Publications from the Jónsson research group

Citation overview in Google Scholar and in ResearcherID

Recent publications:

2024

'Decoherence and vibrational energy relaxation of the electronically excited PtPOP complex in solution', B. O. Birgisson, A. O. Dohn, H. Jónsson and G. Levi, J. Chem. Phys. (submitted).

'A Neural-Network-Based Selective Configuration Interaction Approach to Molecular Electronic Structure', Y. L. A. Schmerwitz, L. Thirion, G. Levi, E. Ö. Jónsson, P. Bilous, H. Jónsson and P. Hansmann, (submitted). Early manuscript available on arXiv at https://arxiv.org/pdf/2406.08154.

'From AC-STEM Image to 3D Structure: A Systematic Analysis of the Au55 nanocluster', K. S. Bersha, A. Pena-Torres and H. Jónsson, (submitted). Manuscript available on arXiv.

'Calculations of Ag Adatom Diffusion on Si(100) Reveal Fast Migration Along Dimer Rows and Explain Facile Dimer Formation at Low Temperature', A. Pena-Torres, M. Stamatakis and H. Jónsson, (submitted). Manuscript available on arXiv.

'Identification of Mechanisms of Magnetic Transitions Using an Efficient Method for Converging on First Order Saddle Points', M. Sallermann, H. Schrautzer, P. Bessarab and H. Jónsson, (submitted). Manuscript available on arXiv.

'Silver Electrodes Are Highly Selective for CO in CO2 Electroreduction due to Interplay between Voltage Dependent Kinetics and Thermodynamics', M. Re Fiorentin, F. Risplendi, C. Salvini, J. Zeng, G. Cicero and H. Jónsson, J. Phys. Chem. Letters 15, 11538 (2024). Manuscript available on arXiv.

'Doping-induced Enhancement of Hydrogen Evolution at MoS2 Electrodes', S. Hanslin, H. Jónsson and J. Akola, ChemPhysChem (in an issue honoring Jens K. Nørskov) 16, e202400349 (2024). Manuscript available on arXiv.

'Saddle Point Search Algorithms for Variational Density Functional Calculations of Excited Electronic States with Self- Interaction Correction', Y. L. A. Schmerwitz, N. O. Ollé, G. Levi and H. Jónsson, Proceedings of the Platform for Advanced Scientific Computing Conference, PASC '24, (Association for Computing Machinery, New York, NY, USA), article 19 (2024). Manuscript available on arXiv.

'Characterization of Deformational Isomerization Potential and Interconversion Dynamics with Ultrafast X-ray Solution Scattering', N. E. Powers-Riggs, B. O. Birgisson, S. L. Raj, et al., Journal of the American Chemical Society 146, 13962 (2024). Manuscript available on ChemRxiv.

'Single Atom Substituents in Copper Surfaces May Adsorb Multiple CO Molecules', M. A. H. Christiansen, A. Pena-Torres, E. Ö. Jónsson, and H. Jónsson, J. Phys. Chem. Letters 15, 5654 (2024). Manuscript available on arXiv.

'GPAW: Open Python Package for Electronic-structure Calculations', J. J. Mortensen, A. H. Larsen, M. Kuisma, A. V. Ivanov, et al., J. Chem. Phys. 160, 092503 (2024). Manuscript available on arXiv.

'Evidence of Sharp Transitions Between Octahedral and Capped Trigonal Prism States of the Solvation Shell of Fe+3(aq)', A. Goswami, A. Pena-Torres, E. Ö. Jónsson, S. A. Egorov, and H. Jónsson, J. Chem. Phys. Letters 15, 4523 (2024). Manuscript available on arXiv.

'Improved Initialisation of Optimal Path Calculations Using Sequential Traversal over the Image Dependent Pair Potential Surface', Y. L. A. Schmerwitz, V. Ásgeirsson and H. Jónsson, J. Chem. Theory Comput. 20, 155 (2024). Manuscript available on arXiv.

2023

'Sulfur-deficient Edges as Active Sites for Hydrogen Evolution on MoS2', S. Hanslin, H. Jónsson and J. Akola, Phys. Chem. Chem. Phys. 25, 32541 (2023). Open access.

'Orbital-optimized Density Functional Calculations of Molecular Rydberg Excited States with Real Space Grid Representation and Self-Interaction Correction', A. E. Sigurdarson, Y. L. A. Schmerwitz, D. K. V. Tveiten, G. Levi and H. Jónsson, J. Chem. Phys. 159, 214109 (2023), John P. Perdew festschrift. Manuscript available on arXiv.

'Electronic Excitations of the Charged Nitrogen-Vacancy Center in Diamond Obtained Using Time-Independent Variational Density Functional Calculations', A. V. Ivanov, Y. L. A. Schmerwitz, G. Levi and H. Jónsson, SciPost Physics 15, 009 (2023). Manuscript available on arXiv.

'Calculations of Excited Electronic States by Converging on Saddle Points Using Generalized Mode Following', Y. L. A. Schmerwitz, G. Levi and H. Jónsson, J. Chem. Theory Comput. 19, 3634 (2023). Manuscript available on arXiv.

'Is Doped MoS2 Basal Plane an Efficient Hydrogen Evolution Catalyst? Calculations of Voltage-Dependent Activation Energy', S. Hanslin, H. Jónsson and J. Akola, Phys. Chem. Chem. Phys. 25, 15162 (2023). Manuscript available on arXiv.

'On the Challenge of Obtaining an Accurate Solvation Energy Estimate in Simulations of Electrocatalysis', B. Kirchhoff, E. Ö. Jónsson, T. Jacob and H. Jónsson, Topics in Catalysis, 66, 1244 (2023). Open access.

