| 1 | ;; |
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| 2 | ;; |
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| 3 | ;; nemx documentation for the Chicken Scheme module system. |
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| 4 | ;; |
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| 5 | ;; |
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| 6 | ;; This program is free software: you can redistribute it and/or |
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| 7 | ;; modify it under the terms of the GNU General Public License as |
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| 8 | ;; published by the Free Software Foundation, either version 3 of the |
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| 9 | ;; License, or (at your option) any later version. |
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| 10 | ;; |
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| 11 | ;; This program is distributed in the hope that it will be useful, but |
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| 12 | ;; WITHOUT ANY WARRANTY; without even the implied warranty of |
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| 13 | ;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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| 14 | ;; General Public License for more details. |
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| 15 | ;; |
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| 16 | ;; A full copy of the GPL license can be found at |
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| 17 | ;; <http://www.gnu.org/licenses/>. |
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| 18 | ;; |
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| 19 | ;; |
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| 20 | |
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| 21 | |
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| 22 | (use eggdoc) |
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| 23 | |
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| 24 | (define doc |
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| 25 | `((eggdoc:begin |
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| 26 | |
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| 27 | (name "nemo") |
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| 28 | |
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| 29 | (description "Neuron model description language.") |
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| 30 | |
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| 31 | (author (url "http://chicken.wiki.br/ivan raikov" "Ivan Raikov")) |
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| 32 | |
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| 33 | (history |
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| 34 | (version "1.0" "Initial release")) |
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| 35 | |
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| 36 | |
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| 37 | (requires (url "args.html" "args") |
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| 38 | (url "datatype.html" "datatype") |
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| 39 | (url "digraph.html" "digraph") |
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| 40 | (url "environments.html" "environments") |
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| 41 | (url "graph-bfs.html""graph-bfs") |
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| 42 | (url "graph-cycles.html" "graph-cycles") |
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| 43 | (url "matchable.html" "matchable") |
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| 44 | (url "mathh.html" "mathh") |
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| 45 | (url "strictly-pretty.html" "strictly-pretty") |
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| 46 | (url "sxml-tools.html" "sxml-tools") |
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| 47 | (url "sxml-transforms.html" "sxml-transforms") |
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| 48 | (url "syntax-case.html" "syntax-case") |
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| 49 | (url "varsubst.html" "varsubst") |
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| 50 | (url "vector-lib.html" "vector-lib")) |
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| 51 | |
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| 52 | |
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| 53 | (usage "nemo [options...] [input files ...]") |
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| 54 | (download "nemo.egg") |
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| 55 | |
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| 56 | (documentation |
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| 57 | |
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| 58 | (p (tt "NEMO") " is a program that reads an on channel description " |
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| 59 | "in a format based on ChannelML and generates a corresponding description " |
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| 60 | "in the [[http://www.neuron.yale.edu/neuron/docs/help/neuron/nmodl/nmodl.html|NMODL]] " |
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| 61 | "language used by the [[http://www.neuron.yale.edu/neuron/|NEURON]] simulator. ") |
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| 62 | |
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| 63 | (subsection "Options" |
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| 64 | (p (symbol-table |
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| 65 | (describe "-i FORMAT" "specify input format (xml, sxml, s-exp)") |
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| 66 | (describe "--xml[=FILE]" "write XML output to file (default: <model-name>.xml") |
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| 67 | (describe "--sxml[=FILE]" "write SXML output to file (default: <model-name>.sxml") |
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| 68 | (describe "--nmodl[=FILE]" "write NMODL output to file (default: <model-name>.mod") |
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| 69 | (describe "--nmodl-method=METHOD" "specify NMODL integration method (cnexp, derivimplicit)") |
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| 70 | (describe "-t" "use interpolation tables in generated code") |
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| 71 | (describe "-h, --help" "print help")))) |
