Category: News Releases

A Scientist’s Life: Jennifer Smith

Jennifer Smith is a coral reef ecologist at Scripps Institution of Oceanography at the University of California San Diego since 2008. She received her PhD from the University of Hawaii in botany and ecology, evolution and conservation biology where she spent six years studying human impacts on coral reefs of the Hawaiian Islands. Following graduation, she participated in the first Scripps Line Islands Expedition in 2005 prior to starting postdoctoral research at the National Center for Ecological Analysis and Synthesis at UC Santa Barbara.

explorations now: What do you do for a living?

Jennifer Smith:  I’m a marine ecologist and I spend much my time trying to understand what factors are important in structuring marine communities. I largely work in shallow coastal ecosystems so systems that require scuba diving in order to study them and primarily in warm tropical seas where you find coral reefs.

Coral reefs are among the most important ecosystems on the planet. They provide a number of really important ecosystem services to humans such as fisheries and tourism. They support a huge amount of biodiversity and provide coastal protection from erosion. My research is really focused on trying to understand the factors that affect coral reefs, how humans specifically affect them through things like overfishing and pollution. I’m also interested in global impacts such as how warming and ocean acidification are currently affecting these systems so that we may be able to develop better management strategies for ensuring that these systems are with us for future generations.

en: What are the main questions in your field?

JS:   While it’s often portrayed that every coral reef on the planet is going to be extinct in the next 50 or 100 years, in fact if you go to remote locations around the world, you find that there are coral reefs that are still thriving, coral reefs that still have excessive amounts of living coral, and we’ve seen evidence those systems can actually recover from disturbance events rather rapidly. Even though the media portrays coral reefs as these very susceptible and fragile systems, they have been around for millennia, so there’s no reason to expect that with one disturbance event, they’re going to fall off the face of the earth.

We’re really interested in trying to understand what makes these systems resilient, how can we try to build some of this resilience into other places where people live. How can we better manage fisheries? How can we better manage water quality to give these coral reef systems as much strength as possible to ensure that they can recover from future warming events, which is inevitable with climate change?

en: What are the tools you use in field research?

JS: Being a coral reef ecologist in this day and age is really exciting because technology is advancing rapidly and there are so many neat new tools that we get to use to study these systems to increase our ability to capture data and to process information. We use an imaging system where we essentially just take a camera underwater and take thousands of pictures of the reef. We call it “lawn mowing the reef” because you go back and forth in a grid-like pattern. You bring all those images home with you, you stitch them together using commercially available software, and you can essentially build a 3D model of any coral reef on the planet. We then can go on a virtual dive in these 3D models. We can study these reefs in a way that has never been possible before.

Once we have the 3D models of a coral reef, we partner with scientists at the UC San Diego’s Jacobs School of Engineering, Cultural Heritage Engineering Initiative (CHEI), who have built custom software that allows us to actually move in that 3D space to extract data. This is really novel. There really isn’t any commercially available software that allows scientists to do this so by partnering with these experts, we’ve been able to essentially extract data and information out of these 3D models that we would never have been able to do before.

en: Why did you come to Scripps?

JS: Scripps is home to so many brilliant scientists working on such a diversity of issues. That really opens up the research potential for any given scientist including myself. There are so many collaborative opportunities to work with sensor developers, software engineers, climate scientists that allow us to ask questions that we never would have before been able to do. For example working with Jules Jaffe’s lab, we now have an underwater microscope so instead of bringing organisms into the lab, we can bring the microscope into the field and view live organisms underwater in their natural environment. We can make measurements using autonomous sensors that can collect data from remote parts of the world through collaborations with Todd Martz’ lab. I find Scripps to be a very welcoming and collaborative environment and there are just numerous opportunities to interact, to collaborate, to ask questions that we could never ask as independent scientists.

In this day and age with all of the technological advancements that are currently occurring, there’s a unique opportunity for scientists to take advantage of some of these technologies and to interact and collaborate with partners and folks whom perhaps we would never have interacted with before. I was recently on a panel at South by Southwest talking about the use of technology for studying coral reefs and for coral reef conservation and it opened up numerous doors talking with audiences that I would have never interacted with on my own as a coral reef scientist and so that was really exciting to see the people that are building some of these technologies. People who are the forefront of Facebook and a whole variety of other media platforms are really interested in trying to help us communicate the coral reef story. Using social media in new and unique creative ways I think is really important for us as scientists to try to reach out and build a network to ensure that the messages are getting out to the public.

Many people are passionate about coral reefs because they scuba dive and like to visit these wonderful incredibly biodiverse ecosystems and therefore many people are actually really concerned about their well-being and their future on the planet. So I find it incredibly important for us as scientists studying these systems to communicate our results and to share our findings with the general public. I think we need to get more positive messages out into the public so that people have hope that there are actions we can take to ensure that these reef systems will be around for future generations.

This article is a reproduction of an articled published by Scripps Institution of Oceanography at the University of California San Diego. The original article can be found here.

The human powered submarine team pose in front of their submarine. UC San Diego undergraduates design and build a submarine in hopes of racing it at the International Submarine Races against other universities.

San Diego, April 26, 2018 – A group of roughly 20 undergraduate students –bonded by bondo, fiberglass skin and their innate desire to build –are hoping to enter their human-powered submarine in the European International Submarine Races in the summer.

The unveiling of their design will take place Thursday April 26 at 7 p.m. and will include a brief presentation describing the race and its guidelines. The team will also show off the new and improved design that they plan to compete with this summer. Industry professionals and researchers from the Scripps Institution of Oceanography and other UC San Diego entities will be in attendance to offer advice to and share their passion for engineering with these students.

This isn’t the first time that UCSD has participated in the European International Submarine races. Back in 2000, UCSD broke the world record for the class One Person non propellor with a dolphin fin boat called “subsonic” going four mph.

