ReDiClusData - Revision history

Bradley Monk: Changing image note: SAP cluster for PSD2. For most simulations the starting SAP cluster size for this PSD is 6x6 or 36 SAP molecules. The diffusion rate 'D

2013-08-24T20:04:08Z

Changing image note: SAP cluster for PSD2. For most simulations the starting SAP cluster size for this PSD is 6x6 or 36 SAP molecules. The diffusion rate 'D

← Older revision		Revision as of 13:04, 24 August 2013
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	{{ImageNoteEnd\|id=3}}		{{ImageNoteEnd\|id=3}}
	{{ImageNote\|id=4\|x=260\|y=229\|w=67\|h=59\|dimx=768\|dimy=576\|style=2}}		{{ImageNote\|id=4\|x=260\|y=229\|w=67\|h=59\|dimx=768\|dimy=576\|style=2}}
	SAP cluster at PSD2~~, note~~ the ~~number of~~ SAP molecules ~~expressed at~~ the ~~surface~~ of ~~PSD2~~ (~~6x6~~) ~~is initially less than PSD1~~.		SAP cluster for PSD2. For most simulations the starting SAP cluster size for this PSD is 6x6 or 36 SAP molecules. The diffusion rate 'D' of the extrasynaptic area (D.es) is scaled in the PSD (D.psd) by the current total number of SAPs present (SAP.t), such that [D.psd = D.ec/SAP.t]. So if D.es = .3 µm²/s and there are 10 SAPs in PSD2, then D.psd2 = .03 µm²/s.
	{{ImageNoteEnd\|id=4}}		{{ImageNoteEnd\|id=4}}
	{{ImageNote\|id=5\|x=509\|y=75\|w=69\|h=71\|dimx=768\|dimy=576\|style=2}}		{{ImageNote\|id=5\|x=509\|y=75\|w=69\|h=71\|dimx=768\|dimy=576\|style=2}}

Bradley Monk: Changing image note: SAP cluster for PSD1. For most simulations the starting SAP cluster size for this PSD is 7x7 or 49 SAP molecules. The diffusion rate 'D

2013-08-24T20:02:51Z

Changing image note: SAP cluster for PSD1. For most simulations the starting SAP cluster size for this PSD is 7x7 or 49 SAP molecules. The diffusion rate 'D

← Older revision		Revision as of 13:02, 24 August 2013
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	{{ImageNoteEnd\|id=2}}		{{ImageNoteEnd\|id=2}}
	{{ImageNote\|id=3\|x=143\|y=223\|w=77\|h=66\|dimx=768\|dimy=576\|style=2}}		{{ImageNote\|id=3\|x=143\|y=223\|w=77\|h=66\|dimx=768\|dimy=576\|style=2}}
	SAP cluster for PSD1~~, note~~ the size is ~~initially bigger than PSD2~~		SAP cluster for PSD1. For most simulations the starting SAP cluster size for this PSD is 7x7 or 49 SAP molecules. The diffusion rate 'D' of the extrasynaptic area (D.es) is scaled in the PSD (D.psd) by the current total number of SAPs present (SAP.t), such that [D.psd = D.ec/SAP.t]. So if D.es = .3 µm²/s and there are 10 SAPs in PSD1, then D.psd1 = .03 µm²/s.
	{{ImageNoteEnd\|id=3}}		{{ImageNoteEnd\|id=3}}
	{{ImageNote\|id=4\|x=260\|y=229\|w=67\|h=59\|dimx=768\|dimy=576\|style=2}}		{{ImageNote\|id=4\|x=260\|y=229\|w=67\|h=59\|dimx=768\|dimy=576\|style=2}}

Bradley Monk: Adding image note: This figure will appear in some simulations. It represents the timeline of SAP growth and shrinking the PSD areas. The blue line represen

2013-08-21T00:37:22Z

Adding image note: This figure will appear in some simulations. It represents the timeline of SAP growth and shrinking the PSD areas. The blue line represen

