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
A.N. BONDAR, J.C. SMITH & M. ELSTNER. Mechanism of a proton pump analyzed with computer simulations. Theoretical Chemistry Accounts. In Press.
A. N. BONDAR and J.C. SMITH. Water molecules in short- and long-distance proton transfer steps of bacteriorhodopsin proton pumping. Israel Journal of Chemistry. In Press.
M. SAHARAY, H.-B. GUO, J.C. SMITH and H. GUO. QM/MM Analysis of Cellulase Active Sites and Actions of the Enzymes on Substrates. Biofuels: ACS. In press.
L. PETRIDIS, J. XU, M. CROWLEY, J.C. SMITH and X. CHENG. Atomistic Simulation of Lignocellulosic Biomass and Associated Cellulosomal Protein Complexes Biofuels: ACS. In press.
K. MORITSUGU & J.C. SMITH. REACH Coarse-Grained Normal Mode Analysis of Protein Dimer Interaction Dynamics. Biophysical Journal. 87, 1158-1167 (2009).
T. NEUSIUS, I.M. SOKOLOV & J.C. SMITH. Subdiffusion in time-averaged, confined random walks. Physical Review E. In press.
M. KRISHNAN & J.C. SMITH. Response of Small-Scale, Methyl Rotors to Protein-Ligand Association : A Simulation Analysis of Calmodulin-Peptide Binding. Journal of the American Chemical Society. In press.
J.P. ULMSCHNEIDER, J.C. SMITH, A. KILLIAN and M.B. ULMSCHNEIDER. Folding of membrane-embedded peptides. Journal of Chemical Theory and Computation. In press.
R. SCHULZ, B. LINDNER, L. PETRIDIS & J.C. SMITH. Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer. Journal of Chemical Theory and Computation. In press.
P. IMHOF, S. FISCHER & J.C. SMITH. Catalytic Mechanism of DNA backbone cleavage by the restriction enzyme EcoRV: A quantum mechanical/molecular mechanical analysis" Biochemistry. In press.
J. PARKS, H. GUO, C. MOMANY, L. LIANG, S. MILLER, A. SUMMERS and J.C. SMITH. Mechanism of Hg-C protonolysis in the organomercurial lyase MerB. Journal of the American Chemical Society. In press.
Q. XU, Y. CHU, H.-B. GUO, J.C. SMITH & H. GUO. Energy Triplets for Writing Epigenetic Marks: Insights from QM/MM Free Energy Simulations of Protein Lysine Methyltransferases. Chemistry: A European Journal. In press.
L. PETRIDIS & J.C. SMITH. A molecular mechanics force field for lignin. Journal of Computational Chemistry. 30(3):457-67 (2009)
R. SCHULZ, M. KRISHNAN, I. DAIDONE and J.C. SMITH Instantaneous Normal Modes and the Protein Glass Transition. Biophysical Journal. 96(2):476-84 (2009)
T. SPLETTSTOESSER, F. NOE, T. ODA & J.C. SMITH. Nucleotide-dependence of G-actin conformation from multiple molecular dynamics simulations and observation of a putatively polymerization-competent superclosed state. Proteins: Structure, Function and Dynamics. 180, 1188-1195 (2009).
K. MORITSUGU and J. C. SMITH, REACH: A Program for Coarse-Grained Biomolecular Simulation, Computer Physics Communications 180, 1188-1195 (2009).
J. XU., M. CROWLEY & J.C. SMITH Building a Foundation for Structure-Based Cellulosome Design for Cellulosic Ethanol: Insight into Cohesin-Dockerin Complexation from Computer Simulation. Protein Science. 18(5):949-959 (2009).
P. PHATAK, J.S. FRAEMCKE, M. WANKO, M. HOFFMANN, P. STRODEL, J.C. SMITH, S. SUHAI, A.-N. BONDAR & M. ELSTNER. Long-Distance Proton Transfer with a Break in the Bacteriorhodopsin Active Site. Journal of the American Chemical Society. 131 (20), 7064–7078 (2009).
M. KRISHNAN, R. SCHULZ & SMITH JC. Protein Dynamical Transition : Role of Methyl Dynamics and Local Diffusion Theory and Applications of Computational Chemistry 2008. AIP Conference Proceedings 1102 122-131 (2009).
