Macromolecular crowding has profound effects on the mobility of proteins, with strong implications on the rates of intracellular processes. To describe the dynamics of crowded environments, detailed molecular models are needed, capturing the structures and interactions arising in the crowded system. In this work, we present OPEPv7, which is a coarse-grained force field at amino-acid resolution, suited for rigid-body simulations of the structure and dynamics of crowded solutions formed by globular proteins. Using the OPEP protein model as a starting point, we have refined the intermolecular interactions to match the experimentally observed dynamical slowdown caused by crowding. The resulting force field successfully reproduces the diffusion slowdown in homogeneous and heterogeneous protein solutions at different crowding conditions. Coupled with the lattice Boltzmann technique, it allows the study of dynamical phenomena in protein assemblies and opens the way for the in silico rheology of protein solutions.

Mucociliary clearance is the first defense mechanism of the respiratory tract against inhaled particles. This mechanism is based on the collective beating motion of cilia at the surface of epithelial cells. Impaired clearance, either caused by malfunctioning or absent cilia, or mucus defects, is a symptom of many respiratory diseases. Here, by exploiting the lattice Boltzmann particle dynamics technique, we develop a model to simulate the dynamics of multiciliated cells in a two-layer fluid. First, we tuned our model to reproduce the characteristic length- and time-scales of the cilia beating. We then check for the emergence of the metachronal wave as a consequence of hydrodynamic mediated correlations between beating cilia. Finally, we tune the viscosity of the top fluid layer to simulate the mucus flow upon cilia beating, and evaluate the pushing efficiency of a carpet of cilia. With this work, we build a realistic framework that can be used to explore several important physiological aspects of mucociliary clearance.

Polyelectrolytes can electrophoretically be driven through nanopores in order to be detected. The respective translocation events are often very fast and the process needs to be controlled to promote efficient detection. To this end, we attempt to control the translocation dynamics by coating the inner surface of a nanopore. For this, different charge distributions are chosen that result in substantial variations of the pore–polymer interactions. In addition and in view of the existing detection modalities, experimental settings, and nanopore materials, different types of sensors inside the nanopore have been considered to probe the translocation process and its temporal spread. The respective transport of polyelectrolytes through the coated nanopores is modeled through a multi-physics computational scheme that incorporates a mesoscopic/electrokinetic description for the solvent and particle-based scheme for the polymer. This investigation could underline the interplay between sensing modality, nanopore material, and detection accuracy. The electro-osmotic flow and electrophoretic motion in a pore are analyzed together with the polymeric temporal and spatial fluctuations unraveling their correlations and pathways to optimize the translocation speed and dynamics. Accordingly, this work sketches pathways in order to tune the pore–polymer interactions in order to control the translocation dynamics and, in the long run, errors in their measurements.

In this paper, the authors give a different and more precise analysis of the stability of the classical Gauss-Laguerre quadrature rule for the Cauchy P.V. integrals on the half line. Moreover, in order to obtain this result they give some new estimates for the distance of the zeros of the Laguerre polynomials that can be useful also in other contests.

In this paper we provide emission estimates due to vehicular traffic via Generic Second OrderModels. We generalize them to model road networks with merge and diverge junctions. Theprocedure consists on solving the Riemann Problem at junction assuming the maximization ofthe flow and a priority rule for the incoming roads. We provide some numerical results for asingle-lane roundabout and we propose an application of the given procedure to estimate theproduction of nitrogen oxides (NOx) emission rates. In particular, we show that the presence ofa traffic lights produces a 28% increase in the NOx emissions with respect to the roundabout.

