Diagram shows components -- Sensay A, Antilles, and Sensay B -- arranged parallel to each other within an outer structure. The dimensions of the outer structure are labeled. It is 117mm long by 25 mm wide by 25 mm deep.

Miami faculty, small company team up to develop smaller, faster, more efficient computing device

We’ve all seen the message tacked onto the end of emails: “Please consider the environment before printing.” For those who do, indeed, consider the environment, digital often seems the better choice. Not printing that email saves a tree. Buying the digital version of a movie bypasses plastic waste. Holding a videoconference avoids the carbon emissions associated with travel to a face-to-face meeting.

But while having many of our digital possessions tucked away in the cloud may mean they leave virtually no footprint on our personal environments, they nevertheless leave a sizable footprint on the global environment. That’s because “the cloud” is actually millions of networked servers housed in huge data centers. According to an article in Yale Environment 360, “The biggest [data centers], covering a million square feet or more, consume as much power as a city of a million people. In total, they eat up more than 2 percent of the world’s electricity and emit roughly as much CO2 as the airline industry.”

Obviously, there’s no question of turning back; for environmental better or worse, digital is here to stay. So, where the analog world may have beat a path to the door of the inventor of a better mousetrap, the online world may beat a path to the door of the inventor of a better data center. That could end up being a team of researchers from Miami University and their industrial partner, Look Dynamics.

Powering artificial intelligence

The Miami researchers – Dave Hartup, Gokhan Sahin, and Chi-Hao Cheng in the Department of Electrical and Computer Engineering; John Femiani in the Department of Computer and Software Engineering; and Anthony Rapp in the Department of Physics – are working with photonic processing company Look Dynamics on a project funded by the U.S. Department of Defense’s Defense Advanced Research Projects Agency (DARPA). The project aims to create computing hardware that is not only smaller and more energy-efficient, but also faster, enabling higher performance hardware for artificial intelligence (AI) systems.

According to Hartup, AI, and specifically deep learning, are “hot topics” in engineering because of their use in technologies such as autonomous vehicles, advanced medical imaging, and remote sensing. But generating the powerful algorithms behind that AI requires computers that consume large amounts of energy and space. These issues of sustainability (all those data centers!) and portability limit the application of AI to applications where power and space are readily available.

In collaboration with Look Dynamics, Hartup, Sahin, Cheng, Femiani, and Rapp – along with undergraduate students Owen Hichens and Janelle Ghanem – are helping to overcome these limitations by creating hardware that functions in a completely different way from conventional computers.

A prototype of the novel AI optical processing hardware being developed by Miami University researchers and Look Dynamics.

Replacing electrons with photons

Conventional computers and devices that are controlled by conventional computers – like smart TVs, gaming consoles, and microwaves – are sometimes called “electronics” because they function by moving electrons along circuits. The flow of electrons is controlled by computer chip components called transistors. To process large amounts of information, computer chips contain many transistors, but adding too many slows down processing speeds. And using more transistors results in higher power consumption and generates more heat, which must then be dissipated by fans, which require even more power. So far, scientific advances have enabled a steady increase in the number of transistors on each computer chip, but there’s consensus among electrical engineers that a hard limit is on the horizon.

What the Miami team and Look Dynamics are working on is optical computing hardware. Instead of electrons, optical computing devices rely on photons, particles that make up light. Because photons are transmitted in free space, they are unconstrained by the need for circuits and transistors. As a result, optical systems are able to achieve a high degree of what electrical engineers and computer scientists call “parallelism,” efficiently performing many calculations and carrying out many processes simultaneously.

“The hardware we’re working on can implement AI algorithms 1,000 times faster with 1,000 times less power,” Hartup says, “and it’s 500 to 1,000 times smaller than conventional hardware.”

That’s exactly what’s needed to expand the use of AI to new applications where power and space are limited. New contexts require new AI algorithms, and the more efficiently those algorithms can be implemented, the more quickly technologies can be brought to market. Smaller algorithmic computing devices enable more portable, wearable, or seamlessly integrated technologies.

Enabling new AI applications

Hartup says portable technologies are of particular interest to project sponsor DARPA. Many of the things that AI is really good at enabling, like image recognition and the detection and tracking of moving objects, have obvious relevance to defense. That relevance is sometimes lost if the technology can’t be applied in the field.

“If you’re talking about something like advanced AI algorithms for image processing, you’re not going to carry around a rack of electronics capable of doing that,” Hartup says. “It’s too big and heavy. But with an optical system, it’s small enough and light enough to carry around.”

In the context of data centers, optical computers’ small size means improved sustainability. Swapping out conventional systems with smaller, faster optical ones could allow the physical footprint of data centers to be maintained or reduced, even as the proliferation of AI-enabled technologies ratchets up demand for computing capacity. And because optical computers use less electricity, data centers’ carbon footprints could shrink as well.

For all the complex technology involved, what the Miami-Look Dynamics team is doing boils down to something very simple: applying new design – optics – to make an existing, useful thing – a computer – even more useful. Metaphorically speaking, they’re building a better mousetrap, and DARPA has been the first to take what will surely become a well beaten path to their door.

Images courtesy of Dave Hartup.

Portraits of Rick Page and Dominik Konkolewicz

Miami chemists’ breakthrough technique enables design at the interface of chemistry and biology

A technique developed by Miami University associate professors of chemistry and biochemistry Dominik Konkolewicz and Rick Page may help enable more rapid and efficient development of new materials for use in pharmaceuticals, biofuels, and other applications.

Konkolewicz and Page’s technique uses nuclear magnetic resonance (NMR) technology to illuminate how proteins and synthetic polymers interact in chemical substances known as bioconjugates.

Why bioconjugates are useful

Proteins can be used to catalyze chemical reactions that are useful in many applications. For example, protein enzymes are used to produce high-fructose corn syrup and insulin is used to treat diabetes. But some proteins are active for only a very short time or they break down easily, so it’s just not practical – or cost-effective – to use them. Protein bioconjugates overcome proteins’ limitations by attaching synthetic molecules, often polymers, to the protein.

“Proteins have fantastic performance,” Konkolewicz says, “but there’s not a lot of flexibility in the chemistry we can put into a protein. Polymers offer a huge diversity of structure and function that we can incorporate in to extend the life of the protein or enhance its ability to withstand extreme conditions.”

