Advances in geometrical parametrization and reduced order models and methods for computational fluid dynamics problems in applied sciences and engineering: Overview and perspectives

Several problems in applied sciences and engineering require reduction techniques in order to allow computational tools to be employed in the daily practice, especially in iterative procedures such as optimization or sensitivity analysis. Reduced order methods need to face increasingly complex problems in computational mechanics, especially into a multiphysics setting. Several issues should be faced: stability of the approximation, efficient treatment of nonlinearities, uniqueness or possible bifurcations of the state solutions, proper coupling between fields, as well as offline-online computing, computational savings and certification of errors as measure of accuracy. Moreover, efficient geometrical parametrization techniques should be devised to efficiently face shape optimization problems, as well as shape reconstruction and shape assimilation problems. A related aspect deals with the management of parametrized interfaces in multiphysics problems, such as fluid-structure interaction problems, and also a domain decomposition based approach for complex parametrized networks. We present some illustrative industrial and biomedical problems as examples of recent advances on methodological developments

Breakdown rates and macroinvertebrate colonisation of alder (Alnus glutinosa) leaves in an acid lake (Lake Orta, N Italy), before, during and after a liming intervention

To test the effectiveness of the liming intervention on Lake Orta, the speed of leaves decay and of colonisation processes by macrobenthonic fauna were studied on alder leaves (Alnus glutinosa) placed on the bottom of the lake and recovered after appropriate time intervals. Experiments were performed at two sites (North and South) and two depths (-3 and –18 m), during three successive winters: 1988-1989 (pre-liming), 1989-1990 (liming), 1990-1991 (post-liming). Two main results emerged: 1) alder leaves, which are known to have a medium to high decaying speed in a number of aquatic environments, behave in Lake Orta as a low speed species. Decaying processes in the three years are significantly different only in station N3, where the mean breakdown rate in 1988- 1989 is more than twice that measured in the two subsequent winters. 2) The species richness of colonising benthic fauna is low: the community is made up almost exclusively of Chironomidae, which form 70 to 100% of the whole population; among them, the genus Phenopsectra is always present, while Tanytarsus was collected only during the first year and in the less deep sampling sites. The mean population abundances were higher before liming

Modelling micropollutant cycle in Lake Como in a winter scenario: Implications for water use and reuse, ecosystem services, and the EU zero pollution action plan

The fate and effects of 42 pharmaceuticals was studied in Lake Como (Italy), in wastewater treatment plants delivering water to the lake, in two rivers and in potable water obtained from lake water. Lake Como is one of the deepest and largest lakes in Northern Italy, serving important ecosystem services (i.e., drinking water, recreational, industrial, irrigation uses), some of which are currently at risk giving the current water scarcity and climate change scenarios. The highest concentrations measured in lake water were those of diclofenac, followed by carbamazepine, its metabolite, and clarithromycin. The data measured allowed to calibrate and run a fugacity-based lake model, which showed that the most important chemical load generally comes from the advective water from the north of the lake, rather than from the direct wastewater treatment plant (WWTP) discharges. This indicates that only an important reduction of chemical discharge (reduced use or extensive treatment) at a drainage basin level could significantly reduce concentrations in water. This has strong implications on how to implement the EU zero pollution action plan to significantly improve water ecosystem and human health protection

Driver mutations (JAK2V617F, MPLW515L/K or CALR), pentraxin-3 and C-reactive protein in essential thrombocythemia and polycythemia vera

