Coacervate droplets are considered a plausible model for protocells due to their spontaneous formation and ability to compartmentalize macromolecules such as nucleic acid and peptides. Although experimental studies have observed and synthesized coacervates under different laboratory conditions, little is known about their structure. Here we present atomistic molecular dynamic simulations of the interactions between water and oppositely charged proteins that cluster together in a salt-dependent process. Observing such liquid-liquid phase separation on an atomic level would serve as a model for the initial stages of complex coacervate formation. Molecular Dynamics was used to compute diagnostics of the structure at different NaCl concentrations. Limitation of this study are the time constraint and cell size. Modelling coacervate formation is not only important to the origins of life research, but it would also deepen our understanding of membraneless organelles, their role in diseases, and many other fields such as material sciences.
How did you choose your research topic and/or design your research question? (200 words)
During my research fellowship at the Harvard Origins of Life Initiative last summer, I investigated the syntheses of organic compounds from inorganic matters using photochemical pathways. I became curious about the next step for life to arise: without some type of compartmentalization, these newly synthesized organic compound would not have been able to reach sufficiently high concentrations in the water bodies to maintain chemical reactions necessary for the formation of complex pathways in biological systems. I decided to propose my own thesis project and started looking for potential supervisors across all science departments at Western. After finding a suitable supervisor, I gained permission from my course professor and Biophysics Department Undergraduate Chair to work with the Chemistry department for this project.
My supervisor Dr. Styliani Consta is an expert of chemistry in small volumes, from droplets to biological cells. Given her expertise, I proposed a project studying coacervate droplet formation as a model for the earliest form of cellular compartmentalization. My background in Biophysics and Biochemistry both greatly contributed to my understanding of the topic, system design for computer simulations, and ability to analyze and display our results in a simple, visually pleasing way.
How did you find library/archives services and resources for your research topic? (200 words)
As part of the course lectures, we had a librarian who taught us information searching skills on OMNI catalogue and other commonly used databases, and search strategies such as keyword searches using Boolean Operators. I identified keywords relevant to my project and gathered synonyms:
- keywords: polyelectrolyte, coacervate droplets, computational statistical mechanics
- Advanced final search (sample): ("polyelectrolyte*"[All Fields] OR "macromolecule*"[All Fields] OR (("amino"[All Fields] OR "aminos"[All Fields]) AND "acid*"[All Fields]) OR "peptide*"[All Fields]) AND ((("coacervate"[All Fields] OR "coacervated"[All Fields] OR "coacervates"[All Fields]...)
This strategy provided me with highly relevant results and saved a lot of time during literature review.
I learnt how to critically evaluate the credibility of different journals by their impact factors, checking authors' h-index and article metrics before using it as a reference. I mainly used Google Scholar and Web of Science to find these information. I also kept the limitations of these metrics in mind during my searches, especially because there is still limited research on this topic.
I was also introduced to Mendeley and Zotero for citations; Mendeley was very helpful as I did not have to worry about the order of in-text citation and the references being affected during the final writing and editing process.
What library/archives services and resources did you use to perform your research? (200 words)
Since I had to learn about the basis of soft condensed matter physics from scratch to aid my research project, I looked up the location of some textbooks in Taylor Library and went there. A librarian kindly showed me how to find these books and I browsed through all the section over the course of a few days and checked out two books: "Soft Matter Physics" by Mohamed Daoud and "Soft Condensed Matter" by Richard Jones. I read through the first book cover-to-cover and used the second book as a reference for mathematical details, which both deepened my understanding on the topic.
During literature review I like to look up the original articles referenced by other papers, so Western Libraries' online catalogs became my go-to source of access. This research topic has publications that spans over a century, and understanding its history is essential for justifying the reason and importance of re-visiting the topic using modern computing power and experimental techniques. In some cases, the article/book I was looking for is unavailable through Western Libraries, I would then use my access through Harvard Library, and the combination of both provided me with almost all the background informations I need.
"On the Origins of Life — Modelling the Initial Stages of Complex Coacervate Droplet Formation,"
Western Libraries Undergraduate Research Awards (WLURAs): Vol. 2023, Article 5.
Available at: https://ir.lib.uwo.ca/wlura/vol2023/iss1/5