@article{WeberFischerDamerauetal.2020, author = {Weber, Marie-Christin and Fischer, Lisa and Damerau, Alexandra and Ponomarev, Igor and Pfeiffenberger, Moritz and Gaber, Timo and G{\"o}tschel, Sebastian and Lang, Jens and R{\"o}blitz, Susanna and Buttgereit, Frank and Ehrig, Rainald and Lang, Annemarie}, title = {Macroscale mesenchymal condensation to study cytokine-driven cellular and matrix-related changes during cartilage degradation}, volume = {12}, journal = {Biofabrication}, number = {4}, doi = {10.1088/1758-5090/aba08f}, year = {2020}, abstract = {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.}, language = {en} } @article{WeberFischerDamerauetal.2019, author = {Weber, Marie-Christin and Fischer, Lisa and Damerau, Alexandra and Ponomarev, Igor and Pfeiffenberger, Moritz and Gaber, Timo and G{\"o}tschel, Sebastian and Lang, Jens and R{\"o}blitz, Susanna and Buttgereit, Frank and Ehrig, Rainald and Lang, Annemarie}, title = {In vitro and in silico modeling of cellular and matrix-related changes during the early phase of osteoarthritis}, journal = {BioRxiv}, doi = {10.1101/725317}, year = {2019}, abstract = {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.}, language = {en} } @misc{FranzoneDeuflhardErdmannetal.2005, author = {Franzone, Piero Colli and Deuflhard, Peter and Erdmann, Bodo and Lang, Jens and Pavarino, Luca Franco}, title = {Adaptivity in Space and Time for Reaction-Diffusion Systems in Electrocardiology}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-8649}, number = {05-30}, year = {2005}, abstract = {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.}, language = {en} } @misc{ErdmannLangMateraetal.2006, author = {Erdmann, Bodo and Lang, Jens and Matera, Sebastian and Wilmanski, Krzysztof}, title = {Adaptive Linearly Implicit Methods for Linear Poroelastic Equations}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-9312}, number = {06-37}, year = {2006}, abstract = {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.}, language = {en} } @article{LangErdmannSeebass1999, author = {Lang, Jens and Erdmann, Bodo and Seebaß, Martin}, title = {Impact of Nonlinear Heat Tansfer on Temperature Control in Regional Hypertermia}, volume = {46}, journal = {IEEE Trans. Biomed. Engrg.}, doi = {10.1109/10.784145}, pages = {1129 -- 1138}, year = {1999}, language = {en} } @inproceedings{BirkenheuerBlunkBreuersetal.2011, author = {Birkenheuer, Georg and Blunk, Dirk and Breuers, Sebastian and Brinkmann, Andre and Fels, Gregor and Gesing, Sandra and Grunzke, Richard and Herres-Pawlis, Sonja and Kohlbacher, Oliver and Kr{\"u}ger, Jens and Lang, Ulrich and Packschies, Lars and M{\"u}ller-Pfefferkorn, Ralph and Sch{\"a}fer, Patrick and Schuster, Johannes and Steinke, Thomas and Warzecha, Klaus Dieter and Wewior, Martin}, title = {MoSGrid: Progress of Workflow driven Chemical Simulations}, volume = {826}, booktitle = {Proc. of Grid Workflow Workshop 2011, Cologne, Germany}, publisher = {CEUR Workshop Proceedings}, year = {2011}, language = {en} } @article{BirkenheuerBlunkBreuersetal.2011, author = {Birkenheuer, Georg and Blunk, Dirk and Breuers, Sebastian and Brinkmann, Andre and dos Santos Vieira, Ines and Fels, Gregor and Gesing, Sandra and Grunzke, Richard and Herres-Pawlis, Sonja and Kohlbacher, Oliver and Kr{\"u}ger, Jens and Lang, Ulrich and Packschies, Lars and M{\"u}ller-Pfefferkorn, Ralph and Sch{\"a}fer, Patrick and Schmalz, Hans-G{\"u}nther and Steinke, Thomas and Warzecha, Klaus Dieter and Wewior, Martin}, title = {A Molecular Simulation Grid as new tool for Computational Chemistry, Biology and Material Science}, volume = {3}, journal = {Journal of Cheminformatics 2011}, number = {Suppl 1}, doi = {10.1186/1758-2946-3-S1-P14}, year = {2011}, language = {en} } @article{BirkenheuerBlunkBreuersetal.2012, author = {Birkenheuer, Georg and Blunk, Dirk and Breuers, Sebastian and Brinkmann, Andr{\´e} and dos Santos Vieira, Ines and Fels, Gregor and Gesing, Sandra and Grunzke, Richard and Herres-Pawlis, Sonja and Kohlbacher, Oliver and Kr{\"u}ger, Jens and Lang, Ulrich and Packschies, Lars and M{\"u}ller-Pfefferkorn, Ralph and Sch{\"a}fer, Patrick and Steinke, Thomas and Warzecha, Klaus Dieter and Wewior, Martin}, title = {MoSGrid: efficient data management and a standardized data exchange format for molecular simulations in a grid environment}, volume = {4}, journal = {Journal of Cheminformatics}, number = {Suppl 1}, doi = {10.1186/1758-2946-4-S1-P21}, pages = {21}, year = {2012}, language = {en} } @inproceedings{ErdmannKoberLangetal.2002, author = {Erdmann, Bodo and Kober, C. and Lang, Jens and Deuflhard, Peter and Zeilhofer, J. and Sader, Robert}, title = {Efficient and Reliable Finite Element Methods for Simulation of the Human Mandible}, booktitle = {proceedings of 9th Workshop on The Finite Element Method in Biomedical Engineering, Biomechanics and Related Fields}, address = {Ulm, Germany}, year = {2002}, language = {en} } @inproceedings{ErdmannLangRoitzschetal.1998, author = {Erdmann, Bodo and Lang, Jens and Roitzsch, Rainer and Lourenco, Maria Jos{\´e} and Rosa, S. and de Castro, C.A. and Albuquerque, C.