Members of the Lab

Graduate Students and Postdocs


Brent Rogaski

B.S. Bioengineering, Penn State (2008)
M.S. Chemical Engineering, UMD (2011)

Research Topics

Simulation studies of the lipid transport protein of yeast, Osh4. Detailed studies on how lipids bind to this protein and long simulations of Osh4 with model anionic lipid membranes. He also was involved in developing organelle membrane models of yeast.

Placement

Western Services Corp. (Power Plant Design, Frederick, MD.)


Kunal Pandit

B.S. Chemical Engineering, UMD (2009)
M.S. Chemical Engineering, UMD (2012)
Ph.D. Chemical Engineering, UMD (2015)

Research Topics

Development of model E. coli membrane models for the cytoplasmic membrane. MD simulations of a secondary active transporter, Mhp1.

Placement

Ph.D. program at UMD with Profs. Raghavan and White (BioE).
Current: New York Genome Center


Pushkar Pendse

Ph.D. Chemical Engineering, UMD (2013)
B. Chem. Eng., Institute of Chemical Technology, Mumbai, India
(2007)

Research Topics

Pushkar's research consists of molecular simulations of an important model for secondary active membrane transport proteins, i.e., lactose permease (LacY). He has aided in the development of a new method to predict conformational changes in LacY towards the periplasmic-open state. This method has potential for use with other membrane proteins. His additional interests in LacY are in probing the binding affinity of sugars and proton translocation mechanisms.

Placement

Postdoctoral appointment in Dr. Grabe Lab at the University of Pittsburgh (move to UC-SF).
Current: Pfizer (in Singapore)


Xiaohong Zhuang

Ph.D. Chemical Engineering, UMD (2016)
B.S. The City College of New York (Chemical Engineering, 2012)

Research Topics

Investigated the temperature dependence of lipid bilayers and CHARMM36 for 80+ lipids. She developed in house codes for analysis. She studied the secondary active transporters (SATs) LacY and compared to DEER experiments. She also developed a lipid soy membrane model.

Placement

Postdoctoral appointment in Naval Research Lab.


Rehan Choudhary

M.S. Chemical Engineering, UMD (2017)
B.S. The City College of New York (Chemical Engineering, 2012)

Research Topics

He developed an evaporation model for applications to predict enviromental spills.

Placement

Department of Energy (U.S.A.).


Viviana Monje-Galvan

Ph.D. Chemical Engineering, UMD (2017)
M.S. Chemical Engineering, UMD (2014)

B.S. Chemical Engineering, UMD (2012)

Research Topics

Viviana began her research in my lab as an undergraduate and continued research as a M.S. and Ph.D. student. As an undergraduate, she aided in testing a new lipid force field for polyunsaturted fatty acid (PUFA) chains. She then worked on researchering yeast membrane models of the plasma membrane, trans-Golgi Network and endoplasmic reticulum. She also worked on studies of the important lipid transport protein, Osh4, and collaborative work with Dr. Mikhail Anisimov on characterizing solutions with hydrotropes.

Placement

Postdoctoral Fellow (NIH) in Dr. Greg Voth's Lab at U. Chicago.


Pouyan Khakbaz

Ph.D. Chemical Engineering, UMD (2018)
M.S. University of California-Irvine (Chemical and Biochemical Engineering, 2011-2012)
B.S. Sharif University of Technology (Chemical Engineering, 2011)

Research Topics

Pouyan did his master's at UC-Irvine and research with Prof. Hung Nguyen. His research initial work at UMD involved studies of secondary active transporters (SATs), such as, lactose permease and Mhp1. He moved on to work on modeling the E. coli cytoplasmic membrane for use in investigating its tolerance to produced chemicals like ethanol. He also simulated condensed phases of PC lipids to study the structure of the ripple and gel phases. Pouyan also collaborated with Dr. Berger (U. Virginia) on Plexin dimerization of the transmembrane and juxtamembrane regions of this large protein.

Placement

Postdoctoral Fellow in Prof. Shukla's Lab at U. Illinois Urbana-Champaign.


Nick Guros

Ph.D. Chemical Engineering, UMD (2019)
B.S. Cornell University (Chemical Engineering)

Research Topics

Modeling of hemolysin, 5HT3, and CDK5 for applications to biosensing. Nick was co-advised by Arvind Balijepalli from NIST. The focus of Nick's reserach is to use all-atom molecular simulations of the hemolysin pore, 5HT3 structure and function and CDK5. He also worked on developing a Field-Effect Transitor (FET) to do expeirmental measurments of chemicals bound to these proteins.

