Applications of Computational Models on Studying Particulate Systems

Particulate systems have been widely studied because of its various phenomena and tight relationship with industry applications. In this dissertation, two types of computational models have been adopted to study two problems with different particulate systems: granular self-organization inside a cylinder driven by an orbital-shaker and the optimal design of bypass line for an industrial-scale 8‑leg polyolefin loop reactor. In the first study, behavior of both single particle and multiple particles in a rotating cylinder has been modeled by discrete element method (DEM) to understand the mechanism of granular self-organization. Sets of studies have then been performed to study the effect of different parameters. This work may benefit the design and operation of equipment involving such kind of granular systems. Further, it serves as the validation of DEM modelling framework on a complex dynamical system with several degrees of self-organization in granular systems. In the second study, CFD simulations were applied to design optimal bypass line for a polyolefin 8-leg loop reactor. 2D CFD simulations were performed to qualitatively compare the slug dissipation processes of three types of bypass line connections. Then, 3D simulations were used to compare the effect of installation angle on the withdrawal rate of the solid phase into the bypass line. By combining these approaches, an optimal design of bypass line was recommended for the loop reactor considered in this study. This design approach can also be generally applied to design bypass lines for other loop reactor configurations

eIF1A/eIF5B Interaction Network and its Functions in Translation Initiation Complex Assembly and Remodeling

Eukaryotic translation initiation is a highly regulated process involving multiple steps, from 43S pre-initiation complex (PIC) assembly, to ribosomal subunit joining. Subunit joining is controlled by the G-protein eukaryotic translation initiation factor 5B (eIF5B). Another protein, eIF1A, is involved in virtually all steps, including subunit joining. The intrinsically disordered eIF1A C-terminal tail (eIF1A-CTT) binds to eIF5B Domain-4 (eIF5B-D4). The ribosomal complex undergoes conformational rearrangements at every step of translation initiation; however, the underlying molecular mechanisms are poorly understood. Here we report three novel interactions involving eIF5B and eIF1A: (i) a second binding interface between eIF5B and eIF1A; (ii) a dynamic intramolecular interaction in eIF1A between the folded domain and eIF1A-CTT; and (iii) an intramolecular interaction between eIF5B-D3 and -D4. The intramolecular interactions within eIF1A and eIF5B interfere with one or both eIF5B/eIF1A contact interfaces, but are disrupted on the ribosome at different stages of translation initiation. Therefore, our results indicate that the interactions between eIF1A and eIF5B are being continuously rearranged during translation initiation. We present a model how the dynamic eIF1A/eIF5B interaction network can promote remodeling of the translation initiation complexes, and the roles in the process played by intrinsically disordered protein segments

Network medicine links SARS-CoV-2/COVID-19 infection to brain microvascular injury and neuroinflammation in dementia-like cognitive impairment

Background Dementia-like cognitive impairment is an increasingly reported complication of SARS-CoV-2 infection. However, the underlying mechanisms responsible for this complication remain unclear. A better understanding of causative processes by which COVID-19 may lead to cognitive impairment is essential for developing preventive and therapeutic interventions. Methods In this study, we conducted a network-based, multimodal omics comparison of COVID-19 and neurologic complications. We constructed the SARS-CoV-2 virus-host interactome from protein-protein interaction assay and CRISPR-Cas9-based genetic assay results and compared network-based relationships therein with those of known neurological manifestations using network proximity measures. We also investigated the transcriptomic profiles (including single-cell/nuclei RNA-sequencing) of Alzheimer’s disease (AD) marker genes from patients infected with COVID-19, as well as the prevalence of SARS-CoV-2 entry factors in the brains of AD patients not infected with SARS-CoV-2. Results We found significant network-based relationships between COVID-19 and neuroinflammation and brain microvascular injury pathways and processes which are implicated in AD. We also detected aberrant expression of AD biomarkers in the cerebrospinal fluid and blood of patients with COVID-19. While transcriptomic analyses showed relatively low expression of SARS-CoV-2 entry factors in human brain, neuroinflammatory changes were pronounced. In addition, single-nucleus transcriptomic analyses showed that expression of SARS-CoV-2 host factors (BSG and FURIN) and antiviral defense genes (LY6E, IFITM2, IFITM3, and IFNAR1) was elevated in brain endothelial cells of AD patients and healthy controls relative to neurons and other cell types, suggesting a possible role for brain microvascular injury in COVID-19-mediated cognitive impairment. Overall, individuals with the AD risk allele APOE E4/E4 displayed reduced expression of antiviral defense genes compared to APOE E3/E3 individuals. Conclusion Our results suggest significant mechanistic overlap between AD and COVID-19, centered on neuroinflammation and microvascular injury. These results help improve our understanding of COVID-19-associated neurological manifestations and provide guidance for future development of preventive or treatment interventions, although causal relationship and mechanistic pathways between COVID-19 and AD need future investigations

