National Nanotechnology Infrastructure Network

National Nanotechnology Infrastructure Network

Serving Nanoscale Science, Engineering & Technology

NNIN Computational Publications ---full listing

Currently over 180 publications have been made possible through the NNIN computation effort.  Please contact one of our staff  to see how we can help your research.


  1. K. Kamiya, M. Yang, S. Park, B. Magyari-Kope, Y. Nishi, M. Niwa, and K. Shiraishi, "ON-OFF switching mechanism of resistive random access memories based on the formation and disruption of oxygen vacancy conducting channels", Applied Physics Letters, 100, 073502, (2012).
  2. A. Hermann, N. W. Ashcroft, and R. Hoffmann, "Making Sense of Boron-Rich Binary Be-B Phases", Inorganic Chemistry, Article ASAP (2012).
  3. G. Grimvall, B. Magyari-Kope, V. Ozolins, and K. Persson, "Lattice instabilities in metallic elements", Reviews of Modern Physics, 84, 945 (2012).
  4. A. Hermann, B. L. Ivanov, N. W. Aschroft, and R. Hoffmann, "LiBeBe: A predicted phase with structural and electronic pecularities", Physical Review B, 86, 014104 (2012).
  5. K. X. Wang, Z. Yu, V. Liu, Y. Cui, and S. Fan, "Absorption enhancement in ultra-thin crystalline silicon solar cells with anti-reflection and light trapping nanogratings", Nano Letters, 12, 1616 (2012).
  6. A. Hmiel and Y. Xue, "Quantum confinement and surface relaxation effects in rutile TiO2 nanowires", Physical Review B, 85, 235461 (2012).
  7. Z. Boekelheide, D. A. Stewart, and F. Hellmann, "Chemical ordering in Cr3Al and relation to semiconducting behavior", Physical Review B, 86, 085120 (2012).
  8. W. Li, N. Mingo, L. Lindsay, D. A. Broido, D. A. Stewart, and N. A. Kathcho, "Thermal conductivity of diamond nanowires from first principles", Physical Review B, 85, 195436 (2012).
  9. A. Hermann, N. W. Ashcroft, and R. Hoffmann, "High Pressure Ices", Proceedings of the National Academy of Sciences, 109, 745 (2012).
  10. B. Magyari-Kope, S. G. Park, H.-D. Lee and Y. Nishi, "First principle calculations of oxygen vacancy ordering effects in resistance change memory materials incorporating binary transition metal oxides", J. Mat. Sci., 47, 7498 (2012).
  11. S. E. Burkhardt, M. A. Lowe, S. Conte, W. Zhou, H. Qian, G. G. Rodriguez-Calero, J. Gao, R.G. Hennig, and H. D. Abruna, "Tailored redox functionality of small organics for pseudocapacitive electrodes", Energy and Environmental Science, 5, 7176 (2012).
  12. M. T. Ong and E. J. Reed, "Engineered Piezoelectricity in Graphene", ACS Nano, 6, 1387, (2012)
  13. D. A. Stewart, "A Cautionary Tale of Two Basis Sets and Graphene", Computing in Science and Engineering, 14, 55 (2012).
  14. E. J. Reed, "Electron-Ion Coupling in Shocked Energetic Materials", J. Phys. Chem. C, 116, 2205 (2012).
  15. M. Yamamoto, H. Takagi, M. Stopa, and S. Tarucha, "Hydrodynamic rectified drag current in a quantum wire induced by Wigner crystallization", Physical Review B, 85, 041308 (2012).
  16. Z. Boekelheide, T. Saerbeck, A. Stampfl, R. A. Robinson, D. A. Stewart, and F. Hellman, "Antiferromagnetism in Cr3Al and relation to semiconducting behavior", Physical Review B, 85, 094413 (2012).
  17. D. A. Stewart and K. A. Mkhoyan "Graphene Oxide: Synthesis, Characterization, Electronic Structure, and Applications" (Book Chapter), Graphene Nanoelectronics, Nanoscience and Technology, Part 2, 435-464, Springer, editor Hassan Raza, 2012.
  18. V. Labet, P. Gonzalez-Morelos, and R. Hoffmann, "A fresh look at dense hydrogen under pressure. I.  An introduction to the problem and an index probing equalization of H-H distances", J. Phys. Chem., 136, 074501 (2012).
  19. V. Labet, R. Hoffmann, and N. W. Ashcroft, "A fresh look at dense hydrogen under pressure. II. Chemical and physical models aiding our understanding of evolving H-H separations", J. Phys. Chem., 136, 074502 (2012).
  20. V. Labet, R. Hoffmann, and N. W. Ashcroft, "A fresh look at dense hydrogen under pressure. III. Two competing effects and the resulting intra-molecular H-H separation in solid hydrogen under pressure", J. Phys. Chem., 136, 074503 (2012).
  21. V. Labet, R. Hoffmann, and N. W. Ashcroft, "A fresh look at dense hydrogen under pressure. IV. Two structural models on the road from paired to monoatomic hydrogen, via a possible non-crystalline phase", J. Phys. Chem., 136, 074504 (2012).
  22. D. Duncan, B. Magyari-Kope, and Y. Nishi, “Ab initio modeling of the resistance switching mechanism in RRAM devices: case study of hafnium oxide (HfO2)”, MRS Proc. 1430, 980 (2012).
  23. L. Zhao, S.-G. Park, B. Magyari-Köpe and Y. Nishi, First principles investigation of the conductive filament configuration in rutile TiO2−x ReRAM”, MRS Proc.1430,1103 (2012).
  24. J. A. Taillon, W. W. Tipton, R. G. Hennig, "Ab initio discovery of novel crystal structure stability in barium and sodium-calcium compounds under pressure using DFT", arXiv, cond-mat 1207.3320 (2012).
