This file was created by the TYPO3 extension bib --- Timezone: CEST Creation date: 2024-04-19 Creation time: 06-54-44 --- Number of references 149 article BocklerdMSSBKBWTTWGSG2024 Measurement 2024 4 7 232 8.41, 8.4, MetHyInfra https://doi.org/10.1016/j.measurement.2024.114675 H.-B.Böckler M.de Huu R.Maury S.Schmelter M.D.Schakel O.Büker J.Kutin G.Bobovnik C.Wedler J.P.M.Trusler M.Thol S.Weiss C.Günz D.Schumann F.Gugole article WinklerNFHLDB2023 Metrology 2023 12 26 3 1 1-28 8.4,8.41,8.43, UQ https://doi.org/10.3390/metrology3010001 BenjaminWinkler ClaudiaNagel NandoFarchmin SebastianHeidenreich AxelLoewe OlafDössel MarkusBär article MehariS2023 IEEE J Biomed Health Inform 2023 11 7 27 11 5326-5334 8.4, 8.41 10.1109/JBHI.2023.3310989 TemesgenMehari NilsStrodthoff article GilletteGNBWWBSDPL2023 Scientific Data 2023 8 8 10 531 (2023) 8.4,8.41,8.43 https://doi.org/10.1038/s41597-023-02416-4 KarliGillette Matthias A. F.Gsell ClaudiaNagel JuleBender BenjaminWinkler Steven E.Williams MarkusBär TobiasSchäffter OlafDössel GernotPlank AxelLoewe article WeissenbrunnerESS2023 Metrologia 2023 7 17 8.4,8.41,Flow, UQ accepted DOI 10.1088/1681-7575/ace7d6 AndreasWeissenbrunner Ann-KathrinEkat MartinStraka SonjaSchmelter article StrodthoffMNASGKHDLBS2023 Scientific Data 2023 5 13 10 279 8.4,8.41 https://doi.org/10.1038/s41597-023-02153-8 NilsStrodthoff TemesgenMehari ClaudiaNagel Philip J.Aston AshishSundar ClausGraff Jørgen K.Kanters WilhelmHaverkamp OlafDössel AxelLoewe MarkusBär TobiasSchaeffter article WeissPBOS2023 Elsevier International Journal of Hydrogen Energy 2023 3 30 8.41,Flow accepted https://doi.org/10.1016/j.ijhydene.2023.03.073 S.Weiss J.Polansky M.Bär K.Oberleithner S.Schmelter article WebnerPKS2023 International Journal of Multiphase Flow 2023 1 158 104278 8.41,8.4, Flow 10.1016/j.ijmultiphaseflow.2022.104278 10.1016/j.ijmultiphaseflow.2022.104278 F.Webner J.Polansky S.Knotek S.Schmelter phdthesis Olbrich2022 2022 12 20 8.4, 8.41, flow TU Berlin https://doi.org/10.14279/depositonce-16659 MarcOlbrich conference SchmelterKOB2022 2022 10 21 8.4,8.41,Flow 19th International Flow Measurement Conference (FLOMEKO) Chongqing, China 19th International Flow Measurement Conference (FLOMEKO) 17-21.10.2022 S.Schmelter S.Knotek M.Olbrich M.Bär conference WeissMOBS2022 2022 10 21 8.4,8.41,Flow 19th International Flow Measurement Conference (FLOMEKO) Chongqing, China 19th International Flow Measurement Conference (FLOMEKO) 17-21.10.2022 S.Weiss B.Mickan K.Oberleithner M.Bär S.Schmelter conference BocklerdMSSB2022 2022 10 8.4,8.41,Flow 19th International Flow Measurement Conference (FLOMEKO) Chongqing, China 19th International Flow Measurement Conference (FLOMEKO) 17-21.10.2022 H.-B.Böckler M.de Huu R.Maury S.Schmelter M.D.Schakel O.Büker article OlbrichRKLvBOS2022 International Journal of Multiphase Flow 2022 9 10 8.4,8.41,Flow,ML https://doi.org/10.1016/j.ijmultiphaseflow.2022.104247 M.Olbrich L.Riazy T.Kretz T.Leonard D.S.van Putten M.Bär K.Oberleithner S.Schmelter article BuranNB2022 New Journal of Physics 2022 8 23 24 August 2022 8.4,8.41 https://doi.org/10.1088/1367-2630/ac8571 P.Buran T.Niedermayer M.Bär article StrakaWKHS2022 Metrology 2022 7 18 2 3 335-359 8.41,8.4,Flow,UQ https://doi.org/10.3390/metrology2030021 MartinStraka AndreasWeissenbrunner ChristianKoglin ChristianHöhne SonjaSchmelter article PolanskyS2022 Archives of Thermodynamics 2022 3 1 43 1 21-43 Multiphase flow, Stratified flow, Turbulence damping, Computational fluid dynamics, OpenFOAM, Reynolds-averaged Navier–Stokes, Detached eddy simulation, Delayed detached eddy simulation 8.4,8.41,Flow http://journals.pan.pl/Content/122890/PDF/art02_internet.pdf 10.24425/ather.2022.140923 JiriPolansky SonjaSchmelter article MehariS2021 Computers in Biology and Medicine 2021 12 18 141 105114 8.4,8.41,ML https://doi.org/10.1016/j.compbiomed.2021.105114 TMehari NStrodthoff article KhmelinskaiaFYPS2021 Advanced Materials Interfaces 2021 10 18 8 24 2101094 8.4, 8.41 https://doi.org/10.1002/admi.202101094 AKhmelinskaia H GFranquelim RYaadav E PPetrov PSchwille article KnotekSO2021 Measurement: Sensors 2021 9 28 18 100317 8.4,8.41,Flow 2665-9174 10.1016/j.measen.2021.100317 StanislavKnotek SonjaSchmelter MarcOlbrich article SchmelterOKB2021 Measurement: Sensors 2021 9 23 18 100154 8.4,8.41,Flow 2665-9174 10.1016/j.measen.2021.100154 SonjaSchmelter MarcOlbrich StanislavKnotek MarkusBär article OlbrichHLSBOS2021 Measurement: Sensors 2021 9 22 18 100222 8.4,8.41,Flow 2665-9174 10.1016/j.measen.2021.100222 MarcOlbrich AndrewHunt TerriLeonard DennisS. van Putten MarkusBär KilianOberleithner SonjaSchmelter article LeydenUMYPGPBA2021 BMC Biology 2021 4 13 19 72 8.4,8.41 https://doi.org/10.1186/s12915-021-00997-3 F.Leyden S.Uthishtran U. K.Moorthi H. M.York A.Patil H.Gandhi Eugene. P.Petrov T.Bornschlögl S.Arumugam article SmudaGHN2021 Int J Mol Sci . 