This paper reports, for the first time, the computational performance of SequenceL for mesoscale simulations of large numbers of particles in a microfluidic device via the lattice-Boltzmann method. The performance of SequenceL simulations was assessed against the optimized serial and parallelized (via OpenMP directives) FORTRAN90 simulations. At present, OpenMP directives were not included in interparticle and particle-wall repulsive (steric) interaction calculations due to difficulties that arose from inter-iteration dependencies between consecutive iterations of the do-loops. SequenceL simulations, on the other hand, relied on built-in automatic parallelism. Under these conditions, numerical simulations revealed that the parallelized FORTRAN90 outran the performance of SequenceL by a factor of 2.5 or more when the number of particles was 100 or less. SequenceL, however, outran the performance of the parallelized FORTRAN90 by a factor of 1.3 when the number of particles was 300. Our results show that when the number of particles increased by 30-fold, the computational time of SequenceL simulations increased linearly by a factor of 1.5, as compared to a 3.2-fold increase in serial and a 7.7-fold increase in parallelized FORTRAN90 simulations. Considering SequenceL's efficient built-in parallelism that led to a relatively small increase in computational time with increased number of particles, it could be a promising programming language for computationally-efficient mesoscale simulations of large numbers of particles in microfluidic experiments. (C) 2016 Elsevier B.V. All rights reserved.

In this paper, an alternative approach to implement initial and boundary conditions in the lattice Boltzmann method is presented. The main idea is to approximate the nonequilibrium component of distribution functions as a third-order power series in the lattice velocities and formulate a procedure to determine boundary node distributions by using fluid variables, consistent with such an expansion. The velocity shift associated with the body force effects is included in this scheme, along with an approximation to determine the mass density in complex geometries. Different strategies based on the present scheme are developed to implement velocity and pressure conditions for arbitrarily shaped boundaries, using the D2Q9, D3Q15, D3Q19 and D3Q27 lattices, in two and three space dimensions, respectively. The proposed treatment is tested against several well-established problems, showing second-order spatial accuracy and often improved behavior as compared to various existing methods, with no appreciable computational overhead.

We revisit the integer lattice (IL) method to numerically solve the Vlasov-Poisson equations, and show that a slight variant of the method is a very easy, viable, and efficient numerical approach to study the dynamics of self-gravitating, collisionless systems. The distribution function lives in a discretized lattice phase-space, and each time-step in the simulation corresponds to a simple permutation of the lattice sites. Hence, the method is Lagrangian, conservative, and fully time-reversible. IL complements other existing methods, such as N-body/ particle mesh (computationally efficient, but affected by Monte Carlo sampling noise and two-body relaxation) and finite volume (FV) direct integration schemes (expensive, accurate but diffusive). We also present improvements to the FV scheme, using a moving-mesh approach inspired by IL, to reduce numerical diffusion and the time-step criterion. Being a direct integration scheme like FV, IL is memory limited (memory requirement for a full 3D problem scales as N-6, where N is the resolution per linear phase- space dimension). However, we describe a new technique for achieving N-4 scaling. The method offers promise for investigating the full 6D phase- space of collisionless systems of stars and dark matter.

We use highly resolved numerical simulations to study turbulent Rayleigh-Benard convection in a cell with sinusoidally rough upper and lower surfaces in two dimensions for Pr = 1 and Ra = [4 x 10(6), 3 x 10(9)]. By varying the wavelength. at a fixed amplitude, we find an optimal wavelength lambda(opt) for which the Nusselt-Rayleigh scaling relation is (Nu - 1 proportional to Ra-0.483), maximizing the heat flux. This is consistent with the upper bound of Goluskin and Doering [J. Fluid Mech. 804, 370 (2016)] who prove that Nu can grow no faster than O(Ra-1/2) as Ra -> infinity, and thus with the concept that roughness facilitates the attainment of the so-called ultimate regime. Our data nearly achieve the largest growth rate permitted by the bound. When lambda << lambda(opt) and lambda >> lambda(opt), the planar case is recovered, demonstrating how controlling the wall geometry manipulates the interaction between the boundary layers and the core flow. Finally, for each Ra, we choose the maximum Nu among all., thus optimizing over all lambda, to find Nu(opt) - 1 = 0.01xRa(0.444).