  25. D. S. Conti, J. Grashik, L. Yang, L. Wu, S. R. P. da Rocha, "Solvation in hydrofluoroalkanes: how can ethanol help?", Journal of Pharmacy and Pharmacology, 64, 1236 (2012).
  26. A. N. Mlinar, P. M. Zimmerman, F. E. Celik, M. Head-Gordon, A. T. Bell, "Effects of Bronsted-acid site proximity on the oligomerization of propene in H-MFI", Journal of Catalysis, 288, 65 (2012).
  27. G. Tian, S. J. Teat, Z. Zhang, and L. Rao, "Sequestering of uranium from seawater: binding strenght and modes of uranyl complexes with glutarimidedioxime", Dalton Trans., Advanced Article (2012).
  28. Q. Zhang, Z. Zhang, Z. Zhu, U. Schwingenschlogl, and Y. Cui, "Exotic topological insulator states and topological phase transitions in Sb3Sb3-Bi2Se3 heterostructures", ACS Nano, 6, 2345 (2012).
  29. H. Lin, Y. W. Wen, C. X. Zhang, L. L. Zhang, Y. H. Huang, B. Shan, and R. Chen, "A GGA+U study of electronic conductivity and lithium diffusion in vanadium doped LiFePO4", Solid State Comm., 152, 999 (2012).
  30. J. Cao, Z. Xie, X. B. Duan, Y. Dong, Z. Wang, J. Xu, B. Liang, B. Shan, J. Ye, D. Chen, and G. Shen, "Visible-light-driven photocatalytic and photoelectrochemical properties of porous SnSx (x=1,2) architectures", CrystEngComm, 14, 3163 (2012).
  31. B. Suo, A. Dong, H. Han, Y. Lei, and Y. Wang, "Theoretical study of the electronic structure of iridium monoxide", Chemical Physics Letters, Accepted manuscript, (2012). 
  32. R. Chen, Z. Chen, B. Ma, X. Hao, N. Kapur, J. Hyun, K. Cho, and B. Shan, "Comparison of CO adsorption on Pt(111) and Pd(111) Surfaces: A First-Principles Based Lattice Gas Monte-Carlo Study", Theoretical and Computational Chemistry, 987, 77 (2012).
  33.  K.-H. Xue, Y. Nishi, P. Blaise, G. Molas, G. Ghibaudo, L. Fonseca, and B. De Salvo, Study on oxygen vacancy chains in monoclinic hafnia for application to Resistive Random Access Memories”, 2nd International Conference on Advanced Materials Modelling (ICAMM), No. P32, Nantes, France, June 14-16 (2012).
  34. K. Shiraishi, K. Yamaguchi, M. Yang, S. G. Park, K. Kamiya, Y. Shigeta, B. Magyari-Köpe, M. Niwa, 
and Y. Nishi, “Computational study toward micro electronics engineering”, Proc. 28th Int. Conf. Microel. (MIEL 2012) (2012).
  35. S. Gupta, B. Vincent, D. Lin, M. Gunji, A. Firrincieli, F. Gencarelli, B. Magyari-Köpe, B. Yang, B. 
Douhard, J. Delmotte, A. Franquet, M. Caymax, J. Dekoster, Y. Nishi, K. Saraswat, “GeSn channel nMOSFETs: material potential and technological outlook”, Tech. Digest, VLSI, (2012).


  1. A. Miura, M. Lowe, B. M. Leonard, C. V. Subban, Y. Masubuchi, S. Kikkawa, R. Dronskowski, R. G. Hennig, H. D. Abruna, F. J. DiSalvo, "Silver dilafossite nitride, AgTaN2?", Journal of Solid State Chemistry, 184 7 (2011).
  2. D. Kong, Y. Chen, J. J. Cha, Q. Zhang, J. G. Analytis, K. Lai, Z. Liu, S. S. Hong, K. J. Koshi, S.-K. Mo, Z. Hussain, I. R. Fisher, Z.-X. Shen, Y. Cui, "Ambipolar field effect in the ternary topological insulator (Bi(x)Sb(1-x)2Te3 by composition tuning", Nature Nanotechnology, 6, 705 (2011).
  3. V. Labet and R. Hoffmann, "Molecular models for WH6 under pressure", New Journal of Chemistry, 35, 2349 (2011).
  4. C. S. Ruiz-Vargas, H. L. Zhuang, P. Y. Huang, A. M. van der Zande, S. Garg, P. L. McEuen, D. A. Muller, R. G. Hennig, and J. Park, "Softened Elastic Response and Unzipping in Chemical Vapor Deposition Graphene Membranes", Nano Letters, 11, 2259 (2011).
  5. A. Kundu, N. Mingo, D. A. Broido, and D. A. Stewart, "The role of lighter and heavier embedded nanoparticles on the thermal conductivity of SiGe alloys", Physical Review B, 84, 125426 (2011).
  6. X.-D. Wen, L. Hand, V. Labet, T. Yang, R. Hoffmann, N. W. Ashcroft, A. R. Oganov, and A. O. Lyakhov, "Graphane sheets and crystals under pressure", Proceedings of the National Academy of Sciences (USA), 108, 6833 (2011).
  7. S.-H. Wu, S. E. Burkhardt, J. Yao, Y.-W. Zhong, H. D. Abruna, "Near-infrared absorbing and emitting Ru(II)-Pt(II) hetrodimetallic complexes of DPDPZ (DPDPZ = 2,3-Di(pyridyl)-5,6-diphenylpyrazine)", Inorganic Chemistry, 50, 3959 (2011).
  8. X.-D. Wen, R. Hoffmann, and N. W. Ashcroft, "Benzene under high pressure: a story of molecular crystals transforming to saturated networks, with a possible intermediate metallic phase", Journal of the American Chemical Society, 133, 9023, (2011).
