Jensen-Feynman approach to the statistics of interacting electrons

Faussurier et al. [Phys. Rev. E 65, 016403 (2001)] proposed to use a variational principle relying on Jensen-Feynman (or Gibbs-Bogoliubov) inequality in order to optimize the accounting for two-particle interactions in the calculation of canonical partition functions. It consists in a decomposition into a reference electron system and a first-order correction. The procedure appears to be very efficient in order to evaluate the free energy and the orbital populations. In this work, we present numerical applications of the method and propose to extend it using a reference energy which includes the interaction between two electrons inside a given orbital. This is possible thanks to our efficient recursion relation for the calculation of partition functions. We also show that a linear reference energy, however, is usually sufficient to achieve a good precision and that the most promising way to improve the approach of Faussurier et al. is to apply Jensen's inequality to a more convenient convex function.Comment: submitted to Physical Review

Verifying Temporal Regular Properties of Abstractions of Term Rewriting Systems

The tree automaton completion is an algorithm used for proving safety properties of systems that can be modeled by a term rewriting system. This representation and verification technique works well for proving properties of infinite systems like cryptographic protocols or more recently on Java Bytecode programs. This algorithm computes a tree automaton which represents a (regular) over approximation of the set of reachable terms by rewriting initial terms. This approach is limited by the lack of information about rewriting relation between terms. Actually, terms in relation by rewriting are in the same equivalence class: there are recognized by the same state in the tree automaton. Our objective is to produce an automaton embedding an abstraction of the rewriting relation sufficient to prove temporal properties of the term rewriting system. We propose to extend the algorithm to produce an automaton having more equivalence classes to distinguish a term or a subterm from its successors w.r.t. rewriting. While ground transitions are used to recognize equivalence classes of terms, epsilon-transitions represent the rewriting relation between terms. From the completed automaton, it is possible to automatically build a Kripke structure abstracting the rewriting sequence. States of the Kripke structure are states of the tree automaton and the transition relation is given by the set of epsilon-transitions. States of the Kripke structure are labelled by the set of terms recognized using ground transitions. On this Kripke structure, we define the Regular Linear Temporal Logic (R-LTL) for expressing properties. Such properties can then be checked using standard model checking algorithms. The only difference between LTL and R-LTL is that predicates are replaced by regular sets of acceptable terms

Identification and structural characterisation of a partially arabinosylated lipoarabinomannan variant isolated from a Corynebacterium glutamicum ubiAmutant

Arabinan polysaccharide side-chains are present in both Mycobacterium tuberculosis and Corynebacterium glutamicum in the heteropolysaccharide arabinogalactan (AG), and in M. tuberculosis in the lipoglycan, lipoarabinomannan (LAM). Herein, we show by quantitative sugar and glycosyl linkage analysis that C. glutamicum possesses a much smaller LAM version, Cg-LAM, characterised by single t-Araf residues linked to th

Characterization of anomalous Zeeman patterns in complex atomic spectra

The modeling of complex atomic spectra is a difficult task, due to the huge number of levels and lines involved. In the presence of a magnetic field, the computation becomes even more difficult. The anomalous Zeeman pattern is a superposition of many absorption or emission profiles with different Zeeman relative strengths, shifts, widths, asymmetries and sharpnesses. We propose a statistical approach to study the effect of a magnetic field on the broadening of spectral lines and transition arrays in atomic spectra. In this model, the sigma and pi profiles are described using the moments of the Zeeman components, which depend on quantum numbers and Land\'{e} factors. A graphical calculation of these moments, together with a statistical modeling of Zeeman profiles as expansions in terms of Hermite polynomials are presented. It is shown that the procedure is more efficient, in terms of convergence and validity range, than the Taylor-series expansion in powers of the magnetic field which was suggested in the past. Finally, a simple approximate method to estimate the contribution of a magnetic field to the width of transition arrays is proposed. It relies on our recently published recursive technique for the numbering of LS-terms of an arbitrary configuration.Comment: submitted to Physical Review

PIM2 Induced COX-2 and MMP-9 Expression in Macrophages Requires PI3K and Notch1 Signaling

Activation of inflammatory immune responses during granuloma formation by the host upon infection of mycobacteria is one of the crucial steps that is often associated with tissue remodeling and breakdown of the extracellular matrix. In these complex processes, cyclooxygenase-2 (COX-2) plays a major role in chronic inflammation and matrix metalloproteinase-9 (MMP-9) significantly in tissue remodeling. In this study, we investigated the molecular mechanisms underlying Phosphatidyl-myo-inositol dimannosides (PIM2), an integral component of the mycobacterial envelope, triggered COX-2 and MMP-9 expression in macrophages. PIM2 triggers the activation of Phosphoinositide-3 Kinase (PI3K) and Notch1 signaling leading to COX-2 and MMP-9 expression in a Toll-like receptor 2 (TLR2)-MyD88 dependent manner. Notch1 signaling perturbations data demonstrate the involvement of the cross-talk with members of PI3K and Mitogen activated protein kinase pathway. Enforced expression of the cleaved Notch1 in macrophages induces the expression of COX-2 and MMP-9. PIM2 triggered significant p65 nuclear factor -κB (NF-κB) nuclear translocation that was dependent on activation of PI3K or Notch1 signaling. Furthermore, COX-2 and MMP-9 expression requires Notch1 mediated recruitment of Suppressor of Hairless (CSL) and NF-κB to respective promoters. Inhibition of PIM2 induced COX-2 resulted in marked reduction in MMP-9 expression clearly implicating the role of COX-2 dependent signaling events in driving the MMP-9 expression. Taken together, these data implicate PI3K and Notch1 signaling as obligatory early proximal signaling events during PIM2 induced COX-2 and MMP-9 expression in macrophages

