Papers published since start of research program at UC Davis:

37. Eastman, P.; Swails, J.; Chodera, J. D.; McGibbon, R. T.; Zhao, Y.; Beauchamp, K. A.; Wang, L. P.; Simmonett, A. C.; Harrigan, M. P.; Stern, C. D.; Wiewiora, R. P.; Brooks, B. R.; Pande, V. S. (2017) “OpenMM 7: Rapid development of high performance algorithms for molecular dynamics”, PLOS Comput. Biol. 13, e1005659. (DOI, PDF)

36. Huang, J.; Mei, Y.; König, G.; Simmonett, A. C.; Pickard IV, F. C.; Wu, Q.; Wang, L.-P.; MacKerell Jr., A. D.; Brooks, B. R.; Shao, Y. (2017) “An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches”, J. Chem. Theory Comput. 13, 679–695. (DOI, PDF)

35. Wang, L.-P.; McKiernan, K. A.; Gomes, J.; Beauchamp, K. A.; Head-Gordon, T.; Rice, J. E.; Swope, W. C.; Martínez, T. J.; Pande, V. S. (2017) "Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15", J. Phys. Chem. B 4023–4039. (DOI, PDF)

34. Khedri, Z.; Xiao, A.; Yu, H.; Landig, C. S.; Li, W.; Diaz, S.; Wasik, B. R.; Parrish, C. R.; Wang, L.-P.; Varki, A; Chen, X. (2017) “A Chemical Biology Solution to Problems with Studying Biologically Important but Unstable 9-O-Acetyl Sialic Acids”, ACS Chem. Biol. 12, 214–224. (DOI, PDF)

33. McKiernan, K. A.; Wang L.-P.; Pande V. S. (2016) “Training and Validation of a Liquid-Crystalline Phospholipid Bilayer Force Field”, J. Chem. Theory Comput. 12, 5960–5967. (DOI, PDF)

32. Albaugh, A.; Boateng, H. A.; Bradshaw, R. T.; Demerdash, O. N.; Dziedzic, J.; Mao, Y. Z.; Margul, D. T.; Swails, J.; Zeng, Q.; Case, D. A.; Eastman, P.; Wang, L.-P.; Essex, J. W.; Head-Gordon, M.; Pande, V. S.; Ponder, J. W.; Shao, Y. H.; Skylaris, C. K.; Todorov, I. T.; Tuckerman, M. E.; Head-Gordon, T. (2016) “Advanced Potential Energy Surfaces for Molecular Simulation”, J. Phys. Chem. B 120, 9811-9832. (DOI, PDF)

31. Wang C.-Y.; Liao X.; Wang L.-P.; Wang C.-H.; Manga M. (2016) “Large earthquakes create permeability by breaching aquitards”, J. Chem. Phys. 144, 214108. (DOI, PDF)

30. Wang L.-P.*; Song C. C. (2016) “Geometry optimization made simple with translation and rotation coordinates”, J. Chem. Phys. 144, 214108. (DOI, PDF)

29. Song C. C., Wang L.-P., Martínez T. J. (2016) “Automated Code Engine for Graphical Processing Units: Application to the Effective Core Potential Integrals and Gradients”, J. Chem. Theory Comput. 12, 92-106. (DOI, PDF)

28. Wang L.-P.; McGibbon R. T.; Pande V. S.; Martínez T. J. (2016) “Automated Discovery and Refinement of Reactive Molecular Dynamics Pathways”, J. Chem. Theory Comput. 12, 638-649. (DOI, PDF)

27. McGibbon R. T.; Beauchamp K. A.; Harrigan M. P.; Klein C.; Swails J. M.; Hernández C. X.; Schwantes C. R.; Wang L.-P.; Lane T. J.; Pande V. S. (2015) “MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories”, Biophys. J. 109, 1528-1532. (DOI, PDF)

26. Song C. C.; Wang L.-P.; Sachse T.; Preiss J.; Presselt M; Martinez T. J. (2015) “Efficient implementation of effective core potential integrals and gradients on graphical processing units”, J. Chem. Phys. 143, 014114. (DOIPDF)

25. Rui Q.*; Wang L.-P.*; Wang Q.; Pande V. S.; Ren P. (2015) “United polarizable multipole water model for molecular mechanics simulation”, J. Chem. Phys. 143, 014504. (DOI, PDF)

Papers published prior to start of research program at UC Davis:

* Equal contributions.       

24. Kokkila Schumacher S. I. L.; Hohenstein E. G.; Parrish R. M.; Wang L.-P.; Martinez T. J. (2015) “ Tensor hypercontraction second-order Møller−Plesset perturbation theory: grid optimization and reaction energies”, J. Chem. Theory. Comput., Article ASAP. (DOI, PDF)

23. Welborn M.; Chen J.; Wang L.-P.; Van Voorhis T. (2015) “Why many semiempirical molecular orbital theories fail for liquid water and how to fix them”, J. Comput. Chem. 36, 934-939. (DOI, PDF)

22. Laury M. L.*; Wang L.-P.*; Pande V. S.; Head-Gordon T.; Ponder J. W. (2015) “Revised parameters for the AMOEBA polarizable atomic multipole water model”, J. Phys. Chem. B, Article ASAP. (DOI, PDF)

* Equal contributions.       

21. Wang L.-P.; Titov A.; McGibbon R.; Liu F.; Pande V. S.; Martinez T. J. (2014) “Discovering chemistry with an ab initio nanoreactor”, Nature Chemistry 6, 1044-1048.* (DOI, PDF

* Highlighted in Nov. 10, 2014 issue of Chemical & Engineering News.

