Journal of Physics},
year = {2019},
month = {1},
day = {31},
volume = {21},
number = {1},
pages = {013037},
tags = {8.4,8.41},
DOI = {10.1088\%2F1367-2630\%2Faaff09},
author = {Reinken, H and Heidenreich, S and B{\"a}r, M and Klapp, S. H. L}
}
@Article { KulawiakLBE2018,
title = {Oscillatory motion of a droplet in an active poroelastic two-phase model},
journal = {Journal of Physics D: Applied Physics},
year = {2019},
month = {1},
day = {1},
volume = {52},
number = {1},
pages = {014004},
tags = {8.4,8.41},
DOI = {10.1088/1361-6463/aae41d},
author = {Kulawiak, D A and L{\"o}ber, J and B{\"a}r, M and Engel, H}
}
@Article { OlbrichSROBS2018,
title = {Validation of simulations in multiphase flow metrology by comparison with experimental video observation},
journal = {J. Phys.: Conf. Series},
year = {2018},
month = {11},
day = {1},
volume = {1065},
number = {9},
pages = {092015},
tags = {8.4,8.41,Flow},
DOI = {10.1088/1742-6596/1065/9/092015},
author = {Olbrich, M and Schmeyer, E and Riazy, L and Oberleithner, K and B{\"a}r, M and Schmelter, S}
}
@Article { SchmelterOSB2018,
title = {Validation of multiphase flow simulations by comparison with experimental video observations},
journal = {Proceedings of the North Sea Flow Measurement Workshop 2018},
year = {2018},
month = {11},
day = {1},
tags = {8.4,8.41,Flow},
author = {Schmelter, S and Olbrich, M and Schmeyer, E and B{\"a}r, M}
}
@Article { HeidenreichGB2018,
title = {Bayesian approach to determine critical dimensions from scatterometric measurements},
journal = {Metrologia},
year = {2018},
month = {10},
day = {19},
volume = {55},
number = {6},
pages = {201},
tags = {8.4,8.41,8.43, UQ},
DOI = {10.1088/1681-7575/aae41c},
author = {Heidenreich, S and Gross, H and B{\"a}r, M}
}
@Article { ArielSRHBB2018,
title = {Collective dynamics of two-dimensional swimming bacteria: Experiments and models},
journal = {PHYSICAL REVIEW E},
year = {2018},
month = {9},
day = {24},
volume = {98},
number = {3},
pages = {032415},
tags = {8.4,8.41},
DOI = {10.1103/PhysRevE.98.032415},
author = {Ariel, G and Sidortsov, M and Ryan, S D and Heidenreich, S and B{\"a}r, M and Be'er, A}
}
@Article { BeckerFNRMB2018,
title = {Local control of globally competing patterns in coupled Swift–Hohenberg equations},
journal = {Chaos: An Interdisciplinary Journal of Nonlinear Science},
year = {2018},
month = {4},
day = {30},
volume = {28},
number = {4},
pages = {043121},
tags = {8.4, 8.41, 8.43},
DOI = {10.1063/1.5018139},
author = {Becker, M and Frenzel, T and Niedermayer, T and Reichelt, S and Mielke, A and B{\"a}r, M}
}
@Article { ReinkenKBH2018,
title = {Derivation of a hydrodynamic theory for mesoscale dynamics in microswimmer suspensions},
journal = {Physical Review E 97},
year = {2018},
month = {2},
day = {22},
volume = {97},
number = {2},
pages = {022613},
tags = {8.4, 8.41, Active fluids, hydrodynamics theory, microswimmers},
DOI = {10.1103/PhysRevE.97.022613},
author = {Reinken, H and Klapp, S H L and B{\"a}r, M and Heidenreich, S}
}
@Article { StrakaFEK2018,
title = {Hybrid simulation of a segmental orifice plate},
journal = {Flow Measurement and Instrumentation},
year = {2018},
month = {2},
day = {14},
volume = {60},
pages = {124--133},
tags = {8.4,8.41,Flow},
DOI = {10.1016/j.flowmeasinst.2018.02.006},
author = {Straka, M and Fiebach, A and Eichler, T and Koglin, C}
}
@Article { GiengerBN2018,
title = {Extinction spectra of suspensions of microspheres: determination of the spectral refractive index and particle size distribution with nanometer accuracy},
journal = {Applied Optics},
year = {2018},
month = {1},
day = {1},
volume = {57},
number = {2},
pages = {344 -- 355},
tags = {8.4,8.41,Cyto},
DOI = {10.1364/AO.57.000344},
author = {Gienger, J and B{\"a}r, M and Neukammer, J}
}
@Article { BuranBN2017,
title = {Control of electrical turbulence by periodic excitation of cardiac tissue},
journal = {Chaos},
year = {2017},
month = {11},
day = {19},
volume = {27},
number = {11},
pages = {113110},
tags = {8.4,8.43,8.41},
DOI = {10.1063/1.5010787},
author = {Buran, P and B{\"a}r, M and Alonso, S and Niedermayer, T}
}
@Article { AlonsoREB2017,
title = {Mechanochemical pattern formation in simple models of active viscoelastic fluids and solids},
journal = {Journal of Physics D: Applied Physics},
year = {2017},
month = {10},
day = {3},
volume = {50},
number = {43},
pages = {434004},
tags = {8.4,8.41},
DOI = {10.1088/1361-6463/aa8a1d},
author = {Alonso, S and Radszuweit, M and Engel, H and B{\"a}r, M}
}
@Article { BarE2018,
title = {Mathematics and Statistics for Digitalization},
journal = {PTB Mitteilungen},
year = {2017},
month = {10},
day = {1},
volume = {127},
number = {4},
pages = {69--74},
tags = {8.4,8.41,8.42},
url = {https://www.ptb.de/cms/fileadmin/internet/publikationen/ptb_mitteilungen/mitt2017/Heft4/PTB-Mitteilungen_2017_Heft_4.pdf},
author = {B{\"a}r, M and Elster, C}
}
@Article { WeissenbrunnerFJT2017,
title = {A coupled numerical and laser optical method for on-site calibration of flow meters},
journal = {Eccomas Proceedia UNCECOMP},
year = {2017},
month = {6},
day = {17},
number = {5393},
pages = {576--587},
tags = {8.4,8.41,Flow},
DOI = {10.7712/120217.5393.16913},
author = {Weissenbrunner, A and Fiebach, A and Juling, M and Thamsen, P U}
}
@Article { GrossHB2016,
title = {Impact of different stochastic line edge roughness patterns on measurements in scatterometry - a simulation study},
journal = {Measurement},
year = {2017},
month = {2},
day = {1},
volume = {98},
pages = {339--346},
tags = {8.4,8.41,Scatter-Inv},
DOI = {10.1016/j.measurement.2016.08.027},
author = {Gross, H and Heidenreich, S and B{\"a}r, M}
}
@Article { HeidenreichGBW2016,
title = {Uncertainty propagation in computationally expensive models: A survey of sampling methods and application to scatterometry},
journal = {Measurement},
year = {2017},
month = {2},
day = {1},
volume = {97},
number = {79--87},
tags = {8.4,8.41,UQ},
DOI = {10.1016/j.measurement.2016.06.009},
author = {Heidenreich, S and Gross, H and B{\"a}r, M and Wright, L}
}
@Article { GiengerGNB2016,
title = {Determining the refractive index of humanhemoglobin solutions by Kramers–Kronig relations with an improved absorption model.},
journal = {Applied Optics},
year = {2016},
month = {11},
day = {25},
volume = {55},
number = {31},
pages = {8951--8961},
tags = {8.4,8.41,Cyto},
DOI = {10.1364/AO.55.008951},
author = {Gienger, J and Gro{\ss}, H and Neukammer, J and B{\"a}r, M}
}
@Article { AlonsoWB2016,
title = {Reentry and Ectopic Pacemakers Emerge in aThree-Dimensional Model for a Slab of Cardiac Tissue with Diffuse Microfibrosis nearthe Percolation Threshold},
journal = {PLOS One},
year = {2016},
month = {11},
day = {25},
volume = {11},
number = {11},
tags = {8.4,8.41,8.43},
DOI = {10.1371/journal.pone.0166972},
author = {Alonso, S and Weber dos Santos, R and B{\"a}r, M}
}
@Article { GrosmannPB2016_2,
title = {Mesoscale pattern formation of self-propelled rodswith velocity reversal},
journal = {Phys. Rev. E},
year = {2016},
month = {11},
day = {25},
volume = {94},
number = {5},
pages = {050602},
tags = {8.4,8.43,8.41},
DOI = {10.1103/PhysRevE.94.050602},
author = {Gro{\ss}mann, R and Peruani, F and B{\"a}r, M}
}
@Article { FiebachSKS2016,
title = {Numerical simulation of multiphase flow in a vertically mounted Venturi flow meter},
journal = {Proceedings of the 17th International Flow Measurement Conference FLOMEKO 2016},
year = {2016},
month = {9},
day = {29},
tags = {8.4,8.41,Flow},
author = {Fiebach, A and Schmeyer, E and Knotek, S and Schmelter, S}
}
@Article { KnotekFS2016,
title = {Numerical simulation of multiphase flows in large horizontal pipes},
journal = {Proceedings of the 17th International Flow Measurement Conference FLOMEKO 2016},
year = {2016},
month = {9},
day = {29},
tags = {8.4,8.41,Flow},
author = {Knotek, S and Fiebach, A and Schmelter, S}
}
@Article { HeidenreichDKB2016,
title = {Hydrodynamic length-scale selection in microswimmer suspensions},
journal = {Physical Review E},
year = {2016},
month = {8},
day = {29},
volume = {94},
number = {2},
pages = {020601},
tags = {8.4,8.41,ActFluid},
DOI = {10.1103/PhysRevE.94.020601},
author = {Heidenreich, S and Dunkel, J and Klapp, H.L and B{\"a}r, M}
}
@Article { AlonsoBE2016,
title = {Nonlinear physics of electrical wave propagation in the heart: a review},
journal = {Reports on Progress in Physics},
year = {2016},
month = {8},
day = {29},
volume = {79},
number = {9},
pages = {096601},
tags = {8.4,8.41,8.43,Herz},
DOI = {10.1088/0034-4885/79/9/096601},
author = {Alonso, S and B{\"a}r, M and Echebarria, B}
}
@Article { AlonsoB2016,
title = {Reentry produced by small-scale heterogeneities in a discrete model of cardiac tissue},
journal = {Journal of Physics: Conference Series},
year = {2016},
month = {8},
day = {29},
volume = {727},
number = {1},
pages = {012002},
tags = {8.4,8.41,8.43,Herz},
DOI = {10.1088/1742-6596/727/1/012002},
author = {Alonso, S and B{\"a}r, M}
}
@Article { WeissenbrunnerFSMTL2016,
title = {Simulation-based determination of systematic errors of flow meters due to uncertain inflow conditions},
journal = {Flow Measurement and Instrumentation},
year = {2016},
month = {8},
day = {29},
tags = {8.4,8.41,Flow,UQ},
state = {in_preparation},
DOI = {10.1016/j.flowmeasinst.2016.07.011},
author = {Weissenbrunner, A and Fiebach, A and Schmelter, S and B{\"a}r, M and Thamsen, P.U and Lederer, T}
}
@Article { GrosmannPB2013,
title = {Superdiffusion, large-scale synchronization, and topological defects},
journal = {Phys. Rev. E},
year = {2016},
month = {4},
day = {31},
volume = {93},
keywords = {8.43},
tags = {8.4,8.43,8.41},
DOI = {10.1103/PhysRevE.93.040102},
author = {Gro{\ss}mann, R and Peruani, F and B{\"a}r, M}
}
@Article { GrosmannPB2016,
title = {Diffusion properties of active particles with directional reversal},
journal = {New J. Phys},
year = {2016},
month = {4},
day = {31},
volume = {18},
keywords = {8.43},
tags = {8.4,8.43,8.41},
DOI = {10.1088/1367-2630/18/4/043009},
author = {Gro{\ss}mann, R and Peruani, F and B{\"a}r, M}
}
@Article { Alonso_PhysD_2015,
title = {Oscillations and uniaxial mechanochemical waves in a model of an active poroelastic medium: Application to deformation patterns in protoplasmic droplets of Physarum polycephalum},
journal = {Physica D},
year = {2016},
month = {4},
day = {1},
volume = {318},
pages = {58-69},
tags = {8.41, Spatio-Diff, ActFluid},
DOI = {10.1016/j.physd.2015.09.017},
author = {Alonso, S and Strachauer, U and Radszuweit, M and B{\"a}r, M and Hauser, M.J.B}
}
@Article { Schmelter_2016_1,
title = {Polynomchaos zur Unsicherheitsquantifizierung in Str{\"o}mungssimulationen f{\"u}r metrologische Anwendungen},
journal = {tm-Technisches Messen},
year = {2016},
month = {1},
day = {8},
volume = {83},
number = {2},
pages = {71-76},
tags = {8.41, Flow, UQ},
web_url = {http://www.degruyter.com/view/j/teme.2016.83.issue-2/teme-2015-0109/teme-2015-0109.xml},
author = {Schmelter, S and Fiebach, A and Weissenbrunner, A}
}
@Article { Lindner_JFE2015,
title = {A Computational Fluid Dynamics Study on the Gas Mixing Capabilities of a Multiple Inlet System},
journal = {J. Fluids Eng},
year = {2016},
month = {1},
day = {5},
volume = {138},
number = {3},
pages = {031302},
keywords = {8.41, Flow},
tags = {8.41, Flow},
DOI = {10.1115/1.4031380},
author = {Lindner, G and Schmelter, S and Model, R and Nowak, A and Ebert, V and B{\"a}r, M}
}
@Article { e73c330da32016_3,
title = {Reconstructing interaction potentials in thin films from real-space images},
journal = {Phys. Rev. E},
year = {2016},
volume = {93},
number = {4},
pages = {043306},
tags = {8.4,8.41},
DOI = {10.1103/PhysRevE.93.043306},
author = {Gienger, J and Severin, N and Rabe, J and Sokolov, I M}
}
@Article { SH,
title = {Generalized Swift-Hohenberg models for dense active suspensions},
journal = {Eur. Phys. J. E},
year = {2016},
volume = {39},
number = {10},
pages = {97},
tags = {8.4,8.41,ActFluid},
