Using the generalized interpolation material point method for fluid-solid interactions induced by surface tension

This thesis is devoted to the development of new, Generalized Interpolation Material Point Method (GIMP)-based algorithms for handling surface tension and contact (wetting) in fluid-solid interaction (FSI) problems at small scales. In these problems, surface tension becomes so dominant that its influence on both fluids and solids must be considered. Since analytical solutions for most engineering problems are usually unavailable, numerical methods are needed to describe and predict complicated time-dependent states in the solid and fluid involved due to surface tension effects. Traditional computational methods for handling fluid-solid interactions may not be effective due to their weakness in solving large-deformation problems and the complicated coupling of two different types of computational frameworks: one for solid, and the other for fluid. On the contrary, GIMP, a mesh-free algorithm for solid mechanics problems, is numerically effective in handling problems involving large deformations and fracture. Here we extend the capability of GIMP to handle fluid dynamics problems with surface tension, and to develop a new contact algorithm to deal with the wetting boundary conditions that include the modeling of contact angle and slip near the triple points where the three phases -- fluid, solid, and vapor -- meet. The error of the new GIMP algorithm for FSI problems at small scales, as verified by various benchmark problems, generally falls within the 5% range. In this thesis, we have successfully extended the capability of GIMP for handling FSI problems under surface tension in a one-solver numerical framework, a unique and innovative approach.Chapter 1. Introduction -- Chapter 2. Using the generalized interpolation material point method for fluid dynamics at low reynolds numbers -- Chapter 3. On the modeling of surface tension and its applications by the generalized interpolation material point method -- Chapter 4. Using the generalized interpolation material point method for fluid-solid interactions induced by surface tension -- Chapter 5. Conclusions

Creep of grouted anchors in ice-rich silt

Thesis (M.S.) University of Alaska Fairbanks, 2011Creep is a critical consideration for designing anchors in ice-rich silt. In this study, creep was evaluated for grouted anchors in ice-rich silt by laboratory tests. A total of nineteen staged-load pullout tests were conducted on smooth grouted anchors. The anchors were loaded until either a tertiary creep stage or the capacity of the load system was reached. Soil temperatures evaluated in this study ranged from 32 °F to 26.6 °F. It was found that the onset of tertiary creep for smooth anchors was around 0.03 inches, which was much smaller than that suggested in the literature for rough anchors (1.0 inch). Given the same shear stress and soil temperature, the observed creep displacement rates for smooth anchors were greater than those given by the existing design guidelines for rough anchors. A new creep model was proposed in which soil temperature was included as an additional variable. Model parameters were developed as a function of soil temperature and moisture contents by using the test data. The model predictions were compared with the laboratory tests. It was found that the creep displacement rates decreased with the decreasing of soil moisture contents and temperature. Based on the analysis of laboratory test data, design charts were provided to give the allowable pullout capacity for smooth anchors in ice-rich silt.Alaska Department of Transportation & Public Facilities and Alaska University Transportation Center1. Introduction -- 1.1. Objectives of the research -- 1.2. Research methodology -- 2. Literature review -- 2.1. Background on grouted anchors -- 2.2. Creep behavior of grouted anchors -- 2.3. Factors influencing creep of anchors in permafrost -- 2.4. Existing theories for creep in frozen soil -- 2.5. Design for anchor capacity -- 2.6. Anchor load tests in permafrost -- 3. Anchor load tests and test results -- 3.1. Soil preparation -- 3.2. Laboratory creep test setup -- 3.3. Anchor installation methods -- 3.4. Testing procedures -- 3.5. Test results -- 4. Data analysis and discussion -- 4.1. Comparison with rough anchors based on the design guidelines -- 4.2. Development of a time-dependent creep equations -- 4.3. Effect of soil moisture content and temperature -- 4.4. Design example -- 4.5. Design charts -- 5. Conclusions and recommendations -- 5.1. Conclusions -- 5.2. Recommendations -- References -- Appendix A: Anchor load tests in the laboratory -- A.1. Test anchor configurations and fabrications -- A.2. Load frame configurations and calibrations -- A.3. Displacement measurement -- A.4. Testing procedures -- Appendix B: Anchor load test results -- B.1. Load conditions -- B.2. Creep curves from the nineteen load tests -- Appendix C: Data regression results

