arXiv subjects

Constantinos Simserides

Publications and source records attributed to Constantinos Simserides.

12 recordsLinked to original sources

arXiv2025

Psychoacoustic study of simple-tone dyads: frequency ratio and pitch

This study investigates how listeners perceive consonance and dissonance in dyads composed of simple (sine) tones, focusing on the effects of frequency ratio ($R$) and mean frequency ($F$). Seventy adult participants - categorized by musical training, gender, and age group - rated randomly ordered dyads using binary preference responses (``like'' or ``dislike''). Dyads represented standard Western intervals but were constructed with sine tones rather than musical notes, preserving interval ratios while varying absolute pitch. Statistical analyses reveal a consistent decrease in preference with increasing mean frequency, regardless of interval class or participant group. Octaves, fifths, fourths, and sixths showed a nearly linear decline in preference with increasing $F$. Major seconds were among the least preferred. Musicians rated octaves and certain consonant intervals more positively than non-musicians, while gender and age groups exhibited different sensitivity to high frequencies. The findings suggest that both interval structure and pitch range shape the perception of consonance in simple-tone dyads, with possible psychoacoustic explanations involving frequency sensitivity and auditory fatigue at higher frequencies.

q-bio.NC↗

arXiv2025

QuantumDNA: A Python Package for Analyzing Quantum Charge Dynamics in DNA and Exploring Its Biological Relevance

The study of DNA charge dynamics is a highly interdisciplinary field that bridges physics, chemistry, biology, and medicine, and plays a critical role in processes such as DNA damage detection, protein-DNA interactions, and DNA-based nanotechnology. However, despite significant advances in each of these areas, knowledge often remains inaccessible to other scientific communities, limiting the broader impact of advances across disciplines. To bridge this gap, we present QuantumDNA, an open-source Python package for simulating DNA charge transfer (CT) and excited states using quantum-physical methods. QuantumDNA combines an efficient Linear Combination of Atomic Orbitals (LCAO) approach with tight-binding (TB) models, incorporating open quantum systems techniques to account for environmental effects. This approach allows rapid yet accurate analysis of large DNA ensembles, enabling statistical studies of genetic and epigenetic phenomena. To ensure accessibility, the package features a graphical user interface (GUI), making it suitable for researchers across disciplines.

q-bio.BM↗

arXiv2025

Influence of transition mutations and disorder on charge localization and transfer along B-DNA sequences

We illuminate the influence of transition mutations and disorder on charge localization and transfer along B-DNA sequences. Homopolymers are the best for charge transfer (cf. Refs.~ \cite{LVBMS:2018, MLTS:2019}). Hence, we consider as flawless a homopolymer sequence and then disturb it, introducing transition mutations and disorder. We exclude the possibility of charge transfer via the backbone that will be addressed soon in another work. We employ the Tight Binding (TB) Wire model to study the influence of transition mutations and the TB Fishbone Wire model to evaluate the influence of disorder emanating either from the $\pi$ path or from the backbone. For the TB Wire parameters, we employ the parametrization created in Ref.~\cite{MLS:2023}, where another TB at atomic level was used, considering all valence orbitals of all atoms. We calculate the HOMO and LUMO regime eigenenergies and eigenvectors, the participation ratio (a measure of the localization of each eigenstate), the time-dependent probability to find the carrier at each site, the mean over time probability at each site, and the mean transfer rate from site to site. Transition mutations increase localization in terms of participation ratio and impede charge transfer in terms of mean probability and transfer rates, provided the TB parameters involving mutated sites are significantly modified relative to the original. Disorder leads to severe modifications of participation ratios, i.e., increase of localization. Relevant changes occur on eigenenergies, mean probabilities at each site, and transfer rates.

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↗

arXiv2018

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↗

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 $\beta$ for exponential fits $k(d)$, where $d$ is the charge transfer distance, and the exponent $\eta$ 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 $\beta$ and $\eta$. 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↗

arXiv2013

Charge transfer along DNA dimers, trimers and polymers

The transfer of electrons and holes along DNA dimers, trimers and polymers is described at the base-pair level, using the relevant on-site energies of the base-pairs and the hopping parameters between successive base-pairs. The temporal and spatial evolution of carriers along a $N$ base-pair DNA segment is determined, solving a system of $N$ coupled differential equations. Useful physical quantities are calculated including the pure mean carrier transfer rate $k$, the inverse decay length $\beta$ used for exponential fit ($k = k_0 \textrm{exp}(-\beta d)$) of the transfer rate as a function of the charge transfer distance $d = N \times$ 3.4 {\AA} and the exponent $\eta$ used for a power law fit ($k = k_0' N^{-\eta}$) of the transfer rate as function of the number of monomers $N$. Among others, the electron and hole transfer along the polymers poly(dG)-poly(dC), poly(dA)-poly(dT), GCGCGC..., ATATAT... is studied. $\beta$ ($\eta$) falls in the range $\approx$ 0.2 - 2 {\AA}$^{-1}$ (1.7 - 17), $k_0$ ($k_0'$) is usually $\approx 10^{-2}$-10$^{-1}$ ($ 10^{-2}$-10$^{-1}$) PHz although, generally, it falls in the wider range $\approx 10^{-4}$-10 ($10^{-4}$-10$^3$) PHz. The results are compared with past predictions and experiments. Our approach illustrates to which extent a specific DNA segment can serve as an efficient medium for charge transfer.

