Gabriel Wittum

Universität Heidelberg, Heidelburg, Baden-Württemberg, Germany

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Publications (136)156.01 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: The automated mapping of program functionality to intuitive user interfaces is a highly challenging task. Nevertheless it is a promising way to significantly improve software quality by simplifying the development process. This paper describes a method for a declarative and fully automated creation of graphical user interfaces from Java objects, i.e. the information accessible via the Java Reflection API. For this purpose we created the Visual Reflection Library (VRL). VRL interfaces are able to represent complex workflows and allow for a certain degree of visual programming. We start by describing an application: the development of an interactive user interface for the simulation system UG. By shortly discussing the requirements for such an interface, we will explain the reasons for creating VRL and the benefits we gained from it. After that we give an overview of our methods and show several applications. We end by summarizing our results and giving a future outlook.
    Computing and Visualization in Science 12/2014;
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    ABSTRACT: In this paper we describe the concept of the renewed software package UG, that is used as a flexible simulation framework for the solution of partial differential equations. A general overview of the concepts of the new implementation is given: The modularization of the software package into several libraries libGrid, libAlgebra, libDiscretization and pcl is described and all major modules are discussed in detail. User backends through scripting and visual editing are briefly considered and examples show the new features of the current implementation.
    Computing and Visualization in Science 12/2014;
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    ABSTRACT: The morphology of presynaptic specializations can vary greatly ranging from classical single-release-site boutons in the central nervous system to boutons of various sizes harboring multiple vesicle release sites. Multi-release-site boutons can be found in several neural contexts, for example at the neuromuscular junction (NMJ) of body wall muscles of Drosophila larvae. These NMJs are built by two motor neurons forming two types of glutamatergic multi-release-site boutons with two typical diameters. However, it is unknown why these distinct nerve terminal configurations are used on the same postsynaptic muscle fiber. To systematically dissect the biophysical properties of these boutons we developed a full three-dimensional model of such boutons, their release sites and transmitter-harboring vesicles and analyzed the local vesicle dynamics of various configurations during stimulation. Here we show that the rate of transmission of a bouton is primarily limited by diffusion-based vesicle movements and that the probability of vesicle release and the size of a bouton affect bouton-performance in distinct temporal domains allowing for an optimal transmission of the neural signals at different time scales. A comparison of our in silico simulations with in vivo recordings of the natural motor pattern of both neurons revealed that the bouton properties resemble a well-tuned cooperation of the parameters release probability and bouton size, enabling a reliable transmission of the prevailing firing-pattern at diffusion-limited boutons. Our findings indicate that the prevailing firing-pattern of a neuron may determine the physiological and morphological parameters required for its synaptic terminals.
    Frontiers in Computational Neuroscience 09/2014; 8:101. · 2.23 Impact Factor
  • Ivo Muha, Bernd Linke, Gabriel Wittum
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    ABSTRACT: The focus of this work is the development of a model for the estimation of methane emissions for storage tanks of biogas plants. Those can be estimated depending on (i) hydraulic retention time in the digester, (ii) an arbitrary removal rate of the digestate from the storage tank and (iii) arbitrary temperature conditions in the storage tank. Furthermore, the model is capable of considering an arbitrary mixture of manure and crops in the input material. The model was validated by data from 21 full scale biogas plants in Germany digesting cow manure and crops. A realistic scenario for the removal rate and temperature conditions in the storage tank was then investigated and special emphasis was given to the effect of hydraulic retention time and proportion of crops in the mixture on the input VS methane yield from the digester and the storage tank.
    Bioresource Technology 08/2014; · 5.04 Impact Factor
  • Mathematics and Mechanics of Solids 01/2014; · 0.86 Impact Factor
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    ABSTRACT: The application of X-radiography in ceramic studies is becoming an increasingly valued method. Using the potential of industrial X-ray computed tomography (CT) for non-destructive testing as an archaeometric or archaeological method in pottery studies, especially regarding aspects such as manufacturing techniques or pottery fabrics, requires controlled data-acquisition and post-processing by scientific computing adjusted to archaeological issues. The first results of this evaluation project show that, despite the difficulties inherent in CT technology, considerable information can be extracted for pottery analysis. The application of surface morphology reconstructions and volumetric measurements based on CT data will open a new field in future non-invasive archaeology.
    Craft and science: International perspectives on archaeological ceramics, UCL Qatar Series in Archaeology and Cultural Heritage. 01/2014; 1:253-262.
