Biomolecular simulations: From dynamics and mechanisms to computational assays of biological activity
Biomolecular simulation is increasingly central to understanding and designing biological
molecules and their interactions. Detailed, physics‐based simulation methods are …
molecules and their interactions. Detailed, physics‐based simulation methods are …
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 …
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 …
Single-molecule visualization of twin-supercoiled domains generated during transcription
Transcription-coupled supercoiling of DNA is a key factor in chromosome compaction and
the regulation of genetic processes in all domains of life. It has become common knowledge …
the regulation of genetic processes in all domains of life. It has become common knowledge …
Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides
In the cell, DNA is arranged into highly-organised and topologically-constrained
(supercoiled) structures. It remains unclear how this supercoiling affects the detailed double …
(supercoiled) structures. It remains unclear how this supercoiling affects the detailed double …
A molecular view of DNA flexibility
DNA dynamics can only be understood by taking into account its complex mechanical
behavior at different length scales. At the micrometer level, the mechanical properties of …
behavior at different length scales. At the micrometer level, the mechanical properties of …
Coarse-grained modelling of the structural properties of DNA origami
We use the oxDNA coarse-grained model to provide a detailed characterization of the
fundamental structural properties of DNA origami, focussing on archetypal 2D and 3D …
fundamental structural properties of DNA origami, focussing on archetypal 2D and 3D …
Force-induced rupture of a DNA duplex: from fundamentals to force sensors
The rupture of double-stranded DNA under stress is a key process in biophysics and
nanotechnology. In this article, we consider the shear-induced rupture of short DNA …
nanotechnology. In this article, we consider the shear-induced rupture of short DNA …
Probing the mechanical properties, conformational changes, and interactions of nucleic acids with magnetic tweezers
Nucleic acids are central to the storage and transmission of genetic information. Mechanical
properties, along with their sequence, both enable and fundamentally constrain the …
properties, along with their sequence, both enable and fundamentally constrain the …
The temperature dependence of the helical twist of DNA
F Kriegel, C Matek, T Dršata, K Kulenkampff… - Nucleic acids …, 2018 - academic.oup.com
DNA is the carrier of all cellular genetic information and increasingly used in
nanotechnology. Quantitative understanding and optimization of its functions requires …
nanotechnology. Quantitative understanding and optimization of its functions requires …