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With University of North Texas Affiliation

  1. B. Pampel, S. Holbach, L. Hartung, and O. Valsson
    Sampling Rare Event Energy Landscapes via Birth-Death Augmented Dynamics
    Preprint – arXiv:2209.00607 (2022)
    DOI: 10.48550/arXiv.2209.00607
    arXiv: 2209.00607
    Dataset: DOI
    Simulation Code (v0.3.1): DOI
    Simulation Code on Github: bpampel/bdld
    Simulation Code - Documentation

  2. L. M. Ghiringhelli, C. Baldauf, …, O. Valsson, C. Wöll, and M. Scheffler (see full author list in paper)
    Shared Metadata for Data-Centric Materials Science
    Preprint – arXiv:2205.14774 (2022)
    DOI: 10.48550/arXiv.2205.14774
    arXiv: 2205.14774

  3. J. Hénin, T. Lelièvre, M. R. Shirts, O. Valsson, and L. Delemotte
    Enhanced Sampling Methods for Molecular Dynamics Simulations
    LiveCoMS. 4, 1583 (2022)
    DOI: 10.33011/livecoms.4.1.1583
    arXiv: 2205.14774
    Article Code Repository on Github: jhenin/Methods-for-enhanced-sampling-and-free-energy-calculations

  4. N. Petersen, M. Girard, A. Riedinger, and O. Valsson
    The Crucial Role of Solvation Forces in the Steric Stabilization of Nanoplatelets
    Nano Lett. (2022)
    DOI: 10.1021/acs.nanolett.2c02848
    ChemRxiv: 10.26434/chemrxiv-2022-mw1cs-v3
    Dataset: DOI

  5. J. Rydzewski, M. Chen, T. K. Ghosh, and O. Valsson
    Reweighted Manifold Learning of Collective Variables from Enhanced Sampling Simulations
    J. Chem. Theory Comput. 18, 7179–7192 (2022)
    DOI: 10.1021/acs.jctc.2c00873
    arXiv: 2207.14554

  6. B. Pampel and O. Valsson
    Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials
    J. Chem. Theory Comput. 18, 4127-4141 (2022)
    DOI: 10.1021/acs.jctc.2c00197
    arXiv: 2202.13459
    Dataset: DOI
    PLUMED-NEST: plumID:22.001

Prior to joining University of North Texas

  1. A. Iscen, N. Forero-Martinez, O. Valsson, and K. Kremer
    Acrylic Paints: An Atomistic View of Polymer Structure and Effects of Environmental Pollutants
    J. Phys. Chem. B, 125, 10854 (2021)
    DOI: 10.1021/acs.jpcb.1c05188

  2. J. Rydzewski and O. Valsson
    Multiscale Reweighted Stochastic Embedding: Deep Learning of Collective Variables for Enhanced Sampling
    J. Phys. Chem. A, 125, 6286 (2021)
    DOI: 10.1021/acs.jpca.1c02869
    arXiv: 2007.06377
    Dataset: DOI
    PLUMED-NEST: plumID:21.023

  3. C. Liu, J. G. Brandenburg, O.Valsson, K. Kremer, and T. Bereau
    Free-energy landscape of polymer-crystal polymorphism
    Soft Matter, 16, 9683 (2020)
    DOI: 10.1039/D0SM01342K
    arXiv: 2007.11867

  4. A. Halder, S. Kumar, O. Valsson, and G. Reddy
    Mg2+ Sensing by an RNA Fragment: Role of Mg2+ Coordinated Water Molecules
    J. Chem. Theory Comput. 16, 6702 (2020)
    DOI: 10.1021/acs.jctc.0c00589
    bioRxiv: 10.1101/2020.06.04.133371

  5. O. Valsson and M. Parrinello
    Variationally Enhanced Sampling
    Handbook of Materials Modeling - Methods: Theory and Modeling
    Second Edition (2020) (Editors: W. Andreoni and S. Yip)
    DOI: 10.1007/978-3-319-44677-6_50

  6. Omar Valsson as part of the PLUMED consortium
    Promoting Transparency and Reproducibility in Enhanced Molecular Simulations
    Nature Methods 16, 670 (2019)
    DOI: 10.1038/s41592-019-0506-8

  7. J. Rydzewski and O. Valsson
    Finding Multiple Reaction Pathways of Ligand Unbinding
    J. Chem. Phys. 150, 221101 (2019)
    DOI: 10.1063/1.5108638
    arXiv: 1808.08089
    PLUMED-NEST: plumID:19.066

  8. Y. Wong, O. Valsson, P. Tiwary, M. Parrinello, and K. Lindroff-Larsen
    Frequency Adaptive Metadynamics for the Calculation of Rare-Event Kinetics
    J. Chem. Phys. 149, 072309 (2018)
    Special Topic on Enhanced sampling for Molecular Systems
    DOI: 10.1063/1.5024679
    arXiv: 1802.04182

  9. C. Perego, O. Valsson, and M. Parrinello
    Chemical Potential Calculations in Non-Homogeneous Liquids
    J. Chem. Phys. 149, 072305 (2018)
    Special Topic on Enhanced sampling for Molecular Systems
    DOI: 10.1063/1.5024631
    arXiv: 1804.03477

  10. F. Palazzesi, O. Valsson, and M. Parrinello
    Conformational Entropy as Collective Variable for Proteins
    J. Phys. Chem. Lett. 8, 4752-4756 (2017)
    DOI: 10.1021/acs.jpclett.7b01770
    arXiv: 1704.03344

  11. P. M. Piaggi, O. Valsson, and M. Parrinello
    Enhancing Entropy and Enthalpy Fluctuations to Drive Crystallization in Atomistic Simulations
    Phys. Rev. Lett. 119, 015701 (2017)
    DOI: 10.1103/PhysRevLett.119.015701
    Erratum: 10.1103/PhysRevLett.125.159902
    arXiv: 1612.03235

