List of Publications

  1. Preprints
  2. Peer-reviewed publications
  3. Other publications

Preprints

This includes preprints that have not been peer-reviewed and published.

  1. Antalík, A.; Levy, A.; Kvedaravičiūtė, S.; Johnson, S. K.; Carrasco-Busturia, D.; Raghavan, B.; Mouvet, F.; Acocella, A.; S., D.; Gavini, V.; Mandelli, D.; Ippoliti, E.; Meloni, S.; Carloni, P.; Rothlisberger, U.; Olsen, J. M. H. MiMiC: A High-Performance Framework for Multiscale Molecular Dynamics Simulations, 2024.

Peer-reviewed publications

  1. Carrasco-Busturia, D.; Ippoliti, E.; Meloni, S.; Rothlisberger, U.; Olsen, J. M. H. Multiscale Biomolecular Simulations in the Exascale Era. Curr. Opin. Struct. Biol. 2024, 86, 102821.
  2. Carrasco-Busturia, D.; Olsen, J. M. H. Polarizable Embedding Potentials through Molecular Fractionation with Conjugate Caps Including Hydrogen Bonds. J. Chem. Theory Comput. 2023, 19, 6510–6520.
  3. Kvedaravičiūtė, S.; Carrasco-Busturia, D.; Møller, K. B.; Olsen, J. M. H. Polarizable Embedding without Artificial Boundary Polarization. J. Chem. Theory Comput. 2023, 19, 5122–5141.
  4. Raghavan, B.; Schackert, F. K.; Levy, A.; Johnson, S. K.; Ippoliti, E.; Mandelli, D.; Olsen, J. M. H.; Rothlisberger, U.; Carloni, P. MiMiCPy: An Efficient Toolkit for MiMiC-Based QM/MM Simulations. J. Chem. Inf. Model. 2023, 63, 1406–1412.
  5. Wu, H.; Ma, Z.; Li, M.; Lu, H.; Tang, A.; Zhou, E.; Wen, J.; Sun, Y.; Tress, W.; Olsen, J. M. H.; Meloni, S.; Bo, Z.; Tang, Z. Impact of Donor Halogenation on Reorganization Energies and Voltage Losses in Bulk-Heterojunction Solar Cells. Energy Environ. Sci. 2023, 16, 1277–1290.
  6. Church, J. R.; Olsen, J. M. H.; Schapiro, I. Induction Effects on the Absorption Maxima of Photoreceptor Proteins. Biophysics and Physicobiology 2023, 20, e201007.
  7. Church, J. R.; Amoyal, G. S.; Borin, V. A.; Adam, S.; Olsen, J. M. H.; Schapiro, I. Deciphering the Spectral Tuning Mechanism in Proteorhodopsin: The Dominant Role of Electrostatics Instead of Chromophore Geometry. Chem. Eur. J. 2022, 28, e202200139.
  8. Church, J. R.; Olsen, J. M. H.; Schapiro, I. The Impact of Retinal Configuration on the Protein–Chromophore Interactions in Bistable Jumping Spider Rhodopsin-1. Molecules 2022, 27, 71.
  9. Kirsch, T.; Olsen, J. M. H.; Bolnykh, V.; Meloni, S.; Ippoliti, E.; Rothlisberger, U.; Cascella, M.; Gauss, J. Wavefunction-Based Electrostatic-Embedding QM/MM Using CFOUR through MiMiC. J. Chem. Theory Comput. 2022, 18, 13–24.
  10. Scheurer, M.; Reinholdt, P.; Olsen, J. M. H.; Dreuw, A.; Kongsted, J. Efficient Open-Source Implementations of Linear-Scaling Polarizable Embedding: Use Octrees to Save the Trees. J. Chem. Theory Comput. 2021, 17, 3445–3454.
  11. Dundas, K. O. H. M.; Beerepoot, M. T. P.; Ringholm, M.; Reine, S.; Bast, R.; List, N. H.; Kongsted, J.; Ruud, K.; Olsen, J. M. H. Harmonic Infrared and Raman Spectra in Molecular Environments Using the Polarizable Embedding Model. J. Chem Theory Comput. 2021, 17, 3599–3617.
