Related papers: Bio-Polymer Hairpin Loops Sustained by Polarons
Small polaron behavior in a two dimensional honeycomb net is studied by applying the strong coupling perturbative method to the Holstein molecular crystal model. We find that small optical polarons can be mobile also if the electrons are…
The structure and dynamics of a range of polystyrene sulphonate comb polyelectrolytes with well defined chain architectures were examined with static light scattering, dynamic light scattering, small angle neutron/X-ray scattering, particle…
We consider a polaron model where molecular \emph{rotations} are important. Here, the usual hopping between neighboring sites is affected directly by the electron-phonon interaction via a {\em twist-dependent} hopping amplitude. This model…
We study the electric properties of single-stranded DNA molecules with hairpin-like shapes in the presence of a magnetic flux. It is shown that the current amplitude can be modulated by the applied field. The details of the electric…
We study the electronic transport through short DNA chains with various sequences of base pairs between voltage-biased leads. The strong coupling of the charge carriers to local vibrations of the base pairs leads to the formation of…
Layered superatomic semiconductors, whose buildings blocks are atomically precise molecular clusters, exhibit interesting electronic and vibrational properties. In recent work [Science 382, 438 (2023)], transient reflection microscopy…
The accurate knowledge of the elastic properties of single-stranded DNA (ssDNA) is key to characterize the thermodynamics of molecular reactions that are studied by force spectroscopy methods where DNA is mechanically unfolded. Examples…
The present {\em ab initio} study shows that in BaBiO$_3$, Bi$^{3+}$ sites can trap two holes from the valence band to form Bi$^{5+}$ cations. The trapping is accompanied by large local lattice distortions, therefore the composite particle…
We consider how beads can diffuse along a chain that wraps them, without becoming displaced from the chain; our proposed mechanism is analogous to the reptation of "stored length" in more familiar situations of polymer dynamics. The problem…
Polarons are composite quasiparticles comprising electronic charge carriers taken together with the alterations they induce in surrounding condensed matter. Strong-coupling polarons form when electronic charge carriers become self-trapped:…
We use a recently developed coarse-grained model for DNA to study kissing complexes formed by hybridization of complementary hairpin loops. The binding of the loops is topologically constrained because their linking number must remain…
A simple model of a circularly closed dsDNA in a poor solvent is considered as an example of a semi-flexible polymer with self-attraction. To find the ground states, the conformational energy is computed as a sum of the bending and…
Polymer filaments form the foundation of biology from cell scaffolding to DNA. Their study and fabrication play an important role in a wide range of processes from tissue engineering to molecular machines. We present a simple method to…
A theory is presented of DNA hairpins enclosed in a nanochannel. A hairpin becomes constrained as it approaches the wall of a channel which leads to an entropic force causing the hairpin to tighten. The free energy of the hairpin computed…
Many charged polymers, including nucleic acids, are locally stiff. Their bending rigidity -- quantified by the persistence length --, depends crucially on Coulombic features, such as the ionic strength of the solution which offers a…
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 the same footing, based on a single general physical principle. As…
We systematically explore the self-assembly of semi-flexible polymers in deformable spherical confinement across a wide regime of chain stiffness, contour lengths and packing fractions by means of coarse-grained molecular dynamics…
Advances in DNA nanotechnology have stimulated the search for simple motifs that can be used to control the properties of DNA nanostructures. One such motif, which has been used extensively in structures such as polyhedral cages,…
Effect of bending anisotropy on a planar DNA loop, using energy minimization and neglecting entropic effects, is studied. We show that the anisotropy results in polygonal shape of the loop and increasing the anisotropy makes the edges…
Quantun spin transport through a short DNA chain connected to ferromagnetic electrodes has been investigated by the transfer matrix method. We describe the system by a tight-binding model where the parameters are extracted from the…