David L. Mobley


OBJECTIVE
I recently moved to a faculty position in the Department of Chemistry at the University of New Orleans. For more details see my web page there, though this web page is at least presently still maintained.


EDUCATION
Ph.D. University of California at Davis, Physics, 2004. Advisers: Daniel Cox, Rajiv Singh.
M.S. University of California at Davis, Physics, 2001.
B.S. University of California at Davis, Physics, 2000, with high honors.

PROFESSIONAL AND RESEARCH EXPERIENCE
2008- Assistant Professor, Chemistry, University of New Orleans.
2004-2008 Postdoctoral Researcher, UC San Francisco, under Ken Dill.
2003-2004 Graduate Research Assistant, UC Davis, with Daniel Cox and Rajiv Singh.
Fall 2003 Graduate Fellow, Kavli Institute for Theoretical Physics, Santa Barbara, attending "Pattern Formation in Physics and Biology".
2001-2003 National Science Foundation NEAT-IGERT Fellow, UC Davis
2001-2003 Undergraduate Research Assistant, UC Davis, with Winston Ko

TEACHING EXPERIENCE
2006 Supervising and training several graduate students
2001 General Physics Discussion/Laboratory B; UC Davis
2000-2001 Electronic Instrumentation Laboratory A, B; UC Davis
2000 General Science, Sacramento High School, with Howard Hughes Medical Institute Science Teaching Internship from UC Davis
1997-1998 Tutor, Physics, Shasta College

HONORS, AWARDS, AND FELLOWSHIPS
Fall 2003 Graduate Fellowship, Kavli Institute for Theoretical Physics, Santa Barbara
2001-2003 National Science Foundation NEAT-IGERT Fellowship, UC Davis
2000-2001 UC Davis Physics Department Award
2000 Saxon-Patten Prize, University of California, Davis
2000 Departmental Citation in Physics, Physics Department, University of California, Davis
2000 Howard Hughes Medical Institute Science Teaching Internship

