Bradley Monk: Redirected page to ReDiClus

2013-10-09T00:38:06Z

Redirected page to ReDiClus

← Older revision		Revision as of 17:38, 8 October 2013
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	~~<big><big>'''Re'''ceptor '''Di'''ffusion & '''Clus'''ter Model - ReDiClus Model </big></big>~~		#REDIRECT [[ReDiClus]]



	~~==Diffusion and Cluster Model of LTP==~~
	~~{{ExpandBox\|Diffusion and Cluster Model of LTP\|~~

	~~{{Box\|font=120%\|width=40%\|float=left\|text=12px\|Model Space\|~~
	~~;The model is simulated in a 3D space with the following parameters:~~
	* There is a 3D XYZ coordinate grid
	* The X-Y plane has {{Button\|60x60}} area
	* The X-Y plane consists of real numbers: {{Button\|-30 to +30}}
	* The Z axis is only 2 levels: {{Button\|0 and -1}}
	** 0 represents the membrane surface
	** -1 represents intracellular space
	}}
	~~{{Box\|font=120%\|width=40%\|float=left\|text=12px\|Particle Types\|~~
	~~; There are 2 types of particles in the simulation~~
	* 'Red' particle dots represent AMPA receptors
	** Red dots can randomly diffuse anywhere on the X-Y plane
	** Red dots only diffuse on the surface {{Button\|Z {{=}} 0}}
	* 'Blue' particle dots represent PSD-95 molecules
	** Blue dots are contained in predefined PSD areas and cannot leave
	** Blue dots can exist at the surface {{Button\|Z {{=}} 0}} or intracellularly {{Button\|Z {{=}} -1}}
	}}

	~~{{Box\|font=120%\|width=95%\|float=left\|text=12px\|Visual Representations\|~~
	[[~~File:3D Model.png\|500px]][[File:Model 3d space.png\|500px]]~~
	}}

	~~{{Box\|font=120%\|width=95%\|float=left\|text=12px\|two independent processes\|~~
	~~; In this model, there are two independently occurring processes.~~
	* 1. Blue dots can be expressed at the surface or internalized within their PSD area
	** The Blue dot internalization/externalization rate properties are set by the Shouval cluster model equations.
	* 2. Red dots diffuse on the X-Y plane with brownian motion
	** Each Red dot has an initial step size randomly drawn from a normal distribution with a {{Button\|mean {{=}} 1}} and {{Button\|sd {{=}} .2}}


	~~; The step size for Red dots is dynamically altered when it's located in a PSD area~~
	* 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
	* The more Blue dots at the surface, the more the step size is reduced
	* The current step size function is:
	** {{Button\| {{math\| ''f''(<var>R<sub>step</sub></var>) {{=}} <var>R</var> * (10*(1 &frasl; <var>B<sub>n</sub></var>))}} }}
	*** where R<sub>step</sub> is the baseline Red dot step size
	*** where B<sub>n</sub> is number of Blue dots currently expressed at the PSD surface

	~~; Several screen shots of the dynamic graphs in the model~~
	~~: {{Fig\|[[File:Matlab Sim3.png]]}}~~
	~~: {{Fig\|[[File:Matlab Sim2.png]]}}~~
	}}


	~~{{Box\|font=120%\|width=95%\|float=left\|text=12px\|MEAN SQUARED DISPLACEMENT\|~~

	~~{{Pop3\|<HTML><embed src="http://bradleymonk.com/media/MSD.mp4" height="500" width="640" autoplay="false"></HTML>\|REDICLUS\|ANIMATION\|SEE ANIMATION}}~~


	~~;Brownian Motion Mean Squared Displacement~~
	* The goal of this calculation is to relate the simulated particle diffusion to real world values, namely velocity.
	*Particle velocity will be a function of MSD {{Button\|''x'' units ²&frasl;s}} which scales on space (units) and time (s) parameters.
	* 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)
	*a step size of {{Button\|1 unit/step}} will produce a brownian motion MSD of {{Button\|~0.52 ±0.2 units ²/s}}
	*empirical observations show that reasonable values for MSD are:
	** PSD 0.01 µm ²/s
	** synaptic 0.05 µm ²/s
	** extrasynaptic 0.1 µm ²/s

	*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.
	*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

	}}


	~~}}<!-- END MODEL -->~~


	~~{{ExpandBox\|ReDiClus MODEL DATA RESULTS\|~~

	~~[[ReDiClusData]]~~

	~~}}<!-- END MODEL -->~~

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

	~~{{:Neural Anatomy}}~~

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



	~~{{PageHead\|[[Malinow]]\|[[Molecular Methods]]\|[[Quantum Dots]]\|[[Choquet]]\|[[AMPAR]]}}~~
	~~[[Category:Malinow]] [[Category:~~ReDiClus]]

Bradley Monk: Created page with "'''Re'''ceptor '''Di'''ffusion & '''Clus'''ter Model - ReDiClus Model ==Diffusion and Cluster Model of LTP== {{ExpandBox|Diffusion and Cluster Model ..."

