Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Random Walk Formula

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Random Walk Formula

General Modeling Idea

The 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.


Figure 1. Modeling the random walk on DNA origami as one dimensional random walk. Cyan, markers. Blue, Track 1. Red, Track 2. White, DNA staples only. Five-pointed star, walker goal. Each step is modeled as walking from one rectangle to an adjacent one. SP 10, 22, 34 indicate different starting positions. Note that in the cases of SP22 and SP34, there are no tracks to the left of starting positions.

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.

Figure 2. A line segment with N+1 distinct sites. The walker starts the random walk at i and is reflected at N with a probability of β. The random walk ends once it reaches site 0.

Random Walk Formula

Two 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(t-1;i-1) + r·h(t-1;i) + p·h(t-1; 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,...,N-1\!} . 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(t-1;N)+ βh(t-1; N-1) \!}

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=1}^∞ h(t;1)s^t} , 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 \!}

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) = \frac {q^i s^i T_i (s)} {T_0 (s)}, 0\leqslant i < N \!}

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 H_N (s) = \frac {\beta q^{N-1} s^N (\lambda_1 - \lambda_2)} {T_0 (s)},\!}

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 ^{N-i}-\lambda_2 ^{N-i})-\beta p s^2 (\lambda_1 ^{N-i-1}-\lambda_2 ^{N-i-1})\!}

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{{(1-rs)}^2-4 p q s^2} +1-rs ).\!}

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

References

  • Feller, W. (1971). An introduction to probability theory and its applications.
  • Netus, M. (1963). Absorption probabilities for a random walk between a reflecting and an absorbing barrier. Bull. Soc. Math. Belgique, 15, 253-258.