Refereed Journal Papers

1. Comparison of the serial and parallel algorithms of generalized ensemble simulations: An analytical approach (PDF)
   S Park (2008), Physical Review E 77, 016709.


2. Theory for an order-driven disruption of the liquid state in water
   J L England, S Park, V S Pande (2008), Journal of Chemical Physics 128, 044503.


3. Folding and misfolding of the collagen triple helix: Markov analysis of molecular dynamics simulations (PDF)
   S Park, T E Klein, V S Pande (2007), Biophysical Journal 93, 4108-4115.


4. Persistent voids: A new structural metric for membrane fusion
   P Kasson, A Zomorodian, S Park, N Singhal, L J Guibas, V S Pande (2007), Bioinformatics 23, 1753-1759.


5. Choosing weights for simulated tempering (PDF)
   S Park, V S Pande (2007), Physical Review E 76, 016703.


6. Bayesian update method for adaptive weighted sampling (PDF)
   S Park, D L Ensign, V S Pande (2006), Physical Review E 74, 066703.


7. Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics
   G Jayachandran, M R Shirts, S Park, V S Pande (2006), Journal of Chemical Physics 125, 084901.


8. Validation of Markov state models using Shannon's entropy (PDF)
   S Park, V S Pande (2006), Journal of Chemical Physics 124, 054118.


9. A new set of molecular mechanics parameters for hydroxyproline and its use in molecular dynamics simulations of collagen-like peptides (PDF)
   S Park, R J Radmer, T E Klein, V S Pande (2005), Journal of Computational Chemistry 26, 1612-1616.


10. Foldamer dynamics expressed via Markov state models: I. Explicit solvent molecular dynamics simulations in acetonitrile, chloroform, methanol, and water
    S P Elmer, S Park, V S Pande (2005), Journal of Chemical Physics 123, 114902.


11. Foldamer dynamics expressed via Markov state models: II. State space decomposition
    S P Elmer, S Park, V S Pande (2005), Journal of Chemical Physics 123, 114903.


12. Calculating potentials of mean force from steered molecular dynamics simulations (PDF)
    S Park, K Schulten (2004), Journal of Chemical Physics 120, 5946-5961.


13. Excitation migration in trimeric cyanobacterial photosystem I
    M K Sener, S Park, D Lu, A Damjanovic, T Ritz, P Fromme, K Schulten (2004), Journal of Chemical Physics 120, 11183-11195.


14. Free energy calculation from steered molecular dynamics simulations using Jarzynski's equality (PDF)
    S Park, F Khalili-Araghi, E Tajkhorshid, K Schulten (2003), Journal of Chemical Physics 119, 3559-3566.


15. Reaction paths based on mean first-passage times (PDF)
    S Park, M K Sener, D Lu, K Schulten (2003), Journal of Chemical Physics 119, 1313-1319.


16. Energetics of glycerol conduction through aquaglyceroporin GlpF (PDF)
    M O Jensen, S Park, E Tajkhorshid, K Schulten (2002), Proceedings of the National Academy of Sciences of the USA 99, 6731-6736.


17. Robustness and optimality of light harvesting in cyanobacterial photosystem I
    M K Sener, D Lu, T Ritz, S Park, P Fromme, K Schulten (2002), Journal of Physical Chemistry B 106, 7948-7960.


18. Kinetics of excitation migration and trapping in the photosynthetic unit of purple bacteria
    T Ritz, S Park, K Schulten (2001), Journal of Physical Chemistry B 105, 8259-8267.


19. Entropic sampling and natural selection in biological evolution
    M Y Choi, H Y Lee, D Kim, S Park (1997), Journal of Physics A: Mathematical and General 30, L749-L755.

Others

1. Ph.D. Thesis - Extracting equilibrium from nonequilibrium: free energy calculation from steered molecular dynamics simulations (PDF)
   S Park (2004), University of Illinois Urbana-Champaign.