Already there is some commercial development of bioconjugates, such as antibody-drug conjugates used to treat cancer, although the guidelines for how to improve the performance of these substances remains elusive.

Developing new, useful bioconjugates is often difficult and expensive because the process traditionally relies on trial and error: scientists throw a lot of polymer candidates against a proverbial wall of proteins to see what “sticks” in the form of enhanced performance. But just as it doesn’t make sense to throw a tennis ball at a Sheetrocked wall expecting it to stick, it doesn’t make sense to throw certain polymers at certain proteins expecting them to stick.

Accelerating development through rational design

We understand the nature of tennis balls and drywall well enough to know that “sticking” is not a possible outcome of their interaction, but Page says that scientists don’t always understand the nature of proteins and polymers well enough to make similar predictions when it comes to bioconjugation.

“In many cases, we know the structure of the protein, but we don’t know the structure of the polymer. We don’t know what shape it is, where it attaches to the protein, or how it wraps around or interacts with the protein,” Page says.

What’s needed, Konkolewicz and Page say, is a set of rules that would enable rational design of new bioconjugates. Such rules would allow chemists to look at the structure of a target protein and design a polymer molecule of the right size, shape, and function to fit it specifically.

Schematic showing a synthetic polymer (teal tube) conjugated to a protein (cluster of red, blue, and grey spheres). The purple sleeve on the polymer is a reporting group, the key to Konkolewicz and Page’s technique.

“It would be great to be able to say, ‘Okay, here’s the protein I have. Here are the ways I need to stabilize it, and here are the sorts of polymers we can use for that,’” Page says.

The technique Page and Konkolewicz have developed is the first step in enabling the establishment of such a set of rules.

While previous techniques for examining interactions between proteins and polymers in bioconjugates relied on, for instance, neutron beams – very expensive equipment available at a limited number of facilities around the world – the Miami chemists’ technique uses readily available nuclear magnetic resonance (NMR) technology. The key to the technique is placing reporting groups on the synthetic polymers. These reporting groups act something like beacons, allowing researchers to see how close a polymer is to a protein, when the bioconjugate is in an NMR instrument.

The accessibility of NMR technology is important because it vastly increases the capacity of the research community to make discoveries.

“We can’t look at every relevant protein ourselves,” Konkolewicz says. “We’d have to live for 500 years to do that. By making it accessible, we allow other groups to examine their proteins of interest – catalytic proteins, like our lab focuses on, or therapeutic proteins, or whatever type they study. This technique provides scale.”

A breakthrough made possible by Miami’s unique environment

Fundamentally, Konkolewicz and Page’s technique enables chemists from around the globe to collaborate on the establishment of a set of design rules to guide more rapid development of bioconjugates that are both effective and affordable for use in industrial applications, including pharmaceuticals and biofuels. That’s a fitting outcome for a research effort that was itself born out of collaboration.

It’s been historically uncommon for scientists from different subfields to team up as Konkolewicz, a synthetic chemist, and Page, a biochemist, have. Konkolewicz and Page say their advance owes to the fact that Miami University fosters collaboration and encourages exploration across a broad range of expertise.

“The environment that we have here at Miami, and the ability and encouragement for groups to collaborate with each other here, has really set us up in the right environment to come up with this breakthrough technique,” Page says.

Another aspect of Miami’s unique environment is the deep involvement of undergraduate students in research. Four undergraduate students from Konkolewicz’s and Page’s labs were named as authors of an article reporting on their technique, which was recently published in the open-access flagship Royal Society of Chemistry journal, Chemical Science:

  • Caleb Kozuszek, a biochemistry major who worked in Konkolewicz’s lab prior to his graduation in 2020
  • Ryan Parnell, a biochemistry major who worked in Konkolewicz’s lab prior to his graduation in 2020
  • Jonathan Montgomery, a biochemistry major who worked in Page’s lab prior to his graduation in 2020
  • Nicholas Damon, a biology major who worked in Konkolewicz’s lab prior to his graduation in 2018

In addition to mentoring undergraduate members of their respective teams, PhD students Kevin Burridge (Konkolewicz’s lab) and Ben Shurina (Page’s lab) made other substantial contributions to the work and are named as the publication’s first and second authors, respectively. Jamie VanPelt, a former PhD student of Page’s who graduated in 2018, is also named as an author.

Page and Konkolewicz say Miami’s commitment to facilitating research collaborations is further reflected in the level of support they have received from professional staff in the university’s facilities, including EPR instrumentation specialist Rob McCarrick and NMR/MS specialist Theresa Ramelot, both of whom are named as authors on the Chemical Science article.

Konkolewicz and Page’s research was supported by a grant from the U.S. Army Research Office.

Originally appeared as a “Top Story” on Miami University’s News & Events website.

Photos of Rick Page and Dominik Konkolewicz by Miami University. Schematic provided by the Konkolewicz lab.

Portraits of Dominik Konkolewicz and Rick Page flank an image of coronaviruses.

Two Miami University researchers receive NSF RAPID grant to develop coronavirus-attacking materials

Materials will help limit indirect contact transmission of COVID-19

Two Miami University researchers in protein, polymer and materials chemistry received a Rapid Response Research (RAPID) grant from the National Science Foundation (NSF) for a project that will address the spread of the novel coronavirus.

They received $181,849 to develop materials that can be used to prevent indirect contact transmission of the SARS-CoV-2 coronavirus responsible for COVID-19.

Dominik Konkolewicz and Rick Page, both associate professors of chemistry and biochemistry, are the primary and co-investigators of the project.

Reduce indirect contact transmission of COVID-19

The virus responsible for the COVID-19 pandemic is especially concerning for indirect contact transmission, since it can remain active on various surfaces for extended periods of time, Konkolewicz said.

If a person infected with COVID-19 deposits active viral particles (droplets or aerosols) on frequently touched surfaces, the disease can be transmitted if an uninfected person picks up the active viruses from the contaminated surface.

In this way, the disease can be spread even if the two individuals do not ever come in direct contact with each other. Since the virus can remain active on surfaces for days, there is an increased risk of indirect contact transmission.

To help limit this, Konkolewicz and Page will develop materials that can capture and inactivate the coronavirus on surfaces.

Capture and inactivate the virus

Through their work in synthetic polymer chemistry and protein chemistry, the researchers plan two complementary approaches in developing coronavirus-attacking materials:

Inactivate: One approach is to disrupt the lipid layer/lipid envelope in the coronavirus. This lipid envelope is critical to the structure of the virus and also to its infection mechanism. “If we disrupt the lipids, we can inactivate the coronavirus, such that it cannot infect a new individual,” Konkolewicz said. (Handwashing with soap is one example of disrupting the lipid layer to inactivate the virus).