Creep Behavior of Shallow Anchors in Ice-rich Silt

Grouted anchors have become a common technique in the application of earth retention systems, slope stability problems and tie-down structures in unfrozen soils due to its cost and time efficiency. However, within much of Alaska area, permafrost is a common type of soil and might contain large amount of visible ice. The highly time and temperature dependent properties of ice-rich soil make it a challenge for the application of anchors in permafrost area. This project valuates the effect of water content and temperature on the creep behavior of shallow anchors in cold room lab. Also, field test was conducted to determine effectiveness of three types of grouting materials, including Bentonite clay, Microsil Anchor Grout and special cement formula. The temperature along the anchor was monitored to evaluate the degradation of the surrounding frozen soil. Research results may be applicable in the design of shallow anchors in ice-rich permafrost at various ice content and temperature range. Also, the load distribution and the pullout test results could give a general guidance for the shallow anchor design in permafrost area.Table of Contents - iv List of Figures - viii List of Tables - xiv Chapter 1 Introduction - 1 1.1 General - 1 1.2 Problem Statement - 1 1.3 Objective - 2 1.4 Research Methodology - 2 Chapter 2 Literature Review - 4 2.1 Background on Grouted Anchors - 4 2.2 Creep Theory - 5 1. General Creep Behavior - 5 2. Creep Behavior of Ice - 6 3. Creep behavior of Frozen Soils - 8 2.3 Grouted Anchor Design in Permafrost - 10 1. Grouted Anchor Design Considerations - 11 2. Grouted Anchor Design in Ice-rich Soil - 14 Chapter 3 Laboratory Test - 19 3.1 Laboratory Pullout Test Preparation - 19 1. Soil Preparation - 19 2. Grouted Anchor Preparation - 20 3. Load Frame Preparation - 23 4. Calibration of the Testing Equipment - 26 3.2 Laboratory Pullout Test Procedures - 28 1. Preparing Anchor Test Specimens - 28 2. Load Frame Setup - 31 3. Testing Procedure Outline - 32 Chapter 4 Field Tests of Anchor in CRREL Permafrost Tunnel - 34 4.1 Test Site Overview - 34 1. Introduction to Testing Site - 34 2. CRREL Permafrost Tunnel Geology - 36 3. Anchor Test Location within Permafrost Tunnel - 37 4.2 Testing Equipment - 39 1. Strain Sensors - 40 2. LVDT - 42 4.3 Borehole Drilling Process - 43 1. Drilling Borehole and Drilling System Layout - 43 2. Drilling machine setup - 46 3. Drilling procedure - 48 4. Drilling sequence - 50 4.4 Anchor Preparation and Installation - 51 1. HPI Strain Gage Installation - 52 2. Geokon Strain Gage Installation - 55 3. Anchor Installation Process - 57 4. Backfill Material Preparation and Grouting - 58 5. Backfill Material Mixing - 59 4.5 Loading System Setup - 62 1. Loading system for shallow anchor - 62 2. Loading system for duckbill - 68 4.6 Data Acquisition System Setup - 69 4.7 Duckbill Removal and Anchor Pullout Test - 71 1. Duckbill Removal - 71 2. Pullout Test System Setup - 72 Chapter 5 Test Results and Data Analysis - 75 5.1 Laboratory Pullout Test Results and Analysis (UAF Laboratory) 75 1. Effect of Temperature and Water Content - 77 2. Design Chats for Creep Rate at Different Temperature and Water Content - 78 5.2 Grouting Temperature Test Results and Analysis (Permafrost Tunnel) - 79 5.3 Duckbill Test Results and Analysis (Permafrost Tunnel) - 85 5.4 Load Distribution along Anchor Shaft for Bar-Type Anchors (Permafrost Tunnel) - 88 5.5 Displacement vs. Time Curves (Permafrost Tunnel) - 98 5.6 Pullout Test Results and Analysis - 103 Chapter 6 Conclusion and Recommendation - 111 6.1 Conclusions - 111 6.2 Recommendations - 112 References - 113 Appendix A Displacement vs. Time Curves - 116 Appendix B Grouting Temperature - 123 Appendix C Load Distribution - 126 Appendix D Displacement vs. Time Curve Revision - 134 Appendix E Pullout Test Results - 14

Transcriptomic down-regulation of immune system components in barrier and hematopoietic tissues after lipopolysaccharide injection in antarctic notothenia coriiceps