  9. F. Zhou, A. L. Moore, J. Bolinsson, A. Persson, L. Froberg, M. T. Pettes, H. Kong, L. Rabenberg, P. Caroff, D. A. Stewart, N. Mingo, K. A. Dick, L. Samuelson, H. Linke, and L. Shi, "Thermal conductivity of indium arsenside nanowires with wurtzite and zinc blende phases", Physical Review B, 83, 205416 (2011).
  10. S. E. Burkhardt, S. Conte, G. Rodriguez-Calero, M. A. Lowe, H. Qian, W. Zhou, R. G. Hennig, H. D. Abruna, "Towards organic energy storage: characterization of 2,5-bis(methythio)thieno[3,2-b]thiophene", Journal of Materials Chemistry, 21, 9553 (2011).
  11. T. Luo, C. Zhang, Z. Zhang, Y. Zhu, and J. Li, "Rational designs of crystal solid-solution materials for lithium-ion batteries", Physica Status Solidi (b), 248, 2027 (2011).
  12. P. M. Zimmerman, Z. Zhang, and C. B. Musgrave, "Dynamic mechanisms for ammonia borane thermolysis in solvent: deviation from gas-phase minimum-energy pathways", Journal of Physical Chemistry Letters, 2, 276 (2011).
  13. B. Magyari-Kope, M. Tendulkar, S. Park, H. Lee, and Y. Nishi, "Resistive switching mechanisms in random access memory devices incorporating transition metal oxides: TiO2, NiO and Pr0:7Ca0:3MnO3", Nanotechnology, 22, 254029 (2011).
  14. S. Park, B. Magyari-Kope, and Y. Nishi, "The impact of oxygen vacancies on the formation of a conductive channel in rutile TiO2", IEEE Electron Device Letters, 32, 197 (2011).
  15. P. M. Zimmerman, F. Bell, D. Casanova, M. Head-Gordon, "Mechanism for singlet fission in pentacene and tetracene: from single exciton to two triplets", J. Am. Chem. Soc., 133, 19944 (2011).
  16. D. Stuck, T. A. Baker, P. M. Zimmerman, W. Kurlancheek, M. Head-Gordon, "On the nature of electron correlation in C60", J. Chem. Phys., 135, 194306 (2011).
  17. P. M. Zimmerman, M. Head-Gordon, A. T. Bell, "Selection and Validation of Charge and Leonard-Jones Parameters for QM/MM simulations of hydrocarbon interactions with zeolite", J. Chem. Theory Comput. 7, 1695 (2011).
  18. G. Tian, L. Martin, Z. Zhang, and L. Rao, "Thermodynamic, spectroscopic, and computational studies of lathanide complexation with diethylenetriaminepentaacetic acid: Temperature effect and coordination modes", Inorganic Chemistry, 50, 3087 (2011).
  19. Z. Z. Chen, B. Shan, R. Chen, "Electronic origin of the phase transition in ternary alloy Mo(Si1-x,Alx)2", Appl. Phys. Lett., 98, 101903 (2011).
  20. S. Gupta, R. Chen, B. Magyari-Kope, H. Lin, A. Nainani, Y. Nishi, J. Harris, K. C. Saraswat, "GeSn Technology: Extending the Ge Electronics Roadmap", Tech. Digest IEEE IEDM, (2011).
  21. B. Magyari-Kope, S. Park, H. Lee, Y. Nishi, "Understanding the switching mechanism in RRAM devices and the dielectric breakdown of ultrathin high-k gate stacks from first principles", ECS Trans. - ULSI vs TFT, 37 (2011).
  22. S. G. Park, B. Magyari-Kope, Y. Nishi, "Theoretical Study of the Resistance Switching Mechanism in Rutle TiO(2-x) for ReRAM: the role of oxygen vacancies and hydrogen impurities", Tech. Digest VLSI Tech. Symp. (2011).
  23. R. Olivares-Amaya, M. Stopa, X. Andrade, M. A. Watson, and A. Aspuru-Guzik, "Anion Stabilization in Electrostatic Environments", Journal of Physical Chemistry Letters, 2, 682 (2011).
  24. K. Yamada, M. Stopa, T. Hatano, T. Yamaguchi, T. Ota, Y. Tokura, and S. Tarucha, "Geometric blockade in a quantum dot coupled to two-dimensional and three-dimensional electron gases", Physical Review B, 84, 201303 (2011).
  25. H. Chen and A. Alexander-Katz, "Dynamics of Polymers in Flowing Colloidal Suspensions", Physical Review Letters, 107, 128301 (2011).
  26. G. S. Lee, N. Filipovic, L. F. Miele, M. Lin, D. Collings-Simpson, B. Gibney, M. A. Konerding, A. Tsuda, and S. J. Mentzer, "Intravascular pillars and pruning in the extraembryonic vessles of chick embryos", Developmental Dynamics, 240 1335 (2011).
  27. M. Kojic, I. Vlastelica, B. Stojanovic, V. Rankovic, and A. Tsuda, "Characteristics of biological membranes of lung microstructure", Contemporary Materials, (2011) in press.
  28. F. S. Henry and A. Tsuda, "Low reynolds number flow in an expanding alveolated duct", Computational Bioengineering, (2011) in press.
  29. N. Moore, M. Leeser, and L. Smith King, "Adaptable Two-Dimensional Sliding Windows on NVIDIA GPUs with Runtime Compilation", Symposium on Application Accelerators in High Performance Computing (SAAHPC), July 2011 (Winner Best Paper Award).


  1. X.-D. Wen, T. J. Cahill, N. M. Gerovac, M. J. Bucknum, and R. Hoffmann, "Playing the Quantum Chemical Slot Machine: An Exploration of ABX2 Compounds", Inorganic Chemistry, 49, 249 (2010).
  2. D. A. Stewart, "New type of magnetic tunnel junction based on tunneling through a reduced symmetry oxide: FeCo|Mg3B2O6|FeCo", Nano Letters, 10, 263 (2010).