Structural characterization of a partially arabinosylated lipoarabinomannan variant isolated from a Corynebacterium glutamicum ubiA mutant

Arabinan polysaccharide side-chains are present in both Mycobacterium tuberculosis and Corynebacterium glutamicum in the heteropolysaccharide arabinogalactan (AG), and in M. tuberculosis in the lipoglycan lipoarabinomannan (LAM). This study shows by quantitative sugar and glycosyl linkage analysis that C. glutamicum possesses a much smaller LAM version, Cg-LAM, characterized by single t-Araf residues linked to the α(1→6)-linked mannan backbone. MALDI-TOF MS showed an average molecular mass of 13 800–15 400 Da for Cg-LAM. The biosynthetic origin of Araf residues found in the extracytoplasmic arabinan domain of AG and LAM is well known to be provided by decaprenyl-monophosphoryl-d-arabinose (DPA). However, the characterization of LAM in a C. glutamicum : : ubiA mutant devoid of prenyltransferase activity and devoid of DPA-dependent arabinan deposition into AG revealed partial formation of LAM, albeit with a slightly altered molecular mass. These data suggest that in addition to DPA utilization as an Araf donor, alternative pathways exist in Corynebacterianeae for Araf delivery, possibly via an unknown sugar nucleotide

Abstraction-based Malware Analysis Using Rewriting and Model Checking

International audienceWe propose a formal approach for the detection of high-level malware behaviors. Our technique uses a rewriting-based abstraction mechanism, producing abstracted forms of program traces, independent of the program implementation. It then allows us to handle similar be- haviors in a generic way and thus to be robust with respect to variants. These behaviors, defined as combinations of patterns given in a signa- ture, are detected by model-checking on the high-level representation of the program. We work on unbounded sets of traces, which makes our technique useful not only for dynamic analysis, considering one trace at a time, but also for static analysis, considering a set of traces inferred from a control flow graph. Abstracting traces with rewriting systems on first order terms with variables allows us in particular to model dataflow and to detect information leak

Measurement of XUV-absorption spectra of ZnS radiatively heated foils

Time-resolved absorption of zinc sulfide (ZnS) and aluminum in the XUV-range has been measured. Thin foils in conditions close to local thermodynamic equilibrium were heated by radiation from laser-irradiated gold spherical cavities. Analysis of the aluminum foil radiative hydrodynamic expansion, based on the detailed atomic calculations of its absorption spectra, showed that the cavity emitted flux that heated the absorption foils corresponds to a radiation temperature in the range 55 60 eV. Comparison of the ZnS absorption spectra with calculations based on a superconfiguration approach identified the presence of species Zn6+ - Zn8+ and S5+ - S6+. Based on the validation of the radiative source simulations, experimental spectra were then compared to calculations performed by post-processing the radiative hydrodynamic simulations of ZnS. Satisfying agreement is found when temperature gradients are accounted for

Lipoglycans Contribute to Innate Immune Detection of Mycobacteria

Innate immune recognition is based on the detection, by pattern recognition receptors (PRRs), of molecular structures that are unique to microorganisms. Lipoglycans are macromolecules specific to the cell envelope of mycobacteria and related genera. They have been described to be ligands, as purified molecules, of several PRRs, including the C-type lectins Mannose Receptor and DC-SIGN, as well as TLR2. However, whether they are really sensed by these receptors in the context of a bacterium infection remains unclear. To address this question, we used the model organism Mycobacterium smegmatis to generate mutants altered for the production of lipoglycans. Since their biosynthesis cannot be fully abrogated, we manipulated the biosynthesis pathway of GDP-Mannose to obtain some strains with either augmented (∼1.7 fold) or reduced (∼2 fold) production of lipoglycans. Interestingly, infection experiments demonstrated a direct correlation between the amount of lipoglycans in the bacterial cell envelope on one hand and the magnitude of innate immune signaling in TLR2 reporter cells, monocyte/macrophage THP-1 cell line and human dendritic cells, as revealed by NF-κB activation and IL-8 production, on the other hand. These data establish that lipoglycans are bona fide Microbe-Associated Molecular Patterns contributing to innate immune detection of mycobacteria, via TLR2 among other PRRs