Air Quality Modeling at CHPC
Collaboration between the Utah Division of Air Quality (UDAQ) and the University of Utah’s Center for High Performance Computing (CHPC) now gives the air quality modeling group at UDAQ access to advanced computing resources. This cooperative agreement began with a request from the Utah office of the Bureau of Land Management (BLM) for consultation on air quality modeling to support environmental impact analysis needed to process natural gas drilling permits in the Uintah Basin. This collaboration between UDAQ and CHPC is now a critical element in UDAQ’s ability to conduct air quality modeling for a wide variety of applications throughout the state, from the urbanized Wasatch Front to energy production areas of the Uintah Basin.
HIPAA-compliant Servers at CHPC
CHPC’s security expert Wayne Bradford, along with John Hurdle, Bernie LaSalle and Julio Facelli at BMI, has published a case study of the HIPAA-compliant environment at CHPC. The study shows “how an HPC can be re-engineered to accommodate clinical data while retaining its utility in computationally intensive tasks such as data mining, machine learning, and statistics.” Access to CHPC’s secured servers requires double authentication: first, users must have access to the CHPC virtual private network; and, second, users must be listed in the HPC network information service directory. Additional security is provided by housing the physical hardware in our data center that has controlled room access. All CHPC employees and the users of the secured servers are required to take the U’s Health Insurance Portability and Accountability Act training. The HIPAA-compliant environment is put to good use. Wayne reports that “in the first 3 years, researcher count has increased from 6 to 58.”
You can read his full case study here:
Mapping the Universe with CHPC Resources
The Sloan Digital Sky Survey makes use of the University of Utah's Center for High Performance Computing (CHPC) parallel computing resources to help with its mission to map the Universe, from our Galaxy and beyond. Building on fourteen years of discovery, the fourth phase of SDSS (SDSS-IV) recently had its first public data release, DR13. In SDSS-IV the survey expands its reach in three different ways:
- We observe millions of stars in both the Northern and Southern skies by including a second telescope in Chile. Now SDSS uses both the 2.5m SDSS telescope in New Mexico, and the 2.5m du Pont Telescope in Las Campanas, Chile.
- We observe millions of galaxies and quasars at previously unexplored distances to map the large scale structure in the Universe 5 billion years ago, and to understand the nature of Dark Energy.
- We use new instrumentation to collect high resolution spectra within 10,000 nearby galaxies, to discover how galaxies grow and evolve over billions of years of cosmic history.
University of Utah astronomers are a core part of this international collaboration. Joel Brownstein, Professor of Physics and Astronomy, is the Science Archive Scientist, making sure that the SDSS data reduction pipelines run smoothly, and that the data products are easily accessible both within the team and publicly. Prof. Kyle Dawson and postdoctoral fellows are also involved, working on instrumentation to map the distant Universe.
Autism Research within CHPC’s Protected Environment
The Utah Autism and Developmental Disabilities Monitoring Project (UT-ADDM) headed by Deborah Bilder, M.D. and William McMahon, M.D. in the Department of Psychiatry at the University of Utah’s School of Medicine, uses CHPC’s robust protected environment that allows researchers using protected health information (PHI) to gather, process and store data, increasing user productivity and compliance. In addition to access to high performance computing power, other tangible benefits for researchers using PHI is that the CHPC handles systems management issues, such as rapid response to electrical power issues, provision of reliable cooling and heating, VPN support for a work-anywhere computing experience, and ensuring a hardened, secure environment compared to office computers or departmental servers. For the institution this resource allows much better compliance and reduces the vulnerabilities of exposure of PHI data.
A New Role for Proteins
DNA encodes RNAs and RNAs encode proteins. This flow of cellular information is commonly referred to as the Central Dogma of Molecular Biology. However, a team of researchers discovered a notable exception to this rule where a protein can direct the synthesis of another protein, without an RNA template. This unusual mode of protein synthesis only occurs after normal protein synthesis has failed and appears to send a distress signal to the cell that something has gone awry.
The researchers first detected template-free protein synthesis by visualizing it directly by using a technique known as electron cryo-microscopy (cryo-EM). The image analysis, performed on the University of Utah Center for High Performance Computing cluster, required processing hundreds of thousands of 2D images to compute a 3D reconstruction of the cellular assembly. Once the researchers analyzed the structure and performed follow-up biochemical experiments, they knew they had stumbled upon an unexpected discovery. "In this case, we have a protein playing a role similar to that filled by messenger RNA," says Adam Frost, M.D., Ph.D., assistant professor at University of California, San Francisco (UCSF) and adjunct professor of biochemistry at the University of Utah, who led the research team. "I love this story because it blurs the lines of what we thought proteins could do." This work was featured in the January 2, 2015 issue of Science.
