In this paper we present a new multi-scale method for reproducing traffic flow which couples a first-order macroscopic model with a second-order microscopic model, avoiding any interface or boundary conditions between them. The multi-scale model is characterized by the fact that microscopic and macroscopic descriptions are not spatially separated. On the contrary, the macro-scale is always active while the micro-scale is activated only if needed by the traffic conditions. The Euler-Godunov scheme associated to the model is conservative and it is able to reproduce typical traffic phenomena like stop & go waves.

Background. The three terms "panic", "irrationality", and "herding" are ubiquitous in the crowd dynamics literature and have a strong influence on both modelling and management practices. The terms are also commonly shared between the scientific and nonscientific domains. The pervasiveness of the use of these terms is to the point where their underlying assumptions have often been treated as common knowledge by both experts and lay persons. Yet, at the same time, the literature on crowd dynamics presents ample debate, contradiction, and inconsistency on these topics. Method. This review is the first to systematically revisit these three terms in a unified study to highlight the scope of this debate. We extracted from peer-reviewed journal articles direct quotes that offer a definition, conceptualisation, or supporting/contradicting evidence on these terms and/or their underlying theories. To further examine the suitability of the term herding, a secondary and more detailed analysis is also conducted on studies that have specifically investigated this phenomenon in empirical settings. Results. The review shows that (i) there is no consensus on the definition for the terms panic and irrationality and that (ii) the literature is highly divided along discipline lines on how accurate these theories/terminologies are for describing human escape behaviour. The review reveals a complete division and disconnection between studies published by social scientists and those from the physical science domain and also between studies whose main focus is on numerical simulation versus those with empirical focus. (iii) Despite the ambiguity of the definitions and the missing consensus in the literature, these terms are still increasingly and persistently mentioned in crowd evacuation studies. (iv) Different to panic and irrationality, there is relative consistency in definitions of the term herding, with the term usually being associated with '(blind) imitation'. However, based on the findings of empirical studies, we argue why, despite the relative consistency in meaning, (v) the term herding itself lacks adequate nuance and accuracy for describing the role of 'social influence' in escape behaviour. Our conclusions also emphasise the importance of distinguishing between the social influence on various aspects of evacuation behaviour and avoiding generalisation across various behavioural layers. Conclusions. We argue that the use of these three terms in the scientific literature does not contribute constructively to extending the knowledge or to improving the modelling capabilities in the field of crowd dynamics. This is largely due to the ambiguity of these terms, the overly simplistic nature of their assumptions, or the fact that the theories they represent are not readily verifiable. Recommendations. We suggest that it would be beneficial for advancing this research field that the phenomena related to these three terms are clearly defined by more tangible and quantifiable terms and be formulated as verifiable hypotheses, so they can be operationalized for empirical testing.

The High-throughput Chromosome Conformation Capture (Hi-C) technique combines the power of the Next Generation Sequencing technologies with chromosome conformation capture approach to study the 3D chromatin organization at the genome-wide scale. Although such a technique is quite recent, many tools are already available for pre-processing and analyzing Hi-C data, allowing to identify chromatin loops, topological associating domains and A/B compartments. However, only a few of them provide an exhaustive analysis pipeline or allow to easily integrate and visualize other omic layers. Moreover, most of the available tools are designed for expert users, who have great confidence with command-line applications. In this paper, we present HiCeekR (https://github.com/lucidif/HiCeekR), a novel R Graphical User Interface (GUI) that allows researchers to easily perform a complete Hi-C data analysis. With the aid of the Shiny libraries, it integrates several R/Bioconductor packages for Hi-C data analysis and visualization, guiding the user during the entire process. Here, we describe its architecture and functionalities, then illustrate its capabilities using a publicly available dataset

The properties of a semiflexible polymer with fixed ends exposed to oscillatory shear flow are investigated by simulations. The two-dimensionally confined polymer is modeled as a linear bead-spring chain, and the interaction with the fluid is described by the Brownian multiparticle collision dynamics approach. For small shear rates, the tethering of the ends leads to a more-or-less linear oscillatory response. However, at high shear rates, we found a strongly nonlinear reaction, with a polymer (partially) wrapped around the fixation points. This leads to an overall shrinkage of the polymer. Dynamically, the location probability of the polymer center-of-mass position is largest on a spatial curve resembling a limacon, although with an inhomogeneous distribution. We found shear-induced modifications of the normal-mode correlation functions, with a frequency doubling at high shear rates. Interestingly, an even-odd asymmetry for the Cartesian components of the correlation functions appears, with rather similar spectra for odd x- and even y-modes and vice versa. Overall, our simulations yielded an intriguing nonlinear behavior of tethered semiflexible polymers under oscillatory shear flow.

