SOM research
Escalona, Yerko, Drazen Petrov, and Chris Oostenbrink. 2023. “Exploring the Macroscopic Properties of Humic Substances using Modeling and Molecular Simulations [accepted].” Agronomy MDPI, 2023.
Edgar Galica-Andres, Escalona, Yerko, Drazen Petrov, and Chris Oostenbrink. “Molecular Dynamics Simulations up to Earth: Modeling of Soil Organic Matter [accepted].” Comprehensive Computational Chemistry, 2023.
Escalona, Yerko, Drazen Petrov and Chris Oostenbrink. 2021. “Modeling soil organic matter: Changes in macroscopic properties due to microscopic changes.” Geochimica Et Cosmochimica Acta 307: 228–41. https://doi.org/10.1016/j.gca.2021.05.035.
Escalona, Yerko, Drazen Petrov and Chris Oostenbrink. 2021. “Vienna soil organic matter modeler 2 (VSOMM2).” Journal of Molecular Graphics and Modelling 103: 107817. https://doi.org/10.1016/j.jmgm.2020.107817.
Gotsmy, Mathias, Escalona, Yerko, Chris Oostenbrink, and Drazen Petrov. 2021. “Exploring the structure and dynamics of proteins in soil organic matter.” Proteins: Structure, Function and Bioinformatics, no. February: 925–36. https://doi.org/10.1002/prot.26070.
Galicia-Andrés, Edgar, Escalona, Yerko, Chris Oostenbrink, Daniel Tunega, and Martin H. Gerzabek. 2021. “Soil organic matter stabilization at molecular scale: The role of metal cations and hydrogen bonds.” Geoderma 401 (June): 115237. https://doi.org/10.1016/j.geoderma.2021.115237.
Graphene research
Escalona, Yerko, Nicolas Espinoza, Chris Oostenbrink, and Jose Antonio Garate. 2022. “On the effects of induced polarizability at the water-graphene interface via classical charge-on-spring models.” Phys. Chem. Chem. Phys., 2022,24, 7748-7758. https://doi.org/10.1039/D1CP05573A.
Garate, Jose Antonio, Alejandro Bernardin, Escalona, Yerko, Carlos Yanez, Niall J. English, and Tomas Perez-Acle. 2019. “Orientational and Folding Thermodynamics via Electric Dipole Moment Restraining.” Journal of Physical Chemistry B 123 (12): 2599–2608. https://doi.org/10.1021/acs.jpcb.8b09374.
GJC research
Escalona, Yerko, Jose A Garate, Raul Araya-Secchi, Tien Huynh, Ruhong Zhou, and Tomas Perez-Acle. 2016. “Exploring the Membrane Potential of Simple Dual-Membrane Systems as Models for Gap-Junction Channels.” Biophysical Journal 110 (12): 2678–88. https://doi.org/10.1016/j.bpj.2016.05.005.
Escalona, Yerko, Jose A Garate, and Tomas Perez-Acle. 2015. “Exploring the membrane potential of a simple dual membrane system by using a constant electric field.” BMC Bioinformatics 16 (Suppl 8): A5. https://doi.org/10.1186/1471-2105-16-S8-A5.
Vargas, Anibal A, Bruno A Cisterna, Fujiko Saavedra-Leiva, Carolina Urrutia, Luis A Cea, Alex H Vielma, Sebastian E Gutierrez-Maldonado, et al. 2017. “On Biophysical Properties and Sensitivity to Gap Junction Blockers of Connexin 39 Hemichannels Expressed in HeLa Cells.” Frontiers in Physiology. https://doi.org/10.3389/fphys.2017.00038.
Villanelo, F, Escalona, Y, C Pareja-Barrueto, J A Garate, I M Skerrett, and T Perez-Acle. 2017. “Accessing gap-junction channel structure- function relationships through molecular modeling and simulations.” BMC Cell Biology 28 (Suppl 1): 1–15. https://doi.org/10.1186/s12860-016-0121-9.
Brennan, Matthew J, Jennifer Karcz, Nicholas R Vaughn, Yvonne Woolwine-Cunningham, Adam D DePriest, Escalona, Yerko, Tomas Perez-Acle, and I Martha Skerrett. 2015. “Tryptophan scanning reveals dense packing of connexin transmembrane domains in gap junction channels composed of connexin32.” Journal of Biological Chemistry 290 (28): 17074–84. https://doi.org/10.1074/jbc.M115.650747.
Araya-Secchi, Raul, Tomas Perez-Acle, Seung Gu Kang, Tien Huynh, Alejandro Bernardin, Escalona, Yerko, Jose Antonio Garate, et al. 2014. “Characterization of a novel water pocket inside the human Cx26 hemichannel structure.” Biophysical Journal 107 (3): 599–612. https://doi.org/10.1016/j.bpj.2014.05.037.