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25 pages, 859 KiB  
Article
Entanglement and Generalized Berry Geometrical Phases in Quantum Gravity
by Diego J. Cirilo-Lombardo and Norma G. Sanchez
Symmetry 2024, 16(8), 1026; https://doi.org/10.3390/sym16081026 (registering DOI) - 12 Aug 2024
Abstract
A new formalism is introduced that makes it possible to elucidate the physical and geometric content of quantum space–time. It is based on the Minimum Group Representation Principle (MGRP). Within this framework, new results for entanglement and geometrical/topological phases are found and implemented [...] Read more.
A new formalism is introduced that makes it possible to elucidate the physical and geometric content of quantum space–time. It is based on the Minimum Group Representation Principle (MGRP). Within this framework, new results for entanglement and geometrical/topological phases are found and implemented in cosmological and black hole space–times. Our main results here are as follows: (i) We find the Berry phases for inflation and for the cosmological perturbations and express them in terms of the observables, such as the spectral scalar and tensor indices, nS and nT, and the tensor-to-scalar ratio r. The Berry phase for de Sitter inflation is imaginary with the sign describing the exponential acceleration. (ii) The pure entangled states in the minimum group (metaplectic) Mp(n) representation for quantum de Sitter space–time and black holes are found. (iii) For entanglement, the relation between the Schmidt type representation and the physical states of the Mp(n) group is found: This is a new non-diagonal coherent state representation complementary to the known Sudarshan diagonal one. (iv) Mean value generators of Mp(2) are related to the adiabatic invariant and topological charge of the space–time, (matrix element of the transition <t<). (v) The basic even and odd n-sectors of the Hilbert space are intrinsic to the quantum space–time and its discrete levels (in particular, continuum for n), they do not require any extrinsic generation process such as the standard Schrodinger cat states, and are entangled. (vi) The gravity or cosmological on one side and another of the Planck scale are entangled. Examples: The quantum primordial trans-Planckian de Sitter vacuum and the classical late de Sitter vacuum today; the central quantum gravity region and the external classical gravity region of black holes. The classical and quantum dual gravity regions of the space–time are entangled. (vii) The general classical-quantum gravity duality is associated with the Metaplectic Mp(n) group symmetry which provides the complete full covering of the phase space and of the quantum space–time mapped from it. Full article
(This article belongs to the Section Physics)
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Figure 1
<p>Chiral-antichiral oscillation (zitterbebegung) giving the pattern of cat states from first principles. The asymmetry in the pattern can be seen, marking a preferential temporal evolution.</p>
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<p>3D picture of the chiral-antichiral oscillation (cat states pattern).</p>
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<p>The three images show from top to down the entangled coherent state where the degree of entaglement varies as a function of time from the highest to the lowest degree controlled by the overlap <math display="inline"><semantics> <mfenced separators="" open="&#x2329;" close="&#x232A;"> <mi>α</mi> <mspace width="0.166667em"/> <mo>|</mo> <mspace width="0.166667em"/> <mi>β</mi> </mfenced> </semantics></math>. Here <math display="inline"><semantics> <mrow> <mo>(</mo> <mi>x</mi> <mo>,</mo> <mi>y</mi> <mo>)</mo> </mrow> </semantics></math> correspond to <math display="inline"><semantics> <mrow> <mo form="prefix">Re</mo> <mspace width="0.166667em"/> <mover accent="true"> <mi>α</mi> <mo>˜</mo> </mover> </mrow> </semantics></math> and <math display="inline"><semantics> <mrow> <mo form="prefix">Im</mo> <mspace width="0.166667em"/> <mover accent="true"> <mi>α</mi> <mo>˜</mo> </mover> </mrow> </semantics></math>.</p>
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28 pages, 6642 KiB  
Article
Boolean Modeling of Biological Network Applied to Protein–Protein Interaction Network of Autism Patients
by Leena Nezamuldeen and Mohsin Saleet Jafri
Biology 2024, 13(8), 606; https://doi.org/10.3390/biology13080606 (registering DOI) - 10 Aug 2024
Viewed by 215
Abstract
Cellular molecules interact with one another in a structured manner, defining a regulatory network topology that describes cellular mechanisms. Genetic mutations alter these networks’ pathways, generating complex disorders such as autism spectrum disorder (ASD). Boolean models have assisted in understanding biological system dynamics [...] Read more.
Cellular molecules interact with one another in a structured manner, defining a regulatory network topology that describes cellular mechanisms. Genetic mutations alter these networks’ pathways, generating complex disorders such as autism spectrum disorder (ASD). Boolean models have assisted in understanding biological system dynamics since Kauffman’s 1969 discovery, and various analytical tools for regulatory networks have been developed. This study examined the protein–protein interaction network created in our previous publication of four ASD patients using the SPIDDOR R package, a Boolean model-based method. The aim is to examine how patients’ genetic variations in INTS6L, USP9X, RSK4, FGF5, FLNA, SUMF1, and IDS affect mTOR and Wnt cell signaling convergence. The Boolean network analysis revealed abnormal activation levels of essential proteins such as β-catenin, MTORC1, RPS6, eIF4E, Cadherin, and SMAD. These proteins affect gene expression, translation, cell adhesion, shape, and migration. Patients 1 and 2 showed consistent patterns of increased β-catenin activity and decreased MTORC1, RPS6, and eIF4E activity. However, patient 2 had an independent decrease in Cadherin and SMAD activity due to the FLNA mutation. Patients 3 and 4 have an abnormal activation of the mTOR pathway, which includes the MTORC1, RPS6, and eIF4E genes. The shared mTOR pathway behavior in these patients is explained by a shared mutation in two closely related proteins (SUMF1 and IDS). Diverse activities in β-catenin, MTORC1, RPS6, eIF4E, Cadherin, and SMAD contributed to the reported phenotype in these individuals. Furthermore, it unveiled the potential therapeutic options that could be suggested to these individuals. Full article
(This article belongs to the Section Bioinformatics)
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<p>Schematic representation of the mutated proteins in four patients colored with red, green, cyan, and brown with arrangements of their roles on Wnt and mTOR signaling pathways [<a href="#B33-biology-13-00606" class="html-bibr">33</a>].</p>
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<p>Schematic representation of the algorithm developed in SPIDDOR library in R using the asynchronous method. (<b>A</b>) The output of the dynamic evolution function. The rows represent the nodes, and the columns represent the 100 iterations. (<b>B</b>) The output of the average simulation function. The probability of each node to be ON calculated from 2500 (N) simulations.</p>
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<p>The oscillation of the proteins involved in cell adhesion or DNA transcription and translation in the Boolean system for 2500 simulations in every 100 time steps. The blue color shows when all the proteins are at 100% of their functional effect. The green color when the mutation-like effect was introduced to proteins with variants in each patient to delay their activation by 50%. The red color when the mutation-like effect was introduced to proteins with variants in each patient to knock out their activation.</p>
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<p>The averages of the datapoints that represent the curves in the Boolean system (<a href="#biology-13-00606-f004" class="html-fig">Figure 4</a>): (<b>A</b>) Showing the oscillation average of each protein in each patient; (<b>B</b>) Showing the oscillation average of each protein combined by patients.</p>
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<p>The knockout heatmap representing the perturbation indexes PIs as a result of knocking out each node in the system (columns) and their effect on the other nodes in the network (rows). The heatmap is scaled and colored as follows: PI values close to 1 are taking the value of 0 and colored in gray, PI values between 1.25 and 2 are taking the value of 1 and colored in light orange, PI values greater than 2 are taking the value of 2 and colored in dark orange, PI values between 0.5 and 0.8 are taking the value of −1 and colored in light blue, and PI values less than 0.5 are taking the value of −2 and colored in dark blue.</p>
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<p>Multiple sequence alignment of the residues around beta strands 1 and 2 in the ligand FGF1-19 identified in [<a href="#B59-biology-13-00606" class="html-bibr">59</a>] using NCBI COBALT and visualized with alignment viewer. The colored symbols are to ease comparison of same amino acid residue down the columns (yellow was recolored to black using onlinepngtools.com—accessed on 28 June 2024). The mutated residue (red box) in FGF5 is adjacent to the conserved domain. All sequences come from human cells, except FGF15, which is from mouse brain cells.</p>
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19 pages, 6004 KiB  
Article
An Evaluation Model for Node Influence Based on Heuristic Spatiotemporal Features
by Sheng Jin, Yuzhi Xiao, Jiaxin Han and Tao Huang
Entropy 2024, 26(8), 676; https://doi.org/10.3390/e26080676 (registering DOI) - 10 Aug 2024
Viewed by 248
Abstract
The accurate assessment of node influence is of vital significance for enhancing system stability. Given the structural redundancy problem triggered by the network topology deviation when an empirical network is copied, as well as the dynamic characteristics of the empirical network itself, it [...] Read more.
