Above: Digital Elevation Model (DEM) showing preferred paths of water flow on a tilled field. The project is part of the new Applied and Scientific Visualization Program at RENCI@NC State.

RALEIGH, December 16, 2010—Two North Carolina State University research teams will work with RENCI visual analytics experts through the new RENCI@NC State Faculty Engagement Program in Applied Scientific and Information Visualization.

The program is an effort to expand the use of visualization tools and technologies among NC State researchers.  Each research team will receive up to $12,000 to support their work over the next year and will be expected to develop new research methods, models, applications or prototypes that can lead to larger projects supported by grant money.

The projects are:

• Visualization and analysis tool for biomolecular structure exploration Yaroslava Yingling, Ph.D., department of materials science and engineering

Prof. Yingling’s research group will work with RENCI Senior Research Software Developer and visualization expert Hong Yi to build a 3D visualization tool to study the structure of various complex proteins. The tool will be able to solve a variety of problems in the biological sciences. The initial research will focus on understanding protein complexes that synthesize cellulose. Cellulose is the foundational component of all plant cell walls.  Because it converts sunlight into renewable, storable energy, understanding and manipulating cellulose could help scientists find ways to produce energy from algae, bacteria and other plants or create new bio-renewable materials for manufacturing, medicine and other uses.

Yi and Yingling will create a visual 3D mapping tool that allows researchers to compare the sequential and structural differences between cellulose synthase proteins from different plants.  The research team will also visualize the results of molecular dynamics simulations in order to understand the relationship between mutations caused by a change in a single amino acid and changes to the protein structure.  Because these single amino acid mutations are functionally important to the protein, a better understanding of their impact on the protein structure could help scientists learn to manipulate cellulose synthesis.

“Three dimensional comparisons of protein structure can provide many insights into protein functions and how to manipulate proteins to better understand the effects of mutations,” said Yingling. “Current visualization techniques lack simple and clean tools that allow the use of 3D structural information to analyze the genetic alignments and mutations. We want to work with RENCI to create a tool that uses spatial distance in the 3D structure to create images that are much more useful for analysis.”

• Visualization of terrain evolution: from animations to space-time cube
  Helena Mitasova, Ph.D., department of marine, earth and atmospheric sciences
  Margery F. Overton, Ph.D., department of civil, construction and environmental engineering
  Laura Tateosian, department of parks, recreation and tourism management

Prof. Mitasova and her research team plan to use high-resolution elevation data of North Carolina’s coast obtained from Light Detection and Ranging (LiDAR) remote sensing technology to create 3D models of the dynamics of coastal terrain. Working with RENCI’s Sidharth Thakur, a senior research software developer and visualization expert, the researchers will create visual, geographically accurate digital elevation models (DEMs) of the topography of the Outer Banks over time in order to study the effects of large events (such as hurricanes and storm surge) and long-term phenomena (such as winds and rising sea levels) on the terrain of the Outer Banks.

Understanding the dynamics of terrain evolution will build a better understanding of the risks of associated with coastal storms, flooding and erosion. The visual models will also make it easier for researchers and public officials to communicate the impacts of storms and floods to citizens and could be used to guide the development of sustainable land use plans and emergency plans.

“LiDAR surveys have generated elevation data of unprecedented resolution and have given us new opportunities to study evolution of topography as a dynamic, three-dimensional process,” said Mitasova. “But these massive datasets cannot be visualized at full spatial and temporal resolutions using traditional techniques. We are turning to RENCI to develop new approaches and tools to extract and visualize information captured by these unique data sets.”

About RENCI@NC State

RENCI@North Carolina State opened in 2006 in the Partners 1 Building on Centennial Campus. The facility supports NC State faculty members interested in using visualization technology and advanced computational methods to explore issues in science and engineering. The center includes a 14-foot-by-8-foot, high resolution, rear projection display wall and connects to other RENCI centers for video conferencing, group-to-group interactions and real-time data sharing. For more on RENCI, see www.renci.org.

A new Renaissance Computing Institute (RENCI) animation created from a mathematical model shows a black hole moving supersonically through an interstellar gas cloud. This phenomenon often occurs in multiple star systems, where a companion star provides the gas cloud. The gravity of the black hole pulls the gas inward. Early on in the process, a wake forms behind the black hole, much like the wake behind a motorboat. Unlike a motorboat wake, it begins to move back and forth after a while until it whips all the way around the black hole, forming an accretion disk of gas falling into the hole.