'Stability of Magnetic Skyrmions: Systematic Calculations of the Effect of Size from Nanometer Scale to Microns', M. N. Potkina, I. S. Lobanov, H. Jónsson and V. M. Uzdin, Phys. Rev. B 107, 184414 (2023). Manuscript available on arXiv.

'A General-purpose Machine Learning Pt Interatomic Potential for an Accurate Description of Bulk, Surfaces and Nanoparticles', J. Kloppenburg, L. B. Pártay, H. Jónsson and M. A. Caro, J. Chem. Phys. 158, 134704 (2023). Manuscript available on arXiv.

'Electric Field Induced Release of Guest Molecules from Clathrate Hydrates and Its Consequences for Electrochemical CO2 Conversion', M. Lyu, Z. Li, M. Van den Bossche, H. Jónsson and C. Rose-Petruck, Chemical Physics 568, 111839 (2023). Manuscript available on ChemRxiv.

'Stability of Hopfions in Bulk Magnets with Competing Exchange Interactions', M. Sallermann, H. Jónsson and S. Blügel, Phys. Rev. B 107, 104404 (2023). Manuscript available on arXiv.

2022

'New Insights Into the Volume Isotope Effect of Ice Ih From Polarizable Many-Body Potentials', S. Rasti, E. Ö. Jónsson, H. Jónsson and J. Meyer, J. Phys. Chem. Letters 13, 11831 (2022). Open source.

'Development of a Polarizable Force Field for Acetonitrile Based on a Single-Center Multipole Expansion', H. Myneni, E. Ö. Jónsson, H. Jónsson and A. O. Dohn, J. Phys. Chem. B 126, 9339 (2022). Manuscript available on ChemRxiv.

'Transferable Potential Function for Flexible H2O Molecules Based on the Single Center Multipole Expansion', E. Ö. Jónsson, S. Rasti, M. Galynska, J. Meyer and H. Jónsson, J. Chem. Theory Comput. 18, 7528 (2022). Manuscript available on arXiv.

'Kinetic Monte Carlo Simulation Studies of the Shape of Islands on Close-packed Surfaces', G. S. Sun and H. Jónsson, Journal of the Electrochemical Society 169, 102503 (2022).

'Reassignment of Magic Numbers for Icosahedral Au Clusters: 310, 564, 928 and 1426', J. Kloppenburg, A. Pedersen, K. Laasonen, M. Caro and H. Jónsson, Nanoscale, 14, 9053 (2022).

'Simulations of the Electrochemical Oxidation of Pt Nanoparticles of Various Shapes', B. Kirchhoff, C. Jung, H. Jónsson, D. Fantauzzi and T. Jacob. J. Phys. Chem. C 126, 6773 (2022). Manuscript available on arXiv.

'Variational Density Functional Calculations of Excited States: Conical Intersection and Avoided Crossing in Ethylene Bond Twisting', Y. L. A. Schmerwitz, A. V. Ivanov, E. Ö. Jónsson, H. Jónsson and Gianluca Levi, J. Phys. Chem. Letters 13, 3990 (2022). Manuscript available on arXiv.

'Indirect Mechanism of Au adatom Diffusion on the Si(100) Surface', A. Pena-Torres, A. Ali, M. Stamatakis and H. Jónsson, Phys. Rev. B 105, 205411 (2022). Manuscript available on arXiv.

'Mechanism of Interlayer Transport on a Growing Au(111) Surface: 2D vs. 3D Growth', A. Ali and H. Jónsson, Surfaces and Interfaces 31, 101944 (2022).

'Lifetime of Skyrmions in Discrete Systems with Infinitesimal Lattice Constant', M. N. Potkina, I. S. Lobanov, H. Jónsson and V. M. Uzdin, Journal of Magnetism and Magnetic Materials 549, 168974 (2022). Manuscript available on arXiv.

2021

'Observation of Electric-Field-Induced Liberation of Guest Molecules From Clathrate Hydrate', Z. Li, M. Lyu, H. Jónsson and C. Rose-Petruck, J. Phys. Chem. Letters 12, 10410 (2021).

'Elastic Collision Based Dynamic Partitioning Scheme for Hybrid Simulations', B. Kirchhoff, E. Ö. Jónsson, A. O. Dohn, T. Jacob and H. Jónsson, J. Chem. Theory Comput. 17, 5863 (2021). Manuscript available on arXiv.

'Assessment of the Accuracy of Density Functionals for Calculating Oxygen Reduction Reaction on Nitrogen Doped Graphene', B. Kirchhoff, A. Ivanov, E. Skúlason, D. Fantauzzi, T. Jacob and H. Jónsson, J. Chem. Theory Comput. 17, 6405 (2021). Manuscript available on arXiv.

'Nudged Elastic Band Method for Molecular Reactions Using Energy-Weighted Springs Combined with Eigenvector Following', V. Ásgeirsson, B. O. Birgisson, R. Bjornsson, U. Becker, F. Neese, C. Riplinger and H. Jónsson, J. Chem. Theory Comput. 17, 4929 (2021). Manuscript available on arXiv.

'Method for Calculating Excited Electronic States Using Density Functionals and Direct Orbital Optimization with Real Space Grid or Plane-Wave Basis Set', A. V. Ivanov, G. Levi, E. Ö. Jónsson and H. Jónsson, J. Chem. Theory Comput. 17, 5034 (2021). Manuscript available on arXiv.

'Mn Dimer can be Described Accurately with Density Functional Calculations when Self-interaction Correction is Applied', A. V. Ivanov, T. Ghosh, E. Ö. Jónsson and H. Jónsson, J. Phys. Chem. Letters 12, 4240 (2021). Manuscript available on arXiv.

