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Volumn , Issue OCT, 2013, Pages

Efficient calculation of the quasi-static electrical potential on a tetrahedral mesh and its implementation in STEPS

Author keywords

3D electrical potential; Complex morphology; Efficient node ordering; Membrane potential; Multiscale simulation; Spatial stochastic simulation; Tetrahedral meshes

Indexed keywords

COMPLEX MORPHOLOGY; ELECTRICAL POTENTIAL; MEMBRANE POTENTIALS; MULTI-SCALE SIMULATION; NODE ORDERING; SPATIAL STOCHASTIC SIMULATIONS; TETRAHEDRAL MESHES;

EID: 84884916603     PISSN: 16625188     EISSN: None     Source Type: Journal    
DOI: 10.3389/fncom.2013.00129     Document Type: Article
Times cited : (8)

References (33)
  • 1
    • 84884919826 scopus 로고    scopus 로고
    • Stochastic calcium mechanisms cause dendritic calcium spike variability
    • doi: 10.1523/JNEUROSCI.1722-13.2013
    • Anwar, H., Hepburn, I., Nedelescu, H., Chen, W., and De Schutter, E. (2013). Stochastic calcium mechanisms cause dendritic calcium spike variability. J. Neurosci. 33, 15848-15867. doi: 10.1523/JNEUROSCI.1722-13.2013
    • (2013) J. Neurosci , vol.33 , pp. 15848-15867
    • Anwar, H.1    Hepburn, I.2    Nedelescu, H.3    Chen, W.4    De Schutter, E.5
  • 2
    • 80053202815 scopus 로고    scopus 로고
    • Multiscale interactions between chemical and electric signaling in LTP induction, LTP reversal and dendritic excitability
    • doi: 10.1016/j.neunet.2011.05.001
    • Bhalla, U. S. (2011). Multiscale interactions between chemical and electric signaling in LTP induction, LTP reversal and dendritic excitability. Neural Netw. 24, 943-949. doi: 10.1016/j.neunet.2011.05.001
    • (2011) Neural Netw , vol.24 , pp. 943-949
    • Bhalla, U.S.1
  • 3
    • 0026784596 scopus 로고
    • Rallpacks: A set of benchmarks for neuronal simulators
    • doi: 10.1016/0166-2236(92)90009-W
    • Bhalla, U. S., Bilitch, D. H., and Bower, J. M. (1992). Rallpacks: a set of benchmarks for neuronal simulators. Trends Neurosci. 15, 453-458. doi: 10.1016/0166-2236(92)90009-W
    • (1992) Trends Neurosci , vol.15 , pp. 453-458
    • Bhalla, U.S.1    Bilitch, D.H.2    Bower, J.M.3
  • 4
    • 84888103732 scopus 로고    scopus 로고
    • Connecting MOOSE and NeuroRD through MUSIC: Towards a communication framework for multi-scale modeling
    • doi: 10.1186/1471-2202-12-S1-P77
    • Brandi, M., Brocke, E., Talukdar, H., Hanke, M., Bhalla, U. S., Kotaleski, J., et al. (2011). Connecting MOOSE and NeuroRD through MUSIC: towards a communication framework for multi-scale modeling. BMC Neurosci. 12(Suppl 1):P77. doi: 10.1186/1471-2202-12-S1-P77.
    • (2011) BMC Neurosci , vol.12 , Issue.SUPPL. 1 , pp. 77
    • Brandi, M.1    Brocke, E.2    Talukdar, H.3    Hanke, M.4    Bhalla, U.S.5    Kotaleski, J.6
  • 5
    • 84862101988 scopus 로고    scopus 로고
    • The origin of extracellular fields and currents-EEG, ECoG, LFP and spikes
    • doi: 10.1038/nrn3241
    • Buzsáki, G., Anastassiou, C. A., and Koch, C. (2012). The origin of extracellular fields and currents-EEG, ECoG, LFP and spikes. Nat. Rev. Neurosci. 13, 407-420. doi: 10.1038/nrn3241
    • (2012) Nat. Rev. Neurosci , vol.13 , pp. 407-420
    • Buzsáki, G.1    Anastassiou, C.A.2    Koch, C.3
  • 6
    • 77956290907 scopus 로고    scopus 로고
    • Determining K+ channel activation curves from K+ channel currents often requires the Goldman-Hodgkin-Katz equation
    • doi: 10.3389/neuro.03.020.2009
