References and models cited by this paper

References and models that cite this paper

Allbritton NL, Meyer T, Stryer L (1992) Range of messenger action of calcium ion and inositol 1,4,5-trisphosphate. Science 258:1812-5 [PubMed]

Andrews SS, Addy NJ, Brent R, Arkin AP (2010) Detailed simulations of cell biology with Smoldyn 2.1. PLoS Comput Biol 6:e1000705 [Journal] [PubMed]

Anwar H, Hepburn I, Nedelescu H, Chen W, De Schutter E (2013) Stochastic calcium mechanisms cause dendritic calcium spike variability. J Neurosci 33:15848-67 [Journal] [PubMed]

Arellano JI, Benavides-Piccione R, Defelipe J, Yuste R (2007) Ultrastructure of dendritic spines: correlation between synaptic and spine morphologies. Front Neurosci 1:131-43 [Journal] [PubMed]

Ascoli GA (2006) Mobilizing the base of neuroscience data: the case of neuronal morphologies. Nat Rev Neurosci 7:318-24 [Journal] [PubMed]

Bading H (2000) Transcription-dependent neuronal plasticity: The nuclear calcium hypothesis. Eur J Biochem 267:5280-3 [Journal] [PubMed]

Balls GT, Baden SB (2004) A large scale monte carlo simulator for cellular microphysiology Proceedings of the 18th International Parallel and Distributed Processing Symposium

Bastian P, Birken K, Johannsen K, Lang S, Neuss N, Rentz-reichert H (1997) UG – A flexible software toolbox for solving partial differential equations Comp.Vis.Sci. 1:27-40

Bentley JL (1975) Multidimensional binary search trees used for associative searching Communications Of ACM 18:509-517

Blackwell KT, Wallace LJ, Kim B, Oliveira RF, Koh W (2013) Modeling spatial aspects of intracellular dopamine signaling. Methods Mol Biol 964:61-75 [Journal] [PubMed]

Bower JM, Beeman D (1998) The Book Of Genesis: Exploring Realistic Neural Models With The General Neural Simulation System

Brandi M, Brocke E, Talukdar HA, Hanke M, Bhalla US, Kotaleski JH (2011) Connecting MOOSE and NeuroRD through MUSIC: towards a communication framework for multi-scale modeling BMC Neurosci. 12(Suppl 1):77

Broser PJ, Schulte R, Lang S, Roth A, Helmchen F, Waters J, Sakmann B, Wittum G (2004) Nonlinear anisotropic diffusion filtering of three-dimensional image data from two-photon microscopy. J Biomed Opt 9:1253-64 [Journal] [PubMed]

Burette AC, Lesperance T, Crum J, Martone M, Volkmann N, Ellisman MH, Weinberg RJ (2012) Electron tomographic analysis of synaptic ultrastructure. J Comp Neurol 520:2697-711 [Journal] [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 Comput Biol [Journal] [PubMed]

Carnevale NT, Hines ML (2006) The NEURON Book [Journal]

Chen X, Winters C, Azzam R, Li X, Galbraith JA, Leapman RD, Reese TS (2008) Organization of the core structure of the postsynaptic density. Proc Natl Acad Sci U S A 105:4453-8 [Journal] [PubMed]

Clapham DE (2007) Calcium signaling. Cell 131:1047-58 [Journal] [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

Djurfeldt M, Hjorth J, Eppler JM, Dudani N, Helias M, Potjans TC, Bhalla US, Diesmann M, Kotaleski JH, Ekeberg O (2010) Run-time interoperability between neuronal network simulators based on the MUSIC framework. Neuroinformatics 8:43-60 [Journal] [PubMed]

Egelman DM, Montague PR (1999) Calcium dynamics in the extracellular space of mammalian neural tissue. Biophys J 76:1856-67 [PubMed]

Eggermann E, Bucurenciu I, Goswami SP, Jonas P (2011) Nanodomain coupling between Ca²? channels and sensors of exocytosis at fast mammalian synapses. Nat Rev Neurosci 13:7-21 [Journal] [PubMed]

Eymard R, Gallouet TR, Herin R (2000) eds, North Holland, 2000, 715-1022. The finite volume method in Handbook of Numerical Analysis, Ciarlet Ph:Lions JL, ed. pp.713

Gewaltig M-O, Diesmann M (2007) NEST (Neural Simulation Tool) Scholarpedia 2:1430