← Older revision		Revision as of 17:37, 20 August 2013
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	These bar graphs represent the number of AMPAR (red) particles in a defined region: EC (extracellular), PSD1, PSD2, and PSDT (the total combined number of receptors in both PSD areas). In most simulations, if PSDT > 50, PSD clusters tend to shrink, and if PSDT < 30 SAP clusters tend to grow. This is due to the repulsion lattice changes, globally, based on the total number of receptors in synapses.		These bar graphs represent the number of AMPAR (red) particles in a defined region: EC (extracellular), PSD1, PSD2, and PSDT (the total combined number of receptors in both PSD areas). In most simulations, if PSDT > 50, PSD clusters tend to shrink, and if PSDT < 30 SAP clusters tend to grow. This is due to the repulsion lattice changes, globally, based on the total number of receptors in synapses.
	{{ImageNoteEnd\|id=9}}		{{ImageNoteEnd\|id=9}}
			{{ImageNote\|id=10\|x=349\|y=463\|w=348\|h=112\|dimx=768\|dimy=576\|style=2}}
			This figure will appear in some simulations. It represents the timeline of SAP growth and shrinking the PSD areas. The blue line represents PSD1. This particular figure represents a simulated 20 minutes of activity.
			{{ImageNoteEnd\|id=10}}
	</div>		</div>

Bradley Monk: Adding image note: These bar graphs represent the number of AMPAR (red) particles in a defined region: EC (extracellular), PSD1, PSD2, and PSDT (the total c

2013-08-21T00:35:00Z

Adding image note: These bar graphs represent the number of AMPAR (red) particles in a defined region: EC (extracellular), PSD1, PSD2, and PSDT (the total c

← Older revision		Revision as of 17:35, 20 August 2013
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	This is the diffusion rate meter (aka D-Ometer) for PSD2. It provides information on the moment-to-moment diffusion rate inside PSD2. Note the meter is log scaled from .001 µm²/s to 1.0 µm²/s.		This is the diffusion rate meter (aka D-Ometer) for PSD2. It provides information on the moment-to-moment diffusion rate inside PSD2. Note the meter is log scaled from .001 µm²/s to 1.0 µm²/s.
	{{ImageNoteEnd\|id=8}}		{{ImageNoteEnd\|id=8}}
			{{ImageNote\|id=9\|x=146\|y=448\|w=187\|h=77\|dimx=768\|dimy=576\|style=2}}
			These bar graphs represent the number of AMPAR (red) particles in a defined region: EC (extracellular), PSD1, PSD2, and PSDT (the total combined number of receptors in both PSD areas). In most simulations, if PSDT > 50, PSD clusters tend to shrink, and if PSDT < 30 SAP clusters tend to grow. This is due to the repulsion lattice changes, globally, based on the total number of receptors in synapses.
			{{ImageNoteEnd\|id=9}}
	</div>		</div>

Bradley Monk: Adding image note: This is the diffusion rate meter (aka D-Ometer) for PSD2. It provides information on the moment-to-moment diffusion rate inside PSD2. Not

2013-08-21T00:29:45Z

Adding image note: This is the diffusion rate meter (aka D-Ometer) for PSD2. It provides information on the moment-to-moment diffusion rate inside PSD2. Not

← Older revision		Revision as of 17:29, 20 August 2013
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	This is the diffusion rate meter (aka D-Ometer) for PSD1. It provides information on the moment-to-moment diffusion rate inside PSD1. Note the meter is log scaled from .001 µm²/s to 1.0 µm²/s.		This is the diffusion rate meter (aka D-Ometer) for PSD1. It provides information on the moment-to-moment diffusion rate inside PSD1. Note the meter is log scaled from .001 µm²/s to 1.0 µm²/s.
	{{ImageNoteEnd\|id=7}}		{{ImageNoteEnd\|id=7}}
			{{ImageNote\|id=8\|x=252\|y=334\|w=81\|h=78\|dimx=768\|dimy=576\|style=2}}
			This is the diffusion rate meter (aka D-Ometer) for PSD2. It provides information on the moment-to-moment diffusion rate inside PSD2. Note the meter is log scaled from .001 µm²/s to 1.0 µm²/s.
			{{ImageNoteEnd\|id=8}}
	</div>		</div>

