Publications

90. J.I. Mendieta-Moreno, D.G. Trabada, J. Mendieta, J.P. Lewis, P. Gómez-Puertas, and J. Ortega. 2016. “Quantum Mechanics/Molecular Mechanics Free Energy Maps and Nonadiabatic Simulations for a Photochemical Reaction in DNA: Cyclobutane Thymine Dimer. J. Phys. Chem. Lett. 7:4391-4397. DOI: 10.1021/acs.jpclett.6b02168

89.
C. Wang, L. Wang, J. Zhang, H. Wang, J.P. Lewis, and F.-S. Xiao. 2016. Product selectivity controlled by zeolite crystals in biomass hydrogenation over a palladium catalyst. J. Am. Chem. Soc. 138:7880-7883. DOI: 10.1021/jacs.6b04951

88. L. Wang, J. Zhang, H. Wang, Y. Shao, X. Liu, Y.-Q. Wang, J.P. Lewis, F.-S. Xiao. 2016. “Outstanding activity and selectivity in nitroarene hydrogenation over Au nanoparticles on the edge/corner of anatase,” ACS Catalysis. 6:4110-4116. DOI: 10.1021/acscatal.6b00530

87. V. Zobač, J.P. Lewis, and P. Jelínek. 2016. “Non-adiabatic molecular dynamics simulations of opening reaction of molecular junctions,” Nanotechnology 27:285202. DOI: 10.1088/0957-4484/27/28/285202

86. O. Ranasingha, H. Wang, V. Zobač, P. Jelínek, G. Panapitiya, A.J. Neukirch, O.V. Prezhdo, and J.P. Lewis. 2016. “Slow relaxation of surface excitations in Au55: The key to efficient plasmonic heating in Au/TiO2,” J. Phys. Chem. Lett. 7:1563-1569. DOI: 10.1021/acs.jpclett.6b00283

85. I. Karki, H. Wang, N.R. Giese, B.W. Wilson, J.P. Lewis, and T. Gullion. 2015 “Tripeptides on gold nanoparticles: Structural differences between two reverse sequences as determined by solid-state NMR and DFT calculations,” J. Phys. Chem. 119:11998-12006. DOI: 10.1021/acs.jpcb.5b04299

84. O.K. Ranasingha, C. Wang, P.R. Ohodnicki, Jr. J.W. Lekse, J.P. Lewis, and C. Matranga. 2015. “Synthesis, characterization, and photocatalytic activity of Au-ZnO nanopyramids,” J. Mat. Chem. A. 3:15141. DOI: 10.1039/c5ta01344e

83. L. Wang, H. Wang, A.E. Rice, W. Zheng, X. Li, M. Chen, X. Meng, J.P. Lewis, and F.-S. Xiao. 2015. “
Design and preparation of supported Au catalyst with enhanced catalytic activities by rationally positioning Au nanoparticles on anatase,” J. Phys. Chem. Lett., 6:2345-2349. DOI: 10.1021/acs.jpclett.5b00655

82. V. Zobač, J.P. Lewis, E. Abad, J.I. Mendieta-Moreno, P. Hapala, P. Jelínek, and J. Ortega. 2015. “Photo-induced reactions from efficient molecular dynamics with electronic transitions using the FIREBALL local-orbital density functional theory formalism,” J. Phys.: Cond. Mat. 27:175002. DOI:10.1088/0953-8984/27/17/175002

81. A.J. Neukirch, J. Park, V. Zobac, H. Wang, P. Jelinek, O.V. Prezhdo, H.-C. Zhou, and J.P. Lewis. 2015. “
Calculated photo-isomerization efficiencies of functionalized azobenzene derivatives in solar energy materials: azo-functional organic linkers for porous coordinated polymers,” J. Phys.: Cond. Matt. 27:134208. Special Issue - Theory of Solar Energy Materials. DOI:10.1088/0953-8984/27/13/134208

80. J. Lekse, B.J. Haycock, J.P. Lewis, and C. Matranga. 2014. “The effect of electronic structure changes in NaInO2 and NaIn0.9Fe0.1O2 on the photoreduction of methylene blue", J. Mater. Chem. A, 2014,2, 9331-9337. DOI: 10.1039/C4TA00906

