Massive simulation reveals how a bacterial organelle converts sunlight to chemical energy

November 15, 2019

Researchers from ASU’s Biodesign Institute, in collaboration with colleagues from the University of Illinois, report that they have successfully simulated every atom of a light-harvesting structure in a photosynthetic bacterium that generates energy for the organism. The simulated organelle behaves just like its counterpart in nature, the researchers report.

The work is a major step toward understanding how some biological structures convert sunlight into chemical energy, a biological innovation that is essential to life, the researchers said. They report their findings in the journal Cell Researchers used supercomputers to construct a 136 million-atom model of the chromatophore, a primitive light-harvesting structure in purple bacteria. The simulated organelle behaved just as it does in nature, the team reports. Graphic by Christopher Maffeo Download Full Image

The research team, originally led by University of Illinois physics professor Klaus Schulten, continued the work after Schulten’s death in 2016. The study fulfills, in part, Schulten’s decades-long dream of discovering the mechanisms by which atomic-level interactions build and animate living systems.

Schulten decided very early in his career to study photosynthetic systems. Schulten and research scientist Melih Sener, a co-author, have modeled the chromatophore, a photosynthetic organelle that produces chemical energy in the form of a molecule known as ATP, with the help of experimental data from Neil Hunter from the University of Sheffield in a decade-long collaboration. Schulten was fascinated with the chromatophore from purple bacteria as one of the most primitive biological light-harvesting apparatus known.

“He was a physicist; he wanted to understand biology at the physics level,” said Illinois biochemistry professor Emad Tajkhorshid, a co-author on the new study. “But then he realized biology only works if you put all of the complexity into the model. And the only way to do that was with supercomputers.”

Over the years, Schulten recruited and supported collaborators at Illinois and elsewhere to help him tackle the challenge. The team constructed a 136 million-atom hybrid model of the chromatophore using structural and spectroscopic data derived by long-term collaborator Hunter. The effort required a colossal amount of supercomputer power over a period of four years. The work was conducted on the Titan and Summit supercomputer at the Oak Ridge National Laboratory in Knoxville, Tennessee, and on Blue Waters, which is housed at the National Center for Supercomputing Applications at the University of Illinois.

Schulten and his colleagues had already conducted molecular simulations of many of the individual protein and lipid components of the chromatophore, which produces the ATP needed to power a living cell.

“The chromatophore has an antenna, a battery and a motor,” said the article's lead author, Abhishek Singharoy, who worked with Schulten at Illinois as a Beckman Fellow and CPLC Fellow before moving to Arizona State University in Tempe in December 2017. The antenna harvests light, the battery directs that energy to the motor and the motor cranks out ATP, said Singharoy, who is now a researcher in the Biodesign Center for Applied Structural Discovery and professor in the School of Molecular Sciences at ASU. John Vant and Jonathan Nguyen, fellow researchers in the Singharoy lab, also participated in the new study. Singharoy has focused on state-of-the-art computational approaches for capturing cell-scale biological responses with atomic precision. For the current study, his group was able to parse the data from ORNL’s massive Summit supercomputer using the Agave cluster, a high-performance computing resource at ASU.

ASU research team (from left): Jonathan Nguyen, Abhishek Singharoy and John W. Vant, framed by a graphic of the chromatophore molecule they modeled using supercomputing resources. Photo by Shireen Dooling

Figuring out how the system worked required putting all the parts together, said Illinois physics professor Aleksei Aksimentiev, who guided the project to completion after Schulten’s death. This meant dissecting the chromatophore with every tool available to science, from laboratory experiments to electron microscopy, to programming innovations that broke down the computing challenge into manageable steps, Aksimentiev said.

Once they had a working model of the chromatophore, the researchers watched simulations that revealed how the organelle functioned under different scenarios. They changed the concentration of salt in its environment, for example, to see how it coped with stress.

When they exposed their simulated organelle to conditions that it typically experiences in the cell, they were surprised by how it behaved. It immediately became less spherical, and certain proteins embedded in the membrane began to clump together.

“We started with a perfect sphere, but very rapidly it became imperfect, with flat areas and little areas with high curvatures,” Aksimentiev said. “And all of that, our calculations reveal, has a biological role.”

The protein arrangement creates patches of positive and negative charges that facilitate the distribution of electrons across the system, the researchers said. The electrons are ultimately swapped for protons that drive an enzyme known as an ATP synthase, the motor that produces ATP.

“Chromatophore structure is like a circuit diagram,” said study co-author Melih Sener, a research scientist at the Beckman Institute for Advanced Science and Technology, where much of the computational work was conducted. “If you know how energy and charges travel in it, you know how this machine works. Chromatophore is basically an electronic device.”

The study confirms that, at the atomic scale, physics drives biology, the researchers said. The work will inform future studies of more complex energy-generating organelles in other microorganisms, and in plants and animals, they said. And it will advance scientists’ understanding of nature’s solution to a perpetual human problem: how to efficiently extract energy from one’s environment without poisoning oneself.

The research was made possible through the National Institutes of Health Center for Macromolecular Modeling and Bioinformatics and the National Science Foundation Center for the Physics of Living Cells, both at the University of Illinois. Aksimentiev and Tajkhorshid also are also affiliates of the Beckman Institute. All the computations were supported by first Schulten’s and then Singharoy’s Innovative and Novel Computational Impact on Theory and Experiment (INCITE) grant with the Department of Energy. The Arizona leg of the work in Singharoy’s laboratory was also supported by Research Corporation for Science Advancement and the Gordon and Betty Moore Foundation.

