Related papers: Characterising DNA T-motifs by Simulation and Expe…
DNA supercoiling plays an important role in a variety of cellular processes. The torsional stress related with supercoiling may be also involved in gene regulation through the local structure and dynamics of the double helix. To check this…
Nucleic acids are highly deformable helical molecules constantly stretched, twisted and bent in their biological functioning. Single molecule experiments have shown that double stranded (ds)-RNA and standard ds-DNA have opposite…
The sticking of a soft polystyrene colloidal particle to a planar glass plate was studied by a microrheological technique using an optical tweezer to trap the particle and a piezoelectric-stage to position the plate and to sinusoidally…
We present a self-contained theory for the mechanical response of DNA in single molecule experiments. Our model is based on a 1D continuum description of the DNA molecule and accounts both for its elasticity and for DNA-DNA electrostatic…
By combining analytical results and simulations of various coarse-grained models we investigate the minimal energy shape of DNA minicircles which are torsionally constrained by an imposed over or undertwist. We show that twist-bend…
The observation by Ke et al. [Science 338, 1177 (2012)] that large numbers of short, pre-designed DNA strands can assemble into three-dimensional target structures came as a great surprise, as no colloidal self-assembling system has ever…
Introducing superconductivity in topological materials can lead to innovative electronic phases and device functionalities. Here, we present a new strategy for quantum engineering of superconducting junctions in moire materials through…
In equilibrium self-assembly, microscopic building blocks spontaneously self-organize into stable structures as dictated by their interaction potentials, which limits the accessible structural features to those that correspond to global…
Twisted bilayers of two-dimensional materials have emerged as a highly tunable platform for studying broken symmetry phases. While most interest has been focused on emergent states in systems whose constituent monolayers do not feature…
Motor proteins drive persistent motion and self-organisation of cytoskeletal filaments. However, state-of-the-art microscopy techniques and continuum modelling approaches focus on large length and time scales. Here, we perform…
We present an analytically solvable model for self-assembly of a molecular complex on a filament. The process is driven by a seed molecule that undergoes facilitated diffusion, which is a search strategy that combines diffusion in…
We study different configurations of permanent magnets and ferromagnetic circuit, in order to optimize the magnetic field for the so-called ``magnetic tweezers'' technique, for studing mechanical properties of DNA molecules. The magnetic…
We address the question of whether dualities formulated in continuum field theory can be realised exactly at finite lattice spacing, rather than only emerging in the infrared. In this context, we construct a lattice framework for a…
The response of a short DNA segment to bending is studied, taking into account the anisotropy in the bending rigidities caused by the double-helical structure. It is shown that the anisotropy introduces an effective nonlinear twist-bend…
The stability and dynamics of a double-stranded DNA (dsDNA) is affected by the preferential occupancy of small monovalent molecular ions. Small metal and molecular ions such as sodium and alkyl ammonium have crucial biological functions in…
Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…
Inspired by recent successes using single-stranded DNA tiles to produce complex structures, we develop a two-step coarse-graining approach that uses detailed thermodynamic calculations with oxDNA, a nucleotide-based model of DNA, to…
Composites of flexible and rigid polymers are ubiquitous in biology and industry alike, yet the physical principles determining their mechanical properties are far from understood. Here, we couple force spectroscopy with large-scale…
Engineering the synthetic nanopores through lipid bilayer membrane to access the interior of a cell is a long persisting challenge in biotechnology. Here, we demonstrate the stability and dynamics of a tile-based 6-helix DNA nanotube (DNT)…
We present the results of high temperature 500 K Molecular Dynamics simulations of the DNA i-motif. The essential dynamics and the main unfolding pathways are compared to a biased metadynamics simulation at 300 K. Our results indicate a…