The accurate assessment of node influence is of vital significance for enhancing system stability. Given the structural redundancy problem triggered by the network topology deviation when an empirical network is copied, as well as the dynamic characteristics of the empirical network itself, it is difficult for traditional static assessment methods to effectively capture the dynamic evolution of node influence. Therefore, we propose a heuristic-based spatiotemporal feature node influence assessment model (HEIST). First, the zero-model method is applied to optimize the network-copying process and reduce the noise interference caused by network structure redundancy. Second, the copied network is divided into subnets, and feature modeling is performed to enhance the node influence differentiation. Third, node influence is quantified based on the spatiotemporal depth-perception module, which has a built-in local and global two-layer structure. At the local level, a graph convolutional neural network (GCN) is used to improve the spatial perception of node influence; it fuses the feature changes of the nodes in the subnetwork variation, combining this method with a long- and short-term memory network (LSTM) to enhance its ability to capture the depth evolution of node influence and improve the robustness of the assessment. Finally, a heuristic assessment algorithm is used to jointly optimize the influence strength of the nodes at different stages and quantify the node influence via a nonlinear optimization function. The experiments show that the Kendall coefficients exceed 90% in multiple datasets, proving that the model has good generalization performance in empirical networks. Full article
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<p>Study overview.</p>
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<p>Node influence assessment process diagram.</p>
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<p>Nodal spatiotemporal feature construction maps.</p>
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<p>Plot of the scale of impact on the network when the HEIST model is compared to other models with high-impact nodes selected as propagation sources.</p>
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<p>Analysis of propagation in a small network.</p>
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<p>Visualization of different network structures.</p>
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<p>Graph of the effect of different training network training tests.</p>
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20 pages, 8984 KiB  
Article
Numerical Study on the Heat Dissipation Performance of Diamond Microchannels under High Heat Flux Density
by Jiwen Zhao, Kunlong Zhao, Xiaobin Hao, Yicun Li, Sen Zhang, Benjian Liu, Bing Dai, Wenxin Cao and Jiaqi Zhu
Processes 2024, 12(8), 1675; https://doi.org/10.3390/pr12081675 (registering DOI) - 9 Aug 2024
Viewed by 283
Abstract
Heat dissipation significantly limits semiconductor component performance improvement. Thermal management devices are pivotal for electronic chip heat dissipation, with the enhanced thermal conductivity of materials being crucial for their effectiveness. This study focuses on single-crystal diamond, renowned for its exceptional natural thermal conductivity, [...] Read more.
Heat dissipation significantly limits semiconductor component performance improvement. Thermal management devices are pivotal for electronic chip heat dissipation, with the enhanced thermal conductivity of materials being crucial for their effectiveness. This study focuses on single-crystal diamond, renowned for its exceptional natural thermal conductivity, investigating diamond microchannels using finite element simulations. Initially, a validated mathematical model for microchannel flow heat transfer was established. Subsequently, the heat dissipation performance of typical microchannel materials was analyzed, highlighting the diamond’s impact. This study also explores diamond microchannel topologies under high-power conditions, revealing unmatched advantages in ultra-high heat flux density dissipation. At 800 W/cm2 and inlet flow rates of 0.4–1 m/s, diamond microchannels exhibit lower maximum temperatures compared to pure copper microchannels by 7.0, 7.2, 7.4, and 7.5 °C, respectively. Rectangular cross-section microchannels demonstrate superior heat dissipation, considering diamond processing costs. The exploration of angular structures with varying parameters shows significant temperature reductions with increasing complexity, such as a 2.4 °C drop at i = 4. The analysis of shape parameter ki indicates optimal heat dissipation performance at ki = 1.1. This research offers crucial insights for developing and optimizing diamond microchannel devices under ultra-high-heat-flux-density conditions, guiding future advancements in thermal management technology. Full article
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<p>Boundary conditions set in the model.</p>
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<p>Grid division: (<b>a</b>) overall grid division and (<b>b</b>) microchannel region grid division.</p>
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<p>Grid division with different densities: (<b>a</b>) Plan A, (<b>b</b>) Plan B, (<b>c</b>) Plan C, and (<b>d</b>) Plan D.</p>
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<p>Calculation model validation: (<b>a</b>) geometric structure of microchannels; (<b>b</b>) comparison of experimental and simulated average wall temperatures along the channel direction (normal direction from the inlet to the outlet) [<a href="#B38-processes-12-01675" class="html-bibr">38</a>].</p>
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<p>Relationship between maximum temperature and heat flux density of microchannels under different flow rate conditions: (<b>a</b>) silicon, (<b>b</b>) copper, (<b>c</b>) LTCC, and (<b>d</b>) aluminum.</p>
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<p>Comparison of maximum temperatures of different substrate materials at various heat flux densities.</p>
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<p>Comparison of heat dissipation performance of diamonds with different thermal conductivities.</p>
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<p>Heat dissipation performance of diamond microchannels with varying thermal conductivity.</p>
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<p>Influence of cross-sectional shape on heat dissipation performance: (<b>a</b>) schematic of microchannel model and (<b>b</b>) impact of cross-sectional variation on heat dissipation performance.</p>
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<p>The effect of microchannel expansion on heat dissipation performance: (<b>a</b>) microchannel model and (<b>b</b>) influence of <span class="html-italic">k</span><sub>1</sub> on the heat dissipation performance of microchannels.</p>
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<p>Temperature distribution of microchannels under different <span class="html-italic">k</span><sub>1</sub> values.</p>
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<p>Flow velocity distributions of microchannels under different <span class="html-italic">k</span><sub>1</sub> values.</p>
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<p>Pressure distribution of microchannels under different <span class="html-italic">k</span><sub>1</sub> values.</p>
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<p>The influence of different numbers of diamond-shaped (hourglass-shaped) microchannels on heat dissipation performance: (<b>a1</b>–<b>c1</b>) models of diamond-shaped (hourglass-shaped) microchannels with different numbers and (<b>a2</b>–<b>c2</b>) heat dissipation performance of diamond-shaped (hourglass-shaped) microchannels with different numbers.</p>
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<p>Effects of different numbers of diamond-shaped (hourglass-shaped) microchannels on maximum flow velocity and pressure: (<b>a1</b>–<b>c1</b>) effects on flow velocity; (<b>a2</b>–<b>c2</b>) effects on maximum pressure.</p>
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19 pages, 3142 KiB  
Article
Dynamic Radiant Barrier for Modulating Heat Transfer and Reducing Building Energy Usage
by Tyler R. Stevens, Behzad Parsi, Rydge B. Mulford and Nathan B. Crane
Energies 2024, 17(16), 3959; https://doi.org/10.3390/en17163959 (registering DOI) - 9 Aug 2024
Viewed by 258
Abstract
Buildings consume significant energy, much of which is used for heating and cooling. Insulation reduces undesired heat transfer to save on heating and cooling energy usage. Radiant barriers are a type of insulation technology that reduces radiant heat absorbed by a structure. Applying [...] Read more.
