Related papers: Conformation dependent electronic transport in a D…
We study DNA self-assembly and DNA computation using a coarse-grained DNA model within the directional dynamic bonding framework {[}C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012){]}. In our model, a single nucleotide or domain is…
We examine the conformations of a model for a short segment of closed DNA. The molecule is represented as a cylindrically symmetric elastic rod with a constraint corresponding to a specification of the linking number. We obtain analytic…
We employ two Tight-Binding (TB) approaches to study the electronic structure and hole or electron transfer in B-DNA monomer polymers and dimer polymers made up of $N$ monomers (base pairs): (I) at the base-pair level, using the on-site…
The structural origin of the size of the 11 nm nucleosomal disc is addressed. On the nanometer length-scale the organization of DNA as chromatin in the chromosomes involves a coiling of DNA around the histone core of the nucleosome. We…
In this study, we compare the charge transport properties of multiple (double stranded) dsRNA sequences with corresponding dsDNA sequences. Recent studies have presented a contradictory picture of relative charge transport efficiencies in…
The pair interaction between two stiff parallel linear DNA molecules depends not only on the distance between their axes but on their azimuthal orientation. The positional and orientational order in columnar B-DNA assemblies in solution is…
The question of whether DNA is intrinsically conducting or not is still a challenge. The ongoing debate on DNA molecules as an electronic material has so far underestimated a key distinction of the system: the role of base pairing (inter…
We investigate the formation process of nonlinear vibrational modes representing broad H-bridge multi--site breathers in a DNA--shaped double strand. Within a network model of the double helix we take individual motions of the bases within…
Double-stranded DNA (dsDNA) has been established as an efficient medium for charge migration, bringing it to the forefront of the field of molecular electronics as well as biological research. The charge migration rate is controlled by the…
The temperature dependence of DNA flexibility is studied in the presence of stretching and unzipping forces. Two classes of models are considered. In one case the origin of elasticity is entropic due to the polymeric correlations, and in…
The two strands of the DNA double helix can be `unzipped' by application of 15 pN force. We analyze the dynamics of unzipping and rezipping, for the case where the molecule ends are separated and re-approached at constant velocity. For…
Recent ultrafast experiments have implicated that intrachain base-stacking rather than base-pairing mediate the fate and transport of photoexcited species in DNA chains. Here use an $SU(2)\otimes SU(2)$ lattice model which incorporates both…
We use X-ray scattering and molecular simulations to investigate the structural properties of complexes of multivalent cationic lipids and DNA molecules. At low mole fraction of neutral lipids (NLs), $\Phi_{\rm NL}$, the complexes show…
The aim of the present paper is the study of the entropic elasticity of the dsDNA molecule, having a cristallographic length L of the order of 10 to 30 persistence lengths A, when it is subject to spatial obstructions. We have not tried to…
The symmetries of the DNA double helix require a new term in its linear response to stress: the coupling between twist and stretch. Recent experiments with torsionally-constrained single molecules give the first direct measurement of this…
Positions of protons in DNA hydrogen bonds are fundamental for the fidelity of the replication process. Because the hydrogen bond is partially covalent the electronic structure of DNA plays an important role in the replication process.…
DNA flexibility is a key determinant of biological function, from nucleosome positioning to transcriptional regulation, motivating a direct measurement of the bend-torque response of individual DNA molecules. In this work, DNA bending is…
We present a numerical analysis of a DNA hydrogel that consists of three-valent Y-shaped DNA molecules. The building blocks self-assemble fully reversibly from complementary single-stranded DNA segments. We compare melting curves from both…
We investigate the influence of a dissipative environment which effectively comprises the effects of counterions and hydration shells, on the transport properties of short \DNA wires. Their electronic structure is captured by a…
The effect of sequence heterogeneity on polynucleotide translocation across a pore and on simple models of molecular motors such as helicases, DNA polymerase/exonuclease and RNA polymerase is studied in detail. Pore translocation of RNA or…