We investigate the long-time properties of the two-dimensional inviscid Boussinesq equations near a stably stratified Couette flow, for an initial Gevrey perturbation of size ?. Under the classical Miles-Howard stability condition on the Richardson number, we prove that the system experiences a shear-buoyancy instability: the density variation and velocity undergo an O(t-1/2) inviscid damping while the vorticity and density gradient grow as O(t1/2). The result holds at least until the natural, nonlinear timescale t??-2. Notice that the density behaves very differently from a passive scalar, as can be seen from the inviscid damping and slower gradient growth. The proof relies on several ingredients: (A) a suitable symmetrization that makes the linear terms amenable to energy methods and takes into account the classical Miles-Howard spectral stability condition; (B) a variation of the Fourier time-dependent energy method introduced for the inviscid, homogeneous Couette flow problem developed on a toy model adapted to the Boussinesq equations, i.e. tracking the potential nonlinear echo chains in the symmetrized variables despite the vorticity growth.

We present a simple model describing the chemical aggression undergone by calcium carbonate rocks in presence of acid atmosphere. A large literature is available on the deterioration processes of building stones, in particular in connection with problems concerning historical buildings in the field of Cultural Heritage. It is well known that the greatest aggression is caused by sulfur dioxide and nitrate. In this paper we consider the corrosion caused by sulphur dioxide, which, reacting with calcium carbonate, produces gypsum. The model proposed is obtained by considering both the diffusive and convective effects of propagation and assuming that the porous medium is saturated with a compressible fluid having an assigned polytropic constitutive equation for the pressure. The qualitative behavior of the one dimensional solutions in the fastreaction limit is performed.

WeinvestigatethelinearstabilityofshearsneartheCouetteflowforaclassof2Dincompressible stably stratified fluids. Our main result consists of nearly optimal decay rates for perturbations of stationary states whose velocities are monotone shear flows (U (y), 0) and have an exponential density profile. In the case of the Couette flow U(y) = y, we recover the rates predicted by Hartman in 1975, by adopting an explicit point-wise approach in frequency space. As a by-product, this implies optimal decay rates as well as Lyapunov instability in L2 for the vorticity. For the previously unexplored case of more general shear flows close to Couette, the inviscid damping results follow by a weighted energy estimate. Each outcome concerning the stably stratified regime applies to the Boussinesq equations as well. Remarkably, our results hold under the celebrated Miles-Howard criterion for stratified fluids.

This paper presents a sparse factorization for the delay Vandermonde matrix (DVM) and a faster, exact, radix-2, and completely recursive DVM algorithm to realize millimeter wave beamformers in wireless communication networks. The proposed algorithm will reduce the complexity of $N$-beam wideband beamformers from $\mathcal{O}(N^2)$ to $\mathcal{O}(N {\rm\: log\:} N)$. The scaled DVM algorithm is at least 97$\%$ faster than the brute-force scale DVM by a vector product. The signal flow graphs of the scaled DVM algorithm are shown to elaborate the simplicity of the proposed algorithm. The proposed lower complexity DVM algorithm can be used to design simple signal flow graph and realize in very large scale integrated circuit architecture with the significant reduction of chip area and power consumption. Moreover, the realization of the faster DVM algorithm through analog integrated circuits will be addressed . Finally, the proposed DVM algorithm will be utilized to obtain a low-complexity approximate transform for beamforming

The PRISMA (PRecursore IperSpettrale della Missione Applicativa) hyperspectral satellite, launched by the Italian Space Agency (ASI) is presently operational on a global scale. The mission includes the hyperspectral imager PRISMA working in the 400-2500 nm spectral range with 234 bands and a panchromatic (PAN) camera (400-750 nm). In the context of this work, we intend to determine the two noise components (photon and thermal noise) and assess SNR with an image based approach. Results show that the SNR evaluation assessed through the collected images is coherent with the mission requirements and that the PRISMA noise components, derived on the fragmented Pignola test site, in Southern Italy, are comparable to the ones derived on the Rail Road Valley calibration site.

