Equilibrium mechanisms of self-limiting assembly
Self-assembly is a ubiquitous process in synthetic and biological systems, broadly defined
as the spontaneous organization of multiple subunits (macromolecules, particles, etc.) into …
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 …
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 …
controlling reaction kinetics. Although the dependence of strand displacement kinetics on …
Microscopic Evidence for Liquid-Liquid Separation in Supersaturated CaCO3 Solutions
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 …
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
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 …
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 …
operation of many dynamic DNA devices depends on toehold-mediated strand …
DNA hybridization kinetics: zippering, internal displacement and sequence dependence
Although the thermodynamics of DNA hybridization is generally well established, the
kinetics of this classic transition is less well understood. Providing such understanding has …
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
Elucidating the population dynamics of correlated electron-hole pairs (bound excitons) in
semiconducting quantum dots (QDs) is key for developing our fundamental understanding of …
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 …
molecular systems. Designing out-of-equilibrium architectures, however, requires a more …
Base triplet stepping by the Rad51/RecA family of recombinases
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 …
life, but the physical basis for these reactions remains poorly defined. Using single-molecule …