Capture: The other approach is to capture and trap the coronavirus spike proteins within the synthetic material. This way the virus cannot leave and provide a path for a new infection.

Combined: The researchers will also develop materials with both capture and inactivation capabilities. This two-pronged approach tethers the virus to the surface to allow for increased opportunities to attack and inactivate it, Page said.

The new materials they develop could be adapted or coated onto existing high touch surfaces to limit indirect contact transmission, Konkolewicz said. The polymers will form a tough network to ensure the material performs for an extended period of time.

Konkolewicz and Page will also develop content on the importance of polymer materials in healthcare applications. This will be distributed through YouTube channels for accessibility to the public.

About the researchers

Konkolewicz researches responsive, or “smart” polymer materials and materials that contain both synthetic and biological components. He was awarded an NSF CAREER Award for self-healing polymers in 2018. He was named a 2018 Young Investigator by the American Chemical Society-Polymer, Materials Science, and Engineering section and he received the 2018 Polymer Chemistry Emerging Investigator Award. He and his research team have multiple research collaborations with colleagues in chemistry, biochemistry, chemical engineering and mechanical engineering. He was named a Miami University Junior Faculty Scholar in 2018.

Follow Konkolewicz on Twitter @PolyKonkol.

Page researches the structure, dynamics and mechanisms of action for proteins in a range of biologic and synthetic systems. He was named a Miami University Junior Faculty Scholar in 2016. He received an NSF Career grant in 2016 for his research on protein quality control. In 2018 he received a five-year MIRA (Maximizing Investigator’s Research Award) — one of Miami’s first two — that supports his research projects on protein quality control and antibiotic resistance. He has multiple research collaborations with colleagues in chemistry, biochemistry and bioengineering.

Follow Page on Twitter @ThePageLab.

NSF RAPID grants

The grant for “RAPID: Viral Particle Disrupting and Sequestering Polymer Materials applied to Coronaviruses,” will support the research of Page and Konkolewicz for one year and support three graduate students.

RAPID grants give the NSF a way to help fight the pandemic by supporting scientists doing relevant work across many disciplines, according to the foundation. They may be funded for up to $200,000 and up to one year in duration, with an average award size of $89,000.

In March Congress gave NSF an extra $75 million in the CARES Act stimulus funding to spend on research projects that will help “prevent, prepare for, and respond” to the novel coronavirus.

Written by Susan Meikle, Miami University News and Communications. Originally appeared as a “Top Story” on  Miami University’s News and Events website.

Photos of Dominik Konkolewicz and Rick Page by Miami University Photo Services. Image of coronaviruses by By U.S. Army. Public domain.

Portrait of Andrew Jones

Miami researchers discover process to sustainably produce psilocybin — a drug candidate that could help treat depression

Alexandra Adams working in the Jones Lab.
Junior Alexandra (Lexie) Adams is the lead author in a published article of the Jones Lab’s findings in a scientific journal.

A team of undergraduate students author published article

Andrew Jones at Miami University and his team of students may have developed a research first.

Through metabolic engineering, they discovered a way to sustainably produce a promising drug candidate to help patients with treatment-resistant depression.

Their findings, titled “In vivo production of psilocybin in E. coli,” are published in the journal Metabolic Engineering.

Psilocybin is now in clinical trials, and medical professionals see promising results for its use in treating addiction, depression, and post-traumatic stress disorder in humans.

Jones, assistant professor in Miami’s Department of Chemical, Paper, and Biomedical Engineering, believed he could come up with a process using genetically engineered bacteria to produce the drug candidate.

The chemical, psilocybin, is naturally found in a specific mushroom, Psilocybe cubensis. Jones said to mass produce psilocybin from its natural mushroom host would require extensive real estate and time. Currently, alternative synthetic chemical production methods are used but are very expensive. Jones, the principal investigator of this research, wanted a solution that maintains biological integrity and reduces production costs.

Finding an optimal organic host

Through metabolic engineering, which finds ways to increase a cell’s ability to produce a compound of interest, his team of students developed a series of experiments to identify optimal psilocybin production conditions. The recently published article describes their work to optimize the production of psilocybin in the Escherichia coli bacteria. The team is using a well-known E. coli strain that is engineered for safe lab production.

“We are taking the DNA from the mushroom that encodes its ability to make this product and putting it in E. coli,” he said. “It’s similar to the way you make beer, through a fermentation process. We are effectively taking the technology that allows for scale and speed of production and applying it to our psilocybin-producing E. coli.”

Their end result is a significant step toward demonstrating the feasibility of producing this drug economically from a biological source.

“What’s exciting is the speed at which we were able to achieve our high production. Over the course of this study we improved production from only a few milligrams per liter to over a gram per liter, a near 500-fold increase,” Jones said.

He gives much credit and praise to his students who designed many of the experiments performed during the 18-month-long study.

“A big part of my job is training undergraduates to do this work. The basic idea was mine, but much of the experimental design fell on the students. Early on, I would help guide them in the experimental design process. Toward the end, they were becoming more independent. That’s the type of student we want as they near graduation,” Jones said.

Learning to run laboratory experiments

Lead author Alexandra (Lexie) Adams, a junior chemical engineering major, became a member of the research team her freshman year, just as the Jones Lab was getting started. Patient and meticulous, Jones worked with the admittedly nervous Adams on the basics of laboratory research. It paid off.

The initial work was done in the summer of 2018 as Adams and another undergraduate student co-author, Nicholas Kaplan, took part in Miami’s Undergraduate Summer Scholars Program. The program provides funding to students for undergraduate research.

Both students, working on separate studies, learned the ins and outs of research, gaining confidence and learning lessons as the summer progressed.

Kaplan, a junior chemical engineering major, studied the feasibility of cyanobacteria as another potential metabolic engineering host. His findings showed mixed results, and it was decided that the lab team would focus on Adams’ psilocybin in E. coli project.

Celebrating a research breakthrough

Adams remembers when they saw the breakthrough in their research. Their goal was to transfer the DNA from the mushroom and see activity in the E. coli host.

“Once we transferred the DNA, we saw [a tiny] peak emerge in our data. We knew we had done something huge,” she said.