  3. F. Petruzielo, J. Toulouse, and C. J. Umrigar, "Compact and Flexible Basis Functions for Quantum Monte Carlo Calculations", Journal of Chemical Physics, 132, 094109 (2010).
  4. N. Mingo, K. Esfarjani, D. A. Broido, and D. A. Stewart, "Cluster scattering effects on phonon conduction in graphene", Physical Review B, 81, 045408 (2010).
  5. X.-D. Wen, T. J. Cahill, and R. Hoffmann, "Exploring Group 14 Structures: 1D to 2D to 3D", Chemistry - A European Journal, 16, 6555 (2010).
  6. S. K. Baur, J. Shumway, and E. J. Mueller, "Fulde-Ferrell-Larkin-Ovchinnikov versus Bose-Fermi mixture in a polarized one-dimensional Fermi gas at a Feshbach resonance: A three-body study", Physical Review A 81 033628 (2010).
  7. G. C. Rodriguez-Calero, M. A. Lowe, Y. Kiya, and H. D. Abruna, "Electrochemical and Computational Studies of the Electrocatalytic Effect of Conducting Polymers towards the Redox Reactions of Thiadiazole-Based Thiolate Compounds", Journal of Physical Chemistry C, 111 6169 (2010).
  8. J. J. Choi, J. Luria, B.-R. Hyun, A. C. Bartnik, L. Sun, Y.-F. Lim, J. A. Marohn, F. W. Wise, and T. Hanrath, "Photogenerated Exciton Dissociation in Highly Coupled Lead Salt Nanocrystal Assemblies", Nano Letters, 10, 1805 (2010).
  9. P. Gonzalez-Morelos, R. Hoffmann, and N. W. Ashcroft, "Segregation into Layers: A General Problem for Structural Instability under Pressure: Exemplified by SnH4", ChemPhysChem, 11, 3105 (2010).
  10. P. E. Hopkins, M. L. Bauer, J. C. Duda, J. L. Smoyer, T. S. English, P. M. Norris, T. E. Beechem, and D. A. Stewart, "Ultrafast properties of gold under conditions of strong electron-phonon nonequilibrium", Journal of Applied Physics, 108, 104907 (2010).
  11. Z. Boekelheide, A. X. Gray, C. Papp, B. Balke, D. A. Stewart, S. Ueda, K. Kobayashi, F. Hellmann, and C. S. Fadley, "Band gap and electronic structure of an epitaxial, semiconducting Cr0.80Al0.20 thin film", Physical Review Letters, 105, 236404 (2010).
  12. S. E. Burkhardt, G. C. Rodrigues-Calero, M. A. Lowe, Y. Kiya, R. G. Hennig, and H. D. Abruna, "Theoretical and electrochemical analysis of poly(3,4-alkylenedioxythiphenes): Electron-donating effects and onset of p-doped conductivity", Journal of Physical Chemistry C, 114, 16776 (2010).
  13. J. J. Cha, Z. Yu, E. Smith, M. Couillard, S. Fan, and D. A. Muller, "Mapping local optical densities of states in silicon photonics structures with nanoscale electron spectroscopy", Physical Review B, 81, 113102 (2010).
  14. C. Barthel, M. Kjaergaard, J. Medford, M. Stopa, C. M. Marcus, M. P. Hanson, and A. C. Gossard, "Fast sensing of double-dot charge arrangement and spin state with a radio-frequency sensor quantum dot", Physical Review B, 81 161308 (2010).
  15. M. Gullans, J. J. Krich, J. M. Taylor, H. Bluhm, B. I. Halperin, C. M. Marcus, M. Stopa, A. Yacoby, and M. D. Lukin, "Dynamic nuclear polarization in double quantum dots", Physical Review Letters, 104, 226807 (2010).
  16. P. Rebentrost, M. Stopa, and A. Aspuru-Guzik, "Forster coupling in nanoparticle excitonic circuits", Nano Letters, 10, 2849 (2010).
  17. M. Stopa, J. J. Krich, and A. Yacoby, "Inhomogeneous nuclear spin flips: Feedback mechanisms between electronic states in a double quantum dot and the underlying nuclear spin bath", Physical Review B, 81, 041304 (2010).
  18. P. M. Zimmerman, Z. Zhang, and C. B. Musgrave, "Simultaneous 2H transfer as a mechanism for efficient CO2 reduction", Inorganic Chemistry, 49, 8724 (2010).
  19. P. M. Zimmerman, Z. Zhang, and C. B. Musgrave, "Singlet fission in pentacene through multiple exiton quantum states", Nature Chemistry, 2, 648 (2010).
  20. H.-D. Lee, B. Magyari-Kope, and Y. Nishi, "Model of metallic filament formation and nupture in NiO for unipolar switching", Physical Review B, 81, 193202 (2010).
  21. S. G. Park, B. Magyari-Kope, and Y. Nishi, "Electron correlation effects in reduced rutile TiO2 within the LDA+U method", Physical Review B, 82, 115109 (2010)
  22. L. Leem, A. Srivastava, S. Li, B. Magyari-Kope, G. Iannaccone, J. S. Harris, G. Fiori, "Multi-scale simulations of partially unzipped CNT heterojunction tunneling field effect transistor", Techn. Digest, IEDM, 2010.
  23. S. Mijalovich, M. Kojic, and A. Tsuda, "Particle-induced indentation of the alveolar epithelium caused by surface tension forces", Journal of Applied Physiology, 109, 1179 (2010).
  24. G. S. Lee, N. Filipovic, L. F. Miele, M. Lin, D. Collings-Simpson, B. Gibney, M. A. Konerding, A. Tsuda, S. J. Mentzer, "Blood flow shapes intravascular pillar geometry in the chick chorioallantoic membrane", Journal of Angiogenesis Research, 2, 11 (2010).
