Welcome to the Biomolecular Simulations Lab

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.


Jan 16, 2024
A paper Stephanie contributed called "Bioorthogonal click labeling of an amber-free HIV-1 provirus for in-virus single molecule imaging" was Published! Cell Chemical Biology Congrats!
Jan 5, 2024
Asal Behzadnezhad joined the lab as a Ph.D student in the CEMB. Welcome, Asal!
Jan 4, 2024
Reza Taghavi joined the lab as a Ph.D student in the MSEN. Welcome, Reza!
Jan 3, 2024
Dr.Hope Woods joins the lab as a postdoctoral fellow. Welcome Hope! 
Dec 1, 2023
Ehsaneh Won First Place in MSEN Poster Presentation Contest. Congrats Ehsaneh!
Jun 29, 2023
Goolsby, Curtis; Losey, James; Fakharzadeh, Ashkan; Xu, Yuchen; Düker, Marie-Christine; Getmansky Sherman, Mila; Matteson, David; Moradi, Mahmoud's paper called ” Addressing the Embeddability Problem in Transition Rate Estimation " was Published! The Journal of Physical Chemistry Congrats all!
Jun 19, 2023
M Benton, M Furr, V Govind Kumar, A Polasa, F Gao, C-D Heyes, T-K Suresh Kumar, M Moradi's paper called ” cpSRP43 is both highly flexible and stable: Structural insights using a combined experimental and computational approach " was published! Journal of Chemical Information and Modeling Congrats all!
May 30, 2023
Shadi, Ugochi, and Ehsaneh’s paper called "The Alternating Access Mechanism in Mammalian Multidrug Resistance Transporters and Their Bacterial Homologs" was punblished in Membranes! Membranes Co$
May 25, 2023
Stephanie, Joseph, and Adithya's paper on the rocker-switch mechanism in the major facilitator superfamily was selected as the cover of Membranes! Membranes Congrats all!
May 15, 2023
Ahmed Shubbar joined the lab. Welcome Ahmed!
May 8, 2023
Ehsan Khodadadi joined the lab. Welcome Ehsan!
May 3, 2023
Ugochi defended her masters in Cellular and Molecular Biology. Congrats Ugochi!
May 1, 2023
Samuel Wamwere Mwatha joined the lab. Welcome Samuel!
Apr 25, 2023
Stephanie, Joseph, and Adithya's paper called "Ins and Outs of Rocker Switch Mechanism in Major Facilitator Superfamily of Transporters" was punblished in Membranes! Membranes Co$
Mar 3, 2023
Ugochi, Shadi, and Ehsaneh's paper called "Cholesterol in Class C GPCRs:Role, Relevance, and Localization" was punblished in Membranes! Membranes Congrats Ugochi, Shadi, and Ehsaneh!
Feb 23, 2023
Group dinner at Pacific Catch in La Jolla, CA.
Feb 18-23, 2023
The lab attended the 2023 Biophysical Society Annual Meeting in San Diego, CA!
Jan 16, 2023
Adithya's paper called "Towards A Purely Physics-based Computational Binding Affinity Estimation"" was published in Nature Computational Science.Nature Computational Science Congrats Adithya!

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