79. J.I. Mendieta-Moreno, R.C. Walker, J.P. Lewis, P. Gómez-Puertas, J. Mendieta, and J. Ortega. 2014. “An efficient local-orbital DFT QM/MM method for biomolecular systems: FIREBALL/AMBER,” J. Chem. Theory Comp. 10:2185-2193. DOI: 10.1021/ct500033w

78.
B.J. Haycock, G. Lander, M. K. Rice, K. Prasai, B. Prasai, D. A. Drabold, and J.P. Lewis. 2014.  "High-throughput evaluation in nitrogen doping of amorphous titanium dioxide", Phys. Stat. Solidi (b) 6:1225–1230. DOI:10.1002/pssb.201451010

77. B.J. Haycock, M.K. Rice, and J.P. Lewis. 2014. “High-throughput approach to calculate properties of CuGa1-xFexO2 delafossite oxides,” Comp. Mat. Sci86: 155-164.  DOI:10.1016/j.commatsci.2014.01.024

76. L. Wang, H. Wang, F. Liu, J. Zhang, Q. Sun, J.P. Lewis, L. Zhu, X. Meng, and F.-S. Xiao. 2014. “Selective catalytic production of 5-hydroxymethylfurfural from glucose by adjusting catalyst wettability,” Chem. Sus. Chem., 7:402-406. (Most accessed article: #12/15 in Jan 2014) DOI: 10.1002/cssc.201301076

75. A.J. Neukirch, L.C. Shamberger, E. Abad, B.J. Haycock, H. Wang, J. Ortega, O.V. Prezhdo, and J.P. Lewis. 2014. "Ab initio non-adiabatic simulations of the photo-isomerization of cis-stilbene and cis-azobenzene," J. Chem. Theory Comp., 10: 14-23. (Most accessed article: #16/20 in Dec 2013) DOI: 10.1021/ct4009816

74. C. Wang, O. Ranasingha, S.Natesakhawat, P.R. Ohodnicki, Jr., M. Andio, J.P. Lewis, C. Matranga. 2013. “Visible light plasmonic heating of Au/ZnO for the photocatalytic reduction of CO2,” Nanoscale 5:6968-6974. DOI: 10.1039/c3nr02001k

73. E. Abad, J.P. Lewis, V. Zobač, P. Hapala, P. Jelínek, and J. Ortega. 2013. “Calculation of non-adiabatic coupling vectors in a local-orbital basis set,” J. Chem. Phys. 138:154106. DOI: 10.1063/1.4801511

72. L. Wang, H. Wang, W. Zhang, J. Zhang, D.S. Su, J.P. Lewis, X. J. Meng, and F.S. Xiao. 2013. "Aerobic homo-coupling of phenylboronic acid on Mg-Al mixed oxides supported Au nanoparticles", J. Catal. 298:186-197.DOI: 10.1016/j.jcat.2012.11.020 

71. J.A. Carr, H. Wang, A. Abraham, T. Gullion, and J.P. Lewis. 2012. “L-cysteine interaction with Au55 nanoparticle,” J. Phys. Chem. C. 116:25816-25823. DOI: DOI:10.1021/jp308215n

70. B.J. Haycock, D.G. Trabada, J. Ortega, J.D. O’Mahony and J.P. Lewis. 2012. "Metallisation of the K-overlayer on the β-SiC(100) c(4X2) surface", J. Phys: Cond. Matt. 24:485001. DOI: 10.1088/0953-8984/24/48/485001

69. A. Michalkova Scott, T. Petrova, Kh. Odbadrakh, D.M. Nicholson, M. Fuentes-Cabrera, J.P. Lewis, F.C. Hill, and J. Leszczynski. 2012. “Molecular simulations of adsorption of RDX and TATP on IRMOF-1(Be),” J. Mol. Model. 18:3363-3378. DOI: 10.1007/s00894-011-1338-3

68. B. Prasai, B. Cai, M.K. Underwood, J.P. Lewis, and D.A. Drabold. 2012. “Properties of amorphous and crystalline titanium dioxide from first principles,” J. Mater. Sci. 47:7515-7521. DOI: 10.1007/s10853-012-6439-6