In the wide scenario of the optimization techniques, a large number of algorithms are inspired by natural processes, in many different ways. One of the latest is the Imperialist Competitive Algorithm (ICA) Atashpaz-Gargari and Lucas (2007), judged by their authors as very efficient and competitive with other popular optimization algorithms. However, its diffusion is still limited, so that it has not yet been adequately studied. In this paper, we have investigated the convergence properties of the ICA algorithm, observing the effect of the various coefficients and their role in the global convergence. Some modifications, including the coupling with a local search method, have been listed/suggested and then tested on a suite of standard algebraic test functions, verifying the improvements on the speed of convergence of the original algorithm. An application to naval design has been also included, in order to check the ability to solve realistic problems.

Particle Swarm Optimization is an evolutionary optimization algorithm, largely studied during the years: analysis of convergence, determination of the optimal coefficients, hybridization of the original algorithm and also the determination of the best relationship structure between the swarm elements (topology) have been investigated largely. Unfortunately, all these studies have been produced separately, and the same coefficients, derived for the original topology of the algorithm, have been always applied. The intent of this paper is to identify the best set of coefficients for different topological structures. A large suite of objective functions are considered and the best compromise coefficients are identified for each topology. Results are finally compared on the base of a practical ship design application.

The role of comics in science communications has been subject of a number of recent papers. While some debate on an accepted definition of what constitutes a science comics is still ongoing, the role of comics in science outreach is now universally recognized. [1] Here we present the Comics&Science comic books published by CNR Edizioni and edited by Roberto Natalini and Andrea Plazzi. The Comics&Science concept was implemented in the first place as a section of the Lucca Comics&Games festival, followed by the printed series in 2013. Comics&Science's philosophy is to have science elements, ideas and "bits" integrated into cartoons by the best professional writers and artists. The story must be fun, entertaining and overall artistically and aesthetically significant. Each issue is completed by articles and pieces about and around the topics touched by the story. A Comics&Science issue almost always starts with the cartoonist visiting a research lab/facility. Tipically, the artist has little or no formal scientific background and up to now this has proved to be an effective starting point for exchanging opinions and a cross-debate of sorts. Following the Comics&Science "protocol", Italian hugely popular cartoonist Zerocalcare (millions of books sold in the last few years) visited the Elettra and Fermi light sources prior to working to his "Light Issue", co-edited by the Istituto di Struttura della Materia-CNR (ISM- CNR) and Elettra Sincrotrone Trieste. The upcoming Comics&Science issue (Fall 2019) will be featuring a Periodic Table-inspired story by writer Giovanni Eccher and artist Sergio Ponchione, as a joint venture between the Department of Chemical Science and Technology of Materials (CNR-DSCTM) and the Young Chemists Group and the Group for the Diffusion of the Chemistry Culture of the Italian Chemical Society.

In this paper, an adaptive method for copy-move forgery detection and localization in digital images is proposed. The method employs wavelet transform with non constant Q factor and characterizes image pixels through the multiscale behavior of corresponding wavelet coefficients. The detection of forged regions is then performed by considering similar those pixels having the same multiscale behavior. The method is pointwise and the length of pixel features vector is image dependent, allowing for a more precise and fast detection of forged regions. The qualitative and quantitative evaluation of the experimental results reveals that the proposed method outperforms some existing transform-based methods in terms of performance and execution time.