Buildings consume significant energy, much of which is used for heating and cooling. Insulation reduces undesired heat transfer to save on heating and cooling energy usage. Radiant barriers are a type of insulation technology that reduces radiant heat absorbed by a structure. Applying radiant barriers to buildings reduces costs and improves both energy efficiency and occupant comfort. However, homes often have favorable thermal gradients that could also be used to reduce energy usage if the insulation properties were switched dynamically. This article introduces two dynamic radiant barriers intended for residential attics, which can switch between reflecting and transmitting states as needed. These radiant barriers are manufactured as a single deformable assembly using sheet materials and are compatible with various actuation mechanisms. The efficacy of these radiant barriers is reported based on a hotbox experiment and numerical calculations. The experimental results demonstrate that both proposed dynamic radiant barrier designs increase effective thermal resistance by factors of approximately 2 when comparing insulating to conducting states, and by approximately 4 when comparing the insulating state to the case without a radiant barrier. Additionally, the dynamic radiant barriers achieve heat flux reductions up to 41.9% in the insulating state compared to tests without a dynamic radiant barrier. Full article
(This article belongs to the Section G: Energy and Buildings)
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<p>Conceptual designs of the two dynamic radiant barrier designs: Accordion and S-Curve.</p>
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<p>Two dynamic radiant barrier designs: Accordion fold and S-Curve. The DRBs in this image are made from polyethylene and metalized polyester.</p>
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<p>(<b>a</b>) Manufactured and exploded views of Accordion and S-Curve DRBs. Black represents the LDPE, while blue and teal are used to differentiate the segments formed by cutting each reflective sheet. (<b>b</b>) Dimensions for LDPE and aluminum components, with units in mm.</p>
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<p>A conceptual design of the simplified Accordion DRB which uses a single folded reflective sheet instead of multiple bonded sheets.</p>
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<p>The manufactured, simplified Accordion DRB using LDPE and ten aluminum sheets in the manufactured (insulating) and deployed (conducting) states. Blue tape is used to hold down the DRB.</p>
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<p>Isometric view and cross-section of the hotbox used to measure the effective transmissivity of the proposed DRBs. Thermocouples are placed on each side of both particleboard layers to estimate the heat fluxes. The insulation has a reflective layer, and the representation of the insulating DRB is scaled to emphasize its location.</p>
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<p>Labeled cross-section of hotbox setup for corresponding dimensions listed in <a href="#energies-17-03959-t001" class="html-table">Table 1</a>. Shades of grey indicate the distinct sections of insulation.</p>
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<p>Schematic figures of the FEA hotbox and boundary conditions of the system for the 2D simulation.</p>
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<p>Averaged temperature distribution across particleboards in the control group (No DRB) during testing.</p>
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<p>A comparison of the experimental data, between the control test (without DRB) and the Accordion and S-Curve DRB configurations. Plots represent (<b>a</b>) the heat flux measurements, (<b>b</b>) ratio of heat flux across the lower particleboard, (<b>c</b>) the thermal resistance measurements, and (<b>d</b>) ratios of thermal resistance. Ins and Con refer to the insulating (manufactured) and conducting (deployed) states of the DRB.</p>
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<p>Steady–state temperature profiles of the hotbox without DRB.</p>
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<p>Heat flux from simulation and experiment through the bottom particleboard (between surfaces 3 and 4).</p>
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11 pages, 7955 KiB  
Article
Grating Bio-Microelectromechanical Platform Architecture for Multiple Biomarker Detection
by Fahimeh Marvi, Kian Jafari and Mohamad Sawan
Biosensors 2024, 14(8), 385; https://doi.org/10.3390/bios14080385 - 9 Aug 2024
Viewed by 246
Abstract
A label-free biosensor based on a tunable MEMS metamaterial structure is proposed in this paper. The adopted structure is a one-dimensional array of metamaterial gratings with movable and fixed fingers. The moving unit of the optical detection system is a component of the [...] Read more.
A label-free biosensor based on a tunable MEMS metamaterial structure is proposed in this paper. The adopted structure is a one-dimensional array of metamaterial gratings with movable and fixed fingers. The moving unit of the optical detection system is a component of the MEMS structure, driven by the surface stress effect. Thus, these suspended optical nanoribbons can be moved and change the grating pattern by the biological bonds that happened on the modified cantilever surface. Such structural variations lead to significant changes in the optical response of the metamaterial system under illuminating angled light and subsequently shift its resonance wavelength spectrum. As a result, the proposed biosensor shows appropriate analytical characteristics, including the mechanical sensitivity of Sm = 11.55 μm/Nm−1, the optical sensitivity of So = Δλ/Δd = 0.7 translated to So = Δλ/Δσ = 8.08 μm/Nm−1, and the quality factor of Q = 102.7. Also, considering the importance of multi-biomarker detection, a specific design of the proposed topology has been introduced as an array for identifying different biomolecules. Based on the conducted modeling and analyses, the presented device poses the capability of detecting multiple biomarkers of disease at very low concentrations with proper precision in fluidic environments, offering a suitable bio-platform for lab-on-chip structures. Full article
(This article belongs to the Special Issue Micro-nano Optic-Based Biosensing Technology and Strategy)
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<p>Schematic of the proposed optical BioMEMS platform for biosensing of target analytes: (<b>a</b>) 3D design of the biosensor topology, and (<b>b</b>) a description of the physical parameters of its suspended MEMS framework (under displacements in the Z-direction).</p>
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<p>Simulated mechanical sensitivity of the suspended cantilever under applied surface stresses.</p>
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<p>Modal analysis of the proposed BioMEMS structure to estimate its bandwidth considering the first resonant frequency of f<sub>r1</sub> = 876.9 Hz.</p>
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<p>Optical pattern of the proposed grating metamaterials: (<b>a</b>) a top view for physical parameter description and (<b>b</b>) a cross-section view to explain the tuning mechanism under cantilever displacement.</p>
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<p>A compromise between the sensitivity and Figure of Merit (FOM) of the sensor (based on minimizing the FWHM) by optimizing several effective parameters of the proposed optical design, including (<b>a</b>) the incident angle and (<b>b</b>) the width of movable nanoribbons under different incident angles.</p>
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<p>Simulated optical spectrum of the proposed tunable metamaterial gratings: (<b>a</b>) different resonances of the optical pattern in its wavelength spectrum under TE mode excitation (incident angle of 50 degrees), and (<b>b</b>) a cross-view of the electric field distribution of incident light in the desired resonant wavelength for a part (three cells) of the periodic pattern (λ = 2.055 μm).</p>
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<p>Wavelength changes in the movable grating metamaterials induced by several cantilever deflections.</p>
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<p>A schematic of the proposed BioMEMS platform for multiplex detection of biomarkers, highlighting: (<b>A</b>) an array of functionalized cantilevers by different specific bioreceptors; (<b>B</b>) biological markers; and (<b>C</b>) illuminated light and its reflection for wavelength modulation.</p>
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<p>Wavelength modulation of three optical patterns with different grating periods in a specific spectrum to simultaneously measure various concentrations of different biomarkers.</p>
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28 pages, 1533 KiB  
Article
Evaluating Federated Learning Simulators: A Comparative Analysis of Horizontal and Vertical Approaches
by Ismail M. Elshair, Tariq Jamil Saifullah Khanzada, Muhammad Farrukh Shahid and Shahbaz Siddiqui
Sensors 2024, 24(16), 5149; https://doi.org/10.3390/s24165149 - 9 Aug 2024
Viewed by 391
Abstract
Federated learning (FL) is a decentralized machine learning approach whereby each device is allowed to train local models, eliminating the requirement for centralized data collecting and ensuring data privacy. Unlike typical typical centralized machine learning, collaborative model training in FL involves aggregating updates [...] Read more.
