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.