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| 72 | |
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| 73 | (subsection "Model description language" |
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| 74 | (p "The following constructs comprise the model description language: ") |
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| 75 | (p (symbol-table |
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| 76 | (describe "(INPUT {ID | (ID [AS LOCAL-ID] [FROM NAMESPACE])} ... )" |
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| 77 | "declare an imported quantity") |
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| 78 | (describe "(OUTPUT ID)" |
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| 79 | "declare that an existing quantity be exported") |
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| 80 | (describe "(CONST ID = EXPR)" |
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| 81 | "declare a constant quantity (its value will be computed at declaration time)") |
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| 82 | (describe "(DEFUN ID ({ARG-ID} ... ) BODY)" |
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| 83 | "declare a function (an expression with no free variables)") |
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| 84 | (describe "(ASGN ID = EXPR)" |
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| 85 | "declare an assigned quantity (an expression that can refer to other quantities in the system)") |
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| 86 | (describe "(STATE-COMPLEX ID TRANSITIONS INITIAL OPEN)" |
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| 87 | "declare a state complex quantity") |
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| 88 | (describe "(COMPONENT (TYPE ID) (NAME ID) ELEMENTS)" |
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| 89 | "declare a system component (a quantity that can contain other quantities)") |
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| 90 | ) |
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| 91 | )) |
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| 92 | |
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| 93 | ) |
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| 94 | (examples (pre #<<EOF |
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| 95 | |
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| 96 | ;; Akemann and Knoepfel, J.Neurosci. 26 (2006) 4602 |
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| 97 | |
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| 98 | (nemo-model PotIhCa |
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| 99 | ((input v cai cao) |
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| 100 | |
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| 101 | (const Vrest = -68) |
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| 102 | (const diam = 20) |
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| 103 | (const celsius = 24) |
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| 104 | |
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| 105 | (const temp_adj = (pow 3 (/ (- celsius 22) 10))) |
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| 106 | |
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| 107 | (defun ghk (v celsius ci co) |
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| 108 | (let ((F 96485.0) (R 8.3145)) |
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| 109 | (let ((zeta (/ (* 2e-3 F v) (* R (+ 273.19 celsius))))) |
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| 110 | (if (< (abs (- 1.0 (exp (neg zeta)))) 1e-6) |
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| 111 | (* 1e-6 (* 2 F) (- ci (* co (exp (neg zeta)))) (+ 1.0 (/ zeta 2))) |
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| 112 | (/ (* 1e-6 (* 2 zeta F) (- ci (* co (exp (neg zeta))))) (- 1.0 (exp (neg zeta)))))))) |
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| 113 | |
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| 114 | |
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| 115 | (component (type ion-channel) (name Kv1) |
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| 116 | |
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| 117 | (component (type gate) |
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| 118 | |
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| 119 | ;; rate functions |
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| 120 | (defun Kv1_amf (v) |
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| 121 | (let ((cma 0.12889) |
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| 122 | (cka -33.90877) |
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| 123 | (cva 45)) |
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| 124 | (* cma (exp (neg (/ (+ v cva) cka)))))) |
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| 125 | |
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| 126 | (defun Kv1_bmf (v) |
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| 127 | (let ((cmb 0.12889) |
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| 128 | (ckb 12.42101) |
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| 129 | (cvb 45)) |
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| 130 | (* cmb (exp (neg (/ (+ v cvb) ckb)))))) |
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| 131 | |
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| 132 | (hh-ionic-conductance |
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| 133 | (Kv1 ;; ion name: exported variables will be of the form {ion}_{id} |
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| 134 | (initial-m (/ (Kv1_amf Vrest) (+ (Kv1_amf Vrest) (Kv1_bmf Vrest)))) |
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| 135 | (m-power 4) |
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| 136 | (h-power 0) |
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| 137 | (m-alpha (* temp_adj (Kv1_amf v) )) |
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| 138 | (m-beta (* temp_adj (Kv1_bmf v) ))) |
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| 139 | |
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| 140 | )) |
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| 141 | |
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| 142 | |
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| 143 | |
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| 144 | (component (type pore) |
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| 145 | (const gbar_Kv1 = 0.011) |
