Publications

Google Scholar Link

23) Mechanistic Insights into Passive Membrane Permeability of Drug-like Molecules from a Weighted Ensemble of Trajectories

S. Zhang, J. P. Thompson, J. Xia, A. T. Bogetti, F. York, A. G. Skillman, L. T. Chong, D. N. LeBard, J. Chem. Inf. Model., XX, XXX-XXX (2022). (link)

22) WESTPA 2.0: High-Performance Upgrades for Weighted Ensemble Simulations and Analysis of Longer-Timescale Applications

J. D. Russo, S. Zhang, J. M. G. Leung, A. T. Bogetti, J. P. Thompson, A. J. DeGrave, P. A. Torrillo, A. J. Pratt, K. F. Wong, J. Xia, J. Copperman, J. L. Adelman, M. C. Zwier, D. N. LeBard, D. M. Zuckerman, L. T. Chong, , J. Chem. Theor. Comput., 18(2), 638-649 (2022). (link)

21) Accurate modeling of scaffold hopping transformations in drug discovery

L. Wang, Y. Deng, Y. Wu, B. Kim, D. N LeBard, D. Wandschneider, M. Beachy, R. A Friesner, Bob Abel, J. Chem. Theor. Comput., 13(1), 42-54 (2017). (link)

20) TCR Triggering by pMHC Ligands Tethered on Surfaces via Poly(Ethylene Glycol) Depends on Polymer Length

Z. Ma, D. N. LeBard*, S. M. Loverde*, K. A. Sharp, M. L. Klein, D. E. Discher, T. H. Finkel, PLoS One, 9(11), e112292(2104) DOI: 10.1371/journal.pone.0112292 (2014). (link)

* Joint second author

19) Advancing simulations of biological materials: applications of coarse-grained models on graphics processing unit hardware

D. N. LeBard*, Molecular Simulation, 40(10-11), 802-820, DOI: 10.1080/08927022.2014.899700 (2014). (link)

* Invited article for a special issue on Recent Advances in Molecular Biology

18) Magnesium-dependent RNA binding to the PA endonuclease domain of the avian influenza polymerase

S. Xiao, M. L. Klein, D. N. LeBard, B. G. Levine, H. Liang, C. M. MacDermaid, M. Alfonso-Prieto, J. Phys. Chem. B., 118(4), 873-889, DOI: 10.1021/jp408383g (2014). (link)

17) Coulomb soup of bioenergetics: Electron transfer in a bacterial bc1 complex

D. R. Martin, D. N. LeBard, D. V. Matyushov, J. Phys. Chem. Lett., 4, 3602-3606, DOI: 10.1021/jz401910e (2013). (link)

16) Protein dynamics to optimize and control bacterial photosynthesis

D. N. LeBard, D. R. Martin, S. Lin, N. W. Woodbury, D. V. Matyushov, Chem. Sci., 4, 4127-4136, DOI: 10.1039/C3SC51327K (2013). (link)

Inside back cover article

15) Exploring volatile general anesthetic binding to a closed membrane-bound bacterial voltage-gated sodium channel via computation

S. G. Raju*, A. F. Barber*, D. N. LeBard*, M. L. Klein, V. Carnevale, PLoS Comput. Biol., 9(6), e1003090 (2013), DOI: 10.1371/journal.pcbi.1003090 (link)

* Joint first author

14) General anesthetics predicted to block the GLIC pore with micromolar affinity

D. N. LeBard*, J. Hénin*, R. G. Eckenhoff, M. L. Klein, G. Brannigan, PLoS Comput. Biol., 8(6), e1002532 (2012), DOI: 10.1371/journal.pcbi.1002532 (link)

* Joint first author

13) Surfactant concentration effects on micellar properties

A. Jusufi, D. N. LeBard, B. G. Levine, and M. L. Klein, J. Phys. Chem. B, 116(3), 987-991 (2012). (link)

12) Premicelles and monomer exchange in aqueous surfactant solutions above and below the critical micelle concentration

D. N. LeBard*, B. G. Levine*, R. H. DeVane, W. Shinoda, M. L. Klein, Chem. Phys. Lett., 522, 38-42 (2012). (link)

* Joint first author

11) Self-assembly of coarse-grained ionic surfactants accelerated by graphics processing unitsD. N. LeBard*, B. G. Levine*, P. Mertmann, S. A. Barr, A. Jusufi, S. Sanders, M. L. Klein, and and A. Z. Panagiotopoulos, Soft Matter, 8(8), 2385-2397 (2012). (link)

* Joint first author

Cover article

10) Micellization studied by GPU-accelerated coarse-grained molecular dynamics

B. G. Levine*, D. N. LeBard*, R. H. DeVane, W. Shinoda, A. Kohlmeyer, M. L. Klein, J. Chem. Theor. Comput., 7(12), 4135-4145 (2011). (link)

* Joint first author

9) Protein-water electrostatics and principles of bioenergeticsD. N. LeBard, D. V. Matyushov, Phys. Chem. Chem. Phys., 12, 15335-15348 (2010). (link)

Cover article, invited perspective

8) Multiple binding sites for the general anesthetic isoflurane identified in the nicotinic acetylcholine receptor transmembrane domain

G. Brannigan, D. N. LeBard, J. Hénin, R. G. Eckenhoff, and M. L. Klein, Proc. Natl. Acad. Sci., 107(32), 14122-14127 (2010). (link)

7) Ferroelectric hydration shells around proteins: Electrostatics of the protein−water interface

D. N. LeBard and D. V. Matyushov, J. Phys. Chem. B, 114(28), 9246-9258 (2010). (link)

6) Energetics of bacterial photosynthesis

D. N. LeBard and D. V. Matyushov, J. Phys. Chem. B, 113(36), 12424-12437 (2009). (link)

5) Dynamical transition, hydrophobic interface, and the temperature dependence of electrostatic fluctuations in proteins

D. N. LeBard and D. V. Matyushov, Phys. Rev. E, 78, 061901 (2008). (link)

4) Redox entropy of plastocyanin: Developing a microscopic view of mesoscopic solvation

D. N. LeBard and D. V. Matyushov, J. Chem. Phys., 128, 155106 (2008). (link)

3) Energetics and kinetics of primary charge separation in bacterial photosynthesis

D. N. LeBard, V. Kapko, and D. V. Matyushov, J. Phys. Chem. B, 112(33), 10322-10342 (2008). (link)

Cover article

2) Glassy protein dynamics and gigantic solvent reorganization energy of plastocyanin

D. N. LeBard and D.V. Matyushov, J. Phys. Chem. B, 112(16), 5218-5227 (2008). (link)

Cover article

1) Solvent reorganization energy of charge transfer in DNA hairpins

D. N. LeBard, M. Lilichenko, D. V. Matyushov, Yu. A. Berlin, and M. A. Ratner, J. Phys. Chem. B, 107(51), 14509-14520 (2003) (link)