  25. S. Haber, D. Yitzhak, and A. Tsuda, "Trajectories and Deposition Sites of Spherical Particles Moving Inside Rhythmically Expanding Alveoli under Gravity-Free Conditions", J. Aerosol Med. Pulm. Drug Delivery, 23, 405 (2010).
  26. F. S Henry and A. Tsuda, "Flow and particle tracks in model acini", ASME J. Biomedical Engineering, 132, 101001 (2010).


  1. K. Mkhoyan, A. Contryman, J. Silcox, D. A. Stewart, E. Goki, C. Mattevi, S. Miller, M. Chhowalla, "Atomic and Electronic Structure of Graphene-Oxide", Nano Letters, 9 1058 (2009)
  2. B. Magyari-Kope, S. Park, L. Colombo, Y. Nishi, and K. J. Cho, "Ab-initio study of Al-Ni bilayers on SiO2: Implications to effective work function modulation in gate stacks", Journal of Applied Physics 105 013711 (2009)
  3. D. A. Stewart, I. Savic, and N. Mingo, "First principles calculation of the isotope effect on boron nitride nanotube thermal conductivity", Nano Letters, 9 81 (2009).
  4. X.-D. Wen, T. J. Cahill, and R. Hoffmann, "Element lines: Bonding in the Ternary Gold Polyphoshides, AuMP with M= Pb, Tl, or Hg", Journal of the American Chemical Society, 131, 2199 (2009).
  5. A. Ward, D. A. Broido, D. A. Stewart, G. Deinzer, "Ab-initio theory of the lattice thermal conductivity in diamond", Physical Review B, 80 125203 (2009)
  6. P. E. Hopkins and D. A. Stewart, "Contribution of d-band electrons to ballistic transport and scattering during electron-phonon nonequilibrium in nanoscale Au films using an ab-initio density of states", Journal of Applied Physics, 106, 053512 (2009)
  7. I. Arslan, J. K. Hyun, R. Erni, M. N. Fairchild, S. D. Hersee, and D. A. Muller, "Using Electrons as a High-Resolution Probe of Optical Modes in Individual Nanowires", Nano Letters, 9, 4073 (2009).
  8. K. J. Donald, M. Hargittai, R. Hoffmann, "Group 12 Dihalides: Structural Predilections from Gas to Solids", Chemistry - A European Journal, 15, 158 (2009).
  9. Image Charge and Dipole Combination Model for the Schottky Barrier Tuning at the Dopant Segregated Metal/Semiconductor Interface, L. Geng, B. Magyari-Kope, Y. Nishi, IEEE Electron Device Letters 30, 963, 2009.
  10. High quality GeO2/Ge interface formed by SPA radical oxidation and uniaxial stress engineering for high performance Ge NMOSFETs, M. Kobayashi, T. Irisawa, B. Magyari-Kope, Y. Sun, K. Saraswat, H. -S.P.Wong, P. Pianetta and Y. Nishi, Tech. Digest of VLSI Tech. Symp. p76, 2009.
  11. Uniaxial Stress Engineering for High Performance Ge NMOSFET, M. Kobayashi, T. Irisawa, B. Magyari-Kope, K. Saraswat, H. S. P. Wong and Y. Nishi, IEEE Trans. Electron Devices, 2009.
  12. Lattice and electronic effects of charged defects in rutile TiO2x from ab initio calculations, S. Park, B. Magyari-Kope, and Y. Nishi, Mat. Res. Soc. Symp. Proc., 2009.
  13. Excited states of methylene from quantum Monte Carlo, Paul M. Zimmerman, Julien Toulouse, Zhiyong Zhang, Charles B. Musgrave, and C. J. Umrigar, J. Chem. Phys. 131, 124103 (2009)
  14. The Energetics of C-H Bonds Formed at Single-Walled Carbon Nanotubes, Anton Nikitin, Zhiyong Zhang, and Anders Nilsson, Nano Lett., 9, 1301-1306 (2009).
  15. Fermi Level Unpinning and Schottky Barrier Modification by Ti, Sc and V Incorporation at NiSi2/Si Interface, L. Geng, B. Magyari-Kope, Z. Zhang, and Y. Nishi, Chinese Phys. Lett., 26(3), 037306 (2009)
  16. The Role of Free N-Heterocyclic Carbene (NHC) in the Catalytic Dehydrogenation of Ammonia-Borane in the Nickel NHC System, Paul M. Zimmerman, Ankan Paul, Zhiyong Zhang, and Charles B. Musgrave, Angew. Chem. Int. Ed., 48, 2201-2205 (2009)
  17. Configuration Interaction Studies on the Electronic States of the CUO Molecule, T. Yang, R. Tyagi, Z. Zhang, and Russell Pitzer, Molecular Physics, 107, 1193-1195 (2009)
  18. Oligomerization and autocatalysis of NH2BH2 with ammonia-borane, Paul Zimmerman, Ankan Paul, Zhiyong Zhang, and Charles Musgrave, Inorg. Chem., 48, 1069-1081 (2009)
  19. C. R. Muller, L. Worschech, S. Lang, M. Stopa, and A. Forchel, "Quantized rectification in a quantum dot nanojunction", Physical Review B, 80, 075317 (2009).
  20. S. K. Saikin, R. Olivares-Amaya, D. Rappoport, M. Stopa, and A. Aspuru-Guzik, "On the chemical bonding effects in the Raman response: Benzenethiol adsorbed on silver clusters", Physical Chemistry Chemical Physics, 11, 9401 (2009).
  21. F. S. Henry, F. E. Laine-Pearson, and A. Tsuda, "Hamiltonian Chaos in a model alveolus", ASME J. Biomechanical Engineering, 131, 011006 (2009).