The environmental conditions and isolation in the Antarctic have driven the evolution of a unique biodiversity at a macro to microorganism scale. Here, we investigated the possible adaptation of the teleost Notothenia coriiceps immune system to the cold environment and unique microbial community of the Southern Ocean. The fish immune system was stimulated through an intraperitoneal injection of lipopolysaccharide (LPS 0111:B4 from E. coli) and the tissue transcriptomic response and plasma biochemistry were analyzed 7 days later and compared to a sham injected control. Gene transcription in the head-kidney, intestine and skin was significantly modified by LPS, although tissues showed different responsiveness, with the duodenum most modified and the skin the least modified. The most modified processes in head-kidney, duodenum and skin were related to cell metabolism (up-regulated) and the immune system (comprising 30% of differentially expressed genes). The immune processes identified were mostly down-regulated, particularly interleukins and pattern recognition receptors (PRRs), nucleotide-binding oligomerization domain-like receptors and mannose receptors, unlike the toll-like receptors response commonly described in other teleost fish. The modified transcriptional response was not mirrored by a modified systemic response, as the circulating levels of enzymes of innate immunity, lysozyme and antiproteases, were not significantly different from the untreated and sham control fish. In conclusion, while the N. coriiceps immune system shares many features with other teleosts there are also some specificities. Further studies should better characterize the PRRs and their role in Antarctic teleosts, as well as the importance of the LPS source and its consequences for immune activation in teleosts.info:eu-repo/semantics/publishedVersio

Evolution of IFN subgroups in bony fish - 2. analysis of subgroup appearance and expansion in teleost fish with a focus on salmonids

Acknowledgements FL was supported by a Newton International Fellowship funded by the Academy of Medical Sciences, UK (AMS, NIF004\1036). Thanks go to Mingli Liu (Shanghai Ocean University) for help with the bioinformatics analysis of the Icefish/Toothfish, and to Drs Dan Macqueen and Manu Gundappa (Roslin Institute, University of Edinburgh) for helpful discussions and advice on the analysis.Peer reviewedPostprin

Toll-like receptor evolution: does temperature matter?

Toll-like receptors (TLRs) recognize conserved pathogen-associated molecular patterns (PAMPs) and are an ancient and well-conserved group of pattern recognition receptors (PRRs). The isolation of the Antarctic continent and its unique teleost fish and microbiota prompted the present investigation into Tlr evolution. Gene homologues of tlr members in teleosts from temperate regions were present in the genome of Antarctic Nototheniidae and the non-Antarctic sister lineage Bovichtidae. Overall, in Nototheniidae apart from D. mawsoni, no major tlr gene family expansion or contraction occurred. Instead, lineage and species-specific changes in the ectodomain and LRR of Tlrs occurred, particularly in the Tlr11 superfamily that is well represented in fish. Positive selective pressure and associated sequence modifications in the TLR ectodomain and within the leucine-rich repeats (LRR), important for pathogen recognition, occurred in Tlr5, Tlr8, Tlr13, Tlr21, Tlr22, and Tlr23 presumably associated with the unique Antarctic microbiota. Exposure to lipopolysaccharide (Escherichia coli O111:B4) Gram negative bacteria did not modify tlr gene expression in N. rossii head-kidney or anterior intestine, although increased water temperature (+4 degrees C) had a significant effect.PTDC/BIAANM/3484/2014; 41761134050; FCT-NSFC/0002/2016; FACC PROPOLAR (2016/2017);info:eu-repo/semantics/publishedVersio

Transcriptome analysis of Immune Response against Streptococcus agalactiae infection in the Nile Tilapia GIFT Strain

Streptococcus agalactiae (group B streptococcus, GBS), a broad-spectrum pathogen, causes great economic losses in fish aquaculture, especially the industry of tilapia. Until now, the knowledge of the immune response mechanism against S. agalactiae infection in tilapia has been limited. In the present study, the gill transcriptome of the tilapia from the GBS and the phosphate buffered saline (PBS) groups were sequenced. The transcriptomic analysis results presented the differentially expressed genes (DEGs) at different time points (DEGs number, 6 h: 2122, 9 h: 1851, 15 h: 1791, and 18 h: 2395) after GBS injection, and significantly enriched immune-related gene ontology (GO) terms such as the innate immune response. The significantly enriched immune pathways included the Toll-like receptor signaling pathway, the nucleotide oligomerization domain (NOD)-like receptor signaling pathway, the cytosolic-DNA sensing pathway, and the intestinal immune network for Immunoglobulin A (IgA) production. Most of the DEGs in Toll-like receptor signaling, NOD-like receptor signaling, and cytosolic-DNA sensing pathways presented upregulations at 18 h, which indicated that the innate immune pathways were activated. Two immune-related pathways (phagosome and cell adhesion molecules) were significantly enriched at all time points, suggesting that these two pathways might also play important roles in the immune response against the GBS infection. The results of HE staining showed that the gills of tilapia were damaged seriously at 9 h post-infection, which might be due to the possibility of pyroptosis resulting from the changes of DEGs in the NODlike receptor signaling pathway. This study provided new insight into the mechanisms of gill damage in fish infected with S. agalactiae.info:eu-repo/semantics/publishedVersio