Graham L (1999) Interpretations of Data and Mechanisms for Hippocampal Pyramidal Cell Models Models of Cortical Circuits Cerebral Cortex 13:19-138

Grillo A, Logashenko D, Stichel S, Andwittum G (2010) Simulation of density-driven flow in fractured porous media Advances in Water Resources 33:1494-1507

Hackbusch W (1985) Multi-Grid Methods

Hackbusch W (2003) Multi-Grid Methods and Applications Springer Computational Mathematics

Hansen S, Henning A, Naegel A, Heisig M, Wittum G, Neumann D, Kostka KH, Zbytovska J, Lehr CM, Schaefer UF (2008) In-silico model of skin penetration based on experimentally determined input parameters. Part I: experimental determination of partition and diffusion coefficients. Eur J Pharm Biopharm 68:352-67 [Journal] [PubMed]

Hayashi Y, Majewska AK (2005) Dendritic spine geometry: functional implication and regulation. Neuron 46:529-32 [Journal] [PubMed]

Helmchen F, Imoto K, Sakmann B (1996) Ca2+ buffering and action potential-evoked Ca2+ signaling in dendrites of pyramidal neurons. Biophys J 70:1069-81 [Journal] [PubMed]

Heppner I, Lampe M, Nagel A, Reiter S, Rupp M, Vogel A (2013) Software Framework ug4: Parallel Multigrid on the Hermit Supercomputer High Performance Computing in Science and Engineering :434-449

Hines ML, Carnevale NT (2003) NEURON simulation environment The Handbook of Brain Theory and Neural Networks (2nd Ed)

HODGKIN AL, HUXLEY AF (1952) A quantitative description of membrane current and its application to conduction and excitation in nerve. J Physiol 117:500-44 [Journal] [PubMed]

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. 14:181-186

Kanamori T, Kanai MI, Dairyo Y, Yasunaga K, Morikawa RK, Emoto K (2013) Compartmentalized calcium transients trigger dendrite pruning in Drosophila sensory neurons. Science 340:1475-8 [Journal] [PubMed]

Katona G, Kaszás A, Turi GF, Hájos N, Tamás G, Vizi ES, Rózsa B (2011) Roller Coaster Scanning reveals spontaneous triggering of dendritic spikes in CA1 interneurons. Proc Natl Acad Sci U S A 108:2148-53 [Journal] [PubMed]

Kerr RA, Bartol TM, Kaminsky B, Dittrich M, Chang JC, Baden SB, Sejnowski TJ, Stiles JR (2008) FAST MONTE CARLO SIMULATION METHODS FOR BIOLOGICAL REACTION-DIFFUSION SYSTEMS IN SOLUTION AND ON SURFACES. SIAM J Sci Comput 30:3126 [Journal] [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 79:275-84 [PubMed]

Korkotian E, Segal M (1999) Release of calcium from stores alters the morphology of dendritic spines in cultured hippocampal neurons. Proc Natl Acad Sci U S A 96:12068-72 [PubMed]

Lee DT (1997) Worst-Case Analysis for Region and Partial Region Searches in Multidimensional Binary Search Trees and Balanced Quad Trees Acta Inf 9:23-29

Maravall M, Mainen ZF, Sabatini BL, Svoboda K (2000) Estimating intracellular calcium concentrations and buffering without wavelength ratioing. Biophys J 78:2655-67 [Journal] [PubMed]

McDougal RA, Hines ML, Lytton WW (2013) Water-tight membranes from neuronal morphology files. J Neurosci Methods 220:167-78 [Journal] [PubMed]

McDougal RA, Hines ML, Lytton WW (2013) Reaction-diffusion in the NEURON simulator. Front Neuroinform 7:28 [Journal] [PubMed]

Migliore M, Morse TM, Davison AP, Marenco L, Shepherd GM, Hines ML (2003) ModelDB: making models publicly accessible to support computational neuroscience. Neuroinformatics 1:135-9 [Journal] [PubMed]

Milner B, Squire LR, Kandel ER (1998) Cognitive neuroscience and the study of memory. Neuron 20:445-68 [PubMed]

Mount D, Arya S (2012) ANN Library

Muha I, Grillo A, Heisig M, Schonberg M, Linke B, Wittum G (2012) Mathematical modeling of process liquid flow and acetoclastic methanogenesis under mesophilic conditions in a two-phase biogas reactor. Bioresour Technol 106:1-9

