Simulation Environment: XPPAUT

  1. A computational model of a small DRG neuron to explore pain (Verma et al. 2019, 2020)
  2. A Computational Model of Bidirectional Plasticity Regulation by betaCaMKII (Pinto et al. 2019)
  3. A mathematical model of evoked calcium dynamics in astrocytes (Handy et al 2017)
  4. A model for early afterdepolarizations in the cardiomyocyte action potential (Kimrey et al., 2022)
  5. A model for pituitary GH(3) lactotroph (Wu and Chang 2005)
  6. A model for recurrent spreading depolarizations (Conte et al. 2017)
  7. A novel mechanism for ramping bursts based on slow negative feedback in model respiratory neurons (John et al., accepted)
  8. A simplified model of NMDA oscillations in lamprey locomotor neurons (Huss et al. 2008)
  9. A theory of ongoing activity in V1 (Goldberg et al 2004)
  10. Action potential of adult rat ventricle (Wang et al. 2008)
  11. Action potential of striated muscle fiber (Adrian et al 1970)
  12. Actions of Rotenone on ionic currents and MEPPs in Mouse Hippocampal Neurons (Huang et al 2018)
  13. Activity patterns in a subthalamopallidal network of the basal ganglia model (Terman et al 2002)
  14. Allosteric gating of K channels (Horrigan et al 1999)
  15. An ion-based model for swelling of neurons and astrocytes (Hubel & Ullah 2016)
  16. An ODE model of the inspiratory & sigh rhythms (Borrus et al., 2024)
  17. Anoxic depolarization, recovery: effect of brain regions and extracellular space (Hubel et al. 2016)
  18. Aplysia LTF model (Liu et al, 2020; Zhang et al, 2021; Liu et al 2022)
  19. Basal ganglia-corticothalamic (BGCT) network (Chen et al., 2014)
  20. Biophysical models of AWCon and RMD C. elegans neurons (M. Nicoletti at al. 2019)
  21. Ca(2+) oscillations based on Ca-induced Ca-release (Dupont et al 1991)
  22. Ca-dependent K Channel: kinetics from rat muscle (Moczydlowski, Latorre 1983) XPP
  23. CA1 pyramidal cell: I_NaP and I_M contributions to somatic bursting (Golomb et al 2006)
  24. CA3 pyramidal cell: rhythmogenesis in a reduced Traub model (Pinsky, Rinzel 1994)
  25. CaMKII system exhibiting bistability with respect to calcium (Graupner and Brunel 2007)
  26. Cardiac action potential based on Luo-Rudy phase 1 model (Luo and Rudy 1991), (Wu 2004)
  27. Circadian clock model based on protein sequestration (simple version) (Kim & Forger 2012)
  28. Circadian clock model in mammals (detailed version) (Kim & Forger 2012)
  29. ClC-2 channels regulate neuronal excitability, not intracellular Cl- levels (Ratte & Prescott 2011)
  30. Consequences of HERG mutations in the long QT syndrome (Clancy, Rudy 2001)
  31. Contribution of ATP-sensitive potassium channels in the neuronal network (Huang et al. 2009)
  32. Control of vibrissa motoneuron firing (Harish and Golomb 2010)
  33. Criticality,degeneracy in injury-induced changes in primary afferent excitability (Ratte et al 2014)
  34. Deterministic chaos in a mathematical model of a snail neuron (Komendantov and Kononenko 1996)
  35. Dopaminergic cell bursting model (Kuznetsov et al 2006)
  36. Dorsal root ganglion (primary somatosensory) neurons (Rho & Prescott 2012)
  37. Double boundary value problem (A. Bose and J.E. Rubin, 2015)
  38. Drosophila 3rd instar larval aCC motoneuron (Gunay et al. 2015)
  39. Dynamics of ramping bursts in a respiratory pre-Botzinger Complex model (Abdulla et al, 2021)
  40. Dynamics of Spike Initiation (Prescott et al. 2008)
  41. Effect of riluzole on action potential in cultured human skeletal muscle cells (Wang YJ et al. 2008)
  42. Effect of slowly inactivating IKdr to delayed firing of action potentials (Wu et al. 2008)
  43. Effect of trp-like current on APs during exposure to sinusoidal voltage (Chen et al. 2010)
  44. Effects of eugenol on the firing of action potentials in NG108-15 neurons (Huang et al. 2011)
  45. Efffect of propofol on potassium current in cardiac H9c2 cells (Liu et al. 2008)