DOI = {10.1140/epje/i2016-16097-2},
author = {Oza, AU and Heidenreich, S and Dunkel, J}
}
@Article { e73c330da32016_2,
title = {Numerical prediction of the flow rate through a flow meter with uncertain inflow profile},
journal = {Proceedings of Imeko 2015 XXI World Congress Measurement in Research and Industry},
year = {2015},
month = {11},
day = {30},
tags = {8.41, Flow, UQ},
author = {Weissenbrunner, A and Fiebach, A and Schmelter, S and Straka, M and B{\"a}r, M and Lederer, T}
}
@Article { Grossmann_EPJ2015_2,
title = {A geometric approach to self-propelled motion in isotropic \& anisotropic environments},
journal = {Eur. Phys. J - Special Topics},
year = {2015},
month = {1},
day = {9},
volume = {224},
number = {7},
pages = {1377-1394},
tags = {8.41, ActMatter},
DOI = {10.1140/epjst/e2015-02465-0},
author = {Gro{\ss}mann, R and Peruani, F and B{\"a}r, M}
}
@Article { heidenreich2015bayesian,
title = {Bayesian approach to the statistical inverse problem of scatterometry: Comparison of three surrogate models},
journal = {International Journal for Uncertainty Quantification},
year = {2015},
month = {1},
day = {8},
pages = {511},
tags = {8.41, Scatter-Inv, UQ},
DOI = {10.1615/Int.J.UncertaintyQuantification.2015013050},
author = {Heidenreich, S and Gross, H and B{\"a}r, M}
}
@Article { Radszu_PRE2015,
title = {Cardiac contraction induces discordant alternans and localized block},
journal = {Phys. Rev. E},
year = {2015},
month = {1},
day = {7},
volume = {91},
pages = {022703},
tags = {8.41, Herz},
DOI = {10.1103/PhysRevE.91.022703},
author = {Radszuweit, M and Alvarez-Lacalle, E and B{\"a}r, M and Echebarria, B}
}
@Article { Bosse_TM2015,
title = {Challenges in nanometrology: high precision measurement of position and size},
journal = {Technisches Messen},
year = {2015},
month = {1},
day = {6},
volume = {82},
pages = {346-358},
tags = {8.41, Scatter-Inv},
url = {10.1515/teme-2015-0002},
author = {Bosse, H and Bodermann, B and Dai, G and Fl{\"u}gge, J and Frase, C. G and Gross, H and H{\"a}{\ss}ler-Grohne, W and K{\"o}chert, P and K{\"o}nning, R and Scholze, F and Weichert, C}
}
@Article { Schmelt_JCF2015,
title = {Numerical prediction of the influence of uncertain inflow conditions in pipes by polynomial chaos},
journal = {Int. J. Comp. Fluid. Dyn.},
year = {2015},
month = {1},
day = {5},
volume = {29},
number = {6-8},
pages = {411-422},
tags = {8.41, Flow, UQ},
DOI = {10.1080/10618562.2015.1112899},
author = {Schmelter, S and Fiebach, A and Model, R and B{\"a}r, M}
}
@Article { Grossmann_EPJE2015,
title = {Pattern formation in active particle systems due to competing alignment interactions},
journal = {Eur. Phys. J - Special Topics},
year = {2015},
month = {1},
day = {4},
volume = {224},
number = {7},
pages = {1325-1347},
tags = {8.41,ActMatter,8.43},
DOI = {10.1140/epjst/e2015-02462-3},
author = {Gro{\ss}mann, R and Romanczuk, P and B{\"a}r, M and Schimansky-Geier, L}
}
@Article { Gross2015,
title = {Modeling aspects to improve the solution of the inverse problem in scatterometry},
journal = {Cont. Dyn. S. - S},
year = {2015},
month = {1},
day = {3},
volume = {8},
pages = {497-519},
tags = {8.41,Scatter-Inv},
DOI = {10.3934/dcdss.2015.8.497},
author = {Gro{\ss}, H and Heidenreich, S and Henn, M-A and B{\"a}r, M and Rathsfeld, A}
}
@Article { Siebert_PRE2014,
title = {Dynamics of reation-diffusion patterns controlled by asymmetric nonlocal coupling as a limiting case of differential advection},
journal = {Phys. Rev. E},
year = {2014},
volume = {89},
pages = {052909},
tags = {8.41, RD},
DOI = {10.1103/PhysRevE.89.052909},
author = {Siebert, J and Alonso, S and B{\"a}r, M and Sch{\"o}ll, E}
}
@Article { Meyer2014,
title = {Active Brownian agents with concentration-dependent chemotactic sensitivity},
journal = {Phys. Rev. E},
year = {2014},
volume = {89},
number = {2},
pages = {022711},
abstract = {We study a biologically motivated model of overdamped, autochemotactic Brownian agents with concentration-dependent chemotactic sensitivity. The agents in our model move stochastically and produce a chemical ligand at their current position. The ligand concentration obeys a reaction-diffusion equation and acts as a chemoattractant for the agents, which bias their motion towards higher concentrations of the dynamically altered chemical field. We explore the impact of concentration-dependent response to chemoattractant gradients on large-scale pattern formation, by deriving a coarse-grained macroscopic description of the individual-based model, and compare the conditions for emergence of inhomogeneous solutions for different variants of the chemotactic sensitivity. We focus primarily on the so-called receptor-law sensitivity, which models a nonlinear decrease of chemotactic sensitivity with increasing ligand concentration. Our results reveal qualitative differences between the receptor law, the constant chemotactic response, and the so-called log law, with respect to stability of the homogeneous solution, as well as the emergence of different patterns (labyrinthine structures, clusters, and bubbles) via spinodal decomposition or nucleation. We discuss two limiting cases, where the model can be reduced to the dynamics of single species: (I) the agent density governed by a density-dependent effective diffusion coefficient and (II) the ligand field with an effective bistable, time-dependent reaction rate. In the end, we turn to single clusters of agents, studying domain growth and determining mean characteristics of the stationary inhomogeneous state. Analytical results are confirmed and extended by large-scale GPU simulations of the individual based model.},
keywords = {,Biological,Biomimetic Materials,Biomimetic Materials: chemistry,Biomimetic Materials: metabolism,Chemical,Chemotaxis,Chemotaxis: drug effects,Chemotaxis: physiology,Computer Simulation,Diffusion,Dose-Response Relationship,Drug,Escherichia coli,Escherichia coli: physiology,Models,Statistical,non-linear dynamics},
tags = {8.41, SPP},
web_url = {http://www.ncbi.nlm.nih.gov/pubmed/25353513},
ISSN = {1550-2376},
DOI = {10.1103/PhysRevE.89.022711},
author = {Meyer, M and Schimansky-Geier, L and Romanczuk, P}
}
@Article { Wendt2014,
title = {Untersuchungen zum Temperaturverhalten von Fl{\"u}ssigkeiten in gro{\ss}en Lagertanks},
journal = {Technische Sicherheit},
year = {2014},
volume = {11},
pages = {13--17},
keywords = {8.41},
tags = {8.41, Flow},
author = {Wendt, G and Jost, R and Schmelter, S and Werner, D}
}
@Article { Schuler2014,
title = {Spatio-temporal dynamics induced by competing instabilities in two asymmetrically coupled nonlinear evolution equations},
journal = {Chaos},
year = {2014},
volume = {24},
number = {4},
pages = {043142},
abstract = {Pattern formation often occurs in spatially extended physical, biological, and chemical systems due to an instability of the homogeneous steady state. The type of the instability usually prescribes the resulting spatio-temporal patterns and their characteristic length scales. However, patterns resulting from the simultaneous occurrence of instabilities cannot be expected to be simple superposition of the patterns associated with the considered instabilities. To address this issue, we design two simple models composed by two asymmetrically coupled equations of non-conserved (Swift-Hohenberg equations) or conserved (Cahn-Hilliard equations) order parameters with different characteristic wave lengths. The patterns arising in these systems range from coexisting static patterns of different wavelengths to traveling waves. A linear stability analysis allows to derive a two parameter phase diagram for the studied models, in particular, revealing for the Swift-Hohenberg equations, a co-dimension two bifurcation point of Turing and wave instability and a region of coexistence of stationary and traveling patterns. The nonlinear dynamics of the coupled evolution equations is investigated by performing accurate numerical simulations. These reveal more complex patterns, ranging from traveling waves with embedded Turing patterns domains to spatio-temporal chaos, and a wide hysteretic region, where waves or Turing patterns coexist. For the coupled Cahn-Hilliard equations the presence of a weak coupling is sufficient to arrest the coarsening process and to lead to the emergence of purely periodic patterns. The final states are characterized by domains with a characteristic length, which diverges logarithmically with the coupling amplitude.},
keywords = {Computer Simulation,Feedback,Models, Theoretical,Nonlinear Dynamics,Oscillometry,Oscillometry: methods,Spatio-Temporal Analysis,non-linear dynamics,spatio-temporal},
tags = {8.41, RD, 8.43},
web_url = {http://scitation.aip.org/content/aip/journal/chaos/24/4/10.1063/1.4905017},
publisher = {AIP Publishing},
ISSN = {1089-7682},
DOI = {10.1063/1.4905017},
author = {Sch{\"u}ler, D and Alonso, S. and Torcini, A and B{\"a}r, M}
}
@Article { Radszuweit2014,
title = {An active poroelastic model for mechanochemical patterns in protoplasmic droplets of Physarum polycephalum},
journal = {PloS one},
year = {2014},
volume = {9},
number = {6},
pages = {e99220},
abstract = {Motivated by recent experimental studies, we derive and analyze a two-dimensional model for the contraction patterns observed in protoplasmic droplets of Physarum polycephalum. The model couples a description of an active poroelastic two-phase medium with equations describing the spatiotemporal dynamics of the intracellular free calcium concentration. The poroelastic medium is assumed to consist of an active viscoelastic solid representing the cytoskeleton and a viscous fluid describing the cytosol. The equations for the poroelastic medium are obtained from continuum force balance and include the relevant mechanical fields and an incompressibility condition for the two-phase medium. The reaction-diffusion equations for the calcium dynamics in the protoplasm of Physarum are extended by advective transport due to the flow of the cytosol generated by mechanical stress. Moreover, we assume that the active tension in the solid cytoskeleton is regulated by the calcium concentration in the fluid phase at the same location, which introduces a mechanochemical coupling. A linear stability analysis of the homogeneous state without deformation and cytosolic flows exhibits an oscillatory Turing instability for a large enough mechanochemical coupling strength. Numerical simulations of the model equations reproduce a large variety of wave patterns, including traveling and standing waves, turbulent patterns, rotating spirals and antiphase oscillations in line with experimental observations of contraction patterns in the protoplasmic droplets.},
keywords = {,Biological,Biomechanical Phenomena,Calcium,Calcium: metabolism,Cytoplasm,Cytoplasm: physiology,Cytoskeleton,Cytoskeleton: physiology,Elasticity,Mechanical,Models,Physarum polycephalum,Physarum polycephalum: cytology,Physarum polycephalum: physiology,Stress,pattern formation},
tags = {8.41, ActMatter, ActFluid},
web_url = {http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0099220},
publisher = {Public Library of Science},
ISSN = {1932-6203},
DOI = {10.1371/journal.pone.0099220},
author = {Radszuweit, M and Engel, H and B{\"a}r, M}
}
@Article { Dai2014,
title = {Measurements of CD and sidewall profile of EUV photomask structures using CD-AFM and tilting-AFM},
journal = {Meas. Sci. Tech.},
year = {2014},
volume = {25},
number = {4},
pages = {044002},
keywords = {Scatterometrie},
tags = {8.41,Scatter-EUV},
web_url = {http://iopscience.iop.org/article/10.1088/0957-0233/25/4/044002},
publisher = {IOP Publishing},
language = {en},
ISSN = {0957-0233},
DOI = {10.1088/0957-0233/25/4/044002},
author = {Dai, G and Hahm, K and Scholze, F and Henn, M-A and Gro{\ss}, H and Fluegge, J and Bosse, H}
}
@Article { Alonso2014,
title = {Modeling domain formation of MARCKS and protein kinase C at cellular membranes},
