1,649 results on '"Olson, C. A."'
Search Results
2. Direct spectroscopic evidence for mixed-valence Tl in the low carrier-density superconductor Pb$_{1-x}$Tl$_x$Te
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Walmsley, P., Liu, C., Palczewski, A. D., Giraldo-Gallo, P., Olson, C. G., Fisher, I. R., and Kaminski, A.
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Condensed Matter - Superconductivity - Abstract
Upon doping with Tl the narrow band-gap semiconductor PbTe exhibits anomalously high temperature superconductivity despite a very low carrier density as well as signatures of the Kondo effect despite an absence of magnetic moments. These phenomena have been explained by invoking 2$e$ fluctuations of the valence of the Tl dopants but a direct measurement of the mixed-valency implied by such a mechanism has not been reported to date. In this work we present the unambiguous observation of multiple valences of Tl in Tl-doped PbTe via photo emission spectroscopy measurements. It is shown via our quantitative analysis that the suppression of the carrier density at compositions exhibiting superconductivity and Kondo-like behaviour is fully accounted for by mixed valency, thus arguing strongly against a self-compensation scenario proposed elsewhere for this material and strengthening the case for valence fluctuation models. In addition to the identification of Tl$^+$ and Tl$^{3+}$ a possible third intermediate local charge-density is tentatively suggested by full fits to the data, the implications of which are discussed in the context of the charge-Kondo effect., Comment: 5 pages, 3 figures
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- 2018
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3. Multi-objective utilization of wood waste recycled from construction and demolition (C&D): Products and characterization
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Khodaei, H., Olson, C., Patino, D., Rico, J., Jin, Q., and Boateng, A.
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- 2022
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4. Rapid identification of neutralizing antibodies against SARS-CoV-2 variants by mRNA display
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Tanaka, Shiho, Olson, C. Anders, Barnes, Christopher O., Higashide, Wendy, Gonzalez, Marcos, Taft, Justin, Richardson, Ashley, Martin-Fernandez, Marta, Bogunovic, Dusan, Gnanapragasam, Priyanthi N.P., Bjorkman, Pamela J., Spilman, Patricia, Niazi, Kayvan, Rabizadeh, Shahrooz, and Soon-Shiong, Patrick
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- 2022
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5. Correction: Functional Constraint Profiling of a Viral Protein Reveals Discordance of Evolutionary Conservation and Functionality.
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Wu, Nicholas C, Olson, C Anders, Du, Yushen, Le, Shuai, Tran, Kevin, Remenyi, Roland, Gong, Danyang, Al-Mawsawi, Laith Q, Qi, Hangfei, Wu, Ting-Ting, and Sun, Ren
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Developmental Biology ,Genetics - Abstract
[This corrects the article DOI: 10.1371/journal.pgen.1005310.].
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- 2017
6. Systematic identification of anti-interferon function on hepatitis C virus genome reveals p7 as an immune evasion protein
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Qi, Hangfei, Chu, Virginia, Wu, Nicholas C, Chen, Zugen, Truong, Shawna, Brar, Gurpreet, Su, Sheng-Yao, Du, Yushen, Arumugaswami, Vaithilingaraja, Olson, C Anders, Chen, Shu-Hua, Lin, Chung-Yen, Wu, Ting-Ting, and Sun, Ren
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Medical Microbiology ,Biomedical and Clinical Sciences ,Biological Sciences ,Immunology ,Digestive Diseases ,Hepatitis ,Chronic Liver Disease and Cirrhosis ,Liver Disease ,Genetics ,Infectious Diseases ,Emerging Infectious Diseases ,Hepatitis - C ,Biotechnology ,Aetiology ,2.1 Biological and endogenous factors ,Infection ,Inflammatory and immune system ,Good Health and Well Being ,CRISPR-Cas Systems ,Cell Line ,Gene Expression Profiling ,Gene Knockout Techniques ,Gene Library ,Genome ,Viral ,Hepacivirus ,Hepatitis C ,Host-Pathogen Interactions ,Humans ,Immune Evasion ,Immunity ,Innate ,Interferons ,Liver ,Membrane Potential ,Mitochondrial ,Mitochondrial Proteins ,Mutagenesis ,Insertional ,Signal Transduction ,Viral Proteins ,Virus Replication ,HCV ,innate immune evasion mechanism ,IF6-16 antiviral function ,high-throughput mutagenesis ,p7 ion channel protein - Abstract
Hepatitis C virus (HCV) encodes mechanisms to evade the multilayered antiviral actions of the host immune system. Great progress has been made in elucidating the strategies HCV employs to down-regulate interferon (IFN) production, impede IFN signaling transduction, and impair IFN-stimulated gene (ISG) expression. However, there is a limited understanding of the mechanisms governing how viral proteins counteract the antiviral functions of downstream IFN effectors due to the lack of an efficient approach to identify such interactions systematically. To study the mechanisms by which HCV antagonizes the IFN responses, we have developed a high-throughput profiling platform that enables mapping of HCV sequences critical for anti-IFN function at high resolution. Genome-wide profiling performed with a 15-nt insertion mutant library of HCV showed that mutations in the p7 region conferred high levels of IFN sensitivity, which could be alleviated by the expression of WT p7 protein. This finding suggests that p7 protein of HCV has an immune evasion function. By screening a liver-specific ISG library, we identified that IFI6-16 significantly inhibits the replication of p7 mutant viruses without affecting WT virus replication. In contrast, knockout of IFI6-16 reversed the IFN hypersensitivity of p7 mutant virus. In addition, p7 was found to be coimmunoprecipitated with IFI6-16 and to counteract the function of IFI6-16 by depolarizing the mitochondria potential. Our data suggest that p7 is a critical immune evasion protein that suppresses the antiviral IFN function by counteracting the function of IFI6-16.
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- 2017
7. Adaptation in protein fitness landscapes is facilitated by indirect paths.
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Wu, Nicholas C, Dai, Lei, Olson, C Anders, Lloyd-Smith, James O, and Sun, Ren
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Bacterial Proteins ,Evolution ,Molecular ,Mutation ,adaptive evolution ,deep sequencing ,epistasis ,evolutionary biology ,fitness landscape ,genomics ,none ,saturation mutagenesis ,Evolution ,Molecular ,Genetics ,Biochemistry and Cell Biology - Abstract
The structure of fitness landscapes is critical for understanding adaptive protein evolution. Previous empirical studies on fitness landscapes were confined to either the neighborhood around the wild type sequence, involving mostly single and double mutants, or a combinatorially complete subgraph involving only two amino acids at each site. In reality, the dimensionality of protein sequence space is higher (20(L)) and there may be higher-order interactions among more than two sites. Here we experimentally characterized the fitness landscape of four sites in protein GB1, containing 20(4) = 160,000 variants. We found that while reciprocal sign epistasis blocked many direct paths of adaptation, such evolutionary traps could be circumvented by indirect paths through genotype space involving gain and subsequent loss of mutations. These indirect paths alleviate the constraint on adaptive protein evolution, suggesting that the heretofore neglected dimensions of sequence space may change our views on how proteins evolve.
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- 2016
8. Functional Constraint Profiling of a Viral Protein Reveals Discordance of Evolutionary Conservation and Functionality.
