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Open Access Publications from the University of California

Scholarly Works (10 results)

  • Thesis
  • Peer Reviewed
UC Berkeley Electronic Theses and Dissertations (2015)

This dissertation broadly describes efforts related to materials discovery, design and optimization

using a first-principles approach based on density functional theory (DFT).

The two main application areas comprise transition-metal alloys and functional materials.

The research involving transition-metal alloys aims at finding cost-effective replacement

strategies for rhenium (Re). Elemental Re exhibits profuse deformation twinning under

mechanical loads and has a high ductility. It is shown that the twinning characteristics of

Re and its ductility are correlated with its anomalously low (11-21) twin-boundary energy.

The origin of this twin-energy anomaly is related to the presence of icosahedral structural

units on the (11-21) twin boundary. These structural units are stabilized near d-band fillings

corresponding to Re. The (11-21) twin-boundary energy can be lowered further by

decreasing the d-band filling with respect to elemental Re. This increases the intrinsic

ductility according to three independent ductility parameters employed in this work: i)

Pugh's ratio of bulk to shear modulus, ii) Yoo's ratio of surface to twin energy and iii) an

ideal-strength criterion. Based on new insights in the relation between d-band filling, defect

energies and intrinsic ductility, several candidate alloys for Re replacement are proposed.

Ru-based alloys with additions of Ta, W and Re are shown to be potential replacement

candidates. The last part of this dissertation describes high-throughput calculations that

have culminated in the two largest databases of elastic and piezoelectric tensor properties

available to-date. The workflow for doing such calculations is described, along with various

checks to ensure the accuracy of the calculated physical properties. The database with

elastic-tensor properties is expected to be of use in a number of fields where discovery of

new materials with desired values of elastic stiffness or (lattice) thermal conductivity are of

interest. Further, data mining and machine learning can be applied to better understand

elastic properties and their physical descriptors. Several novel piezoelectric materials are

discovered as part of this work. Some of these exhibit a high intrinsic piezoelectric response

and may serve as a starting point for a process in which the piezoelectric response is optimized

by alloying and microstructure engineering. As such, this database can support a search for future

replacement candidates of the widely used piezoelectric materials such as Pb(ZrxTi1􀀀-x)O3 (PZT) that contain lead.