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| 146 | (output gbar_Kv1 )) |
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| 147 | |
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| 148 | (component (type permeating-substance) (name k) |
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| 149 | (const e_Kv1 = -85) |
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| 150 | (output e_Kv1 )) |
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| 151 | |
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| 152 | ) ;; end Kv1 current |
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| 153 | |
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| 154 | |
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| 155 | (component (type ion-channel) (name Kv4) |
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| 156 | |
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| 157 | (component (type gate) |
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| 158 | |
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| 159 | ;; rate functions |
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| 160 | |
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| 161 | |
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| 162 | (defun Kv4_amf (v) |
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| 163 | (let ((can 0.15743) |
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| 164 | (ckan -32.19976) |
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| 165 | (cvan 57)) |
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| 166 | (* can (exp (neg (/ (+ v cvan) ckan)))))) |
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| 167 | |
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| 168 | |
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| 169 | (defun Kv4_bmf (v) |
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| 170 | (let ((cbn 0.15743) |
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| 171 | (ckbn 37.51346) |
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| 172 | (cvbn 57)) |
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| 173 | (* cbn (exp (neg (/ (+ v cvbn) ckbn)))))) |
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| 174 | |
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| 175 | |
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| 176 | (defun Kv4_ahf (v) |
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| 177 | (let ((cah 0.01342) |
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| 178 | (ckah -7.86476) |
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| 179 | (cvah 60)) |
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| 180 | (/ cah (+ 1.0 (exp (neg (/ (+ v cvah) ckah))))))) |
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| 181 | |
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| 182 | |
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| 183 | (defun Kv4_bhf (v) |
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| 184 | (let ((cbh 0.04477) |
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| 185 | (ckbh 11.3615) |
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| 186 | (cvbh 54)) |
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| 187 | (/ cbh (+ 1.0 (exp (neg (/ (+ v cvbh) ckbh))))))) |
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| 188 | |
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| 189 | (hh-ionic-conductance |
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| 190 | (Kv4 ;; ion name: exported variables will be of the form {ion}_{id} |
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| 191 | (initial-m (/ (Kv4_amf Vrest) (+ (Kv4_amf Vrest) (Kv4_bmf Vrest)))) |
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| 192 | (initial-h (/ (Kv4_ahf Vrest) (+ (Kv4_ahf Vrest) (Kv4_bhf Vrest))) ) |
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| 193 | (m-power 4) |
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| 194 | (h-power 1) |
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| 195 | (m-alpha (* temp_adj (Kv4_amf v))) |
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| 196 | (m-beta (* temp_adj (Kv4_bmf v))) |
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| 197 | (h-alpha (* temp_adj (Kv4_ahf v))) |
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| 198 | (h-beta (* temp_adj (Kv4_bhf v))) |
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| 199 | )) |
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| 200 | |
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| 201 | ) |
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| 202 | |
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| 203 | (component (type pore) |
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| 204 | (const gbar_Kv4 = 0.0039) |
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| 205 | (output gbar_Kv4 )) |
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| 206 | |
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| 207 | (component (type permeating-substance) (name k) |
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| 208 | (const e_Kv4 = -85) |
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| 209 | (output e_Kv4 )) |
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| 210 | |
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| 211 | ) ;; end Kv4 current |
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| 212 | |
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| 213 | |
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| 214 | |
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| 215 | (component (type ion-channel) (name Ih) |
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| 216 | |
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| 217 | (component (type gate) |
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| 218 | |
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| 219 | ;; rate functions |
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| 220 | |
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| 221 | (defun Ih_inf (v) |
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| 222 | (let ((cvn 90.1) |
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| 223 | (ckn -9.9)) |
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| 224 | (/ 1.0 (+ 1.0 (exp (neg (/ (+ v cvn) ckn) )))))) |
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| 225 | |
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| 226 | (defun Ih_tau (v) |
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| 227 | (let ((cct 190) |
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| 228 | (cat 720) |
