Ongoing Research

(links to download models provided for model pubs)

Trainee names in green

  • Three interactive talks at, Online conference: (i) A Aberbach, B Latimer, DB Headley, SS Nair (2020) Optimizing detailed L5 pyramidal cell model in the rodent motor cortex to predict in vivo characteristics  (Adin is a high school student mentored by Ben); N Opsal, P Canfield, T Banks, SS Nair (2020) Segregation of current modules for efficient and accurate single neuron models; D Dopp, Z Chen, D Headley, SS Nair (2020) Automated estimation of morphology of a neocortical neuron using in vivo LFP records.
  • Vekaria et al. (2020) Recommender-as-a-service with chatbot guided domain-science knowledge discovery in a science gateway, Concurrency and Computation: Practice and Experience, Wiley Press (in press)
  • Feng FLi Y, Latimer B, Zhang C, Nair SS, Hu Z (2020) Prediction of maximum algal productivity in membrane bioreactors with a light-dependent growth model, Science of the Total Environment (in press) Link
  • Guntu V, Latimer B, Shappell E, Schulz D, Nair SS (2020) Challenges in modeling the neural control of LUT, Chapter in Bladder Physiology , Appukuttan and Manchanda (Editors), (in review) PDF.
  • Joshi SR, Headley DB, Ho, KC, Pare D, Nair SS (2019) Classification of brainwaves using convolutional neural network, Proc. 27th European Signal Processing Conf (EUSPICO), A Coruña, Spain. pp. 1-5.
  • Eight posters at the Neuroscience 2019, Annual Meeting of the Society for Neuroscience, Oct 19-23, 2019, Chicago, IL: (i) F Feng, D Headley, V Kanta, D Pare, SS Nair: Closed-loop control of gamma oscillations in BLA – a computational perspective; (ii) Z Chen, F Feng, D Headley, KC Ho, D Pare, SS Nair: Detection and characterization of gamma bursts in LFP signals; (iii) V Guntu, T Banks, A Hummos, SS Nair: Characterizing resonant and synchronizing mechanisms in a hippocampal theta model; (iv) D Dopp, J Wang, P Samarth, D Kick, D Schulz, SS Nair: Structure of large cells in crab cardiac ganglion – a computational study; (v) E Shappel, B Latimer, T Banks, V Guntu, D Schulz, SS Nair: Computational modeling of the neural circuit of a rodent lower urinary tract; (vi) Q Wei, Z Chen, T Banks, B Latimer, Z Chen, SS Nair: Automating development of biophysical single cell and network models; (vii) T Banks, B Latimer, Z Chen, Z Lyu, Z Chen, D Dopp, A Fotoohighiam, P Calyam, T Joshi, D Xu, SS Nair: Software Automation for research and training in neural engineering; (viii) E Shappell, B Latimer, SS Nair: Neural engineering lesson plans for grades 5-12.
  • Feng FHeadley DB, Amir A, Kanta V, Chen Z, Pare D, Nair SS (2019) Gamma oscillations in the basolateral amygdala: biophysical mechanisms and computational consequences, eNeuro 6(1) e0388-18.2018 1–25  PDF   Source Code at Model DB
  • Latimer B, Bergin DB, Guntu V, Schulz DJ, Nair SS (2019), Integrating model-based approaches into a neuroscience curriculum – An interdisciplinary neuroscience course in engineering, IEEE Transactions on Education 62(1) 48-56  PDF
  • Lane BJ, Kick DR, Wilson DK, Nair SS, Schulz DJ (2018) Dopamine maintains network synchrony via direct modulation of gap junctions in the crustacean cardiac ganglion, eLife 10.7554/eLife.39368.001   PDF
  • Latimer B, Bergin DB, Guntu V, Schulz DJ, Nair SS (2018), Open source software tools for teaching neuroscience, Journal of Undergraduate Neuroscience Education 16(3):A197-A202PDF
  • Calyam P, Nair SS (2018) Science gateway development to aid cyber and software automation for neuroscience researchers and educators, 13th Gateway Computing Environments Conference (Gateways), Austin, TX (Sept 25-27, 2018)