physics.bio-ph↗

arXiv2012

Density of states and extent of wave function: two crucial factors for small polaron hopping conductivity in 1D

We introduce a theoretical model to scrutinize the conductivity of small polarons in one-dimensional disordered systems, focusing on two crucial --as will be demonstrated-- factors: the density of states and the spatial extent of the electronic wave function. The investigation is performed for any temperature up to 300 K and under electric field of arbitrary strength up to the polaron dissociation limit. To accomplish this task we combine analytical work with numerical calculations.

cond-mat.dis-nn↗

arXiv2008

Empirical LCAO parameters for $π$ molecular orbitals in planar organic molecules

We present a parametrization within a simplified LCAO model (a type of Hueckel model) for the description of $π$ molecular orbitals in organic molecules containing $π$-bonds between carbon, nitrogen, or oxygen atoms with $sp^2$ hybridization, which we show to be quite accurate in predicting the energy of the highest occupied $π$ orbital and the first $π$-$π*$ transition energy for a large set of organic compounds. We provide four empirical parameter values for the diagonal matrix elements of the LCAO description, corresponding to atoms of carbon, nitrogen with one $p_z$ electron, nitrogen with two $p_z$ electrons, and oxygen. The bond-length dependent formula (proportional to $1/d^2$) of Harrison is used for the non-diagonal matrix elements between neighboring atoms. The predictions of our calculations have been tested against available experimental results in more than sixty organic molecules, including benzene and its derivatives, polyacenes, aromatic hydrocarbons of various geometries, polyenes, ketones, aldehydes, azabenzenes, nucleic acid bases and others. The comparison is rather successful, taking into account the small number of parameters and the simplicity of the LCAO method, involving only $p_z$ atomic orbitals, which leads even to analytical calculations in some cases.

physics.chem-ph↗

arXiv2008

Purely orbital diamagnetic to paramagnetic fluctuation of quasi two-dimensional carriers under in-plane magnetic field

An external magnetic field, $H$, applied parallel to a quasi two-dimensional system modifies quantitatively and qualitatively the density of states. Using a self-consistent numerical approach, we study how this affects the entropy, $S$, the free energy, $F$, and the magnetization, $M$, for different sheet carrier concentrations, $N_s$. As a prototype system we employ III-V double quantum wells. We find that although $M$ is mainly in the opposite direction of $H$, the system is not linear. Surprisingly $\partial M / \partial H$ swings between negative and positive values, i.e., we predict an entirely orbital diamagnetic to paramagnetic fluctuation. This phenomenon is important compared to the ideal de Haas-van Alphen effect i.e. the corresponding phenomenon under perpendicular magnetic field.

cond-mat.mtrl-sci↗

arXiv2007

Quasi two-dimensional carriers in dilute-magnetic-semiconductor quantum wells under in-plane magnetic field

Due to the competition between spatial and magnetic confinement, the density of states of a quasi two-dimensional system deviates from the ideal step-like form both quantitatively and qualitatively. We study how this affects the spin-subband populations and the spin-polarization as functions of the temperature, $T$, and the in-plane magnetic field, $B$, for narrow to wide dilute-magnetic-semiconductor quantum wells. We focus on the quantum well width, the magnitude of the spin-spin exchange interaction, and the sheet carrier concentration dependence. We look for ranges where the system is completely spin-polarized. Increasing $T$, the carrier spin-splitting, $U_{oσ}$, decreases, while increasing $B$, $U_{oσ}$ increases. Moreover, due to the density of states modification, all energetically higher subbands become gradually depopulated.

cond-mat.mtrl-sci↗

arXiv2007

Spin-subband populations and spin polarization of quasi two-dimensional carriers under in-plane magnetic field

Under an in-plane magnetic field, the density of states of quasi two-dimensional carriers deviates from the occasionally stereotypic step-like form both quantitatively and qualitatively. For the first time, we study how this affects the spin-subband populations and the spin-polarization as functions of the temperature, T, and the in-plane magnetic field, B, for narrow to wide dilute-magnetic-semiconductor quantum wells. We examine a wide range of material and structural parameters, focusing on the quantum well width, the magnitude of the spin-spin exchange interaction, and the sheet carrier concentration. Generally, increasing T, the carrier spin-splitting, U, decreases, augmenting the influence of the minority-spin carriers. Increasing B, U increases and accordingly carriers populate majority-spin subbands while they abandon minority-spin subbands. Furthermore, in line with the density of states modification, all energetically higher subbands become gradually depopulated. We also indicate the ranges where the system is completely spin-polarized.

cond-mat.mtrl-sci↗