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

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.

 

 

 

 

 

 

Tyler Cline

B.S/M.S. Student at University of Maryland-College Park (Chemical Engineering, 2017-)

Research Topics

Tyler studies the binding of antimicrobial peptides (AMPs) to model membranes of the inner membrane of E. coli. He collaborates with Dr. Stephanie Nagle at Carnegie Mellon University. The goal of this work is to probe the mechanism and stucture of a designed AMP.

 

 

 

 

 

 

Mahdi Ghorbani

Ph.D. Student at University of Maryland-College Park (Chemical Engineering 2017-)
B.S. University of Tehran (Chemical Engineering)

Research Topics

Mahdi is starting his research on studies to improve yeast membrane chemical tolerance in collaboration with Laura Jarboe at Iowa State University. He is also interested in lipid transport in the cell and studies of the Osh4 membrane protein.

 

 

 

 

 

 

Yalun Yu

Ph.D. Student at University of Maryland-College Park (Biophysics 2017-)
B.S. Fudan University, China (Physics)

Research Topics

Yalun is a biophysics rotation student with past experience with molecular simulation. He is currently working 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.

 

 

 

 

 

 

 

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.

 

 

 

 

 

 

 

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

Mechanical Engineering
Class of 2020

Research Topics

Linnea is stuyding an Osh4 peptide and antimicrobial peptides and how they disturb the membrane.

 

 

 

Moore

Emma Moore

Bioengineering
Class of 2020

Research Topics

Emma is studying peripherial myelin sheath and developing simulation models to probe its structure and function.

 

 

 

Hiner

Chris Hiner

Bioengineering
Class of 2019

Research Topics

Chris is styding the structural and electrostatic characters of the protein, CDK5 in collaboration with Nick Guros.

 

 

 

Moyer

Lauren Moyer

Bioengineering
Class of 2020

Research Topics

Lauren is working with Linnea on studying antimicrobial peptides and their interaction with cell membranes.

 

 

 

 

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 cellular membrane concentration profile.

 

 

 

 

Zakaria

Muhamad Zakaria

Al-Huda School in College Park

Research Topics

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