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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]
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]
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]
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 (1 ed.) https://doi.org/10.1007/978-1-4939-9608-7_11
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]
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]
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.
Membership / relevant position
Perez de Alba Ortiz, A. (2023-). member, KNCV.
Talk / presentation
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.
Others
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, ...).
2021
Pérez de Alba Ortíz, A. (2021). Traversing the free-energy pathways of intricate biomolecular processes: Enhanced simulation development and applications. [Thesis, fully internal, Universiteit van Amsterdam]. [details]
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