Quantification of the HIV viral reservoir is critical to understanding HIV latency, advancing patient care and ultimately achieving a cure. To quantify the reservoir, a new metric was recently introduced, which quantified cells carrying multiply spliced HIV RNA. The developed assay, Tat/rev Induced Limiting Dilution Assay (TILDA), enables quantification of cells containing multiply-spliced HIV ...

The stochastic modelling of biological systems, coupled with Monte Carlo simulation of models, is an increasingly popular technique in bioinformatics. The simulation-analysis workflow may result computationally expensive reducing the interactivity required in the model tuning. In this work, we advocate the high-level software design as a vehicle for building efficient and portable parallel simu...

We consider optimization of computational grids for petroleum reservoir flow simulations. In this context grid quality is determined by two independent error sources. On the one hand there is a loss of precision caused by upscaling of geological data from the fine geological grid to the coarser computational grid, and on the other hand there are numerical errors induced by a non-regular computa...

Wettability has a strong influence on multi-phase flow behavior through reservoir rock. Reservoir rocks tend to have spatially varying wettability. Prior contact with oil, are almost always naturally water-wet. As oil invades the pore-space over geologic time, initial water-wet state may be altered in certain locations due adhesion of substances within phase grains. Mechanisms wettability alter...

the karkheh dam reservoir with a capacity of more than 5 billion cubic meter is the largest dam in iran with both agricultural and drinking usages. its hydrodynamics and water quality were modeled and simulated to analyze the total maximum daily load (tmdl) of total dissolved solids (tds). the simulation was supported with measurements of temperature and tds measurements during two years. a lat...

Seismic reservoir characterization aims to transform obtained seismic signatures into reservoir properties such as lithofacies and pore fluids. We propose a Markov chain Monte Carlo (McMC) workflow consistent with geology, well‐logs, seismic data and rock‐physics information. The workflow uses a multiple‐point geostatistical method for generating realizations from the prior distribution...

Problems in modeling and simulation require significantly different workflow management technologies than standard grid-based workflow management systems. Computational scientists typically interact with simulation software in a feedback driven way were solutions and workflows are developed iteratively and simultaneously. This work describes common activities in workflows and how combinations o...

Petroleum resources are found within sedimentary rocks that have a sufficient interconnected void space to store and transmit fluids. The actual flow of liquid and gas phases occurs on a micrometer scale in the void space between rock grains. On the other hand, the hydrocarbon is typically carried in rock zones that are a few tens of meters thick but extend several kilometers in the lateral dir...