Bradley Monk: Adding image note: This is the diffusion rate meter (aka D-Ometer) for PSD1. It provides information on the moment-to-moment diffusion rate inside PSD1. Not

2013-08-21T00:29:09Z

Adding image note: This is the diffusion rate meter (aka D-Ometer) for PSD1. It provides information on the moment-to-moment diffusion rate inside PSD1. Not

← Older revision		Revision as of 17:29, 20 August 2013
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	PSD2: post synaptic density area "2". This PSD area is 6x6 units (1 unit equals 1 nm). The AMPAR 'red' particle diffusion rate in the PSD areas are scaled as a function of the total SAP expressed at their surface (D.psd = D.ec/SAP). So if the extracellular diffusion rate is 0.3 µm²/s and there are 10 SAP molecules in PSD2, then PSD2 diffusion rate would be D.psd = .3/10 = 0.03 µm²/s which are empirically relevant values. In some experiments run in this model, you may see a set of blue particles appear at varied intervals. These represent calcium influx which impact the repulsion lattice for SAP cluster growth.		PSD2: post synaptic density area "2". This PSD area is 6x6 units (1 unit equals 1 nm). The AMPAR 'red' particle diffusion rate in the PSD areas are scaled as a function of the total SAP expressed at their surface (D.psd = D.ec/SAP). So if the extracellular diffusion rate is 0.3 µm²/s and there are 10 SAP molecules in PSD2, then PSD2 diffusion rate would be D.psd = .3/10 = 0.03 µm²/s which are empirically relevant values. In some experiments run in this model, you may see a set of blue particles appear at varied intervals. These represent calcium influx which impact the repulsion lattice for SAP cluster growth.
	{{ImageNoteEnd\|id=6}}		{{ImageNoteEnd\|id=6}}
			{{ImageNote\|id=7\|x=142\|y=337\|w=79\|h=77\|dimx=768\|dimy=576\|style=2}}
			This is the diffusion rate meter (aka D-Ometer) for PSD1. It provides information on the moment-to-moment diffusion rate inside PSD1. Note the meter is log scaled from .001 µm²/s to 1.0 µm²/s.
			{{ImageNoteEnd\|id=7}}
	</div>		</div>

Bradley Monk: Changing image note: PSD2: post synaptic density area "2". This PSD area is 6x6 units (1 unit equals 1 nm). The AMPAR 'red' particle diffusion rate in the P

2013-08-21T00:26:18Z

Changing image note: PSD2: post synaptic density area "2". This PSD area is 6x6 units (1 unit equals 1 nm). The AMPAR 'red' particle diffusion rate in the P

← Older revision		Revision as of 17:26, 20 August 2013
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	{{ImageNote\|id=6\|x=506\|y=367\|w=75\|h=75\|dimx=768\|dimy=576\|style=2}}		{{ImageNote\|id=6\|x=506\|y=367\|w=75\|h=75\|dimx=768\|dimy=576\|style=2}}
	PSD2: post synaptic density area "2". This PSD area is 6x6 units (1 unit equals 1 nm). The AMPAR 'red' particle diffusion rate in the PSD areas are scaled as a function of the total SAP expressed at their surface (D.psd = D.ec/SAP). So if the extracellular diffusion rate is 0.3 µm²/s and there are 10 SAP molecules in PSD2, then PSD2 diffusion rate would be D.psd = .3/10 = 0.03 µm²/s which are empirically relevant values.		PSD2: post synaptic density area "2". This PSD area is 6x6 units (1 unit equals 1 nm). The AMPAR 'red' particle diffusion rate in the PSD areas are scaled as a function of the total SAP expressed at their surface (D.psd = D.ec/SAP). So if the extracellular diffusion rate is 0.3 µm²/s and there are 10 SAP molecules in PSD2, then PSD2 diffusion rate would be D.psd = .3/10 = 0.03 µm²/s which are empirically relevant values. In some experiments run in this model, you may see a set of blue particles appear at varied intervals. These represent calcium influx which impact the repulsion lattice for SAP cluster growth.
	{{ImageNoteEnd\|id=6}}		{{ImageNoteEnd\|id=6}}
	</div>		</div>