  22. J. Sznitman, T. Heimsch, J. H. Wildhaber, A. Tsuda, and T. Rosgen, "Respiratory flow phenomena and gravitational sedimentation in a three-dimensional space-filling model of the pulmonary acinar tree", ASME J. Biomechanical Engineering, 131, 031010 (2009).
  23. A. Maleshchenko, A. Tsuda, and S. Haber, "Propagation and breakup of liquid menisci and aerosol generation in small airways", J. Aerosol Med. Pulm Drug Deliv., 22, 341 (2009).
  24. N. Filipovic, A. Tsuda, G. S. Lee, L. F. Miele, M. Lin, M. A. Konerding, and S. J. Mentzer, "Computational Flow Dynamics in a Geometric Model of Intussusceptive Angiogenesis", Microvasc. Res., 78, 286, (2009).
  25. A. D. Maestro, B. Rosenow, and S. Sachdev, "Theory of the pairbreaking superconductor-metal transition in nanowires", Annals of Physics, 324, 523 (2009).


  1. N. Mingo, D. A. Stewart, D. A. Broido, and D. Srivastava, "Phonon transmission through defects in carbon nanotubes from first principles", Physical Review B, 77, 033418 (2008).
  2. J. Toulouse and C. J. Umrigar, "Full optimization of Jastrow-Slater wave functions with applications to the first-row atoms and homonuclear diatomic molecules", Journal of Chemical Physics, 128, 174101 (2008)
  3. D. A. Stewart, "Ab-initio investigation of phonon dispersion and anomalies in palladium", New Journal of Physics, 10, 043025 (2008).
  4. E. K. Yu, D. A. Stewart, and S. Tiwari, "Ab-initio study of polarizability and induced charge densities in multilayer graphene films", Physical Review B, 77, 195406 (2008).
  5. W. A. Al-Saidi and C. J. Umrigar, "Fixed node diffusion Monte Carlo study of the structures of m-benzene", Journal of Chemical Physics, 128, 154324 (2008).
  6. I. Savic, N. Mingo, and D. A. Stewart, "Phonon transport in isotope-disordered carbon and boron-nitride nanotubes: Is localization observable?", Physical Review Letters, 101, 165502 (2008).
  7. A. E. Litovitz, I. Keresztes, and B. K. Carpenter, "Evidence for nonstatistical dynamics in the Wolff rearrangement of a carbene", Journal of the American Chemical Society, 130, 12085 (2008).
  8. W. A. Al-Saidi, "Variational and diffusion Monte Carlo study of post-d group 13-17 elements", Journal of Chemical Physics, 129, 064316 (2008).
  9. I. Savic, D. A. Stewart, and N. Mingo, "Thermal conduction mechanisms in boron nitride nanotubes: few shell versus all-shell conduction", Physical Review B, 78, 235434 (2008).
  10. W. L. Wang, S. Meng, and E. Kaxiras, "Graphene nanoflakes with large spin", Nano Letters, 8, 241 (2008).
  11. W. Gao, T. A. Baker, L. Zhou, D. S. Pinnaduwage, E. Kaxiras, and C. M. Friend, "Chlorine Adsorption on Au(111): Chlorine Overlayer or Surface Chloride?", Journal of the American Chemical Society, 130, 3560 (2008).
  12. T. A. Baker, C. M. Friend, and E. Kaxiras, "Nature of Cl bonding on the Au(111) surface: Evidence of a mainly covalent interaction", Journal of the American Chemical Society, 130, 3720 (2008).
  13. M. Bernaschi, S. Melchionna, S. Succi, M. Fyta, and E. Kaxiras, "Quantized Current Blockade and Hydrodynamic Correlations in Biopolymer Translocation through Nanopores: Evidence from Multiscale Simulations", Nano Letters, 8, 1115 (2008).
  14. A. Gali, M. Fyta, and E. Kaxiras, "Ab-initio supercell calculations on nitrogen-vacancy center in diamond: Electron structure and hyperfine tensors", Physical Review B, 77, 155206 (2008).
  15. M. Stopa and C. M. Marcus, "Magnetic field control of exchange and noise immunity in double quantum dots", Nano Letters, 8, 1778 (2008).
  16. M. Fyta, E. Kaxiras, S. Melchionna, and S. Succi, "Multiscale simulation of nanobiological flows", Computing in Science and Engineering, 10, 10 (2008).
  17. "First-principles study of resistance switching in rutile TiO2 with oxygen vacancy", S. Park, B. Magyari-K¨ope, and Y. Nishi NVMTS (Non-Volatile Memory Technology Symposium2008), 9th Annual, 1-5, 2008.
  18. Ab Initio Modeling of Schottky Barrier Height Tuning by Yttrium at Nickel Silicide/Silicon Interface, Li Geng, Blanka Magyari-Kope, Zhiyong Zhang, and Yoshio Nishi, IEEE Electron Device Lett., 29, 746 (2008)
  19. C-H Bond Formation at the Surface of Graphite Studied with Core Level Spectroscopy, Anton Nikitin, Lars Naslund, Zhiyong Zhang, and Anders Nilsson, Surf. Sci., 602, 2575-2580 (2008)
  20. Quantum dot properties in the multiband envelope-function approximation using boundary conditions based upon first principles quantum calculations, Curt A. Flory, Charles B. Musgrave, and Zhiyong Zhang, Phys. Rev. B, 77, 205312 (2008)
  21. Hydrogen Storage in Carbon Nanotubes Through the Formation of C-H Bonds, A. Nikitin, X. Li, Z. Zhang, D. Mann, H. Ogasawara, H. Dai, and A. Nilsson, Nano Lett., 8, 162 (2008)
  22. A. D. Maestro, B. Rosenow, N. Shah, and S. Sachdev, "Universal thermal and electrical transport near the superconductor-metal quantum phase transition in nanowires", Physical Review B, 77 180501 (2008).
