Pattern recognition in the nucleation kinetics of non-equilibrium self-assembly

CG Evans, J O'Brien, E Winfree, A Murugan - Nature, 2024 - nature.com
Inspired by biology's most sophisticated computer, the brain, neural networks constitute a
profound reformulation of computational principles,–. Analogous high-dimensional, highly …

[HTML][HTML] The art of designing DNA nanostructures with CAD software

M Glaser, S Deb, F Seier, A Agrawal, T Liedl… - Molecules, 2021 - mdpi.com
Since the arrival of DNA nanotechnology nearly 40 years ago, the field has progressed from
its beginnings of envisioning rather simple DNA structures having a branched, multi-strand …

Spatiotemporal control of coacervate formation within liposomes

S Deshpande, F Brandenburg, A Lau, MGF Last… - Nature …, 2019 - nature.com
Liquid-liquid phase separation (LLPS), especially coacervation, plays a crucial role in cell
biology, as it forms numerous membraneless organelles in cells. Coacervates play an …

Models and simulations of structural DNA nanotechnology reveal fundamental principles of self-assembly

A Cumberworth, A Reinhardt - Chemical Society Reviews, 2025 - pubs.rsc.org
DNA is not only a centrally important molecule in biology: the specificity of bonding that
allows it to be the primary information storage medium for life has also allowed it to become …

Branching crisscross polymerization of single-stranded dna slats

J Deng, D Minev, A Ershova… - Journal of the American …, 2024 - ACS Publications
Controlling where and when self-assembly happens is crucial in both biological and
synthetic systems as it optimizes the utilization of available resources. We previously …

Differentiable molecular simulations for control and learning

W Wang, S Axelrod, R Gómez-Bombarelli - arxiv preprint arxiv …, 2020 - arxiv.org
Molecular dynamics simulations use statistical mechanics at the atomistic scale to enable
both the elucidation of fundamental mechanisms and the engineering of matter for desired …

Hydrogen-Bonded Fibrous Nanotubes Assembled from Trigonal Prismatic Building Blocks

S Mahapatra, D Qian, R Zhang, S Yang… - Journal of the …, 2024 - ACS Publications
In reticular chemistry, molecular building blocks are designed to create crystalline open
frameworks. A key principle of reticular chemistry is that the most symmetrical networks are …

Spatial control of irreversible protein aggregation

C Weber, T Michaels, L Mahadevan - Elife, 2019 - elifesciences.org
Liquid cellular compartments form in the cyto-or nucleoplasm and can regulate aberrant
protein aggregation. Yet, the mechanisms by which these compartments affect protein …

Temperature protocols to guide selective self-assembly of competing structures

A Bupathy, D Frenkel, S Sastry - Proceedings of the National Academy of …, 2022 - pnas.org
Multicomponent self-assembly mixtures offer the possibility of encoding multiple target
structures with the same set of interacting components. Selective retrieval of one of the …

Probing the formation kinetics and thermodynamics with rationally designed analytical tools enables one-pot synthesis and purification of a tetrahedral DNA …

L Gao, L Liu, Y Tian, Q Yang, P Wu, C Fan… - Analytical …, 2021 - ACS Publications
The development of robust analytical tools capable of probing the formation kinetics and
thermodynamics of DNA nanostructures is a crucial step toward better understanding and …