67. J.W. Lekse, M.K. Underwood, J.P. Lewis, and C. Matranga. 2012. “Synthesis, characterization, electronic structure and photocatalytic behavior of CuGaO2 and CuGa1- xFexO2 (x = 0.05, 0.10, 0.15, 0.20) delafossites,” J. Phys. Chem. C. 116:1865-1872. DOI: 10.1021/jp2087225

66. J.P. Lewis, P. Jelínek, J. Ortega, A.A. Demkov, D.G. Trabada, B. Haycock, H. Wang, G. Adams, J.K. Tomfohr, E. Abad, H. Wang, and D.A. Drabold. 2011. “Advances and applications in the FIREBALL ab-initio tight-binding molecular-dynamics formalism,” Phys. Stat. Sol. B. 248:1989-2007 DOI: 10.1002/pssb.201147259

65. B. Haycock and J.P. Lewis. 2011. “Failure of potassium dimer formation on the β- SiC(100)-c(4x2) surface,” Phys. Stat. Sol. B. 248:2072-2075. DOI: 10.1002/pssb.201147170

64. H. Wang and J.P. Lewis. 2011. “Reactive sites of faceted anatase nanoparticles,” Phys. Stat. Sol. B. 248:2037-2043. DOI: 10.1002/pssb.201147134

63. L. Wang, H. Wang, P. Hapala, L.F. Zhu, L.M. Ren, X.J. Meng, J.P. Lewis, and F.S. Xiao. 2011. “Superior catalytic properties in aerobic oxidation of olefins over Au nanoparticles on pyrrolidone-modified SBA-15,” J. Catal. 281:30-39. DOI: 10.1016/j.jcat.2011.03.029

62. V. Vongsutilers, D. Phillips, K. Shaughnessy, N. Thomsen, J.P. Lewis, and P.M. Gannett. 2011. “The conformational effect of para-substituted C8-arylguanine adducts on the B/Z-DNA equilibrium,” Biophys. Chem. 154:41-48. DOI: 10.1016/j.bpc.2010.12.006

61. Z. Shan, H. Wang, X. Meng, S. Liu, L. Wang, C. Wang, F. Li, J.P. Lewis, and F.-S.Xiao. 2011. “Designed synthesis of TS-1 crystals with controllable b-oriented length,” Chem. Comm. 47:1048-1050. DOI: 10.1039/c0cc03613g 

60. J. B. Keith, J. R. Fennick, D. R. Nelson, C. E. Junkermeier, J. Y.-Y. Lin, C.-W. Li, M. M. McKerns, J. P. Lewis, and B. Fultz. 2010. “AtomSim: web–deployed atomistic dynamics simulator,” J. Appl. Cryst. 43:1553-1559. DOI: 10.1107/S0021889810037209 

59. R. Xiong, Kh. Odbadrakh, A. Michalkova, J.P. Luna, T. Petrova, D.J. Keffer, D.M. Nicholson, M.A. Fuentes-Cabrera, J.P. Lewis and J. Leszczynski. 2010. “Evaluation of functionalized isoreticular metal organic frameworks (IRMOFs) as smart nanoporous preconcentrators of RDX,” Sens. Actuators B. 148:459-468. DOI: 10.1016/j.snb.2010.05.064

58. N.Q. Wu, J. Wang, D. N. Tafen, J.-G. Zheng, J. P. Lewis, S. Leonard, and A. Manivannan. 2010. "Shape-enhanced photocatalytic activity of single-crystalline anatase TiO2 (101) nanobelts." J. Am. Chem. Soc. 132:6679-6685. DOI: 10.1021/ja909456f

57. Kh. Odbadrakh, D.M. Nicholson, and J.P. Lewis. 2010. “Interaction of the explosive molecules RDX and TATP with IRMOF-8,” J. Phys. Chem. 114: 7535-7540. DOI: 10.1021/jp906192g

56. F. Inam, J.P. Lewis, and D.A. Drabold. 2010. “Hidden structure in amorphous solids,” Phys. Stat. Sol. A. 207:599-604. DOI: 10.1002/pssa.200982877

