The regularized lattice BGK (RLBGK) is validated against high-accuracy spectral Chebyshev methods for lid-driven cavity flows. RLBGK is shown to provide a viable alternative to standard lattice BGK schemes, with significant enhancement of numerical stability at a very moderate computational extra-cost. © 2014 World Scientific Publishing Company.

A conference on the occasion of the 60th birthday of Maurizio Falcone

Bioventing is a technology used to abate the presence of pollutants in the subsoil. Microorganisms biodegrade the pollutant but the biochemical reaction requires oxygen and so an air ow is induced in the subsoil by means of injection and/or extraction wells. Costs, final result and decontamination time are reliant on contaminant type, soil permeability and several other factors, but oxygen subsoil concentration plays a very important role. For this reason a rational choice of well location and ow rate is required. The mathematical definition of the optimal design problem will be setup starting from a simplified mathematical model describing the bioventing system. A formal definition of decontaminated subsoil will be given and the set of system control variables will be identified. Several optimimization strategies such as cost minimization, removal rate maximization and time optimization will be mathematically described.

Bioventing is a clean-up technology essentially used to remove hydrocarboon from polluted subsoil by the action of microorganism. The model is based on the theory of fluid flows in porous media and on the mathematical description of population dynamics. The numerical results of a simplified model will be described.

The nucleation mechanisms of methane hydrates are studied using well-tempered metadynamics and restrained molecular dynamics. The collective variables we used to follow the process are the methane-methane and methane-water coordination numbers, from which we computed the corresponding Landau free energy surface. This surface is characterized by two minima, corresponding to the two-phase methane bubble/water solution and clathrate crystal, and a transition state. The clathrate crystal is of type II, while in the simulation conditions (T = 273 K and P = 500 atm) the most stable phase should be type I. We constructed the steepest ascent/descent path connecting the two-phase methane bubble/water solution to the clathrate state and passing through the transition state. We interpret this path as the nucleation path, which shows four phases. First, the concentration of solvated methane increases in the aqueous domain via diffusion through the methane-water interface. Second units of methane molecules solvated in water meet to form an unstructured cluster. Third, the water content of the nucleus decreases to a value compatible with the type II methane clathrate hydrate composition. Finally, a reordering process of solvated methane and water molecules occurs in a manner consistent with the "blob" hypothesis (Jacobson, L. C.; Hujo, W.; Molinero, V. J Am. Chem. Soc. 2010, 132, 11806-11811).

The formation of methane-hydrate precursors at large planar water-methane interfaces has been studied using massively parallel molecular dynamics in systems of varying size from around 10 000 to almost 7 x 10(6) molecules. This process took two distinct steps. First, the concentration of solvated methane clusters increases just inside the aqueous domain via slow diffusion from the methane-water interface, forming "clusters" of solvated methane molecules. Second, the re-ordering process of solvated methane and water molecules takes place in a manner very roughly consistent with the "blob" hypothesis, although with important differences, to form hydrate precursors, necessary for subsequent hydrate nucleation and crystallisation. It was found that larger system sizes serve to promote the formation rate of precursors. (C) 2014 AIP Publishing LLC.

In this study, the immersed boundary-thermal lattice Boltzmann method has been used to simulate non-Newtonian fluid flow over a heated circular cylinder. The direct-forcing algorithm has been employed to couple the off-lattice obstacles and on-lattice fluid nodes. To investigate the effect of boundary sharpness, two different diffuse interface schemes are considered to interpolate the velocity and temperature between the boundary and computational grid points. The lattice Boltzmann equation with split-forcing term is applied to consider the effects of the discrete lattice and the body force to the momentum flux, simultaneously. A method for calculating the Nusselt number based on diffuse interface schemes is developed. The rheological and thermal properties of non-Newtonian fluids are investigated under the different power-law indices and Reynolds numbers. The effect of numerical parameters on the accuracy of the proposed method has been investigated in detail. Results show that the rheological and thermal properties of non-Newtonian fluids in the presence of a heated immersed body can be suitably captured using the immersed boundary thermal lattice Boltzmann method.

