Leabra Bio Conversions

	A	B	C	D	E	F
1	These functions convert biological units to the normalized units used in Leabra equations
2
3	Conversion factors:
4		Dimension	Biological unit	offset	multiplier	notes
5		current	amp	0	1.00E-08	10 nA base unit
6		voltage	volt	0.1	0.1	norm range: -100mV to 0mV -> 0 to 1
7		time	sec	0	0.001	msec
8		conductance	siemens = amp / volt	0	1.00E-07
9		capacitance	farad = (sec * amp) / volt	0	1.00E-10
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12	Category	Parameter	Value	Bio unit	Norm Value
13	Potentials
14		Resting potential	-70	mV	0.3
15		E_l (leak)	-70	mV	0.3
16		E_e (excitatation)	0	mV	1
17		E_i (inhibition)	-75	mV	0.25
18		E hyperpolarized	-90	mV	0.1	can use for K reversal for GABA-B / GIRK for example
19		Spike thr	-50	mV	0.5
20		Exp Spike thr	20	mV	1.2
21			-60		0.4	-60
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23
24	Conductances
25		g_l (leak)	10	nS	0.1
26		gbar_e (excitation)	100	nS	1.0	max conductance for all inputs
27		gbar_i (inhibition)	100	nS	1.0
28		g_e syn	1	nS	0.01	nominal synaptic-level conductance
29
30		Values below are from Urakubo et al, 2008, based on Migliore et al, 1999 and Poirazi et al, 2003
31		gbar_nmda	50	nS	0.50	nominal value per Froemke & Dan, 2002; Urakubo et al, 2008
32		gbar_nmda eff	15	nS	0.15	this is the value that reproduces Urakubo sim data
33		gbar_vgcc distal	146	nS	1.46
34		gbar_vgcc proximal	3.2	nS	0.03
35		gbar_vgcc soma	93	nS	0.93
36		gbar_vgcc psd distal eff	12	nS	0.12	value that reproduces Urakubo sim data
37		gbar_ak distal	48.67	nS	0.49	ramps up from 7.5 to 48.67 linearly as distance progresses, per Migliore et al, 1999; Poirazi et al, 2003; Urakubo et al, 2008
38		gbar_ak proximal	7.5	nS	0.08
39		gbar_ak eff	4.8	nS	0.05	applying a similar rescaling as applied to vgcc -- unclear exactly what drives this rescaling, but likely needed to keep consistent. could be .1
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41	Capacitance (dt)
42		C	281	pF	2.81	this is Vm_tau rate constant for Vm changes
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45	Brunel&Wang, 2001 NMDA
46		g_ampa_ext	2.08	nS	0.02080	all are synapse-level conductances
47		g_ampa_rec	0.104	nS	0.00104
48		g_nmda	0.327	nS	0.00327
49		g_gaba	1.25	nS	0.01250
50		g_l (leak)	25	nS	0.25
51		Cm pyramid	500	pF	5.00
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53
54	Conductance decay time constants
55		AMPA rise	0.5	ms	0	instant rise time
56		AMPA decay	5	ms	5	SahHestrinNicoll90 has 4-8ms mostly
57		GABA rise	0.5	ms	0	instant rise time
58		GABA decay	7	ms	7	XiangHuguenardPrince98 has 6-7
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60
61	Axonal conduction delays		http://www.scholarpedia.org/article/Axonal_conduction_delay
62		Thalamocortical	1.2	ms
63		Corticocortical	2.3	ms
64		Corpus callosum	10	ms
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