CIS Computing & Information Services

Research Projects

The following research projects have made extensive use of CCV resources:

NSF, NIH, DoD, etc.: DNA/RNA Research
The Gerbi Lab

This research develops new methods to identify origins of DNA replication and amplification as well as investigation into ribosomal RNA structures and processing. more

RI STAC Grant: Bringing Planktonic Holograms to Life
Melissa Omand (URI/GSO) and Tom Sgouros (Brown/CCV)

The Holoyurt project will further the identification and analysis of phytoplankton using a laser-holographic microscope. We are developing a method of estimating the carbon content of the suspended phytoplankton in the water, something that is only possible now through laborious chemical analysis of water samples.

R/V Falkor Ben Knörlein, a CCV visualization scientist, accompanied Professor Melissa Omand on a four-week Pacific expedition on the Research Vessel Falkor in January to fine-tune the software.

LLNL, etc.: Stochastic Electronic Structure Theory
The Rubenstein Group

Our group is focused on developing electronic structure methods that are at once highly accurate and scale well with system size to enable theory-driven materials design. Specific topics include modeling transition metals, spin-orbit coupling, hot electrons, and quantum computers. more

NSF, AFOSR, DOE, etc.: Stochastic multiscale mathematics
Karniadakis Lab

Research interests focus on stochastic multiscale mathematics and modeling of physical and biological systems. Current thrusts include machine learning and scientific computing, stochastic simulation, fractional PDEs, and multiscale modeling of complex systems (e.g., the brain). We solve problems in 100 dimensions! We work on sickle cell anemia and also on modeling malaria from first principles. Our new area is neurovascular coupling in the brain, i.e., bridging the gap between neuroscience and vascular mechanics. more

ONR grants: Catalyst Design
The Peterson Group

The reactivity of heterogeneous catalysts is dictated by their atomic configurations, electronic structure, and the interaction with adsorbates. Our laboratory utilizes high-performance computing to understand the reactivity of existing catalysts and to develop design principles for new catalysts. Our experimental facilities include synthesis capabilities, a high-pressure reaction cell, and electrochemical / analytical testing facilities.

Brown University Senior Honors Thesis: embryonic development of Crepidula fornicata
Advisor: Professor Kristi Wharton, Molecular Biology, Department of Cell Biology and Biochemistry

Beatrice Steinert, with two concentrations (Biology and Science & Society) chose for her honors thesis project to recreate a 19th century experiment by the embryologist Edwin Grant Conklin, to collect, study and sketch the embryonic developmental stages of Crepidula fornicata, commonly known as the slipper snail. Using a confocal microscope, Steinert collected images from embryos, digitally compiling them into a model for viewing in the CCV YURT. Wearing special glasses, she can manipulate a 3D embryo, flip it over, walk around it, and even go inside.

Galaxies in Abell 2029 DoE/NFS/NASA: Dark Matter in Galaxy Clusters
Dell'Antonio Group

Galaxy clusters are the biggest stable structures in the Universe. Their principal component is dark matter, whose distribution can be studied via gravitational lensing. By studying the small distortions in the shapes of millions of galaxies behind the clusters, the Dell’Antonio group is mapping out how the dark matter is distributed in clusters, and how the clumping differs for clusters that we observe today compared to more distant clusters that we observe earlier in the Universe history. We are also using simulations of galaxy cluster observations to validate gravitational lensing mass reconstruction techniques.

Rapid visual processing NSF: Visual Perception, Brain Science, Computer Vision
Serre Laboratory

Primates can recognize objects and visual scenes in the blink of an eye. The Serre lab develops computational models to explain the brain mechanisms underlying this unique ability. Our long-term goal is to help realize one of the oldest dreams in artificial intelligence: to reverse-engineer the brain and build machines that can see and interpret the visual world as well as humans do. Achieving such an ambitious goal would give scientists a powerful tool to uncover and understand key mechanisms of human perception and cognition and create a new generation of “seeing” machines. To tackle this problem, the Serre lab combines experimental and computational work to try to answer fundamental questions in visual perception from invariant visual recognition as well as color, motion and depth processing to attention and eye movements. In addition, an active area of research in the Serre lab is the development of computer vision systems for the automated analysis of animal and human behavioral data.

