Vol. 69 No. 3 May-Jun (2023): Revista Mexicana de Física

REVISTA MEXICANA DE FÍSICA, year 69, issue 3, May-June 2023. Bimonthly Journal published by Sociedad Mexicana de Física, A. C. Departamento de Física, 2º Piso, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, Alcaldía Coyacán, C.P. 04510, Ciudad de México. Apartado Postal 70-348. Tel. (+52)55-5622-4946, https://rmf.smf.mx/ojs/rmf, e-mail: rmf@ciencias.unam.mx. Chief Editor: Alfredo Raya Montaño. INDAUTOR Certificate of Reserve: 04-2021-102913424600-203, e-ISSN: 2683-2224, granted by Instituto Nacional del Derecho de Autor. Responsible for the last update of this issue, Technical Staff of Sociedad Mexicana de Física, A. C., 2o. Piso, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, C.P. 04510, Coyoacán, CDMX. Date of last modification, May 1st., 2023.

Published: 2023-05-01

04 Atomic and Molecular Physics

  • Radial solution of Schrödinger equation with Hulthen-Yukawa-Inverse quadratic potential in a Point-Like defect under AB-flux field

    Faizuddin Ahmed
    030401 1–10
    Abstract:

    In this paper, we determine the approximate eigenvalue solution of the non-relativistic wave equation in the presence of the Aharonov-Bohm flux field with Hulthen-Yukawa-Inverse Quadratic potential in a topological defect via point-like global monopole (PGM) geometry. We use the Greene-Aldrich improved approximation scheme into the centrifugal and reciprocal terms appear in the radial Schrödinger equation. We then solve this radial equation using the parametric Nikiforov-Uvarov method and analyze the effects on the eigenvalue solution. We see that the energy levels and the radial wave functions get modified by the topological defect of a point-like global monopole and the magnetic flux field that shows an analogue of the Aharonov-Bohm effect for the bound state. Finally, we utilize the eigenvalue solution to some potential models, such as Hulthen potential, Hulthen plus Yukawa potential, and Hulthen plus inverse quadratic potential and discuss the results.

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06 Fluid Dynamics

  • Stirnol Engine: A combination of Nitinol (shape memory alloy) and Gamma Stirling Engine

    H. Arif, A. Shah, T. A. Hussain Ratlamwala, K. Kamal, M. Ahmed
    030601 1–8
    Abstract:

    Global pursuit to meet emergent energy demands necessitates finding simple and cost effective solutions. A promising solution is the application of renewable energy with thermo-mechanical conversion systems such as Stirling engines. Considerable effort is in hand at industry and academia domains to stimulate the development of Stirling technology. Foregoing, this paper focuses on modelling of Low Temperature Difference (LTD) gamma-type Stirling engine and investigating means of enhancing its performance through integration of Nitinol spring. The CFD models were comprehensively developed to simulate the engine, which have been subsequently validated through experimental data. The results reveal that addition of Nitinol Spring enhances the overall efficiency of engine demonstrating affirmative impact of shape memory alloy towards performance output of Stirling engine.

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07 Gravitation, Mathematical Physics and Field Theory

  • A static spherically symmetric perfect fluid solution to model the interior of stars

    Gabino Estevez Delgado , Joaquin Estevez Delgado, Elivet Aguilar Campuzano
    030701 1–8
    Abstract:

    An exact solution for modeling the interior of stars with perfect fluid is presented, the geometry of their interior is described by a static and spherically symmetric regular space-time. The hydrostatic functions are physically acceptable for the compactness rate u = GM/c2R ∈ (0, 0.3183497], the speed of sound is a monotonically decreasing function, positive and lower than the speed of light, which implies that the condition of causality is not violated, meanwhile the stability of the solution is guaranteed due to the adiabatic index γ > 3.08387 and it is a monotonically increasing function. The analysis of the solution is presented graphically for specific values of the compactness on the interval u ∈ [0.2509338, 0.3183497] with the minimum value of this interval associated to the neutron star PSR J0348+0432, for observational data which generates the maximum compactness when the radius is minimal R = 12.062 km and the mass is maximum M = 2.05 M¯, generating a value of the central density ρc = 7.520589 × 1017 kg/m3