Bradley Monk: Adding image note: PSD2: post synaptic density area "2". This PSD area is 6x6 units (1 unit equals 1 nm). The AMPAR 'red' particle diffusion rate in the PSD

2013-08-21T00:24:15Z

Adding image note: PSD2: post synaptic density area "2". This PSD area is 6x6 units (1 unit equals 1 nm). The AMPAR 'red' particle diffusion rate in the PSD

← Older revision		Revision as of 17:24, 20 August 2013
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	PSD1: post synaptic density area "1". This PSD area is 6x6 units (1 unit equals 1 nm). The AMPAR 'red' particle diffusion rate in the PSD areas are scaled as a function of the total SAP expressed at their surface (D.psd = D.ec/SAP). So if the extracellular diffusion rate is 0.3 µm²/s and there are 10 SAP molecules in PSD1, then PSD1 diffusion rate would be D.psd = .3/10 = 0.03 µm²/s which are empirically relevant values.		PSD1: post synaptic density area "1". This PSD area is 6x6 units (1 unit equals 1 nm). The AMPAR 'red' particle diffusion rate in the PSD areas are scaled as a function of the total SAP expressed at their surface (D.psd = D.ec/SAP). So if the extracellular diffusion rate is 0.3 µm²/s and there are 10 SAP molecules in PSD1, then PSD1 diffusion rate would be D.psd = .3/10 = 0.03 µm²/s which are empirically relevant values.
	{{ImageNoteEnd\|id=5}}		{{ImageNoteEnd\|id=5}}
			{{ImageNote\|id=6\|x=506\|y=367\|w=75\|h=75\|dimx=768\|dimy=576\|style=2}}
			PSD2: post synaptic density area "2". This PSD area is 6x6 units (1 unit equals 1 nm). The AMPAR 'red' particle diffusion rate in the PSD areas are scaled as a function of the total SAP expressed at their surface (D.psd = D.ec/SAP). So if the extracellular diffusion rate is 0.3 µm²/s and there are 10 SAP molecules in PSD2, then PSD2 diffusion rate would be D.psd = .3/10 = 0.03 µm²/s which are empirically relevant values.
			{{ImageNoteEnd\|id=6}}
	</div>		</div>

Bradley Monk: Adding image note: PSD1: post synaptic density area "1". This PSD area is 6x6 units (1 unit equals 1 nm). The AMPAR 'red' particle diffusion rate in the PSD

2013-08-21T00:22:53Z

Adding image note: PSD1: post synaptic density area "1". This PSD area is 6x6 units (1 unit equals 1 nm). The AMPAR 'red' particle diffusion rate in the PSD

← Older revision		Revision as of 17:22, 20 August 2013
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	SAP cluster at PSD2, note the number of SAP molecules expressed at the surface of PSD2 (6x6) is initially less than PSD1.		SAP cluster at PSD2, note the number of SAP molecules expressed at the surface of PSD2 (6x6) is initially less than PSD1.
	{{ImageNoteEnd\|id=4}}		{{ImageNoteEnd\|id=4}}
			{{ImageNote\|id=5\|x=509\|y=75\|w=69\|h=71\|dimx=768\|dimy=576\|style=2}}
			PSD1: post synaptic density area "1". This PSD area is 6x6 units (1 unit equals 1 nm). The AMPAR 'red' particle diffusion rate in the PSD areas are scaled as a function of the total SAP expressed at their surface (D.psd = D.ec/SAP). So if the extracellular diffusion rate is 0.3 µm²/s and there are 10 SAP molecules in PSD1, then PSD1 diffusion rate would be D.psd = .3/10 = 0.03 µm²/s which are empirically relevant values.
			{{ImageNoteEnd\|id=5}}
	</div>		</div>

Bradley Monk: Adding image note: SAP cluster at PSD2, note the number of SAP molecules expressed at the surface of PSD2 (6x6) is initially less than PSD1.

