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Open Access Publications from the University of California

Scholarly Works (34 results)

  • Thesis
  • Peer Reviewed
UC Davis Electronic Theses and Dissertations (2023)

Viscous flow is a crucial part of Computational Fluid Dynamics simulations, where the viscous drag is significant and separation might occur, in particular, in regions of adverse pressure gradient. Predicting the separation bubbles with computer simulation can lead to deeper understanding of the flow structure and assist relevant designs. To narrow the scope, this thesis targets the 2D Steady viscous laminar flow. Benchmark problems in both separated and attached flow are simulated for validation purposes. Stream function and vorticity formulation of both Navier-Stokes equations and Boundary-Layer equations are used to enforce conservation of mass and momentum equations. A formulation of parabolized Navier-Stokes equations is also investigated as the intermediate step. For separated flows, FLARE approximation may provide a less accurate but inexpensive solution (where the convective term is cancelled for negative velocity, hence, a marching procedure can be used).

    Cover page: Numerical Simulations of 2D Steady Laminar Compressible and Incompressible Flows with Separation
    • Article
    Technical Completion Reports (1996)

    The effort that led to this report is twofold. First, it deals with the development of fundamental transport equations and their solutions; they describe the effect of low-permeability zones on the motion and spread of contaminant plumes in high-permeability porous layers. Second, it concerns the development of an analytical multi phase-transport model that describes leaching of pesticides in soils and their fate and transport in groundwater. Using Monte Carlo simulations, the effect of stochastic precipitation, random adsorption, and random (bio )chemical reaction, on the probability distributions of the herbicide Simazine, is investigated under conditions typical to the City of Fresno in California.

    The transport equations that are developed in Chapter 2 describe the capacitance of low permeability layers to store and release reactive constituents by diffusion and mechanical mixing. It is shown that under quasi-steady conditions and a mean flow parallel to the bedding, lateral solute transfer between thin layers is governed by the phenomenological first-order rate model, with a uniquely defined mass transfer rate coefficient, modified to account for reactive constituents. Two-dimensional analytical solutions are obtained in Chapter 3 for the first-order rate model in an infinite porous medium, using the methods of Fourier and Laplace transforms. and superposition. The solutions consider a rectangular area at the source with (l) an instantaneous release of a contaminant mass, and (2) an exponentially-decaying source concentration, applied at a fixed rate. Comparison of the theory with tracer chloride levels at the Borden aquifer indicates that the first-order rate model can describe adequately the dispersion process, on the basis of lateral or transverse diffusive mass transfer between layers.

    In the second effort (Chapter 4), a multiphase transport model is developed with the objective of investigating the impact of soil environment, physical and (bio )chemical processes, especially, volatilization, crop uptake, and agricultural practices on long-term vulnerability of groundwater to contamination by pesticides. The soil is separated into root and intermediate vadose zones, each with uniform properties. Transport in each soil zone is modeled on the basis of complete mixing, by spatial averaging the related point multi phase-transport partial differential equation (i.e., linear-reservoir models). Transport in the aquifer, however, is modeled by a two-dimensional advection-dispersion transport equation, considering adsorption and firstorder decay rate. Vaporization in the soil is accounted for by assuming liquid-vapor phase partitioning using Henry's law, and vapor flux (volatilization) from the soil surface is modeled by diffusion through an air boundary layer. Sorption of liquid-phase solutes by crops is described by a linear relationship that is valid for first-order (passive) crop uptake. The model is applied to five pesticides (Atrazine, Brornacil, Chlordane, Heptachlor, and Lindane), and the potential for pesticides contamination of groundwater is investigated for sandy and clayey soils. Simulation results show that groundwater contamination can be substantially reduced for clayey soil environments, where bio(chemical) degradation and volatilization are most efficient as natural loss pathways for the pesticides. Also, uptake by crops can be a significant mechanism for attenuating exposure levels in groundwater, especially in a sandy soil environment and for relatively persisting pesticides. Further, simulations indicate that changing agricultural practices can have a profound effect on vulnerability of groundwater to mobile and relatively persisting pesticides.

    The deterministic model is integrated with the Monte Carlo method in Chapter 5, to obtain the probability density function, mean, and standard deviation of the concentrations in groundwater, due to random adsorption and stochastic precipitation. The distribution coefficient, which is used to calculate the retardation factor for equilibrium adsorption, is assumed to be normally distributed, and the precipitation is modeled by fitting an ARIMA model to an observed time series. Consequently, the results of the analysis are also probability distribution functions for the concentration of the contaminant. which are useful representations for regulation and management purposes. The stochastic model is applied to data typical to the Fresno area in California, to assess the impact of herbicide Simazine on groundwater quality. The results show that predicted concentrations exhibit non-Gaussian probability distributions and standard deviations of the order of magnitude of the estimated means. Further, predictions made on the basis of averaged values of input parameters may substantially overestimate in transient, and later underestimate, the actual mean (ensemble) of the contaminant levels in groundwater. The results also highlight the importance of accounting for the mechanism of preferential flow.

