Publications from the Jónsson research group

Listed by topic

Recent publications in reverse time order:

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A. Pedersen and H. Jónsson, `Efficient Sampling of Saddle Points with the Minimum-Mode Following Method', Journal of Scientific Computing (to be submitted 2009).

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A. Pedersen, G. Henkelman, J. Schøts and H. Jónsson, `Long timescale simulation of a Grain boundary in copper', New Journal of Physics 11, 073034 (2009). (article in pdf format).

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S. Andersson, G. Nyman, A. Arnaldsson, U. Manthe and H. Jónsson, `Comparison of Quantum Dynamics and Quantum Transition State Theory Estimates of the H + CH4 Reaction Rate', J. Phys. Chem. A 113, 4468 (2009). (article in pdf format).

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A. Pedersen and H. Jónsson, `Simulations of Hydrogen Diffusion at Grain Boundaries in Aluminum', Acta Materialia 57, 4036 (2009). (article in pdf format).

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A. Pedersen and H. Jónsson, `Distributed Implementation of the Adaptive Kinetic Monte Carlo Method', Mathematics and Computers in Simulation (in press 2009). (article in pdf format).

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A. Pedersen, L. Pizzagalli and H. Jónsson, `Finding mechanism of transitions in complex systems: Formation and migration of dislocation kinks in a silicon crystal', Journal of Physics Condensed Matter 21, 084210 (2009). (article in pdf format).

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L. Pizzagalli, A. Pedersen, A. Arnaldsson, H. Jónsson and P. Beauchamp, `Theoretical study of kinks on screw dislocation in silicon', Physical Review B 77, 064106 (2008). (article in pdf format).

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H. D. Flosadóttir, H. Jónsson and O. Ingólfsson, 'Simulations of the fragmentation of the [V-H]- anions as formed upon DEA to L-valine', J. Phys.: Conf. Ser. 115, 012014 (2008). (article in pdf format).

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L. Pizzagalli, P. Beauchamp and H. Jónsson, `Calculations of dislocation mobility using nudged elastic band method and first principles DFT calculations', Philosophical Magazine 88, 91 (2008). (article in pdf format).

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Helga Dögg Flosadóttir, Stephan Denifl, Nina Wendt, Andreas Mauracher, Arntraud Bacher, H. Jónsson, Paul Scheier and Oddur Ingólfsson, `Combined experimental and theoretical study on the nature and the metastable decay pathways of the amino acid ion fragment [M-H]-', Angew. Chem. Int. Ed. 46, 8057 (2007). (article in pdf format).

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E. Skúlason, G. S. Karlberg, J. Rossmeisl, T. Bligaard, J. Greeley, H. Jónsson and J. K. Nørskov, `Density functional theory calculations for the hydrogen evolution reaction in an electrochemical double layer on the Pt(111) electrode', Physical Chemistry Chemical Physics, 9, 3241 (2007). (article in pdf format and supplementary material format).

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L. Xu, C. T. Campbell, H. Jónsson and G. Henkelman, `Kinetic Monte Carlo simulations of Pd deposition and island growth in MgO(100)', Surf. Sci. 601, 3133 (2007). (article in pdf format).

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A. Hellman, et al (summary of EC network), 'Predicting Catalysis: Understanding ammonia synthesis from first-principles calculations', J. Phys. Chem. B, 110, 17719 (2006). (article in pdf format).

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F. Óskarsson, E. S. Aradóttir and H. Jónsson, `Calculations of release temperature of hydrogen storage materials', Prepr. Pap.-Am. Chem. Soc., Div. Fuel Chem., vol. 51, (2006). (article in pdf format).

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F. Óskarsson, W. Stier and H. Jónsson, 'Calculations of the binding energy and diffusion of hydrogen in pure magnesium metal and magnesium hydride', submitted to Phys. Rev. B. (article in pdf format).

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F. Óskarsson and H. Jónsson, 'The effect of light impurities on the binding energy of hydrogen in magnesium metal and magnesium hydride', submitted to Phys. Rev. B. (article in pdf format).

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R. Van Ginhoven, H. Jónsson and L. R. Corrales, `Characterization of exciton self-trapping in amorphous silica', J. Non-Cryst. Solids, vol. 352, p. 2589 (2006). (article in pdf format).

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L. Xu, G. Henkelman, C. T. Campbell and H. Jónsson, `Pd diffusion on MgO(100): the role of defects and small cluster mobility', Surf. Sci., vol. 600, p. 1351 (2006). (article in pdf format).