  • Zhang Y, Calyam P, Joshi T, Nair SS, Xu D (2018) Domain-specific topic model for knowledge discovery through conversational agents in data intensive scientific communities, IEEE International Workshop on Conversational Agents and Chatbots with Machine Learning (ChatbotML), in conjunction with IEEE Big Data, Seattle, WA (Dec 10-13, 2018)
  • Six posters at Neuroscience 2018, Annual Meeting of the Society for Neuroscience, Nov 3-7, 2018, San Diego CA: Closed loop control of gamma oscillations in BLA – a computational perspective; Artificial neural networks for prediction of the local field potential; Alteration of IL-BLA connectivity by stimulation – a computational perspective; Interplay of resonant and synchronizing generators in a hippocampal theta model; A new model for large cells of the crab cardiac ganglion; Network model of the dynamics of the neural circuitry controlling micturition.
  • Latimer B, Banks T, Feng F, Ankathatti A, Calyam P and Nair S , Sept. 6-7, 2018: Software automation for biologically realistic neuro big data simulations. Poster In: Big Data Neuroscience Workshop organized by the Advanced Computational Neuroscience Network (ACNN), Case Western Reserve University, Cleveland, OH.
  • Hummos A, Nair SS (2017) An integrative model of the intrinsic hippocampal theta rhythm, PLoS ONE 12(8): e0182648  PDF   Source Code at Model DB
  • Guntu V, Feng F, Alturki A, Nair A, Samarth PS, Nair SS (2017) Amygdala Models, Chapter in Computational Models of Brain and Behavior, John Wiley and Sons (in press)
  • Five posters at the Annual Meeting of the Society for Neuroscience, Nov 11-15, 2017, Washington DC: Gamma oscillations in BLA – a computational perspective; Formation of tone responsive cells in a central amygdala model during fear conditioning; Characterizing conductance variations in model crab cardiac ganglion large cells; Variation across network output, excitatory post synaptic potentials, ionic conductances, and ion channel and receptor mRNAs within motor neurons of the crustacean cardiac ganglion; Modeling the dynamics of the neural circuitry controlling micturition. PDF
  • Nair SS, Pare D, Vicentic A (2016) Biologically-based neural circuit modeling for the study of fear learning and extinction, npj Science of Learning 1:16015 PDF
  • Lane BJ, Samarth PS, Ransdell JL, Nair SS, Schulz DJ (2016) Synergistic plasticity of intrinsic conductance and electrical coupling restores synchrony in an intact motor network, eLife 5:e16879  PDF
  • Alturki A, Feng F, Nair A, Guntu V, Nair SS (2016) Distinct current modules shape cellular dynamics in model neurons, Neuroscience 334: 309-331. PDF  AUDIO SLIDES   Source Code at Model DB
  • Samarth PS, Ball JM, Unal G, Pare D, Nair SS (2016) Mechanisms of memory storage in a model perirhinal network, Brain Structure & Function, DOI 10.1007/s00429-016-1210-4. PDF
  • Feng F, Samarth PS, Pare D, Nair SS (2016) Mechanisms underlying the formation of the amygdalar fear memory trace: a computational perspective, Neuroscience 322:370-376. PDF   AUDIO SLIDES
  • Kim D, Samarth PS, Feng F, Pare D, Nair SS (2016) Synaptic competition in the lateral amygdala and the stimulus specificity of conditioned fear: A biophysical modeling study, Brain Structure & Function, 221:2163–2182. PDF
  • Hummos A, Nair SS (2015) Multiple mechanisms of theta rhythm generation in a model of the hippocampus, BMC Neuroscience 16(Suppl 1):O17  doi:10.1186/1471-2202-16-S1-O17PDF
  • Two posters at the Annual Meeting of the Society for Neuroscience, Oct 17-21, 2015, Chicago, IL: Distinct current modules shape cellular dynamics in model neurons; Biophysical model of perirhinal cortex reveals memory storage mechanism. PDF
  • Hummos A, Franklin CC, Nair SS (2014) Intrinsic mechanisms stabilize encoding and retrieval circuits differentially in a hippocampal network model, Hippocampus 24(12):1430-48. PDF   Source Code at Model DB
