**You are required to write your own code for this project.** While
you may discuss the project with your fellow students, you may not
borrow code from anyone else.

- Koene, R. A. and Hasselmo, M. E. (2007) First-in-first-out item replacement
in a model of short-term memory based on persistent spiking.
*Cerebral Cortex*17:1766-1781. - Koene, R. A. and Hasselmo, M. E. (2008) Consequences of parameter
differences in a model of short-term persistent spiking buffers
provided by pyramidal cells in entorhinal cortex.
*Brain Research*1202:54-67.

- Koene, R. A. and Hasselmo, M. E. (2005) An integrate-and-fire model of
prefrontal cortex neuronal activity during performance of
goal-directed decision making.
*Cerebral Cortex*15:1964-1981. - Koene, R. A. and Hasselmo, M. E. (2008) Reversed
and forward buffering of behavioral spike sequences enables retrospective and prospective retrieval in hippocampal
regions CA3 and CA1.
*Neural Networks*21(2-3):276-288.

**NOTE: Verify your calculation of
anorm.** To solve for anorm directly, calculate the value of
the bi-exponential term in gi(t) for all t from 0 up to the value of
tau_fall, in increments of 0.01 msec. Find the maximum of these
values. Set anorm equal to the reciprocal of the maximum. Once
you've done that, you will have guaranteed that g_{i}(t) has a
maximum value of G_{i}. The position of the maximum in the
list of values will give you t_{max}, which you only need for
your conductance plots; it's not needed for the simulation itself.
Compare the value you get for t_{max} with the value from your
corrected equation from Step 1. How close is the match?

`currents`

whose first entry,
for the AHP current, looks like this:
In this example,c.AHP = 1; currents(c.AHP).tau_rise = 1e-4; currents(c.AHP).tau_fall = 30; currents(c.AHP).G = 23; currents(c.AHP).Erev = -90; currents(c.AHP).anorm = find_anorm(currents(c.AHP));

`find_anorm`

is a function that computes
anorm, as described in Step 2 above. You will find it advantageous to
declare `c`

and `currents`

to be global variables.
**NOTE: Changes to parameter
values:** For the ADP current, use tau_rise = 135 - 1e-4, and
tau_fall = 135. For the theta current, use tau_fall = 8. For the
gamma current, use G=150.

The table of parameters in the paper shows the leak conductance
as 111, but the text says that g_{leak} =
C/τ_{leak}, which might lead you to infer that the value
should be 1/9 = 0.111. They messed up on the units. The 111 value is
correct. In general, don't worry about getting the units right; just
use the numbers in Table 1.

Create a struct array to describe the set of pyramidal cells in your model. Two values you must keep for each cell are: its current membrane voltage V, and the time it last emitted a spike. You may wish to keep additional values around, such as a state indicator (normal, spiking, or refractory), the cell's current total conductance, and the most recent voltage adjustment, ΔV.

At the start of your simulation you will specify the number of
pyramidal cells P, and the length of the simulation run in
milliseconds Assume that time starts at t=0 and advances in increments
of Δt = 1 msec. From this you can calculate the number of
steps S in the simulation. Create an array `timeline`

of
length S containing the time (in msec) at each step, and a history array
`Vhist`

of size P × S that will hold the
membrane voltage of each pyramidal cell at each time step. You will use
`Vhist`

for plotting the results of your simulation.

Write a function `updatePyramid(p,i)`

where p is the
pyramidal cell number (from 1 to P) and i is the current time step
(from 1 to S). Your function should compute the new membrane voltage
V(t+Δt) based on the previous voltage V(t) and the current
conductances g_{i}(t). Start with a very simple cell that
just has a leak current.

Write the first version of the main loop of your simulation. It should progress through all the time steps, recalculating the membrane voltage of each pyramidal cell at each step. Set the cell's initial membrane voltage to something other than the resting potential of -60 mV. When the main loop finishes, plot the membrane voltage history and verify that the cell settled to its resting potential.

Theta modulation from the medial septum is simulated by a series of
theta "spikes"; each spike triggers an inhibitory conductance. Create
an array `thetaSpikes`

of size S containing, for each
entry, the time of the most recent theta spike. (At a theta frequency
of 8 Hz, the last theta spike time should stay the same for 125 msec,
then jump ahead by 125 msec., etc.)

