Members of the Lab
Graduate Students and Postdocs
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Brent Rogaski B.S. Bioengineering, Penn State (2008) 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.) |
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Kunal Pandit B.S. Chemical Engineering, UMD (2009) 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 |
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Pushkar Pendse Ph.D. Chemical Engineering, UMD (2013) 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) |
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Xiaohong Zhuang Ph.D. Chemical Engineering, UMD (2016) 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. |
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Rehan Choudhary M.S. Chemical Engineering, UMD (2017) Research Topics He developed an evaporation model for applications to predict enviromental spills. Placement Department of Energy (U.S.A.). Current: Manager at EPA |
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Viviana Monje-Galvan Ph.D. Chemical Engineering, UMD (2017) 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. Current: Assistant Professor (University of Buffalo, NY) |
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Pouyan Khakbaz Ph.D. Chemical Engineering, UMD (2018) 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. Current: Principal Scientist (Amgen) |
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Nick Guros Ph.D. Chemical Engineering, UMD (2019) 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. |
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Allison Leonard Ph.D. Biophysics, UMD (2019) 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. |
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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 Green Generation (Bethesda, MD) |
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Indrani Bera Postdoc, UMD (2015-2019) 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) |
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Omid Davoudi M.S. University of Maryland, College Park ( Chemical Engineering, 2019-2023) 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 TBD |
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Mahdi Ghorbani Ph.D. Chemical Engineering UMD (July 2022) 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) Current: Machine Learning Scientist (Expedition Medicine) |
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Yalun Yu Ph.D. Biophysics, UMD (July 2022) 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 |
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Robert Allsopp Ph.D. Chemical Engineering, UMD (December 2023) Research Topics Rob worked on studying membrane active peptides from the Osh4 protein that are involved in how this protein binds to yeast cell organelles. He discovered aiming to discover new binding motifs of this protein to further our understanding of intracellular lipid transport via membrane contact sites. He continued Tyler Cline's work on an antimicrobial peptide in collaboration with Dr. S-T. Nagle at CMU to probe how this interacts with inner membranes of bacteria. Other research projects include work on FGF and how sugars effect the activity of this protein and how this relates to tramatic brain injury and work on serotonin receptor and how conotoxin peptides influence its structure. Placement Postdoc at NIST (Curt Meuse's Lab) |
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Sharmistha Karmakar Ph.D. Indian Association for the Cultivation of Science (IACS), Kolkata, Inida (2019) Research Topics Sharmistha's worke on simulating the lipid transport mechanism within cells. Her focus was on a model protein in yeast, Osh4, and how it binds to anionic membrane models. She also focused on how this protein can simulanteouly bind to two membranes to form membrane contact sites . Placement Postdoc at Idaho National Laboratory (Integrated Energy & Storage Systems) |
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Niamh Carlin B.E./M.E. student at University College Dublin (2020-2025) Research Topics Niamh joins UMD as part of her M.E. program to gain a 12-week experience in research. She was part of a joint project with Prof. Karlsson on cell penetrating peptides (CPPs) where she modeled the CPPs with computational tools. Placement TBD (finish her M.E. at UCD in 2025) |
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Tejaswi Tammareddy Ph.D. in Chemical Engineering, UMD (December 2024) Research Topics Tejaswi used simulations to probe biotech applications with studies of nanopores for her M.S. work. Her Ph.D. research was on CDK5 with its importance to neurological diseases and specifically Alzheimer's Disease. She worked with Dr. Cardone (NIST) on investigating inhibotors of the toxic p25 cleaved product of CDK5. Placement Scientist, Computational Chemistry (SilcsBio) |
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Jieyon Min Ph.D. in Biophysics, UMD (March 2025) Research Topics Jiyeon was co-advised student with Dr. Bernie Brooks' Lab at NIH. In my lab, she focused on measuring the free energy of binding of inositol molecules to model Arg peptides and compared with ITC experiments. This led to an adjustment to the lipid force field. She also has worked on lipid nanoparticle research. In Dr. Brooks' lab her focus was on machine learning. Placement U. Copenhagen postdoc (Simon Rasmussen's lab in bioinfomatics) |