LATE NEWS

Many improvements have been made since the NeuronC simulator was first described in J. Neuroscience Methods in 1992.

Highlights

  • The simulator runs several channel types including Markov sequential-state versions of Hodgkin-Huxley Na, K, KA, Kca and Ih channels. AMPA, NMDA, cGMP, and GABA ligand-gated Markov channels.

  • Calcium T- and L-type channels, diffusion, dynamic buffering, membrane transporters, and realistic Ca currents from GHK equations.

  • Channel types contain individual data structures for unitary conductance, rate functions, temperature dependence of conductance and rates, relative permeabilities to major ions, and sensitivities to receptor ligands.

  • Synaptic and voltage-gated channel functions can implement Markov channel descriptions. Noise kinetics derived from Markov description.

  • Synaptic, channel, and photoreceptor noise can originate in independent noise generators to maintain the same noise waveshape with changes to the neural circuit.

  • Johnson (thermal) noise in membrane conductance.

  • Synaptic temporal functions can be low or high-pass. The postsynaptic function can include a Hill coefficient and a second-messenger with sign inversion and threshold nonlinearity.

  • Photoreceptors have adaptation through feedback from calcium.

  • The photoreceptor spectral sensitivity functions have been improved with second-order interpolation from sensitivity tables and turtle cone functions (default=primate). Photoreceptors can be speeded up or slowed down, and their state can be stored and recalled to save on equilibration time. Stimuli and optical blur can be generated at any scale (default=1 um) to allow very fine resolution.

  • The simulator generates realistic images of neural circuits with the use of the "povray" ray tracer (available free).

  • The simulation language includes dynamically-allocated local arrays and variables. Values can be numeric, text string, and can be scalar (single-valued) or array.

  • File open, close, and scanf, fscanf, sscanf statements.

  • Tapered cables.

  • Function that returns the minimum distance between two neural elements.

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    December, 1998 additions:

  • Dynamic calcium buffering.
  • Default unitary conductance for each channel type.
  • Temperature dependence of unitary conductance, Ca pump, Ca exchanger, Ca buffering.
  • Markov channel types for postsynaptic mechanism.
  • Multiple neurotransmitter types, affinity for postsynaptic receptors.
  • Permeabilities of channels to major ions.
  • Use of GHK current equation to define Ca currents.
  • Use of GHK voltage equation to define reversal potential for Na, K, and Ca channels.
  • Membrane voltage offset generated optionally by external Ca concentration.
  • Johnson noise with independent random noise generator for each compartment.

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    October, 1998 additions:

  • Membrane channel definition code improved to simplify adding new channel types.
  • Na type 2 channel from Vandenberg and Bezanilla, 1991.
  • AMPA, NMDA, cGMP, and GABA Markov channels.
  • Integrate-and-fire Markov channel.
  • Number of shells in Ca diffusion model can be varied.
  • Weighted neurotransmitter action for multiple ligands.

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    July, 1998 additions:

  • Set Q10 for Na channels = 2 (instead of 3 for K chans).
  • Corrected ion current in Ca-Na exchanger.
  • Modified KA kinetics to be more like Fohlmeister & Miller (1997)
  • Tapered cables.
  • Function to return 3D distance between 2 neural elements.

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    April, 1998 additions:

  • Sequential-state versions of Hodgkin-Huxley Na and K channels, KA, Kca, Ih channels.
  • Sequential-state channels can produce Markov state noise with noise kinetics set by rate functions.
  • Synaptic vesicle fluctuation noise is set by Poisson function with optional refractory period.
  • Synaptic vesicle noise can be set by Gamma function for more regularity.
  • Synaptic and Hodgkin-Huxley channels can produce 2-state Markov noise with Lorenzian rolloff frequency.
  • Synaptic temporal filters can be low-pass or high-pass with arbitrary order and time constants.
  • Postsynaptic binding of neurotransmitter can be cooperative (Hill coeff can be > 1)
  • Postsynaptic second-messenger cascade can include sign inversion and threshold nonlinearity.
  • Photoreceptor sensitivity functions include turtle cone spectral sensitivities.
  • Photoreceptor spectral sensitivity functions include second-order interpolation.
  • Simulation language contains array operators +, -, *, /, print

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    July, 1997 additions:

  • Voltage-gated gap junctions with optional rectification.
  • Photoreceptor impulse response duration can be set faster or slower.
  • State of photoreceptors can be saved and restored for fast equilibration.
  • Drag'n drop NeuronC files and commands with 'xfm' and 'tkdesk'
  • Stim file can be compressed with gzip.
  • Simulation language includes local dynamically allocated arrays.
  • Simulator includes DOS version.
  • Simulator can be run as subroutine from standard C program with access to simulator variables and arrays.

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    Jan, 1995 additions:

  • Calcium channels, compartments, and diffusion.
  • Ca-sensitive K channels.
  • Independent noise generators for individual photoreceptors and synapses.
  • Stimuli and optical blur can be set to any scale for finer resolution.
  • 3D surfaces rendered by ray-tracing with "povray".
  • Windowed trimming of neural elements.