The ESA-ESRIN contract no. 21719/08/I-OL covered the activities performed between April 2008 and July 2014 by the L2 sub-group of the MIPAS Quality Working Group. The main objective of this project was to monitor the quality of MIPAS L2 products, to improve the performances of the L2 ESA processor, used for both the near real time analysis during ENVISAT mission and for the off-line analysis, and to enlarge the list of retrieved species. In particular, three different versions of the MIPAS operational processor were finalized: IPF V5, ML2PP V6 and ML2PP V7, leading to significant improvements in the quality of the products and in their diagnostics, to an increase of the number of processed scans, and to an enlargement of the list of provided products. With respect to IPF V4.1&2, used to process only the first two years of MIPAS measurements (2002-2004, Full Resolution (FR) measurements) and validated with respect to correlative measurements (Ridolfi et al., 2006, Cortesi et al., 2007, Wang et al., 2007, Payan et al., 2009, Wetzel et al., 2007, Wetzel et al., 2013, all contained in the MIPAS special issue), IPF V5: o performs the analysis of the full mission (both FR and Optimized Resolution (OR) measurements, characterized by a reduced spectral resolution but finer spatial resolution) after the introduction of an a posteriori regularization with self-adapting threshold aimed to reduce instabilities of the retrieval with measurements of the OR phase (due to sampling intervals finer than the instantaneous field of view of the instrument and the choice of using a retrieval grid aligned with the vertical sampling of the measurements); o provides as output Averaging Kernel (AK) for each scan. Products of ML2PP V6 are very similar to the ones of V5 in terms of bias, but are characterized by: o an improved diagnostics, since the Covariance Matrix and the AK matrix are computed taking into account all iterations performed during the retrieval (this is needed if the final Marquardt parameter is different from zero). Furthermore, horizontal AKs are provided for each latitude band and each season. o additional four new species, namely CFC-11, CFC-12, N2O5 and ClONO2. MIPAS ESA processor products V7 are characterized by: o reduced time dependent calibration error due to non-linearities (coming from using new L1 data, V7); o availability of retrieval altitude grid characterized by a very small bias after correction with ECMWF pressure/altitude relationship; o new microwindows for FR measurements with an increased information content and leading to a reduction of the detected bias in the FR measurements for CH4, N2O and CFC-12; o larger stability, given by the new approach for retrieving continuum (the continuum transmission is fitted instead of the continuum cross-section), and new regularization with altitude dependent regularization strength; o lower bias of CFC-11, due to proper handling of COCl2 interfering species in the retrieval o better representation of the measurements, proven by the fact that a smaller chi-square is obtained for most of the species; o better handling of diurnally varying interfering species, coming from the use of diurnally varying Initial Guess profiles; o products of five new species (HCFC-22, CFC-14, COF2, CCl4 and HCN) available. Concerning V7 products, preliminary verifications have been performed only on the diagnostic dataset V7, including more than 4000 orbits: the Non-Linearity correction performed in the L1 files introduces a drift in V7 profiles with respect to previous versions, that corrects for the instrumental drift present in previous datasets. Some problems have also been identified: V7 FR Temperature profiles in polar and midlatitude regions presents a negative bias of about 0.5-1K with respect to both V6 products and correlative measurements coming from the Non-Linearity correction. In the tropics in general V7 Temperature has a positive bias with respect to previous versions, for both FR and OR measurements, and this seems to come from the new approach for handling continuum. A new version of the spectroscopic database has been finalized, with improvements in H2O, HNO3, COCl2 and C3H8. The new version of the spectroscopic database will be used for the final reprocessing of the whole MIPAS mission in the frame of the subsequent contract. A large effort was spent for improving the quality of the MIPAS L2 products, but further improvements have been identified as needed to reduce some systematic errors of the products and to fully exploit the information contained in MIPAS measurements. One of the main problems identified so far is the error due to the horizontal inhomogeneities that are not currently taken into account by the algorithm. The quality of the retrieval is affected by the horizontal gradients but from the analysis of single scans no enough information is contained in the measurements to retrieve the gradients. Considering that the code will be used only for a reanalysis, the choice has been to take advantage of the information on horizontal gradients of both temperature and target species from previous reprocessing or ECMWF reanalysis and to modify the forward model in order to handle the externally provided gradients. Another important objective is the full exploitation of MIPAS measurements that implies the retrieval of weaker and weaker species, whose interference from other species cannot be disentangled. To this purpose the possibility of performing a multi-target retrieval is crucial. Furthermore, we have to consider that the vertical profile retrieval of weak species requires the use of some constraint for the attainment of a fast and useful product and it can be useful to have the possibility of tuning or removing it as needed during the average procedure. To this purpose Optimal Estimation seems to be more apt than the current approach where the constraint is determined with a self-consistent method, difficult to rebuild. For very weak species a posteriori averages of retrieved profiles after removing a priori constrain, as studied in the frame of this project, can be also considered. Validation of ML2PP V7 and further investigations aimed to solve these open issues will be completed in the frame of the subsequent contract.