    • Clay, J. R. (2009). Determining K+ channel activation curves from K+ channel currents often requires the Goldman-Hodgkin-Katz equation. Front Cell. Neurosci. 3:20. doi: 10.3389/neuro.03.020.2009.
    • (2009) Front Cell. Neurosci , vol.3 , pp. 20
    • Clay, J.R.1
  • 7
    • 0030105583 scopus 로고    scopus 로고
    • CVODE, a stiff/nonstiff ODE solver in C
    • Cohen, S. D., and Hindmarsh, A. C. (1996). CVODE, a stiff/nonstiff ODE solver in C. Comput. Phys. 10, 138-143.
    • (1996) Comput. Phys , vol.10 , pp. 138-143
    • Cohen, S.D.1    Hindmarsh, A.C.2
  • 8
    • 84855374368 scopus 로고    scopus 로고
    • Python as a federation tool for GENESIS 3.0
    • doi: 10.1371/journal.pone.0029018
    • Cornelis, H., Rodriguez, A. L., Coop, A. D., and Bower, J. M. (2012). Python as a federation tool for GENESIS 3.0. PLoS ONE 7:e29018. doi: 10.1371/journal.pone.0029018.
    • (2012) PLoS ONE , vol.7
    • Cornelis, H.1    Rodriguez, A.L.2    Coop, A.D.3    Bower, J.M.4
  • 10
    • 79960648395 scopus 로고    scopus 로고
    • Modeling intracellular calcium dynamics
    • in ed E. De Schutter (Cambridge, MA: The MIT Press)
    • De Schutter, E. (2010). "Modeling intracellular calcium dynamics, " in Computational Modeling Methods for Neuroscientists, ed E. De Schutter (Cambridge, MA: The MIT Press), 93-105.
    • (2010) Computational Modeling Methods for Neuroscientists , pp. 93-105
    • De Schutter, E.1
  • 11
    • 77953106373 scopus 로고    scopus 로고
    • Run-time interoperability between neuronal network simulators based on the MUSIC framework
    • doi: 10.1007/s12021-010-9064-z
    • Djurfeldt, M., Hjorth, J., Eppler, J. M., Dudani, N., Helias, M., Potjans, T. C., et al. (2010). Run-time interoperability between neuronal network simulators based on the MUSIC framework. Neuroinformatics 8, 43-60. doi: 10.1007/s12021-010-9064-z.
    • (2010) Neuroinformatics , vol.8 , pp. 43-60
    • Djurfeldt, M.1    Hjorth, J.2    Eppler, J.M.3    Dudani, N.4    Helias, M.5    Potjans, T.C.6
  • 12
    • 52049125960 scopus 로고    scopus 로고
    • Control of K(Ca) channels by calcium nano/microdomains
    • doi: 10.1016/j.neuron.2008.09.001
    • Fakler, B., and Adelman, J. P. (2008). Control of K(Ca) channels by calcium nano/microdomains. Neuron 59, 873-881. doi: 10.1016/j.neuron.2008.09.001
    • (2008) Neuron , vol.59 , pp. 873-881
    • Fakler, B.1    Adelman, J.P.2
  • 13
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • doi: 10.1021/j100540a008
    • Gillespie, D. T. (1977). Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81, 2340-2361. doi: 10.1021/j100540a008
    • (1977) J. Phys. Chem , vol.81 , pp. 2340-2361
    • Gillespie, D.T.1
  • 14
    • 85012319658 scopus 로고
    • Potential, impedance, and rectification in membranes
    • doi: 10.1085/jgp.27.1.37
    • Goldman, D. E. (1943). Potential, impedance, and rectification in membranes. J. Gen. Physiol. 27, 37-60. doi: 10.1085/jgp.27.1.37
    • (1943) J. Gen. Physiol , vol.27 , pp. 37-60
    • Goldman, D.E.1
  • 15
    • 84860653775 scopus 로고    scopus 로고
    • STEPS: Efficient simulation of stochastic reaction-diffusion models in realistic morphologies
    • doi: 10.1186/1752-0509-6-36
    • Hepburn, I., Chen, W., Wils, S., and De Schutter, E. (2012). STEPS: efficient simulation of stochastic reaction-diffusion models in realistic morphologies. BMC Syst. Biol. 6:36. doi: 10.1186/1752-0509-6-36
    • (2012) BMC Syst. Biol , vol.6 , pp. 36
    • Hepburn, I.1    Chen, W.2    Wils, S.3    De Schutter, E.4
