Justin A. Lemkul

Curriculum Vitae

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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

2016	The Wiley Computers in Chemistry Outstanding Postdoc Award (ACS COMP Division)
2014 - 2017	Ruth L. Kirschstein National Research Service Award (NIH F32)
2013	Outstanding Dissertation in Science, Technology, Engineering, and Mathematics
2012	Outstanding Doctoral Student in the College of Agriculture and Life Sciences
2011	Kendall W. King Memorial Scholarship, outstanding senior graduate student in Biochemistry
2010	1^st place poster (Student Biomedical category), 6^th Annual VCOM Research Day
2009	James F. Eheart Travel Scholarship
2008	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
2007	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
8^th 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	Co-Instructor 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	HTML, LaTeX

Publications

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]