Function Formalism Research Articles

Dynamics of Elementary Steps on Metal Surfaces at High Coverages: The Prevalence and Kinetic Competence of Contiguous Bare-Atom Ensembles.

The rate of elementary steps on densely-covered surfaces depends sensitively on repulsive interactions within dense adlayers, situations ubiquitous in practice and with kinetic consequences seldom captured by Langmuirian treatments of surface catalysis. This study develops an ensemble-based method that assesses how such repulsion influences the prevalence and kinetic competence of bare-atom ensembles of different size. Chemisorbed CO (CO*) is used as an example because it forms dense adlayers on metal nanoparticles during CO2 hydrogenation (CO2-H2) and other reactions, leading to significant repulsion that weakens the binding of CO* and kinetically-relevant transition states (TS). This approach is enabled by density functional theory and probability formalisms and describes the prevalence of ensembles of contiguous bare atoms from their formation energy (via CO* desorption); it then determines their competence in stabilizing the TS and mediating the reaction rates. The specific conclusions reflect the extent to which a given TS and CO* desorbed to form bare ensembles "sense" repulsion and the contribution of each ensemble size to each reaction channel mediated by distinct TS structures. These formalisms are illustrated by assessing the relative contributions, kinetic relevance, and ensemble size requirements for two CO2-H2 routes (direct and H-assisted CO2 activation to CO and H2O) on Ru nanoparticles, but they are not restricted to specific bound species or reaction channels. This method is essential to assess the kinetic relevance of elementary steps in a given catalytic sequence and to determine the contributions from parallel reaction channels at the crowded surfaces that prevail in the practice of surface catalysis.

Complex scaling method applied to the study of the Swanson Hamiltonian in the broken PT-symmetry phase

In this work, we study the non-PT symmetry phase of the Swanson Hamiltonian in the framework of the Complex Scaling Method. By constructing a bi-orthogonality relation, we apply the formalism of the response function to analyse the time evolution of different initial wave packages. The Wigner Functions, mean value of operators, and the probabilities of survival and persistence for the different wave packages are evaluated as a function of time. We analyse in detail the time evolution in the neighbourhood of Exceptional Points. We derive a continuity equation for the system. We compare the results obtained using the Complex Scaling Method to the ones obtained by working in a Rigged Hilbert Space.

Dynamics of proton tunneling in Hydrogen-Bonded systems through Green's function formalism

This study proposes a new theoretical model based on Green's function formalism for studying proton tunneling via hydrogen bonding. This approach allows calculating the tunneling probability and the tunneling energy that proton transfer occurs along a given path inferred a priori. The method is extended to multiple protons tunneling, characterizing the behaviour of some biological molecules. Specifically, the cases of the proton transfer in the Fujicurin A molecule and the double proton tunneling in the Guanine-Cytosine base-pair are investigated. The new approach is an alternative to those present in the literature. It allows straightforwardly predicting the mechanisms of intramolecular and intermolecular proton transfers involving the rearrangement of conjugated electrons.

A frugal machine-intelligent paper sensor for quantification of glucose through standalone desktop application: A computational and experimental approach

A paper-based electrochemical sensor utilizing MoS2 as sensing material is developed to quantitatively estimate glucose in a complex extracellular fluid matrix. The contribution of MoS2 as sensing material is substantiated in the context of density functional theory formalism. The molecular modelling of MoS2 and glucose interaction is elucidated through the theoretical estimation of non-covalent interactions and charge density difference plots. The charge transfer phenomenon during the oxidation of glucose molecule in electrochemical experiments is verified through electronic band structure analysis and frontier orbital theory. The electrochemical responses indicate that the sensor exhibits an average accuracy of nearly 96%, with a quantification limit of 100 nM. Furthermore, the chronoamperometric measurements highlight the superior sensitivity of the device in presence of various perturbing molecules. The obtained DPV responses were integrated with a robust machine learning-driven standalone app GluQuantify. This app precisely predicts the glucose concentrations in serum samples. The utilization of GluQuantify substantially elevates the overall accuracy of the sensing platform to 99% and automates the detection process. The application also enhances the resolution of the sensor to 0.01 µM, which mitigates the sensor resolution-related issues in manual estimation.