Federated learning (FL) is a decentralized machine learning approach whereby each device is allowed to train local models, eliminating the requirement for centralized data collecting and ensuring data privacy. Unlike typical typical centralized machine learning, collaborative model training in FL involves aggregating updates from various devices without sending raw data. This ensures data privacy and security while collecting a collective learning from distributed data sources. These devices in FL models exhibit high efficacy in terms of privacy protection, scalability, and robustness, which is contingent upon the success of communication and collaboration. This paper explore the various topologies of both decentralized or centralized in the context of FL. In this respect, we investigated and explored in detail the evaluation of four widly used end-to-end FL frameworks: FedML, Flower, Flute, and PySyft. We specifically focused on vertical and horizontal FL systems using a logistic regression model that aggregated by the FedAvg algorithm. specifically, we conducted experiments on two images datasets, MNIST and Fashion-MNIST, to evaluate their efficiency and performance. Our paper provides initial findings on how to effectively combine horizontal and vertical solutions to address common difficulties, such as managing model synchronization and communication overhead. Our research indicates the trade-offs that exist in the performance of several simulation frameworks for federated learning. Full article
(This article belongs to the Section Intelligent Sensors)
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<p>The steps to complete training cycle within classic centralized learning.</p>
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<p>Centralized FL: hierarchical topology.</p>
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<p>Decentralized FL: P2P topology.</p>
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<p>Decentralized FL: ring topology.</p>
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<p>Logistic regression using FedAvg in HFL.</p>
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<p>MNIST dataset representation.</p>
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<p>Class distribution of MNIST dataset.</p>
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<p>Fashion MNIST dataset representation.</p>
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<p>Class distribution of Fashion-MNIST dataset.</p>
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<p>The performance of the simulators on the MNIST dataset.</p>
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<p>The performance of the simulators on the Fashion-MNIST dataset.</p>
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9 pages, 274 KiB  
Article
Remarks on the Quantum Effects of Screw Dislocation Topology and Missing Magnetic Flux
by Knut Bakke
Condens. Matter 2024, 9(3), 33; https://doi.org/10.3390/condmat9030033 - 8 Aug 2024
Viewed by 301
Abstract
We revisit the interaction between a point charge and an inhomogeneous magnetic field that yields the magnetic quantum dot system. This magnetic field is defined by filling the whole space, except for a region of radius r0. Then, we assume that [...] Read more.
We revisit the interaction between a point charge and an inhomogeneous magnetic field that yields the magnetic quantum dot system. This magnetic field is defined by filling the whole space, except for a region of radius r0. Then, we assume that there is an impenetrable potential wall located at r0 and discuss the quantum effects of screw dislocation topology and the missing magnetic flux. We first show that Landau levels can be achieved even though there is the presence of an impenetrable potential wall. We go further by discussing the confinement of a point charge to a cylindrical wire. In both cases, we show Aharonov–Bohm-type effects for bound states can be obtained from the influence of the screw dislocation topology and the missing magnetic flux. Later, we discuss the influence of the screw dislocation topology and the missing magnetic flux on the magnetization and the persistent currents. Full article
(This article belongs to the Section Condensed Matter Theory)
15 pages, 1199 KiB  
Review
The Systematics and Evolution of Gymnosperms with an Emphasis on a Few Problematic Taxa
by Yong Yang, Zhi Yang and David Kay Ferguson
Plants 2024, 13(16), 2196; https://doi.org/10.3390/plants13162196 - 8 Aug 2024
Viewed by 235
Abstract
Gymnosperms originated in the Middle Devonian and have experienced a long evolutionary history with pulses of speciation and extinction, which resulted in the four morphologically distinct extant groups, i.e., cycads, Ginkgo, conifers and gnetophytes. For over a century, the systematic relationships within [...] Read more.
Gymnosperms originated in the Middle Devonian and have experienced a long evolutionary history with pulses of speciation and extinction, which resulted in the four morphologically distinct extant groups, i.e., cycads, Ginkgo, conifers and gnetophytes. For over a century, the systematic relationships within the extant gymnosperms have been debated because different authors emphasized different characters. Recent phylogenomic studies of gymnosperms have given a consistent topology, which aligns well with extant gymnosperms classified into three classes, five subclasses, eight orders, and 13 families. Here, we review the historical opinions of systematics of gymnosperms with special reference to several problematic taxa and reconsider the evolution of some key morphological characters previously emphasized by taxonomists within a phylogenomic context. We conclude that (1) cycads contain two families, i.e., the Cycadaceae and the Zamiaceae; (2) Ginkgo is sister to cycads but not to conifers, with the similarities between Ginkgo and conifers being the result of parallel evolution including a monopodial growth pattern, pycnoxylic wood in long shoots, and the compound female cones, and the reproductive similarities between Ginkgo and cycads are either synapomorphic or plesiomorphic, e.g., the boat-shaped pollen, the branched pollen tube, and the flagellate sperms; (3) conifers are paraphyletic with gnetophytes nested within them, thus gnetophytes are derived conifers, and our newly delimited coniferophytes are equivalent to the Pinopsida and include three subclasses, i.e., Pinidae, Gnetidae, and Cupressidae; (4) fleshy cones of conifers originated multiple times, the Podocarpaceae are sister to the Araucariaceae, the Cephalotaxaceae and the Taxaceae comprise a small clade, which is sister to the Cupressaceae; (5) the Cephalotaxaceae are distinct from the Taxaceae, because the former family possesses typical female cones and the fleshy part of the seed is derived from the fleshiness of integument, while the latter family has reduced female cones and preserves no traces of the seed scale complexes. Full article
(This article belongs to the Section Plant Systematics, Taxonomy, Nomenclature and Classification)
