Jógvan Magnus Haugaard Olsen

Publications

• A combined quantum mechanics/molecular mechanics study of the one- and two-photon absorption in the green fluorescent protein DOI: 10.1039/c2cp23537d
• A polarizable embedding DFT study of one-photon absorption in fluorescent proteins DOI: 10.1039/c3cp44659j
• Amyloid Fibril-Induced Structural and Spectral Modifications in the Thioflavin-T Optical Probe DOI: 10.1021/jz3018557
• Computational protocols for prediction of solute NMR relative chemical shifts. A case study of L-tryptophan in aqueous solution DOI: 10.1002/jcc.21867
• Molecular-Level Insight into the Spectral Tuning Mechanism of the DsRed Chromophore DOI: 10.1021/jz3014858
• PERI–CC2: A Polarizable Embedded RI-CC2 Method DOI: 10.1021/ct3003749
• Parallelization of the polarizable embedding scheme for higher-order response functions DOI: 10.1080/00268976.2012.721016
• Performance of popular XC-functionals for the description of excitation energies in GFP-like chromophore models DOI: 10.1002/qua.23059
• Photoabsorption of Acridine Yellow and Proflavin Bound to Human Serum Albumin Studied by Means of Quantum Mechanics/Molecular Dynamics DOI: 10.1021/jp311863x
• Solvatochromic shifts vs nanosolvation patterns: Uracil in water as a test case DOI: 10.1016/j.comptc.2011.07.020
• A polarizable embedding DFT study of one-photon absorption in fluorescent proteins DOI: 10.1039/c3cp44659j
• Amyloid fibril-induced structural and spectral modifications in the thioflavin-T optical probe DOI: 10.1021/jz3018557
• Computational screening of one- and two-photon spectrally tuned channelrhodopsin mutants DOI: 10.1039/c3cp44350g
• Photoabsorption of acridine yellow and proflavin bound to human serum albumin studied by means of quantum mechanics/molecular dynamics DOI: 10.1021/jp311863x
• A combined quantum mechanics/molecular mechanics study of the one- and two-photon absorption in the green fluorescent protein DOI: 10.1039/c2cp23537d
• Molecular-level insight into the spectral tuning mechanism of the dsred chromophore DOI: 10.1021/jz3014858
• PERI-CC2: A polarizable embedded RI-CC2 method DOI: 10.1021/ct3003749
• Parallelization of the polarizable embedding scheme for higher-order response functions DOI: 10.1080/00268976.2012.721016
• Performance of popular XC-functionals for the description of excitation energies in GFP-like chromophore models DOI: 10.1002/qua.23059
• Computational protocols for prediction of solute NMR relative chemical shifts. A case study of L -tryptophan in aqueous solution DOI: 10.1002/jcc.21867
• Molecular Properties through Polarizable Embedding DOI: 10.1016/B978-0-12-386013-2.00003-6
• Solvation effects on electronic transitions: Exploring the performance of advanced solvent potentials in polarizable embedding calculations DOI: 10.1021/ct200258g
• Solvatochromic shifts vs nanosolvation patterns: Uracil in water as a test case DOI: 10.1016/j.comptc.2011.07.020
• Excited states in solution through polarizable embedding DOI: 10.1021/ct1003803
• Solvatochromic shifts in uracil: A combined MD-QM/MM study DOI: 10.1021/ct900502s
• Accuracy of Protein Embedding Potentials: An Analysis in Terms of Electrostatic Potentials
• Cost-Effective Potential for Accurate Polarizable Embedding Calculations in Protein Environments
• Embedding Potentials Of Aqueous Acrolein
• Dataset for the article "Cost-effective Potential for Accurate Polarizable Embedding Calculations in Protein Environments"
• Embedding Potentials Of Aqueous 4-Nitrophenolate
• Averaged Solvent Embedding Potential Parameters for Multiscale Modeling of Molecular Properties
• Molecular Basis of CLC Antiporter Inhibition by Fluoride
• Dataset for the article "MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry"
• MiMiC: A Novel Framework for Multiscale Modeling in Computational Chemistry
• Response properties of embedded molecules through the polarizable embedding model
• MiMiC: Multiscale Modeling in Computational Chemistry
• The DIRAC code for relativistic molecular calculations
• Relativistic Polarizable Embedding
• 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.
• An averaged polarizable potential for multiscale modeling in phospholipid membranes.
