ReDiClusData: Difference between revisions

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-{{Molecular Pathway Tree}}
+{{ReDiClusTree}}
 <div class="wpImageAnnotatorEnable">
-<span class="wpImageAnnotatorPageName" style="display:none;">ReDiClus Data</span>
+<span class="wpImageAnnotatorPageName" style="display:none;">[[ReDiClusData]]</span>
-<span class="wpImageAnnotatorFullName" style="display:none;">ReDiClus Data</span>
+<span class="wpImageAnnotatorFullName" style="display:none;">[[ReDiClusData]]</span>
-<div class="wpImageAnnotatorFile">[[File:1Simulation.png]]</div>
+<div class="wpImageAnnotatorFile">[[File:ReDiClusData1.png]]</div>
-<div style="display:none;"><div><div><!--Dummy marker to have image notes inserted below this line-->{{ImageNoteEnd|id=-1}}
+<div style="display:none;"><div><div><!--IMAGE NOTES BELOW -->{{ImageNoteEnd|id=-1}}
+{{ImageNote|id=1|x=156|y=33|w=147|h=103|dimx=768|dimy=576|style=2}}
-</div>
+D Surface Plot
+{{ImageNoteEnd|id=1}}
+{{ImageNote|id=2|x=459|y=187|w=145|h=130|dimx=768|dimy=576|style=2}}
+D surface plot with PSD areas marked with boxes
+{{ImageNoteEnd|id=2}}
+{{ImageNote|id=3|x=143|y=223|w=77|h=66|dimx=768|dimy=576|style=2}}
+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}}
+{{ImageNote|id=4|x=260|y=229|w=67|h=59|dimx=768|dimy=576|style=2}}
+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}}
+{{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}}
+{{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. 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}}
+{{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}}
+{{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}}
+{{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}}
+{{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>
@@ Line 14: / Line 42: @@
 {| class="wikitable" border="1"
   |-
-  |<!--Col1--><center>[[File:LTP1.png|95px|link=Connectome1]]</center>
+  |<!--Col1--><center>[[File:ReDiClusData1.png|95px|link=1Simulation]]</center>
-  |<!--Col2--><center>[[File:LTP2.png|95px|link=Connectome2]]</center>
+  |<!--Col1--><center>[[File:ReDiClusData1.png|95px|link=1Simulation]]</center>
-  |<!--Col3--><center>[[File:PICK1.png|95px|link=Connectome3]]</center>
+  |<!--Col1--><center>[[File:ReDiClusData1.png|95px|link=1Simulation]]</center>
-  |<!--Col1--><center>[[File:PKA1.png|95px|link=Connectome4]]</center>
+  |<!--Col1--><center>[[File:ReDiClusData1.png|95px|link=1Simulation]]</center>
-  |<!--Col2--><center>[[File:LTP.png|95px|link=Connectome6]]</center>
+  |<!--Col1--><center>[[File:ReDiClusData1.png|95px|link=1Simulation]]</center>
- |<!--Col3--><center>[[File:Brainatlas8.jpg|95px|link=Connectome8]]</center>
+  |<!--Col1--><center>[[File:ReDiClusData1.png|95px|link=1Simulation]]</center>
-  |<!--Col1--><center>[[File:Brainatlas9.jpg|95px|link=Connectome9]]</center>
+  |<!--Col1--><center>[[File:ReDiClusData1.png|95px|link=1Simulation]]</center>
-  |<!--Col1--><center>[[File:Brainatlas10.jpg|95px|link=Connectome10]]</center>
+  |<!--Col1--><center>[[File:ReDiClusData1.png|95px|link=1Simulation]]</center>
-  |<!--Col1--><center>[[File:Brainatlas12.jpg|95px|link=Connectome12]]</center>
- |<!--Col1--><center>[[File:Brainatlas15.jpg|95px|link=Connectome15]]</center>
   |-
-  |<!--Col1--><center><small>[[Connectome1]]</small></center>
+  |<!--Col1--><center><small>[[ReDiClusData1]]</small></center>
-  |<!--Col2--><center><small>[[Connectome2]]</small></center>
+  |<!--Col2--><center><small>[[ReDiClusData1]]</small></center>
-  |<!--Col3--><center><small>[[Connectome3]]</small></center>
+  |<!--Col3--><center><small>[[ReDiClusData1]]</small></center>
-  |<!--Col1--><center><small>[[Connectome4]]</small></center>
+  |<!--Col1--><center><small>[[ReDiClusData1]]</small></center>
-  |<!--Col2--><center><small>[[Connectome6]]</small></center>
+  |<!--Col2--><center><small>[[ReDiClusData1]]</small></center>
-  |<!--Col3--><center><small>[[Connectome8]]</small></center>
+  |<!--Col3--><center><small>[[ReDiClusData1]]</small></center>
-  |<!--Col1--><center><small>[[Connectome9]]</small></center>
+  |<!--Col1--><center><small>[[ReDiClusData1]]</small></center>
-  |<!--Col2--><center><small>[[Connectome10]]</small></center>
+  |<!--Col2--><center><small>[[ReDiClusData1]]</small></center>
- |<!--Col3--><center><small>[[Connectome12]]</small></center>
- |<!--Col1--><center><small>[[Connectome15]]</small></center>
   |}

Latest revision as of 12:04, 24 August 2013

{{#tree:id=ReDiClusTree|openlevels=2|root=ReDiClusTree|

ReDiClus
- ReDiClusData
- Mean Squared Displacement
Malinow
Choquet
Molecular Methods
- Quantum Dots
- Mean Squared Displacement

}}

ReDiClusData ReDiClusData

156

147

103

768

576

3D Surface Plot

459

187

145

130

768

576

2D surface plot with PSD areas marked with boxes

143

223

768

576

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.

260

229

768

576

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.

509

768

576

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.

506

367

768

576

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.

142

337

768

576

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.

252

334

768

576

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.

146

448

187

768

576

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.

349

463

348

112

768

576

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.

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ReDiClusData1	ReDiClusData1	ReDiClusData1	ReDiClusData1	ReDiClusData1	ReDiClusData1	ReDiClusData1	ReDiClusData1

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ReDiClusData: Difference between revisions

Latest revision as of 12:04, 24 August 2013

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