    Cover page: First-Principles Approach to Materials Discovery, Design and Optimization: Applications to Transition-Metal Alloys and Functional Materials
    • Article
    • Peer Reviewed
    UC Berkeley Previously Published Works (2017)
    Auxetics comprise a rare family of materials that manifest negative Poisson's ratio, which causes an expansion instead of contraction under tension. Most known homogeneously auxetic materials are porous foams or artificial macrostructures and there are few examples of inorganic materials that exhibit this behavior as polycrystalline solids. It is now possible to accelerate the discovery of materials with target properties, such as auxetics, using high-throughput computations, open databases, and efficient search algorithms. Candidates exhibiting features correlating with auxetic behavior were chosen from the set of more than 67 000 materials in the Materials Project database. Poisson's ratios were derived from the calculated elastic tensor of each material in this reduced set of compounds. We report that this strategy results in the prediction of three previously unidentified homogeneously auxetic materials as well as a number of compounds with a near-zero homogeneous Poisson's ratio, which are here denoted "anepirretic materials".There are very few inorganic materials with auxetic homogenous Poisson's ratio in polycrystalline form. Here authors develop an approach to screening materials databases for target properties such as negative Poisson's ratio by using stability and structural motifs to predict new instances of homogenous auxetic behavior as well as a number of materials with near-zero Poisson's ratio.
      • Article
      • Peer Reviewed
      UC Berkeley Previously Published Works (2015)
      Piezoelectric materials are used in numerous applications requiring a coupling between electrical fields and mechanical strain. Despite the technological importance of this class of materials, for only a small fraction of all inorganic compounds which display compatible crystallographic symmetry, has piezoelectricity been characterized experimentally or computationally. In this work we employ first-principles calculations based on density functional perturbation theory to compute the piezoelectric tensors for nearly a thousand compounds, thereby increasing the available data for this property by more than an order of magnitude. The results are compared to select experimental data to establish the accuracy of the calculated properties. The details of the calculations are also presented, along with a description of the format of the database developed to make these computational results publicly available. In addition, the ways in which the database can be accessed and applied in materials development efforts are described.
        Cover page: A database to enable discovery and design of piezoelectric materials
        • Article
        • Peer Reviewed
        UC Berkeley Previously Published Works (2016)
        Materials scientists increasingly employ machine or statistical learning (SL) techniques to accelerate materials discovery and design. Such pursuits benefit from pooling training data across, and thus being able to generalize predictions over, k-nary compounds of diverse chemistries and structures. This work presents a SL framework that addresses challenges in materials science applications, where datasets are diverse but of modest size, and extreme values are often of interest. Our advances include the application of power or Hölder means to construct descriptors that generalize over chemistry and crystal structure, and the incorporation of multivariate local regression within a gradient boosting framework. The approach is demonstrated by developing SL models to predict bulk and shear moduli (K and G, respectively) for polycrystalline inorganic compounds, using 1,940 compounds from a growing database of calculated elastic moduli for metals, semiconductors and insulators. The usefulness of the models is illustrated by screening for superhard materials.
          Cover page: A Statistical Learning Framework for Materials Science: Application to Elastic Moduli of k-nary Inorganic Polycrystalline Compounds
          • Article
          • Peer Reviewed
          UC Davis Previously Published Works (2012)
          A large number of hypothetical genes potentially encoding small proteins of unknown function are annotated in the Brucella abortus genome. Individual deletion of 30 of these genes identified four mutants, in BAB1_0355, BAB2_0726, BAB2_0470, and BAB2_0450 that were highly attenuated for infection. BAB2_0726, an YbgT-family protein located at the 3' end of the cydAB genes encoding cytochrome bd ubiquinal oxidase, was designated cydX. A B. abortus cydX mutant lacked cytochrome bd oxidase activity, as shown by increased sensitivity to H(2)O(2), decreased acid tolerance and increased resistance to killing by respiratory inhibitors. The C terminus, but not the N terminus, of CydX was located in the periplasm, suggesting that CydX is an integral cytoplasmic membrane protein. Phenotypic analysis of the cydX mutant, therefore, suggested that CydX is required for full function of cytochrome bd oxidase, possibly via regulation of its assembly or activity.
            Cover page: The small protein CydX is required for function of cytochrome bd oxidase in Brucella abortus
            • Article
            • Peer Reviewed
            UC Berkeley Previously Published Works (2015)
            The elastic constant tensor of an inorganic compound provides a complete description of the response of the material to external stresses in the elastic limit. It thus provides fundamental insight into the nature of the bonding in the material, and it is known to correlate with many mechanical properties. Despite the importance of the elastic constant tensor, it has been measured for a very small fraction of all known inorganic compounds, a situation that limits the ability of materials scientists to develop new materials with targeted mechanical responses. To address this deficiency, we present here the largest database of calculated elastic properties for inorganic compounds to date. The database currently contains full elastic information for 1,181 inorganic compounds, and this number is growing steadily. The methods used to develop the database are described, as are results of tests that establish the accuracy of the data. In addition, we document the database format and describe the different ways it can be accessed and analyzed in efforts related to materials discovery and design.
              Cover page: Charting the complete elastic properties of inorganic crystalline compounds
              • Article
              • Peer Reviewed
              UC Davis Previously Published Works (2019)
              Subversion of endoplasmic reticulum (ER) function is a feature shared by multiple intracellular bacteria and viruses, and in many cases this disruption of cellular function activates pathways of the unfolded protein response (UPR). In the case of infection with Brucella abortus, the etiologic agent of brucellosis, the unfolded protein response in the infected placenta contributes to placentitis and abortion, leading to pathogen transmission. Here we show that B. abortus infection of pregnant mice led to death of infected placental trophoblasts in a manner that depended on the VirB type IV secretion system (T4SS) and its effector VceC. The trophoblast death program required the ER stress-induced transcription factor CHOP. While NOD1/NOD2 expression in macrophages contributed to ER stress-induced inflammation, these receptors did not play a role in trophoblast death. Both placentitis and abortion were independent of apoptosis-associated Speck-like protein containing a caspase activation and recruitment domain (ASC). These studies show that B. abortus uses its T4SS to induce cell-type-specific responses to ER stress in trophoblasts that trigger placental inflammation and abortion. Our results suggest further that in B. abortus the T4SS and its effectors are under selection as bacterial transmission factors.IMPORTANCEBrucella abortus infects the placenta of pregnant cows, where it replicates to high levels and triggers abortion of the calf. The aborted material is highly infectious and transmits infection to both cows and humans, but very little is known about how B. abortus causes abortion. By studying this infection in pregnant mice, we discovered that B. abortus kills trophoblasts, which are important cells for maintaining pregnancy. This killing required an injected bacterial protein (VceC) that triggered an endoplasmic reticulum (ER) stress response in the trophoblast. By inhibiting ER stress or infecting mice that lack CHOP, a protein induced by ER stress, we could prevent death of trophoblasts, reduce inflammation, and increase the viability of the pups. Our results suggest that B. abortus injects VceC into placental trophoblasts to promote its transmission by abortion.
                Cover page: Brucella abortus Infection of Placental Trophoblasts Triggers Endoplasmic Reticulum Stress-Mediated Cell Death and Fetal Loss via Type IV Secretion System-Dependent Activation of CHOP
                • Article
                • Peer Reviewed
                UC Davis Previously Published Works (2013)
                Host cytokine responses to Brucella abortus infection are elicited predominantly by the deployment of a type IV secretion system (T4SS). However, the mechanism by which the T4SS elicits inflammation remains unknown. Here we show that translocation of the T4SS substrate VceC into host cells induces proinflammatory responses. Ectopically expressed VceC interacted with the endoplasmic reticulum (ER) chaperone BiP/Grp78 and localized to the ER of HeLa cells. ER localization of VceC required a transmembrane domain in its N terminus. Notably, the expression of VceC resulted in reorganization of ER structures. In macrophages, VceC was required for B. abortus-induced inflammation by induction of the unfolded protein response by a process requiring inositol-requiring transmembrane kinase/endonuclease 1. Altogether, these findings suggest that translocation of the T4SS effector VceC induces ER stress, which results in the induction of proinflammatory host cell responses during B. abortus infection. IMPORTANCE Brucella species are pathogens that require a type IV secretion system (T4SS) to survive in host cells and to maintain chronic infection. By as-yet-unknown pathways, the T4SS also elicits inflammatory responses in infected cells. Here we show that inflammation caused by the T4SS results in part from the sensing of a T4SS substrate, VceC, that localizes to the endoplasmic reticulum (ER), an intracellular site of Brucella replication. Possibly via binding of the ER chaperone BiP, VceC causes ER stress with concomitant expression of proinflammatory cytokines. Thus, induction of the unfolded protein response may represent a novel pathway by which host cells can detect pathogens deploying a T4SS.
                  Cover page: Sensing of Bacterial Type IV Secretion via the Unfolded Protein Response
                  • Article
                  • Peer Reviewed
                  UCLA Previously Published Works (2019)

