arXiv subjects

Ashkan Shekaari

Publications and source records attributed to Ashkan Shekaari.

11 recordsLinked to original sources

arXiv2026

Structural, electronic, and optical properties of 2D $\alpha$-graphdiyne from first-principles

The structural, electronic, and optical properties of monolayer $\alpha$-graphdiyne ($\alpha$-GDY) are systematically investigated using density-functional theory within the plane-wave pseudopotential formalism. The electronic band structure reveals a gapless Dirac crossing at the K point, indicating Dirac-semimetallic behavior within the PBE/GGA framework. The calculated total and orbital-projected density of states show that the electronic states near the Fermi level are dominated by the carbon $2p$ orbitals, while the contribution of the $2s$ orbitals is comparatively weak. The optical response exhibits pronounced polarization dependence. The in-plane dielectric function displays a strong low-energy electronic response and negative values of its real part, whereas the out-of-plane component remains positive throughout the investigated energy range. Consistently, the absorption coefficient, extinction coefficient, reflectivity, and electron energy-loss spectra reveal pronounced optical anisotropy. The calculated plasma frequencies are approximately $3.21$~eV for in-plane polarization and $1.06$~eV for out-of-plane polarization, highlighting the strongly anisotropic electronic response of the monolayer. These findings demonstrate that $\alpha$-GDY combines Dirac-like electronic behavior with highly anisotropic optical properties, indicating its potential relevance to polarization-sensitive optoelectronic, plasmonic, and nanoelectronic applications.

cond-mat.mtrl-sci↗

arXiv2025

Electronic structure of SLSiN under charge density modulation

First-principles density-functional theory calculations were carried out to assess how incremental unit-cell charging alters the electronic behavior of SLSiN (single-layer Si$_3$N$_4$). The net charge per cell was systematically tuned from $n\,=\,0$ (the neutral/reference configuration) to $n\,=\,\pm\,1,\pm\,2$, and $\pm\,3$ elementary charges, and for each charged configuration the band structure and density of states were evaluated at the PBE level. In its neutral state, SLSiN exhibits zero electronegativity, signifying both its indifference to additional electron density and its intrinsic stability when integrated into heterostructures. Altogether, these results reveal that precise control of the charge density can drive SLSiN across an insulator-to-metal transition.

cond-mat.mtrl-sci↗

arXiv2024

Electronic structure of molybdenene from first principles

Density functional theory has been applied to investigate the electronic structure and lattice stability of molybdenene monolayer in both its hexagonal and triclinic phases, within ultrasoft pseudopotential approach. In agreement with experimental findings, it has been found that either phase is metallic. Analyzing partial density of states has revealed that the $d$ valence orbitals of molybdenum atoms have had the largest contribution to such a metallic property, due to being half-empty as well as being the outermost. Phonon-dispersion calculations also have led to negative frequencies for either phase, showing lattice instability, as reported in the experimental literature.

cond-mat.mtrl-sci↗

arXiv2024

Interaction between U-shaped amyloid beta fibril and semiconducting silicon nitride monolayer

Motivated by some recent works showing the ability of semiconducting monolayers to disintegrate the structures of biological fibrils, we have applied molecular dynamics (MD) simulations in both classical and quantum regimes to investigate whether semiconducting Si$_3$N$_4$ monolayer has the same ability on interaction with U-shaped amyloid beta (A$\beta$) fibril. In agreement with the literature, we found that disintegration began from the last chain (E) due to the rather strong interaction between the monolayer and the fibril residues numbered from 17 to 28 on the very chain, also engaging the next chain (D) over time. As a result, the $\beta$-sheet-rich content of chain E considerably decreases on interaction with the monolayer, turning into other secondary-structure types including turn and coil, in accordance with experimental findings. Results endorse the view that semiconducting Si$_3$N$_4$ monolayer has the potential of destabilizing the structure and conformation of U-shaped amyloid beta fibrils.

cond-mat.soft↗

arXiv2021

Mechanical stretching of amyloid Abeta11-42 fibrils using steered molecular dynamics

Mechanical strength of amyloid beta fibrils has been known to be correlated with neuronal cell death. Here, we resorted to steered molecular dynamics (SMD) simulations to mechanically stretch a single S-shape amyloid beta Abeta11-42 dodecamer fibril in vacuum. It was found that the weakest sites at which the fibril was ruptured due to mechanical extension were exclusively at the interfaces of alanine and glutamic acid distributed throughout the fibril. It was also revealed that the free energy required to unfold the fibril to form a long linear conformation is equivalent to ~ 210 eV, being several thousand times larger than thermal voltage at room temperature. As a consequence, within solution a larger free energy is needed for such a maximal stretching based on the fact that amyloid beta fibrils are structurally more stable in solution due to the interplay between their hydrophobic cores and solution's entropy.