  12. M. Invernizzi, O. Valsson, and M. Parrinello
    Coarse Graining from Variationally Enhanced Sampling Applied to the Ginzburg–Landau Model
    Proc. Natl. Acad. Sci. USA 114, 3370-3374 (2017)
    DOI: 10.1073/pnas.1618455114

  13. G. Piccini, J. McCarty, O. Valsson, and M. Parrinello
    Variational Flooding Study of a SN2 Reaction
    J. Phys. Chem. Lett. 8, 580–583 (2017)
    DOI: 10.1021/acs.jpclett.6b02852

  14. R. Guareschi, O. Valsson, C. Curutchet, B. Mennucci, and C. Filippi
    Electrostatic versus Resonance Interactions in Photoreceptor Proteins: the Case of Rhodopsin
    J. Phys. Chem. Lett. 7, 4547–4553 (2016)
    DOI: 10.1021/acs.jpclett.6b02043

  15. P. Shaffer, O. Valsson, and M. Parrinello
    Hierarchical Protein Free Energy Landscapes from Variationally Enhanced Sampling
    J. Chem. Theory Comput. 12, 5751–5757 (2016)
    DOI: 10.1021/acs.jctc.6b00786

  16. P. M. Piaggi, O. Valsson, and M. Parrinello
    A Variational Approach to Nucleation Simulation
    Farad. Discuss. 195, 557-568 (2016)
    DOI: 10.1039/C6FD00127K

  17. J. McCarty, O. Valsson, and M. Parrinello
    Bespoke Bias for Obtaining Free Energy Differences within Variationally Enhanced Sampling
    J. Chem. Theory Comput. 12, 2162-2169 (2016)
    DOI: 10.1021/acs.jctc.6b00125

  18. O. Valsson, P. Tiwary, and M. Parrinello
    Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint
    Annu. Rev. Phys. Chem. 67, 159-184 (2016)
    DOI: 10.1146/annurev-physchem-040215-112229

  19. P. Shaffer, O. Valsson and M. Parrinello
    Enhanced, Targeted Sampling of High-Dimensional Free-Energy Landscapes using Variationally Enhanced Sampling, with an Application to Chignolin
    Proc. Natl. Acad. Sci. USA 113, 1150-1155 (2016)
    DOI: 10.1073/pnas.1519712113

  20. J. McCarty, O. Valsson, P. Tiwary, and M. Parrinello
    Variationally Optimized Free-Energy Flooding for Rate Calculation
    Phys. Rev. Lett. 115, 070601 (2015)
    DOI: 10.1103/PhysRevLett.115.070601
    arXiv: 1506.02545

  21. O. Valsson and M. Parrinello
    Well-Tempered Variational Approach to Enhanced Sampling
    J. Chem. Theory Comput. 11, 1996-2002 (2015)
    DOI: 10.1021/acs.jctc.5b00076

  22. O. Valsson, C. Filippi, and M. E. Casida
    Regarding the Use and Misuse of Retinal Protonated Schiff Base Photochemistry as a Test Case for Time-Dependent Density-Functional Theory
    J. Chem. Phys. 142, 144104 (2015)
    DOI: 10.1063/1.4916354

  23. O. Valsson and M. Parrinello
    Variational Approach to Enhanced Sampling and Free Energy Calculations
    Phys. Rev. Lett. 113, 090601 (2014)
    DOI: 10.1103/PhysRevLett.113.090601
    arXiv: 1407.0477

  24. O. Valsson and M. Parrinello
    Thermodynamical Description of a Quasi-First-Order Phase Transition from the Well-Tempered Ensemble
    J. Chem. Theory Comput. 9, 5267-5276 (2013)
    DOI: 10.1021/ct400859f

  25. C. Daday, C. König, O. Valsson, J. Neugebauer, and C. Filippi
    State-Specific Embedding Potentials for Excitation-Energy Calculations
    J. Chem. Theory Comput. 9, 2355-2367 (2013)
    DOI: 10.1021/ct400086a

  26. O. Valsson, P. Campomanes, I. Tavernelli, U. Röthlisberger, and C. Filippi
    Rhodopsin Absorption from First Principles: Bypassing Common Pitfalls
    J. Chem. Theory Comput. 9, 2441-2454 (2013)
    DOI: 10.1021/ct3010408

  27. O. Valsson, C. Angeli, and C. Filippi
    Excitation Energies of Retinal Chromophores: Critical Role of the Structural Model
    Phys. Chem. Chem. Phys. 14, 11015-11020 (2012)
    DOI: 10.1039/C2CP41387F

  28. O. Valsson and C. Filippi
    Gas-Phase Retinal Spectroscopy: Temperature Effects Are But a Mirage
    J. Phys. Chem. Lett. 3, 908-912 (2012)
    DOI: 10.1021/jz300183g

  29. R. Send, O. Valsson, and C. Filippi
    Electronic Excitations of Simple Cyanine Dyes: Reconciling Density Functional and Wave Function Methods
    J. Chem. Theory Comput. 7, 444-455 (2011)
    DOI: 10.1021/ct1006295

  30. O. Valsson and C. Filippi
    Photoisomerization of Model Retinal Chromophores: Insight From Quantum Monte Carlo and Multiconfigurational Perturbation Theory
    J. Chem. Theory Comput. 6, 1275-1292 (2010)
    DOI: 10.1021/ct900692y

  31. O. Valsson, CS. Tang, and V. Gudmundsson
    Coherent Switching by Detuning a Side-Coupled Quantum-Dot System
    Phys. Rev. B 78, 165318 (2008)
    DOI: 10.1103/PhysRevB.78.165318