2013-08-21T00:09:00Z

Adding image note: SAP cluster at PSD2, note the number of SAP molecules expressed at the surface of PSD2 (6x6) is initially less than PSD1.

← Older revision		Revision as of 17:09, 20 August 2013
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	SAP cluster for PSD1, note the size is initially bigger than PSD2		SAP cluster for PSD1, note the size is initially bigger than PSD2
	{{ImageNoteEnd\|id=3}}		{{ImageNoteEnd\|id=3}}
			{{ImageNote\|id=4\|x=260\|y=229\|w=67\|h=59\|dimx=768\|dimy=576\|style=2}}
			SAP cluster at PSD2, note the number of SAP molecules expressed at the surface of PSD2 (6x6) is initially less than PSD1.
			{{ImageNoteEnd\|id=4}}
	</div>		</div>

← Older revision		Revision as of 13:04, 24 August 2013
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	{{ImageNote\|id=4\|x=260\|y=229\|w=67\|h=59\|dimx=768\|dimy=576\|style=2}}		{{ImageNote\|id=4\|x=260\|y=229\|w=67\|h=59\|dimx=768\|dimy=576\|style=2}}
	SAP cluster at PSD2~~, note~~ the ~~number of~~ SAP molecules ~~expressed at~~ the ~~surface~~ of ~~PSD2~~ (~~6x6~~) ~~is initially less than PSD1~~.		SAP cluster for PSD2. For most simulations the starting SAP cluster size for this PSD is 6x6 or 36 SAP molecules. The diffusion rate 'D' of the extrasynaptic area (D.es) is scaled in the PSD (D.psd) by the current total number of SAPs present (SAP.t), such that [D.psd = D.ec/SAP.t]. So if D.es = .3 µm²/s and there are 10 SAPs in PSD2, then D.psd2 = .03 µm²/s.
	{{ImageNoteEnd\|id=4}}		{{ImageNoteEnd\|id=4}}
	{{ImageNote\|id=5\|x=509\|y=75\|w=69\|h=71\|dimx=768\|dimy=576\|style=2}}		{{ImageNote\|id=5\|x=509\|y=75\|w=69\|h=71\|dimx=768\|dimy=576\|style=2}}

← Older revision		Revision as of 13:02, 24 August 2013
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	{{ImageNote\|id=3\|x=143\|y=223\|w=77\|h=66\|dimx=768\|dimy=576\|style=2}}		{{ImageNote\|id=3\|x=143\|y=223\|w=77\|h=66\|dimx=768\|dimy=576\|style=2}}
	SAP cluster for PSD1~~, note~~ the size is ~~initially bigger than PSD2~~		SAP cluster for PSD1. For most simulations the starting SAP cluster size for this PSD is 7x7 or 49 SAP molecules. The diffusion rate 'D' of the extrasynaptic area (D.es) is scaled in the PSD (D.psd) by the current total number of SAPs present (SAP.t), such that [D.psd = D.ec/SAP.t]. So if D.es = .3 µm²/s and there are 10 SAPs in PSD1, then D.psd1 = .03 µm²/s.
	{{ImageNoteEnd\|id=3}}		{{ImageNoteEnd\|id=3}}
	{{ImageNote\|id=4\|x=260\|y=229\|w=67\|h=59\|dimx=768\|dimy=576\|style=2}}		{{ImageNote\|id=4\|x=260\|y=229\|w=67\|h=59\|dimx=768\|dimy=576\|style=2}}