ReDiClus - Revision history

Bradley Monk at 09:21, 4 September 2013

2013-09-04T09:21:20Z

← Older revision		Revision as of 02:21, 4 September 2013
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	[[File:RediclusGUI.png\|thumb\|left\|500px\|Screen Shot of the ReDiClus Matlab GUI interface]][[File:Rediclusoutput.png\|thumb\|500px\|Screen Shot of a final [[ReDiClusData\|data output]] from a simulated-30 min of receptor diffusion (took approximately 15 seconds to generate)]]		[[File:RediclusGUI.png\|thumb\|left\|500px\|Screen Shot of the ReDiClus Matlab GUI interface]][[File:Rediclusoutput.png\|thumb\|500px\|Screen Shot of a final [[ReDiClusData\|data output]] from a simulated-30 min of receptor diffusion (took approximately 15 seconds to generate)]]


	~~{{Clear}}~~

	~~==Neural Anatomy==~~
	~~{{ExpandBox\|Quantitative Physiology of the Dendrite\|~~

	~~{{:Neural Anatomy}}~~

	~~}}<!-- END QUANTITATIVE REVIEW -->~~

Bradley Monk: /* ReDiClus in Matlab */

2013-09-04T08:38:39Z

ReDiClus in Matlab

← Older revision		Revision as of 01:38, 4 September 2013
Line 227:		Line 227:


	[[File:RediclusGUI.png\|thumb\|left\|~~600px~~\|Screen Shot of the ReDiClus Matlab GUI interface]][[File:Rediclusoutput.png\|thumb\|~~600px~~\|Screen Shot of a final [[ReDiClusData\|data output]] from a simulated-30 min of receptor diffusion (took approximately 15 seconds to generate)]]		[[File:RediclusGUI.png\|thumb\|left\|500px\|Screen Shot of the ReDiClus Matlab GUI interface]][[File:Rediclusoutput.png\|thumb\|500px\|Screen Shot of a final [[ReDiClusData\|data output]] from a simulated-30 min of receptor diffusion (took approximately 15 seconds to generate)]]

Bradley Monk: /* Data Generation */

2013-09-04T08:37:16Z

Data Generation

← Older revision		Revision as of 01:37, 4 September 2013
Line 190:		Line 190:


	==~~Data Generation~~==		==ReDiClus in Matlab==

	<div class="wpImageAnnotatorEnable">		<div class="wpImageAnnotatorEnable">
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	~~{\| class="wikitable" border="1"~~		[[File:RediclusGUI.png\|thumb\|left\|600px\|Screen Shot of the ReDiClus Matlab GUI interface]][[File:Rediclusoutput.png\|thumb\|600px\|Screen Shot of a final [[ReDiClusData\|data output]] from a simulated-30 min of receptor diffusion (took approximately 15 seconds to generate)]]
	\|-
	~~\|<!--Col1--><center>~~[[File:~~ReDiClusData1~~.png\|~~95px\|link=1Simulation]]</center>~~
	\|~~<!--Col1--><center>[[File:ReDiClusData1.png~~\|~~95px~~\|~~link=1Simulation~~]]~~</center>~~
	~~\|<!--Col1--><center>~~[[File:~~ReDiClusData1~~.png\|~~95px~~\|~~link=1Simulation]]</center>~~
	\|~~<!--Col1--><center>~~[[~~File:ReDiClusData1.png~~\|~~95px\|link=1Simulation~~]]~~</center>~~
	~~\|<!-~~-~~Col1--><center>[[File:ReDiClusData1.png\|95px\|link=1Simulation]]</center>~~
	~~\|<!--Col1--><center>[[File:ReDiClusData1.png\|95px\|link=1Simulation~~]]~~</center>~~
	~~\|<!--Col1--><center>[[File:ReDiClusData1.png\|95px\|link=1Simulation]]</center>~~
	~~\|<!--Col1--><center>[[File:ReDiClusData1.png\|95px\|link=1Simulation]]</center>~~
	\|-
	~~\|<!--Col1--><center><small>[[ReDiClusData1]]</small></center>~~
	~~\|<!--Col2--><center><small>[[ReDiClusData1]]</small></center>~~
	~~\|<!--Col3--><center><small>[[ReDiClusData1]]</small></center>~~
	~~\|<!--Col1--><center><small>[[ReDiClusData1]]</small></center>~~
	~~\|<!--Col2--><center><small>[[ReDiClusData1]]</small></center>~~
	~~\|<!--Col3--><center><small>[[ReDiClusData1]]</small></center>~~
	~~\|<!--Col1--><center><small>[[ReDiClusData1]]</small></center>~~
	~~\|<!--Col2--><center><small>[[ReDiClusData1]]</small></center>~~
	\|}


