Dezhe Jin Group

Department of Physics and Center for Neural Engineering
Penn State University

Research Overview

Consisting of a large number of intricately connected neurons, the brain is one of the most sophisticated dynamical systems in nature. Understanding how the brain computes is at the forefront of current scientific research. Research in our group focuses on theoretical analysis of biological neural networks and computational models of song generation in songbirds, speech recognition in humans, and learning and memory in the hippocampus. The modeling is done in close collaboration with experimental groups.



  • Dezhe Jin, Associate Professor of Physics


  • Seth Hulsey
  • Sumithra Surendralal
  • Leonardo Tavares
  • Yevhen Eugene Tupikov
  • Dominick DiMercurio II


  • Phillip Schafer (PhD, 2014)
  • Jason Wittenbach (PhD, 2014)
  • Aaron Miller (PhD, 2012)
  • David Fraser (PhD, 2009)
  • Linli Wang (PhD, 2009)
  • Joseph Jun (postdoc, 2004-2006)
  • Wonil Chang (Visitor from Korean Advanced Instite of Science and Technology, 2006-2007)
  • Tarik Salameh (Undergraduate student, 2011-2012)
  • David Vidmar (Undergraduate Honors Thesis, 2011-2012)
  • Greg Diehl (Undergraduate student, 2006-2007)
  • David Van Maaden (Undergraduate Honors Thesis, 2008-2009)

  • Courses

  • Phys557, Electrodynamics I (graduate level) Syllabus
  • Phys530, Classical Mechanics (graduate level) Syllabus
  • Phys597B, Computational Neuroscience (graduate level) Syllabus
  • Phys212, Electricity and Magnetism (undergraduate level) Syllabus