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Wu, Nicholas C, Olson, C Anders, Du, Yushen, Le, Shuai, Tran, Kevin, Remenyi, Roland, Gong, Danyang, Al-Mawsawi, Laith Q, Qi, Hangfei, Wu, Ting-Ting, and Sun, Ren
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Cell Line ,Humans ,Influenza A virus ,Influenza B virus ,Viral Proteins ,Sequence Analysis ,DNA ,Computational Biology ,Base Sequence ,Conserved Sequence ,Gene Library ,Biological Evolution ,HEK293 Cells ,RNA-Dependent RNA Polymerase ,Vaccine Related ,Biodefense ,Infectious Diseases ,Biotechnology ,Influenza ,Pneumonia & Influenza ,Emerging Infectious Diseases ,Genetics ,Prevention ,2.2 Factors relating to the physical environment ,Infection ,Developmental Biology - Abstract
Viruses often encode proteins with multiple functions due to their compact genomes. Existing approaches to identify functional residues largely rely on sequence conservation analysis. Inferring functional residues from sequence conservation can produce false positives, in which the conserved residues are functionally silent, or false negatives, where functional residues are not identified since they are species-specific and therefore non-conserved. Furthermore, the tedious process of constructing and analyzing individual mutations limits the number of residues that can be examined in a single study. Here, we developed a systematic approach to identify the functional residues of a viral protein by coupling experimental fitness profiling with protein stability prediction using the influenza virus polymerase PA subunit as the target protein. We identified a significant number of functional residues that were influenza type-specific and were evolutionarily non-conserved among different influenza types. Our results indicate that type-specific functional residues are prevalent and may not otherwise be identified by sequence conservation analysis alone. More importantly, this technique can be adapted to any viral (and potentially non-viral) protein where structural information is available.
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- 2015
9. Intranasal plus subcutaneous prime vaccination with a dual antigen COVID-19 vaccine elicits T-cell and antibody responses in mice
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Rice, Adrian, Verma, Mohit, Shin, Annie, Zakin, Lise, Sieling, Peter, Tanaka, Shiho, Balint, Joseph, Dinkins, Kyle, Adisetiyo, Helty, Morimoto, Brett, Higashide, Wendy, Anders Olson, C., Mody, Shivani, Spilman, Patricia, Gabitzsch, Elizabeth, Safrit, Jeffrey T., Rabizadeh, Shahrooz, Niazi, Kayvan, and Soon-Shiong, Patrick
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- 2021
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10. An ACE2 Triple Decoy that neutralizes SARS-CoV-2 shows enhanced affinity for virus variants
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Tanaka, Shiho, Nelson, Gard, Olson, C. Anders, Buzko, Oleksandr, Higashide, Wendy, Shin, Annie, Gonzalez, Marcos, Taft, Justin, Patel, Roosheel, Buta, Sofija, Richardson, Ashley, Bogunovic, Dusan, Spilman, Patricia, Niazi, Kayvan, Rabizadeh, Shahrooz, and Soon-Shiong, Patrick
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- 2021
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11. A Comprehensive Biophysical Description of Pairwise Epistasis throughout an Entire Protein Domain
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Olson, C Anders, Wu, Nicholas C, and Sun, Ren
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Biochemistry and Cell Biology ,Biological Sciences ,Genetics ,Bacterial Proteins ,Epistasis ,Genetic ,Evolution ,Molecular ,Models ,Genetic ,Models ,Molecular ,Mutation ,Protein Stability ,Protein Structure ,Tertiary ,Medical and Health Sciences ,Psychology and Cognitive Sciences ,Developmental Biology ,Biological sciences ,Biomedical and clinical sciences ,Psychology - Abstract
BackgroundNonadditivity in fitness effects from two or more mutations, termed epistasis, can result in compensation of deleterious mutations or negation of beneficial mutations. Recent evidence shows the importance of epistasis in individual evolutionary pathways. However, an unresolved question in molecular evolution is how often and how significantly fitness effects change in alternative genetic backgrounds.ResultsTo answer this question, we quantified the effects of all single mutations and double mutations between all positions in the IgG-binding domain of protein G (GB1). By observing the first two steps of all possible evolutionary pathways using this fitness profile, we were able to characterize the extent and magnitude of pairwise epistasis throughout an entire protein molecule. Furthermore, we developed a novel approach to quantitatively determine the effects of single mutations on structural stability (ΔΔGU). This enabled determination of the importance of stability effects in functional epistasis.ConclusionsOur results illustrate common biophysical mechanisms for occurrences of positive and negative epistasis. Our results show pervasive positive epistasis within a conformationally dynamic network of residues. The stability analysis shows that significant negative epistasis, which is more common than positive epistasis, mostly occurs between combinations of destabilizing mutations. Furthermore, we show that although significant positive epistasis is rare, many deleterious mutations are beneficial in at least one alternative mutational background. The distribution of conditionally beneficial mutations throughout the domain demonstrates that the functional portion of sequence space can be significantly expanded by epistasis.
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- 2014
12. A Comprehensive Functional Map of the Hepatitis C Virus Genome Provides a Resource for Probing Viral Proteins
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Remenyi, Roland, Qi, Hangfei, Su, Sheng-Yao, Chen, Zugen, Wu, Nicholas C, Arumugaswami, Vaithilingaraja, Truong, Shawna, Chu, Virginia, Stokelman, Tamar, Lo, Hung-Hao, Olson, C Anders, Wu, Ting-Ting, Chen, Shu-Hwa, Lin, Chung-Yen, and Sun, Ren
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Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Liver Disease ,Chronic Liver Disease and Cirrhosis ,Digestive Diseases ,Biotechnology ,Hepatitis - C ,Human Genome ,Emerging Infectious Diseases ,Hepatitis ,Infectious Diseases ,2.2 Factors relating to the physical environment ,Infection ,Good Health and Well Being ,Cell Line ,Chromosome Mapping ,Cloning ,Molecular ,DNA Transposable Elements ,DNA ,Viral ,Gene Library ,Genome ,Viral ,Hepacivirus ,High-Throughput Nucleotide Sequencing ,Humans ,Mutagenesis ,Insertional ,Plasmids ,Sequence Analysis ,DNA ,Transcription ,Genetic ,Transfection ,Viral Proteins ,Virus Replication ,Microbiology ,Biochemistry and cell biology ,Medical microbiology - Abstract
UnlabelledPairing high-throughput sequencing technologies with high-throughput mutagenesis enables genome-wide investigations of pathogenic organisms. Knowledge of the specific functions of protein domains encoded by the genome of the hepatitis C virus (HCV), a major human pathogen that contributes to liver disease worldwide, remains limited to insight from small-scale studies. To enhance the capabilities of HCV researchers, we have obtained a high-resolution functional map of the entire viral genome by combining transposon-based insertional mutagenesis with next-generation sequencing. We generated a library of 8,398 mutagenized HCV clones, each containing one 15-nucleotide sequence inserted at a unique genomic position. We passaged this library in hepatic cells, recovered virus pools, and simultaneously assayed the abundance of mutant viruses in each pool by next-generation sequencing. To illustrate the validity of the functional profile, we compared the genetic footprints of viral proteins with previously solved protein structures. Moreover, we show the utility of these genetic footprints in the identification of candidate regions for epitope tag insertion. In a second application, we screened the genetic footprints for phenotypes that reflected defects in later steps of the viral life cycle. We confirmed that viruses with insertions in a region of the nonstructural protein NS4B had a defect in infectivity while maintaining genome replication. Overall, our genome-wide HCV mutant library and the genetic footprints obtained by high-resolution profiling represent valuable new resources for the research community that can direct the attention of investigators toward unidentified roles of individual protein domains.ImportanceOur insertional mutagenesis library provides a resource that illustrates the effects of relatively small insertions on local protein structure and HCV viability. We have also generated complementary resources, including a website (http://hangfei.bol.ucla.edu) and a panel of epitope-tagged mutant viruses that should enhance the research capabilities of investigators studying HCV. Researchers can now detect epitope-tagged viral proteins by established antibodies, which will allow biochemical studies of HCV proteins for which antibodies are not readily available. Furthermore, researchers can now quickly look up genotype-phenotype relationships and base further mechanistic studies on the residue-by-residue information from the functional profile. More broadly, this approach offers a general strategy for the systematic functional characterization of viruses on the genome scale.
