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(Adding image note: These items will be used as the baseline parameters for the PSD-95 clusters. If ''Homeostatic Scaling'' is turned ON, these values will r)
 
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==GUI Interface==
==GUI Interface==


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<span class="wpImageAnnotatorPageName" style="display:none;">[[ReDiClus]]</span>
<span class="wpImageAnnotatorPageName" style="display:none;">[[RedicGUI]]</span>
<span class="wpImageAnnotatorFullName" style="display:none;">[[ReDiClus]]</span>
<span class="wpImageAnnotatorFullName" style="display:none;">[[RedicGUI]]</span>
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* base: 100
* Represents the total number of AMPAR particles to simulate.
 
 
By default, these particles will behave like GluR2, in that, the entire PSD and periPSD region will have one unified diffusion rate scalar. If 'Use GluR1 receptors' is selected as a Run Item, this total number will allocate exactly half of the particles to the GluR1 pool and half to the GluR2 pool. So at the base value of 100, with 'Use GluR1 receptors' checked, there will be 50 particles representing GluR1 and 50 representing GluR2.
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* base: 1000
* Total number of iterations to run the main loop function of the simulation.
 
This value represents the number of 'steps' or 'seconds' being simulated. Each iteration of the main loop performs many functions, but its most basic function is to generate random, but diffusion rate-dependent, step sizes for each particle; and then update each particle's location accordingly.
 
A note on processing speed:
If either of the Run Items 'View Live 2D Plot' or  'View Live 2D Plot' are selected (ON), to simulate 1000 steps, it takes roughly 100 seconds on my macbook pro laptop¹ and about 10 seconds on my custom built desktop². The big difference between the two is due to graphics rendering (the custom desktop has better specs in all categories, but an especially better graphics card). Keep your hardware in mind when choosing these step values.


When the Run Items 'View Live 2D Plot' or  'View Live 2D Plot' are not selected (OFF), it takes about 20 seconds to run 5000 steps on my macbook pro laptop.


==ReDiClus in Matlab==
Long story short, the live graphics 2D and 3D plot will make the simulation run much slower. If you are only interested in seeing the final output graphs, turn the 2D and 3D plots OFF and save yourself the time.


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* ¹Brad's Macbook Pro: Intel 2.4 GHz i7 quad-core, 8 GB RAM, and AMD Radeon HD 6770M 1GB dedicated graphics.
<span class="wpImageAnnotatorPageName" style="display:none;">[[ReDiClus]]</span>
* ²Brad's Custom Desktop: Overclocked & Watercooled 4.1 GHz i7 Quadcore Bloomfield, Asus TS Supercomputer motherboard, Asus NVIDIA CUDA graphics card, Intel solid state HDD. See full specs for the [[Computer]]
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<div class="wpImageAnnotatorFile">[[File:Redicluslive.png]]</div>
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Live 3D simulation space
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2D surface plot with PSD areas marked with boxes
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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.
* base: 0.3
* diffusion rate coefficient for the extrasynaptic (ES) non-PSD regions of the simulation.
 
 
This value is used to generate the baseline diffusion rate for all particles in the model. This rate will be used when the particles are in ES space regardless of which Run Items are selected. All other diffusion rates are scaled from this baseline value.
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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.
* base: 0.03
* diffusion rate coefficients for the PSD and periPSD zones.  
* '''Run Item Dependents'''
** PSD-96 Clusters (OFF)
** Homeostatic Regulation (OFF)
** Manually set step size (OFF)
 
 
These diffusion rate coefficients will be used only when the Run Items 'Homeostatic regulation' and 'PSD-95 Clusters' are not selected (OFF).
 
If you want to use these values, DO NOT select the Run Item - 'Manually set step size' unless you want all particles to take the same exact step size for every step throughout the entire simulation  (i.e. step sizes will not be random). A fixed-manual step size is not necessary to generate diffusion rates at the value entered into these fields.
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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.
* base: 60 and 30
* specifies a high and low tolerance range for total particles in PSDs
** inside this range, Clusters will run at baseline values
** outside of this range, Clusters will temporarily adjust several parameters leading to growth or shrinking.
* '''Run Item Dependents:'''
** PSD-95 Clusters (ON)
** Homeostatic Regulation (ON)
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Keep these unchecked (OFF). These are experimental items, and may cause the simulation to produce odd behavior.
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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.
When checked (ON), these will provide visuals for a live 2D or 3D simulation. Keep in mind, these both require a high amount of processor time to render, which can significantly slow down the simulation. If you are only interested in the final output, turn them off.
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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.
When checked (ON) this will make half of the AMPAR dots perform like GluR1 particles. The only major difference between GluR1 and the default (GluR2) particle, is that GluR1 particles have a faster diffusion rate in the PSD (center) region compared to the periPSD (periphery) region. Currently, this diffusion rate differences is scaled such that, for GluR2 only, the periPSD diffusion rate is 2x the PSD (center) diffusion rate
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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 is a short sanity check of diffusion rate values. When this is checked, it overrides the values for all other Parameters and Run Items except for ''Particle Diffusion Rates (D)''. It will generate 100 particles and run them through 100 steps at the diffusion rate for the item specified in the dropdown menu. It will then track the paths of those molecules and compute the MSD and D for those paths. It can be used as a check to make sure the diffusion rate specified is actually producing particle diffusion at the desired rate.
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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.
When this is checked (ON), when the total number of particles in PSD areas falls outside of the ''Homeostatic tolerance' range specified, this function will make adjustments to several parameters controlling Cluster growth and stability.
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When checked, the diffusion rate of the PSDs will be set by a PSD-95 cluster simulation instead of the manually entered value. I did this because there's no reason to have both a manually set PSD diffusion rate and the cluster simulation running at the same time (since the clusters would be having no influence on anything happening in the diffusion simulation -- essentially you'd just be running two independent simulations).
Because the default starting cluster size is 7x7, or 49 total cluster molecules, and diffusion is scaled as a function of both the extrasynaptic diffusion rate (you do specify this) in the following way:
psd.D = D.es / N.cluster
psd.D = 3 / 49 = .05
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This will cause a burst of 100 Calcium-representing particles to appear in PSD2. This will influence several parameters related to the cluster simulation, briefly giving the cluster a higher potential for growth. The effects of this function are the most dramatic when homeostatic scaling is turned on, and when a burst happens during a "scaling-down" period. I will be adding several fields to the GUI providing more control over this run item directly from the GUI.
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This run item will trace one particle over the specified number of steps drawing the particle path as it moves.
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This run item will delete all particles in PSD1 at exactly 950 steps into the simulation. I will soon add more control over this function from the GUI.
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These items will be used as the baseline parameters for the PSD-95 clusters. If ''Homeostatic Scaling'' is turned ON, these values will remain the baseline values while the total number of AMPAR particles in PSDs is within the range of high and low ''Homeostatic tolerance' values specified by the user. When the total AMPAR particles in PSDs is outside of this range, the Cluster parameters will be adjusted allowing for growth or shrinking. When the total number of AMPAR particles in PSDs returns to a value within the tolerance range, the values set here will be restored.
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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)]]
 
 
==ReDiClus in Matlab==
 




Latest revision as of 18:30, 7 September 2013

GUI Interface



ReDiClus in Matlab

Malinow Molecular Methods Quantum Dots Choquet AMPAR
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