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Running simulations

In this section we will step through 2 different simulations using the matlab code. In the First simulation we will stimulate several cells in an assembly and several "noise" cells. Then the assembly will activate, shut down the noise and eventually die out. In the second we will have to different assemblies "compete".

Simulation 1

I have created a code called pattern _ maker.m which is an easy way to get a matrix will a designated number of cells, number of patterns, and number of cells per pattern. We will start with a network with 50 excitatory cells and train it with 8 patterns, containing 8 cells in each pattern. Type help pattern _ maker into a matlab prompt to get the details:

>> help pattern_maker pattern_maker.m - creates a pattern matrix. Each row represents a pattern with 1's for active cells, 0's for inactive cells. pattern = pattern_maker(n_cells,n_patterns,n_active) where: n_cells = number of cells n_pattern = number of patterns n_active = number active units per pattern output: pattern = n_patterns x n_cells matrix with each row a randomized pattern with n_active units

Now lets create a variable pp which will store the pattern matrix.

>> pp = pattern_maker(50,8,8);

Now that we have a pattern we can run the main piece of code that will do the simulation: LF _ network.m. Note that many of the parameters are only accessible in the code and would have to be directly edited if the user wishes to change them.

>> help LF_network LF_network.m - This function runs the Lansner-Fransen type simulations as detailed in their paper - "Modelling Hebbian cell assemblies comprised of cortical neurons". There are an equal number of excitory and inhibitory cells. Each excitory cell has a companion inhibitory cell which synapses onto it. The network is trained with different patterns loaded in. Then its calls a code which produces connection strengths. Positive strengths form Excitory to Excitory connections. Negative strengths form connections from Excitory to Inhibitory cells. [v_ex,v_in] = LF_network(dt,Tcutoff,Tfin,I0,stim_cells,Patterns) where: dt = time step Tcutoff = time cutoff for stimulated cells Tfin = time end simulation I0 = stimulation size for cells stim_cells = vector of cells recieving stimulus Patterns = matrix where each row is a pattern the network is trained with returns: v_ex = Voltages for excitory cells, indexed as ve(cell,timestep,compartment)v_in = Voltages for inhibitory cells, indexed as vi(cell,timestep,compartment)ex. pp = pattern_maker(50,8,8) [v_ex, v_in] = LF_network(.01,50,350,1,[1 6 8 10 25],pp);

As explained in the help file above one must choose the cell numbers to stimulate. In order to pick several cells in one assembly we will enter the following command to get the indices of one of the patterns:

>> find(p(1,:)==1) ans = 19 23 28 29 32 35 36 42

Thus we will choose to stimulate cells 19, 23, 28, 29 and add the noise stimuli of cells 45, 46, and 47. The simulation will last for 350 ms and the stimulation will last for 50 ms. A 1.5 nA stimulus is injected into each respective cell soma. After the output is saved we load the results in a code which displays the results: viewer.m.

Questions & Answers

where we get a research paper on Nano chemistry....?
Maira Reply
what are the products of Nano chemistry?
Maira Reply
There are lots of products of nano chemistry... Like nano coatings.....carbon fiber.. And lots of others..
learn
Even nanotechnology is pretty much all about chemistry... Its the chemistry on quantum or atomic level
learn
Google
da
no nanotechnology is also a part of physics and maths it requires angle formulas and some pressure regarding concepts
Bhagvanji
hey
Giriraj
Preparation and Applications of Nanomaterial for Drug Delivery
Hafiz Reply
revolt
da
Application of nanotechnology in medicine
what is variations in raman spectra for nanomaterials
Jyoti Reply
I only see partial conversation and what's the question here!
Crow Reply
what about nanotechnology for water purification
RAW Reply
please someone correct me if I'm wrong but I think one can use nanoparticles, specially silver nanoparticles for water treatment.
Damian
yes that's correct
Professor
I think
Professor
Nasa has use it in the 60's, copper as water purification in the moon travel.
Alexandre
nanocopper obvius
Alexandre
what is the stm
Brian Reply
is there industrial application of fullrenes. What is the method to prepare fullrene on large scale.?
Rafiq
industrial application...? mmm I think on the medical side as drug carrier, but you should go deeper on your research, I may be wrong
Damian
How we are making nano material?
LITNING Reply
what is a peer
LITNING Reply
What is meant by 'nano scale'?
LITNING Reply
What is STMs full form?
LITNING
scanning tunneling microscope
Sahil
how nano science is used for hydrophobicity
Santosh
Do u think that Graphene and Fullrene fiber can be used to make Air Plane body structure the lightest and strongest. Rafiq
Rafiq
what is differents between GO and RGO?
Mahi
what is simplest way to understand the applications of nano robots used to detect the cancer affected cell of human body.? How this robot is carried to required site of body cell.? what will be the carrier material and how can be detected that correct delivery of drug is done Rafiq
Rafiq
if virus is killing to make ARTIFICIAL DNA OF GRAPHENE FOR KILLED THE VIRUS .THIS IS OUR ASSUMPTION
Anam
analytical skills graphene is prepared to kill any type viruses .
Anam
Any one who tell me about Preparation and application of Nanomaterial for drug Delivery
Hafiz
what is Nano technology ?
Bob Reply
write examples of Nano molecule?
Bob
The nanotechnology is as new science, to scale nanometric
brayan
nanotechnology is the study, desing, synthesis, manipulation and application of materials and functional systems through control of matter at nanoscale
Damian
Is there any normative that regulates the use of silver nanoparticles?
Damian Reply
what king of growth are you checking .?
Renato
What fields keep nano created devices from performing or assimulating ? Magnetic fields ? Are do they assimilate ?
Stoney Reply
why we need to study biomolecules, molecular biology in nanotechnology?
Adin Reply
?
Kyle
yes I'm doing my masters in nanotechnology, we are being studying all these domains as well..
Adin
why?
Adin
what school?
Kyle
biomolecules are e building blocks of every organics and inorganic materials.
Joe
how did you get the value of 2000N.What calculations are needed to arrive at it
Smarajit Reply
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Source:  OpenStax, The art of the pfug. OpenStax CNX. Jun 05, 2013 Download for free at http://cnx.org/content/col10523/1.34
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