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Chemical and Biomolecular Engineering

Diwakar Shukla, Blue Waters Assistant Professor in the Department of Chemical and Biomolecular Engineering, has been chosen to receive a 2020 Dean’s Award for Excellence in Research from the Grainger College of Engineering.

The awards were established to honor faculty for outstanding research. Four assistant professors are chosen by their peers based on who has conducted the most outstanding research during the last academic year. In addition, four associate professors are chosen for their outstanding research over the past five academic years. Professor Shukla will be honored at the college’s faculty awards ceremony on April 27.

The Shukla Group uses and develops theoretical and computational chemistry tools to understand biophysical processes in plants. In particular, his research program focuses on understanding how plants sense and cope with stressful environmental conditions.

Shukla Group members, February 2020. First row, left to right: Diwakar Shukla, Matthew Chan, Jiming Chen, Jiangyan Feng, Soumajit Dutta, Brianna Sobecks, Xuenan Mi and Amisha Patel. Second row, left to right: Balaji Selvam, Chuankai Zhao, Prateek Bansal, Austin T. Weigle, Pouyan Khakbaz, Shriyaa Mittal, Zhengyuan Xue and Yazeed Alfawaz.

In 2018-19 and 2019-20 academic years, Dr. Shukla has received seven faculty awards including early-career investigator awards from the American Chemical Society, American Institute of Chemical Engineers, National Science Foundation and Alfred P. Sloan Foundation. He was selected as the NCSA faculty fellow for 2019-2020, Fellow of the Center for Advance Study for 2020-21 and received the Excellence in Teaching award (2019) from the School of chemical sciences.

“I am honored to receive this recognition on behalf of the outstanding students in my group, collaborators, and mentors at Illinois. They inspire me every day by their excellence and enthusiasm for research,” he said.

Shukla joined the Illinois faculty in 2015. He received his PhD in Chemical Engineering from the Massachusetts Institute of Technology and was postdoctoral fellow in the Department of Chemistry at Stanford University. He holds affiliate appointments in the Department of Plant Biology, National Center for Supercomputing Applications, Center for Biophysics & Quantitative Biology, and the Beckman Institute for Advanced Science and Technology.

Diwakar Shukla – professor of chemical and bimolecular engineering

Blue Waters Assistant Professor Diwakar Shukla has been named a Fellow with the University of Illinois Center for Advanced Study for 2020-2021.

Each year the Center for Advanced Study appoints fellows to the center, which provides one semester of release time for creative work. Fellows are selected from among untenured faculty of all departments and colleges to carry out self-initiated programs of scholarly research or professional activity. Fellows also participate in a yearly roundtable discussion of research interests and are invited to deliver a future CAS presentation.

Shukla was selected for his research proposal, “Unraveling the Molecular Magic of Witchweed.” Witchweed is a parasitic weed which destroys $10 billion worth of crops such as corn, sugar cane, and rice annually. It detects its host plants by using strigolactone, a plant hormone released by the host plant into the soil. Witchweed then absorbs nutrients from its host and kills it. His research group is seeking to understand the molecular processes responsible for strigolactone sensitivity in witchweed and use this knowledge to design precise and potent inhibitors to prevent witchweed germination. An inhibitor for witchweed will help to reduce crop losses and improve food security in witchweed-vulnerable regions.

Shukla joined the Illinois faculty in 2015. His group develops and employs computational chemistry approaches to decipher the mechanisms of regulation of protein function with applications in the field of plant biology and medicine. His appointment as a 2020-21 CAS fellow is pending approval by the University of Illinois Board of Trustees.

Congratulations, Dr. Shukla!

Congratulations to Blue Waters Assistant Professor Diwakar Shukla, who has been selected for a 2019 School of Chemical Sciences Teaching Award! He joins several graduate students from the Department of Chemical and Biomolecular Engineering who were also recognized for their teaching excellence in the 2018-19 academic year. The ChBE graduate students chosen for the award include Madeleine Biagioli, Matthew Chan, Nicholas Troescher, and Dylan Walsh.

Diwakar Shukla

In the announcement, school director Jonathan Sweedler said the award recognizes the entire scope of our educational efforts, from course development to in-class instruction.

“Excellence in teaching is not only intellectually satisfying, but our instructional efforts immeasurably strengthen our research mission,” he said.

The school also recognized Donald DeCoste, teaching associate professor in the Department of Chemistry, and the following PhD students in chemistry: Laura Daigh, Reshmi Dani, Clare Leahy, and Zane Thornburg.

