Research in the Baker Lab

Overview of the group

First and foremost, the Baker lab is committed to training the next generation of scientists. The lab works closely with undergraduate students, giving them the opportunity to learn about and contribute to the lab's research. Undergraduate students drive the lab's research forward, and present on their work at local, regional, and national meetings. They also have an opportunity to become part of interdisciplinary projects with our broad range of national and international collaborators.

Importantly, no prior experience with research or computation is necessary!!! We are always looking for interested students as early as your first year as an undergraduate at TCNJ! So please reach out and say hello in-person or via email!

Research in the Baker Lab lies at the interface of physical chemistry, biochemistry, biology, physics, and computer science. The lab focuses on the development and application of computational methods to study the structure, dynamics, and function of complex biomolecular systems. We are particularly interested in protein filaments called pili, which are hair-like filaments that bacteria and archaea use to move around and adhere to surfaces. In many microorganisms, pili are also essential for pathogenesis, the process by which bacteria cause disease. We also investigate the properties of ionic liquids and the influence that they have on protein and biomembrane structure and dynamics.

The Baker Lab uses a variety of computational methods, including all-atom and coarse-grained molecular dynamics simulations, statistical mechanics, and machine learning, to study these systems. Our work has important implications for the development of new and more effective ways to prevent and treat bacterial infections, for example by  developing new drugs or therapies that target and prevent bacteria from adhering to surfaces and causing infections. The fundamental understanding of biomolecular systems that we obtain can also guide us in the design of novel bioinspired materials.

What will students learn?

Undergraduate students who work in the Baker Lab will learn a variety of skills, including:

• Molecular biology and biochemistry: Students will learn about the structure and function of biological molecules, such as proteins, DNA, and RNA. They will also learn how biomolecular structure and function are related to important biological processes at the molecular scale.

• Computational chemistry and physics: Students will learn about the fundamental principles of chemistry and physics that underlie molecular simulations. They will also learn about the various computational methods that are used to simulate biological systems.

• Computer science and programming: Students will learn about the computer science and programming skills that are necessary to develop and run molecular simulations and AI/ML algorithms applied to biomolecular problems. They will also learn about how to use High Performance Computing resources to run large-scale simulations. They will do this on our very own supercomputer at TCNJ, the Electronic Laboratory for Science and Analysis (ELSA)!

• Data analysis and visualization: Students will learn how to analyze and visualize the data that is generated by molecular simulations and AI/ML algorithms. They will also learn how to communicate their findings to other scientists and the public.

In addition to these specific skills, students who work in the Baker Lab will also develop a number of transferable skills, such as problem-solving, critical thinking, and teamwork. They will also learn about the scientific process and how to conduct research!