Polaron states in a CuO chain

We introduce a one-dimensional model for a CuO chain, with holes and $S=1/2$ spins localized in $3d_{x^2-y^2}$ orbitals, and $p_\sigma$ oxygen orbitals without holes in the ground state. We consider a single hole doped at an oxygen site and study its propagation by spin-flip processes. We develop the Green's function method and treat the hole-spin coupling in the self-consistent Born approximation, similar to that successfully used to study polarons in the regular $t$-$J$ model. We present an analytical solution of the problem and investigate whether the numerical integration is a good approximation to this solution.Comment: 3 pages, 2 figures, Physics of Magnetism, Pozna\'n 201

Exact spectral function for hole-magnon coupling in the ferromagnetic CuO3_3-like chain

We present the exact spectral function for a single oxygen hole with spin opposite to ferromagnetic order within a one-dimensional CuO$_{3}$-like spin chain. We find that local Kondo-like exchange interaction generates five different states in the strong coupling regime. It stabilizes a spin polaron which is a bound state of a moving charge dressed by magnon excitations, with essentially the same dispersion as predicted by mean field theory. We then examine in detail the evolution of the spectral function for increasing strength of the hole-magnon interaction. We also demonstrate that the $s$ and $p$ symmetry of orbital states in the conduction band are essentially equivalent to each other and find that the simplified models do not suffice to reproduce subtle aspects of hole-magnon coupling in the charge-transfer model.Comment: 9 pages, 5 figure

Orbiton-magnon interplay in the spin-orbital polarons of KCuF3 and LaMnO3

We present a quasi-analytical solution of a spin-orbital model of KCuF$_{3}$, using the variational method for Green's functions. By analyzing the spectra for different partial bosonic compositions as well as the full solution, we show that hole propagation needs both orbiton and magnon excitations to develop, but the orbitons dominate the picture. We further elucidate the role of the different bosons by analyzing the self-energies for simplified models, establishing that because of the nature of the spin-orbital ground state, magnons alone do not produce a full quasiparticle band, in contrast to orbitons. Finally, using the electron-hole transformation between the $e_g$ states of KCuF$_3$ and LaMnO$_3$ we suggest the qualitative scenario for photoemission experiments in LaMnO$_3$.Comment: 8 pages, 4 figures, accepted by Physical Review

The Green function variational approximation: Significance of physical constraints

We present a calculation of the spectral properties of a single charge doped at a Cu($3d$) site of the Cu-F plane in KCuF$_{3}$. The problem is treated by generating the equations of motion for the Green's function by means of subsequent Dyson expansions and solving the resulting set of equations. This method, dubbed the variational approximation, is both very dependable and flexible, since it is a systematic expansion with precise control over elementary physical processes. It allows for deep insight into the underlying physics of polaron formation as well as for inclusion of many physical constraints, such as excluding crossing diagrams and double occupation constraint, which are not included in the Self-Consistent Born Approximation. Here we examine the role and importance of such constraints by analyzing various spectral functions obtained in second order VA.Comment: 5 pages, 1 figur

Quantum versus classical polarons in a ferromagnetic CuO3_3-like chain

We present an exact solution for an itinerant hole added into the oxygen orbitals of a CuO$_{3}$-like ferromagnetic chain. Using the Green's function method, the quantum polarons obtained for the Heisenberg SU(2) interaction between localized Cu spins are compared with the polarons in the Ising chain. We find that magnons with large energy are favorable towards quasiparticle existence, even in the case of relatively modest electron-magnon coupling. We observe two quasiparticle states with dispersion $\sim 2t$ each, which emerge from the incoherent continuum when the exchange coupling $J$ increases. Quantum fluctuations in the spin system modify the incoherent part of the spectrum and change the spectral function qualitatively, beyond the bands derived from the perturbation theory.Comment: 4 pages, 4 figures, 21 references, conference pape

Interferon-stimulated gene (ISG)-expression screening reveals the specific antibunyaviral activity of ISG20