Other members of the team included graduate Zhangyue ‘Tom’ Wei (Miami ’19), graduate John ‘Jack’ Brinton (BS Miami ’17, MS Miami ’19), junior Chantal Monnier, senior Alexis Enacopol, and staff member Theresa Ramelot, instrumentation specialist.

Both Adams and Kaplan continue to work with Jones. The students are leading projects that build on the recent success of the psilocybin work. Each of them is starting to pass down what they have learned in the lab by mentoring new undergraduate students who join the Jones Lab.

“It’s important for [the new students] to understand the big picture so they see the reasons for the different steps of the experiments,” Kaplan said.

Jones is pursuing the next phase of this research by studying ways to make the E. coli bacteria a better host — the next step toward enabling sustainable production at levels required by the pharmaceutical industry.

Written by Carole Johnson, Miami University News and Communications. Originally appeared as a “Top Story” on  Miami University’s News and Events website.

Photos by Miami University Photo Services.

Maria Gonzalez and now-former student Matthew Bezbatchenko process pond samples.

25 years of ecosystem research on Acton Lake supported by NSF

Mike Vanni (center) and Miami students (left to right) Isabelle Anderson, Ashley Mickens, and Ferdos Abdulkader collect samples from Acton Lake in the summer of 2018.

A team of Miami University scientists, led by Mike Vanni, professor of biology, received its fourth National Science Foundation Long Term Research in Environmental Biology (NSF LTREB) grant in support of long-term research at Acton Lake, a reservoir in Oxford, Ohio.

The LTREB grant provides $634,999 over the next five years for Vanni and his research team. It is the only LTREB project currently funded in Ohio.

The research looks at how long-term changes in agriculture affect streams and lakes, using the Acton Lake watershed as a model system.

The research team

Vanni has studied Acton Lake and its watershed for more than 25 years. His research on Acton Lake has been supported continuously since 1994 by the NSF, with the past 15 years through the NSF LTREB award program (researchers can only apply for an LTREB grant after they have six years of data from their study sites).

Maria Gonzalez, professor of biology, is a co-principal investigator of the project. Bart Grudzinski, assistant professor of geography, joined Gonzalez and Vanni this year, replacing original team member Bill Renwick, now professor emeritus of geography.

Long-term agricultural changes affect streams and lake

Little is known about long-term effects of agricultural changes on streams and lakes, Vanni said.

The practice of conservation tillage, which involves plowing the soil less frequently to reduce sediment runoff, was encouraged in the watershed area by the USDA in the early 1990s.

Similar changes are occurring in agriculture throughout the Midwest.

This practice strongly affected nutrients and sediments in streams that feed downstream Acton Lake, the researchers found.

They found an increase in the abundance of bottom-feeding fish, such as gizzard shad. These fish consume sediments and excrete nutrients into the water, providing more sources of nutrients for algae growth.

The amount of algae is controlled mostly by concentrations of sediment in the water and the abundance of bottom-feeding fish, Vanni said.

The LTREB research explores the long-term changes in these interactions.

“We wanted to compare how much nitrogen and phosphorous were coming in from the watershed, versus what was being supplied by the fish,” Vanni said. “We thought that movement of nutrients through the fish could be really important—and it turns out that it is.”

Decades of data reveal unexpected trends

Decades of data have revealed some surprises that would not have been detected in the short term. Research shows that stratification of nutrients in soil due to conservation tillage may be having unintended consequences in the Acton watershed. These effects are also seen in the Lake Erie watershed, according to Vanni. (See below for recent publications from the research team on storm events and on contrasting long-term trends in nutrient loads.)

Climate change and summer storms

Changes in agriculture are also mediated by climate change. Very wet springs followed by very dry summers have become more common in recent years in the Midwest, according to Vanni. This also affects nutrient input.

Water temperatures are increasing faster than the air temperature in some lakes, Vanni said. But in our area — and in similar agricultural landscapes — the effects of changing precipitation patterns on nutrients and sediments may be more important than the effects of temperature.

Big storms bring in a lot of the nutrients. In Acton Lake, more than half of the nutrients that come in one year can come in a matter of about 10 days, Vanni said. Learn more on the Acton LTREB Blog.

Long-term environmental research — more important now than ever

Long-term environmental research is fundamental to understanding an ecosystem’s response to environmental change. It is key to informing policy decisions about natural resources and environmental issues, especially in response to climate change.

After the first and second decades of their research, Vanni and his team discovered unexpected trends in nutrient and sediment inputs in Acton Lake.

“Now, what is going to happen after the third decade? Things can change and surprise us,” Vanni said.

Research opportunities for 100+ students over the years

The Acton Lake LTREB project has provided research opportunities for more than 100 Miami undergraduate students over the years, on projects mentored by Vanni, Gonzalez, Renwick and Grudzinski.

Many of these students conducted research full time in the summers, supported by fellowships from Miami’s Undergraduate Summer Scholars or Miami Hughes Intern programs. Others were supported by NSF REU (Research Experiences for Undergraduates) supplements to the LTREB grants.

Students from universities around the country have also contributed to this research through Miami’s REU Site on Ecology in Human-Dominated Landscapes.

Current/recent undergraduate students:

Martina Rogers, junior chemistry major, works with Vanni. This past summer she was funded through a Research Experience for Undergraduates (REU) supplement from Vanni’s previous LTREB grant.

Ashley Mickens, senior geology and environmental earth sciences major and sustainability co-major and a French minor, worked with Vanni in summer 2018 as a member of the Ecology REU program.

Ferdos Abdulkader, junior kinesiology major and premedical studies co-major, also worked with Vanni in summer 2018, funded through his REU supplement.

Isabelle Anderson (Miami ’19), currently a doctoral student at Baylor University, was a 2018 Undergraduate Summer Scholar with Vanni. She is first author of a paper with Vanni and others recently accepted in Limnology and Oceanography, the top aquatic sciences journal.

Josh Tivins, a junior biology major and previous Miami Regionals student, currently works with Gonzalez. He was a 2019 Miami Hughes intern.

Izzy Aristizabal, senior geography major and sustainability co-major, and Claire Stock, junior environmental earth science major and sustainability co-major, work with Grudzinski.

Current graduate students:

Tanner Williamson is a doctoral candidate advised by Vanni. He is the recipient of the 2019 Biology Dissertation Scholar Award. Graduate student Carrie Ann Sharitt is also advised by Vanni.

