TY - JOUR A1 - Schöneich, Marc A1 - Stommel, Markus A1 - Kratz, Andrea A1 - Zobel, Valentin A1 - Scheuermann, Gerik A1 - Hotz, Ingrid A1 - Burgeth, Bernhard T1 - Optimization strategy for the design of ribbed plastic components JF - International Journal of Plastics Technology Y1 - 2014 IS - 10 SP - 160 EP - 175 ER - TY - GEN A1 - Wilson, David A1 - Bücher, Pia A1 - Grewe, Carl Martin A1 - Mocanu, Valentin A1 - Anglin, Carolyn A1 - Zachow, Stefan A1 - Dunbar, Michael T1 - Validation of Three Dimensional Models of the Distal Femur Created from Surgical Navigation Data T2 - Orthopedic Research Society Annual Meeting Y1 - 2015 CY - Las Vegas, Nevada ER - TY - CHAP A1 - Dean, Mason N. A1 - Seidel, R. A1 - Knötel, David A1 - Lyons, K. A1 - Baum, Daniel A1 - Weaver, James C. A1 - Fratzl, Peter T1 - To build a shark: 3D tiling laws of tessellated cartilage T2 - Abstract in Integrative and Comparative Biology; conference Society of Integrative and Comparative Biology annual meeting, January 3-7, 2016, Portland, USA N2 - The endoskeleton of sharks and rays (elasmobranchs) is comprised of a cartilaginous core, covered by thousands of mineralized tiles, called tesserae. Characterizing the relationship between tesseral morphometrics, skeletal growth and mechanics is challenging because tesserae are small (a few hundred micrometers wide), anchored to the surrounding tissue in complex three-dimensional ways, and occur in huge numbers. We integrate material property, histology, electron microscopy and synchrotron and laboratory µCT scans of skeletal elements from an ontogenetic series of round stingray Urobatis halleri, to gain insights into the generation and maintenance of a natural tessellated system. Using a custom-made semiautomatic segmentation algorithm, we present the first quantitative and 3d description of tesserae across whole skeletal elements. The tessellation is not interlocking or regular, with tesserae showing a great range of shapes, sizes and number of neighbors. This is partly region-dependent: for example, thick, columnar tesserae are arranged in series along convex edges with small radius of curvature (RoC), whereas more brick- or disc-shaped tesserae are found in planar/flatter areas. Comparison of the tessellation across ontogeny, shows that in younger animals, the forming tesseral network is less densely packed, appearing as a covering of separate, poorly mineralized islands that grow together with age to form a complete surface. Some gaps in the tessellation are localized to specific regions in all samples, indicating they are real features, perhaps either regions of delayed mineralization or of tendon insertion. We will use the structure of elasmobranch skeletons as a road map for understanding shark and ray skeletal mechanics, but also to extract fundamental engineering principles for tiled composite materials. Y1 - 2016 UR - https://academic.oup.com/icb/article-pdf/56/suppl_1/e1/9102603/icw002.pdf VL - 56 (suppl 1) ER - TY - THES A1 - Lindow, Norbert T1 - Visual Analysis of Atomic Structures Based on the Hard-Sphere Model N2 - Visualization and Analysis of atomic compositions is essential to understand the structure and functionality of molecules. There exist versatile areas of applications, from fundamental researches in biophysics and materials science to drug development in pharmaceutics. For most applications, the hard-sphere model is the most often used molecular model. Although the model is a quite simple approximation of reality, it enables investigating important physical properties in a purely geometrical manner. Furthermore, large data sets with thousands up to millions of atoms can be visualized and analyzed. In addition to an adequate and efficient visualization of the data, the extraction of important structures plays a major role. For the investigation of biomolecules, such as proteins, especially the analysis of cavities and their dynamics is of high interest. Substrates can bind in cavities, thereby inducing changes in the function of the protein. Another example is the transport of substrates through membrane proteins by the dynamics of the cavities. For both, the visualization as well as the analysis of cavities, the following contributions will be presented in this thesis: 1. The rendering of smooth molecular surfaces for the analysis of cavities is accelerated and visually improved, which allows showing dynamic proteins. On the other hand, techniques are proposed to interactively render large static biological structures and inorganic materials up to atomic resolution for the first time. 2. A Voronoi-based method is presented to extract molecular cavities. The procedure comes with a high geometrical accuracy by a comparatively fast computation time. Additionally, new methods are presented to visualize and highlight the cavities within the molecular structure. In a further step, the techniques are extended for dynamic molecular data to trace cavities over time and visualize topological changes. 