Uncovering the secrets of Darwin’s pigeons
Centuries of selective breeding have generated a tremendous diversity among the 300+ breeds of domestic rock pigeon (Columba livia), an organism that Charles Darwin proposed as an exemplary model for evolution under selection. This variation gives us the opportunity to better understand the process of vertebrate development, and to investigate how those processes evolve over time. Until recently, however, the specific molecular mechanisms responsible for phenotypic differences among pigeon breeds were a complete mystery.
To identify genetic changes responsible for novel traits among pigeon breeds, researchers from the Shapiro lab at the University of Utah Department of Biology utilized resources at CHPC to identify genetic differences in the genomes of over 100 diverse pigeons, which were then compared to pinpoint which genetic differences are most-closely associated with specific traits. These analyses require high performance computing to processes terabytes of genomic data. Without the large scale computing resources available at CHPC, identifying genetic differences among pigeons would take years, rather than days. Through these studies, surprising links between genes responsible for trait evolution in pigeons and genes responsible for genetic disorders in humans have been found. These results help researchers better understand mechanisms of evolution on a level that Charles Darwin could only have imagined.
Imaging Magma Reservoir beneath Yellowstone Park
The supervolcano that lies beneath Yellowstone National Park is one of the world’s largest active volcanoes. University of Utah seismologists Fan-Chi Lin, Hsin-Hua Huang, Robert B. Smith and Jamie Farrell have used advanced seismic imaging techniques to develop a more complete view of the magma chamber beneath this supervolcano, extending the known range from 12 miles underground to 28 miles. For the study the researchers used new methods to combine the seismic information from two sources. Data from local quakes and shallower crust were provided by University of Utah Seismographic Stations surrounding Yellowstone. Information on the deeper structures was provided by the NSF-funded EarthScope array of seismometers across the US.
Their recent study, as reported in the May 15, 2015 issue of Science, reveals that along with the previously known upper magma chamber there is also a second previously unknown second reservoir that is deeper and nearly 5 times larger than the upper chamber, as depicted in the cross-section illustration which cuts from the southwest to the northeast under Yellowstone. This study provides the first complete view of the plumbing system that supplies hot and partly molten rock from the Yellowstone hotspot to the Yellowstone supervolcano. Together these chambers have enough magma to fill the Grand Canyon nearly 14 times. Using resources at the Center for High Performance Computing, new 3D models are being developed to provide greater insight into the potential seismic and volcanic hazards presented by this supervolcano.
Computational Fluid Dynamic Simulation of a Novel Flash Ironmaking Technology
The U.S. steel industry needs a new technology that produces steel from iron ore with lower greenhouse gas emission and energy consumption. At the University of Utah, Prof. Hong Yong Sohn and his team have conceived of a drastically novel idea for an alternative method called the Flash Ironmaking Technology to replace the century-old blast furnace process. This new technology eliminates the highly problematic cokemaking and pelletization/sintering steps from the current ironmaking processes by directly utilizing iron ore concentrates, which are in abundance in the United States.
Using CHPC resources, the Sohn group is developing high-resolution computational fluid dynamics (CFD) simulations to select the optimal operating conditions for testing and subsequently reduce the testing time and effort. Simulation results will be used to analyze the results from the flash reactors. Also of high importance, the results of the simulations will assist in the subsequent design of an industrial-scale pilot facility and eventual full-scale commercial plant.
An Analysis of Tobacco and Food Purchases
Professor John Hurdle, Biomedical Informatics, has developed QualMART, a tool for helping grocery stores promote healthy eating habits for their customers. To validate the effectiveness of this tool, the group conducted a study that compared tobacco purchases and the quality of food purchases. They classified household grocery transactions in the Atlanta region, based on whether shoppers had ever purchased tobacco, and then applied their novel food purchase quality scoring measure to evaluate the household food environment. The master database with 15 months’ shopping activity from over 100,000 households nationally is housed on a HIPAA-compliant cluster at CHPC (accessed via Swasey).
The graphic shows the difference between ‘ever’ and ‘never’ tobacco purchasing groups is significant, with green areas indicating higher food quality scores and grey and red showing lower quality scores, aggregated by the zip code of the grocery shopping location.
This study validated the group's data-driven grocery food quality scoring design as the findings reproduce results from other studies in the scientific literature showing that tobacco users have lower overall diet quality compared to people who do not use tobacco.
