## Getting Started with Electrophysiology

These steps will guide you through the creation of a new Electrophysiology model using the model editor, compile the model on a remote server, solve a problem on that server, using the client/server architecture of Continuity and setup an anatomically accurate rabbit ventricular mesh with orthotropic conductivity using your newly created model.

### Continuity Client/Server

Install Continuity on the Cluster (follow "Getting started with Electrophysiology on a cluster").

- Run Continuity from the server as a client only and load the Electrophysiology module.

### Model Editor

Add a new model by

*Fenton and Karma, 1998, Chaos, 8, 20-47.*- Go to Electrophysiology - Edit - Ionic Model - Add new model
Name your model as

**EP_Fenton_Karma_model**- Add the Author's name and details about the model
Switch tab to

**Edit equations**and setup your EP model as follows:- CONSTANTS
u_v = 0.04

u_csi = 0.85

tau_si = 30

k = 10

u_c = 0.13

Cm = 1

g_fi_max = 4

tau_w_plus = 870

tau_w_minus = 41

V_0 = -85

V_fi = 15

tau_v_plus = 3.33

tau_v1_minus = 1250

tau_v2_minus = 19.6

tau_r = 33

tau_0 = 12.5

u_v = 0.04

u_csi = 0.85

tau_d = Cm/g_fi_max

- GATING_PARAMETERS
q = HeavisideEq(u-u_v)

p = HeavisideEq(u-u_c)

tau_v_minus = q*tau_v1_minus + (1-q)*tau_v2_minus

- CURRENTS
J_si = - w * (1 + tanh(k*(u-u_csi))) / (2*tau_si)

J_so = u*(1-p)/tau_0 + p/tau_r

J_fi = -v*p*(1-u)*(u-u_c)/tau_d

I_fi = J_fi*Cm*(V_fi - V_0)

I_si = J_si * Cm * (V_fi - V_0)

I_so = J_so * Cm * (V_fi - V_0)

- STIMULUS
J_stim = stim_amp * HeavisideEq( t - t_start ) * (1 - HeavisideEq( t - t_end))

I_stim = J_stim * Cm * (V_fi - V_0)

- STATE_VARIABLES
du_dt = - (J_fi + J_so + J_si - J_stim)

dv_dt = ((1-p) * (1-v)/ tau_v_minus) - (p*v/tau_v_plus) (as spatially coupled variable)

dw_dt = ((1-p)*(1-w)/tau_w_minus) - (p*w/tau_w_plus)

- CONSTANTS
- Set your Initial Values and Set the Parameters properly
You can also find a text file with the model here

Switch to the

**Compile**tab and Save and Compile your model and**Submit**

### Model Setup

Start with Rabbit_model

**Load**the file,**Send**,**Calculate Mesh**,**Render**lines- A few things need to be noticed:
- Integration/collocation points are 2 rather than 3
TriCubic Hermite basis function (should be the first basis selected)

TriLinear Lagrange Basis function should be defined too

- Go to View - Edit Dimensions and Apply Marked Recommendations
- Go to View - Set Divisions to maybe 4
- Go to View - Change Renderer and make sure that you are using Open Mesh
Open the

**Nodes**form and verify that:**Fiber Fields**are defined: (**Mesh > Edit > Material Coordinates > Mat Coord Standard**and the Fiber, Transverse and Sheet parameters are setup to the right Fields)**Field 1**contains the stimuli at the desired nodes. To verify this you can render the Field. To set it up click "Change list" and Apply value**15.0**to node list**.*stim.***of**Field 1 Value****Field 2**has a Tri-Cubic basis function and is set to the value of the resting Voltage of the cell model

- Render Surfaces (that is necessary to solve)

#### Diffusion Tensor Transformation

- The Conductivity is a diagonal matrix at the fiber angle orientation and is defined as:
(f11) Dfiber

0

0

0

f(22) Dtransverse

0

0

0

f(33) Dsheet

To Calculate the conductivity tensor (

**Electrophysiology > Edit > Conductivity Model > Standard Conductivity**) and setup the values for f11, f22 and f33 using either a constant value or a field and**Submit**(If you want to define a higher conductivity for the endocardial nodes, simply define it on a field by clicking "Change list" in the**Nodes**form and Apply value for all nodes list and then Apply a higher value to node list containing**.*endo.***of**Field 3 Value**. You should setup**f22**on**Fields 4**and**f33**on**Field 5**respectively for an orthotropic conduction).- Recalculate mesh
- Setup Ionic Model
Choose

**Your Model**- u = Field 2
- Stim_Amp = Field 1

**Send****Initialize****Calculate Constraints**(Fix out of plane...)**Reset >**Save,reset, and reload**Recalculate Mesh****Initialize****Electrophysiology > Solve > Integration**Setup the Duration of your stimulus (at least 300ms recommended for this simulation), select the name of your**Output**file. Go to**> Output**and increase the number of display solutions to at least 20.**Calculate**Retrieve your solution and

**Render Solution**(make sure to use -85.0 and 15.0 for Max and Min value)

## Potential Gotchas?

- Must calculate mesh after changing basis functions of fields
- Maybe memory error with too many frames?
- The solution was written at the server and it needs to be retrieved by the client
- Rendering frames is somewhat slow