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08 High Energy Physics

  • The influence of noncommutativity on the energy spectra of bosonic particles in the framework of the DKGE with improved spatially-dependent mass including mixed scalar-vector Coulomb potentials in the ERQM symmetries

    Abdelmadjid Maireche
    030801 1–16
    Abstract:

    The bound state solutions of the deformed Klien-Gordon equation (DKGE) have been determined in the extended relativistic quantum mechanics ERQM symmetries using the improved spatially-dependent mass Coulomb potential with mixed scalar-vector Coulomb potentials (ISDM-SVCPs) model. The spatially-dependent mass Coulomb potential, as well as a combination of ((1/(r³)) and (1/(r⁴))), are included in the ISDM-SVCPs model, which is coupled with the coupling LΘ, which explains the interaction of the physical features of the system with the topological deformations of space-time. The new relativistic energy eigenvalues for the ISDM-CP have been derived using the parametric Bopp's shift method and standard perturbation theory. Quantum numbers (j,l,s,m), mixed potential depths (q/s_{c},m₀,m₁), and noncommutativity parameters (Θ,τ,χ) seemed to affect the new values we obtained. Within the framework of relativistic extended quantum mechanics, we have addressed certain significant particular instances that we hope will be valuable to the specialized researcher. In DKGE symmetries, we've also looked at the improved pure scalar Coulomb-like potential. The formulation of total energy was also discovered in the context of extended symmetries, which unified the energies of bosonic particles and antiparticles into a single mathematical formula. When the three simultaneous limits (Θ,τ,χ) were applied, we recovered the normal results of relativistic in the literature (0,0,0).

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  • Soft breaking of the µ ↔ τ symmetry by S4 ⊗ Z2

    J. D. García-Aguilar, A. E. Pozas Ramírez, M. M. Suárez Castañeda, J. C. Gómez-Izquierdo
    030802 1–20
    Abstract:

    The µ ↔ τ symmetry has been ruled out by its predictions on the reactor and atmospheric angles, nevertheless, a breaking of this symmetry might provide correct values. For that reason, we build a non-renormalizable lepton model where the mixings arise from the spontaneous breaking of the S4 ⊗ Z2 discrete group, subsequently the µ ↔ τ symmetry is broken in the effective neutrino mass matrix, that comes from the type II see-saw mechanism. As main result, the reactor and atmospheric angles are corrected and their values are in good agreement with the experimental data for the inverted hierarchy. Furthermore, we point out a link between the atmospheric angle and reactor one. In the quark sector, under certain assumptions, the generalized Fritzsch textures shape to the quark mass matrices so that the CKM matrix values are guaranteed.

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  • B − L model with D5 × Z4 symmetry for lepton mass hierarchy and mixing

    Vien Vo Van
    030803 1–17
    Abstract:

    We propose a gauge B−L model with D5×Z4 for explaining the lepton mass and mixing through the type-I seesaw mechanism. The model can predict the neutrino masses and mixing angles including the Dirac and Majorana CP phases in good agreement with the experimental data. The model also predicts the effective neutrino parameters in highly consistent with the current constraints.

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10 Material Sciences

  • Optical and structural properties of graphene oxide-incorporated polyvinylpyrrolidone/copper ternary nanocomposites (PVP/Cu/GO) films

    Augustine Agobi, Alexander Ikeuba, Azubike Ekpunobi, Imosobome Lucky IKhioya, Kuffre Imoh Udofia, Joseph Effiom-Edem Ntibi, Chiaghanam Ndubuisi Ozoemena, M. A. Abua
    031001 1–9
    Abstract:

    Novel ternary nanocomposite films based on polyvinylpyrrolidone copper nanoparticles graphene oxide (PVP/Cu/GO) were prepared using electrochemical deposition technique on Fluorine doped tin oxide (FTO) substrate. This facile and effective approach has been proven to be very useful for the fabrication of inexpensive, high-performance electrochemical devices.  To achieve uniform deposition of the nanocomposite films, the three components of the nanocomposites were mixed under controlled conditions. The impact of different GO loading on the PVP/Cu/GO composites was measured using UV–visible spectroscopy, X-Ray Diffraction (XRD) spectroscopy, SEM, EDX, and four-point probe techniques to evaluate their optical, structural, morphological, compositional, and electrical properties, respectively. UV-visible analysis shows that the optical band gap (Eg) of the nanocomposite decreased from 3.51 to 2.02 eV with increasing GO loading. All of the nanocomposites showed UV absorbance of ≈450 nm. According to the XRD results, the GO materials were very well dispersed in the PVP/Cu/GO composites, while also revealing the crystalline nature of the nanocomposites. The SEM results revealed spherical-shaped grains of the deposited films, while the EDX results revealed the major elements deposited. Four-point probe analysis of the nanocomposites revealed slight increase in conductivity with low GO content, thus confirming the semiconducting properties of the nanocomposites with the GO content. The obtained results herein shows that the PVP/Cu/GO nanocomposites are successfully synthesized with attractive physiochemical properties suitable for the fabrication of organic electronic devices and photovoltaic devices.

     

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  • Physical properties of spray pyrolysed ZnO thin films obtained from nitrate, acetate and chloride precursors: Comparative study for Solar Cell Applications

    K. Salim, W. Azzaoui
    031002 1–8
    Abstract:

    ZnO thin films prepared using zinc chloride, zinc acetate and zinc nitrate precursors have been successfully synthesized by Spray Pyrolysis method. Films depositions were carried out on glass substrates at 350◦C. Structural properties of ZnO films were investigated by X-ray diffraction (XRD), confirming that all precursors have an Hexagonal Wurtzite structure. The obtained films were oriented along the preferential (002) crystallographic plane. The phase purity was also confirmed by X-ray photoelectron spectroscopy (XPS), Ultra Violet-Visible, and Energy Dispersive X-ray spectroscopy measurements (EDX). The optical measurement revealed that films have average transmittance of 58%, 78% and 65% for zinc chloride, zinc acetate and zinc nitrate, respectively. The band gap values obtained are 3.19, 3.17 and 3.23 eV for ZnO films using zinc acetate, zinc chloride and zinc nitrate precursors, respectively. Additionally, the refractive index and extinction coefficient of the ZnO films for all precursors have been explored.

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  • Catching CO2 pollutant gas through nanocomposite formed by chitosan with non-circular C16 carbon double ring: VAMP study

    Juan Horacio Pacheco-Sánchez, F. J. Isidro-Ortega, I.-P. Zaragoza
    031003 1–8
    Abstract:

    VAMP study for catching CO2 on nanocomposite generated by chitosan with non-circular C16 carbon ring, for contributing to distinguish the need for ambient air cleaning. Our aim is to modify porosity of chitosan as adsorbent of pollutant agents. At this time our searching is for taking profit of chitosan and carbon rings as new nanocomposite to be applied on air cleaning of pollutant gas, as it is carbon dioxide (CO2). In here, a new material is proposed for pollutant gas capture to reduce atmospheric CO2 levels. Particularly, C16 double carbon ring is responsible for catching CO2, while on the one side chitosan is only capable to break CO2 molecules, on the other side it can be surrounded by carbon ring molecules to catch more CO2, pollutant molecules.

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  • Water adsorption on rutile titanium dioxide (110): Theoretical study of the effect of surface oxygen vacancies and water flux in the steady state case

    Fatima Bouzidi, Moustafa Tadjine, Abderrezak Berbri , Ahmed Bouhekka
    031004 1–9
    Abstract:

    The aim purpose of the present work is highlighting the impact of surface oxygen vacancies and H2O flux on the behavior of water adsorption at the rutile titanium dioxide (110). Therefore, a theoretical model, based on molecular and dissociation mechanisms at different surface atomic sites, was formulated in a system of partial differential coupled equations. The proposed model used to study, in an atomic scale, this complex phenomenon of adsorption governed by several factors including surface vacancies defects and water flux. The findings of the solution of the system of equations in the steady state case, presented in this paper, strongly indicated that the rate coverage of surface oxygen vacancies has an important role in the dissociation of H2O as well as the flux which is a key factor in the behavior of water adsorption on the TiO2 (110) and the rate coverage of OH groups.