DoE/NSF grants: Molecular Dynamics Research
Peter Weber Laboratory

Research investigates molecular reactions on a very fundamental level. While most of Chemistry is based on chemical reactions, the truth is that scientists are still striving to understand how they work. In our research, we develop new methods of investigating molecular reactions and then apply them to important model systems. Our research explores fundamental molecular processes in the broadest sense. We have developed two highly time-resolved techniques to explore molecular dynamics from two different perspectives.

DoE/NSF/others:LUX Dark Matter Experiment
Rick Gaitskell's Brown Particle Astrophysics Group

The LUX Dark Matter Experiment is a ⅓ tonne liquid xenon dual phase TPC located 1 mile underground at the Sanford Underground Research Facility in Lead, SD. LUX is currently the most sensitive dark matter direct detection experiment in the world. Looking for the very rare dark matter particle (“WIMP”) interactions requires the detector to be the quietest place in the world.

CAVE Writing Class
Professor John Cayley, Literary Arts

This class merges this technology with one of humanity’s oldest technologies—the written word—to unleash creativity and explore new modes of literary expression. In this class users read, listen and interact with virtual reality literature while immersed in the 3-D environment such as the one in this image showing the virtual poem, “Cubes.”

Dunn Lab completes evolutionary tree for mollusks
October, 2011 (press release)

In a paper in Nature, researchers from the Casey Dunn Lab (Department of Ecology and Evolutionary Biology) and collaborating institutions have compiled the most comprehensive evolutionary tree for mollusks to date. Their analysis surprisingly places two enigmatic groups, cephalopods and monoplacophorans, as sister clades. The team has also shown that there was a single origin for shelled mollusks.

NSF Grant: XROMM: X-ray Reconstruction of Moving Morphology
Elizabeth Brainerd

This project intends to establish a community of researchers that use X-ray Motion Analysis (XMA) data and X-ray Reconstruction of Moving Morphology (XROMM) analysis, train them in methods for collecting and processing these data through workshops, establish a set of standards for these data and methods, and establish a web-based data portal where researchers can deposit data and share data with collaborators and perform various computing tasks.

NSF MRI Grant: Development of a Next-Generation Interactive Virtual Reality Display Environment for Science
David Laidlaw, Jan Hesthaven, Andy van Dam, George Karniadakis

The proposed instrument will be used primarily for research involving visualization of scientific data, but will also enhance through use in academic courses and projects in the arts that depend on immersive environments. The investigators in the scientific visualization projects will investigate new models and hypotheses, develop working prototypes of new visualization and interaction methods, evaluate the prototypes, and apply them to their scientific problems.

Evolutionary Gene Networks unravel the genetic mechanisms that enable parasites to thrive
March, 2011

The Lane Lab (Department of Biological Sciences, University of Rhode Island) focuses on genome evolution and reduction in parasites. Parasitic organisms have independently evolved in every major lineage of life on Earth, but despite both the medical, economic and agricultural impacts of parasites, very little is known about the process by which a species adopts a parasitic life style.

Examining H1N1 Through Its Information Entropy
William A. Thompson, Andy Martwick, Joel K. Weltman, "In the Spotlight" article in the IEEE-SPM, May, 2010

As reported by CNN in October 2009, the declaration of the H1N1 swine flu pandemic as a national emergency in the USA highlights the magnitude and continuing spread of the first pandemic flu outbreak in forty years. The H1N1 swine flu pandemic that began in March 2009 is the most recent outbreak of influenza A to threaten the human species. Type A influenza viruses, including the H1N1 of the current pandemic, are the cause of the most frequent and most serious influenza infections in humans.

DoD Grant: PTSD
Roy K. Aaron M.D., Andy van Dam

The intent of this project is to extend technology to allow a more systematic evaluation of patient response to stimuli in the virtual environment, and to enable new treatment modality (e.g., group therapy). It will enable a more evidence-based design of treatment protocols, potentially lowering costs, increasing efficacy and improving the quality of life for many veterans and otherwise disabling post-traumatic psychological illness.

NASA/AISR Grant: ADVISER (Advanced Visualization in Solar System Exploration and Research)
James W. Head III, Sam Fulcomer, Andy van Dam

The overall goal of ADVISER is to virtually place the geoscientist on planetary surfaces, and provide the tools necessary to explore and take measurements within this environment. This has proven to be useful enough in exploring planetary surfaces that it has now been incorporated into the Brown University Geology course GEO 5: “Mars, Moon, and Earth”.

FluidVis and Cave Vox
Dr. Robbert Creton

The FluidVis 3D visualization system, supported by CCV, has been used for teaching, research, and outreach activities in our facility.