Research

GOLDEN, Colo., June 23, 2015 – A team led by a Mines research professor of physics has been awarded $3 million by the Department of Energy to study the deterioration of canisters used for storing spent nuclear fuel.

Primary investigator Zeev Shayer’s team includes faculty from the Department of Metallurgical and Materials Engineering: Professors David Olson and Stephen Liu, and Assistant Professor Zhenzhen Yu.

Meet Sam Spiegel, the director of the Center for Innovative Teaching and Learning (CITL) at Colorado School of Mines. The center—started by Applied Mathematics and Statistics professor Gus Greivel and Physics professor Pat Kohl—is part of Mines’ Strategic Plan initiative to further the school’s STEM reputation, expand research opportunities and increase graduation rates.

Spiegel sees the CITL as a way to enhance faculty connections, provide them with resources and form an active learning community at Mines.

“The pieces that get me excited are real and rich conversations about teaching and learning,” said Spiegel. “I am looking forward to getting involved in the design aspects and supporting faculty and students in changing, growing and enhancing their experiences at Mines.”

The CITL will offer resources in coaching, course review, curricula design, grant support, learning communities, teaching observations and teaching professional development.

“There are quite a number of Mines faculty trying new things and the center is here to be a resource to support them,” Spiegel said. “CITL can provide support and guidance to refine instruction. For those faculty that want more intensive support, we will be offering one-on-one coaching.”

An example of support around course design will happen this summer when Spiegel will work with Department of Chemistry and Geochemistry professors Renee Falconer and Allison Castner to redesign a freshman course with a more active learning style, focusing on furthering student engagement on conceptual learning.

On April 21, Spiegel presented a pedagogy seminar with Chief Information Officer Michael Erickson on how CCIT and CITL plan to collaborate to support faculty and advance teaching and learning at Mines. The CITL will offer seminars this summer on producing educational videos and the science of teaching. The center will also meet with the Office of Academic Affairs to examine student data in efforts to produce consistencies in student learning experiences.

“If you were to put a GoPro on a student and watch them across a week, would their experiences be consistent—particularly at a freshman and sophomore level?” asked Spiegel, who will see the freshman experience firsthand when he serves as a faculty mentor for CSM101 in the fall.

Visit the CITL’s website for information on pedagogy seminars and updates at citl.mines.edu.

Spiegel comes to Mines with 15 years specializing in science education and transforming systems—his past experiences ranging from middle school to university graduate levels. Prior to Mines, Spiegel served as Chair of the Disciplinary Literacy in Science Team at the Institute for Learning and Associate Director for the Swanson School of Engineering's Engineering Education Research Center at the University of Pittsburgh.

 

Contact:
Kathleen Morton, Communications Coordinator / 303-273-3088 / KMorton@mines.edu
Karen Gilbert, Director of Public Relations / 303-273-3541 / KGilbert@mines.edu

With plenty of humor, Physics Professor Reuben Collins shared insights into the world of academic publishing, particularly the challenges it is facing, via his Faculty Senate Distinguished Lecture on March 26.

Collins opened with the story of how he came to be editor-in-chief of Applied Physics Letters. A year-and-a-half ago, “I was interested in trying something different,” he said. He’d always enjoyed writing, so he took up an offer to update a textbook. Then a colleague called and asked him to apply for the APL post.

“I didn’t know what that was,” Collins said. “So I said ‘yes.’”

He was offered the job last summer and – because he was new to editing a large journal – started as an associate editor, reviewing papers. He then took over as top editor in September. “That’s when I realized what I had said ‘yes’ to,” Collins said.

As editor-in-chief, Collins is responsible for setting the direction of the journal, defining standards and maintaining ethics, hiring and managing staff, and overseeing the process of reviewing papers. But his favorite duty, Collins said, is “I get to pick the cover art.”

Above all, Collins’ job is making sure Applied Physics Letters “services the community represents.” And that comes with plenty of challenges.

“We live in a metric-happy world,” Collins said. “We want to reduce everything to one number.” He shared the story of a friend whose work for the past year – papers, conferences, lab accomplishments – was summed up in one phrase that would determine her pay: “2-plus.” For colleges and universities, that might be ranking in U.S. News and World Report.

In the field of scientific journals, that all-important metric is “impact factor,” determined by the average number of citations received for each paper a journal published in the previous two years.

Unfortunately, some journals are rejecting most of the papers they receive even before sending them out for review, in an effort to increase their impact factor, Collins said. He implied that this was a disservice to the scientific community, given that out of all these rejected papers, surely some were worthy of publication.

