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UMD Researchers Use Simulation Tool to Observe Molecular Behavior

New approach delivers “unprecedented levels of atomistic detail.”


Robert Herschbach , 410-245-8959


From targeted drug delivery to oil extraction, engineers are finding ways to use miniscule particles, known as nanoparticles, that can interact with substances in various ways, such as causing them to adhere. Doing so requires an understanding of how the particle surfaces behave—and that can be tricky, given the submicroscopic scales involved. Often, conventional experimental methods aren’t able to deliver sufficiency precise data.

Simulation Tool

Researchers at UMD, led by associate professor of mechanical engineering Siddhartha Das, have been utilizing a simulation tool to model the behavior of individual atoms and molecules. With this approach, “we’re able to obtain unprecedented levels of atomistic detail for problems of great engineering and biomedical significance,” Das said.

The team has now published key findings in the journal Matter, a Cell Press publication. A paper appearing in the journal details how Das and the research team—which also includes Dr. Peter W. Chung, Parth Rakesh Desai, Sai Ankit Etha, Turash Haque Pial, Harnoor Singh Sachar, and Yanbin Wang—were able to employ molecular dynamics to simulate, with unprecedented atomistic detail, the behavior of long, charged molecules (often known as polyelectrolytes or PEs) when they are attached to surfaces and attain configurations that resemble the bristles of our toothbrushes.

Such architectures are known as PE brushes. “What PE brushes do is modify the properties of the surfaces in order to create the desired interactions. This is called ‘functionalizing the surfaces,’” Das said.

Such ‘functionalization’ is used to attribute a variety of capabilities to surfaces, such as nanochannel walls or nanoparticle surfaces, for applications ranging from sensing and rectification to drug delivery and oil recovery.

“This is one of the earliest studies to probe the intriguing behavior of PE brushes with such a remarkable level of atomistic resolution,” Das said. “It allows us to provide an unprecedented description of the ions and water molecules with atomistic resolution: this enables a better understanding of the behavior of the PE brushes, which in turn will help us to significantly improve the different applications where the PE-brush-grafted surfaces are employed.”

Their work has broad relevance to scientists seeking to manipulate various kinds of surfaces and particles so they can be used for different purposes—for example, water harvesting, in which rain and moisture is collected for human use, or in recovering oil from tiny niches inside rocks. Scientists developing treatments for cancer also seek to manipulate the surfaces of submicroscopic particles in order to use them in identifying sick cells.

Through running their simulations, the team observed two specific phenomena: an “ultraconfinement effect,” leading to changes in distribution, structure, and properties, and a water-in-salt-like scenario, in which water molecules become replaced by molecules from the brushes.

Das wrote the paper together with Sachar, a PhD student in the mechanical engineering department. Sachar and fellow doctoral student Pial ran the simulations, while the data was analyzed by PhD students Desai, Etha, and Wang, and by Chung, an associate professor of mechanical engineering. The Deepthought2 High-Performance Computing cluster provided computational support.

Their work was supported by a grant from the U.S. Department of Energy. The paper will be published on Volume 2, Issue 6 of the journal, with a publication date of June 3, and is currently available online at


Mechanical Engineering Research

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A. James Clark School of Engineering

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