Electronic structure, absorption spectra and oxidation dynamics in polyynes and dicyanopolyynes.

The advent of femtosecond to attosecond experimental tools has made now possible to study such ultrafast carrier dynamics, , the spatial and temporal charge density evolution, after an initial oxidation or reduction in molecules, candidates for atomic wires like polyynes and dicyanopolyynes. Here, we study the electronic structure and hole transfer in symmetric molecules containing carbon, nitrogen and hydrogen, the first members in the series of polyynic carbynes and dicyanopolyynes, using methods based on density functional theory (DFT): constrained DFT (CDFT), time-dependent DFT (TDDFT) and real-time TDDFT (RT-TDDFT), with Löwdin population analysis, comparing many levels of theory and obtaining convergence of the results. For the same purposes, we develop a tight binding (TB) variant using all valence orbitals of all atoms.

Charge transport in a double-stranded DNA: Effects of helical symmetry and long-range hopping.

Within a tight-binding framework, we examine conformation-dependent charge transport properties of the DNA double-helix, including helical symmetry and the possibility of multiple charge conduction pathways. Using techniques based on the Green's function method, we inspect changes in the localization properties of DNA in the presence of long-range hopping, with varying disorder strength. We study three characteristic DNA sequences, two periodic and one random.

Electronic Structure and Hole Transfer of All B-DNA Dimers and Homopolymers, via the Fishbone-Wire Model.

We employ the Tight Binding Fishbone-Wire Model to study the electronic structure and coherent transfer of a hole (the absence of an electron created by oxidation) in all possible ideal B-DNA dimers as well as in homopolymers (one base pair repeated along the whole sequence with purine on purine). The sites considered are the base pairs and the deoxyriboses, with no backbone disorder. For the time-independent problem, we calculate the eigenspectra and the density of states.

Charge transport properties of ideal and natural DNA segments, as mutation detectors.

DNA sequences of ideal and natural geometries are examined, studying their charge transport properties as mutation detectors. Ideal means textbook geometry. Natural means naturally distorted sequences; geometry taken from available databases.

Energy Transport along -Helix Protein Chains: External Drives and Multifractal Analysis.

Energy transport within biological systems is critical for biological functions in living cells and for technological applications in molecular motors. Biological systems have very complex dynamics supporting a large number of biochemical and biophysical processes. In the current work, we study the energy transport along protein chains.

Cyclo[18]carbon including zero-point motion: ground state, first singlet and triplet excitations, and hole transfer.

Recent synthesis of cyclo[18]carbon has spurred increasing interest in carbon rings. We focus on a comparative inspection of ground and excited states, as well as of hole transfer properties of cumulenic and polyynic cyclo[18]carbon Density Functional Theory (DFT), time-dependent DFT (TD-DFT) and real-time time-dependent DFT (RT-TDDFT). Zero-point vibrations are also accounted for, using a Monte Carlo sampling technique and a less exact, yet mode-resolved, quadratic approximation.

LCAO Electronic Structure of Nucleic Acid Bases and Other Heterocycles and Transfer Integrals in B-DNA, Including Structural Variability.

To describe the molecular electronic structure of nucleic acid bases and other heterocycles, we employ the Linear Combination of Atomic Orbitals (LCAO) method, considering the molecular wave function as a linear combination of all valence orbitals, i.e., 2s, 2px, 2py, 2pz orbitals for C, N, and O atoms and 1s orbital for H atoms.

Effects of Structural Dynamics on Charge Carrier Transfer in B-DNA: A Combined MD and RT-TDDFT Study.

Hole transfer along the axis of duplex DNA has been the focus of physical chemistry research for decades, with implications in diverse fields, from nanotechnology to cell oxidative damage. Computational approaches are particularly amenable for this problem, to complement experimental data for interpretation of transfer mechanisms. To be predictive, computational results need to account for the inherent mobility of biological molecules during the time frame of experimental measurements.

Hole Transfer in Open Carbynes.

We investigate hole transfer in open carbynes, i.e., carbon atomic nanowires, using Real-Time Time-Dependent Density Functional Theory (RT-TDDFT).

Publisher's Note: Electronic structure and carrier transfer in B-DNA monomer polymers and dimer polymers: Stationary and time-dependent aspects of a wire model versus an extended ladder model [Phys. Rev. E 94, 062403 (2016)].

This corrects the article DOI: 10.1103/PhysRevE.94.

Quasi-Periodic and Fractal Polymers: Energy Structure and Carrier Transfer.

We study the energy structure and the coherent transfer of an extra electron or hole along aperiodic polymers made of monomers, with fixed boundaries, using B-DNA as our prototype system. We use a Tight-Binding wire model, where a site is a monomer (e.g.

