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--- Timezone: CET
Creation date: 2022-11-28
Creation time: 03-18-14
--- Number of references
169
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8.41, RD
10.1103/PhysRevE.89.052909
JSiebert
SAlonso
MBär
ESchöll
article
Meyer2014
Active Brownian agents with concentration-dependent chemotactic sensitivity
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
Untersuchungen zum Temperaturverhalten von Flüssigkeiten in großen Lagertanks
Technische Sicherheit
2014
11
13--17
8.41
8.41, Flow
GWendt
RJost
SSchmelter
DWerner
article
Schuler2014
Spatio-temporal dynamics induced by competing instabilities in two asymmetrically coupled nonlinear evolution equations
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
An active poroelastic model for mechanochemical patterns in protoplasmic droplets of Physarum polycephalum
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
Measurements of CD and sidewall profile of EUV photomask structures using CD-AFM and tilting-AFM
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
Modeling domain formation of MARCKS and protein kinase C at cellular membranes
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
Vortex arrays and mesoscale turbulence of self-propelled particles
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
Heidenreich2014a
A surrogate model enables a Bayesian approach to the inverse problem of scatterometry
J. Phys. Conf. Ser.
2014
490
1
012007
8.41,Bayes,Scatter-Inv,Regression,8.42, UQ
http://iopscience.iop.org/article/10.1088/1742-6596/490/1/012007
IOP Publishing
en
1742-6596
10.1088/1742-6596/490/1/012007
SHeidenreich
HGross
M-AHenn
CElster
MBär
article
John2014
Traveling waves and global oscillations triggered by attractive molecular interactions in an excitable system
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
Henn2014
Improved reconstruction of critical dimensions in extreme ultraviolet scatterometry by modeling systematic errors
Measurement Science and Technology
2014
25
4
044003
8.41,Scatter-Inv,Scatterometrie, 8.42
http://iopscience.iop.org/article/10.1088/0957-0233/25/4/044003
IOP Publishing
en
0957-0233
10.1088/0957-0233/25/4/044003
M-AHenn
HGross
SHeidenreich
FScholze
CElster
MBär
article
Heidenreich2014
Numerical simulations of a minimal model for the fluid dynamics of dense bacterial suspensions
J.Phys.: Conf. Ser.
2014
490
1
012126
8.41,fluid dynamics
8.41, ActFluid
http://iopscience.iop.org/article/10.1088/1742-6596/490/1/012126
IOP Publishing
en
1742-6596
10.1088/1742-6596/490/1/012126
SHeidenreich
S H LKlapp
MBär
article
Gross2014
Modelling line edge roughness in periodic line-space structures by Fourier optics to improve scatterometry
J. Europ.Opt. Soci.Rap. Pub.
2014
9
14003
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, â€™non-roughâ€™ 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 σ<prt>\_</prt> 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.
Scatterometrie,Scatterometry,atomic force microscopy,line edge roughness,power spectrum density
8.41,Scatter-Inv
http://www.jeos.org/index.php/jeos<prt>\_</prt>rp/article/view/14003
en
1990-2573
10.2971/jeos.2014.14003
HGroß
SHeidenreich
M-AHenn
GDai
FScholze
MBär
article
Fiebach2014
Uniform global bounds for solutions of an implicit Voronoi finite volume method for reactionâ€“diffusion problems
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
Numerical investigation of temperature distributions in large storage tanks
Proceedings of Flomeko 2013 16th International Flow Measurement Conference
2013
12
31
8.41, Flow
SSchmelter
RModel
GWendt
MBär
article
Heiden_PRL2013
Fluid Dynamics of Bacterial Turbulence
Phys. Rev. Lett.
2013
110
228102
8.41, ActFluid
10.1103/PhysRevLett.110.228102
JDunkel
SHeidenreich
KDrescher
H. HWensink
MBär
R. EGoldstein
article
Radszuweit2013
Intracellular mechanochemical waves in an active poroelastic model
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
A kinetic model and scaling properties of non-equilibrium clustering of self-propelled particles
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
A standard to test the dynamics of vacuum gauges in the millisecond range
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
Dunkel2013
Minimal continuum theories of structure formation in dense active fluids
New J. Phys.