2021 2 10 22 4 1753 8.4,8.41,Cyto 10.3390/ijms22041753 KSmuda JGienger PHönicke JNeukammer article SchmelterKOFB2021 Metrologia 2021 1 21 58 1 014003 8.4,8.41,Flow 10.1088/1681-7575/abd1c9 SSchmelter SKnotek MOlbrich AFiebach MBär article SchmidtFSSLS2021 Magnetic Resonance in Medicine 2021 85 6 3154-3168 8.4,8.41,Flow 10.1002/mrm.28641 SSchmidt SFlassbeck SSchmelter ESchmeyer M ELadd SSchmitter article OlbrichSBSOS2020 Flow Measurement and Instrumentation 2020 10 16 76 101814 8.4,8.41,Flow 10.1016/j.flowmeasinst.2020.101814 MOlbrich ESchmeyer MBär MSieber KOberleithner SSchmelter article OlbrichBOS2020 International Journal of Multiphase Flow 2020 9 6 134 103453 8.4,8.41,Flow 10.1016/j.ijmultiphaseflow.2020.103453 MOlbrich MBär KOberleithner SSchmelter article SchmelterOSB2020 Flow Measurement and Instrumentation 2020 3 10 73 101722 8.4,8.41,Flow 10.1016/j.flowmeasinst.2020.101722 SSchmelter MOlbrich ESchmeyer MBär article GiengerGOBN2019 Biomedical Optics Express 2019 9 1 10 9 4531 -- 4550 8.4,8.41,Cyto 10.1364/BOE.10.004531 JGienger HGross VOst MBär JNeukammer article SchmelterOSB2019 Proceedings of the 18th International Flow Measurement Conference FLOMEKO 2019 2019 7 1 8.4,8.41,Flow SSchmelter MOlbrich ESchmeyer MBär article OlbrichSBSOS2019 Proceedings of the 18th International Flow Measurement Conference FLOMEKO 2019 2019 7 1 8.4,8.41,Flow MOlbrich ESchmeyer MBär MSieber KOberleithner SSchmelter article KulawiakLBE2019 PLoS One 2019 5 14 14 8 8.4,8.41 10.1101/638312 D AKulawiak JLöber MBär HEngel article RiazySOAvNS2019 Magnetic Resonance in Medicine 2019 4 16 advance online publication 8.4,8.41, flow 10.1002/mrm.27756 LRiazy TSchäffter MOlbrich J ASchueler Fv. Knobelsdorff-Brenkenhoff TNiendorf JSchulz-Menger article GiengerSMBN2019 Scientific Reports 2019 3 15 9 8.4,8.41,Cyto 10.1038/s41598-019-38767-5 JGienger KSmuda RMüller MBär JNeukammer article AlvesdBd2019 Front. Physiol. 2019 3 14 10 177 8.4,8.41 10.3389/fphys.2019.00177 J. RAlves R. A. Bde Queiroz MBär R. Wdos Santos article KulawiakLBE2018 Journal of Physics D: Applied Physics 2019 1 1 52 1 014004 8.4,8.41 10.1088/1361-6463/aae41d D AKulawiak JLöber MBär HEngel article OlbrichSROBS2018 J. Phys.: Conf. Series 2018 11 1 1065 9 092015 8.4,8.41,Flow 10.1088/1742-6596/1065/9/092015 MOlbrich ESchmeyer LRiazy KOberleithner MBär SSchmelter article SchmelterOSB2018 Proceedings of the North Sea Flow Measurement Workshop 2018 2018 11 1 8.4,8.41,Flow SSchmelter MOlbrich ESchmeyer MBär article BeckerFNRMB2018 Chaos: An Interdisciplinary Journal of Nonlinear Science 2018 4 30 28 4 043121 8.4, 8.41, 8.43 10.1063/1.5018139 MBecker TFrenzel TNiedermayer SReichelt AMielke MBär article StrakaFEK2018 Flow Measurement and Instrumentation 2018 2 14 60 124--133 8.4,8.41,Flow,UQ 10.1016/j.flowmeasinst.2018.02.006 MStraka AFiebach TEichler CKoglin article GiengerBN2018 Applied Optics 2018 1 1 57 2 344 -- 355 8.4,8.41,Cyto 10.1364/AO.57.000344 JGienger MBär JNeukammer article BuranBN2017 Chaos 2017 11 19 27 11 113110 8.4,8.43,8.41 10.1063/1.5010787 PBuran MBär SAlonso TNiedermayer article AlonsoREB2017 Journal of Physics D: Applied Physics 2017 10 3 50 43 434004 8.4,8.41 10.1088/1361-6463/aa8a1d SAlonso MRadszuweit HEngel MBär article BarE2018 PTB Mitteilungen 2017 10 1 127 4 69--74 8.4,8.41,8.42 https://www.ptb.de/cms/fileadmin/internet/publikationen/ptb_mitteilungen/mitt2017/Heft4/PTB-Mitteilungen_2017_Heft_4.pdf MBär CElster article WeissenbrunnerFJT2017 Eccomas Proceedia UNCECOMP 2017 6 17 5393 576--587 8.4,8.41,Flow,UQ 10.7712/120217.5393.16913 AWeissenbrunner AFiebach MJuling P UThamsen article GiengerGNB2016 Applied Optics 2016 11 25 55 31 8951--8961 8.4,8.41,Cyto 10.1364/AO.55.008951 JGienger HGroß JNeukammer MBär article AlonsoWB2016 PLOS One 2016 11 25 11 11 8.4,8.41,8.43 10.1371/journal.pone.0166972 SAlonso RWeber dos Santos MBär article GrosmannPB2016_2 Phys. Rev. E 2016 11 25 94 5 050602 8.4,8.43,8.41 10.1103/PhysRevE.94.050602 RGroßmann FPeruani MBär article FiebachSKS2016 Proceedings of the 17th International Flow Measurement Conference FLOMEKO 2016 2016 9 29 8.4,8.41,Flow AFiebach ESchmeyer SKnotek SSchmelter article KnotekFS2016 Proceedings of the 17th