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Open Access Publications from the University of California

Scholarly Works (40 results)

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

Ionic liquids (ILs) have many advantages compared to conventional organic compounds in terms of biological, chemical, physical, and thermal properties. Therefore, ILs are considered as promising green engineering liquids for replacement of commonly used volatile organic compounds that offer a convenient solution to challenges associated with both solvent emission and catalytic recycling for a diverse range of applications. Here, we primarily focus on ILs as lubricants and lubricant additives.

For the application in tribology as lubricants/lubricant additives, phosphonium ILs have been the rising star of the ILs family as they have been reported to exhibit lower wear and friction, as well as superior resistance to corrosion and tribo-corrosion. They are more stable in strongly basic media and more thermally stable than other ILs. Also, importantly, some phosphonium ILs can be less toxic and biodegradable than conventional organic compounds.

The physico-chemical properties of phosphonium ILs are tunable depending upon the combination of cation and anion employed. Changes in properties in turn affect the performance of phosphonium ILs as lubricants and lubricant additives. Although there have been many investigations into the relationship between IL properties and ion chemistry/structure, the selection of cations and anions for phosphonium ILs is still very much trial-and-error. To optimize phosphonium ILs for lubrication, a full understanding of the relationship between chemistry/structure and material properties of is phosphonium ILs required. Toward this goal, classical and reactive molecular dynamics simulations are employed to study the molecular scale mechanisms underlying the mechanical response of phosphonium ILs with different cation and anion combinations.

First, a non-reactive force field was used to predict bulk properties, including density, viscosity, and ionic conductivity. The accuracy of the modeling approach was evaluated by comparing to experiment/literature data. In particular, the effect of anions on these bulk properties was analyzed. The high accuracy in predicting bulk properties provided confidence for using this force field to investigate the wetting behavior and frictional behavior. Then the wetting behavior of phosphonium ILs on iron was studied for different cation-anion pairs to investigate the interaction of phosphonium ILs with solid surfaces. Results showed that contact angle was affected by the anion and increased as benzoate < salicylate < saccharinate longer alkyl chains in the cations led to lower contact angle. The trends were explained in terms of adhesive and cohesive energies in the simulations, and then correlated to the atomic scale differences between the anions and cations. Since the effectiveness of lubricants depends on their frictional behavior, viscous friction that is entirely determined by the fluid properties was investigated for different phosphonium cations. It was found that viscous friction is highly related to cation alkyl chains and chain asymmetry under the same operating condition. A predictive model of viscous friction for tetraalkylphosphonium ILs was then established to capture the effect of cation moiety and operating conditions. Lastly, in many applications, ILs are in direct contact with a metal surface and form a solid-liquid interface and possible corrosion could occur. The origins of corrosion behavior for trihexyltetradecylphosphonium benzoate and trihexyltetradecylphosphonium salicylate on ferrous surfaces was analyzed using reactive molecular dynamics simulations based on the types of bonding and orientation of the anions relative to the surface. It was found that salicylate had more possible bonding scenarios and was more likely to be tilted on the surface than benzoate, affecting the localization of surface-anion bonds and anion coverage density which could affect corrosion mechanisms.

Overall, the results of these studies revealed direct correlations between tribological properties of phosphonium ILs and cation and anion chemistry. The structure-property relationship obtained from this study can ultimately be used to guide the design of high performance phosphonium ILs lubricants.

    Cover page: Understanding Structure-property Relationships between Tribological Properties and Chemistry of Phosphonium Ionic Liquids
    • Thesis
    • Peer Reviewed
    UCLA Electronic Theses and Dissertations (2016)

