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15 pages, 2339 KiB  
Article
A Comparative Study and Numerical Solutions for the Fractional Modified Lorenz–Stenflo System Using Two Methods
by Mohamed Elbadri, Mohamed A. Abdoon, Abdulrahman B. M. Alzahrani, Rania Saadeh and Mohammed Berir
Axioms 2025, 14(1), 20; https://doi.org/10.3390/axioms14010020 (registering DOI) - 30 Dec 2024
Abstract
This paper provides a solution to the new fractional-order Lorenz–Stenflo model using the adaptive predictor–corrector approach and the ρ-Laplace New Iterative Method (LρNIM), representing an extensive comparison between both techniques with RK4 related to accuracy and [...] Read more.
This paper provides a solution to the new fractional-order Lorenz–Stenflo model using the adaptive predictor–corrector approach and the ρ-Laplace New Iterative Method (LρNIM), representing an extensive comparison between both techniques with RK4 related to accuracy and error analysis. The results show that the suggested approaches allow one to be more accurate in analyzing the dynamics of the system. These techniques also produce results that are comparable to the results of other approximate techniques. The techniques can, thus, be used on a wider class of systems in order to provide more accurate results. These techniques also appropriately identify chaotic attractors in the system. These techniques can be applied to solve various numerical problems arising in science and engineering in the future. Full article
(This article belongs to the Special Issue Fractional Differential Equation and Its Applications)
14 pages, 526 KiB  
Article
Engineered Phage Enables Efficient Control of Gene Expression upon Infection of the Host Cell
by Ting Wei, Wangsheng Lai, Qian Chen and Chenjian Sun
Int. J. Mol. Sci. 2025, 26(1), 250; https://doi.org/10.3390/ijms26010250 (registering DOI) - 30 Dec 2024
Abstract
Recently, we developed a spatial phage-assisted continuous evolution (SPACE) system. This system utilizes chemotaxis coupled with the growth of motile bacteria during their spatial range expansion in soft agar to provide fresh host cells for iterative phage infection and selection pressure for preserving [...] Read more.
Recently, we developed a spatial phage-assisted continuous evolution (SPACE) system. This system utilizes chemotaxis coupled with the growth of motile bacteria during their spatial range expansion in soft agar to provide fresh host cells for iterative phage infection and selection pressure for preserving evolved genes of interest carried by phage mutants. Controllable mutagenesis activated only in a subpopulation of the migrating cells is essential in this system to efficiently generate mutated progeny phages from which desired individuals are selected during the directed evolution process. But, the widely adopted small molecule-dependent inducible system could hardly fulfill this purpose because it always affects all cells homogeneously. In this study, we developed a phage infection-induced gene expression system using modified Escherichia coli (E. coli) phage shock protein operon or sigma factors from Bacillus subtilis. Results showed that this system enabled efficient control of gene expression upon phage infection with dynamic output ranges from small to large using combinations of different engineered phages and corresponding promoters. This system was incorporated into SPACE to function as a phage infection-induced mutagenesis module and successfully facilitated the evolution of T7 RNA polymerase, which generated diverse mutants with altered promoter recognition specificity. We expect that phage infection-induced gene expression system could be further extended to more applications involving partial induction in a portion of a population and targeted induction in specific strains among a mixed bacterial community, which provides an important complement to small molecule-dependent inducible systems. Full article
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Figure 1

Figure 1
<p>Application of the phage shock protein (<span class="html-italic">psp</span>) operon for construction of phage-inducible gene expression circuit. (<b>A</b>) Structure and working mechanism of <span class="html-italic">psp</span> operon in <span class="html-italic">E. coli</span>. Phage represents filamentous phage M13, of which the infection of <span class="html-italic">E. coli</span> cells activates the <span class="html-italic">psp</span> operon via a phage pIV-dependent signaling cascade. Psp, phage shock protein; UAS, upstream activating sequence; IHF BS, integration host factor binding site; TSS, transcription start site. (<b>B</b>) Design of a fluorescent gene expression system activated by phage infection using <span class="html-italic">psp</span> operon. The <span class="html-italic">E. coli</span> cells carry a reporter plasmid (RP), which harbors <span class="html-italic">gfp</span> under the control of the <span class="html-italic">psp</span> promoter. (<b>C</b>) Two versions of phages are used to activate the expression of <span class="html-italic">gfp</span> and the fluorescence intensity of their host cells across time after phage infection. Wild-type M13 was used in (<b>1</b>), and AP1-SPT7, which carries a T7 RNA polymerase gene in place of <span class="html-italic">gIII</span> and only produces infectious progeny phages in the presence of an accessory plasmid carrying <span class="html-italic">gIII</span> downstream of the T7 promoter, was used in (<b>2</b>). Native promoters are not annotated in the schematic diagram of the circuit design. The fluorescence intensity was normalized by the corresponding OD<sub>600</sub> value at each time point. The starting time point of the plots was set at 50 min after phage inoculation when the OD<sub>600</sub> values became significant enough to give stable normalized intensity values. Solid circle (●) represents the experimental group in which both <span class="html-italic">E. coli</span> FM15 cells and phages were added. Open circle (○) represents the control group in which only FM15 cells were added. The mean for two or three replicates is shown in the plot.</p>
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<p>Modification of the <span class="html-italic">psp</span> operon for construction of phage-inducible gene expression circuit. (<b>A</b>) Construction of <span class="html-italic">E. coli</span> FM20 strain by deleting the native <span class="html-italic">psp</span> operon from FM15 genome with CRISPR-Cas system. FM20 was used as the bacterial host for the genetic circuit design using a modified <span class="html-italic">psp</span> operon. (<b>B</b>) Design of a fluorescent gene expression system activated by phage infection using the modified <span class="html-italic">psp</span> operon consisting only of the <span class="html-italic">psp</span> promoter without other <span class="html-italic">psp</span> genes and <span class="html-italic">pspF</span> carried by the activator phage. (<b>C</b>) Two versions of phages are used to activate the expression of <span class="html-italic">gfp</span> and the fluorescence intensity of their host cells across time after phage infection. AP2-SPT7F carries the T7 RNA polymerase gene followed by <span class="html-italic">pspF</span> in place of <span class="html-italic">gIII</span>. For further control of infectious progeny phage reproduction, <span class="html-italic">gII</span> and <span class="html-italic">gV</span>, two more phage genes were deleted, and <span class="html-italic">pspF</span> was inserted instead to construct another version of activator phage, AP3-SPF. Correspondingly, accessory plasmid pLAasc22 carrying <span class="html-italic">gIII</span>, <span class="html-italic">gII</span>, and <span class="html-italic">gV</span> downstream of the T7 promoter was constructed to enable the reproduction of AP3-SPF. Native promoters are not annotated in the schematic diagram of the circuit design. The fluorescence intensity was normalized by the corresponding OD<sub>600</sub> value at each time point. Solid circle (●) represents the experimental group in which both <span class="html-italic">E. coli</span> FM15 cells and phages were added. Open circle (○) represents the control group in which only FM15 cells were added. The mean for three replicates is shown in the plot.</p>
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<p>Construction of phage-inducible gene expression circuit using heterologous sigma factors. (<b>A</b>) Schematic design of a fluorescent gene expression system in <span class="html-italic">E. coli</span> activated by phage infection using heterologous sigma factors and promoters from <span class="html-italic">Bacillus</span>. These sigma factors are expected to bind the host core RNA polymerase (RNAP) and form a holoenzyme to recognize/transcribe specifically from its cognate promoter to yield an orthogonal expression system. (<b>B</b>) Three versions of phages are used to activate the expression of <span class="html-italic">gfp</span> and the fluorescence intensity of their host cells across time after phage infection. AP4-SPSF and AP5-SPSB carry the T7 RNAP gene in place of phage <span class="html-italic">gIII</span> and genes of <span class="html-italic">Bacillus</span> sigma factors B and F, respectively, in place of phage <span class="html-italic">gII</span>-<span class="html-italic">gV</span>. These two phages both rely on accessory plasmid pLAasc22 carrying <span class="html-italic">gIII</span>, <span class="html-italic">gII</span>, and <span class="html-italic">gV</span> downstream of the T7 promoter to reproduce. AP6-SPJSF was derived from AP1-SPT7 by inserting the gene of sigma factor F controlled by a strong synthetic promoter J23100 (<a href="https://parts.igem.org/Part:BBa_J23100" target="_blank">https://parts.igem.org/Part:BBa_J23100</a> (accessed on 26 November 2020)) downstream of the T7 RNAP gene. This activator can also use accessory plasmid pLAasc1 to reproduce. Native promoters are not annotated in the schematic diagram of the circuit design. The fluorescence intensity was normalized by the corresponding OD<sub>600</sub> value at each time point. Solid circle (●) represents the experimental group in which both <span class="html-italic">E. coli</span> FM15 cells and phages were added. Open circle (○) represents the control group in which only FM15 cells were added. The mean for three replicates is shown in the plot.</p>