We prove a dimension-invariant imbedding estimate for Sobolev spaces of first order into a small Lebesgue space, and we establish the optimality of its fundamental function. Namely, for any 1 < p < ?, the inequality with a constant c_p, related to the imbedding of W_0^{1,p}(B_n) into Y_p(0,1), where Yp(0,1) is a rearrangement-invariant Banach function space independent of the dimension n, B_n is the ball in R^n of measure 1 and c_p is a constant independent of n, is satisfied by the small Lebesgue space L(p,p? /2 (0, 1). Moreover, we show that the smallest space Yp (0, 1) (in the sense of the continuous imbedding) such that (*) is true has the fundamental function equivalent to that of L(p,p?/2(0,1). As a byproduct of our results, we get that the space Lp (log L)p/2 is optimal in the framework of the Orlicz spaces satisfying the imbedding inequality.

Gene expression data from high-throughput assays, such as microarray, are often used to predict cancer survival. However, available datasets consist of a small number of samples (n patients) and a large number of gene expression data (p predictors). Therefore, the main challenge is to cope with the high-dimensionality. Moreover, genes are co-regulated and their expression levels are expected to be highly correlated. In order to face these two issues, network based approaches have been proposed. In our analysis, we compare four network penalized Cox models for high-dimensional survival data aimed to determine pathway structures and biomarkers involved in cancer progression. Using these network-based models, it is possible to obtain a deeper understanding of the gene-regulatory networks and investigate the gene signatures related to the cancer survival time. We evaluate cancer survival prediction to illustrate the benefits and drawbacks of the network techniques and to understand how patient features (i.e. age, gender and coexisting diseases-comorbidity) can influence cancer treatment, detection and outcome. In particular, we show results obtained in simulation and real cancer datasets using the Functional Linkage network, as network prior information.

A hydro-kinetic scheme for water-like fluids, based on a lattice version of the Boltzmann equation, is presented and applied to the popular TIP3P model of liquid water. By proceeding in much larger steps than molecular dynamics, the scheme proves to be very effective in attaining global minima of classical pair potentials with directional and radial interactions, as confirmed by further simulations using the three-dimensional Ben-Naim water potential. The scheme is shown to reproduce the propensity of water to form nearly four hydrogen bonds per molecule, as well as their statistical distribution in the presence of thermal fluctuations, at a linear cost of computational time with the system size. This journal is © the Partner Organisations 2014.

We review recent advances on the mesoscopic modeling of water-like fluids, based on the lattice Boltzmann (LB) methodology. The main idea is to enrich the basic LB (hydro)-dynamics with angular degrees of freedom responding to suitable directional potentials between water-like molecules. The model is shown to reproduce some microscopic features of liquid water, such as an average number of hydrogen bonds per molecules (HBs) between 3 and 4, as well as a qualitatively correct statistics of the hydrogen bond angle as a function of the temperature. Future developments, based on the coupling the present water-like LB model with the dynamics of suspended bodies, such as biopolymers, may open new angles of attack to the simulation of complex biofluidic problems, such as protein folding and aggregation, and the motion of large biomolecules in complex cellular environments.