Optical Emission Spectra of Molecular Excitonic Polariton Computed at the First‐Principles Level QED‐TDDFT

In microcavity, strong coupling between light and molecules leads to the formation of hybrid excitations, i.e., the polaritons, or exciton‐polaritons. Such coupling may alter the energy landscape of the system and the optical properties of the material, making it an effective approach for controlling the light emission from molecular materials. However, due to the complexity of vibrational modes, spectroscopic calculations for organic exciton‐polaritons remain to be challenging. In this work, based on the linear‐response quantum‐electrodynamical time‐dependent density functional theory (QED‐TDDFT), we employ the thermal vibrational correlation function (TVCF) formalism to calculate the molecular optical spectrum of the lower polaritons (LP) at first‐principles level for three molecules, i.e., anthracene, distyrylbenzenes (DSB), and rubrene. The polaron decoupling effect is confirmed from our first‐principles computations. The theoretical emission spectra of LP provide fruitful insights for molecular and device design in microcavities that are otherwise hindered due to the lack of vibrational information.

Electroluminescence Rectification and High Harmonic Generation in Molecular Junctions.

The field of molecular electronics has emerged from efforts to understand electron propagation through single molecules and to use them in electronic circuits. Serving as a testbed for advanced theoretical methods, it reveals a significant discrepancy between the operational time scales of experiments (static to GHz frequencies) and theoretical models (femtoseconds). Utilizing a recently developed time-linear nonequilibrium Green function formalism, we model molecular junctions on experimentally accessible time scales. Our study focuses on the quantum pump effect in a benzenedithiol molecule connected to two copper electrodes and coupled with cavity photons. By calculating both electric and photonic current responses to an ac bias voltage, we observe pronounced electroluminescence and high harmonic generation in this setup. The mechanism of the latter effect is more analogous to that from solids than from isolated molecules, with even harmonics being suppressed or enhanced depending on the symmetry of the driving field.

Contribution to the study of the CoFeTi Asquaternary Heusler material's structural, electronic, and magnetic properties

By simulating the structural, electronic, and magnetic properties of the QuateryCoFeTiAs Heusler compound, we presented a theoretical investigation in this work The calculations were performed using the generalized gradient (GGA) approximation and the WIEN2k code's application of the augmented plane wave method (FP-LAPW)which is based on density functional formalism (DFT). The results are consistent with important theoretical calculations.Our results showed that this compound conforms with the (Slater-Pauling) Mtot = (ZT - 24) μB rule and is a half-metallic material.

A Meshless And Binless Approach To Compute Statistics In 3D Ensemble PTV

We propose a method to obtain super-resolution of turbulent statistics for three-dimensional ensemble particle tracking velocimetry (EPTV). Our approach is “meshless” because it does not require a grid to compute derivatives, and it is “binless” because it does not require bins to compute local statistics. The method combines the constrained radial basis function (RBF) formalism introduced in Sperotto et al. (Meas Sci Technol, 33:094005, 2022) with a kernel estimate approach for the ensemble average of the RBF regressions. The computational cost for the RBF regression is alleviated with the partition of unity method (PUM). We compare the newly proposed method with traditional binning-based approaches such as Gaussian weighting (Agüí and Jiménez, JFM, 185:447-468, 1987) and local polynomial fitting (Agüera et al, Meas Sci Technol, 27:124011, 2016). The results on experimental data of an underwater jet show a better resolution of spatial gradients of turbulent stresses while at the same time yielding an analytical expression which results in super-resolution of statistical quantities.

Theoretical prediction of the potential of using two-dimensional V2S2 as an effective anode for alkali metal ion batteries

This study investigates proper anode of alkali metal-ion batteries (MIBs) in response of urgent demand for effective devices for storing energy. The 2D V2S2 system can be a potential material as a MIB anode. We have employed the density functional formalism to examine the energetical, dynamic, mechanical, and thermal stability of pristine V2S2 monolayer. The pristine monolayer has inherent metallicity, which satisfies one of the criteria for being an electrode material. The electrical and structural characteristics of the V2S2 systems with the adsorbates of alkali metals and the charge transfer within the system are explored. The barriers of Li, Na, and K migration are computed as 0.42 eV, 0.12 eV, and 0.14 eV, respectively. In addition, our predicted systems demonstrate a significant theoretical capacity of 968.9 mAh/g of the lithium and sodium atoms. The computed open-circuit voltages support that this monolayer can be a practical 2D anode.