  23. A. D. Maestro, B. Rosenow, M. Mueller, and S. Sachdev, "Infinite randomness fixed point of the superconductor-metal quantum phase transition", Physical Review Letters, 101, 035701 (2008).

2007 (Articles with * are from the 2006 NNIN/C Synergy Conference)

  1. K. E. Aidala, R. E. Parrott, T. Kramer, E. J. Heller, R. M. Westervelt, M. P. Hanson, and A. C. Gossard, "Imaging magnetic focusing of coherent electron waves", Nature Physics, 3, 464 (2007).
  2. J. Toulouse, C. J. Umrigar, "Optimization of quantum Monte Carlo wave functions by energy minimization", Journal of Chemical Physics, 126, 084102 (2007)
  3. * M. Prakash and E. P. Giannelis, "Mechanism of heat transport in nanofluids", Journal of Computer-Aided Material Design, 14, 109 (2007)
  4. D. A. Stewart, "Magnetism in Coaxial Palladium Nanowires", Journal of Applied Physics, 101, 09D503 (2007)
  5. C. J. Umrigar, J. Toulouse, C. Filippi, S. Sorella, R. G. Hennig, "Alleviation of the Fermion-sign problem by optimization of many-body wave functions", Physical Review Letters, 98, 110201 (2007)
  6. J. Toulouse, R. Assaraf, C. J. Umrigar, "Zero-variance zero-bias quantum Monte Carlo estimators of the spherically and system-averaged pair density", Journal of Chemical Physics, 126, 244112 (2007)
  7. M. R. Lee and P. M. Fauchet, "Two-dimensional silicon photonic crystal based biosensing platform for protein detection", Optics Express, 15, 4530 (2007)
  8. G. Merino, K. J. Donald, J. D'Acchioli, and R. Hoffmann, "The Many Ways to Have a Quintuple Bond", Journal of the American Chemical Society (JACS), 129, 15295 (2007)
  9. D. A. Broido, M. Malorny, G. Birner, N. Mingo, and D. A. Stewart, "Intrinsic lattice thermal conductivity of semiconductors from first principles", Applied Physics Letters, 91, 231922 (2007)
  10. J. J. Cha, M. Weyland, J.-F. Briere, I. P. Daykov, T. A. Arias, and D. A. Muller, "Three-dimensional imaging of carbon nanotubes deformed by metal islands", Nano Letters, 7 3770 (2007)
  11. A. Ghosal, A. D. Guclu, C. J. Umrigar, D. Ullmo, and H. U. Baranger, "Incipient Wigner localization in circular quantum dots", Physical Review B, 76, 085341 (2007)
  12. J. Y. Vaishnav, J. D. Walls, M. Apratim, and E. J. Heller, "Matter-wave scattering and guiding by atomic arrays", Physical Review A, 76, 013620 (2007)
  13. S. Meng, P. Maragakis, C. Papaloukas, and E. Kaxiras, "DNA nucleoside interaction and identification with carbon nanotubes", Nano Letters, 7, 45 (2007).
  14. S. Meng, W. L. Wang, P. Maragakis, and E. Kaxiras, "Determination of DNA-base orientation on carbon nanotubes through directional optical absorbance", Nano Letters, 7, 2312 (2007)
  15. S. Melchionna, M. G. Fyta, E. Kaxiras, and S. Succi, "Exploring DNA translocation through a nanopore via a multiscale lattice-boltzmann molecular-dynamics methodology", Int. Journal of Modern Physics C, 18, 685 (2007)
  16. R. L. Barnett, P. Maragakis, A. Turner, M. Fyta, and E. Kaxiras, "Multiscale model of electronic behavior and localization in stretched dry DNA", Journal of Materials Science, 42, 1573 (2007)
  17. S. Luscher, L. S. Moore, T. Rejec, Y. Meir, H. Shtrikman, and D. Goldhaber-Gordon, "Charge rearrangement and screening in a quantum point contact", Physical Review Letters, 98, 196805 (2007)
  18. S. Brozell, R. Shepard, and Z. Zhang, "Spin-orbit interaction with nonlinear wave functions", Int. J. of Quant. Chem., 107, 3191 (2007).
  19. Z. Zhang and K. J. Cho, "Ab-initio study of hydrogen interaction with pure and nitrogen doped carbon nanotubes", Physical Review B, 75, 075420 (2007).
  20. * M. Stopa, "Synergy between experiment and computation in nanoscale science", J. Comp.-Aided Materials Design 14, 1 (2007).
  21. * Z. Abidin, N. Matsue, and T. Henmi, "Differential formation of allophane and imogolite: experimental and molecular orbital study", J. Comp.-Aided Materials Design, 14, 5 (2007)
  22. * W. J. Adams, T. Pong, N. A. Geisse, S. P. Sheehy, B. Diop-Frimpong, and K. K. Parker, "Engineering design of a cardiac myocyte", J. Comp.-Aided Materials Design, 14, 19 (2007)
  23. * C. Aramphongphun and J. M. Castro, "Microfluidics and rheology of carbon black suspensions for In-Mold Coating applications: some insights into the slip flow phenomena", J. Comp.-Aided Materials Design, 14, 31 (2007)
  24. * O. Citfja, "An experimentally justified confining potential for electrons in two-dimensional semiconductor quantum dots", J. Comp-Aided Materials Design, 14, 37 (2007).
  25. * H. Manzano, A. Ayuela, and J. S. Dolado, "On the formation of cementitious C-S-H nanoparticles", J. Comp-Aided Materials Design, 14, 45 (2007).
  26. * A. A. Hassanali and S. J. Singer, "Static and dynamic properties of the water/amorphous silica interface: a model for the undissociated surface", J. Comp-Aided Materials Design, 14, 53 (2007)
  27. * M. Encinosa and M. Jack, "Dipole and solenoidal magnetic moments of electronic surface currents on toroidal nanostructures", J. Comp-Aided Materials Design, 14, 65 (2007).