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<p>Different hypotheses on phylogenetic relationships of seed plant groups. (<b>A</b>) anthophyte scenario indicating that gnetophytes and angiosperms comprise a clade sister to cycads; (<b>B</b>) neo-englerian scenario suggesting that gnetophytes and angiosperms comprise a clade sister to conifers; (<b>C</b>,<b>D</b>), gnetifer hypothesis implying that gnetophytes are sister to conifers, (<b>C</b>) differs from (<b>D</b>) in the relationship of <span class="html-italic">Ginkgo</span>; (<b>E</b>,<b>F</b>), gnepine hypothesis suggesting that conifers are paraphyletic with gnetophytes sister to the Pinaceae, (<b>E</b>) differs from (<b>F</b>) in the position of <span class="html-italic">Ginkgo</span>; (<b>G</b>), gnecup hypothesis indicating that conifers are paraphyletic with gnetophytes sister to cupressophytes; (<b>H</b>), gnetophytes-other gymnosperms hypothesis suggesting that gymnosperms constitute a monophyletic group and gnetophytes are sister to a clade including the rest gymnosperm groups; (<b>I</b>), gnetophytes-other seed plants hypothesis denoting that gymnosperms are paraphyletic and gnetophytes are sister to a clade encompassing other seed plant groups. Colored branches and abbreviations display the jumping groups of seed plants. Abbreviations: ANG: angiosperms; CYC: cycadophytes; GIN: <span class="html-italic">Ginkgo</span>; GNE: gnetophtyes; PIN: Pinaceae; CUP: cupressophytes.</p>
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<p>Female cone characters and phylogenomic relationships of extant families of gymnosperms. (<b>A</b>) <span class="html-italic">Cycas panzhihuaensis</span>; (<b>B</b>) <span class="html-italic">Ginkgo biloba</span>; (<b>C</b>) <span class="html-italic">Araucaria cunninghamii</span>; (<b>D</b>) <span class="html-italic">Podocarpus macrophyllus</span>; (<b>E</b>) <span class="html-italic">Sciadopitys verticillata</span>; (<b>F</b>) <span class="html-italic">Sequoiadendron giganteum</span>; (<b>G</b>) <span class="html-italic">Sabina chinensis</span>; (<b>H</b>) <span class="html-italic">Cephalotaxus sinensis</span>; (<b>I</b>) <span class="html-italic">Taxus cuspidata</span>; (<b>J</b>) <span class="html-italic">Pinus tabuliformis</span>; (<b>K</b>) <span class="html-italic">Ephedra rhytidosperma</span>; (<b>L</b>) <span class="html-italic">Welwitschia mirabilis</span>; (<b>M</b>) <span class="html-italic">Gnetum gnemon</span>.</p>
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<p>Historical classifications of conifers. (<b>A</b>) Keng [<a href="#B44-plants-13-02196" class="html-bibr">44</a>]; (<b>B</b>) Florin [<a href="#B87-plants-13-02196" class="html-bibr">87</a>]; (<b>C</b>) Cheng and Fu [<a href="#B46-plants-13-02196" class="html-bibr">46</a>].</p>
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19 pages, 1303 KiB  
Article
Natural Language Processing for Hardware Security: Case of Hardware Trojan Detection in FPGAs
by Jaya Dofe, Wafi Danesh, Vaishnavi More and Aaditya Chaudhari
Cryptography 2024, 8(3), 36; https://doi.org/10.3390/cryptography8030036 - 8 Aug 2024
Viewed by 329
Abstract
Field-programmable gate arrays (FPGAs) offer the inherent ability to reconfigure at runtime, making them ideal for applications such as data centers, cloud computing, and edge computing. This reconfiguration, often achieved through remote access, enables efficient resource utilization but also introduces critical security vulnerabilities. [...] Read more.
Field-programmable gate arrays (FPGAs) offer the inherent ability to reconfigure at runtime, making them ideal for applications such as data centers, cloud computing, and edge computing. This reconfiguration, often achieved through remote access, enables efficient resource utilization but also introduces critical security vulnerabilities. An adversary could exploit this access to insert a dormant hardware trojan (HT) into the configuration bitstream, bypassing conventional security and verification measures. To address this security threat, we propose a supervised learning approach using deep recurrent neural networks (RNNs) for HT detection within FPGA configuration bitstreams. We explore two RNN architectures: basic RNN and long short-term memory (LSTM) networks. Our proposed method analyzes bitstream patterns, to identify anomalies indicative of malicious modifications. We evaluated the effectiveness on ISCAS 85 benchmark circuits of varying sizes and topologies, implemented on a Xilinx Artix-7 FPGA. The experimental results revealed that the basic RNN model showed lower accuracy in identifying HT-compromised bitstreams for most circuits. In contrast, the LSTM model achieved a significantly higher average accuracy of 93.5%. These results demonstrate that the LSTM model is more successful for HT detection in FPGA bitstreams. This research paves the way for using RNN architectures for HT detection in FPGAs, eliminating the need for time-consuming and resource-intensive reverse engineering or performance-degrading bitstream conversions. Full article
(This article belongs to the Special Issue Emerging Topics in Hardware Security)
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<p>Concept of a bitstream protocol stack for Xilinx 7 series FPGAs.</p>
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<p>Xilinx configuration file formats. (Note: For (1), (2), (3) please refer to [<a href="#B22-cryptography-08-00036" class="html-bibr">22</a>]).</p>
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<p>Steps in 7-series FPGA configuration.</p>
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<p>Type 1 packet header format for Xilinx 7-series FPGA.</p>
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<p>Opcode for Type 1 packet header.</p>
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<p>Type 2 packet header format for Xilinx 7-series FPGA.</p>
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<p>Frame address register description.</p>
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<p>Conventional RNN architecture.</p>
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<p>Hidden layer for conventional RNN.</p>
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<p>Cell for LSTM architecture.</p>
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<p>The .<span class="html-italic">bit</span> file format.</p>
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<p>Data preprocessing algorithm.</p>
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<p>Training RNN models on preprocessed bitstreams.</p>
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<p>Training and validation accuracy over training epochs for RNN with step size 16.</p>
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<p>Training and validation accuracy over training epochs for LSTM with step size 16.</p>
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<p>Step size and accuracy trends for LSTM.</p>
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<p>Example of latched RO.</p>
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<p>Training and validation accuracy vs. step size for c17 benchmark.</p>
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<p>Comparison of c17 performance metrics for step sizes 8 and 16.</p>
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14 pages, 44406 KiB  
Article
Engineering In-Co3O4/H-SSZ-39(OA) Catalyst for CH4-SCR of NOx: Mild Oxalic Acid (OA) Leaching and Co3O4 Modification
by Guanyu Chen, Weixin Zhang, Rongshu Zhu, Yanpeng Chen, Minghu Zhao and Mei Hong
Molecules 2024, 29(16), 3747; https://doi.org/10.3390/molecules29163747 - 7 Aug 2024
Viewed by 298
Abstract
Zeolite-based catalysts efficiently catalyze the selective catalytic reduction of NOx with methane (CH4-SCR) for the environmentally friendly removal of nitrogen oxides, but suffer severe deactivation in high-temperature SO2- and H2O-containing flue gas. In this work, SSZ-39 [...] Read more.