For this year’s race, the team chose to design and build a dolphin-fin submarine because it is an innovative challenge that requires an unconventional propulsion mechanism: a six-bar linkage optimized using a genetic algorithm. The team is also using biomimicry to inspire the design of their propulsion fin, specifically multi-material 3D printing to mimic the flexible trailing edge of a dolphin tail.

The team’s first iteration of steering fins was made possible through a collaboration with the Qualcomm Institute’s DroneLab. Structural Engineering Professor Falko Kuester, the director of the DroneLab provided the students with use of the 3-D printers to create their submarine parts.

For club-member Tobin Gutermuth, this project and the research required to complete it has given him a boost of confidence.

“This project has given myself and many of my other teammates the confidence that we can go into the world, recognize a complex problem, break it down, and come up with a novel engineering solution,” Gutermuth said. “It gives us tremendous confidence to design, build, and test a product of our own.”

Media Contacts

Tiffany Fox
(858) 246-0353

San Diego, April 12, 2018 – War-fighting innovation and the future that such innovation would make possible were the focus of four days of talks, tours and workshops as part of the United States’ Marine Corps Hybrid Logistics Symposium, held from Feb. 26 to Mar. 1 at the UC San Diego Qualcomm Institute.

Hosted by the Marine Corps Deputy Commandant for Installations and Logistics Michael Dana (in partnership with UC San Diego), the first-ever symposium comprised a series of interconnected briefs, panels and breakout groups that focused on identifying the people, processes and equipment — in other words, hybrid logistics — that the next generation of Marines will need in 2025 and beyond. One hundred Marines and sailors, including junior enlisted, junior officer and civilian Marines joined UC San Diego students and faculty — including UC San Diego Chancellor Pradeep Khosla — at the symposium.

United States Marines erxploring CHEI’s Wide Angle Virtual Environment (WAVE)

Also present were key private industry partners, including Microsoft, which provided insights into how to solve some of the military’s most difficult logistical challenges.

“Moving toward a hybrid logistics model will require a logistics community that questions conventional wisdom without ignoring the realities of the modern battlefield,” said Lt. Gen. Dana. “The Hybrid Logistics Symposium is the first step toward getting feedback on our processes from some of our brightest Marine logisticians.”

Hybrid Logistics, as the Marines describe it, is the blending of proven logistical tactics with innovative methods of sustaining Marines in combat. It consists of five areas of focus:

  • Additive manufacturing (the industrial version of 3D printing)
  • Unmanned logistics systems (eg drones)
  • Smart logistics
  • Expeditionary energy
  • Expeditionary medicine

Several of the symposium’s discussions and tours of the Qualcomm Institute’s headquarters in Atkinson Hall were directly related to these focus areas, from demonstrations of QI’s SunCAVE and Vroom visualization tools, a visit to the QI Drone Lab and a tour of the Additive Rocket Company (ARC) facilities in the QI Innovation Space. (ARC manufactures rockets using 3D metal printing technologies.)

“There’s a lot of interest and a lot of work on 3D printing, not only elements that don’t need to have very strong structural properties, but also things with structural properties you want to engineer, to be able to embed electronics and sensors even as you print these things and addressing the whole design chain in a significant new way,” said QI Director Ramesh Rao. “I think there’s a lot that is going to be taking place here in the near future beyond what was presented.”

Electrical and Computer Engineering Prof. Todd Hylton, a QI affiliate and the Executive Director of the Contextual Robotics Institute discussed complexity in the management of systems during a panel discussion on day one of the symposium titled “Where Will the World Be in 2025.” Hylton spoke about replacing regular hierarchical system organization to match the system that needs to be managed or influenced, highlighting the necessity of the five domains: vehicles, people and applications, project management, data analysis and distribution, policy planning and infrastructure.

Another major topic of discussion during the panel was the impact of climate change on the future. Mark A. Merrifield, the Executive Director at the Center for Climate Change Impacts and Adaptations and Professor at the Scripps Institute of Oceanography spoke about the scientific basis for global warming and climate change. Merrifield remarked that the stress climate change will put on the system is completely unprecedented, with some regions of the world getting warmer while others experience stress on their crops.

“Where we’ll be by 2025 is mainly reflecting the amount of carbon we’ve burned over the past century and we will over the next seven years or so,” said Merrifield. “Changes we make now likewise will change what the future of this scenario will be.”

This food scarcity, along with large population movements from coastal cities and a resulting rise in income inequality are problems that could lead to possible global conflicts, warned Barbara Walter, a professor of Political Science at the School of Global Policy and Strategy.

Dr. Gary S. Firestein, director of the UC San Diego Altman Clinical and Translational Research Institute (ACTRI) and the Associate Vice Chancellor of Translational Medicine at UC San Diego, explained how the migration of mosquitos to northern regions including the United States may lead to a greater prevalence of vector-borne diseases.

Hylton pointed out how inequalities between nations and the desire for underdeveloped nations to foster development makes it difficult to find sources of clean energy and, in tandem, incentives to eliminate the increase in fossil fuels.

The panel preceded multitude of presentations, such as “Design Thinking and Expeditionary Energy,” that described how these challenges would affect the Marine Corps and subsequent ways the military would need to change its structure to accommodate such changes. Mark Valentine, Chief of Staff for Microsoft’s Department of Defense, described to the Marines the function of wearable technologies today and their potential usage in the future, while ECE Prof. Patrick Mercier (a QI affiliate) described his research with energy-efficient biomedical interfaces, wireless circuits and power electronics. Firestein suggested this research could be instrumental in using the  human body to power devices via the extraction of energy from the inner ear’s potassium current.

The Marines brainstormed for their challenge presentations, in efforts to conceive of innovative practices that could be used to replace current methods and approaches to hybrid logistics.

Later in the program came a shift in focus to address the notion of innovation. Morgan Plumber, managing director of the MD5 National Security Technology Accelerator at the US Department of Defense, commented on the cultural shift needed to instill the necessity and importance of innovation to the Marines.