journal = {Eur. Phys. J. E},
year = {2014},
volume = {2},
number = {1},
pages = {1},
keywords = {pattern formation},
tags = {8.41, membrane},
web_url = {http://link.springer.com/10.1140/epjnbp14},
ISSN = {2195-0008},
DOI = {10.1140/epjnbp14},
author = {Alonso, S and B{\"a}r, M}
}
@Article { Grossmann2014,
title = {Vortex arrays and mesoscale turbulence of self-propelled particles},
journal = {Phys. Rev. Lett.},
year = {2014},
volume = {113},
number = {25},
pages = {258104},
abstract = {Inspired by the Turing mechanism for pattern formation, we propose a simple self-propelled particle model with short-range alignment and antialignment at larger distances. It is able to produce orientationally ordered states, periodic vortex patterns, and mesoscale turbulence, which resembles observations in dense suspensions of swimming bacteria. The model allows a systematic derivation and analysis of a kinetic theory as well as hydrodynamic equations for density and momentum fields. A phase diagram with regions of pattern formation as well as orientational order is obtained from a linear stability analysis of these continuum equations. Microscopic Langevin simulations of self-propelled particles are in agreement with these findings.},
keywords = {pattern formation,turbulence},
tags = {8.41,ActMatt,8.43},
web_url = {http://www.ncbi.nlm.nih.gov/pubmed/25554911},
ISSN = {1079-7114},
DOI = {10.1103/PhysRevLett.113.258104},
author = {Gro{\ss}mann, R and Romanczuk, P and B{\"a}r, M and Schimansky-Geier, L}
}
@Article { Heidenreich2014a,
title = {A surrogate model enables a Bayesian approach to the inverse problem of scatterometry},
journal = {J. Phys. Conf. Ser.},
year = {2014},
volume = {490},
number = {1},
pages = {012007},
tags = {8.41,Bayes,Scatter-Inv,Regression,8.42, UQ},
web_url = {http://iopscience.iop.org/article/10.1088/1742-6596/490/1/012007},
publisher = {IOP Publishing},
language = {en},
ISSN = {1742-6596},
DOI = {10.1088/1742-6596/490/1/012007},
author = {Heidenreich, S and Gross, H and Henn, M-A and Elster, C and B{\"a}r, M}
}
@Article { John2014,
title = {Traveling waves and global oscillations triggered by attractive molecular interactions in an excitable system},
journal = {Phys. Rev. E},
year = {2014},
volume = {90},
number = {5-1},
pages = {052913},
abstract = {During pattern formation in spatially extended systems, different mechanisms with different characteristic length scales, e.g., reaction-diffusion processes or molecular interactions, can be active. Such multiscale effects may generate new phenomena, which are not observed in systems where pattern formation occurs on a single scale. Here, we derive and analyze a reaction-diffusion model of the FitzHugh-Nagumo type with short-range attractive molecular interactions of the activator species. The model exhibits a wave instability. Simulations in one and two dimensions show traveling waves with a wavelength set by the parameters of the molecular interaction in the model. In two dimensions, simulations reveal a labyrinthine arrangement of the waves in systems with isotropic diffusion, whereas parallel bands of counterpropagating waves are formed in simulations of a model with anisotropic diffusion. The latter findings are in good qualitative agreement with experimental observation in the catalytic NO+H{\textbackslash_}\{\{\}2{\}} reaction on an anisotropic Rh(110) surface. In addition we have identified a transition regime in the simulations, where a short scale instability triggers global oscillations in an excitable regime.},
keywords = {pattern formation},
tags = {8.41, exc-media},
web_url = {http://www.ncbi.nlm.nih.gov/pubmed/25493864},
ISSN = {1550-2376},
DOI = {10.1103/PhysRevE.90.052913},
author = {John, K and Alonso, S. and B{\"a}r, M}
}
@Article { Henn2014,
title = {Improved reconstruction of critical dimensions in extreme ultraviolet scatterometry by modeling systematic errors},
journal = {Measurement Science and Technology},
year = {2014},
volume = {25},
number = {4},
pages = {044003},
tags = {8.41,Scatter-Inv,Scatterometrie, 8.42},
web_url = {http://iopscience.iop.org/article/10.1088/0957-0233/25/4/044003},
publisher = {IOP Publishing},
language = {en},
ISSN = {0957-0233},
DOI = {10.1088/0957-0233/25/4/044003},
author = {Henn, M-A and Gross, H and Heidenreich, S and Scholze, F and Elster, C and B{\"a}r, M}
}
@Article { Heidenreich2014,
title = {Numerical simulations of a minimal model for the fluid dynamics of dense bacterial suspensions},
journal = {J.Phys.: Conf. Ser.},
year = {2014},
volume = {490},
number = {1},
pages = {012126},
keywords = {8.41,fluid dynamics},
tags = {8.41, ActFluid},
web_url = {http://iopscience.iop.org/article/10.1088/1742-6596/490/1/012126},
publisher = {IOP Publishing},
language = {en},
ISSN = {1742-6596},
DOI = {10.1088/1742-6596/490/1/012126},
author = {Heidenreich, S and Klapp, S H L and B{\"a}r, M}
}
@Article { Gross2014,
title = {Modelling line edge roughness in periodic line-space structures by Fourier optics to improve scatterometry},
journal = {J. Europ.Opt. Soci.Rap. Pub.},
year = {2014},
volume = {9},
pages = {14003},
abstract = {In the present paper, we propose a 2D-Fourier transform method as a simple and efficient algorithm for stochastical and numerical studies to investigate the systematic impacts of line edge roughness on light diffraction pattern of periodic line-space structures. The key concept is the generation of ensembles of rough apertures composed of many slits, to calculate the irradiance of the illuminated rough apertures far away from the aperture plane, and a comparison of their light intensities to those of the undisturbed, {\^a}{\euro}™non-rough{\^a}{\euro}™ aperture. We apply the Fraunhofer approximation and interpret the rough apertures as binary 2D-gratings to compute their diffraction patterns very efficiently as the 2D-Fourier transform of the light distribution of the source plane. The rough edges of the aperture slits are generated by means of power spectrum density (PSD) functions, which are often used in metrology of rough geometries. The mean efficiencies of the rough apertures reveal a systematic exponential decrease for higher diffraction orders if compared to the diffraction pattern of the unperturbed aperture. This confirms former results, obtained by rigorous calculations with computational expensive finite element methods (FEM) for a simplified roughness model. The implicated model extension for scatterometry by an exponential damping factor for the calculated efficiencies allows to determine the standard deviation \(\sigma\){\textbackslash_} r of line edge roughness along with the critical dimensions (CDs), i.e., line widths, heights and other profile properties in the sub-micrometer range. First comparisons with the corresponding roughness value determined by 3D atomic force microscopy (3D AFM) reveal encouraging results.},
keywords = {Scatterometrie,Scatterometry,atomic force microscopy,line edge roughness,power spectrum density},
tags = {8.41,Scatter-Inv},
web_url = {http://www.jeos.org/index.php/jeos{\textbackslash_}rp/article/view/14003},
language = {en},
ISSN = {1990-2573},
DOI = {10.2971/jeos.2014.14003},
author = {Gro{\ss}, H and Heidenreich, S and Henn, M-A and Dai, G and Scholze, F and B{\"a}r, M}
}
@Article { Fiebach2014,
title = {Uniform global bounds for solutions of an implicit Voronoi finite volume method for reaction{\^a}{\euro}“diffusion problems},
journal = {Numerische Mathematik},
year = {2014},
volume = {128},
number = {1},
pages = {31--72},
keywords = {finite elements,finite volumes,voronoi},
tags = {8.41},
web_url = {http://link.springer.com/10.1007/s00211-014-0604-6},
ISSN = {0029-599X},
DOI = {10.1007/s00211-014-0604-6},
author = {Fiebach, A and Glitzky, A and Linke, A}
}
@Article { f3ee8757792015,
title = {Numerical investigation of temperature distributions in large storage tanks},
journal = {Proceedings of Flomeko 2013 16th International Flow Measurement Conference},
year = {2013},
month = {12},
day = {31},
tags = {8.41, Flow},
author = {Schmelter, S and Model, R and Wendt, G and B{\"a}r, M}
}
@Article { Heiden_PRL2013,
title = {Fluid Dynamics of Bacterial Turbulence},
journal = {Phys. Rev. Lett.},
year = {2013},
volume = {110},
pages = {228102},
tags = {8.41, ActFluid},
DOI = {10.1103/PhysRevLett.110.228102},
author = {Dunkel, J and Heidenreich, S and Drescher, K and Wensink, H. H and B{\"a}r, M and Goldstein, R. E}
}
@Article { Radszuweit2013,
title = {Intracellular mechanochemical waves in an active poroelastic model},
journal = {Phys. Rev. Lett.},
year = {2013},
volume = {110},
number = {13},
pages = {138102},
abstract = {Many processes in living cells are controlled by biochemical substances regulating active stresses. The cytoplasm is an active material with both viscoelastic and liquid properties. We incorporate the active stress into a two-phase model of the cytoplasm which accounts for the spatiotemporal dynamics of the cytoskeleton and the cytosol. The cytoskeleton is described as a solid matrix that together with the cytosol as an interstitial fluid constitutes a poroelastic material. We find different forms of mechanochemical waves including traveling, standing, and rotating waves by employing linear stability analysis and numerical simulations in one and two spatial dimensions.},
keywords = {Biological,Biomechanical Phenomena,Cell Physiological Phenomena,Cytoplasm,Cytoplasm: chemistry,Cytoskeleton,Cytoskeleton: chemistry,Elasticity,Extracellular Fluid,Extracellular Fluid: chemistry,Models,Viscosity},
tags = {8.41, ActMatt, ActFluid},
web_url = {http://www.ncbi.nlm.nih.gov/pubmed/23581377},
ISSN = {1079-7114},
DOI = {10.1103/PhysRevLett.110.138102},
author = {Radszuweit, M and Alonso, S. and Engel, H and B{\"a}r, M}
}
@Article { Peruani2013,
title = {A kinetic model and scaling properties of non-equilibrium clustering of self-propelled particles},
journal = {New J. Phys.},
year = {2013},
volume = {15},
number = {6},
pages = {065009},
tags = {8.41, SPP},
web_url = {http://iopscience.iop.org/article/10.1088/1367-2630/15/6/065009},
publisher = {IOP Publishing},
language = {en},
ISBN = {doi:10.1088/1367-2630/15/6/065009},
ISSN = {1367-2630},
DOI = {10.1088/1367-2630/15/6/065009},
author = {Peruani, F and B{\"a}r, M}
}
@Article { Jousten2014,
title = {A standard to test the dynamics of vacuum gauges in the millisecond range},
journal = {Vacuum},
year = {2013},
volume = {100},
pages = {14--17},
abstract = {Vacuum gauges that control fast processes in industrial applications, e.g. load locks, should immediately react to pressure changes. To study the response time of vacuum gauges to rapid pressure changes, a dynamic vacuum standard was developed where the pressure may change from 100 kPa to 100 Pa within 20 ms in a step-wise manner or within longer times up to 1 s in a predictable manner. This is accomplished by a very fast opening gate valve DN40 and exchangeable orifices and ducts through which the mass flow rate can be calculated by gas flow simulation software. A simple physical model can be used to approximate the calculations. Experiments have been performed with capacitance diaphragm gauges with improved electronics to give a read-out every 0.7 ms. Preliminary results indicate that their response time is at most 1.7 ms, but may be significantly less.},
keywords = {Choked flow,Dynamic pressure,Response time,Vacuum gauge,Vacuum metrology},
tags = {8.41,Flow},
url = {fileadmin/internet/fachabteilungen/abteilung_8/8.4_mathematische_modellierung/8.42/DYNAMIK/842_dynamik_Sensors_2010_10_7621.pdf},
web_url = {http://www.sciencedirect.com/science/article/pii/S0042207X13002546},
ISSN = {0042207X},
DOI = {10.1016/j.vacuum.2013.07.037},
author = {Jousten, K and Pantazis, S and Buthig, J and Model, R and W{\"u}est, M and Iwicki, J}
}
@Article { Dunkel2013,
title = {Minimal continuum theories of structure formation in dense active fluids},