Extend your `updatePyramid`

function to include the theta
current. Rerun the simulation and verify that theta ipsp's are
present.

In the example plot above, created with P=2 (two pyramidal cells) and an S value of around 510, the black asterisks mark theta cell spikes. You can see that each theta spike briefly hyperpolarizes the pyramidal cells due to the inhibitory conductance.

`inputSpikes`

that contains the last spike time of an input
to each of the P pyramidal cells. These spikes will control an
"input" current whose parameters are not listed in Table 1, but you
can find them on p. 3 of the "Reverse and Forward Buffering" paper;
use 0 mV as the reversal potential.
Modify the `updatePyramid`

function to include the AHP,
ADP, and input currents, and add logic to make the cell spike if the
membrane voltage goes above threshold. When the cell enters the
"spiking" state it should hold its membrane voltage at 0 mV for 1
millisecond; then it should enter a refractory state for **2
milliseconds** where it refuses to spike no matter what the membrane
voltage is. When the refractory period is over, the cell should
return to its normal state and can spike again if the membrane voltage
goes above threshold.

Write a function `setInput(p,ts)`

that sets up an input
spike for pyramidal cell number p at time ts by writing appropriate
values into the `inputSpikes`

array. You call this
function at the beginning of your simulation for each input spike you
want to apply. Note that since `inputSpikes(p,i)`

encodes
the time of the *last* spike up to and including step i of the
simulation, when you add a spike to the array you must modify all the
succeeding entries on that row.

Set up an input spike for the first pyramidal cell at time t=100, and
run your simulation with two cells. Verify that the first cell fires
repeatedly while the second one remains inactive, but both cells show
theta ipsps. **Note: you must set the firing
rate threshold to -57 mV rather than the -50 mV value given in the
paper.**

Now set up an input to the second pyramidal cell at time t=225. Run the simulation again. Notice that the relative spike times of the two pyramidal cells are not stable. We will fix this in the next step.

To implement the gamma interneuron you will need to create a variable
`gammaNeuron`

containing the same kind of structure as a
pyramidal cell. (There is only one of these interneurons in the
simulation so you don't need an array of them.) This neuron should
receive excitatory input from the pyramidal cells, which you can model
as a single input current using the last spike time of the most
recently-fired pyramidal cell.

Write an `updateGamma`

function to update the state of the
gamma interneuron, using the appropriate parameters for that neuron instead
of the ones for the pyramidal cell.

Modify your `updatePyramid`

function to include inhibitory
input from the gamma interneuron. Modify your display code to display
the gamma interneuron's firing.

In the above plot, the black asterisks mark theta cell spikes, and the membrane voltage of the gamma cell is shown as a black line. The first input is at t=100 msec and the second at t=475 msec. The gamma cell trace is scaled and translated downward to get it out of the way of the pyramidal cell voltage traces.

Run your simulation with four pyramidal cells for 1510 time steps. Input should come at t=100 for the first cell, t=225 for the second, t=355 for the third, and t=605 for the fourth. Verify that the relative spike times are stable.

`spikestats`

that is called after the simulation has run,
and prints out the following statistics separately for each pyramidal cell:
- Time of each spike
- Inter-spike interval for each spike, i.e., the time between this spike and the previous one
- Phase of each spike relative to the theta cycle

- The answers to the questions posed in the text above.
- Plots of your anorm functions.
- A screen capture of the plot your simulation produces.
- The output of the spikestats function.
- Your MATLAB code.

- See this suggestion about global variables.
- In order for gamma inhibition to work correctly you must have the
correct value of anorm; the instructions for
`find_anorm`

specify that you should search for the maximum conductance using t values in increments of 0.01 msec. If you use increments of 1 msec you will get a poor result. Also, for the gamma current, the G parameter must be increased from 100 to 150. - The conductance parameters given here were tuned for Δt = 1 msec. To use a finer-scale Δt value, which would reduce quantization error, the conductances would have to be tweaked a bit. You're not being asked to do that.
- The table of parameters in the paper shows the leak conductance
as 111, but the text says that g
_{leak}= C/τ_{leak}, which might lead you to infer that the value should be 1/9 = 0.111. They messed up on the units. The 111 value is correct. In general, don't worry about getting the units right; just use the numbers in Table 1. - Be sure to use a 2 millisecond refractory period.

Dave Touretzky Last modified: Wed Dec 23 23:17:35 EST 2015