diff --git a/docs/formulation.tex b/docs/formulation.tex index 3275b658be483d37dfe494d094cde87d962d1700..84cb4ac06177891c1f68d3009c1dc48a6ac8dedd 100644 --- a/docs/formulation.tex +++ b/docs/formulation.tex @@ -211,6 +211,63 @@ is the area of the surface between two adjacent segments $i$ and $j$, and \end{equation} is the lateral area of the conical frustrum describing segment $i$. +%------------------------------------------------------------------------------- +\subsubsection{Time Stepping} +%------------------------------------------------------------------------------- +The finite volume discretization approximates spatial derivatives, reducing the original continuous formulation into the set of ODEs, with one ODE for each compartment, in equation~\eq{eq:ode}. +Here we employ an implicit euler temporal integration sheme, wherby the temporal derivative on the lhs is approximated using forward differences +\begin{align} + \sigma_i c_m \frac{V_i^{k+1}-V_i^{k}}{\Delta t} + = & -\sum_{j\in\mathcal{N}_i} {\frac{\sigma_{i,j}}{r_L \Delta x_{i,j}} (V_i^{k+1}-V_j^{k+1})} \nonumber \\ + & - \sigma_i\cdot(i_m(V_i^{k}) - i_e), + \label{eq:ode_subs} +\end{align} +Where $V^k$ is the value of $V$ in compartment $i$ at time step $k$. +Note that on the rhs the value of $V$ at the target time step $k+1$ is used, with the exception of calculating the ion channel and synaptic currents $i_m$. +The current $i_m$ is often a nonlinear function of voltage, so if it was formulated in terms of $V^{k+1}$ the system in~\eq{eq:ode_subs} would be nonlinear, requiring Newton iterations to resolve. + +The equations can be rearranged to have all unknown voltage values on the lhs, and values that can be calculated directly on the rhs: +\begin{align} + & V_i^{k+1} + \sum_{j\in\mathcal{N}_i} {\frac{\alpha_{ij}}{\sigma_i} (V_i^{k+1}-V_j^{k+1})} + \nonumber \\ + = & V_i^k - \frac{2\Delta t}{ac_m}(i_m^{k} - i_e), + \label{eq:ode_linsys} +\end{align} +where the value +\begin{equation} + \alpha_{ij} = \alpha_{ji} = \frac{\Delta t \sigma_{ij}}{ c_m \Delta x_{ij}} + \label{eq:alpha_linsys} +\end{equation} +is a constant that can be computed for each interface between adjacent compartments during set up. + +%------------------------------------------------------------------------------- +\subsubsection{Example: unbranched uniform cable} +%------------------------------------------------------------------------------- +For an unrbanched uniform cable of constant radius $a$, with length $L$ and $n$ compartments, the linear system for internal compartments (i.e. not at the end points of the cable) is simplified by the following observations +\begin{align} + \Delta x_{ij} &= \Delta x = \frac{L}{n-1}, \nonumber \\ + \sigma_{ij} &= \pi a^2, \nonumber \\ + \sigma_{i} &= 2 \pi a \Delta x, \nonumber \\ + \alpha_{ij} &= \frac{\pi a^2\Delta t}{c_m\Delta x}, \nonumber \\ + \frac{\alpha_{ij}}{\sigma_i} + &= \frac{a\Delta t}{2c_m\Delta x^2}. \nonumber +\end{align} +With these simplifications, the lhs of the linear system is +\begin{align} + & V_i^{k+1} + \beta (V_i^{k+1}-V_{i+1}^{k+1}) + \beta (V_i^{k+1}-V_{i-1}^{k+1}) + \nonumber \\ + = & (1+2\beta)V_i^{k+1} - \beta V_{i+1}^{k+1} - \beta V_{i-1}^{k+1}. +\end{align} +where $\beta=\frac{a\Delta t}{2c_m\Delta x^2}$. + +The end points of the cable, i.e. the compartments for $x_1$ and $x_n$, have to be handled differently. +If we assume that a no-flux boundary condition, i.e. $\vv{J}\cdot\vv{n}=0$, is imposed at the end of the cable, the lhs of the linear system are +\begin{align} + (1+2\beta)V_1^{k+1} - 2\beta V_{2}^{k+1}, \quad\quad & \text{left} \nonumber \\ + (1+2\beta)V_n^{k+1} - 2\beta V_{n-1}^{k+1}, \quad\quad & \text{right} \nonumber +\end{align} +where we note that the ratio $\alpha_{ij}/\sigma_{i}=2\beta$ because the surface area of the control volumes at the boundary are half those on the interior. + %------------------------------------------------------------------------------- \subsubsection{Handling branches} %-------------------------------------------------------------------------------