journal = {New J. Phys.},
year = {2013},
volume = {15},
number = {4},
pages = {045016},
tags = {8.41, ActFluid},
web_url = {http://iopscience.iop.org/article/10.1088/1367-2630/15/4/045016},
publisher = {IOP Publishing},
language = {en},
ISSN = {1367-2630},
DOI = {10.1088/1367-2630/15/4/045016},
author = {Dunkel, J and Heidenreich, S and B{\"a}r, M and Goldstein, R E}
}
@Article { Dahmlow2013,
title = {Twists of opposite handedness on a scroll wave},
journal = {Phys. Rev. Lett.},
year = {2013},
volume = {110},
number = {23},
pages = {234102},
abstract = {The dynamic interaction of scroll waves in the Belousov-Zhabotinsky reaction with a vertically orientated gradient of excitability is studied by optical tomography. This study focuses on scroll waves, whose filaments were oriented almost perpendicular to the gradient. Whereas scroll waves with filaments exactly perpendicular to the gradient remain unaffected, filaments with a component parallel to the gradient develop a twist. Scroll waves with U-shaped filaments exhibit twists starting from both of its ends, resulting in scroll waves whose filaments display a pair of twists of opposite handedness. These twists are separated by a nodal plane where the filament remains straight and untwisted. The experimental findings were reproduced by numerical simulations using the Oregonator model and a linear gradient of excitability almost perpendicular to the orientation of the filament.},
keywords = {Arrhythmias,Cardiac,Cardiac: physiopathology,Heart,Heart: physiology,Models,Theoretical},
tags = {8.41,Herz},
web_url = {http://www.ncbi.nlm.nih.gov/pubmed/25167496},
ISSN = {1079-7114},
DOI = {10.1103/PhysRevLett.110.234102},
author = {D{\"a}hmlow, P and Alonso, S. and B{\"a}r, M and Hauser, M J B}
}
@Article { Alonso2013,
title = {Negative tension of scroll wave filaments and turbulence in three-dimensional excitable media and application in cardiac dynamics},
journal = {Bull. Math. Biol.},
year = {2013},
volume = {75},
number = {8},
pages = {1351--76},
abstract = {Scroll waves are vortices that occur in three-dimensional excitable media. Scroll waves have been observed in a variety of systems including cardiac tissue, where they are associated with cardiac arrhythmias. The disorganization of scroll waves into chaotic behavior is thought to be the mechanism of ventricular fibrillation, whose lethality is widely known. One possible mechanism for this process of scroll wave instability is negative filament tension. It was discovered in 1987 in a simple two variables model of an excitable medium. Since that time, negative filament tension of scroll waves and the resulting complex, often turbulent dynamics was studied in many generic models of excitable media as well as in physiologically realistic models of cardiac tissue. In this article, we review the work in this area from the first simulations in FitzHugh-Nagumo type models to recent studies involving detailed ionic models of cardiac tissue. We discuss the relation of negative filament tension and tissue excitability and the effects of discreteness in the tissue on the filament tension. Finally, we consider the application of the negative tension mechanism to computational cardiology, where it may be regarded as a fundamental mechanism that explains differences in the onset of arrhythmias in thin and thick tissue.},
keywords = {8.41,Animals,Arrhythmias,Cardiac,Cardiac: etiology,Cardiac: physiopathology,Cardiovascular,Electrophysiological Phenomena,Excitation Contraction Coupling,Heart Conduction System,Heart Conduction System: physiology,Hemorheology,Humans,Imaging,Mathematical Concepts,Models,Myocardial Contraction,Three-Dimensional},
tags = {8.41, Herz},
web_url = {http://www.ncbi.nlm.nih.gov/pubmed/22829178},
ISSN = {1522-9602},
DOI = {10.1007/s11538-012-9748-7},
author = {Alonso, S and Panfilov, A V}
}
@Article { Alonso2013a,
title = {Reentry near the percolation threshold in a heterogeneous discrete model for cardiac tissue},
journal = {Phys. Rev. Lett.},
year = {2013},
volume = {110},
number = {15},
pages = {158101},
abstract = {Arrhythmias in cardiac tissue are related to irregular electrical wave propagation in the heart. Cardiac tissue is formed by a discrete cell network, which is often heterogeneous. A localized region with a fraction of nonconducting links surrounded by homogeneous conducting tissue can become a source of reentry and ectopic beats. Extensive simulations in a discrete model of cardiac tissue show that a wave crossing a heterogeneous region of cardiac tissue can disintegrate into irregular patterns, provided the fraction of nonconducting links is close to the percolation threshold of the cell network. The dependence of the reentry probability on this fraction, the system size, and the degree of excitability can be inferred from the size distribution of nonconducting clusters near the percolation threshold.},
keywords = {Action Potentials,Cardiovascular,Computer Simulation,Heart,Heart: physiology,Models},
tags = {8.41, Herz, 8.43},
web_url = {http://www.ncbi.nlm.nih.gov/pubmed/25167313},
ISSN = {1079-7114},
DOI = {10.1103/PhysRevLett.110.158101},
author = {Alonso, S and B{\"a}r, M}
}
@Article { Aranson2013,
title = {Viewpoint: The Aquatic Dance of Bacteria},
journal = {Physics},
year = {2013},
volume = {6},
tags = {8.41, ActMatter},
web_url = {http://physics.aps.org/articles/v6/61},
publisher = {American Physical Society},
language = {en},
author = {Aranson, I}
}
@Phdthesis { Radszuweit2013a,
title = {An Active Poroelastic Model for Cytoplasm and Pattern Formation in Protoplasmic Droplets of Physarum Polycephalum},
year = {2013},
tags = {8.41, ActMatter},
school = {TU Berlin},
author = {Radszuweit, M}
}
@Phdthesis { Henn_Thesis,
title = {Statistical Approaches to the Inverse Problem of Scatterometry},
year = {2013},
keywords = {8.41,8.42,Scatter-Inv,Scatterometrie},
tags = {8.41,Scatter-Inv},
school = {TU Berlin},
author = {Henn, M-A}
}
@Phdthesis { Fiebach2013,
title = {A dissipative finite volume scheme for reaction-diffusion systems in heterogeneous materials},
year = {2013},
keywords = {discrete Moser iteration,dissipative finite volume scheme,heterogeneous materials,reaction-diffusion systems},
tags = {8.41},
web_url = {http://www.diss.fu-berlin.de/diss/receive/FUDISS{\textbackslash_}thesis{\textbackslash_}000000096910},
language = {English},
author = {Fiebach, A}
}
@Article { Peruani2012,
title = {Collective Motion and Nonequilibrium Cluster Formation in Colonies of Gliding Bacteria},
journal = {Phys. Rev. Lett.},
year = {2012},
volume = {108},
number = {9},
pages = {098102},
tags = {8.41, SPP, 8.43},
web_url = {http://link.aps.org/doi/10.1103/PhysRevLett.108.098102},
ISSN = {0031-9007},
DOI = {10.1103/PhysRevLett.108.098102},
author = {Peruani, F and Starru{\ss}, J and Jakovljevic, V and S{\o}gaard-Andersen, L and Deutsch, A and B{\"a}r, M}
}
@Article { Lober2012,
title = {Front propagation in one-dimensional spatially periodic bistable media},
journal = {Phys. Rev. E},
year = {2012},
volume = {86},
number = {6 Pt 2},
pages = {066210},
abstract = {Front propagation in heterogeneous bistable media is studied using the Schl{{\"o}}gl model as a representative example. Spatially periodic modulations in the parameters of the bistable kinetics are taken into account perturbatively. Depending on the ratio L/l (L is the spatial period of the heterogeneity, l is the front width), appropriate singular perturbation techniques are applied to derive an ordinary differential equation for the position of the front in the presence of the heterogeneities. From this equation, the dependence of the average propagation speed on L/l as well as on the modulation amplitude is calculated. The analytical results obtained predict velocity overshoot, different cases of propagation failure, and the propagation speed for very large spatial periods in quantitative agreement with the results of direct numerical simulations of the underlying reaction-diffusion equation.},
tags = {8.41, exc-media},
web_url = {http://www.ncbi.nlm.nih.gov/pubmed/23368027},
ISSN = {1550-2376},
DOI = {10.1103/PhysRevE.86.066210},
author = {L{\"o}ber, J and B{\"a}r, M and Engel, H}
}
@Article { Wensink2012,
title = {Meso-scale turbulence in living fluids},
journal = {Proc. Natl. Acad. Sci. U.S.A.},
year = {2012},
volume = {109},
number = {36},
pages = {14308--13},
abstract = {Turbulence is ubiquitous, from oceanic currents to small-scale biological and quantum systems. Self-sustained turbulent motion in microbial suspensions presents an intriguing example of collective dynamical behavior among the simplest forms of life and is important for fluid mixing and molecular transport on the microscale. The mathematical characterization of turbulence phenomena in active nonequilibrium fluids proves even more difficult than for conventional liquids or gases. It is not known which features of turbulent phases in living matter are universal or system-specific or which generalizations of the Navier-Stokes equations are able to describe them adequately. Here, we combine experiments, particle simulations, and continuum theory to identify the statistical properties of self-sustained meso-scale turbulence in active systems. To study how dimensionality and boundary conditions affect collective bacterial dynamics, we measured energy spectra and structure functions in dense Bacillus subtilis suspensions in quasi-2D and 3D geometries. Our experimental results for the bacterial flow statistics agree well with predictions from a minimal model for self-propelled rods, suggesting that at high concentrations the collective motion of the bacteria is dominated by short-range interactions. To provide a basis for future theoretical studies, we propose a minimal continuum model for incompressible bacterial flow. A detailed numerical analysis of the 2D case shows that this theory can reproduce many of the experimentally observed features of self-sustained active turbulence.},
keywords = {Bacillus subtilis,Bacillus subtilis: physiology,Biological,Biomechanical Phenomena,Computer Simulation,Culture Media,Culture Media: chemistry,Hydrodynamics,Models,Movement,Movement: physiology},
tags = {8.41, ActFluid},
web_url = {http://www.pnas.org/content/109/36/14308},
ISSN = {1091-6490},
DOI = {10.1073/pnas.1202032109},
author = {Wensink, H H and Dunkel, J and Heidenreich, S and Drescher, K and Goldstein, R E and L{\"o}wen, H and Yeomans, J M}
}
@Article { Romanczuk2012,
title = {Active Brownian particles},
journal = {Eur. Phys. J. - Special Topics},
year = {2012},
volume = {202},
number = {1},
pages = {1--162},
tags = {8.41, SSP},
web_url = {http://www.springerlink.com/index/10.1140/epjst/e2012-01529-y},
ISSN = {1951-6355},
DOI = {10.1140/epjst/e2012-01529-y},
author = {Romanczuk, P and B{\"a}r, M and Ebeling, W and Lindner, B and Schimansky-Geier, L}
}
@Article { Starruss2012,
title = {Pattern-formation mechanisms in motility mutants of Myxococcus xanthus},
journal = {Interface focus},
year = {2012},
volume = {2},
number = {6},
pages = {774--85},