The improvement of the readability of time-frequency transforms is an important topic in the field of fast-oscillating signal processing. The reassignment method is often used due to its adaptivity to different transforms and nice formal properties. However, it strongly depends on the selection of the analysis window and it requires the computation of the same transform using three different but well-defined windows. The aim of this work is to provide a simple method for spectrogram reassignment, named FIRST (Fast Iterative and Robust Reassignment Thinning), with comparable or better precision than classical reassignment method, a reduced computational effort, and a near independence of the adopted analysis window. To this aim, the time-frequency evolution of a multicomponent signal is formally provided and, based on this law, only a subset of time-frequency points is used to improve spectrogram readability. Those points are the ones less influenced by interfering components. Preliminary results show that the proposed method can efficiently reassign spectrograms more accurately than the classical method in the case of interfering signal components, with a significant gain in terms of required computational effort.

Marine species reproduce and compete while being advected by turbulent flows. It is largely unknown, both theoretically and experimentally, how population dynamics and genetics are changed by the presence of fluid flows. Discrete agent-based simulations in continuous space allow for accurate treatment of advection and number fluctuations, but can be computationally expensive for even modest organism densities. In this report, we propose an algorithm to overcome some of these challenges. We first provide a thorough validation of the algorithm in one and two dimensions without flow. Next, we focus on the case of weakly compressible flows in two dimensions. This models organisms such as phytoplankton living at a specific depth in the three-dimensional, incompressible ocean experiencing upwelling and/or downwelling events. We show that organisms born at sources in a two-dimensional time-independent flow experience an increase in fixation probability.

The dynamics of inertial particles in Rayleigh-Benard convection, where both particles and fluid exhibit thermal expansion, is studied using direct numerical simulations (DNS) in the soft-turbulence regime. We consider the effect of particles with a thermal expansion coefficient larger than that of the fluid, causing particles to become lighter than the fluid near the hot bottom plate and heavier than the fluid near the cold top plate. Because of the opposite directions of the net Archimedes' force on particles and fluid, particles deposited at the plate now experience a relative force towards the bulk. The characteristic time for this motion towards the bulk to happen, quantified as the time particles spend inside the thermal boundary layers (BLs) at the plates, is shown to depend on the thermal response time, tau T. In particular, the residence time is constant for small thermal response times, tau T less than or similar to 1, and increasing with tau T for larger thermal response times, tau T greater than or similar to 1. Also, the thermal BL residence time is increasing with decreasing K. A one-dimensional (1D) model is developed, where particles experience thermal inertia and their motion is purely dependent on the buoyancy force. Although the values do not match one-to-one, this highly simplified 1D model does predict a regime of a constant thermal BL residence time for smaller thermal response times and a regime of increasing residence time with tau T for larger response times, thus explaining the trends in the DNS data well.

In Rayleigh-Bénard convection (RBC) for fluids with Prandtl number Pr1, rotation beyond a critical (small) rotation rate is known to cause a sudden enhancement of heat transfer, which can be explained by a change in the character of the boundary layer (BL) dynamics near the top and bottom plates of the convection cell. Namely, with increasing rotation rate, the BL signature suddenly changes from Prandtl-Blasius type to Ekman type. The transition from a constant heat transfer to an almost linearly increasing heat transfer with increasing rotation rate is known to be sharp and the critical Rossby number Roc occurs typically in the range 2.3Roc2.9 (for Rayleigh number Ra=1.3×109, Pr=6.7, and a convection cell with aspect ratio ?=DH=1, with D the diameter and H the height of the cell). The explanation of the sharp transition in the heat transfer points to the change in the dominant flow structure. At 1/Ro1/Roc (slow rotation), the well-known large-scale circulation (LSC) is found: a single domain-filling convection roll made up of many individual thermal plumes. At 1/Ro1/Roc (rapid rotation), the LSC vanishes and is replaced with a collection of swirling plumes that align with the rotation axis. In this paper, by numerically studying Lagrangian acceleration statistics, related to the small-scale properties of the flow structures, we reveal that this transition between these different dominant flow structures happens at a second critical Rossby number, Roc2?2.25 (different from Roc1?2.7 for the sharp transition in the Nusselt number Nu; both values for the parameter settings of our present numerical study). When statistical data of Lagrangian tracers near the top plate are collected, it is found that the root-mean-square values and the kurtosis of the horizontal acceleration of these tracers show a sudden increase at Roc2. To better understand the nature of this transition we compute joint statistics of the Lagrangian velocity and acceleration of fluid particles and vertical vorticity near the top plate. It is found that for Ro2.25 there is hardly any correlation between the vertical vorticity and extreme acceleration events of fluid particles. For Ro2.25, however, vortical regions are much more prominent and extreme horizontal acceleration events are now correlated to large values of positive (cyclonic) vorticity. This suggests that the observed sudden transition in the acceleration statistics is related to thermal plumes with cyclonic vorticity developing in the Ekman BL and subsequently becoming mature and entering the bulk of the flow for Ro2.25.