Decoding the spermatogonial stem cell niche under physiological and recovery conditions in adult mice and humans

The intricate interaction between spermatogonial stem cell (SSC) and testicular niche is essential for maintaining SSC homeostasis; however, this interaction remains largely uncharacterized. In this study, to characterize the underlying signaling pathways and related paracrine factors, we delineated the intercellular interactions between SSC and niche cell in both adult mice and humans under physiological conditions and dissected the niche-derived regulation of SSC maintenance under recovery conditions, thus uncovering the essential role of C-C motif chemokine ligand 24 and insulin-like growth factor binding protein 7 in SSC maintenance. We also established the clinical relevance of specific paracrine factors in human fertility. Collectively, our work on decoding the adult SSC niche serves as a valuable reference for future studies on the aetiology, diagnosis, and treatment of male infertility.</p

A Genome Wide Association Study Identifies Common Variants Associated with Lipid Levels in the Chinese Population

Plasma lipid levels are important risk factors for cardiovascular disease and are influenced by genetic and environmental factors. Recent genome wide association studies (GWAS) have identified several lipid-associated loci, but these loci have been identified primarily in European populations. In order to identify genetic markers for lipid levels in a Chinese population and analyze the heterogeneity between Europeans and Asians, especially Chinese, we performed a meta-analysis of two genome wide association studies on four common lipid traits including total cholesterol (TC), triglycerides (TG), low-density lipoprotein cholesterol (LDL) and high-density lipoprotein cholesterol (HDL) in a Han Chinese population totaling 3,451 healthy subjects. Replication was performed in an additional 8,830 subjects of Han Chinese ethnicity. We replicated eight loci associated with lipid levels previously reported in a European population. The loci genome wide significantly associated with TC were near DOCK7, HMGCR and ABO; those genome wide significantly associated with TG were near APOA1/C3/A4/A5 and LPL; those genome wide significantly associated with LDL were near HMGCR, ABO and TOMM40; and those genome wide significantly associated with HDL were near LPL, LIPC and CETP. In addition, an additive genotype score of eight SNPs representing the eight loci that were found to be associated with lipid levels was associated with higher TC, TG and LDL levels (P = 5.52×10-16, 1.38×10-6 and 5.59×10-9, respectively). These findings suggest the cumulative effects of multiple genetic loci on plasma lipid levels. Comparisons with previous GWAS of lipids highlight heterogeneity in allele frequency and in effect size for some loci between Chinese and European populations. The results from our GWAS provided comprehensive and convincing evidence of the genetic determinants of plasma lipid levels in a Chinese population

Association Study of the β2-Adrenergic Receptor Gene Polymorphisms and Hypertension in the Northern Han Chinese

Background: The beta 2-adrenergic receptor (ADRB2) gene has been widely researched as a candidate gene for essential hypertension (EH), but no consensus has been reached in different ethnicities. The aim of the present study was to evaluate the possible association between the ADRB2 gene polymorphisms and the EH risk in the Northern Han Chinese population. Methodology/Principal Findings: This study included 747 hypertensive subjects and 390 healthy volunteers as control subjects in the Northern Han Chinese. Genotyping was performed to identify the C-47T, A46G and C79G polymorphisms of the ADRB2 gene. G allelic frequency of A46G polymorphism was significantly higher in hypertensive subjects (P = 0.011, OR = 1.287, 95% CI [1.059-1.565]) than that in controls. Significant association could also be found in dominant genetic model (GG+AG vs. AA, P = 0.006, OR = 1.497, 95% CI [1.121-1.998]), in homozygote comparison (GG vs. AA, P = 0.025, OR = 1.568, 95% CI [1.059-2.322]), and in additive genetic model (GG vs. AG vs. AA, P = 0.012, OR = 1.282, 95% CI [1.056-1.555]). Subgroup analyses performed by gender suggested that this association could be found in male, but not in female. Stratification analyses by obesity showed that A46G polymorphism was related to the prevalence of hypertension in the obese population (GG vs. AG vs. AA, P&lt;0.001, OR = 1.645, 95% CI [1.258-2.151]). Significant interaction was found between A46G genotypes and body mass index on EH risk. No significant association could be found between C-47T or C79G polymorphism and EH risk. Linkage disequilibrium was detected between the C-47T, A46G and C79G polymorphisms. Haplotype analyses observed that the T-47-A46-C79 haplotype was a protective haplotype for EH, while the T-47-G46-C79 haplotype increased the risk. Conclusions/Significances: We revealed that the ADRB2 A46G polymorphism might increase the risk for EH in the Northern Han Chinese population.Multidisciplinary SciencesSCI(E)7ARTICLE4null

