Laboratory of Molecular & Thermodynamic Modeling

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Alumni of the Research Group


High School Students

 

Allen Cheng

Poolesville High School in the Science, Math, and Computer Science magnet program (June 2011)

Research Topics

First, worked on develping a GUI-based program for obtaining gas hydrate phase diagrams with the Klauda/Sandler fugacity-based model. Then, studied asphaletene aggregation with model compounds.

Placement

B.S. UMD (Materials Science and Engineering)

Josh Nichols

Eleanor Roosevelt High School in the Science and Technology (S/T) program (June 2013)

Research Topics

Investigated the accuracy of the CHARMM36 lipid force field as a funciton of temperture for PC lipids.

Placement

B.S. UMD (Chemical and Biomolecular Engineering)

Michael Lu

Eleanor Roosevelt High School in the Science and Technology (S/T) program (June 2014)

Research Topics

Investigated the accuracy of the CHARMM36 lipid force field for a ceramide lipid.

Placement

B.S. UMD (Undecided Engineering)

Ou

Anna Ou

Montgomery Blair High School, Silver Spring, MD
Science, Math, Computer Science Magnet Program
(May 2014-June 2016)

Research Topics

Anna focused on MD simulations of PUFA lipids (18:2 and 18:3 chains) with modeling of soybean plasma membranes.

Placement

B.S. UC-Berekely (Molecular Biology-Premed)

 

 

 

 

Marsandi

Michelle Marsandi

Eleanor Roosevelt High School in the Science and Technology (S/T) program (Fall 2016-Spring 2017)

Research Topics

Michelle focused on chemical stress on bacterial membranes.

Placement

UMD

 

 

Selvadoss

Andrew Selvadoss

Poolesville High School in the Science, Mathematics, and Computer Science magnet program (June 2018)

Research Topics

Andrew studied the effects of ethanol and a dual bilayer setup to mimic the cellular membrane concentration profile.

Placement

TBD

Boughter

Muhamad Zakaria

Al-Huda School in College Park, MD
(May 2017-May 2018)

Research Topics

Muhamad probed the effects of octanoic acid on model E. coli membranes to better understand bacterial tolerance to chemical production..

Placement

B.S. UC-Berekely (Molecular Biology-Premed)

 


Undergraduate Students

 

Glenn Guglietta

B.S. Chemical Engineering, UMD (2009)

Research Topics

Initial studies on H2 storage in Gas Hydrates.

Placement

Ph.D. program at Drexel University.

 

Joseph Lim

B.S. Chemical Engineering & Biochemistry, UMD (2010)
Sc.D. Chemical Engineering & MIT (2015)

Research Topics

Simulation studies of model yeast and Chyladmida membranes. MD simulations of the peripherial membranes protein Osh4.

Awards: UMD Bioscience Day (2008) best poster (Biochem/Biophys) and HHMI Undergrad Fellowship (2009-2010)

Placement

Ph.D. program at MIT. (NSF Graduate Fellow in ChemE, graduated)
Current: Yale Medical School

 

Joseph O'Connor

B.S. Chemical Engineering, UMD (2010)

Research Topics

Simulation studies DMPC/cholesterol bilayer with a majority of cholesterol. Interactions of AQP0 with these model membranes.

Placement

TBD

 

Arpan A. Bandyopadhyay

B.S. Chemical Engineering, IIT-Bombay (2012)

Research Topics

Thermodynamic modeling of gas hydrates in electrolyte solutions.

Placement

Ph.D. program at the University of Minnesota.

 

Ivy Muregi

B.S. Chemical Engineering, UMD (2012)

Research Topics

Studies of model asphaletene aggregration in water and organic solvents.

Placement

Consultanting engineer at Accenture

 

Diana Villanueva

B.S. Chemical Engineering, UMD (2013)

Research Topics

Diana aided in force field development and interesting studies of oxidized lipids. She has tested a new united atom chain model for the CHARMM lipid force field. However, her main project was studies of oxidized lipid models and how these influence bilayer properties. Her research has indicated how the oxidized lipids can alter the stability of lipid membranes.

Award: Travel award to the ACC "Meeting of Minds" Research Conference (2011)

Placement

GSK (Rockville, MD) as a Biopharmaceutical Manufacturing Engineer

 

Robert Pullen

B.S. Chemical Engineering, UMD (2013)

Research Topics

Rob began simulations of lipid bilayers and the influence of their stability with ethanol. The applications to this are for studying the effects of byproducts of biofuels production.