But some journals have found a balance, Collins said – publishing many papers, which is good for the community; earning many citations, which benefits both the author and the community; and rating a high impact factor, which benefits the journal and authors.

Collins calls these “Good Science Citizen Journals,” a group he doesn’t put Applied Physics Letters in just yet. He said APL is still publishing too many papers, and many that don’t receive citations. “I want to move us into the good citizenship zone.”

Competition from the big science publishers is another challenge, with so many new journals being launched on what seems like a monthly basis. There’s also the push for open access – where the public can read and use publicly funded scientific research for free. Collins has also seen plagiarism, double-publishing, and other ethical issues crop up as editor-in-chief.

One current problem that will eventually turn into a boon for publishers is globalization, Collins said. In recent years, China has become a leading producer of scientific papers, though most of them end up unpublished. He sees this changing in the future, much like Japan changed its reputation from producer of cheap goods to leading manufacturer of electronics and cars.

“China will do the same thing,” he said. “Publishers have to hitch their wagon to that.”

The Faculty Senate Distinguished Lecturer Award, established in 1990, is an opportunity for faculty to honor outstanding colleagues. Recipients are selected from faculty nominations, and are invited to present on a topic of their choice. They also receive a plaque, and a gift to their discretionary account.

In addition to serving as professor and APL editor-in-chief, Collins is associate director of the Renewable Energy Materials Research Science and Engineering Center, and director of the Center for Solar and Electronic Materials.

Contact: 
Mark Ramirez, Communications Specialist, College of Applied Science & Engineering | 303-383-2622 | ramirez@mines.edu
Karen Gilbert, Director of Public Relations, Colorado School of Mines | 303-273-3541 | kgilbert@mines.edu
Kathleen Morton, Communications Coordinator, Colorado School of Mines | 303-273-3088 | kmorton@mines.edu

We spend 90 percent of our time indoors (according to the EPA) without realizing that the air we breathe could be potentially dangerous to our long-term health. Civil and Environmental Engineering professor Tissa Illangasekare has spent the last five years researching how volatile organic compounds, which are commonly entrapped as non-aqueous phase liquids (NAPLs) or dissolved into groundwater to produce plumes, affect our indoor air concentration.

“We drink so many liters of water a day, but we inhale so many thousands of liters of air,” Illangasekare said. (According to the EPA, the average American inhales close to 3,000 gallons a day.) “Sometimes we go to a contaminated site, test the water and we find it’s clean but later we go inside the building and find the vapor is contaminated.”

In 2009, Illangasekare and his research group, including a collaborator from the U.S. Air Force Academy, received funding from the Department of Defense Strategic Environmental Research and Development Program Office. The funding allowed the researchers to improve their understanding of the processes and mechanisms controlling vapor generation from entrapped NAPL sources and groundwater plumes, their subsequent migration through the subsurface, and their attenuation in naturally heterogeneous vadose zones under various natural physical, climatic, and geochemical conditions.

As the director of the Center for Experimental Study of Subsurface Environmental Processes, Illangasekare has an advantage. In his lab, he works with students to control experiments in multiscale test systems, studying vapor and airflow through unsaturated soils. The tanks are instrumented with soil moisture, relative humidity and temperature sensors. Using computation models, Illangasekare can predict how various climates affect soil concentrations expected to be found in a building. 

Their hypothesis was that some of this variability could originate from weather and hydrologic cycle dynamics, such as surface heating, rainfall and water table fluctuation.

“We learned how contaminant vapors move preferentially through the ground and make their way into people’s basements or crawl spaces,” said Kathleen Smits, a professor in the Department of Civil and Environmental Engineering, who has worked with Illangasekare for the past five years. “We also discovered how this is influenced by changes in climate (e.g. temperature, wind conditions and precipitation).”

In April 2014, Illangasekare received the 2012 European Geosciences Union's Henry Darcy Medal for his scientific contributions in water resources research and water resources engineering and management. Two months later, he was one of the coauthors on a report to the Strategic Environmental Research and Development Program on “Vapor Intrusion From Entrapped NAPL Sources and Groundwater Plumes: Process Understanding and Improved Modeling Tools for Pathway Assessment.”

“Our research has contributed to fundamentally understanding what’s happening to this system, which will help decision makers and regulatory agencies give better guidelines on how to manage these sites,” he said.

Illangasekare’s research will impact closure decisions on waste sites based on vapor intrusion risks.

