Editorial Introduction of a special issue

In this paper an in silico study of the behavior of an active polar emulsion is reported, focusing on the case of a highly off-symmetric ratio between the polar (active) and passive components, both for the extensile and contractile case. In absence of activity the system is characterized by an hexatic-ordered droplets phase. We find that small extensile activity is able to enhance the hexatic order in the array of droplets with respect to the passive case, while increasing activity aster-like rotating droplets appear. In contractile systems activity creates shear flows and elongated structures are formed.

This paper considers a hub location problem where several carriers operate on a shared network to satisfy a given demand represented by a set of commodities. Possible cooperative strategies are studied where carriers can share resources or swap their respective commodities to produce tangible cost savings while fully satisfying the existing demand. Three different collaborative policies are introduced and discussed, and mixed integer programming formulations are provided for each of them. Theoretical analyses are developed in order to assess the potential savings of each model with respect to traditional non-collaborative approaches. An empirical performance comparison on state-of-art sets of instances offers a complementary viewpoint. The influence of several diverse problem parameters on the performance is analyzed to identify those operational settings enabling the highest possible savings for the considered collaborative hub location models. The number of carriers and the number of open hubs have shown to play a key role; depending on the collaborative strategy, savings of up to 50% can be obtained as the number of carriers increases or the number of open hubs decreases.

The exploration and analysis of Web graphs has flourished in the recent past, producing a large number of relevant and interesting research results. However, the unique characteristics of the Tor network demand for specific algorithms to explore and analyze it. Tor is an anonymity network that allows offering and accessing various Internet resources while guaranteeing a high degree of provider and user anonymity. So far the attention of the research community has focused on assessing the security of the Tor infrastructure. Most research work on the Tor network aimed at discovering protocol vulnerabilities to de-anonymize users and services, while little or no information is available about the topology of the Tor Web graph or the relationship between pages' content and topological structure. With our work we aim at addressing such lack of information. We describe the topology of the Tor Web graph measuring both global and local properties by means of well-known metrics that require due to the size of the network, high performance algorithms. We consider three different snapshots obtained by extensively crawling Tor three times over a 5 months time frame. Finally we present a correlation analysis of pages' semantics and topology, discussing novel insights about the Tor Web organization and its content. Our findings show that the Tor graph presents some of the character- istics of social and surface web graphs, along with a few unique peculiarities.

Morphometric, biochemical and genetic analyses were conducted on Olea europaea L. of Campania, an area of Southern Italy highly suited to the cultivation of olive trees and the production of extra virgin olive oil (EVOO). We aimed to characterize the distribution of morphological, biochemical and genetic diversity in this area and to develop a practical tool to aid traceability of oils. Phenotypes were characterized using morphometric data of drupes and leaves; biochemical and genetic diversity were assessed on the basis of the fatty acid composition of the EVOOs and with microsatellite markers, respectively. We provide an open-source tool as a novel R package titled 'OliveR', useful in performing multivariate data analysis using a point and click interactive approach. These analyses highlight a clear correlation among the morphological, biochemical and genetic profiles of samples with four collection sites, and confirm that Southern Italy represents a wide reservoir of phenotypic and genetic variability.

In this paper, we deal with a group variable in size of pedestrians moving in a unknown confined environment and searching for an exit. Pedestrian dynamics are simulated by means of a recently introduced microscopic (agent-based) model, characterized by an exploration phase and an egress phase. First, we study the model to reveal the role of its main parameters and its qualitative properties. Second, we tackle a robust optimization problem by means of the Particle Swarm Optimization method, aiming at reducing the time-to-target by adding in the walking area multiple obstacles optimally placed and shaped. Robustness is sought against the number of people in the group, which is an uncertain quantity described by a random variable with given probability density distribution.

We review the state of the art of active fluids with particular attention to hydrodynamic continuous models and to the use of Lattice Boltzmann Methods (LBM) in this field. We present the thermodynamics of active fluids, in terms of liquid crystals modelling adapted to describe large-scale organization of active systems, as well as other effective phenomenological models. We discuss how LBM can be implemented to solve the hydrodynamics of active matter, starting from the case of a simple fluid, for which we explicitly recover the continuous equations by means of Chapman-Enskog expansion. Going beyond this simple case, we summarize how LBM can be used to treat complex and active fluids. We then review recent developments concerning some relevant topics in active matter that have been studied by means of LBM: spontaneous flow, self-propelled droplets, active emulsions, rheology, active turbulence, and active colloids.

