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Open Access Publications from the University of California

Scholarly Works (10 results)

  • Article
  • Peer Reviewed
UC Davis Previously Published Works (2016)
The study of protein mass transport via atomistic simulation requires time and length scales beyond the computational capabilities of modern computer systems. The raspberry model for colloidal particles in combination with the mesoscopic hydrodynamic method of lattice Boltzmann facilitates coarse-grained simulations that are on the order of microseconds and hundreds of nanometers for the study of diffusive transport of protein-like colloid particles. The raspberry model reproduces linearity in resistance to motion versus particle size and correct enhanced drag within cylindrical pores at off-center coordinates for spherical particles. Owing to the high aspect ratio of many proteins, ellipsoidal raspberry colloid particles were constructed and reproduced the geometric resistance factors of Perrin and of Happel and Brenner in the laboratory-frame and in the moving body-frame. Accurate body-frame rotations during diffusive motion have been captured for the first time using projections of displacements. The spatial discretization of the fluid leads to a renormalization of the hydrodynamic radius, however, the data describes a self-consistent hydrodynamic frame within this renormalized system.
    • Article
    • Peer Reviewed
    UC Davis Previously Published Works (2016)
    The supplementary material, in the form of one pdf file, is available from the journal web page at http://dx.doi.org/10.1140/epjst/e2016-02676-9 The Publishers regret this mistake and apologize for any inconvenience caused.
      • Thesis
      • Peer Reviewed
      UC Berkeley Electronic Theses and Dissertations (2012)

      This document summarizes the development of an integral perturbation solution of the equations governing momentum transport in microchannels between disks of multiple-disk drag turbines such as the Tesla turbine. This analysis allows a parametric study of turbine performance based on several nondimensional parameters. The results of this analysis are then compared to two sets of test data published in previous work and by other projects. The results are further compared to Computational Fluid Dynamics (CFD) simulations. Finally, expected performance and potential applications of these devices are discussed in light of the results developed.

      Analysis of this type of flow problem is a key element in the optimal design of Tesla drag-type turbines for geothermal, waste heat, energy harvesting, or solar alternative energy applications. In multiple-disk turbines, high speed flow enters tangentially at the outer radius of cylindrical microchannels formed by closely spaced parallel disks, spiraling through the channel to an exhaust at a small radius or at the center of the disk. Previous investigations have generally developed models based on simplifying idealizations of the flow in these circumstances. Here, beginning with the momentum and continuity equations for incompressible and steady flow in cylindrical coordinates, an integral solution scheme is developed that leads to a dimensionless perturbation series solution that retains the full complement of momentum and viscous effects to consistent levels of approximation in the series solution. This more rigorous approach indicates all dimensionless parameters that affect flow and transport, and allows a direct assessment of the relative importance of viscous, pressure, and momentum effects in different directions in the flow. The resulting lowest-order equations are solved explicitly and higher order terms in the series solutions are determined numerically.

      Enhancement of rotor drag in this type of turbine enhances energy conversion efficiency. A modified version of the integral perturbation analysis is presented that incorporates the effects of enhanced drag due to surface microstructuring. Results of the model analysis for smooth disk walls are shown to agree well with experimental performance data for two prototype Tesla turbines, and predictions of performance models developed in earlier investigations. Specifically, experimental efficiencies corelate well with those predicted by the integral perturbation solution, deviating by an average of 29% and a maximum of 52%. Model predictions indicate that enhancement of disk drag by strategic microstructuring of the disk surfaces can significantly increase turbine efficiency. Exploratory calculations with the model indicate that turbine efficiencies exceeding 75% can be achieved by designing for optimal ranges of the governing dimensionless parameters.

      The same parametric trends in performance are compared to test data for a micro-scale Tesla turbine with water as a working fluid. Experimental efficiencies again correlate well with those predicted by the integral perturbation solution. Exerimental efficiencies show a mean deviation of 52% with efficiencies predicted by the model, and a max deviation of 65%. A Computational Fluid Dynamics (CFD) model is then compared to both the analytical and experimental turbine efficiencies. The CFD solutions of the flow field are then used to help reconcile areas where the analytical predictions do not match experimental data. CFD predicted efficiencies match the efficiencies predicted by the integral perturbation solution very closely, deviating by an average of only 18%.

      Based on the results of the CFD simulations and experimental data, conclusions are made about the validity of the integral perturbation solution. The model accurately predicts the flow inside the rotor, but a better treatment of the flow in the inlet to the turbine is necessary. Despite this, the integral perturbation solution is shown to be capable of directing high efficiency turbine design, and design strategies and parameter ranges that result in high efficiency devices are outlined.

        Cover page: Theory and Performance of Tesla Turbines
        • Article
        • Peer Reviewed
        UC Davis Previously Published Works (2017)
        The polymer poly(N-isopropylacrylamide) (PNIPAM) is studied using a novel combination of multiscale modeling methodologies. We develop an iterative Boltzmann inversion potential of concentrated PNIPAM solutions and combine it with lattice Boltzmann as a Navier-Stokes equation solver for the solvent. We study in detail the influence of the methodology on statics and dynamics of the system. The combination is successful and significantly simpler and faster than other mapping techniques for polymer solution while keeping the correct hydrodynamics. The model can semiquantitatively describe the correct phase behavior and polymer dynamics.
          Cover page: Development and Application of a Coarse-Grained Model for PNIPAM by Iterative Boltzmann Inversion and Its Combination with Lattice Boltzmann Hydrodynamics
          • Article
          • Peer Reviewed
          UC Davis Previously Published Works (2022)

          Background

          Young children exposed to high-dose vitamin A supplements (VAS) and vitamin A (VA)-fortified foods may be at risk of high VA intake and high VA total body stores (TBS).