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| 229 | (cvt 81.5) |
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| 230 | (ckt 11.9)) |
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| 231 | (+ cct (* cat (exp (neg (pow (/ (+ v cvt) ckt) 2))))))) |
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| 232 | |
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| 233 | (hh-ionic-conductance |
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| 234 | (Ih ;; ion name: exported variables will be of the form {ion}_{id} |
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| 235 | (initial-m (Ih_inf Vrest)) |
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| 236 | (m-power 1) |
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| 237 | (h-power 0) |
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| 238 | (m-inf (Ih_inf v)) |
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| 239 | (m-tau (/ (Ih_tau v) temp_adj)) |
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| 240 | )) |
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| 241 | |
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| 242 | ) |
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| 243 | |
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| 244 | (component (type pore) |
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| 245 | (const gbar_Ih = 0.0002) |
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| 246 | (output gbar_Ih )) |
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| 247 | |
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| 248 | (component (type permeating-substance) (name non-specific) |
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| 249 | (const e_Ih = -30) |
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| 250 | (output e_Ih )) |
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| 251 | |
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| 252 | ) ;; end Ih current |
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| 253 | |
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| 254 | (component (type ion-channel) (name CaP) |
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| 255 | |
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| 256 | (component (type gate) |
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| 257 | |
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| 258 | ;; rate functions |
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| 259 | (defun CaP_inf (v) |
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| 260 | (let ((cv 19) (ck 5.5)) |
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| 261 | (/ 1.0 (+ 1.0 (exp (neg (/ (+ v cv) ck))))))) |
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| 262 | |
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| 263 | (defun CaP_tau (v) |
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| 264 | (if (> v -50) |
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| 265 | (* 1e3 (+ 0.000191 (* 0.00376 (pow (exp (neg (/ (+ v 41.9) 27.8))) 2)))) |
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| 266 | (* 1e3 (+ 0.00026367 (* 0.1278 (exp (* 0.10327 v))))))) |
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| 267 | |
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| 268 | (hh-ionic-conductance |
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| 269 | (CaP ;; ion name: exported variables will be of the form {ion}_{id} |
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| 270 | (initial-m (CaP_inf Vrest)) |
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| 271 | (m-power 1) |
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| 272 | (h-power 0) |
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| 273 | (m-inf (CaP_inf v)) |
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| 274 | (m-tau (/ (CaP_tau v) temp_adj)))) |
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| 275 | |
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| 276 | ) |
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| 277 | |
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| 278 | (component (type pore) |
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| 279 | (const gmax_CaP = 0.01667) |
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| 280 | (gbar_CaP = (* gmax_CaP (ghk v celsius cai cao))) |
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| 281 | (output gbar_CaP )) |
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| 282 | |
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| 283 | (component (type accumulating-substance) (name ca) ) |
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| 284 | |
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| 285 | |
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| 286 | ) ;; end CaP current |
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| 287 | |
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| 288 | |
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| 289 | (component (type ion-channel) (name CaBK) |
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| 290 | |
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| 291 | (component (type gate) |
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| 292 | |
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| 293 | ;; rate functions |
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| 294 | |
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| 295 | (defun CaBK_zinf (ca) |
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| 296 | (let ((zhalf 0.001)) |
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| 297 | (/ 1 (+ 1 (/ zhalf ca))))) |
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| 298 | |
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| 299 | (const CaBK_ztau = 1.0) |
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| 300 | |
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| 301 | (defun CaBK_minf (v) |
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| 302 | (let ((cvm 28.9) |
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| 303 | (ckm 6.2)) |
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| 304 | (/ 1.0 (+ 1.0 (exp (neg (/ (+ v 5.0 cvm) ckm))))))) |
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| 305 | |
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| 306 | (defun CaBK_mtau (v) |
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| 307 | (let ((ctm 0.000505) |
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| 308 | (cvtm1 86.4) |
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| 309 | (cktm1 -10.1) |
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| 310 | (cvtm2 -33.3) |
