Related papers: Twist-bend instability for toroidal DNA condensate…
Toroidal modes in the form of so-called Hopfions, with two independent winding numbers, a hidden one (twist, s), which characterizes a circular vortex thread embedded into a three-dimensional soliton, and the vorticity around the vertical…
To characterize the thermodynamical equilibrium of DNA chains interacting with a solution of non-specific binding proteins, a Flory-Huggins free energy model was implemented. We explored the dependence on DNA and protein concentrations of…
To study the elastic properties of rod-like DNA nanostructures, we perform long simulations of these structure using the oxDNA coarse-grained model. By analysing the fluctuations in these trajectories we obtain estimates of the bend and…
When a swollen, thermoresponsive polymer gel is heated in a solvent bath, it expels solvent and deswells. When this heating is slow, deswelling proceeds homogeneously, as observed in a toroid-shaped gel that changes volume whilst…
The self-similar collapse of 3D and quasi-2D atom condensates with negative scattering length is examined. 3D condensates are shown to blow up following the scenario of {\it weak collapse}: The inner core of the condensate diverges with an…
Despite their considerable practical and biological applications, the link between molecular properties, assembly conditions and self-organized structure in confined polymer solutions remains elusive. Here, we explore the lyotropic nematic…
We investigate the dynamics of the collapse of a single copolymer chain, when the solvent quality is suddenly quenched from good to poor. We employ Brownian dynamics simulations of a bead-spring chain model and incorporate fluctuating…
Bundles of stiff filaments are ubiquitous in the living world, found both in the cytoskeleton and in the extracellular medium. These bundles are typically held together by smaller cross-linking molecules. We demonstrate analytically,…
Concentrated solutions of short blunt-ended DNA duplexes, down to 6 base pairs, are known to order into the nematic liquid crystal phase. This self-assembly is due to the stacking interactions between the duplex terminals that promotes…
The effect of dipolar orientation with respect to the condensate plane on the mean-field dynamics of dipolar Bose-Einstein condensates in a pancake-shaped confinement is discussed. The stability of a quasi-two-dimensional condensate, with…
It is well-established that many physical properties of DNA at sufficiently long length scales can be understood by means of simple polymer models. One of the most widely used elasticity models for DNA is the twistable worm-like chain…
In layered materials, a common mode of deformation involves buckling of the layers under tensile deformation in the direction perpendicular to the layers. The instability mechanism, which operates in elastic materials from geological to…
We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with…
In this work, we combine coarse-grained Brownian dynamics simulations and mean-field theory to study supercoiling dynamics, as well as the steady-state profiles of twist and writhe, in an open DNA polymer where one of the free ends is…
Twisted two-dimensional (2D) layered materials exhibit many novel and unique phenomena, such as insulation and superconductivity transition, and superlubricity. However, the effect of twisting on these phenomena remains unclear. A key…
We study the dynamics of a polymer when it is quenched from a $\theta$ solvent into a good or bad solvent by means of a Langevin equation. The variation of the radius of gyration is studied as a function of time. For the first stage of…
The torsional elasticity of semiflexible polymers like DNA is of biological significance. A mathematical treatment of this problem was begun by Fuller using the relation between link, twist and writhe, but progress has been hindered by the…
The phase behaviour of two-component bottle-brush polymers with fully flexible backbones under poor solvent conditions is studied via molecular-dynamics simulations, using a coarse-grained bead-spring model and side chains of up to $N=40$…
Short DNA linkers are increasingly being exploited for driving specific self-assembly of Brownian objects. DNA-functionalised colloids can assemble into ordered or amorphous materials with tailored morphology. Recently, the same approach…
Under special conditions bacteria excrete an attractant and aggregate. The high density regions initially collapse into cylindrical structures, which subsequently destabilize and break up into spherical aggregates. This paper presents a…