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- 2014
13. High-Throughput Identification of Loss-of-Function Mutations for Anti-Interferon Activity in the Influenza A Virus NS Segment
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Wu, Nicholas C, Young, Arthur P, Al-Mawsawi, Laith Q, Olson, C Anders, Feng, Jun, Qi, Hangfei, Luan, Harding H, Li, Xinmin, Wu, Ting-Ting, and Sun, Ren
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Medical Microbiology ,Biomedical and Clinical Sciences ,Genetics ,Biological Sciences ,Emerging Infectious Diseases ,Prevention ,Biotechnology ,Infectious Diseases ,Vaccine Related ,High-Throughput Nucleotide Sequencing ,Influenza A virus ,Interferon Type I ,Molecular Biology ,Mutation ,RNA ,Viral ,Viral Nonstructural Proteins ,Virology ,Agricultural and Veterinary Sciences ,Medical and Health Sciences ,Agricultural ,veterinary and food sciences ,Biological sciences ,Biomedical and clinical sciences - Abstract
UnlabelledViral proteins often display several functions which require multiple assays to dissect their genetic basis. Here, we describe a systematic approach to screen for loss-of-function mutations that confer a fitness disadvantage under a specified growth condition. Our methodology was achieved by genetically monitoring a mutant library under two growth conditions, with and without interferon, by deep sequencing. We employed a molecular tagging technique to distinguish true mutations from sequencing error. This approach enabled us to identify mutations that were negatively selected against, in addition to those that were positively selected for. Using this technique, we identified loss-of-function mutations in the influenza A virus NS segment that were sensitive to type I interferon in a high-throughput fashion. Mechanistic characterization further showed that a single substitution, D92Y, resulted in the inability of NS to inhibit RIG-I ubiquitination. The approach described in this study can be applied under any specified condition for any virus that can be genetically manipulated.ImportanceTraditional genetics focuses on a single genotype-phenotype relationship, whereas high-throughput genetics permits phenotypic characterization of numerous mutants in parallel. High-throughput genetics often involves monitoring of a mutant library with deep sequencing. However, deep sequencing suffers from a high error rate (∼0.1 to 1%), which is usually higher than the occurrence frequency for individual point mutations within a mutant library. Therefore, only mutations that confer a fitness advantage can be identified with confidence due to an enrichment in the occurrence frequency. In contrast, it is impossible to identify deleterious mutations using most next-generation sequencing techniques. In this study, we have applied a molecular tagging technique to distinguish true mutations from sequencing errors. It enabled us to identify mutations that underwent negative selection, in addition to mutations that experienced positive selection. This study provides a proof of concept by screening for loss-of-function mutations on the influenza A virus NS segment that are involved in its anti-interferon activity.
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- 2014
14. High-throughput profiling of influenza A virus hemagglutinin gene at single-nucleotide resolution.
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Wu, Nicholas C, Young, Arthur P, Al-Mawsawi, Laith Q, Olson, C Anders, Feng, Jun, Qi, Hangfei, Chen, Shu-Hwa, Lu, I-Hsuan, Lin, Chung-Yen, Chin, Robert G, Luan, Harding H, Nguyen, Nguyen, Nelson, Stanley F, Li, Xinmin, Wu, Ting-Ting, and Sun, Ren
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Cell Line ,Humans ,Hemagglutinin Glycoproteins ,Influenza Virus ,Binding Sites ,Protein Conformation ,Structure-Activity Relationship ,Phenotype ,Mutation ,Polymorphism ,Single Nucleotide ,Models ,Molecular ,Influenza A Virus ,H1N1 Subtype ,Protein Interaction Domains and Motifs ,High-Throughput Nucleotide Sequencing ,Pneumonia & Influenza ,Influenza ,Biodefense ,Infectious Diseases ,Emerging Infectious Diseases ,Immunization ,Prevention ,Vaccine Related ,Biotechnology ,Genetics ,Human Genome ,2.2 Factors relating to the physical environment ,Infection - Abstract
Genetic research on influenza virus biology has been informed in large part by nucleotide variants present in seasonal or pandemic samples, or individual mutants generated in the laboratory, leaving a substantial part of the genome uncharacterized. Here, we have developed a single-nucleotide resolution genetic approach to interrogate the fitness effect of point mutations in 98% of the amino acid positions in the influenza A virus hemagglutinin (HA) gene. Our HA fitness map provides a reference to identify indispensable regions to aid in drug and vaccine design as targeting these regions will increase the genetic barrier for the emergence of escape mutations. This study offers a new platform for studying genome dynamics, structure-function relationships, virus-host interactions, and can further rational drug and vaccine design. Our approach can also be applied to any virus that can be genetically manipulated.
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- 2014
15. A quantitative high-resolution genetic profile rapidly identifies sequence determinants of hepatitis C viral fitness and drug sensitivity.
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Qi, Hangfei, Olson, C Anders, Wu, Nicholas C, Ke, Ruian, Loverdo, Claude, Chu, Virginia, Truong, Shawna, Remenyi, Roland, Chen, Zugen, Du, Yushen, Su, Sheng-Yao, Al-Mawsawi, Laith Q, Wu, Ting-Ting, Chen, Shu-Hua, Lin, Chung-Yen, Zhong, Weidong, Lloyd-Smith, James O, and Sun, Ren
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Cell Line ,Humans ,Hepacivirus ,Hepatitis C ,Imidazoles ,Viral Nonstructural Proteins ,Gene Expression Profiling ,Drug Resistance ,Viral ,Virus Replication ,Genetic Fitness ,Liver Disease ,Drug Abuse (NIDA Only) ,Digestive Diseases ,Infectious Diseases ,Chronic Liver Disease and Cirrhosis ,Genetics ,Biotechnology ,Prevention ,Emerging Infectious Diseases ,Hepatitis - C ,Antimicrobial Resistance ,Human Genome ,Substance Abuse ,Hepatitis ,5.1 Pharmaceuticals ,Infection ,Virology ,Microbiology ,Immunology ,Medical Microbiology - Abstract
Widely used chemical genetic screens have greatly facilitated the identification of many antiviral agents. However, the regions of interaction and inhibitory mechanisms of many therapeutic candidates have yet to be elucidated. Previous chemical screens identified Daclatasvir (BMS-790052) as a potent nonstructural protein 5A (NS5A) inhibitor for Hepatitis C virus (HCV) infection with an unclear inhibitory mechanism. Here we have developed a quantitative high-resolution genetic (qHRG) approach to systematically map the drug-protein interactions between Daclatasvir and NS5A and profile genetic barriers to Daclatasvir resistance. We implemented saturation mutagenesis in combination with next-generation sequencing technology to systematically quantify the effect of every possible amino acid substitution in the drug-targeted region (domain IA of NS5A) on replication fitness and sensitivity to Daclatasvir. This enabled determination of the residues governing drug-protein interactions. The relative fitness and drug sensitivity profiles also provide a comprehensive reference of the genetic barriers for all possible single amino acid changes during viral evolution, which we utilized to predict clinical outcomes using mathematical models. We envision that this high-resolution profiling methodology will be useful for next-generation drug development to select drugs with higher fitness costs to resistance, and also for informing the rational use of drugs based on viral variant spectra from patients.
