Allbritton NL, Meyer T, Stryer L. (1992). Range of messenger action of calcium ion and inositol 1,4,5-trisphosphate. Science (New York, N.Y.). 258 [PubMed]
Andrews SS, Addy NJ, Brent R, Arkin AP. (2010). Detailed simulations of cell biology with Smoldyn 2.1. PLoS computational biology. 6 [PubMed]
Anwar H, Hepburn I, Nedelescu H, Chen W, De Schutter E. (2013). Stochastic calcium mechanisms cause dendritic calcium spike variability. The Journal of neuroscience : the official journal of the Society for Neuroscience. 33 [PubMed]
Arellano JI, Benavides-Piccione R, Defelipe J, Yuste R. (2007). Ultrastructure of dendritic spines: correlation between synaptic and spine morphologies. Frontiers in neuroscience. 1 [PubMed]
Arya S, Mount D. (2012). ANN Library.
Ascoli GA. (2006). Mobilizing the base of neuroscience data: the case of neuronal morphologies. Nature reviews. Neuroscience. 7 [PubMed]
Baden SB, Balls GT. (2004). A large scale monte carlo simulator for cellular microphysiology Proceedings of the 18th International Parallel and Distributed Processing Symposium.
Bading H. (2000). Transcription-dependent neuronal plasticity: The nuclear calcium hypothesis. European journal of biochemistry. 267 [PubMed]
Bentley JL. (1975). Multidimensional binary search trees used for associative searching Communications Of ACM. 18
Bhalla US et al. (2011). Connecting MOOSE and NeuroRD through MUSIC: towards a communication framework for multi-scale modeling BMC Neurosci.. 12(Suppl 1)
Blackwell KT, Wallace LJ, Kim B, Oliveira RF, Koh W. (2013). Modeling spatial aspects of intracellular dopamine signaling. Methods in molecular biology (Clifton, N.J.). 964 [PubMed]
Bower JM, Beeman D. (1998). The Book Of Genesis: Exploring Realistic Neural Models With The General Neural Simulation System.
Broser PJ et al. (2004). Nonlinear anisotropic diffusion filtering of three-dimensional image data from two-photon microscopy. Journal of biomedical optics. 9 [PubMed]
Burette AC et al. (2012). Electron tomographic analysis of synaptic ultrastructure. The Journal of comparative neurology. 520 [PubMed]
Cannon RC, O'Donnell C, Nolan MF. (2010). Stochastic ion channel gating in dendritic neurons: morphology dependence and probabilistic synaptic activation of dendritic spikes. PLoS computational biology. 6 [PubMed]
Chen X et al. (2008). Organization of the core structure of the postsynaptic density. Proceedings of the National Academy of Sciences of the United States of America. 105 [PubMed]
Clapham DE. (2007). Calcium signaling. Cell. 131 [PubMed]
Cormen TH, Leiserson CE, Andrivest RL. (2011). Introduction to Algorithms.
Cormen TH, Leiserson CE, Rivest RR. (1990). Introduction to algorithms..
Deuflhard P, Andweiser M. (2011). Adaptive Lösung partieller Differentialgleichungen Numerische Mathematik 3.
Diesmann M, Gewaltig M-O. (2007). NEST (Neural Simulation Tool) Scholarpedia. 2
Djurfeldt M et al. (2010). Run-time interoperability between neuronal network simulators based on the MUSIC framework. Neuroinformatics. 8 [PubMed]
Egelman DM, Montague PR. (1999). Calcium dynamics in the extracellular space of mammalian neural tissue. Biophysical journal. 76 [PubMed]
Eggermann E, Bucurenciu I, Goswami SP, Jonas P. (2011). Nanodomain coupling between Ca²? channels and sensors of exocytosis at fast mammalian synapses. Nature reviews. Neuroscience. 13 [PubMed]
Eymard R, Gallouet TR, Herin R. (2000). eds, North Holland, 2000, 715-1022. The finite volume method in Handbook of Numerical Analysis. 7
Gao F et al. (2013). Virtual Cell: computational tools for modeling in cell biology. Wiley Interdiscip Rev Syst Biol Med. 4
Graham L. (1999). Interpretations of Data and Mechanisms for Hippocampal Pyramidal Cell Models Models of Cortical Circuits Cerebral Cortex. 13
Grillo A, Logashenko D, Stichel S, Andwittum G. (2010). Simulation of density-driven flow in fractured porous media Advances in Water Resources. 33
HODGKIN AL, HUXLEY AF. (1952). A quantitative description of membrane current and its application to conduction and excitation in nerve. The Journal of physiology. 117 [PubMed]
Hackbusch W. (1985). Multi-Grid Methods.
Hackbusch W. (2003). Multi-Grid Methods and Applications Springer Computational Mathematics.