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<p>Spatial continuous directed evolution (SPACE) experiment using different versions of mutagenesis modules. (<b>A</b>) Two versions of activator phages carrying the T7 RNA polymerase (RNAP) gene as the target gene to be evolved and either the native phage <span class="html-italic">gIV</span> or <span class="html-italic">Bacillus</span> sigma factor gene of which the protein product can activate the expression of mutator genes from corresponding mutagenesis plasmids (pLM1/pLM2). (<b>B</b>) Upon phage infection, the mutagenesis process becomes active and leads to the production of various T7 RNAP mutants. Mutants with improved activity to recognize and transcribe from the target promoter 1C12 will lead to stronger infectious progeny phage propagation and will, in turn, produce a larger fan-shaped infection area with lower cell density on the bacterial lawn in the SPACE experiment. Evolved T7 RNAP mutant genes carried by sampled phages were sequenced, and the amino acid (AA) changes detected in these mutants are listed alongside the images of the SPACE agar plates from which the mutants were isolated. Photographs of a quarter of the semi-solid agar plate are shown in the Figure. Scale bar represents 1 cm.</p>
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17 pages, 1647 KiB  
Article
A Multi-Player Framework for Sustainable Traffic Optimization in the Era of Digital Transportation
by Areti Kotsi, Ioannis Politis, Emmanouil Chaniotakis and Evangelos Mitsakis
Infrastructures 2025, 10(1), 6; https://doi.org/10.3390/infrastructures10010006 (registering DOI) - 30 Dec 2024
Abstract
Nowadays, traffic management challenges in the era of digital transport are rising, as the interactions of various stakeholders providing such technologies play a pivotal role in shaping traffic dynamics. The objective of this paper was to present a game-theory-based framework for modeling and [...] Read more.
Nowadays, traffic management challenges in the era of digital transport are rising, as the interactions of various stakeholders providing such technologies play a pivotal role in shaping traffic dynamics. The objective of this paper was to present a game-theory-based framework for modeling and optimizing urban traffic in road networks, considering the co-existence and interactions of different players composed of drivers of conventional vehicles, central governing authorities with traffic management capabilities, and competitive or cooperative connected mobility private service providers. The scope of this work was to explore and present the outcomes of diverse mixed equilibrium conditions in the road network of the city of Thessaloniki (Greece), integrating the principles of user equilibrium, system optimum, and Cournot oligopoly. The impacts of varying network attributes were systematically analyzed to provide quantitative indicators representing the overall network performance. Analysis of the results provided insights into the sensitivity and the resilience of the road network under various prevalence schemes of drivers of conventional vehicles, representing the user equilibrium characteristics, or drivers relying on traffic guidance provided by a central governing authority, representing the system optimum principles as well as the cooperation and competition schemes of private connected mobility providers with certain market shares in the network. Full article
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Figure 1

Figure 1
<p>Methodological framework.</p>
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<p>Link flows per player and link average “perceived cost”—travel time per player.</p>
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<p>CN dominant link flows (orange font) in the Thessaloniki road network.</p>
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23 pages, 5735 KiB  
Article
Application of Computational Fluid Dynamics and Semi-Empirical Speed Loss Prediction for Weather Routing
by Chih-Wen Cheng, Yu-An Tzeng, Ming-Hsiung Chang, Shang-Chi Liu, Ho-King Cheung and Ching-Yeh Hsin
J. Mar. Sci. Eng. 2025, 13(1), 42; https://doi.org/10.3390/jmse13010042 (registering DOI) - 30 Dec 2024
Abstract
This study presents an optimized system for ship route planning. Computational fluid dynamics simulations were used to modify Kwon’s semi-empirical speed loss estimation method, enabling efficient route planning under variable sea conditions. The study focused on improving the prediction of speed loss in [...] Read more.
This study presents an optimized system for ship route planning. Computational fluid dynamics simulations were used to modify Kwon’s semi-empirical speed loss estimation method, enabling efficient route planning under variable sea conditions. The study focused on improving the prediction of speed loss in irregular waves for container ships and further applying this to ship-optimized voyage planning. Dynamic programming was used for optimized voyage planning by modifying the ship course in response to meteorological data; this approach could balance both energy efficiency and safety. The modified speed loss predictions aligned closely with the simulation results, enhancing the reliability of weather routing decisions. Case studies for trans-Pacific and trans-Atlantic voyages demonstrated that the proposed system could significantly reduce the voyage time. These findings highlight the potential of real-time updates in voyage planning. The proposed system is a valuable tool for captains and fleet managers. The applicability of this system can be further broadened by validating it on different ship types. Full article
19 pages, 1884 KiB  
Article
Dual-Layer Path Planning Model for Autonomous Vehicles in Urban Road Networks Using an Improved Deep Q-Network Algorithm with Proportional–Integral–Derivative Control
by Guoji Xu, Lingling Chen, Xiaohui Zhao, Wengang Liu, Yue Yu, Fusen Huang, Yifan Wang and Yifan Chen
Electronics 2025, 14(1), 116; https://doi.org/10.3390/electronics14010116 (registering DOI) - 30 Dec 2024
Abstract
With the continuous progress of intelligent transportation systems and automated driving technologies, complex urban road environments put forward higher requirements on the real-time characteristic and accuracy of path planning algorithms. Traditional single-layer path planning methods struggle to effectively handle the complexity of road [...] Read more.
With the continuous progress of intelligent transportation systems and automated driving technologies, complex urban road environments put forward higher requirements on the real-time characteristic and accuracy of path planning algorithms. Traditional single-layer path planning methods struggle to effectively handle the complexity of road and lane networks, leading to high computational complexity and suboptimal planning outcomes. To address this issue, we propose a dual-layer path planning model. First, at the road level, we employ the A* algorithm to efficiently determine the optimal macroscopic route, reducing computational overhead. At the lane level, we introduce a Proportional–Integral–Derivative Q-network (PIDQN) based on deep reinforcement learning, which leverages PID control mechanisms to enhance lane selection accuracy and adaptability. By incorporating proportional, integral, and derivative control, PIDQN effectively handles dynamic environments and avoids local optima, ensuring stable and faster convergence. Compared with traditional Deep Q-Network (DQN) and Q-learning algorithms, PIDQN demonstrates significant improvements in success rate and convergence speed in path planning tasks. Using high-precision maps in real-world environments and Python for simulation experiments, we verify the superiority of this approach in complex urban road networks, and we compare the performance of traditional A* algorithms and two-layer planning algorithms. The results show that the two-layer planning algorithm outperforms the traditional A* algorithm and provides a more robust and efficient solution for self-driving car navigation. Full article
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Figure 1
<p>Map model conversion.</p>
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<p>PIDQN.</p>
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<p>Urban road network.</p>
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<p>Global planning results.</p>
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<p>Global planning results.</p>
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<p>Reward value.</p>
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<p>Number of successes.</p>
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<p>Parametric analysis.</p>
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24 pages, 2096 KiB  
Article
Human Activity Recognition Using Graph Structures and Deep Neural Networks
by Abed Al Raoof K. Bsoul
Computers 2025, 14(1), 9; https://doi.org/10.3390/computers14010009 (registering DOI) - 30 Dec 2024
Abstract
Human activity recognition (HAR) systems are essential in healthcare, surveillance, and sports analytics, enabling automated movement analysis. This research presents a novel HAR system combining graph structures with deep neural networks to capture both spatial and temporal patterns in activities. While CNN-based models [...] Read more.