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G. Henkelman, A. Arnaldsson and H. Jónsson, `Theoretical calculations of CH4 and H2 associative desorption from Ni(111): could subsurface hydrogen play an important role?', J. Chem. Phys., vol. 124, p. 044706 (2006). (article in pdf format).

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G. Henkelman, A. Arnaldsson and H. Jónsson, `A fast and robust algorithm for Bader decomposition of charge density', Comp. Mat. Sci. 36, 354 (2006). (abstract, article in pdf format, additional info).

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E. R. Batista, P. Ayotte, A. Bilic, B. D. Kay and H. Jónsson, `What Determines the Sticking Probability of Water Molecules on Ice?', Phys. Rev. Letters, vol. 95, 223201 (2005). (article in pdf format).

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L. Xu, G. Henkelman, C. T. Campbell and H. Jónsson, `Small Pd clusters, up to the tetramer at least, are highly mobile on the MgO(100) surface', Phys. Rev. Letters, vol 95, page 146103 (2005). (abstract, article in pdf format).

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R. M. Van Ginhoven, H. Jónsson and L. R. Corrales, `Cleavage and Recovery of Molecular Water in Silica', J. Phys. Chem. B, vol. 109, p. 10936 (2005). (abstract, article in pdf format).

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R. M. Van Ginhoven, L. R. Corrales and H. Jónsson, `Silica glass structure generation for ab initio calculations', Phys. Rev. B vol. 71, 024208 (2005). (abstract, article in pdf format).

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W. Stier, L. G. Camargo, F. Óskarsson and H. Jónsson, `Hydrogen storage in magnesium based alloys', Prepr. Pap.-Am. Chem. Soc., Div. Fuel Chem., vol. 50(1), page 15 (2005). (article in pdf format).

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T. Bligaard and H. Jónsson, `Optimization of hyperplanar transition states: Application to 2D test problems', Comp. Phys. Commun., vol. 169, p. 284 (2005). (abstract, article in pdf format).

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J. K. Norskov, J. Rossmeisl, A. Logadóttir, L. Lindqvist, J. R. Kitchin, T. Bligaard and H. Jónsson, `Origin of the overpotential for oxygen reduction at a fuel-cell cathode', J. Phys. Chem. B vol. 108, p. 17886 (2004). (article in pdf format).

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R. A. Olsen, G. J. Kroes, G. Henkelman, A. Arnaldsson and H. Jónsson, `Comparison of methods for finding saddle points without knowledge of the final states', J. Chem. Phys. vol. 121, 9776 (2004). (abstract, article in pdf format).

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R. M. Van Ginhoven, H. Jónsson, K. A. Peterson, M. Dupuis, and L. R. Corrales, `An ab initio study of self-trapped excitons in alpha-quartz', J. Chem. Phys. vol. 118, 6582 (2003). (abstract, article in pdf format).

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F. Gao, G. Henkelman, W. J. Weber, L. R. Corrales and H. Jónsson, `Finding Possible Transition States of Defects in Silicon-Carbide and Alpha-Iron using the Dimer Method', Nucl. Instr. and Meth. in Phys. Res. B, vol. 202, p. 1 (2003). (article in pdf format).

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G. Henkelman and H. Jónsson, `Multiple time scale simulations of metal crystal growth reveal importance of multi-atom surface processes', Phys. Rev. Letters, Vol. 90, p. 116101 (2003). (abstract, article in pdf format).

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G. Henkelman and H. Jónsson, `Long time scale simulations of Al(100) crystal growth', in "Atomistic Aspects of Epitaxial Growth", M. Kotrla et al. (eds.), page 63 (Kluwer, Netherlands, 2002). (abstract)

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Blas Uberuaga, Graeme Henkelman, H. Jónsson, Scott Dunham, W. Windl and R. Stumpf, `Theoretical Studies of Self-Diffusion and Dopant Clustering in Semiconductors', Physica Status Solidi B, 233, 24 (2002). (abstract, the article in pdf format).