  • 17
    • 0041898981 scopus 로고    scopus 로고
    • Elementary properties of ions in solution
    • in ed B. Hille (Sunderland, MA: Sinauer Associates)
    • Hille, B. (2001b). "Elementary properties of ions in solution, " in Ion Channels of Excitable Membranes, ed B. Hille (Sunderland, MA: Sinauer Associates), 309-345.
    • (2001) Ion Channels of Excitable Membranes , pp. 309-345
    • Hille, B.1
  • 18
    • 16544378541 scopus 로고    scopus 로고
    • Calcium dynamics, epithelial transport, and intercellular coupling
    • in ed B. Hille (Sunderland, MA: Sinauer Associates)
    • Hille, B. (2001c). "Calcium dynamics, epithelial transport, and intercellular coupling, " in Ion Channels of Excitable Membranes, ed B. Hille (Sunderland, MA: Sinauer Associates), 269-306.
    • (2001) Ion Channels of Excitable Membranes , pp. 269-306
    • Hille, B.1
  • 19
    • 0035080096 scopus 로고    scopus 로고
    • NEURON: A tool for neuroscientists
    • doi: 10.1177/107385840100700207
    • Hines, M. L., and Carnevale, N. T. (2001). NEURON: a tool for neuroscientists. Neuroscientist 7, 123-135. doi: 10.1177/107385840100700207.
    • (2001) Neuroscientist , vol.7 , pp. 123-135
    • Hines, M.L.1    Carnevale, N.T.2
  • 20
    • 78651026696 scopus 로고
    • The effect of sodium ions on the electrical activity of the giant axon of the squid
    • Hodgkin, A. L., and Katz, B. (1949). The effect of sodium ions on the electrical activity of the giant axon of the squid. J. Physiol. 108, 37-77.
    • (1949) J. Physiol , vol.108 , pp. 37-77
    • Hodgkin, A.L.1    Katz, B.2
  • 21
    • 0036400557 scopus 로고    scopus 로고
    • Voltage and concentration dependence of Ca(2+) permeability in recombinant glutamate receptor subtypes
    • doi: 10.1113/jphysiol.2001.012897
    • Jatzke, C., Watanabe, J., and Wollmuth, L. P. (2002). Voltage and concentration dependence of Ca(2+) permeability in recombinant glutamate receptor subtypes. J. Physiol. 538, 25-39. doi: 10.1113/jphysiol.2001.012897
    • (2002) J. Physiol , vol.538 , pp. 25-39
    • Jatzke, C.1    Watanabe, J.2    Wollmuth, L.P.3
  • 22
    • 1842588624 scopus 로고    scopus 로고
    • From Maxwell's equations to the cable equation and beyond
    • doi: 10.1016/j.pbiomolbio.2003.08.001
    • Lindsay, K. A., Rosenberg, J. R., and Tucker, G. (2004). From Maxwell's equations to the cable equation and beyond. Progr. Biophys. Mol. Biol. 85, 71-116. doi: 10.1016/j.pbiomolbio.2003.08.001.
    • (2004) Progr. Biophys. Mol. Biol , vol.85 , pp. 71-116
    • Lindsay, K.A.1    Rosenberg, J.R.2    Tucker, G.3
  • 23
    • 0031052442 scopus 로고    scopus 로고
    • Conductivity noise in transmembrane ion channels due to ion concentration fluctuations via diffusion
    • doi: 10.1016/S0006-3495(97)78764-2
    • Mak, D. O., and Webb, W. W. (1997). Conductivity noise in transmembrane ion channels due to ion concentration fluctuations via diffusion. Biophys. J. 72, 1153-1164. doi: 10.1016/S0006-3495(97)78764-2.
    • (1997) Biophys. J , vol.72 , pp. 1153-1164
    • Mak, D.O.1    Webb, W.W.2
  • 26
    • 0000208310 scopus 로고
    • Branching dendritic trees and motoneuron membrane resistivity
    • doi: 10.1016/0014-4886(59)90046-9
    • Rall, W. (1959). Branching dendritic trees and motoneuron membrane resistivity. Exp. Neurol. 1, 491-527. doi: 10.1016/0014-4886(59)90046-9
    • (1959) Exp. Neurol , vol.1 , pp. 491-527
    • Rall, W.1
  • 27
    • 77949823666 scopus 로고    scopus 로고