Zeolite-based catalysts efficiently catalyze the selective catalytic reduction of NOx with methane (CH4-SCR) for the environmentally friendly removal of nitrogen oxides, but suffer severe deactivation in high-temperature SO2- and H2O-containing flue gas. In this work, SSZ-39 zeolite (AEI topology) with high hydrothermal stability is reported for preparing CH4-SCR catalysts. Mild acid leaching with oxalic acid (OA) not only modulates the Si/Al ratio of commercial SSZ-39 to a suitable value, but also removes some extra-framework Al atoms, introducing a small number of mesopores into the zeolite that alleviate diffusion limitation. Additional Co3O4 modification during indium exchange further enhances the catalytic activity of the resulting In-Co3O4/H-SSZ-39(OA). The optimized sample exhibits remarkable performance in CH4-SCR under a gas hourly space velocity (GHSV) of 24,000 h−1 and in the presence of 5 vol% H2O. Even under harsh SO2- and H2O-containing high-temperature conditions, it shows satisfactory stability. Catalysts containing Co3O4 components demonstrate much higher CH4 conversion. The strong mutual interaction between Co3O4 and Brønsted acid sites, confirmed by the temperature-programmed desorption of NO (NO-TPD), enables more stable NxOy species to be retained in In-Co3O4/H-SSZ-39(OA) to supply further reactions at high temperatures. Full article
(This article belongs to the Special Issue Zeolites and Porous Materials: Synthesis, Properties and Applications)
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<p>Effects of oxalic acid concentration, etching time, and etching temperature in acid etching post-treatment on the (<b>a</b>–<b>c</b>) NO<span class="html-italic"><sub>x</sub></span> conversion, (<b>d</b>–<b>f</b>) CH<sub>4</sub> conversion, and (<b>g</b>–<b>i</b>) CH<sub>4</sub> selectivity of the resulting catalysts for dry CH<sub>4</sub>-SCR. Reaction conditions: [NO] = 400 ppm, [CH<sub>4</sub>] = 600 ppm, [O<sub>2</sub>] = 10 vol%, Ar balance, GHSV = 24,000 h<sup>−1</sup>.</p>
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<p>Effect of the Co<sub>3</sub>O<sub>4</sub> to H-SSZ-39(OA) mass ratio on the (<b>a</b>) NO<span class="html-italic"><sub>x</sub></span> conversion and (<b>b</b>) CH<sub>4</sub> conversion of the resulting catalysts under wet conditions. Reaction conditions: [NO] = 400 ppm, [CH<sub>4</sub>] = 600 ppm, [O<sub>2</sub>] = 10 vol%, [H<sub>2</sub>O] = 5 vol%, Ar balance, GHSV = 24,000 h<sup>−1</sup>. (<b>c</b>) Recyclability test of In-Co<sub>3</sub>O<sub>4</sub>/H-SSZ-39(OA) under harsh H<sub>2</sub>O- and SO<sub>2</sub>-containing conditions. Reaction conditions: [NO] = 400 ppm, [CH<sub>4</sub>] = 600 ppm, [O<sub>2</sub>] = 10 vol%, [H<sub>2</sub>O] = 5 vol%, [SO<sub>2</sub>] = 50 ppm, Ar balance, GHSV = 12,000 h<sup>−1</sup>. (<b>d</b>) Stability test of In-Co<sub>3</sub>O<sub>4</sub>/H-SSZ-39(OA) under harsh H<sub>2</sub>O- and SO<sub>2</sub>-containing conditions. Reaction conditions: [NO] = 400 ppm, [CH<sub>4</sub>] = 600 ppm, [O<sub>2</sub>] = 10 vol%, [H<sub>2</sub>O] = 5 vol%, [SO<sub>2</sub>] = 50 ppm, Ar balance, GHSV = 12,000 h<sup>−1</sup>, <span class="html-italic">T</span> = 600 °C.</p>
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<p>SEM images of (<b>a</b>) Pristine H-SSZ-39, (<b>b</b>) In/H-SSZ-39(OA), and (<b>c</b>) In-Co<sub>3</sub>O<sub>4</sub>/H-SSZ-39(OA). HRTEM images of (<b>d</b>) Pristine H-SSZ-39, (<b>e</b>) In/H-SSZ-39(OA), and (<b>f</b>) In-Co<sub>3</sub>O<sub>4</sub>/H-SSZ-39(OA). (<b>g</b>) PXRD patterns, (<b>h</b>) N<sub>2</sub> adsorption–desorption isotherms, and (<b>i</b>) NLDFT PSD curves of samples.</p>
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<p>(<b>a</b>) <sup>27</sup>Al MAS SSNMR and (<b>b</b>) <sup>29</sup>Si MAS SSNMR of Pristine H-SSZ-39 and In/H-SSZ-39(OA).</p>
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<p>High-resolution XPS spectra of (<b>a</b>) In 3d region and (<b>b</b>) Co 2p region.</p>
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<p>(<b>a</b>) NH<sub>3</sub>-TPD profiles and (<b>b</b>) NO-TPD profiles of samples.</p>
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12 pages, 12974 KiB  
Article
Effect of Ca, Ba, Be, Mg, and Sr Substitution on Electronic and Optical Properties of XNb2Bi2O9 for Energy Conversion Application Using Generalized Gradient Approximation–Perdew–Burke–Ernzerhof
by Fatima Kainat, Nawishta Jabeen, Ali Yaqoob, Najam Ul Hassan, Ahmad Hussain and Mohamed E. Khalifa
Crystals 2024, 14(8), 710; https://doi.org/10.3390/cryst14080710 - 7 Aug 2024
Viewed by 279
Abstract
Bismuth layered structure ferroelectrics (BLSFs), also known as Aurivillius phase materials, are ideal for energy-efficient applications, particularly for solar cells. This work reports the first comprehensive detailed theoretical study on the fascinating structural, electronic, and optical properties of XNb2Bi2O [...] Read more.
Bismuth layered structure ferroelectrics (BLSFs), also known as Aurivillius phase materials, are ideal for energy-efficient applications, particularly for solar cells. This work reports the first comprehensive detailed theoretical study on the fascinating structural, electronic, and optical properties of XNb2Bi2O9 (X = Ca, Ba, Be, Mg, Sr). The Perdew–Burke–Ernzerhof approach and generalized gradient approximation (GGA) are implemented to thoroughly investigate the structural, bandgap, optical, and electronic properties of the compounds. The optical conductivity, band topologies, dielectric function, bandgap values, absorption coefficient, reflectivity, extinction coefficient, refractive index, and partial and total densities of states are thoroughly investigated from a photovoltaics standpoint. The material exhibits distinct behaviors, including significant optical anisotropy and an elevated absorption coefficient > 105 cm−1 in the region of visible; ultraviolet energy is observed, the elevated transparency lies in the visible and infrared regions for the imaginary portion of the dielectric function, and peaks in the optical spectra caused by inter-band transitions are detected. According to the data reported, it becomes obvious that XNb2Bi2O9 (X = Ca, Ba, Be, Mg, and Sr) is a suitable candidate for implementation in solar energy conversion applications. Full article
(This article belongs to the Section Materials for Energy Applications)
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<p>Crystal structure of bismuth layered structure ferroelectrics (BLSFs) with generalized formula (Bi<sub>2</sub>O<sub>2</sub>)<sup>2+</sup>(A<sub>n−1</sub>B<sub>n</sub>O<sub>3n+1</sub>)<sup>2–</sup>.</p>
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<p>Band structure of BLSFs family: (<b>a</b>) CaNb<sub>2</sub>Bi<sub>2</sub>O<sub>9</sub>; (<b>b</b>) BaNb<sub>2</sub>Bi<sub>2</sub>O<sub>9</sub>; (<b>c</b>) BeNb<sub>2</sub>Bi<sub>2</sub>O<sub>9</sub>; (<b>d</b>) MgNb<sub>2</sub>Bi<sub>2</sub>O<sub>9</sub>; and (<b>e</b>) SrNb<sub>2</sub>Bi<sub>2</sub>O<sub>9</sub>.</p>
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<p>Density of states of (<b>a</b>) CaNb<sub>2</sub>Bi<sub>2</sub>O<sub>9</sub>, (<b>b</b>) BaNb<sub>2</sub>Bi<sub>2</sub>O<sub>9</sub>, (<b>c</b>) BeNb<sub>2</sub>Bi<sub>2</sub>O<sub>9</sub>, (<b>d</b>) MgNb<sub>2</sub>Bi<sub>2</sub>O<sub>9</sub>, and (<b>e</b>) SrNb<sub>2</sub>Bi<sub>2</sub>O<sub>9</sub>.</p>
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<p>Partial density of states (PDOS) of (<b>a</b>) CaNb<sub>2</sub>Bi<sub>2</sub>O<sub>9</sub>, (<b>b</b>) BaNb<sub>2</sub>Bi<sub>2</sub>O<sub>9</sub>, (<b>c</b>) BeNb<sub>2</sub>Bi<sub>2</sub>O<sub>9</sub>, (<b>d</b>) MgNb<sub>2</sub>Bi<sub>2</sub>O<sub>9</sub>, and (<b>e</b>) SrNb<sub>2</sub>Bi<sub>2</sub>O<sub>9</sub>.</p>
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<p>Optical properties of XNb<sub>2</sub>Bi<sub>2</sub>O<sub>9</sub> with X = Ca, Ba, Be, Mg, and Sr, (<b>a</b>) refractive index, (<b>b</b>) extinction coefficient, (<b>c</b>) absorption (cm<sup>−1</sup>), and (<b>d</b>) reflectivity.</p>
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<p>(<b>a</b>) The real part of the dielectric function, (<b>b</b>) imaginary part of the dielectric function, (<b>c</b>) optical conductivity, and (<b>d</b>) loss function of CaNb<sub>2</sub>Bi<sub>2</sub>O<sub>9</sub>, BaNb<sub>2</sub>Bi<sub>2</sub>O<sub>9</sub>, BeNb<sub>2</sub>Bi<sub>2</sub>O<sub>9</sub>, MgNb<sub>2</sub>Bi<sub>2</sub>O<sub>9,</sub> and SrNb<sub>2</sub>Bi<sub>2</sub>O<sub>9</sub>.</p>
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24 pages, 2407 KiB  
Article
An Enhanced Active Access-Point Configuration Algorithm Using the Throughput Request Satisfaction Method for an Energy-Efficient Wireless Local-Area Network
by Bin Wu, Nobuo Funabiki, Dezheng Kong, Xuan Wang, Taishiro Seto and Yu-Cheng Fan
Symmetry 2024, 16(8), 1005; https://doi.org/10.3390/sym16081005 - 7 Aug 2024
Viewed by 334
Abstract
Wireless Local-Area Networks (WLANs), as a popular internet access solution, are widely used in numerous places, including enterprises, campuses, and public venues. As the number of devices increases, large-scale deployments will cause the problem of dense wireless networks, including a lot of [...] Read more.