    In mammals, injury-induced inflammation is mediated by Toll-like receptor (TLR)/NF-κB signaling in blood cells. Although Toll signaling is conserved in Drosophila, how the blood system senses and responds to injury remains largely unknown. By contrast, Toll pathway activation in the context of humoral immunity has been well characterized in Drosophila, focusing primarily on the adult fat body. In this study, we show that epidermal injury in Drosophila larvae causes rapid activation of Toll signaling in blood cells, and is largely independent of the pathway that is known to activate Toll in response to infection. We also show that Jun kinase signaling is activated by injury rapidly under control of Toll signaling, but only Toll contribute to the delayed downstream activation of cytokine-like signaling. It has been previously shown that epidermal injury causes blood cell differentiation in Drosophila; however the underlying molecular mechanism was unknown. Our work demonstrates that Toll and cytokine-like (JAK/STAT) signaling are required sequentially for injury-induced blood cell differentiation. Future studies aiming at understanding how epidermal injury initiates signals that leads to Toll activation may be of specific relevance to similar scenarios in mammalian injury responses.

      Cover page: Sequential activation of NFkB, JNK, and cytokine signaling in the Drosophila blood system in response to distal injury
      • Article
      • Peer Reviewed
      UCLA Previously Published Works (2014)
      Analyses of the Drosophila hematopoietic system are becoming more and more prevalent as developmental and functional parallels with vertebrate blood cells become more evident. Investigative work on the fly blood system has, out of necessity, led to the identification of new molecular markers for blood cell types and lineages and to the refinement of useful molecular genetic tools and analytical methods. This review briefly describes the Drosophila hematopoietic system at different developmental stages, summarizes the major useful cell markers and tools for each stage, and provides basic protocols for practical analysis of circulating blood cells and of the lymph gland, the larval hematopoietic organ.
        Cover page: Drosophila hematopoiesis: Markers and methods for molecular genetic analysis
        • Article
        • Peer Reviewed
        UC Riverside Previously Published Works (2020)
        Software vulnerabilities are now reported at an unprecedented speed due to the recent development of automated vulnerability hunting tools. However, fixing vulnerabilities still mainly depends on programmers' manual efforts. Developers need to deeply understand the vulnerability and try to affect the system's functions as little as possible. In this paper, with the advancement of Neural Machine Translation (NMT) techniques, we provide a novel approach called SeqTrans to exploit historical vulnerability fixes to provide suggestions and automatically fix the source code. To capture the contextual information around the vulnerable code, we propose to leverage data flow dependencies to construct code sequences and fed them into the state-of-the-art transformer model. The fine-tuning strategy has been introduced to overcome the small sample size problem. We evaluate SeqTrans on a dataset containing 1,282 commits that fix 624 vulnerabilities in 205 Java projects. Results show that the accuracy of SeqTrans outperforms the latest techniques and achieves 23.3% in statement-level fix and 25.3% in CVE-level fix. In the meantime, we look deep inside the result and observe that NMT model performs very well in certain kinds of vulnerabilities like CWE-287 (Improper Authentication) and CWE-863 (Incorrect Authorization).
          Cover page: SeqTrans: Automatic Vulnerability Fix via Sequence to Sequence Learning
          • Article
          • Peer Reviewed
          UC San Diego Previously Published Works (2013)
          Automated electron microscopy (EM) image analysis techniques can be tremendously helpful for connectomics research. In this paper, we extend our previous work [1] and propose a fully automatic method to utilize inter-section information for intra-section neuron segmentation of EM image stacks. A watershed merge forest is built via the watershed transform with each tree representing the region merging hierarchy of one 2D section in the stack. A section classifier is learned to identify the most likely region correspondence between adjacent sections. The inter-section information from such correspondence is incorporated to update the potentials of tree nodes. We resolve the merge forest using these potentials together with consistency constraints to acquire the final segmentation of the whole stack. We demonstrate that our method leads to notable segmentation accuracy improvement by experimenting with two types of EM image data sets.
            Cover page: Watershed Merge Forest Classification for Electron Microscopy Image Stack Segmentation
            • Article
            • Peer Reviewed
            UC Merced Previously Published Works (2022)
            The wettability of ionic liquids (ILs) is relevant to their use in various applications. However, a mechanistic understanding of how the cation-anion pair affects wettability is still evolving. Here, focusing on phosphonium ILs, wettability was characterized in terms of contact angle using experiments and classical molecular dynamics simulations. Both experiments and simulations showed that the contact angle was affected by the anion and increased as benzoate < salicylate < saccharinate. Further, the simulations showed that the contact angle decreased with increasing cation alkyl chain length for these anions paired with five different tetra-alkyl-phosphonium cations. The trends were explained in terms of adhesive and cohesive energies in the simulations and then correlated to the atomic scale differences between the anions and the cations.
            • 1 supplemental PDF
            Cover page: Effect of Ion Pair on Contact Angle for Phosphonium Ionic Liquids
            • Article
            • Peer Reviewed
            UC Merced Previously Published Works (2023)
            • 1 supplemental PDF
            Cover page: The effect of Fe-anion interactions on corrosion of ferrous surfaces by phosphonium ionic liquidsCreative Commons 'BY-NC-ND' version 4.0 license
            • Article
            • Peer Reviewed
            UCLA Previously Published Works (2022)
            Inflammatory response in Drosophila to sterile (axenic) injury in embryos and adults has received some attention in recent years, and most concentrate on the events at the injury site. Here we focus on the effect sterile injury has on the hematopoietic organ, the lymph gland, and the circulating blood cells in the larva, the developmental stage at which major events of hematopoiesis are evident. In mammals, injury activates Toll-like receptor/NF-κB signaling in macrophages, which then express and secrete secondary, proinflammatory cytokines. In Drosophila larvae, distal puncture injury of the body wall epidermis causes a rapid activation of Toll and Jun kinase (JNK) signaling throughout the hematopoietic system and the differentiation of a unique blood cell type, the lamellocyte. Furthermore, we find that Toll and JNK signaling are coupled in their activation. Secondary to this Toll/JNK response, a cytokine, Upd3, is induced as a Toll pathway transcriptional target, which then promotes JAK/STAT signaling within the blood cells. Toll and JAK/STAT signaling are required for the emergence of the injury-induced lamellocytes. This is akin to the derivation of specialized macrophages in mammalian systems. Upstream, at the injury site, a Duox- and peroxide-dependent signal causes the activation of the proteases Grass and SPE, needed for the activation of the Toll-ligand Spz, but microbial sensors or the proteases most closely associated with them during septic injury are not involved in the axenic inflammatory response.
              Cover page: Injury-induced inflammatory signaling and hematopoiesis in Drosophila
              • Article
              • Peer Reviewed
              UC Riverside Previously Published Works (2018)
                Cover page: Coordinating the operations of smart buildings in smart grids
                • Article
                • Peer Reviewed
                UC San Diego Previously Published Works (2015)