}, title = {Simulation of the Transient Heating in an Unsymmetrical Coated Hot-Strip Sensor With a Self-Adaptive Finite Element Method}, volume = {1}, booktitle = {Proc. 5th Asian Thermophysical Properties Conference}, editor = {Kim, M. and Ro, S.}, address = {Seoul, South Corea}, pages = {91 -- 94}, year = {1998}, language = {en} } @inproceedings{ErdmannLangSeebass1997, author = {Erdmann, Bodo and Lang, Jens and Seebass, Martin}, title = {Adaptive Solutions of Nonlinear Parabolic Equations with Application to Hyperthermia Treatments}, booktitle = {CHT'97}, editor = {de Vahl Davis, G. and Leonardi, E.}, address = {Cesme, Turkey}, pages = {103 -- 110}, year = {1997}, language = {en} } @inproceedings{ErdmannLangSeebass1998, author = {Erdmann, Bodo and Lang, Jens and Seebass, Martin}, title = {Optimization of Temperature Distributions for Regional Hyperthermia based on a Nonlinear Heat Transfer Model}, volume = {858}, booktitle = {Biotransport}, editor = {Diller, K.}, pages = {36 -- 46}, year = {1998}, language = {en} } @article{ErdmannLangSeebass1999, author = {Erdmann, Bodo and Lang, Jens and Seebass, Martin}, title = {The Impact of a Nonlinear Heat Transfer Model for Temperature Control in Regional Hyperthermia}, volume = {49}, journal = {IEEE Transactions on Biomedical Engineering}, number = {9}, pages = {1129 -- 1138}, year = {1999}, language = {en} } @inproceedings{LangErdmannRoitzsch1997, author = {Lang, Jens and Erdmann, Bodo and Roitzsch, Rainer}, title = {Adaptive Time-Space Discretization for Combustion Problems}, booktitle = {15th IMACS World Congress on Scientific Computation, Modelling and Applied Mathematics, Vol. 2, Numerical Mathematics}, editor = {Sydow, Achim}, publisher = {Wissenschaft und Technik Verlag, Berlin}, pages = {49 -- 155}, year = {1997}, language = {en} } @inproceedings{LangErdmannRoitzsch1997, author = {Lang, Jens and Erdmann, Bodo and Roitzsch, Rainer}, title = {Three-Dimensional Fully Adaptive Solution of Thermo-Diffusive Flame Propagation Problems}, booktitle = {Numerical Methods in Thermal Problems}, editor = {Lewis, R.}, publisher = {Pineridge Press, Swansea, UK}, pages = {857 -- 862}, year = {1997}, language = {en} } @incollection{LangErdmannKoberetal.2003, author = {Lang, Jens and Erdmann, Bodo and Kober, Cornelia and Deuflhard, Peter and Sader, Robert and Zeilhofer, Hans-Florian}, title = {Effiziente und zuverl{\"a}ssige Finite-Elemente-Methoden zur Simulation des menschlichen Unterkiefers}, volume = {1}, booktitle = {Berichte des IZWR - Interdisziplin{\"a}res Zentrum f{\"u}r Wissenschaftliches Rechnen}, editor = {Alt, Walter and Hermann, Martin}, publisher = {Universit{\"a}t Jena}, address = {Germany}, pages = {49 -- 57}, year = {2003}, language = {en} } @inproceedings{KoberErdmannLangetal.2004, author = {Kober, C. and Erdmann, Bodo and Lang, Jens and Sader, Robert and Zeilhofer, Hans-Florian}, title = {Sensitivity of the Temporomandibular Joint Capsule for the Structural Behaviour of the Human Mandible}, volume = {49-2}, booktitle = {Proc. BMT 2004}, address = {Ilmenau, Deutschland}, pages = {372 -- 373}, year = {2004}, language = {en} } @inproceedings{KoberErdmannLangetal.2004, author = {Kober, C. and Erdmann, Bodo and Lang, Jens and Sader, Robert and Zeilhofer, Hans-Florian}, title = {Adaptive Finite Element Simulation of the Human Mandible Using a New Physiological Model of the Masticatory Muscles}, volume = {4}, booktitle = {Proc. of 75th Annual Meeting of the GAMM}, number = {1}, pages = {332 -- 333}, year = {2004}, language = {en} } @inproceedings{RoitzschLangErdmann1998, author = {Roitzsch, Rainer and Lang, Jens and Erdmann, Bodo}, title = {The Benefits of Modularization}, booktitle = {Proc. 14th GAMM-Seminar Kiel on 'Concepts of Numerical Software}, publisher = {did not appear}, year = {1998}, language = {en} } @misc{LangErdmannRoitzsch1997, author = {Lang, Jens and Erdmann, Bodo and Roitzsch, Rainer}, title = {Three-Dimensional Fully Adaptive Solution of Thermo-Diffusive Flame Propagation Problems}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-2879}, number = {SC-97-18}, year = {1997}, abstract = {In this paper we present a self--adaptive finite element method to solve flame propagation problems in 3D. An implicit time integrator of Rosenbrock type is coupled with a multilevel approach in space. The proposed method is applied to an unsteady thermo--diffusive combustion model to demonstrate its potential for the solution of complicated problems.}, language = {en} }