Publications

RCSG ACCOMPLISHMENTS

The Research Computing Support Group (RCSG) at UT San Antonio has been published in a range of materials showcasing their contributions to computational research. These publications highlight innovative methodologies, case studies, and collaborative projects, providing valuable insights and advancements in the field of research computing.

 

ACKNOWLEDGING OUR SUPPORT:

If you'd like to acknowledge our computing resources or support, please be sure to refer to our environment as ARC and the university as "The University of Texas at San Antonio" or "UT San Antonio." 

PUBLISHED RESEARCH

 Avidani, Y., Angert, A., Davidson, C., Xia, X., Gao, Y., & Amrani, A. (2024). Sulfur isotopic fractionation during hydrolysis of carbonyl sulfide. Marine Chemistry, 267, 104458. https://doi.org/10.1016/j.marchem.2024.104458

 

Bagherian, A., Abbasi Ghiri, A., Ramzanpour, M., Wallace, J., Elashy, S., & Seidi, M. (2025). Position-based assessment of head impact frequency, severity, type, and location in high school American football. Frontiers in Bioengineering and Biotechnology, 12. https://doi.org/10.3389/fbioe.2024.1500786 

 

Castillo, O., Mancillas, J., Hughes, W., & Brancaleon, L. (2022). Characterization of the interaction of metal-protoporphyrins photosensitizers with β-lactoglobulin. Biophysical Chemistry, 106918. https://doi.org/10.1016/j.bpc.2022.106918 

 

Cheng, K., Chen, I. C., Cheng, C. E., Mutoji, K., Hale, B. J., Hermann, B. P., Geyer, C. B., Oatley, J. M., & McCarrey, J. R. (2020). Unique epigenetic programming distinguishes regenerative spermatogonial stem cells in the developing mouse testis. iScience, 23(10), 101596. https://doi.org/10.1016/j.isci.2020.101596 

 

Fenner, K., Redgate, A., & Brancaleon, L. (2022). A 200 nanoseconds all-atom simulation of the pH-dependent EF loop transition in bovine β-lactoglobulin: The role of the orientation of the E89 side chain. Journal of Biomolecular Structure and Dynamics, 40(1), 549–564. https://doi.org/10.1080/07391102.2020.1817785 

 

Garcia, I., & Morales Escalante, J. (2025). Physics informed neural networks for a Wigner-Fokker-Planck model of open quantum systems. In M. Paszynski, A. S. Barnard, & Y. J. Zhang (Eds.), Computational Science – ICCS 2025 Workshops (Lecture Notes in Computer Science, Vol. 15909). Springer. https://doi.org/10.1007/978-3-031-97564-6_22

 

Kumaresan, V., Hung, C. Y., Hermann, B. P., & Seshu, J. (2025). Role of dual specificity phosphatase 1 (DUSP1) in influencing inflammatory pathways in macrophages modulated by Borrelia burgdorferi lipoproteins. bioRxiv. https://doi.org/10.1101/2024.11.20.624562

 

Kumaresan, V., Ingle, T. M., Kilgore, N., Zhang, G., Hermann, B. P., & Seshu, J. (2023). Cellular and transcriptome signatures unveiled by single-cell RNA-Seq following ex vivo infection of murine splenocytes with Borrelia burgdorferi. Frontiers in Immunology, 14, 1296580. https://doi.org/10.3389/fimmu.2023.1296580

 

Lee, J., Toujani, C., Tang, Y., Lee, R., Cureño Hernandez, K. E., Guilliams, B. F., Pochan, D. J., Ramírez-Hernández, A., & Herrera-Alonso, M. (2025). Nonequilibrium solution-based assemblies from bottlebrush block copolymers for drug delivery. ACS Nano, 19(19), 18556–18569. https://doi.org/10.1021/acsnano.5c02267

 

Montaño-Priede, J. L., & Large, N. (2022). Photonic band structure calculation of 3D-finite nanostructured supercrystals. Nanoscale Advances, 4(21), 4589–4596. https://doi.org/10.1039/D2NA00538G 

 

Montaño-Priede, J. L., Mlayah, A., & Large, N. (2022). Raman energy density in the context of acoustoplasmonics. Physical Review B, 106(16), 165425. https://doi.org/10.1103/PhysRevB.106.165425

 

Mondal, S., Montaño-Priede, J. L., Nguyen, V. T., Park, S., Choi, J., Doan, V. H. M., Vo, T. M. T., Vo, T. H., Large, N., Kim, C.-S., & Oh, J. (2022). Computational analysis of drug-free silver triangular nanoprism theranostic probe plasmonic behavior for in-situ tumor imaging and photothermal therapy. Journal of Advanced Research, 41, 23–38. https://doi.org/10.1016/j.jare.2022.02.006 

 

Olivares, E., & Wilson, C. J. (2025). Neuronal and network resonance in the external globus pallidus. Journal of Neurophysiology, 134(2), 794–813. https://doi.org/10.1152/jn.00270.2025

 

Olivares, E., Higgs, M. H., & Wilson, C. J. (2022). Local inhibition in a model of the indirect pathway globus pallidus network slows and deregularizes background firing, but sharpens and synchronizes responses to striatal input. Journal of Computational Neuroscience, 50(2), 251–272. https://doi.org/10.1007/s10827-022-00814-y

 

Olivares, E., Wilson, C. J., & Goldberg, J. A. (2024). Phase delays between mouse globus pallidus neurons entrained by common oscillatory drive arise from their intrinsic properties, not their coupling. eNeuro, 11(5). https://doi.org/10.1523/ENEURO.0187-24.2024

 

