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Welcome!» Faculty and Research» Jeremy C. Smith


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. K. SANGHA, L. PETRIDIS, J. C. SMITH, A. ZIEBELL and J. M. PARKS. Molecular simulation as a tool for studying lignin Environmental Progress and Sustainable Energy. 31 (1) 47-54 (2012)

M. BISWAS, T. WOCJAN, J. LANGOWSKI & J.C. SMITH. DNA bending potentials for loop-mediated nucleosome repositioning by M. Biswas, EPL 97 38004 (2012)

K. VOLTZ, J. TRYLSKA, N. CALIMET, J.C. SMITH and J. LANGOWSKI. Unwrapping of nucleosomal DNA ends: a multiscale molecular dynamics study. Biophysical Journal. 102(4):849-58 (2012)

B. LINDNER and J.C. SMITH. Sassena - X-ray and Neutron Scattering Calculations from Molecular Dynamics Trajectories using Massively Parallel Computers. Computer Physics Communications. 183(7) 1491-1501 (2012)

N. SMOLIN, R. BIEHL, G.R. KNELLER, D. RICHTER & J.C. SMITH. Functional Domain Motions in Proteins on the ~1-100ns Timescale: Comparison of Neutron Spin Echo Spectroscopy of Phosphoglycerate Kinase with Molecular Dynamics Simulation. Biophysical Journal. 102(5), 1108-1117 (2012).

X. CHENG, J.M. PARKS, L. PETRIDIS, B. LINDNER, R. SCHULZ, H.B. GUO, G. SRINIVAS and J.C. Smith. Molecular Simulation in the Energy Biosciences. In Innovations in Biomolecular Modeling and Simulations Vol. 1.  RSC Publishing. Ed. T. Schlick. 87-112. (2012)

M. KRISHNAN & J.C. SMITH Reconstruction of Protein Side-Chain Conformational Free Energy Surfaces From NMR-Derived Methyl Axis Order Parameters. Journal of Physical Chemistry B. 116(14):4124-33 (2012)

L. HONG, X. CHENG, D. C. GLASS & J.C. SMITH Surface hydration amplifies single-well protein atom diffusion propagating into the macromolecular core. Physical Review Letters. 108, 238102 (2012)

T BEREZNIAK, A. JAESCHKE, J.C. SMITH & P. IMHOF. Stereoselection in the Diels-Alderase Ribozyme: A Molecular Dynamics Study. Journal of Computational Chemistry. 33(19):1603-14 (2012)

R. POOL, K.A.FEENSTRA, M. HOEFLING, R. SCHULZ, J.C. SMITH & J. HERINGA. 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. In press.

Y. ZHENG, Y. MIAO, J. BAUDRY, N. JAIN and J.C. SMITH  Derivation of Mean-Square Displacements for Protein Dynamics from Elastic Incoherent Neutron Scattering. Journal of Physical Chemistry B.  In Press.

A. SANGHA, J. PARKS, R. STANDAERT, A. ZIEBELL,  M. DAVIS  & J.C. SMITH. Radical Coupling Reactions in Lignin Synthesis: A DFT study. Journal of Physical Chemistry B.  In Press.

S.R. ELLINGSON, S. DAKSHANAMURTHY, M. BROWN, J.C. SMITH & J. BAUDRY Accelerating Virtual High-Throughput Ligand Docking: Screening One Million Compounds Using a Petascale Supercomputer. Concurrency and Computation: Practice and Experience. In press.

P. LANGAN,  B. R. EVANS,  M. FOSTON,  W. T. HELLER,  H. O’NEILL, L.PETRIDIS,  S. V. PINGALI, A. J. RAGAUSKAS,  J. C. SMITH,  V. S. URBAN, B. DAVISON. Neutron Technologies for Bioenergy Research. Industrial Biotechnology. In Press.

J. P. ULMSCHNEIDER, J.C. SMITH, M.B. ULMSCHNEIDER, A. ULRICH & E. STRANDBERG. Re-orientation and dimerization of the membrane-bound antimicrobial peptidePGLa from microsecond all-atom MD simulations. Biophysical Journal. In Press

D. GLASS, K. MORITSUGU, X. CHENG & J.C. SMITH. REACH coarse-grained simulation of a cellulose fiber. Biomacromolecules. In press

J.D. NICKELS, H. O’NEILL, L. HONG, M. TYAGI, G. EHLERS, K. WEISS, Q. ZHANG, Z. YI, E. MAMANTOV, J.C. SMITH & A. SOKOLOV.  Dynamics of a Protein and its Hydration Water: Neutron Scattering Studies on Fully Deuterated GFP. Biophysical Journal. In Press.

I. DAIDONE, C. IACOBUCCI, S.E. MCCLAIN & J.C. SMITH. Alteration of Water Structure by Peptide Clusters Revealed by Neutron Scattering in the  Small Angle Region (below 1 A**-1). Biophysical Journal. In press.

Collignon B, Schulz R, Smith J, and Baudry J. Task-Parallel MPI Implementation of Autodock4 for Docking of Very Large Databases of Compounds Using High Performance Super-Computers. Journal of Computational Chemistry. (in press)

Guo HB, Parks J, Johs A, and Smith J. Mercury Detoxification by Bacteria: Simulations of Transcription Activation and Mercury-Carbon Bond Cleavage in Modeling of Molecular Properties. Springer. (in press)

Noe F, Doose S, Daidone I, Lollmann M, Sauer M, Chodera J, and Smith J . Dynamical Fingerprints: Probing Individual Relaxation Processes in Biomolecular Dynamics with Simulations and Kinetic Experiments. Proceedings of the National Academy of Sciences. (in press)

Parks J, Imhof P, and Smith J. Understanding Enzyme Catalysis Using Computer Simulation. Wiley. Encyclopedia of Catalysis, 2nd edition. (in press)

Prinz JH, Held M, Smith J, and Noe F. Efficient Computation, Sensitivity and Error Analysis of Committor Probabilities for Complex
Dynamical Processes. Multiscale Modeling and Simulation. (in press)

Smith J, Krishnan M, Petridis L, and Smolin N. Structure and Dynamics of Biological Systems: Integration of Neutron Scattering with
Computer Simulation. Dynamics of Soft Matter. (in press)

Splettstoesser T, Holmes K, Noe F, and Smith J. Structural Modeling and Molecular Dynamics Simulation of the Actin Filament. PROTEINS: Structure, Function, and Bioinformatics. (in press)

Bondar AN, Fischer S, and Smith J. Water Pathways in the Bacteriorhodopsin Proton Pump. Journal of Membrane Biology, 239(1-2):73-84. (2011)

Neusius T, Daidone I, Sokolov I, and Smith J. Configurational Subdiffusion of Peptides: A Network Study. Physical Review E, 83:021902. (2011)

Petridis L, Pingali SV, Urban V, Heller W, O' Neil H, Foston M, Ragauskas A, and Smith J. Self-similar multiscale structure of lignin revealed by neutron scattering and molecular dynamics simulation. Physical Review E, 83:061911. (2011)

Jeremy C. Smith, Ph.D.

 

Contact Information

Office:
Oak Ridge National Laboratory
Phone: (865) 574-9635

Email:smithjc@ornl.gov