“If you believe that talent and ideas are equitably spread against geography and race and gender, then the notion that you have an entire force under arms that’s composed of less than half of one percent of this nation’s population is a pretty good indicator that we’re not accessing all of the talent and ideas and tech that we need,” Plumber said. “We talk about innovation in the context of, ‘Oh, wouldn’t it be cool.’ But there’s actually a deeply existential component to innovation that the department faces which is how do you bring people home alive.”

Of emerging importance to war-fighting and hybrid logistics is the concept of Smart Cities. Deputy Chief Operating Officer for the City of San Diego David Graham described how the city of San Diego is working towards advancing sensor technologies and the Internet of Things to become a hyper-connected Smart City and elaborated on the worldwide race to attain this distinction. In January of 2000, Graham noted, the City of San Diego had gone broke, but used that as a starting point to become a better San Diego.

“Disaster and problems will breed back innovation if you can take that as your challenge,” Graham said, adding that technology and innovation must always remain about the people they serve.

The culmination of the Hybrid Logistics Symposium were a series of challenge presentations, an effort to conceive of innovative practices that could be used to replace current methods and approaches to hybrid logistics.

The winning group suggested a “Marine Corps Innovation Hub,” an online crowdsourcing platform to emphasize collaboration and promote a more free exchange of ideas among Marines. The Leadership and participants at the conference expressed collective interest in planning and executing Hybrid Logistics using drones, high-speed networks created by university researchers for often entirely different purposes.

Media Contacts

Tiffany Fox
(858) 246-0353

San Diego, March 23, 2018 – PBS NewsHour aired the first of a two-part series tonight on the Bermuda 100 Challenge, a joint initiative between the University of California San Diego’s Cultural Heritage Engineering Initiative (CHEI), the Bermuda Government’s Marine Heritage Section of the Department of Environment and Natural Resources and Look Bermuda. The second part in the series, which will heavily feature QI technologies, airs tomorrow night at 7 p.m. on San Diego’s KPBS and at 6 p.m. on KPBS2. Watch the first part of the series here.

Viewing Mary Celestia Bermuda on UC San Diego’s WAVE virtual reality display

The chief aim of the Bermuda 100 project is to document 100 or more historic shipwrecks and distinct natural habitats in the waters surrounding Bermuda to promote conservation efforts and open the sites to both real and ‘virtual’ tourism from interested students, researchers and travelers from around the world.

One shipwreck that has already drawn the interest of archaeologists, marine biologists and divers alike is the Mary Celestia, an iron-hulled steamship from the American Civil War that sank in 1864

Dr. Philippe Rouja with Jeffrey Brown at wrecks of the ‘Norkoplin’ and ‘Emma Davis’

PBS News Hour’s Senior Correspondent & Chief Arts Correspondent Jeffrey Brown and his team spent a day at the Qualcomm Institute (QI), where CHEI is based, with the project’s principal investigator, Structural Engineering Professor and CHEI Director Falko Kuester, as well as CHEI Development Engineers Vid Petrovic and Eric Lo. While there, Brown was able to view the shipwrecks and related artifacts on QI’s suite of ultra high-resolution displays, including the Vroom display wall, the WAVE and the SunCAVE virtual reality environments.

Brown later spent three days in Bermuda with local project PI and Custodian of Historic Wrecks Dr. Philippe Max Rouja, where he experienced the shipwrecks in person, “demonstrating the promise of this new and developing technology,” said Rouja.

“The vision behind the Bermuda 100 Challenge is to create the science, technology and engineering foundation needed to scale the documentation of submerged cultural heritage up globally. Given that there are millions of shipwrecks, while hundreds of thousands are considered archaeologically significant, there is a lot more to be explored, discovered and preserved,” added Kuester.

PBS NewsHour has an average of 1.1 million nightly viewers. San Diego residents can watch the broadcast on KPBS or on-demand at

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Media Contacts
Tiffany Fox
(858) 246-0353

San Diego, March 19, 2018 – The Cultural Heritage Engineering Initiative (CHEI), based at the University of California San Diego, has received $225,000 from San Diego-based entrepreneur Brian Strauss to enable digital visualization technologies that make it possible to see cultural heritage sites and artifacts in entirely new ways – like “the La Brea tar pits without the tar.”

Brian Strauss and Dominique Rissolo, pictured on site at Hoyo Negro, Mexico

The funds – which contribute to the Campaign for UC San Diego – will go primarily toward financing expeditions and field work at Mexico’s Hoyo Negro underwater cave site, where the remains of a young Paleo-American woman (dubbed “Naia” by researchers) were found last year alongside fossils of extinct Ice Age megafauna such as saber-tooth cats and huge Shasta ground sloths.

“This funding will help us breathe new life into MesoAmerican studies,” said CHEI Director Falko Kuester, a professor of Structural Engineering at UC San Diego. “The Strauss family’s generous donation will allow us to dive in – both literally and digitally – to get this field work done.”

CHEI’s work at the Hoyo Negro site can be compared to forensic science, or what the researchers describe as “CSI archaeology” – a means of using advanced visualization technologies such as LiDAR (Light Detection And Ranging) laser technology and structure-from-motion photogrammetry techniques to capture and then “stitch together” a digital recreation of the cave site. From the comfort of dry land (and using CHEI’s advanced 3D visualization displays) the researchers can then reveal previously hidden or difficult-to-access information about this remote and hostile environment.

“Instead of deducing what happened, as one might do at the scene of a crash – there’s a smashed-up car, there’s a skid mark, there’s a tree – we can draw conclusions from the data itself,” explained Dominique Rissolo, co-director of the Hoyo Negro Underwater Archaeology Project, special projects coordinator for CHEI and an expert in Maya archaeology.