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  • A comparison of viscoelastic behavior of engineering elastomers under different stress and temperature

    Jocelyn Arlet Juárez Hernández, Jonathan Allan Sotomayor-del-Moral, Orlando Susarrey-Huerta, Leonardo Israel Farfán-Cabrera, Juan Benito Pascual-Francisco
    031005 1–9
    Abstract:

    In this work, a comparison of the viscoelastic creep behavior of five engineering elastomers (Ethylene-Propylene-Diene Monomer, Flouroelastomer, nitrile butadiene rubber, silicon rubber and neoprene/chloroprene rubber) is presented. Creep tests at different stress levels and temperatures were conducted using a “home-built” creep test device. A commercial equipment of Digital Image Correlation technique was implemented for the measurement of the time-dependent strains. The linear viscoelastic behavior regimes were determined by evaluating the creep compliance for each stress and temperature condition. Then, the creep curves obtained were fitted to a characteristic creep model, enabling the calculation of the viscoelastic parameters of each material. It was observed that the tested elastomers exhibited different elastic and viscous parameters, which were found to decrease with temperature. Particularly, it was observed that silicon rubber showed large instantaneous (elastic) strain and a small viscous deformation, whereas the Flouroelastomer rubber exhibited moderate strain curves, even at very high temperatures (100 °C and 120 °C), showing the highest creep resistance and the wider regime of linear viscoelastic behavior.  

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11 Medical Physics

  • Analysis of factors that affect radiation dose level during interventional cardiology procedures using logistic regression

    Edrees Harki, Zhala S. Rashid
    031101 1–8
    Abstract:

    Interventional cardiology procedures (ICP) are considered some of the main medical procedures in which patients are exposed to high doses of radiation. The aim of this study was to examine how to control the level of radiation exposure and to analyse and study the factors affecting the increase in radiation exposure from the specified level using a regression method. The results model correctly predicted that in 80.0%, 90.5%, and 95.2% of the cases, there were routine dose area product (DAP) levels, and in 64.3%, 33.3%, and 77.8% of cases, there were high levels of DAP, giving an overall percentage, correct prediction rate of 72.45%, 73.35%, and 90.0%, for coronary angiography (CA), percutaneous coronary intervention (PCI), and combined CA with PCI (CA/PCI), respectively. All the factors studied in this research, namely Kv, mA, Fluoroscopy Time (FT) and Body Mass Index (BMI), have a significant relationship with the DAP level. We concluded that regression analysis is a reliable method for evaluating the user protocol in a center or hospital and identifying variables that have an effect on the dose area product level in interventional cardiology.

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  • Effect of transverse magnetic field on dose distributions of yttrium 90 skin patch source

    Hakan Epik
    031102 1–6
    Abstract:

    The total dose absorbed on the tumor cell from the skin patch sources used in clinical superficial brachytherapy should be limited within the target tumor volume in order to minimize the potential side effects. Average range of the beta particles within tissue may exceed the thickness of a superficial skin tumor beyond the target tumor volume, causing side effects by damaging the deeper located healthy tissue and the bone underneath the tumor. It is desired to minimize the possible side effects by selecting a short-range radionuclide. Administering the treatment under an external magnetic field is another option for reducing side effects. To achieve this, in this study, the percentage deep dose (PDD) and transverse dose profile (TDP) distributions of the skin patch source labeled with Yttrium 90 (90Y) using the GEANT4-based GAMOS Monte Carlo code were examined before and after applying magnetic field, and it was evaluated  whether it was possible to limit the dose within a certain volume or not.

    Simulation results showed that, along with the application of a transverse magnetic field, the dose values increased by 7.2% and 3.1% respectively at 0.25 mm and 1.0 mm depths whereas it decreased by 9.4%, 25.0%, 41.8% and 57.6%, at 2.0 mm, 3.0 mm, 4.0 mm and 5.0 mm depths respectively on the central axis from the surface of the tissue phantom with respect to the 0 T values of the field.  In case of a superficial skin tumor with a thickness of 3.0 mm from the skin surface, the amount of dose accumulated in the tumor volume for 0 T value of the transverse magnetic field was 89% of the total dose, while it increased to 98% at the intensity of 1.5 T, and the dose received by the healthy tissue under the tumor decreased by 10.1%.

