Electrostatic interactions play an essential role in molecular and cellular processes that include signal transmission at synaptic junctions, ion-transport, molecular recognition, and stability and function of DNA, RNA and proteins. Of paramount biological importance is the collective behavior of ions, molecules, and macromolecules having inhomogeneous charge distributions in the aqueous crowded environment of a living cell. Central to this environment is water, which is a complex solvent with non-bulk properties near ions, molecules and water-biopolymer interfaces. The main challenge for modeling electrostatics, as the core calculation of Molecular Dynamics and Monte Carlo simulations, is to balance the accuracy of interactions among charges and the efficiency required for realistic biological systems. For all-atom simulations the Ewald method is currently the most accurate method for large enough system where periodic boundary effects are negligible. Unfortunately, the simulation of a macromolecule requires a large simulation volume, making the Ewald method and similar methods too expensive while a smaller system size compromises accuracy. Meanwhile, modeling the solvent using continuum electrostatics is much faster, but accuracy is compromised by neglecting molecular scale inhomogeneity, such as atomic details near the surface of the solute. ? ? ?

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
1R01GM083600-01
Application #
7413778
Study Section
Special Emphasis Panel (ZGM1-CBCB-5 (BM))
Program Officer
Wehrle, Janna P
Project Start
2007-08-06
Project End
2011-07-31
Budget Start
2007-08-06
Budget End
2008-07-31
Support Year
1
Fiscal Year
2007
Total Cost
$360,000
Indirect Cost
Name
University of North Carolina Charlotte
Department
Biostatistics & Other Math Sci
Type
Schools of Arts and Sciences
DUNS #
066300096
City
Charlotte
State
NC
Country
United States
Zip Code
28223
Baker, Katherine; Baumketner, Andrij; Lin, Yuchun et al. (2013) ICSM: An order N method for calculating electrostatic interactions added to TINKER. Comput Phys Commun 184:19-26
Deng, Shaozhong; Xue, Changfeng; Baumketner, Andriy et al. (2013) Generalized image charge solvation model for electrostatic interactions in molecular dynamics simulations of aqueous solutions. J Comput Phys 245:84-106
Song, Wei; Lin, Yuchun; Baumketner, Andrij et al. (2013) Effect of the Reaction Field on Molecular Forces and Torques Revealed by an Image-Charge Solvation Model. Commun Comput Phys 13:129-149
Ni, Boris; Baumketner, Andrij (2013) Reduced atomic pair-interaction design (RAPID) model for simulations of proteins. J Chem Phys 138:064102
Baumketner, Andrij (2012) The mechanism of the converter domain rotation in the recovery stroke of myosin motor protein. Proteins 80:2701-10
Baumketner, Andrij (2012) Interactions between relay helix and Src homology 1 (SH1) domain helix drive the converter domain rotation during the recovery stroke of myosin II. Proteins 80:1569-81
Lin, Yuchun; Baumketner, Andrij; Song, Wei et al. (2011) Ionic solvation studied by image-charge reaction field method. J Chem Phys 134:044105
Baumketner, Andrij; Nesmelov, Yuri (2011) Early stages of the recovery stroke in myosin II studied by molecular dynamics simulations. Protein Sci 20:2013-22
Xu, Zhenli; Cai, Wei; Cheng, Xiaolin (2011) Image Charge Method for Reaction Fields in a Hybrid Ion-Channel Model. Commun Comput Phys 9:1056-1070
Ni, Boris; Baumketner, Andrij (2011) Effect of atom- and group-based truncations on biomolecules simulated with reaction-field electrostatics. J Mol Model 17:2883-93

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