A model study of momentum-selective Mott physics

The Fermi liquid theory is a central concept in modern condensed matter physics used to describe conventional metals. A state of this universality class consists of well-defined quasiparticles, which occupy a finite number of states within a Fermi volume defined in momentum space. According to the Luttinger’s theorem, such a state encloses a Fermi volume proportional to the electron density modulo the filled bands if no symmetry is broken. In the past decades strong deviations from Fermi liquid theory have been observed in the scaling behavior of thermodynamic observables in different materials, among which are for instance cuprates and iron pnictides. This thesis is about two prototypical systems that can not be described by Fermi liquid theory. The first part of this work investigates two-dimensional effective models, which are in a Mott insulating state at half-filling and have a finite conductivity when doped with holes. In such a Mott insulating state, the charge carriers are strongly localized due to the Coulomb repulsion. Hence, strong correlations are assumed to have a strong impact on the formation of the ground state, also in the regime of small hole concentration. In a first project we have used a so-called spinon dopon mean-field theory to represent the two-dimensional Fermi-Hubbard model with strong on-site repulsive interaction in effective degrees of freedom, in which the holes can be embedded into a quantum spin liquid. The corresponding SU(2) invariant ground state belongs to the class of fractionalized Fermi liquids. In a second project we investigate a quantum dimer model, an effective model based on a Hilbert space spanned by short range singlets and bound states of holes and spins. The focus here is on the calculation of the hole-part of the electron spectral function by using exact diagonalization and its comparison with two analytic methods, a diagrammatic computation based on the Bethe-Salpeter equation and a so-called two-mode approximation. The electron spectral function shows a similar analytic form in momentum space between nodal and antinodal point when compared to results from photoemission spectroscopy experiments on cuprates. Furthermore, in a subsequent work we calculate the exact ground state of the quantum dimer model along a certain parameter line. In order to analyze the behavior of the elctron spectral function when increasing the density of holes, we investigate the Fermi-Hubbard model in a current project using a dynamical mean-field approach. To solve the 4-site cluster impurity problem, we use a numerical renormalization group approach. However, numerical limitations force us to restrict the analysis to spin-polarized baths. According to the spectral data, the system is similar to the SU(2) invariant case at half-filling in a Mott insulating state and posseses a momentum-selective energy gap at finite doping. The topology of the Fermi surface shows a Lifshitz transition when increasing the hole concentration. Here, the curvature of the Fermi surface changes from electron- to hole-like. For comparison we apply the dynamical mean-field theory also to the quantum dimer model and observe that the electron spectral functions at finite doping are qualitatively similar to that of the two-dimensional Fermi-Hubbard model. The second half of the work is about Tomonaga-Luttinger liquid theory, which is used to describe the low-energy effective degrees of freedom of one-dimensional systems. Here, we first discuss a conceptional extension of the operator-based bosonization theory for one-dimensional systems. This extension is especially suited for inhomogeneous one-dimensional systems. First, we investigate a one-dimensional system with a local interation potential and compute an exact solution of the single particle propagator at T = 0. The critical exponent of the single particle propagator has an unconventional form as a function of the microscopic Tomonaga-Luttinger parameters, which is not covered by the original Luttinger paradigm postulated by F. Duncan M. Haldane. In a second project on one-dimensional systems, we study the impact of scattering processes among bosonic low-energy excitations on the thermalization process. Such scattering processes are irrelevant on large length scales, however strongly affect the dynamics. In our analytic analysis we focus on a experimental setup, where a one-dimensional Bose gas is instantaneously splitted in two identical, however strongly correlated, halves of one-dimensional electronic systems. In the following, the corresponding non-equilibrium state runs through multiple regimes in time, such as a metastable prethermalization regime. However, above a certain threshold in time such scattering processes cause an effective thermalization of the system. In order to demonstrate this, we compute the kinetic equation in the Keldysh field integral formalism from a diagrammatic expansion based on a self-consistent Born approximation