MIPAS is a Fourier Transform spectrometer that measured the atmospheric limb emission spectra in the middle infrared on board the ENVISAT satellite. These measurements allowed the global monitoring of the three-dimensional (latitude, longitude and altitude) distribution of temperature and of the concentrations of many species, during both day and night, for 10 years, from July 2002 to April 2012. MIPAS measurements allowed to study the atmosphere from the upper troposphere to the stratosphere and above, up to the thermosphere. The interest in these measurements goes beyond the end of the mission, as they can be used in long time series of data to determine changes in atmospheric composition and in our planet's climate. Furthermore, if the Changing-Atmosphere Infra-Red Tomography Explorer (CAIRT) mission, one of four candidates for Earth Explorer 11, will be selected, MIPAS data will constitute a benchmark for these measurements. CAIRT exploits indeed the heritage of MIPAS on ENVISAT, but allows to measure the composition of the atmosphere with unprecedented three-dimensional resolution being the first imaging Fourier Transform spectrometer sounding the limb of the atmosphere from space. For the last reanalysis of the whole MIPAS mission, a significant effort was made by the MIPAS Quality Working Group, supported by ESA, to improve both L1 [1] and L2 processors, as well as spectroscopy and Level 2 Initial Guess profiles [2], with the objectives of obtaining L2 products with increased accuracy, better temporal stability, and a larger number of retrieved species. The main improvements of L1 processor were related to the radiometric calibration and pointing. With these new processors a MIPAS full mission reprocessing has been recently performed ([1] and [3]). The quality of this final operational data set has been assessed with comprehensive validation studies including comparisons to ground-based in-situ and balloon-borne measurements. The dataset containing the new version 8 of both L1 and L2 products and covering the entire MIPAS operational lifetime period (2002-2012) is available at ESA Earth Online web site.This paper will focus on the lessons learnt, on the quality of the reprocessed data, on the remaining problems, and on further improvements that could improve the quality of both MIPAS L1 and L2 datasets.[1] Kleinert et al. Kleinert, A., Birk, M., Perron, G., and Wagner, G.: Level 1b error budget for MIPAS on ENVISAT, Atmos. Meas. Tech., 11, 5657-5672,https://doi.org/10.5194/amt-11-5657-2018, 2018 [2] Raspollini, P., Arnone, E., Barbara, F., Bianchini, M., Carli, B., Ceccherini, S., Chipperfield, M. P., Dehn, A., Della Fera, S., Dinelli, B. M., Dudhia, A., Flaud, J.-M., Gai, M., Kiefer, M., López-Puertas, M., Moore, D. P., Piro, A., Remedios, J. J., Ridolfi, M., Sembhi, H., Sgheri, L., and Zoppetti, N.: Level 2 processor and auxiliary data for ESA Version 8 final full mission analysis of MIPAS measurements on ENVISAT, Atmos. Meas. Tech. Discuss. [preprint], https://doi.org/10.5194/amt-2021-235, in review, 2021. [3] Dinelli, B. M., Raspollini, P., Gai, M., Sgheri, L., Ridolfi, M., Ceccherini, S., Barbara, F., Zoppetti, N., Castelli, E., Papandrea, E., Pettinari, P., Dehn, A., Dudhia, A., Kiefer, M., Piro, A., Flaud, J.-M., Lopez-Puertas, M., Moore, D., Remedios, J., and Bianchini, M.: The ESA MIPAS/ENVISAT Level2-v8 dataset: 10 years of measurements retrieved with ORM v8.22, Atmos. Meas. Tech. Discuss. [preprint], https://doi.org/10.5194/amt-2021-215, accepted, 2021.

The capability to simulate a two-way coupled interaction between a rarefied gas and an arbitrary-shaped colloidal particle is important for many practical applications, such as aerospace engineering, lung drug delivery, and semiconductor manufacturing. By means of numerical simulations based on the direct-simulation Monte Carlo (DSMC) method, we investigate the influence of the orientation of the particle and rarefaction on the drag and lift coefficients, in the case of prolate and oblate ellipsoidal particles immersed in a uniform ambient flow. This is done by modeling the solid particles using a cut-cell algorithm embedded within our DSMC solver. In this approach, the surface of the particle is described by its analytical expression and the microscopic gas-solid interactions are computed exactly using a ray-tracing technique. The measured drag and lift coefficients are used to extend the correlations, based on the sine-squared drag law, available in the continuum regime to the rarefied regime, focusing on the transitional and free-molecular regimes. The functional forms of the correlations for the ellipsoidal particles are chosen as a generalization from the spherical case. We show that the fits over the data from numerical simulations can be extended to regimes outside the simulated range of Kn. Our approach allows to achieve a higher precision when compared with existing predictive models from the literature. Finally, we underline the importance of this work in providing correlations for nonspherical particles that can be used for point-particle Euler-Lagrangian simulations to address the problem of contamination from finite-size particles in high-tech mechanical systems.

