PhD-project 3b: Nucleobase-driven synthetic self-replication: computational modelling
PhD student: Mark van der Klok
Supervisors: Onck / Otto
The aim of this project is to assist the development of new nucleobase-containing self-replicators, by computationally studying their structure, nucleobase accessibility and self-assembly. By performing a detailed analysis we try to understand the underlying mechanisms and interactions and to correlate simulation readouts with replication propensity.
We use molecular dynamics simulations to study the self-replicators, their fiber structure and their self-assembly process. To study fiber structures at shorter length scales, we use simulations at the atomistic scale. Additionally, we work on larger-scale simulations using our newly-developed 4-bead-per-aminoacid (4BPA) coarse-grained force field.