Conceptual Properties of Islamic Economic Modeling: Complexity, Nonlinearity, and Endogeneity in Epistemological Perspectives

This paper introduces a new perspective of economic reasoning and analysis pertaining to situations of complexity combined with nonlinearity and endogenous relations among interacting, integrating and evolutionary entities. The entities comprise multi-variables representing different embedded systems that encompass economy, society, science, and ethics. In the emergent model of endogenous inter-causal relationships between such entities the ontological perspective assumes the nature of evaluating inter-causal intra- and inters- systemic relations by means of formalism belonging to functional ontology of mathematical forms (Gruber, 1993), as opposed to invoking metaphysical ontological speculation. The functional ontological approach to structure and formalize leads to a new framework of economic reasoning in the presence of embedded systems that continuously participate and complement, as opposed to being subjected to the central postulate of marginal rate of substitution and exogenous treatment of knowledge in mainstream economics. The continuous phenomenon of interaction, integration, and evolutionary (IIE) learning in such inter-causal systems establish ethical endogeneity. Thus, philosophical background of economic reasoning is invoked in the functional epistemological formalism of the interactive, integrative, and evolutionary systems. That is sush systems are characterized by IIE-learning processes induced by the episteme of unity of knowledge.

Effects of Photon Recycling and Luminescent Coupling in All‐Perovskite Tandem Solar Cells Assessed by Full Opto‐electronic Simulation

The impact of photon recycling (PR) and of luminescent coupling (LC) on the photovoltaic performance of all‐perovskite tandem solar cells is analyzed by the means of optical and full opto‐electronic device simulation. Optical processes are assessed using a comprehensive Green function formalism that considers wave optical effects also in emission. Starting from a consistent fit of experimental sub‐cell and tandem characteristics, the effects of re‐absorption are propagated from the optical limit to a situation with consideration of realistic charge transport across the entire tandem device. This also provides insight into the origin of performance losses due to sub‐cell and interconnection quality.

Chirality-Induced Spin Selectivity: Analysis of Density Functional Theory Calculations.

Chirality-induced spin selectivity (CISS), which was demonstrated in several molecular and material systems, has drawn much interest recently. The phenomenon, described in electron transport by the difference in the transport rate of electrons of opposite spins through a chiral system, is however not fully understood. Herein, we employed density functional theory in conjunction with spin-orbit coupling to evaluate the percent spin-polarization in a device setup with finite electrodes at zero bias, using an electron transport program developed in-house. To study the interface effects and the level of theory considered, we investigated a helical oligopeptide chain, an intrinsically chiral gold cluster, and a helicene model system that was previously studied (Zöllner et al. J. Chem. Theory Comput. 2020, 16, 7357-7371). We find that the magnitude of the spin-polarization depends on the chiral system-electrode interface that is modeled by varying the interface boundary between the system's regions, on the method of calculating spin-orbit coupling, and on the exchange-correlation functional, e.g., the amount of exact exchange in the hybrid functionals. In addition, to assess the effects of bias, we employ the nonequilibrium Green's function formalism in the Quantum Atomistix Toolkit program, showing that the spin-flip terms could be important in calculating the CISS effect. Although understanding CISS in comparison to experiment is still not resolved, our study provides intrinsic responses from first-principles calculations.

Cascading failures in bipartite networks with directional support links.

We study the cascading failures in a system of two interdependent networks whose internetwork supply links are directional. We will show that, by utilizing generating function formalism, the cascading process can be modeled by a set of recursive relations. Most importantly, the functions involved in these relations are solely dependent upon the choice of the degree distribution of ingoing links. Simulation results in the limit of very large networks based on different choices of degree distributions for outgoing links, e.g., Kronecker delta, Poisson and Pareto, are indeed identical and are in excellent agreement with the theory. However, for Pareto distribution with the shape parameter 1<α<2, the convergence is slow. In general, directional networks can be more vulnerable or less vulnerable than their bidirectional counterparts. For three special settings of interdependent networks, we analytically compare their vulnerability. For practical applications it is important to predict if a system responds to the size of the initial attack continuously or if there is catastrophic collapse of the system if the attack exceeds a specific transition size. We analytically show that systems with lower average degrees are more resilient against this abrupt transition. We also establish an equivalence of this transition with the liquid-gas transition in statistical mechanics. In the last section, we derive the set of recursive relation to describe the cascading process where the initial attack is not restricted to a single network.