  12. Mroginski, M.-A.; Adam, S.; Amoyal, G. S.; Barnoy, A.; Bondar, A.-N.; Borin, V. A.; Church, J. R.; Domratcheva, T.; Ensing, B.; Fanelli, F.; Ferré, N.; Filiba, O.; Pedraza-González, L.; González, R.; González-Espinoza, C. E.; Kar, R. K.; Kemmler, L.; Kim, S. S.; Kongsted, J.; Krylov, A. I.; Lahav, Y.; Lazaratos, M.; NasserEddin, Q.; Navizet, I.; Nemukhin, A.; Olivucci, M.; Olsen, J. M. H.; Alba Ortíz, A. Pérez de; Pieri, E.; Rao, A. G.; Rhee, Y. M.; Ricardi, N.; Sen, S.; Solov’yov, I. A.; De Vico, L.; Wesolowski, T. A.; Wiebeler, C.; Yang, X.; Schapiro, I. Frontiers in Multiscale Modeling of Photoreceptor Proteins. Photochem. Photobiol. 2021, 97, 243–269.
  13. Reinholdt, P.; Jørgensen, F. K.; Kongsted, J.; Olsen, J. M. H. Polarizable Density Embedding for Large Biomolecular Systems. J. Chem. Theory Comput. 2020, 16, 5999–6006.
  14. Capelli, R.; Lyu, W.; Bolnykh, V.; Meloni, S.; Olsen, J. M. H.; Rothlisberger, U.; Parrinello, M.; Carloni, P. Accuracy of Molecular Simulation-Based Predictions of k_off Values: A Metadynamics Study. J. Phys. Chem. Lett. 2020, 11, 6373–6381.
  15. Rossano-Tapia, M.; Olsen, J. M. H.; Brown, A. Two-Photon Absorption Cross-Sections in Fluorescent Proteins Containing Non-Canonical Chromophores Using Polarizable QM/MM. Front. Mol. Biosci. 2020, 7, 111.
  16. Olsen, J. M. H.; Reine, S.; Vahtras, O.; Kjellgren, E.; Reinholdt, P.; Hjorth Dundas, K. O.; Li, X.; Cukras, J.; Ringholm, M.; Hedegård, E. D.; Di Remigio, R.; List, N. H.; Faber, R.; Cabral Tenorio, B. N.; Bast, R.; Pedersen, T. B.; Rinkevicius, Z.; Sauer, S. P. A.; Mikkelsen, K. V.; Kongsted, J.; Coriani, S.; Ruud, K.; Helgaker, T.; Jensen, H. J. A.; Norman, P. Dalton Project: A Python Platform for Molecular- and Electronic-Structure Simulations of Complex Systems. J. Chem. Phys. 2020, 152, 214115.
  17. Saue, T.; Bast, R.; Gomes, A. S. P.; Jensen, H. J. A.; Visscher, L.; Aucar, I. A.; Di Remigio, R.; Dyall, K. G.; Eliav, E.; Fasshauer, E.; Fleig, T.; Halbert, L.; Hedegård, E. D.; Helmich-Paris, B.; Iliaš, M.; Jacob, C. R.; Knecht, S.; Laerdahl, J. K.; Vidal, M. L.; Nayak, M. K.; Olejniczak, M.; Olsen, J. M. H.; Pernpointner, M.; Senjean, B.; Shee, A.; Sunaga, A.; Stralen, J. N. P. van. The DIRAC Code for Relativistic Molecular Calculations. J. Chem. Phys. 2020, 152, 204104.
  18. Chiariello, M. G.; Bolnykh, V.; Ippoliti, E.; Meloni, S.; Olsen, J. M. H.; Beck, T.; Rothlisberger, U.; Fahlke, C.; Carloni, P. Molecular Basis of CLC Antiporter Inhibition by Fluoride. J. Am. Chem. Soc. 2020, 142, 7254–7258.
  19. Bolnykh, V.; Olsen, J. M. H.; Meloni, S.; Bircher, M. P.; Ippoliti, E.; Carloni, P.; Rothlisberger, U. MiMiC: Multiscale Modeling in Computational Chemistry. Front. Mol. Biosci. 2020, 7, 45.
  20. Khah, A. M.; Reinholdt, P.; Olsen, J. M. H.; Kongsted, J.; Hättig, C. Avoiding Electron Spill-Out in QM/MM Calculations on Excited States with Simple Pseudopotentials. J. Chem. Theory Comput. 2020, 16, 1373–1381.
