Behavioral simulation and synthesis of biological neuron systems using synthesizable VHDL

Neurons are complex biological entities which form the basis of nervous systems. Insight can be gained into neuron behavior through the use of computer models and as a result many such models have been developed. However, there exists a trade-off between biological accuracy and simulation time with the most realistic results requiring extensive computation. To address this issue, a novel approach is described in this paper that allows complex models of real biological systems to be simulated at a speed greater than real time and with excellent accuracy. The approach is based on a specially developed neuron model VHDL library which allows complex neuron systems to be implemented on field programmable gate array (FPGA) hardware. The locomotion system of the nematode Caenorhabditis elegans is used as a case study and the measured results show that the real time FPGA based implementation performs 288 times faster than traditional ModelSim simulations for the same accuracy

Yield improvement using configurable analogue transistors (CATs)

Continued process scaling has led to significant yield and reliability challenges for today’s designers. Analogue circuits are particularly susceptible to poor variation, driving the need for new yield resilient techniques in this area. This paper describes a new configurable analogue transistor structure and supporting methodology that facilitates variation compensation at the post-manufacture stage. The approach has demonstrated significant yield improvements and can be applied to any analogue circui

Behavioral simulation and synthesis of biological neuron systems using synthesizable VHDL

Neurons are complex biological entities which form the basis of nervous systems. Insight can be gained into neuron behavior through the use of computer models and as a result many such models have been developed. However, there exists a trade-off between biological accuracy and simulation time with the most realistic results requiring extensive computation. To address this issue, a novel approach is described in this paper that allows complex models of real biological systems to be simulated at a speed greater than real time and with excellent accuracy. The approach is based on a specially developed neuron model VHDL library which allows complex neuron systems to be implemented on field programmable gate array (FPGA) hardware. The locomotion system of the nematode Caenorhabditis elegans is used as a case study and the measured results show that the real time FPGA based implementation performs 288 times faster than traditional ModelSim simulations for the same accuracy

Bedload abrasion and the in situ fragmentation of bivalve shells

The aim of this study was to determine how Unio bivalve shells fragment within the channel of the Sakmara River (southern Urals, Russia). The Sakmara River has an abundant bivalve population and a highly variable flow regime which, at low flow, allowed much of the channel bed to be examined. A large data set of 1013 shells (Unio sp.) was examined and these were shown to have consistent patterns of orientation, aspect, shell abrasion, perforation and fracture. The close spatial relationship between areas of shell abrasion, shell perforation and shell fracture showed that they form part of a continuum whereby areas of abrasion evolve into perforations and perforations coalesce and enlarge into fractures. The mechanism of shell damage proposed is one of abrasion in place, whereby the shell remains stationary on the surface of the point bar and is impacted by bedload. Underpinning this process are the hydrodynamic properties of the bivalve shell, with consistency in the orientation and aspect of the valve in a flowing current producing consistency in the distribution of damage on the shell surface. Valves preferentially lie in a convex-up position and orientate in the flow such that the umbo faces upstream. The elevated, upstream-facing umbo region is exposed to particle impact and is the first to be abraded and perforated. The vulnerability of the umbo to perforation is greatly increased by the thinness of the shell at the umbo cavity. The in situ abrasion process is enhanced by the development of an armoured gravel bed which restricts valve mobility and maintains shells within the abrasion zone at the sediment-water interface. The in situ abrasion process shows that broken shells are not a reliable indicator of long distance transport. The study also raises the issue that tumbling barrel experiments, which are generally used to simulate shell abrasion, will not replicate the type of directionally focused sand-blasting which appears to be the principal cause of shell fragmentation in the Sakmara River

A new approach to define surface/sub-surface transition in gravel beds

The vertical structure of river beds varies temporally and spatially in response to hydraulic regime, sediment mobility, grain size distribution and faunal interaction. Implicit are changes to the active layer depth and bed porosity, both critical in describing processes such as armour layer development, surface-subsurface exchange processes and siltation/ sealing. Whilst measurements of the bed surface are increasingly informed by quantitative and spatial measurement techniques (e.g., laser displacement scanning), material opacity has precluded the full 3D bed structure analysis required to accurately define the surface-subsurface transition. To overcome this problem, this paper provides magnetic resonance imaging (MRI) data of vertical bed porosity profiles. Uniform and bimodal (σ g = 2.1) sand-gravel beds are considered following restructuring under sub-threshold flow durations of 60 and 960 minutes. MRI data are compared to traditional 2.5D laser displacement scans and six robust definitions of the surface-subsurface transition are provided; these form the focus of discussion