abstract = {Formation of spatial patterns of cells is a recurring theme in biology and often depends on regulated cell motility. Motility of the rod-shaped cells of the bacterium Myxococcus xanthus depends on two motility machineries, type IV pili (giving rise to S-motility) and the gliding motility apparatus (giving rise to A-motility). Cell motility is regulated by occasional reversals. Moving M. xanthus cells can organize into spreading colonies or spore-filled fruiting bodies, depending on their nutritional status. To ultimately understand these two pattern-formation processes and the contributions by the two motility machineries, as well as the cell reversal machinery, we analyse spatial self-organization in three M. xanthus strains: (i) a mutant that moves unidirectionally without reversing by the A-motility system only, (ii) a unidirectional mutant that is also equipped with the S-motility system, and (iii) the wild-type that, in addition to the two motility systems, occasionally reverses its direction of movement. The mutant moving by means of the A-engine illustrates that collective motion in the form of large moving clusters can arise in gliding bacteria owing to steric interactions of the rod-shaped cells, without the need of invoking any biochemical signal regulation. The two-engine strain mutant reveals that the same phenomenon emerges when both motility systems are present, and as long as cells exhibit unidirectional motion only. From the study of these two strains, we conclude that unidirectional cell motion induces the formation of large moving clusters at low and intermediate densities, while it results in vortex formation at very high densities. These findings are consistent with what is known from self-propelled rod models, which strongly suggests that the combined effect of self-propulsion and volume exclusion interactions is the pattern-formation mechanism leading to the observed phenomena. On the other hand, we learn that when cells occasionally reverse their moving direction, as observed in the wild-type, cells form small but strongly elongated clusters and self-organize into a mesh-like structure at high enough densities. These results have been obtained from a careful analysis of the cluster statistics of ensembles of cells, and analysed in the light of a coagulation Smoluchowski equation with fragmentation.},
keywords = {,pattern formation},
tags = {8.41,SPP},
web_url = {http://rsfs.royalsocietypublishing.org/content/2/6/774},
ISSN = {2042-8901},
DOI = {10.1098/rsfs.2012.0034},
author = {Starru{\ss}, J and Peruani, F and Jakovljevic, V and S{\o}gaard-Andersen, L and Deutsch, A and B{\"a}r, M}
}
@Article { Bodermann2012,
title = {Nanometrology at PTB in support of process control of nanoscale features in semiconductor manufacturing},
journal = {International Journal of Nanomanufacturing},
year = {2012},
volume = {8},
number = {1},
abstract = {We report on recent developments at the PTB in the field of dimensional nanometrology with a special focus on instrumentation, measurement and simulation methods, and standards which are used in semiconductor lithography manufacturing processes. Important dimensional measurands to be controlled precisely during the high volume manufacturing processes of nanoscale features (< 32 nm node) are the positions and widths of features on lithographic masks and wafers as well as the relative positioning or overlay of features.},
keywords = {Nanometrology},
tags = {8.41,Scatter-Inv},
author = {Bodermann, B and Scholze, F and Fl{\"u}gge, J and Gro{\ss}, H and Bosse, H}
}
@Article { Bar2012,
title = {Synchronization and complex dynamics of oscillators with delayed pulse coupling},
journal = {Angewandte Chemie (International ed. in English)},
year = {2012},
volume = {51},
number = {38},
pages = {9489--90},
tags = {8.41, NonDyn},
web_url = {http://www.ncbi.nlm.nih.gov/pubmed/22915494},
ISSN = {1521-3773},
DOI = {10.1002/anie.201205214},
author = {B{\"a}r, M and Sch{\"o}ll, E and Torcini, A}
}
@Article { Henn2012a,
title = {Improved grating reconstruction by determination of line roughness in extreme ultraviolet scatterometry},
journal = {Opt. Lett.},
year = {2012},
volume = {37},
number = {24},
pages = {5229--5231},
keywords = {8.41,Scatter-Inv},
tags = {8.41,Scatter-Inv},
DOI = {10.1364/OL.37.005229},
author = {Henn, M-A and Heidenreich, S and Gro{\ss}, H and Rathsfeld, A and Scholze, F and B{\"a}r, M}
}
@Article { Henn2012,
title = {A maximum likelihood approach to the inverse problem of scatterometry},
journal = {Optics Express},
year = {2012},
volume = {20},
number = {12},
pages = {12771-86},
abstract = {Scatterometry is frequently used as a non-imaging indirect optical method to reconstruct the critical dimensions (CD) of periodic nanostructures. A particular promising direction is EUV scatterometry with wavelengths in the range of 13 - 14 nm. The conventional approach to determine CDs is the minimization of a least squares function (LSQ). In this paper, we introduce an alternative method based on the maximum likelihood estimation (MLE) that determines the statistical error model parameters directly from measurement data. By using simulation data, we show that the MLE method is able to correct the systematic errors present in LSQ results and improves the accuracy of scatterometry. In a second step, the MLE approach is applied to measurement data from both extreme ultraviolet (EUV) and deep ultraviolet (DUV) scatterometry. Using MLE removes the systematic disagreement of EUV with other methods such as scanning electron microscopy and gives consistent results for DUV.},
tags = {8.41,Diffraction gratings,Metrology,Scatter-Inv,Scatterometrie,8.42},
web_url = {http://www.osapublishing.org/viewmedia.cfm?uri=oe-20-12-12771{\&}seq=0{\&}html=true},
publisher = {Optical Society of America},
language = {EN},
ISSN = {1094-4087},
DOI = {10.1364/OE.20.012771},
author = {Henn, M-A and Gross, H and Scholze, F and Wurm, M and Elster, C and B{\"a}r, M}
}
@Article { GrosHHRB2012,
title = {Modeling of line roughness and its impact on the diffraction intensities and the reconstructed critical dimensions in scatterometry},
journal = {Appl. Opt.},
year = {2012},
volume = {51},
number = {30},
pages = {7384--94},
abstract = {We investigate the impact of line-edge and line-width roughness (LER, LWR) on the measured diffraction intensities in angular resolved extreme ultraviolet (EUV) scatterometry for a periodic line-space structure designed for EUV lithography. LER and LWR with typical amplitudes of a few nanometers were previously neglected in the course of the profile reconstruction. The two-dimensional (2D) rigorous numerical simulations of the diffraction process for periodic structures are carried out with the finite element method providing a numerical solution of the 2D Helmholtz equation. To model roughness, multiple calculations are performed for domains with large periods, containing many pairs of line and space with stochastically chosen line and space widths. A systematic decrease of the mean efficiencies for higher diffraction orders along with increasing variances is observed and established for different degrees of roughness. In particular, we obtain simple analytical expressions for the bias in the mean efficiencies and the additional uncertainty contribution stemming from the presence of LER and/or LWR. As a consequence this bias can easily be included into the reconstruction model to provide accurate values for the evaluated profile parameters. We resolve the sensitivity of the reconstruction from this bias by using simulated data with LER/LWR perturbed efficiencies for multiple reconstructions. If the scattering efficiencies are bias-corrected, significant improvements are found in the reconstructed bottom and top widths toward the nominal values.},
keywords = {8.41,Diffraction gratings,Metrology,Scatter-Inv,Scatterometrie},
tags = {8.41,Scatter-Inv},
web_url = {http://www.osapublishing.org/viewmedia.cfm?uri=ao-51-30-7384{\&}seq=0{\&}html=true},
publisher = {Optical Society of America},
language = {EN},
ISSN = {1539-4522},
DOI = {10.1364/AO.51.007384},
author = {Gro{\ss}, H and Henn, M-A and Heidenreich, S and Rathsfeld, A and B{\"a}r, M}
}
@Inbook { Model_2012,
title = {Numerical simulations and turbulent modelling for application in flow metrology},
year = {2012},
volume = {84},
tags = {8.41, Flow},
editor = {F. Pavese, M. B{\"a}r, J.-R. Filtz, A. B. Forbes, L. Pendrill and K. Shirono},
publisher = {World Scientific, New Jersey},
author = {Model, R and Schmelter, S and Lindner, G and B{\"a}r, M}
}
@Inbook { Gross2012,
title = {Stochastic modeling aspects for an improved solution of the inverse problem in scatterometry},
year = {2012},
keywords = {8.41,Scatter-Inv},
tags = {8.41,Scatter-Inv},
editor = {F. Pavese, M. B{\"a}r, J.-R. Filtz, A. B. Forbes, L. Pendrill, K. Shirono},
publisher = {World Scientific New Jersey},
booktitle = {Advanced Mathematical \& Computational Tools in Metrology and Testing IX},
author = {Gro{\ss}, H and Henn, M-A and Rathsfeld, A and B{\"a}r, M}
}
@Inproceedings { Bodermann2012a,
title = {First steps towards a scatterometry reference standard},
year = {2012},
keywords = {8.41,Scatter-Inv},
tags = {8.41,Scatter-Inv},
booktitle = {SPIE Proc.},
author = {Bodermann, B and Hansen, P-E and Burger, S and Henn, M-A and Gross, H and Scholze, F and Endres, J and Wurm, M}
}
@Article { Peruani2011,
title = {Polar vs. apolar alignment in systems of polar self-propelled particles},
journal = {J. Phys.: Conf. Ser.},
year = {2011},
volume = {297},
number = {1},
pages = {012014},
tags = {8.41, SPP},
web_url = {http://iopscience.iop.org/article/10.1088/1742-6596/297/1/012014},
publisher = {IOP Publishing},
language = {en},
ISSN = {1742-6596},
DOI = {10.1088/1742-6596/297/1/012014},
author = {Peruani, F and Ginelli, F and B{\"a}r, M and Chat{\'e}, H}
}
@Article { Kupitz2011,
title = {Surfactant-induced gradients in the three-dimensional Belousov-Zhabotinsky reaction},
journal = {Phys. Review. E},
year = {2011},
volume = {84},
number = {5 Pt 2},
pages = {056210},
abstract = {Scroll waves are prominent patterns formed in three-dimensional excitable media, and they are frequently considered highly relevant for some types of cardiac arrhythmias. Experimentally, scroll wave dynamics is often studied by optical tomography in the Belousov-Zhabotinsky reaction, which produces CO(2) as an undesired product. Addition of small concentrations of a surfactant to the reaction medium is a popular method to suppress or retard CO(2) bubble formation. We show that in closed reactors even these low concentrations of surfactants are sufficient to generate vertical gradients of excitability which are due to gradients in CO(2) concentration. In reactors open to the atmosphere such gradients can be avoided. The gradients induce a twist on vertically oriented scroll waves, while a twist is absent in scroll waves in a gradient-free medium. The effects of the CO(2) gradients are reproduced by a numerical study, where we extend the Oregonator model to account for the production of CO(2) and for its advection against the direction of gravity. The numerical simulations confirm the role of solubilized CO(2) as the source of the vertical gradient of excitability in reactors closed to the atmosphere.},
keywords = {Algorithms,Animals,Arrhythmias,Biophysics,Biophysics: methods,Bioreactors,Carbon Dioxide,Carbon Dioxide: chemistry,Cardiac,Cardiac: physiopathology,Culture Media,Gases,Humans,Micelles,Models,Sodium Dodecyl Sulfate,Sodium Dodecyl Sulfate: chemistry,Statistical,Surface-Active Agents,Surface-Active Agents: chemistry,Theoretical,Time Factors},
tags = {8.41, RD},
web_url = {http://www.ncbi.nlm.nih.gov/pubmed/22181487},
ISSN = {1550-2376},
DOI = {10.1103/PhysRevE.84.056210},
author = {Kupitz, D and Alonso, S. and B{\"a}r, M and Hauser, M J B}
}
@Article { Echebarria2011,
title = {Supernormal conduction in cardiac tissue promotes concordant alternans and action potential bunching},
journal = {Phys. Rev. E},
year = {2011},
volume = {83},
number = {4 Pt 1},
pages = {040902},
abstract = {Supernormal conduction (SNC) in excitable cardiac tissue refers to an increase of pulse (or action potential) velocity with decreasing distance to the preceding pulse. Here we employ a simple ionic model to study the effect of SNC on the propagation of action potentials (APs) and the phenomenology of alternans in excitable cardiac tissue. We use bifurcation analysis and simulations to study attraction between propagating APs caused by SNC that leads to AP pairs and bunching. It is shown that SNC stabilizes concordant alternans in arbitrarily long paced one-dimensional cables. As a consequence, spiral waves in two-dimensional tissue simulations exhibit straight nodal lines for SNC in contrast to spiraling ones in the case of normal conduction.},
