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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

what is the stm
Brian Reply
is there industrial application of fullrenes. What is the method to prepare fullrene on large scale.?
industrial application...? mmm I think on the medical side as drug carrier, but you should go deeper on your research, I may be wrong
How we are making nano material?
what is a peer
What is meant by 'nano scale'?
What is STMs full form?
scanning tunneling microscope
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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
what is Nano technology ?
Bob Reply
write examples of Nano molecule?
The nanotechnology is as new science, to scale nanometric
nanotechnology is the study, desing, synthesis, manipulation and application of materials and functional systems through control of matter at nanoscale
Is there any normative that regulates the use of silver nanoparticles?
Damian Reply
what king of growth are you checking .?
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Stoney Reply
why we need to study biomolecules, molecular biology in nanotechnology?
Adin Reply
yes I'm doing my masters in nanotechnology, we are being studying all these domains as well..
what school?
biomolecules are e building blocks of every organics and inorganic materials.
anyone know any internet site where one can find nanotechnology papers?
Damian Reply
sciencedirect big data base
Introduction about quantum dots in nanotechnology
Praveena Reply
what does nano mean?
Anassong Reply
nano basically means 10^(-9). nanometer is a unit to measure length.
do you think it's worthwhile in the long term to study the effects and possibilities of nanotechnology on viral treatment?
Damian Reply
absolutely yes
how to know photocatalytic properties of tio2 nanoparticles...what to do now
Akash Reply
it is a goid question and i want to know the answer as well
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Do somebody tell me a best nano engineering book for beginners?
s. Reply
there is no specific books for beginners but there is book called principle of nanotechnology
how can I make nanorobot?
what is fullerene does it is used to make bukky balls
Devang Reply
are you nano engineer ?
fullerene is a bucky ball aka Carbon 60 molecule. It was name by the architect Fuller. He design the geodesic dome. it resembles a soccer ball.
what is the actual application of fullerenes nowadays?
That is a great question Damian. best way to answer that question is to Google it. there are hundreds of applications for buck minister fullerenes, from medical to aerospace. you can also find plenty of research papers that will give you great detail on the potential applications of fullerenes.
how did you get the value of 2000N.What calculations are needed to arrive at it
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