• Embedding beyond electrostatics-The role of wave function confinement
• A QM/MM and QM/QM/MM study of Kerr, Cotton–Mouton and Jones linear birefringences in liquid acetonitrile
• Open-ended response theory with polarizable embedding: multiphoton absorption in biomolecular systems
• Excited states in large molecular systems through polarizable embedding
• The Impact of Retinal Configuration on the Protein–Chromophore Interactions in Bistable Jumping Spider Rhodopsin-1
• Supporting Information: Exclusion lists for single lipids
• Polarizable Embedding Combined with the Algebraic Diagrammatic Construction: Tackling Excited States in Biomolecular Systems
• Embedding Potentials Of Aqueous Formamide
• Dataset For The Tutorial: "Response Properties Of Embedded Molecules Through The Polarizable Embedding Model"
• Importance of Accurate Structures for Quantum Chemistry Embedding Methods: Which Strategy Is Better?
• The Quality of the Embedding Potential Is Decisive for Minimal Quantum Region Size in Embedding Calculations: The Case of the Green Fluorescent Protein
• Modeling Electronic Circular Dichroism within the Polarizable Embedding Approach
• Optimization and transferability of non-electrostatic repulsion in the polarizable density embedding model
• Modeling the absorption spectrum of the permanganate ion in vacuum and in aqueous solution
• Dataset for the manuscript: Two-photon Absorption Cross-sections in Fluorescent Proteins Containing Non-canonical Chromophores Using Polarizable QM/MM
• Computational Approach for Studying Optical Properties of DNA Systems in Solution
• Dalton Project: A Python platform for molecular- and electronic-structure simulations of complex systems
• Two-Photon Absorption Cross-Sections in Fluorescent Proteins Containing Non-canonical Chromophores Using Polarizable QM/MM
• Polarizable Density Embedding Coupled Cluster Method
• PyFraME: Python framework for Fragment-based Multiscale Embedding
• Accuracy of Molecular Simulation-Based Predictions of koff Values: A Metadynamics Study
• Avoiding Electron Spill-Out in QM/MM Calculations on Excited States with Simple Pseudopotentials
• Frontiers in Multiscale Modeling of Photoreceptor Proteins
• Polarizable Density Embedding: A Solution to the Electron Spill-Out Problem in Multiscale Modeling
• Extreme Scalability of DFT-Based QM/MM MD Simulations Using MiMiC
• CPPE: An Open-Source C++ and Python Library for Polarizable Embedding
• PElib: The Polarizable Embedding library
• Efficient Open-Source Implementations of Linear-Scaling Polarizable Embedding: Use Octrees to Save the Trees
• Harmonic Infrared and Raman Spectra in Molecular Environments Using the Polarizable Embedding Model
• Polarizable Density Embedding for Large Biomolecular Systems
• Multipole moments for embedding potentials: Exploring different atomic allocation algorithms
• Analysis of computational models for an accurate study of electronic excitations in GFP
• The Impact of Retinal Configuration on the Protein-Chromophore Interactions in Bistable Jumping Spider Rhodopsin-1
• PElib: The Polarizable Embedding library
• Wavefunction-Based Electrostatic-Embedding QM/MM Using CFOUR through MiMiC
• Solvation Effects on Electronic Transitions: Exploring the Performance of Advanced Solvent Potentials in Polarizable Embedding Calculations
• Nuclear Magnetic Shielding Constants from Quantum Mechanical/Molecular Mechanical Calculations Using Polarizable Embedding: Role of the Embedding Potential
• A combined quantum mechanics/molecular mechanics study of the one- and two-photon absorption in the green fluorescent protein
• Photodissociation of OCS: Deviations between theory and experiment, and the importance of higher order correlation effects
• Quantifying electron transfer reactions in biological systems: what interactions play the major role?