What has mystified scientists since 1988 is the seemingly erratic rotation of accretion disks in the computer-generated models. In some cases the model shows the disk rotating for a time in one direction, then suddenly switching directions. The disk’s spin may remain stable for a time and then abruptly reverse direction again. The reversal may repeat several times.

Astrophysicists refer to this accretion disk about face as “flip-flop instability” and have debated its possible causes for years. Some suggest the phenomenon doesn’t actually occur but is a flaw in the model itself. Yet flip-flop instability has shown up in numerous different studies, leading some scientists to suggest it is the cause of stellar flares and bursts of energy that haven’t otherwise been explained.

North Carolina State University researchers John Blondin and T. Chris Pope generated the data used to construct this visualization. Their computer simulations exploit the power of high-performance computers available through the National Science Foundation’s TeraGrid to explore flip-flop instability at an unprecedented level of detail and scientific sophistication. In a paper published June 30 in the Astrophysical Journal, they conclude that the flip-flop instability is real and not an anomaly of computer models.

In the animation, created by Steve Chall of the RENCI’s North Carolina State Engagement Center, the gas cloud swirls around the black hole at the center, creating an accretion disk around the black hole. At first, the disk spins counterclockwise and then very rapidly reverses to a clockwise direction. The background colors in the animation represent pressure, from green for low through blue, violet, red and finally pale yellow for the highest pressure. Spheres emitted from 10 equally spaced sources upstream from the black hole (far right) show the velocities of representative particles in the gas cloud. Pale yellow spheres exhibit the least velocity, through red, violet and up to blue for the fastest-moving particles.

Credits: Numerical simulation: Dr. John Blondin and T. Chris Pope, department of physics, North Carolina State University. Visualization: Steve Chall, Renaissance Computing Institute NC State. This research was supported in part by a grant from the National Science Foundation, by an NC State Undergraduate Research Award to T. Chris Pope, and by computing resources at the Texas Advanced Computing Center.

The NC State node of BEN, consisting of Infinera digital optical networking hardware, connects campus researchers to the experimental network through RENCI at NC State.

RALEIGH, NC, March 11, 2009—RENCI’s NC State engagement center recently completed upgrades to support the installation of the Breakable Experimental Network (BEN). BEN serves as a test bed for experimentation with new networking technologies that will help make networked communications faster, easier and more reliable. BEN is “breakable” because it is not meant to be a stable commercial network, such as those that keep the commercial Internet running. Instead BEN allows network researchers to experiment with disruptive technologies—those that are likely to have a major impact in the years to come and thereby disrupt standard operating procedures for networks.

The new network connects RENCI facilities at NC State, Duke University, UNC Chapel Hill, RENCI’s main office at Europa Center in Chapel Hill, and MCNC in Research Triangle Park. RENCI administers the network and provides access to the fiber for researchers at the Triangle area campuses through its engagement centers. With funding from the National Science Foundation, RENCI and Duke are using BEN as a test bed for the Global Environment for Network Innovations (GENI) project. GENI’s aim is to forge new solutions to problems facing today’s Internet including inadequate security, reliability, manageability and scalability.

RENCI at NC State also upgraded its 170-inch by 96-inch visualization display wall into a fully digital system that more accurately adjusts images on the screen. The display system uses 16 projectors and can display images at a resolution of 5,120 by 2,880 pixels.

The visualization wall allows researchers to view large-scale, time-dependent data as color-coded visual simulations of complicated processes, from astrophysical phenomena to the relationships among documents in a large data archive.

For more on BEN, see http://ben.renci.org.

For more on GENI, see http://www.geni.net

RENCI…Catalyst for Innovation
The Renaissance Computing Institute, a multi-institutional organization, brings together multidisciplinary experts and advanced technological capabilities to address pressing research issues and to find solutions to complex problems that affect the quality of life in North Carolina, our nation and the world. RENCI leverages its expertise and resources in leading edge computing, visualization, networking and data technologies to catalyze new collaborations and solve problems. Founded in 2004 as a major collaborative venture of Duke University, North Carolina State University, the University of North Carolina at Chapel Hill and the state of North Carolina, RENCI is a statewide virtual organization.