'Direct Energy Minimization Based on Exponential Transformation in Density Functional Calculations of Finite and Extended Systems', A. V. Ivanov, E. Ö. Jónsson, T. Vegge and H. Jónsson, Computer Physics Communications 267, 108047 (2021). Manuscript available on arXiv.

'Competing HCOOH and CO Pathways in CO2 Electroreduction at Copper Electrodes: Calculations of Voltage Dependent Activation Energy', M. Van den Bossche, C. Rose-Petruck, and H. Jónsson, J. Phys. Chem. C 125, 13802 (2021).

'Localized and Delocalized States of a Diamine Cation: Resolution of a Controversy', M. Galynska, H. Jónsson and R. Björnsson, Journal of Physical Chemistry Letters 12, 1250 (2021). Open access.

'Fast and Robust Algorithm for the Energy Minimization of Spin Systems Applied to Analysis of High Temperature Spin Configurations in Terms of Skyrmion Density', A. V. Ivanov, V. M. Uzdin and H. Jónsson, Comp. Phys. Commun. 260, 107749 (2021). Manuscript available on arXiv.

2020

'Variational Density Functional Calculations of Excited States via Direct Optimization', G. Levi, A. V. Ivanov and H. Jónsson, J. Chem. Theo. Comput. 16, 6968 (2020). Manuscript available on arXiv.

'Skyrmions in Antiferromagnets: Thermal Stability and the Effect of External Field and Impurities', M. N. Potkina, I. S. Lobanov, H. Jónsson and V. M. Uzdin, Journal of Applied Physics 127, 213906 (2020). Manuscript available on arXiv.

'Variational Calculations of Excited States via Direct Optimization of the Orbitals in DFT', G. Levi, A. V. Ivanov and H. Jónsson, Faraday Discussions 224, 448 (2020). Available on journal web site.

'Stability of Long-lived Antiskyrmions in Mn-Pt-Sn Tetragonal Heusler Material', M. N. Potkina, I. S. Lobanov, O. A. Tretiakov, H. Jónsson and V. M. Uzdin, Phys. Rev. B 102, 134430 (2020). Manuscript available on arXiv.

'Magnetic Skyrmion Annihilation by Quantum Mechanical Tunneling', S. M. Vlasov, P.F. Bessarab, I. S. Lobanov, M. N. Potkina, V. M. Uzdin and H. Jónsson, New Journal of Physics 22, 083013 (2020). Manuscript available on journal web site.

'Coupled Quasi-Monopoles in Chiral Magnets', G.P. Müller, F.N. Rybakov, H. Jónsson, S. Blügel and N.S. Kiselev, Phys. Rev. B 101, 184405 (2020). Manuscript available on arXiv.

'NWChem: Past, Present, and Future', E. Aprà, E. J. Bylaska, W. A. de Jong, et al. J. Chem. Phys. 152, 184102 (2020). Accepted manuscript.

'Efficient Optimization Method for Finding Minimum Energy Paths of Magnetic Transitions', A. V. Ivanov, D. Dagbartsson, J. Tranchida, M. Uzdin and H. Jónsson, Journal of Physics: Condensed Matter 32, 345901 (2020). Manuscript available on arXiv.

'Fully Self-Consistent Calculations of Magnetic Structure Within Non-collinear Alexander-Anderson Model', A. V. Ivanov, P. F. Bessarab, V. M. Uzdin and H. Jónsson, Nanosystems: Physics, Chemistry, Mathematics 11, 65 (2020). Open access at journal web site.

'Atomic and Electronic Structure of a Vacancy in Amorphous Silicon', A. Pedersen, L. Pizzagalli and H. Jónsson, Phys. Rev. B 101, 054204 (2020). Manuscript available on arXiv.

'Minimum Mode Saddle Point Searches Using Gaussian Process Regression with Inverse-distance Covariance Function', O-P. Koistinen, V. Ásgeirsson, A. Vehtari and H. Jónsson. J. Chem. Theo. Comput. 16, 499 (2020). Manuscript available on ChemRxiv.

'On the Role of Solvent and Methyl Substituents in the Excited-State Dynamics of a Copper Phenanthroline Photosensitizer', G.Levi, E. Biasin, A. O. Dohn, and H. Jónsson. Phys. Chem. Chem. Phys. 22, 748 (2020). Manuscript available at OpinVisindi.

2019

'Effect of H adsorption on the Magnetic Properties of an Fe Island on a W(110) Surface', M. Melander and H. Jónsson. Phys Rev. B 100, 174431 (2019). Manuscript available on ChemRxiv.

'Simulations of the Oxidation and Degradation of Platinum Electrocatalysts', B. Kirchhoff, L. Braunwarth, H. Jónsson, D. Fantauzzi and T. Jacob. Small 15, 1905159 (2019).

'Polarizable Embedding with a Transferable H2O Potential Function I: Formulation and Tests on Dimer', E.Ö. Jónsson, A. O. Dohn, and H. Jónsson. J. Chem. Theo. Comput. 15, 6562(2019). Manuscript available on ChemRxiv.

'Polarizable Embedding with a Transferable H2O Potential Function II: Application to (H2O)n Clusters and Liquid Water', A. O. Dohn, E. Ö. Jónsson and H. Jónsson. J. Chem. Theo. Comput. 15, 6578 (2019). Manuscript available on ChemRxiv.

'Nudged Elastic Band Calculations Accelerated with Gaussian Process Regression Based on Inverse Inter-atomic Distances', O-P. Koistinen, V. Ásgeirsson, A. Vehtari and H. Jónsson. J. Chem. Theo. Comput. 15, 6738 (2019). Manuscript available on ChemRxiv.

'Elucidation of Temperature-programmed Desorption of High-coverage Hydrogen on Pt(211), Pt(221), Pt(533) and Pt(553) based on Density Functional Theory Calculations', M. J. Kolb, A. L. Garden, C. Badan, E. Skúlason, L. B.F. Juurlink, H Jónsson and M. T. M. Koper. Phys. Chem. Chem. Phys. 21, 17142 (2019).