A model study of momentum-selective Mott physics

The Fermi liquid theory is a central concept in modern condensed matter physics used to describe conventional metals. A state of this universality class consists of well-defined quasiparticles, which occupy a finite number of states within a Fermi volume defined in momentum space. According to the Luttinger’s theorem, such a state encloses a Fermi volume proportional to the electron density modulo the filled bands if no symmetry is broken. In the past decades strong deviations from Fermi liquid theory have been observed in the scaling behavior of thermodynamic observables in different materials, among which are for instance cuprates and iron pnictides. This thesis is about two prototypical systems that can not be described by Fermi liquid theory. The first part of this work investigates two-dimensional effective models, which are in a Mott insulating state at half-filling and have a finite conductivity when doped with holes. In such a Mott insulating state, the charge carriers are strongly localized due to the Coulomb repulsion. Hence, strong correlations are assumed to have a strong impact on the formation of the ground state, also in the regime of small hole concentration. In a first project we have used a so-called spinon dopon mean-field theory to represent the two-dimensional Fermi-Hubbard model with strong on-site repulsive interaction in effective degrees of freedom, in which the holes can be embedded into a quantum spin liquid. The corresponding SU(2) invariant ground state belongs to the class of fractionalized Fermi liquids. In a second project we investigate a quantum dimer model, an effective model based on a Hilbert space spanned by short range singlets and bound states of holes and spins. The focus here is on the calculation of the hole-part of the electron spectral function by using exact diagonalization and its comparison with two analytic methods, a diagrammatic computation based on the Bethe-Salpeter equation and a so-called two-mode approximation. The electron spectral function shows a similar analytic form in momentum space between nodal and antinodal point when compared to results from photoemission spectroscopy experiments on cuprates. Furthermore, in a subsequent work we calculate the exact ground state of the quantum dimer model along a certain parameter line. In order to analyze the behavior of the elctron spectral function when increasing the density of holes, we investigate the Fermi-Hubbard model in a current project using a dynamical mean-field approach. To solve the 4-site cluster impurity problem, we use a numerical renormalization group approach. However, numerical limitations force us to restrict the analysis to spin-polarized baths. According to the spectral data, the system is similar to the SU(2) invariant case at half-filling in a Mott insulating state and posseses a momentum-selective energy gap at finite doping. The topology of the Fermi surface shows a Lifshitz transition when increasing the hole concentration. Here, the curvature of the Fermi surface changes from electron- to hole-like. For comparison we apply the dynamical mean-field theory also to the quantum dimer model and observe that the electron spectral functions at finite doping are qualitatively similar to that of the two-dimensional Fermi-Hubbard model. The second half of the work is about Tomonaga-Luttinger liquid theory, which is used to describe the low-energy effective degrees of freedom of one-dimensional systems. Here, we first discuss a conceptional extension of the operator-based bosonization theory for one-dimensional systems. This extension is especially suited for inhomogeneous one-dimensional systems. First, we investigate a one-dimensional system with a local interation potential and compute an exact solution of the single particle propagator at T = 0. The critical exponent of the single particle propagator has an unconventional form as a function of the microscopic Tomonaga-Luttinger parameters, which is not covered by the original Luttinger paradigm postulated by F. Duncan M. Haldane. In a second project on one-dimensional systems, we study the impact of scattering processes among bosonic low-energy excitations on the thermalization process. Such scattering processes are irrelevant on large length scales, however strongly affect the dynamics. In our analytic analysis we focus on a experimental setup, where a one-dimensional Bose gas is instantaneously splitted in two identical, however strongly correlated, halves of one-dimensional electronic systems. In the following, the corresponding non-equilibrium state runs through multiple regimes in time, such as a metastable prethermalization regime. However, above a certain threshold in time such scattering processes cause an effective thermalization of the system. In order to demonstrate this, we compute the kinetic equation in the Keldysh field integral formalism from a diagrammatic expansion based on a self-consistent Born approximation

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

Time-resolved dual transcriptomics reveal early induced Nicotiana benthamiana root genes and conserved infection-promoting Phytophthora palmivora effectors