20. Wang L.-P.; Martinez T. J.; Pande V. S. (2014) “Building force fields – an automatic, systematic and reproducible approach”, J. Phys. Chem. Lett. 4, 1885-1891. (DOI, PDF)

19. Mavros M.; Tsuchimochi T.; Kowalczyk T.; McIsaac A.; Wang L.-P.; Van Voorhis T. (2014) “What can density functional theory tell us about artificial catalytic water splitting?” Inorg. Chem. 53, 6386-6397. (DOI, PDF)

18. Mu X.; Wang Q.; Wang L.-P.; Fried S. D.; Piquemal J. P.; Dalby K. N.; Ren P. (2014) “Modeling Organochlorine Compounds and the σ-Hole Effect Using a Polarizable Multipole Force Field”, J. Phys. Chem. B 118, 6456-6465. (DOI, PDF)

17.  Fried S. D.; Wang L.-P.; Boxer S. G.; Ren P.; Pande V. S. (2013) “Calculations of the Electric Fields in Liquid Solutions”, J. Phys. Chem. B 117, 16236-16248. (DOI, PDF)

16.  Wang L.-P.; Tofan D.; Chen J.; Van Voorhis T.; Cummins C. C. (2013) “A pathway to diphosphorous from the dissociation of photoexcited tetraphosphorus”, RSC Advances 3, 23166-23171. (DOI, PDF)

15.  Wang L.-P.; Head-Gordon T.; Ponder J. W.; Ren P.; Chodera J. D.; Eastman P. K.; Martinez T. J.; Pande V. S. (2013) “Systematic Improvement of a Classical Molecular Model of Water”, J. Phys. Chem. B 117, 9956-9972. (DOI, PDF)

14.  Wang C.-Y.; Wang L.-P.; Manga M.; Wang C.-H.; Chen C.-H. (2013) “Basin-scale transport of heat and fluid induced by earthquakes”, Geophys. Res. Lett. 40, 3893-3897. (DOI, PDF)

13.  Wang C.-Y.; Chen W.-P.; Wang L.-P. (2013) “Temperature beneath Tibet”, Earth. Planet. Sci. Lett. 375, 326-337. (DOI, PDF)

12.  Wang L.-P.; Chen J.; Van Voorhis T. (2013) “Systematic Parameterization of Polarizable Force Fields from Quantum Chemistry Data”, J. Chem. Theory Comput. 9, 452-460. (DOI, PDF)

11. Eastman P.; Friedrichs M. S.; Chodera J. D.; Radmer R. J.; Bruns C. M.; Ku J. P.; Beauchamp K. A.; Lane T. J.; Wang L.-P.; Shukla D.; Tye T.; Houston M.; Stich M.; Klein C.; Shirts M. R.; Pande V. S. “OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation”, J. Chem. Theory Comput. 9, 461-469. (DOI, PDF)

10.  Wang L.-P.; Van Voorhis T. (2012) “A Polarizable QM/MM Explicit Solvent Model for Computational Electrochemistry in Water”, J. Chem. Theory Comput. 8, 610-617. (DOI, PDF)

9.    Kowalczyk T.; Wang L.-P.; Van Voorhis T. (2011) “Simulation of solution phase electron transfer in a compact donor-acceptor dyad”, J. Phys. Chem. B. 115, 12135. (DOI, PDF)

8.    Wang L.-P.; Van Voorhis T. (2011) “Direct-Coupling O2 Bond Forming a Pathway in Cobalt Oxide Water Oxidation Catalysts”, J. Phys. Chem. Lett. 2, 2200-2204. (DOI, PDF)

7.    Yost S. R.; Wang L.-P.; Van Voorhis T. (2011) “Molecular Insight Into the Energy Levels at the Organic Donor/Acceptor Interface: A Quantum Mechanics/Molecular Mechanics Study”, J. Phys. Chem. C 115, 14431-14436. (DOI, PDF)

6.    Wang L.-P.; Wu Q.; Van Voorhis T. (2010) “Acid-Base Mechanism for Ruthenium Water Oxidation Catalysts”, Inorg. Chem. 49, 4543-4553. (DOI, PDF)

5.    Wang L.-P.; Van Voorhis T. (2010) “Hybrid ensembles for improved force matching”, J. Chem. Phys. 133, 231101. (DOI, PDF)

4.    Difley S.; Wang L.-P.; Yeganeh S.; Yost S. R.; Van Voorhis T. (2010) “Electronic Properties of Disordered Organic Semiconductors via QM/MM Simulations”, Acc. Chem. Res. 43, 955-1004 and front cover. (DOI, PDF)

3.    Van Voorhis T.; Kowalczyk T.; Kaduk B.; Wang L.-P.; Cheng C. L.; Wu Q. (2010) “The Diabatic Picture of Electron Transfer, Reaction Barriers, and Molecular Dynamics”, Ann. Rev. Phys. Chem. 61, 149-170. (DOI, PDF)

2.    Khine M.; Ionescu-Zanetti C.; Blatz A.; Wang L.-P.; Lee L. P. (2007) “Single cell electroporation arrays with real-time monitoring and feedback control”, Lab on a Chip 7, 457-462. (DOI, PDF)

1.    Ionescu-Zanetti C.; Wang L.-P.; Di Carlo D.; Hung P.; Di Blas A.; Hughey R.; Lee L. P. (2005) “Alkaline hemolysis fragility is dependent on cell shape: Results from a morphology tracker”, Cytometry 65A, 116-123. (DOI, PDF)