Prediction of Crystal Structures from First Principle Calculations
Using CHPC resources a team of researchers from the University of Utah and the University of Buenos Aires has demonstrated that it is possible to predict the crystal structures of a biomedical molecule using solely first principles calculations. The results on glycine polymorphs shown in the figure were obtained using the Genetic Algorithms search implemented in Modified Genetic Algorithm for Crystals coupled with the local optimization and energy evaluation provided by Quantum Espresso. All three of the ambient pressure stable glycine polymorphs were found in the same energetic ordering as observed experimentally. The agreement between the experimental and predicted structures is of such accuracy that they are visually almost indistinguishable.
The ability to accomplish this goal has far reaching implications well beyond just intellectual curiosity. Crystal structure prediction can be used to obtain an understanding of the principles that control crystal growth. More practically, the ability to successfully predict crystal structures and energetics based on computation alone will have a significant impact in many industries for which crystal structure and stability plays a critical role in product formulation and manufacturing, including pharmaceuticals, agrochemicals, pigments, dyes and explosives.
Lund AM, Pagola GI, Orendt AM, Ferraro, MB, Facelli, JC (2015). Crystal structure prediction from first principles: The crystal structure of glycine. Chemical Physics Letters, 626, 20-24.
Watching Nanomaterials Assemble at CHPC
By Prof. Michael Grünwald, Grünwald Research Group, Department of Chemistry
My son and I like to build remote control cars. The path that leads from a disordered pile of plastic parts and metal screws to a new race car is straightforward and fun: step after step, we collect the pieces that need to be assembled and put them together according to the instructions. In fact, this assembly strategy is the blueprint for much human building activity and applies almost generally to the construction of houses, machines, furniture (in particular the Swedish kind), and many other objects of our daily lives.
Large objects, that is. Building small things, as it turns out, requires a strikingly different approach. Consider, for instance, the "objects" illustrated in Figure 1: A porous crystal structure made from intricately arranged metal ions and organic molecules (a "metal-organic framework"), and an ordered arrangement of nanoparticles (a "superstructure"), which themselves consist of many thousands of atoms. These structures are examples of "nanomaterials", objects that derive their unusual properties from their fascinating microscopic structure. Because of their large pores, metal-organic frameworks like the one in Figure 1a can be used to store hydrogen gas, filter CO2, or separate molecules by shape. Depending on the kinds of nanoparticles used, superstructures such as the one in Figure 1b can be used to alter the direction of light, or act as new kinds of solar cells.
Read the full article in the newsletter
Cataloging the Interactions of Insects and Plants
By Thomas Kursar, Department of Biology
Multiscale Modeling of Anion-exchange Membrane for Fuel Cells
By Jibao Lu, Liam Jacobson, Justin Hooper, Hongchao Pan, Dmitry Bedrov, and Valeria Molinero, University of Utah; Kyle Grew and Joshua McClure, US Army Research Laboratory; and Wei Zhang and Adri Duin, Pennsylvania State University
Analyzing and Predicting Stream Properties
By Milada Majerova and Bethany Neilson, Utah Water Research Laboratory, Utah State University
Clean Coal: Powered by Exascale
By Philip J. Smith and Michal Hradisky, CCMSC
The mission of the Carbon-Capture Multidisciplinary Simulation Center (CCMSC) at the University of Utah is to demonstrate the use of exascale uncertainty quantification (UQ) predictive simulation science to accelerate deployment of low-cost, low-emission electric power generation to meet the growing energy needs in the United States and throughout the world. The two main objectives, advancing simulation science to exascale with UQ-predictivity in real engineering systems and use of high-performance computing (HPC) and predictive science to achieve a societal impact, are linked together through an overarching problem: simulation of an existing 1,000 MW coal-fired ultra-supercritical (USC) boiler and simulation of a design 500 MW oxy-coal advanced ultra-supercritical (AUSC) boiler.
Read the full article in the newsletter
Changes in Neuronal Membrane Properties Lead to Suppression of Hippocampal Ripples
By Eric D. Melonakos, John A. White, and Fernando R. Fernandez, Department of Bioengineering
Center for High Performance Computing resources were used to study the effects of cholinergic inputs to the hippocampus on patterns of brain activity.