Muha I, Nagel A, Stichel S, Grillo A, Heisig M, Wittum G (2011) Effective diffusivity in membranes with tetrakaidekahedral cells and implications for the permeability of human stratum corneum. J. Memb. Sci. 368:18-25

Muller D, Nikonenko I, Jourdain P, Alberi S (2002) LTP, memory and structural plasticity. Curr Mol Med 2:605-11 [PubMed]

Murase S, Schuman EM (1999) The role of cell adhesion molecules in synaptic plasticity and memory. Curr Opin Cell Biol 11:549-53 [PubMed]

Naegel A, Hansen S, Neumann D, Lehr CM, Schaefer UF, Wittum G, Heisig M (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. Eur J Pharm Biopharm 68:368-79 [Journal] [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. Eur J Pharm Biopharm 72:332-8 [Journal] [PubMed]

Nägerl UV, Novo D, Mody I, Vergara JL (2000) Binding kinetics of calbindin-D(28k) determined by flash photolysis of caged Ca(2+) Biophys J 79:3009-18 [Journal] [PubMed]

Oliveira RF, Terrin A, Di Benedetto G, Cannon RC, Koh W, Kim M, Zaccolo M, Blackwell KT (2010) The role of type 4 phosphodiesterases in generating microdomains of cAMP: large scale stochastic simulations. PLoS One 5:e11725 [Journal] [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. J Comp Neurol 519:1338-54 [Journal] [PubMed]

Pumplin DW, Reese TS, Llinás R (1981) Are the presynaptic membrane particles the calcium channels? Proc Natl Acad Sci U S A 78:7210-3 [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. J Biomed Opt 13:014009 [Journal] [PubMed]

Ray S, Bhalla US (2008) PyMOOSE: Interoperable Scripting in Python for MOOSE. Front Neuroinform 2:6 [Journal] [PubMed]

Resasco DC, Gao F, Morgan F, Novak IL, Schaff JC, Slepchenko BM (2013) Virtual Cell: computational tools for modeling in cell biology. Wiley Interdiscip Rev Syst Biol Med 4:129-40

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 75:856-880

Silver RA, Lamb AG, Bolsover SR (1990) Calcium hotspots caused by L-channel clustering promote morphological changes in neuronal growth cones. Nature 343:751-4 [Journal] [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. J Neurosci 17:190-203 [PubMed]

Tada T, Sheng M (2006) Molecular mechanisms of dendritic spine morphogenesis. Curr Opin Neurobiol 16:95-101 [Journal] [PubMed]

Tai CY, Kim SA, Schuman EM (2008) Cadherins and synaptic plasticity. Curr Opin Cell Biol 20:567-75 [Journal] [PubMed]

Takahashi A, Camacho P, Lechleiter JD, Herman B (1999) Measurement of intracellular calcium. Physiol Rev 79:1089-125 [Journal] [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. Curr Opin Neurobiol 14:297-304 [Journal] [PubMed]

Vogel A,Reiter S,Rupp M,Nägel A,Wittum G (2013) UG 4: a novel flexible software system for simulating PDE based models on high performance computers Computing and Visualization in Science 16(4):165-179 [Journal]

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 67:367

West AE, Griffith EC, Greenberg ME (2002) Regulation of transcription factors by neuronal activity. Nat Rev Neurosci 3:921-31 [Journal] [PubMed]

Wikipedia (2012) K-dtree Wikipedia,The Free Encyclopedia

Wils S, De Schutter E (2009) STEPS: Modeling and Simulating Complex Reaction-Diffusion Systems with Python. Front Neuroinform 3:15 [Journal] [PubMed]

Wittmann M, Queisser G, Eder A, Wiegert JS, Bengtson CP, Hellwig A, Wittum G, Bading H (2009) Synaptic activity induces dramatic changes in the geometry of the cell nucleus: interplay between nuclear structure, histone H3 phosphorylation, and nuclear calcium signaling. J Neurosci 29:14687-700 [Journal] [PubMed]

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 11:137-48 [Journal] [PubMed]

Xylouris K (2013) Generalized cable equation for signal processing in neurons PhD Thesis

Xylouris K, Queisser G, Wittum G (2007) A Three-Dimensional Mathematical Model of Active Signal Processing in Axons Comp. Vis. Sci. 13:409-418

Mörschel K, Breit M, Queisser G (2017) Generating Neuron Geometries for Detailed Three-Dimensional Simulations Using AnaMorph. Neuroinformatics 15:247-269 [Journal] [PubMed]