International Flow Measurement Conference FLOMEKO 2016 2016 9 29 8.4,8.41,Flow SKnotek AFiebach SSchmelter article AlonsoBE2016 Reports on Progress in Physics 2016 8 29 79 9 096601 8.4,8.41,8.43,Herz 10.1088/0034-4885/79/9/096601 SAlonso MBär BEchebarria article AlonsoB2016 Journal of Physics: Conference Series 2016 8 29 727 1 012002 8.4,8.41,8.43,Herz 10.1088/1742-6596/727/1/012002 SAlonso MBär article WeissenbrunnerFSMTL2016 Flow Measurement and Instrumentation 2016 8 29 8.4,8.41,Flow,UQ in_preparation 10.1016/j.flowmeasinst.2016.07.011 AWeissenbrunner AFiebach SSchmelter MBär P.UThamsen TLederer article GrosmannPB2013 Phys. Rev. E 2016 4 31 93 8.43 8.4,8.43,8.41 10.1103/PhysRevE.93.040102 RGroßmann FPeruani MBär article GrosmannPB2016 New J. Phys 2016 4 31 18 8.43 8.4,8.43,8.41 10.1088/1367-2630/18/4/043009 RGroßmann FPeruani MBär article Alonso_PhysD_2015 Physica D 2016 4 1 318 58-69 8.41, Spatio-Diff, ActFluid 10.1016/j.physd.2015.09.017 SAlonso UStrachauer MRadszuweit MBär M.J.BHauser article Schmelter_2016_1 tm-Technisches Messen 2016 1 8 83 2 71-76 8.41, Flow, UQ http://www.degruyter.com/view/j/teme.2016.83.issue-2/teme-2015-0109/teme-2015-0109.xml SSchmelter AFiebach AWeissenbrunner article Lindner_JFE2015 J. Fluids Eng 2016 1 5 138 3 031302 8.41, Flow 8.41, Flow 10.1115/1.4031380 GLindner SSchmelter RModel ANowak VEbert MBär article e73c330da32016_3 Phys. Rev. E 2016 93 4 043306 8.4,8.41 10.1103/PhysRevE.93.043306 JGienger NSeverin JRabe I MSokolov article e73c330da32016_2 Proceedings of Imeko 2015 XXI World Congress Measurement in Research and Industry 2015 11 30 8.41, Flow, UQ AWeissenbrunner AFiebach SSchmelter MStraka MBär TLederer article Grossmann_EPJ2015_2 Eur. Phys. J - Special Topics 2015 1 9 224 7 1377-1394 8.41, ActMatter 10.1140/epjst/e2015-02465-0 RGroßmann FPeruani MBär article Radszu_PRE2015 Phys. Rev. E 2015 1 7 91 022703 8.41, Herz 10.1103/PhysRevE.91.022703 MRadszuweit EAlvarez-Lacalle MBär BEchebarria article Bosse_TM2015 Technisches Messen 2015 1 6 82 346-358 8.41, Scatter-Inv 10.1515/teme-2015-0002 HBosse BBodermann GDai JFlügge C. GFrase HGross WHäßler-Grohne PKöchert RKönning FScholze CWeichert article Schmelt_JCF2015 Int. J. Comp. Fluid. Dyn. 2015 1 5 29 6-8 411-422 8.41, Flow, UQ 10.1080/10618562.2015.1112899 SSchmelter AFiebach RModel MBär article Grossmann_EPJE2015 Eur. Phys. J - Special Topics 2015 1 4 224 7 1325-1347 8.41,ActMatter,8.43 10.1140/epjst/e2015-02462-3 RGroßmann PRomanczuk MBär LSchimansky-Geier article Siebert_PRE2014 Phys. Rev. E 2014 89 052909 8.41, RD 10.1103/PhysRevE.89.052909 JSiebert SAlonso MBär ESchöll article Meyer2014 Phys. Rev. E 2014 89 2 022711 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. ,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 8.41, SPP http://www.ncbi.nlm.nih.gov/pubmed/25353513 1550-2376 10.1103/PhysRevE.89.022711 MMeyer LSchimansky-Geier PRomanczuk article Wendt2014 Technische Sicherheit 2014 11 13--17 8.41 8.41, Flow GWendt RJost SSchmelter DWerner article Schuler2014 Chaos 2014 24 4 043142 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. Computer Simulation,Feedback,Models, Theoretical,Nonlinear Dynamics,Oscillometry,Oscillometry: methods,Spatio-Temporal Analysis,non-linear dynamics,spatio-temporal 8.41, RD, 8.43 http://scitation.aip.org/content/aip/journal/chaos/24/4/10.1063/1.4905017 AIP Publishing 1089-7682 10.1063/1.4905017 DSchüler S.Alonso ATorcini MBär article Radszuweit2014 PloS one 2014 9 6 e99220 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. ,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 8.41, ActMatter, ActFluid http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0099220 Public Library of Science 1932-6203 10.1371/journal.pone.0099220 MRadszuweit HEngel MBär article Dai2014 Meas. Sci. Tech. 2014 25 4 044002 Scatterometrie 8.41,Scatter-EUV http://iopscience.iop.org/article/10.1088/0957-0233/25/4/044002 IOP Publishing en 0957-0233 10.1088/0957-0233/25/4/044002 GDai KHahm FScholze M-AHenn HGroß JFluegge HBosse article Alonso2014 Eur. Phys. J. E 2014 2 1 1 pattern formation 8.41, membrane http://link.springer.com/10.1140/epjnbp14 2195-0008 10.1140/epjnbp14 SAlonso MBär article Grossmann2014 Phys. Rev. Lett. 2014 113 25 258104 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. pattern formation,turbulence 8.41,ActMatt,8.43 http://www.ncbi.nlm.nih.gov/pubmed/25554911 1079-7114 10.1103/PhysRevLett.113.258104 RGroßmann PRomanczuk MBär LSchimansky-Geier article John2014 Phys. Rev. E 2014 90 5-1 052913 