Interplay of superconductivity and magnetism in the Fe1+yTe1‐xSex iron‐based superconductor: A theoretical study

AbstractThe competition between superconductivity and magnetism has been studied for the ongoing investigation of mechanisms in unconventional superconductors. Fe1+yTe1−xSex is distinct among iron‐based superconductors due to its structural simplicity, comprising solely FeTe/Se layers that are favorable for probing the superconductivity mechanism. The main goal of this article is to focus on the computational investigation of the interplay of magnetism and superconductivity in the Fe1+yTe1−xSex multiband superconductor. From the electronic structure of the Fe1+yTe1−xSex superconductor, a two‐band Hamiltonian model was considered to examine the interplay of magnetism and superconductivity in the Fe1+yTe1‐xSex superconductor. Using Green's function formalism with the Hamiltonian model, the mathematical statements for the superconducting (Sc) gap parameter, spin density wave (SDW) ordering parameter, Sc and magnetic transitional temperatures have been obtained. Using these mathematical expressions, the phase diagram of transition temperatures versus the gap parameters for the Fe1+yTe1‐xSex superconductor has been plotted. The intersection region in the phase diagram of transition temperatures as a function of the SDW order parameter has been plotted to show the possible interplay of superconductivity and magnetism in a Fe1+yTe1‐xSex iron‐based superconductor.

Temperature dependence analysis of intersubband absorption in asymmetric ZnO/MgZnO quantum wells: Potential for terahertz emission applications

In this paper, in ZnO/MgxZn1−xO quantum well structures, with 20% of Mg, we have calculated the electronic states of confined levels and the intersubband absorption coefficient with or without the effect of non-parabolicity. We use the finite difference approach to do our computations inside the envelope function formalism approximation. The results show that the wavelength range covered by the E12 transition (9–16 μm) is mid-infrared to far-infrared. According to our findings, ZnO/MgZnO quantum well structures, which have extremely similar lattice characteristics and the benefit of an unconstrained structure, have E23 transition energies that provide terahertz frequencies (1.1—20THz) that are utilized in airport security and explosives detection. This promotes intersubband photonic structure design and epitaxial development. Furthermore, we have examined the impact of temperature on the Fermi level and the load carrier population inside each level for these remarkable structures. In addition, each transition's oscillation force and intersubband absorption are considered.

Electron–phonon coupling and a resonant-like optical observation of a band inversion in topological crystal insulator Pb1−x Sn x Se

The optical reflectivity of n-type Pb0.865Sn0.135Se and Pb0.75Sn0.25Se solid solutions was measured in the THz spectral region energetically corresponding to optical phonon excitations and in the temperature range from 40 K to 280 K. The first solid solution exhibits an open energy gap with trivial band ordering at all temperatures, while for the second one the transition from trivial insulator to topological crystal insulator phase is expected. The analysis of Pb0.75Sn0.25Se data performed within the dynamic dielectric function formalism revealed an anomaly of resonance-like character in the temperature dependence of LO phonon frequency. The formula for LO phonon energy renormalization reproduced observed anomaly for energy gap equal to zero, the phase transition occurred at T 0 = (172 ± 2) K. This effect was absent for Pb0.865Sn0.135Se. Present results show that reflectivity measurements in the THz range in the vicinity of LO phonon frequency can be valuable experimental method for precise determining of band inversion temperature in narrow-gap topological materials.

Development of an innovative diffraction scattering theory of X-rays and electrons in imperfect crystals.

Fundamental equations describing the X-ray and electron diffraction scattering in imperfect crystals have been derived in the form of the matrix Fredholm-Volterra integral equation of the second kind. A theoretical approach has been developed using the perfect-crystal Green function formalism. In contrast, another approach utilizes the wavefield eigenfunctions related to the diagonalized matrix propagators of the conventional Takagi-Taupin and Howie-Whelan equations. Using the Liouville-Neumann-type series formalism for building up the matrix Fredholm-Volterra integral equation solutions, the general resolvent function solutions of the X-ray and electron diffraction boundary-valued Cauchy problems have been obtained. Based on the resolvent-type solutions, the aim is to reveal the features of the diffraction scattering onto the crystal lattice defects, including the mechanisms of intra- and interbranch wave scattering in the strongly deformed regions in the vicinity of crystal lattice defect cores. Using the two-stage resolvent solution of the second order, this approach has been supported by straightforward calculation of the electron bright- and dark-field contrasts of an edge dislocation in a thick foil. The results obtained for the bright- and dark-field profiles of the edge dislocation are discussed and compared with analogous ones numerically calculated by Howie & Whelan [Proc. R. Soc. A (1962), 267, 206].