cond-mat.soft↗

arXiv2021

Biocompatibility of 2D Silicon Nitride: Interaction at the Nano-Bio interface

Determining potential abilities of nanostructures to induce toxicity to biological molecules is still a convoluted challenge in the realm of nanomedicine. Based on the unprecedented achievements of twodimensional nanomaterials in nearly all areas of applied sciences particularly medicine, we carried out all-atom molecular dynamics simulations to assess the biologically-important, yet-unmapped issue of the biocompatibility of 2D, hexagonal \b{eta}-Si3N4 nanosheet via investigating its possible cross interactions with both human serum albumin (HSA) and p53 tumor suppressor. Examining the conventional MD indicators in the presence and absence of the monolayer revealed that hexagonal Si3N4 nanosheet weakly binds to these two proteins without inducing any important, dramatic change to their secondary structures, revealing accordingly the biological compatibility of the monolayer in case it is released as therapeutics or carriers in vivo. This finding was also broadly supported by the related, time-dependent behaviors of the protein-monolayer as well as the protein-water interaction energies.

physics.bio-ph↗

arXiv2021

Theory and Simulation of the Ising Model

We have provided a concise introduction to the Ising model as one of the most important models in statistical mechanics and in studying the phenomenon of phase transition. The required theoretical background and derivation of the Hamiltonian of the model have also been presented. We finally have discussed the computational method and details to numerically solve the two- and three-dimensional Ising problems using Monte Carlo simulations. The related computer codes in both Python and Fortran, as well as a simulation trick to visualize the spin lattice, have also been provided.

cond-mat.stat-mech↗

arXiv2021

A concise introduction to molecular dynamics simulation: theory and programming

We provided a concise and self-contained introduction to molecular dynamics (MD) simulation, which involves a body of fundamentals needed for all MD users. The associated computer code, simulating a gas of classical particles interacting via the Lennard-Jones pairwise potential, was also written in Python programming language in both top-down and function-based designs.

cond-mat.mtrl-sci↗

arXiv2021

Temperature: The ignored factor in quantum mechanics

We have developed a theoretical formalism to introduce temperature as a parameter into the framework of non-relativistic quantum mechanics using the laws of classical thermodynamics and the canonical ensemble scheme of statistical mechanics. A self-consistent Hamiltonian has then been constructed for a given quantum many-body system which includes the effect of temperature in the form of correction terms added to the corresponding zero-temperature Hamiltonian of the system. Investigating some quantum mechanical systems with exact zero-temperature solutions including the particle-in-a-box model, the free particle, and the harmonic oscillator within our finite-temperature approach up to the first order of self-consistency has led to temperature-dependent Hamiltonians describing these systems above absolute zero without encountering any physically unacceptable brand of behavior for their wave functions and energy spectra. Results firmly support the view that a quantum mechanical system at a finite temperature behaves as if it is in a zero-temperature excited state.

quant-ph↗

arXiv2021

Temperature as perturbation in quantum mechanics

The perturbative approach was adopted to develop a temperature-dependent version of non-relativistic quantum mechanics in the limit of low-enough temperatures. A generalized, self-consistent Hamiltonian was therefore constructed for an arbitrary quantum-mechanical system in a way that the ground-state Hamiltonian turned out to be just a limiting case at absolute zero. The weak-coupling term connecting the system of interest and its immediate environment was accordingly treated as the perturbation. Applying the obtained generalized Hamiltonian to some typical quantum systems with exact zero-temperature solutions, including the free particle in a box, the free particle in vacuum, and the harmonic oscillator, up to the first order of self-consistency, therefore corrected their associated Hamiltonians, energy spectrums, and wavefunctions to be consistent with the low-temperature limit. Further investigation revealed some kind of quantum tunneling effect by a residual probability for the free particle in a box, as a chief consequence of thermally coupling to the reservoir. The possible effects of thermal environment on the main properties of the wavefunctions were also thoroughly examined and discussed.

quant-ph↗

arXiv2021

Thermodynamic equilibrium of biological macromolecules under mechanical constraints

Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic equilibrium with the surrounding is attained. However, in some important cases, we have to equilibrate the system of interest in the constant presence of certain constraints, being referred to as constrained equilibration in the present work. A clear illustration of this type is a single amyloid \b{eta}-strand or RNA, when the reaction coordinate is defined as the distance between the two ends of the strand and we are interested in carrying out replica-exchange umbrella sampling to map the associated free energy profile as the dependent quantity of interest. In such cases, each sample has to be equilibrated with the two ends fixed. Here, we introduced a simulation trick to perform this so-called constrained equilibration using steered molecular dynamics. We then applied this method to equilibrate a single, stretched \b{eta}-strand of an amyloid beta dodecamer fibril with fixed ends. Examining the associated curves of the total energy and the force exerted on the practically-fixed SMD atom over the total timespan broadly supported the validity of this kind of equilibration.

cond-mat.soft↗