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12 Nuclear Physics

  • Comprehensive examination of the elastic scattering angular distributions of 10C+4He, 27Al, 58Ni and 208Pb using various potentials.

    M. N. El-Hammamy, Awad Ibraheem, M. El-Azab Farid, E. F. Elshamy, Sh. Hamada
    031201 1–13
    Abstract:

    The recently measured elastic scattering angular distributions for 10C + 4He, 10C + 27Al, 10C + 58Ni and 10C + 208Pb nuclear systems are investigated in the current study using various potentials based on phenomenological, semi microscopic as well as microscopic approaches. The implemented potentials are: optical potential, double folding potentials based on both Sao Paulo and CDM3Y6 interactions with and without taking into account the effect of the rearrangement term, as well as the cluster folding potential. The cluster nature of 10C as a core of 9B with a valence proton orbiting this core is applied to generate the cluster folding potentials for the different considered systems. The concerned experimental data is fairly reproduced with all the aforementioned potentials.

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13 Optics

  • Complex Fourier demodulation approach for the dual rotation polarizer-analyzer polarimeter

    J. Cervantes-L., G. A. Parra Escamilla, J. L. Flores Núñez, D. I. Serrano Garcia
    031301 1–6
    Abstract:

    In this research, we propose a demodulation algorithm for the dual rotation polarizer-analyzer polarimeter. The proposal retrieves the partial Mueller matrix from the complex coefficients, theoretically calculated from the Fourier transform of the output intensity. As calibration parameters, the initial orientations of the polarizer-analyzer are used. Experimental results for air and a rotating dichroic film polarizer show our proposal's feasibility.

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  • Star shape interferometer with reduced vibration sensitivity

    Juan de la Rosa, Eduardo Gomez, Victor Manuel Valenzuela
    031302 1–9
    Abstract:

    An optical interferometer has a high sensitivity to displacements of the mirrors and other optical elements, something that becomes a source of fluctuations in situations where one is only interested in the phase change due to a sample inserted in one of the paths. A Sagnac interferometer minimizes this sensitivity by having the two beams follow opposite trajectories, so that a mirror displacement gives a similar phase change for both paths, but makes it impossible to insert an element that affects only one path. We present a new kind of interferometer, the Star interferometer, where the two beams still interact with all the optical elements while having different trajectories. We obtain a common phase change in both trajectories by having a different number of turns for each path. Having independent access to both trajectories makes it possible to determine the phase change due to a sample inserted in one of the paths, opening new possibilities for interferometric configurations that maintain a reduced sensitivity to displacements of the optical elements.

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16 Solid State Physics

  • Production of Al2O3-SiC composites from micrometer α-Al2O3 powder obtained via sol-gel

    Quetzalmaflor Miranda, I. I. López López, J. Lemus Ruiz, A. Contreras-Cuevas, J. Zárate-Medina
    031601 1–6
    Abstract:

    Alumina (Al2O3) is an advanced ceramic material developed for different applications as refractories, precision tools, pacemaker, etc. Solid state sintering of alumina or matrix ceramic composites (CMCs) compacts starts from powders. Once method to produce high quality aluminum oxide powders is the sol-gel technique. Alumina begins as pseudo-crystallized aluminum hydroxide gel which is produced under moderate reaction conditions trough a colloidal suspension. In this work, Al2O3 powder was produced by precipitation of pseudoboehmite (PB) through sol-gel process. Subsequently, a mixture of Al2O3/SiC powders with 5 wt.% of SiC as reinforcement was produced. This mixture was used to manufacture green compacts by uniaxial pressing at 440 MPa. Afterward, some samples were applied a heat treatment (pre-sintered) at 1200°C for 6 h in air. Sintering was carried out in a vertical dilatometer Linseis L75 V up to 1500°C for 2h under argon atmosphere. Pseudobohemite, alumina powders and Al2O3/SiC composites were characterized through X-ray diffraction technique and Scanning Electron Microscopy (SEM). Dilatometric shrinkage data into densification curves obtained were analyzed. Images obtained with SEM showed a uniform Al2O3 powder morphology of submicron size, otherwise Al2O3/SiC composite images showed the interaction of the reinforcement particles on the ceramic matrix. Experimental results demonstrated the pre-sintering reduce the decomposition of SiC particles on the compact surface. This behavior was attributed to formation of SiO2 around the reinforcement particle due it act as protective barrier.