BACKGROUND: The driver mutations JAK2V617F, MPLW515L/K and CALR influence disease phenotype of myeloproliferative neoplasms (MPNs) and might sustain a condition of chronic inflammation. Pentraxin 3 (PTX3) and high-sensitivity C-reactive protein (hs-CRP) are inflammatory biomarkers potentially useful for refining prognostic classification of MPNs. METHODS: We evaluated 305 with essential thrombocythemia (ET) and 172 polycythemia vera (PV) patients diagnosed according to the 2016 WHO criteria and with full molecular characterization for driver mutations. RESULTS: PTX3 levels were significantly increased in carriers of homozygous JAK2V617F mutation compared to all the other genotypes and triple negative ET patients, while hs-CRP levels were independent of the mutational profile. The risk of haematological evolution and death from any cause was about 2- and 1.5-fold increased in individuals with high PTX-3 levels, while the thrombosis rate tended to be lower. High hs-CRP levels were associated with risk of haematological evolution, death and also major thrombosis. After sequential adjustment for potential confounders (age, gender, diagnosis and treatments) and the presence of JAK2V617F homozygous status, high hs-CRP levels remained significant for all outcomes, while JAK2V617F homozygous status as well as treatments were the factors independently accounting for adverse outcomes among patients with high PTX3 levels. CONCLUSIONS: These results provide evidence that JAK2V617F mutation influences MPN-associated inflammation with a strong correlation between allele burden and PTX3 levels. Plasma levels of hs-CRP and PTX3 might be of prognostic value for patients with ET and PV, but their validation in future prospective studies is needed

Free-form deformation, mesh morphing and reduced-order methods: enablers for efficient aerodynamic shape optimisation

The work provides an integrated pipeline for the model order reduction of turbulent flows around parametrised geometries in aerodynamics. In particular, Free-Form Deformation is applied for geometry parametrisation, whereas two different reduced-order models based on Proper Orthogonal Decomposition (POD) are employed in order to speed-up the full-order simulations: the first method exploits POD with interpolation, while the second one is based on domain decomposition. For the sampling of the parameter space, we adopt a Greedy strategy coupled with Constrained Centroidal Voronoi Tessellations, in order to guarantee a good compromise between space exploration and exploitation. The proposed framework is tested on an industrially relevant application, i.e. the front-bumper morphing of the DrivAer car model, using the finite-volume method for the full-order resolution of the Reynolds-Averaged Navier-Stokes equations

Pilot scale validation campaign of gel dosimetry for pre-treatment quality assurance in stereotactic radiotherapy

Purpose: Complex stereotactic radiotherapy treatment plans require prior verification. A gel dosimetry system was developed and tested to serve as a high-resolution 3D dosimeter for Quality Assurance (QA) purposes.Materials and Methods: A modified version of a polyacrylamide polymer gel dosimeter based on chemical response inhibition was employed. Different sample geometries (cuvettes and phantoms) were manufactured for calibration and QA acquisitions. Irradiations were performed with a Varian Trilogy linac, and analyses of irradiated gel dosimeters were performed via MRI with a 1.5 T Philips Achieva at 1 mm3 or 2 mm3 isotropic spatial resolution. To assess reliability of polymer gel data, 54 stereotactic clinical treatment plans were delivered both on dosimetric gel phantoms and on the Delta4 dosimeter. Results from the two devices were evaluated through a global gamma index over a range of acceptance criteria and compared with each other.Results: A quantitative and tunable control of dosimetric gel response sensitivity was achieved through chemical inhibition. An optimized MRI analysis protocol allowed to acquire high resolution phantom dose data in time -frames of approximate to 1 h. Conversion of gel dosimeter data into absorbed dose was achieved through internal calibration. Polymer gel dosimeters (2 mm3 resolution) and Delta4 presented an agreement within 4.8 % and 2.7 % at the 3 %/1 mm and 2 %/2 mm gamma criteria, respectively.Conclusions: Gel dosimeters appear as promising tools for high resolution 3D QA. Added complexity of the gel dosimetry protocol may be justifiable in case of small target volumes and steep dose gradients

Driver mutations (JAK2V617F, MPLW515L/K or CALR), pentraxin-3 and C-reactive protein in essential thrombocythemia and polycythemia vera