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- 2014
16. Modelling clinical data shows active tissue concentration of daclatasvir is 10-fold lower than its plasma concentration
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Ke, Ruian, Loverdo, Claude, Qi, Hangfei, Olson, C Anders, Wu, Nicholas C, Sun, Ren, and Lloyd-Smith, James O
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Biomedical and Clinical Sciences ,Oncology and Carcinogenesis ,Liver Disease ,Digestive Diseases ,Prevention ,5.1 Pharmaceuticals ,Development of treatments and therapeutic interventions ,Infection ,Good Health and Well Being ,Antiviral Agents ,Carbamates ,Clinical Trials as Topic ,Hepacivirus ,Humans ,Imidazoles ,Models ,Theoretical ,Plasma ,Pyrrolidines ,Valine ,Viral Load ,hepatitis C virus ,resistance ,pharmacokinetics/pharmacodynamics ,mathematical modeling ,Microbiology ,Medical Microbiology ,Pharmacology and Pharmaceutical Sciences ,Clinical sciences ,Pharmacology and pharmaceutical sciences - Abstract
ObjectivesDaclatasvir is a highly potent inhibitor of hepatitis C virus. We estimated the active tissue concentration of daclatasvir in vivo.MethodsWe developed a mathematical model incorporating pharmacokinetic/pharmacodynamic and viral dynamics. By fitting the model to clinical data reported previously, we estimated the ratio between plasma drug concentration and active tissue concentration in vivo.ResultsThe modelling results show that the active tissue concentration of daclatasvir is ∼9% of the concentration measured in plasma (95% CI 1%-29%).ConclusionsUsing plasma concentrations as surrogates for clinical recommendations may lead to substantial underestimation of the risk of resistance.
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- 2014
17. HIV-1 Quasispecies Delineation by Tag Linkage Deep Sequencing
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Wu, Nicholas C, De La Cruz, Justin, Al-Mawsawi, Laith Q, Olson, C Anders, Qi, Hangfei, Luan, Harding H, Nguyen, Nguyen, Du, Yushen, Le, Shuai, Wu, Ting-Ting, Li, Xinmin, Lewis, Martha J, Yang, Otto O, and Sun, Ren
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Biological Sciences ,Bioinformatics and Computational Biology ,HIV/AIDS ,Genetics ,Infectious Diseases ,Clinical Research ,Biotechnology ,Genome ,Viral ,HIV-1 ,High-Throughput Nucleotide Sequencing ,Reproducibility of Results ,General Science & Technology - Abstract
Trade-offs between throughput, read length, and error rates in high-throughput sequencing limit certain applications such as monitoring viral quasispecies. Here, we describe a molecular-based tag linkage method that allows assemblage of short sequence reads into long DNA fragments. It enables haplotype phasing with high accuracy and sensitivity to interrogate individual viral sequences in a quasispecies. This approach is demonstrated to deduce ∼ 2000 unique 1.3 kb viral sequences from HIV-1 quasispecies in vivo and after passaging ex vivo with a detection limit of ∼ 0.005% to ∼ 0.001%. Reproducibility of the method is validated quantitatively and qualitatively by a technical replicate. This approach can improve monitoring of the genetic architecture and evolution dynamics in any quasispecies population.
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- 2014
18. Eulerian CFD simulation of biomass thermal conversion in an indirect slow pyrolysis rotary kiln unit to produce biochar from recycled waste wood
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Khodaei, H., primary, Álvarez-Bermúdez, C., additional, Chapela, S., additional, Olson, C., additional, MacKenzie, M.D., additional, Gomez, M.A., additional, and Porteiro, J., additional
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- 2023
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19. Angle-resolved photoemission study of USb2: the 5f band structure
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Guziewicz, E., Durakiewicz, T., Butterfield, M. T., Olson, C. G., Joyce, J. J., Arko, A. J., Sarrao, J. L., Moore, D. P., and Morales, L.
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Condensed Matter - Abstract
Single crystal antiferromagnetic USb2 was studied at 15K by angle-resolved photoemission with an overall energy resolution of 24 meV. The measurements unambiguously show the dispersion of extremely narrow bands situated near the Fermi level. The peak at the Fermi level represents the narrowest feature observed in 5f-electron photoemission to date. The natural linewidth of the feature just below the Fermi level is not greater than 10 meV. Normal emission data indicate a three dimensional aspect to the electronic structure of this layered material., Comment: 22 pages including figures
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- 2003
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20. Electronic structures of UTSn (T=Ni, Pd) using photoemission spectroscopy
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Kang, J. -S., Wi, S. C., Kim, J. H., McEwen, K. A., Olson, C. G., Shim, J. H., and Min, B. I.
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Condensed Matter - Materials Science - Abstract
The electronic structures of the localized $5f$ systems UTSn (T=Ni, Pd) have been investigated using photoemission spectroscopy (PES). The extracted U $5f$ PES spectra of UTSn (T=Ni, Pd) exhibit a broad peak centered at $\sim 0.3$ eV below $\rm E_F$ with rather small spectral weight near $\rm E_F$ (N$_f$($\rm E_F$)). The small N$_f$($\rm E_F$) in UTSn is found to be correlated with the T $d$ PES spectra that have a very low density of states (DOS) near $\rm E_F$. The high-resolution PES spectra for UTSn provide the V-shaped reduced metallic DOS near $\rm E_F$ but do not reveal any appreciable changes in their electronic structures across the magnetic phase transitions. A possible origin for the reduced N$_f$($\rm E_F$) in UTSn is ascribed to the hybridization to the very low T $d$ DOS at $\rm E_F$. Comparison of the measured PES spectra to the LSDA+$U$ band structure calculation reveals a reasonably good agreement for UPdSn, but not so for UNiSn., Comment: 7 pages, 6 figures
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- 2003
21. Reply to Comment on: 'Spontaneous breaking of time-reversal symmetry in the pseudogap state of a high-Tc superconductor'
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Kaminski, A., Rosenkranz, S., Fretwell, H. M., Campuzano, J. C., Li, Z. Z., Raffy, H., Cullen, W. G., You, H., Olson, C. G., Varma, C. M., and Hoechst, H.
