# Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Random Walk Formula

(Difference between revisions)
 Revision as of 08:47, 2 October 2011 (view source) (→General Modeling Idea)← Previous diff Revision as of 08:49, 2 October 2011 (view source) (→Random Walk Formula)Next diff → Line 3: Line 3: __TOC__ __TOC__ ==General Modeling Idea== ==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 the adjacent one. Various formulae had been developed to model this process, but none of them can perfectly match our situation (Weesakul, 1961; Hardin & Sweet, 1969; Alessandro Blasi, 1976; Ahmed El-Shehawy, 1992). + 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 the adjacent one. Line 11: Line 11: [[Image:RW.bmp|thumb|center|800px|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.  ]] [[Image:RW.bmp|thumb|center|800px|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.  ]] + + {{Template:DeoxyriboNucleicAwesomeFooter}} {{Template:DeoxyriboNucleicAwesomeFooter}}

## Revision as of 08:49, 2 October 2011

Friday, August 22, 2014

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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 the 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.