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2009

This folder holds the following references to publications, sorted by year and author.

There are 23 references in this bibliography folder.

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Bondar AN, and Smith JC (2009).
Water Molecules in Short- and Long-Distance Proton Transfer Steps of Bacteriorhodopsin Proton Pumping.
Israel Journal of Chemistry, 49(2):155-161.

Cheng X, Ivanov I, Wang HL, Sine SM, and McCammon JA (2009).
Molecular-Dynamics Simulations of ELIC - a Prokaryotic Homologue of the Nicotinic Acetylcholine Receptor.
Biophysical Journal, 96(11):4502-4513.

Krishnan M, and Smith JC (2009).
Response of Small-Scale, Methyl Rotors to Protein-Ligand Association: A Simulation Analysis of Calmodulin-Peptide Binding.
Journal of the American Chemical Society, 131(29):10083-10091.

Krishnan M, Schulz R, and Smith JC (2009).
Protein Dynamical Transition: Role of Methyl Dynamics and Local Diffusion.
Theory and Applications of Computational Chemistry 2008. AIP Conference Proceedings, 1102:122-131.

Moritsugu K, and Smith JC (2009).
REACH: A Program for Coarse-Grained Biomolecular Simulation.
Computer Physics Communications, 180(7):1188-1195.

Moritsugu K, Kurkal-Siebert V, and Smith JC (2009).
REACH Coarse-Grained Normal Mode Analysis of Protein Dimer Interaction Dynamics.
Biophyical Journal, 97(4):1158-1167.

Neusius T, Sokolov IM, and Smith JC (2009).
Subdiffusion in Time-Averaged, Confined Random Walks.
Physical Review E, 80:011109.

Parks JM, Guo H, Momany C, Liang L, Miller SM, Summers AO, and Smith JC (2009).
Mechanism of Hg−C Protonolysis in the Organomercurial Lyase MerB.
Journal of the American Chemical Society, 131(37):13278-13285.

Petridis L, and Smith JC (2009).
A Molecular Mechanics Force Field for Lignin.
Journal of Computational Chemistry, 30(3):457-467.

Phatak P, Fraemcke JS, Wanko M, Hoffmann M, Strodel P, Smith JC, Suhai S, Bondar AN, and Elstner M (2009).
Long-Distance Proton Transfer with a Break in the Bacteriorhodopsin Active Site.
Journal of the American Chemical Society, 131(20):7064-7078.

Schulz R, Krishnan M, Daidone I, and Smith JC (2009).
Instantaneous Normal Modes and the Protein Glass Transition.
Biophysical Journal, 96(2):476–484.

Schulz R, Lindner B, Petridis L, and Smith JC (2009).
Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer.
Journal of Chemical Theory and Computation, 5(10):2798-2808.

Shen T, Langan P, French A, Johnson GP, and Gnanakaran S (2009).
Conformational Flexibility of Soluble Cellulose Oligomers: Chain Length and Temperature Dependence.
Journal of the American Chemical Society, 131(41):14786–14794.

Smith JC (2009).
Supercomputers Tackle Biofuel Production Problems.
SciDAC Review(15):34-45.

Spies A, Reese JG, Dodd D, Pankow KL, Blanke SR, and Baudry J (2009).
Determinants of Catalytic Power and Ligand Binding in Glutamate Racemase.
Journal of the American Chemical Society, 131(14):5274-5284.

Splettstoesser T, Noé F, Oda T, and Smith JC (2009).
Nucleotide-Dependence of G-Actin Conformation from Multiple Molecular Dynamics Simulations and Observation of a Putatively Polymerization-Competent Superclosed State.
Proteins: Structure, Function, and Bioinformatics, 76(2):353-364.

Thukral L, Smith JC, and Daidone I (2009).
Common Folding Mechanism of a Beta-Hairpin Peptide via Non-Native Turn Formation Revealed by Unbiased Molecular Dynamics Simulations.
Journal of the American Chemical Society, 131(50):18147–18152.

Ulmschneider JP, Smith JC, Killian A, and Ulmschneider MB (2009).
Peptide Partitioning and Folding into Lipid Bilayers.
Journal of Chemical Theory and Computation, 5(9):2202-2205.

Xu Q, Chu Y, Guo HB, Smith JC, and Guo H (2009).
Energy Triplets for Writing Epigenetic Marks: Insights from QM/MM Free Energy Simulations of Protein Lysine Methyltransferases.
Chemistry: A European Journal, 15(46):12596-12599.

Xu Q, Ye X, Li LY, Cheng ZM, and Guo H (2009).
Structural Basis for the Action of Xyloglucan Endotransglycosylases/hydrolases: Insights from Homology Modeling.
Interdisciplinary Sciences: Computational Life Sciences, 2(2):133-139.

 
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