Deconstructing synthetic biology across scales: a conceptual approach for training synthetic biologists

AS Karim, DM Brown, CM Archuleta, S Grannan… - Nature …, 2024 - nature.com
Synthetic biology allows us to reuse, repurpose, and reconfigure biological systems to
address society's most pressing challenges. Developing biotechnologies in this way …

Nanomanufacturing: a perspective

JA Liddle, GM Gallatin - ACS nano, 2016 - ACS Publications
Nanomanufacturing, the commercially scalable and economically sustainable mass
production of nanoscale materials and devices, represents the tangible outcome of the …

Failure mechanisms in DNA self-assembly: barriers to single-fold yield

JM Majikes, PN Patrone, AJ Kearsley, M Zwolak… - ACS …, 2021 - ACS Publications
Understanding the folding process of DNA origami is a critical stepping stone to the broader
implementation of nucleic acid nanofabrication technology but is notably nontrivial. Origami …

Kinetics and thermodynamics of Watson–Crick base pairing driven DNA origami dimerization

J Zenk, C Tuntivate, R Schulman - Journal of the American …, 2016 - ACS Publications
We investigate the kinetics and thermodynamics of DNA origami dimerization using flat
rectangle origami components and different architectures of Watson–Crick complementary …

Discovering optimal kinetic pathways for self-assembly using automatic differentiation

A Jhaveri, S Loggia, Y Qian… - Proceedings of the …, 2024 - National Acad Sciences
Macromolecular complexes are often composed of diverse subunits. The self-assembly of
these subunits is inherently nonequilibrium and must avoid kinetic traps to achieve high …

Direct observation and rational design of nucleation behavior in addressable self-assembly

M Sajfutdinow, WM Jacobs… - Proceedings of the …, 2018 - National Acad Sciences
To optimize a self-assembly reaction, it is essential to understand the factors that govern its
pathway. Here, we examine the influence of nucleation pathways in a model system for …

DNA brick self-assembly with an off-lattice potential

A Reinhardt, D Frenkel - Soft Matter, 2016 - pubs.rsc.org
We report Monte Carlo simulations of a simple off-lattice patchy-particle model for DNA
'bricks'. We relate the parameters that characterise this model with the binding free energy of …

The energy landscape for the self-assembly of a two-dimensional DNA origami complex

J Fern, J Lu, R Schulman - ACS nano, 2016 - ACS Publications
While the self-assembly of different types of DNA origami into well-defined complexes could
produce nanostructures on which thousands of locations can be independently …

Effects of co-ordination number on the nucleation behaviour in many-component self-assembly

A Reinhardt, CP Ho, D Frenkel - Faraday Discussions, 2016 - pubs.rsc.org
We report canonical and grand-canonical lattice Monte Carlo simulations of the self-
assembly of addressable structures comprising hundreds of distinct component types. The …

Typical stochastic paths in the transient assembly of fibrous materials

SB Nicholson, RA Bone, JR Green - The Journal of Physical …, 2019 - ACS Publications
When chemically fueled, molecular self-assembly can sustain dynamic aggregates of
polymeric fibers—hydrogels—with tunable properties. If the fuel supply is finite, the hydrogel …