  21. Reinholdt, P.; Kjellgren, E. R.; Steinmann, C.; Olsen, J. M. H. Cost-Effective Potential for Accurate Polarizable Embedding Calculations in Protein Environments. J. Chem. Theory Comput. 2020, 16, 1162–1174.
  22. Scheurer, M.; Reinholdt, P.; Kjellgren, E. R.; Olsen, J. M. H.; Dreuw, A.; Kongsted, J. CPPE: An Open-Source C++ and Python Library for Polarizable Embedding. J. Chem. Theory Comput. 2019, 15, 6154–6163.
  23. Bolnykh, V.; Olsen, J. M. H.; Meloni, S.; Bircher, M. P.; Ippoliti, E.; Carloni, P.; Rothlisberger, U. Extreme Scalability of DFT-Based QM/MM MD Simulations Using MiMiC. J. Chem. Theory Comput. 2019, 15, 5601–5613.
  24. Olsen, J. M. H.; Bolnykh, V.; Meloni, S.; Ippoliti, E.; Bircher, M. P.; Carloni, P.; Rothlisberger, U. MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry. J. Chem. Theory Comput. 2019, 15, 3810–3823.
  25. Scheurer, M.; Herbst, M. F.; Reinholdt, P.; Olsen, J. M. H.; Dreuw, A.; Kongsted, J. Polarizable Embedding Combined with the Algebraic Diagrammatic Construction: Tackling Excited States in Biomolecular Systems. J. Chem. Theory Comput. 2018, 14, 4870–4883.
  26. Steinmann, C.; Reinholdt, P.; Nørby, M. S.; Kongsted, J.; Olsen, J. M. H. Response Properties of Embedded Molecules through the Polarizable Embedding Model. Int. J. Quantum Chem. 2018, 119, e25717.
  27. Kjellgren, E. R.; Olsen, J. M. H.; Kongsted, J. Importance of Accurate Structures for Quantum Chemistry Embedding Methods: Which Strategy Is Better? J. Chem. Theory Comput. 2018, 14, 4309–4319.
  28. Hršak, D.; Olsen, J. M. H.; Kongsted, J. Polarizable Density Embedding Coupled Cluster Method. J. Chem. Theory Comput. 2018, 14, 1351–1360.
  29. Fahleson, T.; Olsen, J. M. H.; Norman, P.; Rizzo, A. A QM/MM and QM/QM/MM Study of Kerr, Cotton–Mouton and Jones Linear Birefringences in Liquid Acetonitrile. Phys. Chem. Chem. Phys. 2018, 20, 3831–3840.
  30. Reinholdt, R.; Kongsted, J.; Olsen, J. M. H. Polarizable Density Embedding: A Solution to the Electron Spill-Out Problem in Multiscale Modeling. J. Phys. Chem. Lett. 2017, 8, 5949–5958.
  31. Nåbo, L. J.; Olsen, J. M. H.; Martı́nez T. J.; Kongsted, J. The Quality of the Embedding Potential Is Decisive for Minimal Quantum Region Size in Embedding Calculations: The Case of the Green Fluorescent Protein. J. Chem. Theory Comput. 2017, 13, 6230–6236.
  32. Nørby, M. S.; Olsen, J. M. H.; Steinmann, C.; Kongsted, J. Modeling Electronic Circular Dichroism within the Polarizable Embedding Approach. J. Chem. Theory Comput. 2017, 13, 4442–4451.
  33. Hršak, D.; Olsen, J. M. H.; Kongsted, J. Optimization and Transferability of Non-Electrostatic Repulsion in the Polarizable Density Embedding Model. J. Comput. Chem. 2017, 38, 2108–2117.
  34. Olsen, J. M. H.; Hedegård, E. D. Modeling the Absorption Spectrum of the Permanganate Ion in Vacuum and in Aqueous Solution. Phys. Chem. Chem. Phys. 2017, 19, 15870–15875.
  35. Hedegård, E. D.; Bast, R.; Kongsted, J.; Olsen, J. M. H.; Jensen, H. J. \relax A. Relativistic Polarizable Embedding. J. Chem. Theory Comput. 2017, 13, 2870–2880.