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Condensed Matter - Strongly Correlated Electrons ,Condensed Matter - Superconductivity - Abstract
In a recent comment [1], Armitage and Hu have suggested that our experiment observing dichroism in angle resolved photoemission (ARPES) [2] could not be conclusively interpreted as arising from time reversal symmetry breaking, arguing that our observations are likely due to structural effects. The concerns expressed by Armitage and Hu that our results could be due to a change in the mirror plane are as important as they are obvious. In fact the first part of their comment merely restates the results of Simon and Varma [3] about the relationship and contrast of effects due to time reversal symmetry breaking and those caused by crystallographic changes. In any test of time reversal symmetry one must ensure that parity alone is not inducing the observed changes. We have indeed considered this issue very carefully in the course of our study [2] and it is precisely the lack of temperature dependent structural changes significant enough to explain the magnitude of the observed dichroism that forced us to conclude that time reversal symmetry breaking is the only plausible explanation. Furthermore, recent experiments by Borisenko, et al. [4] confirm that changes in the mirror plane are unmeasurably small.
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- 2003
22. Metastability and Transient Effects in Vortex Matter Near a Decoupling Transition
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Olson, C. J., Reichhardt, C., Scalettar, R. T., Zimanyi, G. T., and Gronbech-Jensen, N.
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Condensed Matter - Superconductivity - Abstract
We examine metastable and transient effects both above and below the first-order decoupling line in a 3D simulation of magnetically interacting pancake vortices. We observe pronounced transient and history effects as well as supercooling and superheating between the 3D coupled, ordered and 2D decoupled, disordered phases. In the disordered supercooled state as a function of DC driving, reordering occurs through the formation of growing moving channels of the ordered phase. No channels form in the superheated region; instead the ordered state is homogeneously destroyed. When a sequence of current pulses is applied we observe memory effects. We find a ramp rate dependence of the V(I) curves on both sides of the decoupling transition. The critical current that we obtain depends on how the system is prepared., Comment: 10 pages, 15 postscript figures, version to appear in PRB
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- 2003
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23. Resonant photoemission spectroscopy study of insulator-to-metal transition in Cr- and Ru-doped Nd_{1/2}A_{1/2}Mn_{1-y} O_{3} (A=Ca, Sr)
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Kang, J. -S., Kim, J. H., Sekiyama, A., Kasai, S., Suga, S., Han, S. W., Kim, K. H., Choi, E. J., Kimura, T., Muro, T., Saitoh, Y., Olson, C. G., Shim, J. H., and Min, B. I.
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Condensed Matter - Strongly Correlated Electrons - Abstract
Electronic structures of very dilute Cr- or Ru-doped Nd_{1/2}A_{1/2}MnO_{3} (NAMO; A=Ca, Sr) manganites have been investigated using the Mn and Cr 2p -> 3d resonant photoemission spectroscopy (PES). All the Cr- and Ru-doped NAMO systems exhibit the clear metallic Fermi edges in the Mn e_g spectra near E_F, consistent with their metallic ground states. The Cr 3d states with t^3_{2g} configuration are at ~ 1.3 eV below E_F, and the Cr e_{g} states do not participate in the formation of the band near E_F. Cr- and Ru-induced ferromagnetism and insulator-to-metal transitions can be understood with their measured electronic structures., Comment: 4 pages, 4 figures
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- 2002
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24. Bulk-sensitive photoemission spectroscopy of A_2FeMoO_6 double perovskites (A=Sr, Ba)
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Kang, J. -S., Kim, J. H., Sekiyama, A., Kasai, S., Suga, S., Han, S. W., Kim, K. H., Muro, T., Saitoh, Y., Hwang, C., Olson, C. G., Park, B. J., Lee, B. W., Shim, J. H., Park, J. H., and Min, B. I.
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Condensed Matter - Materials Science ,Condensed Matter - Strongly Correlated Electrons - Abstract
Electronic structures of Sr_2FeMoO_6 (SFMO) and Ba_2FeMoO_6 (BFMO) double perovskites have been investigated using the Fe 2p->3d resonant photoemission spectroscopy (PES) and the Cooper minimum in the Mo 4d photoionization cross section. The states close to the Fermi level are found to have strongly mixed Mo-Fe t_{2g} character, suggesting that the Fe valence is far from pure 3+. The Fe 2p_{3/2} XAS spectra indicate the mixed-valent Fe^{3+}-Fe^{2+} configurations, and the larger Fe^{2+} component for BFMO than for SFMO, suggesting a kind of double exchange interaction. The valence-band PES spectra reveal good agreement with the LSDA+U calculation., Comment: 4 pages, 3 figures
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- 2002
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25. Spontaneous time reversal symmetry breaking in the pseudogap state of high-Tc superconductors
- Author
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Kaminski, A., Rosenkranz, S., Fretwell, H. M., Campuzano, J. C., Li, Z., Raffy, H., Cullen, W. G., You, H., Olson, C. G., Varma, C. M., and H"ochst, H.
- Subjects
Condensed Matter - Strongly Correlated Electrons - Abstract
When matter undergoes a phase transition from one state to another, usually a change in symmetry is observed, as some of the symmetries exhibited are said to be spontaneously broken. The superconducting phase transition in the underdoped high-Tc superconductors is rather unusual, in that it is not a mean-field transition as other superconducting transitions are. Instead, it is observed that a pseudo-gap in the electronic excitation spectrum appears at temperatures T* higher than Tc, while phase coherence, and superconductivity, are established at Tc (Refs. 1, 2). One would then wish to understand if T* is just a crossover, controlled by fluctuations in order which will set in at the lower Tc (Refs. 3, 4), or whether some symmetry is spontaneously broken at T* (Refs. 5-10). Here, using angle-resolved photoemission with circularly polarized light, we find that, in the pseudogap state, left-circularly polarized photons give a different photocurrent than right-circularly polarized photons, and therefore the state below T* is rather unusual, in that it breaks time reversal symmetry11. This observation of a phase transition at T* provides the answer to a major mystery of the phase diagram of the cuprates. The appearance of the anomalies below T* must be related to the order parameter that sets in at this characteristic temperature ., Comment: 11 pages, 4 figures
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- 2002
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26. Novel Colloidal Crystalline States on Two Dimensional Periodic Substrates
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Reichhardt, C. and Olson, C. J.
- Subjects
Condensed Matter - Soft Condensed Matter - Abstract
We show using numerical simulations that a rich variety of novel colloidal crystalline states are realized on square and triangular two dimensional periodic substrates which can be experimentally created using crossed laser arrays. When there are more colloids than potential substrate minima, multiple colloids are trapped at each substrate minima and act as a single particle with a rotational degree of freedom, giving rise to a new type of orientational order. We call these states colloidal molecular crystals. A two-step melting can also occur in which individual colloidal molecules initially rotate, destroying the overall orientational order, followed by the onset of inter-well colloidal hopping., Comment: 4 pages, 4 postscript figures
- Published
- 2002
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27. Transverse Phase Locking for Vortex Motion in Square and Triangular Pinning Arrays
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Reichhardt, C. and Olson, C. J.