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    ABSTRACT: We develop a numerical technique for variable-density flow in fractured porous media, in which fractures are (d − 1)-dimensional manifolds, with d being the dimension of the ambient space. The PDEs of variable-density flow are firstly presented in the same form for both the fractures and the enclosing medium. Then, the equations defined in the fractures are averaged along the fracture width and formulated in (d − 1)-dimensions. The resulting PDEs are solved together with those defined in the enclosing medium, which maintain their d-dimensional form. The discretisation of the coupled system of d- and (d − 1)-dimensional PDEs follows a finite-volume method requiring a special construction of the discretisation grid, obtained by the algorithm explained in this paper. The accuracy of our technique is tested by comparing the produced results with those obtained in simulations in which the fractures maintain dimension d. In all simulations the fractured medium is three-dimensional.
    International Journal of Computational Science and Engineering 01/2014; 9(5/6):416-432.
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    ABSTRACT: The scope of this manuscript is to investigate the role of the Forchheimer correction in the description of variable-density flow in fractured porous media. A fractured porous medium, which shall be also referred to as “the embedding medium”, represents a flow region that is made macroscopically heterogeneous by the presence of fractures. Fractures are assumed to be filled with a porous medium characterized by flow properties that differ appreciably from those of the embedding medium. The fluid, which is free to move in the pore space of the entire flow region, is a mixture of water and brine. Flow is assumed to be a consequence of the variability of the fluid mass density in response to the generally nonuniform distribution of brine, which is subject to diffusion and convection. The fractures are assumed to be thin in comparison with the characteristic sizes of the embedding medium. Within this framework, some benchmark problems are solved by adopting two approaches: (i) the fractures are treated as thin but $\mathrm{d}$ -dimensional flow subregions, with $d$ being the geometric dimension of the embedding medium; (ii) the fractures are regarded as $(\mathrm{d}-1)$ -dimensional manifolds. In the first approach, the equations of variable-density flow are written in the same, $d$ -dimensional form both in the fractures and in the embedding medium. In the second approach, instead, new equations are obtained by averaging the $\mathrm{d}$ -dimensional ones over the fracture width. The reliability of the second approach is discussed by comparing the results of the $(\mathrm{d}-1)$ -dimensional numerical simulations of the selected benchmark problems with those obtained by using the $d$ -dimensional approach. Moreover, the deviations of the results determined by accounting for the Forchheimer correction to flow velocity are compared with those predicted by Darcy’s law.
    Computing and Visualization in Science 08/2013;
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    ABSTRACT: A sophisticated combination of noise reducing, segmentation and meshgeneration methods provides the reconstruction of the surface morphology fromthree dimensional computed tomography scans of archaeological data as triangularsurface meshes. The highly parallelized GPU-enabled implementation of the algo-rithm processes large data sets in only a few minutes, allowing the systematic recon-struction of various objects. Rendering of the generated triangular meshes and thecalculation of the surface area and the volume of the reconstructed items or selectedparts of interest, can be done in real time. Those items can also be exchanged byscientists around the world and can be investigated without manipulating the irre-placeable artifacts. The application of computed tomography and the developmentof archaeological adjusted post processing of the acquired volumetric data enablea non-destructive investigation of the entire object regarding shape, manufacturingtechniques or material textures. The reconstructions can also serve as a basis forvirtual exhibitions.
    Edited by Hans Georg Bock; Willi Jäger; Michael Winckler, 08/2013; Springer., ISBN: 978-3-642-28021-4
  • Bioresource Technology. 01/2013; 132:414-418.
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    ABSTRACT: In this article a mathematical model is introduced, which estimates the distribution of the four anaerobic digestion phases (hydrolysis, acidogenesis, acetogenesis and methanogenesis) that occur among the leach bed reactor and the anaerobic filter of a biogas plant. It is shown that only the hydrolysis takes place in the first stage (leach bed reactor), while all other anaerobic digestion phases take place in both reactor stages. It turns out that, besides the usually measured raw materials of the acetogenesis and the methanogenesis phases (organic acids), it is also necessary to analyze the process liquid for raw materials of the acidogenesis phase, i.e., sugars, fatty acids, amino acids, etc. The introduced model can be used to monitor the inhibition of the anaerobic digestion phases in reactor stages and can, thus, help to improve the control system of biogas plants.
