diff --git a/readme.txt b/README.md similarity index 51% rename from readme.txt rename to README.md index 2cae418..0158a99 100644 --- a/readme.txt +++ b/README.md @@ -1,67 +1,71 @@ -This model reproduces Figure 6a and 6b and Supplementary Figure 5b of -the article - -"State and location dependence of action potential metabolic cost in -cortical pyramidal neurons". Nature Neuroscience (2012) -doi:10.1038/nn.3132 - -When the folder is compiled using the mknrndll script the simulation -can be started with "mosinit.hoc". - -The newly developed model of the axonal K+ currents (Kv1_axonal.mod) -was based on step evoked K+ currents including activation, -deactivation and inactivation protocols as well as steady state -curves. To describe the activation, eight Hodgkin-Huxley gates were -used (n^8). To describe the biphasic inactivation and recovery from -inactivation, two populations of channels with different -Hodgkin-Huxley inactivation gates were used (n^8*h1^+n^8*h2). - -To analyze the AP efficiency and the ATP usage on a subcellular level, -the Na+/K+ charge overlap, the excess Na+ influx and the ATP usage -were calculated as RANGE variables (charge.mod). - -Executing "ch()" in the terminal shell (see charge.hoc) will print -average ATP usage per cellular compartment as shown below (some of the -information is exported into text files). - -------------------------------------------------------------------------- - -The Na influx was analyzed from 517.000000 to 535.000000 ms -Required ATP molecules to pump Na ions out: -Total: 1.998503e+08 -Soma: 1.416016e+07 -Basal dendrite: 4.609883e+07 -Apical dendrite: 9.149446e+07 -Axon Initial Segment: 2.498228e+07 -Axon collaterals: 2.095502e+07 -Myelin: 7.227968e+05 -Node: 1.436733e+06 - -------------------------------------------------------------------------- -------------------------------------------------------------------------- - -Required ATP molecules to pump Na ions out per um^2: -Total: 2.818287e+03 -Soma: 6.810007e+03 -Basal dendrite: 2.531221e+03 -Apical dendrite: 2.213969e+03 -Axon Initial Segment: 5.531797e+04 -Axon collaterals: 3.932075e+03 -Myelin: 2.081271e+02 -Node: 3.517895e+04 -------------------------------------------------------------------------- -Total area (um^2): 7.091197e+04 -Soma area (um^2): 2.079316e+03 -------------------------------------------------------------------------- - -For questions please contact s.hallermann@eni-g.de or -m.kole@nin.knaw.nl - - -June 12th 2012, Stefan Hallermann - -20140226 ModelDB Administrator: To prevent collision with NEURON's -"charge" the "charge" mechanism has been changed to "charge_" with -changes in the hoc code. The charge in names of files was left -unchanged. - +This model reproduces Figure 6a and 6b and Supplementary Figure 5b of +the article + +# "State and location dependence of action potential metabolic cost in cortical pyramidal neurons". *Nature Neuroscience* (2012) +doi:10.1038/nn.3132 + +When the folder is compiled using the mknrndll script the simulation +can be started with "mosinit.hoc". + +The newly developed model of the axonal K+ currents (Kv1_axonal.mod) +was based on step evoked K+ currents including activation, +deactivation and inactivation protocols as well as steady state +curves. To describe the activation, eight Hodgkin-Huxley gates were +used (n^8). To describe the biphasic inactivation and recovery from +inactivation, two populations of channels with different +Hodgkin-Huxley inactivation gates were used (n^8*h1^+n^8*h2). + +To analyze the AP efficiency and the ATP usage on a subcellular level, +the Na+/K+ charge overlap, the excess Na+ influx and the ATP usage +were calculated as RANGE variables (charge.mod). + +Executing "ch()" in the terminal shell (see charge.hoc) will print +average ATP usage per cellular compartment as shown below (some of the +information is exported into text files). + +------------------------------------------------------------------------- + +The Na influx was analyzed from 517.000000 to 535.000000 ms +Required ATP molecules to pump Na ions out: +Total: 1.998503e+08 +Soma: 1.416016e+07 +Basal dendrite: 4.609883e+07 +Apical dendrite: 9.149446e+07 +Axon Initial Segment: 2.498228e+07 +Axon collaterals: 2.095502e+07 +Myelin: 7.227968e+05 +Node: 1.436733e+06 + +------------------------------------------------------------------------- +------------------------------------------------------------------------- + +Required ATP molecules to pump Na ions out per um^2: +Total: 2.818287e+03 +Soma: 6.810007e+03 +Basal dendrite: 2.531221e+03 +Apical dendrite: 2.213969e+03 +Axon Initial Segment: 5.531797e+04 +Axon collaterals: 3.932075e+03 +Myelin: 2.081271e+02 +Node: 3.517895e+04 + +------------------------------------------------------------------------- + +Total area (um^2): 7.091197e+04 +Soma area (um^2): 2.079316e+03 + +------------------------------------------------------------------------- + +For questions please contact s.hallermann@eni-g.de or +m.kole@nin.knaw.nl + +June 12th 2012, Stefan Hallermann + +## Changelog + +20140226 ModelDB Administrator: To prevent collision with NEURON's +"charge" the "charge" mechanism has been changed to "charge_" with +changes in the hoc code. The charge in names of files was left +unchanged. + +20250709 Converted README to Markdown.