 

Congratulations to Assistant Professor Diwakar Shukla! He has been chosen for a 2019-2020 Faculty Fellowship from the National Center for Supercomputing Applications (NCSA).

Diwakar Shukla

The NCSA Faculty Fellowship is a competitive program for faculty and researchers at the University of Illinois at Urbana-Champaign which provides seed funding for new collaborations that include NCSA staff as integral contributors to the project.

Shukla and NCSA collaborator Luigi Marini will work on the project, “Enabling Long-Term Reuse of Experimental and Computational Datasets on Protein Dynamics,” which aims to have a transformative impact on how protein science is conducted by experimental and computational research groups.

In Shukla’s proposal, he writes that modern molecular simulations of proteins on high-performance computing resources such as Blue Waters generate extensive atomistic-detailed information about protein dynamics, which could be leveraged for obtaining insights about molecular origin of human diseases, design of therapeutics, bioengineering of plants. However, the key challenge is to convert the terabytes of biomolecular dynamics data generated on supercomputers into a format accessible to an experimental researcher.

“In this proposal, we present an approach that not only generates suggestions for optimal experiments based on simulation data (e.g. for validation of simulations) but also integrates the existing experimental and simulation information to generate comprehensive models of protein dynamics that are missing from the current literature. We have developed algorithms that provide an approach that maximizes information gain for the design of experiments given simulation data. We propose to work with NCSA collaborators to implement a cloud-based platform and a user interface for this proposed service. NCSA will benefit from working on this project by gaining more expertise in applying cyberinfrastructure in the realm of biomolecular dynamics. The biggest impact of the proposed study is that it provides an accessible tool for experimental researchers to help harness the knowledge hidden in the big protein simulation datasets generated using Blue Waters and other high performance computing resources. This work will have a transformative impact on how protein science is conducted by experimental and computational research groups.”

Shukla is among seven named for the 2019-2020 academic school year.
Additional abstracts can be found here.

The National Center for Supercomputing Applications (NCSA) at the University of Illinois at Urbana-Champaign provides supercomputing and advanced digital resources for the nation’s science enterprise. At NCSA, University of Illinois faculty, staff, students, and collaborators from around the globe use advanced digital resources to address research grand challenges for the benefit of science and society. NCSA has been advancing one third of the Fortune 50® for more than 30 years by bringing industry, researchers, and students together to solve grand challenges at rapid speed and scale.

Two Illinois scientists are among 126 recipients of the 2019 Sloan Research Fellowships from the Alfred P. Sloan Foundation. According to the foundation, the awards “honor early career scholars whose achievements mark them as among the most promising researchers in their fields.”

This year’s Illinois recipients are chemical and biomolecular engineering professor Diwakar Shukla and electrical and computer engineering professor Haitham Al-Hassanieh.

Diwakar Shukla

Shukla uses physics-based models and techniques to understand complex biological processes such as the regulation of protein structure and function, with applications in food security and human health. He joined the Illinois faculty as a Blue Waters professor in 2015. He is an affiliate of the department of plant biology, the Center for Biophysics and Quantitative Biology, and the National Center for Supercomputing Applications. He is a graduate of the Indian Institute of Technology in Mumbai and received a Ph.D. from MIT. The fellowship will support his work in chemistry.

Al-Hassanieh works on designing systems and algorithms for wireless networking and mobile sensing in order to enhance and scale connectivity in future networks and the “internet of things.” He received a Ph.D. from the Massachusetts Institute of Technology and joined the U. of I. faculty in 2016. He is an affiliate of the department of computer science and of the Coordinated Science Laboratory. He also leads the Systems and Networking Research Group. The fellowship will support his work in computer science.

“Sloan Research Fellows are the best young scientists working today,” said Alfred P. Sloan Foundation president Adam F. Falk. “Sloan Fellows stand out for their creativity, for their hard work, for the importance of the issues they tackle, and the energy and innovation with which they tackle them.”

A full list of the 2019 Fellows is available at the Sloan Foundation website.

Congratulations to Jee-Wei Emily Chen, Chemical and Biomolecular Engineering graduate student in Professor Brendan Harley’s lab. Her image, “A Rising Moon Above the Mountain” was named winner of the School of Chemical Sciences’ 2018 Science Image Challenge.

The annual research image competition is sponsored by the School of Chemical Sciences and open to graduate and undergraduate students, postdoctoral associates/fellows, and staff members, excluding faculty members.

