Reconstruction and simulation of neocortical microcircuitry

We present a first-draft digital reconstruction of the microcircuitry of somatosensory cortex of juvenile rat. The reconstruction uses cellular and synaptic organizing principles to algorithmically reconstruct detailed anatomy and physiology from sparse experimental data. An objective anatomical method defines a neocortical volume of 0.29 ± 0.01 mm3 containing ∼31,000 neurons, and patch-clamp studies identify 55 layer-specific morphological and 207 morpho-electrical neuron subtypes. When digitally reconstructed neurons are positioned in the volume and synapse formation is restricted to biological bouton densities and numbers of synapses per connection, their overlapping arbors form ∼8 million connections with ∼37 million synapses. Simulations reproduce an array of in vitro and in vivo experiments without parameter tuning. Additionally, we find a spectrum of network states with a sharp transition from synchronous to asynchronous activity, modulated by physiological mechanisms. The spectrum of network states, dynamically reconfigured around this transition, supports diverse information processing strategies

Computer Simulation and Advanced Visualisation of DNA.

This project has investigated the major forces responsible for the folding of DNA or RNA polypeptide chains, in order to form the stable geometrical structure of the double helix and to find out the potential curvature in the 3-Dimensional (3D) structure of DNA, where the sequence is poly-A, poly-C, i.e. poly-single or double nucleotide. Two different algorithms have been developed. Each algorithm implements the Monte Carlo annealing method and has been used to model and minimize linear, single and double stranded B-DNA sequences. The force field used is composed of a limited number of bonded and non-bonded interactions. A variety of DNA sequences and sizes was investigated containing coding and non-coding, random and real, homogeneous or heterogeneous sequences in the range 2 to 40 base pairs. During the work different graphical display methods and algorithms for large macromolecules were investigated by using in most cases the OpenGL graphics library. The advantages and disadvantages of different programming language and graphical systems for molecular visualization have been studied. Software has been developed using OpenGL, VCL and Win32 programming interfaces to allow visualization of macromolecules such as DNA in mono and stereo using both Red/Green and VR glasses

Keyword based indexing and searching over storage resource broker

A keyword based metadata indexing and searching facility for Storage Resource Broker (SRB) is presented here. SRB is a popular data grid based storage system that provides means to store data and associate metadata information with the stored data. The metadata storage system in SRB is modeled on the attribute-value pair representation. This data structure enables SRB to be used as a general purpose data management platform for a variety of application domains. However, the generic representation of metadata storage mechanism also proves to be a limitation for applications that depend on the extensive use of the associated metadata in order to provide customized search and query operations. The presented work addresses this limitation by providing a keyword based indexing system over the metadata stored in the SRB system. The system is tightly coupled with the SRB metadata catalog; thereby ensuring that the keyword indexes are always kept updated to reflect changes in the host SRB system

Analysis of labelled compounds by mass spectroscopy in the presence of heavy isotopes at natural abundance: the NAIC program

A program is described, which allows the intensity contributions from naturally occurring heavy isotopes to be eliminated from the mass spectrometric ions of an artificially labelled compound. This allows the accurate measurement of the isotopomer distribution of the compound and hence its percentage isotopic abundance. In the case of radioactively labelled compounds the specific radioactivity can then be derived from the abundance data. The program utilizes a graphical user interface based upon the C++ Builder 6.0 environment and VCL library