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  1. Multiphoton Absorption Spectra of Channelrhodopsin-2 via Multiscale Simulation Methods

    Article • October 2025, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  2. Multiphoton Absorption Spectra of Channelrhodopsin-2 via Multiscale Simulation Methods

    Article • October 2025, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  3. Workflow for Harmonic IR and Raman Spectra of Embedded Systems: The PE-QM Approach

    Article • The Journal of Physical Chemistry A, July 2025, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  4. OpenMM–MiMiC Interface for Efficient and Flexible Multiscale Simulations

    Article • Journal of Chemical Information and Modeling, June 2025, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  5. Making Puzzle Pieces Fit or Reshaping MiMiC for Multiscale Simulations with CP2K and More

    Article • Journal of Chemical Information and Modeling, May 2025, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  6. Multiscale Molecular Dynamics Simulations with the MiMiC Framework

    Article • CHIMIA International Journal for Chemistry, April 2025, Swiss Chemical Society

    Jógvan Magnus Haugaard Olsen

  7. Multiphoton Absorption Spectra of Channelrhodopsin-2 via Multiscale Simulation Methods

    Article • March 2025, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  8. Assessing the Partial Hessian Approximation in QM/MM-Based Vibrational Analysis

    Article • Journal of Chemical Theory and Computation, October 2024, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  9. Assessing the Partial Hessian Approximation in QM/MM-based Vibrational Analysis

    Article • October 2024, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  10. Benchmarks and Workflow for Harmonic IR and Raman Spectra

    Article • August 2024, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  11. MiMiC: A high-performance framework for multiscale molecular dynamics simulations

    Article • The Journal of Chemical Physics, July 2024, American Institute of Physics

    Jógvan Magnus Haugaard Olsen

  12. Assessing the Partial Hessian Approximation in QM/MM-based Vibrational Analysis

    Article • July 2024, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  13. A fully-polarizable KS-DFT/AMOEBA embedding scheme for plane wave basis sets through the MiMiC framework

    Article • July 2024, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  14. Multiscale biomolecular simulations in the exascale era

    Article • Current Opinion in Structural Biology, June 2024, Elsevier

    Jógvan Magnus Haugaard Olsen

  15. Polarizable Embedding Potentials through Molecular Fractionation with Conjugate Caps Including Hydrogen Bonds

    Article • Journal of Chemical Theory and Computation, September 2023, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  16. Polarizable Embedding without Artificial Boundary Polarization

    Article • Journal of Chemical Theory and Computation, July 2023, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  17. Polarizable Embedding with Periodic Boundary Conditions

    Article • March 2023, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  18. Polarizable Embedding Potentials through Molecular Fractionation with Conjugate Caps Including Hydrogen Bonds

    Article • February 2023, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  19. MiMiCPy: An Efficient Toolkit for MiMiC-Based QM/MM Simulations

    Article • Journal of Chemical Information and Modeling, February 2023, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  20. Impact of donor halogenation on reorganization energies and voltage losses in bulk-heterojunction solar cells

    Article • Energy & Environmental Science, January 2023, Royal Society of Chemistry

    Jógvan Magnus Haugaard Olsen

  21. Induction effects on the absorption maxima of photoreceptor proteins

    Article • Biophysics and Physicobiology, January 2023, Biophysical Society of Japan

    Jógvan Magnus Haugaard Olsen

  22. Deciphering the Spectral Tuning Mechanism in Proteorhodopsin: The Dominant Role of Electrostatics Instead of Chromophore Geometry

    Article • Chemistry - A European Journal, April 2022, Wiley

    Jógvan Magnus Haugaard Olsen

  23. The Impact of Retinal Configuration on the Protein–Chromophore Interactions in Bistable Jumping Spider Rhodopsin-1

    Article • Molecules, December 2021, MDPI AG

    Jógvan Magnus Haugaard Olsen

  24. Wavefunction-Based Electrostatic-Embedding QM/MM Using CFOUR through MiMiC

    Article • Journal of Chemical Theory and Computation, December 2021, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  25. The Impact of Retinal Configuration on the Protein-Chromophore Interactions in Bistable Jumping Spider Rhodopsin-1

    Article • November 2021, MDPI AG

    Jógvan Magnus Haugaard Olsen

  26. Harmonic Infrared and Raman Spectra in Molecular Environments Using the Polarizable Embedding Model

    Article • Journal of Chemical Theory and Computation, May 2021, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  27. Efficient Open-Source Implementations of Linear-Scaling Polarizable Embedding: Use Octrees to Save the Trees

    Article • Journal of Chemical Theory and Computation, May 2021, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  28. Efficient Open-Source Implementations of Linear-Scaling Polarizable Embedding: Use Octrees to Save the Trees

