List of Papers using RMG

"2x4 GaP(100) surface: atomic structure and optical anisotropy", A. M. Frisch, W. G. Schmidt, J. Bernholc, M. Pristovsek, N. Esser and W. Richter, Phys. Rev. B 60, 2488 (1999).

"Mechanical Properties and Electronic Transport in Carbon Nanotubes", J. Bernholc, M. Buongiorno Nardelli, J.-L. Fattebert, D. Orlikowski, R. Roland and Q. Zhao, in "Nanotubes," edited by D. Tomanek and R. J. Enbody, Kluwer Academic Publishing (2000).

"GaP(001) and InP(001): Reflectance anisotropy and surface geometry", N. Esser, W. G. Schmidt, J. Bernholc, A. M. Frisch, P. Vogt, M. Zorn, M. Pristovsek, W. Richter, F. Bechstedt, Th. Hannappel and S. Visbeck, J. Vac. Sci. Techn. B 17, 1691 (1999).

"(001) surfaces of GaP and InP: Structural motifs, electronic states and optical signatures", W. G. Schmidt, J. Bernholc and F. Bechstedt, Appl. Surf. Sci. 166, 179 (2000).

"Self-energy effects in the optical anisotropy of GaP(001)", W.G. Schmidt, J. L. Fattebert, J. Bernholc and F. Bechstedt, Surf. Rev. Lett. 6, 1159 (1999).

"Angle resolved photoemission spectroscopy of the InP(001) surface", A. M. Frisch, P. Vogt, S. Visbeck, Th. Hannappel, F. Willig, W. Braun, W. Richter, J. Bernholc, W. G. Schmidt and N. Esser Appl. Surf. Sci. 166, 224 (2000).

"Understanding reflectance anisotropy: Surface-state signatures and bulk-related features in the optical spectrum of InP(001)(2x4)", W. G. Schmidt, N. Esser, A. M. Frisch, P. Vogt, J. Bernholc, F. Bechstedt, M. Zorn, Th. Hannappel, S. Visbeck, F. Willig, W. Richter, Phys. Rev. B 61, R16335 (2000).

"Towards grid-based O(N) DFT methods: optimized non-orthogonal orbitals and multigrid acceleration", J.-L. Fattebert and J. Bernholc, Phys. Rev. B 62, 1713 (2000).

"Step-induced optical anisotropy of Si(111):H surfaces", W. G. Schmidt and J. Bernholc, Phys. Rev. B, 61, 7604 (2000).

"Understanding reflectance anisotropy: Surface-state signatures and bulk-related features", W. G. Schmidt, F. Bechstedt, and J. Bernholc, J. Vac. Sci. Tech. B 18, 2215 (2000).

"Terrace and step contributions to the surface optical anisotropy of Si(001)", W.G. Schmidt, F. Bechstedt and J. Bernholc, Phys. Rev. B 63, 45322 (2001).

"Terrace and step contributions to the surface optical anisotropy of Si(001)", W.G. Schmidt, F. Bechstedt and J. Bernholc, Proc. 25th Intern. Conf. Phys. Semicond., Springer-Verlag, Berlin, 299 (2001).

"Optical anisotropy of the SiC(001) (3x2) surface: evidence for the two-adlayer asymmetric-dimer model", W. Lu, W. G. Schmidt, E. L. Briggs, and J. Bernholc, Phys. Rev. Lett. 85, 4381 (2000).

"An O(N) real-space method for ab initio quantum transport calculations: application to carbon nanotube-metal contacts", M. Buongiorno Nardelli, J.-L. Fattebert, and J. Bernholc, Phys. Rev. B 64, 245423 (2001).

"Ultimate strength of carbon nanotubes: a theoretical study", Q. Zhao, M. Buongiorno Nardelli and J. Bernholc, Phys. Rev. B 65, 144105 (2002).

"GaAs(001) Surface Reconstructions: Geometries, Chemical Bonding and Optical Properties", W.G. Schmidt, F. Bechstedt, and J. Bernholc, Appl. Surf. Sci. 190, 264 (2002).

