Related papers: Twist-bend instability for toroidal DNA condensate…
We use numerical simulations to study tangentially active flexible ring polymers with different knot topologies. Simple, unknotted active rings display a transition from an extended phase to a collapsed one upon increasing the degree of…
We present a scaling theory describing the collapse of a homopolymer chain in poor solvent. At time t after the beginning of the collapse, the original Gaussian chain of length N is streamlined to form N/g segments of length R(t), each…
The stability of copolymer tethers is investigated theoretically. Self-assembly of diblockor triblock copolymers can lead to tubular polymersomes which are known experimentallyto undergo shape instability under thermal, chemical and tension…
We study the structures of a ribbon or ladder polymer immersed in poor solvents. The anisotropic bending rigidity coupled with the surface tension leads ribbon polymers to spontaneous formation of highly anisotropic condensates in poor…
We study the elastic response of a worm-like polymer chain with reversible kink-like structural defects. This is a generic model for (a) the double-stranded DNA with sharp bends induced by binding of certain proteins, and (b) effects of…
Recent work indicates that twist-bend coupling plays an important role in DNA micromechanics. Here we investigate its effect on bent DNA. We provide an analytical solution of the minimum-energy shape of circular DNA, showing that twist-bend…
Bending of DNA from a straight rod to a circular form in presence of any of the mono-, di-, tri- or tetravalent counterions has been simulated in strong Coulomb coupling environment employing a previously developed energy minimization…
The sequence-dependent elasticity of double-helical DNA on a nm length scale can be captured by the rigid base-pair model, whose strains are the relative position and orientation of adjacent base-pairs. Corresponding elastic potentials have…
Although the free energy of a genome packing into a virus is dominated by DNA-DNA interactions, ordering of the DNA inside the capsid is elasticity-driven, suggesting general solutions with DNA organized into spool-like domains. Using…
We examine the condensed states of a simple semiflexible copolymer in which there are two monomer types that are immiscible with each other and with the solvent. Although this is similar to the well known problem of collapse for a…
The thermodynamic properties of DNA circular molecules are investigated by a new path integral computational method which treats in the real space the fundamental forces stabilizing the molecule. The base pair and stacking contributions to…
Depositing monolayer graphene on a transition metal dichalcogenide (TMD) semiconductor substrate has been shown to change the dynamics of the electronic states in graphene, inducing spin orbit coupling (SOC) and staggered potential effects.…
In the present work, crystallization in melts and poor-solvent solutions of semiflexible polymers with different concentration was studied by means of dissipative particle dynamics simulation technique. We use a coarse-grained polymer model…
Semiflexible polymers in poor solvents exhibit a rich variety of collapsed morphologies, including globules, toroids, and rodlike bundles, arising from the competition between attractive interactions and chain stiffness. Computer…
DNA torsion dynamics is essential in the transcription process; simple models for it have been proposed by several authors, in particular Yakushevich (Y model). These are strongly related to models of DNA separation dynamics such as the one…
By equilibrating condensed DNA arrays against reservoirs of known osmotic stress and examining them with several structural probes, it has been possible to achieve a detailed thermodynamic and structural characterization of the change…
When colloidal particles are vertically confined to a gap of between 1.3-1.6 particle diameters, they pack into buckled crystals of particles in either "up" or "down" states. Neighboring particles tend to occupy opposite states, analogous…
We consider the folding of a self-avoiding homopolymer on a lattice, with saturating hydrogen bond interactions. Our goal is to numerically evaluate the statistical distribution of the topological genus of pseudoknotted configurations. The…
Lattice relaxation in twistronic bilayers with close lattice parameters and almost perfect crystallographic alignment of the layers results in the transformation of moir\'e pattern into a sequence of preferential stacking domains and domain…
We investigate the rotational properties of a dipolar Bose-Einstein condensate trapped in a toroidal geometry. Studying the ground states in the rotating frame and at fixed angular momenta, we observe that the condensate acts in distinctly…