Human activity recognition (HAR) systems are essential in healthcare, surveillance, and sports analytics, enabling automated movement analysis. This research presents a novel HAR system combining graph structures with deep neural networks to capture both spatial and temporal patterns in activities. While CNN-based models excel at spatial feature extraction, they struggle with temporal dynamics, limiting their ability to classify complex actions. To address this, we applied the Firefly Optimization Algorithm to fine-tune the hyperparameters of both the graph-based model and a CNN baseline for comparison. The optimized graph-based system, evaluated on the UCF101 and Kinetics-400 datasets, achieved 88.9% accuracy with balanced precision, recall, and F1-scores, outperforming the baseline. It demonstrated robustness across diverse activities, including sports, household routines, and musical performances. This study highlights the potential of graph-based HAR systems for real-world applications, with future work focused on multi-modal data integration and improved handling of occlusions to enhance adaptability and performance. Full article
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Figure 1
<p>System architecture of the proposed methodology.</p>
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<p>Temporal evolution of right wrist and nose coordinates during a waving motion.</p>
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<p>Heatmap of average relative velocities between joint pairs during right-hand waving motion.</p>
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<p>Architecture of the CNN model.</p>
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<p>Training and validation accuracy before and after optimization.</p>
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<p>Overall performance of the system and by action category.</p>
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<p>Results of the optimized graph-based model and baseline CNN model.</p>
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23 pages, 5881 KiB  
Article
Impact of Wetting-Drying Cycles on Soil Intra-Aggregate Pore Architecture Under Different Management Systems
by Luiz F. Pires, Jocenei A. T. de Oliveira, José V. Gaspareto, Adolfo N. D. Posadas and André L. F. Lourenço
AgriEngineering 2025, 7(1), 9; https://doi.org/10.3390/agriengineering7010009 (registering DOI) - 30 Dec 2024
Abstract
In many soil processes, including solute and gas dynamics, the architecture of intra-aggregate pores is a crucial component. Soil management practices and wetting-drying (W-D) cycles, the latter having a significant impact on pore aggregation, are two key factors that shape pore structure. This [...] Read more.
In many soil processes, including solute and gas dynamics, the architecture of intra-aggregate pores is a crucial component. Soil management practices and wetting-drying (W-D) cycles, the latter having a significant impact on pore aggregation, are two key factors that shape pore structure. This study examines the effects of W-D cycles on the architecture of intra-aggregate pores under three different soil management systems: no-tillage (NT), minimum tillage (MT), and conventional tillage (CT). The soil samples were subjected to 0 and 12 W-D cycles, and the resulting pore structures were scanned using X-ray micro-computed tomography, generating reconstructed 3D volumetric data. The data analyses were conducted in terms of multifractal spectra, normalized Shannon entropy, lacunarity, porosity, anisotropy, connectivity, and tortuosity. The multifractal parameters of capacity, correlation, and information dimensions showed mean values of approximately 2.77, 2.75, and 2.75 when considering the different management practices and W-D cycles; 3D lacunarity decreased mainly for the smallest boxes between 0 and 12 W-D cycles for CT and NT, with the opposite behavior for MT. The normalized 3D Shannon entropy showed differences of less than 2% before and after the W-D cycles for MT and NT, with differences of 5% for CT. The imaged porosity showed reductions of approximately 50% after 12 W-D cycles for CT and NT. Generally, the largest pores (>0.1 mm3) contributed the most to porosity for all management practices before and after W-D cycles. Anisotropy increased by 9% and 2% for MT and CT after the cycles and decreased by 23% for NT. Pore connectivity showed a downward trend after 12 W-D cycles for CT and NT. Regarding the pore shape, the greatest contribution to porosity and number of pores was due to triaxial-shaped pores for both 0 and 12 W-D cycles for all management practices. The results demonstrate that, within the resolution limits of the microtomography analysis, pore architecture remained resilient to changes, despite some observable trends in specific parameters. Full article
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Figure 1

Figure 1
<p>Location of the State of Paraná on the map of Brazil, the municipality of Ponta Grossa on the map of Paraná, and the experimental area where the samples were collected. IAPAR: “Instituto de Desenvolvimento Rural do Paraná”; CT: conventional tillage; NT: no tillage; MT: minimum tillage.</p>
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<p>Three-dimensional images of the soil pore system (terracotta color) for the following conditions: (<b>a</b>,<b>b</b>) minimum tillage for 0 and 12 wetting and drying (W-D) cycles; (<b>c</b>,<b>d</b>) conventional tillage for 0 and 12 W-D cycles; (<b>e</b>,<b>f</b>) no tillage for 0 and 12 W-D cycles.</p>
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<p>Three-dimensional Shannon entropy (<math display="inline"><semantics> <mrow> <msup> <mi>H</mi> <mo>*</mo> </msup> <mrow> <mo>(</mo> <mi>ε</mi> <mo>)</mo> </mrow> </mrow> </semantics></math>) and lacunarity (<math display="inline"><semantics> <mrow> <mi>L</mi> <mi>n</mi> <mo>(</mo> <mo>Λ</mo> </mrow> </semantics></math>)) curves for the following conditions: (<b>a</b>,<b>b</b>) minimum tillage for 0 and 12 wetting and drying (W-D) cycles; (<b>c</b>,<b>d</b>) conventional tillage for 0 and 12 W-D cycles; (<b>e</b>,<b>f</b>) no tillage for 0 and 12 W-D cycles. The error bars represent the standard deviation from the mean.</p>
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<p>Variation in the capacity dimension (<math display="inline"><semantics> <msub> <mi>D</mi> <mn>0</mn> </msub> </semantics></math>) as a function of the application of wetting and drying cycles (W-D) for the following conditions: (<b>a</b>) minimum tillage for 0 and 12 W-D cycles; (<b>b</b>) conventional tillage for 0 and 12 W-D cycles; (<b>c</b>) no tillage for 0 and 12 W-D cycles. NS: non-significant differences determined by a <span class="html-italic">t</span>-test (<math display="inline"><semantics> <mrow> <mi>p</mi> <mo>&lt;</mo> <mn>0.05</mn> </mrow> </semantics></math>).</p>
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<p>Variation in porosity (<math display="inline"><semantics> <mo>Φ</mo> </semantics></math>) and pore size distribution (<math display="inline"><semantics> <mrow> <mo>Φ</mo> <mo>−</mo> <mi>s</mi> <mi>i</mi> <mi>z</mi> <mi>e</mi> </mrow> </semantics></math>) as a function of the application of wetting and drying cycles (W-D) for the following conditions: (<b>a</b>,<b>b</b>) minimum tillage for 0 and 12 W-D cycles; (<b>c</b>,<b>d</b>) conventional tillage for 0 and 12 W-D cycles; (<b>e</b>,<b>f</b>) no-tillage for 0 and 12 W-D cycles. NS: non-significant differences by <span class="html-italic">t</span>-test (<math display="inline"><semantics> <mrow> <mi>p</mi> <mo>&lt;</mo> <mn>0.05</mn> </mrow> </semantics></math>).</p>
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<p>Variation in the degree of anisotropy (DA) and number of pores (NP) as a function of the application of wetting and drying cycles (W-D) for the following conditions: (<b>a</b>,<b>b</b>) minimum tillage for 0 and 12 W-D cycles; (<b>c</b>,<b>d</b>) conventional tillage for 0 and 12 W-D cycles; (<b>e</b>,<b>f</b>) no tillage for 0 and 12 W-D cycles. NS: non-significant differences determined by a <span class="html-italic">t</span>-test (<math display="inline"><semantics> <mrow> <mi>p</mi> <mo>&lt;</mo> <mn>0.05</mn> </mrow> </semantics></math>).</p>
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<p>Variation in pore connectivity (C) and tortuosity (<math display="inline"><semantics> <mi>τ</mi> </semantics></math>) as a function of the application of wetting and drying cycles (W-D) for the following conditions: (<b>a</b>,<b>b</b>) minimum tillage for 0 and 12 W-D cycles; (<b>c</b>,<b>d</b>) conventional tillage for 0 and 12 W-D cycles; (<b>e</b>,<b>f</b>) no- tillage for 0 and 12 W-D cycles. NS: non-significant differences determined by a <span class="html-italic">t</span>-test (<math display="inline"><semantics> <mrow> <mi>p</mi> <mo>&lt;</mo> <mn>0.05</mn> </mrow> </semantics></math>).</p>
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<p>Contribution of the different pore shapes to the volume (VP-S) and number of pores (NP-S) for the following conditions: (<b>a</b>,<b>b</b>) minimum tillage for 0 and 12 wetting and drying (W-D) cycles; (<b>c</b>,<b>d</b>) conventional tillage for 0 and 12 W-D cycles; (<b>e</b>,<b>f</b>) no-tillage for 0 and 12 W-D cycles. Eq.: equant; Pr.: prolate; Ob.: oblate; Tr.: triaxial. NS: non-significant differences by <span class="html-italic">t</span>-test (<math display="inline"><semantics> <mrow> <mi>p</mi> <mo>&lt;</mo> <mn>0.05</mn> </mrow> </semantics></math>).</p>
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<p>Diagram for extracting the soil aggregate sample. (1) Soil sample inside the cylinder; (2) volume of soil carefully extracted from the cylinder; (3) soil aggregate extracted from the center of the sample.</p>
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<p>Multifractal spectra for samples subjected to different (0 and 12) wetting and drying 565 cycles (W-D). MT: minimum tillage; CT: conventional tillage; NT: no tillage; R: replicate.</p>
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20 pages, 4737 KiB  
Article
Multi-Stage Hybrid Planning Method for Charging Stations Based on Graph Auto-Encoder
by Andrew Y. Wu, Juai Wu and Yui-yip Lau
Electronics 2025, 14(1), 114; https://doi.org/10.3390/electronics14010114 (registering DOI) - 30 Dec 2024
Abstract
To improve the operational efficiency of electric vehicle (EV) charging infrastructure, this paper proposes a multi-stage hybrid planning method for charging stations (CSs) based on graph auto-encoder (GAE). First, the network topology and dynamic interaction process of the coupled “Vehicle-Station-Network” system are characterized [...] Read more.