2013
15
4
045016
8.41, ActFluid
http://iopscience.iop.org/article/10.1088/1367-2630/15/4/045016
IOP Publishing
en
1367-2630
10.1088/1367-2630/15/4/045016
JDunkel
SHeidenreich
MBär
R EGoldstein
article
Dahmlow2013
Twists of opposite handedness on a scroll wave
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
Negative tension of scroll wave filaments and turbulence in three-dimensional excitable media and application in cardiac dynamics
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
Reentry near the percolation threshold in a heterogeneous discrete model for cardiac tissue
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
Viewpoint: The Aquatic Dance of Bacteria
Physics
2013
6
8.41, ActMatter
http://physics.aps.org/articles/v6/61
American Physical Society
en
IAranson
phdthesis
Radszuweit2013a
An Active Poroelastic Model for Cytoplasm and Pattern Formation in Protoplasmic Droplets of Physarum Polycephalum
2013
8.41, ActMatter
TU Berlin
MRadszuweit
phdthesis
Henn_Thesis
Statistical Approaches to the Inverse Problem of Scatterometry
2013
8.41,8.42,Scatter-Inv,Scatterometrie
8.41,Scatter-Inv
TU Berlin
M-AHenn
phdthesis
Fiebach2013
A dissipative finite volume scheme for reaction-diffusion systems in heterogeneous materials
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
Collective Motion and Nonequilibrium Cluster Formation in Colonies of Gliding Bacteria
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
Front propagation in one-dimensional spatially periodic bistable media
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
Wensink2012
Meso-scale turbulence in living fluids
Proc. Natl. Acad. Sci. U.S.A.
2012
109
36
14308--13
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.
Bacillus subtilis,Bacillus subtilis: physiology,Biological,Biomechanical Phenomena,Computer Simulation,Culture Media,Culture Media: chemistry,Hydrodynamics,Models,Movement,Movement: physiology
8.41, ActFluid
http://www.pnas.org/content/109/36/14308
1091-6490
10.1073/pnas.1202032109
H HWensink
JDunkel
SHeidenreich
KDrescher
R EGoldstein
HLöwen
J MYeomans
article
Romanczuk2012
Active Brownian particles
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
Pattern-formation mechanisms in motility mutants of Myxococcus xanthus
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
Nanometrology at PTB in support of process control of nanoscale features in semiconductor manufacturing
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 (< 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
Synchronization and complex dynamics of oscillators with delayed pulse coupling
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
article
Henn2012a
Improved grating reconstruction by determination of line roughness in extreme ultraviolet scatterometry
Opt. Lett.
2012
37
24
5229--5231
8.41,Scatter-Inv
8.41,Scatter-Inv
10.1364/OL.37.005229
M-AHenn
SHeidenreich
HGroß
ARathsfeld
FScholze
MBär
article
Henn2012
A maximum likelihood approach to the inverse problem of scatterometry
Optics Express
2012
20
12
12771-86
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.
8.41,Diffraction gratings,Metrology,Scatter-Inv,Scatterometrie,8.42
http://www.osapublishing.org/viewmedia.cfm?uri=oe-20-12-12771<prt>&</prt>seq=0<prt>&</prt>html=true
Optical Society of America
EN
1094-4087
10.1364/OE.20.012771
M-AHenn
HGross
FScholze
MWurm
CElster
MBär
article
GrosHHRB2012
Modeling of line roughness and its impact on the diffraction intensities and the reconstructed critical dimensions in scatterometry
Appl. Opt.
2012
51
30
7384--94
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.
8.41,Diffraction gratings,Metrology,Scatter-Inv,Scatterometrie
8.41,Scatter-Inv
http://www.osapublishing.org/viewmedia.cfm?uri=ao-51-30-7384<prt>&</prt>seq=0<prt>&</prt>html=true
Optical Society of America
EN
1539-4522
10.1364/AO.51.007384
HGroß
M-AHenn
SHeidenreich
ARathsfeld
MBär
inbook
Model_2012
Numerical simulations and turbulent modelling for application in flow metrology
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
Stochastic modeling aspects for an improved solution of the inverse problem in scatterometry
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
inproceedings
Bodermann2012a
First steps towards a scatterometry reference standard
2012
8.41,Scatter-Inv
8.41,Scatter-Inv
SPIE Proc.
