notes from analytical exploration of effects of chain length on mRNA variability

The details of this approach are not valid, since we require reversability to use this form for the variance.

excised text from review draft:

% Using Sanchez Approach
Since only one state in the gestation cycle is transcriptionally competent, all but one element of $\vec{r}$ in equations \ref{eq:Sanchez2} and \ref{eq:Sanchez3} is zero. The mean expression level has the simple form,
\begin{equation}
\mu_m = \frac{k_t}{\delta} \frac{1}{ \sum\limits_{i=1}^N i k_b^{N-i} k_f^{i-1} }
\end{equation}

Consequently the second moment of the mRNA distribution depends only on the $(N,N)$ element of inverted, modified transition matrix,
\begin{equation}
<m^2> = \mu_m – 1/\delta*kt^2 \frac{1}{\sum\limits_{i=1}^N i k_b^{N-i} k_f^{i-1} \left[(M^T-\delta \mathbb{I})\right]_{N,N}}
\end{equation}

Denoting $A_{N,N} = \left[(M^T-\delta \mathbb{I})\right]_{N,N}$ and denoting by $B$ submatrix generated by leaving off the last row and last column from $A$,

\begin{equation}
A^{-1}{N,N} = \frac{\det(B)}{\det{A}} = \frac{\det(B)}{\det(B) (-k_f-k_b-\delta-B{N,1}^{-1}k_f^2 – B_{N,N}^{-1} k_f k_b)}
\end{equation}
which since $B$ is tridiagonal we can evaluate by solving the recurrence relation for the inverse of tridiagonal matrices as presented by \citet{Usmani1994}. The resulting explicit expressions for the second moment, the variance, and the coefficient of variation as a function of the rate parameters is not especially compact.

%\begin{equation}
%A^{-1}{N,N} = \left( -k_f -k_b – \delta – (-1)^N k_f^N\frac{1}{theta{N-1}} – \frac{\theta_{N-2}}{\theta_{N-1}} k_f k_b \right)^{-1}
%\end{equation}
%Note that $\theta_{i}$ come from the solutions of the recurrence relation, and that $\theta_{N-1} = \det(B)$.

%\begin{equation}
%\right[(M^T – \delta \mathbb{I})^{-1}\left]{ij} =
%\begin{cases}
%(-1)^{i+j}b_i\ldots b
{j-1},\theta_{i-1}\phi_{j+1}/\theta_n & \text{if } i \leq j\
%(-1)^{i+j}c_j\ldots c_{i-1},\theta_{j-1}\phi_{i+1}/\theta_n & \text{if } i \g j\
%\end{cases}
%\end{equation}
%Where $b_i = k_b$, $c_i=k_f$ and the $\theta_i$ and $\phi_i$ are given by the recurrence relation,
%\begin{equation}
%\theta_i = a_i \theta_{i-1} = b_{i-1}c_{i-1}\theta_{i-2}
%\end{equation}

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