Fluid dynamics in intrinsically curved geometries is encountered in many physical systems in nature, ranging from microscopic bio-membranes all the way up to general relativity at cosmological scales. Despite the diversity of applications, all of these systems share a common feature: the free motion of particles is affected by inertial forces originating from the curvature of the embedding space. Here we reveal a fundamental process underlying fluid dynamics in curved spaces: the free motion of fluids, in the complete absence of solid walls or obstacles, exhibits loss of energy due exclusively to the intrinsic curvature of space. We find that local sources of curvature generate viscous stresses as a result of the inertial forces. The curvature-induced viscous forces are shown to cause hitherto unnoticed and yet appreciable energy dissipation, which might play a significant role for a variety of physical systems involving fluid dynamics in curved spaces.

In this work, a hybrid lattice Boltzmann method (HLBM) is proposed, where the standard lattice Boltzmann implementation based on the Bhatnagar-Gross-Krook (LBGK) approximation is combined together with an unstructured finite-volume lattice Boltzmann model. The method is constructed on an overlapping grid system, which allows the coexistence of a uniform lattice nodes spacing and a coordinate-free lattice structure. The natural adaptivity of the hybrid grid system makes the method particularly suitable to handle problems involving complex geometries. Moreover, the provided scheme ensures a high-accuracy solution near walls, given the capability of the unstructured submodel of achieving the desired level of refinement in a very flexible way. For these reasons, the HLBM represents a prospective tool for solving multiscale problems. The proposed method is here applied to the benchmark problem of a two-dimensional flow past a circular cylinder for a wide range of Reynolds numbers and its numerical performances are measured and compared with the standard LBGK ones.

Growth in static and controlled environments such as a Petri dish can be used to study the spatial population dynamics of microorganisms. However, natural populations such as marine microbes experience fluid advection and often grow up in heterogeneous environments. We investigate a generalized Fisher-Kolmogorov-Petrovsky-Piscounov (FKPP) equation describing single species population subject to a constant flow field and quenched random spatially inhomogeneous growth rates with a fertile overall growth condition. We analytically and numerically demonstrate that the non-equilibrium steady-state population density develops a flow-driven striation pattern. The striations are highly asymmetric with a longitudinal correlation length that diverges linearly with the flow speed and a transverse correlation length that approaches a finite velocity-independent value. Linear response theory is developed to study the statistics of the steady states. Theoretical predictions show excellent agreement with the numerical steady states of the generalized FKPP equation obtained from Lattice Boltzmann simulations. These findings suggest that, although the growth disorder can be spatially uncorrelated, correlated population structures with striations emerge naturally at sufficiently strong advection. (C) 2016 Elsevier B.V. All rights reserved.

