Please use this identifier to cite or link to this item: http://scholarbank.nus.edu.sg/handle/10635/13264
Title: Monte Carlo simulation of a supercoiled double-stranded DNA model
Authors: CHUNG WENG YEW
Keywords: Monte Carlo DNA Double-Stranded Writhe Linking
Issue Date: 2-Jun-2008
Source: CHUNG WENG YEW (2008-06-02). Monte Carlo simulation of a supercoiled double-stranded DNA model. ScholarBank@NUS Repository.
Abstract: An efficient Monte Carlo Metropolis simulation [Monte Carlo et al, 1953] wasconducted on the double stranded DNA model proposed by [Zhang et al, 2000]. Themodel was mathematically discussed in detail and the calculation time for the energycomponents were improved. The mathematical characteristic of the writhe calculationwas also examined and a fast algorithm which reduces the writhe calculation by 45-55% was presented. The method was verified with the conventional algorithm and thecalculated writhe was found to be accurate within usable limits. The force versusextension and supercoiling degree versus extension relationships of the model werealso investigated and verified with the experimental results published by [Strick et al,1998]. The results obtained from the simulation coincide reasonably with theexperimental measurements.
URI: http://scholarbank.nus.edu.sg/handle/10635/13264
Appears in Collections:Master's Theses (Open)

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1. Chapter - Cover & Title.pdf15.58 kBAdobe PDF

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2. Chapter i - Acknowledgements.pdf11.18 kBAdobe PDF

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3. Chapter ii - Table of Contents.pdf28.9 kBAdobe PDF

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4. Chapter iii - Summary.pdf23.55 kBAdobe PDF

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5. Chapter iv - List of Tables.pdf13.58 kBAdobe PDF

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6. Chapter v - List of Figures.pdf26.29 kBAdobe PDF

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7. Chapter vi - References.pdf25.57 kBAdobe PDF

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8. Chapter 1 - Introduction.pdf37.73 kBAdobe PDF

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9. Chapter 2 - Statistical Mechanics.pdf164.85 kBAdobe PDF

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10. Chapter 3 - DNA Model.pdf152.49 kBAdobe PDF

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11. Chapter 4 - Move Generations.pdf100.92 kBAdobe PDF

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12. Chapter 5 - Supercoiling Degree of DNA.pdf459.69 kBAdobe PDF

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13. Chapter 6 - MC Metropolis Simulation.pdf154.64 kBAdobe PDF

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14. Chapter 7 - Conclusion.pdf32.43 kBAdobe PDF

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15. Chapter A - Simulation Flow Chart.pdf33.35 kBAdobe PDF

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