TY - JOUR A1 - Weber, Marie-Christin A1 - Fischer, Lisa A1 - Damerau, Alexandra A1 - Ponomarev, Igor A1 - Pfeiffenberger, Moritz A1 - Gaber, Timo A1 - Götschel, Sebastian A1 - Lang, Jens A1 - Röblitz, Susanna A1 - Buttgereit, Frank A1 - Ehrig, Rainald A1 - Lang, Annemarie T1 - Macroscale mesenchymal condensation to study cytokine-driven cellular and matrix-related changes during cartilage degradation JF - Biofabrication N2 - Understanding the pathophysiological processes of cartilage degradation requires adequate model systems to develop therapeutic strategies towards osteoarthritis (OA). Although different in vitro or in vivo models have been described, further comprehensive approaches are needed to study specific disease aspects. This study aimed to combine in vitro and in silico modeling based on a tissue-engineering approach using mesenchymal condensation to mimic cytokine-induced cellular and matrix-related changes during cartilage degradation. Thus, scaffold-free cartilage-like constructs (SFCCs) were produced based on self-organization of mesenchymal stromal cells (mesenchymal condensation) and i) characterized regarding their cellular and matrix composition or secondly ii) treated with interleukin-1β (IL-1β) and tumor necrosis factor α (TNFα) for 3 weeks to simulate OA-related matrix degradation. In addition, an existing mathematical model based on partial differential equations was optimized and transferred to the underlying settings to simulate distribution of IL-1β, type II collagen degradation and cell number reduction. By combining in vitro and in silico methods, we aim to develop a valid, efficient alternative approach to examine and predict disease progression and effects of new therapeutics. Y1 - 2020 U6 - https://doi.org/10.1088/1758-5090/aba08f VL - 12 IS - 4 ER - TY - JOUR A1 - Weber, Marie-Christin A1 - Fischer, Lisa A1 - Damerau, Alexandra A1 - Ponomarev, Igor A1 - Pfeiffenberger, Moritz A1 - Gaber, Timo A1 - Götschel, Sebastian A1 - Lang, Jens A1 - Röblitz, Susanna A1 - Buttgereit, Frank A1 - Ehrig, Rainald A1 - Lang, Annemarie T1 - In vitro and in silico modeling of cellular and matrix-related changes during the early phase of osteoarthritis JF - BioRxiv N2 - Understanding the pathophysiological processes of osteoarthritis (OA) require adequate model systems. Although different in vitro or in vivo models have been described, further comprehensive approaches are needed to study specific parts of the disease. This study aimed to combine in vitro and in silico modeling to describe cellular and matrix-related changes during the early phase of OA. We developed an in vitro OA model based on scaffold-free cartilage-like constructs (SFCCs), which was mathematically modeled using a partial differential equation (PDE) system to resemble the processes during the onset of OA. SFCCs were produced from mesenchymal stromal cells and analyzed weekly by histology and qPCR to characterize the cellular and matrix-related composition. To simulate the early phase of OA, SFCCs were treated with interleukin-1β (IL-1β), tumor necrosis factor α (TNFα) and examined after 3 weeks or cultivated another 3 weeks without inflammatory cytokines to validate the regeneration potential. Mathematical modeling was performed in parallel to the in vitro experiments. SFCCs expressed cartilage-specific markers, and after stimulation an increased expression of inflammatory markers, matrix degrading enzymes, a loss of collagen II (Col-2) and a reduced cell density was observed which could be partially reversed by retraction of stimulation. Based on the PDEs, the distribution processes within the SFCCs, including those of IL-1β, Col-2 degradation and cell number reduction was simulated. By combining in vitro and in silico methods, we aimed to develop a valid, efficient alternative approach to examine and predict disease progression and new therapeutic strategies. Y1 - 2019 U6 - https://doi.org/10.1101/725317 ER - TY - GEN A1 - Franzone, Piero Colli A1 - Deuflhard, Peter A1 - Erdmann, Bodo A1 - Lang, Jens A1 - Pavarino, Luca Franco T1 - Adaptivity in Space and Time for Reaction-Diffusion Systems in Electrocardiology N2 - Adaptive numerical methods in space and time are introduced and studied for multiscale cardiac reaction-diffusion models in three dimensions. The evolution of a complete heartbeat, from the excitation to the recovery phase, is simulated with both the anisotropic Bidomain and Monodomain models, coupled with either a variant of the simple FitzHugh-Nagumo model or the more complex phase-I Luo-Rudy ionic model. The simulations are performed with the {\sc kardos} library, that employs adaptive finite elements in space and adaptive linearly implicit methods in time. The numerical results show that this adaptive method successfully solves these complex cardiac