Heather Luken and Xiu Gao, master’s students in biology, are advised by Gonzalez.

Tessa Farthing is a master’s degree student in geography and geographic information science, advised by Grudzinski.

Recent publications from the research team include:

“Stream Nitrogen And Phosphorus Loads Are Differentially Affected By Storm Events And The Difference May Be Exacerbated By Conservation Tillage”

“Stream Nitrogen, Phosphorus, and Sediment Concentrations Show Contrasting Long-term Trends Associated with Agricultural Change.”

Written by Susan Meikle, Miami University News and Communications. Originally appeared as a “Top Story” on  Miami University’s News and Events website.

Photos by Jeff Sabo, Miami University Photo Services.


Michael Loadenthal reviews work performed by Prosecution Project team members at a work session

The Prosecution Project aided by Research Computing Support group

Prosecution Project team members (from left) Sarah Carrier, Olivia Sellegren, Meekael Hailu, and Morgan Demboski, discuss data at a work session.

For all the time, effort, and resources devoted to thwarting terrorism, it’s surprisingly difficult to get a complete view of sociopolitical violence in the United States. The Anti-Defamation League and the Southern Poverty Law Center monitor racist and white nationalist violence. The Center for Biomedical Research collects data on attacks against animal testing facilities. The University of Maryland tracks international incidents of terrorism in its Global Terrorism Database. But because none of these groups’ datasets interface with any other’s, information remains siloed and analysis of broader relationships is stymied.

Michael Loadenthal is trying to break down those silos. A visiting assistant professor of sociology and social justice studies at Miami University, Loadenthal directs the Prosecution Project, which seeks to understand how terrorism, extremism, and hate crimes are prosecuted in the U.S. justice system. The Prosecution Project’s dataset includes all crimes of political violence, without regard to the identity of the targets or the ideology of the perpetrators, so it paints a uniquely comprehensive picture.

“We’re looking to understand the patterns that exist between who a criminal defendant is, who commits crimes motivated by sociopolitical violence, and how that relates to the crime they committed and the way it’s prosecuted,” Loadenthal says.

Altogether, Loadenthal and his project team — which consists entirely of his current and former undergraduate students — account for 46 variables in each case they add to their dataset. Each case is coded by two members of the project’s coding team. After review of the initial coding by at least two senior members of the analysis team, the data are then reviewed by an auditor. So far, the team has fully coded and reviewed about 40% of the 5,000 cases they have identified. Once the dataset is fully processed, Loadenthal intends to make it available to the public.

Working toward that goal has required Loadenthal to figure a way around some technical roadblocks. One place he turned for help is Miami’s Research Computing Support group, particularly Greg Reese, senior research computing support specialist.

Among other things, Reese developed a custom audit program that Loadenthal says “helps machine some of the irregularity out of the data.” Reese’s program reads the data the project team has collected and checks it against a set of defined rules — about 30 in all — to find irregularities or incongruences. Certain mistakes, like an extra space typed after a defendant’s name, will cause a computer to classify data incorrectly. (A computer treats “John Jones ” — with a space after “Jones” — and “John Jones” — no space after “Jones” — as two different people, for instance.) Reese’s audit program searches for such mistakes and flags them so they can be corrected to improve the integrity of the overall dataset.

Loadenthal is grateful for Reese’s willingness not only to listen to the specific challenges the Prosecution Project faces, but also to develop custom solutions.

“I’ve seen Greg learn different aspects of new computer languages in order to code what we need,” Loadenthal says. “He’s taught himself new skill sets in order to accommodate us. Instead of trying to use something he’s already familiar with — let’s say C++ — he adapted and learned Python, which is better suited to what we’re doing.”

Reese’s impulse for inclusivity fits something of a theme for the Prosecution Project, which has remarkably diverse personnel. Although most members of Loadenthal’s 60-person team identify as female, they otherwise represent the gamut of student demographics and identities.

“We have a highly diverse research team that closely resembles the world off-campus,” Loadenthal says. “Our students represent a variety of races, ethnicities, nationalities, and religions. They don’t all conform to binary notions of gender. In addition, they represent a broad set of academic majors, from biology to English to political science to sociology.”

Loadenthal isn’t sure why the Prosecution Project’s team is so diverse. Diversity is more common in the social justice studies and upper-level sociology classes Loadenthal teaches than in the university as a whole, but beyond that, the team’s diversity doesn’t result from any active recruiting strategy. Students self-select to participate in the project — he waits for them to approach him.

The key to the team’s diversity may lie in diverse students’ inherent interest in finding answers to questions about systemic inequalities, which tend not to work out in their favor. Loadenthal says one of his early goals for the Prosecution Project was to explain sentencing disparities. He acknowledges that many members of his team expected to find that nationality, religion, and race play a role. And while they did find that African-, Asian-, and Middle Eastern-born, Muslim defendants with foreign-sounding names often receive harsher sentences than American-born, Christian defendants of European descent, they also found that simple xenophobia didn’t fully explain the differences. Loadenthal is committed to making Prosecution Project data available to other researchers who can help develop more nuanced explanations.

“This project is the only one that co-mingles and assimilates data points so you can make comparisons between ideologies and not restrict it to one particular movement,” Loadenthal says. “That’s the main goal, to ask questions that aren’t specific to one interest group.”

Written by Heather Beattey Johnston, Associate Director of Research Communications, Office for the Advancement of Research and Scholarship, Miami University.

Photos by Miami University Photo Services.


Kevin Ruiz works with equipment in the lab of Andrea Kravats

NSF-funded program gives students from around the country access to Miami faculty and state-of-the-art resources

Miami sophomore zoology major Ty Cooley searches for amphibians at Shaker Trace Wetlands in Harrison, Ohio.

They ventured from Iowa, North Carolina, Puerto Rico and other communities to study at Miami University during the summer as part of the NSF-funded Research Experience for Undergraduates (REU) program. Miami students also are eligible to apply to the program. Some undergraduate researchers came to take advantage of equipment and resources that might not be available at their universities. Others came to be mentored by a specific faculty member. They all gained valuable research experiences, connections and the thrill of scientific adventure.

Here are a few of their stories.

Laser mystique

Samir Bali looks back fondly to 2006 when his baby, of sorts, was born. You won’t find arms, legs or even a stray hair on Penelope. Think more twisting wires, camera lenses and laser beams.

