Related papers: DNA confined in a two-dimensional strip geometry
A new N-dimensional vector space of DNA sequences over the Galois field of the 64 codons (GF(64)) was recently presented. Now, in order to include deletions and insertions (indel mutations), we have defined a new Galois field over the set…
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,…
Interplay between structure and function in atomically thin crystalline nanoribbons is sensitive to their conformations yet the ability to prescribe them is a formidable challenge. Here, we report a novel paradigm for controlled nucleation…
A DNA-protein complex modelled by a semiflexible chain and an attractive spherical core is studied in the situation when an external stretching force is acting on one end monomer of the chain while the other end monomer is kept fixed in…
Topological entanglements in polymers are mimicked by sliding rings (slip-links) which enforce pair contacts between monomers. We study the force-extension curve for linear polymers in which slip-links create additional loops of variable…
We use large scale Monte Carlo simulations to test scaling theories for the electrostatic persistence length $l_e$ of isolated, uniformly charged polymers with \DH intrachain interactions in the limit where the screening length…
We present an interpretation of recent experimental measurements of dmu/dn in suspended bilayer graphene samples. We demonstrate that the data may be quantitatively described by assuming a spatially varying band gap induced by local…
Diffusion of a polymer in a gel is studied within the framework of de Gennes' model for reptation. Our results for the scaling of the diffusion coefficient D and the longest relaxation time tau are markedly different from the most recently…
A theory is presented for the binding of small molecules such as surfactants to semiflexible polymers. The persistence length is assumed to be large compared to the monomer size but much smaller than the total chain length. Such polymers…
We consider a long, semiflexible polymer, with persistence length $P$ and contour length $L$, fluctuating in a narrow cylindrical channel of diameter $D$. In the regime $D\ll P\ll L$ the free energy of confinement $\Delta F$ and the length…
Molecular topology of polymers plays a key role in determining their physical properties. We studied herein the topological effects on the static and dynamic properties of a 2D catenated network of DNA rings called a kinetoplast.…
The density crossover scaling of various thermodynamic properties of solutions and melts of self-avoiding and highly flexible polymer chains without chain intersections confined to strictly two dimensions is investigated by means of…
We investigate the effects excluded volume on the stretching of a single DNA in solution. We find that for small force F, the extension h is not linear in F but proportion to F^{\chi}, with \chi=(1-\nu)/\nu, where \nu is the well-known…
Gauge-theory approach to describe Dirac fermions on a disclinated flexible membrane beyond the inextensional limit is formulated. The elastic membrane is considered as an embedding of 2D surface into R^3. The disclination is incorporated…
We study a model of two layers, each consisting of a d-dimensional elastic object driven over a random substrate, and mutually interacting through a viscous coupling. For this model, the mean-field theory (i.e. a fully connected model)…
An analytic expression is derived for the distribution $G(\vec{R})$ of the end-to-end distance $\vec{R}$ of semiflexible polymers in external potentials to elucidate the effect of confinement on the mechanical and statistical properties of…
We show that the collapsed globular phase of a polymer accommodates a scale-free incompatibility graph of its contacts. The degree distribution of this network is found to decay with the exponent $\gamma = 1/(2-c)$ up to a cut-off degree…
The phase behavior of liquids confined in a slit geometry does not reveal a crossover from a three to a two-dimensional behavior as the gap size decreases. Indeed, the prototypical two-dimensional hexatic phase only occurs in liquids…
We directly visualize single polymers with persistence lengths ranging from $\ell_p=0.05$ to 16 $\mu$m, dissolved in the nematic phase of rod-like {\it fd} virus. Polymers with sufficiently large persistence length undergo a coil-rod…
The cage model for polymer reptation, proposed by Evans and Edwards, and its recent extension to model DNA electrophoresis, are studied by numerically exact computation of the drift velocities for polymers with a length L of up to 15…