Laboratory of Molecular & Thermodynamic Modeling

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Group Members


Interested in working in the lab?

For new graduate students, please go to the New Projects section. Otherwise please contact Dr. Jeff Klauda at (301) 405-1320 or jbklauda@umd.edu for information on available positions.

Postdocs

Indrani Bera

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 has also been testing the use of this software with the CHARMM36 lipid force field. She has also been involved with running MARTINI simulations of Plexin dimerization. Her current work is on secondary active transporters (uniporters) and predicting structural changes.

 

 

Michael Kio

Ph.D. Cranfield University, United Kingdom (2015)
Aerospace Research (Computational Fluid Dynamics)

Research Topics

Mike's research focuses on nanoparticle interaction with lipid bilayers for studies of drug delivery

 

 

Graduate Students

Viviana Monje-Galvan

Ph.D. Student at University of Maryland-College Park (Chemical Engineering, 2014-)
M.S. Student at University of Maryland-College Park (Chemical Engineering, 2014)
B.S. University of Maryland-College Park (Chemical Engineering, 2012)

Research Topics

Viviana's began her research in my lab as an undergraduate and is continuing research as a Master's student. As an undergraduate, she aided in testing a new lipid force field for polyunsaturted fatty acid (PUFA) chains. She is currently begining research on yeast membrane models of the plasma membrane and endoplasmic reticulum. These will be used in future studies of an important lipid transport protein, Osh4.

 

 

 

 

 

Pouyan Khakbaz

Ph.D. Student at University of Maryland-College Park (Chemical Engineering, 2013-)
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 at UMD involves studies of secondary active transporters (SATs), such as, lactose permease and Mhp1. He is testing a new method developed in Dr. Klauda's lab to enchance conformational sampling of these SAT proteins.

 

 

 

 

 

Nick Guros

Ph.D. Student at University of Maryland-College Park (Chemical Engineering 2015-)
B.S. Cornell University (Chemical Engineering)

Research Topics

Modeling of hemolysin for applications to biosensing. Nick is co-advised by Arvind Balijepalli from NIST. The focus of Nick's reserach is to use all-atom molecular simulations of the hemolysin pore with various analytes. These simulations will aid in more coarse-grained modeling with a Brownian Dynamics model to study a wide range of analytes.

 

 

 

 

 

 

Allison Leonard

Ph.D. Student at University of Maryland-College Park (Biophysics, 2015-)
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 is researching the energetics of beryllium binding to phosphoserine in lipid bilayers, and the effects of ether linkages on bilayer properties. Dr. Sergei Sukharev is co-advising her work on Beryllium. Previously, she did theoretical research in non-equilibrium quantum work distributions.

 

 

 

 

 

 

 

Undergraduate Students

Wildermuth

Ky Wildermuth

Chemical Engineering and minor in Physics
Class of 2017

Research Topics

Ky is 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 is also involved in code development for quantifying lipid packing defects and website development.

 

 

 

 

 

 

 

Chu

Monica Chu

Bioengineering
Class of 2018

Research Topics

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

 

 

 

 

 

Gavrilenko

Lenny Fobe

Chemical Engineering
Class of 2018

Research Topics

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

 

 

 

 

Mesfin

Nebeyu Mesfin

Chemical Engineering
Class of 2019

Research Topics

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

 

 

 

 

 

 

Wang

Eric Wang

Bioengineering
Class of 2019

Research Topics

Eric is studying the effect of cholesterol added to sphingomyelin membranes in comparison with experiment.

 

 

 

 

 

 

Wang

Kirellos N. Abou Elsaad

Chemical Enginering
Class of 2018

Research Topics

Kirellos is studying formation and growth of cyclohexane/benzene/methane hydrates with molecular simulations.

 

 

 

Warburton

Linnea Warburton

Bioengineering
Class of 2020

Research Topics

Linnea is stuyding antimicrobial peptides and how they disturb the membrane.

 

 

 

 

High School Students

Selvadoss

Andrew Selvadoss

Poolesville High School in the Science, Mathematics, and Computer Science magnet program

Research Topics

Andrew is studying the effects of ethanol and a dual bilayer setup to mimic the celluar membrane concentration profile.