Wireless Local-Area Networks (WLANs), as a popular internet access solution, are widely used in numerous places, including enterprises, campuses, and public venues. As the number of devices increases, large-scale deployments will cause the problem of dense wireless networks, including a lot of energy consumption. Thus, the optimization of energy-efficient wireless AP devices has become a focal point of attention. To reduce energy consumption, we have proposed the active access-point (AP) configuration algorithm for WLANs using APs with a dual interface. This uses the greedy algorithm combined with the local search optimization method to find the minimum number of activated APs while satisfying the minimum throughput constraint. However, the previous algorithm basically satisfies only the average throughput among the multiple hosts associated with one AP, wherein some hosts may not reach the required one. In this paper, to overcome this limitation, we propose an enhanced active AP configuration algorithm by incorporating the throughput request satisfaction method that controls the actual throughput at the target value (target throughput) for every host by applying traffic shaping. The target throughput is calculated from the single and concurrent communicating throughput of each host based on channel occupancy time. The minimum throughput constraint will be iteratively adjusted to obtain the required target throughput and achieve the fair throughput allocation. For evaluations, we conducted simulations using the WIMNET simulator and experiments using the testbed system with a Raspberry Pi 4B for APs in four topology cases with five APs and ten hosts. The results show that the proposed method always achieved the required minimum throughput in simulations as well as in experiments, while minimizing the number of active APs. Thus, the validity and effectiveness of our proposal were confirmed. Full article
(This article belongs to the Special Issue Next-Generation Green Wireless Networks and Industrial IoT)
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<p>Flow of enhanced active AP configuration algorithm.</p>
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<p>Topology of the testbed system.</p>
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<p>Device locations in network fields. The red triangle in the figure indicates the location of the AP (Access Point), while the blue circle denotes the host location. Case 1 and Case 2 refer to locations in the Engineering Building #2 at Okayama University, and Case 3 and Case 4 refer to the Graduate School of Natural Sciences Building at Okayama University.</p>
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<p>Experimental results for <span class="html-italic">Case 1</span>.</p>
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<p>Experimental results for <span class="html-italic">Case 2</span>.</p>
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<p>Experimental results for <span class="html-italic">Case 3</span>.</p>
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<p>Experimental results for <span class="html-italic">Case 4</span>.</p>
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<p>Throughput distributions for the previous and enhanced algorithms.</p>
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18 pages, 3650 KiB  
Article
Ensuring Topological Data-Structure Preservation under Autoencoder Compression Due to Latent Space Regularization in Gauss–Legendre Nodes
by Chethan Krishnamurthy Ramanaik, Anna Willmann, Juan-Esteban Suarez Cardona, Pia Hanfeld, Nico Hoffmann and Michael Hecht
Axioms 2024, 13(8), 535; https://doi.org/10.3390/axioms13080535 - 7 Aug 2024
Viewed by 392
Abstract
We formulate a data-independent latent space regularization constraint for general unsupervised autoencoders. The regularization relies on sampling the autoencoder Jacobian at Legendre nodes, which are the centers of the Gauss–Legendre quadrature. Revisiting this classic allows us to prove that regularized autoencoders ensure a [...] Read more.
We formulate a data-independent latent space regularization constraint for general unsupervised autoencoders. The regularization relies on sampling the autoencoder Jacobian at Legendre nodes, which are the centers of the Gauss–Legendre quadrature. Revisiting this classic allows us to prove that regularized autoencoders ensure a one-to-one re-embedding of the initial data manifold into its latent representation. Demonstrations show that previously proposed regularization strategies, such as contractive autoencoding, cause topological defects even in simple examples, as do convolutional-based (variational) autoencoders. In contrast, topological preservation is ensured by standard multilayer perceptron neural networks when regularized using our approach. This observation extends from the classic FashionMNIST dataset to (low-resolution) MRI brain scans, suggesting that reliable low-dimensional representations of complex high-dimensional datasets can be achieved using this regularization technique. Full article
(This article belongs to the Special Issue Differential Geometry and Its Application II)
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<p>Illustration of the latent representation <math display="inline"><semantics> <mrow> <msup> <mi mathvariant="script">D</mi> <mo>′</mo> </msup> <mo>=</mo> <mi>φ</mi> <mrow> <mo>(</mo> <mi mathvariant="script">D</mi> <mo>)</mo> </mrow> <mo>⊆</mo> <msub> <mo>Ω</mo> <msub> <mi>m</mi> <mn>1</mn> </msub> </msub> </mrow> </semantics></math> of the data manifold <math display="inline"><semantics> <mrow> <mi mathvariant="script">D</mi> <mo>⊆</mo> <msub> <mo>Ω</mo> <msub> <mi>m</mi> <mn>2</mn> </msub> </msub> </mrow> </semantics></math>, <math display="inline"><semantics> <mrow> <mi>dim</mi> <mi mathvariant="script">D</mi> <mo>=</mo> <msub> <mi>m</mi> <mn>0</mn> </msub> <mo>&lt;</mo> <msub> <mi>m</mi> <mn>1</mn> </msub> <mo>&lt;</mo> <msub> <mi>m</mi> <mn>2</mn> </msub> <mo>∈</mo> <mi mathvariant="double-struck">N</mi> </mrow> </semantics></math> given by the autoencoder <math display="inline"><semantics> <mrow> <mo>(</mo> <mi>φ</mi> <mo>,</mo> <mi>ν</mi> <mo>)</mo> </mrow> </semantics></math>. The decoder is a one-to-one mapping of the hypercube <math display="inline"><semantics> <msub> <mo>Ω</mo> <msub> <mi>m</mi> <mn>1</mn> </msub> </msub> </semantics></math> to its image <math display="inline"><semantics> <mrow> <mi>ν</mi> <mo>(</mo> <msub> <mo>Ω</mo> <msub> <mi>m</mi> <mn>1</mn> </msub> </msub> <mo>)</mo> <mo>⊃</mo> <mi mathvariant="script">D</mi> </mrow> </semantics></math>, including <math display="inline"><semantics> <mi mathvariant="script">D</mi> </semantics></math> in its interior and consequently guaranteeing Equation (<a href="#FD1-axioms-13-00535" class="html-disp-formula">1</a>).</p>
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<p>Circle reconstruction using various autoencoder models.</p>
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<p>Torus reconstruction using various autoencoder models, <math display="inline"><semantics> <mrow> <mi>dim</mi> <mo>=</mo> <mn>15</mn> </mrow> </semantics></math>.</p>