  • Jason Wittenbach, Kristofer E. Bouchard, Michael S. Brainard, Dezhe Z. Jin, "An adapting auditory-motor feedback loop can contribute to generating vocal repetition", PLoS Computational Biology, 11, e1004471 (2015). (PDF)
  • Yisi Zhang, Jason D. Wittenbach, Dezhe Z. Jin, Alexay Kozhevnikov, "Temperature manipulation in songbird brain implicates the premotor nucleus HVC in birdsong syntax", arXiv:1501.06108 (2015).
  • Phillip B. Schafer and Dezhe Z. Jin, "Noise-robust speech recognition through auditory feature detection and spike sequence decoding", Neural Computation, 26, 523 (2014). (PDF)
  • Arik Kershenbaum, Ann E. Bowles, Todd M. Freeberg, Dezhe Z. Jin, Adriano R. Lameira, and Kirsten Bohn, "Animal vocal sequences: not the Markov chains we thought they were", Proceedings of the Royal Society B: Biological Sciences, 281, 20141370 (2014). (PDF)
  • Arik Kershenbaum et al, "Acoustic sequences in non-human animals: a tutorial review and prospectus”, Biological Reviews, doi: 10.1111/brv.12160 (2014). (PDF)
  • Aaron Miller and Dezhe Z. Jin, "Potentiation decay of synapses and the length distributions of synfire chains self-organized in recurrent neural networks", Physical Review E, 80, 062716 (2013). (PDF)
  • Dezhe Z. Jin, "The Neural Basis of Birdsong Syntax", in Progress in Cognitive Science: From Cellular Mechanisms to Computational Theories, Edited by Zhong-lin Lu and Yuejia Luo, Peking University Press (2013). (PDF)
  • Dezhe Z. Jin and Alexay A. Kozhevnikov, "A compact statistical model of the song syntax in Bengalese finch", PLoS Computational Biology, 7, e1001108 (2011). (PDF)
  • Michael A. Long, Dezhe Z. Jin, and Michale S. Fee, "Support for a synaptic chain model of sequence generation from intracellular recordings in the singing bird", Nature, 468, 394 (2010). (PDF, SI)
  • Theresa M. Desrochers, Dezhe Z. Jin, Noah D. Goodman, and Ann M. Graybiel, "Optimal habits can develop spontaneously through sensitivity to local cost", Proceedings of National Academy of Science, 107, 20512 (2010). (PDF, SI)
  • Dezhe Z. Jin, "Generating variable birdsong syllable sequences with branching chain networks in avian premotor nucleus HVC", Physical Review E, 80, 051902 (2009). (PDF)
  • Dezhe Z. Jin, Naotaka Fujii, and Ann M. Graybiel, "Neural representation of time in cortico-basal ganglia circuits", Proceedings of National Academy of Science, 106, 19156 (2009). (PDF, SI)
  • Wonil Chang and Dezhe Z. Jin, "Spike propagation in driven chain networks with dominant global inhibition", Physical Review E, 79, 051917 (2009). (PDF)
  • Dezhe Z. Jin, "Decoding spatiotemporal spike sequences via the finite state automata dynamics of spiking neural networks", New Journal of Physics, 10, 015010 (2008). (PDF)
  • Joseph K. Jun and Dezhe Z. Jin, "Development of neural circuitry for precise temporal sequences through spontaneous activity, axon remodeling, and synaptic plasticity", PLoS ONE, 2, e723 (2007). (PDF). Download the code related to the paper, written by Aaron Miller, from the Model Database maintained at Yale University.
  • Dezhe Z. Jin, Fethi M. Ramazanoglu, and H. Sebastian Seung, "Intrinsic bursting enhances the robustness of a neural network model of sequence generation by avian brain area HVC", Journal of Computational Neuroscience, 23(3), 283-99 (2007). (PDF)
  • Brandon J. Farley, Hongbo Yu, Dezhe Z. Jin, and Mriganka Sur, "Alteration of visual input results in a coordinated reorganization of multiple visual cortex maps", Journal of Neuroscience, 19, 10299-10310 (2007). (PDF)
  • Dezhe Z. Jin, Valentin Dragoi, Mriganka Sur, and H. Sebastian Seung, "The tilt aftereffect and adaptation-induced changes in orientation tuning in visual cortex", Journal of Neurophysiology, 94, 4038-4050 (2005). (PDF)
  • Terra D. Barnes, Yasuo Kubota, Dan Hu, Dezhe Z. Jin and Ann M. Graybiel, "Activity of striatal neurons reflects dynamic encoding and recoding of procedural memories", Nature, 437, 1158-1161 (2005). (PDF)
  • Hongbo Yu, Brandon J. Farley, Dezhe Z. Jin, and Mriganka Sur, "The coordinated mapping of visual space and response features in visual cortex", Neuron, 47, 267 (2005). (PDF)
  • Dezhe Z. Jin, "Spiking neural network for recognizing spatiotemporal sequences of spikes", Physical Review E, 69, 021905 (2004). (PDF)
  • Dezhe Z. Jin, "Fast convergence of spike sequences to periodic patterns in recurrent networks", Physical Review Letters, 89, 208102 (2002). (PDF)
  • Dezhe Z. Jin and H. Sebastian Seung, "Fast computation with spikes in a recurrent neural network", Physical Review E, 65, 051922 (2002). (PDF)
  • Carson C. Chow, Dezhe Z. Jin, and Alessandro Treves, "Is the world full of circles?", Journal of Vision, 2, 571 (2002). (PDF)
  • Daniel H. E. Dubin and Dezhe Z. Jin, "Collisional diffusion in a 2-dimensional point vortex gas", Physics Letters A, 284, 112 (2001). (PDF)
  • Dezhe Z. Jin and Daniel H. E. Dubin, "Point vortex dynamics within a background vorticity patch", Physics of Fluids, 13, 677 (2001). (PDF)
  • Dezhe Z. Jin and Daniel H. E. Dubin, "Characteristics of two-dimensional turbulence that self-organizes into vortex crystals", Physical Review Letters, 84, 1443 (2000). (PDF)
  • Dezhe Z. Jin and Daniel H. E. Dubin, "Theory of vortex crystal formation in two-dimensional turbulence", Physics of Plasmas, 7, 1719 (2000). (PDF)
  • Dezhe Z. Jin and Daniel H. E. Dubin, "Regional maximum entropy theory of vortex crystal formation", Physical Review Letters, 80, 4434 (1998). (PDF)

    Dezhe Jin
    Associate Professor of Physics
    contact: dzj2

    Department of Physics
    Penn State
    104 Davey Lab
    University Park, PA 16802-6300