Tutorial Exercises and Demonstrations
Tutorial v14 for Neurosim v5.5 (June 2023)
Version
NOTE: The tutorials in this section are written for an earlier version of Neurosim. Tutorials for the latest version (and links to earlier versions) are available here.
If you are actually running Neurosim v5-5-2, you are strongly recommended to install the free upgrade to the latest version.
Tooltips
Within the tutorial text there are occasional tooltips indicated thus This is a tooltip.. If you hover over one of these (or tap it on a touch screen), hopefully-useful information will show.
Parameter files
Within the tutorials there are links to the parameter files displayed thus.
You can download or run Be aware that if you run a file directly from the browser, each file will start a new instance of Neurosim. Also note that with some browsers a local copy of the file may be downloaded to your default Download folder. To prevent disk clutter, you may want to delete these files after you finish your simulation session. parameter files (depending on your browser configuration) by clicking on the link. However, if you would rather download all the parameter files at once and store them locally on your computer, they are available in the compressed file samples-5-5.zip.
There are 5 core tutorial topics:
There are implementation details about the algorithms and methods used in Neurosim
Click on a link in the Contents below to go to a particular topic.
Note: there is much more material here than would be needed or useful for most undergraduate courses. If you are a teacher using Neurosim, you should just select the activities you deem appropriate – and of course feel free to adjust them and/or write your own.
Contents
Passive Properties
Resting potential
Nernst equation
Potassium Equilibrium Potential
Temperature Dependence
Concentration Gradient Dependence
Goldman equation
Simple Goldman
Full Goldman
Chloride
Chloride Regulation
Steady State versus Equilibrium: Pumps
Electrogenic Pumps
Permeability vs Conductance
Conductance Asymmetry: Rectification
Spherical Cells: The Membrane as a Resistor-Capacitor (RC) Circuit
Basic RC Properties
Leakage and Capacitive Currents
Input Resistance
Input Resistance is Size Dependent
Membrane Time Constant
Quantifying the Membrane Time Constant
Reality Checks
Measuring the Time Constant
The Falling Phase
Time Constant is Size Independent
Temporal summation: Why the Time Constant Matters
Low-Pass Filter
Phase Delay
Axons and Dendrites: Conduction of Passive Signals
Attenuation and Delay: Basic Properties
The Space (Length) Constant: Attenuation with Distance
Voltage vs Distance Display
Diameter Affects the Space Constant
Why is the Space Constant Diameter-Sensitive?
Spatial Summation: Why the Space Constant Matters
Conduction Velocity
The Time Constant: Time Delay with Distance
Temporal Summation: Why the Time Constant Matters
Input Resistance
The Cable Equation
Non-Uniform Diameter: A Compartmental Model
Spatial Summation
Passive Property Units
Action Potentials (Spikes)
Conceptual Summary
Static (Non-Propagating) Spikes
Threshold: All or None?
Sodium Dependence of Spikes
Analysing the Results
Hyperkalaemia
Spike Currents and Conductances
Blocking Sodium and Potassium Channels
Molecular Events and Patch Recordings
Single Channel Patch Recording
Micro and Macro Conductance
The HH Model in Action
Strength-Duration Curve
Rheobase and Chronaxie
Cause of the Strength-Duration Relationship
Ramp Stimulus
Refractory Period
Threshold Accommodation
Rebound Excitation
Post-Inhibitory Facilitation
Pacemaker (continuous spiking)
Spike Propagation (Conduction)
Basic Conduction Features
Conduction Velocity
Spike Collision
Spike Spatial Distribution
Passive vs Active Conduction
Refractory Conduction
Myelination and Saltatory Conduction
Voltage clamp
Theory of the Voltage Clamp
Voltage Clamp Currents: Ionic, Capacitive, Gating
Classic HH Experiments
Sodium I/V Curve
Sodium Equilibrium Potential
Sodium Inactivation
Potassium I/V Curve
Tail Currents
Capacitive Current
Why a Constant Voltage Matters
Space-Clamp Problems
Single Channel Patch Recording
Conductance
Micro and Macro Conductance
Current
Beyond Basic HH Models