  36. Witzke, S.; List, N. H.; Olsen, J. M. H.; Steinmann, C.; Petersen, M.; Beerepoot, M. T. P.; Kongsted, J. An Averaged Polarizable Potential for Multiscale Modeling in Phospholipid Membranes. J. Comput. Chem. 2017, 38, 601–611.
  37. Steinmann, C.; Bratholm, L. A.; Olsen, J. M. H.; Kongsted, J. Automated Fragmentation Polarizable Embedding Density Functional Theory (PE-DFT) Calculations of Nuclear Magnetic Resonance (NMR) Shielding Constants of Proteins with Application to Chemical Shift Predictions. J. Chem. Theory Comput. 2017, 13, 525–536.
  38. Steindal, A. H.; Beerepoot, M. T. P.; Ringholm, M.; List, N. H.; Ruud, K.; Kongsted, J.; Olsen, J. M. H. Open-Ended Response Theory with Polarizable Embedding: Multiphoton Absorption in Biomolecular Systems. Phys. Chem. Chem. Phys. 2016, 18, 28339–28352.
  39. Nåbo, L. J.; Olsen, J. M. H.; List, N. H.; Solanko, L. M.; Wüstner, D.; Kongsted, J. Embedding beyond Electrostatics—The Role of Wave Function Confinement. J. Chem. Phys. 2016, 145, 104102.
  40. Nørby, M. S.; Steinmann, C.; Olsen, J. M. H.; Li, H.; Kongsted, J. Computational Approach for Studying Optical Properties of DNA Systems in Solution. J. Chem. Theory Comput. 2016, 12, 5050–5057.
  41. List, N. H.; Olsen, J. M. H.; Kongsted, J. Excited States in Large Molecular Systems through Polarizable Embedding. Phys. Chem. Chem. Phys. 2016, 18, 20234–20250.
  42. Nørby, M. S.; Olsen, J. M. H.; Kongsted, J.; Jensen, H. J. \relax A. Multipole Moments for Embedding Potentials: Exploring Different Atomic Allocation Algorithms. J. Comp. Chem. 2016, 37, 1887–1896.
  43. Beerepoot, M. T. P.; Steindal, A. H.; List, N. H.; Kongsted, J.; Olsen, J. M. H. Averaged Solvent Embedding Potential Parameters for Multiscale Modeling of Molecular Properties. J Chem. Theory Comput. 2016, 12, 1684–1695.
  44. Rasmussen, E.; Olsen, J. M. H.; Solov’yov, I. Quantifying Electron Transfer Reactions in Biological Systems: What Interactions Play the Major Role? Scientific Reports 2016, 5, 18446.
  45. Olsen, J. M. H.; List, N. H.; Kristensen, K.; Kongsted, J. Accuracy of Protein Embedding Potentials: An Analysis in Terms of Electrostatic Potentials. J. Chem. Theory Comput. 2015, 11, 1832–1842.
  46. Hedegård, E. D.; Olsen, J. M. H.; Knecht, S.; Kongsted, J.; Jensen, H. J. \relax A. Polarizable Embedding with a Multiconfiguration Short-Range Density Functional Theory Linear Response Method. J. Chem. Phys. 2015, 142, 114113.
  47. Olsen, J. M. H.; Steinmann, C.; Ruud, K.; Kongsted, J. Polarizable Density Embedding: A New QM/QM/MM-Based Computational Strategy. J. Phys. Chem. A 2015, 119, 5344–5355.
  48. List, N. H.; Beerepoot, M. T. P.; Olsen, J. M. H.; Gao, B.; Ruud, K.; Jensen, H. J. \relax A.; Kongsted, J. Molecular Quantum Mechanical Gradients within the Polarizable Embedding Approach—Application to the Internal Vibrational Stark Shift of Acetophenone. J. Chem. Phys. 2015, 142, 034119.
  49. Schwabe, T.; Beerepoot, M. T. P.; Olsen, J. M. H.; Kongsted, J. Analysis of Computational Models for an Accurate Study of Electronic Excitations in GFP. Phys. Chem. Chem. Phys. 2015, 17, 2582–2588.
  50. Schmidt, J. A.; Olsen, J. M. H. Photodissociation of OCS: Deviations between Theory and Experiment, and the Importance of Higher Order Correlation Effects. J. Chem. Phys. 2014, 141, 184310.
