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Biomolecular Simulations Group

Research in Biomolecular Simulations Group (Moradi Lab) is centered around two inter-related questions: (i) how do proteins function by changing their conformation and undergoing concerted motions? and (ii) how can we simulate these functionally important conformational changes at an atomic level?

We develop and employ Molecular Dynamics (MD) based enhanced sampling techniques to tackle both problems. Answering these questions would shed light on the structure-function relationships in proteins, and could improve our understanding of disease at a molecular level. We attempt to narrow the gap between the state-of-the-art computational methodologies and biologically/biomedically relevant applications.

We are particularly interested in the study of large-scale conformational changes of proteins such as those involved in membrane transport and signal transduction. A novel combination of nonequilibrium and equilibrium MD based techniques are employed to reconstruct the slow biomolecular processes such as inward- to outward-facing structural transition of membrane transporters at an atomic level.

Spike Proteins

The active configuration of SARS CoV-2 (left) remaining active, while the active of cofiguration of SARS CoV1 (right) moves to an inactive state.

Blue Waters Symposium, June 2018, Sunriver, OR Free Energy Workshop, Sep. 2017, Urbana, IL Free Energy Workshop, Sep. 2017, Urbana, IL
Blue Waters Symposium, June 2019, Sunriver, OR Free Energy Workshop, Sep. 2018, Urbana, IL Free Energy Workshop, Sep. 2018, Urbana, IL

Lab News:

Oct 16, 2020 A UARK Newswire article featured a story on the work done in the biomolecular simulation lab on modeling the hemagglutinin protein of the influenza virus.
Sep 27, 2020 An article in IEEE Spectrum on the contributions of AI and other computational techniques to the study of SARS CoV-2 and vaccine development mentions the work done in the Biomolecular Simulations Group.
Aug 21, 2020 Shadi Asadian joins the lab as a Cell and Molecular Biology Ph.D. student. Welcome to the lab!
Jun 15, 2020 The Pittsburgh Supercomputing Center's website published a news story on the Biomolecular Simulation Lab's work on the coronavirus glycoproteins. The group has used computing resources on the Anton 2 supercomputer, as part of the COVID-19 HPC Research Consortium, to quickly simulate large all-atom protein systems.
Jun 3, 2020 UARK News shared Dr. Moradi on a new episode of the Short Talks from the Hill to discuss the lab's research on SARS CoV-1 and SARS CoV-2.
May 20, 2020 Research comparing the spike proteins from CoV-1 and CoV-2 was highlighted in the Texas Advanced Computing Center News.
May 18, 2020 An E&E News article on the efforts of the COVID-19 HPC Consortium to indentify theraputic drugs highlights the group's research as evidence that structural difference between CoV-1 and CoV-2 require new theraputic targets.
May 15, 2020 The COVID-19 HPC Consortium blog highlighted the research being done in the Moradi lab to identify behavioral differences between the SARS CoV-1 and CoV-2.
Apr 16, 2020 Dr. Moradi is interviewed with other scientists in U.S. News & World Report for the research being done on the SARS CoV2 spike protein using supercomputers.
Apr 14, 2020 A story in the UARK Newswire on SARS CoV-2 simulations done in the Biomolecular Simulation Lab highlights the use of supercomputers made available through the COVID-19 HPC Consortium for research on conformational changes of the spike protein.
Mar 9, 2020 Alaa El-Khouly, a Master of Biomedical Engineering student, joins the lab. Welcome, Alaa!
Feb 15, 2020 Lab members attend the 2020 Biophysical Society Anual Meeting in San Diego, CA.
Feb 6, 2020 Dr. Moradi receives the Faculty Early Career Development Program (CAREER) award from the National Science Foundation.
Jan 24, 2020 Ugochi Isu was approved as a CHBC Ph.D. candidate after passing her cumulative examinations.
Jan 13, 2020 Ph.D. student Matthew Brownd joins the lab. Welcome, Matthew!
Dec 2,2019 Vivek Govind Kumar passed his CEMB candidacy exam.
Nov 20, 2019 Dr. James Losey joins the lab as a Postdoctoral Research Fellow.
Oct 9, 2019 Newswire write-up on the recent publication in Scientific Reports.
Sep 18, 2019 The manuscript from Moradi Lab with an undergraduate first author is accepted for publication at Scientific Reports (preprint). Congrats Thomas!
Sep 17, 2019 Moradi Lab receives an NSF grant on "Atomic-level Structural Dynamics in Catalysts". This is part of a collaborative grant to support an interdiscilinary research project involving six different labs across the US with expertise in data science, computational techniques, materials science, and biophysics.
Mar 13, 2019 Moradi Lab (and 5 other labs across the US) are awarded access to Blue Waters supercomputer at University of Illinois by Great Lakes Consortium for Petascale Computation (GLCPC) .