“The positioning of fossils tell a story about how and when the structure formed and allows us to study the spatial and temporal context,” he continued. “Virtual access gives us the ability to teleport researchers to this cave site and allow them to dive the entire cave as it exists now. ”

Using this suite of digital tools, the researchers were able to determine that Naia fell into what, at the time, was shallow water, as evidenced by the conditions of her remains, which indicate how her body came to rest on the floor of the cave. Researchers were able to determine that Naia lived 13.000 years ago, making her the earliest mostly complete human found so far in the Americas.

Brian Strauss, son of Paul and Anita Strauss, made the donation to CHEI after hearing a talk on cave archaeology given by Rissolo at the San Diego Natural History Museum, where Rissolo was serving as a consultant for the museum’s exhibition on the Maya (the family previously donated $100,000 to the project). Strauss said that when he heard about CHEI’s work in Mexico he didn’t want to merely fund the project, he wanted to be a part of it: to work with the archaeologists and master divers in their efforts to document the site. Strauss has now been a part of four excursions to Quintana Roo, the area of the Yucatan Peninsula where the cave is located.

Because the CHEI researchers are also surveying and documenting the cave site itself in addition to the human and animal remains, their work has broader implications for climate scientists.

“This work bumps up against what people would call ‘natural heritage’ and allows us to look at the anthropogenic factors at play,” said Rissolo. “Creating a paleo-environmental reconstruction of the site allows us to look at mineral deposits in the cave, which helps researchers understand what the climate was like back then and what sea-level rise might have been like 6.000 years ago.”

“This is a time capsule, not just a time snapshot,” added Kuester. “It’s like a message in a bottle, only the bottle is cracked and there is seepage. We have to preserve the message.”

“This gift is truly transformational in a day and age where philanthropy might have to become the critical enabler towards keeping our world cultural heritage alive and creating a means to pass it on to future generations, given the dwindling or non-existent public and federal resources to do so,” added Kuester. “As such, Brian truly answered CHEI’s call to action of ‘If not now, when?’ and ‘If not us/you, who?’ because ultimately we do owe it to our children to create a future for the past.”

Media Contacts
Tiffany Fox
(858) 246-0353

February 15, 2018

A collaborative group of researchers from the University of California San Diego traveled to Turin, Italy recently to digitally map an entire portion of the city—complete with historic architecture, expansive murals and stunning works of art.

From left, Eric Lo and Dominique Rissolo of the UC San Diego Cultural Heritage Engineering Initiative with Polytechnic University students in Italy. Photo by Farshid Bazmandegan

Digital data will be used by students and researchers on campus to explore the site’s buildings and artifacts, ultimately recreating an interactive, virtual-reality experience. Through high-resolution images and 3D models, students can study all the pieces together without the difficulty of travel to the site, nor fear of losing objects to passing time.

“The idea is to create a model— a digital surrogate—of these structures that allows us to interact with them, to analyze them, to annotate them and to make measurements to

really understand their state of health,” said Dominique Rissolo, an archaeologist and assistant research scientist at the UC San Diego Qualcomm Institute. “We have a unique capability here on campus … that allows us to go one step beyond the model to actually create the digital surrogate.”

The work is being conducted as a project of the Cultural Heritage Engineering Initiative at the Qualcomm Institute, organized by researchers at the institute, Division of Arts and Humanitiesand Turin’s Polytechnic University.

From left, Eric Lo, structural engineering Ph.D. student Michael Hess and Falko Kuester in the WAVE lab navigating the Turin virtual reality. Photo by Erik Jepsen/UC San Diego Publications

Trip findings are an extension of Division of Arts and Humanities Dean Cristina Della Coletta’s research on the historical significance of the 1911 Turin International, the world’s fair that took place in the city’s Parco del Valentino. With a goal to visually recreate the 1911 fair, the team digitally captured a majority of the park, which includes a medieval village and the Castello del Valentino, or “Valentino Castle”—home to Polytechnic University’s architecture department.

“For the first time, we really have a wide array of expertise that is brought to bear on the project: we have engineers, working with architects, working with cultural historians,” Della Coletta said. “This is a winning combination.”

Researchers digitally mapped a portion of Turin’s Parco del Valentino, the location of the 1911 World’s Fair. The park includes a medieval village called Borgo Medievale, pictured here. Photo by Farshid Bazmandegan

Led by Della Coletta, Rissolo, Falko Kuester and Vid Petrovic, the Turin fieldwork brings together engineering students and arts and humanities students for the betterment of both. Cross training these students, Kuester said, creates empowered and dynamic learning: just as the cultural preservation work is important, honing and testing new technical skills in the field and classroom is equally as important.

“The exciting part for us, as educators, is that we get to work with talented students from a broad range of disciplines—disciplines that historically do not really collaborate together as much,” said Kuester, the Kinsella Heritage Engineering Director at Qualcomm Institute and professor at the UC San Diego Jacobs School of Engineering.

“By doing this, and being able to put on these different lenses, our students get to learn to speak each other’s language [and] to communicate in ways we were never required to do before,” he said. “Our students, in the process, are becoming more complete human beings and innovators.”

Considered the initial steps in recreating the structures of the 1911 Turin World’s Fair, Rissolo said the team collected field data by using terrestrial laser scanners, structure-from-motion photogrammetry and stereo spherical giga-pixel imaging. Taking several scans from many different perspectives in the park allows the team to process the data quickly and with a high degree of certainty. They collected thousands of images, and use advanced software on campus to create digital models of the structures.

“The most important takeaway for our students is the ability to connect theory and practice, whether it is in the archives or in the digital lab,” said Della Coletta, who participated in the data gathering during fall quarter. “What makes the project meaningful is the ability of our students to learn by doing.”

With a first round of digital information collected, the researchers have been busy on campus recreating a 3D model of the buildings, both inside and out. Viewing the models at the university’s WAVE lab, Qualcomm Institute research and development engineer Eric Lo said the results were a good representation of what he saw on the ground in Italy, but some data was missing. Once the 3D models are created, gaps appear, giving the team an overview of what to record on future trips.