- Subjects
Condensed Matter - Superconductivity - Abstract
We analyze transverse phase locking for vortex motion in a superconductor with a longitudinal DC drive and a transverse AC drive. For both square and triangular arrays we observe a variety of fractional phase locking steps in the velocity versus DC drive which correspond to stable vortex orbits. The locking steps are more pronounced for the triangular arrays which is due to the fact that the vortex motion has a periodic transverse velocity component even for zero transverse AC drive. All the steps increase monotonically in width with AC amplitude. We confirm that the width of some fractional steps in the square arrays scales as the square of the AC driving amplitude. In addition we demonstrate scaling in the velocity versus applied DC driving curves at depinning and on the main step, similar to that seen for phase locking in charge-density wave systems. The phase locking steps are most prominent for commensurate vortex fillings where the interstitial vortices form symmetrical ground states. For increasing temperature, the fractional steps are washed out very quickly, while the main step gains a linear component and disappears at melting. For triangular pinning arrays we again observe transverse phase locking, with the main and several of the fractional step widths scaling linearly with AC amplitude., Comment: 10 pages, 14 postscript figures
- Published
- 2002
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28. Colloidal Dynamics on Disordered Substrates
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Reichhardt, C. and Olson, C. J.
- Subjects
Condensed Matter - Soft Condensed Matter - Abstract
Using Langevin simulations we examine driven colloids interacting with quenched disorder. For weak substrates the colloids form an ordered state and depin elastically. For increasing substrate strength we find a sharp crossover to inhomogeneous depinning and a substantial increase in the depinning force, analogous to the peak effect in superconductors. The velocity versus driving force curve shows criticality at depinning, with a change in scaling exponent occuring at the order to disorder crossover. Upon application of a sudden pulse of driving force, pronounced transients appear in the disordered regime which are due to the formation of long-lived colloidal flow channels., Comment: 4 pages, 4 postscript figures
- Published
- 2001
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29. Depinning and Dynamics of Systems with Competing Interactions in Quenched Disorder
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Reichhardt, C., Olson, C. J., Martin, I., and Bishop, A. R.
- Subjects
Condensed Matter - Mesoscale and Nanoscale Physics ,Condensed Matter - Disordered Systems and Neural Networks - Abstract
We examine the depinning and driven dynamics of a system in which there is a competition between long range Coulomb repulsive and short range attractive interactions. In the absence of disorder the system forms Wigner crystal, stripe, and clump phases as the attractive interaction is increased. With quenched disorder, these phases are fragmented and there is a finite depinning threshold. The stripe phase is the most strongly pinned and shows hysteretic transport properties. At higher drives beyond depinning, a dynamical reordering transition occurs in all the phases, which is associated with a characteristic transport signature., Comment: 4 pages, 4 postscript figures
- Published
- 2001
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30. Vortex Pinball Under Crossed AC Drives in Superconductors with Periodic Pinning Arrays
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Reichhardt, C. and Olson, C. J.
- Subjects
Condensed Matter - Superconductivity - Abstract
Vortices driven with both a transverse and a longitudinal AC drive which are out of phase are shown to exhibit a novel commensuration-incommensuration effect when interacting with periodic substrates. For different AC driving parameters, the motion of the vortices forms commensurate orbits with the periodicity of the pinning array. When the commensurate orbits are present, there is a finite DC critical depinning threshold, while for the incommensurate phases the vortices are delocalized and the DC depinning threshold is absent., Comment: 4 pages, 4 postscript figures
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- 2001
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31. Rectification and Phase Locking for Particles on Two Dimensional Periodic Substrates
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Reichhardt, C., Olson, C. J., and Hastings, M. B.
- Subjects
Condensed Matter - Statistical Mechanics ,Condensed Matter - Soft Condensed Matter - Abstract
We show that a novel rectification phenomena is possible for overdamped particles interacting with a 2D periodic substrate and driven with a longitudinal DC drive and a circular AC drive. As a function of DC amplitude, the longitudinal velocity increases in a series of quantized steps with transverse rectification occuring near these transitions. We present a simple model that captures the quantization and rectification behaviors., Comment: 4 pages, 4 postscript figures
- Published
- 2001
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32. Ratchet-Induced Segregation and Transport of Non-Spherical Grains
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Wambaugh, J. F., Reichhardt, C., and Olson, C. J.
- Subjects
Condensed Matter - Abstract
We consider through simulations the behavior of elongated grains on a vibrating ratchet-shaped base. We observe differences in layer velocity profile and in net grain velocity for grains that are composed of one, two, or three colinear spheres. In the case of mixtures of different species of grains, we demonstrate layer-by-layer variation in the average velocity as well as layer segregation of species, and show that horizontal separation of the species can be achieved using this geometry. We also find that the addition of a small number of shorter grains to a sample of long grains provides a lubrication effect that increases the velocity of the long grains., Comment: 8 pages, 7 postscript figures
- Published
- 2001
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33. Bulk Band Gaps in Divalent Hexaborides
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Denlinger, J. D., Clack, J. A., Allen, J. W., Gweon, G. -H., Poirier, D. M., Olson, C. G., Sarrao, J. L., Bianchi, A. D., and Fisk, Z.
- Subjects
Condensed Matter - Strongly Correlated Electrons - Abstract
Complementary angle-resolved photoemission and bulk-sensitive k-resolved resonant inelastic x-ray scattering of divalent hexaborides reveal a >1 eV X-point gap between the valence and conduction bands, in contradiction to the band overlap assumed in several models of their novel ferromagnetism. This semiconducting gap implies that carriers detected in transport measurements arise from defects, and the measured location of the bulk Fermi level at the bottom of the conduction band implicates boron vacancies as the origin of the excess electrons. The measured band structure and X-point gap in CaB_6 additionally provide a stringent test case for proper inclusion of many-body effects in quasi-particle band calculations., Comment: 4 pages, 3 figures; new RIXS analysis; accepted for publication in PRL
- Published
- 2001
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34. ARPES Study of X-Point Band Overlaps in LaB$_6$ and SmB$_6$ - Contrast to SrB$_6$ and EuB$_6$
- Author
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Mo, S. -K., Gweon, G. -H., Denlinger, J. D., Kim, H. -D., Allen, J. W., Olson, C. G., Höchst, H., Sarrao, J. L., and Fisk, Z.
- Subjects
Condensed Matter - Strongly Correlated Electrons - Abstract
In contrast to our recent finding of an X-point band gap in divalent hexaborides, we report here that angle resolved photoemission spectroscopy (ARPES) data shows that the gap is absent for trivalent LaB$_6$ and is absent or nearly so for mixed valent SmB$_6$. This finding demonstrates a nontrivial evolution of the band structure from divalent to trivalent hexaborides., Comment: submitted to SCES '01
- Published
- 2001
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35. Photoemission view of electron fractionalization in quasi-one dimensional metal Li$_{0.9}$Mo$_6$O$_{17}$
- Author
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Gweon, G. -H., Denlinger, J. D., Olson, C. G., Höchst, H., Marcus, J., and Schlenker, C.
- Subjects
Condensed Matter - Strongly Correlated Electrons - Abstract
We report Luttinger liquid line shapes better revealed by new angle resolved photoemission data taken with a much improved angle resolution on a quasi-1-dimensional metal Li$_{0.9}$Mo$_6$O$_{17}$. The new data indicate a larger spinon velocity than our previous lower resolution data indicated., Comment: submitted to SCES '01
- Published
- 2001
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36. Commensurate and Incommensurate Vortex Lattice Melting in Periodic Pinning Arrays
- Author
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Reichhardt, C., Olson, C. J., Scalettar, R. T., and Zimanyi, G. T.