    • PyMOOSE: Interoperable scripting in python for MOOSE
    • doi: 10.3389/neuro.11.006.2008
    • Ray, S., and Bhalla, U. S. (2008). PyMOOSE: interoperable scripting in python for MOOSE. Front. Neuroinformatics 2:6. doi: 10.3389/neuro.11.006.2008
    • (2008) Front. Neuroinformatics , vol.2 , pp. 6
    • Ray, S.1    Bhalla, U.S.2
  • 28
    • 33751019968 scopus 로고    scopus 로고
    • Anomolous diffusion in purkinje cell dendrites caused by spines
    • doi: 10.1016/j.neuron.2006.10.025
    • Santamaria, F., Wils, S., De Schutter, E., and Augustine, G. J. (2006). Anomolous diffusion in purkinje cell dendrites caused by spines. Neuron 52, 635-648. doi: 10.1016/j.neuron.2006.10.025.
    • (2006) Neuron , vol.52 , pp. 635-648
    • Santamaria, F.1    Wils, S.2    De Schutter, E.3    Augustine, G.J.4
  • 29
    • 33845693161 scopus 로고    scopus 로고
    • Evidence for a large conductance voltage gated cationic channel in rough endoplasmic reticulum of rat hepatocytes
    • doi: 10.1016/j.abb.2006.10.012
    • Sepehri, H., Eliassi, A., Sauvé, R., Ashrafpour, M., and Saghiri, R. (2007). Evidence for a large conductance voltage gated cationic channel in rough endoplasmic reticulum of rat hepatocytes. Arch. Biochem. Biophys. 457, 35-40. doi: 10.1016/j.abb.2006.10.012
    • (2007) Arch. Biochem. Biophys , vol.457 , pp. 35-40
    • Sepehri, H.1    Eliassi, A.2    Sauvé, R.3    Ashrafpour, M.4    Saghiri, R.5
  • 30
    • 41849091113 scopus 로고    scopus 로고
    • Electrotonic signals along intracellular membranes may interconnect dendritic spines and nucleus
    • doi: 10.1371/journal.pcbi.1000036
    • Shemer, I., Brinne, B., Tegnér, J., and Grillner, S. (2008). Electrotonic signals along intracellular membranes may interconnect dendritic spines and nucleus. PLOS Comput. Biol. 4:e1000036. doi: 10.1371/journal.pcbi.1000036
    • (2008) PLOS Comput. Biol , vol.4
    • Shemer, I.1    Brinne, B.2    Tegnér, J.3    Grillner, S.4
  • 31
    • 0031849860 scopus 로고    scopus 로고
    • The intracellular potassium and chloride channels: Properties, pharmacology and function (Review)
    • doi: 10.3109/09687689809027518
    • Szewczyk, A. (1998). The intracellular potassium and chloride channels: properties, pharmacology and function (Review). Mol. Membr. Biol. 15, 49-58. doi: 10.3109/09687689809027518
    • (1998) Mol. Membr. Biol , vol.15 , pp. 49-58
    • Szewczyk, A.1
  • 32
    • 0026337757 scopus 로고
    • Single-channel, macroscopic, and gating currents from sodium channels in the squid giant axon
    • doi: 10.1016/S0006-3495(91)82185-3
    • Vandenberg, C. A., and Bezanilla, F. (1991). Single-channel, macroscopic, and gating currents from sodium channels in the squid giant axon. Biophys. J. 60, 1499-1510. doi: 10.1016/S0006-3495(91)82185-3
    • (1991) Biophys. J , vol.60 , pp. 1499-1510
    • Vandenberg, C.A.1    Bezanilla, F.2
  • 33
    • 3042832113 scopus 로고    scopus 로고
    • Fast and slow voltage-dependent dynamics of magnesium block in the NMDA receptor: The asymmetric trapping block model
    • doi: 10.1523/JNEUROSCI.1380-04.2004
    • Vargas-Caballero, M., and Robinson, H. P. C. (2004). Fast and slow voltage-dependent dynamics of magnesium block in the NMDA receptor: the asymmetric trapping block model. J. Neurosci. 24, 6171-6180. doi: 10.1523/JNEUROSCI.1380-04.2004
    • (2004) J. Neurosci , vol.24 , pp. 6171-6180
    • Vargas-Caballero, M.1    Robinson, H.P.C.2


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