“Ultimately, it’s a map to the site, but a map that also tells us what else to map in order to first create the best possible digital surrogate, combining site geometry, building materials and overall state of health, as well as its art and history,” Kuester said.

The Turin team also included Department of Visual Arts alumnus Farshid Bazmandegan and students at Italy’s Polytechnic University, headed by geomatics professor Filiberto Chiabrando. The Polytechnic team continues to digitally document historic structures in the park.

“The approach that we will follow in this project is very interesting, since it’s connected to the cultural heritage, [and] it’s connected to the humanities as well. This is a fruitful collaboration that we have started,” Chiabrando said. “The most important thing is to merge different backgrounds, and different experiences. A multidisciplinary approach is the best way.”

The images will ultimately recreate a “digital map” of the buildings, both outside and in—as shown here in the researcher’s planning book. Photo by Farshid Bazmandegan

The Cultural Heritage Engineering Initiative at UC San Diego brings the power of student-driven engineering to the study and preservation of historic structures, archaeological sites, art and other artifacts. There are multiple projects underway, from visualizing shipwrecks near Bermuda to the Hearing Seascapes initiative with Department of Music professor Lei Liang.

“It’s a phenomenal opportunity to have the Division of Arts and Humanities partner with the Cultural Heritage Engineering Initiative, the Jacobs School of Engineering and, on top of that, the Polytechnic University in Turin,” said Della Coletta. “What better place to engage in a project that connects engineering and technology with the humanities.”

San Diego, February 9, 2018 – PBS Nova has featured work by a team of researchers at the UC San Diego Qualcomm Institute in a recent article in its NOVA NEXT online publication.

Diver Alberto Nava in the SunCAVE.

In the article, titled “How VR Helped Archaeologists Excavate a Fossil-Rich Submerged Cave,” QI Research Scientist Dominique Rissolo describes his team’s work at the QI Cultural Heritage Engineering Initiative (CHEI) to visualize – in high-resolution 3D – ancient human and animal remains found in Hoyo Negro, an underwater cave on Mexico’s Yucatan peninsula.

The remains were discovered by lead diver Alberto Nava and his colleagues on the floor of a flooded pit 130 feet from the surface. Among them were parts of more than 30 animal skeletons, including the nearly intact skull and skeleton of a teenage girl of around 16 who had fallen to her death in the pit at the end of the last Ice Age some 13,000 years ago. Also found were fossils of Ice Age megafauna such as saber-tooth cats and huge Shasta ground sloths.

The researchers used the state-of-the art SunCAVE (Cave Automatic Virtual Environment) at QI, which allowed scientists associated with a NOVA documentary to interact with, map and measure the fossils, as well as plan future diving missions. QI and CHEI  are an integral part of the Hoyo Negro Project – working with the technical dive time to develop optimal image acquisition strategies, creating the high-resolution digital models, and powering the visual analytics necessary to bring this remote site to the scientific community.

The QI effort is being led by Rissolo, an archaeologist who has been working in the Yucatan for 25 years, as well as cultural heritage engineering specialists Falko Kuester, Vid Petrovic and Eric Lo. Many of the researchers studying the site’s diverse Ice Age fauna will never have a chance to go there. Not only has the virtual “twin” of the site enabled paleontologists to study the bones remotely, but they are making discoveries in the data – bones and tell-tale features that have eluded detection by divers at the bottom of the deep dark pit.

Exploring an environment that only few have seen before, yet to be the first to see it as a whole and in its full beauty, combining site-scale context with the finest possible details captured by its digital twin for in-depth analysis, is truly transformative, says Falko Kuester, Professor for Visualization and Virtual Reality at CHEI.

“Not only is the virtual cave essential for a comprehensive fossil inventory,” writes NOVA Next writer Evan Hadingham, “it enables the team to take measurements and print accurate 3D replicas of specific bones, including Naia’s skull.” Explorers on the most recent National Geographic-funded mission to Hoyo Negro used the virtual SunCAVE to plan their excursion in detail, which ultimately allowed them to bring up parts of eleven ancient animals, some of them previously unknown.

To watch a documentary film about Hoyo Negro, visit

And to see QI’s Hoyo Negro website, visit

San Diego, February 6, 2018 – “Lost Treasures of the Maya Snake Kings,” a new one-hour National Geographic special premiering today at 9/8 p.m. central, shows how LiDAR laser imaging technology is revolutionizing archaeology and features the WAVE data visualization  technology created by researchers at the University of California San Diego Qualcomm Institute (QI). Albert Yu-Min Lin, an affiliate of QI, is the host of the program.

The documentary explores what’s being hailed as a “major breakthrough” in Maya archaeology: the identification of ruins of more than 60,000 houses, palaces, elevated highways, and other human-made features that have been hidden for centuries under the jungles of northern Guatemala. The work was conducted by researchers of the PACUNAM LiDAR initiative.

Using a powerful technology known as LiDAR (short for “Light Detection And Ranging”), scholars digitally removed the tree canopy from aerial images of the now-unpopulated landscape, revealing the ruins of a sprawling pre-Columbian civilization that was far more complex and interconnected than most Maya specialists had supposed.

“The LiDAR images make it clear that this entire region was a settlement system whose scale and population density had been grossly underestimated,” said Thomas Garrison, an Ithaca College archaeologist and National Geographic Explorer who specializes in using digital technology for archaeological research.

Garrison is part of a consortium of researchers who are participating in the project, which was spearheaded by the PACUNAM Foundation, a Guatemalan nonprofit that fosters scientific research, sustainable development, and cultural heritage preservation.

