GPU-accelerated simulations of mass-action kinetics models with cupSODA

In the last years, graphics processing units (GPUs) witnessed ever growing applications for a wide range of computational analyses in the field of life sciences. Despite its large potentiality, GPU computing risks remaining a niche for specialists, due to the programming and optimization skills it requires. In this work we present cupSODA, a simulator of biological systems that exploits the remarkable memory bandwidth and computational capability of GPUs. cupSODA allows to efficiently execute in parallel large numbers of simulations, which are usually required to investigate the emergent dynamics of a given biological system under different conditions. cupSODA works by automatically deriving the system of ordinary differential equations from a reaction-based mechanistic model, defined according to the mass-action kinetics, and then exploiting the numerical integration algorithm, LSODA. We show that cupSODA can achieve a \(86 \times \) speedup on GPUs with respect to equivalent executions of LSODA on the CPU.     

NUMERICAL SIMULATION OF INTERMITTENT AND CONTINUOUS DEEP-BED DRYING OF BIOLOGICAL MATERIALS

This paper presents a simulation study of dryers. A two-dimensional deep-bed drying model, which incorporates modifications in existing one-dimensional models, has been developed and has the capability of handling both non-uniform velocity profiles and material properties dependence on temperature and moisture content. A corn drying system was simulated in order to analyze its temporal and spatial drying behavior. Both intermittent and continuous drying were simulated. The results showed that continuous drying is more efficient than intermittent drying with respect to drying time. However, intermittent drying led to more uniform temperature and moisture distributions, which improve grain quality. The model can be easily extended to three-dimensional drying analysis.     

Morphological aberrations in therapy-resistant partial epilepsy (TRPE). Confocal laser scanning and 3D reconstructions of Lucifer Yellow injected atypical pyramidal neurons in epileptic human cortex

Epileptic temporal and parietal cortices, removed from 6 patients with therapy-resistant (intractable) partial epilepsy (TRPE) during neurosurgery, were studied. Neurons (40-50 in each slice) in laminae I-VI and white matter were injected with Lucifer Yellow (LY). Samples were examined in a confocal laser scanning microscope (BioRad [Richmond, CA] MRC 600), and individual cells were scanned at 0.1-2 microns incremental levels. 2D maximal linear projection was used for overview. Frames (50-60) of scanned neurons were transformed into 3D volumes, using VoxelView software on a Silicone Graphics workstation, and rotated. All samples contained pyramidal neurons with duplicated apical dendrites, additional basal dendrites, or were misplaced in a horizontal position in the white matter. Rarely were such cells observed in normal cases. The relation between the observations and the disease is discussed. The attempt to simultaneously apply immunofluorescence was successful concerning synaptic vesicle antigens. This approach will be used for a detailed study of the synaptology of this disease.