diff --git a/docs/report.tex b/docs/report.tex index 54d93c8dcfd449fe70b095113e2a1930b12cf4e7..0f816e1c25a7aa22b7199df27a0cd3d8216f9dc2 100644 --- a/docs/report.tex +++ b/docs/report.tex @@ -72,6 +72,9 @@ \newcommand{\dder}[2]{\frac{\deriv{#1}}{\deriv{#2}}} \newcommand{\vv}[1]{\bm{#1}\xspace} +\newcommand{\unit}[1]{\left[{#1}\right]} +\newcommand{\txtunit}[1]{$\left[{#1}\right]$} + %---------------------------------------------------------------------------------------- % ARTICLE INFORMATION %---------------------------------------------------------------------------------------- diff --git a/docs/symbols.tex b/docs/symbols.tex index 19db4a374eb9a3697bcb8971ca2cca9e0b40877e..e12b55820da048ffef27bb790fca4e0b363ba23e 100644 --- a/docs/symbols.tex +++ b/docs/symbols.tex @@ -1,3 +1,113 @@ +%------------------------------------------------------------------------------- +%\subsubsection{Balancing Units} +%------------------------------------------------------------------------------- +Ensuring that units are balanced and correct requires care. +Take the description of the nonlinear system of ODEs that arises from the finite volume discretisation +\begin{equation} + \label{eq:linsys_FV} + V_i^{k+1} + \sum_{j\in\mathcal{N}_i} {\frac{\Delta t \alpha_{ij}}{\sigma_i} (V_i^{k+1}-V_j^{k+1})} + = V_i^k - \frac{\Delta t}{c_m}(i_m^{k} - i_e). +\end{equation} +The choice of units for a parameter, e.g. $\mu m^2$ or $m^2$ for the area $\sigma_{ij}$, introduces a constant of proportionality wherever it is used ($10^{-12}$ in the case of $\mu m^2 \rightarrow m^2$). +Wherever terms are added in \eq{eq:linsys_FV} the units must be checked, and constants of proportionality balanced. + +First, appropriate units for each of the parameters and variables are chosen in~\tbl{tbl:units}. +We try to use the same units as NEURON, except for the specific membrane capacitance $c_m$, for which $F\cdot m^{-2}$ is used in place of $nF\cdot mm^{-2}$. +In \eq{eq:linsys_FV} we choose units of $mV \equiv 10^{-3}V$ for each term because of the $V_i$ terms on either side of the equation. + +\begin{table}[hp!] +\begin{tabular}{lllr} + \hline + term & units & normalized units & NEURON \\ + \hline + $t$ & $ms$ & $10^{-3} \cdot s$ & yes \\ + $V$ & $mV$ & $10^{-3} \cdot V$ & yes \\ + $a,~\Delta x$ & $\mu m$ & $10^{-6} \cdot m$ & yes \\ + $\sigma_{i},~\sigma_{ij}$ & $\mu m^2$ & $10^{-12} \cdot m^2$ & yes \\ + $c_m$ & $F\cdot m^{-2}$ & $s\cdot A\cdot V^{-1}\cdot m^{-2}$ & no \\ + $r_L$ & $\Omega\cdot cm$ & $ 10^{-2} \cdot A^{-1}\cdot V\cdot m$ & yes \\ + $\overline{g}$ & $S\cdot cm^{-2}$ & $10^{4} \cdot A\cdot V^{-1}\cdot m^{-2}$ & yes \\ + $I_e$ & $nA$ & $10^{-9} \cdot A$ & yes \\ + \hline +\end{tabular} +\caption{The units chosen for parameters and variables in NEST MC. The NEURON column indicates whether the same units have been used as NEURON.} +\label{tbl:units} +\end{table} + +%------------------------------------------ +\subsubsection{current terms} +%------------------------------------------ +Membrane current is calculated as follows $i_m = \overline{g}(E-V)$, with units +\begin{align} + \unit{ i_m } &= \unit{ \overline{g} } \unit{ V } \nonumber \\ + &= 10^{4} \cdot A\cdot V^{-1}\cdot m^{-2} \cdot 10^{-3} \cdot V \nonumber \\ + &= 10 \cdot A \cdot m^{-2}. \label{eq:im_unit} +\end{align} +The injected current $I_e$ has units $nA$, which has to be expressed in terms of current per unit area $i_e=I_e / \sigma_i$ with units +\begin{align} + \unit{ i_e } &= \unit{ I_e } \unit{ \sigma_i }^{-1} \nonumber \\ + &= 10^{-9}\cdot A \cdot 10^{12} \cdot m^{-2} \nonumber \\ + &= 10^{3} \cdot A \cdot m ^{-2}, \label{eq:ie_unit} +\end{align} +which must be scaled by $10^2$ to match $i_m$ in \eq{eq:im_unit}. + +The units for the flux coefficent can be calculated as follows: +\begin{align} + \unit{ \frac{\Delta t}{c_m} } &= 10^{-3} \cdot s \cdot s^{-1}\cdot A^{-1}\cdot V\cdot m^2 \nonumber \\ + &= 10^{-3} \cdot A^{-1} \cdot V\cdot m^2. \label{eq:dtcm_unit} +\end{align} +From \eq{eq:im_unit} and \eq{eq:dtcm_unit} that the units of the full current term are +\begin{align} + \unit{ \frac{\Delta t}{c_m}\left(i_m - i_e\right) } + &= 10^{-3} \cdot A^{-1} \cdot V\cdot m^2 \cdot 10 \cdot A \cdot m^{-2} \nonumber \\ + &= 10^{-2} \cdot V, +\end{align} +which must be scaled by $10$ to match the units of $mV\equiv10^{-3}V$. +%------------------------------------------ +\subsubsection{flux terms} +%------------------------------------------ +The coefficients in the linear system have the units +\begin{equation} + \unit{ \frac{\Delta t\alpha_{ij}}{\sigma_i} } + = + \unit{ \frac{\Delta t \sigma_{ij} } {c_m r_L \Delta x_{ij} \sigma_i} } + = + \unit{ \frac{\Delta t } {c_m r_L \Delta x_{ij} } }, +\end{equation} +where we we simplify by noting that $\unit{\sigma_{ij}}=\unit{\sigma_i}$. +The units of the term $c_m r_L$ on the denominator are calculated as follows +\begin{align} + \unit{c_m r_L} + &= s \cdot A \cdot V^{-1} \cdot m^{-2} \cdot 10^{-2} \cdot A^{-1} \cdot V \cdot m \nonumber \\ + &= 10^{-2} \cdot s \cdot m^{-1}, +\end{align} +so the units of the denominator are +\begin{align} + \unit{c_m r_L \Delta x_{ij}} + &= 10^{-2} \cdot s \cdot m^{-1} \cdot 10^{-6} \cdot m \nonumber \\ + &= 10^{-8} \cdot s, +\end{align} +and hence +\begin{align} + \unit{\frac{\Delta t } {c_m r_L \Delta x_{ij} }} + &= 10^{8} \cdot s^{-1} \cdot 10^{-3} \cdot s \nonumber \\ + &= 10^{5}. +\end{align} + +So, the terms with $\alpha_{ij}$ must be scaled by $10^5$ to match the units of $mV$. +%------------------------------------------ +\subsubsection{discretization with scaling} +%------------------------------------------ +Here is something that I wish the NEURON documentation had provided: +\begin{align} +& V_i^{k+1} + \sum_{j\in\mathcal{N}_i} {10^5 \cdot \frac{\Delta t \alpha_{ij}}{\sigma_i} (V_i^{k+1}-V_j^{k+1})} \nonumber \\ +& = V_i^k - 10\cdot \frac{\Delta t}{c_m}(i_m^{k} - 10^2\cdot I_e/\sigma_i). +\end{align} +%------------------------------------------ +\subsection{Supplementary Unit Information} +%------------------------------------------ +Here is some information about units scraped from Wikipedia for convenience. + \begin{table*}[htp!] \begin{center} @@ -15,6 +125,8 @@ \hline \end{tabular} + \vspace{20pt} + \begin{tabular}{llll} \hline symbol & unit & equivalents & SI base \\ @@ -44,27 +156,4 @@ \end{center} \caption{Symbols and quantities.} \end{table*} -%------------------------------------------------------------------------------- -\subsubsection{Units} -%------------------------------------------------------------------------------- -Reffering to the cable equation first defined in~\eq{eq:cable} -\begin{equation*} - c_m \pder{V}{t} = \frac{1}{2\pi a r_{L}} \pder{}{x} \left( a^2 \pder{V}{x} \right) - i_m + i_e, -\end{equation*} - -If the units are taken to be -\begin{itemize} - \item $c_m = F\cdot cm^{-2}$ - \item $V = V$ - \item $a = cm$ - \item $r_L = \Omega\cdot cm$ -\end{itemize} -Then the units of each term in equation are $A\cdot cm^{-2}$. -In practice, the units above are not used, for example distances are usually measured in $\mu m$ and areas in $cm^2$. -But if we work term-by-term, scaling for these factors is manageable. - -A useful identity to use when performing the dimensional analysis relates capacitance and resistance -\begin{equation*} - 1~F = 1~\Omega^{-1} \cdot s -\end{equation*}