S. E. MCLAIN, A. K. SOPER, I. DAIDONE, J. C. SMITH and A. WATTS, Charge based interactions between peptides observed as the dominant force for association in aqueous solution. Angewandte Chemie Intl. Ed. 47 9059-9062 (2008).
V. BECKER, D. SENGUPTA, R. KETTELER, G. M. ULLMANN,_ J. C. SMITH & U. KLINGMÜLLER.Packing density of the erythropoietin receptor transmembrane domain correlates with amplification of biological responses. Biochemistry 47 (45) 11771-11782 (2008).
A.N. BONDAR, J. BAUDRY, S. SUHAI. S. FISCHER and J.C. SMITH. Key role of water molecules in bacteriorhodopsin proton transfer reactions. Journal of Physical Chemistry B 112(47):14729-41 (2008)
K. MORITSUGU & J.C. SMITH. REACH Coarse-Grained Biomolecular Simulation: Transferability between Different Protein Structural Classes. Biophysical Journal 95 4 1639-1648 (2008).
L. PETRIDIS & J.C. SMITH, Cellulosic ethanol: progress towards a simulation model of lignocellulosic biomass Journal of Physics Conference Series 125 012055 (2008)
D. SENGUPTA, J.C. SMITH & M. ULLMANN, Partitioning of Amino-acid Analogues in a Five-slab Membrane Model Biochimica et Biophysica Acta – Biomembranes. 1778 (10) 2234-2243 (2008).
F. NOE, I. DAIDONE, J.C. SMITH, A. DI NOLA & A. AMADEI, Solvent Electrostriction-Driven Peptide Folding Revealed by Quasi Gaussian Entropy Theory and Molecular Dynamics Simulation. Journal of Physical Chemistry B. 112 35 11155-11163 (2008)
D. R. NUTT & J.C. SMITH, Dual function of the hydration layer around an antifreeze protein revealed by atomistic molecular dynamics simulations. Journal of the American Chemical Society. 130(39)13066-13073 (2008)
K. VOLTZ, J. TRYLSKA, V. TOZZINI, V. KURKAL-SIEBERT, J.C. SMITH and J. LANGOWSKI. Coarse-Grained Force field for the Nucleosome from Self-Consistent Multiscaling. Journal of Computational Chemistry. 29(9):1429-39 (2008).
L MEINHOLD, D. CLEMENT, M. TEHEI, R. DANIEL, J.L. FINNEY & J.C. SMITH. Protein dynamics and stability: The distribution of atomic fluctuations in thermophilic and mesophilic dihydrofolate reductase derived using elastic incoherent neutron scattering. Biophysical Journal.. 94(12):4812-8 (2008).
V. KURKAL-SIEBERT, R. AGARWAL & J.C. SMITH. Hydration-dependent dynamical transition in protein:protein interactions at ~240K. Physical Review Letters. 100 13 138102 (2008).
M. KRISHNAN, V. KURKAL-SIEBERT & J.C. SMITH. Methyl Group Dynamics and the Onset of Anharmonicity in Myoglobin. Journal of Physical Chemistry B. 112(17):5522-33 (2008).
T. NEUSIUS, I. DAIDONE, I.M. SOKOLOV & J.C. SMITH. Subdiffusion in peptides originates from fractal-like structure of configuration space. Physical Review Letters. 100 18 188103 (2008).
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):1786-1801 (2007).
A.N. BONDAR, S. SUHAI, S. FISCHER, J.C. SMITH and 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).
S. MESENTEAN, S. KOPPOLE, J.C. SMITH and 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 and J.C. SMITH. Transition Networks: A Unifying Theme for Molecular Simulation and Computer Science. In: Mathematical Modeling of Biological Systems, Volume I. A. Deutsch, L. Brusch, H. Byrne, G. de Vries and H.-P. Herzel (eds). Birkhäuser, Boston, 125-144 (2007).
L. MEINHOLD and J.C. SMITH. Protein Dynamics from X-ray Crystallography: Anisotropic, Global motion in Diffuse Scattering Patterns. Proteins: Structure, Function and Bioinformatics 66 (4):941-953 (2007).
