arXiv subjects

Konstantinos Lambropoulos

Publications and source records attributed to Konstantinos Lambropoulos.

3 recordsLinked to original sources

arXiv2019

Periodic, quasi-periodic, fractal, Kolakoski and random binary polymers: Energy structure and carrier transport

We study periodic, quasi-periodic (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). We use B-DNA as our prototype system. All sequences have purines, guanine (G) or adenine (A) on the same strand, i.e., our prototype binary alphabet is (G,A). Our aim is to examine the influence of sequence intricacy and magnitude of parameters on energy structure, localization and charge transport. We study quantities such as autocorrelation function, eigenspectra, density of states, Lyapunov exponents, transmission coefficients and current-voltage curves. We show that the degree of sequence intricacy and the presence of correlations decisively affect the aforementioned physical properties. Periodic segments have enhanced transport properties. Specifically, in homogeneous sequences transport efficiency is maximum. There are several deterministic aperiodic sequences that can support significant currents, depending on the Fermi level of the leads. Random sequences is the less efficient category.

cond-mat.soft↗

arXiv2019

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 $N$ 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., in DNA, a base pair). We consider quasi-periodic (Fibonacci, Thue-Morse, Double-Period, Rudin-Shapiro) and fractal (Cantor Set, Asymmetric Cantor Set) polymers made of the same monomer (I polymers) or made of different monomers (D polymers). For all types of such polymers, we calculate the HOMO and LUMO eigenspectrum, the HOMO-LUMO gap and the density of states. We examine the mean over time probability to find the carrier at each monomer, the frequency content of carrier transfer (Fourier spectra, weighted mean frequency of each monomer, total weighted mean frequency of the polymer), and the pure mean transfer rate $k$. Our results reveal that there is a correspondence between the degree of structural complexity and the transfer properties. I polymers are more favorable for charge transfer than D polymers. We compare $k(N)$ of quasi-periodic and fractal sequences with that of periodic sequences (including homopolymers) as well as with randomly shuffled sequences. Finally, we discuss aspects of experimental results on charge transfer rates in DNA with respect to our coherent pure mean transfer rates.

cond-mat.soft↗

arXiv2015

Unbiased charge oscillations in DNA monomer-polymers and dimer-polymers

We call {\it 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. We employ a tight-binding (TB) approach at the base-pair level to readily determine the spatiotemporal evolution of a single extra carrier along a $N$ base-pair polymer. We study HOMO and LUMO eigenspectra as well as the mean over time probabilities to find the carrier at a particular monomer. We use the pure mean transfer rate $k$ to evaluate the easiness of charge transfer. The inverse decay length $β$ for exponential fits $k(d)$, where $d$ is the charge transfer distance, and the exponent $η$ for power law fits $k(N)$ are computed; generally power law fits are better. We illustrate that increasing the number of different parameters involved in the TB description, the fall of $k(d)$ or $k(N)$ becomes steeper and show the range covered by $β$ and $η$. Finally, both for the time-independent and the time-dependent problem, we analyze the {\it palindromicity} and the {\it degree of eigenspectrum dependence} of the probabilities to find the carrier at a particular monomer.

physics.bio-ph↗