- Subjects
Condensed Matter - Superconductivity - Abstract
We examine the melting of commensurate and incommensurate vortex lattices interacting with square pinning arrays through the use of numerical simulations. For weak pinning strength in the commensurate case we observe an order-order transition from a commensurate square vortex lattice to a triangular floating solid phase as a function of temperature. This floating solid phase melts into a liquid at still higher temperature. For strong pinning there is only a single transition from the square pinned lattice to the liquid state. For strong pinning in the incommensurate case, we observe a multi-stage melting in which the interstitial vortices become mobile first, followed by the melting of the entire lattice, consistent with recent imaging experiments. The initial motion of vortices in the incommensurate phase occurs by an exchange process of interstitial vortices with vortices located at the pinning sites. We have also examined the vortex melting behavior for higher matching fields and find that a coexistence of a commensurate pinned vortex lattice with an interstitial vortex liquid occurs while at higher temperatures the entire vortex lattice melts. For triangular arrays at incommensurate fields higher than the first matching field we observe that the initial vortex motion can occur through a novel correlated ring excitation where a number of vortices can rotate around a pinned vortex. We also discuss the relevance of our results to recent experiments of colloidal particles interacting with periodic trap arrays., Comment: 8 figures
- Published
- 2001
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37. ARPES Line Shapes in FL and non-FL Quasi-Low-Dimensional Inorganic Metals
- Author
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Gweon, G. -H., Denlinger, J. D., Allen, J. W., Claessen, R., Olson, C. G., Hoechst, H., Marcus, J., Schlenker, C., and Schneemeyer, L. F.
- Subjects
Condensed Matter - Strongly Correlated Electrons ,Condensed Matter - Materials Science - Abstract
Quasi-low-dimensional (quasi-low-D) inorganic materials are not only ideally suited for angle resolved photoemission spectroscopy (ARPES) but also they offer a rich ground for studying key concepts for the emerging paradigm of non-Fermi liquid (non-FL) physics. In this article, we discuss the ARPES technique applied to three quasi-low-D inorganic metals: a paradigm Fermi liquid (FL) material TiTe$_{2}$, a well-known quasi-1D charge density wave (CDW) material K$_{0.3}$MoO$_{3}$ and a quasi-1D non-CDW material Li$_{0.9}$Mo$_{6}$O$_{17}$. With TiTe$_2$, we establish that a many body theoretical interpretation of the ARPES line shape is possible. We also address the fundamental question of how to accurately determine the {\bf k}$_F$ value from ARPES. Both K$_{0.3}$MoO$_{3}$ and Li$_{0.9}$Mo$_{6}$O$_{17}$ show quasi-1D electronic structures with non-FL line shapes. A CDW gap opening is observed for K$_{0.3}$MoO$_{3}$, whereas no gap is observed for Li$_{0.9}$Mo$_{6}$O$_{17}$. We show, however, that the standard CDW theory, even with strong fluctuations, is not sufficient to describe the non-FL line shapes of K$_{0.3}$MoO$_{3}$. We argue that a Luttinger liquid (LL) model is relevant for both bronzes, but also point out difficulties encountered in comparing data with theory. We interpret this situation to mean that a more complete and realistic theory is necessary to understand these data., Comment: 23 pages, including 21 figures; to appear in a special issue of J. Elec. Spectr. Rel. Phenom
- Published
- 2001
38. Dynamic Ordering and Transverse Depinning of a Driven Elastic String in a Disordered Media
- Author
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Reichhardt, C. and Olson, C. J.
- Subjects
Condensed Matter - Abstract
We examine the dynamics of an elastic string interacting with quenched disorder driven perpendicular and parallel to the string. We show that the string is the most disordered at the depinning transition but with increasing drive partial ordering is regained. For low drives the noise power is high and we observe a 1/f^2 noise signature crossing over to a white noise character with low power at higher drives. For the parallel driven moving string there is a finite transverse critical depinning force with the depinning transition occuring by the formation of running kinks., Comment: 4 pages, 4 postscript figures
- Published
- 2001
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39. Collective Interaction-Driven Ratchet for Transporting Flux Quanta
- Author
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Olson, C. J., Reichhardt, C., Janko, B., and Nori, Franco
- Subjects
Condensed Matter - Superconductivity - Abstract
We propose and study a novel way to produce a DC transport of vortices when applying an AC electrical current to a sample. Specifically, we study superconductors with a graduated random pinning density, which transports interacting vortices as a ratchet system. We show that a ratchet effect appears as a consequence of the long range interactions between the vortices. The pinned vortices create an asymmetric periodic flux density profile, which results in an asymmetric effective potential for the unpinned interstitial vortices. The latter exhibit a net longitudinal rectification under an applied transverse AC electric current., Comment: 4 pages, 5 postscript figures
- Published
- 2001
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40. Effect of Grain Geometry on Angle of Repose and Dynamics
- Author
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Olson, C. J., Reichhardt, C., McCloskey, M., and Zieve, R. J.
- Subjects
Condensed Matter - Disordered Systems and Neural Networks ,Condensed Matter - Soft Condensed Matter - Abstract
With simulation and experiment we examine the effect of grain anisotropy on the angle of repose in a two-dimensional geometry. We find that the structure of the granular packing can be directly controlled by changing the aspect ratio of the grains, and that the specific type of order strongly affects the angle of repose and the resulting dynamics. The angle of repose is largest for dimer grains, and is smaller for both monomer and trimer grains. The motion of a collapsing grain heap consists of large scale collective shear when monomer grains are considered, but occurs via tumbling of grains on the surface for dimers, and via disorderly bulk tumbling for trimer grains., Comment: 4 pages, 4 postscript figures
- Published
- 2000
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41. Critical depinning force and vortex lattice order in disordered superconductors
- Author
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Olson, C. J., Reichhardt, C., and Bhattacharya, S.
- Subjects
Condensed Matter - Superconductivity - Abstract
We simulate the ordering of vortices and its effects on the critical current in superconductors with varied vortex-vortex interaction strength and varied pinning strengths for a two-dimensional system. For strong pinning the vortex lattice is always disordered and the critical depinning force only weakly increases with decreasing vortex-vortex interactions. For weak pinning the vortex lattice is defect free until the vortex-vortex interactions have been reduced to a low value, when defects begin to appear with a simultaneous rapid increase in the critical depinning force. In each case the depinning force shows a maximum for non-interacting vortices. The relative height of the peak increases and the peak width decreases for decreasing pinning strength in excellent agreement with experimental trends associated with the peak effect. We show that scaling relations exist between the distance between defects in the vortex lattice and the critical depinning force., Comment: 5 pages, 6 figures
- Published
- 2000
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42. Hysteretic depinning and dynamical melting for magnetically interacting vortices in disordered layered superconductors
- Author
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Olson, C. J., Reichhardt, C., and Vinokur, V. M.