55. Kh. Odbadrakh, D.M. Nicholson, T. Tetyana, A. Michalkova, J. Leszczynski, and J.P. Lewis. 2010. “Interactions of cyclotrimethylene trinitramine (RDX) with metal-organic framework IRMOF-1,” J. Phys. Chem. 114: 3732-3726. DOI: 10.1021/jp905459h

54. R. Xiong, D.J. Keffer, M. Fuentes-Cabrera, D.M. Nicholson, A. Michalkova, T. Petrova, J. Leszczynski, Kh. Odbadrakh, B.L. Doss, and J.P. Lewis. 2010. “Effect of charge distribution on RDX adsorption in IRMOF-10,” Langmuir. 26:5942-5950. DOI: 10.1021/la9039013

53. H. Wang and J.P. Lewis. 2009. “Localization of frontier orbitals on anatase nanoparticles impacts water adsorption,” J. Phys. Chem. C. 113:16631-16637. DOI: 10.1021/jp905489s

52. J. Wang, D. N. Tafen, J. P. Lewis, Z. Hong, A. Manivannan, M. Zhi, M. Li, N.Q. Wu. 2009. "Origin of the photocatalytic activity of nitrogen-doped TiO2 nanobelts." J. Am. Chem. Soc. 131:12290-12227. DOI: 10.1021/ja903781h

51. D. Tafen and J. P. Lewis. 2009. "Structure, stability, and electronic properties of thin TiO2 nanowires." Phys. Rev. B 80:014104.  DOI: 10.1103/PhysRevB.80.014104 
Selected for publication to Virtual Journal of Biological Physics Research (http://www.vjbio.org) v. 20, issue 1. Selected for display on the front page of the journal web site (http://prb.aps.org) in the feature named "Kaleidoscope" (appearing permamently in the archive page (http://prb.aps.org/ kaleidoscope).

50. C.E. Junkermeier, G.W. Bryant, and J.P. Lewis. 2009. “Amorphous nature of small CdS nanoparticles: Molecular-dynamics simulations,” Phys. Rev. B. 79:125323. DOI: 10.1103/PhysRevB.79.125323

49. D. Tafen, J. Wang, N. Wu, and J.P. Lewis. 2009. “Visible light photocatalytic activity in nitrogen-doped TiO2 nanobelts,” Appl. Phys. Let. 94:093101. DOI: 10.1063/1.3093820

48. J.B. Keith, J.R. Fennick, C.E. Junkermeier, D.R. Nelson, and J.P. Lewis. 2009. “A web-deployed interface for performing ab initio molecular dynamics, optimization, and electronic structure in FIREBALL,” Comp. Phys. Comm. 180:418-426. DOI: 10.1016/j.cpc.2008.10.007

47. H. Wang, T.E. Cheatham, III, P.M. Gannett, and J.P. Lewis. 2009. “Differential electronic states observed during the A-B DNA duplex conformational transitions,” Soft Mat. 5:685-690. DOI: 10.1039/B800462E

46. N. Ma, B.R. Cooper, J.P. Lewis, and B.S. Kang. 2008. “Criteria for ductility in Cr alloys based on electronic structures,” Appl. Phys. Let. 93:241903. DOI: 10.1063/1.2981575

45. Z.-G. Wei, H.-X. Zhang, Q.-S. Li, and J.P. Lewis. 2008. “Theoretical study on the surface energy of TiO2 rutile(110),” Chemical Journal of Chinese Universities. 29:824-826. Link

44. C.E. Junkermeier, G.W. Bryant, and J.P. Lewis. 2008. “Ab initio tight-binding analysis of CdS nanocrystals,” Phys. Rev. B. 77:205125. DOI: 10.1103/PhysRevB.77.205125

43. H. Wang, J. Stalnaker, H. Chevreau and J.P. Lewis. 2008. “Potential of Mean Force Calculations Using Ab Initio Tight-binding Molecular Dynamics: Application to N-NO 2 bond dissociation in DMNA and HMX,” Chem. Phys. Let. 457: 26-30. DOI: 10.1016/j.cplett.2008.03.064

