Prediction and simulation on DNA strand displacement for the analysis of DNA nanotechnology

Abstract

The objective of this work is to study the simulation techniques to simulate the time interval between displacements of deoxyribonucleic acid (DNA) strands efficiently and predict the simulation. In this work, two algorithms are proposed. The first proposed algorithm, modified Viterbi algorithm (MVA), is used to find sequence of hidden states and predict the sequence for the hidden DNA structure. Another proposed algorithm, modified Gillespie algorithm (MGA), integrates the stochastic processes such as Gillespie algorithm (GA) and next reaction method (NRM), is used to simulate the displacement of strands efficiently. The dataset used in this work is Droshipilla melanogaster. The output is the simulation of time interval between the strands. When the time interval between the strands increases the number of molecules also increases according to the time. This work resulted the simulated time interval between the displacements of strands and obtained the efficient simulation of strand displacement for the prediction of molecular structure and interaction between molecules.