Juan Pablo Alvarado ’23


Civil and Environmental Engineering

Project Title

Biofilm Droplet

Presentation Link

View Juan Pablo's Presentation

Certificate(s): Materials Science and Engineering

As the availability of fresh water becomes increasingly scarce and unpredictable, we must understand the natural phenomena driving the availability and behavior of water in soils. Scientists have recently realized the important role of biofilms in soil water availability. However, attempts to model biofilm-soil dynamics are limited by a poor understanding of the interactions of these components at the molecular level. My project focused on creating molecular dynamics simulations to better understand the molecular interactions between biofilms and clay in aqueous systems. We hypothesized that the presence of both biofilms and clay would lead to synergistic dynamics that would have implications for water transport and retention. I learned how to create and run simulations using GROMACS, an open-source software that simulates the Newtonian equations of motion for systems with hundreds to millions of atoms, while also troubleshooting errors. Once I learned GROMACS, I primarily worked on fine-tuning my system to produce the desired raw data. After studying such a system and reading numerous papers on biofilms, this is a topic that I would like to further explore through my senior independent research.

* This internship is connected to the HMEI Water and the Environment Challenge project, “Microphysics of Water in Secondary Organic Aerosol.”

Internship Year


Project Category

Water and the Environment


Interfacial Water Group, Department of Civil and Environmental Engineering, Princeton University


Ian Bourg, Assistant Professor of Civil and Environmental Engineering and the High Meadows Environmental Institute; Avery Agles, Ph.D. candidate, Chemical and Biological Engineering