A Comparison of Murine Smooth Muscle Cells Generated from Embryonic versus Induced Pluripotent Stem Cells

Smooth muscle cell (SMC) differentiation and dedifferentiation play a critical role in the pathogenesis of cardiovascular diseases. The lack of a good and simple in vitro SMC differentiation system has hampered the progress of SMC field for years. The generation of such an in vitro system would be invaluable for exploring molecular mechanisms of SMC differentiation and dedifferentiation. Recently, the establishment of induced pluripotent stem (iPS) cells has offered a novel therapeutic strategy to generate patient-specific stem cell lines. Here we have investigated whether iPS cells are able to differentiate into SMCs in vitro. Mouse iPS cell (O9 and TT025) monolayers were treated with 105 mol/L all-trans retinoid acid (RA). After 8 days of RA treatment, we found that >40% of the O9 iPS cells expressed the SMC-markers including SMα-actin and SM myosin heavy chain. Also, we documented that iPS-derived SMCs acquired SMC functional characteristics including contraction and calcium influx in response to stimuli. Moreover, our results indicated that there were differences in SMC-specific gene expression patterns between SMCs derived from O9 and TT025 iPS as well as normal embryonic stem cells. These differences might be due to disparity in the current iPS technology. Taken together, our data have established a simple iPS-SMC system to generate SMCs in vitro, which has tremendous potential to generate individualized SMCs for vascular tissue engineering and personalized drug screening.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/78153/1/scd.2008.0179.pd

Molecular analysis of phosphomannomutase (PMM) genes reveals a unique PMM duplication event in diverse Triticeae species and the main PMM isozymes in bread wheat tissues

BACKGROUND: Phosphomannomutase (PMM) is an essential enzyme in eukaryotes. However, little is known about PMM gene and function in crop plants. Here, we report molecular evolutionary and biochemical analysis of PMM genes in bread wheat and related Triticeae species. RESULTS: Two sets of homoeologous PMM genes (TaPMM-1 and 2) were found in bread wheat, and two corresponding PMM genes were identified in the diploid progenitors of bread wheat and many other diploid Triticeae species. The duplication event yielding PMM-1 and 2 occurred before the radiation of diploid Triticeae genomes. The PMM gene family in wheat and relatives may evolve largely under purifying selection. Among the six TaPMM genes, the transcript levels of PMM-1 members were comparatively high and their recombinant proteins were all enzymatically active. However, PMM-2 homoeologs exhibited lower transcript levels, two of which were also inactive. TaPMM-A1, B1 and D1 were probably the main active isozymes in bread wheat tissues. The three isozymes differed from their counterparts in barley and Brachypodium distachyon in being more tolerant to elevated test temperatures. CONCLUSION: Our work identified the genes encoding PMM isozymes in bread wheat and relatives, uncovered a unique PMM duplication event in diverse Triticeae species, and revealed the main active PMM isozymes in bread wheat tissues. The knowledge obtained here improves the understanding of PMM evolution in eukaryotic organisms, and may facilitate further investigations of PMM function in the temperature adaptability of bread wheat

An animal model of SARS produced by infection of Macaca mulatta with SARS coronavirus.

A new SARS animal model was established by inoculating SARS coronavirus (SARS-CoV) into rhesus macaques (Macaca mulatta) through the nasal cavity. Pathological pulmonary changes were successively detected on days 5-60 after virus inoculation. All eight animals showed a transient fever 2-3 days after inoculation. Immunological, molecular biological, and pathological studies support the establishment of this SARS animal model. Firstly, SARS-CoV-specific IgGs were detected in the sera of macaques from 11 to 60 days after inoculation. Secondly, SARS-CoV RNA could be detected in pharyngeal swab samples using nested RT-PCR in all infected animals from 5 days after virus inoculation. Finally, histopathological changes of interstitial pneumonia were found in the lungs during the 60 days after viral inoculation: these changes were less marked at later time points, indicating that an active healing process together with resolution of an acute inflammatory response was taking place in these animals. This animal model should provide insight into the mechanisms of SARS-CoV-related pulmonary disease and greatly facilitate the development of vaccines and therapeutics against SARS