PUBLICATIONS
1. D. L. Mobley, D. L. Cox, R. R. P. Singh, R. V. Kulkarni and A. Slepoy. "Simulations of Oligomeric Intermediates in Prion Diseases", Biophysical Journal 85, 2213-2223, 2003. (PDF)
2. D. L. Mobley, D. L. Cox, R. R. P. Singh, M. W. Maddox, M. L. Longo. "Modeling Amyloid Beta Peptide Insertion into Lipid Bilayers", Biophysical Journal 86, 3585-3597, 2004. (PDF)
3. D. L. Mobley, "Models of Cooperative Dynamics from Biomolecules to Magnets". Dissertation, University of California, Davis, July 2004. (PDF)
4. D. L. Mobley, C. R. Pike, J. E. Davies, D. L. Cox, R. R. P. Singh, "Hysteresis loops of Co-Pt perpendicular magnetic multilayers", Journal of Physics: Condensed Matter 16, 5897-5906, 2004. (PDF)
5. D. L. Mobley, J. D. Chodera, K. A. Dill. "On the use of orientational restraints and symmetry number corrections in alchemical free energy calculations", Journal of Chemical Physics 125:084902, 2006. Selected for the Virtual Journal of Biological Physics Research 12(5), 2006. (DOI, PDF)
6. A. M. Stein, T. Demuth, D. Mobley, M. Berens, and L. Sander. "A Mathematical Model of Glioblastoma Tumor Spheroid Invasion in a 3-D in vitro Experiment", Biophysical Journal 92:356 (2007). (PDF)
7. D. L. Mobley, E. Dumont, J. D. Chodera and K. A. Dill", "Comparison of charge models for fixed-charge force fields: Small-molecule hydration free energies in explicit solvent", J. Phys. Chem. B. 111:2242-2254 (2007) (DOI)
8. D. L. Mobley, J. D. Chodera, and K. A. Dill, "Confine and Release: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change", Journal of Chemical Theory and Computation 3(4):1231-1235 (2007). (DOI). One of the Top 25 Most Downloaded articles, July-September, 2007. One of the 2007 Most-Accessed Articles.
9. D. L. Mobley, A. P. Graves, J. D. Chodera, A. C. McReynolds, B. K. Shoichet and K. A. Dill, "Predicting absolute ligand binding free energies to a simple model site," Journal of Molecular Biology 371(4):1118-1134 (2007). (DOI). One of the Top 25 Hottest Articles, July-September, 2007.
10. M. R. Shirts, D. L. Mobley, and J. D. Chodera. "Alchemical free energy calculations: Ready for prime time?", Annual Reports in Computational Chemistry 3:41-59 (2007). (DOI, PDF)
11. M. R. Shirts*, D. L. Mobley*, J. D. Chodera, and V. S. Pande. "Accurate and efficient corrections for missing dispersion interactions in molecular simulations", J. Phys. Chem. B 111:13052-13063 (2007). * - These authors contributed equally to this work. (DOI)
12. T. Steinbrecher, D. L. Mobley, and D. A. Case. "Non-linear scaling schemes for Lennard-Jones interactions in free energy calculations", J. Chem. Phys. 127: 214108 (2007). (DOI) Selected for the Virtual Journal of Biological Physics 14 (12), 2007.
13. D. L. Mobley, J. D. Chodera, and K. A. Dill. "Entropy and conformational change in implicit solvent simulations of small molecules", J. Phys. Chem. B 112:938-946 (2008). (DOI, supporting information, small molecule test set, stored Amber trajectories (600 MB)).
14. A. Nicholls*, D. L. Mobley*, J. P. Guthrie, J. D. Chodera, C. I. Bayly, M. D. Cooper, and V. S. Pande. "Predicting small-molecule solvation free energies: a blind challenge test for computational chemistry", J. Med. Chem. 51: 769-779 (2008) (DOI). * - These authors contributed equally to this work.
15. D. L. Mobley, A. Barber II, C. Fennell, and K. A. Dill. "Charge asymmetries in hydration of polar solutes", J. Phys. Chem. B 112: 2405-2414, 2008. (DOI, Supporting Information).
16. D. L. Mobley, C. I. Bayly, M. D. Cooper, M. R. Shirts, and K. A. Dill. "Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge force fields", J. Chem. Theory Comput. 5: 350-358, 2009. (DOI, Supporting info PDF, mol2 files with partial charges, parameter and coordinate files).
17. D. L. Mobley and K. A. Dill. "The binding of small molecule ligands to proteins: 'What you see' is not always 'what you get'" Structure 17(4): 489-498, 2009 (DOI).
18. M. R. Shirts, D. L. Mobley and Scott P. Brown. "Free energy calculations in structure-based drug design", forthcoming in "Structure Based Drug Design", Cambridge University Press, edited by Kenneth M. Merz, Dagmar Ringe and Charles H. Reynolds (PDF preprint)
19. D. L. Mobley, C. I. Bayly, M. D. Cooper, and K. A. Dill. "Predictions of hydration free energies from all-atom molecular dynamics simulations", J. Phys. Chem. B 113:4533-4537, 2009. (DOI)
20. C. L. McClendon, G. Friedland, D. L. Mobley, H. Amirkhani, and M. P. Jacobson. "Quantifying correlations between allosteric sites in thermodynamic ensembles", J. Chem. Theory Comput. 5: 2486-2502, 2009. (DOI)
21. S. E. Boyce*, D. L. Mobley*, G. Rocklin, A. P. Graves, K. A. Dill, and B. K. Shoichet. "Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site", J. Mol. Biol. 394:747-763, 2009. (DOI) * - contributed equally.
22. J. Ponder, C. Wu, V. Pande, M. Schneiders, D. L. Mobley, I. Haque, D. Lambrecht, R. Distasio Jr., M. Head-Gordon, G. Clark, M. Johnson, T. Head-Gordon. "Current status of the AMOEBA polarizable force field", J. Phys. Chem. B. 114:2549-2564, 2010. (DOI)
23. Pavel V. Klimovich and D. L. Mobley, "Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations", J. Comp. Aided Mol. Design 24:307, 2010. (DOI)

 

RESEARCH INTERESTS

 

Computational drug design/lead optimization

Protein-ligand interactions

Free-energy calculations -- application and methodology

Allostery in proteins

Molecular biology of disease

Noise and small number fluctuations in biological systems

Molecular mechanics force fields and solvation models

INVITED PRESENTATIONS
1. Theoretical and Computational Molecular Biophysics Group, The Scripps Research Institute, San Diego, December 2003
2. St. Jude Children's Research Hospital seminar, January, 2004
3. Center for Theoretical Biological Physics seminar, UC San Diego, January, 2004.
4. Short talk, Protein Misaggregation: From Biomolecules to Neurodegeneration, Boston, Febuary, 2004.
5. Biophysics seminar, UC Davis, February 2004
6. Science Colloquium, Shasta College, Redding, CA, March, 2004
7. ICAM Workshop on Lifelike Matter, April, 2004, Santa Fe, N.M.
8. UC Davis Condensed Matter Physics Seminar, January, 2006
9. ACS National Meeting, "Computers in Chemistry: Free Energy Calculations in Drug Discovery", September, 2006
10. Seminar, SGX Pharmaceuticals, San Diego, February, 2007
11. Computational Science Seminar, Florida State University, September, 2007
12. OpenEye CUP Meeting, Santa Fe, NM, March 2008

CONTACT

Mailing Address:
Department of Chemistry
University of New Orleans
New Orleans, LA 70148

Phone: (504) 383-3662

E-mail: dmobley@gmail.com