BBodermann
P-EHansen
SBurger
M-AHenn
HGross
FScholze
JEndres
MWurm
article
Peruani2011
Polar vs. apolar alignment in systems of polar self-propelled particles
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
Surfactant-induced gradients in the three-dimensional Belousov-Zhabotinsky reaction
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
Supernormal conduction in cardiac tissue promotes concordant alternans and action potential bunching
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
Complex wave patterns in an effective reaction-diffusion model for chemical reactions in microemulsions
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.BaÌˆr, 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
Oscillations in the lateral pressure of lipid monolayers induced by nonlinear chemical dynamics of the second messengers MARCKS and protein kinase C
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
Effects of reduced discrete coupling on filament tension in excitable media
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
Untersuchungen zur Explosionsgefahr beim Umschlag von Kerosin Jet A-1
Technische Sicherheit
2011
1
18--27
8.41, Flow
HFörster
WGünther
GLindner
RModel
incollection
Bodermann2011a
Charakterisierung von Nanostrukturen aund Substraten der Halbleiterindustrie
2011
8.41,Nanometrology
8.41, Scatter-Inv
PTB-Mitteilungen 2/2011 "Themenschwerpunkt Nanometrologie"
BBodermann
JFlügge
HGroß
inproceedings
Schmelt2011
Numerical investigation of turbulent natural convection in differentially heated square cavity
2011
1389
106-109
8.41, Flow
AIP Conf. Proc.
S.Schmelter
G.Lindner
G.Wendt
R.Model
inproceedings
Bodermann2011
Joint Research on Scatterometry and AFM Wafer Metrology
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
Improved geometry reconstruction and uncertainty evaluation for extreme ultraviolet (EUV) scatterometry based on maximum likelihood estimation
2011
8.41,Scatter-Inv
8.41,Scatter-Inv
SPIE Proc. 80830N
M-AHenn
HGroß
FScholze
CElster
MBär
article
Fruhner_CC2010
Modelling the influence of cardiac motion on electrical excitation and the magnetocardiogram
Comp. Cardiology
2010
37
867
8.41, Herz
SFruhner
HEngel
MBär
article
Peruani2011a
Cluster dynamics and cluster size distributions in systems of self-propelled particles
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
A model for oscillations and pattern formation in protoplasmic droplets of Physarum polycephalum
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
Wave propagation in heterogeneous bistable and excitable media
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
Self-organization processes at active interfaces
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
Phase separation and bistability in a three-dimensional model for protein domain formation at biomembranes
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
Investigations on a robust profile model for the reconstruction of 2D periodic absorber lines in scatterometry
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
Hyponormal and strongly hyponormal matrices in inner product spaces
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
Large-scale collective properties of self-propelled rods
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
Profile reconstruction in extreme ultraviolet (EUV) scatterometry: modeling and uncertainty estimates
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
On numerical reconstruction of lithographic masks in DUV scatterometry
2009
8.41,Scatter-Inv
8.41,Scatter-Inv
SPIE Proc. 7390
M-AHenn
RModel
MBär
MWurm
BBodermann
ARathsfeld
HGroß
url
DIPOG
DIPOG Homepage
2009
8.41,Scatter-Inv
http://www.wias-berlin.de/software/DIPOG
2015-11-25
JElschner
HHinder
ARathsfeld
GSchmidt
article
Model2008
A scatterometry inverse problem in optical mask metrology
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
Sensitivity analysis for indirect measurement in scatterometry and the reconstruction of periodic grating structures
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>&</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
Computational methods estimating uncertainties for profile reconstruction in scatterometry
2008
6995OT-1 – 6995OT-9
8.41, Scatter-Inv
Proc. SPIE6995
HGross
ARathsfeld
FScholze
RModel
MBär
inproceedings
Gross2008
Modellbildung, Bestimmung der Messunsicherheit und Validierung für diskrete inverse Probleme am Beispiel der Scatterometrie
2008
337--346
8.41, Scatter-Inv
Sensoren und Messsystem 2008
HGroß
RModel
FScholze
MWurm
BBodermann
MBär
ARathsfeld
article
Bauer2007