keywords = {Action Potentials,Action Potentials: physiology,Animals,Biological Clocks,Biological Clocks: physiology,Cardiovascular,Computer Simulation,Heart Conduction System,Heart Conduction System: physiology,Humans,Models},
tags = {8.41, Herz},
web_url = {http://www.ncbi.nlm.nih.gov/pubmed/21599107},
ISSN = {1550-2376},
DOI = {10.1103/PhysRevE.83.040902},
author = {Echebarria, B and R{\"o}der, G and Engel, H and Davidsen, J and B{\"a}r, M}
}
@Article { Alonso2011a,
title = {Complex wave patterns in an effective reaction-diffusion model for chemical reactions in microemulsions},
journal = {J. Chem. Phys.},
year = {2011},
volume = {134},
number = {9},
pages = {094117},
abstract = {An effective medium theory is employed to derive a simple qualitative model of a pattern forming chemical reaction in a microemulsion. This spatially heterogeneous system is composed of water nanodroplets randomly distributed in oil. While some steps of the reaction are performed only inside the droplets, the transport through the extended medium occurs by diffusion of intermediate chemical reactants as well as by collisions of the droplets. We start to model the system with heterogeneous reaction-diffusion equations and then derive an equivalent effective spatially homogeneous reaction-diffusion model by using earlier results on homogenization in heterogeneous reaction-diffusion systems [S.Alonso, M.Ba{\`I}ˆr, and R.Kapral, J. Chem. Phys. 134, 214102 (2009)]. We study the linear stability of the spatially homogeneous state in the resulting effective model and obtain a phase diagram of pattern formation, that is qualitatively similar to earlier experimental results for the Belousov-Zhabotinsky reaction in an aerosol OT (AOT)-water-in-oil microemulsion [V.K.Vanag and I.R.Epstein, Phys. Rev. Lett. 87, 228301 (2001)]. Moreover, we reproduce many patterns that have been observed in experiments with the Belousov-Zhabotinsky reaction in an AOT oil-in-water microemulsion by direct numerical simulations.},
keywords = {Aerosols,Aerosols: chemistry,Chemical,Diffusion,Emulsions,Emulsions: chemistry,Models,Oils,Oils: chemistry,Water,Water: chemistry},
tags = {8.41, RD},
web_url = {http://scitation.aip.org/content/aip/journal/jcp/134/9/10.1063/1.3559154},
publisher = {AIP Publishing},
ISSN = {1089-7690},
DOI = {10.1063/1.3559154},
author = {Alonso, S. and John, K and B{\"a}r, M}
}
@Article { Alonso2011,
title = {Oscillations in the lateral pressure of lipid monolayers induced by nonlinear chemical dynamics of the second messengers MARCKS and protein kinase C},
journal = {Biophys. J.},
year = {2011},
volume = {100},
number = {4},
pages = {939--47},
abstract = {The binding of the MARCKS peptide to the lipid monolayer containing PIP(2) increases the lateral pressure of the monolayer. The unbinding dynamics modulated by protein kinase C leads to oscillations in lateral pressure of lipid monolayers. These periodic dynamics can be attributed to changes in the crystalline lipid domain size. We have developed a mathematical model to explain these observations based on the changes in the physical structure of the monolayer by the translocation of MARCKS peptide. The model indicates that changes in lipid domain size drives these oscillations. The model is extended to an open system that sustains chemical oscillations.},
keywords = {Biological,Biological Transport,Computer Simulation,Fluorescence,Intracellular Signaling Peptides and Proteins,Intracellular Signaling Peptides and Proteins: met,Lipids,Lipids: chemistry,Membrane Proteins,Membrane Proteins: metabolism,Microscopy,Models,Nonlinear Dynamics,Phosphorylation,Pressure,Protein Kinase C,Protein Kinase C: metabolism,Second Messenger Systems,Time Factors},
tags = {8.41,membrane},
web_url = {http://www.sciencedirect.com/science/article/pii/S0006349510052197},
ISSN = {1542-0086},
DOI = {10.1016/j.bpj.2010.12.3702},
author = {Alonso, S. and Dietrich, U and H{\"a}ndel, C and K{\"a}s, J A and B{\"a}r, M}
}
@Article { Alonso2011c,
title = {Effects of reduced discrete coupling on filament tension in excitable media},
journal = {Chaos},
year = {2011},
volume = {21},
number = {1},
pages = {013118},
abstract = {Wave propagation in the heart has a discrete nature, because it is mediated by discrete intercellular connections via gap junctions. Although effects of discreteness on wave propagation have been studied for planar traveling waves and vortexes (spiral waves) in two dimensions, its possible effects on vortexes (scroll waves) in three dimensions are not yet explored. In this article, we study the effect of discrete cell coupling on the filament dynamics in a generic model of an excitable medium. We find that reduced cell coupling decreases the line tension of scroll wave filaments and may induce negative filament tension instability in three-dimensional excitable lattices.},
tags = {8.41 exc-media},
web_url = {http://scitation.aip.org/content/aip/journal/chaos/21/1/10.1063/1.3551500},
publisher = {AIP Publishing},
ISSN = {1089-7682},
DOI = {10.1063/1.3551500},
author = {Alonso, S. and B{\"a}r, M and Panfilov, AlV}
}
@Article { Forster2011,
title = {Untersuchungen zur Explosionsgefahr beim Umschlag von Kerosin Jet A-1},
journal = {Technische Sicherheit},
year = {2011},
volume = {1},
pages = {18--27},
tags = {8.41, Flow},
author = {F{\"o}rster, H and G{\"u}nther, W and Lindner, G and Model, R}
}
@Incollection { Bodermann2011a,
title = {Charakterisierung von Nanostrukturen aund Substraten der Halbleiterindustrie},
year = {2011},
keywords = {8.41,Nanometrology},
tags = {8.41, Scatter-Inv},
booktitle = {PTB-Mitteilungen 2/2011 ''Themenschwerpunkt Nanometrologie''},
author = {Bodermann, B and Fl{\"u}gge, J and Gro{\ss}, H}
}
@Inproceedings { Schmelt2011,
title = {Numerical investigation of turbulent natural convection in differentially heated square cavity},
year = {2011},
volume = {1389},
pages = {106-109},
tags = {8.41, Flow},
booktitle = {AIP Conf. Proc.},
author = {Schmelter, S. and Lindner, G. and Wendt, G. and Model, R.}
}
@Inproceedings { Bodermann2011,
title = {Joint Research on Scatterometry and AFM Wafer Metrology},
year = {2011},
volume = {1395},
number = {1},
pages = {319--323},
abstract = {Supported by the European Commission and EURAMET, a consortium of 10 participants from national metrology institutes, universities and companies has started a joint research project with the aim of overcoming current challenges in optical scatterometry for traceable linewidth metrology. Both experimental and modelling methods will be enhanced and different methods will be compared with each other and with specially adapted atomic force microscopy (AFM) and scanning electron microscopy (SEM) measurement systems in measurement comparisons. Additionally novel methods for sophisticated data analysis will be developed and investigated to reach significant reductions of the measurement uncertainties in critical dimension (CD) metrology. One final goal will be the realisation of a wafer based reference standard material for calibration of scatterometers.},
keywords = {8.41,Scatterometrie},
tags = {8.41, Scatter-Inv},
web_url = {http://scitation.aip.org/content/aip/proceeding/aipcp/10.1063/1.3657910},
booktitle = {AIP Conf. Proc.},
ISSN = {1551-7616},
DOI = {10.1063/1.3657910},
author = {Bodermann, B and Buhr, E and Danzebrink, H-U and B{\"a}r, M and Scholze, F and Krumrey, M and Wurm, M and Klapetek, P and Hansen, P-E and Korpelainen, V and van Veghel, M and Yacoot, A and Siitonen, S and El Gawhary, O and Burger, S and Saastamoinen, T and Seiler, D G and Diebold, A C and McDonald, R and Chabli, A and Secula, E M}
}
@Inproceedings { Henn2011,
title = {Improved geometry reconstruction and uncertainty evaluation for extreme ultraviolet (EUV) scatterometry based on maximum likelihood estimation},
year = {2011},
keywords = {8.41,Scatter-Inv},
tags = {8.41,Scatter-Inv},
booktitle = {SPIE Proc. 80830N},
author = {Henn, M-A and Gro{\ss}, H and Scholze, F and Elster, C and B{\"a}r, M}
}
@Article { Fruhner_CC2010,
title = {Modelling the influence of cardiac motion on electrical excitation and the magnetocardiogram},
journal = {Comp. Cardiology},
year = {2010},
volume = {37},
pages = {867},
tags = {8.41, Herz},
author = {Fruhner, S and Engel, H and B{\"a}r, M}
}
@Article { Peruani2011a,
title = {Cluster dynamics and cluster size distributions in systems of self-propelled particles},
journal = {Eur. Phys. J-Special Topics},
year = {2010},
volume = {191},
number = {1},
pages = {173--185},
tags = {8.41, SSP},
web_url = {http://www.springerlink.com/index/10.1140/epjst/e2010-01349-1},
ISSN = {1951-6355},
DOI = {10.1140/epjst/e2010-01349-1},
author = {Peruani, F and Schimansky-Geier, L and B{\"a}r, M}
}
@Article { Radszuweit2011,
title = {A model for oscillations and pattern formation in protoplasmic droplets of Physarum polycephalum},
journal = {Eur. Phys. J. - Special Topics},
year = {2010},
volume = {191},
number = {1},
pages = {159--172},
keywords = {8.41,pattern formation},
tags = {8.41, ActMatter, ActFluid},
web_url = {http://www.springerlink.com/index/10.1140/epjst/e2010-01348-2},
ISSN = {1951-6355},
DOI = {10.1140/epjst/e2010-01348-2},
author = {Radszuweit, M and Engel, H and B{\"a}r, M}
}
@Article { Alonso2010a,
title = {Wave propagation in heterogeneous bistable and excitable media},
journal = {Eur. Phys. J. - Special Topics},
year = {2010},
volume = {187},
number = {1},
pages = {31--40},
tags = {8.41, exc-Media},
web_url = {http://www.springerlink.com/index/10.1140/epjst/e2010-01268-1},
ISSN = {1951-6355},
DOI = {10.1140/epjst/e2010-01268-1},
author = {Alonso, S and L{\"o}ber, J and B{\"a}r, M and Engel, H}
}
@Article { Alonso2011b,
title = {Self-organization processes at active interfaces},
journal = {The European Physical Journal Special Topics},
year = {2010},
volume = {191},
number = {1},
pages = {131--145},
tags = {8.41, SO},
web_url = {http://www.springerlink.com/index/10.1140/epjst/e2010-01346-4},
ISSN = {1951-6355},
DOI = {10.1140/epjst/e2010-01346-4},
author = {Alonso, S and Chen, H-Y and B{\"a}r, M and Mikhailov, A S}
}
@Article { Alonso2010,
title = {Phase separation and bistability in a three-dimensional model for protein domain formation at biomembranes},
journal = {Phys. Biol.},
year = {2010},
volume = {7},
number = {4},
pages = {046012},
abstract = {Proteins in living cells interact with membranes. They may bind to or unbind from the membrane to the cytosol depending on the lipid composition of the membrane and their interaction with cytosolic enzymes. Moreover, proteins can accumulate at the membrane and assemble in spatial domains. Here, a simple model of protein cycling at biomembranes is studied, when the total number of proteins is conserved. Specifically, we consider the spatio-temporal dynamics of MARCKS proteins and their interactions with enzymes facilitating translocation from and rebinding to the membrane. The model exhibits two qualitatively different mechanisms of protein domain formation: phase separation related to a long-wave instability of a membrane state with homogeneous protein coverage and stable coexistence of two states with different homogeneous protein coverage in bistable media. We evaluate the impact of the cytosolic volume on the occurrence of protein pattern formation by simulations in a three-dimensional model. We show that the explicit treatment of the volume in the model leads to an effective rescaling of the reaction rates. For a simplified model of protein cycling, we can derive analytical expressions for the rescaling coefficients and verify them by direct simulations with the complete three-dimensional model.},
keywords = {Cell Membrane,Cell Membrane: chemistry,Cytosol,Cytosol: chemistry,Diffusion,Membrane Lipids,Membrane Lipids: chemistry,Membrane Proteins,Membrane Proteins: chemistry,Models,Molecular},
