Curriculum Vitae

For a full version of my CV, click here.
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Education and Appointments

July 2013 - Present

Postdoctoral Fellow
Department of Pharmaceutical Sciences
University of Maryland, Baltimore
Advisor: Dr. Alexander D. MacKerell, Jr.

May 2012 - May 2013

Research Scientist
Department of Biochemistry
Virginia Tech

Aug 2007 - May 2012

Ph.D., Biochemistry
Virginia Tech
Advisor: Dr. David R. Bevan

Aug 2003 - May 2007

B.S., Biochemistry In Honors, Summa Cum Laude
Minor in Chemistry
Concentration in Biotechnology
Virginia Tech

Awards and Honors


The Wiley Computers in Chemistry Outstanding Postdoc Award (ACS COMP Division)

2014 - 2017

Ruth L. Kirschstein National Research Service Award (NIH F32)


Outstanding Dissertation in Science, Technology, Engineering, and Mathematics


Outstanding Doctoral Student in the College of Agriculture and Life Sciences


Kendall W. King Memorial Scholarship, outstanding senior graduate student in Biochemistry


1st place poster (Student Biomedical category), 6th Annual VCOM Research Day


James F. Eheart Travel Scholarship


Bruce M. Anderson Graduate Award, outstanding first-year graduate student in Biochemistry

2008 - 2010

NSF MILES-IGERT Training Grant for research in oxidative processes

2007 - 2012

ICTAS Doctoral Scholar Graduate Fellowship


James Lewis Howe Award, outstanding senior in Biochemistry awarded by the Blue Ridge Chapter of the ACS

2005, 2006

R. W. Engel Scholarship for excellence in Biochemistry

2003 - 2007

Dean's List

Teaching Experience

April 2015

Guest Lecturer
PHAR 621 Molecular Biophysics
University of Maryland, Baltimore

August 2014

Lecturer and Mentor
8th Annual q-bio Summer School
University of New Mexico

September 2013

Tutorial Instructor
2013 USA GROMACS Conference and Workshop
University of Virginia

February 2013

Guest Lecturer
BCHM 4116 General Biochemistry
Virginia Tech

Fall 2011

Course Discussion Leader
BCHM 1014 Introduction to Biochemistry
Virginia Tech

December 2010

Guest Lecturer
BIOL 274 Structural Biology
Washington & Lee University

Fall 2009

BCHM 5984 Applications of Molecular Modeling
Virginia Tech

Spring 2009

Teaching Assistant
BCHM 4116 General Biochemistry
Virginia Tech

2006 - 2007

Teaching Assistant
CHEM 1035/1036 General Chemistry
Virginia Tech

2004 - 2007

Chemistry Learning Center Tutor
Department of Chemistry
Virginia Tech

Skills and Software

Molecular dynamics

GROMACS (developer), NAMD, CHARMM, OpenMM

Quantum mechanics

Gaussian, Q-Chem, MolPro

Programming languages

Perl, C, C++

Markup languages



  1. J.A. Lemkul and A.D. MacKerell, Jr. (2017) "Polarizable Force Field for DNA Based on the Classical Drude Oscillator: I. Refinement Using Quantum Mechanical Base Stacking and Conformational Energetics." J. Chem. Theory Comput. 13 (5): 2053-2071. [Abstract]

  2. J.A. Lemkul and A.D. MacKerell, Jr. (2017) "Polarizable Force Field for DNA Based on the Classical Drude Oscillator: II. Microsecond Molecular Dynamics Simulations of Duplex DNA." J. Chem. Theory Comput. 13 (5): 2072-2085. [Abstract]

  3. J.A. Lemkul and A.D. MacKerell, Jr. (2016) "Balancing the Interactions of Mg2+ in Aqueous Solution and with Nucleic Acid Moieties For a Polarizable Force Field Based on the Classical Drude Oscillator Model." J. Phys. Chem. B 120 (44): 11436-11448. [Abstract]

  4. J.A. Lemkul, S.K. Lakkaraju, and A.D. MacKerell, Jr. (2016) "Characterization of Mg2+ Distributions around RNA in Solution." ACS Omega 1 (4): 680-688. [Full Text]

  5. I. Soteras, F.-Y. Lin, K. Vanommeslaeghe, J.A. Lemkul, K.A. Armacost, C.L. Brooks III, and A.D. MacKerell, Jr. (2016) "Parametrization of Halogen Bonds in the CHARMM General Force Field: Improved Treatment of Protein-Ligand Interactions." Bioorg. Med. Chem. 24 (20): 4812-4825. [Abstract]

  6. J.A. Lemkul, J. Huang, B. Roux, and A.D. MacKerell, Jr. (2016) "An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications." Chem. Rev. 116 (9): 4983-5013. [Full Text]

  7. J. Lee, X. Cheng, J. Swails, M.S. Yeom, P. Eastman, J.A. Lemkul, S. Wei, J. Buckner, J.C. Jeong, Y. Qi, S. Jo, V. Pande, D.A. Case, C.L. Brooks III, A.D. MacKerell, Jr., J.B. Klauda, and W. Im. (2016) "CHARMM-GUI Input Generation for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations using the CHARMM Force Fields." J. Chem. Theory Comput. 12 (1): 405-413. [Full Text]

  8. S.K. Lakkaraju, J.A. Lemkul, J. Huang, and A.D. MacKerell, Jr. (2016) "DIRECT-ID: An Automated Method to Identify and Quantify Conformational Variations - Application to β2-adrenergic GPCR." J. Comput Chem. 37 (4): 416-425. [Abstract]