Working closely with National Geographic Explorers, QI’s Cultural Heritage Engineering Initiative (CHEI) was launched in 2007 and has since created a comprehensive toolbox and talent pool that brings the power of student-driven science and engineering to the study and preservation of archaeological sites, monuments, historic structures and other artifacts. QI researchers have a history of working on various ground based and drone based LiDAR imaging projects in Guatemala. Lin, along with his collaborators in the QI Engineers for Exploration program —co-directors Ryan Kastner and Curt Schurgers — collaborated with Garrison to lead teams of students on expeditions over the past four years to the jungles of Guatemala to test out various platforms for mapping and imaging. QI Staff Engineer Eric Lo and Ph.D. student  Dominique Meyer were also instrumental in these field expeditions.

Two of the CHEI visualization displays used to visualize the LiDAR imagery
Researchers examine LiDAR imagery from Guatemala on two of the visualization displays (including the WAVE, at right) in the lab of the QI Cultural Heritage Engineering Initiative.

“Engineering and exploration go hand in hand — National Geographic was co-founded by the Alexander Graham Bell who invented the telephone,” said Lin. “The things we create allow us to go further, and with the exponential rate of innovation today this truly is the new golden age of exploration.”

The Qualcomm Institute is a leader in visualization technologies that make it possible to look at data at a massive scale. Researchers at CHEI — including Falko Kuester, Vid Petrovic, Eric Lo, Christopher McFarland, Jurgen Schulze, Greg Dawe, Joel Polizzi, Joe Keefe and Tom DeFanti — played a primary role in developing CHEI’s hardware and software toolbox, including the 70-megapixel Wide Angle Virtual Environment (WAVE), which is featured heavily in the documentary. The team at CHEI also developed the VisCore visual analytics engine that allows archaeologists to use virtual reality to literally walk into the arena of data-enabled scientific discovery, as featured in the “Lost Treasures of the Maya Snake Kings.”

“Turning big-data into insights and action is one of the truly transformative elements that our team enables,” says CHEI Director Kuester. “Lots of data is being acquired and simulated these days, but making sense of it all is a completely different story. The opportunity to work in highly interdisciplinary teams that change to state of knowledge is where it gets truly exciting.”

An advanced civilization

The PACUNAM project mapped more than 800 square miles (2,100 square kilometers) of the Maya Biosphere Reserve in the Petén region of Guatemala, producing the largest LiDAR data set ever obtained for archaeological research.

The results suggest that Central America supported an advanced civilization that was, at its peak some 1,200 years ago, more comparable to sophisticated cultures such as ancient Greece or China than to the scattered and sparsely populated city states that ground-based research had long suggested.

In addition to hundreds of previously unknown structures, the LiDAR images show raised highways connecting urban centers and quarries. Complex irrigation and terracing systems supported intensive agriculture capable of feeding masses of workers who dramatically reshaped the landscape.

The ancient Maya never used the wheel or beasts of burden, yet “this was a civilization that was literally moving mountains,” said Marcello Canuto, a Tulane University archaeologist and National Geographic Explorer who participated in the project.

“We’ve had this western conceit that complex civilizations can’t flourish in the tropics, that the tropics are where civilizations go to die,” said Canuto, who conducts archaeological research at a Guatemalan site known as La Corona. “But with the new LiDAR-based evidence from Central America and [Cambodia’s] Angkor Wat, we now have to consider that complex societies may have formed in the tropics and made their way outward from there.”

Surprising insights

“LiDAR is revolutionizing archaeology the way the Hubble Space Telescope revolutionized astronomy,” said Francisco Estrada-Belli, a Tulane University archaeologist and National Geographic Explorer. “We’ll need 100 years to go through all [the data] and really understand what we’re seeing.”

Already, though, the survey has yielded surprising insights into settlement patterns, inter-urban connectivity, and militarization in the Maya Lowlands. At its peak in the Maya classic period (approximately A.D. 250–900), the civilization covered an area about twice the size of medieval England, but it was far more densely populated.

“Most people had been comfortable with population estimates of around 5 million,” said Estrada-Belli, who directs a multi-disciplinary archaeological project at Holmul, Guatemala. “With this new data it’s no longer unreasonable to think that there were 10 to 15 million people there—including many living in low-lying, swampy areas that many of us had thought uninhabitable.”

Virtually all the Maya cities were connected by causeways wide enough to suggest that they were heavily trafficked and used for trade and other forms of regional interaction. These highways were elevated to allow easy passage even during rainy seasons. In a part of the world where there is usually too much or too little precipitation, the flow of water was meticulously planned and controlled via canals, dikes, and reservoirs.

Among the most surprising findings was the ubiquity of defensive walls, ramparts, terraces, and fortresses. “Warfare wasn’t only happening toward the end of the civilization,” said Garrison. “It was large-scale and systematic, and it endured over many years.”

The survey also revealed thousands of pits dug by modern-day looters. “Many of these new sites are only new to us; they are not new to looters,” said Marianne Hernandez, president of the PACUNAM Foundation. (Read “Losing Maya Heritage to Looters.”)

Environmental degradation is another concern. Guatemala is losing more than 10 percent of its forests annually, and habitat loss has accelerated along its border with Mexico as trespassers burn and clear land for agriculture and human settlement.

“By identifying these sites and helping to understand who these ancient people were, we hope to raise awareness of the value of protecting these places,” Hernandez said.

The survey is the first phase of the PACUNAM LiDAR Initiative, a three-year project that will eventually map more than 5,000 square miles (14,000 square kilometers) of Guatemala’s lowlands, part of a pre-Columbian settlement system that extended north to the Gulf of Mexico.

“The ambition and the impact of this project is just incredible,” said Kathryn Reese-Taylor, a University of Calgary archaeologist and Maya specialist who was not associated with the PACUNAM survey. “After decades of combing through the forests, no archaeologists had stumbled across these sites. More importantly, we never had the big picture that this data set gives us. It really pulls back the veil and helps us see the civilization as the ancient Maya saw it.