“Rising Moon Above the Mountain”

Description: This is a Scanning Electron Microscope (SEM) image of gelatin hydrogel added with false color composite with a glioblastoma brain tumor microshperoid environmental electron scanning microscope (ESEM) image. The tumor mimetic microspheroid embedded in the brain-mimetic hydrogel will allow us to visualize tumor therapeutic responses. Acknowledgement: SEM and ESEM image was taken at the Beckman Institute with assistance from Cate Wallace.

Students, faculty, and staff are invited to attend the SCS VizLab’s open house to celebrate the winner and finalists.

SCS VizLab Open House

151 Noyes Lab

2-4 p.m. Tuesday, Dec. 11

2:30 p.m. awards presentation

Refreshments will be provided.

In addition to Chen’s winning image, four finalists were named.

“Fire and Ice,” Marley Dewey, Harley Lab

Description: An environmental scanning electron microscope image of a poly(lactic acid) 3D print (blue) within a porous mineralized collagen scaffold (red). 3D prints are used to reinforce the soft mineralized collagen scaffold, which is used for bone regeneration of large missing bone defects in the skull and jaw.

 

“Feathers of the Ocean,” Prapti Kafle, Diao Lab

Description: Presented is a cross-polarized microscopy image of nanothin films of an anti-cancer drug ellipticine on edible polymer-pullulan. The film, produced by solution shearing of the drug solution under highly non-equilibrium conditions, embraces an elegant morphology with oriented needles and spherulites, that resembles feathers of a bird, camouflaging in the ocean.

 

“Molecular Machinery,” Matthew Chan, Shukla Lab

Description: Proteins are intricate molecular machines. Shown here, the serotonin transporter undergoes conformational changes to transport serotonin and ions across the membrane. Using computational simulations, we can visualize the complex dynamics to understand of how these molecular machines can be regulated. Image was based on simulation results and drawn in Illustrator.

 

“Molecular Dynamics of Cytochrome P450 with Endogenous Inhibitor Virodhamine,” Andres Arango, Tajkhorshid Lab, Center for Biophysics and Quantitative Biology

Description: Cytochrome P450s (CYPs) are responsible for the metabolism of many exogenous and endogenous biomolecules. This image depicts the molecular dynamics simulations virodhamine, an endogenous inhibitor of CYP2J2, the predominant CYP in heart tissue.

Congratulations to Blue Waters Assistant Professor Diwakar Shukla, who has been awarded a National Science Foundation Faculty Early Career Development (CAREER) Award.

The award will provide five years of support for Shukla’s efforts in developing new algorithms and their applications to the field of computational biology. NSF CAREER Awards are prestigious and competitive awards given to junior faculty who exemplify the role of teacher-scholar through outstanding research, excellent education, and the integration of education and research within the context of the mission of their respective organizations.

The Shukla Group in December 2017. First row (left to right): Prof. Diwakar Shukla, Dr. Balaji Selvam, Jiming Chen, Jiangyan Feng, Zahra Shamsi, Matthew Chan and Faisal Aldukhi. Second row (left to right): Alexander Moffett, Chuankai Zhao, Kevin Cheng, Qihua Chen and Shriyaa Mittal.

The title of his project is “Reinforcement Learning of the Free Energy Landscapes of Proteins.” It addresses a critical challenge of sampling large-scale conformational dynamics in molecular simulations and develops a computational approach likely to have broad impact on understanding the dynamics underlying protein function.

“The research effort aims to apply the proposed methodologies to investigate proteins that play a critical role in the environment (sugar transport in plants) and human health (neurotransmitter transport in human brain), but in which limited structural or dynamic information about them is available. Therefore, this project will provide new information critical for regulating their activity,” Shukla said.

“I would like to thank my students and collaborators for their hard work and passion that has contributed significantly towards the ideas and research plans to be executed as part of this award,” Shukla said. “My group is excited about both the intellectual and educational components of this award,” he said.

The Shukla Group develops and employs computational chemistry approaches to decipher the mechanisms of regulation of protein function which play a critical role in governing cellular and organismal behavior. Shukla joined the Illinois faculty in 2015. He received his PhD in Chemical Engineering from the Massachusetts Institute of Technology and was postdoctoral fellow in the Department of Chemistry at Stanford University.

The proposed outreach efforts are focused on engaging children from Champaign and Urbana schools, specifically in educating them about how proteins function as molecular machines in our body.

