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Abstract This study leverages reactive molecular dynamics simulations to enhance undergraduate education and research in materials science. Focusing on the oxidation processes of a variety of energetic metal nanoparticles, including Al, Cu, Mg, and Ti, two undergraduate students led the scientific inquiry. They conducted literature reviews, ran simulations, validated assumptions, and analyzed results, deepening their understanding of material behaviors and strengthening their STEM identity. Through these hands-on experiences, the students successfully investigated the energetic properties of these nanoparticles, demonstrating the effectiveness of this approach in promoting inquiry-based learning. This work underscores the transformative potential of computational simulations in advancing computational materials research, fostering diversity, and preparing undergraduates for future contributions to computational modeling-driven science. Graphical abstract 

Digital controls is a topic often learned through a highly theoretical, almost purely mathematical approach which students struggle to master. Project-based learning is one potentially effective way to address this issue, and hands-on learning as a component of projects can make it even more effective. However, access to equipment for hands-on learning can present significant challenges. To address this issue, we have designed and developed two novel prototypes of hands-on equipment for learning controls that are open-source, inexpensive to produce, and portable. They are suitable for use in undergraduate and graduate-level digital embedded control systems courses. These newly developed devices are a pendulum driven by a dc motor, and a straight-line mechanism consisting of a board, two links, and a dc motor. Control of the devices was used as the primary basis for a class project given to students. 

Drone simulators are often used to reduce training costs and prepare operators for various ad-hoc scenarios, as well as to test the quality of algorithmic and communication aspects in collaborative scenarios. An important aspect of drone missions in simulated (as well as real life) environments is the operational lifetime of a given drone, in both solo and collaborative fleet settings. Its importance stems from the fact that the capacity of the on-board batteries in untethered (i.e., free-flying) drones determines the range and/or the length of the trajectory that a drone can travel in the course of its surveilance or delivery missions. Most of the existing simulators incorporate some kind of a consumption model based on different parameters of the drone and its flight trajectory. However, to our knowledge, the existing simulators are not capable of incorporating data obtained from actual physical measurements/observations into the consumption model. In this work, we take a first step towards enabling the (users of) drones simulator to incorporate the speed and direction of the wind into the model and monitor its impact on the battery consumption as the direction of the flight changes relative to the wind. We have also developed a proof-of-concept implementation with DJI Mavic 3 and Parrot ANAFI drones. 

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent responsible for coronavirus disease 2019 (COVID-19), has affected the lives of billions and killed millions of infected people. This virus has been demonstrated to have different outcomes among individuals, with some of them presenting a mild infection, while others present severe symptoms or even death. The identification of the molecular states related to the severity of a COVID-19 infection has become of the utmost importance to understanding the differences in critical immune response. In this study, we computationally processed a set of publicly available single-cell RNA-Seq (scRNA-Seq) data of 12 Bronchoalveolar Lavage Fluid (BALF) samples diagnosed as having a mild, severe, or no infection, and generated a high-quality dataset that consists of 63,734 cells, each with 23,916 genes. We extended the cell-type and sub-type composition identification and our analysis showed significant differences in cell-type composition in mild and severe groups compared to the normal. Importantly, inflammatory responses were dramatically elevated in the severe group, which was evidenced by the significant increase in macrophages, from 10.56% in the normal group to 20.97% in the mild group and 34.15% in the severe group. As an indicator of immune defense, populations of T cells accounted for 24.76% in the mild group and decreased to 7.35% in the severe group. To verify these findings, we developed several artificial neural networks (ANNs) and graph convolutional neural network (GCNN) models. We showed that the GCNN models reach a prediction accuracy of the infection of 91.16% using data from subtypes of macrophages. Overall, our study indicates significant differences in the gene expression profiles of inflammatory response and immune cells of severely infected patients. 

Abstract Background Macrophages show versatile functions in innate immunity, infectious diseases, and progression of cancers and cardiovascular diseases. These versatile functions of macrophages are conducted by different macrophage phenotypes classified as classically activated macrophages and alternatively activated macrophages due to different stimuli in the complex in vivo cytokine environment. Dissecting the regulation of macrophage activations will have a significant impact on disease progression and therapeutic strategy. Mathematical modeling of macrophage activation can improve the understanding of this biological process through quantitative analysis and provide guidance to facilitate future experimental design. However, few results have been reported for a complete model of macrophage activation patterns. Results We globally searched and reviewed literature for macrophage activation from PubMed databases and screened the published experimental results. Temporal in vitro macrophage cytokine expression profiles from published results were selected to establish Boolean network models for macrophage activation patterns in response to three different stimuli. A combination of modeling methods including clustering, binarization, linear programming (LP), Boolean function determination, and semi-tensor product was applied to establish Boolean networks to quantify three macrophage activation patterns. The structure of the networks was confirmed based on protein-protein-interaction databases, pathway databases, and published experimental results. Computational predictions of the network evolution were compared against real experimental results to validate the effectiveness of the Boolean network models. Conclusion Three macrophage activation core evolution maps were established based on the Boolean networks using Matlab. Cytokine signatures of macrophage activation patterns were identified, providing a possible determination of macrophage activations using extracellular cytokine measurements.