                Background

                In the area of connectomics, there is a significant gap between the time required for data acquisition and dense reconstruction of the neural processes contained in the same dataset. Automatic methods are able to eliminate this timing gap, but the state-of-the-art accuracy so far is insufficient for use without user corrections. If completed naively, this process of correction can be tedious and time consuming.

                New method

                We present a new semi-automatic method that can be used to perform 3D segmentation of neurites in EM image stacks. It utilizes an automatic method that creates a hierarchical structure for recommended merges of superpixels. The user is then guided through each predicted region to quickly identify errors and establish correct links.

                Results

                We tested our method on three datasets with both novice and expert users. Accuracy and timing were compared with published automatic, semi-automatic, and manual results.

                Comparison with existing methods

                Post-automatic correction methods have also been used in Mishchenko et al. (2010) and Haehn et al. (2014). These methods do not provide navigation or suggestions in the manner we present. Other semi-automatic methods require user input prior to the automatic segmentation such as Jeong et al. (2009) and Cardona et al. (2010) and are inherently different than our method.

                Conclusion

                Using this method on the three datasets, novice users achieved accuracy exceeding state-of-the-art automatic results, and expert users achieved accuracy on par with full manual labeling but with a 70% time improvement when compared with other examples in publication.
                  Cover page: Efficient semi-automatic 3D segmentation for neuron tracing in electron microscopy images
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