Theoretical study on the structure, spectroscopic, and current–voltage behavior of 11-Cis and Trans retinal isomers in rhodopsin

In this study, the electronic transport properties of 11-Cis and Trans retinal, components of rhodopsin, were investigated as optical molecular switches using the nonequilibrium Green’s function (NEGF) formalism combined with first-principles density functional theory (DFT). These isomers, which can be reversibly converted into each other, were examined in detail. The structural and spectroscopic properties, including infrared (IR), Raman, nuclear magnetic resonance (NMR), and ultraviolet (UV) spectra, were analyzed using the hybrid B3LYP/6–311 + + G** level of theory. Complete vibrational assignments were performed for both forms utilizing the scaled quantum mechanical force field (SQMFF) methodology. To evaluate the conductivity of these molecules, we utilized current–voltage (I-V) characteristics, transmission spectra, molecular projected self-consistent Hamiltonian (MPSH), HOMO–LUMO gap, and second-order interaction energies (E2). The trendline extrapolation of the current–voltage plots confirmed our findings. We investigated the effect of different electrodes (Ag, Au, Pt) and various connection sites (hollow, top, bridge) on conductivity. The Ag electrode with the hollow site exhibited the highest efficiency. Our results indicate that the Cis form has higher conductivity than the Trans form.

Jiezi: An open-source Python software for simulating quantum transport based on non-equilibrium Green's function formalism

We present a Python-based open-source library named Jiezi, which provides the means of simulating the electronic transport properties of nanoscaled devices on the atomistic level. The key feature of Jiezi lies in its core algorithm, i.e., self-consistent orchestration between the non-equilibrium Green's function (NEGF) method and a Poisson's equation solver. Beyond the construction of the tight-binding (TB) Hamiltonian with empirical parameters for conventional materials, the package offers a comprehensive framework for constructing the Wannier-based Hamiltonian matrix, enabling the investigation of novel materials and their heterostructures. To expedite the solution of NEGF systems, a methodology based on renormalization theory is proposed for reducing the dimension of the Hamiltonian matrix. Additionally, we adopt a non-linear Poisson equation solver with no analytical approximation in this software. The software facilitates seamless integration with external tools for geometry and mesh generation and post-processing. In this paper, we present the main capabilities and workflow by demonstrating with a simulation for the carbon nanotube field-effect transistor (CNTFET). Program summaryProgram Title: JieziCPC Library link to program files:https://doi.org/10.17632/nk79kbtww4.1Developer's repository link:https://github.com/Jiezi-negf/JieziLicensing provisions: GPLv3Programming language: PythonNature of problem: Simulates the quantum transport property of nano-scaled transistors based on the predefined device structure and the material composition.Solution method: Solves the coupled Schrödinger equation and Poisson equation by NEGF and finite element method.

Advancing molecular modeling and reverse vaccinology in broad-spectrum yellow fever virus vaccine development

Yellow fever outbreaks are prevalent, particularly in endemic regions. Given the lack of an established treatment for this disease, significant attention has been directed toward managing this arbovirus. In response, we developed a multiepitope vaccine designed to elicit an immune response, utilizing advanced immunoinformatic and molecular modeling techniques. To achieve this, we predicted B- and T-cell epitopes using the sequences from all structural (E, prM, and C) and nonstructural proteins of 196 YFV strains. Through comprehensive analysis, we identified 10 cytotoxic T-lymphocyte (CTL) and 5T-helper (Th) epitopes that exhibited overlap with B-lymphocyte epitopes. These epitopes were further evaluated for their affinity to a wide range of human leukocyte antigen system alleles and were rigorously tested for antigenicity, immunogenicity, allergenicity, toxicity, and conservation. These epitopes were linked to an adjuvant (β\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\beta$$\\end{document}-defensin) and to each other using ligands, resulting in a vaccine sequence with appropriate physicochemical properties. The 3D structure of this sequence was created, improved, and quality checked; then it was anchored to the Toll-like receptor. Molecular Dynamics and Quantum Mechanics/Molecular Mechanics simulations were employed to enhance the accuracy of docking calculations, with the QM portion of the simulations carried out utilizing the density functional theory formalism. Moreover, the inoculation model was able to provide an optimal codon sequence that was inserted into the pET-28a( +) vector for in silico cloning and could even stimulate highly relevant humoral and cellular immunological responses. Overall, these results suggest that the designed multi-epitope vaccine can serve as prophylaxis against the yellow fever virus.