  51. Aidas, K.; Angeli, C.; Bak, K. L.; Bakken, V.; Bast, R.; Boman, L.; Christiansen, O.; Cimiraglia, R.; Coriani, S.; Dahle, P.; Dalskov, E. K.; Ekström, U.; Enevoldsen, T.; Eriksen, J. J.; Ettenhuber, P.; Fernández, B.; Ferrighi, L.; Fliegl, H.; Frediani, L.; Hald, K.; Halkier, A.; Hättig, C.; Heiberg, H.; Helgaker, T.; Hennum, A. C.; Hettema, H.; Hjertenæs, E.; Høst, S.; Høyvik, I.-M.; Iozzi, M. F.; Jansík, B.; Jensen, H. J. A.; Jonsson, D.; Jørgensen, P.; Kauczor, J.; Kirpekar, S.; Kjærgaard, T.; Klopper, W.; Knecht, S.; Kobayashi, R.; Koch, H.; Kongsted, J.; Krapp, A.; Kristensen, K.; Ligabue, A.; Lutnæs, O. B.; Melo, J. I.; Mikkelsen, K. V.; Myhre, R. H.; Neiss, C.; Nielsen, C. B.; Norman, P.; Olsen, J.; Olsen, J. M. H.; Osted, A.; Packer, M. J.; Pawlowski, F.; Pedersen, T. B.; Provasi, P. F.; Reine, S.; Rinkevicius, Z.; Ruden, T. A.; Ruud, K.; Rybkin, V. V.; Sałek, P.; Samson, C. C. M.; Merás, A. S. de; Saue, T.; Sauer, S. P. A.; Schimmelpfennig, B.; Sneskov, K.; Steindal, A. H.; Sylvester-Hvid, K. O.; Taylor, P. R.; Teale, A. M.; Tellgren, E. I.; Tew, D. P.; Thorvaldsen, A. J.; Thøgersen, L.; Vahtras, O.; Watson, M. A.; Wilson, D. J. D.; Ziolkowski, M.; Ågren, H. The Dalton Quantum Chemistry Program System. WIREs Comput. Mol. Sci. 2014, 4, 269–284.
  52. Poongavanam, V.; Olsen, J. M. H.; Kongsted, J. Binding Free Energy Based Structural Dynamics Analysis of HIV-1 RT RNase H-Inhibitor Complexes. Integr. Biol. 2014, 6, 1010–1022.
  53. Beerepoot, M. T. P.; Steindal, A. H.; Ruud, K.; Olsen, J. M. H.; Kongsted, J. Convergence of Environment Polarization Effects in Multiscale Modeling of Excitation Energies. Comp. Theor. Chem. 2014, 1040-1041, 304–311.
  54. Pedersen, M. N.; Hedegård, E. D.; Olsen, J. M. H.; Kauczor, J.; Norman, P.; Kongsted, J. Damped Response Theory in Combination with Polarizable Environments: The Polarizable Embedding Complex Polarization Propagator Method. J. Chem. Theory Comput. 2014, 10, 1164–1171.
  55. Steinmann, C.; Olsen, J. M. H.; Kongsted, J. Nuclear Magnetic Shielding Constants from Quantum Mechanical/Molecular Mechanical Calculations Using Polarizable Embedding: Role of the Embedding Potential. J. Chem. Theory Comput. 2014, 10, 981–988.
  56. Sneskov, K.; Olsen, J. M. H.; Schwabe, T.; Hättig, C.; Christiansen, O.; Kongsted, J. Computational Screening of One- and Two-Photon Spectrally Tuned Channelrhodopsin Mutants. Phys. Chem. Chem. Phys. 2013, 15, 7567–7576.
  57. Beerepoot, M. T. P.; Steindal, A. H.; Kongsted, J.; Brandsdal, B. O.; Frediani, L.; Ruud, K.; Olsen, J. M. H. A Polarizable Embedding DFT Study of One-Photon Absorption in Fluorescent Proteins. Phys. Chem. Chem. Phys. 2013, 15, 4735–4743.