Hansen S et al. (2008). In-silico model of skin penetration based on experimentally determined input parameters. Part I: experimental determination of partition and diffusion coefficients. European journal of pharmaceutics and biopharmaceutics : official journal of Arbeitsgemeinschaft fur Pharmazeutische Verfahrenstechnik e.V. 68 [PubMed]
Hayashi Y, Majewska AK. (2005). Dendritic spine geometry: functional implication and regulation. Neuron. 46 [PubMed]
Helmchen F, Imoto K, Sakmann B. (1996). Ca2+ buffering and action potential-evoked Ca2+ signaling in dendrites of pyramidal neurons. Biophysical journal. 70 [PubMed]
Hines ML, Carnevale NT. (2003). NEURON simulation environment The Handbook of Brain Theory and Neural Networks (2nd Ed).
Hines ML, Carnevale NT. (2006). The NEURON Book.
Ierusalimschy R, Celes W, Defigueiredo LH. (2013). Lua: The Programming Language.
Jungblut D, Queisser G, Andwittum G. (2011). Inertia Based Filtering of High Resolution Images Using a GPU Cluster Comp. Vis. Sci.. 14
Kanamori T et al. (2013). Compartmentalized calcium transients trigger dendrite pruning in Drosophila sensory neurons. Science (New York, N.Y.). 340 [PubMed]
Katona G et al. (2011). Roller Coaster Scanning reveals spontaneous triggering of dendritic spikes in CA1 interneurons. Proceedings of the National Academy of Sciences of the United States of America. 108 [PubMed]
Kerr RA et al. (2008). FAST MONTE CARLO SIMULATION METHODS FOR BIOLOGICAL REACTION-DIFFUSION SYSTEMS IN SOLUTION AND ON SURFACES. SIAM journal on scientific computing : a publication of the Society for Industrial and Applied Mathematics. 30 [PubMed]
Kits KS, Dreijer AM, Lodder JC, Borgdorff A, Wadman WJ. (1997). High intracellular calcium levels during and after electrical discharges in molluscan peptidergic neurons. Neuroscience. 79 [PubMed]
Korkotian E, Segal M. (1999). Release of calcium from stores alters the morphology of dendritic spines in cultured hippocampal neurons. Proceedings of the National Academy of Sciences of the United States of America. 96 [PubMed]
Lang S et al. (1997). UG – A flexible software toolbox for solving partial differential equations Comp.Vis.Sci.. 1
Lee DT. (1997). Worst-Case Analysis for Region and Partial Region Searches in Multidimensional Binary Search Trees and Balanced Quad Trees Acta Inf. 9
Maravall M, Mainen ZF, Sabatini BL, Svoboda K. (2000). Estimating intracellular calcium concentrations and buffering without wavelength ratioing. Biophysical journal. 78 [PubMed]
McDougal RA, Hines ML, Lytton WW. (2013). Water-tight membranes from neuronal morphology files. Journal of neuroscience methods. 220 [PubMed]
McDougal RA, Hines ML, Lytton WW. (2013). Reaction-diffusion in the NEURON simulator. Frontiers in neuroinformatics. 7 [PubMed]
Migliore M et al. (2003). ModelDB: making models publicly accessible to support computational neuroscience. Neuroinformatics. 1 [PubMed]
Milner B, Squire LR, Kandel ER. (1998). Cognitive neuroscience and the study of memory. Neuron. 20 [PubMed]
Muller D, Nikonenko I, Jourdain P, Alberi S. (2002). LTP, memory and structural plasticity. Current molecular medicine. 2 [PubMed]
Murase S, Schuman EM. (1999). The role of cell adhesion molecules in synaptic plasticity and memory. Current opinion in cell biology. 11 [PubMed]
Naegel A et al. (2008). In-silico model of skin penetration based on experimentally determined input parameters. Part II: mathematical modelling of in-vitro diffusion experiments. Identification of critical input parameters. European journal of pharmaceutics and biopharmaceutics : official journal of Arbeitsgemeinschaft fur Pharmazeutische Verfahrenstechnik e.V. 68 [PubMed]
Naegel A, Heisig M, Wittum G. (2009). A comparison of two- and three-dimensional models for the simulation of the permeability of human stratum corneum. European journal of pharmaceutics and biopharmaceutics : official journal of Arbeitsgemeinschaft fur Pharmazeutische Verfahrenstechnik e.V. 72 [PubMed]
Nägerl UV, Novo D, Mody I, Vergara JL. (2000). Binding kinetics of calbindin-D(28k) determined by flash photolysis of caged Ca(2+) Biophysical journal. 79 [PubMed]
Oliveira RF et al. (2010). The role of type 4 phosphodiesterases in generating microdomains of cAMP: large scale stochastic simulations. PloS one. 5 [PubMed]
Popov VI, Kleschevnikov AM, Klimenko OA, Stewart MG, Belichenko PV. (2011). Three-dimensional synaptic ultrastructure in the dentate gyrus and hippocampal area CA3 in the Ts65Dn mouse model of Down syndrome. The Journal of comparative neurology. 519 [PubMed]
Pumplin DW, Reese TS, Llinás R. (1981). Are the presynaptic membrane particles the calcium channels? Proceedings of the National Academy of Sciences of the United States of America. 78 [PubMed]
Queisser G, Wittmann M, Bading H, Wittum G. (2008). Filtering, reconstruction, and measurement of the geometry of nuclei from hippocampal neurons based on confocal microscopy data. Journal of biomedical optics. 13 [PubMed]
Ray S, Bhalla US. (2008). PyMOOSE: Interoperable Scripting in Python for MOOSE. Frontiers in neuroinformatics. 2 [PubMed]
Reiter S et al. (2013). Software Framework ug4: Parallel Multigrid on the Hermit Supercomputer High Performance Computing in Science and Engineering.
