Thermodynamics of a pseudoknot polymer formation
Date Issued
2004
Date
2004
Author(s)
Mau, You-Chun
DOI
zh-TW
Abstract
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.
Subjects
蒙地卡羅模擬法
熱力性質
pseudoknot polymer
Monte Carlo simulation
Type
thesis
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