Research on the Mobile Refrigeration System at a High Temperature Working Face of an Underground Mine

With an increase in mining depth, the problem of heat damage in metal mine working face has become increasingly prominent. In order to effectively reduce the temperature of the working face and provide a comfortable working environment for the miners, based on the concept of “cooling on demand”, a mobile refrigeration system for high-temperature working face was designed, and a field test was carried out in Dahongshan Copper Mine, Yunnan Province. At the same time, based on the experimental conditions, the parameter optimization research of the mobile refrigeration system was carried out. The results showed that: (1) The mobile refrigeration system could reduce the wet bulb temperature of the working face at the test site to below 30 °C, which is in line with the “Safety Regulations for Metal and Non-Metallic Mines” (GB16423-2020); (2) when the diameter of the air supply pipe was 600 mm and the air supply velocity was 12 m/s, the target cooling area could meet the continuous operation requirements stipulated in the “Safety Regulations for Metal and Non-metallic Mines” in China; (3) for every 2 °C decrease in supply air temperature, the average wet bulb temperature in the target cooling area decreased by 0.9 °C; (4) for every 10% decrease in supply air humidity, the wet bulb temperature and relative humidity in the target cooling area decreased by 0.76 °C and 4.38% on average, respectively. The research results provide new ideas and methods for the prevention and control of heat damage in metal mines

A Vibration-Based MEMS Piezoelectric Energy Harvester and Power Conditioning Circuit

This paper presents a micro-electro-mechanical system (MEMS) piezoelectric power generator array for vibration energy harvesting. A complete design flow of the vibration-based energy harvester using the finite element method (FEM) is proposed. The modal analysis is selected to calculate the resonant frequency of the harvester, and harmonic analysis is performed to investigate the influence of the geometric parameters on the output voltage. Based on simulation results, a MEMS Pb(Zr,Ti)O3 (PZT) cantilever array with an integrated large Si proof mass is designed and fabricated to improve output voltage and power. Test results show that the fabricated generator, with five cantilever beams (with unit dimensions of about 3 × 2.4 × 0.05 mm3) and an individual integrated Si mass dimension of about 8 × 12.4 × 0.5 mm3, produces a output power of 66.75 μW, or a power density of 5.19 μW∙mm−3∙g−2 with an optimal resistive load of 220 kΩ from 5 m/s2 vibration acceleration at its resonant frequency of 234.5 Hz. In view of high internal impedance characteristic of the PZT generator, an efficient autonomous power conditioning circuit, with the function of impedance matching, energy storage and voltage regulation, is then presented, finding that the efficiency of the energy storage is greatly improved and up to 64.95%. The proposed self-supplied energy generator with power conditioning circuit could provide a very promising complete power supply solution for wireless sensor node loads

A Hybrid Indoor Ambient Light and Vibration Energy Harvester for Wireless Sensor Nodes

To take advantage of applications where both light and vibration energy are available, a hybrid indoor ambient light and vibration energy harvesting scheme is proposed in this paper. This scheme uses only one power conditioning circuit to condition the combined output power harvested from both energy sources so as to reduce the power dissipation. In order to more accurately predict the instantaneous power harvested from the solar panel, an improved five-parameter model for small-scale solar panel applying in low light illumination is presented. The output voltage is increased by using the MEMS piezoelectric cantilever arrays architecture. It overcomes the disadvantage of traditional MEMS vibration energy harvester with low voltage output. The implementation of the maximum power point tracking (MPPT) for indoor ambient light is implemented using analog discrete components, which improves the whole harvester efficiency significantly compared to the digital signal processor. The output power of the vibration energy harvester is improved by using the impedance matching technique. An efficient mechanism of energy accumulation and bleed-off is also discussed. Experiment results obtained from an amorphous-silicon (a-Si) solar panel of 4.8 × 2.0 cm2 and a fabricated piezoelectric MEMS generator of 11 × 12.4 mm2 show that the hybrid energy harvester achieves a maximum efficiency around 76.7%