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Graeme Henkelman, Blas Uberuaga, Scott Dunham and H. Jónsson, `Simulations of dopant clustering in silicon: Dimer calculations using DFT forces', 2nd International Conference on Computational Nanoscience and Nanotechnology, April 2002, p. 144 (2002). (abstract, the article in pdf format)

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G. Henkelman and H. Jónsson, `Long time scale kinetic Monte Carlo simulations without lattice approximation and predefined event table', J. Chem. Phys., Vol. 115, p. 9657 (2001). (abstract, the article in pdf format)

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G. Henkelman and H. Jónsson, `Simulations of long time scale dynamics using the dimer method', Mat. Res. Soc. Symp. Proc. 677, AA8.1.1 (2001). (abstract, the article in pdf format)

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L. R. Corrales, J. Song, R. M. VanGinhoven, and H. Jónsson, `Computational studies of self-trapped excitons in silica', NATO Advanced Studies Institute Proceedings on "Defects in SiO2 and related dielectrics: Science and technology" held in Erice, Italy. Eds: G. Pacchioni et al. Pages 329-337 (Kluwer Academic, Dordrecht, 2000). (abstract)

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J. Song, L. R. Corrales, G. Kresse, and H. Jónsson, `Migration of O-vacancies in alpha-quartz: The effect of excitons and electron holes', Physical Review B , Vol. 64, p. 134102 (2001). (abstract, the article, color figures and more info).

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G. H. Jóhannesson and H. Jónsson, `Optimization of Hyperplanar Transition States', Journal of Chemical Physics, Vol. 115, p. 9644 (2001). (abstract, the article in pdf format)

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E. Batista and H. Jónsson, `Diffusion and Island Formation on the Ice Ih Basal Plane Surface', Computational Materials Science, vol. 20, page 325 (2001) (abstract, and article in pdf format)

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G. Henkelman and H. Jónsson, `Theoretical calculations of dissociative adsorption of methane on an Ir(111) surface', Physical Review Letters Vol. 86, p. 664 (2001). (abstract, article in pdf format)

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G. Henkelman, B. Uberuaga and H. Jónsson, `A Climbing-Image NEB Method for Finding Saddle Points and Minimum Energy Paths', J. Chem. Phys. Vol. 113, p. 9901 (2000). (abstract, article in pdf format)

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G. Henkelman and H. Jónsson, `Improved Tangent Estimate in the NEB Method for Finding Minimum Energy Paths and Saddle Points', J. Chem. Phys. Vol. 113, p. 9978 (2000). (abstract, article in pdf format)

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J. Song, R. vanGinhoven, L. R. Corrales, and H. Jónsson, `Self-trapped Excitons at the Quartz(0001) Surface', Faraday Discuss. vol. 117, p. 303 (2000). (abstract, pdf file with article, pdf file with discussions)

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G. Henkelman, G. Jóhannesson, and H. Jónsson, `Methods for Finding Saddle Points and Minimum Energy Paths', Progress on Theoretical Chemistry and Physics, ed. S. D. Schwartz (Kluwar Academic Publishers, 2000). (abstract, and chapter in pdf format)

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H. Jónsson, `Theoretical Studies of Atomic Scale Processes Relevant to Crystal Growth', Annual Review of Physical Chemistry, 51, 623 (2000). (abstract, article in pdf format )

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J. Song, H. Jónsson, and L. R. Corrales, `Self-Trapped Excitons in Quartz', Nucl. Inst. Meth. Phys. Res. B, vol. 166-167, p. 453 (2000), (abstract, article in pdf format)

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L. R. Corrales, H. Jónsson, J. Song, and R. M. VanGinhoven, `A Comparative Study of Oxygen Vacancy Migration Pathways in Crystalline Polymorphs of Silica', in "Waste Management Science and Technology in the Ceramic and Nuclear Industries", G. L. Smith, G. T. Chandler and B. Mobasher, eds. (The American Ceramics Society, Westerville, Ohio). (abstract, article in pdf format)

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B.P. Uberuaga, M. Leskovar, A. P. Smith, H. Jónsson, and M. Olmstead `Diffusion of Ge below the Si(100) surface: Theory and Experiment', Physical Review Letters, vol. 84, p. 2441 (2000). (abstract, a article in pdf format)

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E.R. Batista S. Xantheas and H. Jónsson `Electric Fields in Ice and Near Water Clusters' Journal of Chemical Physics, vol. 112, p. 3285 (2000). (abstract, a article in pdf format)

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B.P. Uberuaga, E.R. Batista and H. Jónsson `Elastic Sheet Method for Identifying Atoms in Molecules' Journal of Chemical Physics, Vol. 111, p. 10664 (1999). (abstract, and a article in pdf format)

