This short-term research project aims to initiate a collaboration between Taiwan and countries from SouthEast Asia on the study of Molecular Life Science. The study essentially addresses processes concerning the maintenance of genetic integrity and diversity by considering complicated interplay between biomolecules (e.g., protein and DNA). These processes include “homologous recombination”, “site-specific recombination” and so forth.

Homologous recombination (HR) accounts for new recombinations of DNA sequences in the repair of DNA breaks, crosslinks and collapsed replication forks; they are carried out through homology search. Site-specific recombination (SSR), on the other hand, occurs between DNA with no extensive homology at special sites; it is carried out via strand exchange between segments. Both of these two processes play a key role in generating genetic diversity from bacteria to humans. Although there are currently many crystal structures and EM structures of their multiple assemblies available, the detailed step-by-step process is still not clear.

In this project, we plan to develop a simulation protocol for studying these processes using state-of-the-art molecular dynamics simulation techniques. The mentee will be learning to use the coarse-grained force field, Associative-memory, Water-mediated, Structure and Energy Model (AWSEM), and related computation tools to build complex protein-DNA assemblies and simulate their dynamics to full molecular details. To initiate the project, the mentee will be invited to visit Tamkang University in Taiwan for up to 3~6 months.