Periodic, quasiperiodic, fractal, Kolakoski, and random binary polymers: Energy structure and carrier transport.

We study periodic, quasiperiodic (Thue-Morse, Fibonacci, period doubling, Rudin-Shapiro), fractal (Cantor, generalized Cantor), Kolakoski, and random binary sequences using a tight-binding wire model, where a site is a monomer (e.g., in DNA, a base pair).

Electronic structure and charge transport properties of atomic carbon wires.

Atomic carbon wires represent the ultimate one-atom-thick one-dimensional structure. We use a Tight-binding (TB) approach to determine the electronic structure of polyynic and cumulenic carbynes, in terms of their dispersion relations (for cyclic boundaries), eigenspectra (for fixed boundaries) and density of states (DOS). We further derive the transmission coefficient at zero-bias by attaching the carbynes to semi-infinite metallic leads, and demonstrate the effect of the coupling strength and asymmetry to the transparency of the system to incident carriers.

Electronic structure and carrier transfer in B-DNA monomer polymers and dimer polymers: Stationary and time-dependent aspects of a wire model versus an extended ladder model.

We employ two tight-binding (TB) approaches to systematically 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 onsite energies of base pairs and the hopping integrals between successive base pairs, i.e., a wire model and (II) at the single-base level, using the onsite energies of the bases and the hopping integrals between neighboring bases, i.

Wire and extended ladder model predict THz oscillations in DNA monomers, dimers and trimers.

We call monomer a B-DNA base pair and study, analytically and numerically, electron or hole oscillations in monomers, dimers and trimers. We employ two tight binding (TB) approaches: (I) at the base-pair level, using the on-site energies of the base pairs and the hopping parameters between successive base pairs i.e.

Publisher's Note: Unbiased charge oscillations in B-DNA: Monomer polymers and dimer polymers [Phys. Rev. E 92, 032725 (2015)].

This corrects the article DOI: 10.1103/PhysRevE.92.

Unbiased charge oscillations in B-DNA: monomer polymers and dimer polymers.

We call monomer a B-DNA base pair and examine, analytically and numerically, electron or hole oscillations in monomer and dimer polymers, i.e., periodic sequences with repetition unit made of one or two monomers.

Near-field optical properties of quantum dots, applications and perspectives.

Recent years have witnessed tremendous research in quantum dots as excellent models of quantum physics at the nanoscale and as excellent candidates for various applications based on their optoelectronic properties. This review intends to present theoretical and experimental investigations of the near-field optical properties of these structures, and their multimodal applications such as biosensors, biological labels, optical fibers, switches and sensors, visual displays, photovoltaic devices and related patents.

Electronic parameters for charge transfer along DNA.

We systematically examine all the tight-binding parameters pertinent to charge transfer along DNA. The pi molecular structure of the four DNA bases (adenine, thymine, cytosine, and guanine) is investigated by using the linear combination of atomic orbitals method with a recently introduced parametrization. The HOMO and LUMO wave functions and energies of DNA bases are discussed and then used for calculating the corresponding wave functions of the two B-DNA base-pairs (adenine-thymine and guanine-cytosine).

Principal thermodynamic properties of quasi-two-dimensional carriers under in-plane magnetic field.

An external magnetic field, H, applied parallel to a quasi-two-dimensional carrier system modifies quantitatively and qualitatively the density of states. We examine how this affects primary thermodynamic properties, namely, the entropy, S, the internal and free energy, U and F, the magnetization, M, and the magnetic susceptibility, χ(m), using a self-consistent numerical approach. Although M is mainly in the opposite direction to H, the system is not linear.

Effects of the task of categorizing FM direction on auditory evoked magnetic fields in the human auditory cortex.

We examined effects of the task of categorizing linear frequency-modulated (FM) sweeps into rising and falling on auditory evoked magnetic fields (AEFs) from the human auditory cortex, recorded by means of whole-head magnetoencephalography. AEFs in this task condition were compared with those in a passive condition where subjects had been asked to just passively listen to the same stimulus material. We found that the M100-peak latency was significantly shorter for the task condition than for the passive condition in the left but not in the right hemisphere.

Theory of spontaneous emission of quantum dots in the linear regime.

We develop a fully quantum-mechanical theory for the interaction of light and electron-hole excitations in semiconductor quantum dots. Our theoretical analysis results in an expression for the photoluminescence intensity of quantum dots in the linear regime. Taking into account the single-particle Hamiltonian, the free-photon Hamiltonian, the electron-hole interaction Hamiltonian, and the interaction of carriers with light, and applying the Heisenberg equation of motion to the photon number expectation values, to the carrier distribution functions and to the correlation term between the photon generation (destruction) and electron-hole pair, we obtain a set of luminescence equations.