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<prt>\_</prt>{{}2<prt>}</prt> 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. pattern formation 8.41, exc-media http://www.ncbi.nlm.nih.gov/pubmed/25493864 1550-2376 10.1103/PhysRevE.90.052913 KJohn S.Alonso MBär article Fiebach2014 Numerische Mathematik 2014 128 1 31--72 finite elements,finite volumes,voronoi 8.41 http://link.springer.com/10.1007/s00211-014-0604-6 0029-599X 10.1007/s00211-014-0604-6 AFiebach AGlitzky ALinke article f3ee8757792015 Proceedings of Flomeko 2013 16th International Flow Measurement Conference 2013 12 31 8.41, Flow SSchmelter RModel GWendt MBär article Radszuweit2013 Phys. Rev. Lett. 2013 110 13 138102 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. Biological,Biomechanical Phenomena,Cell Physiological Phenomena,Cytoplasm,Cytoplasm: chemistry,Cytoskeleton,Cytoskeleton: chemistry,Elasticity,Extracellular Fluid,Extracellular Fluid: chemistry,Models,Viscosity 8.41, ActMatt, ActFluid http://www.ncbi.nlm.nih.gov/pubmed/23581377 1079-7114 10.1103/PhysRevLett.110.138102 MRadszuweit S.Alonso HEngel MBär article Peruani2013 New J. Phys. 2013 15 6 065009 8.41, SPP http://iopscience.iop.org/article/10.1088/1367-2630/15/6/065009 IOP Publishing en doi:10.1088/1367-2630/15/6/065009 1367-2630 10.1088/1367-2630/15/6/065009 FPeruani MBär article Jousten2014 Vacuum 2013 100 14--17 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. Choked flow,Dynamic pressure,Response time,Vacuum gauge,Vacuum metrology 8.41,Flow fileadmin/internet/fachabteilungen/abteilung_8/8.4_mathematische_modellierung/8.42/DYNAMIK/842_dynamik_Sensors_2010_10_7621.pdf http://www.sciencedirect.com/science/article/pii/S0042207X13002546 0042207X 10.1016/j.vacuum.2013.07.037 KJousten SPantazis JButhig RModel MWüest JIwicki article Dahmlow2013 Phys. Rev. Lett. 2013 110 23 234102 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. Arrhythmias,Cardiac,Cardiac: physiopathology,Heart,Heart: physiology,Models,Theoretical 8.41,Herz http://www.ncbi.nlm.nih.gov/pubmed/25167496 1079-7114 10.1103/PhysRevLett.110.234102 PDähmlow S.Alonso MBär M J BHauser article Alonso2013 Bull. Math. Biol. 2013 75 8 1351--76 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. 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 8.41, Herz http://www.ncbi.nlm.nih.gov/pubmed/22829178 1522-9602 10.1007/s11538-012-9748-7 SAlonso A VPanfilov article Alonso2013a Phys. Rev. Lett. 2013 110 15 158101 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. Action Potentials,Cardiovascular,Computer Simulation,Heart,Heart: physiology,Models 8.41, Herz, 8.43 http://www.ncbi.nlm.nih.gov/pubmed/25167313 1079-7114 10.1103/PhysRevLett.110.158101 SAlonso MBär article Aranson2013 Physics 2013 6 8.41, ActMatter http://physics.aps.org/articles/v6/61 American Physical Society en IAranson phdthesis Radszuweit2013a 2013 8.41, ActMatter TU Berlin MRadszuweit phdthesis Henn_Thesis 2013 8.41,8.42,Scatter-Inv,Scatterometrie 8.41,Scatter-Inv TU Berlin M-AHenn phdthesis Fiebach2013 2013 discrete Moser iteration,dissipative finite volume scheme,heterogeneous materials,reaction-diffusion systems 8.41 http://www.diss.fu-berlin.de/diss/receive/FUDISS<prt>\_</prt>thesis<prt>\_</prt>000000096910 English AFiebach article Peruani2012 Phys. Rev. Lett. 2012 108 9 098102 8.41, SPP, 8.43 http://link.aps.org/doi/10.1103/PhysRevLett.108.098102 0031-9007 10.1103/PhysRevLett.108.098102 FPeruani JStarruß VJakovljevic LSøgaard-Andersen ADeutsch MBär article Lober2012 Phys. Rev. E 2012 86 6 Pt 2 066210 Front propagation in heterogeneous bistable media is studied using the Schl<prt>ö</prt>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. 8.41, exc-media http://www.ncbi.nlm.nih.gov/pubmed/23368027 1550-2376 10.1103/PhysRevE.86.066210 JLöber MBär HEngel article Romanczuk2012 Eur. Phys. J. - Special Topics 2012 202 1 1--162 8.41, SSP http://www.springerlink.com/index/10.1140/epjst/e2012-01529-y 1951-6355 10.1140/epjst/e2012-01529-y PRomanczuk MBär WEbeling BLindner LSchimansky-Geier article Starruss2012 Interface focus 2012 2 6 774--85 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. ,pattern formation 8.41,SPP http://rsfs.royalsocietypublishing.org/content/2/6/774 2042-8901 10.1098/rsfs.2012.0034 JStarruß FPeruani VJakovljevic LSøgaard-Andersen ADeutsch MBär article Bodermann2012 International Journal of Nanomanufacturing 2012 8 1 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 (&lt; 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. Nanometrology 8.41,Scatter-Inv BBodermann FScholze JFlügge HGroß HBosse article Bar2012 Angewandte Chemie (International ed. in English) 2012 51 38 9489--90 8.41, NonDyn http://www.ncbi.nlm.nih.gov/pubmed/22915494 1521-3773 10.1002/anie.201205214 MBär ESchöll ATorcini inbook Model_2012 2012 84 8.41, Flow F. Pavese, M. Bär, J.