Physics – Biological Physics
Scientific paper
2011-03-06
Physics
Biological Physics
5 main pages, 3 main figures, 10 pages for additional information. The DNA system is not appropriate for testing the theorem.
Scientific paper
Jarzynski's equality [1] allows us to investigate free energy landscapes (FELs) by constructing distributions of work performed on a system from an initial ensemble of states to final states. This work is experimentally measured by extension-versus-force (EVF) curves. We proposed a new approach that enables us to reconstruct such FELs without necessity of measuring EVF curves. We proved that any free energy changes could be computed by measuring the fluctuations of a harmonic external potential in final states. The main assumption of our proof is that one should probably treat a potential's minimum {\lambda} (thought to be control parameter) and time in separate and independent manners. We recovered Jarzynski's equality from the introduction of a double Heaviside function. We then applied the approach in molecular dynamics (MD) simulations to compute the free energy barrier of breaking DNA base pairs (bps). The free energy barrier for breaking a CG bp in our simulations is identified as 1.7 +/- 0.2 kcal/mol that is in a very beautiful agreement with experimental values [2-4] of about 1.9 to 2.1 kcal/mol. Interestingly, the history of our computed free energies probably represents a favorable transition pathway.
No associations
LandOfFree
Potential Fluctuation Equality for Free Energy Evaluation does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.
If you have personal experience with Potential Fluctuation Equality for Free Energy Evaluation, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Potential Fluctuation Equality for Free Energy Evaluation will most certainly appreciate the feedback.
Profile ID: LFWR-SCP-O-606419