# 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.

### 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)
• 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

• 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