Placement

Ph.D. Program at the University of Tennessee (Knoxville)

Generic

Alan Tran

B.S. Chemistry, UMD (May 2014)

Research Topics

Alan's research ocused on aiding in the development of a new united atom chain model for the CHARMM lipid force field.

Placement

Graduate Studies at UMD and working as a pharmacy technician

Weglein

David Weglein

B.S. Chemical Engineering, UMD (May 2014)

Research Topics

David research involved simulation studies of a bilayer DOPC for future studies of peptide binding.

Placement

TBD

Daristotle

John Daristotle

B.S. Chemical Engineering, UMD (May 2014)

Research Topics

John's reserach involved studies of ethanol and its interaction with model membranes. His focus was on how ethanol influence structural and dynamical properties of POPE bilayers. Ultimate interest in this work is the effect of toxic products/byproducts to cell membrane during biofuels production.

Placement

Ph.D. Bioengineering at UMD

Generic

Sarah Lee

B.S. Chemistry, UMD (May 2014)

Research Topics

Sarah's research initially focused on aiding in the development of a new united atom chain model for the CHARMM lipid force field. This has resulted in faster simulations for systems that do not require the all-atom detail for the acyl-lipid chain. She also studied peptide binding of the ALPS-like motif to membranes under the advisement of Viviana.

Placement

University of Maryland Easter Shore School of Pharmacy (Pharm.D.)

Allsopp

Matthew Allsopp

B.S. Chemical Engineering, UMD (May 2014)

Research Topics

Matthew's interest lied in the self-assembly of amphillic molecules. He probed the ability of the CHARMM-UA force field to describe surfactant self-assembly. He also started work on MD simulations of potential pore-forming lipids.

Placement

M.Eng. Georgia Tech.
Current: Sumitomo Bakelite High Performance Plastics

Makeover

Judah Makover

B.S. Chemical Engineering, UMD (Anticipated May 2015)

Research Topics

Judah studied the thermodynamic properties of model lipid bilayers and the accuracy of the CHARMM36 force field to predict the temperature dependence of these properties.

Placement

Israeli Army

Ndubuisi (Ben) Harbor

B.S. Chemical Engineering, UMD (May 2014)

Research Topics

Ben's research involved studies of ethanol and its interaction with model membranes. His focus has been on how ethanol influence structural and dynamical properties of POPC bilayers. Ultimate applications lie in the areas of biofuels and anesthetics.

Placement

University of Toronto (Master's program)

 

Mengesteab Adera

B.S. Chemical Engineering, UMD (May 2014)

Research Topics

Mengesteab's research has involved studies of a polarizable water model for use in biological and gas hydrate applications. The goal is to have an accurate but efficient water model.

Placement

Schreiber Foods (Production Supervisor)

 

Boughter

Chris Boughter

B.S. Physics, UMD (May 2015)

Research Topics

Chris' initial interest was in alternate energy and alternate energy sources. This resulted in a project of studying a new class of molecules that form quasi-micelles in collaboration with Dr. Anisimov (UMD/IPST). He switched interest to biophysics and studied the influence of cholesterol on lipid bilayer properties of different lipid headgroup and chain types.

Placement

University of Chicago (Ph.D. Biophysics Program)

Hebert

Jacob Hebert

B.S. Chemical Engineering, UMD (May 2015)

Research Topics

Jacob worked on studies on the temperature dependence of the surface tension of alkane/water interfaces. He also studied the effect of side chains to a model for asphalatenes on aggregation.

Placement

Northeastern University (Ph.D. ChemE Program)

Wong

Sook Wong

B.S. Chemical Engineering, UMD (May 2014)

Research Topics

Sook's research focused on a sugar binding domain of a a bacterial protein that is known to enzymatically attack polysaccharides of its host. She is studying the pH binding dependence of binding of HA to this protein.

Placement

ORISE Research Fellow (FDA)

Konas

Ryan Konas

B.S. Chemical Engineering, UMD (May 2015)

Research Topics

Ryan's research involved studies of ethanol and its interaction with model membranes. His focus was on how ethanol influence structural and dynamical properties of POPE, POPC, POPS and mixed bilayers. Ultimate interest in this work is the effect of toxic products/byproducts to cell membrane during production of biofuels and chemicals for single-celled organisms.