Despite the seemingly breakneck speed of technological advancement, current methods of measuring turbid (opaque) substances’ properties are not foolproof. With the help of his dad, Bali, a physics professor at Miami, built and refined a laser-based sensor to solve this problem.

“I was introduced to a physics research lab at the age of 19, and I’ll never forget the sights and sounds when I first walked in — the green, red and orange colors of the lasers, the quiet humming of the vacuum pumps. I remember feeling this powerful sense of intrigue. I enjoy recreating those moments for myself by reliving them with my undergraduate researchers.

— Samir Bali

A prototype like this doesn’t come with an instruction manual.

Before visiting undergraduates Menaka Kumar, from North Carolina State University, and Sydney Rollins, from Whitman College in Washington, could begin investigating turbid media, they first needed to understand how the device works and develop a standard process for using it.

“She [the sensor] was kind of making us mad. We gave her a name so we could call her something,” said Rollins.

Penelope, they quickly realized, requires extensive cleaning. Even the smallest speck of dust skews the results.

After weeks of testing, Kumar and Rollins hoped to turn their attention to melamine – a compound that is virtually indistinguishable from milk when diluted in water. It’s used to produce glues, adhesives and other plastics.

In 2008, melamine was discovered in a Chinese company’s infant milk. Melamine artificially inflates the protein content of a substance and has nearly the same particle size as milk, making it hard to detect. Infants across China who consumed the melamine-contaminated milk developed bladder stones, and several died. The scandal shocked the world and pointed to a need for better contamination detection methods.

“Chemical detection methods are very targeted,” Bali explained, “but you need to know what you’re looking for.”

As with many opaque substances, it’s challenging to determine the properties of liquid melamine. Penelope, they hope, can shine light on this substance to prevent future contamination.

Chemical change

REU student Echo DeVries, a senior at Clarke University in Iowa, was mentored by Hang Ren, Miami assistant professor of chemistry and biochemistry this summer. Their project: measuring the distribution of surface charge on electrodes.

An electrode conducts electricity and allows reactions to occur on its surface when electricity is applied. These electrodes play a key role in electrocatalysis, the process of using electricity to drive chemical reactions. For example, an electrode can be used to convert water to hydrogen fuel. Hydrogen is a clean fuel, which produces no CO2 emissions – the same fuel NASA uses to launch rockets. However, the generation of hydrogen on the electrode surface is not uniform. Hot spots exist that efficiently catalyze this reaction.

That’s where Ren and DeVries’ research comes in.

Different electrode surface charges could cause electrochemical reactions to behave differently. That’s why Ren and DeVries analyzed electrodes’ properties and surface charges.

Down the hall from Ren’s lab, Kevin Ruiz, an REU student from the University of Puerto Rico, explored a different area of chemistry research. Alongside his mentor Andrea Kravats, Miami assistant professor of chemistry and biochemistry, and graduate student Yaa Amankwah, Ruiz studied molecular chaperones, which are proteins that assist in maintaining cellular integrity by folding and unfolding proteins that are misfolded. Incorrect folding of proteins has been linked to degenerative diseases such as Alzheimer’s, Parkinson’s, cancer and Type 2 diabetes. Kravats hopes her lab’s work can one day be used to establish new cancer treatments or therapies.

“ Students are eager to learn and tend to get involved early in their undergraduate careers here, giving them an excellent opportunity to excel in their studies.

— Andrea Kravats

At the University of Puerto Rico, Ruiz is a chemical engineering major, but his goal is to become a biochemical engineer. His summer at Miami provided an opportunity to dig into research he’s excited about.

“I already work with protein purification in Puerto Rico, but not the background of why the protein purifies, how it purifies, how we can separate proteins from others. It has been a really good experience,” he said.

Wetland wonders

Ty Cooley, a Miami University sophomore zoology major, hunched eagerly over a bucket filled with pond water from Shaker Trace Wetlands in Harrison, Ohio, about 20 miles southwest of Oxford. Cooley, originally from New York, gently swirled the bucket’s contents, revealing a host of creatures swimming beneath the algae: mayflies, water mites, water boatmen, glass worms, water scorpions. His eyes lit up as he dug deeper into the bucket and pulled out a large dragonfly larva.

“You see this?” he said, pointing near the arm. “This is where the mouth is located. Let me see if I can get him to- Whoa!” The dragonfly suddenly expanded and thrust an arm-like tongue outward.

Cooley maintained his grip.

“They will shoot out like that, grab stuff, and pull it in. It’s like an alien!”

He’s been bitten by water scorpions. Poked by dragonfly larva. Burned in the scorching July sun. Such is the life of a field researcher, but it is, without question, one chosen gleefully.

Cooley and his mentor, graduate student Jess McQuigg from Mount Vernon, Ohio, are both researchers in biology associate professor Michelle Boone’s amphibian lab. This summer they studied different types of macroinvertebrates in 21 different wetland systems around Hamilton, Butler and Preble counties. Macroinvertebrates are visible to the naked eye but lack a spine. As part of the lab’s larger project, they wanted to see how certain macroinvertebrates affect the density of a pathogen called Batrachochytrium dendrobatidis (Bd or amphibian chytrid fungus for short) in a given wetland.

Bd is responsible for a significant number of amphibian declines and extinctions, and many sources call it the most devastating pathogen in wildlife history. According to research in Boone’s lab, this pathogen exists in about 30% of wetlands in southwest Ohio.

But the team is optimistic that they’ll discover a method for controlling the pathogen. One of the lab’s big goals is to understand how wetlands can be created that are more naturally resistant to Bd.

As the weather turns colder, Cooley and McQuigg will be back in the lab performing DNA analysis to determine the locations and quantities of the pathogen – what McQuigg refers to as their “fall and winter sport.”

Written by Alicia Auhagen, Miami University Marketing and Creative Services. Originally appeared as a “Top Story” on  Miami University’s News and Events website.

Photos by Jeff Sabo, Miami University Photo Services.

Ellen Yezierski in her lab.

$1.9M NSF grant will help teachers stimulate students’ imaginations to improve learning of chemistry

A water molecule, H2O. Liquid water, H2O(I). Covalently bonded molecules held together by intermolecular hydrogen bonds.
An example of the VisChem dynamic visualizations.

With a new $1.9 million grant from the National Science Foundation, Miami University’s Ellen Yezierski aims to help high school chemistry teachers prepare students to become more scientifically literate.