In some important biological phenomena Volterra integral and integrodifferential equations represent an appropriate mathematical model for the description of the dynamics involved (see e.g. [1], and the bibliography therein). In most cases, the kernels of these equations are of convolution type, however, some recent applications, as cell migration and collective motion [4-5], are characterized by kernels with a quasi-convolution form, namely involving a convolution contribution plus a non-convolution term. We focus on problems of this type and exploit some known results about convolution equations [2, 3], in order to describe the asymptotic dynamics of numerical approximations and connect the results to the behaviour of the analytical solution

Purpose: Beckwith-Wiedemann syndrome (BWS) is a developmental disorder caused by dysregulation of the imprinted gene cluster of chromosome 11p15.5 and often associated with loss of methylation (LOM) of the imprinting center 2 (IC2) located in KCNQ1 intron 10. To unravel the etiological mechanisms underlying these epimutations, we searched for genetic variants associated with IC2 LOM. Methods: We looked for cases showing the clinical features of both BWS and long QT syndrome (LQTS), which is often associated with KCNQ1 variants. Pathogenic variants were identified by genomic analysis and targeted sequencing. Functional experiments were performed to link these pathogenic variants to the imprinting defect. Results: We found three rare cases in which complete IC2 LOM is associated with maternal transmission of KCNQ1 variants, two of which were demonstrated to affect KCNQ1 transcription upstream of IC2. As a consequence of KCNQ1 haploinsufficiency, these variants also cause LQTS on both maternal and paternal transmission. Conclusion: These results are consistent with the hypothesis that, similar to what has been demonstrated in mouse, lack of transcription across IC2 results in failure of methylation establishment in the female germline and BWS later in development, and also suggest a new link between LQTS and BWS that is important for genetic counseling.

We investigate the dynamics of a phase-separating binary fluid, containing colloidal dumbbells anchored to the fluid-fluid interface. Extensive lattice Boltzmann-immersed boundary method simulations reveal that the presence of soft dumbbells can significantly affect the curvature dynamics of the interface between phase-separating fluids, even though the coarsening dynamics is left nearly unchanged. In addition, our results show that the curvature dynamics exhibits distinct non-local effects, which might be exploited for the design of new soft mesoscale materials. We point out that the inspection of the statistical dynamics of the curvature can disclose new insights into local inhomogeneities of the binary fluid configuration, as a function of the volume fraction and aspect ratio of the dumbbells.

We discuss the state of art of Lattice Boltzmann (LB) computing, with special focus on prospective LB schemes capable of meeting the forthcoming Exascale challenge. After reviewing the basic notions of LB computing, we discuss current techniques to improve the performance of LB codes on parallel machines and illustrate selected leading-edge applications in the Petascale range. Finally, we put forward a few ideas on how to improve the communication/computation overlap in current largescale LB simulations, as well as possible strategies towards fault-tolerant LB schemes. (C) 2019 Published by Elsevier Ltd.

Fully three-dimensional, time-dependent, direct simulations of the non-ideal Navier-Stokes equations for a two-component fluid shed light into the mechanism which inhibits droplet breakup in step emulsifiers below a critical threshold of the width-to-height (w/h) ratio of the microfluidic nozzle. Below w/h similar to 2.6, the simulations provide evidence of a smooth topological transition of the fluid from the confined rectangular channel geometry to an isotropic (spherical) expansion of the fluid downstream the nozzle step. Above such threshold, the transition from the inner to the outer space involves a series of dynamical rearrangements which keep the free surface in mechanical balance. Such rearrangements also induce a backflow of the ambient fluid which, in turn, leads to jet pinching and ultimately to its rupture, namely, droplet formation. The simulations show remarkable agreement with the experimental value of the threshold, which is found around w/h similar to 2.56. Published under license by AIP Publishing.

This article is part of the theme issue 'Multiscale modelling, simulation and computing: from the desktop to the exascale'. We outline the main ideas behind the numerical modelling of soft flowing crystals, paying special attention to their application to microfluidic devices for the design of novel mesoscale porous materials.

alpha-quartz is one of the most important SiO2 polymorphs because it is the basis of very common minerals, especially for seabed materials with geoscientific importance. The elastic characterization of these materials is particularly relevant when the properties governing phonon and sound propagation are involved. These studies are especially interesting for oil exploration purposes. Recently, we published a new method that constitutes to the best of our knowledge the first attempt to recreate longitudinal and transversal perturbations in a simulation box to observe their propagation through the crystal by means of a set of descriptors [D. Melgar et al., J. Phys. Chem. C 122, 3006-3013 (2018)]. The agreement with the experimental S- and P-wave velocities was rather excellent. Thus, an effort has been undertaken to deepen the particularities of this new methodology. Here, bearing in mind this encouraging initial methodology-development progress, we deepen our knowledge of the particularities of this new methodology in presenting a systematic investigation of the implementation of the perturbation source. This includes new ways of creating the perturbation, as well as analyzing the possible effects the perturbation amplitude could have on the resultant velocities. In addition, different force fields were tested to describe the interatomic interactions. The lack of dependence of the seismic velocities on the way the perturbation is created and the perturbation amplitude, and the good agreement with the experimental results are the main reasons that allow the definition of this new methodology as robust and reliable. These qualities are consolidated by the physical behavior of the calculated velocities in the presence of vacancies and under stress. The development of this method opens up a new line of research of calculating seismic velocities for geophysically relevant materials in a systematic way, with full control not only on the sample features (composition, porosity, vacancies, stress, etc.) but also on the particularities of perturbation itself, as well as determining optimal system-response metrics. Published under license by AIP Publishing.