Grants: P41-GM104601, NIH R01-GM067887, NSF PHY-1430124, MCB1616790,

Written by Diana Yates and Richard Harth

Bringing a network of mentors to ASU students

ASU Mentor Network harnesses the professional expertise of Sun Devil community

November 15, 2019

After Arizona State University student Raj Kanaiyo Thakkar was injured in his first semester of college during a soccer game, he wasn’t able to get around easily to connect to resources and classmates in those pivotal first few weeks of school. But he was able to stay on track, despite a partial knee replacement, thanks to the guidance he received from a mentor, an MBA student he was matched with through the ASU Mentor Network

“It was really helpful for me to have someone who could guide me through that time,” said Thakkar, now a sophomore.   Zhengyu Wei, Tara Boucher and ASU Career Services' Alison Scott Dean pose at an ASU alumni and Career Services event in Seattle From left: Mentee Zhengyu Wei, mentor Tara Boucher and Alison Scott Dean, ASU Career and Professional Development Services associate director for corporate engagement and partnerships for the Western region, at a Seattle CPDS and ASU Alumni event. Download Full Image

His mentor helped him zero in on his major path. At the time, he was a business exploratory major and didn’t know what he wanted to concentrate on. Thakkar decided he wanted to study sustainability and logistics management because his family owns automobile dealerships, so it would be helpful to understand the logistics of the operation. 

“She guided me through it and helped me out. She showed me where resources were and how to plan out the semester,” he said. 

Education and career paths are built on skills and experience but also on relationships and coaching. Having someone to put in a good word, guide you through a process or give advice about your path can be an invaluable leg up.

That’s why in fall 2018 ASU Career and Professional Development Services launched the ASU Mentor Network. The initiative harnesses the professional expertise of the Sun Devil community to offer chances for networking and mentorship to current students and alumni. It was built with the intention of giving students and alumni a platform to make powerful professional connections within the Sun Devil community.

Experiences like Thakkar’s can be pivotal to educational persistence and also career success. Research has shown that people with mentors are more likely to get promoted and more likely to be enrolled in college.

“Our big goal is to have every Sun Devil in the ASU Mentor Network experience one or more meaningful connections that impact their career trajectory,” said Kimberly Scatton, assistant director of ASU Career and Professional Development Services.

Through the ASU Mentor Network, alumni and professionals fill out a profile and set availability preferences. Potential mentees then browse profiles and make a request for a connection. Students and professionals can connect via email, video, through group chats, events and more. Scatton said it’s a growth opportunity for the mentors as well as the mentees, since teaching others solidifies your own leadership and communication skills.

ASU alumna Tara Boucher, who graduated from ASU with a degree in engineering and management technology, said the impact is felt on both sides of the mentoring relationship. She signed up to be a mentor after establishing her career in technology working with the Starbucks corporate office, Visa and USAA because she loves the ASU Polytechnic campus and loves working with students. 

“The feeling of giving back is great,” she said. Boucher advises other alumni to sign up to mentor because it’s an opportunity they won’t want to miss. “They might learn something about themselves,” she said.

Boucher, who lives in San Antonio, connects with students and alumni remotely. Her passion for mentorship started when she was working for the Starbucks corporate office in Seattle. Boucher was one of the first ASU Online mentors for Starbucks partners who were pursuing a degree at ASU through the Starbucks College Achievement Plan.

Boucher said her own career has benefitted from mentorship and that young women especially tend to not know their own potential, so she enjoys encouraging mentees to get on-the-job experience and persist beyond rejection. Boucher said it’s important for people to have someone to bounce ideas off of, especially since young people might not know the boundaries of how much they should share with coworkers.

“It doesn’t always seem appropriate at work to open up and seek advice, so it’s great to be able to offer that to someone,” she said.

Zhengyu Wei, who graduated from ASU in May 2019 with her degree in business analytics, is Boucher’s mentee through the ASU Mentor Network. Wei, who is working as a data service engineer for Microsoft, said the experience has been invaluable.

“It is great that you have a professional mentor who works in the industry and can introduce you to others. Meeting more people means you will have more of a chance to get in the door,” said Wei.

Wei said she especially appreciates the opportunities ASU provides to network in her field, have resume help and get referrals because she was an international student and didn’t have a network built in the United States.

Wei, who now works in the Seattle area, said the connection she made through the ASU Mentor Network goes beyond graduation and even beyond professional development. 

“Long-term mentorship will become a friendship. Not only for careers but life,” said Wei. Boucher and Wei enjoyed connecting in person at a recent ASU Alumni and Career and Professional Development Services meetup in Seattle.

Boucher said that she encourages other Sun Devils to get involved as a professional development opportunity and a way to shake things up.

“I highly encourage people to get out of their desk environment, to get out of their day-to-day routine and try something new … and make that thing be mentoring,” said Boucher.

Mentees such as Thakkar say all ASU students shouldn’t hesitate to take advantage of this resource.

“They’re there for you. …They’ll help you through it and guide you. They know what they’re doing because they’ve been through it,” said Thakkar.

Apply to become a mentor.

Hannah Moulton Belec

Marketing content specialist, Educational Outreach and Student Services