"GaAs(001): Surface structure and optical properties", W. G. Schmidt, F. Bechstedt, K. Fleischer, C. Cobet, N. Esser, W. Richter, J. Bernholc, and G. Onida, Phys. Stat. Sol. 188, 1401 (2001).

"Quantum Transport in Nanotube-Based Structures", M. Buongiorno Nardelli, J.-L. Fattebert, and J. Bernholc, Proc. Mat. Res. Soc. 706, Z8.2 (2002).

"Structure and Energetics of Ga-rich GaAs(001) Surfaces", K. Seino, W. G. Schmidt, F. Bechstedt, and J. Bernholc, Surf. Sci. 507-510, 406 (2002).

"Ab initio investigations of lithium diffusion in carbon nanotube systems", V. Meunier, C. Roland, J. Bernholc, Phys. Rev. Lett. 88, 075506 (2002).

"Cycloaddition reaction vs dimer cleavage at the Si(001): C5H8 interface", W. Lu, W. G. Schmidt and J. Bernholc, Phys. Rev. B 68, 115327 (2003).

"Spontaneous polarization and piezoelectricity in boron nitride nanotubes", S. M. Nakhmanson, V. Meunier, J. Bernholc, M. Buongiorno Nardelli, Phys. Rev. B 67, 235406 (2003).

"Interplay of surface reconstruction and surface electric fields in the optical spectroscopy of GaAs(001)", W. G. Schmidt, F. Bechstedt, W. Lu and J. Bernholc, Phys. Rev. B 66, 085334 (2002).

"Nanowire-induced optical anisotropy of the Si(111)-In surface", S. Wang, W. Lu, W. G. Schmidt and J. Bernholc, Phys. Rev. B 68, 035329 (2003).

"Calculation of surface optical properties: From qualitative understanding to quantitative predictions", W. G. Schmidt, K. Seino, P. H. Hahn, F. Bechstedt, W. Lu, S. Wang, and J. Bernholc, Thin Solid Films 455/456, 764 (2004).

"Atomic Indium nanowires on Si(111): The (4x1)-(8x2)-phase transition studied with Reflectance Anisotropy Spectroscopy", K. Fleischer, S. Chandola, N. Esser, W. Richter, J. F. McGilp, F. Bechstedt, S. Wang, W. Lu, W.G. Schmidt, J. Bernholc, Appl. Surf. Sci. 234, 302 (2004).

"Gallium-rich reconstructions on GaAs(001)", M. Pristovsek, S. Tsukamoto, A. Ohtake, N. Koguchi, B. G. Orr, W. G. Schmidt, and J. Bernholc, Phys. Stat. Sol. (b) 240, 91-98 (2003).

"Ab initio studies of polarization and piezoelectricity in vinylidene fluoride and BN-based polymers", S. M. Nakhmanson, M. Buongiorno Nardelli and J. Bernholc, Phys. Rev. Lett. 92, 115504 (2004).

"Oxidation- and organic-molecule-induced changes of the Si surface optical anisotropy: ab initio predictions", W. G. Schmidt, F. Fuchs, A. Hermann, K. Seino, F. Bechstedt, R. Passmann, M.Wahl, M. Gensch, K. Hinrichs, N. Esser, S. Wang, W. Lu and J. Bernholc, J. Phys.: Condens. Matter 16, S4323 (2004).

"Optical Absorption of Water: Coulomb Effects versus Hydrogen Bonding", P. H. Hahn, W. G. Schmidt, K. Seino, M. Preuss, F. Bechstedt, and J. Bernholc, Phys. Rev. Lett. 94, 037404 (2005), listed also in Virtual Journal of Biological Physics Research, February 1 (2005).

"Carbon nanotube-metal cluster composites: a new road to chemical sensors?", Q. Zhao, M. Buongiorno Nardelli, W. Lu and J. Bernholc, Nano Letters 5, 847 (2005).

"Non-equilibrium quantum transport properties of organic molecules on silicon", W. Lu, V. Meunier, and J. Bernholc, Phys. Rev. Lett. 95, 206805 (2005).

"Electron transport in molecular systems", V. Meunier, W. Lu, J. Bernholc, and B. G. Sumpter, Journal of Physics: Conference Series 16, 283 (2005).