Jan 22, 2019 Newswire Highlights the research conducted in Moradi Lab and published in ACS Central Science: New Insight Into Cell Membranes Could Improve Drug Testing and Design.
Jan 7, 2019 Moradi Lab publishes a research article in ACS Central Science, proposing a novel lipid-dependent mechanism for ABC exporters.
Oct 15,2018 Moradi Lab is awarded access to the specialized supercomputer, Anton 2, housed at the Pittsburgh Supercomputing Center. 57 research labs across the US have been awarded access to Anton in this cycle.
Sep 10-14, 2018 Upcoming Event: Hands-on Workshop on Enhanced Sampling and Free-Energy Calculation at Urbana, IL.
Aug 30, 2018 - Collaborative work on ALS-causing mutations of PFN1 protein was published in Scientific Reports. Moradi Lab collaborated with several Labs at University of Arkansas for Medical Sciences on this project.
Apr 27, 2018 - Moradi Lab (and 8 other labs across the US) are awarded access to Blue Waters supercomputer at University of Illinois by Great Lake Consortium for Petascale Computation (GLCPC).
Feb 22, 2018 - Newswire highlights the collaborative work with the Department of Education at U. Arkansas and Fayetteville High School published at Biochem. Mol. Biol. Educ. in an article: Professors, High School Teachers Study Use of Modeling Software to Boost Science Education.
May 9, 2017 - Moradi's collaborative work with the UIUC team makes it to the headline of Oak Ridge Leadership Computing Facility (OLCF) website: Assembling Life’s Molecular Motor.
Jan 13, 2017 - Arkansas Newswire Headline: U of A chemist develops new theory for explaining the function of proteins.
Jan 6, 2017 - Thomas Harkey receives an Honors College Research Grant for the Spring and Fall 2017 terms.
Dec 13, 2016 - Research conducted in Moradi Lab on the GkPOT transporter and the limitations of molecular dynamics appears in J. Phys. Chem. B.
Dec 9, 2016 - Dr Moradi coauthors a paper on chemomechanical couplings in V–type ATPases, published in J. Am. Chem. Soc.
Nov 18, 2016 - Dr Moradi's paper appears in the Journal of Physical Chemistry Letters: Effective Riemannian Diffusion Model for Conformational Dynamics of Biomolecular Systems.
Arkansas Newswire Headline, Apr. 14, 2020
Spike Protein
Arkansas Newswire Headline, Jan. 22, 2019
Lipid-Dependent Alternating Access

Arkansas Newswire Headline, Jan. 13, 2017
Riemannian Conformational Space
Nov 1, 2016 - Moradi Lab is awarded 460,000 MDUs on molecular dynamics specialized supercomputer Anton 2, housed at the Pittsburgh Supercomputing Center. 52 research labs across the US have been awarded access to Anton in this cycle.
Oct 22, 2016 - Mitchell Benton and Reid Shelton present posters at the 2016 Conference for Arkansas IDeA Network of Biomedical Research Excellence (INBRE).
Sep 19, 2016 - Hamid Tabari joins the lab as a graduate student in CEMB program.
Jun 2, 2016 - Moradi Lab (and 10 other labs across the US) are awarded access to Blue Waters supercomputer at University of Illinois by Great Lake Consortium for Petascale Computation (GLCPC).
May 18, 2016 - Mitchell Benton receives an Honors College Research Grant for the Summer and Fall 2016 terms.
Apr 19, 2016 - Dr Jeevapani Hettige joins the lab as a postdoctoral fellow.
Feb 1, 2016 - Dr Kalyan Immadisetty joins the lab as a postdoctoral fellow.
Nov 7, 2015 - Dr Moradi gives an invited talk at the Joint Southeastern/Southwest ACS Regional Meeting, Memphis, TN.
Sep 29, 2015 - Dr Moradi's recent paper was published in Nature Communications.
In this work, an entire transport process is, for the first time, reconstructed at an atomic level and characterized thermodynamically.
Copyright © 2015, Biomolecular Simulations Group, Department of Chemistry and Biochemistry, University of Arkansas.
These materials are not endorsed, approved, sponsored, or provided by or on behalf of the University of Arkansas, Fayetteville.
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