  28. * Y. Ouyang, Y. Yoon, and J. Guo, "On the current delivery limit of semiconducting carbon nanotubes", J. Comp-Aided Materials Design, 14, 73 (2007).
  29. * S. Kundu, A. Sreedhar, and A. Sanyal, "Forbidden pitches in sub-wavelength lithography and their implications on design", J. Comp-Aided Materials Design, 14, 79 (2007).
  30. * C. May, K. Ensslin, and M. Troyer, "Self-consistent potential calculation for locally oxidized Ga[Al]Al heterostructures", J. Comp-Aided Materials Design, 14, 91 (2007).
  31. * L. Mourokh, A. Smirnov, J. Bird, and M. Stopa, "Fano resonances in the system of coupled point contacts", J. Comp-Aided Materials Design, 14, 97 (2007)
  32. * K. Palandage, "An exact study of pairing fluctuations and phase diagrams in four-site Hubbard nanoclusters", J. Comp-Aided Materials Design, 14, 103 (2007).
  33. * R. Sedmik, I. Vasiljevich, and M. Tajmar, "Detailed parametric study of Casimir forces in the Casimir Polder approximation for nontrivial 3D geometries", J. Comp-Aided Materials Design, 14, 119 (2007).
  34. * N. Shi and R. Ramprasad, "Dielectric properties of nanoscale multi-component systems: a first principles computational study", J. Comp-Aided Materials Design, 14, 133 (2007).
  35. * M. Stilling, K., Stokbro, and K. Flensberg, "Electronic transport in crystalline magnetotunnel junctions: effects of structural disorder", J. Comp-Aided Materials Design, 141 (2007).
  36. * M. Yu, G. W. Fernando, R. Li, F. Papadimitrakopoulos, N. Shi, and R. Ramprasad, "Discrete size series of CdSe quantum dots: a combined computational and experimental investigation", Journal of Comp.-Aided Materials Design, 14, 167 (2007)
  37. * J. K. Stolarczyk, T. Sainsbury, and D. Fitzmaurice, "Evaulation of interactions between functionalised multi-walled carbon nanotubes and ligand-stablised gold nanoparticles using surface element integration", Journal of Comp.-Aided Materials Design, 14, 151 (2007)


  1. J. Feng, W. Grochala, T. Jaron, R. Hoffman, A. Bergara, and N. W. Ashcroft, "Structures and Potential Superconductivity in SiH4 at High Pressure: En Route to Metallic Hydrogen", Physical Review Letters, 96, 017006 (2006).
  2. A. Gondarenko, S. Preble, J. Robinson, L. Chen, H. Lipson, and M. Lipson, "Spontaneous Emergence of Periodic Patterns in a Biologically Inspired Simulation of Photonic Structures", Physical Review Letters, 96, 143904 (2006)
  3. K. J. Donald and R. Hoffmann, "Solid Memory: Structure Preferences in Group 2 Dihalide Monomers, Dimers, and Solids", Journal of the American Chemical Society (JACS), 128, 11236 (2006)
  4. A. H. Edwards, A. C. Pineda, P. A. Schultz, M. G. Martin, A. P. Thompson, H. P. Hjalmarson, and C. J. Umrigar, "Electronic structure of intrinsic defects in crystalline germanium telluride", Physical Review B, 73, 045210 (2006).
  5. A. Ghosal, A. D. Guclu, C. J. Umrigar, D. Ullmo, and H. U. Baranger, "Correlation-induced inhomogeneity in circular quantum dots", Nature Physics, 2, 336 (2006)
  6. J. Hachmann, W. Cardoen, and G. K-L. Chan, "Multireference correlation in long molecules with the quadratic scaling density matrix renormalization group", Journal of Chemical Physics, 125, 144101 (2006)
  7. F. Leonard and D. A. Stewart, "Properties of short channel ballistic carbon nanotube transistors with ohmic contacts", Nanotechnology, 17, 4699 (2006).
  8. M. G. Fyta, S. Melchionna, E. Kaxiras, and S. Succi, "Multiscale coupling of molecular dynamics and hydrodynamics: applications to DNA translocation through a nanopore", Multiscale Modeling and Simulation, 5, 1156 (2006).
  9. M. Yamamoto, M. Stopa., Y. Tokura, Y. Hirayama, S. Tarucha, "Negative Coulomb Drag in a One-Dimensional Wire", Science, 313, 204 (2006).
  10. A. Vidan, M. Stopa, R. M. Westervelt, M. Hanson, A. C. Gossard, "Multipeak Kondo Effect in One- and Two-Electron Quantum Dots", Physical Review Letters, 96, 156802 (2006).
  11. W. G. van der Wiel, M. Stopa, T. Kodera, T. Hatano, and S. Tarucha, "Semiconducting quantum dots for electron spin qubits", New Journal of Physics, 8, 28 (2006).


  1. P. Fallahi, A. C. Bleszynski, R. M. Westervelt, J. Huang, J. D. Walls, E. J. Heller, M. Hanson, and A. C. Gossard, "Imaging a single-electron quantum dot", Nano Letters, 5, 223 (2005)
  2. T. Hatano, M. Stopa, and S. Tarucha, "Single-electron delocalization in hybrid vertical-lateral double quantum dots", Science, 309, 268 (2005)
  3. A. Vidan, R. M. Westervelt, M. Stopa, M. Hanson, A. C. Gossard, "Charging and spin effects in triple dot artificial molecules", Journal of Superconductivity, 18, 223 (2005)
  4. A. Nikitin, H. Ogasawara, D. Mann, Z. Zhang, H. Dai, K. J. Cho, and A. Nilsson, "Hydrogenation of single-walled carbon nanotubes", Physical Review Letters, 95, 225507 (2005).