42. J.R. Fennick, J.B. Keith, R.H. Leonard, T.N. Truong, and J.P. Lewis. 2008. “A cyberenvironment for crystallography and materials science and an integrated use interface to the Crystallography Open Database and Predicted Crystallography Open Database,” J. Appl. Cryst. 41:471-475. DOI: 10.1107/S0021889808000381

41. J.B. Keith, H. Wang, and J.P. Lewis. 2008. “Ab initio free energy of vacancy formation and mass-action kinetics in vis-active TiO2,” J. Phys.: Condens. Mat. (Fast Track) 20:022202. DOI: 10.1088/0953-8984/20/02/022202

40. X. Sun, S. Sengupta, J.L. Peterson, H. Wang, J.P. Lewis, and X. Shi. 2007. “Intermolecular cross-double-Michael addition between nitro and carbonyl activated olefins as a new approach in C-C bond formation,” Org. Let. 9:4495-4498. DOI: 10.1021/ol702059x

39. R. Takahashi, H. Wang, and J.P. Lewis. 2007. “Electronic structures and conductivity in cyclic peptide nanotubes,” J. Phys. Chem. B. 111:9093-9098. DOI: 10.1021/jp0708446

38. H.T. Stokes, J. Gunter, D.M. Hatch, J.-J. Dong, H. Wang, and J.P. Lewis. 2007. “Bilayer sliding mechanism for the wurtzite-to-rocksalt transition,” Phys. Rev. B. 76:012102 DOI: 10.1103/PhysRevB.76.012102

37. B. Keith, H. Alejandro, A. Woolley, and J.P. Lewis. 2007. “Advances and opportunities in electronic structure and charge transfer of polymeric DNA: Basic science and nanotechnology,” Soft Nanomaterials, Ed. H.S. Nalwa (American Scientific, Valencia, California).

36. Z.-G. Wei, H.-X. Zhang, and J.P. Lewis. 2007. “Theoretical study of water decomposition on TiO2 surface,” Chemical Journal of Chinese Universities. 28:350-351.

35. J.B. Keith, H. Wang, D.M. Hatch, and J.P. Lewis. 2006. “Application of computational ceramic engineering to titanium dioxide photocatalysis, defect free energies of formation, and domain averaging engineering of ferroelectrics,” Ceram. Trans. 193:213-223.

34. N.A. Bruque, K. Alam, R.R. Pandey, R.K. Lake, J.P. Lewis, X. Wang, F. Liu, C.S. Ozkan, M. Ozkan, and K.L. Wang. 2006. “Self-assembled carbon nanotubes for electronic circuit and device applications,” J. Nanoelectronics and Optoelectronics. 1:74-81. DOI: 10.1166/jno.2006.007

33. H. Wang, R. Marsh, J.P. Lewis, and R.A. Roemer. 2006. “Electronic transport and localization in short and long DNA,” in Modern Methods for Theoretical Physical Chemisty of Biopolymers, Eds. E.B. Starikow, S. Tanaka, and J.P. Lewis (Elsevier, Amsterdam). DOI: 10.1016/B978-044452220-7/50085-X

32. H. Wang and J.P. Lewis. 2006. “Second-generation photocatalytic materials: anion- doped TiO2,” J. Phys.: Cond. Mat. 18:421-434. DOI: 10.1088/0953-8984/18/2/006

31. E.B. Starikow, J.P. Lewis, and O.F. Sankey. 2005. “Base sequence effects on charge carrier generation in DNA: A theoretical study,” Int. J. Mod. Phys. B. 19:4331-4357. DOI: 10.1142/S0217979205032802

30. N. Bruque, R.R. Pandey, R.K. Lake, H. Wang, and J.P. Lewis. 2005. “Electronic transport through a CNT-pseudopeptide-CNT hybrid material,” Mol. Sim. 31:859-864. DOI:10.1080/08927020500323879

29. P. Jelínek, H. Wang, J.P. Lewis, O.F. Sankey, and J. Ortega. 2005. “A new multi-center approach to the exchange-correlation interactions in ab initio tight-binding methods,” Phys. Rev. B. 71:235101. DOI: 10.1103/PhysRevB.71.235101

