arXiv subjects

Fabio Bonaccorso

Publications and source records attributed to Fabio Bonaccorso.

At least 37 records · Page 2Linked to original sources

arXiv2023

Multiscale Hybrid Modeling of Proteins in Solvent: SARS-CoV2 Spike Protein as test case for Lattice Boltzmann -- All Atom Molecular Dynamics Coupling

Physiological solvent flows surround biological structures triggering therein collective motions. Notable examples are virus/host-cell interactions and solvent-mediated allosteric regulation. The present work describes a multiscale approach joining the Lattice Boltzmann fluid dynamics (for solvent flows) with the all-atom atomistic molecular dynamics (for proteins) to model functional interactions between flows and molecules. We present, as an applicative scenario, the study of the SARS-CoV-2 virus spike glycoprotein protein interacting with the surrounding solvent, modeled as a mesoscopic fluid. The equilibrium properties of the wild-type spike and of the Alpha variant in implicit solvent are described by suitable observables. The mesoscopic solvent description is critically compared to the all-atom solvent model, to quantify the advantages and limitations of the mesoscopic fluid description.

physics.comp-ph↗

arXiv2023

Thread-safe lattice Boltzmann for high-performance computing on GPUs

We present thread-safe, highly-optimized lattice Boltzmann implementations, specifically aimed at exploiting the high memory bandwidth of GPU-based architectures. At variance with standard approaches to LB coding, the proposed strategy, based on the reconstruction of the post-collision distribution via Hermite projection, enforces data locality and avoids the onset of memory dependencies, which may arise during the propagation step, with no need to resort to more complex streaming strategies. The thread-safe lattice Boltzmann achieves peak performances, both in two and three dimensions and it allows to sensibly reduce the allocated memory ( tens of GigaBytes for order billions lattice nodes simulations) by retaining the algorithmic simplicity of standard LB computing. Our findings open attractive prospects for high-performance simulations of complex flows on GPU-based architectures.

cs.DC↗

arXiv2022

Classifying Turbulent Environments via Machine Learning

The problem of classifying turbulent environments from partial observation is key for some theoretical and applied fields, from engineering to earth observation and astrophysics, e.g. to precondition searching of optimal control policies in different turbulent backgrounds, to predict the probability of rare events and/or to infer physical parameters labelling different turbulent set-ups. To achieve such goal one can use different tools depending on the system's knowledge and on the quality and quantity of the accessible data. In this context, we assume to work in a model-free setup completely blind to all dynamical laws, but with a large quantity of (good quality) data for training. As a prototype of complex flows with different attractors, and different multi-scale statistical properties we selected 10 turbulent 'ensembles' by changing the rotation frequency of the frame of reference of the 3d domain and we suppose to have access to a set of partial observations limited to the instantaneous kinetic energy distribution in a 2d plane, as it is often the case in geophysics and astrophysics. We compare results obtained by a Machine Learning (ML) approach consisting of a state-of-the-art Deep Convolutional Neural Network (DCNN) against Bayesian inference which exploits the information on velocity and enstrophy moments. First, we discuss the supremacy of the ML approach, presenting also results at changing the number of training data and of the hyper-parameters. Second, we present an ablation study on the input data aimed to perform a ranking on the importance of the flow features used by the DCNN, helping to identify the main physical contents used by the classifier. Finally, we discuss the main limitations of such data-driven methods and potential interesting applications.

physics.flu-dyn↗

arXiv2022

DropTrack -- automatic droplet tracking using deep learning for microfluidic applications

Deep neural networks are rapidly emerging as data analysis tools, often outperforming the conventional techniques used in complex microfluidic systems. One fundamental analysis frequently desired in microfluidic experiments is counting and tracking the droplets. Specifically, droplet tracking in dense emulsions is challenging as droplets move in tightly packed configurations. Sometimes the individual droplets in these dense clusters are hard to resolve, even for a human observer. Here, two deep learning-based cutting-edge algorithms for object detection (YOLO) and object tracking (DeepSORT) are combined into a single image analysis tool, DropTrack, to track droplets in microfluidic experiments. DropTrack analyzes input videos, extracts droplets' trajectories, and infers other observables of interest, such as droplet numbers. Training an object detector network for droplet recognition with manually annotated images is a labor-intensive task and a persistent bottleneck. This work partly resolves this problem by training object detector networks (YOLOv5) with hybrid datasets containing real and synthetic images. We present an analysis of a double emulsion experiment as a case study to measure DropTrack's performance. For our test case, the YOLO networks trained with 60% synthetic images show similar performance in droplet counting as with the one trained using 100% real images, meanwhile saving the image annotation work by 60%. DropTrack's performance is measured in terms of mean average precision (mAP), mean square error in counting the droplets, and inference speed. The fastest configuration of DropTrack runs inference at about 30 frames per second, well within the standards for real-time image analysis.

