Project Info

Molecular Simulations of Bacterial Microcompartment Proteins

Alex Pak

Project Goals and Description:

This research project aims to use molecular dynamics (MD) simulations to study the self-assembly of or metabolite permeation through bacterial shell proteins. The focus of this study is on bacterial microcompartments (BMCs), which are membrane-less organelles formed through self-assembly that consist of enclosed enzymes surrounded by a protein shell. Prokaryotic cells utilize BMCs for a range of metabolic processes, including carbon fixation, propanediol utilization, and ethanolamine utilization. As naturally occurring analogues, BMCs are intriguing platforms to study physical principles that can be adapted for bottom-up design of catalytic bionanoreactors, which have applications in bioremediation, water treatment, chemical fuel production, and medicine. The goal of this study is to understand how BMC shell proteins differentiate shell morphology or substrate permeation and to explore how modification of these proteins may manipulate BMC properties.

More Information:

Grand Challenge: Develop carbon sequestration methods.
  1. Li et al., “Computational and experimental approaches to controlling bacterial microcompartment assembly,” ACS Cent. Sci., 2021, 7, 658-70.
  2. Mahinthichaichan et al., “Selective permeability of carboxysome shell pores to anionic molecules,” Phys. Chem. B, 2018, 122, 9110-8.

Primary Contacts:

Pak, Alex,  

Student Preparation


The student should have prior knowledge on thermodynamics and molecular biology from formal coursework or self-study. The student should be highly motivated to learn and to develop new skills. Prior experience with programming (Python or C++) or Linux is beneficial but not required.




  • Molecular dynamics simulations
  • Enhanced sampling techniques
  • High-performance computing
  • Dimensional reduction
  • Workflow management (Git, Lab notebooks, etc.)
  • Coding: Python and Bash
  • Literature review
  • Oral/written communication (e.g. presentations and manuscripts)


The student will give brief updates over Slack once a week and have an extended meeting (joint with other group members in the same research area) with the PI every two weeks. The student will also participate in regular biweekly group meetings. The group members and PI will be accessible both in-person and via Slack.


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