“We reduced the pressure by a factor of eight, which is something experimentalists couldn’t do,” said Deborah Levin, researcher in the Department of Aerospace Engineering at the University of Illinois at Urbana-Champaign. “In an actual chamber, they tried to reduce the pressure but couldn’t reduce it that much because the apparatuses are designed to operate within a certain region. They couldn’t operate it if the pressure was too low. When we reduced the pressure in the simulation, we found that the instabilities in the flow calmed down. We still had a lot of the kind of vortical structure — separation bubbles and swirls — they were still there. But the data were more tractable, more understandable in terms of their time variation.”

Levin conducted the research along with her, then, doctoral student Ozgur Tumuklu, and Vassilis Theofilis from the University of Liverpool.

The Direct Simulation Monte Carlo (DSMC) approach, a high-fidelity physical approach was used to simulate the hypersonic flow. But, like any method, it has pros and cons. One con is that it creates the flow by gathering large amounts of collision data, producing reams and reams of particle data, and with it, statistical noise.

The researchers fed the DSMC results into a window proper orthogonal decomposition program, an example of what is known as a reduced order model to make the analyses of the time behavior of the DSMC results much more feasible.

“It’s a very clever method that is more tractable and can reduce computational effort,” Levin said. “Before we had this technique, we’d select three-dimensional data of pressure, density, and temperature, which are varying throughout the whole flow over the external shape of the vehicle. We’d sit at different locations in the flow and collect data at every time step.It winds up being a treasure hunt — you look here, you look there, wherever you think there is a sensitive part of the flow where you could see some changes.

“The main difference in using WPOD is that it organizes all of that spacial data, which is changing as a function of time, and it gives you some idea as to what it thinks are the decay modes,” Levin said.

In addition to the application of this new method to interpret data, the team of researchers gained new knowledge about the chemical reactions that happen in hypersonic flow. The study looked at three types of gas compositions — molecular nitrogen, non-reacting air consisting of molecular nitrogen and oxygen, and reacting air with oxygen dissociation and the nitric oxide exchange reactions.

“We learned about vibrational temperatures,” Levin said. “These are usually very hard to compute. We learned about being able to predict chemical species, like nitric oxide — a compound in the gas phase, that are only present in very small amounts. It’s produced in hypersonic flows in one out of one thousand particles. It’s not a major component, like 79 percent nitrogen, but it’s very important and we wanted to be able to predict it. Using this technique, we were able to do it so much more easily. Because of that we were able to understand what the affect of the chemistry was in the flow that produced the nitric oxide, and how that affected the different stability modes.”

Tumuklu created short videos by saving all of the data in frames, then speeding it up to show how the flow evolves over time. Although difficult to see with an untrained eye, Levin said the video shows the difference in the way the shocks interact for the nitrogen case that has no chemical reactions and the reacting aircase of 79 percent nitrogen and 21 percent oxygen, which is the composition of air in Earth’s atmosphere.

“There is also a feature called the ‘triple point’ represented by a red dot on the video. If you look very closely, at the two videos, the triple point on the nitrogen case never moves; it stays at one location while everything moves about it.

But in the case of the reacting air, the triple point does move. It oscillates back and forth with everything else still moving around it,” Levin said. “This told us what the effective chemical reactions were. They are dumping extra heat or energy into the flow, which changes the instability, the unsteady behavior.

Levin said aircraft designers over design to compensate for not knowing the exact needs — for example, the minimum thickness needed for a heat shield.

“Ultimately, through this basic research, we will get some answers, some rules of thumb for people, who are at the designing level,” she said. “They won’t have to run petascale calculations, but they’ll know that if they have certain shapes at certain positions to the angle of attack, they need to worry about instabilities when designing spacecraft for safe reentry into Earth’s atmosphere or other atmospheres. They may take out a flap or reposition a flap for a control surface to minimize or prevent instabilities.”

This research not only reveals the physics of how elastic spheres interact with water, but it also lays the foundation for the future design of water-walking drones.