To improve the operational efficiency of electric vehicle (EV) charging infrastructure, this paper proposes a multi-stage hybrid planning method for charging stations (CSs) based on graph auto-encoder (GAE). First, the network topology and dynamic interaction process of the coupled “Vehicle-Station-Network” system are characterized as a graph-structured model. Second, in the first stage, a GAE-based deep neural network is used to learn the graph-structured model and identify and classify different charging station (CS) types for the network nodes of the coupled system topology. The candidate CS set is screened out, including fast-charging stations (FCSs), fast-medium-charging stations, medium-charging stations, and slow-charging stations. Then, in the second stage, the candidate CS set is re-optimized using a traditional swarm intelligence algorithm, considering the interests of multiple parties in CS construction. The optimal CS locations and charging pile configurations are determined. Finally, case studies are conducted within a practical traffic zone in Hong Kong, China. The existing CS planning methods rely on simulation topology, which makes it difficult to realize efficient collaboration of charging networks. However, the proposed scheme is based on the realistic geographical space and large-scale traffic topology. The scheme determines the station and pile configuration through multi-stage planning. With the help of an artificial intelligence (AI) algorithm, the user behavior characteristics are captured adaptively, and the distribution rule of established CSs is extracted to provide support for the planning of new CSs. The research results will help the power and transportation departments to reasonably plan charging facilities and promote the coordinated development of EV industry, energy, and transportation systems. Full article
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<p>Overall architecture of the proposed multi-stage hybrid planning method for CSs.</p>
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<p>Loss function for training with different GCLs.</p>
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<p>Classification accuracy of the proposed GAE method for candidate CS nodes.</p>
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<p>Identification result of the candidate CS nodes.</p>
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<p>PSO-based iterative process of CS planning.</p>
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<p>Relationship between the total cost and quantity of CS planning.</p>
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<p>Distribution results of the optimal hybrid planning for CSs.</p>
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<p>Heat map of spatial distribution of pre-post-planning charging demand. (<b>a</b>) Spatial distribution of pre-planning charging demand. (<b>b</b>) Spatial distribution of post-planning charging demand.</p>
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<p>Average traveling and charging costs of users of pre-post-planning.</p>
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<p>Comparison of distribution network loads for different planning methods.</p>
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<p>Comparison of node voltages for different planning methods.</p>
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21 pages, 4425 KiB  
Article
Mechanical Properties of Faecal Sludge and Its Influence on Moisture Retention
by Arun Kumar Rayavellore Suryakumar, Sergio Luis Parra-Angarita, Angélique Léonard, Jonathan Pocock and Santiago Septien
ChemEngineering 2025, 9(1), 2; https://doi.org/10.3390/chemengineering9010002 (registering DOI) - 30 Dec 2024
Abstract
The mechanical properties of faecal sludge (FS) influence its moisture retention characteristics to a greater extent than other properties. A comprehensive fundamental characterisation of the mechanical properties is scarcely discussed in the literature. This research focused on bulk and true densities, porosity, particle [...] Read more.
The mechanical properties of faecal sludge (FS) influence its moisture retention characteristics to a greater extent than other properties. A comprehensive fundamental characterisation of the mechanical properties is scarcely discussed in the literature. This research focused on bulk and true densities, porosity, particle size distribution and zeta-potential, extracellular polymeric substances, rheology and dilatancy, microstructure analysis, and compactibility in the context of using the FS as a substitute for soil in land reclamation and bioremediation processes. FSs from different on-site sanitation systems were collected from around Durban, South Africa. The porosity of the FSs varied between 42% and 63%, with the zeta-potential being negative, below 10 mV. Over 95% of the particles were <1000 µm. With its presence in the inner part of the solid particles, tightly bound extra-cellular polymeric substances (TB-EPSs) influenced the stability of the sludge by tightly attaching to the cell walls, with the highest being in the septic tank with the greywater sample. More proteins than carbohydrates also confirmed characterised the anaerobic nature of the sludge. The results of the textural properties using a penetrometer showed that the initial slope of the positive part of the penetration curve was related to the stiffness of the sludge sample and similar to that of sewage sludge. The dynamic oscillatory measurements exhibited a firm gel-like behaviour with a linear viscoelastic behaviour of the sludges due to the change in EPSs because of anaerobicity. The high-TS samples exhibited the role of moisture as a lubricating agent on the motion of solid particles, leading to dilatancy with reduced moisture, where the yield stress was no longer associated with the viscous forces but with the frictional contacts of solid–solid particle interactions. The filtration–compression cell test showed good compactibility, but the presence of unbound moisture even at a high pressure of 300 kPa meant that not all unbound moisture was easily removable. The moisture retention behaviour of FS was influenced by its mechanical properties, and any interventional changes to these properties can result in the release of the bound moisture of FS. Full article
(This article belongs to the Special Issue Innovative Approaches for the Environmental Chemical Engineering)
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<p>Particle size distribution of all FSs.</p>
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<p>Correlation between PSD and ZP.</p>
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<p>Correlation of TOC with EPSs.</p>
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<p>Experimental penetration curve.</p>
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<p>Experimental shear strain curve.</p>
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<p>Dilatancy of VIP and UDDT sludges.</p>
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<p>The sample height vs. pressure plot for the FS samples.</p>
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<p>DTG curve for VIP and ST-BW pre-FCC and post-FCC.</p>
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<p>Unbound and bound moisture fractions of FSs pre-FCC and post-FCC.</p>
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<p>ESEM microstructural imagery of the FS samples.</p>
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24 pages, 10995 KiB  
Article
Using RES Surpluses to Remove Overburden from Lignite Mines Can Improve the Nation’s Energy Security
by Leszek Jurdziak, Witold Kawalec, Zbigniew Kasztelewicz and Pawel Parczyk
Energies 2025, 18(1), 104; https://doi.org/10.3390/en18010104 (registering DOI) - 30 Dec 2024
Abstract
The increasing use of renewable energy sources, such as wind and solar energy, presents challenges to the stability and efficiency of other energy sources due to their intermittent and unpredictable surpluses. The unintended consequence of stabilizing the power supply system is an increase [...] Read more.
