NJIT_CompNeuro

Analytical and Computational Neuroscience

Math430 and Math635 - Fall 2012

Recommended Reading and Matlab / XPP Codes

Matlab Tutorial (Kohitij Kar)

Matlab Tutorial
Solutions

ODE Examples - Matlab (Jon Guez)

ODEexamples

Introduction to the Neurosciences:

J&W: Chapter 1

Passive Membrane Properties:
J&W: Chapter 2
Membrane Potential. Elmslie, K. S. (2001) Encyclopedia of Life Sciences. John Wiley & Sons, Elmslie, K. S. (2001) Encyclopedia of Life Sciences. John Wiley & Sons, http://www.mrw.interscience.wiley.com/emrw/9780470015902/els/article/a0000182

ODE Examples - Matlab (Jon)

ODEexamples

Introduction to XPP

Jessica's notes on WinPP installation
Bard Ermentrout's XPP website
Bard Ermentrout's XPP tutorial
Passive membrane potential .ode files:

passivemembrane_01
passivemembrane_02
passivemembrane_03
passivemembrane_04
passivemembrane_05,

Dynamics of the passive membrane

.ode files:

passivemembrane_06

Integrate-and-Fire Neurons

D&A: Chapter 5.1-5.4

.ode files:

integrateandfire_01

FitzHugh-Nagumo model: stability analysis

.m file:

TauDelta_Xavier

The Hodgkin-Huxley model

Hodgkin, A. L. and Huxley, A. F. (1952). A quantitative description of membrane current and its application to conduction and excitation in nerve - The Journal of Physioloty, 117, 500-544
Action Potential: Ionic Mechanisms. Elmslie, K. S. (2001) Encyclopedia of Life Sciences. John Wiley & Sons, Elmslie, K. S. (2001) Encyclopedia of Life Sciences. John Wiley & Sons, http://www.mrw.interscience.wiley.com/emrw/9780470015902/els/article/a0000002
J&W: Chapter 6
I: Chapter 2

The cable equation

Passive Propagation of Electrical Signals. Elmslie, K. S. (2005) Encyclopedia of Life Sciences. John Wiley & Sons, Elmslie, K. S. (2005) Encyclopedia of Life Sciences. John Wiley & Sons, http://www.mrw.interscience.wiley.com/emrw/9780470015902/els/article/a0000197
D&A: Chapter 6
K: Chapter 2

Reduced models

Phase Space Analysis of Neuronal Excitability - J. Rinzel & B. Ermentrout, Methods in Neuronal Modeling (C. Koch and I. Segeve, Eds.)

One-dimensional neural systems

I: Chapter 3

Two-dimensional neural systems

I: Chapter 4

Subthreshold oscillations

HGR Talk 1
HGR Talk 2

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Papers for Student Presentations

C. Acker, J. A. White & N. Kopell (2003), 'Synchronization of strongly coupled excitatory neurons: relating network behavior to biophysics', J. Comp. Neurosci., 15:71-90.
D. Terman, N. Kopell & A. Bose (1998), 'Dynamics of two mutually coupled slow inhibitory neurons', Physica D 117:241-275.
X.-J. Wang & G. Buzsaki (1996), 'Gamma oscillation by synaptic inhibition in a hippocampal interneuronal network model', J. Neurosci. 16:6402-6413.
R. J. Butera, J. Rinzel & J. C. Smith (1999), 'Models of respiratory rhythm generation in the pre-Botzinger comples. I. Bursting pacemaker neurons', J. Neurophysiol. 82:382-397.
N. Kopell & D. Somers (1995), 'Anti-phase solutions in relaxation oscillators coupled through excitatory interactions', J. Math. Bio. 33:261-280 D. Terman, N. Kopell & A. Bose (1998), 'Dynamics of two mutually coupled slow inhibitory neurons', Physica D 117:241-275.
S. Schreiber, I. Erchova, U. Heinemann & A. V. M. Herz (2004), 'Subthreshold resonance explains the frequency-dependent integration of periodic as well as random stimuli in the entorhinal cortex', J. Neurophysiol., 92:408-415.
S. Schreiber, J.-M. Fellous, P. Tiesinga & T. Sejnowski (2003). 'Influence of ionic conductances on spike timing reliability of cortical neurons for suprathreshold rhythmic inputs'. J. Neurophysiol., 91:194-205.
D. Golomb & Y. Amitai (1997), 'Propagating neuronal discharges in neocortical slices: computational and experimental study', J. Neurophysiol., 78:1199-1211.

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Books

J&W : "Foundations of Cellular Neurophysiology", by Daniel Johnston and Samuel M.-S. Wu. The MIT Press, 1995. ISBN 0-262-10053-3.

I : "Dynamical Systems in Neuroscience: The Geometry of Excitability and Bursting", by Eugene M. Izhikevich. The MIT Press, 2007. ISBN 0-262-09043-8

K : "Biophysics of Computation - Information processing in single neurons", by Christof Koch. Oxford University Press, 1999. ISBN 0-19-510491-9.

D&A : "Theoretical Neuroscience: Computational and Mathematical Modeling of Neural Systems", by Peter Dayan and Larry F. Abbott. The MIT Press,2001. ISBN 0-262-04199-5

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Department of Mathematical Sciences(DMS).
New Jersey Institute of Technology (NJIT).

Horacio
Last modified: Thu Sep 2 10:45:36 EDT 2010