Computer simulations of bi-continuous two-phase fluids with interspersed dumbbells show that, unlike rigid colloids, soft dumbbells do not lead to arrested coarsening. However, they significantly alter the curvature dynamics of the fluid-fluid interface, whose probability density distributions are shown to exhibit (i) a universal spontaneous transition (observed even in the absence of colloids) from an initial broad-shape distribution towards a highly localized one and (ii) super-diffusive dynamics with long-range effects. Both features may prove useful for the design of novel families of soft porous materials.

We present a mesoscale representation of near-contact interactions between colliding droplets which permits one to reach up to the scale of full microfluidic devices, where such droplets are produced. The method is demonstrated for the case of colliding droplets and the formation of soft flowing crystals in flow-focusing microfluidic devices. This model may open up the possibility of multiscale simulation of microfluidic devices for the production of new droplet and bubble-based mesoscale porous materials.

We present a mesoscale kinetic model for multicomponent flows, augmented with a short range forcing term, aimed at describing the combined effect of surface tension and near-contact interactions operating at the fluid interface level. Such a mesoscale approach is shown to (i) accurately capture the complex dynamics of bouncing colliding droplets for different values of the main governing parameters, (ii) predict quantitatively the effective viscosity of dense emulsions in micro-channels and (iii) simulate the formation of the so-called soft flowing crystals in microfluidic focusers.

The dynamic interaction of complex fluid interfaces is highly sensitive to near-contact interactions occurring at the scale of ten of nanometers. Such interactions are difficult to analyze because they couple self-consistently to the dynamic morphology of the evolving interface, as well as to the hydrodynamics of the interstitial fluid film. In this work, we show that, above a given magnitude threshold, near-contact interactions trigger nontrivial microvorticity patterns, which in turn affect the effective near-contact interactions, giving rise to persistent fluctuating ripples at the fluid interface. In such a regime, near-contact interactions may significantly affect the macroscopic arrangement of emulsion configurations, such as those arising in soft-flowing microfluidic crystals.

Given methane hydrates' importance in marine sediments, as well as the widespread use of seabed acoustic-signaling methods in oil and gas exploration, the elastic characterization of these materials is particularly relevant. A greater understanding of the properties governing phonon, sound, and acoustic propagation would help to better classify methane-hydrate deposits, aiding in their discovery. Recently, we have published a new nonequilibrium molecular-dynamics (NEMD) methodology to recreate longitudinal and transverse perturbations, observing their propagation through a crystalline lattice by various metrics, to study the underlying S- and P-wave velocities (achieving excellent agreement with experiment) [Melgar et al., J. Phys. Chem. 122(5), 3006-3013 (2018); ibid. 150, 084101 (2019)]. Here, we apply these NEMD methods to methane-clathrate systems to study acoustic-propagation characteristics, as well as the lattice elastic behavior. In so doing, we determine S- and P-wave velocities in excellent accord with experiment; we also ascertain the allowable magnitude range of acoustic perturbation and establish a threshold for lattice breakup and hydrate decomposition. Interestingly, upon dissociation, we observe the formation of methane nanobubbles, which agrees with previous studies on the microscopic fundamentals of hydrate dissociation by various means.

The crack density within a fault's damage zone is thought to vary as seismic rupture is approached, as well as in the postseismic period. Moreover, external stress loads, seasonal or tidal, may also change the crack density in rocks, and all such processes can leave detectable signatures on seismic attenuation. Here we show that attenuation time histories from the San Andreas Fault at Parkfield are affected by seasonal loading cycles, as well as by 1.5-3-year periodic variations of creep rates, consistent with Turner et al. (2015, https://biblioproxy.cnr.it:2481/10.1002/2015JB011998), who documented a broad spectral peak, between 1.5 and 4 years, of the spectra calculated over the activity of repeating earthquakes, and over InSAR time series. After the Parkfield main shock, we see a clear modulation between seismic attenuation correlated to tidal forces. Opposite attenuation trends are seen on the two sides of the fault up to the M6.5 2003 San Simeon earthquake, when attenuation changed discontinuously, in the same directions of the relative trends. Attenuation increased steadily of over one year on the SW side of the San Andreas Fault, until the San Simeon earthquake, whereas it decreased steadily on the NE side of the San Andreas Fault, roughly for the six months prior to the event. Random fluctuations are observed up to the 2004 M6 Parkfield main shock, when rebounds in opposite directions are observed, in which attenuation decreased on the SW side, and increased on the NE side.