Bunyaviruses pose a significant threat to human health, prosperity and food security. In response to viral infections, interferons (IFNs) upregulate the expression of hundreds of interferon stimulated genes (ISGs) whose cumulative action can potently inhibit the replication of bunyaviruses. We used a flow cytometry-based method to screen the ability of ∼500 unique ISGs from humans and rhesus macaques to inhibit the replication of Bunyamwera orthobunyavirus (BUNV), the prototype of both the Peribunyaviridae family and Bunyavirales order. Candidates possessing antibunyaviral activity were further examined using a panel of divergent bunyaviruses. Interestingly, one candidate, ISG20, exhibited potent antibunyaviral activity against most viruses examined from the Peribunyaviridae, Hantaviridae and Nairoviridae families, whereas phleboviruses (Phenuiviridae) largely escaped inhibition. Similar to other viruses known to be targeted by ISG20, the antibunyaviral activity of ISG20 is dependent upon its functional ribonuclease activity. Through use of an infectious VLP assay (based on the BUNV minigenome system), we confirmed that gene expression from all 3 viral segments is strongly inhibited by ISG20. Using in vitro evolution, we generated a substantially ISG20-resistant BUNV and mapped the determinants of ISG20 sensitivity/resistance. Taken together, we report that ISG20 is a broad and potent antibunyaviral factor yet some bunyaviruses are remarkably ISG20 resistant. Thus, ISG20 sensitivity/resistance could influence the pathogenesis of bunyaviruses, many of which are emerging viruses of clinical or veterinary significance

A Serpin shapes the extracellular environment to prevent influenza A virus maturation

Interferon-stimulated genes (ISGs) act in concert to provide a tight barrier against viruses. Recent studies have shed light on the contribution of individual ISG effectors to the antiviral state, but most have examined those acting on early, intracellular stages of the viral life cycle. Here, we applied an image-based screen to identify ISGs inhibiting late stages of influenza A virus (IAV) infection. We unraveled a directly antiviral function for the gene SERPINE1, encoding plasminogen activator inhibitor 1 (PAI-1). By targeting extracellular airway proteases, PAI-1 inhibits IAV glycoprotein cleavage, thereby reducing infectivity of progeny viruses. This was biologically relevant for IAV restriction in vivo. Further, partial PAI-1 deficiency, attributable to a polymorphism in human SERPINE1, conferred increased susceptibility to IAV in vitro. Together, our findings reveal that manipulating the extracellular environment to inhibit the last step in a virus life cycle is an important mechanism of the antiviral response

Identification of Interferon-Stimulated Genes with Antiretroviral Activity

SummaryInterferons (IFNs) exert their anti-viral effects by inducing the expression of hundreds of IFN-stimulated genes (ISGs). The activity of known ISGs is insufficient to account for the antiretroviral effects of IFN, suggesting that ISGs with antiretroviral activity are yet to be described. We constructed an arrayed library of ISGs from rhesus macaques and tested the ability of hundreds of individual macaque and human ISGs to inhibit early and late replication steps for 11 members of the retroviridae from various host species. These screens uncovered numerous ISGs with antiretroviral activity at both the early and late stages of virus replication. Detailed analyses of two antiretroviral ISGs indicate that indoleamine 2,3-dioxygenase 1 (IDO1) can inhibit retroviral replication by metabolite depletion while tripartite motif-56 (TRIM56) accentuates ISG induction by IFNα and inhibits the expression of late HIV-1 genes. Overall, these studies reveal numerous host proteins that mediate the antiretroviral activity of IFNs

Acorn: A grid computing system for constraint based modeling and visualization of the genome scale metabolic reaction networks via a web interface

Constraint-based approaches facilitate the prediction of cellular metabolic capabilities, based, in turn on predictions of the repertoire of enzymes encoded in the genome. Recently, genome annotations have been used to reconstruct genome scale metabolic reaction networks for numerous species, including Homo sapiens, which allow simulations that provide valuable insights into topics, including predictions of gene essentiality of pathogens, interpretation of genetic polymorphism in metabolic disease syndromes and suggestions for novel approaches to microbial metabolic engineering. These constraint-based simulations are being integrated with the functional genomics portals, an activity that requires efficient implementation of the constraint-based simulations in the web-based environment