Explicit ions/implicit water generalized Born model for nucleic acids
نویسندگان
چکیده
منابع مشابه
Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules
An explicit ion, implicit water solvent model for molecular dynamics was developed and tested with DNA and RNA simulations. The implicit water model uses the finite difference Poisson (FDP) model with the smooth permittivity method implemented in the OpenEye ZAP libraries. Explicit counter-ions, co-ions, and nucleic acid were treated with a Langevin dynamics molecular dynamics algorithm. Ion el...
متن کاملNew Born Radii Deriving Method for Generalized Born Model
Here we report a method to calculate Born radii, an important parameter used in a Generalized Born model. Traditional methods to derive Born radii are mostly based on a complicated formula, while our method is easier and more direct. Atoms are classified according to their atom type, and the Born radii of each type are obtained by fitting to experimental solvation free energy. The SMARTS langua...
متن کاملNucleic Acids
The first isolation of what we now refer to as DNA was accomplished by Johann Friedrich Miescher circa 1870. He reported finding a weakly acidic substance of unknown function in the nuclei of human white blood cells, and named this material "nuclein". A few years later, Miescher separated nuclein into protein and nucleic acid components. In the 1920's nucleic acids were found to be major compon...
متن کاملNucleic acids.
In: Dyer A, Hudson HG and Williams PA (eds) Ion Exchange Processes: Advances and Applications, p. 39. Cambridge, UK: The Royal Society of Chemistry. Lehto J and Harjula R (1997) Selective separation of radionuclides from nuclear waste solutions with inorganic ion exchangers, React Funct Polym (in press). Navratil JD (1989) Ion exchange technology in spent fuel reprocessing. Journal of Nuclear S...
متن کامل[Nucleic acids].
E wish to suggest a structure for the salt of deoxyribose nucleic acid (D.N.A.). This structure has novel features which are of considerable biological interest. A structure for nucleic acid has already been proposed by Pauling and Corey. They kindly made their manuscript available to us in advance of publication. Their model consists of three intertwined chains, with the phosphates near the fi...
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ژورنال
عنوان ژورنال: The Journal of Chemical Physics
سال: 2018
ISSN: 0021-9606,1089-7690
DOI: 10.1063/1.5027260