From predictive modelling to machine learning and reverse engineering of colloidal self-assembly
M Dijkstra, E Luijten - Nature materials, 2021 - nature.com
An overwhelming diversity of colloidal building blocks with distinct sizes, materials and
tunable interaction potentials are now available for colloidal self-assembly. The application …
tunable interaction potentials are now available for colloidal self-assembly. The application …
A primer on the oxDNA model of DNA: when to use it, how to simulate it and how to interpret the results
The oxDNA model of Deoxyribonucleic acid has been applied widely to systems in biology,
biophysics and nanotechnology. It is currently available via two independent open source …
biophysics and nanotechnology. It is currently available via two independent open source …
Systematic comparison of the structural and dynamic properties of commonly used water models for molecular dynamics simulations
SP Kadaoluwa Pathirannahalage… - Journal of Chemical …, 2021 - ACS Publications
Water is a unique solvent that is ubiquitous in biology and present in a variety of solutions,
mixtures, and materials settings. It therefore forms the basis for all molecular dynamics …
mixtures, and materials settings. It therefore forms the basis for all molecular dynamics …
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 …
Design, optimization and analysis of large DNA and RNA nanostructures through interactive visualization, editing and molecular simulation
This work seeks to remedy two deficiencies in the current nucleic acid nanotechnology
software environment: the lack of both a fast and user-friendly visualization tool and a …
software environment: the lack of both a fast and user-friendly visualization tool and a …
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 …
Localisation of DivIVA by targeting to negatively curved membranes
R Lenarcic, S Halbedel, L Visser, M Shaw, LJ Wu… - The EMBO …, 2009 - embopress.org
DivIVA is a conserved protein in Gram‐positive bacteria and involved in various processes
related to cell growth, cell division and spore formation. DivIVA is specifically targeted to cell …
related to cell growth, cell division and spore formation. DivIVA is specifically targeted to cell …
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 …
Coarse-graining DNA for simulations of DNA nanotechnology
To simulate long time and length scale processes involving DNA it is necessary to use a
coarse-grained description. Here we provide an overview of different approaches to such …
coarse-grained description. Here we provide an overview of different approaches to such …