          Objectives

          TBS and estimated liver VA concentration were compared among children with adequate or high VA intake and different timing of exposure to VAS, and associations between estimated liver VA concentrations and biomarkers of VA toxicity were examined.

          Methods

          Children 12-18 mo of age (n = 123) were selected for 3 groups: 1) retinol intake >600 µg/d and VAS within the past mo, 2) retinol intake >600 µg/d and VAS in the past 3-6 mo, and 3) VA intake 200-500 µg retinol activity equivalents (RAE)/d and VAS in the past 3-6 mo. Dietary intake data were collected to measure VA intakes from complementary foods, breast milk, and low-dose, over-the-counter supplements. TBS were assessed by retinol isotope dilution, and VA toxicity biomarkers were measured. Main outcomes were compared by group.

          Results

          Mean (95% CI) VA intakes excluding VAS were 1184 (942, 1426), 980 (772, 1187), and 627 (530, 724) µg RAE/d, in groups 1-3, respectively; mean VA intake was higher in groups 1 and 2 compared with group 3 (P < 0.05). Geometric mean (GM) (95% CI) TBS were 589 (525, 661), 493 (435, 559), and 466 (411, 528) µmol, respectively. GM TBS and GM liver VA concentrations were higher in group 1 compared with group 3 (liver VA concentration: 1.62 vs. 1.33 µmol/g; P < 0.05). Plasma retinyl ester and 4-oxo-retinoic acid concentrations and serum markers of bone turnover and liver damage did not indicate VA toxicity.

          Conclusions

          In this sample, most children had retinol intakes above the Tolerable Upper Intake Level (UL) and liver VA concentrations above the proposed cutoff for "hypervitaminosis A" (>1 µmol/g liver). There was no evidence of chronic VA toxicity, suggesting that the liver VA cutoff value should be re-evaluated. This trial was registered at www.clinicaltrials.gov as NCT03030339.
            Cover page: Filipino Children with High Usual Vitamin A Intakes and Exposure to Multiple Sources of Vitamin A Have Elevated Total Body Stores of Vitamin A But Do Not Show Clear Evidence of Vitamin A Toxicity
            • Article
            Lawrence Berkeley National Laboratory (2003)

            The proposed SuperNova/Acceleration Probe (SNAP) mission will have a two-meter class telescope delivering diffraction-limited images to an instrumented 0.7 square degree field in the visible and near-infrared wavelength regime. The requirements for the instrument suite and the present configuration of the focal plane concept are presented. A two year R&D phase, largely supported by the Department of Energy, is just beginning. We describe the development activities that are taking place to advance our preparedness for mission proposal in the areas of detectors and electronics.

              Cover page: SNAP Satellite Focal Plane Development
              • Article
              LBL Publications (2003)
              A wide field space-based imaging telescope is necessary to fully exploit the technique of observing dark matter via weak gravitational lensing. This first paper in a three part series outlines the survey strategies and relevant instrumental parameters for such a mission. As a concrete example of hardware design, we consider the proposed Supernova/Acceleration Probe (SNAP). Using SNAP engineering models, we quantify the major contributions to this telescope's Point Spread Function (PSF). These PSF contributions are relevant to any similar wide field space telescope. We further show that the PSF of SNAP or a similar telescope will be smaller than current ground-based PSFs, and more isotropic and stable over time than the PSF of the Hubble Space Telescope. We outline survey strategies for two different regimes - a "wide" 300 square degree survey and a "deep" 15 square degree survey that will accomplish various weak lensing goals including statistical studies and dark matter mapping.
                Cover page: Weak Lensing from Space I: Instrumentation and Survey Strategy
                • Article
                Lawrence Berkeley National Laboratory (2002)
                  Cover page: Overview of the SuperNova/Acceleration probe (SNAP)
                  • Article
                  • Peer Reviewed
                  UC Berkeley Previously Published Works (2004)
                  The Supernova / Acceleration Probe (SNAP) is a proposed space-based experiment designed to study the dark energy and alternative explanations of the acceleration of the Universe's expansion by performing a series of complementary systematics-controlled measurements. We describe a self-consistent reference mission design for building a Type Ia supernova Hubble diagram and for performing a wide-area weak gravitational lensing study. A 2-m wide-field telescope feeds a focal plane consisting of a 0.7 square-degree imager tiled with equal areas of optical CCDs and near infrared sensors, and a high-efficiency low-resolution integral field spectrograph. The SNAP mission will obtain high-signal-to-noise calibrated light-curves and spectra for several thousand supernovae at redshifts between z=0.1 and 1.7. A wide-field survey covering one thousand square degrees resolves ~100 galaxies per square arcminute. If we assume we live in a cosmological-constant-dominated Universe, the matter density, dark energy density, and flatness of space can all be measured with SNAP supernova and weak-lensing measurements to a systematics-limited accuracy of 1%. For a flat universe, the density-to-pressure ratio of dark energy can be similarly measured to 5% for the present value w0 and ~0.1 for the time variation w'. The large survey area, depth, spatial resolution, time-sampling, and nine-band optical to NIR photometry will support additional independent and/or complementary dark-energy measurement approaches as well as a broad range of auxiliary science programs. (Abridged)
                    Cover page: Supernova / Acceleration Probe: A Satellite Experiment to Study the Nature of the Dark Energy
                    • Article
                    • Peer Reviewed
                    UC Davis Previously Published Works (2019)
                    Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.
                      Cover page: Large expert-curated database for benchmarking document similarity detection in biomedical literature search
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