QPTAS and Subexponential Algorithm for Maximum Clique on Disk Graphs

A (unit) disk graph is the intersection graph of closed (unit) disks in the plane. Almost three decades ago, an elegant polynomial-time algorithm was found for Maximum Clique on unit disk graphs [Clark, Colbourn, Johnson; Discrete Mathematics '90]. Since then, it has been an intriguing open question whether or not tractability can be extended to general disk graphs. We show the rather surprising structural result that a disjoint union of cycles is the complement of a disk graph if and only if at most one of those cycles is of odd length. From that, we derive the first QPTAS and subexponential algorithm running in time 2^{O~(n^{2/3})} for Maximum Clique on disk graphs. In stark contrast, Maximum Clique on intersection graphs of filled ellipses or filled triangles is unlikely to have such algorithms, even when the ellipses are close to unit disks. Indeed, we show that there is a constant ratio of approximation which cannot be attained even in time 2^{n^{1-epsilon}}, unless the Exponential Time Hypothesis fails

Designing RNA secondary structures is hard

An RNA sequence is a word over an alphabet on four elements {A, C, G, U} called bases. RNA sequences fold into secondary structures where some bases match one another while others remain unpaired. Pseudoknot-free secondary structures can be represented as well-parenthesized expressions with additional dots, where pairs of matching parentheses symbolize paired bases and dots, unpaired bases. The two fundamental problems in RNA algorithmic are to predict how sequences fold within some model of energy and to design sequences of bases which will fold into targeted secondary structures. Predicting how a given RNA sequence folds into a pseudoknot-free secondary structure is known to be solvable in cubic time since the eighties and in truly subcubic time by a recent result of Bringmann et al. (FOCS 2016), whereas Lyngsø has shown it is NP-complete if pseudoknots are allowed (ICALP 2004). As a stark contrast, it is unknown whether or not designing a given RNA secondary structure is a tractable task; this has been raised as a challenging open question by Anne Condon (ICALP 2003). Because of its crucial importance in a number of fields such as pharmaceutical research and biochemistry, there are dozens of heuristics and software libraries dedicated to RNA secondary structure design. It is therefore rather surprising that the computational complexity of this central problem in bioinformatics has been unsettled for decades. In this paper we show that, in the simplest model of energy which is the Watson-Crick model the design of secondary structures is NP-complete if one adds natural constraints of the form: index i of the sequence has to be labeled by base b. This negative result suggests that the same lower bound holds for more realistic models of energy. It is noteworthy that the additional constraints are by no means artificial: they are provided by all the RNA design pieces of software and they do correspond to the actual practice (see for example the instances of the EteRNA project). Our reduction from a variant of 3-Sat has as main ingredients: arches of parentheses of different widths, a linear order interleaving variables and clauses, and an intended rematching strategy which increases the number of pairs iff the three literals of a same clause are not satisfied. The correctness of the construction is also quite intricate; it relies on the polynomial algorithm for the design of saturated structures – secondary structures without dots – by Haleš et al. (Algorithmica 2016), counting arguments, and a concise case analysis

The eclipsing bursting X-ray binary EXO 0748-676 revisited by XMM-Newton

The bright eclipsing and bursting low-mass X-ray binary EXO 0748-676 has been observed at several occasions by XMM-Newton during the initial calibration and performance verification (CAL/PV) phase. We present here the results obtained from observations with the EPIC cameras. Apart from several type-I X-ray bursts, the source shows a high degree of variability with the presence of soft flares. The wide energy coverage and high sensitivity of XMM-Newton allows for the first time a detailed description of the spectral variability. The source is found to be the superposition of a central (~2 10^8 cm) Comptonized emission, most probably a corona surrounding the inner edge of an accretion disk, associated with a more extended (~3 10^10 cm) thermal halo at a typical temperature of ~0.6 keV with an indication of non-solar abundances. Most of the variations of the source can be accounted for by a variable absorption affecting only the central comptonized component and reaching up to NH ~1.3 10^23 cm^{-2}. The characteristics of the surrounding halo are found compatible with an irradiated atmosphere of an accretion disc which intercepts the central emission due to the system high inclination.Comment: 6 pages, 4 figures, accepted for publication in A&A Letters, XMM special issu

QPTAS and subexponential algorithm for maximum clique on disk graphs

A (unit) disk graph is the intersection graph of closed (unit) disks in the plane. Almost three decades ago, an elegant polynomial-time algorithm was found for \textsc{Maximum Clique} on unit disk graphs [Clark, Colbourn, Johnson; Discrete Mathematics '90]. Since then, it has been an intriguing open question whether or not tractability can be extended to general disk graphs. We show the rather surprising structural result that a disjoint union of cycles is the complement of a disk graph if and only if at most one of those cycles is of odd length. From that, we derive the first QPTAS and subexponential algorithm running in time $2^{\tilde{O}(n^{2/3})}$ for \textsc{Maximum Clique} on disk graphs. In stark contrast, \textsc{Maximum Clique} on intersection graphs of filled ellipses or filled triangles is unlikely to have such algorithms, even when the ellipses are close to unit disks. Indeed, we show that there is a constant ratio of approximation which cannot be attained even in time $2^{n^{1-\varepsilon}}$, unless the Exponential Time Hypothesis fails