 

This summer the Department of Chemical and Biomolecular Engineering brought 24 high school students to campus for the GAMES (Girls’ Adventures in Mathematics, Engineering, and Science) camp. They participated in a variety of activities, including demonstrations, presentations, hands-on activities, and tours which exposed them to the breadth of chemical engineering.

Led by Blue Waters Assistant Professor Diwakar Shukla, the camp’s experiments involving distillation, polymer extrusion, acid rain, starch straining, foaming face wash, and continuous distillation. Professor Diao and members of her lab led the campers in activities making chocolate shapes, drying them, and discussing how chocolate crystallizes. In another session, Professor Mary Kraft and her team led the campers in an activity about gold nanoparticles, during which the students aggregated a gold colloid. Another popular activity was the hydrogel demonstration led by the Hyunjoon Kong Lab, wherein the hydrogels run after each other on top of water. The students also enjoyed making oobleck courtesy of the Simon Rogers Lab.

For more information, check out this article about the camp by the I-STEM education initiative.

Congratulations to Blue Waters Assistant Professor Diwakar Shukla, who has been chosen to receive the 2018 CoMSEF Young Investigator Award for Modeling & Simulation.

Diwakar Shukla
Diwakar Shukla

This award, from the Computational Molecular Science and Engineering Forum of the American Institute of Chemical Engineers, recognizes outstanding research in computational molecular science and engineering, encompassing both methods and applications.

This fall Shukla will deliver a presentation within the CoMSEF plenary session of the AIChE Annual Meeting. His talk is entitled, “Methodologies for enhanced unbiased sampling of the free energy landscapes of proteins.” The abstract follows.

“Protein function is inextricably linked to protein dynamics. As we move from a static structural picture to a dynamic ensemble view of protein structure and function, novel computational paradigms are required for observing and understanding conformational dynamics of proteins and its functional implications. In principle, molecular dynamics simulations can provide the time evolution of atomistic models of proteins, but the long time scales associated with functional dynamics make it difficult to observe rare dynamical transitions on the free energy landscapes associated with protein function. One approach to surmount this challenge is to use reaction coordinate that characterize the rare conformational transitions to sample conformational landscapes more effectively. However, it is not possible to identify reaction coordinate for systems a priori, especially for proteins with limited availability of structural information. Furthermore, different reaction coordinates characterize the free energy barriers at different points on the free energy landscapes. Here, we discuss a set of methodologies outlined in a series of papers from our group, which use evolutionarily coupling between protein residues and machine learning methods to adaptively guide sampling with no alterations to potential energy functions in order to expedite exploration of the free energy landscapes.”

Shukla joined the University of Illinois Department of Chemical and Biomolecular Engineering in 2015. He also is an affiliate faculty member in the Center for Biophysics and Computational Biology, Computational Science & Engineering Program, Department of Plant Biology and National Center for Supercomputing Applications. He started his research career at the Indian Institute of Technology (IIT) Bombay, India, where he received B. Tech and M. Tech. degrees in chemical engineering. He then joined Massachusetts Institute of Technology where he received MS and PhD degrees in chemical engineering under guidance of Prof. Bernhardt Trout followed by a postdoc at Stanford University with Prof. Vijay Pande. He has received several awards for his research including the  CoMSEF Graduate student award from AIChE, Peterson award from the American Chemical Society, Innovation in Biotechnology award from American Association of Pharmaceutical Scientists, OpenEye outstanding junior faculty award in computational chemistry from ACS and the New Innovator Award from the Foundation for Food and Agriculture Research.

Blue Waters Assistant Professor Diwakar Shukla has been selected by a panel of distinguished reviewers to receive the American Chemical Society’s OpenEye Outstanding Junior Faculty Award for Fall 2018.

The competition, organized by the ACS Division of Computers in Chemistry, selects four outstanding tenure-track junior faculty annually for the award. Winners will present their work at the Fall 2018 ACS national meeting. According to ACS, the awards are designed to assist new faculty members in gaining visibility within the COMP community.

Diwakar Shukla

Shukla, a faculty member of Chemical and Biomolecular Engineering at Illinois, focuses his research on understanding complex biological processes using novel physics-based models and techniques. He also is an affiliate faculty member in the Center for Biophysics and Computational Biology, the Computational Science & Engineering Program, the Department of Plant Biology and the National Center for Supercomputing Applications. He joined the faculty in 2015.

He earned his PhD in Chemical Engineering from MIT and completed his postdoctoral studies at Stanford University.

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