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 currently focuses 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. Her future work will involve research on membrane-associated proteins and lipid peroxidation.

 

 

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.

 

 

 

 

 

Xiaohong Zhuang

Ph.D. Student at University of Maryland-College Park (Chemical Engineering, 2013-)
B.S. The City College of New York (Chemical Engineering, 2012)

Research Topics

Xiao recently joined the lab and will be focusing on studies of secondary active transporters (SATs) and their interactions with the membrane.

 

 

 

 

 

 

Rehan Choudhary

M.S. Student at University of Maryland-College Park (Chemical Engineering, 2013-)
B.S. University of Maryland (Chemical Engineering)

Research Topics

Incorporting activity coefficient models into modeling enviromental spills.

 

 

 

 

 

 

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

Mark Adams

Chemical Engineering
Class of 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.

Kang<

Hojin Kang

Computer Science
Class of 2016 (Winter)

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 currently is involved in developing and eductional website for high school and early undergraduates in the general area of molecular biology.

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

Lidiya Gavrilenko

Chemical Engineering
Class of 2016

Research Topics

Lidiya will be continuing work by others in the lab on asphalatene aggregration. Her focus will be to look at important functional groups and how these affect aggregration kinetics and structure.

 

 

 

 

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.

 

 

 

 

Khan

Yusuf Khan

Chemical Engineering
Class of 2017

Research Topics

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

 

 

 

 

 

 

 

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.

 

 

 

 

 

 

 

High School Students

Wang

Michelle Marsandi

Eleanor Roosevelt High School
Science and Technology Program

Research Topics

Michelle 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.