Abstract
The objective of the work presented here is to develop a computational tool designed specifically for the study of the complex mechanisms that occur at chemical synapses. This tool should enable students and researchers (biologists with very little training in computational biology, as well as experienced modelers) worldwide to study the roles of diverse parameters that impact synaptic transmission from presynaptic to postsynaptic depolarization in an integrated modeling platform, using an easy, user-friendly and modular graphical interface.
Key Terms in this Chapter
Java Webstart Application: Java is an object-oriented programming language developed by Sun Microsystems. It allows the development of Webstart applications that can be downloaded from the Internet and run in a platform-independent manner.
AMPA, NMDA, mGluR Receptors: Different subtypes of glutamate receptors. AMPA and NMDA receptors are ionotropic (directly linked to an ion-channel) while the mGluR family of receptors is metabotropic (indirectly linked with ion-channels through signal transduction mechanisms).
Finite Element Method: Finite element method allows the calculation of diffusion in complex spaces by discretizing the continuous computational domain. The diffusion equation is then solved as a series of differential equations in each discretized element of the domain.
Glutamate: Glutamate is the most abundant excitatory neurotransmitter in the mammalian central nervous system. It is stored in vesicles and its release is triggered by nerve impulses.
Chemical Synapses: Chemical synapses are specialized junctions through which cells constituting the nervous system signal to one another and to non-neuronal cells such as muscles or glands. They represent key elements regulating communication between neurons in neural circuits.
Long Term Potentiation: Long Term Potentiation is generally considered to represent a cellular mechanism underlying certain forms of learning and memory. Long term potentiation consists of an increase in the strength of a chemical synapse that lasts from minutes to several days or weeks following a series of short, high-frequency electrical stimuli.
Postsynaptic Density: The postsynaptic density is a membrane specialization that concentrates neurotransmitter receptors and associated proteins to respond rapidly to the presence of neurotransmitter in the space separating the two neurons (referred to as the synaptic cleft).