      Cover page: Modeling and Stochastic Analysis of Contaminant Transport in Soils and Aquifers
      • Article
      • Peer Reviewed
      UC Davis Previously Published Works (2021)
      Despite many preventive measures, including prophylactic antibiotics, periprosthetic joint infection (PJI) remains a devastating complication following arthroplasty, leading to pain, suffering, morbidity and substantial economic burden. Humans have a powerful innate immune system that can effectively control infections, if alerted quickly. Unfortunately, pathogens use many mechanisms to dampen innate immune responses. The study hypothesis was that immunomodulators that can jumpstart and direct innate immune responses (particularly neutrophils) at the surgical site of implant placement would boost immune responses and reduce PJI, even in the absence of antibiotics. To test this hypothesis, N-formyl-methionyl-leucyl-phenylalanine (fMLP) (a potent chemoattractant for phagocytic leukocytes including neutrophils) was used in a mouse model of PJI with Staphylococcus aureus (S. aureus). Mice receiving intramedullary femoral implants were divided into three groups: i) implant alone; ii) implant + S. aureus; iii) implant + fMLP + S. aureus. fMLP treatment reduced S. aureus infection levels by ~ 2-Log orders at day 3. Moreover, fMLP therapy reduced infection-induced peri-implant periosteal reaction, focal cortical loss and areas of inflammatory infiltrate in mice distal femora at day 10. Finally, fMLP treatment reduced pain behaviour and increased weight-bearing at the implant leg in infected mice at day 10. Data indicated that fMLP therapy is a promising novel approach for reducing PJI, if administered locally at surgical sites. Future work will be toward further enhancement and optimisation of an fMLP-based therapeutic approach through combination with antibiotics and/or implant coating with fMLP.
        Cover page: Therapeutic assessment of N-formyl-methionyl-leucyl-phenylalanine (fMLP) in reducing periprosthetic joint infection.
        • Article
        • Peer Reviewed
        UC San Diego Previously Published Works (2020)

        Background and purpose

        Benign prostatic hyperplasia (BPH) is the most common urologic disorder affecting older men, necessitating medical or surgical intervention. Limited data exists regarding the effect these surgeries have on the endourologist's musculoskeletal system following the surgery because of the required difficult posture, prolonged procedures, repetitive movements, and the settings of an adjustable visual display terminal workstation. The aim of our study was to survey the prevalence and possible causes of musculoskeletal disorders among endourologists performing transurethral resection of the prostate (TURP) or laser prostatectomy using either holmium laser enucleation or thulium laser enucleation.

        Materials and methods

        An email inviting all members of the Endourological Society to participate in the survey was sent. The questionnaire included different demographic and practice characteristics, with concern regarding performing either TURP or laser prostatectomy and the incidence and type of musculoskeletal incidents following these surgeries. All responses were collected by a commercially available internet based survey host (www.surveymonkey.com) over a period of 6 weeks.

        Results

        Of the 121 complete responses, 84 (69%) of endourologists complained of a musculoskeletal disorder following TURP or laser prostatectomy. The most frequent complaint was for neck (64%), followed by back (57%), shoulder (48%), hand (40%), and elbow (18%). The average prostate volume turned out to be the most compelling predictor for musculoskeletal disorder occurrence with an average prostate volume of 76 g operated on by the complaining group compared with 59 g in the noncomplaining group. Those with more severe symptoms were linked to a mean prostate size of 80 g (60-146) and constantly complained of shoulder, neck, or back trouble compared with the less-severely complaining group.

