Project Supervisor:
Dr Yulia Timofeeva
Title: Software Tool for Modelling the Dynamics of Branched Neurons
Abstract: Dendrites form the major component of many neural cell types, especially those
found in the human cortex. They form elaborate branching structures, accounting for up to
99% of a cell’s volume. As well as providing contact area for synaptic inputs from other
neurons they endow the cell with rich computational abilities. These arise from the interplay
of the biophysical properties of the dendritic membrane with the dendritic geometry. It
would appear that the brain makes use of different dendritic geometries to build distinct
functional classes of neuron – each distinguished by the complex spatio-temporal dynamics
of cell signalling that they produce. One way to model such cells is with a system of partial
differential equations and appropriate boundary conditions (obeying Kirchoff’s laws). The
existing simulation environments for solving such models are based on methods of numerical
integration and require large amounts of computation. The goal of this project is to develop a
software tool for computing the dynamics of neural cell responses using a recently proposed
theoretical framework which obviates the need for numerical integration. Instead it requires
the computation of terms involving all possible paths between any two points on a graph
describing the dendritic tree. This software tool will be applied to real neuronal geometries,
available from existing public databases. The computational efficiency of this new approach
to modelling single neuron response will be of interest to computational and experimental
neuroscientists alike. The project will involve a substantial amount of programming with an
important component in algorithm optimisation. The end result will be a web-based resource
that naturally interfaces with existing software and databases used in the neuroscience
community, such as NEURON and ModelDB, for the study of branched neurons.