tags = {8.41,Membrane},
web_url = {http://iopscience.iop.org/article/10.1088/1478-3975/7/4/046012},
publisher = {IOP Publishing},
ISBN = {doi:10.1088/1478-3975/7/4/046012},
ISSN = {1478-3975},
DOI = {10.1088/1478-3975/7/4/046012},
author = {Alonso, S and B{\"a}r, M}
}
@Article { Gross2010,
title = {Investigations on a robust profile model for the reconstruction of 2D periodic absorber lines in scatterometry},
journal = {J. Europ. Opt. Soc. Rap. Public.},
year = {2010},
volume = {5},
pages = {10053},
abstract = {Scatterometry as a non-imaging indirect optical method in wafer metrology is applicable to lithography masks designed for extreme ultraviolet (EUV) lithography , where light with wavelengths of about 13.5 nm is applied. The main goal is to reconstruct the critical dimensions (CD) of the mask, i.e., profile parameters such as line width, line height, and side-wall angle, from the measured diffracted light pattern and to estimate the associated uncertainties. The numerical simulation of the diffraction process for periodic 2D structures can be realized by the finite element solution of the two-dimensional Helmholtz equation. The inverse problem is expressed as a non-linear operator equation where the operator maps the sought mask parameters to the efficiencies of the diffracted plane wave modes. To solve this operator equation, the deviation of the measured efficiencies from the ones obtained computationally is minimized by a Gauss-Newton type iterative method. In the present paper, the admissibility of rectangular profile models for the evaluations of CD uniformity is studied. More precisely, several sets of typical measurement data are simulated for trapezoidal shaped EUV masks with different mask signatures characterized by various line widths, heights and side-wall angles slightly smaller than 90 degree. Using these sets, but assuming rectangular structures as the basic profiles of the numerical reconstruction algorithm, approximate line height and width parameters are determined as the critical dimensions of the mask. Finally, the model error due to the simplified shapes is analyzed by checking the deviations of the reconstructed parameters from their nominal values.},
keywords = {Scatterometrie,critical dimensions (CD),inverse problem,profile model,scatterometry},
tags = {8.41,Scatter-Inv},
web_url = {http://www.jeos.org/index.php/jeos{\textbackslash_}rp/article/view/10053},
language = {en},
ISSN = {1990-2573},
DOI = {10.2971/jeos.2010.10053},
author = {Gross, H and Richter, J and Rathsfeld, A and B{\"a}r, M}
}
@Article { Henn2010,
title = {Hyponormal and strongly hyponormal matrices in inner product spaces},
journal = {Linear Algebra and its Applications},
year = {2010},
volume = {433},
number = {6},
pages = {1055--1076},
abstract = {Complex matrices that are structured with respect to a possibly degenerate indefinite inner product are studied. Based on earlier works on normal matrices, the notions of hyponormal and strongly hyponormal matrices are introduced. A full characterization of such matrices is given and it is shown how those matrices are related to different concepts of normal matrices in degenerate inner product spaces. Finally, the existence of invariant semidefinite subspaces for strongly hyponormal matrices is discussed.},
keywords = {Adjoint,Degenerate inner product,H-Hyponormal,Invariant semidefinite subspace,Linear relations,Primary: 15A57,Secondary: 15A63,Strongly H-hyponormal},
tags = {8.41,},
web_url = {http://www.sciencedirect.com/science/article/pii/S0024379510002880},
ISSN = {00243795},
DOI = {10.1016/j.laa.2010.04.050},
author = {Henn, M-A and Mehl, C and Trunk, C}
}
@Article { Ginelli2010,
title = {Large-scale collective properties of self-propelled rods},
journal = {Phys. Rev. Lett.},
year = {2010},
volume = {104},
number = {18},
pages = {184502},
abstract = {We study, in two space dimensions, the collective properties of constant-speed polar point particles interacting locally by nematic alignment in the presence of noise. This minimal approach to self-propelled rods allows one to deal with large numbers of particles, which exhibit a rich phenomenology distinctively different from all other known models for self-propelled particles. Extensive simulations reveal long-range nematic order, phase separation, and space-time chaos mediated by large-scale segregated structures.},
tags = {8.41, SPP, 8.43},
web_url = {http://www.ncbi.nlm.nih.gov/pubmed/20482178},
ISSN = {1079-7114},
DOI = {10.1103/PhysRevLett.104.184502},
author = {Ginelli, F and Peruani, F and B{\"a}r, M and Chat{\'e}, H}
}
@Article { Gross2009,
title = {Profile reconstruction in extreme ultraviolet (EUV) scatterometry: modeling and uncertainty estimates},
journal = {Measurement Science and Technology},
year = {2009},
volume = {20},
number = {10},
pages = {105102},
keywords = {8.41,Scatter-EUV,Scatter-Inv,Scatterometrie},
tags = {8.41,Scatter-Inv},
web_url = {http://iopscience.iop.org/article/10.1088/0957-0233/20/10/105102},
publisher = {IOP Publishing},
language = {en},
ISSN = {0957-0233},
DOI = {10.1088/0957-0233/20/10/105102},
author = {Gross, H and Rathsfeld, A and Scholze, F and B{\"a}r, M}
}
@Inproceedings { Henn2009,
title = {On numerical reconstruction of lithographic masks in DUV scatterometry},
year = {2009},
keywords = {8.41,Scatter-Inv},
tags = {8.41,Scatter-Inv},
booktitle = {SPIE Proc. 7390},
author = {Henn, M-A and Model, R and B{\"a}r, M and Wurm, M and Bodermann, B and Rathsfeld, A and Gro{\ss}, H}
}
@Url { DIPOG,
title = {DIPOG Homepage},
year = {2009},
tags = {8.41,Scatter-Inv},
web_url = {http://www.wias-berlin.de/software/DIPOG},
web_url_date = {2015-11-25},
author = {Elschner, J and Hinder, H and Rathsfeld, A and Schmidt, G}
}
@Article { Model2008,
title = {A scatterometry inverse problem in optical mask metrology},
journal = {Journal of Physics: Conference Series},
year = {2008},
volume = {135},
number = {1},
pages = {012071},
keywords = {8.41,Scatter-Inv,Scatterometrie},
tags = {8.41,Scatter-Inv},
web_url = {http://iopscience.iop.org/article/10.1088/1742-6596/135/1/012071},
publisher = {IOP Publishing},
language = {en},
ISSN = {1742-6596},
DOI = {10.1088/1742-6596/135/1/012071},
author = {Model, R and Rathsfeld, A and Gross, H and Wurm, M and Bodermann, B}
}
@Article { Gross2008,
title = {Sensitivity analysis for indirect measurement in scatterometry and the reconstruction of periodic grating structures},
journal = {Waves in Random and Complex Media},
year = {2008},
volume = {18},
number = {1},
pages = {129--149},
abstract = {We discuss numerical algorithms for the determination of periodic surface structures from light diffraction patterns. With decreasing details of lithography masks, increasing demands on metrology techniques arise. Scatterometry as a non-imaging indirect optical method is applied to simple periodic line structures in order to determine parameters like side-wall angles, heights, top and bottom widths and to evaluate the quality of the manufacturing process. The numerical simulation of diffraction is based on the finite element solution of the Helmholtz equation. The inverse problem seeks to reconstruct the grating geometry from measured diffraction patterns. Restricting the class of gratings and the set of measurements, this inverse problem can be reformulated as a non-linear operator equation in Euclidean spaces. The operator maps the grating parameters to special efficiencies of diffracted plane-wave modes. We employ a Gau{\ss} {\^a}{\euro}“Newton type iterative method to solve this operator equation. The reconstruction ...},
keywords = {8.41,Scatter-Inv,Scatterometrie},
tags = {8.41,Scatter-Inv},
web_url = {http://www.tandfonline.com/doi/abs/10.1080/17455030701481823},
publisher = {Taylor {\&} Francis Group},
language = {en},
ISSN = {1745-5030},
DOI = {10.1080/17455030701481823},
author = {Gro{\ss}, H and Rathsfeld, A}
}
@Inproceedings { Model08,
year = {2008},
volume = {77},
tags = {8.41, Inv-Scatt},
publisher = {Proc. ICIPE 2008},
booktitle = {A scatterometry inverse problem in optical mask technology},
author = {Model, R and Rathsfeld, A and Gross, H and Wurm, M and Bodermann, B}
}
@Inproceedings { Gross_Model08,
title = {Computational methods estimating uncertainties for profile reconstruction in scatterometry},
year = {2008},
pages = {6995OT-1 – 6995OT-9},
tags = {8.41, Scatter-Inv},
publisher = {Proc. SPIE6995},
author = {Gross, H and Rathsfeld, A and Scholze, F and Model, R and B{\"a}r, M}
}
@Inproceedings { Gross2008,
title = {Modellbildung, Bestimmung der Messunsicherheit und Validierung f{\"u}r diskrete inverse Probleme am Beispiel der Scatterometrie},
year = {2008},
pages = {337--346},
tags = {8.41, Scatter-Inv},
booktitle = {Sensoren und Messsystem 2008},
author = {Gro{\ss}, H and Model, R and Scholze, F and Wurm, M and Bodermann, B and B{\"a}r, M and Rathsfeld, A}
}
@Article { Bauer2007,
title = {Alternans and the influence of ionic channel modifications: Cardiac three-dimensional simulations and one-dimensional numerical bifurcation analysis},
journal = {Chaos (Woodbury, N.Y.)},
year = {2007},
volume = {17},
number = {1},
pages = {015104},
abstract = {Cardiac propagation is investigated by simulations using a realistic three-dimensional (3D) geometry including muscle fiber orientation of the ventricles of a rabbit heart and the modified Beeler-Reuter ionic model. Electrical excitation is introduced by a periodic pacing of the lower septum. Depending on the pacing frequency, qualitatively different dynamics are observed, namely, normal heart beat, T-wave alternans, and 2:1 conduction block at small, intermediate, and large pacing frequencies, respectively. In a second step, we performed a numerical stability and bifurcation analysis of a pulse propagating in a one-dimensional (1D) ring of cardiac tissue. The precise onset of the alternans instability is obtained from computer-assisted linear stability analysis of the pulse and computation of the associated spectrum. The critical frequency at the onset of alternans and the profiles of the membrane potential agree well with the ones obtained in the 3D simulations. Next, we computed changes in the wave profiles and in the onset of alternans for the Beeler-Reuter model with modifications of the sodium, calcium, and potassium channels, respectively. For this purpose, we employ the method of numerical bifurcation and stability analysis. While blocking of calcium channels has a stabilizing effect, blocked sodium or potassium channels lead to the occurrence of alternans at lower pacing frequencies. The findings regarding channel blocking are verified within three-dimensional simulations. Altogether, we have found T-wave alternans and conduction block in 3D simulations of a realistic rabbit heart geometry. The onset of alternans has been analyzed by numerical bifurcation and stability analysis of 1D wave trains. By comparing the results of the two approaches, we find that alternans is not strongly influenced by ingredients such as 3D geometry and propagation anisotropy, but depends mostly on the frequency of pacing (frequency of subsequent action potentials). In addition, we have introduced numerical bifurcation and stability analysis as a tool into heart modeling and demonstrated its efficiency in scanning a large set of parameters in the case of models with reduced conductivity. Bifurcation analysis also provides an accurate test for analytical theories of alternans as is demonstrated for the case of the restitution hypothesis.},
keywords = {8.41,Action Potentials,Animals,Arrhythmias, Cardiac,Arrhythmias, Cardiac: physiopathology,Biological Clocks,Computer Simulation,Electric Countershock,Electric Countershock: methods,Heart Conduction System,Heart Conduction System: physiopathology,Heart Ventricles,Heart Ventricles: physiopathology,Humans,Imaging, Three-Dimensional,Ion Channel Gating,Ion Channels,Models, Cardiovascular,Myocardial Contraction,Oscillometry,Oscillometry: methods,Rabbits,Therapy, Computer-Assisted,Therapy, Computer-Assisted: methods},