-R. Filtz, A. B. Forbes, L. Pendrill and K. Shirono World Scientific, New Jersey RModel SSchmelter GLindner MBär inbook Gross2012 2012 8.41,Scatter-Inv 8.41,Scatter-Inv F. Pavese, M. Bär, J.-R. Filtz, A. B. Forbes, L. Pendrill, K. Shirono World Scientific New Jersey Advanced Mathematical & Computational Tools in Metrology and Testing IX HGroß M-AHenn ARathsfeld MBär article Peruani2011 J. Phys.: Conf. Ser. 2011 297 1 012014 8.41, SPP http://iopscience.iop.org/article/10.1088/1742-6596/297/1/012014 IOP Publishing en 1742-6596 10.1088/1742-6596/297/1/012014 FPeruani FGinelli MBär HChaté article Kupitz2011 Phys. Review. E 2011 84 5 Pt 2 056210 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. 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 8.41, RD http://www.ncbi.nlm.nih.gov/pubmed/22181487 1550-2376 10.1103/PhysRevE.84.056210 DKupitz S.Alonso MBär M J BHauser article Echebarria2011 Phys. Rev. E 2011 83 4 Pt 1 040902 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. Action Potentials,Action Potentials: physiology,Animals,Biological Clocks,Biological Clocks: physiology,Cardiovascular,Computer Simulation,Heart Conduction System,Heart Conduction System: physiology,Humans,Models 8.41, Herz http://www.ncbi.nlm.nih.gov/pubmed/21599107 1550-2376 10.1103/PhysRevE.83.040902 BEchebarria GRöder HEngel JDavidsen MBär article Alonso2011a J. Chem. Phys. 2011 134 9 094117 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.Bär, 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. Aerosols,Aerosols: chemistry,Chemical,Diffusion,Emulsions,Emulsions: chemistry,Models,Oils,Oils: chemistry,Water,Water: chemistry 8.41, RD http://scitation.aip.org/content/aip/journal/jcp/134/9/10.1063/1.3559154 AIP Publishing 1089-7690 10.1063/1.3559154 S.Alonso KJohn MBär article Alonso2011 Biophys. J. 2011 100 4 939--47 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. 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 8.41,membrane http://www.sciencedirect.com/science/article/pii/S0006349510052197 1542-0086 10.1016/j.bpj.2010.12.3702 S.Alonso UDietrich CHändel J AKäs MBär article Alonso2011c Chaos 2011 21 1 013118 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. 8.41 exc-media http://scitation.aip.org/content/aip/journal/chaos/21/1/10.1063/1.3551500 AIP Publishing 1089-7682 10.1063/1.3551500 S.Alonso MBär AlVPanfilov article Forster2011 Technische Sicherheit 2011 1 18--27 8.41, Flow HFörster WGünther GLindner RModel incollection Bodermann2011a 2011 8.41,Nanometrology 8.41, Scatter-Inv PTB-Mitteilungen 2/2011 "Themenschwerpunkt Nanometrologie" BBodermann JFlügge HGroß inproceedings Schmelt2011 2011 1389 106-109 8.41, Flow AIP Conf. Proc. S.Schmelter G.Lindner G.Wendt R.Model inproceedings Bodermann2011 2011 1395 1 319--323 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. 8.41,Scatterometrie 8.41, Scatter-Inv http://scitation.aip.org/content/aip/proceeding/aipcp/10.1063/1.3657910 AIP Conf. Proc. 1551-7616 10.1063/1.3657910 BBodermann EBuhr H-UDanzebrink MBär FScholze MKrumrey MWurm PKlapetek P-EHansen VKorpelainen Mvan Veghel AYacoot SSiitonen OEl Gawhary SBurger TSaastamoinen D GSeiler A CDiebold RMcDonald AChabli E MSecula inproceedings Henn2011 2011 8.41,Scatter-Inv 8.41,Scatter-Inv SPIE Proc. 80830N M-AHenn HGroß FScholze CElster MBär article Fruhner_CC2010 Comp. Cardiology 2010 37 867 8.41, Herz SFruhner HEngel MBär article Peruani2011a Eur. Phys. J-Special Topics 2010 191 1 173--185 8.41, SSP http://www.springerlink.com/index/10.1140/epjst/e2010-01349-1 1951-6355 10.1140/epjst/e2010-01349-1 FPeruani LSchimansky-Geier MBär article Radszuweit2011 Eur. Phys. J. - Special Topics 2010 191 1 159--172 8.41,pattern formation 8.41, ActMatter, ActFluid http://www.springerlink.com/index/10.1140/epjst/e2010-01348-2 1951-6355 10.1140/epjst/e2010-01348-2 MRadszuweit HEngel MBär article Alonso2010a Eur. Phys. J. - Special Topics 2010 187 1 31--40 8.41, exc-Media http://www.springerlink.com/index/10.1140/epjst/e2010-01268-1 1951-6355 10.1140/epjst/e2010-01268-1 SAlonso JLöber MBär HEngel article Alonso2011b The European Physical Journal Special Topics 2010 191 1 131--145 8.41, SO http://www.springerlink.com/index/10.1140/epjst/e2010-01346-4 1951-6355 10.1140/epjst/e2010-01346-4 SAlonso H-YChen MBär A SMikhailov article Alonso2010 Phys. Biol. 2010 7 4 046012 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. Cell Membrane,Cell Membrane: chemistry,Cytosol,Cytosol: chemistry,Diffusion,Membrane Lipids,Membrane Lipids: chemistry,Membrane Proteins,Membrane Proteins: chemistry,Models,Molecular 8.41,Membrane http://iopscience.iop.org/article/10.1088/1478-3975/7/4/046012 IOP Publishing doi:10.1088/1478-3975/7/4/046012 1478-3975 10.1088/1478-3975/7/4/046012 SAlonso MBär article Gross2010 J. Europ. Opt. Soc. Rap. Public. 