The increasing use of renewable energy sources, such as wind and solar energy, presents challenges to the stability and efficiency of other energy sources due to their intermittent and unpredictable surpluses. The unintended consequence of stabilizing the power supply system is an increase in emissions and external costs from the suboptimal use of coal power plants. The rising number of RES curtailments needs to be addressed by either the adjusting energy supply from fossil fuel or the flexible energy consumption. In Poland’s energy mix, coal-fired power plants are a critical component in ensuring energy security for the foreseeable future. Using domestic lignite to generate a total power of 8.5 GW can stabilize the national power supply, as it is currently done in Germany, where 15 GW of lignite-fueled power units provide the power supply base for the country. The leading Belchatów power plant comprises 10 retrofitted units and one new unit, with a total rating of 5.5 GW. Access to the new coal deposit, Zloczew, is necessary to ensure its longer operation. The other domestic lignite power plants are located in Central Poland at Patnów (0.47 GW from the new unit and 0.6 GW from its three retrofitted counterparts) and located in the Lusatian lignite basin at Turów (operating a brand new unit rated at 0.5 GW and retrofitted units with a total rating of 1.5 GW). The use of this fuel is currently being penalized as a result of increasing carbon costs. However, the continuous surface mining technology that is used in lignite mines is fully electrified, and large amounts of electric energy are required to remove and dump overburden and mining coal and its conveying to power units (the transport of coal from the new lignite mine Zloczew to the Belchatów power plant would be a long-distance operation). A possible solution to this problem is to focus on the lignite fuel supply operations of these power plants, with extensive simulations of the entire supply chain. A modern lignite mine is operated by one control room, and it can balance the dynamic consumption of surplus renewable energy sources (RESs) and reduce the need for reduction. When a lignite supply chain is operated this way, a high-capacity power bank can be created with energy storage in the form of an open brown coal seam. This would enable an almost emission-free supply of cheap and domestic fossil fuel, making it insensitive to changes in the world prices of energy resources for power units operating at the base of the system. Furthermore, extending the life of relatively new and efficient lignite-fired units in Poland would facilitate the decommissioning of older and exhausted hard coal-fired units. Full article
(This article belongs to the Section H: Geo-Energy)
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<p>Demand and growth for renewable energy, main case 2023–2030 [<a href="#B1-energies-18-00104" class="html-bibr">1</a>].</p>
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<p>Global generation of RES electricity, installed power, and share in total electric energy production, 2023 and 2030 [<a href="#B1-energies-18-00104" class="html-bibr">1</a>].</p>
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<p>RES capacity and RES energy production and hours of operation at full power.</p>
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<p>Solar PV installed power additions and avoided emissions [<a href="#B2-energies-18-00104" class="html-bibr">2</a>].</p>
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<p>Solar PV capacity per capita in Poland 2013–2024 * (W/capita). *—data until September 2024, based on [<a href="#B4-energies-18-00104" class="html-bibr">4</a>].</p>
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<p>Curtailment of solar PV generation on the 1 April (<b>left</b>) and 4 May 2024 (<b>right</b>).</p>
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<p>Monthly wind and solar curtailments in California in GWh [<a href="#B14-energies-18-00104" class="html-bibr">14</a>].</p>
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<p>Relationship between the hourly electricity price on the day-ahead market and the instantaneous share of RES energy in the national demand in May 2024 [<a href="#B16-energies-18-00104" class="html-bibr">16</a>].</p>
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<p>Changes in hourly energy prices during the day on consecutive years 2017–2023 in Poland. WysokieNapiecie.pl. License: CC BY SA 4.0 [<a href="#B17-energies-18-00104" class="html-bibr">17</a>]. Price version of the net load “duck curve” (own modification of the original chart by the authors).</p>
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<p>Hourly electricity prices for individual hours of the next day (day-ahead market) in Poland on 27–28 April 2024 Energy.Instrat.pl (accessed on 20 December 2024). Data: TGE (Polish Power Exchange). License: CCA 4.0 International (CC BY 4.0). Duck additions by the authors [<a href="#B18-energies-18-00104" class="html-bibr">18</a>].</p>
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<p>Total load in Poland on 15 May 2024 (<b>left</b>) and on Wednesdays in the middle of May in previous years (<b>right</b>).</p>
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<p>Distribution of energy production from the example of photovoltaic installation (with a capacity of 3 kW) located in the Małopolska region in Poland on one of the sunny and cloudy days in different months of 2019. Small chart: Comparison of the elevation of the sun during the most characteristic days: summer solstice, equinoxes, and winter solstice [<a href="#B23-energies-18-00104" class="html-bibr">23</a>].</p>
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<p>The height of the sun above the horizon is called an elevation or an altitude angle α [<a href="#B15-energies-18-00104" class="html-bibr">15</a>].</p>
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<p>Global solar photovoltaic (PV) market development (2024–2032) and forecasts up to 2032 [<a href="#B25-energies-18-00104" class="html-bibr">25</a>].</p>
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<p>Summary power of new PV projects with connection to the grid conditions in selected power ranges in MW (based on [<a href="#B28-energies-18-00104" class="html-bibr">28</a>]).</p>
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<p>Global generation of electricity by RES technology for selected countries and regions for 2023 and 2030 [<a href="#B1-energies-18-00104" class="html-bibr">1</a>].</p>
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<p>(<b>A</b>) Calculation of the LCOE for electric energy from a perspective 100% VRE energy mix in Switzerland in 2050, taking into account proactive curtailment (* denotes minimum value of LCOE) [<a href="#B29-energies-18-00104" class="html-bibr">29</a>]. (<b>B</b>) CO<sub>2</sub>-low carbon energy mix in Switzerland, based on [<a href="#B30-energies-18-00104" class="html-bibr">30</a>].</p>
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<p>The visualization of the ultimate pit shell DTM merged with the topography DTM (textured with the geographical map) filled with coal block model cells; colouring represents coal calorific value: red—above 6.5 MJ/kg, yellow—lower values (Datamine Studio OP, version: 3.0.175.0).</p>
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<p>Two general schemes of conveying routes: for the development of the mine (with an external dumpsite) and for the mature mine (with in-pit dumpsite represented by slopes and benches coloured brown); blue strings represent an example of the conveying route on a given pit level; red perimeter outlines the ultimate pit crest—see <a href="#energies-18-00104-f018" class="html-fig">Figure 18</a> (Datamine Studio OP).</p>
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<p>Electric energy consumed by overburden removal within the Life of Mine schedule; bar colors represent the number of mining level (1st—blue, 2nd—orange, etc.).</p>
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17 pages, 12159 KiB  
Article
Numerical Study of Carreau Fluid Flow in Symmetrically Branched Tubes
by Vinicius Pepe, Antonio F. Miguel, Flávia Zinani and Luiz Rocha
Symmetry 2025, 17(1), 48; https://doi.org/10.3390/sym17010048 (registering DOI) - 30 Dec 2024
Abstract
The non-Newtonian Carreau fluid model is a suitable model for pseudoplastic fluids and can be used to characterize fluids not so different from biological fluids, such as the blood, and fluids involved in geological processes, such as lava and magma. These fluids are [...] Read more.
