Computational Neuroscience

2.

Foundations in Neuroscience

2.1.

The Neuron Doctrine

2.1.1.

Historical development

2.1.2.

Cajal's contributions

2.1.3.

Implications for brain organization

2.1.4.

Modern refinements

2.2.

Structure of a Neuron

2.2.1.

2.2.1.1.

Cell body components

2.2.1.2.

Nucleus and organelles

2.2.2.

2.2.2.1.

Dendritic tree structure

2.2.2.2.

Dendritic spines

2.2.2.3.

Signal integration

2.2.3.

2.2.3.1.

Axon hillock and initial segment

2.2.3.2.

2.2.3.3.

2.2.4.

2.2.4.1.

Oligodendrocytes and Schwann cells

2.2.4.2.

Myelination process

2.2.5.

Nodes of Ranvier

2.2.5.1.

Structure and function

2.2.5.2.

Saltatory conduction

2.2.6.

Synaptic terminals

2.2.6.1.

Presynaptic terminals

2.2.6.2.

Synaptic vesicles

2.2.6.3.

2.3.

The Cell Membrane and Ion Channels

2.3.1.

2.3.1.1.

Structure and function

2.3.1.2.

Membrane proteins

2.3.1.3.

Membrane permeability

2.3.2.

2.3.2.1.

Voltage-gated channels

2.3.2.1.1.

Sodium channels

2.3.2.1.2.

Potassium channels

2.3.2.1.3.

Calcium channels

2.3.2.2.

Ligand-gated channels

2.3.2.2.1.

Neurotransmitter receptors

2.3.2.2.2.

Second messenger systems

2.3.2.3.

Mechanically-gated channels

2.3.2.3.1.

Stretch-activated channels

2.3.3.

2.3.3.1.

Sodium-potassium pump

2.3.3.2.

2.3.3.3.

Energy requirements

2.3.4.

2.3.4.1.

Sodium-calcium exchanger

2.3.4.2.

Chloride transporters

2.4.

The Resting Membrane Potential

2.4.1.

Ionic gradients

2.4.1.1.

Sodium gradient

2.4.1.2.

Potassium gradient

2.4.1.3.

Chloride gradient

2.4.1.4.

Calcium gradient

2.4.2.

Nernst Equation

2.4.2.1.

2.4.3.

Goldman-Hodgkin-Katz Equation

2.4.3.1.

Multiple ion permeability

2.4.3.2.

Relative permeabilities

2.4.4.

Role of permeability

2.4.4.1.

Selective permeability

2.4.4.2.

Membrane resistance

2.5.

The Action Potential

2.5.1.

Threshold and All-or-None Principle

2.5.1.1.

Threshold mechanisms

2.5.1.2.

Digital nature of spikes

2.5.2.

Phases of the Action Potential

2.5.2.1.

2.5.2.1.1.

Sodium channel activation

2.5.2.1.2.

Positive feedback

2.5.2.2.

2.5.2.2.1.

Potassium channel activation

2.5.2.2.2.

Sodium channel inactivation

2.5.2.3.

Hyperpolarization

2.5.2.3.1.

Afterhyperpolarization

2.5.2.3.2.

Potassium channel deactivation

2.5.3.

Refractory Period

2.5.3.1.

Absolute refractory period

2.5.3.1.1.

Sodium channel inactivation

2.5.3.2.

Relative refractory period

2.5.3.2.1.

Threshold elevation

2.5.4.

Propagation of action potentials

2.5.4.1.

Continuous conduction

2.5.4.2.

Saltatory conduction

2.5.4.3.

Conduction velocity

2.6.

Synaptic Transmission

2.6.1.

Electrical Synapses

2.6.1.1.

2.6.1.2.

2.6.1.3.

Fast transmission

2.6.1.4.

Bidirectional communication

2.6.2.

Chemical Synapses

2.6.2.1.

Neurotransmitter release

2.6.2.1.1.

Calcium-dependent exocytosis

2.6.2.1.2.

2.6.2.2.

Synaptic vesicles

2.6.2.2.1.

2.6.2.2.2.

Neurotransmitter packaging

2.6.2.3.

2.6.2.3.1.

Neurotransmitter diffusion

2.6.2.3.2.

Clearance mechanisms

2.6.3.

Neurotransmitters

2.6.3.1.

Excitatory neurotransmitters

2.6.3.1.1.

2.6.3.1.2.

2.6.3.2.

Inhibitory neurotransmitters

2.6.3.2.1.

2.6.3.2.2.

2.6.3.3.

Modulatory neurotransmitters

2.6.3.3.1.

2.6.3.3.2.

2.6.3.3.3.

2.6.4.

2.6.4.1.

Ionotropic receptors

2.6.4.1.1.

2.6.4.1.2.

2.6.4.1.3.

GABA-A receptors

2.6.4.2.

Metabotropic receptors

2.6.4.2.1.

G-protein coupled receptors

2.6.4.2.2.

Second messenger cascades

2.6.5.

Postsynaptic Potentials

2.6.5.1.

Excitatory Postsynaptic Potentials

2.6.5.1.1.

EPSP characteristics

2.6.5.1.2.

Glutamate-mediated EPSPs

2.6.5.2.

Inhibitory Postsynaptic Potentials

2.6.5.2.1.

IPSP characteristics

2.6.5.2.2.

GABA-mediated IPSPs

2.6.6.

Synaptic integration

2.6.6.1.

Spatial summation

2.6.6.1.1.

Linear summation

2.6.6.1.2.

Nonlinear interactions

2.6.6.2.

Temporal summation

2.6.6.2.1.

Membrane time constants

2.6.6.2.2.

Facilitation and depression

2.7.

Major Brain Structures and Functions

2.7.1.

Cerebral cortex

2.7.1.1.

Cortical layers

2.7.1.2.

Cortical columns

2.7.1.3.

Functional areas

2.7.2.

2.7.2.1.

2.7.2.2.

2.7.2.3.

Memory formation

2.7.3.

2.7.3.1.

2.7.3.2.

Globus pallidus

2.7.3.3.

Substantia nigra

2.7.3.4.

Motor control circuits

2.7.4.

2.7.4.1.

Cerebellar cortex

2.7.4.2.

Deep cerebellar nuclei

2.7.4.3.

2.7.5.

2.7.5.1.

Thalamic nuclei

2.7.5.2.

Relay functions

2.7.5.3.

Cortical-thalamic loops

2.7.6.

2.7.6.1.

2.7.6.2.

2.7.6.3.

2.7.6.4.

Vital functions

2.7.7.

2.7.7.1.

Gray matter organization

2.7.7.2.

White matter tracts

2.7.7.3.

Reflex circuits

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