| Discovering Collective Variables of Molecular Transitions via Genetic Algorithms and Neural Networks F Hooft, A Pérez de Alba Ortíz, B Ensing Journal of Chemical Theory and Computation 17 (4), 2294-2306, 2021 | 35 | 2021 |
| Advances in enhanced sampling along adaptive paths of collective variables A Pérez de Alba Ortíz, A Tiwari, RC Puthenkalathil, B Ensing The Journal of Chemical Physics 149 (7), 2018 | 35 | 2018 |
| Frontiers in Multiscale Modeling of Photoreceptor Proteins MA Mroginski, S Adam, GS Amoyal, A Barnoy, AN Bondar, VA Borin, ... Photochemistry and Photobiology 97 (2), 243-269, 2021 | 27 | 2021 |
| The Adaptive Path Collective Variable: A Versatile Biasing Approach to Compute the Average Transition Path and Free Energy of Molecular Transitions A Pérez de Alba Ortíz, J Vreede, B Ensing Biomolecular Simulations, 255-290, 2019 | 18* | 2019 |
| Strong Reduction of the Chain Rigidity of Hyaluronan by Selective Binding of Ca2+ Ions G Giubertoni, A Pérez de Alba Ortíz, F Bano, X Zhang, RJ Linhardt, ... Macromolecules 54 (3), 1137-1146, 2021 | 13 | 2021 |
| Atomistic insight into the kinetic pathways for Watson–Crick to Hoogsteen transitions in DNA J Vreede, A Pérez de Alba Ortíz, PG Bolhuis, DWH Swenson Nucleic acids research 47 (21), 11069-11076, 2019 | 13 | 2019 |
| Sequence dependence of transient Hoogsteen base pairing in DNA A Pérez de Alba Ortíz, J Vreede, B Ensing PLOS Computational Biology 18 (5), e1010113, 2022 | 9 | 2022 |
| Peptide Side-COOH Groups Have Two Distinct Conformations under Biorelevant Conditions OO Sofronov, G Giubertoni, A Pérez de Alba Ortíz, B Ensing, HJ Bakker The Journal of Physical Chemistry Letters 11 (9), 3466-3472, 2020 | 8 | 2020 |
| Understanding a key step in CO2 to polymers: The role of alkali hydroxides in formate coupling reactions E Schuler, AP de Alba Ortiz, B Ensing, NR Shiju, GJM Gruter J. Am. Chem. Soc, 2022 | 4 | 2022 |
| Simultaneous sampling of multiple transition channels using adaptive paths of collective variables A Pérez de Alba Ortíz, B Ensing arXiv preprint arXiv:2112.04061, 2021 | 3* | 2021 |
| A Boltzmann generator for the isobaric-isothermal ensemble S van Leeuwen, A Pérez de Alba Ortíz, M Dijkstra arXiv preprint arXiv:2305.08483, 2023 | 1 | 2023 |
| Free energies of the Gln tautomerization and rotation mechanism of dark-state recovery in blue light-using flavin proteins A Perez de Alba Ortiz, C Rovira, B Ensing bioRxiv, 2023.08. 11.551373, 2023 | 1 | 2023 |
| Inverse Design of Crystals and Quasicrystals in a Non-Additive Binary Mixture of Hard Disks EA Bedolla-Montiel, JT Lange, A Pérez de Alba Ortíz, M Dijkstra arXiv preprint arXiv:2403.15277, 2024 | | 2024 |
| Enhanced sampling strategies for molecular simulation of DNA B Mohr, T van Heesch, A Pérez de Alba Ortíz, J Vreede Wiley Interdisciplinary Reviews: Computational Molecular Science 14 (2), e1712, 2024 | | 2024 |
| Supplementary Information for: Sequence-dependence of transient Hoogsteen base-pairing in DNA A Pérez de Alba Ortíz, J Vreede, B Ensing | | 2021 |
| Traversing the free-energy pathways of intricate biomolecular processes: Enhanced simulation development and applications A Pérez de Alba Ortíz | | 2021 |
| From high-dimensional stable-state data to interpretable transition pathways and free-energy profiles A Pérez de Alba Ortíz, T van Heesch, B Ensing LatinXChem 2020, 2020 | | 2020 |
| PLUMED Wrapper for OpenPathSampling A Pérez de Alba Ortíz https://e-cam.readthedocs.io/en/latest/Classical-MD-Modules/modules …, 2018 | | 2018 |
| Adaptive QM/MM simulations of proton transfer in water with an energy based reaction coordinate A Pérez de Alba Ortíz | | 2016 |
| Frontiers in Multiscale Modelling of Photoreceptor Proteins MSLP GONZALEZ, RK KAR, I NAVIZET, JMH OLSEN, MRAPDEA ORTÍZ, ... | | |
Bernd EnsingAssociate Professor of Computational Chemistry, University of AmsterdamVerified email at uva.nl