	~~[[File:RediclusGUI.png\|thumb\|500px]]~~		{{Clear}}
	~~[[File:Rediclusoutput.png\|thumb\|500px]]~~

	~~[[ReDiClusData]] [[Category:ReDiClus]]~~

	==Neural Anatomy==		==Neural Anatomy==

Bradley Monk: Adding image note: This is the boundary for the PSD area of PSD-2. This area has a lower diffusion rate (D) compared to the surrounding periPSD area box. It

2013-09-04T08:32:33Z

Adding image note: This is the boundary for the PSD area of PSD-2. This area has a lower diffusion rate (D) compared to the surrounding periPSD area box. It

← Older revision		Revision as of 01:32, 4 September 2013
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	This the the boundary for the periPSD area, aka the perisynaptic pad for PSD2 that represents a non-PSD portion of a dendritic spine. This area has its own diffusion rate, and separate D-rates for GluR1 and GluR2 particles		This the the boundary for the periPSD area, aka the perisynaptic pad for PSD2 that represents a non-PSD portion of a dendritic spine. This area has its own diffusion rate, and separate D-rates for GluR1 and GluR2 particles
	{{ImageNoteEnd\|id=9}}		{{ImageNoteEnd\|id=9}}
			{{ImageNote\|id=10\|x=595\|y=539\|w=14\|h=58\|dimx=850\|dimy=679\|style=2}}
			This is the boundary for the PSD area of PSD-2. This area has a lower diffusion rate (D) compared to the surrounding periPSD area box. It also has a lower diffusion rate for GluR2 than GluR1 during baseline conditions.
			{{ImageNoteEnd\|id=10}}
	</div>		</div>

Bradley Monk: Removing 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

2013-09-04T08:29:27Z

Removing 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 01:29, 4 September 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=4}}		{{ImageNoteEnd\|id=4}}
	~~{{ImageNote\|id=5\|x=593\|y=541\|w=76\|h=53\|dimx=850\|dimy=679\|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. 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=5}}~~
	{{ImageNote\|id=6\|x=100\|y=437\|w=142\|h=115\|dimx=850\|dimy=679\|style=2}}		{{ImageNote\|id=6\|x=100\|y=437\|w=142\|h=115\|dimx=850\|dimy=679\|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.		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.

Bradley Monk: Adding image note: This the the boundary for the periPSD area, aka the perisynaptic pad for PSD2 that represents a non-PSD portion of a dendritic spine. Thi

2013-09-04T08:28:44Z

Adding image note: This the the boundary for the periPSD area, aka the perisynaptic pad for PSD2 that represents a non-PSD portion of a dendritic spine. Thi

← Older revision		Revision as of 01:28, 4 September 2013
Line 221:		Line 221:
	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=8}}		{{ImageNoteEnd\|id=8}}
			{{ImageNote\|id=9\|x=557\|y=513\|w=17\|h=107\|dimx=850\|dimy=679\|style=2}}
			This the the boundary for the periPSD area, aka the perisynaptic pad for PSD2 that represents a non-PSD portion of a dendritic spine. This area has its own diffusion rate, and separate D-rates for GluR1 and GluR2 particles
			{{ImageNoteEnd\|id=9}}
	</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