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S.G. Srinivasan, J.W. Cahn, H. Jónsson, and G. Kalonji `Excess energy of grain-boundary trijunctions: an atomistic simulation study' Acta Mater., Vol. 47, p. 2821 (1999). (abstract, and article in pdf format)

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E. Batista S. Xantheas and H. Jónsson `Multipole Moments of Water Molecules in Clusters and Ice Ih from First Principles Calculations' Journal of Chemical Physics, Vol. 111, page 6011 (1999). (abstract, and article in pdf format)

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G. Henkelman and H. Jónsson, `A Dimer Method for Finding Saddle Points on High Dimensional Potential Surfaces Using Only First Derivatives', J. Chem. Phys., Vol. 111, page 7010 (1999) (abstract, a article in pdf format, and a post script file with the paper)

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A. P. Esposito, T. Stedl, H. Jónsson, P. J. Reid, and K. A. Peterson, `Absorption and Resonance Raman Study of the 2B1(X)-2A2(A) Transition of Chlorine Dioxide in the Gas Phase', J. Phys. Chem., Vol. 103, p. 1748 (1999) (abstract, article in pdf format)

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E. Batista, H. Jónsson and S. Xantheas, `Molecular multipole moments of water molecules in ice Ih' Journal of Chemical Physics, vol. 109, p. 4546 (1998). (abstract, a article in pdf format and ps file)

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S. Rempe and H. Jónsson, `A Computational Exercise Illustrating Molecular Vibrations and Normal Modes', The Chemical Educator, vol. 3, (1998), http://journals.springer-ny.com/chedr. (abstract, and article in pdf format)

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G. Mills, G. K. Schenter, D. Makarov and H. Jónsson, `RAW Quantum Transition State Theory', in `Classical and Quantum Dynamics in Condensed Phase Simulations', ed. B. J. Berne, G. Ciccotti and D. F. Coker (World Scientific, 1998), page 405. (abstract, a article in pdf format and ps file)

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H. Jónsson, G. Mills, K. W. Jacobsen, `Nudged Elastic Band Method for Finding Minimum Energy Paths of Transitions', in `Classical and Quantum Dynamics in Condensed Phase Simulations', ed. B. J. Berne, G. Ciccotti and D. F. Coker (World Scientific, 1998), page 385. (abstract, a article in pdf format and ps file )

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T. Rasmussen, K.W. Jacobsen, T. Leffers, O.B. Pedersen, S.G. Srinivasan and H. Jónsson, `Atomistic Determination of Cross-Slip Pathway and Energetics', Physical Review Letters, vol. 79, p. 3676 (1997). (abstract, article in pdf format)

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G. Mills, G. K. Schenter, D. Makarov and H. Jónsson, `Generalized Path Integral Based Quantum Transition State Theory', Chemical Physics Letters, vol. 278, p. 91 (1997). (abstract, article in pdf format)

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S. Srivilliputhur, I. Ashok, H. Jónsson, G. Kalonji and J. Zarhojan, `Dynamic-Domain-Decomposition Parallel Molecular Dynamics', Computer Physics Communications, vol. 102, p. 44 (1997). (abstract)

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S. Srivilliputhur, I. Ashok, H. Jónsson, G. Kalonji and J. Zarhojan, `Parallel Short-Range Molecular Dynamics Using Adhara Runtime System', Computer Physics Communications, vol. 102, p. 28 (1997). (abstract)

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Mads R. Sorensen, Karsten W. Jacobsen, and Hannes Jónsson, `Thermal Diffusion Processes in Metal Tip-Surface Interactions: Contact Formation and Adatom Mobility', Physical Review Letters, vol. 77, p. 5067 (1996). (abstract, article in pdf format)

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A.P.Smith and H. Jónsson, `Early Stages of Island Formation During Deposition of Si on Si(100)', Physical Review Letters, vol. 77, p. 1326 (1996). (abstract, article in pdf format)

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B.S. Swartzentruber, A.P.Smith, and H. Jónsson, `Experimental and theoretical study of the rotation rate of Si ad-dimers on the Si(100) surface', Physical Review Letters, vol. 77, p. 2518 (1996). (abstract, article in pdf format)

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P. Nachtigall, K. D. Jordan, A Smith and H. Jónsson, `Investigation of the Reliability of Density Functional Methods: reaction and activation energies for Si-Si bond cleaveage and H2 elimination from Silanes', Journal of Chemical Physics, vol. 104, p. 148 (1996). (abstract, article in pdf format)