The non-Newtonian Carreau fluid model is a suitable model for pseudoplastic fluids and can be used to characterize fluids not so different from biological fluids, such as the blood, and fluids involved in geological processes, such as lava and magma. These fluids are frequently conveyed by complex flow structures, which consist of a network of channels that allow the fluid to flow from one place (source or sink) to a variety of locations or vice versa. These flow networks are not randomly arranged but show self-similarity at different spatial scales. Our work focuses on the design of self-similar branched flow networks that look the same on any scale. The flow is incompressible and stationary with a viscosity following the Carreau model, which is important for the study of complex flow systems. The flow division ratios, the flow resistances at different scales, and the geometric size ratios for maximum flow access are studied, based on Computational Fluid Dynamics (CFD). A special emphasis is placed on investigating the possible incidence of flow asymmetry in these symmetric networks. Our results show that asymmetries may occur for both Newtonian and non-Newtonian fluids and shear-thinning fluids most affect performance results. The lowest flow resistance occurs when the diameters of the parent and daughter ducts are equal, and the more uniform distribution of flow resistance occurs for a ratio between the diameters of the parent and daughter ducts equal to 0.75. Resistances for non-Newtonian fluids are 4.8 to 5.6 times greater than for Newtonian fluids at Reynolds numbers of 100 and 250, respectively. For the design of engineering systems and the assessment of biological systems, it is recommended that the findings presented are taken into account. Full article
(This article belongs to the Special Issue Symmetry in Thermal Fluid Sciences and Energy Applications)
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<p>Self-similar fluidic structure with three symmetric branching levels and circular sections to transport Carreau’s fluids.</p>
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<p>Contours of static pressure for a network designed for a<sub>D</sub> = 0.80.</p>
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<p>Contours of static pressure for a network designed for a<sub>D</sub> = 0.80.</p>
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<p>Dimensionless flow resistance of a Carreau fluid (Equation (18)) versus the diameter ratio a<sub>D</sub> and svelteness index Sv, for Reynolds numbers 100 and 250.</p>
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<p>Dimensionless flow resistance of a Carreau fluid (Equation (18)) versus the diameter ratio a<sub>D</sub> and svelteness index Sv, for Reynolds numbers 100 and 250.</p>
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<p>CNR flow resistances (Equation (19)) versus the diameter ratio a<sub>D</sub> and svelteness index Sv, for Reynolds numbers 100 and 250.</p>
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<p>Euler number (Equation (17)) versus the diameter ratio a<sub>D</sub>, svelteness index Sv, Reynolds number, Carreau number, and rheological parameters.</p>
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<p>Dimensionless flow resistance (R<sub>i</sub>/R<sub>T</sub>) versus diameter ratio for different Reynolds numbers and rheological parameters.</p>
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<p>Dimensionless flow resistance (R<sub>i</sub>/R<sub>T</sub>) for best resistance distributions, versus the diameter ratio a<sub>D</sub> and svelteness index Sv.</p>
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<p>Dimensionless flow partitioning ratio (Equation (20)) for level 1.</p>
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<p>Dimensionless flow partitioning ratio (Equation (20)) for level 2.</p>
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<p>Dimensionless flow partitioning ratio (Equation (20)) for level 3.</p>
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17 pages, 7949 KiB  
Article
Traditional Chinese Medicine Monomer Bakuchiol Attenuates the Pathogenicity of Pseudomonas aeruginosa via Targeting PqsR
by Jing Zeng, Xin Ma, Yu Zheng, Dandan Liu, Wanqing Ning, Wei Xiao, Qian Mao, Zhenqing Bai, Renjun Mao, Juanli Cheng and Jinshui Lin
Int. J. Mol. Sci. 2025, 26(1), 243; https://doi.org/10.3390/ijms26010243 (registering DOI) - 30 Dec 2024
Abstract
As the antibiotic resistance of pathogens becomes increasingly severe, it is becoming more feasible to use methods that suppress the virulence of pathogens rather than exerting selective pressure on their growth. Pseudomonas aeruginosa, a dangerous opportunistic pathogen, infects hosts by producing multiple [...] Read more.
As the antibiotic resistance of pathogens becomes increasingly severe, it is becoming more feasible to use methods that suppress the virulence of pathogens rather than exerting selective pressure on their growth. Pseudomonas aeruginosa, a dangerous opportunistic pathogen, infects hosts by producing multiple virulence factors, which are regulated by quorum-sensing (QS) systems, including the las systems, rhl systems, and pqs systems. This study used the chromosome lacZ transcription fusion reporter model to screen the traditional Chinese medicine monomer library and found that bakuchiol can effectively inhibit the pqs system and related virulence phenotypes of P. aeruginosa, including the production of virulence factors (pyocyanin, hydrogen cyanide, elastase, and lectin) and motility (swarming, swimming, and twitching motility) without affecting its growth. Subsequently, through genetic complementation analysis, we found that bakuchiol inhibited the function of the transcriptional activation protein PqsR of the pqs system in P. aeruginosa in a concentration-dependent manner. Furthermore, molecular dynamics simulation study results indicated that bakuchiol can target PqsR of the pqs system, thereby inhibiting the pqs system. Among the amino acids in PqsR, ALA-168 may be a key amino acid residue in the hydrophobic interaction between PqsR protein and bakuchiol. Finally, in vivo experiments demonstrated that bakuchiol attenuated the pathogenicity of P. aeruginosa to Chinese cabbage (Brassica pekinensis) and Caenorhabditis elegans. In summary, this study suggests that bakuchiol is an effective inhibitor that targets the pqs system of P. aeruginosa, providing a new strategy for addressing P. aeruginosa infections. Full article
(This article belongs to the Special Issue Microbial Infections and Novel Biological Molecules for Treatment)
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<p>The effect of bakuchiol on gene expression related to quorum-sensing systems. (<b>A</b>) Effects of 100 μg/mL of bakuchiol on the expression of QS genes <span class="html-italic">pqsA</span>, <span class="html-italic">rhlI</span>, and <span class="html-italic">lasI</span>. DMSO and calycosin were used as the solvent and Chinese medicine monomer negative controls, respectively. (<b>B</b>) The chemical structural formula of bakuchiol. All data represent the results of at least three independent biological replicates. The error bars represent the standard deviations. Student’s <span class="html-italic">t</span> test; ***: <span class="html-italic">p</span> &lt; 0.001.</p>
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<p>The effect of different concentrations of bakuchiol on the gene expression of <span class="html-italic">pqsA</span>. (<b>A</b>) Levels of <span class="html-italic">pqsA</span> transcription in <span class="html-italic">Pseudomonas aeruginosa</span> wild-type strain with increasing bakuchiol concentration. (<b>B</b>) The half-maximal inhibitory concentration (IC50) levels of bakuchiol on <span class="html-italic">pqsA</span> transcription. The slope of the curve was calculated based on its respective dose–response curves and plotted against the log concentration. All data represent the results of at least three independent biological replicates. The error bars represent the standard deviations.</p>
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<p>The effect of different concentrations of bakuchiol on the <span class="html-italic">pqs</span> system in strains with differential expression of <span class="html-italic">pqsR</span>. (<b>A</b>) Levels of <span class="html-italic">pqsA</span> transcription in strains with differential expression of <span class="html-italic">pqsR</span> exposed to increasing concentrations of bakuchiol. (<b>B</b>,<b>C</b>) The half-maximal inhibitory concentration (IC<sub>50</sub>) levels of <span class="html-italic">pqsA</span> transcription in (<b>B</b>) PAO1 (pBBR1MCS-5) and (<b>C</b>) PAO1 (pBBR1MCS-5-<span class="html-italic">pqsR</span>) exposed to various concentrations of bakuchiol. The slope of the curve was calculated based on its respective dose–response curves and plotted against the log concentration. All data represent the results of at least three independent biological replicates. The error bars represent the standard deviations.</p>
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<p>Molecular docking analysis of bakuchiol and PqsR. (<b>A</b>) Surface mode diagram of bakuchiol and PqsR. (<b>B</b>) Three-dimensional interaction diagram. (<b>C</b>) Two-dimensional interaction diagram. The binding energy is −7.5 kcal/mol.</p>
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<p>Potential target analysis of bakuchiol on PqsR. (<b>A</b>) Levels of <span class="html-italic">pqsA</span> transcription after site-specific mutation of PqsR (with or without bakuchiol addition). (<b>B</b>) Surface mode diagram of bakuchiol and PqsR<sup>A168L</sup>. (<b>C</b>) Three-dimensional interaction diagram. (<b>D</b>) Two-dimensional interaction diagram. Binding energy is −5.64 kcal/mol. All data represent results of at least three independent biological replicates. Error bars represent standard deviations. Student’s <span class="html-italic">t</span> test; ****: <span class="html-italic">p</span> &lt; 0.0001; n.s.: <span class="html-italic">p</span> &gt; 0.05.</p>