2010 5 10053 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. Scatterometrie,critical dimensions (CD),inverse problem,profile model,scatterometry 8.41,Scatter-Inv http://www.jeos.org/index.php/jeos<prt>\_</prt>rp/article/view/10053 en 1990-2573 10.2971/jeos.2010.10053 HGross JRichter ARathsfeld MBär article Henn2010 Linear Algebra and its Applications 2010 433 6 1055--1076 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. Adjoint,Degenerate inner product,H-Hyponormal,Invariant semidefinite subspace,Linear relations,Primary: 15A57,Secondary: 15A63,Strongly H-hyponormal 8.41, http://www.sciencedirect.com/science/article/pii/S0024379510002880 00243795 10.1016/j.laa.2010.04.050 M-AHenn CMehl CTrunk article Ginelli2010 Phys. Rev. Lett. 2010 104 18 184502 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. 8.41, SPP, 8.43 http://www.ncbi.nlm.nih.gov/pubmed/20482178 1079-7114 10.1103/PhysRevLett.104.184502 FGinelli FPeruani MBär HChaté article Gross2009 Measurement Science and Technology 2009 20 10 105102 8.41,Scatter-EUV,Scatter-Inv,Scatterometrie 8.41,Scatter-Inv http://iopscience.iop.org/article/10.1088/0957-0233/20/10/105102 IOP Publishing en 0957-0233 10.1088/0957-0233/20/10/105102 HGross ARathsfeld FScholze MBär inproceedings Henn2009 2009 8.41,Scatter-Inv 8.41,Scatter-Inv SPIE Proc. 7390 M-AHenn RModel MBär MWurm BBodermann ARathsfeld HGroß url DIPOG 2009 8.41,Scatter-Inv http://www.wias-berlin.de/software/DIPOG 2015-11-25 JElschner HHinder ARathsfeld GSchmidt article Model2008 Journal of Physics: Conference Series 2008 135 1 012071 8.41,Scatter-Inv,Scatterometrie 8.41,Scatter-Inv http://iopscience.iop.org/article/10.1088/1742-6596/135/1/012071 IOP Publishing en 1742-6596 10.1088/1742-6596/135/1/012071 RModel ARathsfeld HGross MWurm BBodermann article Gross2008 Waves in Random and Complex Media 2008 18 1 129--149 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 Gauß â€“Newton type iterative method to solve this operator equation. The reconstruction ... 8.41,Scatter-Inv,Scatterometrie 8.41,Scatter-Inv http://www.tandfonline.com/doi/abs/10.1080/17455030701481823 Taylor <prt>&amp;</prt> Francis Group en 1745-5030 10.1080/17455030701481823 HGroß ARathsfeld inproceedings Model08 2008 77 8.41, Inv-Scatt Proc. ICIPE 2008 A scatterometry inverse problem in optical mask technology RModel ARathsfeld HGross MWurm BBodermann inproceedings Gross_Model08 2008 6995OT-1 – 6995OT-9 8.41, Scatter-Inv Proc. SPIE6995 HGross ARathsfeld FScholze RModel MBär inproceedings Gross2008 2008 337--346 8.41, Scatter-Inv Sensoren und Messsystem 2008 HGroß RModel FScholze MWurm BBodermann MBär ARathsfeld article Bauer2007 Chaos (Woodbury, N.Y.) 2007 17 1 015104 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. 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 8.41 http://www.ncbi.nlm.nih.gov/pubmed/17411261 1054-1500 10.1063/1.2715668 SBauer GRöder MBär article Haberkorn2007 2007 8.41 8.41 http://www.researchgate.net/publication/238648406<prt>\_</prt>Analytical<prt>\_</prt>study<prt>\_</prt>of<prt>\_</prt>the<prt>\_</prt>magnetic<prt>\_</prt>field<prt>\_</prt>from<prt>\_</prt>extended<prt>\_</prt>sources<prt>\_</prt>in<prt>\_</prt>subcortic WHaberkorn MBurghoff incollection Gross_Rathsf97 2007 8.41, Scatter-Inv Annual Research Report 2007 HGross ARathsfeld inproceedings Wurm2007 2007 8.41,Scatter-Inv 8.41,Scatter-Inv SPIE Proc. 6617 MWurm BBodermann RModel HGroß inproceedings Gross2007 2007 8.41,Scatter-Inv 8.41,Scatter-Inv SPIE Proc. 6617 HGroß ARathsfeld FScholze MBär UDersch article Model2006 THERMAL CONDUCTIVITY 2006 28 298--308 8.41 8.41 RModel RStosch UHammerschmidt article Nicola2006 Physical review. E, Statistical, nonlinear, and soft matter physics 2006 73 6 Pt 2 066225 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. 