'Spirit: Multifunctional Framework for Atomistic Spin Simulations', G.P. Müller, M. Hoffmann, C. Disselkamp, D. Schürhoff, S. Mavros, M. Sallermann, N.S. Kiselev, H. Jónsson and S. Blügel. Phys. Rev. B 99, 224414 (2019). Manuscript available on arXiv.

'R-NEB: Accelerated Nudged Elastic Band Calculations by use of Reflection Symmetry', Nicolai R. Mathiesen, Hannes Jónsson, Tejs Vegge and Juan Maria García Lastra. J. Chem. Theo. Comput. 15, 3215 (2019).

'Assessment of Constant-potential Implicit Solvation Calculations of Electrochemical Energy Barriers', Maxime Van den Bossche, Egill Skúlason, Christoph Rose-Petruck and Hannes Jónsson. J. Phys. Chem. C 123, 4116 (2019). Manuscript available on ChemRxiv.

'Addition to "Assessment of Constant-Potential Implicit Solvation Calculations of Electrochemical Energy Barriers for H2 Evolution on Pt"', Maxime Van den Bossche, Egill Skúlason, Christoph Rose-Petruck and Hannes Jónsson. J. Phys. Chem. C 123, 15875 (2019). Open access at journal site.

'Density Functional Theory Calculations and Thermodynamic Analysis of the Forsterite Mg2SiO4(010) Surface', Ming Geng and Hannes Jónsson. J. Phys. Chem. C 123, 464 (2019). Manuscript available on arXiv.

'Determination of the Structure and Properties of an Edge Dislocation in Rutile TiO2', Emile Maras, Mitsuhiro Saito, Kazutoshi Inoue, Hannes Jónsson, Yuichi Ikuhara and Keith P. McKenna. Acta Materialia 163, 199 (2019). Open access at journal site.

'Density Functional Theory Calculation and Thermodynamic Analysis of the Bridgmanite Surface Structure', Ming Geng and Hannes Jónsson. Phys. Chem. Chem. Phys. 21, 1009 (2019). Manuscript available on arXiv.

2018

'Models of the Energy Landscape Characterizing an Element of a Shakti Spin Lattice', Unnar B. Arnalds, Sergi Y. Liashko, Pavel F. Bessarab, Valery M. Uzdin and Hannes Jónsson, Nanosystems: Physics, Chemistry Mathematics 9, 711 (2018).

'Reply to ‘The Diamine Cation Is Not a Chemical Example Where Density Functional Theory Fails‘', Xinxin Cheng, Elvar Jónsson, Hannes Jónsson and Peter M. Weber, Nature Communications 9, 5348 (2018). Open access at journal site.

'Duplication, Collapse and Escape of Magnetic Skyrmions Revealed Using a Systematic Saddle Point Search Method', G. P. Müller, P.F. Bessarab, S. M. Vlasov, F. Lux, N. S. Kiselev, V. M. Uzdin, S. Blügel and H. Jónsson, Phys. Rev. Letters 121, 197202 (2018). Manuscript available on arXiv.

'Exploring Potential Energy Surfaces with Saddle Point Searches', V. Ásgeirsson and H. Jónsson, chapter in "Handbook of Materials Modeling. Volume 1 Methods: Theory and Modeling, page 689" (Springer, 2018).

'Long-timescale Simulations: Challenges, Pitfalls, Best Practices, for Development and Applications', G. Henkelman, H. Jónsson, T. Leliévre, N. Mousseau and A. Voter, chapter in "Handbook of Materials Modeling. Volume 1 Methods: Theory and Modeling, page 825" (Springer, 2018).

'Reassignment of ''Magic Numbers'' for Au Clusters of Decahedral and FCC Structural Motifs', A.L. Garden, A. Pedersen and H. Jónsson, Nanoscale 10, 5124 (2018).

'Calculations of Product Selectivity in Electrochemical CO2 Reduction', J. Husssain, H. Jónsson and E. Skúlason, ACS Catalysis 8, 5240 (2018). Open access at journal site.

'Lifetime of Racetrack Skyrmions', P.F. Bessarab, G.P. Müller, I.S. Lobanov, F.N. Rybakov, N.S. Kiselev, H. Jónsson, V.M. Uzdin, S. Blügel, L. Bergqvist and A. Delin, Scientific Reports, 8, 3433 (2018). Open access at journal site.

'The Effect of Confinement and Defects on the Thermal Stability of Skyrmions', V. M. Uzdin, M. N. Potkina, I. S. Lobanov, P. F. Bessarab, H. Jónsson, Physica B 549, 6 (2018). Manuscript available on arXiv.

'Energy Surface and Lifetime of Magnetic Skyrmions', V.M. Uzdin, M.N. Potkina, I.S. Lobanov, P.F. Bessarab, H. Jónsson, Journal of Magnetism and Magnetic Materials 459, 236 (2018). Manuscript available on arXiv.

'Efficient Evaluation of Atom Tunneling Combined with Electronic Structure Calculations', V. Ásgeirsson, A. Arnaldsson and H. Jónsson, J. Chem. Phys. 148, 102334 (2018).

2017

'Calculations of switching field and energy barrier for magnetic islands with perpendicular anisotropy', S. Y. Liashko, H. Jónsson and V.M. Uzdin, Nanosystems: Physics, Chemistry, Mathematics 8, 701 (2017). Open access at journal site.

'Instantons describing tunneling between magnetic states at finite temperature', S.M. Vlasov, P.F. Bessarab, V.M. Uzdin and H. Jónsson, Nanosystems: Physics, Chemistry, Mathematics 8, 746 (2017). Open access at journal site.