  9. J.A. Lemkul, J. Huang, and A.D. Mackerell, Jr. (2015) "Induced Dipole-Dipole Interactions Influence Unfolding Pathways of Wild-Type and Mutant Amyloid β-Peptides." J. Phys. Chem. B 119 (51): 11574-11582. [Full Text]

  10. J.A. Lemkul, B. Roux, D. van der Spoel, and A.D. MacKerell, Jr. (2015) "Implementation of Extended Lagrangian Dynamics in GROMACS for Polarizable Simulations Using the Classical Drude Oscillator Model." J. Comput. Chem. 36 (19): 1473-1479. [Abstract]

  11. J.A. Lemkul, S.N. Lewis, J. Bassaganya-Riera, and D.R. Bevan (2015) "Phosphorylation of PPARγ Affects the Collective Motions of the PPARγ-RXRα-DNA Complex." PLOS ONE 10 (5): e0123984. [Full Text]

  12. S.R. Gerben, J.A. Lemkul, A.M. Brown, and D.R. Bevan (2014) "Comparing Atomistic Molecular Mechanics Force Fields for a Difficult Target: A Case Study of the Amyloid β-Peptide." J. Biomol. Struct. Dyn. 32 (11): 1817-1832. [Abstract]

  13. J.A. Lemkul, A. Savelyev, and A.D. MacKerell, Jr. (2014) "Induced Polarization Influences the Fundamental Forces in DNA Base Flipping." J. Phys. Chem. Lett. 5 (12): 2077-2083. [Full Text] [ACS LiveSlides]

  14. D.G.S. Capelluto, X. Zhao, A. Lucas, J.A. Lemkul, S. Xiao, X. Fu, F. Sun, D.R. Bevan, and C.V. Finkielstein (2014) "Biophysical and molecular dynamics studies of phosphatidic acid binding by the Dvl-2 DEP domain." Biophys. J. 106 (5): 1101-1111. [Abstract]

  15. A.M. Brown, J.A. Lemkul, N. Schaum, and D.R. Bevan (2014) "Simulations of Monomeric Amyloid β-Peptide (1-40) with Varying Solution Conditions and Oxidation State of Met35: Implications for Aggregation." Arch. Biochem. Biophys. 545 (1): 44-62. [Abstract]

  16. J.A. Lemkul and D.R. Bevan (2013) "Aggregation of Alzheimer's Amyloid β-Peptide in Biological Membranes: A Molecular Dynamics Study." Biochemistry 52 (29): 4971-4980. [Abstract]

  17. J.A. Lemkul and D.R. Bevan (2012) "The Role of Molecular Simulations in the Development of Inhibitors of Amyloid β-Peptide Aggregation for the Treatment of Alzheimer's Disease." ACS Chem. Neurosci. 3 (11): 845-856. [Abstract] [Cover Art]

  18. J.A. Lemkul and D.R. Bevan (2012) "Morin Inhibits the Early Stages of Amyloid β-Peptide Aggregation by Altering Tertiary and Quaternary Interactions to Produce 'Off-Pathway' Structures." Biochemistry 51 (30): 5990-6009. [Abstract]

  19. J.A. Lemkul and D.R. Bevan (2011) "Lipid composition influences the release of Alzheimer's amyloid β-peptide from membranes." Protein Sci. 20 (9): 1530-1545. [Abstract]

  20. J.A. Lemkul and D.R. Bevan (2011) "Characterization of Interactions between PilA from Pseudomonas aeruginosa Strain K and a Model Membrane." J. Phys. Chem. B 115 (24): 8004-8008. [Abstract]

  21. J.A. Lemkul, W.J. Allen, and D.R. Bevan (2010) "Practical Considerations for Building GROMOS-Compatible Small Molecule Topologies." J. Chem. Inf. Model. 50 (12): 2221-2235. [Abstract]

  22. J.A. Lemkul and D.R. Bevan (2010) "Destabilizing Alzheimer's Aβ42 Protofibrils with Morin: Mechanistic Insights from Molecular Dynamics Simulations." Biochemistry 49 (18): 3935-3946. [Abstract]

  23. P. Mehere, Q. Han, J.A. Lemkul, C.J. Vavricka, H. Robinson, D.R. Bevan, and J. Li (2010) "Tyrosine Aminotransferase: biochemical and structural properties and molecular dynamics simulations." Protein & Cell 1 (11): 1023-1032. [Abstract]

  24. J.A. Lemkul and D.R. Bevan (2010) "Assessing the Stability of Alzheimer's Amyloid Protofibrils Using Molecular Dynamics." J. Phys. Chem. B 114 (4): 1652-1660. [Abstract]

  25. J.A. Lemkul and D.R. Bevan (2009) "Perturbation of membranes by the amyloid β-peptide - a molecular dynamics study." FEBS J. 276 (11): 3060-3075. [Abstract]

  26. W.J. Allen, J.A. Lemkul, and D.R. Bevan (2009) "GridMAT-MD: A Grid-Based Membrane Analysis Tool for Use With Molecular Dynamics." J. Comput. Chem. 30 (12): 1952-1958. [Abstract]

  27. J.A. Lemkul and D.R. Bevan (2008) "A Comparative Molecular Dynamics Analysis of the Amyloid β-Peptide in a Lipid Bilayer." Arch. Biochem. Biophys. 470 (1): 54-63. [Abstract]

Copyright 2013-2016 by Justin Lemkul