Placement

Job Searching

 

Condon

Josh Condon

B.S. Chemical Engineering, UMD (May 2015)

Research Topics

Sook's research focused on a sugar binding domain of a a bacterial protein that is known to enzymatically attack polysaccharides of its host. She is studying the pH binding dependence of binding of poly-Gluc to this protein.

Placement

Ph.D. program at the University of Delware (Chemical Engineering)

 

Welch

Connor Welch

B.S. Chemical Engineering, UMD (May 2016)

Research Topics

Connor's research involved studies of gas hydrate formation using a newly developed polarizable water model. However, his main focus was in testing the formation of gel and ripple phase lipid bilayers and worked with Pouyan on the phase diagram of these lipid bilayer structures.

Placement

Deloitte Consulting (Business Technology Analyst)

Bacarisas

Francis Bacarisas

B.S. Bioengineering (May 2016)
Class of 2016

Research Topics

Francis tested our newly developed sphingo/ceramide all-atom parameter set. His specific interest was testing ceramide lipid bilayers and mixtures with PC lipids.

Placement

Consulting Firm Job

Ponte

Rui Ponte

B.S. Chemical Engineering and Computer Science (May 2017)
Class of 2017

Research Topics

Rui was involved in testing our CHARMM36UA model for various lipids to verify its accuracy and futher use for more complex lipid membrane models.

Placement

Tetracore, Inc.

Clark

Tylar Clark

B.S. Chemistry (May 2018)
Class of 2018

Research Topics

Tylar was involved in testing the polarizable Drude force field for lipids in CHARMM.

Placement

Johns Hopkins University (Ph.D. Student in Physical Chemistry)

Mark Adams

B.S. Chemical Engineering (May 2016)

Research Topics

Mark is involved in testing our CHARMM36UA model for various lipids to verify its accuracy and futher use for more complex lipid membrane models. He also developed models for the ocular lens.

Placement

Stryker Communications(Integration Specialist)

Kang

Hojin Kang

B.S. Computer Science (December 2016)

Research Topics

Hojin tested the accuracy of the CHARMM36 lipid force field for POPG lipid bilayers. She also worked on testing sphingo lipid bilayers mixed with cholesterol. These studies were important with our development of model membranes of the nerve and ocular lens. She also was involved in developing and eductional website for high school and early undergraduates in the general area of molecular biology.

Placement

Facebook (Seattle, WA)

Kang

Lidiya Gavrilenko

B.S. Chemical Engineering (May 2016)

Research Topics

Lidiya continued work by others in the lab on asphalatene aggregration. She studied important functional groups and how these effect aggregration kinetics and structure.

Placement

Federal Aviation Administration (as a general engineer) working for NextGen

Khan

Yusuf Khan

B.S. Chemical Engineering (May 2017)

Research Topics

Yusuf worked on simulation of ceramide bilayers with different hydroxylations to study the effects on bilayer properties.

Placement

Vici Health Sciences

Chu

Monica Chu

B.S. Bioengineering (May 2018)

Research Topics

Monica was involved in understanding how certain antiobotics interact and potentially partition within cell membranes.

Placement

TBD

Wildermuth

Ky Wildermuth

B.S. Chemial Engineering with Minor in Physics (May 2017)

Research Topics

Ky was involved in running HMMM MD simulations on the ALPS-like peptide of the Osh4 protein of yeast. The focus here is to enhance timescales of binding to membranes. He also developed a code for quantifying lipid packing defects.

Placement

Planisware USA, Inc.

Fobe

Lenny Fobe

B.S. Chemial Engineering and Chemistry (May 2018)

Research Topics

Lenny was working on two projects involving lipid membranes. His initial project studied the effect of pH buffers on lipid bilayer properties. His second project involved the study of pores forming in ceramide bilayers with applicaitons to skin delivery of drugs.

Placement

U. of Colorado-Boulder (Ph.D. Student in Chemical Engineering)

Mesfin

Nebeyu Mesfin

B.S. Chemial Engineering (expected, May 2019)

Research Topics

Nebeyu studied model membranes of E. coli and how mutations in the membrane composition influence membrane properties. The focus was on understnading how to tune the membrane to be toleratant to fuels/chemicals produced by this bacteria.

Placement

TBD

Mesfin

Emma Moore

B.S. Bioengineering (expected, May 2020)

Research Topics

Emma studyied the peripherial myelin sheath and developed simulation models to probe its structure and function.

Placement

TBD

Graduate Students

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.