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<p>FashionMNIST reconstruction with varying levels of Gaussian noise, latent dimension <math display="inline"><semantics> <mrow> <mi>dim</mi> <mo>=</mo> <mn>10</mn> </mrow> </semantics></math>.</p>
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<p>Two show cases of FashionMNIST reconstruction for latent dimension <math display="inline"><semantics> <mrow> <mi>m</mi> <mo>=</mo> <mn>10</mn> </mrow> </semantics></math>. First row shows the input image with vertical, horizontal flips, and <math display="inline"><semantics> <mrow> <mn>0</mn> <mo>%</mo> <mo>,</mo> <mn>10</mn> <mo>%</mo> <mo>,</mo> <mn>20</mn> <mo>%</mo> <mo>,</mo> <mn>50</mn> <mo>%</mo> <mo>,</mo> <mn>70</mn> <mo>%</mo> </mrow> </semantics></math> of Gaussian noise. Rows beneath show the results of (2) MLAP-AE, (3) CNN-AE, (4) MLP-VAE, (5) CNN-VAE, (6) ContraAE, (7) AE-REG, and (8) Hybrid AE-REG.</p>
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<p>FashionMNIST geodesics in latent dimension <math display="inline"><semantics> <mrow> <mi>dim</mi> <mo>=</mo> <mn>4</mn> </mrow> </semantics></math>.</p>
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<p>MRI reconstruction, latent dimension <math display="inline"><semantics> <mrow> <mi>dim</mi> <mo>=</mo> <mn>40</mn> </mrow> </semantics></math>.</p>
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<p>MRI show case. First row shows the input image with vertical, horizontal flips, and <math display="inline"><semantics> <mrow> <mn>0</mn> <mo>%</mo> <mo>,</mo> <mn>10</mn> <mo>%</mo> <mo>,</mo> <mn>20</mn> <mo>%</mo> <mo>,</mo> <mn>50</mn> <mo>%</mo> <mo>,</mo> <mn>70</mn> <mo>%</mo> </mrow> </semantics></math> of Gaussian noise. Rows beneath show the results of (2) MLAP-AE, (3) CNN-AE, (4) MLP-VAE, (5) CNN-VAE, (6) ContraAE, (7) AE-REG, and (8) Hybrid AE-REG.</p>
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<p>MRI geodesics for latent dimension <math display="inline"><semantics> <mrow> <mi>dim</mi> <mo>=</mo> <mn>40</mn> </mrow> </semantics></math> with various levels of Gaussian noise.</p>
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14 pages, 3869 KiB  
Article
Elevational Variation in and Environmental Determinants of Fungal Diversity in Forest Ecosystems of Korean Peninsula
by Lei Chen, Zhi Yu, Mengchen Zhao, Dorsaf Kerfahi, Nan Li, Lingling Shi, Xiwu Qi, Chang-Bae Lee, Ke Dong, Hae-In Lee and Sang-Seob Lee
J. Fungi 2024, 10(8), 556; https://doi.org/10.3390/jof10080556 - 7 Aug 2024
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Abstract
Exploring species diversity along elevational gradients is important for understanding the underlying mechanisms. Our study focused on analyzing the species diversity of fungal communities and their subcommunities at different trophic and taxonomic levels across three high mountains of the Korean Peninsula, each situated [...] Read more.
Exploring species diversity along elevational gradients is important for understanding the underlying mechanisms. Our study focused on analyzing the species diversity of fungal communities and their subcommunities at different trophic and taxonomic levels across three high mountains of the Korean Peninsula, each situated in a different climatic zone. Using high-throughput sequencing, we aimed to assess fungal diversity patterns and investigate the primary environmental factors influencing fungal diversity. Our results indicate that soil fungal diversity exhibits different elevational distribution patterns on different mountains, highlighting the combined effects of climate, soil properties, and geographic topology. Notably, the total and available phosphorus contents in the soil emerged as key determinants in explaining the differences in diversity attributed to soil properties. Despite the varied responses of fungal diversity to elevational gradients among different trophic guilds and taxonomic levels, their primary environmental determinants remained remarkably consistent. In particular, total and available phosphorus contents showed significant correlations with the diversity of the majority of the trophic guilds and taxonomic levels. Our study reveals the absence of a uniform diversity pattern along elevational gradients, underscoring the general sensitivity of fungi to soil conditions. By enriching our understanding of fungal diversity dynamics, this research enhances our comprehension of the formation and maintenance of elevational fungal diversity and the response of microbial communities in mountain ecosystems to climate change. This study provides valuable insights for future ecological studies of similar biotic communities. Full article
(This article belongs to the Special Issue Fungal Communities in Various Environments)
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Figure 1

Figure 1
<p>Sampling site (<b>a</b>) and schematic diagram of sampling points: Mt. Seorak (<b>b</b>), Mt. Jiri (<b>c</b>), and Mt. Halla (<b>d</b>). The green, blue, and red dots represent Mt. Halla, Mt. Jiri, and Mt. Seorak, respectively.</p>
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<p>Elevational patterns of fungal community diversity, including overall and specific phylum, class, and functional diversity, indicated by blue dots, black fitted curves, and gray confidence intervals, respectively. Panels (<b>a</b>–<b>c</b>) represent alpha diversity (Shannon index transformed by z-score) for Mt. Halla, Mt. Jiri, and Mt. Seorak. The quadratic model was selected based on the AIC (refer to <a href="#app1-jof-10-00556" class="html-app">Supplementary Table S1</a>). Blue dots represent the values of the Shannon index transformed by z-score at each sampled sites for each mountain. Solid lines indicate significant trends, while dashed lines represent non-significant trends.</p>
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<p>Variance partitioning analysis (VPA) demonstrates the combined influence of geographical, climatic, and soil properties on the fungal community alpha diversity indices across the three mountains. Panels (<b>a</b>–<b>c</b>) represent Mt. Halla, Mt. Jiri, and Mt. Seorak, respectively. Geographical factors include longitude and latitude; climatic factors include mean annual temperature (MAT) and mean annual precipitation (MAP); and soil properties include pH, total organic carbon (TOC), total nitrogen (TN), NH<sub>4</sub><sup>+</sup>, NO<sub>3</sub><sup>−</sup>, available phosphorus (P<sub>2</sub>O<sub>5</sub>), moisture content, total phosphorus (TP), and soil texture (sand, silt, and clay).</p>
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<p>The correlation between fungal alpha diversity (<b>a</b>), including richness and Chao, Shannon, and Simpson indices), fungal functions (<b>b</b>), and the alpha diversity of dominant fungal phyla and genera (<b>c</b>) with environmental factors across the three mountains. * <span class="html-italic">p</span> &lt; 0.05, ** <span class="html-italic">p</span> &lt; 0.01, and *** <span class="html-italic">p</span> &lt; 0.001.</p>
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