UTSA logo

The Santamaria Computational Neuroscience Laboratory

Main Content

PubMed  Google Scholar  Research Gate

REFEREED JOURNAL PUBLICATIONS

  1. 1. Gimenez, P., Shakya, R. T., Santamaria, F., & Tønnesen, J. (2026). Extracellular space diffusion modelling identifies distinct functional advantages of glutamatergic and GABAergic synapse geometries. Fluids and Barriers of the CNS.
  2. Miller, J. A., Pahlavan, B., Gamboa, B., & Santamaria, F. (2025). Incorporating the thermodynamic effects of temperature and pressure on modeling neuronal gating kinetics. PLoS One, 20(10), e0333592.
  3. Miller, J. A., Pahlavan, B., Gamboa, B., & Santamaria, F. (2025). Incorporating the thermodynamic effects of temperature and pressure on modeling neuronal gating kinetics. PLoS One, 20(10), e0333592.
  4. Nelson, J. S., Meyer, J., Gerkau, N. J., Kafitz, K. W., Ullah, G., Santamaria, F., & Rose, C. R. (2025). Spatio-temporal dynamics of lateral Na+ diffusion in apical dendrites of mouse CA1 pyramidal neurons. Journal of Neuroscience.
  5. Vazquez-Guerrero, P., Tuladhar, R., Psychalinos, C., Elwakil, A., Chacron, M. J., & Santamaria, F. (2024). Fractional order memcapacitive neuromorphic elements reproduce and predict neuronal function. Scientific Reports, 14(1), 5817.
  6. Daniel Levenstein, Veronica A Alvarez, Asohan Amarasingham, Habiba Azab, Zhe Sage Chen, Richard C Gerkin, Andrea Hasenstaub, Ramakrishnan Iyer, Renaud B Jolivet, Sarah Marzen, Joseph D Monaco, Astrid A Prinz, Salma Quraishi, Fidel Santamaria, Sabyasachi Shivkumar, Matthew F Singh, Roger Traub, Horacio G Rotstein, Farzan Nadim, A David Redish. "On the role of theory and modeling in neuroscience." Journal of Neuroscience 43.7 (2023): 1074-1088.
  7. Pahlavan, Bahram, Nicolas Buitrago, and Fidel Santamaria. "Macromolecular rate theory explains the temperature dependence of membrane conductance kinetics." Biophysical Journal 122.3 (2023): 522-532.
  8. Monje-Reyna, Daniela, Jorge Manzo Denes, and Fidel Santamaria. "Effects of environmental enrichment and sexual dimorphism on the expression of cerebellar receptors in C57BL/6 and BTBR+ Itpr3tf/J mice." BMC research notes 15.1 (2022): 1-7.
  9. Rohisha Tuladhar, Paolo Grigolini, Fidel Santamaria. (2022). The allometric propagation of COVID-19 is explained by human travel. Infectious Disease Modelling, Volume 7, Issue 1, Pages 122-133.
  10. Tuladhar R, Stamova I, Santamaria F. Fractional Lotka–Volterra-type Biological Network Cooperation (2020). Entropy 22(9), 970.
  11. Coronel-Escamilla A, Gomez-Aguilar JF, Stamova I, Santamaria F. (2020).Fractional order controllers increase the robustness of closed-loop brain stimulation systems. Chaos, Solitons & Fractals 140. DOI: 10.1016/j.chaos.2020.110149
  12. Vazquez-Guerrero P, Gómez-Aguilar JF, Santamaria F, Escobar-Jiménez RF (2020). Design of a high-gain observer for the synchronization of chimera states in neurons coupled with fractional dynamics. Physica A, 539. DOI: 10.1016/j.physa.2019.122896
  13. Kim EJ, Feng C, Santamaria F, and Kim JH (2019). Impact of auditory experience on the ​structural plasticity of the AIS in the mouse brainstem throughout the lifespan. Frontiers. Cell. Neurosci. 13. DOI: 10.3389/fncel.2019.00456
  14. Vazquez-Guerrero P, Gomez-Aguilar JF, Santamaria F, and Escobar-Jimenez FR (2019). Synchronization patterns with strong memory adaptive control in networks of coupled neurons with chimera states dynamics. Chaos, Solitons and Fractals. DOI: 10.1016/j.chaos.2019.07.057
  15. Stockton D and Santamaria F (2017). Integrating the Allen Brain Institute Cell Types Database into automated neuroscience workflow. Neuroinformatics. DOI: 10.1007/s12021-017-9337-x.
  16. Stockton D and Santamaria F (2016). Automating NEURON simulation deployment in cloud resources. Neuroinformatics. DOI: 10.1007/s12021-016-9315-8
  17. Yang Z and Santamaria F. (2016) Purkinje cell intrinsic excitability increases after synaptic long term depression. J Neurophysiology. DOI: 10.1152/jn.00369.2016
  18. Mohapatra N, Tønnesen J, Vlachos A, Kuner T, Dealers T, Nägerl UV, Santamaria F, and Jedlicka P. (2016) Spines slow down dendritic chloride diffusion and affect short-term ionic plasticity of GABAergic inhibition. Scientific Reports 6:23196. DOI: 10.1038/srep23196.
  19. Teka W, Stockton DB, and Santamaria F. (2016) Power-law dynamics of membrane conductances increase spiking diversity in a Hodgkin-Huxley model. In press PLoS Computational Biology. DOI: 10.1371/journal.pcbi.1004776