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<p>The effect of bakuchiol on the synthesis of pyocyanin by <span class="html-italic">P. aeruginosa</span>. (<b>A</b>) Quantitative estimation of pyocyanin. (<b>B</b>,<b>C</b>) Effects of 80 μg/mL of bakuchiol on the expression of pyocyanin synthesis genes (<span class="html-italic">phzA1</span> and <span class="html-italic">phzA2</span>). DMSO and calycosin were used as the solvent negative control and Chinese medicine monomer negative control, respectively. All data represent the results of at least three independent biological replicates. The error bars represent the standard deviations. Student’s <span class="html-italic">t</span> test; ***: <span class="html-italic">p</span> &lt; 0.001; ****: <span class="html-italic">p</span> &lt; 0.0001.</p>
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<p>The effect of bakuchiol on the expression of various virulence factor genes in <span class="html-italic">P. aeruginosa</span>. (<b>A</b>–<b>C</b>) The effect of bakuchiol on (<b>A</b>) hydrogen cyanide, (<b>B</b>) elastase, and (<b>C</b>) lectin synthesis genes in <span class="html-italic">P. aeruginosa</span>. DMSO and calycosin were used as the solvent negative control and Chinese medicine monomer negative control, respectively. All data represent the results of at least three independent biological replicates. The error bars represent the standard deviations. Student’s <span class="html-italic">t</span> test; ***: <span class="html-italic">p</span> &lt; 0.001; ****: <span class="html-italic">p</span> &lt; 0.0001.</p>
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<p>The effect of bakuchiol on the motility of <span class="html-italic">P. aeruginosa</span>. The effect of bakuchiol on the (<b>A</b>) swarming, (<b>B</b>) swimming, (<b>C</b>) and twitching motility in <span class="html-italic">P. aeruginosa</span>. DMSO and calycosin were used as the solvent negative control and Chinese medicine monomer negative control, respectively. All data represent the results of at least three independent biological replicates. The error bars represent the standard deviations. Student’s <span class="html-italic">t</span> test; **: <span class="html-italic">p</span> &lt; 0.01; ****: <span class="html-italic">p</span> &lt; 0.0001.</p>
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<p>The effect of bakuchiol on the pathogenicity of <span class="html-italic">P. aeruginosa</span>. (<b>A</b>,<b>B</b>) Determination of the (<b>A</b>) survival rate of <span class="html-italic">Caenorhabditis elegans</span> and the (<b>B</b>) decay area of Chinese cabbage (<b>B</b>) in an infection model of <span class="html-italic">P. aeruginosa</span>. All data represent the results of at least three independent biological replicates. The error bars represent the standard deviations. Student’s <span class="html-italic">t</span> test; *: <span class="html-italic">p</span> &lt; 0.05; **: <span class="html-italic">p</span> &lt; 0.01.</p>
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23 pages, 2048 KiB  
Article
Early COVID-19 Pandemic Preparedness: Informing Public Health Interventions and Hospital Capacity Planning Through Participatory Hybrid Simulation Modeling
by Yuan Tian, Jenny Basran, Wade McDonald and Nathaniel D. Osgood
Int. J. Environ. Res. Public Health 2025, 22(1), 39; https://doi.org/10.3390/ijerph22010039 (registering DOI) - 30 Dec 2024
Abstract
We engaged with health sector stakeholders and public health professionals within the health system through a participatory modeling approach to support policy-making in the early COVID-19 pandemic in Saskatchewan, Canada. The objective was to use simulation modeling to guide the implementation of public [...] Read more.
We engaged with health sector stakeholders and public health professionals within the health system through a participatory modeling approach to support policy-making in the early COVID-19 pandemic in Saskatchewan, Canada. The objective was to use simulation modeling to guide the implementation of public health measures and short-term hospital capacity planning to mitigate the disease burden from March to June 2020. We developed a hybrid simulation model combining System Dynamics (SD), discrete-event simulation (DES), and agent-based modeling (ABM). SD models the population-level transmission of COVID-19, ABM simulates individual-level disease progression and contact tracing intervention, and DES captures COVID-19-related hospital patient flow. We examined the impact of mixed mitigation strategies—physical distancing, testing, conventional and digital contact tracing—on COVID-19 transmission and hospital capacity for a worst-case scenario. Modeling results showed that enhanced contact tracing with mass testing in the early pandemic could significantly reduce transmission, mortality, and the peak census of hospital beds and intensive care beds. Using a participatory modeling approach, we not only directly informed policy-making on contact tracing interventions and hospital surge capacity planning for COVID-19 but also helped validate the effectiveness of the interventions adopted by the provincial government. We conclude with a discussion on lessons learned and the novelty of our hybrid approach. Full article
(This article belongs to the Special Issue Pandemic Preparedness: Lessons Learned from COVID-19)
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<p>Hybrid model structure for simulating COVID-19 transmission, disease progression, and COVID-19-related hospital patient flow.</p>
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<p>Comparison of model outputs with observed COVID-19 data in Saskatchewan. MSE: Mean Squared Error.</p>
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<p>Mean census of hospital beds, ICU beds, and ventilators for COVID-19 inpatients under various scenarios, with peak values and 10th and 90th percentile ranges.</p>
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<p>Sensitivity analyses on the basic reproduction number (<math display="inline"><semantics> <msub> <mi>R</mi> <mn>0</mn> </msub> </semantics></math>).</p>
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22 pages, 1580 KiB  
Article
Predictive Forwarding Rule Caching for Latency Reduction in Dynamic SDN
by Doosik Um, Hyung-Seok Park, Hyunho Ryu and Kyung-Joon Park
Sensors 2025, 25(1), 155; https://doi.org/10.3390/s25010155 (registering DOI) - 30 Dec 2024
Abstract
In mission-critical environments such as industrial and military settings, the use of unmanned vehicles is on the rise. These scenarios typically involve a ground control system (GCS) and nodes such as unmanned ground vehicles (UGVs) and unmanned aerial vehicles (UAVs). The GCS and [...] Read more.
In mission-critical environments such as industrial and military settings, the use of unmanned vehicles is on the rise. These scenarios typically involve a ground control system (GCS) and nodes such as unmanned ground vehicles (UGVs) and unmanned aerial vehicles (UAVs). The GCS and nodes exchange different types of information, including control data that direct unmanned vehicle movements and sensor data that capture real-world environmental conditions. The GCS and nodes communicate wirelessly, leading to loss or delays in control and sensor data. Minimizing these issues is crucial to ensure nodes operate as intended over wireless links. In dynamic networks, distributed path calculation methods lead to increased network traffic, as each node independently exchanges control messages to discover new routes. This heightened traffic results in internal interference, causing communication delays and data loss. In contrast, software-defined networking (SDN) offers a centralized approach by calculating paths for all nodes from a single point, reducing network traffic. However, shifting from a distributed to a centralized approach with SDN does not inherently guarantee faster route creation. The speed of generating new routes remains independent of whether the approach is centralized, so SDN does not always lead to faster results. Therefore, a key challenge remains: determining how to create new routes as quickly as possible even within an SDN framework. This paper introduces a caching technique for forwarding rules based on predicted link states in SDN, which was named the CRIMSON (Cashing Routing Information in Mobile SDN Network) algorithm. The CRIMSON algorithm detects network link state changes caused by node mobility and caches new forwarding rules based on predicted topology changes. We validated that the CRIMSON algorithm consistently reduces end-to-end latency by an average of 88.96% and 59.49% compared to conventional reactive and proactive modes, respectively. Full article
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<p>Necessity of forwarding rule updates in dynamic network. In a dynamic network, topology changes and link changes occur as nodes move around. Accordingly, forwarding rules for node-specific communication must be updated.</p>
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<p>Comparison between traditional communication and SDN methods. In a traditional network, a control plane is configured on each node. However, in an SDN environment, only the central controller has a control plane. In this case, the central controller provides the forwarding rules.</p>
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<p>LLDP transmission process for communication between SDN nodes. In an SDN, the SDN controller recognizes new switches through the process of packet-out, deliver LLDP, and packet-in to the switches it already knows.</p>
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<p>Representation of node link states using adjacency matrix. Graph data for each topology are represented as an adjacency matrix. Depending on the number of nodes (<span class="html-italic">n</span>), an <math display="inline"><semantics> <mrow> <mi>n</mi> <mo>×</mo> <mi>n</mi> </mrow> </semantics></math> matrix is formed, where each row and column data represent the connection status between nodes.</p>
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<p>Confusion matrix. The confusion matrix calculates Precision, NPV, Specificity, and Recall using the TP, TN, FP, and FN metrics. This matrix is used to evaluate the performance of classification models.</p>
