Large-scale lattice Boltzmann simulations of complex fluids: advances through the advent of computational grids

During the last two years the RealityGrid project has allowed us to be one of the few scientific groups involved in the development of computational grids. Since smoothly working production grids are not yet available, we have been able to substantially influence the direction of software development and grid deployment within the project. In this paper we review our results from large scale three-dimensional lattice Boltzmann simulations performed over the last two years. We describe how the proactive use of computational steering and advanced job migration and visualization techniques enabled us to do our scientific work more efficiently. The projects reported on in this paper are studies of complex fluid flows under shear or in porous media, as well as large-scale parameter searches, and studies of the self-organisation of liquid cubic mesophases. Movies are available at http://www.ica1.uni-stuttgart.de/~jens/pub/05/05-PhilTransReview.htmlComment: 18 pages, 9 figures, 4 movies available, accepted for publication in Phil. Trans. R. Soc. London Series

Minimal model of self-replicating nanocells: a physically embodied information-free scenario

The building of minimal self-reproducing systems with a physical embodiment (generically called protocells) is a great challenge, with implications for both theory and applied sciences. Although the classical view of a living protocell assumes that it includes information-carrying molecules as an essential ingredient, a dividing cell-like structure can be built from a metabolism-container coupled system, only. An example of such a system, modeled with dissipative particle dynamics, is presented here. This article demonstrates how a simple coupling between a precursor molecule and surfactant molecules forming micelles can experience a growth-division cycle in a predictable manner, and analyzes the influence of crucial parameters on this replication cycle. Implications of these results for origins of cellular life and living technology are outlined.Comment: 9 pages, 10 figure

Lattice-Boltzmann studies of fluid flow in porous media with realistic rock geometries

AbstractWe present results of lattice-Boltzmann simulations to calculate flow in realistic porous media. Two examples are given for lattice-Boltzmann simulations in two- and three-dimensional (2D and 3D) rock samples. First, we show lattice-Boltzmann simulation results of the flow in quasi-two-dimensional micromodels. The third dimension was taken into account using an effective viscous drag force. In this case, we consider a 2D micromodel of Berea sandstone. We calculate the flow field and permeability of the micromodel and find excellent agreement with Microparticle Image Velocimetry (μ-PIV) experiments. Then, we use a particle tracking algorithm to calculate the dispersion of tracer particles in the Berea geometry, using the lattice-Boltzmann flow field.Second, we use lattice-Boltzmann simulations to calculate the flow in Bentheimer sandstone. The data set used in this study was obtained using X-ray microtomography (XMT). First, we consider a single phase flow. We systematically study the effect of system size and validate Darcy’s law from the linear dependence of the flux on the body force exerted. We observe that the values of the permeability measurements as a function of porosity tend to concentrate in a narrower region of the porosity, as the system size of the computational sub-sample increases. Finally, we compute relative permeabilities for binary immiscible fluids in the XMT rock sample

Fruit maturity and antioxidant activity affecting superficial scald development in ‘Abate Fétel’ pears

Superficial scald (SS) is one of the main physiological disorders affecting postharvest of pears. Its onset is linked to oxidative processes. Antioxidant compounds such as ascorbic acid and phenolics could play a key role in preventing SS. Growing environment and fruit quality also have an influence on SS symptoms occurrence. The aim of this project is to understand the relationship between antioxidant activity, phenolic content, and development of SS in ‘Abate Fétel’ pear. Moreover, the effect on SS of fruit maturity at harvest was assessed using multivariate statistical approach. Data were collected in thirty orchards in the EmiliaRomagna region (Italy) in three seasons (2018, 2019 and 2020), and the fruit were stored in a regular atmosphere for 120 days. Antioxidant capacity was determined by 2,2diphenyl1picrylhydrazy (DPPH) method and total phenol content by FolinCiocalteau colorimetric protocol. The results showed that 340 mg of ascorbate/100 g of FW and 300 mg of gallic ac./100 g of FW at least provide good protection against SS. Multivariate analysis indicated that pulp firmness and index of absorbance difference (IAD) seem to keep low the SS occurrence, when at harvest are higher than 6.3 kg and 1.9, respectively. In conclusion, it would be possible to build a forecasting model to control SS that considers preharvest data and content of antioxidants in different orchards, to improve the postharvest management of ‘Abate Fétel’

Performance of HPV DNA testing in the follow-up after treatment of high-grade cervical lesions, adenocarcinoma in situ (AIS) and microinvasive carcinoma

BACKGROUND: Over the last two decades it has become clear that distinct types of human papillomavirus (HPV), the so-called high-risk types (hrHPV), are the major cause of cervical cancer. The hrHPV-DNA testing has shown excellent performance in several clinical applications from screening to the follow-up of conservatively treated patients. METHODS: We conducted a systematic review of the recent literature on the performance of HPV DNA testing in follow-up after treatment of high-grade cervical lesions, adenocarcinoma in situ, and microinvasive carcinoma compared to Pap smear cytology. RESULTS: Observational studies have demonstrated that the high risk hrHPV-DNA test is significantly more sensitive (95%) compared to follow-up cytology(70%) in detecting post-treatment squamous intraepithelial high-grade lesions. Moreover, in patients treated conservatively for cervical adenocarcinoma in situ, the hrHPV-DNA test is the most significant independent predictor of recurrent disease or progression to invasive cancer, and the combination of viral DNA testing and cytology reaches 90% sensitivity in detecting persistent lesions at the first follow-up visit and 100% at the second follow-up visit. The cause of microinvasive squamous cervical carcinoma is increasingly treated with conservative therapies in order to preserve fertility, and an effective strategy allowing early detection of residual or progressive disease has become more and more important in post-treatment follow-up. Primary results seem to indicate that the median time for viral clearance is relatively longer compared with patients treated for CIN and suggest a prolonged surveillance for these patients. However, the potential clinical value of HPV-DNA testing in this clinical setting needs to be confirmed by further observations. CONCLUSIONS: The excellent sensitivity, negative predictive value, and optimal reproducibility of the hrHPV DNA testing, currently is considered a powerful tool in the clinicians’ hands to better manage post-treatment follow-up either in cervical squamous lesion or in situ adenocarcinoma