'Nanocluster structure deduced from AC-STEM images coupled to theoretical modelling', K. Sukuta, M. V. d. Bossche, A. Pedersen and H. Jónsson, Nanosystems: Physics, Chemistry, Mathematics 8, 723 (2017). Open access at journal site.

'A Real-Space Grid Implementation of QM/MM Electrostatic Embedding and Application to a Solvated Diplatinum Complex', A.O. Dohn, E.Ö. Jónsson, G. Levi, J.J. Mortensen, O. Lopez-Acevedo, K.S. Thygesen, K.W. Jacobsen, J. Ulstrup, N. E. Henriksen, K.B. Møller and H. Jónsson, J. Chem. Theo. Comput. 13, 6010 (2017).

'Thermal stability of magnetic states in submicron magnetic islands', S. Y. Liashko, I.S. Lobanov, V.M. Uzdin and H. Jónsson, Nanosystems: Physics, Chemistry, Mathematics 8, 572 (2017). Open access at journal site.

'Truncated minimum energy path method for finding first order saddle points', I.S. Lobanov, M.N. Potkina, H. Jónsson and V.M. Uzdin, Nanosystems: Physics, Chemistry, Mathematics, 8, 586 (2017). Open access at journal site.

'First-principles Green's-function method for surface calculations: a pseudopotential localized basis set approach', S. Smidstrup, D. Stradi, J. Wellendorff, P.A. Khomyakov, U.G. Vej-Hansen, M-E. Lee, T. Ghosh, E. Jónsson, H. Jónsson, K. Stokbro, Phys. Rev. B 96, 195309 (2017). Manuscript available on arXiv.

'The effect of temperature and external field on transitions in elements of kagome spin ice', S. Y. Liashko, H Jónsson and V. M. Uzdin, New Journal of Physics 19, 113008 (2017). Open access at journal site.

'Coherence in Nonradiative Transitions: Internal Conversion in Rydberg-Excited N-Methyl and N-Ethyl Morpholine', Y. Zhang, H. Jónsson and P. M. Weber, Physical Chemistry Chemical Physics 19, 26403 (2017).

'Ultrafast X-ray Absorption Study of Longitudinal-Transverse Phonon Coupling in Electrolyte Aqueous Solution', Y. Jiao, B.W. Adams, A.O. Dohn, C.B. Müller, H. Jónsson and C. Rose-Petruck, Physical Chemistry Chemical Physics 19, 27266 (2017).

'Atomic Scale Formation Mechanism of Edge Dislocation Relieving Lattice Strain in a GeSi overlayer on Si(001)', E. Maras, L. Pizzagalli, T. Ala-Nissila and H. Jónsson, Scientific Reports 7, 11966 (2017). Open access at journal site.

'Calculations of the onset temperature for tunneling in multispin systems', S.M. Vlasov, P.F. Bessarab, V.M. Uzdin and H. Jónsson, Nanosystems: Physics, Chemistry, Mathematics, 8, 454 (2017). Open access at journal web site.

'Magnetic exchange force microscopy: Theoretical analysis of induced magnetization reversals', A. Ivanov, P.F. Bessarab, V.M. Uzdin and H. Jónsson, Nanoscale 9, 13320 (2017). Open access at journal site.

'Nudged Elastic Band Calculations Accelerated with Gaussian Process Regression', O-P. Koistinen, F. Dagbjartsdóttir, V. Ásgeirsson, A. Vehtari, and H. Jónsson, J. Chem. Phys. 147, 152720 (2017). Manuscript available on arXiv.

'An Observation of Structural Wavepacket Motion: the Umbrella Mode in Rydberg-Excited N-Methyl Morpholine', Y. Zhang, S. Deb, H. Jónsson and P.M. Weber, J. Phys. Chem. Letters 8, 3740 (2017).

'Energy surface and transition rates in a hexagonal element of spin ice', S. Y. Liashko, V. M. Uzdin and H Jónsson, Journal of Physics: Conf. Ser. 903, 012006 (2017). Open access at journal site.

'Optimal atomic structure of amorphous silicon obtained from density functional theory calculations', A. Pedersen, L. Pizzagalli and H. Jónsson, New Journal of Physics 19, 063018 (2017). Open access at journal website.

'Atomic scale simulations of heterogeneous electrocatalysis: recent advances', E. Skúlason and H. Jónsson, Advances in Physics X 2, 481 (2017). Open access at journal site.

'Theory and Applications of Generalized Pipek−Mezey Wannier Functions', E.Ö. Jónsson, S. Lehtola, M. J. Puska and H. Jónsson, Journal of Chemical Theory and Computation 13, 460 (2017). Manuscript available on arXiv.

'Long-timescale simulations of tunneling-assisted diffusion of hydrogen on ice surfaces at low temperature', V. Ásgeirsson, H. Jónsson and K. Th. Wikfeldt, J. Phys. Chem. C. 121, 1648 (2017).

'Improved Minimum Mode Following Method for Finding First Order Saddle Points', M.P. Gutiérrez, C. Argáez and H. Jónsson, Journal of Chemical Theory and Computation 13, 125 (2017). See journal web site.

2016

'Minimum energy path calculations with Gaussian process regression', O-P. Koistinen, E. Maras, A. Vehtari, H. Jónsson. Nanosystems: Physics, Chemistry, Mathematics, 7, 925 (2016). pdf file.

'Mechanism and activation energy of magnetic skyrmion annihilation obtained from minimum energy path calculations', I. Lobanov, H. Jónsson and V. M. Uzdin. Phys. Rev. B 94, 174418 (2016). Available at journal web site.

'Crossover temperature for quantum tunnelling in spin systems', S. Vlasov, P. F. Bessarab, V. M. Uzdin and H. Jónsson. Journal of Physics: Conf. Ser. 741, 012183 (2016). Open access at journal web site.