- Subjects
Condensed Matter - Superconductivity - Abstract
We examine the depinning transitions and the temperature versus driving force phase diagram for magnetically interacting pancake vortices in layered superconductors. For strong disorder the initial depinning is plastic followed by a sharp hysteretic transition to a 3D ordered state for increasing driving force. Our results are in good agreement with theoretical predictions for driven anisotropic charge density wave systems. We also show that a temperature induced peak effect in the critical current occurs due to the onset of plasticity between the layers., Comment: 4 pages, 4 postscript figures
- Published
- 2000
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43. Bandgap recovery and electron doping on cleaved [100] surfaces of divalent semi-metal hexaborides
- Author
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Denlinger, J. D., Clack, J. A., Allen, J. W., Gweon, G. -H., Poirier, D. M., Olson, C. G., Sarrao, J. L., and Fisk, Z.
- Subjects
Condensed Matter - Strongly Correlated Electrons - Abstract
This paper has been withdrawn by the authors due to new theoretical evidence and experimental proof that the semiconducting bandgap reported in this paper and ascribed to a surface region is in fact a bulk property of divalent hexaborides. As reported in J. D. Denlinger et al., cond-mat/0107429, which supercedes this paper, bulk-sensitive boron K-edge soft x-ray emission provides a complementary confirmation of the X-point band gap identified by angle-resolved photoemission., Comment: This paper is withdrawn and has been superceded by cond-mat/0107429, showing the band gap to be a bulk property
- Published
- 2000
44. Disordering Transitions in Vortex Matter: Peak Effect and Phase Diagram
- Author
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Olson, C. J., Reichhardt, C., Scalettar, R. T., Zimanyi, G. T., and Gronbech-Jensen, N.
- Subjects
Condensed Matter - Superconductivity - Abstract
Using numerical simulations of magnetically interacting vortices in disordered layered superconductors we obtain the static vortex phase diagram as a function of magnetic field and temperature. For increasing field or temperature, we find a transition from ordered straight vortices to disordered decoupled vortices. This transition is associated with a peak effect in the critical current. For samples with increasing disorder strength the field at which the decoupling occurs decreases. Long range, nonlinear interactions in the c-axis are required to observe the effect., Comment: 4 pages, 4 postscript figures
- Published
- 2000
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45. Non-Fermi liquid angle resolved photoemission lineshapes of Li0.9Mo6O17
- Author
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Gweon, G. -H., Denlinger, J. D., Allen, J. W., Olson, C. G., Hoechst, H., Marcus, J., and Schlenker, C.
- Subjects
Condensed Matter - Strongly Correlated Electrons ,Condensed Matter - Materials Science - Abstract
A recent letter by Xue et al. (PRL v.83, 1235 ('99)) reports a Fermi-Liquid (FL) angle resolved photoemission (ARPES) lineshape for quasi one-dimensional Li0.9Mo6O17, contradicting our report (PRL v.82, 2540 ('99)) of a non-FL lineshape in this material. Xue et al. attributed the difference to the improved angle resolution. In this comment, we point out that this reasoning is flawed. Rather, we find that their data have fundamental differences from other ARPES results and also band theory., Comment: To be published as a PRL Comment
- Published
- 2000
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46. Moving Wigner Glasses and Smectics: Dynamics of Disordered Wigner Crystals
- Author
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Reichhardt, C., Olson, C. J., and Nori, Franco
- Subjects
Condensed Matter - Mesoscale and Nanoscale Physics ,Condensed Matter - Disordered Systems and Neural Networks - Abstract
We examine the dynamics of driven classical Wigner solids interacting with quenched disorder from charged impurities. For strong disorder, the initial motion is plastic -- in the form of crossing winding channels. For increasing drive, the disordered Wigner glass can reorder to a moving Wigner smectic -- with the electrons moving in non-crossing 1D channels. These different dynamic phases can be related to the conduction noise and I(V) curves. For strong disorder, we show criticality in the voltage onset just above depinning. We also obtain the dynamic phase diagram for driven Wigner solids and prove that there is a finite threshold for transverse sliding, recently found experimentally., Comment: 4 pages, 4 postscript figures
- Published
- 2000
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47. No well-defined remnant Fermi surface in Sr2CuO2Cl2
- Author
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Haffner, S., Brammeier, D. M., Olson, C. G., Miller, L. L., and Lynch, D. W.
- Subjects
Condensed Matter - Superconductivity ,Condensed Matter - Strongly Correlated Electrons - Abstract
In angle-resolved photoelectron spectra of the antiferromagnetic insulators Ca2CuO2Cl2 and Sr2CuO2Cl2 a sharp drop of the spectral intensity of the lowest-lying band is observed along a line in k space equivalent to the Fermi surface of the optimally doped high-temperature superconductors. This was interpreted as a signature of the existence of a remnant Fermi surface in the insulating phase of the high-temperature superconductors. In this paper it is shown that the drop of the spectral intensity is not related to the spectral function but is a consequence of the electron-photon matrix element, Comment: 4 pages, 3 figures
- Published
- 2000
- Full Text
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48. Metastability and Transient Effects in Vortex Matter Near a Disorder Driven Transition
- Author
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Olson, C. J., Reichhardt, C., Scalettar, R. T., Zimanyi, G. T., and Gronbech-Jensen, N.
- Subjects
Condensed Matter - Superconductivity - Abstract
We examine metastable and transient effects both above and below the first-order disorder driven decoupling line in a 3D simulation of magnetically interacting pancake vortices. We observe pronounced transient and history effects as well as supercooling and superheating between the ordered and disordered phases. In the disordered supercooled state as a function of DC driving, reordering occurs through the formation of growing moving channels of the ordered phase. We find that hysteresis in V(I) is strongly dependent on the proximity to the decoupling transition line., Comment: 4 pages, 5 postscript figures
- Published
- 2000
49. Driven vortices in 3D layered superconductors: Dynamical ordering along the c-axis
- Author
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Kolton, A. B., Dominguez, D., Olson, C. J., and Gronbech-Jensen, N.
- Subjects
Condensed Matter - Superconductivity ,Condensed Matter - Soft Condensed Matter - Abstract
We study a 3D model of driven vortices in weakly coupled layered superconductors with strong pinning. Above the critical force $F_c$, we find a plastic flow regime in which pancakes in different layers are uncoupled, corresponding to a pancake gas. At a higher $F$, there is an ``smectic flow'' regime with short-range interlayer order, corresponding to an entangled line liquid. Later, the transverse displacements freeze and vortices become correlated along the c-axis, resulting in a transverse solid. Finally, at a force $F_s$ the longitudinal displacements freeze and we find a coherent solid of rigid lines., Comment: 4 pages, 3 postscript figures
- Published
- 2000
- Full Text
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50. Static and dynamic coupling transitions of vortex lattices in disordered anisotropic superconductors
- Author
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Olson, C. J., Zimanyi, G. T., Kolton, A. B., and Gronbech-Jensen, N.
- Subjects
Condensed Matter - Superconductivity - Abstract
We use three-dimensional molecular dynamics simulations of magnetically interacting pancake vortices to study vortex matter in disordered, highly anisotropic materials such as BSCCO. We observe a sharp 2D-3D transition from vortex lines to decoupled pancakes as a function of relative interlayer coupling strength, with an accompanying large increase in the critical current remniscent of a second peak effect. We find that decoupled pancakes, when driven, simultaneously recouple and order into a crystalline-like state at high drives. We construct a dynamic phase diagram and show that the dynamic recoupling transition is associated with a double peak in dV/dI., Comment: 4 pages, 4 postscript figures
- Published
- 2000
- Full Text
- View/download PDF
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