Placement

Scientist at AstraZenca/MedImmune.


Allison Leonard

Ph.D. Biophysics, UMD (2019)
A.P. Physics Teacher (2009-2013)
M.A. Augusta State University (Teaching, 2008)
B.A. North Georgia College & State University (English with minor in Physics, 2006)

Research Topics

Alison researched the energetics of beryllium ion binding to phosphoserine in lipid bilayers, and the effects of ether linkages on bilayer properties. Dr. Sergei Sukharev (UMD/Biology) co-advised her work on beryllium. She also was co-advised by Dr. Rich Pastor (NIH/NHLBI) working on long-range LJ with PME and ion effects on polymers.

Placement

Postdoctoral postition Ed Lyman's lab at the University of Delaware.


Tyler Cline

B.S./M.S. in Chemical Engineering (2018/2019)

Research Topics

Tyler studied the binding of antimicrobial peptides (AMPs) to model membranes of the inner membrane of E. coli. He collaborated with Dr. Stephanie Nagle at Carnegie Mellon University.

Placement

TBD


Indrani Bera

Postdoc, UMD (2015-2019)
Ph.D. Jadavpur University, India (2014)
Structural Biology and Bioinformatics Department, CSIR- Indian Institute of Chemical Biology (CSIR-IICB)
M.S. Birla Institute of Technology, Mesra, India (Bioinformatics, 2008)

Research Topics

Indrani's research first focused on studying sphingomyelin-phospholipid mixed bilayer and how membrane properties are effected by sphingolipids. She has brought to the lab expertise in Gromacs and also tested the use of this software with the CHARMM36 lipid force field. She has also been involved with running MARTINI simulations of Plexin dimerization. She worke on secondary active transporters (uniporters) and predicting structural changes. Her final project involved the study of bio-produced chemicals and their effect on cellular membranes.

Placement

UCD, Dublin (postdoc)


Omid Davoudi

Ph.D. student at University of Maryland, College Park ( Chemical Engineering, 2019-)
M.S. Sharif University of Technology, (Chemical Engineering, 2017-2019)
B.S. Sharif University of Technology, (Chemical Engineering, 2010-2015)

Research Topics

Omid studied mechanosensitive ion channels in bacteria, and working on E. coli mechanosensitive ion channels MscL and MscS specifically. One of the most exciting adaptation processes in nature is the osmoregulation of bacteria in a hyperosmotic environment. In addition, Omid was involved in isothermal titration experiments of divalent cations with model compounds and liposomes. This research was co-advised by Prof. Sukharev from Biophysics program at University of Maryland.

Placement

Transfer Ph.D. to a new Ph.D. lab (Dr. Raghavan/ChBE)


Mahdi Ghorbani

Ph.D. Chemical Engineering UMD (July 2022)
B.S. University of Tehran (Chemical Engineering)

Research Topics

Mahdi started his research on studies to improve yeast membrane chemical tolerance in collaboration with Laura Jarboe at Iowa State University. This research was used to test methods to estimate cell membrane permeability. Mahdi was involved in many projects such as antifugal peptides (in collaboration with Dr. Karlsson's lab), protein aggregration (in collaboration with Dr. Woehl's lab), and free energy predictions, machine learning (simulation analysis and AMP peptide prediction), and plexin proteins. He also did some research on COVID-19 focusing on RBD/ACE2 interaction and the sugar protetcion of the spike protein.

Placement

Postdoc position with Prof. Michael Keiser (UC-San Francisco)


Yalun Yu

Ph.D. Biophysics, UMD (July 2022)
B.S. Fudan University, China (Physics)

Research Topics

Yalun was a biophysics rotation student with past experience with molecular simulation. In my lab, he worked on modeling the Pseudomonas aeruginosa inner membrane with general interest in membrane properties in comparison with E. coli and applications to later look at mechanosensitive transporters. His main project was lipid force field development in collaboration with Dr. Rich Pastor (NIH). He developed a computational algorithm to use thermodynamic reweighting to optimize parameters for the additive and polarizable force field. He also continued work on membrane modeling and developed asymmetric models for plant membranes.

Placement

Scientist at Schrödinger, Inc