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DNA Comparison of Potential Energy, RMS Deviation, Electrostatic Energy

  1. Dec 5, 2008 #1
    1. The problem statement, all variables and given/known data
    I am comparing a normal DNA decamer molecule with one in which the two strands are only connected by the two base pairs on one of the ends. It was determined that the potential energies of both DNA molecules are negative, with values for the normal DNA much more negative than broken DNA. It was also determined that root-mean-squared (RMS) deviations were positive for both DNA molecules (and increasing over time), with values for the broken DNA much more positive than those of the normal DNA. It was also determined that the electrostatic energy for the broken DNA was higher than that of the normal DNA.

    I need help explaining why the potential energies, RMS deviations, and electrostatic energies are the way they are.

    2. Relevant equations
    N/A

    3. The attempt at a solution

    In the normal DNA, the molecules are closer to each other, allowing for more hinderance between the molecules, which affects the potential energies, RMS deviations, and electrostatic energies. I just do not know what else I can include in my answer.
     
  2. jcsd
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