@misc{BojarovskiHegeLieetal.2015, author = {Bojarovski, Stefan and Hege, Hans-Christian and Lie, Han Cheng and Weber, Marcus}, title = {Topological analysis and visualization of scalar functions characterizing conformational transitions of molecules on multiple time-scales}, journal = {Shape Up 2015 - Exercises in Materials Geometry and Topology, 14-18 Sept. 2015, Berlin, Germany}, year = {2015}, abstract = {Molecular processes such as protein folding or ligand-receptor-binding can be understood by analyzing the free energy landscape. Those processes are often metastable, i.e. the molecular systems remain in basins around local minima of the free energy landscape, and in rare cases undergo gauche transitions between metastable states by passing saddle-points of this landscape. By discretizing the configuration space, this can be modeled as a discrete Markov process. One way to compute the transition rates between conformations of a molecular system is by utilizing Transition Path Theory and the concept of committor functions. A fundamental problem from the computational point of view is that many time-scales are involved, ranging from 10^(-14) sec for the fastest motion to 10^(-6) sec or more for conformation changes that cause biological effects. The goal of our work is to provide a better understanding of such transitions in configuration space on various time-scales by analyzing characteristic scalar functions topologically and geometrically. We are developing suitable visualization and interaction techniques to support our analysis. For example, we are analyzing a transition rate indicator function by computing and visualizing its Reeb graph together with the sets of molecular states corresponding to maxima of the transition rate indicator function. A particular challenge is the high dimensionality of the domain which does not allow for a straightforward visualization of the function. The computational topology approach to the analysis of the transition rate indicator functions for a molecular system allows to explore different time scales of the system by utilizing coarser or finer topological partitioning of the function. A specific goal is the development of tools for analyzing the hierarchy of these partitionings. This approach tackles the analysis of a complex and sparse dataset from a different angle than the well-known spectral analysis of Markov State Models.}, language = {en} } @misc{SieberKuhnHegeetal.2015, author = {Sieber, Moritz and Kuhn, Alexander and Hege, Hans-Christian and Paschereit, C. Oliver and Oberleithner, Kilian}, title = {A Graphical Representation of the Spectral Proper Orthogonal Decomposition}, journal = {68th Annual Meeting of the APS Division of Fluid Dynamics, Gallery of Fluid Motion, Nov 22-24, 2015, Boston, MA, USA.}, year = {2015}, abstract = {We consider the spectral proper orthogonal decomposition (SPOD) for experimental data of a turbulent swirling jet. This newly introduced method combines the advantages of spectral methods, such as Fourier decomposition or dynamic mode decomposition, with the energy-ranked proper orthogonal decomposition (POD). This poster visualizes how the modal energy spectrum transitions from the spectral purity of Fourier space to the sparsity of POD space. The transition is achieved by changing a single parameter - the width of the SPOD filter. Each dot in the 3D space corresponds to an SPOD mode pair, where the size and color indicates its spectral coherence. What we notice is that neither the Fourier nor the POD spectrum achieves a clear separation of the dynamic phenomena. Scanning through the graph from the front plane (Fourier) to the back plane (POD), we observe how three highly coherent SPOD modes emerge from the dispersed Fourier spectrum and later branch out into numerous POD modes. The spatial properties of these three individual SPOD modes are displayed in the back of the graph using line integral convolution colored by vorticity. The first two modes correspond to single-helical global instabilities that are well known for these flows. Their coexistence, however, has not been observed until now. The third mode is of double- helical shape and has not been observed so far. For this considered data set and many others, the SPOD is superior in identification of coherent structures in turbulent flows. Hopefully, it gives access to new fluid dynamic phenomena and enriches the available methods.}, language = {en} } @misc{Grewe2015, author = {Grewe, Carl Martin}, title = {3D Digital Morphology of Human Faces}, journal = {Anthropologie der Wahrnehmung. Marsilius-Sommerakademie Heidelberg, 14.