    Bioresource Technology 12/2012; · 5.04 Impact Factor
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    ABSTRACT: Data from 24 full scale biogas plants in Germany digesting cow manure and crops were evaluated. Special emphasis was given to the effect of hydraulic retention time HRT and proportion of crops in the mixture (VS basis) p(VS,Crops)(Inp) on the methane yield from the digester [Formula: see text] and the storage tank [Formula: see text] at 37 and 22°C. The evaluation has shown model parameters for maximal methane yield of manure and crops [Formula: see text] at 270 and 420 Lkg(-1), respectively. For example, at HRT of 60days, maximum methane yield result to 249 and 388 Lkg(-1) for a crop proportion in the input of 0.0 and 1.0, respectively. The calculation of [Formula: see text] considers first order reaction rates and a temperature term f(T). Hence, at any arbitrary temperature in the range of 12°C<T<37°C the values of [Formula: see text] in the course of time can be calculated, which correspond to methane emissions for uncovered storage tanks.
    Bioresource Technology 12/2012; 130C:689-695. · 5.04 Impact Factor
  • Arne Nägel, Michael Heisig, Gabriel Wittum
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    ABSTRACT: In recent years, the combination of computational modeling and experiments has become a useful tool that is proving increasingly powerful for explaining biological complexity. As computational power is increasing, scientists are able to explore ever more complex models in finer detail and to explain very complex real world data. This work provides an overview of one-, two- and three-dimensional diffusion models for penetration into mammalian skin. Besides diffusive transport this includes also binding of substances to skin proteins and metabolism. These models are based on partial differential equations that describe the spatial evolution of the transport process through the biological barrier skin. Furthermore, the work focuses on analytical and numerical techniques for this type of equations such as discretization schemes or homogenization (upscaling) techniques. Finally, the work compares different geometry models with respect to the permeability.
    Advanced drug delivery reviews 11/2012; · 11.96 Impact Factor
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    ABSTRACT: This work investigates in vitro finite dose skin absorption of the model compounds flufenamic acid and caffeine experimentally and mathematically. The mass balance in different skin compartments (donor, stratum corneum (SC), deeper skin layers (DSL), lateral skin parts and acceptor) is analyzed as a function of time. For both substances high amounts were found in the lateral skin compartment after 6 hours of incubation, which emphasizes not to elide these parts in the modeling. Here, three different mathematical models were investigated and tested with the experimental data: a pharmacokinetic model (PK), a detailed microscopic two-dimensional diffusion model (MICRO) and a macroscopic homogenized diffusion model (MACRO). While the PK model was fitted to the experimental data, the MICRO and the MACRO models employed input parameters derived from infinite dose studies to predict the underlying diffusion process. All models could satisfyingly predict or describe the experimental data. The PK model and MACRO model also feature the lateral parts.
    Journal of Controlled Release 10/2012; · 7.63 Impact Factor
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    ABSTRACT: In this paper we present a mathematical diffusion model describing the transient transdermal penetration of two non-volatile substances, the lipophilic flufenamic acid and the hydrophilic caffeine, after finite dosing in an aqueous vehicle system. A striking feature of this microscopic diffusion model is its ability to predict concentration-depth profiles. Relevant input parameters are obtained from a previously published infinite dose study (Naegel et al in Eur J Pharm Biopharm 68:368–379, 2008; Hansen et al in Eur J Pharm Biopharm 68:352–367, 2008). The quality of the model has been evaluated by comparing the concentration-depth profiles in stratum corneum (SC) and deeper skin layers of the experiment with those of the simulation. The results from the experiment and the simulation are in good agreement. The study addresses benefits and shortcomings of the model, and discusses future perspectives such as incorporating different morphological regions of the SC.
    Computing and Visualization in Science 10/2012; 14(7).
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    ABSTRACT: SpineLab is a software tool developed for reconstructing neuronal feature skeletons from three-dimensional single- or multi-photon image stacks. These images often suffer from limited resolution and a low signal-to-noise ratio, making the extraction of morphometric information difficult. To overcome this limitation, we have developed a software tool that offers the possibility to create feature skeletons in various modes-automatically as well as with manual interaction. We have named this novel tool SpineLab. In a first step, an investigator adjusts a set of parameters for automatic analysis in an interactive manner, i.e., with online visual feedback, followed by a second step, in which the neuronal feature skeleton can be modified by hand. We validate the ability of SpineLab to reconstruct the entire dendritic tree of identified GFP-expressing neurons and evaluate the accuracy of dendritic spine detection. We report that SpineLab is capable of significantly facilitating the reconstruction of dendrites and spines. Moreover, the automatic approach appears sufficient to detect spine density changes in time-lapse imaging experiments. Taken together, we conclude that SpineLab is an ideal software tool for partially automatic reconstruction of neural cell morphology.