3. To further improve the accuracy of the approaches mentioned above, a new molecular surface model is presented that shows the accessibility of a substrate. For the first time, the structure and dynamics of the substrate as hard-sphere model is considered for the accessibility computation. In addition to the definition of the surface, an efficient algorithm for its computation is proposed, which additionally allows extracting cavities. The presented algorithms are demonstrated on different molecular data sets. The data sets are either the result of physical or biological experiments or molecular dynamics simulations. Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-63190 ER - TY - JOUR A1 - Günther, Tobias A1 - Kuhn, Alexander A1 - Hege, Hans-Christian A1 - Theisel, Holger T1 - MCFTLE: Monte Carlo Rendering of Finite-Time Lyapunov Exponent Fields JF - Computer Graphics Forum Y1 - 2016 U6 - https://doi.org/10.1111/cgf.12914 N1 - By mistake the fourth author Hans-Christian Hege has been ommitted in the journal publication VL - 35 IS - 3 SP - 381 EP - 390 ER - TY - CHAP A1 - Sagnol, Guillaume A1 - Hege, Hans-Christian A1 - Weiser, Martin T1 - Using sparse kernels to design computer experiments with tunable precision T2 - 22nd Intern. Conf. on Computational Statistics - COMPSTAT 2016, Oviedo, Spain, 23-26 August 2016, Proceedings ISBN 978-90-73592-36-0 Y1 - 2016 SP - 397 EP - 408 ER - TY - GEN A1 - Aboulhassan, Amal A1 - Sicat, Ronell A1 - Baum, Daniel A1 - Wodo, Olga A1 - Hadwiger, Markus T1 - Comparative Visual Analysis of Structure-Performance Relations in Complex Bulk-Heterojunction Morphologies N2 - The structure of Bulk-Heterojunction (BHJ) materials, the main component of organic photovoltaic solar cells, is very complex, and the relationship between structure and performance is still largely an open question. Overall, there is a wide spectrum of fabrication configurations resulting in different BHJ morphologies and correspondingly different performances. Current state- of-the-art methods for assessing the performance of BHJ morphologies are either based on global quantification of morphological features or simply on visual inspection of the morphology based on experimental imaging. This makes finding optimal BHJ structures very challenging. Moreover, finding the optimal fabrication parameters to get an optimal structure is still an open question. In this paper, we propose a visual analysis framework to help answer these questions through comparative visualization and parameter space exploration for local morphology features. With our approach, we enable scientists to explore multivariate correlations between local features and performance indicators of BHJ morphologies. Our framework is built on shape-based clustering of local cubical regions of the morphology that we call patches. This enables correlating the features of clusters with intuition-based performance indicators computed from geometrical and topological features of charge paths. T3 - ZIB-Report - 17-16 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-63239 SN - 1438-0064 ER - TY - GEN A1 - Kaplan, Bernhard A1 - Laufer, Jan A1 - Prohaska, Steffen A1 - Buchmann, Jens T1 - Monte-Carlo-based inversion scheme for 3D quantitative photoacoustic tomography N2 - The goal of quantitative photoacoustic tomography (qPAT) is to recover maps of the chromophore distributions from multiwavelength images of the initial pressure. Model-based inversions that incorporate the physical processes underlying the photoacoustic (PA) signal generation represent a promising approach. Monte-Carlo models of the light transport are computationally expensive, but provide accurate fluence distributions predictions, especially in the ballistic and quasi-ballistic regimes. Here, we focus on the inverse problem of 3D qPAT of blood oxygenation and investigate the application of the Monte-Carlo method in a model-based inversion scheme. A forward model of the light transport based on the MCX simulator and acoustic propagation modeled by the k-Wave toolbox was used to generate a PA image data set acquired in a tissue phantom over a planar detection geometry. The combination of the optical and acoustic models is shown to account for limited-view artifacts. In addition, the errors in the fluence due to, for example, partial volume artifacts and absorbers immediately adjacent to the region of interest are investigated. To accomplish large-scale inversions in 3D, the number of degrees of freedom is reduced by applying image segmentation to the initial pressure distribution to extract a limited number of regions with homogeneous optical parameters. The absorber concentration in the tissue phantom was estimated using a coordinate descent parameter search based on the comparison between measured and modeled PA spectra. The estimated relative concentrations using this approach lie within 5 % compared to the known concentrations. Finally, we discuss the feasibility of this approach to recover the blood oxygenation from experimental data. T3 - ZIB-Report - 17-04 KW - quantitative photoacoustic tomography KW - model-based inversion KW - oxygen saturation