  20. Stockton DB and Santamaria F. (2015) NeuroManager: A workflow analysis based simulation management engine for computational neuroscience. Frontiers in Neuroinformatics Vol. 9(24) DOI:10.3389/fninf.2015.00024
  21. Romero VH, Kereselidze Z, Egido W, Michaelides EA, Santamaria F, and Peralta XG. (2014). Nanoparticle assisted photothermal deformation of individual neuronal organelles and cells. Biomedical Optics Express. Vol. 5(11), pp 4002-4012. DOI:  10.1364/BOE.5.004002.
  22. Salinas K, Kereselidze Z, Peralta XG, Santamaria F. (2014) Transient extracellular application of gold nano-stars increases hippocampal neuronal activity. J. of Nanobiotechnology 12(31) DOI: http://dx.doi.org/10.1186/s12951-014-0031-y.
  23. Teka W, Marinov T, Santamaria, F. (2014). Neuronal Spike Timing Adaptation Described with a Fractional Leaky Integrate-and-Fire Model. PLoS Comput Biol 10(3): e1003526. DOI: 10.1371/journal.pcbi.1003526.
  24. Marinov TM and Santamaria F. (2014) Computational modeling of diffusion in the cerebellum. Prog Mol Biol Transl Sci.123:169-89. DOI: 10.1016/B978-0-12-397897-4.00007-3.
  25. Marinov T, Rodriguez N, Santamaria F. (2013). Fractional Integration Toolbox. Journal of Fractional Calculus and Analysis. Vol 16(3). DOI: 10.2478/s13540-013-0042-7.
  26. Kereselidze Z, Romero VH, Peralta XG, Santamaria F. (2012) Gold nanostar synthesis with a modified silver seed mediated growth method. J. Vis. Exp. (59), e3570, DOI: 10.3791/3570.
  27. Santamaria F, Wils S, De Schutter E, Augustine GJ. (2011) The diffusional properties of dendrites depend on the density of dendritic spines. Eur. J. Neurosci. 34(4) pp561-568. DOI: 10.1111/j.1460-9568.2011.07785.x.
  28. Valdez VM, Phelix CF, Smith MA, Perry G, Santamaria F. (2011) Modeling cholesterol metabolism by gene expression profiling in the hippocampus. Molecular BioSystems. Vol 7, pp 1891-1901. DOI: 10.1039/C0MB00282H.
  29. Santamaria F, Gonzalez J, Augustine GJ, and Ragavachari S. (2010) Quantifying the effects of elastic collisions and non-covalent binding on glutamate receptor trafficking in the post-synaptic density. PLoS Comp. Bio. 6(5), May 2010. DOI: 10.1371/journal.pcbi.1000780.
  30. Coop A, Cornelis H, and Santamaria F. (2010) Quantification of the contribution of dendritic channel activity to information processing in a Purkinje cell model. Front. Comput. Neurosci. 4:6. DOI: 10.3389/fncom.2010.00006.
  31. Valdez CM, Smith MA, Perry G, Phelyx CF, Santamaria F. (2010) Cholesterol homeostasis markers are localized to mouse hippocampal pyramidal and granule layers. Hippocampus. Vol 20(8) pp 902-905.  DOI: 10.1002/hipo.20743.
  32. Santamaria F, Tripp P and Bower JM. (2007) Molecular interneuron feed forward inhibition controls the spread of granule cell activity in the cerebellar cortex. J. Neurophys., 97(1):248-63. DOI: 10.1152/jn.01098.2005
  33. Tanaka K, Kirough L, Santamaria F, Doi T, Ogaswara H, Ellis-Davies G, Kawato M, Augustine GJ. (2007) Ca2+ requirements for cerebellar long-term synaptic depression: role for a postsynaptic leaky integrator. Neuron 54(5):787-800. DOI : 10.1016/j.neuron.2007.05.014
  34. Santamaria F, Wils S, De Schutter E, Augustine GJ. (2006) Anomalous diffusion in Purkinje cell dendrites caused by spines. Neuron 52(4):635-648. DOI:  10.1016/j.neuron.2006.10.025.
  35. Santamaria F and Bower JM. (2005) Background synaptic activity modulates the response of a modeled Purkinje cell to paired afferent input. J. Neurophys. 93: 237-250. DOI: 10.1152/jn.00458.2004
  36. Augustine GJ, Santamaria F, Yamamoto K. (2003) Local calcium signaling in neurons. Neuron 20(2):331-346. DOI: 10.1016/S0896-6273(03)00639-1
  37. Santamaria F, Jaeger D, De Schutter E and Bower JM. (2002)  Modulatory effects of parallel fibers and molecular layer interneuron synaptic activity on the Purkinje cell responses to ascending segment input: A modeling study. J. Comp. Neurosc., 13(3):217-35. DOI:  2010.1023/A:1020266315730
  38. Mocanu OD, Oliver J, Santamaria F and Bower JM. (2000) Branching point effects on the passive properties of the cerebellar granule cell. Neurocomputing 32-33:207-212.  DOI: 10.1016/S0925-2312(00)00165-X
  39. Marsalek P and Santamaria F. (1998) Investigating spike backpropagation induced Ca2+ influx in models of hippocampal and cortical pyramidal neurons. BioSystems 48:147-156. DOI: 10.1016/S0303-2647(98)00060-4

