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 local, 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 several distinct but equally important complex biomolecular systems:

• Bacterial Pili: We study how these hair-like protein-based filaments used by bacteria and archaea to move, adhere to surfaces, drive pathogenesis, and facilitate the transport of DNA.

• Barnacle Proteins: We investigate the molecular mechanics behind robust underwater bioadhesion.

• The Dark Kinome: We are exploring a vast, understudied family of kinase proteins that hold immense potential for uncovering new biological pathways.

• Ionic Liquids: We investigate their unique properties and the influence they have on protein and biomembrane structure and dynamics.

Alongside these core areas, we actively pursue a variety of exciting side projects driven by student curiosity and new interdisciplinary collaborations.

The Baker Lab uses a variety of computational methods, including all-atom and coarse-grained molecular dynamics simulations, statistical mechanics, and machine learning/AI methods, to study these systems. Our work has broad implications across multiple fields. For example, the fundamental understanding we gain from these molecular systems can guide the design of novel bioinspired materials, such as next-generation synthetic adhesives, as well as aid in the development of new therapeutics that prevent bacterial infections or target novel pathways within the dark kinome.

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!