Related papers: Electronic parameters for the hole transfer in DNA…
By combining analytical results and simulations of various coarse-grained models we investigate the minimal energy shape of DNA minicircles which are torsionally constrained by an imposed over or undertwist. We show that twist-bend…
In this work, we investigated the influence of base pairing and {\pi}-{\pi} stacking interactions on electron attachment induced shape resonances in the adenine-thymine (AT) base pair. Resonance positions and widths are computed using a…
Structural changes in giant DNA induced by the addition of the flexible polymer PEG were examined by the method of single-DNA observation. In dilute DNA conditions, individual DNA assumes a compact state via a discrete coil-globule…
Chemical bondings of graphene oxides with oxygen concentration from 1\% to 50\% are investigated using first-principle calculations. Energy gaps are mainly determined by the competition of orbital hybridizations in C-C, O-O, and C-O bonds.…
We propose a model Hamiltonian for describing charge transport through short homogeneous double stranded DNA molecules. We show that the hybridization of the overlapping pi orbitals in the base-pair stack coupled to the backbone is…
Anomalous non-exponential relaxation in hydrated biomolecules is commonly attributed to the complexity of the free-energy landscapes, similarly to polymers and glasses. It was found recently that the hydrogen-bond breathing of terminal DNA…
Coupled colloidal quantum dot molecules composed of two fused CdSe/CdS core/shell sphere monomers were recently presented. Upon fusion, the potential energy landscape is changing into two quantum dots separated by a pre-tuned potential…
We develop a new approach to derive single state tight binding (SSTB) model for electron transport in the vicinity of valence-conduction bands of poly(G)-poly(C) and poly(A)-poly(T) DNA. The SSTB parameters are derived from {\it first…
An ideal nanofabrication method should allow the organization of nanoparticles and molecules with nanometric positional precision, stoichiometric control and well-defined orientation. The DNA origami technique has evolved into a highly…
Long range charge transfer experiments in DNA oligomers and the subsequently measured -- and very diverse -- transport response of DNA wires in solid state experiments exemplifies the need for a thorough theoretical understanding of charge…
During the life cycle of bacterial cells the non-mixing of the two ring-shaped daughter genomes is an important prerequisite for the cell division process. Mimicking the environments inside highly crowded biological cells, we study the…
Using data from contact maps of the DNA-polymer of $E. Coli$ (at kilobase pair resolution) as an input to our model, we introduce cross-links between monomers in a bead-spring model of a ring polymer at very specific points along the chain.…
An 1d model with time-dependent random hopping is proposed to describe charge transport in DNA. It admits to investigate both diffusion of electrons and their tunneling between different sites in DNA. The tunneling appears to be strongly…
Dielectronic and higher-order resonant electron recombination processes including a K-shell excitation were systematically measured at high resolution in electron beam ion traps. Storing highly charged Ar, Fe, and Kr ions, the dependence on…
A model of self-avoiding walk with suitable constraints on self-attraction is developed to describe the conformational behavior of a short RNA or a single stranded DNA molecule that forms hairpin structure and calculate the properties…
A crucial factor determining charge transport in organic semiconductors is the electronic coupling between the molecular constituents, which is heavily influenced by the relative arrangement of the molecules. This renders quinacridone, with…
We call \textit{monomer} a B-DNA base pair and study, analytically and numerically, electron or hole oscillations in \textit{monomers}, \textit{dimers} and \textit{trimers}. We employ two Tight Binding (TB) approaches: (I) at the base-pair…
We report on a study of the interactions between holes and molecular vibrations on dry DNA using photoinduced infrared absorption spectroscopy. Laser photoexcited (PE) holes are found to have a room-temperature lifetime in excess of 1 ms,…
We analyze the electronic structure of the recently synthesized higher-order nickelate Ruddlesden-Popper phases La$_{n+1}$Ni$_n$O$_{3n+1}$ ($n=4-6$) using first-principles calculations. For all materials, our results show large holelike…
We report density-matrix renormalization group calculations of spin gaps in the quarter-filled correlated two-leg rectangular ladder with bond-dimerization along the legs of the ladder. In the small rung-coupling region, dimerization along…