Jeremy C. Smith, Ph.D.
See Also: Center for Molecular Biophysics
A native of Norwich, England, in October 2006 he became the first Governor's Chair at the University of Tennessee and also Director of the Center for Molecular Biophysics at Oak Ridge National Laboratory. He had previously lead research groups in Biomolecular Simulation at the Centre D'Etudes Nucleaires at Saclay, France (1989-1998) and as Chair of Computational Molecular Biophysics at the University of Heidelberg, Germany (1998-2006).
Smith has performed and directed research in high-performance computer simulation of biological macromolecules, neutron scattering in biology, the physics of proteins, bioenergetics and the analysis of structural change in proteins. As of 2007 Smith had published over 200 peer-reviewed scientific articles. (Information retreived from http://cmb.ornl.gov/group/cst)
Selected Publications
D.R. NUTT and J.C. SMITH. Choosing an Appropriate Water Model for Use in Biomolecular Simulations. In "Physics and Chemistry of Ice", RSC Publishing, 451-458 (2007).
L. MEINHOLD, J.C. SMITH., A. KITAO, A. and A.H. ZEWAIL. Picosecond Fluctuating Protein Energy Landscape Mapped by Pressure-Temperature Molecular Dynamics Simulation. Proceedings of the National Academy of Sciences (U.S.A.)..104(44):17261-5 (2007).
A De HATTEN, Z COURNIA, J.C. SMITH & N. METZLER-NOLTE. Force-field development and molecular dynamics simulations of ferrocene-peptide conjugates as a scaffold for hydrogenase mimics.Hydrogenase Mimics. Chemistry.. 13(29):8139-52 (2007).
L. MEINHOLD, F. MERZEL & J.C. SMITH. Lattice Vibrations in Protein Crystals. Physical Review Letters. 28;99(13):138101 (2007).
I. DAIDONE, F. NOE. A DI NOLA and J.C. SMITH. Dehydration-Driven Peptide folding. Proceedings of the National Academy of Sciences (U.S.A.). 104(39):15230-5 (2007)
K. MORITSUGU & J.C. SMITH. REACH: Realistic Extension Algorithm via Covariance Hessian. Biophysical Journal. 93(10):3460-9 (2007)..
D. NUTT & J.C.SMITH. Molecular dynamics simulations of Proteins: can the Water model be Varied? Journal of Chemical Theory and Computation. 3 1550-1560 (2007).
F. NOE, I. HORENKO, C. SCHUETTE & J.C.SMITH. Hierarchical analysis of conformational dynamics in biomolecules: Transition networks of meta-stable states Journal of Chemical Physics. 126(15):155102 (2007).
S. MESENTEAN, S. KOPPOLE, J.C. SMITH, S. FISCHER. The principal motions involved in the coupling mechanism of the recovery stroke of the myosin motor. Journal of Molecular Biology. 367(2):591-602 (2007).
F. NOE, D. KRACHTUS, J.C. SMITH. S. FISCHER, Transition Networks for the Z. COURNIA, G.M. ULLMANN and J.C. SMITH. Differential Effects of Cholesterol, Ergosterol and Lanosterol on a Dipalmitoyl Phosphatidylcholine (DPPC) membrane: A Molecular Dynamics Simulations Study" Journal of Physical Chemistry B, 111(7):1786-801 (2007).
S. KOPPOLE, J.C. SMITH & S. FISCHER, The structural coupling between ATPase activation and recovery stroke in the myosin II motor. Structure. 15(7):825-37 (2007).
A.N. BONDAR, S. SUHAI, S. FISCHER J.C. SMITH, & M. ELSTNER. Suppression of the back proton-transfer from Asp85 to the retinal Schiff base in bacteriorhodopsin: A theoretical analysis of structural elements.
Journal of Structural Biology 157(3):454-69 (2007)
C. TOPHAM & J.C. SMITH. Orientation Preferences of Backbone Secondary Amide Functional Groups in Peptide Nucleic Acid Complexes: Quantum Chemical Calculations Reveal an Intrinsic Preference of Cationic D-Amino Acid-Based Chiral PNA Analogues for the P-form. Biophysical Journal..