“There’s a need for this science to exist. We are training a new generation of scientists and engineers to look at these kinds of problems.”

 

Contact:

Kathleen Morton, Communications Coordinator / 303-273-3088 / kmorton@mines.edu
Karen Gilbert, Director of Public Relations / 303-273-3541 / kgilbert@mines.edu

Colorado School of Mines Mechanical Engineering professor Xiaoli Zhang and graduate student Songpo Li have developed a gaze-contingent-controlled robotic laparoscope system that can help surgeons better perform laparoscopic surgery.

Laparoscopy is an operation performed in the abdomen or pelvis through small incisions with a camera. Laparoscopic instruments (typically 0.5-1 centimeters in diameter) are inserted through small incisions and then operated inside a patient’s body together with a laparoscope that allows the surgeon to see the surgical field on a monitor. Unlike open surgery, laparoscopic surgeries have reduced scarring, lessened blood loss, shorter recovery times and decreased post-operative pain. But due to limitations of holding and positioning the laparoscope, surgeons struggle with physiologic tremors, fatigue and the fulcrum effect.

Zhang and Li’s attention-aware robotic laparoscope aims to eliminate some of these physical and mental burdens.

“The robot arm holds the camera so the surgeon doesn’t have to,” Zhang said, noting that the camera is controlled effortlessly. “Wherever you look, the camera will autonomously follow your viewing attention. It frees the surgeon from laparoscope intervention so the surgeon can focus on instrument manipulation only.”

Their system tracks the surgeon’s viewing attention by analyzing gaze data. When the surgeon’s eyes stop on a new fixation area, the robot adjusts the laparoscope to show a different field of view that focuses on the new area of interest.

To validate the effectiveness of this procedure, the team tested six participants on visualization tasks. Participants reported “they could naturally interact with the field of view without feeling the existence of the robotic laparoscope.”

Zhang and Li anticipate that their technologies could have more than just healthcare applications, such as being used for the disabled and the elderly, who may have difficulty with upper-limb movements.

“Using this system, the surgeon can perform the operation solo, which has great practicability in situations like the battlefield and others with limited human resources,” Li said.

In mid September, Li received the Colorado Innovation S.T.A.R.S. challenge award for “Best Technical Achievement” at the college level during the JeffCo Innovation Faire. Zhang and Li are working with clinical researchers and industry partners to commercialize their attention-aware robotic laparoscope.

 

Contact:

Kathleen Morton, Communications Coordinator / 303-273-3088 / kmorton@mines.edu
Karen Gilbert, Director of Public Relations / 303-273-3541 / kgilbert@mines.edu

This story appears in the 2014-15 issue of Mines' research magazine, "Energy & the Earth."

Colorado School of Mines has been known for its prowess in geology since about 1874. Its reputation in biotechnology has taken just a little bit longer to develop – about 130 years longer, give or take.

Mines is making up for lost time. The school’s faculty, researchers and students haVe shed new light on areas as diverse as the nature of blood clots and the microbial role in rust. They have helped make better artificial limbs and developed laser microscopes capable of capturing video of the inner working of cells. They have reengineered algae to produce biofuels and developed scaffolding that could one day give new cartilage a foothold in creaky knees. In short, biological sciences and engineering have arrived at Mines, and in a big way.

The work is diverse, but there are common threads, said David Marr, who heads Mines’ Department of Chemical and Biological Engineering.

“We are an engineering and technology-focused institution— that’s really where our niche is,” Marr said. “It’s in areas of bioengineering, broadly interpreted, that we have a strong role to play.” Those areas, he added, encompass biomedical applications, biomechanics, biomaterials, environmental biotechnology and biofuels.

Recent hires have bolstered several of these research areas, and curriculum has changed in kind, with courses covering a range of biomedical engineering, biomaterials, environmental biotechnology and biophysics available to undergraduate as well as graduate students. In fall 2013, Mines’ freshman biology course moved to a studio format, where small teams of students sit at workstations equipped with computers, dual monitors, video microscopes, digital cameras and digital balances, as well as with more specialized equipment like micropipettes and oxygen, pH and temperature sensors.

Mines Assistant Professor Nanette Boyle is among the recent arrivals, having signed on in August 2013. Like many at Mines, Boyle considers herself an engineer. But she engineers the genomes of algae and cyanobacteria, microscopic plants using the tools of synthetic biology, systems biology and metabolic engineering.

“The overall goal of my research is to make products that replace petroleum using these photosynthetic organisms,” Boyle said.