Endogenous Burster Neurons
Calcium/Calcium-Dependent Potassium Channels
Phase Resetting
Inactivating Calcium Channels
Channel Kinetics
Conditional bursters
Plateau Potentials
Bi-stable neurons
A Current (Transient Potassium Channels)
Inking in Aplysia
Advanced Kinetics
Voltage-Dependency of Alpha and Beta
Gate Voltage-Dependency
Steady-State Probability
Time Constant of Probability Change
Alpha and Beta during a Spike
Channel Voltage-Dependency
Potassium Channels
Sodium Channels
Putting it all together: finding the membrane potential
Capacitive current (spike)
Non-Ohmic Channels: The GHK Current Equation
Rectification
Conductance
Morris-Lecar: Reduced Kinetics
Equations
Further reduction
Significance
Phase Plane Analysis
Phase Plots of Experimental Data
Synapses
Chemical Synapses
Excitation and Inhibition
Integration
Voltage Clamp
Summation and Facilitation
Depolarising and Silent IPSPs
Non-Spiking Synapses
Voltage-Dependent Synapses (NMDA-type)
NMDA I/V Curve
Hebbian Synapses
Quantal Release
Quantal Size Distribution
Electrical Synapses
Frequency Matters
Size Matters
Rectification
Crayfish
Dendritic Computation
Proximal and Distal Inhibition
Directional Sensitivity
Networks
Central Pattern Generators
Flip-Flop Circuit
Reciprocal Inhibition Oscillator
Multi-Phase Rhythms
Laser Photoinactivation and Optogenetics
Sensory Feedback
Phase Resetting Tests
Tadpole Swimming: A case study
Basic dIN and cIN Properties
The Core Swimming Circuit
Spike-Triggered Display
Swim Initiation
Short-Term Motor Memory and the Sodium Pump
Synchronization and Entrainment
Entrainment
Synchronization
Metachronal Rhythm
Stochastic Resonance
Dithering
Lateral Inhibition
Pre-Synaptic Inhibition
Primary Afferent Depolarization (PAD)
Inhibition mechanism
Antidromic Spikes and the DRR
The Jeffress Model for Auditory Localization
Phase Ambiguity
Learning Networks
Classical Conditioning: Pavlov’s Dog
Associative Learning: Pattern Completion
Hebbian mechanism
Limitations
Facilities for Memory Models
Wilson Cowan Models
Background Theory
Neurosim Implementation
Stable States
Bi-stable output
Hysteresis
Tri-stable output
Tri-stable mechanism
Oscillations
Phase plane analysis
Multi-Unit Models
Synchronizing oscillations
Anti-phase synchronization
Fly larval crawling
Kinetics of Single Ion Channels
Two-State Channels: An Open and Shut Case
Mean Sojourn Duration and Transition Rate Constants
Sojourn Distribution is Exponential
Histogram Analysis
Channel Blocker: Antagonist Effects
Open-Time Distribution
Effect of Blocker Concentration
Closed-Time Distribution is Multi-Exponential
Likelihood and BIC
Why are there 2 Exponentials?
Comparison of Open- and Closed-Time Distributions
What is the Point? A Reminder
A Transmitter-Activated Channel
Open-Time Distributions
Closed-Time Distribution.
Bursts of Open State Conductance
The Acetylcholine Receptor Model
Auto-Correlations
Implementation Details
Neurons
Passive Properties
Noise
Spiking Properties
Integrate-and-fire
Spike Threshold Accommodation
Synaptic connections
Without Integrate-and-Fire
Spike generation
Synaptic connections
Voltage-Dependent Channels
Gates
Non-Gate Models
Calcium and Sodium Channels
Variable Equilibrium Potential
Drugs: Blockers, Activators and Optogenetics
Blockers
Activators
Optogenetics
Calcium Dependent Channels
Intracellular Calcium Concentration
Making a Channel Calcium-Dependent
Sodium Pump
Pump Current Sodium Concentration Dependency
Intracellular Sodium Concentration
Limitations
Synapses
Spiking Chemical Synapse
Delay
Shape
Single exponential
Dual exponential
Facilitation
Voltage-Dependent Synapse
Hebbian Synapses
Learning
Forgetting
Linear forgetting
Augmentation-reduced forgetting
Advanced HH Only
Conductance Decrease Synapse
Extracellular Calcium Concentration
Quantal Release
Non-Spiking Chemical Synapses
Direct
Multi-Stage
Carrier Ions: Calcium and Sodium
Electrical Synapses
Rectifying Electrical Synapses
Drugs: Blockers and Activators
Blockers
Activators
Facilitation
Occlusion
Equations and Integration
Exponential Euler Integration
Integration Components
Adaptive Step Size
Wilson-Cowan Integration
Compartmental Models
Active Currents
Neurosim Implementation
References