ReDiClus: Difference between revisions
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==Data Generation== | ==Data Generation== | ||
{{ReDiClusTree}} | |||
[[ | <div class="wpImageAnnotatorEnable"> | ||
<span class="wpImageAnnotatorPageName" style="display:none;">[[ReDiClus]]</span> | |||
<span class="wpImageAnnotatorFullName" style="display:none;">[[ReDiClus]]</span> | |||
<div class="wpImageAnnotatorFile">[[File:Redicluslive.png]]</div> | |||
<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}} | |||
3D Surface Plot | |||
{{ImageNoteEnd|id=1}} | |||
{{ImageNote|id=2|x=459|y=187|w=145|h=130|dimx=768|dimy=576|style=2}} | |||
2D 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> | |||
{| class="wikitable" border="1" | |||
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|<!--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]] | |||
[[File:Rediclusoutput.png|thumb|500px]] | |||
[[ReDiClusData]] [[Category:ReDiClus]] | |||
==Neural Anatomy== | ==Neural Anatomy== |
Revision as of 00:18, 4 September 2013
ReDiClus - Receptor Diffusion & Cluster Model
Simulation Space
ReDiClus Model Space
Particle Types
Visual Representations
Particle Diffusion
Simulating Molecular Diffusion
Diffusion Equations
Homeostatic Scaling
PSD-95 SAP Cluster Scaling
Physical Properties
ReDiClus Physics
two independent processes
MEAN SQUARED DISPLACEMENT
Data Generation
{{#tree:id=ReDiClusTree|openlevels=2|root=ReDiClusTree|
}}
Neural Anatomy
Quantitative Physiology of the Dendrite
Quantitative Review
The Size of Dendrites
Particle Counts
Diffusion Rates
Images
Choquet 2007 Real Time Receptor Diffusion
Choquet 2007 Real Time Receptor Diffusion Analysis
Receptor Diffusion Rate Best Estimates
Brain Data: Facts and Figures
Estimated Number of Neurons in the Brain of Humans & Other Animals
Brain vs Computer
Facts and Figures
Processor | Transistor count | Date of introduction | Manufacturer | Semiconductor device fabrication|Process | Area |
---|---|---|---|---|---|
Core 2 Duo Wolfdale3M | 230,000,000 | 2008 | Intel | 45 nm | 83 mm² |
Core i7 (Quad) | 731,000,000 (7e8) | 2008 | Intel | 45 nm | 263 mm² |
POWER6 | 789,000,000 | 2007 | IBM | 65 nm | 341 mm² |
WDC 65C02 | 785,000,000 | 2009 | western design center | 0.22 µm | 14 mm² |
Six-Core Opteron 2400 | 904,000,000 | 2009 | AMD | 45 nm | 346 mm² |
16-Core SPARC T3 | 1,000,000,000 (1e9) | 2010 | Sun Oracle Corporation|Oracle | 40 nm | 377 mm² |
Quad-Core plus GPU Sandy Bridge Core i7 | 1,160,000,000 | 2011 | Intel | 32 nm | 216 mm² |
Core i7 (Gulftown) | 1,170,000,000 | 2010 | Intel | 32 nm | 240 mm² |
8-core POWER7 32M L3 | 1,200,000,000 | 2010 | IBM | 45 nm | 567 mm² |
8-Core AMD Bulldozer | 1,200,000,000 | 2012 | AMD | 32nm | 315 mm² |
Quad-Core + GPU AMD Trinity | 1,303,000,000 | 2012 | AMD | 32 nm | 246 mm² |
z196 | 1,400,000,000 | 2010 | IBM | 45 nm | 512 mm² |
Core i7 | 1,400,000,000 | 2012 | Intel | 22 nm | 160 mm² |
Dual-Core Itanium 2 | 1,700,000,000 | 2006 | Intel | 90 nm | 596 mm² |
Six-Core Xeon 7400 | 1,900,000,000 | 2008 | Intel | 45 nm | 503 mm² |
Tukwila | 2,000,000,000 (2e9) | 2010 | Intel | 65 nm | 699 mm² |
8-core POWER7 80M L3 | 2,100,000,000 | 2012 | IBM | 32 nm | 567 mm² |
Six-Core Core i7 and 8-Core Xeon E5 | 2,270,000,000 | 2011 | Intel | 32 nm | 434 mm² |
Nehalem-EX | 2,300,000,000 | 2010 | Intel | 45 nm | 684 mm² |
10-Core Xeon Westmere-EX | 2,600,000,000 | 2011 | Intel | 32 nm | 512 mm² |
zEC12 | 2,750,000,000 | 2012 | IBM | 32 nm | 597 mm² |
Poulson | 3,100,000,000 (3e9) | 2012 | Intel | 32 nm | 544 mm² |
15-Core Xeon Ivy Bridge-EX | 4,310,000,000 (4e9) | 2014 | Intel | 22 nm | |
62-Core Xeon Phi | 5,000,000,000 | 2012 | Intel | 22 nm | |
Xbox One Main SoC | 5,000,000,000 (5e9) | 2013 | Microsoft/AMD | 28 nm | 363 mm² |
STARShiP | Molecular Methods | Quantum Dots | AMPAR | Brownian Motion |
Malinow | Molecular Methods | Quantum Dots | Choquet | AMPAR |