-20. September}, year = {2015}, language = {en} } @misc{TackKobayashiGaueretal.2015, author = {Tack, Alexander and Kobayashi, Yuske and Gauer, Tobias and Schlaefer, Alexander and Werner, Ren{\´e}}, title = {Bewegungsfeldsch{\"a}tzung in artefaktbehafteten 4D-CT-Bilddaten: Vergleich von paar- und gruppenweiser Registrierung}, volume = {Supplement 1}, journal = {21st Annual Meeting of the German-Society-for-Radiation-Oncology}, edition = {191}, publisher = {Springer}, address = {Strahlentherapie und Onkologie}, doi = {10.1007/s00066-015-0847-x}, pages = {65 -- 65}, year = {2015}, abstract = {In der Strahlentherapie von Lungentumoren kann mittels Dosisakkumulation der Einfluss von Atembewegungen auf statisch geplante Dosisverteilungen abgesch{\"a}tzt werden. Grundlage sind 4D-CT-Daten des Patienten, aus denen mittels nicht-linearer Bildregistrierung eine Sequenz von Bewegungsfeldern berechnet wird. Typischerweise werden Methoden der paarweisen Bildregistrierung eingesetzt, d.h. konsekutiv zwei Atemphasen aufeinander registriert. Hierbei erfolgt i.d.R. eine physiologisch nicht plausible Anpassung der Felder an CT-Bewegungsartefakte. Gruppenweise Registrierungsans{\"a}tze ber{\"u}cksichtigen hingegen gleichzeitig s{\"a}mtliche Bilddaten des 4D-CT-Scans und erm{\"o}glichen die Integration von zeitlichen Konsistenzbetrachtungen. In diesem Beitrag wird der potentielle Vorteil der gruppen- im Vergleich zur paarweisen Registrierung in artefaktbehafteten 4D-CT-Daten untersucht.}, language = {de} } @misc{OsterlandBennProhaskaetal.2015, author = {Osterland, Marc and Benn, Andreas and Prohaska, Steffen and Sch{\"u}tte, Christof}, title = {Single Cell Tracking in Phase-Contrast Microscopy}, journal = {EMBL Symposium 2015 - Seeing is Believing - Imaging the Processes of Life}, year = {2015}, abstract = {In this work, we developed an automatic algorithm to analyze cell migration in chemotaxis assays, based on phase-contrast time-lapse microscopy. While manual approaches are still widely used in recent publications, our algorithm is able to track hundreds of single cells per frame. The extracted paths are analysed with traditional geometrical approaches as well as diffusion-driven Markov state models (MSM). Based on these models, a detailed view on spatial and temporal effects is possible. Using our new approach on experimental data, we are able to distinguish between directed migration (e.g. towards a VEGF gradient) and random migration without favored direction. A calculation of the committor probabilities reveals that cells of the whole image area are more likely to migrate directly towards the VEGF than away from it during the first four hours. However, in absence of a chemoattractant, cells migrate more likely to their nearest image border. These conclusions are supported by the spatial mean directions. In a next step, the cell-cell interaction during migration and the migration of cell clusters will be analyzed. Furthermore, we want to observe phenotypical changes during migration based on fluorescence microscopy and machine learning. The algorithm is part of a collaborative platform which brings the experimental expertise of scientists from life sciences and the analytical knowledge of computer scientists together. This platform is built using web-based technologies with a responsive real-time user interface. All data, including raw and metadata as well as the accompanying results, will be stored in a secure and scalable compute cluster. The compute cluster provides sufficient space and computational power for modern image-based experiments and their analyses. Specific versions of data and results can be tagged to keep immutable records for archival.}, language = {en} } @misc{KnoetelSeidelWeaveretal.2015, author = {Kn{\"o}tel, David and Seidel, Ronald and Weaver, James C. and Baum, Daniel and Dean, Mason N.}, title = {Segmentation of the Tessellated Mineralized Endoskeleton of Sharks and Rays}, journal = {Poster, Tomography for Scientific Advancement symposium (ToScA), Manchester, UK, September 3 - 4, 2015}, year = {2015}, abstract = {The cartilaginous endoskeletons of sharks and rays are covered by tiles of mineralized cartilage called tesserae that enclose areas of unmineralized cartilage. These tesselated layers are vital to the growth as well as the material properties of the skeleton, providing both flexibility and strength. An understanding of the principles behind the tiling of the mineralized layer requires a quantitative analysis of shark and ray skeletal tessellation. However, since a single skeletal element comprises several thousand tesserae, manual segmentation is infeasible. We developed an automated segmentation pipeline that, working from micro-CT data, allows quantification of all tesserae in a skeletal element in less than an hour. Our segmentation algorithm relies on aspects we have learned of general tesseral morphology. In micro-CT scans, tesserae usually appear as round or star-shaped plate-like tiles, wider than deep and connected by mineralized intertesseral joints. Based on these observations, we exploit the distance map of the mineralized layer to separate individual tiles using a hierarchical watershed algorithm. Utilizing a two-dimensional distance map that measures the distance in the plane of the mineralized layer only greatly improves the segmentation. We developed post-processing techniques to quickly correct segmentation errors in regions where tesseral shape differs from the assumed shape. Evaluation of our results is done qualitatively by visual comparison with raw datasets, and quantitatively by comparison to manual segmentations. Furthermore, we generate two-dimensional abstractions of the tiling network based on the neighborhood, allowing representation of complex, biological forms as simpler geometries. We apply our newly developed techniques to the analysis of the left and right hyomandibulae of four ages of stingray enabling the first quantitative analyses of the tesseral tiling structure, while clarifying how these patterns develop across ontogeny.