Her project has the potential to impact up to 80,000 high school chemistry students from a broad range of socioeconomic, geographic and racial backgrounds, Yezierski said. It will focus on traditionally underserved groups, including English language learners.

Yezierski, a chemistry education researcher, was awarded the five-year grant for her design research in the teaching and learning of high school chemistry through the use of dynamic visualizations — “VisChem” molecular animations designed by Roy Tasker.

These video animations of the molecular world can bring a new dimension to learning chemistry.

The project will develop teachers’ knowledge and skills to help their students build molecular-level mental models to explain chemical events, Yezierski said.

Currently, chemistry education overemphasizes description and symbols rather than learning to explain chemical phenomena.

Students becoming informed adults for a changing world

Yezierski will recruit 64 high school chemistry teachers from across the country to participate in the professional development program.

They will learn how to effectively use storyboarding and the VisChem approach to lead students from describing chemical phenomena, such as reactions and physical changes, to understanding and explaining their causes.

One goal is to help high school students become more scientifically literate. The focus is on learning how to reason with chemistry concepts and principles, rather than on memorizing facts, Yezierski said.

Ultimately, students will be better prepared to understand science in areas requiring molecular-level perspectives, and to become informed adults in a changing world, Yezierski said. Some areas include understanding the role of carbon dioxide in climate change, changes in DNA in genetically modified organisms (GMOs), antibiotic resistance and drinking water quality.

VisChem Institutes: Molecular animations, storyboarding for understanding

An example of the VisChem dynamic visualizations. The images from video animations of liquid water (above) and boiling water (below) show differences in molecular activity of different physical states of water (images by Roy Tasker from VisChem.com.au).
Three teacher cohorts — one cohort each over the next three summers — will attend the all-expenses-paid VisChem Institute (VCI) on campus developed by Yezierski.

The institutes will be taught by Yezierski and project consultant Roy Tasker, creator of the VisChem dynamic animation system. “Animations of the molecular world can stimulate the imagination, bringing a new dimension to learning chemistry,” Tasker said.

For instance, few students have a “feel” for the average distance between ions (charged particles) in a solution of a given concentration, according to Tasker.

“VisChem animations of ionic solutions bring meaning to the magnitude of the number expressing molarity (concentration of a chemical in solution), in much the same way that people have a ‘feel’ for the length of one meter,” Tasker said.

Design research: Supports teachers’ learning

Yezierski’s design research involves studying how to support teacher groups in learning chemistry content and instructional methods.

Teacher cohorts will be supported during the following year after they attend the VCI. Some will be provided with software to run their own molecular simulations. Eventually all teachers will develop and grow a community of skilled practitioners using the VisChem approach.

In their classrooms, teachers will wear tiny GoPro cameras to collect video clips of their teaching. The clips will provide data about what teaching methods are more effective than others.

Those clips will be studied and evaluated by Yezierski and her team to inform and improve the design of future VCIs and improve chemistry teaching with molecular visualizations.

The time is right

Yezierski has been conducting chemistry education and teacher professional development research for the past 16 years. She is nationally recognized for conducting groundbreaking research that improved instruction and student learning as a direct result of Target Inquiry, a visionary professional development model for high school chemistry teachers.

She has a long history with Tasker, having based her doctoral dissertation research on the use of VisChem dynamic visualizations.

She has recently started to see chemistry teachers become more open to/interested in incorporating dynamic visualizations and storyboarding in their teaching.

This approach aligns with the newest Next Generation Science Standards and the recently updated AP chemistry curriculum, Yezierski said.

The team

Yezierski, professor of chemistry and biochemistry, is also director of Miami’s Center for Teaching Excellence.

She was named an American Chemical Society Fellow in 2016.

An experienced high school chemistry teacher, she taught chemistry for seven years before earning her doctorate from Arizona State University in 2003.

Her research team will include a postdoctoral fellow, two graduate students, several undergrad students and Tasker.

Tasker is a renowned Australian chemistry education researcher. He received the Prime Minister’s Award for Australian University Teacher of the Year in 2011 and the prestigious Australian National Senior Teaching Fellowship in 2014.

He created the VisChem approach in the 1990s, and since then the dynamic visualizations have been adopted by educators and textbook authors internationally.

Written by Susan Meikle, University News Writer/Editor, University Communications and Marketing, Miami University. Originally appeared as a “Top Story” on Miami University’s News and Events website.

Photo of Ellen Yezierski by Jeff Sabo, Miami University Photo Services. VisChem dynamic visualization by Roy Tasker from VisChem.com.au.


Image of Miami University's Office of Research for Undergraduates (ORU). Visible are a wall with "ORU" painted on it and three people standing in a circle in a glass-walled office.

Guest post: Undergraduate experiences enhanced by participating in research

In this post, guest posters Grace Chaney and Micailah Guthrie share their experiences as undergraduate researchers.

Grace Chaney

Kinesiology and pre-medical sciences major; molecular biology minor

Grace Chaney poses with fellow members of Randal Claytor's Muscle Fatigue Lab.
Grace Chaney (front row, second from left) conducts research in the Muscle Fatigue Lab, under the supervision of associate professor of kinesiology and health Randal Claytor (back row, second from right).

There is a quote that says the squat is the perfect analogy for life: “It’s about standing back up after something heavy takes you down.”

During my junior year of high school I had two partial knee reconstructions which resulted in the end of my soccer career. After 13 months of physical rehabilitation, I became fascinated with the body’s ability to heal. Furthermore, its ability to come back from an injury even stronger than it was before.

Fitness became an area of my life where curiosity was welcomed, change was sought out and innovation was abundant. The ability to alter variables in physical activity or nutritional intake and obtain significant and measurable results is astounding to me. I quickly became mesmerized by exercise science research and its applications in exercise programming. In my senior year of high school, I pursued and completed my certification in personal training and small group fitness through the American College of Sports Medicine. Through my certification I am able to help people reach their goals through science-backed research, customized programming and compassion.

My involvement in undergraduate research at Miami University has undoubtedly been one of the most influential experiences of my academic career. It has reinforced my passion for hypothesis driven research while also expanding my interests in translational research exponentially. I have had the privilege to be a part of the Muscle Fatigue Lab in the Department of Kinesiology and Health, under Dr. Randal Claytor. We have been studying acute, local muscle fatigue and muscle fiber activation adaptation patterns from a neuromuscular and external mechanical perspective. We utilize a dynamic single-leg extension model and drop-set training template in order to better understand the muscle fatigue and muscle activation processes. According to The Center for Disease Control and Prevention’s Office of Disease Prevention and Health Promotion, time constraints are one of the leading reasons people give as to why they do not partake in regular physical activity. My current research interests during my undergraduate career are to study training methodologies that minimize time spent exercising while maximizing the health benefits of physical movement.