Stabilised dense emulsions display a rich phenomenology connecting microstructure and rheology. In this work, we study how an emulsion with a finite yield stress can be built via large-scale stirring. By gradually increasing the volume fraction of the dispersed minority phase, under the constant action of a stirring force, we are able to achieve a volume fraction close to 80%. Despite the fact that our system is highly concentrated and not yet turbulent we observe a droplet size distribution consistent with the -10/3 scaling, often associated with inertial range droplets breakup. We report that the polydispersity of droplet sizes correlates with the dynamics of the emulsion formation process. Additionally, we quantify the visco-elastic properties of the dense emulsion finally obtained and we demonstrate the presence of a finite yield stress. The approach reported can pave the way to a quantitative understanding of the complex interplay between the dynamics of mesoscale constituents and the large-scale flow properties of yield stress fluids.

The growth and evolution of microbial populations is often subjected to advection by fluid flows in spatially extended environments, with immediate consequences for questions of spatial population genetics in marine ecology, planktonic diversity and origin of life scenarios. Here, we review recent progress made in understanding this rich problem in the simplified setting of two competing genetic microbial strains subjected to fluid flows. As a pedagogical example we focus on antagonsim, i.e., two killer microorganism strains, each secreting toxins that impede the growth of their competitors (competitive exclusion), in the presence of stationary fluid flows. By solving two coupled reaction-diffusion equations that include advection by simple steady cellular flows composed of characteristic flow motifs in two dimensions (2D), we show how local flow shear and compressibility effects can interact with selective advantage to have a dramatic influence on genetic competition and fixation in spatially distributed populations. We analyze several 1D and 2D flow geometries including sources, sinks, vortices and saddles, and show how simple analytical models of the dynamics of the genetic interface can be used to shed light on the nucleation, coexistence and flow-driven instabilities of genetic drops. By exploiting an analogy with phase separation with nonconserved order parameters, we uncover how these genetic drops harness fluid flows for novel evolutionary strategies, even in the presence of number fluctuations, as confirmed by agent-based simulations as well.

The development of turbulence closure models, parametrizing the influence of small nonresolved scales on the dynamics of large resolved ones, is an outstanding theoretical challenge with vast applicative relevance. We present a closure, based on deep recur- rent neural networks, that quantitatively reproduces, within statistical errors, Eulerian and Lagrangian structure functions and the intermittent statistics of the energy cascade, including those of subgrid fluxes. To achieve high-order statistical accuracy, and thus a stringent statistical test, we employ shell models of turbulence. Our results encourage the development of similar approaches for three-dimensional Navier-Stokes turbulence.

By varying the oil volume fraction, the microscopic droplet size and the macroscopic rheology of emulsions are investigated in a Taylor-Couette turbulent shear flow. Although here oil and water in the emulsions have almost the same physical properties (density and viscosity), unexpectedly, we find that oil-in-water (O/W) and water-in-oil (W/O) emulsions have very distinct hydrodynamic behaviours, i.e. the system is clearly asymmetric. By looking at the micro-scales, the average droplet diameter hardly changes with the oil volume fraction for O/W or for W/O. However, for W/O it is about 50% larger than that of O/W. At the macro-scales, the effective viscosity of O/W is higher when compared to that of W/O. These asymmetric behaviours are expected to be caused by the presence of surface-active contaminants from the walls of the system. By introducing an oil-soluble surfactant at high concentration, remarkably, we recover the symmetry (droplet size and effective viscosity) between O/W and W/O emulsions. Based on this, we suggest a possible mechanism responsible for the initial asymmetry and reach conclusions on emulsions where interfaces are fully covered by the surfactant. Next, we discuss what sets the droplet size in turbulent emulsions. We uncover a -6/5 scaling dependence of the droplet size on the Reynolds number of the flow. Combining the scaling dependence and the droplet Weber number, we conclude that the droplet fragmentation, which determines the droplet size, occurs within the boundary layer and is controlled by the dynamic pressure caused by the gradient of the mean flow, as proposed by Levich (Physicochemical Hydrodynamics, Prentice-Hall, 1962), instead of the dynamic pressure due to turbulent fluctuations, as proposed by Kolmogorov (Dokl. Akad. Nauk. SSSR, vol. 66, 1949, pp. 825-828). The present findings provide an understanding of both the microscopic droplet formation and the macroscopic rheological behaviours in dynamic emulsification, and connects them.