}, language = {en} } @misc{TitschackBaum2015, author = {Titschack, J{\"u}rgen and Baum, Daniel}, title = {Ambient occlusion - a powerful algorithm to segment skeletal intrapores and gastral cavities in dendrophyllid cold-water corals}, journal = {Poster, 31st IAS Meeting of Sedimentology, 2015, June 22-25, Krak{\´o}w, Poland}, year = {2015}, language = {en} } @misc{PoulikakosGutscheMcPeaketal.2015, author = {Poulikakos, Lisa and Gutsche, Philipp and McPeak, Kevin and Burger, Sven and Niegemann, Jens and Hafner, Christian and Norris, David}, title = {A Far-Field Interpretation of the Optical Chirality}, journal = {Frontiers in Nanophotonics (Congressi Stefano Franscini)}, year = {2015}, abstract = {A chiral structure is not super-imposable with its mirror image. Most commonly found in organic molecules, chirality can also occur in other systems, such as electromagnetic fields, where circularly polarized light is the most widespread example. Chiral electromagnetic fields can be a useful tool for biosensing applications. In particular, it has been shown that chiral plasmonic nanostructures have the ability to produce strongly enhanced chiral near-fields. Recently, our group has developed chiral plasmonic nanopyramids, which have the ability to focus chiral near-fields at their tip. This could enable chiral sensing at the single-molecule level. Chiral near-fields can be characterized in terms of the "optical chirality density". This time-even and parity-odd pseudoscalar was first derived by Lipkin and was found to follow a conservation law analogous to the energy conservation of electromagnetic fields. More recently, Tang and Cohen identified the physical meaning of the "optical chirality density" as the degree of asymmetry in the excitation rate of a chiral molecule. However, how this near-field interpretation of the optical chirality could translate into the far-field is not well understood. Here, we formulate a far-field interpretation by investigating the conservation law for optical chirality in matter, and performing time-averaging in analogy to Poynting's Theorem. In parallel to extinction energy, we define the "global chirality" as the sum of chirality dissipation within a material and the chirality flux leaving the system. With finite-element simulations, we place a dipole source at locations of enhanced local chirality and investigate the global chirality and ellipticity of emitted light in the far-field. Interestingly, we find that lossy materials with a complex dielectric function have the ability to generate global chirality when excited by achiral light. In particular, chiral plasmonic nanostructures are found to act as effective global chirality generators. The global interpretation of optical chirality provides a useful tool for biosensing applications with chiral plasmonic nanostructures, where the detection is routinely performed in the far-field.}, language = {en} } @misc{GutscheWolffMirnaziryetal.2015, author = {Gutsche, Philipp and Wolff, Christian and Mirnaziry, Sayyed R. and Poulton, Christopher G.}, title = {Coupled-Mode Equations for Stimulated Brillouin Scattering}, journal = {CUDOS 14th Annual Workshop 2015 Handbook}, year = {2015}, abstract = {Stimulated Brillouin Scattering (SBS) is a third-order nonlinear optical effect which originates from the interplay of acoustics and optics. Recently, SBS has been harnessed in nano-photonic waveguides for applications such as narrow-linewidth lasers and Brillouin dynamic gratings [1]. Since the timescales of both phenomena differ significantly, coupled-mode equations derived from a slowly varying envelope approximation are well suited for numerical investigations of SBS [2]. We use the Relaxation Method (RM) [3] to study the optical power transfer and spatially resolved power distributions in long waveguides in the steady state limit.}, language = {en} } @misc{WilsonBuecherGreweetal.2015, author = {Wilson, David and B{\"u}cher, Pia and Grewe, Carl Martin and Anglin, Carolyn and Zachow, Stefan and Michael, Dunbar}, title = {Validation of Three Dimensional Models of the Distal Femur Created from Surgical Navigation Point Cloud Data}, journal = {15th Annual Meeting of the International Society for Computer Assisted Orthopaedic Surgery (CAOS)}, year = {2015}, language = {en} } @misc{WilsonBuecherGreweetal.2015, author = {Wilson, David and B{\"u}cher, Pia and Grewe, Carl Martin and Mocanu, Valentin and Anglin, Carolyn and Zachow, Stefan and Dunbar, Michael}, title = {Validation of Three Dimensional Models of the Distal Femur Created from Surgical Navigation Data}, journal = {Orthopedic Research Society Annual Meeting}, address = {Las Vegas, Nevada}, year = {2015}, language = {en} }