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Matysiak Lab

Biomolecular Modeling Group


Principal Investigator

Silvina Matysiak, PhD

Assistant Professor of Bioengineering
University of Maryland

Postdoctoral Fellow The University of Texas at Austin
PhD Rice University
BS Instituto Tecnologico de Buenos Aires


Photo of Silvin

Graduate Students

Sai Ganesan, MS

MS University of Washington in St. Louis
BS R.V College of Engineering, Bangalore, India


Project 1: Protein coarse grained modeling: Physics based minimalist models to explore larger biological systems and longer timescales has become increasingly popular. One of the major drawbacks of most coarse grained protein models is the absence of polarization effects and hence the inability to reproduce accurate electrostatic screening. My research is based on implementing the Drude oscillator approach to protein systems to build a polarizable coarse grained force field, that will be suitable for concurrent multiscale simulations. With this approach we will be able to capture changes  in secondary and tertiary structures of the protein.

Project 2: Characterization of antimicrobial peptides in targeting cancer cells: The difference in membrane compositions between normal and cancer cells is a crucial targeting strategy. It has been known that
Phosphatidyl serine (PS, a phospholipid) is found increasingly in the outer luminal leaflet of cancer cells as opposed to the inner cytosolic
leaflet in normal cells. A series of peptides (MAX peptides) have been designed by Dr. Joel Schneider's group (NCI) and Dr. Robert Blumenthal's group (NCI), that can disrupt liposomes with varying concentrations of PS and PC (phosphatidyl choline, another phopholipid found predominantly in the luminal leaflet of all cells). My aim is to understand the underlying physics behind the potential use of MAX peptides in anti-cancer therapy, using a combination of coarse grained and all atom simulations. This project is in collaboration with National Cancer Institute. 

Sai's photo

Hongcheng Xu

BS Nanjing Normal University, China


Project 1: Membrane protein folding: Membrane protein folding is an area not well explored experimentally because of the difficulties in crystallizing membrane proteins. On the other hand, computational methods have been developed to predict membrane structure fold but do not provide information about the driving forces behind membrane protein folding and how the presence of particular lipids can tune the emergence of different folding behavior. Also, membrane protein folding is inaccessible to atomistic molecular dynamics since ~μs simulations are needed to embrace a wider range of membrane processes. Up-to-date coarse-grained models have been used to study the insertion and self-assembly process of peptides with fixed secondary structure. Since the group's coarse-grained model can capture de novo folding, my research aim is to combine it with model membranes to explore the steps in membrane protein folding and how they can be tuned by changing the membrane composition.

Project 2: Hydrogels:  Hydrogels are water-filled 3D surfaces that are solid, responsive and programmable. My research aims at exploring how an hydrogel molecular structure affects its behavior. By using atomistic and coarse-grained simulations we are developing a multiscale model of chitosan to understand its self-assembly behavior.
Hongcheng's photo

Gregory Custer

BS University of Georgia


Project 1: Protein stability : Characterizing the delicate interplay of sequence, solvation, and thermodynamic conditions (temperature, pressure) is of fundamental importance for grasping the limits under which proteins function in the cell and for engineering new functional proteins. My research aims at exploring the relationship of sequence and fold in determining protein stability and understanding the role of solvation in controlling the thermostability of proteins.

Project 2: Micelle formation under extreme conditions : Surfactants are commonly used in a large number of industrial applications because of their remarkable ability to influence the properties of surfaces and interfaces. The goal of this research is to obtain a mechanistic description of the self-assembly of nonionic surfactants and the stability of its aggregates in a wide range of pressures and temperatures.

Undergraduate Students

Sudi Jawahery

Senior UMD



Huntington's disease (HD) is caused by the presence of an extended polyglutamine (polyQ) region at the N-terminus of the huntingtin (htt) protein. Our understanding of the molecular basis of its pathology is limited. My project consists in exploring how the interactions of polyQ peptides with membranes can control pathogenesis by using atomistic molecular dynamics simulations.
Sudi's photo

Michael McCutchen

Junior UMD



My research investigates the self-assembly of surfactants in ionic liquids to characterize its phase diagram and thermodynamic behavior.



Anu's photo
Dr. Anu Nagarajan


Postdoctoral Researcher

National Institute of Health


Matt Matthew Eckler


PhD student
University of Virginia

David photo David Peeler