(6cl) Molecular Simulations of Interfacial Dynamics in Biological Systems

My background is in Chemical Engineering and my research expertise is in Computational Biophysics and Molecular Biology. The focus of my work is to understand the molecular interactions that govern membrane dynamics in terms of lipid-lipid and lipid-protein interactions. The need for accurate lipid composition in membrane modeling has become more apparent in recent years, especially in the context of protein-lipid interaction for cell homeostasis or molecular mechanisms of disease. During my graduate training, I used molecular dynamics simulations to study complex membranes models of eukaryotic cells and their interaction with peripheral membrane proteins. My systems were the first to model eukaryotic membranes with at least 7 lipid species at the all-atom level; these studies showed the diversity of lipid components does affect membrane properties that in turn modify membrane-protein interactions. The common topic among my graduate research projects was the study of molecular interactions at biological interfaces; however, I also explore the behavior of water-oil interfaces in the presence of small alcohols that disrupt said interface. I had the opportunity to work and publish with experienced scientists not only in the computational field, but also experimentalists both in the U.S. as well as international collaborations.

During my postdoctoral training, I am applying my expertise on cell membrane modeling to study the dynamics of assembly and membrane remodeling of viruses from the molecular point of view. I am quantifying protein-protein interactions on the surface of the plasma membrane and predicting how membrane lipids reorganize in response to those interactions. I am expanding my simulation skills to advanced techniques such as enhanced sampling and coarse-grain modeling. The rich background diversity of my current group has indeed enhanced my postdoctoral experience by giving me the opportunity to learn from experts in coarse-graining, machine learning, and the developers of enhance sampling techniques such as advanced metadynamics simulations.

Postdoctoral Projects:

1. “Multi-scale modeling of protein binding and aggregation of the matrix (MA) domain of HIV-1. Elucidating the role of lipidated tails in peripheral membrane proteins on membrane dynamics and lipid sorting.”
2. “Next-generation coarse-grain modeling of relevant biomembrane lipids. Developing models for Cholesterol and charged lipids.”

Advisor: Prof. Gregory A. Voth, Department of Chemistry, University of Chicago, Chicago, IL

PhD Dissertation:

“Computational studies of membrane models and their interaction with a peripheral protein in yeast, & disruption of the water-oil interface by a hydrotrope.”

Advisor: Prof. Jeffery B. Klauda, Chemical and Biomolecular Engineering Department, University of Maryland, College Park, MD.

Successful Proposals: Wrote and directed a proposal for XSEDE Educational Allocation. Assisted in writing and gathering preliminary results for NIH, XSEDE, and Anton/Anton2 (Pittsburgh Supercomputing Center) applications.

Research Interests:

Protein-lipid interactions are key for cell homeostasis and growth, and are involved in key steps of disease progression. Over the past ten years there has been more interest on the dynamics of peripheral membrane proteins with membrane lipids. Molecular dynamics (MD) simulations generate a trajectory based on the thermodynamics and forces that act on a given system. MD is a powerful tool to understand the behavior of a system, interpret experimental data with observations at the atomic/molecular level, and suggest or eliminate experimental targets. Increasing computational power allows us to simulate protein-membrane interactions at relevant length and time scales to understand the inner workings of a given protein and propose mechanisms of action of cellular processes.

As a faculty member I plan to lead a computational research group in molecular biophysics, promote participation of women and minorities in science, encourage interdisciplinary research stablishing strong collaborations with experimentalists, and strengthen existing connections with international scientists to develop international collaborations. The specific research topics in my lab will revolve around membrane modeling, protein-protein and protein-membrane interactions in the context of multi-scale study of liver disease, and molecular biology of onco-viruses. In the future, I would like to incorporate machine learning into the design of simulation experiments and data analysis.

Teaching Interests:

During my years at the University of Maryland as a graduate student, I worked with and mentored both high school and undergraduate students as well as served as a teaching assistant in multiple engineering classes over 4 terms. I am invested in becoming a good mentor and role model for my students; I have participated in seminars and workshops on course design and student-centered teaching. During my postdoctoral tenure, I completed the Certificate for College Teaching at the University of Chicago, for which I took classes in pedagogy, and design and taught a hands-on workshop in molecular dynamics along with a journal club geared towards incoming graduate students in the Biophysical Sciences. In particular, I would like to teach thermodynamics, statistics, introduction to chemical engineering, and design elective courses that introduce and promote computational methods in molecular biology.

Selected Publications (Citations: 683. Google h-index: 7):

1. Monje-Galvan, V.; Warburton, L; Klauda, J.B. Setting-up all-atom molecular dynamics simulations to study the interactions of peripheral membrane proteins with model lipid bilayers in Methods in Molecular Biology Series. Intracellular Lipid Transport. Guillaume Drin, Ed. Springer, (2019)
2. Leonard, A.N.; Wang, E.; Monje-Galvan, V.; Klauda, J.B. Developing and testing of lipid force fields with applications to modeling cellular membranes. Rev. DOI: 10.1021/acs.chemrev/8b00384 (2019)
3. Monje-Galvan, V.; Klauda, J.B. Preferred binding mechanism of Osh4’s amphipathic lipid-packing sensor motif, insights from molecular dynamics. Phys. Chem. B., 122(42): 9713-9723 (2018)
4. Monje-Galvan, V.; Klauda, J.B. 2016. Peripheral Membrane Proteins: Tying the Knot between Experiment and Computation. BBA: Biomembranes, 1858: 1584-1593 (2016).
5. Monje-Galvan, V.; Klauda, J.B. 2015. Modelling Yeast Organelle Membranes and How Lipid Diversity Influences Bilayer Properties. 54(45), 6852-6861 (2015).
6. Wu, E.L.; Cheng, X.; Jo, S.; Rui, H.; Song, K.C.; Davila-Contreras, E.M.; Qi, Y.; Lee, J.; Monje-Galvan, V.; Venable, R.M.; Klauda, J.B.; Im, W. CHARMM-GUI Membrane Builder toward Realistic Biological Membrane Simulations. J. Comput. Chem. 35(27), 1997-2004 (2014).