'Tip-surface interaction and rate of magnetic transitions', A. V. Ivanov, P. F. Bessarab, V. M. Uzdin and H Jónsson. Journal of Physics: Conf. Ser. 741, 012184 (2016). Open access at journal web site.

'Rate of thermal transitions in kagome spin ice', S. Y. Liashko, V. M. Uzdin and H Jónsson, Journal of Physics: Conf. Ser. 741, 012182 (2016). Open access at journal site.

'Efficient dynamical correction of the transition state theory rate estimate for a flat energy barrier', H. Mökkönen, T. Ala-Nissila and H. Jónsson, J. Chem. Phys. 145, 094901 (2016), manuscript.

'The effect of complex-valued optimal orbitals on atomization energies with the Perdew–Zunger self-interaction correction to density functional theory', S. Lehtola, E.Ö. Jónsson, and H. Jónsson, Journal of Chemical Theory and Computation 12, 4296 (2016). See journal site.

'Classical to Quantum Mechanical Tunneling Mechanism Crossover in Thermal Transitions Between Magnetic States', S. Vlasov, P. F. Bessarab, V. Uzdin and H. Jónsson, Faraday Discussions of the Royal Society 195, 93 (2016). Open access at journal site.

'Faraday efficiency and mechanism of electrochemical surface reactions: CO2 reduction and H2 formation on Pt(111)', J. Hussain, H. Jónsson and Egill Skúlason, Faraday Discussions of the Royal Society 195, 619 (2016).

'Complex orbitals, multiple local minima and symmetry breaking in Perdew-Zunger self-interaction corrected density-functional theory calculations', S. Lehtola, M. Head-Gordon and H. Jónsson, Journal of Chemical Theory and Computation 12, 3195 (2016).

'Self-Interaction Corrected Functional Calculations of a Dipole-Bound Molecular Anion', Y. Zhang, P.M. Weber and H. Jónsson, J. Phys. Chem. Letters 7, 2068 (2016). See journal site.

'Charge Localization in a diamine cation: A rigorous test of energy functionals for electronic systems', X. Cheng, Y. Zhang, E.Ö. Jónsson, H. Jónsson and P.M. Weber, Nature Communications 7, 11013 (2016). Open access at journal site.

'Global transition path search for dislocation formation in Ge on Si(001)', E. Maras, O. Trushin, A. Stukowski, T. Ala-Nissila and H. Jónsson, Computer Physics Communications 205, 13 (2016). Manuscript available on arXiv.

'Qualitative Insight and Quantitative Analysis of the Effect of Temperature on the Coercivity of a Magnetic System', M. Moskalenko, P.F. Bessarab, V.M. Uzdin and H. Jónsson, AIP Advances 6, 025213 (2016). Open access at journal site.

'Minimum energy path for the nucleation of misfit dislocations in Ge/Si(100) heteroepitaxy', O. Trushin, E. Maras, A. Stukowski, E. Granato, S.C. Ying, H. Jónsson and T. Ala-Nissila, Modelling and Simulation in Materials Science and Engineering 24, 035007 (2016). Manuscript available on arXiv.

2015

'Computational Study of Electrochemical CO2 Reduction at Transition Metal Electrodes', J. Hussain, E. Skúlason and H. Jónsson, Procedia Computer Science 51, 1865 (2015). Open access at journal website.

'Calculations of Al dopant in alpha-quartz using a variational implementation of the Perdew-Zunger self-interaction correction', H. Gudmundsdóttir, E. Ö. Jónsson and H. Jónsson, New Journal of Physics 17, 083006 (2015). Open access at journal website.

'Towards an optimal gradient-dependent energy functional of the PZ-SIC form', E.Ö. Jónsson, S. Lehtola and H. Jónsson, Procedia Computer Science 51, 1858 (2015). Open access at journal website.

'Corrigendum to diffusion and island formation on the ice Ih basal plane surface', E.R. Batista and H. Jónsson, Computational Materials Science 102, 338 (2015), pdf file.

'Method for finding mechanism and activation energy of magnetic transitions, applied to skyrmion and antivortex annihilation', P.F. Bessarab, V.M. Uzdin and H. Jónsson, Computer Physics Communications 196, 335 (2015), DOI: 10.1016/j.cpc.2015.07.001. Manuscript available on arXiv.

'Long-timescale simulations of H2O admolecule diffusion on Ice Ih(0001) surfaces', A. Pedersen, L.J. Karssemeijer, H. M. Cuppen and H. Jónsson, J. Phys. Chem. C 119, 16528 (2015). Manuscript available on arXiv.

'Transition state theory approach to polymer escape from a one dimensional potential well', H. Mökkönen, T. Ikonen, T. Ala-Nissila and H. Jónsson, J. Chem. Phys. 142, 224906 (2015), Manuscript available on arXiv.

'Improved tight-binding charge transfer model and calculations of energetics of a step on rutile TiO2(110) surface', E. Maras, N. Salles, R. Tétot,T. Ala-Nissila, and H. Jónsson, J. Phys. Chem. C 119, 10391 (2015), manuscript.

'The ultrafast structural pathway of charge transfer in N, N, N’, N’-tetramethylethylenediamine', X. Cheng, Y. Zhang, Y. Gao, H. Jónsson and P.M. Weber, J. Phys. Chem. A 119, 2813 (2015), manuscript.

'Removing external degrees of freedom from transition state search methods using quaternions', M. Melander, K. Laasonen, and H. Jónsson, Journal of Chemical Theory and Computation 11, 1055 (2015). Manuscript available on arXiv.

