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DNA ‘glass transition’ and the LL critical point of water--- a simulation study: 

DNA ‘glass transition’ and the LL critical point of water --- a simulation study

Previous work on DNA: 

Previous work on DNA Glass transition in DNA from molecular dynamics simulations. Norberg J, Nilsson L, Proc Natl Acad Sci U S A. 1996 Sep 17;93(19) Inelastic neutron scattering spectra of DNA-fibers A.P. Sokolov, H. Grimm, A. Kisliuk and A.J. Dianoux J CHem Phys Volume 110, Issue 14, pp. 7053-7057 (1999) Differences of the susceptibility spectra Glass transition T=180-200K, Dynamic crossover T=230K, (MCT ?) Mean square fluctuation T=223 ~ 234K [6 nucleotides: (CGCGCG)2 duplex ] TIP3P

Our Model of DNA: Dickerson Dodecamer: 

Our Model of DNA: Dickerson Dodecamer 12 nucleotides: CGCGAATTCGCG mass:7270.756 amu Drew, H. R., Wing, R. M., Takano, T., Broka, C., Tanaka, S., Itakura, K. & Dickerson, R. E. (1981). Structure of a B-DNA dodecamer: conformation and dynamics. Proc. Natl. Acad. Sci. USA 78, 2179-2183.

Water: TIP5P: 

Water: TIP5P M. W. Mahoney and W. L. Jorgensen, A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions, J. Chem. Phys. 112 (2000) 8910-8922. 1488 water molecules, Hydration:1488*18/7270.756=368%

Simulation: AMBER force field ports for the GROMACS: 

Simulation: AMBER force field ports for the GROMACS Details to see: http://folding.stanford.edu/ffamber/ http://www.gromacs.org/

LL critical point: 

LL critical point Li Liu, Sow-Hsin Chen, Antonio Faraone, Chun-Wan Yen,and Chung-Yuan Mou Phys. Rev. Lett. 95, 117802 (2005) L. Xu, P. Kumar, S. V. Buldyrev, S.-H. Chen, P. H. Poole, F. Sciortino, and H. E. Stanley, "Relation between the Widom Line and the Dynamic Crossover in Systems with a Liquid-Liquid Critical Point,“ Proc. Natl. Acad. Sci. 102, 16558-16562 (2005). Pressure Dependence of Fragile-to-Strong Transition and a Possible Second Critical Point in Supercooled Confined Water TIP5P, ambient pressure T crossover=255K

Results: root mean square fluctuationof DNA atoms (RMSF) : 

Results: root mean square fluctuation of DNA atoms (RMSF) root mean square fluctuation (RMSF, i.e. standard deviation) of atomic positions after first fitting to a reference frame

Results: thermodynamics and dynamics: 

Results: thermodynamics and dynamics Specific Heat of whole system (water+DNA) Diffusion constant of hydration water

Structure change of water:: 

Structure change of water: Radial distribution function Inset: G(r) at first peak as function of T

Structure change of water:: 

Structure change of water: The g(r1) at first peak as function of T, and the slope as function of T

More: root mean square deviation of DNA (RMSD): 

More: root mean square deviation of DNA (RMSD) Each structure from a trajectory is compared to a reference structure dt time ago by least-squares fitting the structures on top of each other.

RMSD as function of time: 

RMSD as function of time

Future work: 

Future work Boson peak Hydrogen bonds melting of bound water molecules on surface of DNA? Molecular group difference of fluctuation? riboses, phosphate, Guanine(G),Cytosine(C), Adenine(A), Thymine(T).