    Article • March 2021, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  29. Efficient Open-Source Implementations of Linear-Scaling Polarizable Embedding: Use Octrees to Save the Trees

    Article • March 2021, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  30. Frontiers in Multiscale Modeling of Photoreceptor Proteins

    Article • Photochemistry and Photobiology, February 2021, Wiley

    Jógvan Magnus Haugaard Olsen

  31. Polarizable Density Embedding for Large Biomolecular Systems

    Article • Journal of Chemical Theory and Computation, September 2020, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  32. Polarizable Density Embedding for Large Biomolecular Systems

    Article • July 2020, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  33. Accuracy of Molecular Simulation-Based Predictions of koff Values: A Metadynamics Study

    Article • The Journal of Physical Chemistry Letters, July 2020, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  34. Two-Photon Absorption Cross-Sections in Fluorescent Proteins Containing Non-canonical Chromophores Using Polarizable QM/MM

    Article • Frontiers in Molecular Biosciences, June 2020, Frontiers

    Jógvan Magnus Haugaard Olsen

  35. Dalton Project: A Python platform for molecular- and electronic-structure simulations of complex systems

    Article • The Journal of Chemical Physics, June 2020, American Institute of Physics

    Jógvan Magnus Haugaard Olsen, Dr Stephan P. A. Sauer

  36. The DIRAC code for relativistic molecular calculations

    Article • The Journal of Chemical Physics, May 2020, American Institute of Physics

    Professor Hans Jørgen Aagaard Jensen, Dr. Ignacio Agustin Aucar, Miroslav Iliaš, Andre Severo Pereira Gomes, Elke Fasshauer, Jógvan Magnus Haugaard Olsen, Ayaki Sunaga

  37. Molecular Basis of CLC Antiporter Inhibition by Fluoride

    Article • Journal of the American Chemical Society, April 2020, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  38. Polarizable Density Embedding for Large Biomolecular Systems

    Article • April 2020, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  39. Polarizable Density Embedding for Large Biomolecular Systems

    Article • April 2020, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  40. On the accuracy of molecular simulation-based predictions of koff values: a Metadynamics study

    Article • March 2020, Cold Spring Harbor Laboratory Press

    Jógvan Magnus Haugaard Olsen

  41. MiMiC: Multiscale Modeling in Computational Chemistry

    Article • Frontiers in Molecular Biosciences, March 2020, Frontiers

    Jógvan Magnus Haugaard Olsen

  42. Avoiding Electron Spill-Out in QM/MM Calculations on Excited States with Simple Pseudopotentials

    Article • Journal of Chemical Theory and Computation, February 2020, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  43. Cost-Effective Potential for Accurate Polarizable Embedding Calculations in Protein Environments

    Article • Journal of Chemical Theory and Computation, January 2020, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  44. CPPE: An Open-Source C++ and Python Library for Polarizable Embedding

    Article • Journal of Chemical Theory and Computation, October 2019, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  45. Extreme Scalability of DFT-Based QM/MM MD Simulations Using MiMiC

    Article • Journal of Chemical Theory and Computation, September 2019, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  46. CPPE: An Open-Source C++ and Python Library for Polarizable Embedding

    Article • July 2019, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  47. CPPE: An Open-Source C++ and Python Library for Polarizable Embedding

    Article • July 2019, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  48. Cost-Effective Potential for Accurate Polarizable Embedding Calculations in Protein Environments

    Article • June 2019, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  49. Cost-Effective Potential for Accurate Polarizable Embedding Calculations in Protein Environments

    Article • June 2019, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  50. MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry

    Article • Journal of Chemical Theory and Computation, May 2019, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  51. Extreme Scalability of DFT-Based QM/MM MD Simulations Using MiMiC

    Article • May 2019, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  52. Extreme Scalability of DFT-Based QM/MM MD Simulations Using MiMiC

    Article • May 2019, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  53. MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry

    Article • January 2019, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  54. MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry

    Article • January 2019, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  55. Response properties of embedded molecules through the polarizable embedding model

    Article • International Journal of Quantum Chemistry, September 2018, Wiley

    Jógvan Magnus Haugaard Olsen

  56. Polarizable Embedding Combined with the Algebraic Diagrammatic Construction: Tackling Excited States in Biomolecular Systems

    Article • Journal of Chemical Theory and Computation, August 2018, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  57. Importance of Accurate Structures for Quantum Chemistry Embedding Methods: Which Strategy Is Better?