'Magic-number gold nanoclusters with diameter 1 to 3.5 nm: Relative stability and catalytic activity for CO oxidation', H. Li, L. Li, A. Pedersen, Y. Gao, N. Khetrapal, H. Jónsson and X.C. Zeng, Nano Letters 15, 682 (2015), (manuscript).

2014

'Molecular reordering processes on ice (0001) surfaces from long timescale simulations', A. Pedersen, K. Th. Wikfeldt, L.J. Karssemeijer, H. M. Cuppen and H. Jónsson, J. Chem. Phys. 141, 234706 (2014), (manuscript in pdf format on arXiv).

'Self-interaction corrected density functional calculations of Rydberg states of molecular clusters: N,N-dimethylisopropylamine', H. Gudmundsdóttir, Y. Zhang, P. M. Weber and H. Jónsson, J. Chem. Phys. 141, 234308 (2014), (manuscript in pdf format).

'Navigation on the energy surface of the noncollinear Alexander-Anderson model', P. F. Bessarab, V. M. Uzdin and H. Jónsson, Nanosystems: Physics, Chemistry, Mathematics 5, 757 (2014), published article.

'Variational, self-consistent implementation of the Perdew–Zunger self-interaction correction with complex optimal orbitals', S. Lehtola and H. Jónsson, Journal of Chemical Theory and Computation 10, 5324 (2014), manuscript in pdf format. Erratum: Figure 2b got misplaced and is simply the same as figure 2c in the published article. An erratum with the correct figure 2 is here, Erratum.

'Adsorption of Water Dimer on Platinum(111): Identification of the –OH···Pt Hydrogen Bond', K. Motobayashi, L. Árnadóttir, C. Matsumoto, E. M. Stuve, H. Jónsson, Y. Kim and M. Kawai, ACS Nano 8, 11583 (2014), manuscript in pdf format.

'Ultrafast Structural Dynamics in Rydberg Excited N,N,N',N'- Tetramethylethylenediamine: Conformation Dependent Electron Lone Pair Interaction and Charge Delocalization', X. Cheng, Y. Zhang, S. Deb, M.P. Minitti, Y. Gao, H. Jónsson and P.M. Weber, Chemical Science 5, 4394 (2014), preprint in pdf format.

'Effect of Magnetic States on the Reactivity of FCC(111) Iron Surface' M. Melander, K. Laasonen, and H. Jónsson, J. Phys. Chem. C 118, 15863 (2014), manuscript in pdf format.

'Improved initial guess for minimum energy path calculations', S. Smidstrup, A. Pedersen, K. Stokbro and H. Jónsson, J. Chem. Phys. 140, 214106 (2014), manuscript on arXiv)).

'Calculations of magnetic states and minimum energy paths of transitions using a non-collinear extension of the Alexander-Anderson model and a magnetic force theorem', P. F. Bessarab, V. M. Uzdin and H. Jónsson, Phys. Rev. B 89, 214424 (2014), manuscript in pdf format.

'EON: Software for long time simulations of atomic scale systems', S.T. Chill, M. Welborn, R. Terrell, L. Zhang, J-C. Berthet, A. Pedersen, H. Jónsson and G. Henkelman, Modelling and Simulation in Materials Science and Engineering 22, 055002 (2014), manuscript in pdf format.

'Polymer escape from a confining potential', Harri Mökkönen, Timo Ikonen, Hannes Jónsson and Tapio Ala-Nissila, J. Chem. Phys. 140, 054907 (2014), manuscript in pdf format.

'Pipek–Mezey orbital localization using various partial charge estimates', S. Lehtola and H. Jónsson, Journal of Chemical Theory and Computation 10, 642 (2014), manuscript in pdf format.

'Catalytic activity of Pt nano-particles for H2 formation', E. Skúlason, A.A. Faraj, L. Kristinsdóttir, J. Hussain, A.L. Garden and H. Jónsson, Topics in Catalysis 57, 273 (2014), manuscript in pdf format, the final publication is available here .

'Geothermal model calibration using a global minimization algorithm based on finding saddle points as well as minima of the objective function', M. Plasencia, A. Pedersen, A. Arnaldsson, J-C. Berthet and H. Jónsson, Computers and Geosciences 65, 110 (2014), manuscript in pdf format, published version.

2013

'The Effect of Hydrogen Adsorption on the Magnetic Properties of a Surface Nanocluster of Iron', P. F. Bessarab, V. M. Uzdin and H. Jónsson, Physical Review B 88, 214407 (2013), (manuscript in pdf format, published version).

'Unitary Optimization of Localized Molecular Orbitals', S. Lehtola and H. Jónsson, Journal of Chemical Theory and Computation 9, 5365 (2013), (manuscript in pdf format).

'Self-interaction corrected density functional calculations of molecular Rydberg states', H. Gudmundsdóttir, Y. Zhang, P. M. Weber and H. Jónsson, J. Chem. Phys. 139, 194102 (2013), (manuscript in pdf format).

'A Transferable H2O Interaction Potential Based on a Single Center Multipole Expansion: SCME', K. T. Wikfeldt, E. R. Batista, F. D. Vila and H. Jónsson, Physical Chemistry Chemical Physics 15, 16542 (2013), (manuscript in pdf format).

'Potential energy surfaces and rates of spin transitions', P. F. Bessarab, V. M. Uzdin and H. Jónsson, Zeitschrift fur Physikalische Chemie 227, 1543 (2013), (manuscript in pdf format).

'Dynamics of basaltic glass dissolution – Capturing microscopic effects in continuum scale models', E.S.P. Aradóttir, B. Sigfússon, E.L. Sonnenthal, G. Björnsson and H. Jónsson, Geochimica et Cosmochimica Acta 121, 311 (2013), (manuscript in pdf format).