Ripples (140–220 Hz) are patterns of brain activity, seen in the local field potential of the hippocampus, that are important for memory consolidation. Cholinergic inputs to the hippocampus from neurons in the medial septum-diagonal band of Broca cause a marked reduction in ripple incidence as rodents switch from memory consolidation to memory encoding behaviors. The mechanism for this disruption in ripple power is not fully understood. Among the major effects of acetylcholine (or carbachol, a cholinomimetic) on hippocampal neurons are 1) an increase in membrane potential, 2) a decrease in the size of spike after hyperpolarization (AHP), and 3) an increase in membrane resistance. Using an existing model of hippocampal ripples that includes 5000 interconnected neurons (Brunel and Wang, 2003), we manipulated these parameters and observed their effects on ripple power. Shown here, the network firing rate and ripple power of the original model (top row; pyramidal neuron data is shown in red, interneuron data is shown in black) undergo marked changes following a decrease in pyramidal neuron AHP size, as well as an increase in the membrane voltage of both types of neurons. These changes could be the means whereby cholinergic input suppresses hippocampal ripples.
Tackling Large Medical Genomics Datasets
By Barry Moore, USTAR Center for Genetic Discovery
The University of Utah has a long and rich history of genetic research that spans decades and has led to the discovery of over 30 genes linked to genetic disease. These Utah discoveries range from relatively common and well-known heritable disease, such as breast cancer linked to BRCA1/BRCA2 genes, to the truly obscure Ogden syndrome, which in 2010 became the first new genetic disease to be described based on genome sequencing. The Utah Genome Project (UGP), together with clinical investigators across the University of Utah, is continuing this tradition of cutting edge genetic research in Utah by launching several large medical genomics projects over the last year. The USTAR Center for Genetic Discovery (UCGD)—the computational engine for the UGP—has partnered with the University’s Center for High Performance Computing (CHPC) to tackle the massive datasets and the large scale computing requirements associated with these projects.
Read the full article in the newsletter
Role of Stacking Disorder in Nucleation, Growth and Stability of Ice
By Laura Lupi, Arpa Hudait, Baron Peters, and Valeria Molinero, Department of Chemistry
Understanding the Carbon Cycle Through Climate Models
By Brett Raczka, Department of Biology
Read the paper in Biogeosciences
Data Assimilation for Improving WRF Performance in Simulating Wintertime Thermal Inversions in the Uintah Basin
By Trang Tran, Huy Tran, and Erik Crosman, Utah State University and University of Utah
Tracking Pressure Features
By Alexander Jacques, MesoWest/SynopticLabs and Atmospheric Sciences
Center for High Performance Computing resources were used to model the progression of a mesoscale gravity wave generated by a large storm system on April 26–27, 2011.
A mesoscale gravity wave, generated by a large storm system in the southern United States, moved northward through the central United States causing short-term changes in surface wind speed and direction. This animation shows efforts to detect and evaluate the negative mesoscale surface pressure perturbation generated by this wave. Detected positive (red contours) and negative (blue contours) perturbations are determined from perturbation analysis grids, generated every 5 minutes, using USArray Transportable Array surface pressure observations (circle markers). Best-track paths for the perturbations are shown via the dotted trajectories. To identify physical phenomena associated with the perturbations, conventional radar imagery was also leveraged. It can be seen here that the detected feature migrates north away from the majority of the precipitation, which is often seen with mesoscale gravity wave features.
Understanding Wind Energy
By Marc Calaf, Wind Energy & Turbulence, Department of Mechanical Engineering
The Wind Energy & Turbulence laboratory attempts to improve the current understanding of wind energy harvesting. The laboratory uses Center for High Performance Computing resources for high-resolution numerical simulations.
Currently we mainly use Large Eddy Simulations, which are capable of resolving most of the atmospheric turbulent scales as well as the wind turbines, providing very good results when compared to the experimental data. We are highly interested in improving the current conception of the land-atmosphere energy exchanges, and our work strives to fill the gaps of our current understanding. It is only by properly capturing the land-atmosphere connection that forces the atmospheric flow aloft that we will be able to reproduce with high accuracy the atmospheric flow.
Tracking Pressure Perturbations Resulting From Thunderstorm Complexes
By Alexander Jacques, MesoWest/SynopticLabs and Atmospheric Sciences
Modeling Ozone Concentration
By Brian Blaylock, Department of Atmospheric Sciences
Genomic Insights Through Computation
By Karen Kapheim, Kapheim Lab, Utah State University
Modeling the Unexpected Formation of a Gyroid
By Carlos Chu-Jon, Grünwald Research Group, Department of Chemistry
Quantifying Contributions from Natural and Non-local Sources to Uintah Basin Ozone
By Huy Tran, Seth Lyman, Trang Tran, and Marc Mansfield, Bingham Entrepreneurship & Energy Research Center