8.41 8.41 http://www.ncbi.nlm.nih.gov/pubmed/16906964 1539-3755 10.1103/PhysRevE.73.066225 E MNicola MBär HEngel article Peruani2006 Physical Review E 2006 74 3 030904 8.41,8.43 8.41,8.43 http://link.aps.org/doi/10.1103/PhysRevE.74.030904 1539-3755 10.1103/PhysRevE.74.030904 FPeruani ADeutsch MBär article Wei2006 Physical review. E, Statistical, nonlinear, and soft matter physics 2006 73 1 Pt 2 016210 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. 8.41 8.41 http://www.ncbi.nlm.nih.gov/pubmed/16486261 1539-3755 10.1103/PhysRevE.73.016210 HWei GLilienkamp JDavidsen MBär RImbihl article Borner2006 Physical biology 2006 3 2 138--46 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. 8.41,Biological,Biological Evolution,Computer Simulation,Linear Models,Models, Biological,Myxococcales,Myxococcales: growth <prt>&amp;</prt> development 8.41 http://www.ncbi.nlm.nih.gov/pubmed/16829700 1478-3975 10.1088/1478-3975/3/2/006 UBörner ADeutsch MBär article Haberkorn2006 Biomagnetic research and technology 2006 4 1 5 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. 8.41 8.41 http://www.biomagres.com/content/4/1/5 BioMed Central Ltd en 1477-044X 10.1186/1477-044X-4-5 WHaberkorn USteinhoff MBurghoff OKosch AMorguet HKoch article Hammerschmidt2006a THERMAL CONDUCTIVITY 2006 28 288--297 8.41 8.41 UHammerschmidt VMeier RModel article Gross2006 Measurement 2006 39 9 782--794 8.41 8.41, Scatter-Inv http://www.researchgate.net/publication/223944217<prt>\_</prt>Mathematical<prt>\_</prt>modelling<prt>\_</prt>of<prt>\_</prt>indirect<prt>\_</prt>measurements<prt>\_</prt>in<prt>\_</prt>scatterometry 02632241 10.1016/j.measurement.2006.04.009 HGroß RModel MBär MWurm BBodermann ARathsfeld incollection Model2006b 2006 8.41,Scatter-Inv 8.41,Scatter-Inv PTB-Mitteilungen 3/2006 RModel HGroß WHaberkorn MBär incollection Bar2006 2006 8.41 8.41 Advanced Mathematical And Computational Tools In Metrology And Testing VII (Series on Advances in Mathematics for Applied Sciences) MBär SBauer RModel RWeber dos Santos incollection Gross2006a 2006 8.41,Scatter-Inv 8.41,Scatter-Inv WIAS Preprint No. 1164 HGroß ARathsfeld incollection Gross2006 2006 60--72 8.41 8.41 Advanced Mathematical and Computational Tools in Metrology VII HGroß VHartmann KJousten GLindner inproceedings Wurm2006 2006 8.41,Scatter-Inv 8.41,Scatter-Inv DGaO-Proc. MWurm BBodermann FScholze CLaubis HGroß ARathsfeld article Model2005b Thermal Conductivity 26/Thermal Expansion 14 2005 346--357 8.41, Flow RModel UHammerschmidt article Model2005 International Journal of Thermophysics 2005 26 1 165--178 8.41 8.41, Flow http://www.researchgate.net/publication/226424470<prt>\_</prt>Thermal<prt>\_</prt>Transport<prt>\_</prt>Properties<prt>\_</prt>of<prt>\_</prt>Layered<prt>\_</prt>Materials<prt>\_</prt>Identification<prt>\_</prt>by<prt>\_</prt>a<prt>\_</prt>New<prt>\_</prt 0195-928X 10.1007/s10765-005-2363-1 RModel article John2005 Eur. Phys. J. E, Soft matter 2005 18 2 183--99 We study chemically driven running droplets on a partially wetting solid substrate by means of coupled evolution equations for the thickness profile of the droplets and the density profile of an adsorbate layer. Two models are introduced corresponding to two qualitatively different types of experiments described in the literature. In both cases an adsorption or desorption reaction underneath the droplets induces a wettability gradient on the substrate and provides the driving force for droplet motion. The difference lies in the behavior of the substrate behind the droplet. In case I the substrate is irreversibly changed whereas in case II it recovers allowing for a periodic droplet movement (as long as the overall system stays far away from equilibrium). Both models allow for a non-saturated and a saturated regime of droplet movement depending on the ratio of the viscous and reactive time scales. In contrast to model I, model II allows for sitting drops at high reaction rate and zero diffusion along the substrate. The transition from running to sitting drops in model II occurs via a super- or subcritical drift-pitchfork bifurcation and may be strongly hysteretic implying a coexistence region of running and sitting drops. 