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P. Bedrossian, A. Smith and H. Jónsson, `Silicon Adatom Binding on Si(100)', Mat. Res. Soc. Symp. Proc., vol. 389, p. 35 (1995). (abstract)

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H. Yan, A. Smith and H. Jónsson, `Electronic and Atomic Sctructure of beta-SiC(100) Surfaces', Surf. Sci., vol. 330, p. 265 (1995). (abstract, article in pdf format)

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J. Wiggs and H. Jónsson, `A Hybrid Decomposition Parallel Implementation of the Car-Parrinello Method', Computer Physics Communications, vol. 87, p. 319 (1995). (abstract, article in pdf format)

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M. Villarba and H. Jónsson, `Atomic Exchange Processes in Sputter Deposition of Pt on Pt(111)', Surface Science, vol. 324, p. 35 (1995). (abstract, article in pdf format)

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H. Jónsson, `Research Level Computers and Software in the Undergraduate Curriculum', Journal of Chemical Education, April 1995. (abstract)

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A. Goldstein and H. Jónsson, `EAM type potentials for HCP metals: Zr', Philosophical Magazine B vol. 71, p. 1041 (1995). (abstract)

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S. Shumway, A. S. Clarke and H. Jónsson, `Molecular Dynamics Simulations of Pressure-induced Glass Transition', Journal of Chemical Physics, vol. 102, p. 1796 (1995). (abstract, article in pdf format)

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A. Smith, J. Wiggs, H. Jónsson, H. Yan, L.R. Corrales, P. Nachtigall, K. Jordan, `Si adatom binding and diffusion on the Si(100) surface: Comparison of ab initio, semi-empirical and empirical potential results.' Journal of Chemical Physics, vol. 102, p. 1044 (1995). (abstract, article in pdf format)

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G. Mills, H. Jónsson and G. K. Schenter, `Reversible Work Based Transition State Theory: Application to H2 Dissociative Adsorption', Surface Science, vol. 324, p. 305 (1995). (abstract, article in pdf format)

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J. Hoekstra, H. Yan, G. Kalonji, and H. Jónsson, `Structure and Properties of Strained Crystalline Multilayers: A Molecular Dynamics Study', Mat. Res. Soc. Symp. Proc., vol. 351, p. 349 (1994). (abstract)

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G. K. Schenter, G. Mills, and H. Jónsson, `Reversible Work Based Quantum Transition State Theory', Journal of Chemical Physics, vol. 101, p. 8964 (1994). (abstract, article in pdf format)

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M. Villarba and H. Jónsson, `Diffusion Mechanisms Relevant to Metal Crystal Growth: Pt/Pt(111) ', Surface Science, vol. 317, p. 15 (1994). (abstract, article in pdf format)

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H. Yan, X. Hu, and H. Jónsson, `Atomic Structure of beta-SiC(100) Surfaces: A Study Using the Tersoff Potential', Surface Science, vol. 316, p. 181 (1994). (abstract, article in pdf format)

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J. Hoekstra, H. Yan, G. Kalonji, and H. Jónsson, `Structural Variations in Strained Crystalline Multilayers', Journal of Materials Research, vol. 9, p. 2190 (1994). (abstract)

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J. Wiggs and H. Jónsson, `A Parallel Implementation of the Car-Parrinello Method by Orbital Decomposition', Computer Physics Communications, vol. 81, p. 1 (1994). (abstract)

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D. Faken and H. Jónsson, `Systematic Analysis of Local Atomic Structure Combined with 3D Computer Graphics', Computational Materials Science, vol. 2, p. 279 (1994). (abstract, article in pdf format)

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G. Mills and H. Jónsson, `Quantum and Thermal Effects in H2 Dissociative Adsorption: Evaluation of Free Energy Barriers in Multidimensional Quantum Systems', Physical Review Letters, vol. 72, p. 1124 (1994). (abstract, article in pdf format)

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M. Villarba and H. Jónsson, `Low Temperature Homoepitaxial Growth of Pt(111) in Simulated Vapor Deposition', Phys. Rev. B vol. 49, p. 2208 (1994). (abstract, article in pdf format)

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A. Clarke and H. Jónsson, `Structural changes accompanying densification of random hard-sphere packings', Phys. Rev. E vol. 47, p. 3975 (1993). (abstract, article in pdf format)

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