Thermodynamics of a pseudoknot polymer formation

• Main Authors: You-Chun Mau, 毛佑群
• Other Authors: Y.-J. Sheng
• Format: Others
• Language: zh-TW
• Published: 2004
• Online Access: http://ndltd.ncl.edu.tw/handle/91759085179540660995

碩士 === 國立臺灣大學 === 高分子科學與工程學研究所 === 92 === The kinetics of conformational fluctuations of a pseudoknot polymer is studied by Monte Carlo simulation. The polymer chain is modeled as having two pair of binding sites at interior with binding energies of -ε1 and -ε2 (ε1 < ε2). Firstly, the length of each section divided by the binding sites are increased proportionally. We find that the rate constants form state 0 to state 2 or 5 scale as N2.48 and the rate constants form state 2 or 5 to state 0 is independent of chain length but proportional to e-ε/kT. The probability of state 2 decreases with increasing chain length and may be zero as N→∞. The four-state system will become a three-state system. In the figure of heat capacity plotted against temperature, two peaks are observed representing the transitions between state 0 and 5, and between 5 and 7. In the second part of the work, the total polymer chain length is fixed as 40 and the length of both end sections is set to be 3. By increasing the distance between pair of binding energy -ε1 and at the same time decreasing the distance between pair of binding energy -ε2,the probability of state 2 increases and the probability of state 5 decreases. This result indicates that we can control the folded forms of a pseudoknot by adjusting the length of each section divided by binding sites on the chain.