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  • Impact of AlN interlayer on the electronic and I-V characteristics of In0.17Al0.83N/GaN HEMTs devices

    Abdelmalek Douara, Abdelaziz Rabehi, Oussama Baitiche
    031602 1–6
    Abstract:

    Here, we study a simulation model of In0.17Al0.83N/GaN passivated high electron mobility transistors (HEMTs) on SiC substrate. The research focused systematically on the effet of AlN interlayer on the electronic and electric characteristics using the Nextnano simulation software. The 2D–electron gas density of  In0.17Al0.83N/AlN/GaN HEMTs is investigated through the dependence on various AlN layer thickness, we report calculations of  I-V characteristics, with 1.5 nm AlN thickness, we find the highest maximum output current of 1.81 A/mm at Vgs  1 V, and more than 450 mS/mm as a transconductance peak. The Results are in agreement with experimental data.

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  • Surface plasmon resonance based on graphene-metal-graphene structure: recurrence relation theory

    Gerardo González de la Cruz
    031603 1–6
    Abstract:

    The last years, graphene has opened exciting new fields in graphene plasmonics, due to the graphene’s unique optoelectronic properties such as long-lived collective excitation, extreme optical confinement in graphene plasmonics and extraordinary light-matter interactions in metamaterials. Therefore, these excellent properties make graphene a favorable candidate for novel plasmonic devices and potential applications in photonics, optoelectronics and sensor technologies. In this work, theoretical investigations are carried out to in Graphene-Metal-Graphene structure for enhanced surface plasmon resonance based on the recurrence relations’ method. We find that the graphene-metal-graphene structure supports both high-energy optical plasmon oscillations and out-of-phase low energy acoustic charge density excitations. Since a high performance of surface plasmon resonance excitations should exhibit a large depth of dip (small reflectivity), the minimum of reflectivity in the hybrid structure can be manipulated dynamically by changing the thickness of the metallic film, the number of the graphene layers and the dielectric proprieties of the surrounding dielectric materials. Based on this principle, different kinds of plasmonic sensors have been designed in previous years.

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  • Theoretical study of [111]-germanium nanowires as anode materials in rechargeable batteries: a density functional theory approach

    Ricardo Jiménez-Sánchez, Pedro Morales-Vergara, Fernando Salazar, Alvaro Miranda, Alejandro Trejo, Ivonne J. Hernández-Hernández, Luis Antonio Pérez, Miguel Cruz-Irisson
    031604 1–6
    Abstract:

    In this work, we present a Density Functional Theory (DFT) study of hydrogen-passivated germanium nanowires grown along the [111] crystallographic direction. The study is performed within the local density approximation (LDA) and the supercell technique. Four different diameters of nanowires were considered and the surface hydrogen atoms were replaced by Li ones using a sequential process. The results indicate that the nanowires have a semiconductor behaviour and the energy band gap diminishes when the number of Li atoms per unit cell increases. The formation energy results reveal that the Li atoms increase the stability of the Ge nanowires, and there is a charge transfer from the Li atoms to the surface Ge atoms. The open circuit voltage values are almost independent of the concentration of Li atoms. On the other hand, the lithium storage capacity results reveal that the Ge nanowires could be good candidates to be incorporated as anodic materials in the new generation of rechargeable batteries.

