Laboratory of Molecular & Thermodynamic Modeling

umd logo

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

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

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.

 

 

 

Unger

Leonard Unger

Mathematics and Music Performance
Class of 2021

Research Topics

Leonard is studying the plasma membrane of the Lyme Bacteria. His initial focus is modeling the unique glycolipids in this bacteria and then will focus on accurate membrane models.

 

 

 

Correa

Juan Correa

Chemical Engineering with Minor in Sustainability
Class of 2021

Research Topics

Juan is simulating the formation of hydrates for potential separation of cyclohexane and benzene. His second project will be the study of hydrates as a tool for carbon sequesterization.

 

 

 

Razi

Niayesh Razi

Chemistry
Class of 2021

Research Topics

Niayesh is running simulations of lipid bilayers and their interaction with drugs. The focus is on antibiotics and how these partition into model lipid membranes.

 

 

 

Harron

Marc Harron

Chemical Engineering
Class of 2020

Research Topics

Marc is simulating the effects of chemicals produced by microbes and how the lipid membrane can be tunned to improve its tolerance to value-added chemicals produced by these microbes.

 

 

 

 

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.