Biomod/2011/Caltech/DeoxyriboNucleicAwesome/Random Walk Formula
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Tuesday, May 30, 2017

Random Walk Formula
General Modeling 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.
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. Random Walk FormulaTwo 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 h(t;i) be the probability that the walker reaches 0 for the first time after t steps given its starting position being i. h(t;i) obeys the following difference equation h(t;i) = qh(t − 1;i − 1) + rh(t − 1;i) + ph(t − 1;i + 1)