Padilla, L. A., León-Islas, A. A., Funkhouser, J., Armas-Pérez, J. C., & Ramírez-Hernández, A. (2021). Dynamics and phase behavior of two-dimensional size-asymmetric binary mixtures of core-softened colloids. The Journal of Chemical Physics, 155(21), 214901. https://doi.org/10.1063/5.0067449 

 

Park, Y., Li, B., & Li, Y. (2023). Crop yield prediction using Bayesian spatially varying coefficient models with functional predictors. Journal of the American Statistical Association, 118(541), 70–83. https://doi.org/10.1080/01621459.2022.2123333 

 

Ramzanpour, M., Jafari, B., Smith, J., Allen, J., & Hajiaghamemar, M. (2023). Comprehensive study of sex-based anatomical variations of human brain and development of sex-specific brain templates. Brain Multiphysics, 4, 100077. https://doi.org/10.1016/j.brain.2023.100077 

 

Renthal, R. (2024). Arthropod repellent interactions with olfactory receptors and ionotropic receptors analyzed by molecular modeling. Current Research in Insect Science, 5, 100082. https://doi.org/10.1016/j.cris.2024.100082 

 

Rigor, J., Kurouski, D., & Large, N. (2022). Plasmonic heating effects in tip-enhanced Raman spectroscopy (TERS). The Journal of Physical Chemistry C, 126(32), 13986–13993. https://doi.org/10.1021/acs.jpcc.2c03881 

 

Salinas-Soto, C. A., Choe, Y., Hur, S.-M., & Ramírez-Hernández, A. (2023). Exploring conformations of comb-like polymers with varying grafting density in dilute solutions. The Journal of Chemical Physics, 159(11), 114901. https://doi.org/10.1063/5.0148986 

 

Salinas-Soto, C. A., Padilla-Gutierrez, C., Herrera-Alonso, M., Urena-Benavides, E., & Ramirez-Hernandez, A. (2024). Structure and organization of amphiphilic mikto-grafted molecular brushes at liquid/liquid planar interfaces. Macromolecules, 57, 2773. https://doi.org/10.1039/D6SM00097E

 

Salinas-Soto, C. A., Zhao, B., & Ramírez-Hernández, A. (2025). Nanopatterning of liquid–liquid interfaces by mikto-grafted molecular brush polymers. Macromolecules, 58(17), 9259–9271. https://doi.org/10.1021/acs.macromol.5c01807

 

Seita, Y., Cheng, K., McCarrey, J. R., Yadu, N., Cheeseman, I. H., Bagwell, A., Ross, C. N., Santana Toro, I., Yen, L. H., Vargas, S., Navara, C. S., Hermann, B. P., & Sasaki, K. (2023). Efficient generation of marmoset primordial germ cell-like cells using induced pluripotent stem cells. eLife, 12, e82263. https://doi.org/10.7554/eLife.82263 

 

Sharma, C., Başağağoğlu, H., Yoosefdoost, I., Wootten, A., Chakraborty-Reddy, D., Bertetti, F. P., Mirchi, A., & Chakraborty, D. (2025). Efficacy of mitigation strategies for aquifer sustainability under climate change. Nature Sustainability, 8(1), 44–53. https://doi.org/10.1038/s41893-024-01477-6 

 

Singh, A., & Hermann, B. P. (2023). Bulk and single-cell RNA-Seq analyses for studies of spermatogonia. Methods in Molecular Biology, 2656, 37–70. https://doi.org/10.1007/978-1-0716-3139-3_4

 

Suzuki, S., McCarrey, J. R., & Hermann, B. P. (2021). Differential RA responsiveness among subsets of mouse late progenitor spermatogonia. Reproduction, 161(6), 645–655. https://doi.org/10.1530/REP-21-0031 

 

Toujani, C., Padilla, L. A., Alhraki, N., Hur, S.-M., & Ramírez-Hernández, A. (2024). Self-assembly of rod-coil-rod block copolymers in a coil-selective solvent: Coarse-grained simulation results. Soft Matter. https://doi.org/10.1039/D4SM00251B 

 

Uboh, N., Vargas, S., Diaz, V. D., & Hermann, B. P. (2025). Spatial transcriptomic analyses of spermatogenesis. Methods in Molecular Biology, 2954, 49–94. https://doi.org/10.1007/978-1-0716-4698-4_3

 

Vásquez–Briceño, A., Pérez–Lemus, G. R., Armas–Pérez, J. C., & Ramírez–Hernández, A. (2025). Multiblock copolymers at liquid–liquid interfaces: Effect of the block sequence on interfacial tension and polymer conformation. Journal of Physical Chemistry B, 129(11), 3041–3052. https://doi.org/10.1021/acs.jpcb.4c07448

 

Vásquez–Briceño, A., Salinas–Soto, C. R., Ureña–Benavides, E., & Ramírez–Hernández, A. (2026). Conformations and interfacial activity of amphiphilic bottlebrush block copolymers at the interface of immiscible liquids. Macromolecules. Advance online publication. https://doi.org/10.1021/acs.macromol.5c03499

 

Xia, X., & Gao, Y. (2023). Determining reaction paths by evaluating kinetic isotopic effects with density functional theory: Example of methane thermogenesis. Journal of Chemical Information and Modeling, 63(9), 2742–2747. https://doi.org/10.1021/acs.jcim.3c00531 

 

Xia, X., & Gao, Y. (2024). Compound-specific, intra-molecular, and clumped 13C fractionations in the thermal generation and decomposition of ethane and propane: A DFT and kinetic investigation. Geochimica et Cosmochimica Acta, 375, 50–63. https://doi.org/10.1016/j.gca.2024.05.001