'Hydrogen adsorption and desorption at the Pt(110)-(1x2) surface: experimental and theoretical study', S. Gudmundsdóttir, E. Skúlason, K-J. Weststrate, L. Juurlink and H. Jónsson, Physical Chemistry Chemical Physics 15, 6323 (2013), (manuscript in pdf format).

'Molecular rearrangement reactions in the gas phase triggered by electron attachment', B. Ómarsson, E. H. Bjarnason, S. A. Haughey, T. A. Field, A. Abramov, P. Klüpfel, H. Jónsson and O. Ingólfsson, Physical Chemistry Chemical Physics 15, 4754 (2013), (manuscript in pdf format).

'Size and Shape Dependence of Thermal Spin Transitions in Nanoislands', P. F. Bessarab, V. M. Uzdin and H. Jónsson, Phys. Rev. Letters 110, 020604 (2013), (manuscript in pdf format).


2012

'Local Density of States Analysis using Bader Decomposition for N2 and CO2 Adsorbed on Pt(110)-(1x2) Electrodes', S. Gudmundsdóttir, W. Tang, G. Henkelman, H. Jónsson and E. Skúlason, J. Chem. Phys. 137, 164705 (2012), (manuscript in pdf format).

'The effect of the Perdew-Zunger self-interaction correction to density functionals on the energetics of small molecules', S. Klüpfel, P. Klüpfel and H. Jónsson, J. Chem. Phys. 137, 124102 (2012), (manuscript in pdf format).

'Geothermal model calibration using a global minimization algorithm based on finding saddle points as well as minima of the objective function', M. Plasencia, A. Pedersen, A. Arnaldsson and H. Jónsson, Proceedings of THOUGH Symposium 2012, Lawrence Berkeley National Laboratory, Sept. (2012), (article in pdf format).

'Long-timescale simulations of diffusion in molecular solids', L.J. Karssemeijer, A. Pedersen, H. Jónsson and H.M. Cuppen, Phys. Chem. Chem. Phys. 14, 10844 (2012), (manuscript in pdf format).

'Harmonic Transition State Theory of Thermal Spin Transitions', P. F. Bessarab, V. M. Uzdin and H. Jónsson, Phys. Rev. B. 85, 184409 (2012), (manuscript in pdf format).

'The effect of coadsorbed water on the stability, configuration and interconversion of formyl (HCO) and hydroxymethylidyne (COH) on Pt(111)', L. Árnadóttir, E. M. Stuve and H. Jónsson, Chem. Phys. Letters 541, 32 (2012), (manuscript in pdf format).

'Reentrant mechanism for associative desorption: H2/Pt(110)-(1x2)', S. Gudmundsdóttir, E. Skúlason and H. Jónsson, Phys. Rev. Letters. 108, 156101 (2012), (manuscript in pdf format).

'Global Optimization of Reservoir Models by Mapping Out Object Function Minima and Saddle Points', M. Plasencia, A. Pedersen, A. Arnaldsson and H. Jónsson, Proceedings of the Thirty-Seventh Workshop on Geothermal Reservoir Engineering at Stanford University, Jan. 30 - Feb. 1 (2012), (manuscript in pdf format).

'Multidimensional reactive transport modeling of CO2 mineral sequestration in basalts at the Hellisheidi geothermal field, Iceland', E.S.P. Aradóttir, E.L. Sonnenthal, G. Björnsson and H. Jónsson, Int. J. Greenhouse Gas Control 9, 24 (2012), (manuscript in pdf format).

'Development and evaluation of a thermodynamic dataset for phases of interest in CO2 mineral sequestration in basaltic rocks', E.S.P. Aradóttir, E.L. Sonnenthal and H. Jónsson, Chemical Geology 304-305, 26 (2012), (manuscript in pdf format).

'A method for finding the ridge between saddle points applied to rare event rate estimates', J. B. Maronsson, H. Jónsson and T. Vegge, Phys. Chem. Chem. Phys. 14, 2884 (2012), (manuscript in pdf format).

'Adsorption of water monomer and clusters on platinum (111) terrace and related steps and kinks II. Surface diffusion', L. Árnadóttir, E. M. Stuve and H. Jónsson, Surface Science 606, 233 (2012), (manuscript in pdf format).

'A theoretical evaluation of possible transition metal electro-catalysts for N2 reduction', E. Skúlason, T. Bligaard, S. Gudmundsdóttir, F. Studt, J. Rossmeisl, F. Abild-Pedersen, T. Vegge, H. Jónsson and J.K. Nørskov, Phys. Chem. Chem. Phys. 14, 1235 (2012), (manuscript in pdf format).

'Path Optimization with Application to Tunneling', D.M. Einarsdóttir, A. Arnaldsson, F. Óskarsson and H. Jónsson, Lecture Notes in Computer Science 7134, 45 (2012), (manuscript in pdf format).

'Optimization of functionals of orthonormal functions in the absence of unitary invariance', P. J. Klüpfel, S. Klüpfel, K. Tsemekhman and H. Jónsson, Lecture Notes in Computer Science 7134, 23 (2012), (manuscript in pdf format).

'Simulated Annealing with Coarse Graining and Distributed Computing', A. Pedersen, J-C. Berthet and H. Jónsson, Lecture Notes in Computer Science 7134, 34 (2012), (manuscript in pdf format).

'Solar hydrogen production with semiconductor metal oxides: New directions in experiment and theory', Á. Valdés, J. Brillet, M. Grätzel, H. Gudmundsdóttir, H.A. Hansen, H. Jónsson, P. Klüpfel, G.-J. Kroes, F. Le Formal, I.C. Man, R.S. Martins, J.K. Nørskov, J. Rossmeisl, K. Sivula, A. Vojvodic and M. Zäch, Phys. Chem. Chem. Phys. 14, 49 (2012), (manuscript in pdf format).


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