    Article • Journal of Chemical Theory and Computation, July 2018, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  58. Polarizable Density Embedding Coupled Cluster Method

    Article • Journal of Chemical Theory and Computation, February 2018, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  59. A QM/MM and QM/QM/MM study of Kerr, Cotton–Mouton and Jones linear birefringences in liquid acetonitrile

    Article • Physical Chemistry Chemical Physics, January 2018, Royal Society of Chemistry

    Jógvan Magnus Haugaard Olsen

  60. Polarizable Density Embedding: A Solution to the Electron Spill-Out Problem in Multiscale Modeling

    Article • The Journal of Physical Chemistry Letters, November 2017, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  61. The Quality of the Embedding Potential Is Decisive for Minimal Quantum Region Size in Embedding Calculations: The Case of the Green Fluorescent Protein

    Article • Journal of Chemical Theory and Computation, November 2017, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen, Todd Martinez

  62. Modeling Electronic Circular Dichroism within the Polarizable Embedding Approach

    Article • Journal of Chemical Theory and Computation, August 2017, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  63. Optimization and transferability of non-electrostatic repulsion in the polarizable density embedding model

    Article • Journal of Computational Chemistry, June 2017, Wiley

    Jógvan Magnus Haugaard Olsen

  64. Relativistic Polarizable Embedding

    Article • Journal of Chemical Theory and Computation, May 2017, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen, Professor Hans Jørgen Aagaard Jensen

  65. An averaged polarizable potential for multiscale modeling in phospholipid membranes

    Article • Journal of Computational Chemistry, February 2017, Wiley

    Jógvan Magnus Haugaard Olsen

  66. 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

    Article • Journal of Chemical Theory and Computation, January 2017, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  67. Modeling the absorption spectrum of the permanganate ion in vacuum and in aqueous solution

    Article • Physical Chemistry Chemical Physics, January 2017, Royal Society of Chemistry

    Jógvan Magnus Haugaard Olsen

  68. Computational Approach for Studying Optical Properties of DNA Systems in Solution

    Article • Journal of Chemical Theory and Computation, September 2016, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  69. Embedding beyond electrostatics—The role of wave function confinement

    Article • The Journal of Chemical Physics, September 2016, American Institute of Physics

    Jógvan Magnus Haugaard Olsen

  70. Multipole moments for embedding potentials: Exploring different atomic allocation algorithms

    Article • Journal of Computational Chemistry, May 2016, Wiley

    Jógvan Magnus Haugaard Olsen, Professor Hans Jørgen Aagaard Jensen

  71. Averaged Solvent Embedding Potential Parameters for Multiscale Modeling of Molecular Properties

    Article • Journal of Chemical Theory and Computation, March 2016, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  72. Correction: Analysis of computational models for an accurate study of electronic excitations in GFP

    Article • Physical Chemistry Chemical Physics, January 2016, Royal Society of Chemistry

    Jógvan Magnus Haugaard Olsen

  73. Excited states in large molecular systems through polarizable embedding

    Article • Physical Chemistry Chemical Physics, January 2016, Royal Society of Chemistry

    Jógvan Magnus Haugaard Olsen

  74. Open-ended response theory with polarizable embedding: multiphoton absorption in biomolecular systems

    Article • Physical Chemistry Chemical Physics, January 2016, Royal Society of Chemistry

    Jógvan Magnus Haugaard Olsen

  75. Quantifying electron transfer reactions in biological systems: what interactions play the major role?

    Article • Scientific Reports, December 2015, Springer Science + Business Media

    Jógvan Magnus Haugaard Olsen

  76. Correction to “Polarizable Density Embedding: A New QM/QM/MM-based Computational Strategy”

    Article • The Journal of Physical Chemistry A, June 2015, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  77. Accuracy of Protein Embedding Potentials: An Analysis in Terms of Electrostatic Potentials

    Article • Journal of Chemical Theory and Computation, April 2015, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  78. Polarizable embedding with a multiconfiguration short-range density functional theory linear response method

    Article • The Journal of Chemical Physics, March 2015, American Institute of Physics

    Jógvan Magnus Haugaard Olsen, Professor Hans Jørgen Aagaard Jensen

  79. Polarizable Density Embedding: A New QM/QM/MM-Based Computational Strategy

    Article • The Journal of Physical Chemistry A, February 2015, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  80. Molecular quantum mechanical gradients within the polarizable embedding approach—Application to the internal vibrational Stark shift of acetophenone

    Article • The Journal of Chemical Physics, January 2015, American Institute of Physics

    Jógvan Magnus Haugaard Olsen, Professor Hans Jørgen Aagaard Jensen

  81. Analysis of computational models for an accurate study of electronic excitations in GFP

    Article • Physical Chemistry Chemical Physics, January 2015, Royal Society of Chemistry

    Tobias Schwabe, Jógvan Magnus Haugaard Olsen

  82. Photodissociation of OCS: Deviations between theory and experiment, and the importance of higher order correlation effects

    Article • The Journal of Chemical Physics, November 2014, American Institute of Physics