  46. Exact mean-field models for Izhikevich networks (Chen and Campbell 2022)
  47. Excitability of DA neurons and their regulation by synaptic input (Morozova et al. 2016a, 2016b)
  48. Excitatory and inhibitory interactions in populations of model neurons (Wilson and Cowan 1972)
  49. Explaining pathological changes in axonal excitability by dynamical analysis (Coggan et al. 2011)
  50. Exploring the role of Kӧlliker-Fuse nucleus in breathing variability via mathematical modeling (John et al., 2023)
  51. External Tufted Cell Model (Ryan Viertel, Alla Borisyuk 2019)
  52. Failure of Deep Brain Stimulation in a basal ganglia neuronal network model (Dovzhenok et al. 2013)
  53. Fast-spiking cortical interneuron (Golomb et al. 2007)
  54. Fully continuous Pinsky-Rinzel model for bifurcation analysis (Atherton et al. 2016)
  55. Glial voltage dynamics driven by Kir & K2P currents (Janjic et al 2023)
  56. HERG K+ channels spike-frequency adaptation (Chiesa et al 1997)
  57. HH-type model of fast-spiking parvalbumin interneurons in spinal dorsal horn (Ma et al, 2023)
  58. High frequency stimulation of the Subthalamic Nucleus (Rubin and Terman 2004)
  59. Hippocampus CA1: Temporal sensitivity of signaling pathways underlying LTP (Kim et al. 2010)
  60. Hodgkin-Huxley simplifed 2D and 3D models (Lundstrom et al. 2009)
  61. Hodgkin-Huxley with dynamic ion concentrations (Hubel and Dahlem, 2014)
  62. How adaptation makes low firing rates robust (Sherman & Ha 2017)
  63. Human sleep/wake cycle (Rempe et al. 2010)
  64. Inhibitory control by an integral feedback signal in prefrontal cortex (Miller and Wang 2006)
  65. Inhibitory control of motoneuron excitability (Venugopal et al 2011)
  66. Initiation of spreading depolarization by GABAergic neuron hyperactivity & NaV 1.1 (Chever et al 21)
  67. Integrated Oscillator Model for pancreatic islet beta-cells (Marinelli et al., 2022)
  68. Interactions among kinase cascades underlying LTP in Aplysia sensory neurons (Zhang et al 2021)
  69. Inverse stochastic resonance of cerebellar Purkinje cell (Buchin et al. 2016)
  70. Ion concentration dynamics as a mechanism for neuronal bursting (Barreto & Cressman 2011)
  71. Kv4.3, Kv1.4 encoded K(+) channel in heart cells (Greenstein et al 2000) (XPP)
  72. Locational influence of dendritic PIC on input-output properties of spinal motoneurons (Kim 2017)
  73. Markovian model for cardiac sodium channel (Clancy, Rudy 2002)
  74. Markovian model for HCN-encoded current regulated by capsazepine (Wong et al., 2024)
  75. Markovian model for SCN8A-encoded channel (Kuo et al 2020)
  76. Markovian model for single-channel recordings of Ik_1 in ventricular cells (Matsuoka et al 2003)
  77. Mauthner cell with two pre-synaptic cells, an inhibitory and an excitatory cell (Orr et al 2021)
  78. Minimal model for human ventricular action potentials (Bueno-Orovio et al 2008)
  79. Model for pancreatic beta-cells (Law et al. 2020)
  80. Model for pancreatic beta-cells with two isoforms of PFK (Marinelli et al., 2022)
  81. Model for pusatile insulin secretion at basal levels of glucose (Fletcher et al, 2022)
  82. Model of a BDNF feedback loop (Zhang et al 2016)
  83. Model of DARPP-32 phosphorylation in striatal medium spiny neurons (Lindskog et al. 2006)
  84. Modeling interactions in Aplysia neuron R15 (Yu et al 2004)
  85. Modeling the effects of dopamine on network synchronization (Komek et al. 2012)
  86. Motoneuron model of self-sustained firing after spinal cord injury (Kurian et al. 2011)
  87. Multiscale model of olfactory receptor neuron in mouse (Dougherty 2009)
  88. Networks of spiking neurons: a review of tools and strategies (Brette et al. 2007)
  89. Neuroprotective Role of Gap Junctions in a Neuron Astrocyte Network Model (Huguet et al 2016)
  90. Nicotinic control of dopamine release in nucleus accumbens (Maex et al. 2014)
  91. Pallidostriatal projections promote beta oscillations (Corbit, Whalen, et al 2016)