• Polarizable embedding with a multiconfiguration short-range density functional theory linear response method
• Computational screening of one- and two-photon spectrally tuned channelrhodopsin mutants
• Damped Response Theory in Combination with Polarizable Environments: The Polarizable Embedding Complex Polarization Propagator Method
• PhD defense lecture on polarizable embedding models
• Molecular Properties through Polarizable Embedding
• Development of Quantum Chemical Methods towards Rationalization and Optimal Design of Photoactive Proteins
• Improved Short-Range Electrostatic Interactions within the Polarizable Embedding Approach
• Convergence of environment polarization effects in multiscale modeling of excitation energies
• Solvatochromic Shifts in Uracil: A Combined MD-QM/MM Study
• Photoabsorption of Acridine Yellow and Proflavin Bound to Human Serum Albumin Studied by Means of Quantum Mechanics/Molecular Dynamics
• Molecular-Level Insight into the Spectral Tuning Mechanism of the DsRed Chromophore
• Computational protocols for prediction of solute NMR relative chemical shifts. A case study of L-tryptophan in aqueous solution
• Excited States in Solution through Polarizable Embedding
• Binding free energy based structural dynamics analysis of HIV-1 RT RNase H-inhibitor complexes
• A polarizable embedding DFT study of one-photon absorption in fluorescent proteins
• Amyloid Fibril-Induced Structural and Spectral Modifications in the Thioflavin-T Optical Probe
• Parallelization of the polarizable embedding scheme for higher-order response functions
• Molecular Properties through Polarizable Embedding
• The Dalton quantum chemistry program system
• Solvatochromic shifts vs nanosolvation patterns: Uracil in water as a test case
• Molecular quantum mechanical gradients within the polarizable embedding approach-Application to the internal vibrational Stark shift of acetophenone
• Polarizable Density Embedding: A New QM/QM/MM-Based Computational Strategy
• PERI-CC2: A Polarizable Embedded RI-CC2 Method
• Performance of popular XC-functionals for the description of excitation energies in GFP-like chromophore models
• Deciphering the Spectral Tuning Mechanism in Proteorhodopsin: The Dominant Role of Electrostatics Instead of Chromophore Geometry
• MiMiC: A Framework for Multiscale Modeling in Computational Chemistry
• MiMiC Communication Library
• MiMiC Communication Library
• Impact of donor halogenation on reorganization energies and voltage losses in bulk-heterojunction solar cells
• MiMiCPy: An Efficient Toolkit for MiMiC-Based QM/MM Simulations
• DIRAC23
• DIRAC23
• Induction effects on the absorption maxima of photoreceptor proteins
• Wavefunction-based electrostatic-embedding QM/MM using CFOUR through MiMiC
• Dataset for the article "Polarizable Embedding without Artificial Boundary Polarization"
• Dataset for the article "Polarizable Embedding without Artificial Boundary Polarization"
• Polarizable Embedding without Artificial Boundary Polarization
• Polarizable Embedding Potentials through Molecular Fractionation with Conjugate Caps Including Hydrogen Bonds
• Optimization and transferability of non‐electrostatic repulsion in the polarizable density embedding model
• Dataset for the article "Polarizable Embedding Potentials through Molecular Fractionation with Conjugate Caps including Hydrogen Bonds"
• Dataset for the article "Polarizable Embedding Potentials through Molecular Fractionation with Conjugate Caps including Hydrogen Bonds"
• DIRAC24
• DIRAC24
• Multiscale biomolecular simulations in the exascale era
• Assessing the Partial Hessian Approximation in QM/MM-based Vibrational Analysis
• Assessing the Partial Hessian Approximation in QM/MM-based Vibrational Analysis
• MiMiC: A high-performance framework for multiscale molecular dynamics simulations
• Dataset for the article "Benchmarks and Workflow for Harmonic IR and Raman Spectra"
• Dataset for the article "Benchmarks and Workflow for Harmonic IR and Raman Spectra"
• A fully-polarizable KS-DFT/AMOEBA embedding scheme for plane wave basis sets through the MiMiC framework
• Benchmarks and Workflow for Harmonic IR and Raman Spectra
• Dataset for the article "Assessing the Partial Hessian Approximation in QM/MM-based Vibrational Analysis"
• Assessing the Partial Hessian Approximation in QM/MM-Based Vibrational Analysis
• Polarizable Embedding with Periodic Boundary Conditions
• Dataset for the article "OpenMM–MiMiC Interface for Efficient and Flexible Multiscale Simulations"
• Dataset for the article "OpenMM–MiMiC Interface for Efficient and Flexible Multiscale Simulations"
• Dataset for the article "Making Puzzle Pieces Fit or Reshaping MiMiC for Multiscale Simulations with CP2K and More"
• Dataset for the article "Making Puzzle Pieces Fit or Reshaping MiMiC for Multiscale Simulations with CP2K and More"
• DIRAC25
• DIRAC25
• Multiphoton Absorption Spectra of Channelrhodopsin-2 via Multiscale Simulation Methods
• Multiscale Molecular Dynamics Simulations with the MiMiC Framework
• Making Puzzle Pieces Fit or Reshaping MiMiC for Multiscale Simulations with CP2K and More