Alternans and the influence of ionic channel modifications: Cardiac three-dimensional simulations and one-dimensional numerical bifurcation analysis
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
Analytical study of the magnetic field from extended sources in subcortical structures
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
Intelligent solutions for complex problems
2007
8.41, Scatter-Inv
Annual Research Report 2007
HGross
ARathsfeld
inproceedings
Wurm2007
Numerical analysis of DUV scatterometry on EUV masks
2007
8.41,Scatter-Inv
8.41,Scatter-Inv
SPIE Proc. 6617
MWurm
BBodermann
RModel
HGroß
inproceedings
Gross2007
Optimal sets of measurement data for profile reconstruction in scatterometry
2007
8.41,Scatter-Inv
8.41,Scatter-Inv
SPIE Proc. 6617
HGroß
ARathsfeld
FScholze
MBär
UDersch
article
Model2006
Improved transient hot strip sensor design by means of FEM simulations
THERMAL CONDUCTIVITY
2006
28
298--308
8.41
8.41
RModel
RStosch
UHammerschmidt
article
Nicola2006
Wave instability induced by nonlocal spatial coupling in a model of the light-sensitive Belousov-Zhabotinsky reaction
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
Nonequilibrium clustering of self-propelled rods
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
Nucleation of spiral wave patterns at surface defects
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
A generalized discrete model linking rippling pattern formation and individual cell reversal statistics in colonies of myxobacteria
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>&</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
Pseudo current density maps of electrophysiological heart, nerve or brain function and their physical basis
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
JANUS: High Temperature Transient Hot Bridge Sensor
THERMAL CONDUCTIVITY
2006
28
288--297
8.41
8.41
UHammerschmidt
VMeier
RModel
article
Gross2006
Mathematical modelling of indirect measurements in scatterometry
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
Inverse Methoden für indirekte Messungen und Partielle-Differentialgleichungs-Modelle
2006
8.41,Scatter-Inv
8.41,Scatter-Inv
PTB-Mitteilungen 3/2006
RModel
HGroß
WHaberkorn
MBär
incollection
Bar2006
Modelling measurement processes in complex systems with partial differential equations: From heat conduction to the heart
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
Sensitivity Analysis for Indirect Measurement in Scatterometry and the Reconstruction of Periodic Grating Structures
2006
8.41,Scatter-Inv
8.41,Scatter-Inv
WIAS Preprint No. 1164
HGroß
ARathsfeld
incollection
Gross2006
Generic system design for measurement databases - Applied to calibrationsin vacuum metrology, biosignals and a template system
2006
60--72
8.41
8.41
Advanced Mathematical and Computational Tools in Metrology VII
HGroß
VHartmann
KJousten
GLindner
inproceedings
Wurm2006
Untersuchungen zur Eignung der EUV-Scatterometrie zur quantitativen Charakterisierung periodischer Strukturen auf Photolithographiemasken
2006
8.41,Scatter-Inv
8.41,Scatter-Inv
DGaO-Proc.
MWurm
BBodermann
FScholze
CLaubis
HGroß
ARathsfeld
article
Model2005b
An identification procedure for thermal transport properties of layered solids by means of transient measurements
Thermal Conductivity 26/Thermal Expansion 14
2005
346--357
8.41, Flow
RModel
UHammerschmidt
article
Model2005
Thermal Transport Properties of Layered Materials: Identification by a New Numerical Algorithm for Transient Measurements
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
Self-propelled running droplets on solid substrates driven by chemical reactions
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
Visualization of action currents propagation in peripheral nerves from the biomagnetic field
Biomed. Tech.
2005
50
1
179--180
8.41
8.41, BioMed
MBurghoff
B MMackert
WHaberkorn
article
John2005b
Travelling lipid domains in a dynamic model for protein-induced pattern formation in biomembranes
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
Alternative mechanisms of structuring biomembranes: self-assembly versus self-organization
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
A simple method for measuring thoron spatial distributions
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
Preconditioning Techniques for the Bidomain Equations
2005
571--580
8.41
Domain Decomposition Methods in Science and Engineering
RWeber dos Santos
inproceedings
Model2005a
The Virtual Experiment Design: Optimizing of the Transient Hot Bridge Sensor
2005
8.41
8.41
Proc. 17th Europ. Conf. on Thermophys. Prop.
RModel
RStosch
UHammerschmidt