92(3):769-86. (2007).
L.MEINHOLD & J.C. SMITH. Protein dynamics from X-ray crystallography: anisotropic, global motion in diffuse scattering patterns.
Proteins.: Structure, Function and Bioinformatics 66(4):941-53. (2007).
Comprehensive Characterization of Complex Conformational Change in proteins. Journal of Chemical Theory and Computation. 2, 840-857 (2006).
J.C. SMITH. Tight in Titin. Structure. 14(3):389-90 (2006).
S. KOPPOLE, J.C. SMITH 7 S. FISCHER. Simulations of the myosin II motor reveal a nucleotide-state sensing element that controls the recovery stroke.
Journal of Molecular Biology. 361(3):604-16 (2006).
V. KURKAL-SIEBERT and J.C. SMITH. Low-Temperature Protein Physics: A Simulation Analysis of Interprotein Vibrations and the Boson Peak at 150K. Journal of the American Chemical Society 128 2356-2364 (2006).
T. EFFERTH, S.M. SCHWARZL, J.C. SMITH and R. OSIEKA. Role of glucose-6-phosphate dehydrogenase for oxidative stress and apoptosis. Cell Death and Differentiation 13 527-528 (2006).
S. SCHWARZL, J.C. SMITH & S. FISCHER. Insights into the chemomechanical coupling of the myosin motor from simulation of its ATP hydrolysis mechanism.
Biochemistry 45(18):5830-47 (2006)
L. WALEWSKI, D. KRACHTUS, S. FISCHER, J.C. SMITH, P. BALA and B. LESYNG. SCC-DFTB Energy Barriers for Single and Double Proton Transfer Processes in the Model Molecular Systems Malonaldehyde and Porphycene. International Journal of Quantum Chemistry 106, 3, 636-640 (2006)
A.N. BONDAR, J.C. SMITH & S. FISCHER. Structural and energetic determinants of proton transfer in bacteriorhodopsin. Photochemical and Photobiological Sciences. 5 547-561 (2006).
M. TEHEI, J.C. SMITH, C. MONK, J. OLLIVIER, M. OETTL, V. KURKAL, J.L. FINNEY and R.M. DANIEL. Dynamics of Immobilized and Native Escherichia coli Dihydrofolate Reductase by Quasielastic Neutron Scattering. Biophysical Journal. 90(3):1090-7 (2006).
S. MESENTEAN, S. FISCHER & J.C. SMITH. Analyzing Large-Scale Structural Change in Proteins: Comparison of Principal Component Projection and Sammon Mapping. Proteins: Structure, Function and Bioinformatics. 64:210-218 (2006)
E. BALOG, J.C.SMITH, D. PERAHIA. Conformational heterogeneity and low-frequency vibrational modes of proteins. Physical Chemistry Chemical Physics.. 8(47) 5543-8 (2006).
V. KURKAL, J.L. FINNEY, R. DANIEL & J.C. SMITH. Enzyme hydration, activity and flexibility : A neutron scattering approach. Journal of Noncrystalline Solids. 352 (42), 4387-4393 (2006).
P. IMHOF, F. NOE, S. FISCHER, J.C. SMITH. AM1/d parameters for Magnesium in Metalloenzymes. Journal of Chemical Theory and Computation. 2(4) 1050 – 1056 (2006).
K. MORITSUGU & J.C.SMITH, Temperature-Dependent Protein Dynamics: A Simulation-Based Probabilistic Diffusion-Vibration Langevin Description. Journal of Physical Chemistry B. 110(11):5807-16 (2006).
F. NOE, M. OSWALD, G. REINELT, S. FISCHER & J.C. SMITH. Computing Best Transition Pathways in High-Dimensional Dynamical Systems: Application to the αL-β-αR Transitions in Octaalanine. Multiscale Modelling and Simulation. 5, 393 (2006).
Contact Information
Office:
Oak Ridge National Laboratory
Phone: (865) 574-9635
Email:smithjc@ornl.gov