Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Random Walk Formula
Tuesday, November 21, 2017

ContentsRandom Walk FormulaModeling IdeaThe random walk on DNA origami can be modeled as one dimensional random walk with a reflecting and an absorbing barrier (Figure 1). Tracks in the same column are grouped into rectangles, and each step is defined as walking from one rectangle to an adjacent one. We are interested in expressing the probability of reaching the walker goal as a function of the number of steps taken.
Consider a random walk on a line segment with N+1 sites denoted by integers (0,1,2, … , N) (Figure 2). The walker starts random walk at site i, 0 < i ≤ N. Let p be the probability for the walker to move one segment to the left, q be the probability for the walker to move one segment to the right. The probability for the walker to stay at a particular site for the next unit time is thus r = 1 – p – q. When the walker reaches site N, the partially reflecting barrier, it has a probability of β to be reflected back to site N – 1, and a probability of α = 1 – β to stay at site N in the next unit time. When reaching site 0, the absorbing barrier, it stays there for 100% probability and the random walk ends. General ApproachTwo assumptions are made in our case. 1) The DNA origami is immune to any free floating walkers in solution, meaning that free floating walkers cannot bind to an origami and starts random walking; 2) walkers are immediately absorbed when reaching the rectangles with WGs, despite the presence of two TR2 in the same rectangle. Let Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle h(t;i)\!} be the probability that the walker reaches 0 for the first time after Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle t\!} steps given its starting position being Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle i\!} . Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle h(t;i)\!} obeys the following difference equation Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle h(t;i) = q·h(t1;i1) + r·h(t1;i) + p·h(t1; i + 1)\!}
for Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle t = 1,2,3,...\!} and Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle i = 1,2,3,...,N1\!} . We define Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle h(t;0)= 1\!} Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle if\!} Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle t = 0\!} ; Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle h(t;0)= 0\!} Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle if\!} Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle t > 0\!} . Also, Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle h(t;i) = 0\!} Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle for\!} Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle t < i\!} . When Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle i = N\!} we have Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle h(t;N) = αh(t1;N)+ βh(t1; N1) \!}
The generating function for Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle h(t;i)\!} can be expressed as Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle H_i (s) = \sum_{t=0}^\infty h(t;1)s^t,s <1 \!}
Following Netus (1963), the explicit expression of the generating function is Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle H_i (s) =\begin{cases} \frac {q^i s^i T_i (s)} {T_0 (s)}, 0\leqslant i < N\\ \frac {\beta q^{N1} s^N (\lambda_1  \lambda_2)} {T_0 (s)},i=N\end{cases}\!}
where Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle T_i (s) = (1\alpha s)(\lambda_1 ^{Ni}\lambda_2 ^{Ni})\beta p s^2 (\lambda_1 ^{Ni1}\lambda_2 ^{Ni1})\!}
and Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle \lambda_{1,2} = \frac {1} {2} ( \pm \sqrt{{(1rs)}^24 p q s^2} +1rs ).\!}
The explicit expression of Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle h(t;i)\!} can thus be deduced from Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle H_i (s)\!} using partial fraction expansion (Feller, 1971). Assume that Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle T_0 (s)\!} has Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle k\!} distinct roots Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle s_1,s_2,..., s_k . H_i (s)\!} can then be decomposed into partial fractions Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle H_i (s) = \frac {\rho_1} {ss_1} + \frac{\rho_2}{ss_2} +...+ \frac {\rho_k}{ss_k} \!}
where Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle \rho_k = \frac {q^i {s_m}^i T_i (S_m)}{{T_0}^' (s_m)}, m\leqslant k \!}
It follows that Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle h(t;i) = \sum_{m=1}^k \frac {\rho_m}{{s_m}^{t+1}} \!}
Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle h(t;N)\!} can be similarly deduced from Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle H_N (s)\!} using the same method. Parameter EstimationPossible positions of walkers on the origami can be grouped into two categories, either in the center of rectangles (Figure 1, Line 2) or at the sides (Figure 1, Lines 1&3), and the values of Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle p\!} , Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle q\!} and Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle r\!} are different in each category. Hence there is a need to find out the distribution of walkers in these two categories in order to estimate Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle p\!} , Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle q\!} and Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle r\!} . Due to the nature of our design, each walker has a probability of 50% to stay at its original track after one branch migration. Assuming no reflecting boundaries, when the walker is in the center (Figure 1, Line 2), the probability of staying in Line 2 after one branch migration is Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle \frac {1}{2}+\frac{1}{2} \times \frac{1}{2}=\frac{3}{4}} , while the probability of going to Lines 1 or 3 is Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle 1 \frac{3}{4}=\frac{1}{4}} . Similarly, when it is in Lines 1 or 3, the probability of staying in the same line after one branch migration is Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle \frac{1}{2}+\frac{1}{2} \times \frac{2}{3}=\frac{5}{6}} while the probability of going to Line 2 is Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle 1 \frac{5}{6}=\frac{1}{6}} . Here we assume no reflecting barrier in the system. The distribution of relative positions of walkers can be modeled using Markov chain as follows. Let Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle v(t) = (a, 1–a)\!} denote the proportion of walkers in Line 2 Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle (a)\!} and Lines 1&3 Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle (1–a)\!} after Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle t\!} branch migrations. Since all the walkers are initially planted in the center, Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle v(0) = (1, 0)\!} . Define the transition matrix Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle M = \begin{pmatrix} 3/4 & 1/4 \\ 1/6 & 5/6 \end{pmatrix}. \!}
It follows that Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle v(t)=v(0). \underbrace{M.M.M...M}_{t} \!}
It was found that Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle \lim_{t \to \infty} v(t)= (0.4,0.6).} Hence at the stable state, 40% of the walkers are in Line 2 while 60% are in Lines 1 or 3. Since Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle v(8) = (0.408,0.592)\!} , the distribution of relative positions of walkers on the origami stabilizes after approximately 8 branch migrations. The overall probabilities Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle p, q, r, \alpha,\beta\!} can thus be calculated (Table 1).
Explicit Expression of FormulaeThe explicit expression for the probability of reaching the walker goal (h(t;i)) as a function of the number of steps taken (t) can then be deduced using the general approach and the estimated parameters. Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle SP10: h(t;12)= \begin{cases} 0, 0\leqslant t < 12\\ \frac{0.0032}{1.0025^{t+1}}  \frac{0.0097}{1.0226^{t+1}} + \frac{0.0166}{1.0639^{t+1}}  \frac{0.02407}{1.1283^{t+1}} + \frac{0.0323}{1.2189^{t+1}} \frac{0.0410}{1.3387^{t+1}} \\ \quad +\frac{0.0494}{1.4908^{t+1}} \frac{0.0556}{1.6753^{t+1}} +\frac{0.0565}{1.8863^{t+1}} \frac{0.0482}{2.1070^{t+1}} +\frac{0.0301}{2.3071^{t+1}} \frac{0.0094}{2.4487^{t+1}} ,t \geqslant 12\end{cases}}
Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle SP22: h(t;8)= \begin{cases} 0, 0\leqslant t < 8\\ \frac{0.0070}{1.0055^{t+1}} \frac{0.0218}{1.0507^{t+1}} +\frac{0.0383}{1.1458^{t+1}} \frac{0.0569}{1.2998^{t+1}} +\frac{0.0751}{1.5222^{t+1}} \frac{0.0838}{1.8117^{t+1}} +\frac{0.0677}{2.1327^{t+1}} \frac{0.0257}{2.3970^{t+1}} ,t \geqslant 8\end{cases}}
Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "https://api.formulasearchengine.com/v1/":): {\displaystyle SP34: h(t;4)= \begin{cases} 0, 0\leqslant t < 4\\ \frac{0.0272}{1.0212^{t+1}} \frac{0.0893}{1.2034^{t+1}} +\frac{0.1522}{1.6168^{t+1}} \frac{0.1094}{2.1994^{t+1}} ,t \geqslant 4\end{cases}}
References