  58. Aidas, K.; Olsen, J. M. H.; Kongsted, J.; Ågren, H. Photoabsorption of Acridine Yellow and Proflavin Bound to Human Serum Albumin Studied by Means of Quantum Mechanics/Molecular Dynamics. J. Phys. Chem. B 2013, 117, 2069–2080.
  59. Murugan, N. A.; Olsen, J. M. H.; Kongsted, J.; Rinkevicius, Z.; Aidas, K.; Ågren, H. Amyloid Fibril-Induced Structural and Spectral Modifications in the Thioflavin-T Optical Probe. J. Phys. Chem. Lett. 2012, 4, 70–77.
  60. List, N. H.; Olsen, J. M. H.; Jensen, H. J. A.; Steindal, A. H.; Kongsted, J. Molecular-Level Insight into the Spectral Tuning Mechanism of the DsRed Chromophore. J. Phys. Chem. Lett. 2012, 3, 3513–3521.
  61. Steindal, A. H.; Olsen, J. M. H.; Ruud, K.; Frediani, L.; Kongsted, J. A Combined Quantum Mechanics/Molecular Mechanics Study of the One-and Two-Photon Absorption in the Green Fluorescent Protein. Phys. Chem. Chem. Phys. 2012, 14, 5440–5451.
  62. Schwabe, T.; Sneskov, K.; Olsen, J. M. H.; Kongsted, J.; Christiansen, O.; Hättig, C. PERI-CC2: A Polarizable Embedded RI-CC2 Method. J. Chem. Theory Comput. 2012, 8, 3274–3283.
  63. Steindal, A. H.; Olsen, J. M. H.; Frediani, L.; Kongsted, J.; Ruud, K. Parallelization of the Polarizable Embedding Scheme for Higher-Order Response Functions. Mol. Phys. 2012, 110, 2579–2586.
  64. List, N. H.; Olsen, J. M.; Rocha-Rinza, T.; Christiansen, O.; Kongsted, J. Performance of Popular XC-Functionals for the Description of Excitation Energies in GFP-like Chromophore Models. Int. J. Quant. Chem. 2012, 112, 789–800.
  65. Olsen, J. M. H.; Kongsted, J. Molecular Properties through Polarizable Embedding. Adv. Quantum Chem. 2011, 61, 107–143.
  66. Schwabe, T.; Olsen, J. M. H.; Sneskov, K.; Kongsted, J.; Christiansen, O. Solvation Effects on Electronic Transitions: Exploring the Performance of Advanced Solvent Potentials in Polarizable Embedding Calculations. J. Chem. Theory Comput. 2011, 7, 2209–2217.
  67. Eriksen, J. J.; Olsen, J. M. H.; Aidas, K.; Ågren, H.; Mikkelsen, K. V.; Kongsted, J. Computational Protocols for Prediction of Solute NMR Relative Chemical Shifts. A Case Study of L-Tryptophan in Aqueous Solution. J. Comp. Chem. 2011, 32, 2853–2864.
  68. Zazza, C.; Olsen, J. M.; Kongsted, J. Solvatochromic Shifts vs Nanosolvation Patterns: Uracil in Water as a Test Case. Comp. Theor. Chem. 2011, 974, 109–116.
  69. Olsen, J. M.; Aidas, K.; Kongsted, J. Excited States in Solution through Polarizable Embedding. J. Chem. Theory Comput. 2010, 6, 3721–3734.
  70. Olsen, J. M.; Aidas, K.; Mikkelsen, K. V.; Kongsted, J. Solvatochromic Shifts in Uracil: A Combined MD-QM/MM Study. J. Chem. Theory Comput. 2009, 6, 249–256.

Other publications

This includes other publications (co)authored by group members that do not include the group leader.

  1. Vester, J.; Despré, V.; Kuleff, A. I. The Role of Symmetric Vibrational Modes in the Decoherence of Correlation-Driven Charge Migration. J. Chem. Phys. 2023, 158, 104305.
  2. Lengvinaitė, D.; Kvedaraviciute, S.; Bielskutė, S.; Klimavicius, V.; Balevicius, V.; Mocci, F.; Laaksonen, A.; Aidas, K. Structural Features of the [C4mim][Cl] Ionic Liquid and Its Mixtures with Water: Insight from a 1H NMR Experimental and QM/MD Study. J. Phys. Chem. B 2021, 125 (48), 13255–13266.