[Crib-list] Reminder: Fri Oct 2 @12pm: MIT CRiBB seminar

[Ian Wang]

Dear all,
Reminder to join us on Friday!

MIT Computational Research in Boston and Beyond (CRIBB) Seminar
https://math.mit.edu/crib/


TITLE: Modeling the Mechanics of DNA Nanostructures in Flow
SPEAKER: Richard Huang (MIT)

DATE: Friday, October 2, 2026
TIME: noon(eastern) - 1pm (eastern)
ZOOM: https://mit.zoom.us/j/91933017072

ABSTRACT: Modern DNA synthesis techniques enable the precise design of heterogeneous DNA nanostructures, with proposed applications in drug delivery, vaccine development, and biosensing. In these applications, particles may encounter flow and spatially varying hydrodynamic forces. However, the relationship between designed particle structure and deformation under these non-uniform forces remains poorly understood. Understanding this relationship requires examining how shape determines force transmission and how local structural transitions enable larger-scale deformation.

In this work, we combine coarse-grained molecular dynamics and mechanistic modeling, using DNA as a canonical polymeric system to investigate deformation under non-uniform forcing. We start by understanding the flow response mechanisms of simple linear and cyclic DNA chains in extensional flow. Distributed drag concentrates tension toward the center of linear duplexes, where base-pair disruption leads to an overstretching transition. Meanwhile, as minicircles deform, the sides straighten and bending becomes concentrated at two opposing tips, producing localized kinks in the overall minicircle structure. Analytical models are developed that account for these responses through DNA elasticity and the distribution of hydrodynamic forces.

We take our understanding and models from simple structures and use them to understand more complex DNA origami nanostructures. For wireframe DNA origami, we investigate how forces are transmitted through connected DNA strands, and how local structural changes contribute to overall particle deformation. This understanding can inform the design of DNA nanostructures with enhanced stability or tailored deformation in their intended flow environments. Together, these studies develop our understanding of the interplay between shape, structural transitions, and deformation under non-uniform forcing.


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