We introduce a novel mesoscopic computational model based on a multiphase-multicomponent lattice Boltzmann method for the simulation of self-phoretic particles in the presence of liquid-liquid interfaces. Our model features fully resolved solvent hydrodynamics, and, thanks to its versatility, it can handle important aspects of the multiphysics of the problem, including particle wettability and differential solubility of the product in the two liquid phases. The method is extensively validated in simple numerical experiments, whose outcome is theoretically predictable, and then applied to the study of the behavior of active particles next to and trapped at interfaces. We show that their motion can be variously steered by tuning relevant control parameters, such as the phoretic mobilities, the contact angle, and the product solubility.

Electrostimulation is the object of the study of a variety of clinical approaches, ranging from bioelectronic medicine where the aim is to elicit the activity of the autonomic nervous system (ANS), to electroacupuncture with the general objective to restore homeostasis, to transcutaneous electrical nerve stimulation (TENS) to control pain and degeneration, to name a few. Among the numerous obstacles preventing from a clear adoption or rejection of these approaches in mainstream clinical practice, is the difficulty in standardizing experimental systems for testing and validation. Consequently, indications on the appropriate magnitude of an effective stimulus (duration, frequency, intensity) remain unclear. To approach this issue we present preliminary results on the differential molecular activity elicited in a 3D bioprinted construct containing fibroblasts and keratinocytes in a collagen matrix, by two diverse types of electrical stimulation (direct and alternate current). Two conditions, physiology and inflammation induced by TNF? perfusion were tested with anelectrobiomedical device. The system mimics a simplified model of skin, the largest and most accessible of our organs, in inflamed or physiological states, treated by electrostimulation. The bioprinted sample is constructed to yield an appropriate number of cell enabling high-throughput screens. We report here our preliminary results on RNA-seq differential expression comparing direct and alternate current stimuli, with a focus on wound healing and inflammation as part of the greater inflammatory pathway. Our construct offer reproducibility of the experience, and direct comparison among potentially numerous conditions and types of stimulation. Our preliminary results shows that electrostimulation offers differential elicitation of biological functions. In particular, direct and alternate current provoke differential activation of proliferation and development associated functions.

In this note, we consider generalizations of the Cucker-Smale dynamical system and we derive rigorously in Wasserstein's type topologies the mean-field limit (and propagation of chaos) to the Vlasov-type equation introduced in [13]. Unlike previous results on the Cucker-Smale model, our approach is not based on the empirical measures, but, using an Eulerian point of view introduced in [9] in the Hamiltonian setting, we show the limit providing explicit constants. Moreover, for non strictly Cucker-Smale particles dynamics, we also give an insight on what induces a flocking behavior of the solution to the Vlasov equation to the - unknown a priori - flocking properties of the original particle system.

Mass currents in astrophysics generate gravitomagnetic fields of enormous complexity. Gravitomagnetichelicity, in direct analogy with magnetic helicity, is a measure of entwining of the gravitomagnetic fieldlines. We discuss gravitomagnetic helicity within the gravitoelectromagnetic (GEM) framework oflinearized general relativity. Furthermore, we employ the spacetime curvature approach to GEM in orderto determine the gravitomagnetic helicity for static observers in Kerr spacetime.