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:
CHPC Resources Aid Study of Massive Galaxies
University of Utah astronomers are using CHPC parallel computing resources to study galaxy evolution and cosmology. Adam Bolton, assistant professor in the department of Physics and Astronomy, and his research group are members of the Baryon Oscillation Spectroscopic Survey (BOSS) project within the international Sloan Digital Sky Survey III (SDSS-III) collaboration. BOSS is currently building the largest ever three-dimensional map of galaxies using a 2.5-meter telescope at Apache Point Observatory (APO) in New Mexico. Researchers are measuring the statistical patterns within this map in order to understand the nature of the mysterious “dark energy” that seems to be accelerating the expansion rate of the universe. Kyle Dawson, another member of the University’s Department of Physics and Astronomy, is also heavily involved in the BOSS project.
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, 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 ne 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 con- struction 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 in- stance, the “objects” illustrated in Figure 1: A porous crys- tal 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, lter 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.