BACKGROUND: Plant-pathogenic oomycetes are responsible for economically important losses in crops worldwide. Phytophthora palmivora, a tropical relative of the potato late blight pathogen, causes rotting diseases in many tropical crops including papaya, cocoa, oil palm, black pepper, rubber, coconut, durian, mango, cassava and citrus. Transcriptomics have helped to identify repertoires of host-translocated microbial effector proteins which counteract defenses and reprogram the host in support of infection. As such, these studies have helped in understanding how pathogens cause diseases. Despite the importance of P. palmivora diseases, genetic resources to allow for disease resistance breeding and identification of microbial effectors are scarce. RESULTS: We employed the model plant Nicotiana benthamiana to study the P. palmivora root infections at the cellular and molecular levels. Time-resolved dual transcriptomics revealed different pathogen and host transcriptome dynamics. De novo assembly of P. palmivora transcriptome and semi-automated prediction and annotation of the secretome enabled robust identification of conserved infection-promoting effectors. We show that one of them, REX3, suppresses plant secretion processes. In a survey for early transcriptionally activated plant genes we identified a N. benthamiana gene specifically induced at infected root tips that encodes a peptide with danger-associated molecular features. CONCLUSIONS: These results constitute a major advance in our understanding of P. palmivora diseases and establish extensive resources for P. palmivora pathogenomics, effector-aided resistance breeding and the generation of induced resistance to Phytophthora root infections. Furthermore, our approach to find infection-relevant secreted genes is transferable to other pathogen-host interactions and not restricted to plants.This work was supported by the Gatsby Charitable Foundation (RG62472), by the Royal Society (RG69135) and by the European Research Council (ERC-2014-STG, H2020, 637537)

Collins and Sivers asymmetries in muonproduction of pions and kaons off transversely polarised protons

Measurements of the Collins and Sivers asymmetries for charged pions and charged and neutral kaons produced in semi-inclusive deep-inelastic scattering of high energy muons off transversely polarised protons are presented. The results were obtained using all the available COMPASS proton data, which were taken in the years 2007 and 2010. The Collins asymmetries exhibit in the valence region a non-zero signal for pions and there are hints of non-zero signal also for kaons. The Sivers asymmetries are found to be positive for positive pions and kaons and compatible with zero otherwise. © 2015

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts.The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that -80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAFPeer reviewe

Sex differences in oncogenic mutational processes

Funder: Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology); doi: https://doi.org/10.13039/501100002790Funder: Genome Canada (Génome Canada); doi: https://doi.org/10.13039/100008762Funder: Canada Foundation for Innovation (Fondation canadienne pour l'innovation); doi: https://doi.org/10.13039/501100000196Funder: Terry Fox Research Institute (Institut de Recherche Terry Fox); doi: https://doi.org/10.13039/501100004376Abstract: Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Sex differences in oncogenic mutational processes

Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.Peer reviewe

Odd and even partial waves of eta pi(-) and eta 'pi(-) in pi(-) p -> eta(('))pi(-)p at 191 GeV/c

Exclusive production of eta pi(-) and eta'pi(-) in has been studied with a 191 GeV/c pi(-) beam impinging on a hydrogen target at COMPASS (CERN). Partial-wave analyses reveal different odd/even angular momentum (L) characteristics in the inspected invariant mass range up to 3 GeV/c(2). A striking similarity between the two systems is observed for the L = 2, 4, 6 intensities (scaled by kinematical factors) and the relative phases. The known resonances a(2)(1320) and a(4)(2040) are in line with this similarity. In contrast, a strong enhancement of eta'pi(-) over eta pi(-) is found for the L = 1, 3, 5 waves, which carry non-qq quantum numbers. The L = 1 intensity peaks at 1.7 GeV/c(2) in in and at 1.4 GeV/c(2) in eta pi(-), the corresponding phase motions with respect to L = 2 are different. (C) 2014 The Authors. Published by Elsevier B.V.DFG [1102]; German Bundesministerium fur Bildung und Forschung; Czech Republic MEYS [ME492, LA242]; SAIL (CSR), Govt. of India; CERN-RFBR [08-02-91009, 12-02-91500]; Portuguese FCT - Fundacao para a Ciencia e Tecnologia [CERN/FP/109323/2009, CERN/FP/116376/2010, CERN/FP/123600/2011]; MEXT; JSPS [18002006, 20540299, 18540281]; Daiko Foundation; Yamada Foundation; DFG; EU [283286]; Israel Science Foundation; Polish NCN [DEC-2011/01/M/ST2/02350