Equilibrium mechanisms of self-limiting assembly

MF Hagan, GM Grason - Reviews of modern physics, 2021 - APS
Self-assembly is a ubiquitous process in synthetic and biological systems, broadly defined
as the spontaneous organization of multiple subunits (macromolecules, particles, etc.) into …

The statistical mechanics of dynamic pathways to self-assembly

S Whitelam, RL Jack - Annual review of physical chemistry, 2015 - annualreviews.org
This review describes some important physical characteristics of the pathways (ie,
dynamical processes) by which molecular, nanoscale, and micrometer-scale self-assembly …

On the biophysics and kinetics of toehold-mediated DNA strand displacement

N Srinivas, TE Ouldridge, P Šulc… - Nucleic acids …, 2013 - academic.oup.com
Dynamic DNA nanotechnology often uses toehold-mediated strand displacement for
controlling reaction kinetics. Although the dependence of strand displacement kinetics on …

Microscopic Evidence for Liquid-Liquid Separation in Supersaturated CaCO3 Solutions

AF Wallace, LO Hedges, A Fernandez-Martinez… - Science, 2013 - science.org
Recent experimental observations of the onset of calcium carbonate (CaCO3) mineralization
suggest the emergence of a population of clusters that are stable rather than unstable as …

Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

BEK Snodin, F Randisi, M Mosayebi, P Šulc… - The Journal of …, 2015 - pubs.aip.org
We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic
acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of …

Programmable energy landscapes for kinetic control of DNA strand displacement

RRF Machinek, TE Ouldridge, NEC Haley… - Nature …, 2014 - nature.com
DNA is used to construct synthetic systems that sense, actuate, move and compute. The
operation of many dynamic DNA devices depends on toehold-mediated strand …

DNA hybridization kinetics: zippering, internal displacement and sequence dependence

TE Ouldridge, P Šulc, F Romano, JPK Doye… - Nucleic acids …, 2013 - academic.oup.com
Although the thermodynamics of DNA hybridization is generally well established, the
kinetics of this classic transition is less well understood. Providing such understanding has …

Ultrafast hole relaxation dynamics in quantum dots revealed by two-dimensional electronic spectroscopy

PJ Brosseau, JJ Geuchies, D Jasrasaria… - Communications …, 2023 - nature.com
Elucidating the population dynamics of correlated electron-hole pairs (bound excitons) in
semiconducting quantum dots (QDs) is key for developing our fundamental understanding of …

Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement

NEC Haley, TE Ouldridge, I Mullor Ruiz… - Nature …, 2020 - nature.com
Recent years have seen great advances in the development of synthetic self-assembling
molecular systems. Designing out-of-equilibrium architectures, however, requires a more …

Base triplet stepping by the Rad51/RecA family of recombinases

JY Lee, T Terakawa, Z Qi, JB Steinfeld, S Redding… - Science, 2015 - science.org
DNA strand exchange plays a central role in genetic recombination across all kingdoms of
life, but the physical basis for these reactions remains poorly defined. Using single-molecule …