"Collective polarization effects in beta-polyvinylidene fluoride and its copolymers with tri- and tetrafluoroethylene", S. M. Nakhmanson, M. Buongiorno Nardelli and J. Bernholc, Phys. Rev. B 72, 115210 (2005).

"Density Functional Theory Studies of Quantum Transport in Molecular Systems", V. Meunier, W. Lu, B. G. Sumpter, J. Bernholc, Intern. J. Quantum Chem. 106, 3334 (2006).

"Atomic Scale Design of Nanostructures", J. Bernholc, W. Lu, S. M. Nakhmanson, P. H. Hahn, V. Meunier, M. Buongiorno Nardelli, and W. G. Schmidt, Molecular Physics, 105, 147 (2007).

"Resonant Coupling and Negative Differential Resistance in Metal/Ferrocenyl-Alkanethiolate/STM structures", S. Wang, W. Lu, Q. Zhao, and J. Bernholc, Phys. Rev. B 74, 195430 (2006). listed also in Virtual Journal of Nanoscale Science & Technology, December 4 (2006).

"Implementation of ultrasoft pseudopotentials in large-scale, grid-based electronic structure calculations", M. Hodak, S. Wang, W. Lu, and J. Bernholc, Phys. Rev. B, 76, 085108 (2007).

"Hybrid ab initio Kohn-Sham DFT/frozen-density orbital-free DFT simulation method suitable for biological systems", M. Hodak, W. Lu, and J. Bernholc, J. Chem. Phys. 128, 014101 (2008).

"Effects of end group functionalization and level alignment on electron transport in molecular devices", G. Kim, S. Wang, W. Lu, M. Buongiorno Nardelli, and J. Bernholc, J. Chem. Phys. 128, 024708 (2008).

"Doping-dependent negative differential resistance in hybrid organic/inorganic Si-porphyrin-Si junctions", F. J. Ribeiro, W. Lu, and J. Bernholc, ACS Nano 2, 1517 (2008).

"Recent developments and applications of the real-space multigrid method", J. Bernholc, M. Hodak, and W. Lu, J. Phys. Condens. Matter 20, 294205 (2008).

"Functional implications of multistage copper binding to the prion protein", M. Hodak, R. Chisnell, W. Lu, and J. Bernholc, Proc. Nat. Acad. Sci. 106, 11576 (2009).

"Performance evaluation for petascale quantum simulation tools", S. Tomov, W. Lu, J. Bernholc, S. Moore, and J. Dongarra, Proceedings of Cray User Group 2009 (CUG09): Compute the Future (2009).

"First-principles methodology for quantum transport in multiterminal junctions", K. K. Saha, W. Lu, J. Bernholc, V. Meunier, J. Chem. Phys. 131, 164105 (2009).

"Insights into prion protein function from atomistic simulations", M. Hodak and J. Bernholc, Prion 4, 13 (2010).

"Electron transport in multiterminal molecular devices: A density functional theory study", K. K. Saha, W. Lu, J. Bernholc, V. Meunier, Phys. Rev. B 81, 125420 (2010).

"Negative Differential Resistance in C60-Based Electronic Devices", X. Zheng, W. Lu, T. A. Abtew, V. Meunier, and J. Bernholc, ACS Nano 4, 7205 (2010).

"Quantum-Interference-Controlled Three-Terminal Molecular Transistors Based on a Single Ring-Shaped Molecule Connected to Graphene Nanoribbon Electrodes", K. K. Saha, B. K. Nikolic, V. Meunier, W. Lu, and J. Bernholc, Phys. Rev. Lett. 105, 236803 (2010).

"Mechanism of copper(II)-induced misfolding of Parkinson's disease protein", F. Rose, M. Hodak, and J. Bernholc, Nature Scientific Reports 1, 11 (2011).

"Hybrid quantum simulations of biomolecules: the role of copper in neurodegenerative diseases", J. Bernholc, M. Hodak, W. Lu, and F. Rose, Proceedings of the 2010 Scientific Discovery through Advanced Computing (SciDAC) Conference, pp. 12-22 (2011).