2013-09-04T03:51:15Z

Created page with "<big><big>'''Re'''ceptor '''Di'''ffusion & '''Clus'''ter Model - ReDiClus Model </big></big> ==Diffusion and Cluster Model of LTP== {{ExpandBox|Diffusion and Cluster Model ..."

New page

<big><big>'''Re'''ceptor '''Di'''ffusion & '''Clus'''ter Model - ReDiClus Model </big></big>

==Diffusion and Cluster Model of LTP==
{{ExpandBox|Diffusion and Cluster Model of LTP|

{{Box|font=120%|width=40%|float=left|text=12px|Model Space|
;The model is simulated in a 3D space with the following parameters:
* There is a 3D XYZ coordinate grid
* The X-Y plane has {{Button|60x60}} area
* The X-Y plane consists of real numbers: {{Button|-30 to +30}}
* The Z axis is only 2 levels: {{Button|0 and -1}}
** 0 represents the membrane surface
** -1 represents intracellular space
}}
{{Box|font=120%|width=40%|float=left|text=12px|Particle Types|
; There are 2 types of particles in the simulation
* 'Red' particle dots represent AMPA receptors
** Red dots can randomly diffuse anywhere on the X-Y plane
** Red dots only diffuse on the surface {{Button|Z {{=}} 0}}
* 'Blue' particle dots represent PSD-95 molecules
** Blue dots are contained in predefined PSD areas and cannot leave
** Blue dots can exist at the surface {{Button|Z {{=}} 0}} or intracellularly {{Button|Z {{=}} -1}}
}}

{{Box|font=120%|width=95%|float=left|text=12px|Visual Representations|
[[File:3D Model.png|500px]][[File:Model 3d space.png|500px]]
}}

{{Box|font=120%|width=95%|float=left|text=12px|two independent processes|
; In this model, there are two independently occurring processes.
* 1. Blue dots can be expressed at the surface or internalized within their PSD area
** The Blue dot internalization/externalization rate properties are set by the Shouval cluster model equations.
* 2. Red dots diffuse on the X-Y plane with brownian motion
** Each Red dot has an initial step size randomly drawn from a normal distribution with a {{Button|mean {{=}} 1}} and {{Button|sd {{=}} .2}}

; The step size for Red dots is dynamically altered when it's located in a PSD area
* 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
* The more Blue dots at the surface, the more the step size is reduced
* The current step size function is:
** {{Button| {{math| ''f''(<var>Rstep</var>) {{=}} <var>R</var> * (10*(1 &frasl; <var>Bn</var>))}} }}
*** where Rstep is the baseline Red dot step size
*** where Bn is number of Blue dots currently expressed at the PSD surface

; Several screen shots of the dynamic graphs in the model
: {{Fig|[[File:Matlab Sim3.png]]}}
: {{Fig|[[File:Matlab Sim2.png]]}}
}}

{{Box|font=120%|width=95%|float=left|text=12px|MEAN SQUARED DISPLACEMENT|

{{Pop3|<HTML><embed src="http://bradleymonk.com/media/MSD.mp4" height="500" width="640" autoplay="false"></HTML>|REDICLUS|ANIMATION|SEE ANIMATION}}

;Brownian Motion Mean Squared Displacement
* The goal of this calculation is to relate the simulated particle diffusion to real world values, namely velocity.
*Particle velocity will be a function of MSD {{Button|''x'' units ²&frasl;s}} which scales on space (units) and time (s) parameters.
* 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)
*a step size of {{Button|1 unit/step}} will produce a brownian motion MSD of {{Button|~0.52 ±0.2 units ²/s}}
*empirical observations show that reasonable values for MSD are:
** PSD 0.01 µm ²/s
** synaptic 0.05 µm ²/s
** extrasynaptic 0.1 µm ²/s

*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.
*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

}}

}}

{{ExpandBox|ReDiClus MODEL DATA RESULTS|

[[ReDiClusData]]

}}

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

{{:Neural Anatomy}}

}}

{{PageHead|[[Malinow]]|[[Molecular Methods]]|[[Quantum Dots]]|[[Choquet]]|[[AMPAR]]}}
[[Category:Malinow]] [[Category:ReDiClus]]

ReDiClus Model - Revision history

Bradley Monk: Redirected page to ReDiClus

Bradley Monk: Created page with "'''Re'''ceptor '''Di'''ffusion & '''Clus'''ter Model - ReDiClus Model ==Diffusion and Cluster Model of LTP== {{ExpandBox|Diffusion and Cluster Model ..."