Double-distribution-function discrete Boltzmann model for combustion

A 2-dimensional discrete Boltzmann model for combustion is presented. Mathematically, the model is composed of two coupled discrete Boltzmann equations for two species and a phenomenological equation for chemical reaction process. Physically, the model is equivalent to a reactive Navier-Stokes model supplemented by a coarse-grained model for the thermodynamic nonequilibrium behaviours. This model adopts 16 discrete velocities. It works for both subsonic and supersonic combustion phenomena with flexible specific heat ratio. To discuss the physical accuracy of the coarse-grained model for nonequilibrium behaviours, three other discrete velocity models are used for comparisons. Numerical results are compared with analytical solutions based on both the first-order and second-order truncations of the distribution function. It is confirmed that the physical accuracy increases with the increasing moment relations needed by nonequlibrium manifestations. Furthermore, compared with the single distribution function model, this model can simulate more details of combustion.Comment: Accepted for publication in Combustion and Flam

GliomaPredict: A Clinically Useful Tool for Assigning Glioma Patients to Specific Molecular Subtypes

Background: Advances in generating genome-wide gene expression data have accelerated the development of molecular-based tumor classification systems. Tools that allow the translation of such molecular classification schemas from research into clinical applications are still missing in the emerging era of personalized medicine. Results: We developed GliomaPredict as a computational tool that allows the fast and reliable classification of glioma patients into one of six previously published stratified subtypes based on sets of extensively validated classifiers derived from hundreds of glioma transcriptomic profiles. Our tool utilizes a principle component analysis (PCA)-based approach to generate a visual representation of the analyses, quantifies the confidence of the underlying subtype assessment and presents results as a printable PDF file. GliomaPredict tool is implemented as a plugin application for the widely-used GenePattern framework. Conclusions: GliomaPredict provides a user-friendly, clinically applicable novel platform for instantly assigning gene expression-based subtype in patients with gliomas thereby aiding in clinical trial design and therapeutic decisionmaking. Implemented as a user-friendly diagnostic tool, we expect that in time GliomaPredict, and tools like it, will become routinely used in translational/clinical research and in the clinical care of patients with gliomas

Master Regulators, Regulatory Networks, and Pathways of Glioblastoma Subtypes

Glioblastoma multiforme (GBM) is the most common malignant brain tumor. GBM samples are classified into subtypes based on their transcriptomic and epigenetic profiles. Despite numerous studies to better characterize GBM biology, a comprehensive study to identify GBM subtype-specific master regulators, gene regulatory networks, and pathways is missing. Here, we used FastMEDUSA to compute master regulators and gene regulatory networks for each GBM subtype. We also ran Gene Set Enrichment Analysis and Ingenuity Pathway Analysis on GBM expression dataset from The Cancer Genome Atlas Project to compute GBM- and GBM subtype-specific pathways. Our analysis was able to recover some of the known master regulators and pathways in GBM as well as some putative novel regulators and pathways, which will aide in our understanding of the unique biology of GBM subtypes

Multiple-Relaxation-Time Lattice Boltzmann Approach to Compressible Flows with Flexible Specific-Heat Ratio and Prandtl Number

A new multiple-relaxation-time lattice Boltzmann scheme for compressible flows with arbitrary specific heat ratio and Prandtl number is presented. In the new scheme, which is based on a two-dimensional 16-discrete-velocity model, the moment space and the corresponding transformation matrix are constructed according to the seven-moment relations associated with the local equilibrium distribution function. In the continuum limit, the model recovers the compressible Navier-Stokes equations with flexible specific-heat ratio and Prandtl number. Numerical experiments show that compressible flows with strong shocks can be simulated by the present model up to Mach numbers $Ma \sim 5$.Comment: Accepted for publication in EP