Dr. A. (Alberto) Pérez de Alba Ortíz
Faculteit der Natuurwetenschappen, Wiskunde en Informatica
Van 't Hoff Institute for Molecular Sciences
Bezoekadres
- Science Park 904
- Kamernummer: C3.259
Postadres
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Postbus 94157
1090 GD Amsterdam
Contactgegevens
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Publicaties
2024
- Bedolla-Montiel, E. A., Lange, J. T., Pérez de Alba Ortíz, A., & Dijkstra, M. (2024). Inverse design of crystals and quasicrystals in a non-additive binary mixture of hard disks. Journal of Chemical Physics, 160(24). https://doi.org/10.1063/5.0210034
Mohr, B., van Heesch, T., Pérez de Alba Ortíz, A., & Vreede, J. (2024). Enhanced sampling strategies for molecular simulation of DNA. Wiley interdisciplinary reviews. Computational molecular science , 14(2), Article e1712. https://doi.org/10.1002/wcms.1712 [details]
2022
- Pérez de Alba Ortíz, A., Vreede, J., & Ensing, B. (2022). Sequence dependence of transient Hoogsteen base pairing in DNA. PLoS Computational Biology, 18(5), Article e1010113. https://doi.org/10.1371/journal.pcbi.1010113 [details]
2021
- Giubertoni, G., Pérez de Alba Ortíz, A., Bano, F., Zhang, X., Linhardt, R. J., Green, D. E., DeAngelis, P. L., Koenderink, G. H., Richter, R. P., Ensing, B., & Bakker, H. J. (2021). Strong Reduction of the Chain Rigidity of Hyaluronan by Selective Binding of Ca2+ Ions. Macromolecules, 54(3), 1137-1146. https://doi.org/10.1021/acs.macromol.0c02242 [details]
- Hooft, F., Pérez de Alba Ortíz, A., & Ensing, B. (2021). Discovering Collective Variables of Molecular Transitions via Genetic Algorithms and Neural Networks. Journal of Chemical Theory and Computation, 17(4), 2294-2306. https://doi.org/10.1021/acs.jctc.0c00981 [details]
- 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., Ferre, N., Filiba, O., Pedraza-Gonzalez, L., Gonzaelez, R., Gonzalez-Espinoza, C. E., Kar, R. K., Kemmler, L., Kim, S. S., Kongsted, J., ... Schapiro, I. (2021). Frontiers in Multiscale Modeling of Photoreceptor Proteins. Photochemistry and Photobiology, 97(2), 243-269. Advance online publication. https://doi.org/10.1111/php.13372 [details]
2020
- Sofronov, O. O., Giubertoni, G., Pérez de Alba Ortiz, A., Ensing, B., & Bakker, H. J. (2020). Peptide Side-COOH Groups Have Two Distinct Conformations under Biorelevant Conditions. Journal of Physical Chemistry Letters, 11(9), 3466-3472. https://doi.org/10.1021/acs.jpclett.0c00711 [details]
2019
- Pérez de Alba Ortíz, A., Vreede, J., & Ensing, B. (2019). The Adaptive Path Collective Variable: A Versatile Biasing Approach to Compute the Average Transition Path and Free Energy of Molecular Transitions. In M. Bonomi, & C. Camilloni (Eds.), Biomolecular Simulations: Methods and Protocols (pp. 255–290). (Methods in Molecular Biology; Vol. 2022). Humana Press. https://doi.org/10.1007/978-1-4939-9608-7_11 [details]
- Vreede, J., Pérez de Alba Ortíz, A., Bolhuis, P. G., & Swenson, D. W. H. (2019). Atomistic insight into the kinetic pathways for Watson-Crick to Hoogsteen transitions in DNA. Nucleic Acids Research, 47(21), 11069-11076. https://doi.org/10.1093/nar/gkz837 [details]
2018
- Pérez de Alba Ortíz, A., Tiwari, A., Puthenkalathil, R. C., & Ensing, B. (2018). Advances in enhanced sampling along adaptive paths of collective variables. Journal of Chemical Physics, 149(7), Article 072320. https://doi.org/10.1063/1.5027392 [details]
Prijs / subsidie
- Pérez de Alba Ortíz, A. (2024). Veni grant: Predicting the risks of nanoplastics for cardiovascular health. https://hims.uva.nl/content/news/2024/07/veni-grant-for-computational-scientist-alberto-perez-de-alba-ortiz.html?origin=4zNaIwCsT1iMc%2FL4U9Sh2Q
- Shahidzadeh, N., Perez de Alba Ortiz, A. & Woutersen, S. (2023). AI4SMM postdoctoral fellowship.
- Bolhuis, P., van Hoof, H., Jabbari Farouji, S., Quattrocchio, F. M., Schall, P. & Perez de Alba Ortiz, A. (2023). AI4SMM postdoctoral fellowship.
Lidmaatschap / relevante positie
- Perez de Alba Ortiz, A. (2023-). member, KNCV.
Spreker
- Perez de Alba Ortiz, A. (speaker) (24-2-2023). Harnessing ML to Sample, Analyze & Engineer Modes in Molecular & Colloidal Systems, AI4Science symposium.
- Perez de Alba Ortiz, A. (speaker) (24-2-2023). Computationally understanding & designing living-like soft matter, Utrecht University Nanoseminar.
- Perez de Alba Ortiz, A. (speaker) (9-12-2020). Unraveling a protein signaling mechanism with enhanced simulation, CHAINS 2020.
Andere
- Perez de Alba Ortiz, A. (participant) (4-4-2023 - 5-4-2023). NWO Physics, Veldhoven (participating in a conference, workshop, ...).
- Perez de Alba Ortiz, A. (participant) (30-1-2023 - 3-2-2023). Designing Soft Matter in and out of Equilibrium, Leiden. Lorentz center workshop (prepared while UU affiliated) (organising a conference, workshop, ...).
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Nevenwerkzaamheden
Geen nevenwerkzaamheden
Mohr, B., van Heesch, T., Pérez de Alba Ortíz, A., & Vreede, J. (2024). Enhanced sampling strategies for molecular simulation of DNA. Wiley interdisciplinary reviews. Computational molecular science , 14(2), Article e1712.