Related papers: Structural stability versus conformational samplin…
In this work we investigate the interplay between coherent and incoherent charge transport in cytosine-guanine (GC) rich DNA molecules. Our objective is to introduce physically grounded approach to dephasing in large molecules and to…
In solution, DNA is a highly charged macromolecule which bears a unit of negative charge on each phosphate of its sugar-phosphate backbone. Although partially compensated by counterions adsorbed at or condensed near it, DNA still produces a…
Using density functional theory calculations, we have examined the structural stability, electronic, magnetic and optical properties of rectangular shaped quantum dots (QDs) of graphene (G), Boron Nitride (BN) and their hybrids. Different…
Modeling the electronic and optical properties of organic semiconductors remains a challenge for theory, despite the remarkable progress achieved in the last three decades. The complexity of these systems, including structural (dis)order…
Structure-function relationships constitute an important tool to investigate the fundamental principles of molecular electronics. Most commonly, this involves identifying a potentially important molecular structural element, followed by…
By means of density functional theory the electronic structure of the MgB2 superconductor was characterised and compared with that of the related iso-structural systems: AlB2, ZrB2, NbB2, and TaB2. Using the full-potential linearized…
We study a genetic regulatory network model developed to demonstrate that genetic robustness can evolve through stabilizing selection for optimal phenotypes. We report preliminary results on whether such selection could result in a…
Multistep denaturation in a short circular DNA molecule is analyzed by a mesoscopic Hamiltonian model which accounts for the helicoidal geometry. Computation of melting profiles by the path integral method suggests that stacking…
We consider the problem of electron transport along a one-dimensional disordered multiple-scattering conductor, and study the electron density for all the electronic levels. A model is proposed for the reduced density matrix of the system…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
We propose using graphene electrodes with hydrogenated edges for solid-state nanopore-based DNA sequencing, and perform molecular dynamics simulations in conjunction with electronic transport calculations to explore the potential merits of…
Quasicrystals are assumed to be electronically stabilized by a Hume-Rothery type mechanism. This explains most of the peculiar properties of quasicrystals. The stabilization is investigated by electronic transport properties, as they depend…
Double-stranded DNA `overstretches' at a pulling force of about 65 pN, increasing in length by a factor of 1.7. The nature of the overstretched state is unknown, despite its considerable importance for DNA's biological function and…
We report an accurate method to determine DNA barcodes from the dwell time measurement of protein tags (barcodes) along the DNA backbone using Brownian dynamics simulation of a model DNA and use a recursive theoretical scheme which improves…
DNA is an astonishing material that can be used as a molecular building block to construct periodic arrays and devices with nanoscale accuracy and precision. Here, we present simple bead-spring model of DNA nanostars having three, four and…
Hybrid systems, which take advantage of low material dimensionality, have great potential for designing nanoscale devices. Quantum dots (QDs) -- a 0D nanostructure -- can be combined with 2D monolayers to achieve success in photovoltaics…
The passage of DNA through a nanopore can be effectively decomposed into two distinct phases, docking and actual translocation. In experiments each phase is characterized by a distinct current signature which allows the discrimination of…
We develop a continuum elastic approach to examining the bending mechanics of semiflexible filaments with a local internal degree of freedom that couples to the bending modulus. We apply this model to study the nonlinear mechanics of a…
We investigate the charge transfer characteristics of one and two excess charges in a DNA base-pair dimer using a model Hamiltonian approach. The electron part comprises diagonal and off-diagonal Coulomb matrix elements such a correlated…
Deep neural networks (DNNs) have excellent representative power and are state of the art classifiers on many tasks. However, they often do not capture their own uncertainties well making them less robust in the real world as they…