We discuss the steps needed to introduce the horizontal gradients in a MTR ORM

Cloud computing offers unprecedented ways to split and offload the workload of parallel algorithms to remote computing nodes. However, such remote parties can potentially misbehave, for instance by providing fake computation results in order to save resources. In turn, these erroneous partial results can affect the timeliness and correctness of the overall outcome of the algorithm. The widely successful cloud approach increases the economic feasibility of leveraging computational redundancy to enforce some degree of assurance about the results. However, naïve solutions that dumbly replicate the same computation over several sets of nodes are not cost-efficient. In this paper, we provide several contributions as for the distribution of workload over (heterogeneous) cloud nodes. In particular, we first formalize the problem of computing a parallel function over a set of nodes; later, we introduce CheR (for Cheating Resilience), a novel approach based upon modelling the assignment of input elements to cloud nodes as a linear integer programming problem aimed at minimizing cost while being resilient against misbehaving nodes. Further, we describe the CheR approach in different scenarios and highlight the novelty with respect to other state-of-the-art solutions. Finally, we present and discuss some experimental results showing the viability and quality of our proposal. © 2014 Springer International Publishing Switzerland.

The use of population dynamics models is essential to provide assessment of the fish abundance and advice on management and strategies for the fisheries. The stock-recruitment curve define the relationship between the spawning stock and the subsequent recruitment, describing nature's regulation of population size, whether or not the populations are being exploited. The two classical relations, established by Ricker and Shepherd, are: R (S) = b1S e-b2S , b1, b2 > 0 (4) R (S) = S b1 + b2Sb3 , b1, b2, b3 > 0 where S is the spawning stock and R is the recruitment, i.e. the amount of offspring coming in the fishing exploitable phase. We present a mathematical model for studying the evolution of an age-structured population living in a bounded domain Ohm ? R. Under suitable assumptions, which are biologically consistent, we prove the well posedness of the system, using a semigroup approach. Numerical methods for the approximation of the solution are under development. This is joint work with Gabriela Marinoschi from Institute of Mathematical Statistics and Applied Mathematics, Romanian Academy, Buchare

Performance of N-ary classification testing (expanding binary false positive/negative, true positive/negative)

This paper aims at building a variational approach to the dynamics of discrete topological singularities in two dimensions, based on I"-convergence. We consider discrete systems, described by scalar functions defined on a square lattice and governed by periodic interaction potentials. Our main motivation comes from XY spin systems, described by the phase parameter, and screw dislocations, described by the displacement function. For these systems, we introduce a discrete notion of vorticity. As the lattice spacing tends to zero we derive the first order I"-limit of the free energy which is referred to as renormalized energy and describes the interaction of vortices. As a byproduct of this analysis, we show that such systems exhibit increasingly many metastable configurations of singularities. Therefore, we propose a variational approach to the depinning and dynamics of discrete vortices, based on minimizing movements. We show that, letting first the lattice spacing and then the time step of the minimizing movements tend to zero, the vortices move according with the gradient flow of the renormalized energy, as in the continuous Ginzburg-Landau framework.

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Methods: Twenty-five infants were recruited and classified as good and non-/low-responders according to serological test results. Whole genome DNA methylation states were profiled by Illumina HumanMethylation 450 K beadchips. Data were processed through quality and dispersion filtering and with differential methylation analysis based on a combination of average methylation differences and non-parametric statistical tests. Results were finally associated to already published transcriptomics and post-transcriptomics to gain further insight. Background: Variable responses to the Hepatitis B Virus (HBV) vaccine have recently been reported as strongly dependent on genetic causes. Yet, the details on such mechanisms of action are still unknown. In parallel, altered DNA methylation states have been uncovered as important contributors to a variety of health conditions. However, methodologies for the analysis of such high-throughput data (epigenomic), especially from the computational point of view, still lack of a gold standard, mostly due to the intrinsic statistical distribution of methylomic data i.e. binomial rather than (pseudo-) normal, which characterizes the better known transcriptomic data. We present in this article our contribution to the challenge of epigenomic data analysis with application to the variable response to the Hepatitis B virus (HBV) vaccine and its most lethal degeneration: hepatocellular carcinoma (HCC).