KW - chromophore concentration KW - photoacoustic imaging KW - Monte Carlo methods for light transport KW - boundary conditions KW - coordinate search Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-62318 SN - 1438-0064 ER - TY - CHAP A1 - Kaplan, Bernhard A1 - Buchmann, Jens A1 - Prohaska, Steffen A1 - Laufer, Jan T1 - Monte-Carlo-based inversion scheme for 3D quantitative photoacoustic tomography T2 - Proc. of SPIE, Photons Plus Ultrasound: Imaging and Sensing 2017 N2 - The goal of quantitative photoacoustic tomography (qPAT) is to recover maps of the chromophore distributions from multiwavelength images of the initial pressure. Model-based inversions that incorporate the physical processes underlying the photoacoustic (PA) signal generation represent a promising approach. Monte-Carlo models of the light transport are computationally expensive, but provide accurate fluence distributions predictions, especially in the ballistic and quasi-ballistic regimes. Here, we focus on the inverse problem of 3D qPAT of blood oxygenation and investigate the application of the Monte-Carlo method in a model-based inversion scheme. A forward model of the light transport based on the MCX simulator and acoustic propagation modeled by the k-Wave toolbox was used to generate a PA image data set acquired in a tissue phantom over a planar detection geometry. The combination of the optical and acoustic models is shown to account for limited-view artifacts. In addition, the errors in the fluence due to, for example, partial volume artifacts and absorbers immediately adjacent to the region of interest are investigated. To accomplish large-scale inversions in 3D, the number of degrees of freedom is reduced by applying image segmentation to the initial pressure distribution to extract a limited number of regions with homogeneous optical parameters. The absorber concentration in the tissue phantom was estimated using a coordinate descent parameter search based on the comparison between measured and modeled PA spectra. The estimated relative concentrations using this approach lie within 5 % compared to the known concentrations. Finally, we discuss the feasibility of this approach to recover the blood oxygenation from experimental data. Y1 - 2017 U6 - https://doi.org/10.1117/12.2251945 VL - 10064 SP - 100645J EP - 100645J-13 ER - TY - JOUR A1 - Lube, Juliane A1 - Flack, Natasha A1 - Cotofana, Sebastian A1 - Özkurtul, Orkun A1 - Woodley, Stephanie A1 - Zachow, Stefan A1 - Hammer, Niels T1 - Pelvic and lower extremity physiological cross-sectional areas: An MRI study of the living young and comparison to published research literature JF - Surgical and Radiologic Anatomy N2 - Purpose: Morphological data pertaining to the pelvis and lower extremity muscles are increasingly being used in biomechanical modeling to compare healthy and pathological conditions. Very few data sets exist that encompass all of the muscles of the lower limb, allowing for comparisons between regions. The aims of this study were to (a) provide physiological cross-sectional area (PCSA) data for the pelvic, thigh, and leg muscles in young, healthy participants, using magnetic resonance imaging (MRI), and (b) to compare these data with summarized PCSAs obtained from the literature. Materials and Methods: Six young and healthy volunteers participated and were scanned using 3 T MRI. PCSAs were calculated from volumetric segmentations obtained bilaterally of 28 muscles/muscle groups of the pelvis, thigh, and leg. These data were compared to published, summarized PCSA data derived from cadaveric, computed tomography, MRI and ultrasound studies. Results: The PCSA of the pelvis, thigh, and leg muscles tended to be 20–130% larger in males than in females, except for the gemelli which were 34% smaller in males, and semitendinosus and triceps surae which did not differ (<20% different). The dominant and the non-dominant sides showed similar and minutely different PCSA with less than 18% difference between sides. Comparison to other studies revealed wide ranges within, and large differences between, the cadaveric and imaging PCSA data. Comparison of the PCSA of this study and published literature revealed major differences in the iliopsoas, gluteus minimus, tensor fasciae latae, gemelli, obturator internus, biceps femoris, quadriceps femoris, and the deep leg flexor muscles. Conclusions: These volume-derived PCSAs of the pelvic and lower limb muscles alongside the data synthesised from the literature may serve as a basis for comparative and biomechanical studies of the living and healthy young, and enable calculation of muscle forces. Comparison of the literature revealed large variations in PCSA from each of the different investigative modalities, hampering omparability between studies. Sample size, age, post-mortem changes of muscle tone, chemical fixation of cadaveric tissues, and the underlying physics of the imaging techniques may potentially influence PCSA calculations. Y1 - 2017 U6 - https://doi.org/10.1007/s00276-016-1807-6 VL - 39 IS - 8 SP - 849 EP - 857 ER -