  • Six posters at the Annual Meeting of the Society for Neuroscience, Nov 14-19, 2014, Washington DC. PDF
  • Pendyam S, Bravo-Rivera C, Burgos-Robles A, Sotres-Bayon F, Quirk GJ, Nair SS (2013) Fear signaling in the prelimbic-amygdala circuit: A computational modeling and recording study, Journal of Neurophysiology 110: 844 – 861. PDF
  • Kim D, Pare D, Nair SS (2013) Assignment of model amygdala neurons to the fear memory trace depends on competitive synaptic interactions, Journal of Neuroscience 33(36):14354 –14358. PDF
  • Kim D, Pare D, Nair SS (2013) Mechanisms contributing to the induction and storage of Pavlovian fear memories in the lateral amygdala, Learning & Memory 20: 421-430. PDF  Source Code at Model DB
  • Ransdell J, Nair SS, Schulz DJ (2013) Neurons within the same network independently achieve conserved output by differentially balancing variable conductance magnitudes, Journal of Neuroscience 33(24):9950 –9956. PDF
  • Six posters at the Annual Meeting of the Society for Neuroscience, Nov 9-13, 2013, San Diego.
  • Ball JM, Hummos A, Nair SS (2012) Role of sensory input distribution and intrinsic connectivity in lateral amygdala during auditory fear conditioning, Neuroscience 224:249–267.  PDF
  • Nair SS (2012) Auditory fear circuits in the amygdala – Insights from computational models, chapter 6 in The Amygdala – A Discrete Multi-Tasking Manager, pg. 141-170, InTech Publishing, Barbara Ferry, Editor. doi:10.5772/47814. PDF
  • Ransdell J, Nair SS, Schulz DJ (2012) Rapid homeostatic plasticity of intrinsic excitability in a central pattern generator network stabilizes functional neural network output, Journal of Neuroscience 32(28):9649-58. PDF
  • Pendyam S, Mohan A, Kalivas PW, Nair SS (2012) Role of perisynaptic parameters in neurotransmitter homeostasis – computational study of a general synapse, Synapse 66(7):608–621. PDF
  • Six posters at the Annual Meeting of the Society for Neuroscience, Oct 13-16, 2012, New Orleans.
  • Moussawi K, Riegel A, Nair S and Kalivas PW (2011) Extracellular glutamate: functional compartments operate in different concentration ranges, Frontiers in Systems Neuroscience 5:94. doi: 10.3389/fnsys.2011.00094  PDF
  • Li G, Amano T, Pare D, Nair SS (2011) Impact of infralimbic inputs on intercalated amygdala neurons: a biophysical modeling study, Learning & Memory 18:226-240 PDF
  • Mohan A, Pendyam S, Kalivas PW, Nair SS (2011) Molecular diffusion model of neurotransmitter homeostasis around synapses supporting gradients, Neural Computation 23:984:1014 PDF
  • Franklin CC, Ball JM, Schulz DJ, Nair SS (2010) Generation and preservation of the slow underlying membrane potential oscillation in model bursting neurons, Journal of Neurophysiology 104: 1589-16410. PDF
  • Ball JM, Franklin CC, Tobin AE, Schulz DJ, Nair SS (2010) Coregulation of ion channel conductances preserves output in a computational model of a crustacean cardiac motor neuron, Journal of Neuroscience 30: 8637-8649. PDF
  • Li G, Nair SS, Quirk GJ (2009) A biologically realistic network model of acquisition and extinction of conditioned fear associations in lateral amygdala neurons, Journal of Neurophysiology 101: 1629-1646. PDF
  • Pendyam S, Mohan A, Kalivas PW, Nair SS (2009) Computational model of extracellular glutamate in the nucleus accumbens incorporates neuroadaptations by chronic cocaine, Neuroscience 158(4):1266-76. PDF
  • Mohan A, Pendyam S, Li G, Kalivas P, Nair SS (2008) Computational models of neuronal networks – Modeling plasticity in Glu transmission due to cocaine, chapter in New Research on Neuronal Networks, Yoshida and Sato (Eds.), Nova Science Publishers, New York, 65-107.
  • Li G, Nair J, Quirk GJ, Nair SS (2008) Computational modeling – a tool for new psychiatric medication development, Psychiatric Annals, 28(4):296-304. PDF