BOOK CHAPTERS

  1. Coronel-Escamilla, Tuladhar R, Santamaria F. Fractional Order Dynamics to study neuronal function. Book Chapter due September 2020. To Appear in "Fractional Order Systems: Mathematics, Design, and Applications for Engineers". Elsevier.
  2. Santamaria F and Peralta XG. (2018). Two applications of Gold nanostars to Hippocampal Neuronal cells: Localized phototermal ablation and stimulation of firing rate. Use of nanoparticles in neuroscience. Santamaria F and Peralta XG eds. Springer.
  3. Weinberg SH and Santamaria F. (2017). History dependent neuronal activity modeled with fractional order dynamics. Computational models of brain and behavior. Moustafa A Ed. Wiley-Blackwell.
  4. Santamaria F. (2015) Cerebellum: Overview. Encyclopedia of Computational Neuroscience. Jung and Jaeger Eds. Springer.
  5. Marinov T and Santamaria F. (2015) Diffusion Equation. Encyclopedia of Computational Neuroscience. Jung and Jaeger Eds. Springer.
  6. Michaelides E and Santamaria F. (2015). Multi-Scale Modeling of Purkinje Cells. Encyclopedia of Computational Neuroscience. Jung and Jaeger Eds. Springer.
  7. Deans H and Santamaria F. (2015). Modeling ion concentrations. Encyclopedia of Computational Neuroscience. Jung and Jaeger Eds. Springer.
  8. Santamaria F, Antunes G, and De Schutter E. (2012) Breakdown of mass-action laws in biochemical computation. Computational Systems Neurobiology, La Novere and Bhalla Eds. Springer.
  9. Santamaria F and Bower JM (2009) Hodgkin-Huxley models. The Encyclopedia of Neuroscience. Squire LR Ed. Elsevier. DOI:10.1016/B978-008045046-9.01413-3

CONFERENCE PROCEDING (refereed)

  1. Stockton DB, Prinz AA, and Santamaria F. Provenance and Reproducibility in the Automation of a Standard Computational Neuroscience Pipeline. P-RECS '19 Proceedings of the 2nd International Workshop on Practical Reproducible Evaluation of Computer Systems. Pages 7-12. Phoenix, AZ, June 24, 2019.
  2. Santamaria F. (2015). Effect of power-law ionic conductances in the Hodgkin and Huxley model (Suppl 1 ed., vol. 16, pp. P250). BMC Neuroscience. DOI: 10.1186/1471-2202-16-S1-P250
  3. Marinov T and Santamaria F (2013). Modeling the effects of anomalous diffusion on synaptic plasticity. BMC Neuroscience 14(1). DOI: 10.1186/1471-2202-14-S1-P343
  4. Deans H and Santamaria F (2012) Modeling the effects of molecular crowding on cerebellar long term depression. BMC Neuroscience 13(1). DOI: 10.1186/1471-2202-13-S1-P47
  5. Coop A, Cornelis H, and Santamaria F (2010). Synaptic activity and excitability modulates information transfer in Purkinje cells: a modeling study. BMC Neuroscience 11(Suppl 1). DOI: 10.1186/1471-2202-11-S1-P165.
  6. Deans H, Sherwood D, and Santamaria F (2010). The effects of molecular crowding on LTD expression. BMC Neuoscience 11 (Suppl 1). DOI: 10.1186/1471-2202-11-S1-P6.
  7. Wang Z, Robbins K, Wang Y, Becker Livi C, Coop AD, Santamaria F, Wendk C, Bower JM (2010). Building an institutional base for Computational Neuroscience: the CBI at UTSA/UTHSCSA. BMC Neuroscience 11 (Suppl 1). · DOI: 10.1186/1471-2202-11-S1-P67

BOOK

Use of nanoparticles in neuroscience. Santamaria F. and Peralta XG, editors. Neuromethods, vol. 135. Springer. 2018. ISBN 978-1-4939-7584-6