                  Background

                  Erythropoietin (EPO) has been reported as a novel determinant of fibroblast growth factor 23 (FGF23) production; however, it is unknown whether FGF23 is stimulated by chronic exposure to EPO or by EPO administration in nonpolycystic chronic kidney disease (CKD) models.

                  Methods

                  We analyzed the effects of chronic EPO on FGF23 in murine models with chronically high EPO levels and normal kidney function. We studied the effects of exogenous EPO on FGF23 in wild-type mice, with and without CKD, injected with EPO. Also, in four independent human CKD cohorts, we evaluated associations between FGF23 and serum EPO levels or exogenous EPO dose.

                  Results

                  Mice with high endogenous EPO have elevated circulating total FGF23, increased disproportionately to intact FGF23, suggesting coupling of increased FGF23 production with increased proteolytic cleavage. Similarly, in wild-type mice with and without CKD, a single exogenous EPO dose acutely increases circulating total FGF23 out of proportion to intact FGF23. In these murine models, the bone marrow is shown to be a novel source of EPO-stimulated FGF23 production. In humans, serum EPO levels and recombinant human EPO dose are positively and independently associated with total FGF23 levels across the spectrum of CKD and after kidney transplantation. In our largest cohort of 680 renal transplant recipients, serum EPO levels are associated with total FGF23, but not intact FGF23, consistent with the effects of EPO on FGF23 production and metabolism observed in our murine models.

                  Conclusion

                  EPO affects FGF23 production and metabolism, which may have important implications for CKD patients.
                    Cover page: Effects of erythropoietin on fibroblast growth factor 23 in mice and humans.
                    • Article
                    • Peer Reviewed
                    UC Davis Previously Published Works (2009)
                    Brucella ovis is a veterinary pathogen associated with epididymitis in sheep. Despite its genetic similarity to the zoonotic pathogens B. abortus, B. melitensis and B. suis, B. ovis does not cause zoonotic disease. Genomic analysis of the type strain ATCC25840 revealed a high percentage of pseudogenes and increased numbers of transposable elements compared to the zoonotic Brucella species, suggesting that genome degradation has occurred concomitant with narrowing of the host range of B. ovis. The absence of genomic island 2, encoding functions required for lipopolysaccharide biosynthesis, as well as inactivation of genes encoding urease, nutrient uptake and utilization, and outer membrane proteins may be factors contributing to the avirulence of B. ovis for humans. A 26.5 kb region of B. ovis ATCC25840 Chromosome II was absent from all the sequenced human pathogenic Brucella genomes, but was present in all of 17 B. ovis isolates tested and in three B. ceti isolates, suggesting that this DNA region may be of use for differentiating B. ovis from other Brucella spp. This is the first genomic analysis of a non-zoonotic Brucella species. The results suggest that inactivation of genes involved in nutrient acquisition and utilization, cell envelope structure and urease may have played a role in narrowing of the tissue tropism and host range of B. ovis.
                      Cover page: Genome Degradation in Brucella ovis Corresponds with Narrowing of Its Host Range and Tissue Tropism
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