A challenging task in the management of Protected Areas is the conservation of natural habitats and native endangered species through the optimization of control strategies for invasive plant or animal species, typically competing for the use of resources in a fragmented habitat [1]. We review two cases of control strategies on the wolf-wild boar populations in a Southern Italy Protected Area belonging to the Natura 2000 network [2,3]. The challenge for the regional authorities is to plan conservation policies able to maintain the population of wolves while limiting the presence of wild boars, here considered invasive because of their harmfulness on cultivated areas. The first strategy [2] considers the impact of control policies on predator-prey dynamics in fragmented habitats by simulating different dynamical scenarios theoretically analysed with the aggregation method. The key warning from the model is that a very careful combination of control - through proper planning programs - and migration processes among patches of habitats - through the existing suitable ecological corridors - must be used in order to limit the wild-boar population while preserving wolves from extinction. The second strategy has been developed to apply the Z-control approach to a generalized predator-prey system [3]. It considers the specific case of indirect control of the prey (invasive) population. The key role of the model design parameter is stressed and the critical values of the design parameter are found, delimiting the parameter range for the successful application of the Z-method. A further development is the optimization of a control strategy by taking into account the spatio-temporal data related to the control problem of an invasive species over a wide natural protected area. That approach will be applied to the Alta Murgia National Park, where a EU LIFE+ project is underway to eradicate Ailanthus altissima, included in the list of the most invasive alien plant species in Europe causing serious damages both in protected and urban areas [4]. The Alta Murgia National Park is one of the study site of an on-going H2020 project (ECOPOTENTIAL). This work has been carried out within the H2020 project `ECOPOTENTIAL: Improving Future Ecosystem Benefits Through Earth Observations', coordinated by CNR-IGG (http://www.ecopotential-project.eu). The project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 641762. Bibliography 1)Baker, C. M., Target the Source: Optimal Spatiotemporal Resource Allocation for Invasive Species Control, CONS. LETTERS, pp 1-8, 2016, doi: 10.1111/conl.12236 2)Lacitignola, D.; Diele, F.; Marangi, C., Dynamical scenarios from a two-patch predator-prey system with human control - Implications for the conservation of the wolf in the Alta Murgia National Park ECOLOGICAL MODELLING, Vol. 316, pp 28-40, 2015, doi: 10.1016/j.ecolmodel.2015.07.027 3)Lacitignola, D.; Diele, F.; Marangi, C.; Provenzale A., On the dynamics of a generalized predator-prey system with Z-type control, MATHEMATICAL BIOSCIENCES, vol. 280, pp 10-23, 2016, doi: 10.1016/j.mbs.2016.07.011 4)Casella F., Vurro M. , Ailanthus altissima (tree of heaven): Spread and harmfulness in a case-study urban area, Arboricultural Journal: The International Journal of Urban Forestry, 35(3), pp 172-181, 2013, doi: 10.1080/03071375.2013.852352

Risultati di un sondaggio sulla rivista Archimede

Atmospheric emissions of Carbon tetrachloride CCl4 are regulated by the Montreal Protocol due to its role as a strong ozone-depleting substance. The molecule has been the subject of recent increased interest as a consequence of the so called ``mystery of CCl4,'' the discrepancy between atmospheric observations and reported production and consumption. Surface measurements of CCl4 atmospheric concentrations have declined at a rate almost three times smaller than its lifetime-limited rate, suggesting persistent atmospheric emissions despite the ban. In this paper, we study CCl4 vertical and zonal distributions in the upper troposphere and lower stratosphere (including the photolytic loss region, 70-20 hPa), its trend, and its stratospheric lifetime using measurements from the Michelson Interferometer for Passive Atmospheric Sounding (MIPAS), which operated onboard the ENVISAT satellite from 2002 to 2012. Specifically, we use the MIPAS data product generated with Version 7 of the Level 2 algorithm operated by the European Space Agency.The CCl4 zonal means show features typical of long-lived species of anthropogenic origin that are destroyed primarily in the stratosphere, with larger quantities in the troposphere and a monotonic decrease with increasing altitude in the stratosphere. In the troposphere, the largest concentrations are observed at the latitudes of major industrial countries (20/50°N). The good agreement we find between MIPAS CCl4 and independent measurements from other satellite and balloon-borne remote sounders proves the reliability of the MIPAS dataset.CCl4 trends are calculated as a function of both latitude and altitude. Negative trends are found at all latitudes in the upper-troposphere / lower-stratosphere region, apart from a region in the Southern mid-latitudes between 50 and 10 hPa where the trend is positive. At the lowest altitudes sounded by MIPAS, we find trends consistent with those determined on the basis of long-term ground-based measurements. For higher altitudes, the trend shows a pronounced asymmetry between Northern and Southern Hemispheres, and the magnitude of the decline rate increases with altitude. At 50 hPa the decline is about 30-35 %/decade, close to the lifetime-limited trend.We use a simplified model assuming tracer-tracer linear correlations to determine CCl4 lifetime in the lower stratosphere. The calculation provides a global average lifetime of 46(38-60) years considering CFC-11 as the reference tracer. This value is consistent with the most recent literature result of 44(36-58) years.

We use high-resolution direct numerical simulations to study the anisotropic contents of a turbulent, statistically homogeneous flow with random transitions among multiple energy containing states. We decompose the velocity correlation functions on different sectors of the three-dimensional group of rotations, SO(3), using a high-precision quadrature. Scaling properties of anisotropic components of longitudinal and transverse velocity fluctuations are accurately measured at changing Reynolds numbers. We show that independently of the anisotropic content of the energy containing eddies, small-scale turbulent fluctuations recover isotropy and universality faster than previously reported in experimental and numerical studies. The discrepancies are ascribed to the presence of highly anisotropic contributions that have either been neglected or measured with less accuracy in the foregoing works. Furthermore, the anomalous anisotropic scaling exponents are devoid of any sign of saturation with increasing order. Our study paves the way to systematically assess persistence of anisotropy in high-Reynolds-number flows.