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<p>System model. This environment includes a GCS and multiple mobile unmanned nodes. The GCS and nodes transmit various types of communication, such as data collection, topology maintenance, and command control.</p>
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<p>CRIMSON flow. CRIMSON is composed of three main steps. The first is topology change detection and generation of the predicted node locations. The second is the creation of a predictive adjacency matrix. The third is caching the forwarding rules for the predicted link states. Through this process, CRIMSON prepares forwarding rules in advance, reflecting the predicted link states.</p>
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<p>CRIMSON flow chart. The analysis of time-series data calculates node movement trends, and if they exceed a threshold, the system predicts the node positions. The system calculates distances between nodes using the predicted positions and checks them against the communication range to generate an adjacency matrix. The matrix updates forwarding rules for both direct and alternative paths.</p>
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<p>Types of topologies used in the simulation. We use five topologies consisting of five nodes with UAV modeling applied. The topology shapes used, from left to right, are linear, v-shaped, trapezoid, star, and pentagon.</p>
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<p>Evaluation of confusion matrix metrics within the threshold range of 0.001 to 0.035. We assess the values of Precision, Recall, NPV, and Specificity throughout this threshold range. Afterward, we select the optimal threshold value that produces the highest average among these four metrics.</p>
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<p>Optimization process for finding the Shiftpoint. This process applies three optimization methods to the average value of the four confusion matrix metrics.</p>
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<p>Latency comparison of CRIMSON based on RTT tests. The comparison includes reactive mode and proactive mode. The simulation measured latency using rtt avg, rtt max, and rtt mdev.</p>
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<p>Evaluation of LLDP usage in CRIMSON. The proposed CRIMSON method indicates a lower LLDP count compared to the proactive mode. In an SDN system, LLDP packets are transmitted when packet processing is not handled. This indicates that CRIMSON performs packet processing effectively in dynamic networks.</p>
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<p>Network latency comparison of CRIMSON at various bandwidths. We conduct RTT tests at 0.5 Mbps, 1 Mbps, 5 Mbps, and 10 Mbps for the proposed CRIMSON algorithm. Simulation results confirm that CRIMSON achieves lower and more stable network latency.</p>
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21 pages, 4502 KiB  
Article
Multi-Scale Robotics: A Numerical Investigation on Mobile Micro-Tweezers for Micro-Manipulation with Extreme Requirements
by Ahmet Fatih Tabak
Micromachines 2025, 16(1), 40; https://doi.org/10.3390/mi16010040 (registering DOI) - 30 Dec 2024
Abstract
An automated micro-tweezers system with a flexible workspace would benefit the intelligent sorting of live cells. Such micro-tweezers could employ a forced vortex strong enough to capture a single cell. Furthermore, addressable control of the position to the vortex would constitute a robotic [...] Read more.
An automated micro-tweezers system with a flexible workspace would benefit the intelligent sorting of live cells. Such micro-tweezers could employ a forced vortex strong enough to capture a single cell. Furthermore, addressable control of the position to the vortex would constitute a robotic system. In this study, a spherical micro-object composed of super paramagnetic particles tightly packed in a non-magnetic resin is rotated with a combined magnetic field of permanent magnets. The said magnetic field is articulated by an open-kinematic chain controlled with a simple adaptive PI-control scheme. A vortex is formed as the spherical particle, assumed to be submerged under the surface of fluid, and follows the position and orientation of the external magnetic field. This forced vortex induces a radial pressure gradient that captures the live cell orbiting around the spherical object combined with the inertial effects. Here, a comprehensive mathematical model is presented to reflect on the dynamics of such micro-tweezer systems. Numerical results demonstrate that it is theoretically possible to capture and tow a bacterium cell while meeting extreme tracking references for motion control. Magnetic and fluid forces on the spherical particle traverse the vortex and the bacterium cell, with orbiting and sporadic collusion of the bacterium cell around the spherical particle, and the positions of the end-effector, i.e., the magnets, are analyzed. Full article
(This article belongs to the Special Issue The 15th Anniversary of Micromachines)
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<p>The three-degrees-of-freedom robotic arm (<b>right</b>) and magnets at the 3rd Link, i.e., the end-effector, hovering above the fluid medium that contains the hydrodynamic tweezers (<b>left</b>). A representative orbit of the bacterium cell around the magnetic particle is denoted by the dashed-circle in orange. The illustrated objects are not equally scaled.</p>
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<p>Hydrodynamic tweezers with the core displacing along the XY-plane in an arbitrary direction, thereby dragging and transforming the orbit of the bacterium instantaneously. Unit vectors of the cylindrical coordinates of the vortex core are denoted by <math display="inline"><semantics> <mrow> <msub> <mrow> <mover> <mi mathvariant="normal">e</mi> <mo>^</mo> </mover> </mrow> <mi>r</mi> </msub> </mrow> </semantics></math> and <math display="inline"><semantics> <mrow> <msub> <mrow> <mover> <mi mathvariant="normal">e</mi> <mo>^</mo> </mover> </mrow> <mi>θ</mi> </msub> </mrow> </semantics></math> in the radial and azimuth directions, respectively.</p>
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<p>Reaction to a sudden change in direction of velocity reference before and after the change in direction occurs, in blue and in red, respectively: (<b>a</b>) position of the tip of the robotic arm; (<b>b</b>) position of the vortex core; (<b>c</b>) position of the bacterium cell; (<b>d</b>) position and orientation of the bacterium cell in the vortex frame in polar coordinates; (<b>e</b>) position vs. orientation of the bacterium cell in the vortex frame; (<b>f</b>) the orientation of the bacterium cell on the XY-plane given by respective Euler angles.</p>
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<p>Reaction to a sudden change in direction of the velocity reference before and after the change in direction occurs, in blue and in red, respectively: (<b>a</b>) azimuthal drag force on the bacterium; (<b>b</b>) radial pressure force on the bacterium; (<b>c</b>) magnetic force on the vortex core; (<b>d</b>) contact force on the bacterium; (<b>e</b>) lubrication force on the bacterium; (<b>f</b>) film damping force on the bacterium.</p>
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<p>Reaction to a sudden change in direction of velocity reference before and after the change in direction occurs, in blue and in red, respectively: (<b>a</b>) tracking error calculated for the vortex core on the XY-plane; (<b>b</b>) computed control signal comparison for traverse on the XY-plane with an inset for the second velocity reference (in red); (<b>c</b>) motor currents for traverse on the XY-plane; (<b>d</b>) amplified PWM signal and motor current for the third degree-of-freedom; (<b>e</b>) magnetic field density felt by the vortex; (<b>f</b>) Brownian noise for the bacterium.</p>
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<p>Reaction to constant and comparatively violent pull by the magnetic field: (<b>a</b>) position of the tip of the robotic arm; (<b>b</b>) position of the vortex core; (<b>c</b>) position of the bacterium cell; (<b>d</b>) position and orientation of the bacterium cell in vortex frame in polar coordinates; (<b>e</b>) position vs. orientation of the bacterium cell in vortex frame; (<b>f</b>) the orientation of the bacterium cell on XY-plane given by respective Euler angles.</p>
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<p>Reaction to constant and comparatively violent pull by the magnetic field: (<b>a</b>) azimuthal drag force on the bacterium; (<b>b</b>) radial pressure force on the bacterium; (<b>c</b>) magnetic force on the vortex core; (<b>d</b>) contact force on the bacterium, with the inset further highlighting the non-zero region; (<b>e</b>) lubrication force on the bacterium; (<b>f</b>) film-damping force on the bacterium, with the inset further highlighting the non-zero region.</p>
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<p>Reaction to constant and comparatively violent pull by the magnetic field: (<b>a</b>) error in tracking calculated for the vortex core on the XY-plane; (<b>b</b>) computed control signal comparison for traverse on the XY-plane (<b>c</b>) motor currents for traverse on the XY-plane; (<b>d</b>) amplified PWM signal and motor current for the third degree-of-freedom; (<b>e</b>) magnetic field density felt by the vortex; (<b>f</b>) Brownian noise on the bacterium.</p>
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<p>SIMULINK schematic to generate PWM signal for a given control signal to drive the associated DC motor.</p>
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<p>PWM signals on the third degree-of-freedom for the control tasks in this study: (<b>a</b>) PWM signals before (in blue) and after (in red) the direction of motion was altered; (<b>b</b>) PWM signal while dragging the vortex core with a relatively greater velocity reference.</p>
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