Selected Other Publications

– Systems & Control, Machine Learning, Uncertainty Modeling/System Identification, ….

Trainee names in green

  • Iyoho A, Jang TS, Gall A, Nair SS (2007) Predicting individual differences in human thermal strain using computational models, ASHRAE Transactions 113(1):586-597.
  • Burd RS, Jang T, Nair SS (2007) Evaluation of the relationship between mechanism of injury and outcome in pediatric trauma, Journal of Trauma and Acute Care Surgery 62(4):1004-14.
  • Burd RS, Jang T, Nair SS (2006) Predicting mortality among injured children using a national trauma database, Journal of Trauma and Acute Care Surgery 60:792-801.
  • Zhang X, Xu W, Nair SS, Chellaboina V (2005) PDE modeling and control of a flexible two-link manipulator, IEEE Transactions on Control Systems Technology 13(2):301-312.
  • Zhang X, Xu W, Nair SS (2004) Comparison of some modeling and control issues for a flexible two-link manipulator. ISA Transactions 43(4): 509-525.
  • Du H, Nair SS (2002) Robust adaptive compensation for a class of nonlinear systems. ASME Journal of Dynamic Systems, Measurement, and Control 124: 231-234.
  • Thornton SB, Nair SS (2000) Parametric studies of human thermal mechanisms and measurements, IEEE Transactions on Biomedical Engineering 47(4):444-451.
  • Du H, Nair SS (1999) Modeling and compensation of low velocity friction with bounds. IEEE Transactions on Control Systems Technology 7(1): 110-121.
  • Swamidass P, Mistry SI, Nair SS (1999) The use of a neural factory to investigate the effect of product line width on manufacturing performance. Management Science 45(11):1524-1538.
  • Nair J, Nair SS, Kashani JH, Reid JC, Mistry SI, Vargas VG (1999) Analysis of the symptoms of depression: A neural network approach, Psychiatry Research, 87:193-201.
  • Vargas V, Du H, Nair SS, Reid JC (1999) Sensitivity analysis for modeling and decision making using neural networks, Intl. Journal of Knowledge-Based Intelligent Engineering Systems vol. 3 (3).
  • Kashani JH, Nair SS, Rao V, Nair J, Reid JC (1996) Relationship of personality, environmental and DICA variables to adolescent hopelessness: A neural network sensitivity approach, Journal of the American Academy of Adolescent and Child Psychiatry 35(5):640-645.
  • Reid JC, Nair SS, Mistry SI, Beitman BD (1996) Effectiveness of stages of change and adinazolam SR in panic disorder: A neural network analysis, Journal of Anxiety Disorders 10(5):331-345.

Peer Reviewed Publications Related to Teaching and K-12

Focus – Professional skills, and Concepts from Cognitive Neuroscience for Grad students; and Neuro-Robotics for K-12


  • Franklin CC, Mohan A, Merle D, Lannin J and Nair SS (2012) Perceptions of professional skills by graduate students— A comparative study between Engineering, Education and Biology, International Journal of Engineering Education 28(3):588-598. PDF
  • Mohan A, Merle D, Jackson C, Lannin J and Nair SS (2010) Professional skills in the engineering curriculum, IEEE Transactions on Education 53(4): 562-571. PDF
  • Bergin D, Khanna SK, Lynch J, and Nair SS (2007) Infusing design into the G6-9 curriculum – Two example cases, International Journal of Engineering Education 23(1):43-49. PDF


Note: Per information from, the neuro-LEGO lessons and activities cited below had a total of 107,765 page views in 2015 (91,336 for the lessons and 16,429 for the activities). During 2015, six of our lessons were among their “top 10” for page views, from over 1400+ lessons and activities hosted at the site.

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