Ben Shirt‐Ediss

Modelling the prebiotic origins of regulation & agency in evolving protocell ecologies

This paper introduces a simulation platform to model how regulation and agency emerge in protocell ecologies under prebiotic conditions.

Optimizing DNA origami assembly through selection of scaffold sequences that minimise off-target interactions

This paper develops a computational method to select DNA origami scaffold sequences that minimize off-target interactions, validated through AFM and optical tweezers experiments.

Light-up split Broccoli aptamer as a versatile tool for RNA assembly monitoring in cell-free TX-TL system, hybrid RNA/DNA origami tagging and DNA biosensing

Reverse Engineering DNA Origami Nanostructure Designs from Raw Scaffold and Staple Sequence Lists

This paper introduces an algorithm to convert raw DNA origami sequences back into schematic designs, enabling easier modification and reuse of existing nanostructures.

Co-transcriptional folding of a bio-orthogonal fluorescent scaffolded RNA origami

This paper demonstrates the in vitro synthesis of scaffolded RNA origami using a single-pot transcription reaction and validates its structure through imaging and simulation.

The PCR Simulator: an on-line application for teaching Design of Experiments and the polymerase chain reaction

The PCR Simulator is a web-based tool that teaches experimental design and PCR by allowing learners to simulate reactions and analyze results quickly.