"Scaling the RMG Quantum Mechanics Code", S. Moore, E. Briggs, M. Hodak, W. Lu, J. Bernholc, C. W. Lee, Proc. Extreme Scaling Workshop (BW-XSEDE '12). University of Illinois at Urbana-Champaign, Champaign, IL, USA, , Article 8 , 6 pages.#

“Enzymatic Mechanism of Copper-Containing Nitrite Reductase,” Y. Li, M. Hodak, and J. Bernholc, ACS Biochemistry, 54, 1233 (2015), http://dx.doi.org/10.1021/bi5007767.

“Charge Transport in DNA Nanowires,” B. Tan, M. Hodak, W. Lu, and J. Bernholc, Phys. Rev. B 92, 075429 (2015), http://link.aps.org/doi/10.1103/PhysRevB.92.075429

“Mechanisms of NH3 and NO2 detection in carbon-nanotube-based sensors: An ab initio investigation,” Y. Li, M. Hodak, W. Lu, and J. Bernholc, Carbon 101, 177 (2016). http://dx.doi.org/10.1016/j.carbon.2016.01.092

“Selective sensing of ethylene and glucose using carbon-nanotube-based sensors: An ab initio investigation,” Y. Li, M. Hodak, W. Lu, and J. Bernholc, Nanoscale 9, 1687-1698 (2017) http://dx.doi.org/10.1039/C6NR07371A

“Controllable conversion of quasi-freestanding polymer chains to graphene nanoribbons,” C. Ma, Z. Xiao, H. Zhang, L. Liang, J. Huang, W. Lu, K. Hong, J. Bernholc, A.-P. Li, Nature Communications 8, 14815 (2017) http://dx.doi.org/10.1038/ncomms14815

“Binding of Copper and Cisplatin to Atox1 Is Mediated by Glutathione through the Formation of Metal−Sulfur Clusters,” N. V. Dolgova, C. Yu, J. P. Cvitkovic, M. Hodak,K. H. Nienaber, K. L. Summers, J. J. H. Cotelesage, J. Bernholc, G. A. Kaminski, I. J. Pickering, G. N. George, and O. Y. Dmitriev. Biochemistry, 56, 3129 (2017), http://dx.doi.org/10.1021/acs.biochem.7b00293

“Design of Atomically Precise Nanoscale Negative Differential Resistance Devices,“ Z. Xiao, C. Ma, J. Huang, L. Liang, W. Lu, K. Hong, B. G. Sumpter, A.-P. Li, J. Bernholc, Adv. Theory Simul. 2, 1800172 (2019), https://onlinelibrary.wiley.com/doi/epdf/10.1002/adts.201800172.

“Direct writing of heterostructures in single atomically precise graphene nanoribbons,” C. Ma, Z. Xiao, J. Huang, L. Liang, W. Lu, K. Hong, B. G. Sumpter, J. Bernholc, A.-P. Li, Phys. Rev. Materials 3, 016001 (2019), https://journals.aps.org/prmaterials/abstract/10.1103/PhysRevMaterials.3.016001.

"Mesh independence of the generalized Davidson algorithm," C. T. Kelley, J. Bernholc, E. Briggs, S. Hamilton, L. Lin, and C. Yang, J. Comp. Phys., 409, 109322 (2020), DOI: 10.1016/j.jcp.2020.109322.

"Large-scale phonon calculations using the real-space multigrid method," J. Zhang, Y. Cheng, W. Lu, E. Briggs, A. J. Ramirez-Cuesta, and J. Bernholc, J. Chem. Theory Comput. 12, 6859 (2019), DOI: 10.1021/acs.jctc.9b00802.

"Local manifestations of thickness-dependent topology and axion edge state in topological magnet MnBi2Te4," F. Lüpke, A. D. Pham, Y. F. Zhao, L.-J. Zhou, W. Lu, E. Briggs, J. Bernholc, M. Kolmer, W. Ko, C.-Z. Chang, P. Ganesh, A.-P. Li, Phys. Rev. B 105, 035423 (2022), DOI: 10.1103/PhysRevB.105.035423.

"Ab initio simulations of metal contacts for graphene-based devices," H. Qin, W. Lu and J. Bernholc, J. Appl. Phys. 131, 214301 (2022), DOI: 10.1063/5.0091028.