2013-09-04T08:25:53Z

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 01:25, 4 September 2013
Line 218:		Line 218:
	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=7}}		{{ImageNoteEnd\|id=7}}
			{{ImageNote\|id=8\|x=124\|y=579\|w=246\|h=72\|dimx=850\|dimy=679\|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=8}}
	</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

2013-09-04T08:25:30Z

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 01:25, 4 September 2013
Line 215:		Line 215:
	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=6}}		{{ImageNoteEnd\|id=6}}
			{{ImageNote\|id=7\|x=254\|y=439\|w=134\|h=113\|dimx=850\|dimy=679\|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=7}}
	</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

2013-09-04T08:25:05Z

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 01:25, 4 September 2013
Line 212:		Line 212:
	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=5}}		{{ImageNoteEnd\|id=5}}
			{{ImageNote\|id=6\|x=100\|y=437\|w=142\|h=115\|dimx=850\|dimy=679\|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=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

2013-09-04T08:24:41Z

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 01:24, 4 September 2013
Line 209:		Line 209:
	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=4}}		{{ImageNoteEnd\|id=4}}
			{{ImageNote\|id=5\|x=593\|y=541\|w=76\|h=53\|dimx=850\|dimy=679\|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. 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=5}}
	</div>		</div>

← Older revision		Revision as of 01:37, 4 September 2013
Line 190:		Line 190:


	==~~Data Generation~~==		==ReDiClus in Matlab==

	<div class="wpImageAnnotatorEnable">		<div class="wpImageAnnotatorEnable">
Line 227:		Line 227:


	~~{\| class="wikitable" border="1"~~		[[File:RediclusGUI.png\|thumb\|left\|600px\|Screen Shot of the ReDiClus Matlab GUI interface]][[File:Rediclusoutput.png\|thumb\|600px\|Screen Shot of a final [[ReDiClusData\|data output]] from a simulated-30 min of receptor diffusion (took approximately 15 seconds to generate)]]
	\|-
	~~\|<!--Col1--><center>~~[[File:~~ReDiClusData1~~.png\|~~95px\|link=1Simulation]]</center>~~
	\|~~<!--Col1--><center>[[File:ReDiClusData1.png~~\|~~95px~~\|~~link=1Simulation~~]]~~</center>~~
	~~\|<!--Col1--><center>~~[[File:~~ReDiClusData1~~.png\|~~95px~~\|~~link=1Simulation]]</center>~~
	\|~~<!--Col1--><center>~~[[~~File:ReDiClusData1.png~~\|~~95px\|link=1Simulation~~]]~~</center>~~
	~~\|<!-~~-~~Col1--><center>[[File:ReDiClusData1.png\|95px\|link=1Simulation]]</center>~~
	~~\|<!--Col1--><center>[[File:ReDiClusData1.png\|95px\|link=1Simulation~~]]~~</center>~~
	~~\|<!--Col1--><center>[[File:ReDiClusData1.png\|95px\|link=1Simulation]]</center>~~
	~~\|<!--Col1--><center>[[File:ReDiClusData1.png\|95px\|link=1Simulation]]</center>~~
	\|-
	~~\|<!--Col1--><center><small>[[ReDiClusData1]]</small></center>~~
	~~\|<!--Col2--><center><small>[[ReDiClusData1]]</small></center>~~
	~~\|<!--Col3--><center><small>[[ReDiClusData1]]</small></center>~~
	~~\|<!--Col1--><center><small>[[ReDiClusData1]]</small></center>~~
	~~\|<!--Col2--><center><small>[[ReDiClusData1]]</small></center>~~
	~~\|<!--Col3--><center><small>[[ReDiClusData1]]</small></center>~~
	~~\|<!--Col1--><center><small>[[ReDiClusData1]]</small></center>~~
	~~\|<!--Col2--><center><small>[[ReDiClusData1]]</small></center>~~
	\|}


	~~[[File:RediclusGUI.png\|thumb\|500px]]~~		{{Clear}}
	~~[[File:Rediclusoutput.png\|thumb\|500px]]~~

	~~[[ReDiClusData]] [[Category:ReDiClus]]~~

	==Neural Anatomy==		==Neural Anatomy==