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ASU professor will develop new pc modeling framework for bio-nanotechnology with NSF CAREER award

January 25, 2023

Petr Šulc, an assistant professor at Arizona State College’s College of Molecular Sciences and the Biodesign Heart for Molecular Design and Biomimetics, has lately earned a College Early Profession Improvement (CAREER) award from the Nationwide Science Basis.

Šulc’s lab is extremely interdisciplinary and broadly applies the strategies of statistical physics and computational modeling to issues in chemistry, biology and nanotechnology. The group develops new multiscale fashions to review interactions between biomolecules, significantly within the context of design and simulations of DNA and RNA nanostructures and gadgets.

Petr Šulc is an assistant professor at Arizona State College’s College of Molecular Sciences and the Biodesign Heart for Molecular Design and Biomimetics. Picture courtesy ASU
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“This analysis award will permit our lab to increase the scope of programs that we examine and permit us to design a brand new class of nanodevices and nanomaterials that incorporate DNA, RNA and proteins, in addition to different molecules,” defined Šulc. “Simply as advanced machines in our on a regular basis use — plans, vehicles and chips in electronics — require refined computer-aided design instruments to verify they carry out a desired operate, there’s a urgent have to have entry to such strategies within the molecular sciences. ”

Professor Tijana Rajh, director of the College of Molecular Sciences, stated, “Petr Šulc and his group are doing extraordinarily revolutionary molecular science, utilizing the strategies of computational chemistry and physics to review DNA and RNA molecules within the context of biology in addition to nanotechnology . Our youthful school members within the College of Molecular Sciences have a rare file of accomplishment, and Professor Šulc is an exemplary on this regard.”

The celebrated CAREER program helps the early profession growth actions of teacher-scholars who most successfully combine analysis and schooling throughout the mission of their group. It supplies five-year analysis grants to every recipient.

Bio-nanotechnology

DNA and RNA are the essential molecules of life. They fulfill many capabilities, together with data storage and knowledge switch in residing cells. Additionally they have promising functions within the area of nanotechnology the place designed DNA and RNA strands are used to assemble nanoscale buildings and gadgets. As Šulc explains, “It’s a little bit like enjoying with Lego blocks besides that every Lego block is just a few nanometers (a millionth of a millimeter) in dimension, and as a substitute of placing every block into the place the place it ought to go, you place them inside a field and shake it randomly till solely the specified construction comes out.”

This course of known as self-assembly, and Šulc and his colleagues use computational modeling and design software program to provide you with the constructing blocks that reliably assemble into the form one desires at nanoscale decision.

“The promising functions of this area embody diagnostics, therapeutics and constructing of latest supplies,” says Šulc. “My lab has developed the software program to design these blocks, and we work carefully with experimental teams at ASU in addition to different universities within the US and Europe. “

They’re additionally within the software of machine studying strategies to organic sequence ensembles and use neural networks to design DNA or RNA sequences that may particularly bind to a goal protein of curiosity, such because the SARS-CoV-2 spike protein.

Video of SMS Junior College Highlight- Petr Šulc

The challenges

Pc-aided design software program is commonly utilized in our macroscale world to design pc chips, vehicles and planes in order that the machine operation can initially be examined and optimized in simulation. Building on the nanoscale, nonetheless, presents a number of challenges. Versus our macroworld, nanostructures are sometimes obtained by self-assembly, the place particular person parts randomly diffuse till they meet and assemble right into a goal construction.

So as to acquire extra advanced buildings that may self-assemble in excessive yields, there’s a want for a brand new simulation framework that may effectively and, on the similar time, precisely signify the meeting and performance of the nanostructures.

Šulc’s lab will develop a brand new modeling framework that’s able to simulating self-assembled DNA nanostructures.

The analysis group will use this new framework to optimize nanostructure meeting for top yield and computationally design new forms of reconfigurable nanostructures. Subsequent, the group will lengthen the modeling platform to permit for the incorporation of different natural/inorganic molecules and supplies.

Total, this award will facilitate the creation of latest nanodevices able to performing advanced duties that will be troublesome to hold out experimentally with no refined modeling platform. It’s going to deliver the sector nearer to large-scale industrial functions.

To understand the schooling element of the challenge, Šulc’s lab will develop new studying alternatives for college college students and most people. The primary effort will contain creating an internet citizen-science platform, the place customers can use the simulation platform to design and optimize buildings themselves, enabling crowdsourcing of nanotechnology designs.

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