Truscott’s team used high-speed cameras to record elastomeric spheres skipping over a tank of water. Water walking occurs when elastic spheres gain significant speed over the first several impacts, causing the sphere to maintain a deformed, oblong shape — like a stone one might find near the shore.

This behavior is characterized by the sphere moving nearly parallel to the water surface with the tip of the oblong shape dipping below the water surface with each rotation while the shorter sides pass just above, giving the impression that the sphere is walking across the water’s surface.

“Although this has been a long study, the new modes we discovered make it easier for us to envision using the technology for practical uses like water-walking drones,” Truscott said.

The team discovered there are two different types of water walking. The first type skips once every full rotation and the other skips twice every full rotation. This distinction can be controlled with an equation that can predict the number of skips that will occur.

Truscott said this research provides new insights to water impact physics — an important area of study in naval operations and maritime and ocean engineering.

Video: https://www.youtube.com/watch?time_continue=1&v=KEgW5w8oUhk

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Extending their calculations to coastal areas around the world, the researchers estimate that this process could add 25 million additional tons of carbon dioxide to the ocean each year, which would account for roughly one percent of the ocean’s total annual carbon dioxide uptake. This effect is not currently included in calculations of how much carbon dioxide is entering the ocean because of the burning of fossil fuels.

Less than half of the carbon dioxide that humans have released over the past 200 years has remained in the atmosphere. The remainder has been absorbed in almost equal proportions by the ocean and terrestrial ecosystems. How quickly carbon dioxide enters the ocean in any particular area depends on a number of factors, including the wind speed, the temperature of the water, and the relative concentrations of carbon dioxide in the surface waters and in the air just above the sea surface.

MBARI has been measuring carbon dioxide concentrations in the air and seawater of Monterey Bay almost continuously since 1993. But it wasn’t until 2017 that researchers began looking carefully at the atmospheric data collected from sea-surface robots. “One of our summer interns, Diego Sancho-Gallegos, analyzed the atmospheric carbon dioxide data from our research moorings and found much higher levels than expected,” explained MBARI Biological Oceanographer Francisco Chavez.

Chavez continued, “If these measurements had been taken on board a ship, researchers would have thought the extra carbon dioxide came from the ship’s engine exhaust system and would have discounted them. But our moorings and surface robots do not release carbon dioxide to the atmosphere.”

In early 2018 MBARI Research Assistant Devon Northcott started working on the data set, analyzing hourly carbon dioxide concentrations in the air over Monterey Bay. He noticed another striking pattern — carbon dioxide concentrations peaked in the early morning.

Although atmospheric scientists had previously noticed early-morning peaks in carbon dioxide concentrations in some cities and agricultural areas, this was the first time such peaks had been measured over ocean waters. The finding also contradicted a common scientific assumption that concentrations of carbon dioxide over ocean areas do not vary much over time or space.

Northcott was able to track down the sources of this extra carbon dioxide using measurements made from a robotic surface vessel called a Wave Glider, which travels back and forth across Monterey Bay making measurements of carbon dioxide in the air and ocean for weeks at a time.

“Because we had measurements from the Wave Glider at many different locations around the bay,” Northcott explained, “I could use the Wave Glider’s position and the speed and direction of the wind to triangulate the direction the carbon dioxide was coming from.”

The data suggested two main sources for the morning peaks in carbon dioxide — the Salinas and Santa Clara Valleys. The Salinas Valley is one of California’s largest agricultural areas, and many plants release carbon dioxide at night, which may explain why there was more carbon dioxide in the air from this region. Santa Clara Valley [aka Silicon Valley] is a dense urban area, where light winds and other atmospheric conditions in the early morning could concentrate carbon dioxide released from cars and factories.

Typical morning breezes blow directly from the Salinas Valley out across Monterey Bay. Morning breezes also carry air from the Santa Clara Valley southward and then west through a gap in the mountains (Hecker Pass) and out across Monterey Bay.

“We had this evidence that the carbon dioxide was coming from an urban area,” explained Northcott. “But when we looked at the scientific literature, there was nothing about air from urban areas affecting the coastal ocean. People had thought about this, but no one had measured it systematically before.”