28. D.M. Hatch, H.T. Stokes, J.-J. Dong, J. Gunter, H. Wang, and J.P. Lewis. 2005. “Bilayer sliding mechanism for the zinc-blende to rocksalt transition in SiC,” Phys. Rev. B. 71:184109. DOI: 10.1103/PhysRevB.71.184109

27. H. Wang and J.P. Lewis. 2005. “Effects of dopant states on photoactivity in carbon- doped TiO2,” J. Phys.: Cond. Mat. 17:L209-L213. DOI: 10.1088/0953-8984/17/21/L01

26. H. Wadati, K. Okazaki, Y. Niimi, A. Fujimori, S. Tanaka, H. Tabata, T. Kawai, J. Pikus and J.P. Lewis. 2005. “Photoemission study of poly(dA)-poly(dT),” Appl. Phys. Let. 86:023901. DOI: 10.1063/1.1850187
(Selected for publication to Virtual Journal of Biological Physics Research (http://www.vjbio.org) v. 9, issue 1)

25. L.E. Fried, R. Manaa, and J.P. Lewis. 2004. “Modeling the reactions of energetic materials in the condensed phase” in Overviews of Recent Research on Energetic Materials, Eds. D. Thompson T. Brill, and R. Shaw (World Scientific, New Jersey). DOI: 10.1002/chin.200643258 4

24. M. Zhao, Y. Xia, J.P. Lewis, and L. Mei. 2004. “Chemical reactivity of single-walled nanotubes to amidogen from density-functional calculations,” J. Phys. Chem. B. 108:9599- 9603. DOI: 10.1021/jp037055i

23. H. Wang, J.P. Lewis, and O.F. Sankey. 2004. “Band-gap tunneling states in DNA,” Phys. Rev. Let. 93:016401. DOI: 10.1103/PhysRevLett.93.016401
(Selected for publication to Virtual Journal of Nanoscale Science and Technology (http://www.vjnano.org) v. 10, issue 2)

22. H.T. Stokes, D.M. Hatch, J-J. Dong, and J.P. Lewis. 2004. “Mechanisms for the reconstructive phase transition between the B1 and B2 structure types in NaCl and PbS”, Phys. Rev. B. 69:174111. DOI: 10.1103/PhysRevB.69.174111

21. M. Zhao, Y. Xia, J.P. Lewis, and Ruiqin Zhang. 2003 “First-principles calculations for nitrogen-containing single-walled carbon nanotubes,” J. Appl. Phys. 94:2398-2402. DOI: 10.1063/1.1593798

20. S.D. Shellman, J.P. Lewis, K.R. Glaesemann, K. Sikorski, and G.A. Voth. 2003. “Massively parallel linear-scaling algorithm in an ab initio local-orbital total-energy method,” J. Comp. Phys. 188: 1-15. DOI: 10.1016/S0021-9991(03)00069-X

19. J.P. Lewis. 2003. “The energetics of intermolecular HONO formation in condensed- phase octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX),” Chem. Phys. Let. 371:588- 593. DOI: 10.1016/S0009-2614(03)00309-9

18. J.P. Lewis, H. Wang, T.E. Cheatham III, E. Starikow, and O.F. Sankey. 2003. “Dynamically amorphous character of electronic states in poly(dA)-poly(dT) DNA,” J. Phys. Chem. B. 107:2581-2587. DOI: 10.1021/jp026772u

17. J.P. Lewis, J. Pikus, T.E. Cheatham III, E. Starikow, H. Wang, J. Tomfohr, and O.F. Sankey. 2002. “A comparison of electronic states in periodic and aperiodic poly(dA)- poly(dT) DNA”, Phys. Stat. Sol. 233:90-100. DOI: 10.1002/1521-3951

16. P. Treesukal, J.P. Lewis, J. Limtrakul, and T.N. Truong. 2001. “A full quantum embedded cluster study of proton siting in chabazite,” Chem. Phys. Let. 350:128-134. DOI: 10.1016/S0009-2614(01)01277-5

15. J.P. Lewis, K.R. Glaesemann, G.A. Voth, J. Fritsch, A.A. Demkov, J. Ortega, and O.F. Sankey. 2001. “Further developments in the local-orbital density functional theory tight- binding method: FIREBALL,” Phys. Rev. B. 64:195103. DOI: 10.1103/PhysRevB.64.195103