San Diego, February 2, 2018,

Performances of Erasure and Hearing Seascapes set for 5-7pm on Feb. 8 at UC San Diego’s Qualcomm Institute

In spring 2017, UC San Diego music professor and former Qualcomm Institute (QI) composer in residence Lei Liang, and Falko Kuester, the institute’s professor of visualization and virtual reality, organized a unique seminar course on “Hearing Seascapes: A Collaborative Seminar on the Sonification of Coral Reefs.” It provided graduate students, primarily from the Music department, with an opportunity to develop multimedia projects to highlight the dangers facing coral reefs in many parts of the world.

Scene from Hearing Seascapes

Out of that seminar course emerged two performance-and-installation works accepted into the Qualcomm Institute’s Initiative for Digital Exploration of Arts & Sciences (IDEAS) 2017-2018 season. The two works will premiere simultaneously in QI’s Atkinson Hall on the UC San Diego campus. The immersive works include:

  • Erasure, an ambitious multimedia installation produced by a robust collaboration among three UC San Diego Music Ph.D. students: Jacob Sundstrom in Computer Music, Fiona Digney in Music Performance, and Anthony Vine in Musical Composition, together with Computer Science and Engineering Ph.D. student Vid Petrovic; and
  • Hearing Seascapes, which combines coral-reef imagery and audio data to generate sound based on the location and viewpoints of endangered coral reefs. The work was co-developed by Lauren Jones, a Music graduate student in Vocal Performance, and Music Ph.D. student Eunjeong Stella Koh, both at UC San Diego.

Hearing Seascapes will be staged in the SunCAVE virtual-reality (VR) room in the Immersive Visualization Lab, and Erasure in the Reconfigurable Media Lab, both on the first floor of QI’s Atkinson Hall. The works will premiere Thursday, February 8, 2018 from 5-7 p.m. in Atkinson Hall, followed by a public reception. The schedule:

  • 5:00pm Erasure and Hearing Seascapes installations open to visitors
  • 5:30pm Music Prof. Lei Liang introduces both teams of artists, followed by artist talks
  • 6:00pm Both installations reopen for viewing; public reception begins in entry hall in front of the Calit2 Theater.

“Over the last several decades, coral-reef ecosystems have suffered significant impacts from both local and global factors,” said Koh. “We aim to convey important messaging to the audience and illuminate data that show the declining health of ocean coral reefs.”


Through an interconnected network of three-dimensional (3D) photomosaic models of coral reefs and spatially as well as electronically processed percussion sounds, a metaphorical ecosystem forms and responds directly to human presence and the temporal history of that presence throughout the work’s existence.

Audio-visual cues label types of coral with unique sounds and painted overlays on top of 3D photomosaic models from the 100 Island Challenge.

Erasure responds negatively to human presence in the installation environment. As more and more people enter the space, the installation begins to break down: the sonic tapestry of percussion sounds contort and particulate, the synthetic biome of coral visualizations begin to morph into unnatural forms, and the entire system mutates – all with the presence of the audience – and members of that audience are aesthetically confronted with their impact on these remote and fragile ecosystems.  The transformation, however, is neither irreversible nor unidirectional. “As viewers leave, the piece rebounds, but more slowly than the rate at which it broke down,” explained Ph.D. student Sandstrom. “The system bounces back from the immediate and long-term human impact, and it reflects the resilience of the reefs to withstand and adapt to global shifts in climate and the ecosystem.”

The visual component of Erasure consists of 3D photomosaic models of coral reefs taken from the 100 Island Challenge, based in the Scripps Institution of Oceanography. These digital reproductions were created by the Challenge’s technical visualization advisors from the Qualcomm Institute’s Cultural Heritage Engineering Initiative (CHEI), jointly with Scripps Oceanography. By rigorously photographing and collecting data from reef sites and rendering the data into 3D computer models using custom software developed by CHEI’s Falko Kuester and Vid Petrovic, students from the Music department were able to observe the reefs from various angles, light levels, and distances.

“These coral reef constructions ebb and flow between their natural state—meticulously constructed synthetic ecosystems—and transformative states: from granulations of the stony corals and polyps into whirling cascades of particles, to fissions of vast reef colonies into splintered slabs that recede in and out of focus,” said  Music’s Anthony Vine. “Lingering traces of the piece in its untouched state float among the remains, and the metaphorical ecosystem appears to be dreaming and longing to return to an undisturbed state.”

The sound-space of Erasure is created from a reservoir of percussion improvisations that both reflect the sounds that might be found in and around a coral-reef environment, as well as poetic expansions that reach beyond the palette of oceanic utterances: scraped and struck limestone tiles, sweeping washes of hands streaked across a bass drum, and the murky drones of rolled bell plates. By manipulating these samples in a simple causal network, emergent behavior materializes to constitute a lush atmosphere of sound. In this way, the behavior of the sound world is not unlike the behavior found in reef ecology: masses of small units combining to create a complex and rich environment.


“Music can bring an image to life, and by giving a voice to the coral reefs, we can help the audience make an emotional connection to ecology and realize the fragility of these reefs,” said Lauren Jones. “The goal of this project is to create an immersive experience for the viewer that allows them to submerge themselves in the world of the coral.”

3D laser scan of coral reef featured in Hearing Seascapes.

Viewers use a joystick to ‘dive’ and explore the reef, controlling the location, viewpoint, depth and speed of navigation. Audience members hear different sounds that represent different species in the data set. Each species has its own specific personality (represented by different sounds). “Coral reefs are living, breathing organisms that are vulnerable to small changes of the surrounding environment and climate,” explained Stella Koh. “We assign the coral reefs a distinct personality by examining certain characteristics such as texture, habit, origin and growth. To convey messages through music, we’ve recorded an underwater dialogue of voices.” The installation was designed to induce conversation between coral reefs and a fish maneuvering through the reefs, and the sound becomes louder or softer depending on how far away it is from the coral.