  92. Persistent Spiking in ACC Neurons (Ratte et al 2018)
  93. PreBotzinger Complex inspiratory neuron with NaP and CAN currents (Park and Rubin 2013)
  94. Prediction for the presence of voltage-gated Ca2+ channels in myelinated central axons (Brown 2003)
  95. Properties of aconitine-induced block of KDR current in NG108-15 neurons (Lin et al. 2008)
  96. Pyramidal neurons switch from integrators to resonators (Prescott et al. 2008)
  97. Relating anatomical and biophysical properties to motoneuron excitabilty (Moustafa et al. 2023)
  98. Reliability of Morris-Lecar neurons with added T, h, and AHP currents (Zeldenrust et al. 2013)
  99. Rescue of plasticity by a computationally predicted protocol (Liu et al. 2013)
  100. Respiratory central pattern generator (mammalian brainstem) (Rubin & Smith 2019)
  101. Respiratory central pattern generator including Kolliker-Fuse nucleus (Wittman et al 2019)
  102. Respiratory central pattern generator network in mammalian brainstem (Rubin et al. 2009)
  103. Respiratory control model with brainstem CPG and sensory feedback (Diekman, Thomas, and Wilson 2017)
  104. Role of active dendrites in rhythmically-firing neurons (Goldberg et al 2006)
  105. Role of KCNQ1 and IKs in cardiac repolarization (Silva, Rudy 2005) (XPP)
  106. Roles of I(A) and morphology in AP prop. in CA1 pyramidal cell dendrites (Acker and White 2007)
  107. Signal fidelity in the rostral nucleus of the solitary tract (Boxwell et al 2018)
  108. Simulation of calcium signaling in fine astrocytic processes (Denizot et al 2019)
  109. Simulation studies on mechanisms of levetiracetam-mediated inhibition of IK(DR) (Huang et al. 2009)
  110. Single neuron with dynamic ion concentrations (Cressman et al. 2009)
  111. Spike trains in Hodgkin–Huxley model and ISIs of acupuncture manipulations (Wang et al. 2008)
  112. Spontaneous calcium oscillations in astrocytes (Lavrentovich and Hemkin 2008)
  113. Spreading depression model for FHM3 with Nav1.1 mutation (Dahlem et al. 2014)
  114. Study of augmented Rubin and Terman 2004 deep brain stim. model in Parkinsons (Pascual et al. 2006)
  115. Subiculum network model with dynamic chloride/potassium homeostasis (Buchin et al 2016)
  116. Synchronization by D4 dopamine receptor-mediated phospholipid methylation (Kuznetsova, Deth 2008)
  117. Synergistic inhibitory action of oxcarbazepine on INa and IK (Huang et al. 2008)
  118. Tapered whiskers are required for active tactile sensation (Hires et al. 2013)
  119. Thalamocortical loop with delay for investigation of absence epilepsy (Liu et al 2019)
  120. The activity phase of postsynaptic neurons (Bose et al 2004)
  121. The role of ATP-sensitive potassium channels in a hippocampal neuron (Huang et al. 2007)
  122. The role of glutamate in neuronal ion homeostasis: spreading depolarization (Hubel et al 2017)
  123. Two-neuron conductance-based model with dynamic ion concentrations to study NaV1.1 channel mutations
  124. Ventricular cell model (Luo Rudy dynamic model) (Luo Rudy 1994) used in (Wang et al 2006) (XPP)
  125. Zebrafish Mauthner escape circuit with dopamine, gaba, and glycine (Clements et al., accepted)
  126. Zonisamide-induced inhibition of the firing of APs in hippocampal neurons (Huang et al. 2007)
http://www.math.pitt.edu/~bard/xpp/xpp.html

XPP (XPPAUT is another name; I (Bard Ermentrout) will use the two interchangeably) is a tool for solving differential equations, difference equations, delay equations, functional equations, boundary value problems, and stochastic equations. It evolved from a chapter written by John Rinzel and me on the qualitative theory of nerve membranes and eventually became a commercial product for MSDOS computers called PHASEPLANE. It is now available as a program running under X11 and Windows. The code brings together a number of useful algorithms and is extremely portable.
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