The researchers see this paper not as a last word, but as a “wake-up call” to other scientists. “This brings up a lot of questions that we hope other researchers will look into,” said Chavez. “One of first and most important things would be to make detailed measurements of carbon dioxide in the atmosphere and ocean in other coastal areas. We need to know if this is a global phenomenon. We would also like to get the atmospheric modelling community involved.”

“We’ve estimated that this could increase the amount of carbon dioxide entering coastal waters by roughly 20 percent,” said Chavez. “This could have an effect on the acidity of seawater in these areas. Unfortunately, we don’t have any good way to measure this increase in acidity because carbon dioxide takes time to enter the ocean and carbon dioxide concentrations vary dramatically in coastal waters.”

“There must be other pollutants in this urban air that are affecting the coastal ocean as well,” he added.

“This is yet another case where the data from MBARI’s autonomous robots and sensors has led us to new and unexpected discoveries,” said Chavez. “Hopefully other scientists will see these results and will want to know if this is happening in their own backyards.”

Their discovery, which was reported in the journal Nature Neuroscience, supports the view that schizophrenia is a developmental disease, one which potentially can be detected and treated even before the onset of symptoms.

“This framework opens the door for several (research) directions,” said the paper’s senior author, Bingshan Li, PhD, associate professor of Molecular Physiology and Biophysics and an investigator in the Vanderbilt Genetics Institute (VGI).

One direction is to determine whether drugs already approved for other, unrelated diseases could be “repurposed” to improve the treatment of schizophrenia. Another is to find in which cell types in the brain these genes are active along the development trajectory.

Ultimately, Li said, “I think we’ll have a better understanding of how prenatally these genes predispose risk and that will give us a hint of how to potentially develop intervention strategies. It’s an ambitious goal … (but) by understanding the mechanism, drug development could be more targeted.”

Schizophrenia is a chronic, severe mental disorder characterized by hallucinations and delusions, “flat” emotional expression and cognitive difficulties. Symptoms usually start between the ages of 16 and 30. Antipsychotic medications can relieve symptoms but there is no cure for the disease.

Genetics plays a major role. While schizophrenia occurs in 1 percent of the population, the risk rises sharply to 50 percent for a person whose identical twin has the disease.

Recent genome-wide association studies (GWAS) have identified more than 100 loci, or fixed positions on different chromosomes, associated with schizophrenia. That may not be where high-risk genes are located, however. The loci could be regulating the activity of the genes at a distance — nearby or very far away.

To solve the problem Li, with first authors Rui Chen, PhD, research instructor in Molecular Physiology and Biophysics, and postdoctoral research fellow Quan Wang, PhD, developed a computational “framework” they called the Integrative Risk Genes Selector.

The framework pulled the top genes from previously reported loci based on their cumulative supporting evidence from multi-dimensional genomics data, as well as gene networks.

Which genes have high rates of mutation? Which are expressed in prenatally? These are the kind of questions a genetic “detective” might ask to identify and narrow the list of “suspects.”

The result was a list of 104 high-risk genes, some of which encode proteins targeted in other diseases by drugs already on the market. One gene is suspected in the development of autism spectrum disorder. “Schizophrenia and autism have shared genetics,” Chen said.

Much work remains to be done. But, said Chen, “our framework can push GWAS a step forward … to further identify genes.” It also could be employed to help track down genetic suspects in other complex diseases.

Also contributing to the study were Li’s lab members Qiang Wei, PhD, Ying Ji, Hai Yang, PhD, VGI investigators Xue Zhong, PhD, Ran Tao, PhD, and James Sutcliffe, PhD, and VGI Director Nancy Cox, PhD. Special thanks go to investigators in the Vanderbilt Center for Neuroscience Drug Discovery — Colleen Niswender, PhD, Branden Stansley, PhD, and center Director P. Jeffrey Conn, PhD — for their critical input.

The study was supported by the Vanderbilt Analysis Center for the Genome Sequencing Program and National Institutes of Health grant HG009086.