Competition between biological species in marine environments is affected by the motion of the surrounding fluid. An effective 2D compressibility can arise, for example, from the convergence and divergence of water masses at the depth at which passively traveling photosynthetic organisms are restricted to live. In this report, we seek to quantitatively study genetics under flow. To this end, we couple an off-lattice agent-based simulation of two populations in 1D to a weakly compressible velocity field--first a sine wave and then a shell model of turbulence. We find for both cases that even in a regime where the overall population structure is approximately unaltered, the flow can significantly diminish the effect of a selective advantage on fixation probabilities. We understand this effect in terms of the enhanced survival of organisms born at sources in the flow and the influence of Fisher genetic waves.

The selective entrapment of mutually annihilating species within a phase-changing carrier fluid is explored by both analytical and numerical means. The model takes full account of the dynamic heterogeneity which arises as a result of the coupling between hydrodynamic transport, dynamic phase-transitions and chemical reactions between the participating species, in the presence of a selective droplet interface. Special attention is paid to the dynamic symmetry breaking between the mass of the two species entrapped within the expanding droplet as a function of time. It is found that selective sources are much more effective symmetry breakers than selective diffusion. The present study may be of interest for a broad variety of advection-diffusion-reaction phenomena with selective fluid interfaces, including the problem of electroweak baryogenesis.

Recent numerical analyses to optimize the design of microfluidic devices for more effective entrapment or segregation of surrogate circulating tumor cells (CTCs) from healthy cells have been reported in the literature without concurrently accommodating the non-Newtonian nature of the body fluid and the non-uniform geometric shapes of the CTCs. Through a series of two-dimensional proof-of-concept simulations with increased levels of complexity (e.g., number of particles, inline obstacles), we investigated the validity of the assumptions of the Newtonian fluid behavior for pseudoplastic fluids and the circular particle shape for different-shaped particles (DSPs) in the context of microfluidics-facilitated shape-based segregation of particles. Simulations with a single DSP revealed that even in the absence of internal geometric complexities of a microfluidics channel, the aforementioned assumptions led to 0.11-0.21W (W is the channel length) errors in lateral displacements of DSPs, up to 3-20% errors in their velocities, and 3-5% errors in their travel times. When these assumptions were applied in simulations involving multiple DSPs in inertial microfluidics with inline obstacles, errors in the lateral displacements of DSPs were as high as 0.78W and in their travel times up to 23% , which led to different (un)symmetric flow and segregation patterns of DSPs. Thus, the fluid type and particle shape should be included in numerical models and experiments to assess the performance of microfluidics for targeted cell (e.g., CTCs) harvesting.

We present an analytical derivation of the transport coefficients of a relativistic gas in (2 + 1) dimensions for both Chapman-Enskog (CE) asymptotics and Grad's expansion methods. We further develop a systematic calibration method, connecting the relaxation time of relativistic kinetic theory to the transport parameters of the associated dissipative hydrodynamic equations. Comparison of our analytical results and numerical simulations shows that the CE method correctly captures dissipative effects, while Grad's method does not, in agreement with previous analyses performed in the (3 + 1)-dimensional case. These results provide a solid basis for accurately calibrated computational studies of relativistic dissipative flows.