14. J.P. Lewis, K.R. Glaesemann, K. VanOpdorp, and G.A. Voth. 2000. “Ab initio calculations of reactive pathways for α-Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (α- HMX),” J. Phys. Chem. A. 104:11384-11389. DOI: 10.1021/jp002173g

13. J.P. Lewis, R.B. Evans, T. Sewell, and G.A. Voth. 2000. “Electronic structure calculation of the structures and energies of the three pure polymorphic forms of crystalline HMX,” J. Phys. Chem. B. 104:1009-1013. DOI: 10.1021/jp9926037

12. T.-S. Lee, J.P. Lewis, and W. Yang. 1999. “A linear-scaling quantum mechanical investigation of cytidine deaminase,” Special Issue: J. Comp. Phys. 151:242-263. DOI: 10.1006/jcph.1999.6219

11. T.-S. Lee, J.P. Lewis, and W. Yang. 1998. “Linear-scaling Quantum Mechanical Calculations of Biological Molecules: The Divide-and-Conquer Approach”, in Special Topic Issue (Invited): Computational Materials Science: Tight-Binding Molecular Dynamics. 12:259-277. DOI: 10.1016/S0927-0256(98)00029-9

10. J.P. Lewis, C.W. Carter, Jr., J. Hermans, W. Pan, T.-S. Lee, and W. Yang. 1998. "Active species for the ground state complex of cytidine deaminase: A linear-scaling quantum mechanical investigation,” J. Am. Chem. Soc. 120:5407-5410. DOI: 10.1021/ja973522w

9. O.F. Sankey, A.A. Demkov, W. Windl, J.H. Fritsch, J.P. Lewis, and M. Fuentes-Cabrera. 1998. “The application of approximate density functionals to complex systems,” Int. J. Quant. Chem. 69:327-340. DOI: 10.1002

8. J.P. Lewis, N.H. Pawley, and O.F. Sankey. 1997. “Theoretical investigation of the cyclic peptide system – cyclo[(D-Ala-Glu-D-Ala-Gln)m=1-4],” J. Phys. Chem. B. 101:10576-10583. DOI: 10.1021/jp9722317

7. J.P. Lewis, P. Ordejón, and O.F. Sankey. 1997. “Electronic-structure-based molecular- dynamics method for large biological systems: Application to the 10 basepair poly(dG) •poly(dC) DNA double helix. Phys Rev. B. 55:6880-6887. DOI: 10.1103/PhysRevB.55.6880

6. J. Ortega, J.P. Lewis, and O.F. Sankey. 1997. “First principles simulations of fluid water: The radial distribution functions,” J. Chem. Phys. 106:3696-3702. DOI: 10.1063/1.474121

5. J.P. Lewis, J. Ortega, and O.F. Sankey. 1995. “A simplified electronic structure method for hydrogen-bonded systems: Application to water and DNA base pairs,” in Computational Medicine, Public Health and Biotechnology: Building a Man in the Machine. (World Scientific, New Jersey).

4. J.P. Lewis and O.F. Sankey. 1995. “Geometry and energetics of DNA basepairs and triplets from first principles quantum molecular realxation,” Biophys. J. 69:1068-1076. DOI: 10.1016/S0006-3495(95)79980-5

3. J. Ortega, J.P. Lewis, and O.F. Sankey. 1994. “Simplified electronic structure model for hydrogen-bonding systems- Water,” Phys. Rev. B. 50: 10516-10530.
DOI: 10.1103/PhysRevB.50.10516

2. S.M. Lindsay, T.W. Jing, J. Pan, D. Lampner, J.P. Lewis, and O.F. Sankey. 1994. “Electron tunneling in electrochemical STM,” in Nanoscale Probes of Solid/Liquid Interfaces. Eds. A.A. Gewirth and H. Siegenthaler. (NATO-ASI).

1. J.P. Lewis and D.J. Smith. 1989. “Structural Rearrangements in small Au particles,” Proceedings of the Electron Microscopy Society of America. 47:640-641.