    Journal of Biomedical Optics 07/2012; 17(7):076007. · 2.75 Impact Factor
  • Alfio Grillo, Salvatore Federico, Gabriel Wittum
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    ABSTRACT: We represent a biological tissue by a multi-constituent, fiber-reinforced material, in which we consider two phases: fluid, and a fiber-reinforced solid. Among the various processes that may occur in such a system, we study growth, mass transfer, and remodeling. To us, mass transfer is the reciprocal exchange of constituents between the phases, growth is the variation of mass of the system in response to interactions with the surrounding environment, and remodeling is the evolution of its internal structure. We embrace the theory according to which these events, which lead to a structural reorganization of the system and anelastic deformations, require the introduction of balance laws, which complete the physical picture offered by the standard ones. The former are said to be non-standard. Our purposes are to determine the rates of anelastic deformation related to mass transfer and growth, and to study fiber reorientation in the case of a statistical distribution of fibers. In particular, we discuss the use of the non-standard balance laws in modeling transfer of mass, and compare our results with a formulation in which such balance laws are not introduced.
    International Journal of Non-Linear Mechanics 03/2012; · 1.46 Impact Factor
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    ABSTRACT: We consider a standard Adaptive Edge Finite Element Method (AEFEM) based on arbitrary order Nédélec edge elements, for three-dimensional indefinite time-harmonic Maxwell equations. We prove that the AEFEM gives a contraction for the sum of the energy error and the scaled error estimator, between two consecutive adaptive loops provided the initial mesh is fine enough. Using the geometric decay, we show that the AEFEM yields the best possible decay rate of the error plus oscillation in terms of the number of degrees of freedom. The main technical contribution of the paper is the establishment of a quasi-orthogonality and a localized a posteriori error estimator.
    Mathematics of Computation 01/2012; 81. · 1.41 Impact Factor
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    ABSTRACT: We investigate salinity- and thermohaline-driven flow in a heterogeneous porous medium in which the heterogeneity is due to the presence of fractures. In our study, fractures delimit thin regions of space occupied by a porous medium whose properties are markedly different from those of the porous medium enclosing them. We formulate some benchmark problems in which fractures are present, and solve them by adopting two approaches: (i) The fractures have the same dimension, d, as the enclosing medium and are said to be d dimensional; (ii) the fractures are viewed as (d − 1)-dimensional manifolds, and the equations of density-driven flow are obtained by averaging the d-dimensional laws over the fracture width. We use both approaches as long as salinity-driven problems are considered, and we use the first approach only for the solution of the thermohaline problems. Our aim is twofold: (a) testing the reliability of the (d − 1)-dimensional approach for the considered examples, and (b) studying the effect of fractures on heat transport.
    Journal of Porous Media 01/2012; 15(5):439-458. · 0.47 Impact Factor
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    ABSTRACT: This work presents an extension of grid generation techniques for finite-volume discretizations of density-driven flow in fractured porous media, in which fractures are considered as low-dimensional manifolds and are resolved by sides of grid elements. The proposed technique introduces additional degrees of freedom for the unknowns assigned to the fractures and thus allows to reconstruct jumps of the solution over a fracture. Through the concept of degenerated elements, the proposed technique can be used for arbitrary junctions of fractures but is sufficiently simple regarding the implementation and allows for the application of conventional numerical solvers. Numerical experiments presented at the end of the paper demonstrate the applicability of this technique in two and three dimensions for complicated fracture networks.
    Computing and Visualization in Science 01/2012; 15(4).

Publication Stats

951 Citations
156.01 Total Impact Points


  • 2002–2014
    • Universität Heidelberg
      • • Institute of Computer Science
      • • Interdisciplinary Center for Neurosciences
      • • Interdisciplinary Center for Scientific Computing
      Heidelburg, Baden-Württemberg, Germany
  • 2008–2013
    • Goethe-Universität Frankfurt am Main
      • Goethe Center for Scientific Computing
      Frankfurt, Hesse, Germany
  • 2012
    • Universität des Saarlandes
      Saarbrücken, Saarland, Germany
  • 2011
    • University of Kragujevac
      Krabujevac, Central Serbia, Serbia
  • 2009
    • ETH Zurich
      Zürich, Zurich, Switzerland
  • 1996–2000
    • Universität Stuttgart
      Stuttgart, Baden-Württemberg, Germany