reaction-diffusion models on three-dimensional domains of moderate sizes. By automatically adapting the spatial meshes and time steps to the proper scales in each phase of the heartbeat, the method accurately resolves the evolution of the intra- and extra-cellular potentials, gating variables and ion concentrations during the excitation, plateau and recovery phases. T3 - ZIB-Report - 05-30 KW - reaction-diffusion equations KW - cardiac Bidomain and Monodomain models KW - adaptive finite elements KW - adaptive time integration Y1 - 2005 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-8649 ER - TY - GEN A1 - Erdmann, Bodo A1 - Lang, Jens A1 - Matera, Sebastian A1 - Wilmanski, Krzysztof T1 - Adaptive Linearly Implicit Methods for Linear Poroelastic Equations N2 - Adaptive numerical methods in time and space are introduced and studied for linear poroelastic models in two and three space dimensions. We present equivalent models for linear poroelasticity and choose both the {\em displacement--pressure} and the {\em stress--pressure} formulation for our computations. Their discretizations are provided by means of linearly implicit schemes in time and linear finite elements in space. Our concept of adaptivity opens a way to a fast and reliable simulation of different loading cases defined by corresponding boundary conditions. We present some examples using our code {\sf Kardos} and show that the method works efficiently. In particular, it could be used in the simulation of some bone healing models. T3 - ZIB-Report - 06-37 KW - Poroelasticity KW - Biot's model KW - bone healing KW - adaptive finite elements KW - adaptive time integration KW - Rosenbrock methods Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9312 ER - TY - JOUR A1 - Lang, Jens A1 - Erdmann, Bodo A1 - Seebaß, Martin T1 - Impact of Nonlinear Heat Tansfer on Temperature Control in Regional Hypertermia JF - IEEE Trans. Biomed. Engrg. Y1 - 1999 U6 - https://doi.org/10.1109/10.784145 VL - 46 SP - 1129 EP - 1138 ER - TY - CHAP A1 - Birkenheuer, Georg A1 - Blunk, Dirk A1 - Breuers, Sebastian A1 - Brinkmann, Andre A1 - Fels, Gregor A1 - Gesing, Sandra A1 - Grunzke, Richard A1 - Herres-Pawlis, Sonja A1 - Kohlbacher, Oliver A1 - Krüger, Jens A1 - Lang, Ulrich A1 - Packschies, Lars A1 - Müller-Pfefferkorn, Ralph A1 - Schäfer, Patrick A1 - Schuster, Johannes A1 - Steinke, Thomas A1 - Warzecha, Klaus Dieter A1 - Wewior, Martin T1 - MoSGrid: Progress of Workflow driven Chemical Simulations T2 - Proc. of Grid Workflow Workshop 2011, Cologne, Germany Y1 - 2011 UR - http://CEUR-WS.org/Vol-826/paper02.pdf VL - 826 PB - CEUR Workshop Proceedings ER - TY - JOUR A1 - Birkenheuer, Georg A1 - Blunk, Dirk A1 - Breuers, Sebastian A1 - Brinkmann, Andre A1 - dos Santos Vieira, Ines A1 - Fels, Gregor A1 - Gesing, Sandra A1 - Grunzke, Richard A1 - Herres-Pawlis, Sonja A1 - Kohlbacher, Oliver A1 - Krüger, Jens A1 - Lang, Ulrich A1 - Packschies, Lars A1 - Müller-Pfefferkorn, Ralph A1 - Schäfer, Patrick A1 - Schmalz, Hans-Günther A1 - Steinke, Thomas A1 - Warzecha, Klaus Dieter A1 - Wewior, Martin T1 - A Molecular Simulation Grid as new tool for Computational Chemistry, Biology and Material Science JF - Journal of Cheminformatics 2011 Y1 - 2011 UR - http://www.jcheminf.com/content/3/S1/P14 U6 - https://doi.org/10.1186/1758-2946-3-S1-P14 VL - 3 IS - Suppl 1 ER - TY - JOUR A1 - Birkenheuer, Georg A1 - Blunk, Dirk A1 - Breuers, Sebastian A1 - Brinkmann, André A1 - dos Santos Vieira, Ines A1 - Fels, Gregor A1 - Gesing, Sandra A1 - Grunzke, Richard A1 - Herres-Pawlis, Sonja A1 - Kohlbacher, Oliver A1 - Krüger, Jens A1 - Lang, Ulrich A1 - Packschies, Lars A1 - Müller-Pfefferkorn, Ralph A1 - Schäfer, Patrick A1 - Steinke, Thomas A1 - Warzecha, Klaus Dieter A1 - Wewior, Martin T1 - MoSGrid: efficient data management and a standardized data exchange format for molecular simulations in a grid environment JF - Journal of Cheminformatics Y1 - 2012 UR - http://www.jcheminf.com/content/4/S1/P21 U6 - https://doi.org/10.1186/1758-2946-4-S1-P21 VL - 4 IS - Suppl 1 SP - 21 ER - TY - CHAP A1 - Erdmann, Bodo A1 - Kober, C. A1 - Lang, Jens A1 - Deuflhard, Peter A1 - Zeilhofer, J. A1 - Sader, Robert T1 - Efficient and Reliable Finite Element Methods for Simulation of the Human Mandible T2 - proceedings of 9th Workshop on The Finite Element Method in Biomedical Engineering, Biomechanics and Related Fields Y1 - 2002 CY - Ulm, Germany ER - TY - CHAP A1 - Erdmann, Bodo A1 - Lang, Jens A1 - Roitzsch, Rainer A1 - Lourenco, Maria José A1 - Rosa, S. A1 - de Castro, C.A. A1 - Albuquerque, C. ED - Kim, M. ED - Ro, S. T1 - Simulation of the Transient Heating in an Unsymmetrical Coated Hot-Strip Sensor With a Self-Adaptive Finite Element Method T2 - Proc. 5th Asian Thermophysical Properties Conference Y1 - 1998 VL - 1 SP - 91 EP - 94 CY - Seoul, South Corea ER -