In her new Alderson Hall lab, stacked incubator shakers swirled the contents of four beakers, their sloshing fluid of varying light green hues under the bright multispectral light. They were filed with the algae Chlamydomonas and the cyanobacteria Synechococcus. Boyle’s work differs from most algae-based biofuel efforts, which aim to fatten up the algae and then harvest them. Rather, she wants to engineer the algae to produce short chain alcohols, isoprene or other hydrocarbons while they keep photosynthesizing away.

“You can get them to create whatever you want if you can find the genes to do it,” Boyle said.

Mines Professor John Spear, a microbiologist, also focuses on the genomics of tiny creatures. The driving questions of his work, though, are big.

“What are the possible benefits of microbes to make human life and/or the environment better?” Spear asked. “How can we put microbes to work in ways we haven’t done before?”

Genetic sequencing has fostered an explosion in what is known of the tree of life, and Spear and colleagues are discovering new organisms at a dizzying pace. In the mid-1980s, there were perhaps 12 known phyla, or kingdoms, of bacteria. Now there are 130 and counting.

“So when you find 10 or 20 phyla of bacteria as we have found in some environments, that’s like walking out your door and discovering plants for the first time,” Spear said.

On the applied side, Spear has focused on a couple of areas, including wastewater treatment and corrosion. Some corrosion is chemical, but microbes, which feed on the electrons metal has to offer, also contribute, to the point that the oil and gas industry has considered flushing wells with antibiotics. Across industry, the failures and replacement costs associated with corrosion cost tens of billions of dollars annually. More precisely understanding the composition and habits of such microbes can help industry develop better countermeasures and lower costs, Spear said.

Much of Mines’ biology-related work involves the biomedical field. A longstanding collaboration involving Marr and Associate Professor Keith Neeves, recently landed a National Institutes of Health grant to study how microbots – tiny spherical machines each about onetwentieth the diameter of a human hair – might be used to deliver clot-busting drugs straight to the blockage in stroke patients. The idea, Marr said, is to inject a swarm of microbots and steer them to clots using magnets outside the body, “A sort of ‘Fantastic Voyage’ kind of thing,” Marr said.

Marr’s Alderson lab has the markings of an experimental physicist’s haunts, with stainless-steel-topped laser tables rife with grids of screw holes, many anchoring lenses and mirrors. The work there focuses on using light and magnetism to, among other things, test the mechanical properties of cells. A floor below, Neeves’ PhD student Abimbola Jarvis bounced between making microfluidic devices of rubbery silicone and adjusting an Olympus microscope where the screen displayed a fluorescence-enhanced time-lapse of a blood clot forming. Neeves’ main interest is in how blood clots form and dissolve, work that has piqued the interest of clinicians at places such as Children’s Hospital Colorado, where Neeves has helped study hemophilia patients.

“We work where physics and hematology meet,” Neeves said.

Down the hall, Assistant Professor Melissa Krebs is working on where joints meet, among other things. She and her students create biopolymers with applications ranging from tissue regeneration (cartilage being one target) to cancer fighting. The trick, she said, is to create polymers that support cell growth or drug delivery for a prescribed amount of time and then dissolve away.

In Krebs’s lab, PhD student Michael Riederer was creating microspheres for use on the drug-delivery side. Among the inputs were genipin, a chemical derived from gardenias, and chitosan from shrimp shells. As the research progresses, he will work on releasing proteins from the microspheres, controlling the pace and volume of release, Krebs said. These proteins might include growth factors for tissue regeneration or growth inhibitors for cancer treatment, she said.

Mines Assistant Professor Anne Silverman works on joints, too, but from a different perspective. With Mines associate professors Anthony Petrella and Joel Bach, she leads Mines’ Center for Biomechanics & Rehabilitation Research.

“The overall theme is improving walking ability in people who have movement disorders,” Silverman said.

Her team takes experimental measurements on patients using near-infrared cameras, voltage sensors to measure muscle excitations and force plates to measure external loads (such as the heel hitting the ground). They then use this data to develop computer simulations of movement. Amputations below the knee have been a focus, but her team also works with patients who have Parkinson’s disease and cerebral palsy. Collaboration partners have ranged from the Center for the Intrepid at Brooke Army Medical Center and the Colorado Neurological Institute at Denver’s Swedish Medical Center.

“We’re creating complex models and simulations of movement to estimate in vivo muscular and joint behavior,” Silverman said. “We’re using an engineering approach to solve biological problems.”

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