Shewchuk JR. (2002). What is a good linear finite element? interpolation, conditioning, anisotropy, and quality measures Proceedings of 11th Intnl Meshing Roundatable University of California at Berkeley.
Si H. (2009). TetGen: a quality tetrahedral mesh generator and three-dimensional delaunay triangulator. Aqualitytetrahedralmeshgeneratorandthree-dimensional Delaunaytriangulator Int J Num Methodseng. 75
Silver RA, Lamb AG, Bolsover SR. (1990). Calcium hotspots caused by L-channel clustering promote morphological changes in neuronal growth cones. Nature. 343 [PubMed]
Spacek J, Harris KM. (1997). Three-dimensional organization of smooth endoplasmic reticulum in hippocampal CA1 dendrites and dendritic spines of the immature and mature rat. The Journal of neuroscience : the official journal of the Society for Neuroscience. 17 [PubMed]
Tada T, Sheng M. (2006). Molecular mechanisms of dendritic spine morphogenesis. Current opinion in neurobiology. 16 [PubMed]
Tai CY, Kim SA, Schuman EM. (2008). Cadherins and synaptic plasticity. Current opinion in cell biology. 20 [PubMed]
Takahashi A, Camacho P, Lechleiter JD, Herman B. (1999). Measurement of intracellular calcium. Physiological reviews. 79 [PubMed]
Thompson JF, Soni BK, Weatherill NP. (2012). Handbook of Grid Generation.
Van Aelst L, Cline HT. (2004). Rho GTPases and activity-dependent dendrite development. Current opinion in neurobiology. 14 [PubMed]
Wald I, Hvran V. (2006). On building fast kd-trees for ray tracing, and on doing that in o(NlogN) IEEE Symposium on Interactive Ray Tracing Amsterdam.
Weinan E, Engquist B, Huang Z. (2003). Heterogeneous multiscale method: A general methodology for multiscale modeling Phys. Rev. B. 67
West AE, Griffith EC, Greenberg ME. (2002). Regulation of transcription factors by neuronal activity. Nature reviews. Neuroscience. 3 [PubMed]
Wikipedi Wikipedia. (2012). K-dtree Wikipedia,The Free Encyclopedia.
Wils S, De Schutter E. (2009). STEPS: Modeling and Simulating Complex Reaction-Diffusion Systems with Python. Frontiers in neuroinformatics. 3 [PubMed]
Wittmann M et al. (2009). Synaptic activity induces dramatic changes in the geometry of the cell nucleus: interplay between nuclear structure, histone H3 phosphorylation, and nuclear calcium signaling. The Journal of neuroscience : the official journal of the Society for Neuroscience. 29 [PubMed]
Wittum G et al. (2012). Mathematical modeling of process liquid flow and acetoclastic methanogenesis under mesophilic conditions in a two-phase biogas reactor. Bioresour Technol. 106
Wittum G et al. (2011). Effective diffusivity in membranes with tetrakaidekahedral cells and implications for the permeability of human stratum corneum. J. Memb. Sci.. 368
Wittum G, Queisser G, Xylouris K. (2007). A Three-Dimensional Mathematical Model of Active Signal Processing in Axons Comp. Vis. Sci.. 13
Wittum G, Reiter S, Rupp M, Vogel A, Nägel A. (2013). UG 4: a novel flexible software system for simulating PDE based models on high performance computers Computing and Visualization in Science. 16(4)
Wolf S, Grein S, Queisser G. (2013). Employing NeuGen 2.0 to automatically generate realistic morphologies of hippocampal neurons and neural networks in 3D. Neuroinformatics. 11 [PubMed]
Xylouris K. (2013). Generalized cable equation for signal processing in neurons PhD Thesis.
Mörschel K, Breit M, Queisser G. (2017). Generating Neuron Geometries for Detailed Three-Dimensional Simulations Using AnaMorph. Neuroinformatics. 15 [PubMed]