tags = {8.41},
web_url = {http://www.ncbi.nlm.nih.gov/pubmed/17411261},
ISSN = {1054-1500},
DOI = {10.1063/1.2715668},
author = {Bauer, S and R{\"o}der, G and B{\"a}r, M}
}
@Article { Haberkorn2007,
title = {Analytical study of the magnetic field from extended sources in subcortical structures},
year = {2007},
keywords = {8.41},
tags = {8.41},
web_url = {http://www.researchgate.net/publication/238648406{\textbackslash_}Analytical{\textbackslash_}study{\textbackslash_}of{\textbackslash_}the{\textbackslash_}magnetic{\textbackslash_}field{\textbackslash_}from{\textbackslash_}extended{\textbackslash_}sources{\textbackslash_}in{\textbackslash_}subcortic},
author = {Haberkorn, W and Burghoff, M}
}
@Incollection { Gross_Rathsf97,
title = {Intelligent solutions for complex problems},
year = {2007},
tags = {8.41, Scatter-Inv},
booktitle = {Annual Research Report 2007},
author = {Gross, H and Rathsfeld, A}
}
@Inproceedings { Wurm2007,
title = {Numerical analysis of DUV scatterometry on EUV masks},
year = {2007},
keywords = {8.41,Scatter-Inv},
tags = {8.41,Scatter-Inv},
booktitle = {SPIE Proc. 6617},
author = {Wurm, M and Bodermann, B and Model, R and Gro{\ss}, H}
}
@Inproceedings { Gross2007,
title = {Optimal sets of measurement data for profile reconstruction in scatterometry},
year = {2007},
keywords = {8.41,Scatter-Inv},
tags = {8.41,Scatter-Inv},
booktitle = {SPIE Proc. 6617},
author = {Gro{\ss}, H and Rathsfeld, A and Scholze, F and B{\"a}r, M and Dersch, U}
}
@Article { Model2006,
title = {Improved transient hot strip sensor design by means of FEM simulations},
journal = {THERMAL CONDUCTIVITY},
year = {2006},
volume = {28},
pages = {298--308},
keywords = {8.41},
tags = {8.41},
author = {Model, R and Stosch, R and Hammerschmidt, U}
}
@Article { Nicola2006,
title = {Wave instability induced by nonlocal spatial coupling in a model of the light-sensitive Belousov-Zhabotinsky reaction},
journal = {Physical review. E, Statistical, nonlinear, and soft matter physics},
year = {2006},
volume = {73},
number = {6 Pt 2},
pages = {066225},
abstract = {We study spatiotemporal patterns resulting from instabilities induced by nonlocal spatial coupling in the Oregonator model of the light-sensitive Belousov-Zhabotinsky reaction. In this system, nonlocal coupling can be externally imposed by means of an optical feedback loop which links the intensity of locally applied illumination with the activity in a certain vicinity of a particular point weighted by a given coupling function. This effect is included in the three-variable Oregonator model by an additional integral term in the photochemically induced bromide flow. A linear stability analysis of this modified Oregonator model predicts that wave and Turing instabilities of the homogeneous steady state can be induced for experimentally realistic parameter values. In particular, we find that a long-range inhibition in the optical feedback leads to a Turing instability, while a long-range activation induces wave patterns. Using a weakly nonlinear analysis, we derive amplitude equations for the wave instability which are valid close to the instability threshold. Therein, we find that the wave instability occurs supercritically or subcritically and that traveling waves are preferred over standing waves. The results of the theoretical analysis are in good agreement with numerical simulations of the model near the wave instability threshold. For larger distances from threshold, a secondary breathing instability is found for traveling waves.},
keywords = {8.41},
tags = {8.41},
web_url = {http://www.ncbi.nlm.nih.gov/pubmed/16906964},
ISSN = {1539-3755},
DOI = {10.1103/PhysRevE.73.066225},
author = {Nicola, E M and B{\"a}r, M and Engel, H}
}
@Article { Peruani2006,
title = {Nonequilibrium clustering of self-propelled rods},
journal = {Physical Review E},
year = {2006},
volume = {74},
number = {3},
pages = {030904},
keywords = {8.41,8.43},
tags = {8.41,8.43},
web_url = {http://link.aps.org/doi/10.1103/PhysRevE.74.030904},
ISSN = {1539-3755},
DOI = {10.1103/PhysRevE.74.030904},
author = {Peruani, F and Deutsch, A and B{\"a}r, M}
}
@Article { Wei2006,
title = {Nucleation of spiral wave patterns at surface defects},
journal = {Physical review. E, Statistical, nonlinear, and soft matter physics},
year = {2006},
volume = {73},
number = {1 Pt 2},
pages = {016210},
abstract = {The nucleation of spiral waves at a surface defect during catalytic CO oxidation on Pt(110) has been studied with a low energy electron microscope system. It is found that reaction fronts originate from a boundary layer between the defect and the surrounding Pt(110) area. The findings are corroborated by numerical simulations within a realistic reaction-diffusion model of the surface reaction.},
keywords = {8.41},
tags = {8.41},
web_url = {http://www.ncbi.nlm.nih.gov/pubmed/16486261},
ISSN = {1539-3755},
DOI = {10.1103/PhysRevE.73.016210},
author = {Wei, H and Lilienkamp, G and Davidsen, J and B{\"a}r, M and Imbihl, R}
}
@Article { Borner2006,
title = {A generalized discrete model linking rippling pattern formation and individual cell reversal statistics in colonies of myxobacteria},
journal = {Physical biology},
year = {2006},
volume = {3},
number = {2},
pages = {138--46},
abstract = {Self-organization processes in multicellular aggregates of bacteria and amoebae offer fascinating insights into the evolution of cooperation and differentiation of cells. During myxobacterial development a variety of spatio-temporal patterns emerges such as counterpropagating waves of cell density that are known as rippling. Recently, several models have been introduced that qualitatively reproduce these patterns. All models include active motion and a collision-triggered reversal of individual bacteria. Here, we present a systematic study of a generalized discrete model that is based on similar assumptions as the continuous model by Igoshin et al (2001 Proc. Natl Acad. Sci. USA 98 14913). We find counterpropagating as well as unidirectional rippling waves in extended regions of the parameter space. If the interaction strength and the degree of cooperativity are large enough, rippling patterns appear even in the absence of a refractory period. We show for the first time that the experimentally observed double peak in the reversal statistics of bacteria in rippling colonies (Welch and Kaiser 2001 Proc. Natl Acad. Sci. USA 98 14907) can be reproduced in simulations of counterpropagating rippling waves which are dominant in experiments. In addition, the reversal statistics in the pre-rippling phase is correctly reproduced.},
keywords = {8.41,Biological,Biological Evolution,Computer Simulation,Linear Models,Models, Biological,Myxococcales,Myxococcales: growth {\&} development},
tags = {8.41},
web_url = {http://www.ncbi.nlm.nih.gov/pubmed/16829700},
ISSN = {1478-3975},
DOI = {10.1088/1478-3975/3/2/006},
author = {B{\"o}rner, U and Deutsch, A and B{\"a}r, M}
}
@Article { Haberkorn2006,
title = {Pseudo current density maps of electrophysiological heart, nerve or brain function and their physical basis},
journal = {Biomagnetic research and technology},
year = {2006},
volume = {4},
number = {1},
pages = {5},
abstract = {BACKGROUND: In recent years the visualization of biomagnetic measurement data by so-called pseudo current density maps or Hosaka-Cohen (HC) transformations became popular. METHODS: The physical basis of these intuitive maps is clarified by means of analytically solvable problems. RESULTS: Examples in magnetocardiography, magnetoencephalography and magnetoneurography demonstrate the usefulness of this method. CONCLUSION: Hardware realizations of the HC-transformation and some similar transformations are discussed which could advantageously support cross-platform comparability of biomagnetic measurements.},
keywords = {8.41},
tags = {8.41},
web_url = {http://www.biomagres.com/content/4/1/5},
publisher = {BioMed Central Ltd},
language = {en},
ISSN = {1477-044X},
DOI = {10.1186/1477-044X-4-5},
author = {Haberkorn, W and Steinhoff, U and Burghoff, M and Kosch, O and Morguet, A and Koch, H}
}
@Article { Hammerschmidt2006a,
title = {JANUS: High Temperature Transient Hot Bridge Sensor},
journal = {THERMAL CONDUCTIVITY},
year = {2006},
volume = {28},
pages = {288--297},
keywords = {8.41},
tags = {8.41},
author = {Hammerschmidt, U and Meier, V and Model, R}
}
@Article { Gross2006,
title = {Mathematical modelling of indirect measurements in scatterometry},
journal = {Measurement},
year = {2006},
volume = {39},
number = {9},
pages = {782--794},
keywords = {8.41},
tags = {8.41, Scatter-Inv},
web_url = {http://www.researchgate.net/publication/223944217{\textbackslash_}Mathematical{\textbackslash_}modelling{\textbackslash_}of{\textbackslash_}indirect{\textbackslash_}measurements{\textbackslash_}in{\textbackslash_}scatterometry},
ISSN = {02632241},
DOI = {10.1016/j.measurement.2006.04.009},
author = {Gro{\ss}, H and Model, R and B{\"a}r, M and Wurm, M and Bodermann, B and Rathsfeld, A}
}
@Incollection { Model2006b,
title = {Inverse Methoden f{\"u}r indirekte Messungen und Partielle-Differentialgleichungs-Modelle},
year = {2006},
keywords = {8.41,Scatter-Inv},
tags = {8.41,Scatter-Inv},
booktitle = {PTB-Mitteilungen 3/2006},
author = {Model, R and Gro{\ss}, H and Haberkorn, W and B{\"a}r, M}
}
@Incollection { Bar2006,
title = {Modelling measurement processes in complex systems with partial differential equations: From heat conduction to the heart},
year = {2006},
keywords = {8.41},
tags = {8.41},
booktitle = {Advanced Mathematical And Computational Tools In Metrology And Testing VII (Series on Advances in Mathematics for Applied Sciences)},
author = {B{\"a}r, M and Bauer, S and Model, R and Weber dos Santos, R}
}
@Incollection { Gross2006a,
title = {Sensitivity Analysis for Indirect Measurement in Scatterometry and the Reconstruction of Periodic Grating Structures},
year = {2006},
keywords = {8.41,Scatter-Inv},
tags = {8.41,Scatter-Inv},
booktitle = {WIAS Preprint No. 1164},
author = {Gro{\ss}, H and Rathsfeld, A}
}
@Incollection { Gross2006,
title = {Generic system design for measurement databases - Applied to calibrationsin vacuum metrology, biosignals and a template system},
year = {2006},
pages = {60--72},
keywords = {8.41},
tags = {8.41},
booktitle = {Advanced Mathematical and Computational Tools in Metrology VII},
author = {Gro{\ss}, H and Hartmann, V and Jousten, K and Lindner, G}
}
@Inproceedings { Wurm2006,
title = {Untersuchungen zur Eignung der EUV-Scatterometrie zur quantitativen Charakterisierung periodischer Strukturen auf Photolithographiemasken},
year = {2006},
keywords = {8.41,Scatter-Inv},
tags = {8.41,Scatter-Inv},
booktitle = {DGaO-Proc.},
author = {Wurm, M and Bodermann, B and Scholze, F and Laubis, C and Gro{\ss}, H and Rathsfeld, A}
}
@Article { Model2005b,
title = {An identification procedure for thermal transport properties of layered solids by means of transient measurements},
journal = {Thermal Conductivity 26/Thermal Expansion 14},
year = {2005},
pages = {346--357},
tags = {8.41, Flow},
author = {Model, R and Hammerschmidt, U}
}
@Article { Model2005,
title = {Thermal Transport Properties of Layered Materials: Identification by a New Numerical Algorithm for Transient Measurements},
journal = {International Journal of Thermophysics},
year = {2005},
volume = {26},
number = {1},
pages = {165--178},
keywords = {8.41},
tags = {8.41, Flow},
web_url = {http://www.researchgate.net/publication/226424470{\textbackslash_}Thermal{\textbackslash_}Transport{\textbackslash_}Properties{\textbackslash_}of{\textbackslash_}Layered{\textbackslash_}Materials{\textbackslash_}Identification{\textbackslash_}by{\textbackslash_}a{\textbackslash_}New{\textbackslash_