Through the Undergraduate Summer Scholars program, and with faculty mentorship, I will have the opportunity this summer to pursue a research proposal of my own creation. The Undergraduate Summer Scholars program allows students to explore the depths of their passion for research while also providing a unique and focused learning opportunity. I am sure it will be a pivotal experience in my time here at Miami. In my remaining years left here as a student I hope to be an Ambassador for the Office of Research for Undergraduates (ORU). I hope to encourage other students to engage in and explore research opportunities both on and off campus. I also want to help current student researchers further develop their involvement with and passion for their field of study. I am excited to be working with the ORU, with individuals who share my passion for research and with an institution dedicated towards cultivating and encouraging investigators in so many different fields of study.

In the future, I hope to pursue a career in medicine. The medical field is the perfect culmination of everything I am looking for in a career. A career in which I can focus on compassion, service, innovation and translational research. My research interests are in intraoperative and postoperative research specifically in the field of orthopedics and sports medicine. I am particularly drawn to studying surgical repair techniques and postoperative protocol and how those can be altered to improve patient outcomes.

My love for hypothesis driven research was born out of a terrible experience but that experience built the foundation for who I am today and the kind of doctor I want to become in the future. I am forever grateful for my injuries — they are a constant reminder that you can stand back up after something heavy takes you down.

Micailah Guthrie

Public health major;  medical sociology and individualized studies minor

Undergraduate student Micailah Guthrie conducted research on the career aspirations of Black South African adolescents as part of a study abroad experience in Durban, South Africa.

This spring semester, I had the amazing opportunity to study in Durban, South Africa with the School for International Training (SIT) through their Community Health and Social Policy program. One of the main features of the SIT’s study abroad programs is that each student is able to conduct research as part of an independent study project (ISP). Based off of my experiences here in South Africa and my personal experiences, I’ve focused my ISP on understanding the personal career aspirations of Black South African adolescents and the pathways of support that they may or may not receive. This qualitative research will be conducted using the method of body mapping, which is an art-based method of data collection that serves as a reflective tool for a person to tell their narrative using their bodies. As I am currently in the ISP period of my study aboard program, I am very excited to review and share my findings.

Also this summer, I’ve have the great opportunity to participate in the Summer Research Opportunity Program at Penn State University, which is a graduate research internship and mentorship for undergraduates. There, I will be working with the College of Health and Human Development’s Dr. Jennifer Graham-Engeland, who directs the Stress & Health lab. I’ll be assisting one of her graduate students on their dissertation project, which focuses on understanding the knowledge gaps of both low and high arousal positive affect in everyday life. I will also be able to explore my own research interests, which lie within health behavior, stress, racial disparities, and personal and familial development.

Photo of Miami University Office of Research for Undergraduates by Miami University Photo Services. Photo of members of the Muscle Fatigue Lab courtesy of Grace Chaney. Photo of Micailah Guthrie courtesy of Michailah Guthrie.

Annette Bollmann explains equipment to a student in her lab.

$5.2 million funds four microbiologists’ research from Acton Lake to Antarctica

DJ Ferguson and Jyoti Kashyap work with liquid in a flask in Ferguson's lab.
Ferguson (right) and doctoral student Jyoti Kashyap

Four Miami University microbiologists — who make up the department’s new microbiology physiology research cluster — collaborate on projects with each other and with more than a dozen researchers from other universities.

Together, they are working on five projects funded by more than $5.2 million in recent grants from three national agencies. Study sites range from nearby Acton Lake to Antarctica.

Microbes — the first living creatures on Earth — are microscopic, single-celled organisms found almost everywhere on Earth including on and inside you.

  • Microbes make up more than 60 percent of Earth’s biomass.
  • An estimated 2-3 billion species of microbes share our planet — but fewer than 0.5 percent (that’s still 10 million) have been identified.
  • Microbes generate at least half of the oxygen we breathe.

From the human gut to the atmosphere

The research projects of Rachael Morgan-Kiss, Annette Bollmann and D.J. Ferguson, associate professors of microbiology, and Xin Wang, assistant professor, explore microbes in projects including:

  • Microbial engineering for the production of biofuels.
  • Manipulating microbial communities to function more efficiently for wastewater treatment.
  • Studying extremophiles to create new engineering targets for artificial photosynthesis.
  • Contributing to long-term research on climate variation in the South Pole.
  • Human gut microbes.

By the numbers:

  • Four faculty mentor nine graduate and 11 undergraduate students on these projects.
  • They collaborate with 13 researchers from 11 universities.
  • One internationally-known artist, Xavier Cortada, is working with students and researchers.

Read their stories:

Click on the links to read their stories in Miami’s Campus News.

Rachael Morgan-Kiss and Xin Wang: “Antarctic algae, alternative photosynthesis and art.”

D.J. Ferguson and Xin Wang: “Microbes, QAs, methane: Top to bottom.”

Annette Bollmann: “Microbial ‘neighbors’ improve ammonia removal in wastewater.”

Xin Wang: “Engineering microbes.”

Spotlight on undergraduate research:

These faculty each mentor several undergraduate research students. Learn more about their research at Miami’s 25th Annual Undergraduate Research Forum, April 23-24.

Morgan-Kiss: All students in her Microbial Ecology (MBI 475/575) class will present posters about their work with samples from Antarctica.

Xavier Cortada, an internationally-known environmental artist based in Miami, Florida, will meet with the class to help them design posters for a broad, general audience.

Ferguson’s lab group: Sarah Soppe, senior microbiology major and Spanish double major, and Claire Papamarcos, senior microbiology major and environmental science co-major.

Bollmann’s lab group: Conor Dolson, senior microbiology major and premedical studies co-major.

Wang’s lab group: Kaya Mernitz, senior microbiology major and premedical studies co-major.

Written by Susan Meikle, University News Writer/Editor, University Communications and Marketing, Miami University. Originally appeared as a “Top Story” on Miami University’s News and Events website.

Photos of D.J. Ferguson and Annette Bollmann by Scott Kissell, Miami University Photo Services.