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| <big><big>'''Re'''ceptor '''Di'''ffusion & '''Clus'''ter Model - ReDiClus Model </big></big>
| | #REDIRECT [[ReDiClus]] |
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| ==Diffusion and Cluster Model of LTP==
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| {{ExpandBox|Diffusion and Cluster Model of LTP|
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| {{Box|font=120%|width=40%|float=left|text=12px|Model Space|
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| ;The model is simulated in a 3D space with the following parameters:
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| * There is a 3D XYZ coordinate grid
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| * The X-Y plane has {{Button|60x60}} area
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| * The X-Y plane consists of real numbers: {{Button|-30 to +30}}
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| * The Z axis is only 2 levels: {{Button|0 and -1}}
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| ** 0 represents the membrane surface
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| ** -1 represents intracellular space
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| }}
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| {{Box|font=120%|width=40%|float=left|text=12px|Particle Types|
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| ; There are 2 types of particles in the simulation
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| * 'Red' particle dots represent AMPA receptors
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| ** Red dots can randomly diffuse anywhere on the X-Y plane
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| ** Red dots only diffuse on the surface {{Button|Z {{=}} 0}}
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| * 'Blue' particle dots represent PSD-95 molecules
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| ** Blue dots are contained in predefined PSD areas and cannot leave
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| ** Blue dots can exist at the surface {{Button|Z {{=}} 0}} or intracellularly {{Button|Z {{=}} -1}}
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| }}
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| {{Box|font=120%|width=95%|float=left|text=12px|Visual Representations|
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| [[File:3D Model.png|500px]][[File:Model 3d space.png|500px]] | |
| }}
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| {{Box|font=120%|width=95%|float=left|text=12px|two independent processes|
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| ; In this model, there are two independently occurring processes.
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| * 1. Blue dots can be expressed at the surface or internalized within their PSD area
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| ** The Blue dot internalization/externalization rate properties are set by the Shouval cluster model equations.
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| * 2. Red dots diffuse on the X-Y plane with brownian motion
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| ** Each Red dot has an initial step size randomly drawn from a normal distribution with a {{Button|mean {{=}} 1}} and {{Button|sd {{=}} .2}}
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| ; The step size for Red dots is dynamically altered when it's located in a PSD area
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| * In a PSD, the step size is reduced by a by some factor based on the number of Blue dots currently expressed at the surface of that PSD
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| * The more Blue dots at the surface, the more the step size is reduced
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| * The current step size function is:
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| ** {{Button| {{math| ''f''(<var>R<sub>step</sub></var>) {{=}} <var>R</var> * (10*(1 ⁄ <var>B<sub>n</sub></var>))}} }}
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| *** where R<sub>step</sub> is the baseline Red dot step size
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| *** where B<sub>n</sub> is number of Blue dots currently expressed at the PSD surface
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| ; Several screen shots of the dynamic graphs in the model
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| : {{Fig|[[File:Matlab Sim3.png]]}}
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| : {{Fig|[[File:Matlab Sim2.png]]}}
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| }}
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| {{Box|font=120%|width=95%|float=left|text=12px|MEAN SQUARED DISPLACEMENT|
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| {{Pop3|<HTML><embed src="http://bradleymonk.com/media/MSD.mp4" height="500" width="640" autoplay="false"></HTML>|REDICLUS|ANIMATION|SEE ANIMATION}}
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| ;Brownian Motion Mean Squared Displacement
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| * The goal of this calculation is to relate the simulated particle diffusion to real world values, namely velocity.
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| *Particle velocity will be a function of MSD {{Button|''x'' units ²⁄s}} which scales on space (units) and time (s) parameters.
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| * Space and time in the model are defined arbitrarily as '''Step_Size''' and '''Step''' where each Step a particle moves a distance randomly chosen from a normal distribution (µ{{=}}1,σ{{=}}.2)
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| *a step size of {{Button|1 unit/step}} will produce a brownian motion MSD of {{Button|~0.52 ±0.2 units ²/s}}
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| *empirical observations show that reasonable values for MSD are:
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| ** PSD 0.01 µm ²/s
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| ** synaptic 0.05 µm ²/s
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| ** extrasynaptic 0.1 µm ²/s
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| *given an MSD of {{Button|0.52 ±0.2 units ²/s}} at the current parameters: 1 step {{=}} 1 unit (at µ{{=}}1,σ{{=}}.2), the model will need to be scaled such that particles move at an extrasynaptic rate of 0.1 µm ²/s.
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| *spines are on average 1 to 10 µm apart, if the model is comparing two spines 1 µm apart, they should be separated by 5 units of model space. This is because the current particle diffusion rate of the model is .5 µm ²/s and the empirical MSD is .1 µm ²/s
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| }}
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| }}<!-- END MODEL -->
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| {{ExpandBox|ReDiClus MODEL DATA RESULTS|
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| [[ReDiClusData]]
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| }}<!-- END MODEL -->
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| ==Neural Anatomy==
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| {{ExpandBox|Quantitative Physiology of the Dendrite|
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| {{:Neural Anatomy}}
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| }}<!-- END QUANTITATIVE REVIEW -->
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| {{PageHead|[[Malinow]]|[[Molecular Methods]]|[[Quantum Dots]]|[[Choquet]]|[[AMPAR]]}}
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| [[Category:Malinow]] [[Category:ReDiClus]]
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