        Conclusions

        A high prevalence of musculoskeletal complaints among urologists performing endourologic prostatectomy was confirmed and was found to be proportionally related to the size of the prostate. The integration of an ergonomic specialist inside the operation room to watch and correct the surgeon's position during endourologic procedures may reduce the endourologist's exposure to these occupational hazards.
          Cover page: Ergonomics and musculoskeletal symptoms in surgeons performing endoscopic procedures for benign prostatic hyperplasia
          • Article
          • Peer Reviewed
          UC Berkeley Previously Published Works (2020)
          Lissencephaly-1 (Lis1) is a key cofactor for dynein-mediated intracellular transport towards the minus-ends of microtubules. It remains unclear whether Lis1 serves as an inhibitor or an activator of mammalian dynein motility. Here we use single-molecule imaging and optical trapping to show that Lis1 does not directly alter the stepping and force production of individual dynein motors assembled with dynactin and a cargo adaptor. Instead, Lis1 promotes the formation of an active complex with dynactin. Lis1 also favours the recruitment of two dyneins to dynactin, resulting in increased velocity, higher force production and more effective competition against kinesin in a tug-of-war. Lis1 dissociates from motile complexes, indicating that its primary role is to orchestrate the assembly of the transport machinery. We propose that Lis1 binding releases dynein from its autoinhibited state, which provides a mechanistic explanation for why Lis1 is required for efficient transport of many dynein-associated cargos in cells.
            Cover page: Lis1 activates dynein motility by modulating its pairing with dynactin
            • Article
            • Peer Reviewed
            UCLA Previously Published Works (2010)
            Abstract Background Genetically-modified (GM) mosquitoes have been proposed as part of an integrated vector control strategy for malaria control. Public acceptance is essential prior to field trials, particularly since mosquitoes are a vector of human disease and genetically modified organisms (GMOs) face strong scepticism in developed and developing nations. Despite this, in sub-Saharan Africa, where the GM mosquito effort is primarily directed, very little data is available on perspectives to GMOs. Here, results are presented of a qualitative survey of public attitudes to GM mosquitoes for malaria control in rural and urban areas of Mali, West Africa between the months of October 2008 and June 2009. Methods The sample consisted of 80 individuals - 30 living in rural communities, 30 living in urban suburbs of Bamako, and 20 Western-trained and traditional health professionals working in Bamako and Bandiagara. Questions were asked about the cause of malaria, heredity and selective breeding. This led to questions about genetic alterations, and acceptable conditions for a release of pest-resistant GM corn and malaria-refractory GM mosquitoes. Finally, participants were asked about the decision-making process in their community. Interviews were transcribed and responses were categorized according to general themes. Results Most participants cited mosquitoes as one of several causes of malaria. The concept of the gene was not widely understood; however selective breeding was understood, allowing limited communication of the concept of genetic modification. Participants were open to a release of pest-resistant GM corn, often wanting to conduct a trial themselves. The concept of a trial was reapplied to GM mosquitoes, although less frequently. Participants wanted to see evidence that GM mosquitoes can reduce malaria prevalence without negative consequences for human health and the environment. For several participants, a mosquito control programme was preferred; however a transgenic release that satisfied certain requirements was usually acceptable. Conclusions Although there were some dissenters, the majority of participants were pragmatic towards a release of GM mosquitoes. An array of social and cultural issues associated with malaria, mosquitoes and genetic engineering became apparent. If these can be successfully addressed, then social acceptance among the populations surveyed seems promising.
            • 3 supplemental files
            Cover page: Perspectives of people in Mali toward genetically-modified mosquitoes for malaria control
            • Peer Reviewed
            UC San Francisco Previously Published Works (2020)
              Cover page: Chapter 2 Echocardiography, Transcranial Doppler, and Oximetry for Imaging and Quantification of PFO-Mediated ShuntsCreative Commons 'BY' version 4.0 license
              • Article
              • Peer Reviewed
              LBL Publications (2022)
              Copper-based delafossite oxides are excellent candidates for the p-type transparent conducting oxide (TCO), which is essential in realizing transparent semiconductor applications. Using angle-resolved photoemission spectroscopy (ARPES), we report the low-energy electronic structure of CuAlO2. We found that the band structure near the valence band top is characterized by hole bands with their maxima along the Brillouin zone boundary. Furthermore, the effective masses along the Γ–M and Γ–K directions were found to be (0.6 ± 0.1) m0 and (0.9 ± 0.1) m0, respectively, which impose an important benchmark against the existing band calculations.
                Cover page: Electronic structure of p-type transparent conducting oxide CuAlO2
                • Article
                • Peer Reviewed
                UC Berkeley Previously Published Works (2019)
                Cytoplasmic dynein is an ATP-driven motor that transports intracellular cargos along microtubules. Dynein adopts an inactive conformation when not attached to a cargo, and motility is activated when dynein assembles with dynactin and a cargo adaptor. It was unclear how active dynein-dynactin complexes step along microtubules and transport cargos under tension. Using single-molecule imaging, we showed that dynein-dynactin advances by taking 8 to 32-nm steps toward the microtubule minus end with frequent sideways and backward steps. Multiple dyneins collectively bear a large amount of tension because the backward stepping rate of dynein is insensitive to load. Recruitment of two dyneins to dynactin increases the force generation and the likelihood of winning against kinesin in a tug-of-war but does not directly affect velocity. Instead, velocity is determined by cargo adaptors and tail-tail interactions between two closely packed dyneins. Our results show that cargo adaptors modulate dynein motility and force generation for a wide range of cellular functions.
                  Cover page: Cargo adaptors regulate stepping and force generation of mammalian dynein–dynactin
                  • Article
                  • Peer Reviewed
                  UC Berkeley Previously Published Works (2019)
                  Cytoplasmic dynein is an ATP-driven motor that transports intracellular cargos along microtubules. Dynein adopts an inactive conformation when not attached to a cargo, and motility is activated when dynein assembles with dynactin and a cargo adaptor. It was unclear how active dynein-dynactin complexes step along microtubules and transport cargos under tension. Using single-molecule imaging, we showed that dynein-dynactin advances by taking 8 to 32-nm steps toward the microtubule minus end with frequent sideways and backward steps. Multiple dyneins collectively bear a large amount of tension because the backward stepping rate of dynein is insensitive to load. Recruitment of two dyneins to dynactin increases the force generation and the likelihood of winning against kinesin in a tug-of-war but does not directly affect velocity. Instead, velocity is determined by cargo adaptors and tail-tail interactions between two closely packed dyneins. Our results show that cargo adaptors modulate dynein motility and force generation for a wide range of cellular functions.
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