Background: The driver mutations JAK2V617F, MPLW515L/K and CALR influence disease phenotype of myeloproliferative neoplasms (MPNs) and might sustain a condition of chronic inflammation. Pentraxin 3 (PTX3) and high-sensitivity C-reactive protein (hs-CRP) are inflammatory biomarkers potentially useful for refining prognostic classification of MPNs. Methods: We evaluated 305 with essential thrombocythemia (ET) and 172 polycythemia vera (PV) patients diagnosed according to the 2016 WHO criteria and with full molecular characterization for driver mutations. Results: PTX3 levels were significantly increased in carriers of homozygous JAK2V617F mutation compared to all the other genotypes and triple negative ET patients, while hs-CRP levels were independent of the mutational profile. The risk of haematological evolution and death from any cause was about 2- and 1.5-fold increased in individuals with high PTX-3 levels, while the thrombosis rate tended to be lower. High hs-CRP levels were associated with risk of haematological evolution, death and also major thrombosis. After sequential adjustment for potential confounders (age, gender, diagnosis and treatments) and the presence of JAK2V617F homozygous status, high hs-CRP levels remained significant for all outcomes, while JAK2V617F homozygous status as well as treatments were the factors independently accounting for adverse outcomes among patients with high PTX3 levels. Conclusions: These results provide evidence that JAK2V617F mutation influences MPN-associated inflammation with a strong correlation between allele burden and PTX3 levels. Plasma levels of hs-CRP and PTX3 might be of prognostic value for patients with ET and PV, but their validation in future prospective studies is needed

Dimension reduction in heterogeneous parametric spaces with application to naval engineering shape design problems

We present the results of the first application in the naval architecture field of a methodology based on active subspaces properties for parameter space reduction. The physical problem considered is the one of the simulation of the hydrodynamic flow past the hull of a ship advancing in calm water. Such problem is extremely relevant at the preliminary stages of the ship design, when several flow simulations are typically carried out by the engineers to assess the dependence of the hull total resistance on the geometrical parameters of the hull, and others related with flows and hull properties. Given the high number of geometric and physical parameters which might affect the total ship drag, the main idea of this work is to employ the active subspaces properties to identify possible lower dimensional structures in the parameter space. Thus, a fully automated procedure has been implemented to produce several small shape perturbations of an original hull CAD geometry, in order to exploit the resulting shapes and to run high fidelity flow simulations with different structural and physical parameters as well, and then collect data for the active subspaces analysis. The free form deformation procedure used to morph the hull shapes, the high fidelity solver based on potential flow theory with fully nonlinear free surface treatment, and the active subspaces analysis tool employed in this work have all been developed and integrated within SISSA mathLab as open source tools. The contribution will also discuss several details of the implementation of such tools, as well as the results of their application to the selected target engineering problem

Involvement of MAF/SPP1 axis in the development of bone marrow fibrosis in PMF patients

Primary myelofibrosis (PMF) is a myeloproliferative neoplasm characterized by hyperplastic megakaryopoiesis and myelofibrosis. We recently described the upregulation of MAF (v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog) in PMF CD34+ hematopoietic progenitor cells (HPCs) compared to healthy donor. Here we demonstrated that MAF is also upregulated in PMF compared with the essential thrombocytemia (ET) and polycytemia vera (PV) HPCs. MAF overexpression and knockdown experiments shed some light into the role of MAF in PMF pathogenesis, by demonstrating that MAF favors the megakaryocyte and monocyte/macrophage commitment of HPCs and leads to the increased expression of proinflammatory and profibrotic mediators. Among them, we focused our further studies on SPP1 and LGALS3. We assessed SPP1 and LGALS3 protein levels in 115 PMF, 47 ET and 24 PV patients plasma samples and we found that SPP1 plasma levels are significantly higher in PMF compared with ET and PV patients. Furthermore, in vitro assays demonstrated that SPP1 promotes fibroblasts and mesenchymal stromal cells proliferation and collagen production. Strikingly, clinical correlation analyses uncovered that higher SPP1 plasma levels in PMF patients correlate with a more severe fibrosis degree and a shorter overall survival. Collectively our data unveil that MAF overexpression contributes to PMF pathogenesis by driving the deranged production of the profibrotic mediator SPP1