Jones and Koh set for themselves three goals with Hearing Seascapes: to display experiments with different aspects of sound and innovative graphic design to create an enjoyable environment for the audiences; to tell an effective and interactive story invoking concepts of adventure, imagination and humor to motivate people to recognize environment health; and to create an inviting seascape with a synergy of voices, images, synthesized sounds and human emotion.

“Based on the notion of acoustic ecology, we want to bring out the positive aspects of sound in the ocean environment,” they noted. “We hope to highlight the importance of engaging in the soundscapes of coral reefs in hopes that our musical voice can make scientific results more accessible to society.”

San Diego, CA, January 25, 2018 — One drone landed on a moving Roomba-like robot while being guided by arm gestures. Another streamed a live, high-definition, 360-degree video feed as it flew overhead. These were some of the demos last week that helped inaugurate the first open-air aerodrome for unmanned aerial vehicles here on campus.

The aerodrome’s inauguration was the first step in what engineers hope will be a new era for drone research at the University of California San Diego. One of their goals is to create a living laboratory for unmanned aerial vehicles by bringing together researchers from across campus, including computer scientists, structural, mechanical, aerospace, electrical and computer engineers and scientists at the Scripps Institution of Oceanography.

(L-R) Contextual Robotics Institute Director Henrik Christensen and mechanical engineering graduate students Aamodh Suresh and Aaron Ma, from the lab of Sonia Martinez and Jorge Cortez, monitor a demo at the aerodrome opening.

“We are bringing everyone together so that one plus one equals substantially more than two,” said Henrik I. Christensen, a professor of computer science at the Jacobs School of Engineering at UC San Diego and the director of the campus’ Contextual Robotics Institute.

The institute oversees the new drone testbed, which is located next to the UC San Diego Powell Structures Lab. It is made up of a 30-foot-tall mesh cage over a 2,500-square-foot outdoor area.

The facility will primarily be open to university research. Projects that could take flight in the new aerodrome include everything from quadcopters built by undergraduate students to balloons designed to monitor conditions inside hurricanes.

A research drone from the DroneLab takes flight in the new drone testbed, which is located next to the UC San Diego Powell Structures Lab. It is made up of a 30-foot-tall mesh cage over a 2,500-square-foot outdoor area.

“We expect to see new research results on control of swarms of small UAVs and on the coordination between humans and robots,” Christensen added. “We will also test entirely new vehicles for long endurance flights.”

The aerodrome is opening not only in response to new University of California regulations governing the use of drones in residential areas but also in response to demand from researchers on campus. The testbed will be equipped with motion capture devices, which will allow researchers to test the quality of their flight control algorithms and will provide ground truth data for all drones.

A second phase will expand the testbed to an indoor 100-foot-tall area, connected to the outdoor testing cage. The expansion, which should take place next year, will result in a unique facility in the United States.

“The opening of the aerodrome is exciting because it enables drone research in a controlled environment, supporting experiments with a multitude of autonomous platforms and payloads as well as control, navigation, guidance and communications strategies,” said Falko Kuester, a professor in the Department of Structural Engineering who leads the DroneLab at the Qualcomm Institute at UC San Diego.

Drones in natural disasters

Kuester and his team are using drones to assess damage after natural disasters—both real and simulated. For example, they developed drone-based imaging techniques to map full-scale buildings before, during and after earthquakes and fires. They subsequently tested these on the world’s largest outdoor shake table here at UC San Diego. The drones acquired images and videos of a six-story building to document damage as a simulated earthquake and then a staged fire unfolded. Powerful algorithms then turned the data the drones collected into detailed three-dimensional models that researchers could literally walk through in a Holodeck-type environment to look for damage.


Dominique Meyer, a graduate student from Falko Kuester’s lab, prepares one of the team’s drones for a demonstration at the opening.

“The ability to develop, test and refine drone-based imaging techniques is critical for our rapid response team,” said Kuester. The team deploys around the world to assist with post-disaster reconnaissance and data collection, as well as the study and preservation of sensitive world heritage sites and ecosystems. They traveled to Puerto Rico after Hurricane Maria and to Mexico after a series of earthquakes hit the country in September.

“Being able to develop and test indoor-outdoor flight transitions, under the broad range of scenarios that can be created within the aerodrome is a game changer for us and will ultimately help with saving lives, following disasters,” Kuester said.

Controlling swarms of robots and drones

Another research team, led by professors Jorge Cortes and Sonia Martinez from the Department of Mechanical and Aerospace Engineering, is working to develop algorithms that allow swarms of robots and drones to work together. The swarms could be used in a wide range of situations, including search and rescue missions, environmental monitoring, and pickup and delivery in transportation. Cortes and Martinez also develop algorithms that allow elements of the swarm to sense, estimate and plan. Robots and drones can then talk to one another to determine the most efficient way to deploy.

(L-R) Contextual Robotics Institute project manager Timothy McConnell; Executive Vice President, Technology Qualcomm Technologies Matthew Grob; Contextual Robotics Institute Director Henrik Christensen; and UC San Diego facilities senior project manager Rita Johnson pose with a drone inside the new open-air aerodrome. 

The algorithms allow one person to control the swarm, acting as somewhat of an orchestra conductor. As a first step, researchers interfaced with the swarm with an app on a tablet. They are now working on controlling the swarm via gestures processed via a motion-tracking bracelet.

The new UAV aerodrome is in part supported by funds from Northrup Grumman and Qualcomm—building on a long-standing collaboration. Qualcomm and UC San Diego created the first FAA-approved sites for drone technology development and testing in early 2016 and Northup Grumman hosted its 2016 Quad Cup Innovation Challenge on the UC San Diego campus.

The campus continues to explore other industry partnerships. The associated research is currently supported by the Army Research Laboratory, Army Corps of Engineers, National Science Foundation (NSF), National Institutes of Standards and Technology (NIST) and Defense Advanced Projects Agency (DARPA).

“There is today a shortage of engineers that have experience with drone technologies,” Christensen said. “The aerodrome will allow us to fill that gap.”