8.41 8.41, http://www.researchgate.net/publication/7538520<prt>\_</prt>Self-propelled<prt>\_</prt>running<prt>\_</prt>droplets<prt>\_</prt>on<prt>\_</prt>solid<prt>\_</prt>substrates<prt>\_</prt>driven<prt>\_</prt>by<prt>\_</prt>chemical<prt>\_</prt>reactions 1292-8941 10.1140/epje/i2005-10039-1 KJohn MBär UThiele article Burghoff2005a Biomed. Tech. 2005 50 1 179--180 8.41 8.41, BioMed MBurghoff B MMackert WHaberkorn article John2005b Physical biology 2005 2 2 123--32 Cell membranes are composed of a mixture of lipids. Many biological processes require the formation of spatial domains in the lipid distribution of the plasma membrane. We have developed a mathematical model that describes the dynamic spatial distribution of acidic lipids in response to the presence of GMC proteins and regulating enzymes. The model encompasses diffusion of lipids and GMC proteins, electrostatic attraction between acidic lipids and GMC proteins as well as the kinetics of membrane attachment/detachment of GMC proteins. If the lipid-protein interaction is strong enough, phase separation occurs in the membrane as a result of free energy minimization and protein/lipid domains are formed. The picture is changed if a constant activity of enzymes is included into the model. We chose the myristoyl-electrostatic switch as a regulatory module. It consists of a protein kinase C that phosphorylates and removes the GMC proteins from the membrane and a phosphatase that dephosphorylates the proteins and enables them to rebind to the membrane. For sufficiently high enzymatic activity, the phase separation is replaced by travelling domains of acidic lipids and proteins. The latter active process is typical for nonequilibrium systems. It allows for a faster restructuring and polarization of the membrane since it acts on a larger length scale than the passive phase separation. The travelling domains can be pinned by spatial gradients in the activity; thus the membrane is able to detect spatial clues and can adapt its polarity dynamically to changes in the environment. 8.41,Biophysics,Biophysics: methods,Cell Membrane,Cell Membrane: metabolism,Chemical,Diffusion,Kinetics,Lipids,Lipids: chemistry,Membrane Lipids,Membrane Lipids: chemistry,Models, Chemical,Models, Statistical,Models, Theoretical,Phosphorylation,Protein Biosynthesis,Protein Interaction Mapping,Protein Kinase C,Protein Kinase C: metabolism,Protein Structure, Tertiary,Statistical,Tertiary,Theoretical,Thermodynamics 8.41 http://www.ncbi.nlm.nih.gov/pubmed/16204864 1478-3975 10.1088/1478-3975/2/2/005 KJohn MBär article John2005a Physical review letters 2005 95 19 198101 We study two mechanisms for the formation of protein patterns near membranes of living cells by mathematical modelling. Self-assembly of protein domains by electrostatic lipid-protein interactions is contrasted with self-organization due to a nonequilibrium biochemical reaction cycle of proteins near the membrane. While both processes lead eventually to quite similar patterns, their evolution occurs on very different length and time scales. Self-assembly produces periodic protein patterns on a spatial scale below 0.1 microm in a few seconds followed by extremely slow coarsening, whereas self-organization results in a pattern wavelength comparable to the typical cell size of 100 microm within a few minutes suggesting different biological functions for the two processes. 8.41,Algorithms,Cell Physiological Phenomena,Membrane Proteins,Membrane Proteins: chemistry,Membranes,Membranes: chemistry,Models, Statistical,Particle Size,Phosphorylation,Statistical 8.41 http://www.ncbi.nlm.nih.gov/pubmed/16384028 0031-9007 10.1103/PhysRevLett.95.198101 KJohn MBär article Gargioni2005 Radiation protection dosimetry 2005 113 3 321--5 A simple but effective method that allows the measurement of the 220Rn spatial distribution in working or living environments using a solid-state detector is presented in this paper. The method is based on measurements of the alpha particles emitted by 216Po (the first 220Rn progeny) directly deposited on the detector surface at different distances from a 220Rn exhalation source. The validity of the method is shown by comparing the results of an experiment, where the 220Rn activity concentration is measured under conditions of diffusion at constant temperature, with finite-element calculations. 8.41,Air Pollution, Indoor,Air Pollution, Indoor: analysis,Algorithms,Alpha Particles,Equipment Design,Equipment Failure Analysis,Occupational Exposure,Occupational Exposure: analysis,Radiation Dosage,Radiation Monitoring,Radiation Monitoring: instrumentation,Radiation Monitoring: methods,Radon,Radon: analysis,Risk Assessment,Risk Assessment: methods,Risk Factors 8.41, http://rpd.oxfordjournals.org/content/113/3/321 0144-8420 10.1093/rpd/nch467 EGargioni RModel incollection DosSantos2005 2005 571--580 8.41 Domain Decomposition Methods in Science and Engineering RWeber dos Santos inproceedings Model2005a 2005 8.41 8.41 Proc. 17th Europ. Conf. on Thermophys. Prop. RModel RStosch UHammerschmidt