The Stokes drag force and the gravity force are usually sufficient to describe the behavior of sub-Kolmogorovsize (or pointlike) heavy particles in turbulence, in particular when the particle-to-fluid density ratio rho(p)/rho(integral) greater than or similar to 10(3) (with rho(p) and rho(f) the particle and fluid density, respectively). This is, in general, not the case for smaller particle-to-fluid density ratios, in particular not for rho(p)/rho(f) greater than or similar to 10(2). In that case the pressure gradient force, added mass effects, and the Basset history force also play important roles. In this study we focus on the understanding of the role of these additional forces, all of hydrodynamic origin, in the settling of particles in turbulence. In order to qualitatively elucidate the complex dynamics of such particles in homogeneous isotropic turbulence, we first focus on the case of settling of such particles in the flow field of a single vortex. After having explored this simplified case we extend our analysis to homogeneous isotropic turbulence. In general, we found that the pressure gradient force leads to a decrease in the settling velocity. This can be qualitatively understood by the fact that this force prevents the particles from sweeping out of vortices, a mechanism known as preferential sweeping which causes enhanced settling. Additionally, we found that the Basset history force can both increase and decrease the enhanced settling, depending on the particle Stokes number. Finally, the role of the nonlinear Stokes drag has been explored, confirming that it affects settling of inertial particles in turbulence, but only in a limited way for the parameter settings used in this investigation.

Vaccination is the most successful and cost-effective method to prevent infectious diseases. However, many vaccine antigens have poor in vivo immunogenic potential and need adjuvants to enhance immune response. The application of systems biology to immunity and vaccinology has yielded crucial insights about how vaccines and adjuvants work. We have previously characterized two safe and powerful delivery systems derived from non-pathogenic prokaryotic organisms: E2 and fd filamentous bacteriophage systems. They elicit an in vivo immune response inducing CD8+ T-cell responses, even in absence of adjuvants or stimuli for dendritic cells' maturation. Nonetheless, a systematic and comparative analysis of the complex gene expression network underlying such activation is missing. Therefore, we compared the transcriptomes of ex vivo isolated bone marrow-derived dendritic cells exposed to these antigen delivery systems. Significant differences emerged, especially for genes involved in innate immunity, co-stimulation, and cytokine production. Results indicate that E2 drives polarization toward the Th2 phenotype, mainly mediated by Irf4, Ccl17, and Ccr4 over-expression. Conversely, fd-scalphaDEC-205 triggers Th1 T cells' polarization through the induction of Il12b, Il12rb, Il6, and other molecules involved in its signal transduction. The data analysis was performed using RNASeqGUI, hence, addressing the increasing need of transparency and reproducibility of computational analysis.

Despite numerous important contributions, the investigation of brain connectivity with magnetoencephalography (MEG) still faces multiple challenges. One critical aspect of source-level connectivity, largely overlooked in the literature, is the putative effect of the choice of the inverse method on the subsequent cortico-cortical coupling analysis. We set out to investigate the impact of three inverse methods on source coherence detection using simulated MEG data. To this end, thousands of randomly located pairs of sources were created. Several parameters were manipulated, including inter- and intra-source correlation strength, source size and spatial configuration. The simulated pairs of sources were then used to generate sensor-level MEG measurements at varying signal-to-noise ratios (SNR). Next, the source level power and coherence maps were calculated using three methods (a) L2-Minimum-Norm Estimate (MNE), (b) Linearly Constrained Minimum Variance (LCMV) beamforming, and (c) Dynamic Imaging of Coherent Sources (DICS) beamforming. The performances of the methods were evaluated using Receiver Operating Characteristic (ROC) curves. The results indicate that beamformers perform better than MNE for coherence reconstructions if the interacting cortical sources consist of point-like sources. On the other hand, MNE provides better connectivity estimation than beamformers, if the interacting sources are simulated as extended cortical patches, where each patch consists of dipoles with identical time series (high intra-patch coherence). However, the performance of the beamformers for interacting patches improves substantially if each patch of active cortex is simulated with only partly coherent time series (partial intra-patch coherence). These results demonstrate that the choice of the inverse method impacts the results of MEG source-space coherence analysis, and that the optimal choice of the inverse solution depends on the spatial and synchronization profile of the interacting cortical sources. The insights revealed here can guide method selection and help improve data interpretation regarding MEG connectivity estimation.