Effect of the reservoir size on gas adsorption in inhomogeneous porous media

We study the influence of the relative size of the reservoir on the adsorption isotherms of a fluid in disordered or inhomogeneous mesoporous solids. We consider both an atomistic model of a fluid in a simple, yet structured pore, whose adsorption isotherms are computed by molecular simulation, and a coarse-grained model for adsorption in a disordered mesoporous material, studied by a density functional approach in a local mean-field approximation. In both cases, the fluid inside the porous solid exchanges matter with a reservoir of gas that is at the same temperature and chemical potential and whose relative size can be varied, and the control parameter is the total number of molecules present in the porous sample and in the reservoir. Varying the relative sizes of the reservoir and the sample may change the shape of the hysteretic isotherms, leading to a "reentrant" behavior compared to the grand-canonical isotherm when the latter displays a jump in density. We relate these phenomena to the organization of the metastable states that are accessible for the adsorbed fluid at a given chemical potential or density.Comment: 16 page

Modeling seismic wave propagation and amplification in 1D/2D/3D linear and nonlinear unbounded media

To analyze seismic wave propagation in geological structures, it is possible to consider various numerical approaches: the finite difference method, the spectral element method, the boundary element method, the finite element method, the finite volume method, etc. All these methods have various advantages and drawbacks. The amplification of seismic waves in surface soil layers is mainly due to the velocity contrast between these layers and, possibly, to topographic effects around crests and hills. The influence of the geometry of alluvial basins on the amplification process is also know to be large. Nevertheless, strong heterogeneities and complex geometries are not easy to take into account with all numerical methods. 2D/3D models are needed in many situations and the efficiency/accuracy of the numerical methods in such cases is in question. Furthermore, the radiation conditions at infinity are not easy to handle with finite differences or finite/spectral elements whereas it is explicitely accounted in the Boundary Element Method. Various absorbing layer methods (e.g. F-PML, M-PML) were recently proposed to attenuate the spurious wave reflections especially in some difficult cases such as shallow numerical models or grazing incidences. Finally, strong earthquakes involve nonlinear effects in surficial soil layers. To model strong ground motion, it is thus necessary to consider the nonlinear dynamic behaviour of soils and simultaneously investigate seismic wave propagation in complex 2D/3D geological structures! Recent advances in numerical formulations and constitutive models in such complex situations are presented and discussed in this paper. A crucial issue is the availability of the field/laboratory data to feed and validate such models.Comment: of International Journal Geomechanics (2010) 1-1

Bounds on positive interior transmission eigenvalues

The paper contains lower bounds on the counting function of the positive eigenvalues of the interior transmission problem when the latter is elliptic. In particular, these bounds justify the existence of an infinite set of interior transmission eigenvalues and provide asymptotic estimates from above on the counting function for the large values of the wave number. They also lead to certain important upper estimates on the first few interior transmission eigenvalues. We consider the classical transmission problem as well as the case when the inhomogeneous medium contains an obstacle.Comment: We corrected inaccuracies cost by the wrong sign in the Green formula (17). In particular, the sign in the definition of \sigma was change

Mesons in a Poincare Covariant Bethe-Salpeter Approach

We develop a covariant approach to describe the low-lying scalar, pseudoscalar, vector and axialvector mesons as quark-antiquark bound states. This approach is based on an effective interaction modeling of the non--perturbative structure of the gluon propagator that enters the quark Schwinger-Dyson and meson Bethe-Salpeter equations. We consistently treat these integral equations by precisely implementing the quark propagator functions that solve the Schwinger-Dyson equations into the Bethe-Salpeter equations in the relevant kinematical region. We extract the meson masses and compute the pion and kaon decay constants. We obtain a quantitatively correct description for pions, kaons and vector mesons while the calculated spectra of scalar and axialvector mesons suggest that their structure is more complex than being quark-antiquark bound states.Comment: 18 pages LaTeX, 5 figures; some changes in the presentation, new results on axial vector mesons in enlarged mixing scheme; version to be published in Physical Review

Characteristics of drug-resistant tuberculosis in Abkhazia (Georgia), a high-prevalence area in Eastern Europe

Although multidrug-resistant (MDR) tuberculosis (TB) is a major public health problem in Eastern Europe, the factors contributing to emergence, spread and containment of MDR-TB are not well defined. Here, we analysed the characteristics of drug-resistant TB in a cross-sectional study in Abkhazia (Georgia) between 2003 and 2005, where standard short-course chemotherapy is supplemented with individualized drug-resistance therapy. Drug susceptibility testing (DST) and molecular typing were carried out for Mycobacterium tuberculosis complex strains from consecutive smear-positive TB patients. Out of 366 patients, 60.4% were resistant to any first-line drugs and 21% had MDR-TB. Overall, 25% of all strains belong to the Beijing genotype, which was found to be strongly associated with the risk of MDR-TB (OR 25.9, 95% CI 10.2-66.0) and transmission (OR 2.8, 95% CI 1.6-5.0). One dominant MDR Beijing clone represents 23% of all MDR-TB cases. The level of MDR-TB did not decline during the study period, coinciding with increasing levels of MDR Beijing strains among previously treated cases. Standard chemotherapy plus individualized drug-resistance therapy, guided by conventional DST, might be not sufficient to control MDR-TB in Eastern Europe in light of the spread of "highly transmissible" MDR Beijing strains circulating in the community

The prominent role of the heaviest fragment in multifragmentation and phase transition for hot nuclei

The role played by the heaviest fragment in partitions of multifragmenting hot nuclei is emphasized. Its size/charge distribution (mean value, fluctuations and shape) gives information on properties of fragmenting nuclei and on the associated phase transition.Comment: 11 pages, Proceedings of IWND09, August 23-25, Shanghai (China