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  • Electronic structure and imaginary dielectric function for 2D GaAs doped with Si amphoteric impurities: A DFT study

    G. J. González-Loera, Karla Arely Rodríguez Magdaleno, F. M. Nava-Maldonado, J. C. Martínez-Orozco
    031605 1–5
    Abstract:

    Without a doubt, the impact of the discovery of 2D systems such as graphene has led to both theoretical and experimental investigations of a large number of materials such as Silicene, Borene, Arsenene, Phosphorene, just to mention some of the most emblematic ones, but other materials and its heterostructures are also of interest. From this point of view, in this work we present the band structure, density of states as well as the imaginary part of the dielectric function of a 2D GaAs system, by means of a density functional theory implementation. The aim of this study is to investigate the basic physical properties for a freestanding 2D GaAs sheet, as well as the effect of Si substitutional atoms, since it has an amphoteric nature in the GaAs, which means that depending on which atom is substituted, this can be an n- or p-type impurity atom. We report, as expected, that the levels do indeed appear near the conduction band (or valence) if the impurity is n-type (or p-type), respectively. Also the density of states due to the impurity is modified as well as the imaginary part of the dielectric function

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17 Thermodynamics and Statistical Physics

  • Dinámica molecular de grano grueso de la proteína tau

    Luciano Robert-Jimenez, Susana Figueroa-Gerstenmaier, Gustavo Basurto-Islas, Salvador Herrera-Velarde
    031701 1–12
    Abstract:

    Currently about 48 million people worldwide live with Alzheimer's disease, the most common form of dementia, and still without cure. This disease is partially due to abnormal posttranslational modifications in the protein tau, that in turn induce its abnormal polymerization, forming fibrils and neurofibrillary tangles. Tau does not have a well-defined structure, known as intrinsically disordered protein. Molecular dynamics is an effective method to study this kind of protein. In this work, molecular dynamics with SIRAH (Southamerican Initiative for a Rapid and Accurate Hamiltonian) force field was employed to model two different systems of tau, each with two protein molecules. In the first system, the two proteins are immersed only in water (represented as an explicit solvent), in the second system, in addition to the solvent, ions were added to investigate if charges presence induce protein self-aggregation. The structural modifications of tau were evaluated from 1 µs trajectory at 310 K. For each system, the proteins showed important changes with respect to the initial configuration; there are some differences in the secondary structure according to the presence or absence of ions. We identify that, in both systems, there is no evidence of tau aggregation. The results validated the use of the SIRAH force field to study large proteins and the capacity to reach temporal and spatial scales close to the experimental studies. In addition, the conformational analysis of the obtained trajectories suggests, for the first time, a molecular dynamics perspective that contributes to the understanding and identification of protein-protein interaction regions.

    Actualmente, a nivel mundial, alrededor de 48 millones de personas padecen la enfermedad de Alzheimer, la forma más común de demencia, para la cual no hay cura. La enfermedad se debe, parcialmente, a las alteraciones postraduccionales que experimenta la proteína tau y que favorecen su polimerización anormal formando fibrillas y marañas neurofibrilares. La tau es una proteína intrínsecamente desordenada, es decir, no posee una estructura bien definida. Una técnica eficaz en el estudio de este tipo de proteínas es la dinámica molecular. En este trabajo se utilizó dinámica molecular empleando el campo de fuerza SIRAH (del inglés: Southamerican Initiative for a Rapid and Accurate Hamiltonian) para modelar dos sistemas distintos de tau, cada uno con dos moléculas de proteína. En el primer sistema las dos proteínas están inmersas únicamente en agua (representada como solvente explícito) y en el segundo sistema, además del solvente, se agregaron iones para investigar la influencia de cargas en la posible agregación de tau. A partir de la trayectoria de 1 μs a una temperatura de 310 K, se analizaron los cambios estructurales que experimentaron los monómeros de tau. En ambos sistemas, las proteínas presentaron cambios importantes respecto a la configuración inicial; existiendo algunas diferencias en la estructura secundaria acorde a la presencia o ausencia de iones. Identificamos que, en ambos sistemas, no hay evidencia de un proceso agregativo. Los resultados validaron el uso del campo de fuerza SIRAH para estudiar proteínas de gran tamaño y la factibilidad de alcanzar escalas temporales y espaciales cercanas a las experimentales. Además, el análisis conformacional de las trayectorias obtenidas ofrece, por primera vez, una perspectiva desde la dinámica molecular de la forma en que interactúan dos proteínas tau completas, lo cual contribuye a la comprensión del fenómeno y a la identificación de las regiones de interacción proteína-proteína.

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