    Jógvan Magnus Haugaard Olsen

  83. Convergence of environment polarization effects in multiscale modeling of excitation energies

    Article • Computational and Theoretical Chemistry, July 2014, Elsevier

    Jógvan Magnus Haugaard Olsen

  84. Nuclear Magnetic Shielding Constants from Quantum Mechanical/Molecular Mechanical Calculations Using Polarizable Embedding: Role of the Embedding Potential

    Article • Journal of Chemical Theory and Computation, February 2014, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  85. Damped Response Theory in Combination with Polarizable Environments: The Polarizable Embedding Complex Polarization Propagator Method

    Article • Journal of Chemical Theory and Computation, February 2014, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  86. Binding free energy based structural dynamics analysis of HIV-1 RT RNase H–inhibitor complexes

    Article • Integrative Biology, January 2014, Oxford University Press (OUP)

    Jógvan Magnus Haugaard Olsen

  87. The Dalton quantum chemistry program system

    Article • Wiley Interdisciplinary Reviews Computational Molecular Science, September 2013, Wiley

    Dr Stephan P. A. Sauer, Andrew Teale, Jógvan Magnus Haugaard Olsen, Professor Hans Jørgen Aagaard Jensen

  88. Photoabsorption of Acridine Yellow and Proflavin Bound to Human Serum Albumin Studied by Means of Quantum Mechanics/Molecular Dynamics

    Article • The Journal of Physical Chemistry B, February 2013, American Chemical Society (ACS)

    Kestutis Aidas, Jógvan Magnus Haugaard Olsen

  89. Computational screening of one- and two-photon spectrally tuned channelrhodopsin mutants

    Article • Physical Chemistry Chemical Physics, January 2013, Royal Society of Chemistry

    Tobias Schwabe, Jógvan Magnus Haugaard Olsen

  90. A polarizable embedding DFT study of one-photon absorption in fluorescent proteins

    Article • Physical Chemistry Chemical Physics, January 2013, Royal Society of Chemistry

    Kenneth Ruud, Jógvan Magnus Haugaard Olsen

  91. Amyloid Fibril-Induced Structural and Spectral Modifications in the Thioflavin-T Optical Probe

    Article • The Journal of Physical Chemistry Letters, December 2012, American Chemical Society (ACS)

    Kestutis Aidas, Jógvan Magnus Haugaard Olsen

  92. Molecular-Level Insight into the Spectral Tuning Mechanism of the DsRed Chromophore

    Article • The Journal of Physical Chemistry Letters, November 2012, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen, Professor Hans Jørgen Aagaard Jensen

  93. Parallelization of the polarizable embedding scheme for higher-order response functions

    Article • Molecular Physics, September 2012, Taylor & Francis

    Jógvan Magnus Haugaard Olsen

  94. PERI–CC2: A Polarizable Embedded RI-CC2 Method

    Article • Journal of Chemical Theory and Computation, August 2012, American Chemical Society (ACS)

    Tobias Schwabe, Jógvan Magnus Haugaard Olsen

  95. A combined quantum mechanics/molecular mechanics study of the one- and two-photon absorption in the green fluorescent protein

    Article • Physical Chemistry Chemical Physics, January 2012, Royal Society of Chemistry

    Kenneth Ruud, Jógvan Magnus Haugaard Olsen

  96. Solvatochromic shifts vs nanosolvation patterns: Uracil in water as a test case

    Article • Computational and Theoretical Chemistry, November 2011, Elsevier

    Jógvan Magnus Haugaard Olsen, Dr Costantino Zazza

  97. Solvation Effects on Electronic Transitions: Exploring the Performance of Advanced Solvent Potentials in Polarizable Embedding Calculations

    Article • Journal of Chemical Theory and Computation, July 2011, American Chemical Society (ACS)

    Tobias Schwabe, Jógvan Magnus Haugaard Olsen

  98. Computational protocols for prediction of solute NMR relative chemical shifts. A case study of L ‐tryptophan in aqueous solution

    Article • Journal of Computational Chemistry, July 2011, Wiley

    Kestutis Aidas, Jógvan Magnus Haugaard Olsen

  99. Performance of popular XC-functionals for the description of excitation energies in GFP-like chromophore models

    Article • International Journal of Quantum Chemistry, April 2011, Wiley

    Jógvan Magnus Haugaard Olsen

  100. Molecular Properties through Polarizable Embedding

    Article • January 2011, Elsevier

    Jógvan Magnus Haugaard Olsen

  101. Excited States in Solution through Polarizable Embedding

    Article • Journal of Chemical Theory and Computation, December 2010, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen

  102. Solvatochromic Shifts in Uracil: A Combined MD-QM/MM Study

    Article • Journal of Chemical Theory and Computation, January 2010, American Chemical Society (ACS)

    Jógvan Magnus Haugaard Olsen