This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. Our group is utilizing large-scale molecular dynamics simulations and electronic structure calculations to study the fundamental aspects of ion solvation in water and near ion channel proteins. The project is funded by the National Science Foundation (CHE-0709560 Modeling specific-ion effects in aqueous solutions and ion channels, 2007-2010). This startup proposal seeks Teragrid resources to 1) perform large-scale polarizable molecular dynamics (MD) simulations of ions in water and channels with the AMBER or NAMD codes 2) use configurations from the MD simulations to perform MP2-level electronic structure calculations (Gaussian03) on clusters involving the ions and the first-shell solvation environment in the external field of more distant solvent molecules and 3) perform large-scale MD simulations of ion channel proteins at high temperatures for potential device applications. In ongoing research, we have developed a new formalism for computing solvation free energies based on quasi-chemical theory. That theory rigorously partitions the free energy into inner-shell, packing, and outer-shell/long-ranged contributions. We have developed an efficient computational strategy for handling each of these three pieces of the free energy, and have applied the methodology to studies of the solvation of molecules and ions in water. The work has allowed us to gain new insights into the driving forces for ion solvation. We have also carefully examined the local solvation structure and have found that some existing polarizable force fields over-estimate anion solvation anisotropy due to over-polarization of the ions. In further work, we have re-examined the anion systems with a QM/MM (quantum mechanics/molecular mechanics) approach involving correlated electron calculations (MP2) on ion/water clusters embedded in surrounding water solution. This work has shown that the anions are less polarized than previously predicted, and that the first-shell waters are affected more by their interactions with other waters than by interactions with the ion. Also, substantial charge transfer can occur between the ions and nearby waters. This work should have significant impacts on our basic understanding of biophysical interactions. In our research, we generate a large number of configurations by classical simulation (AMBER or NAMD) and then examine the ensemble of clusters with the electronic structure calculations. The studies require extensive MD sampling and Gaussian03 MP2 calculations on ion/water clusters with roughly 20 atoms for thousands of configurations. The calculations thus require extensive computational resources. The final project concerns simulations of gramicidin channels at high temperatures. These MD simulations of the peptides in realistic membranes require modeling tens of thousands of atoms for ns time scales. We are interested in studying the transport properties of these membrane channels at high temperatures (up to 100o C) for potential applications in novel fuel cell devices. We request the full allowed 200,000 SUs for these initial studies, to be followed by a full Research Allocation proposal. 5 TB of disk, or 25 TB of tape storage should be sufficient. The NAMD, AMBER, and Gaussian03 codes will be the main software used for this research, so we request resources on the NCSA, SDSC, LONI, and IU sites.

National Institute of Health (NIH)
National Center for Research Resources (NCRR)
Biotechnology Resource Grants (P41)
Project #
Application #
Study Section
Special Emphasis Panel (ZRG1-BCMB-Q (40))
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Carnegie-Mellon University
Biostatistics & Other Math Sci
Schools of Arts and Sciences
United States
Zip Code
Yonkunas, Michael; Buddhadev, Maiti; Flores Canales, Jose C et al. (2017) Configurational Preference of the Glutamate Receptor Ligand Binding Domain Dimers. Biophys J 112:2291-2300
Earley, Lauriel F; Powers, John M; Adachi, Kei et al. (2017) Adeno-associated Virus (AAV) Assembly-Activating Protein Is Not an Essential Requirement for Capsid Assembly of AAV Serotypes 4, 5, and 11. J Virol 91:
Subramanian, Sandeep; Chaparala, Srilakshmi; Avali, Viji et al. (2016) A pilot study on the prevalence of DNA palindromes in breast cancer genomes. BMC Med Genomics 9:73
Ramakrishnan, N; Tourdot, Richard W; Radhakrishnan, Ravi (2016) Thermodynamic free energy methods to investigate shape transitions in bilayer membranes. Int J Adv Eng Sci Appl Math 8:88-100
Zhang, Yimeng; Li, Xiong; Samonds, Jason M et al. (2016) Relating functional connectivity in V1 neural circuits and 3D natural scenes using Boltzmann machines. Vision Res 120:121-31
Lee, Wei-Chung Allen; Bonin, Vincent; Reed, Michael et al. (2016) Anatomy and function of an excitatory network in the visual cortex. Nature 532:370-4
Murty, Vishnu P; Calabro, Finnegan; Luna, Beatriz (2016) The role of experience in adolescent cognitive development: Integration of executive, memory, and mesolimbic systems. Neurosci Biobehav Rev 70:46-58
Lee, Tai Sing (2015) The visual system's internal model of the world. Proc IEEE Inst Electr Electron Eng 103:1359-1378
Kuhlman, Chris J; Anil Kumar, V S; Marathe, Madhav V et al. (2015) Inhibiting diffusion of complex contagions in social networks: theoretical and experimental results. Data Min Knowl Discov 29:423-465
Jurkowitz, Marianne S; Patel, Aalapi; Wu, Lai-Chu et al. (2015) The YhhN protein of Legionella pneumophila is a Lysoplasmalogenase. Biochim Biophys Acta 1848:742-51

Showing the most recent 10 out of 289 publications