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 …

DNA cyclization is a powerful technique to gain insight into the nature of DNA bending.
While the wormlike chain model provides a good description of small to moderate bending …

By combining analytical results and simulations of various coarse-grained models, we
investigate the minimal energy shape of DNA minicircles which are torsionally constrained …

The sequence dependence of the conformational distribution of DNA under various levels of
torsional stress is an important unsolved problem. Combining theory and coarse-grained …

The strong bending of polymers is poorly understood. We propose a general quantitative
framework of polymer bending that includes both the weak and strong bending regimes on …

Kink formation is essential in highly bent DNA complexed with gene regulatory proteins such
as histones to release the bending stress stored within the DNA duplex. Local opening of the …

The innate flexibility of a DNA sequence is quantified by the Jacobson-Stockmayer's J-factor,
which measures the propensity for DNA loop formation. Recent studies of ultra-short DNA …

Annealing between sticky ends of DNA is an intermediate step in ligation. It can also be
utilized to program specific binding sites for DNA tile and origami assembly. This reaction is …

The experimental construction of a double-stranded DNA microcircle of only 42 base pairs
entailed a great deal of ingenuity and hard work. However, figuring out the three …

Multiplexed cloning of long DNA sequences is a valuable technique in many biotechnology
applications, such as long-read genome sequencing and the creation of open reading frame …