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| 311 | (cktm2 10)) |
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| 312 | (+ ctm (/ 1.0 (+ (exp (neg (/ (+ v 5.0 cvtm1) cktm1))) |
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| 313 | (exp (neg (/ (+ v 5.0 cvtm2) cktm2)))))))) |
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| 314 | |
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| 315 | (defun CaBK_hinf (v) |
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| 316 | (let ((ch 0.085) |
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| 317 | (cvh 32) |
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| 318 | (ckh -5.8)) |
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| 319 | (+ ch (/ (- 1.0 ch) (+ 1.0 (exp (neg (/ (+ v 5.0 cvh) ckh)))))))) |
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| 320 | |
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| 321 | (defun CaBK_htau (v) |
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| 322 | (let ((cth 0.0019) |
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| 323 | (cvth1 48.5) |
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| 324 | (ckth1 -5.2) |
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| 325 | (cvth2 -54.2) |
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| 326 | (ckth2 12.9)) |
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| 327 | (+ cth (/ 1.0 ( + (exp (- (/ (+ v cvth1) ckth1))) |
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| 328 | (exp (- (/ (+ v cvth2) ckth2)))))))) |
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| 329 | |
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| 330 | (state-complex |
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| 331 | (CaBK_z |
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| 332 | (transitions (-> zC zO (/ (CaBK_zinf cai) CaBK_ztau)) |
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| 333 | (-> zO zC (/ (- 1 (CaBK_zinf cai)) CaBK_ztau))) |
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| 334 | (initial (CaBK_zinf 1e-4)) |
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| 335 | (open zO) (power 2))) |
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| 336 | |
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| 337 | (output CaBK_z ) |
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| 338 | |
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| 339 | |
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| 340 | (hh-ionic-conductance |
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| 341 | (CaBK ;; ion name: exported variables will be of the form {ion}_{id} |
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| 342 | (initial-m (/ (CaBK_minf Vrest) temp_adj)) |
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| 343 | (initial-h (/ (CaBK_hinf Vrest) temp_adj )) |
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| 344 | (m-power 3) |
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| 345 | (h-power 1) |
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| 346 | (m-inf (/ (CaBK_minf v) temp_adj )) |
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| 347 | (m-tau (/ (CaBK_mtau v) temp_adj )) |
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| 348 | (h-inf (/ (CaBK_hinf v) temp_adj) ) |
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| 349 | (h-tau (/ (CaBK_htau v) temp_adj) ))) |
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| 350 | |
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| 351 | ) |
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| 352 | |
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| 353 | (component (type pore) |
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| 354 | (const gbar_CaBK = 0.014) |
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| 355 | (output gbar_CaBK )) |
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| 356 | |
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| 357 | (component (type permeating-substance) (name k) |
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| 358 | (const e_CaBK = -85) |
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| 359 | (output e_CaBK )) |
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| 360 | |
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| 361 | ) ;; end BK current |
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| 362 | |
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| 363 | |
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| 364 | |
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| 365 | )) ;; end model |
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| 366 | |
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| 367 | EOF |
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| 368 | )) |
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| 369 | |
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| 370 | (license |
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| 371 | "Copyright 2008 Ivan Raikov and the Okinawa Institute of Science and Technology. |
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| 372 | |
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| 373 | This program is free software: you can redistribute it and/or modify |
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| 374 | it under the terms of the GNU General Public License as published by |
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| 375 | the Free Software Foundation, either version 3 of the License, or (at |
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| 376 | your option) any later version. |
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| 377 | |
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| 378 | This program is distributed in the hope that it will be useful, but |
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| 379 | WITHOUT ANY WARRANTY; without even the implied warranty of |
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| 380 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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| 381 | General Public License for more details. |
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| 382 | |
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| 383 | A full copy of the GPL license can be found at |
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| 384 | <http://www.gnu.org/licenses/>.")))) |
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| 385 | |
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| 386 | (if (eggdoc->html doc) (void)) |
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