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Matysiak Lab

Biomolecular Modeling Group


Principal Investigator

Silvina Matysiak, PhD

Associate 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

Abhilash Sahoo

BS/MS Physics, Indian Institute of Science Education and Research,  India


Project: Peptide aggregation

Aggregation of mis-folded proteins on cellular membranes into highly structured forms (amyloid fibrils) is observed in several neurodegenerative diseases like Alzheimer's, Parkinson's and Huntington's. However, the physicochemical forces leading to protein aggregation, specifically the protein-protein and protein-membrane interactions are yet to be fully understood. The multi-step pathway of protein polymerization into aggregates goes through several ephemeral oligomeric structures. The transient nature of these oligomeric intermediates makes experimental characterization extremely difficult. On the other hand, computational studies can provide detailed mechanistic insights about protein aggregation pathway's intermediate structures that are not accessible to wet-lab experiments. My research aims to capture the aggregation behavior of aberrant peptide sequences and it's dependence on environmental conditions through coarse grained molecular dynamics simulations.

Abhilash's photo

Peiyin Lee

BS Specialized Chemistry, University of Illinois at Urbana Champaign


Project : Protein Stability in Ionic Liquids
Modification of solvent environment can be used to improve protein stability. The effects of ionic liquids on proteins have drawn great research interests because of their advantages of high chemical and thermal stability, negligible vapor pressure, and high ionic conductivity. My research focuses on understanding protein stability in ionic liquids from different hydrogen bonding abilities and hydrophobicity with molecular dynamics simulation. With the cooperation with experimental side and the examination of polypeptides having progressively increasing complexity, my aim is to extend time window of protein stability and increase retention of protein activity after extended storage in ionic liquids based on molecular insights that are obtained from the simulation results. 

Peiyin's photo

Riya Samanta

BS/MS Physics, Indian Institute of Science Education and Research,  India


Project: Protein allostery
Protein allostery, also called action at distance where the signal from one site is transmitted to a second, distal site, to alter protein function is a fundamental process in biological systems. How does the information traverses between two faraway sites in a monoallosteric protein? I am currently working on BirA allostery and effects of point mutations in its activity, and applying network science concepts combined with an ensemble view of protein allostery to address this query. Improving the understanding on of the molecular mechanism of allostery, a regulatory mechanism used in very known biological processs will have impact in drug development.

Riya's photo

Suhas Gotla


Project: Chitosan Hydrogels

Chitosan is a carbohydrate polymer derived from chitin, the primary component of fungal cell walls and insect exoskeletons, that forms interconnected hydrogel networks. These chitosan hydrogels are biocompatible and display a range of mechanical properties in different environmental conditions that make suitable for use in biofabrication, tissue engineering, and other biomedical applications. However, it is unclear how surfactants, ionic strength, and other environmental factors elicit different hydrogel properties. The aim of my research is to facilitate the development of novel chitosan-based materials by harnessing the capabilities of coarse grained molecular dynamics to explore the molecular mechanisms that underlie differential hydrogel behavior.

Suhas photo

Undergraduate Students

Neel Sanghvi



Dr. Anu Nagarajan        current position: Schrodinger


Dr. Sai Ganesan             current position: UCSF

Dr. Gregory Custer        current position: Air Force

Dr. Hongcheng Xu         current position: Google


Mariam Adwan

Christopher Look

Mattew Eckler                  current position: IBM

David Peeler                    current position: University of Washington

Michael McCutchen       current position: W.L. Gore

Sudi Jawahery                current position: University of California, Berkeley

Anastasiya Belyaeva     current position: MIT