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2012

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

There are 35 references in this bibliography folder.

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Asztalos A, Daniels M, Sethi A, Shen T, Langan P, Redondo A, and Gnanakaran S (2012).
A Coarse-Grained Model for Synergistic Action of Multiple Enzymes on Cellulose.
Biotechnology for Biofuels, 5(1):55.

Berezniak T, Jaeschke A, Smith JC, and Imhof P (2012).
Stereoselection in the Diels-Alderase Ribozyme: A Molecular Dynamics Study.
Journal of Computational Chemistry, 33(19):1603-1614.

Biswas M, Wocjan T, Langowski J, and Smith JC (2012).
DNA Bending Potentials for Loop-Mediated Nucleosome Repositioning .
Europhysics Letters, 97(3):38004.

Brothers MC, Nesbitt AE, Hallock MJ, Rupasinghe SG, Tang M, Harris J, Baudry J, Schuler MA, and Rienstra CM (2012).
VITAL NMR: Using Chemical Shift Derived Secondary Structure Information for a Limited Set of Amino Acids to Assess Homology Model Accuracy.
Journal of Biomolecular NMR, 52(1):41-56.

Cheng X, and Ivanov I (2012).
Molecular Dynamics.
Methods in Molecular Biology, 929:243-285.

Cheng X, Parks JM, Petridis L, Lindner B, Schulz R, Guo HB, Srinivas G, and Smith JC (2012).
Molecular Simulation in the Energy Biosciences.
In: Innovations in Biomolecular Modeling and Simulations, ed. by T. Schlick. RSC Publishing, chap. 5, pp. 87-114. (ISBN: 978-1-84973-504-9 ).

Daidone I, Iacobucci C, McLain SE, and Smith JC (2012).
Alteration of Water Structure by Peptide Clusters Revealed by Neutron Scattering in the Small-Angle Region (below 1 Å^−1).
Biophysical Journal, 103(7):1518-1524.

Glass DC, Moritsugu K, Cheng X, and Smith JC (2012).
REACH Coarse-Grained Simulation of a Cellulose Fiber.
Biomacromolecules, 13(9):2634–2644.

Guo HB, He F, Gu B, Liang L, and Smith JC (2012).
Time-Dependent Density Functional Theory Assessment of UV Absorption of Benzoic Acid Derivatives.
The Journal of Physical Chemistry A, 116(48):11870–11879.

Hong L, Glass DC, and Smith JC (2012).
Surface Hydration Amplifies Single-Well Protein Atom Diffusion Propagating into the Macromolecular Core.
Physical Review Letters, 108(23):238102.

Johnson QR, Nellas RB, and Shen T (2012).
Solvent-Dependent Gating Motions of an Extremophilic Lipase from Pseudomonas aeruginosa.
Biochemistry, 51(31):6238-6245.

Krishnan M, and Smith JC (2012).
Reconstruction of Protein Side-Chain Conformational Free Energy Surfaces From NMR-Derived Methyl Axis Order Parameters.
The Journal of Physical Chemistry B, 116(14):4124-4133.

Langan P, Evans BR, Foston M, Heller WT, O'Neill H, Petridis L, Pingali SV, Ragauskas AJ, Smith JC, Urban VS, and Davison BH (2012).
Neutron Technologies for Bioenergy Research.
Industrial Biotechnology, 8(4):209-216.

Lindner B, and Smith JC (2012).
Sassena - X-ray and Neutron Scattering Calculations from Molecular Dynamics Trajectories using Massively Parallel Computers.
Computer Physics Communications, 183(7):1491-1501.

Merzel F, Johnson MR, and Smith JC (2012).
Normal Modes and Neutrons: Defining Collective, Functional Biomolecular Motions.
Neutron News, 3(23):26-30.

Miao Y, Yi Z, Cantrell C, Glass DC, Baudry J, and Smith JC (2012).
Coupled Flexibility Change in Cytochrome P450cam Substrate Binding Determined by Neutron Scattering, NMR and Molecular Dynamics Simulation.
Biophysical Journal, 103(10):2167-2176.

Miao Y, Yi Z, Glass DC, Hong L, Tyagi M, Baudry J, Jain N, and Smith JC (2012).
Temperature-Dependent Dynamical Transitions of Different Classes of Amino Acid Residue in a Globular Protein.
Journal of the American Chemical Society, 134(48):19576-19579.

Mintz BJ, and Parks JM (2012).
Benchmark Interaction Energies for Biologically Relevant Noncovalent Complexes Containing Divalent Sulfur.
The Journal of Physical Chemistry A, 116(3):1086-1092.

Nellas RB, Glover MM, Hamelberg D, and Shen T (2012).
High-Pressure Effect on the Dynamics of Solvated Peptides.
The Journal of Chemical Physics, 136:145103.

Nickels JD, O'Neill H, Hong L, Tyagi M, Ehlers G, Weiss KL, Zhang Q, Yi Z, Mamontov E, Smith JC, and Sokolov AP (2012).
Dynamics of a Protein and Its Hydration Water: Neutron Scattering Studies on Fully Deuterated GFP.
Biophysical Journal, 104(7):1566-1575.

Pan J, Cheng X, Heberle FA, Mostofian B, Kucerka N, Drazba P, and Katsaras J (2012).
Interactions between Ether Phospholipids and Cholesterol As Determined by Scattering and Molecular Dynamics Simulations.
The Journal of Physical Chemistry B, 116(51):14829-14838.

Pool R, Heringa J, Hoefling M, Schulz R, and Smith JC (2012).
Enabling Grand-Canonical Monte Carlo: Extending the Flexibility of GROMACS through the GromPy Python Interface Module to the GROMACS Simulation C-library.
Journal of Computational Chemistry, 33(12):1207-1214.

Sangha A, Petridis L, Smith JC, Ziebell A, and Parks JM (2012).
Molecular Simulation as a Tool for Studying Lignin.
Environmental Progress & Sustainable Energy, 31(1):47-54.

 
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