F. NOE, I. HORENKO, C. SCHÜTTE and J.C.SMITH. Hierarchical analysis of conformational dynamics in biomolecules: Transition networks of metastable states The Journal of Chemical Physics 126 (15):155102 (2007).
D.R. NUTT and J.C.SMITH. Molecular dynamics simulations of proteins: can the explicit water model be varied? Journal of Chemical Theory and Computation 3(4) 1550-1560 (2007).
C. TOPHAM and 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).
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).
S. KOPPOLE, J.C. SMITH and S. FISCHER, The structural coupling between ATPase activation and recovery stroke in the myosin II motor. Structure 15 (7): 825-837 (2007).
K. MORITSUGU and J.C. SMITH. Coarse-Grained Biomolecular Simulation with REACH: Realistic Extension Algorithm via Covariance Hessian. Biophysical Journal 93(10):3460-3469 (2007).
X. DE HATTEN, Z. COURNIA, I. HUC, J.C. SMITH and N. METZLER-NOLTE. Force-field development and molecular dynamics simulations of ferrocene-peptide conjugates as a scaffold for hydrogenase mimics. Chemistry 13 (29):8139-8152 (2007).
I. DAIDONE, M. ULMSCHNEIDER, A. DI NOLA, A. AMADEI and J.C. SMITH. Dehydration-Driven Solvent Exposure of Hydrophobic Surfaces as a Driving Force in Peptide Folding. Proceedings of the National Academy of Sciences (U.S.A.) 104 39 15230-15235 (2007).
L. MEINHOLD, F. MERZEL and J.C. SMITH. Lattice dynamics of a protein crystal. Physical Review Letters 99 (13):138101 (2007).
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).
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):1090-1097 (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).
J.C. SMITH, T. BECKER, S. FISCHER, F. NOE, A.L. TOURNIER, G.M. ULLMANN and V. KURKAL. Physical and functional aspects of protein dynamics.Soft Condensed Matter Physics in Molecular and Cell Biology, 225-241, ed. W.C.K. Poon and D. Andelman, Taylor & Francis (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).
K. MORITSUGU and J.C.SMITH. Temperature-Dependent Protein Dynamics: A Simulation-Based Probabilistic Diffusion-Vibration Langevin Description. Journal of Physical Chemistry 110(11):5807-16 (2006).
J.C. SMITH. Tight in Titin. Structure 14 (3):389-90 (2006).
S. SCHWARZL, J.C. SMITH and S. FISCHER. Insights into the chemomechanical coupling of the myosin motor from simulation of its ATP hydrolysis mechanism. Biochemistry 45(18):5830-5847 (2006)
F. NOE, D. KRACHTUS, J.C. SMITH and S. FISCHER. Transition Networks for the Comprehensive Characterization of Complex Conformational Change in proteins. Journal of Chemical Theory and Computation 2 840-857 (2006).
S. MESENTEAN, S. FISCHER and 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).
A.N. BONDAR, J.C. SMITH and S. FISCHER. Structural and energetic determinants of proton transfer in bacteriorhodopsin. Photochemical and Photobiological Sciences 5 547-561 (2006).
P. IMHOF, F. NOE, S. FISCHER and J.C. SMITH. AM1/d parameters for Magnesium in Metalloenzymes. Journal of Chemical Theory and Computation 2 (4) 1050–1056 (2006).
E. BALOG, J.C.SMITH and D. PERAHIA. Conformational heterogeneity and low-frequency vibrational modes of proteins. Physical Chemistry Chemical Physics 8 (47) 5543-5548 (2006).
V. KURKAL-SIEBERT, R. DANIEL, J.L. FINNEY, M. TEHEI, R.V. DUNN and J.C. SMITH. Enzyme hydration, activity and flexibility: A neutron scattering approach. Journal of Noncrystalline Solids 352 (42) 4387-4393 (2006).
F. NOE, M. OSWALD, G. REINELT, S. FISCHER and 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 5 393-419 (2006).
Contact Information
Office:
Oak Ridge National Laboratory
Phone: (865) 574-9635
Email:smithjc@ornl.gov