Motility behavior of an engineered chemosensory particle (ECP) in fluidic environments is driven by its responses to chemical stimuli. One of the challenges to understanding such behaviors lies in tracking changes in chemical signal gradients of chemoattractants and ECP-fluid dynamics as the fluid is continuously disturbed by ECP motion. To address this challenge, we introduce a new multiscale numerical model to simulate chemotactic swimming of an ECP in confined fluidic environments by accounting for motility-induced disturbances in spatiotemporal chemoattractant distributions. The model accommodates advective-diffusive transport of unmixed chemoattractants, ECP-fluid hydrodynamics at the ECP-fluid interface, and spatiotemporal disturbances in the chemoattractant concentrations due to particle motion. Demonstrative simulations are presented with an ECP, mimicking Escherichia coli (E. coli) chemotaxis, released into initially quiescent fluids with different source configurations of the chemoattractants N-methyl-L-aspartate and L-serine. Simulations demonstrate that initial distributions and temporal evolution of chemoattractants and their release modes (instantaneous vs. continuous, point source vs. distributed) dictate time histories of chemotactic motility of an ECP. Chemotactic motility is shown to be largely determined by spatiotemporal variation in chemoattractant concentration gradients due to transient disturbances imposed by ECP-fluid hydrodynamics, an observation not captured in previous numerical studies that relied on static chemoattractant concentration fields.

GOLIAT is an offshore production field that spans from the subsea wells up to a complete process plant installed on a FPSO. Due to the comprehensive instrumentation installed on the plant, it is the perfect case study to test an innovative agent based software architecture able to support production management. The modularity and the scalability provided by the agent based architecture guarantees the applicability of the method to any part of the plant. Each agent is in charge of supervising a specific or a group of equipment and is fed by the real-time data coming from the field. These data are then analysed through Machine Learning and Deep Learning algorithms which are incorporated within the agents. The machine learning algorithms estimate the current state of the equipment and provide a set of KPIs in order to understand both the production efficiency and the health status of the machines. Furthermore, learning from the observations of the state transition paths which happened in the past, the agents are capable of predicting the most likely future state. The latter capability is fundamental to prevent unplanned shutdowns and optimize the maintenance plans. On the basis of the estimated current state, each agent can also provide a list of actions targeted to maximize the efficiency from an "equipment" point of view. The actions coming from all the agents can then be collected and negotiated in order to maximize the production from a "plant" point of view. The negotiating algorithms are implemented in a super-agent that can support a human operator in the day-by-day management tasks of the plant. Even though the negotiating capabilities will be implemented in the future version of the application, the modular nature of the system guarantees an easy integration of the super-agent inside the agent's framework. The paper will present the results of the agent framework in terms of the robustness of state estimation and the correctness of the computed KPIs.

In this paper, we develop a three-dimensional multiple-relaxation-time lattice Boltzmann method (MRT-LBM) based on a set of non-orthogonal basis vectors. Compared with the classical MRT-LBM based on a set of orthogonal basis vectors, the present non-orthogonal MRT-LBM simplifies the transformation between the discrete velocity space and the moment space and exhibits better portability across different lattices. The proposed method is then extended to multiphase flows at large density ratio with tunable surface tension, and its numerical stability and accuracy are well demonstrated by some benchmark cases. Using the proposed method, a practical case of a fuel droplet impacting on a dry surface at high Reynolds and Weber numbers is simulated and the evolution of the spreading film diameter agrees well with the experimental data. Furthermore, another realistic case of a droplet impacting on a super-hydrophobic wall with a cylindrical obstacle is reproduced, which confirms the experimental finding of Liu et al. ["Symmetry breaking in drop bouncing on curved surfaces," Nat. Commun. 6, 10034 (2015)] that the contact time is minimized when the cylinder radius is comparable with the droplet radius.

In this paper, we propose a hybrid lattice Boltzmann method (HLBM) for solving fluid-structure interaction problems. The proposed numerical approach is applied to model the flow induced by a vibrating thin lamina submerged in a viscous quiescent fluid. The hydrodynamic force exerted by the fluid on the solid body is described by means of a complex hydrodynamic function, whose real and imaginary parts are determined via parametric analysis. Numerical results are validated by comparison with those from other numerical as well as experimental works available in the literature. The proposed hybrid approach enhances the capability of lattice Boltzmann methods to solve fluid dynamic problems involving moving geometries.