We study the conformational freedom of a protein made by two rigid domains connected by a flexible linker. The conformational freedom is represented as an unknown probability distribution on the space of allowed states. A new algorithm for the calculation of the maximum allowable probability is proposed, which can be extended to any type of measurements. In this paper we use pseudo contact shifts and residual dipolar coupling. We reconstruct a single central tendency in the distribution and discuss in depth the results.

In this paper, we propose a new mathematical model describing the effect of phosphocitrate (PC) on sodium sulphate crystallization inside bricks. This model describes salt and water transport, and crystal formation in a one dimensional symmetry. This is a preliminary study that takes into account mathematically the effects of inhibitors inside a porous stone. To this aim, we introduce two model parameters: the crystallization rate coefficient, which depends on the nucleation rate, and the specific volume of precipitated salt. These two parameters are determined by numerical fitting of our model for both the case of the brick treated with PC and non treated one.

A notion of "2D well-balanced" for drift-diffusion is proposed. Exactness at steady-state, typical in 1D, is weakened by aliasing errors when deriving "truly 2D" numerical fluxes from local Green's function. A main ingredient for proving that such a property holds is the optimality of the trapezoidal rule for periodic functions. In accordance with practical evidence, a "Bessel scheme" previously introduced in [SIAM J. Numer. Anal. 56 (2018), pp. 2845-2870] is shown to be "2D well-balanced" (along with former algorithms known as "discrete weighted means" or "tailored schemes". Some L-2 stability estimates are established, too.

Systems medicine holds many promises, but has so far provided only a limited number of proofs of principle. To address this road block, possible barriers and challenges of translating systems medicine into clinical practice need to be identified and addressed. The members of the European Cooperation in Science and Technology (COST) Action CA15120 Open Multiscale Systems Medicine (OpenMultiMed) wish to engage the scientific community of systems medicine and multiscale modelling, data science and computing, to provide their feedback in a structured manner. This will result in follow-up white papers and open access resources to accelerate the clinical translation of systems medicine.

This poster describes some activities developed by CNR and its third party within EoCoE

Lower tropospheric ozone (O3) retrievals from nadir sounders is challenging due to the lack of vertical sensitivity of the measurements and towards the lowest layers. If improvements have been made during the last decade, it is still important to explore possibilities to improve the retrieval algorithms themselves. O3 retrieval from nadir satellite observations is an ill-conditioned problem, which requires regularization using constraint matrices. Up to now, most of the retrieval algorithms rely on a fixed constraint. The constraint is determined and fixed beforehand, on the basis of sensitivity tests. This does not allow ones to take advantage of the entire capabilities of the satellite measurements, which vary with the thermal conditions of the observed scenes. To overcome this limitation, we developed a self-adapting and altitude-dependent regularization scheme. A crucial step is the choice of the strength of the constraint. This choice is done during an iterative process and depends on the measurement errors and on the sensitivity of the measurements to the target parameters at the different altitudes. The challenge is to limit the use of a priori constraints to the minimal amount needed to perform the inversion. The algorithm has been tested on synthetic observations matching the future IASI-NG satellite instrument. IASI-NG measurements are simulated on the basis of O3 concentrations taken from an atmospheric model and retrieved using two retrieval schemes (the standard and self-adapting ones). Comparison of the results shows that the sensitivity of the observations to the O3 amount in the lowest layers (given by the degrees of freedom for the solution) is increased, which allows a better description of the ozone distribution, especially in the case of large ozone plumes. Biases are reduced and the spatial correlation is improved. Tentative of application to real observations from IASI, currently onboard the Metop satellite will also be presented.