Faculty PublicationsCollection of scholarship submitted by CSUN facultyhttp://hdl.handle.net/10211.2/3092017-09-24T14:08:39Z2017-09-24T14:08:39ZImplicit solvent calculations with explicit molecular models in amber with 3D-RISMLuchko, Tylerhttp://hdl.handle.net/10211.3/1962652017-09-21T21:28:40Z2012-01-01T00:00:00ZImplicit solvent calculations with explicit molecular models in amber with 3D-RISM
Luchko, Tyler
2012-01-01T00:00:00ZImplicit Solvent Models and Electrostatics in Molecular RecognitionLuchko, TylerCase, David A.http://hdl.handle.net/10211.3/1962642017-09-21T21:30:54Z2012-01-01T00:00:00ZImplicit Solvent Models and Electrostatics in Molecular Recognition
Luchko, Tyler; Case, David A.
2012-01-01T00:00:00ZIon Counting from Explicit-Solvent Simulations and 3D-RISMGiambaşu, GeorgeLuchko, TylerHerschlagYork, Darrin M.Case, David A.http://hdl.handle.net/10211.3/1962502017-09-21T20:45:07Z2014-01-01T00:00:00ZIon Counting from Explicit-Solvent Simulations and 3D-RISM
Giambaşu, George; Luchko, Tyler; Herschlag; York, Darrin M.; Case, David A.
The ionic atmosphere around nucleic acids remains only partially understood at atomic-level detail. Ion counting (IC) experiments provide a quantitative measure of the ionic atmosphere around nucleic acids and, as such, are a natural route for testing quantitative theoretical approaches. In this article, we replicate IC experiments involving duplex DNA in NaCl(aq) using molecular dynamics (MD) simulation, the three-dimensional reference interaction site model (3D-RISM), and nonlinear Poisson-Boltzmann (NLPB) calculations and test against recent buffer-equilibration atomic emission spectroscopy measurements. Further, we outline the statistical mechanical basis for interpreting IC experiments and clarify the use of specific concentration scales. Near physiological concentrations, MD simulation and 3D-RISM estimates are close to experimental results, but at higher concentrations (>0.7 M), both methods underestimate the number of condensed cations and overestimate the number of excluded anions. The effect of DNA charge on ion and water atmosphere extends 20-25 � from its surface, yielding layered density profiles. Overall, ion distributions from 3D-RISMs are relatively close to those from corresponding MD simulations, but with less Na(+) binding in grooves and tighter binding to phosphates. NLPB calculations, on the other hand, systematically underestimate the number of condensed cations at almost all concentrations and yield nearly structureless ion distributions that are qualitatively distinct from those generated by both MD simulation and 3D-RISM. These results suggest that MD simulation and 3D-RISM may be further developed to provide quantitative insight into the characterization of the ion atmosphere around nucleic acids and their effect on structure and stability.
2014-01-01T00:00:00ZSimple electrolyte solutions: Comparison of DRISM and molecular dynamics results for alkali halide solutionsJoung, In SukLuchko, TylerCase, David A.http://hdl.handle.net/10211.3/1962512017-09-21T20:46:07Z2013-01-01T00:00:00ZSimple electrolyte solutions: Comparison of DRISM and molecular dynamics results for alkali halide solutions
Joung, In Suk; Luchko, Tyler; Case, David A.
Using the dielectrically consistent reference interaction site model (DRISM) of molecular solvation, we have calculated structural and thermodynamic information of alkali-halide salts in aqueous solution, as a function of salt concentration. The impact of varying the closure relation used with DRISM is investigated using the partial series expansion of order-n (PSE-n) family of closures, which includes the commonly used hypernetted-chain equation (HNC) and Kovalenko-Hirata closures. Results are compared to explicit molecular dynamics (MD) simulations, using the same force fields, and to experiment. The mean activity coefficients of ions predicted by DRISM agree well with experimental values at concentrations below 0.5 m, especially when using the HNC closure. As individual ion activities (and the corresponding solvation free energies) are not known from experiment, only DRISM and MD results are directly compared and found to have reasonably good agreement. The activity of water directly estimated from DRISM is nearly consistent with values derived from the DRISM ion activities and the Gibbs-Duhem equation, but the changes in the computed pressure as a function of salt concentration dominate these comparisons. Good agreement with experiment is obtained if these pressure changes are ignored. Radial distribution functions of NaCl solution at three concentrations were compared between DRISM and MD simulations. DRISM shows comparable water distribution around the cation, but water structures around the anion deviate from the MD results; this may also be related to the high pressure of the system. Despite some problems, DRISM-PSE-n is an effective tool for investigating thermodynamic properties of simple electrolytes.
2013-01-01T00:00:00Z