cs.CV↗

arXiv2022

Stochastic jetting and dripping in confined soft granular flows

We report new dynamical modes in confined soft granular flows, such as stochastic jetting and dripping, with no counterpart in continuum viscous fluids. The new modes emerge as a result of the propagation of the chaotic behaviour of individual grains -- here, monodisperse emulsion droplets to the level of the entire system as the emulsion is focused into a narrow orifice by an external viscous flow. We observe avalanching dynamics and the formation of remarkably stable jets -- singlefile granular chains -- which occasionally break, resulting in a non-Gaussian distribution of cluster sizes. We find that the sequences of droplet rearrangements that lead to the formation of such chains resemble unfolding of cancer cell clusters in narrow capillaries, overall demonstrating that microfluidic emulsion systems could serve to model various aspects of soft granular flows, including also tissue dynamics at the meso-scale.

cond-mat.soft↗

arXiv2021

LBcuda: a high-performance CUDA port of LBsoft for simulation of colloidal systems

We present LBcuda, a GPU accelerated version of LBsoft, our open-source MPI-based software for the simulation of multi-component colloidal flows. We describe the design principles, the optimization and the resulting performance as compared to the CPU version, using both an average cost GPU and high-end NVidia GPU cards (V100 and the latest A100). The results show a substantial acceleration for the fluid solver reaching up to 200 GLUPS (Giga Lattice Updates Per Second) on a cluster made of 512 A100 NVIDIA cards simulating a grid of eight billion lattice points. These results open attractive prospects for the computational design of new materials based on colloidal particles.

physics.comp-ph↗

arXiv2021

Tracking droplets in soft granular flows with deep learning techniques

The state-of-the-art deep learning-based object recognition YOLO algorithm and object tracking DeepSORT algorithm are combined to analyze digital images from fluid dynamic simulations of multi-core emulsions and soft flowing crystals and to track moving droplets within these complex flows. The YOLO network was trained to recognize the droplets with synthetically prepared data, thereby bypassing the labor-intensive data acquisition process. In both applications, the trained YOLO + DeepSORT procedure performs with high accuracy on the real data from the fluid simulations, with low error levels in the inferred trajectories of the droplets and independently computed ground truth. Moreover, using commonly used desktop GPUs, the developed application is capable of analyzing data at speeds that exceed the typical image acquisition rates of digital cameras (30 fps), opening the interesting prospect of realizing a low-cost and practical tool to study systems with many moving objects, mostly but not exclusively, biological ones. Besides its practical applications, the procedure presented here marks the first step towards the automatic extraction of effective equations of motion of many-body soft flowing systems.

cond-mat.soft↗

arXiv2021

A fast and efficient deep learning procedure for tracking droplet motion in dense microfluidic emulsions

We present a deep learning-based object detection and object tracking algorithm to study droplet motion in dense microfluidic emulsions. The deep learning procedure is shown to correctly predict the droplets' shape and track their motion at competitive rates as compared to standard clustering algorithms, even in the presence of significant deformations. The deep learning technique and tool developed in this work could be used for the general study of the dynamics of biological agents in fluid systems, such as moving cells and self-propelled micro organisms in complex biological flows.

cond-mat.soft↗

arXiv2021

Optimal control of point-to-point navigation in turbulent time-dependent flows using Reinforcement Learning

We present theoretical and numerical results concerning the problem to find the path that minimizes the time to navigate between two given points in a complex fluid under realistic navigation constraints. We contrast deterministic Optimal Navigation (ON) control with stochastic policies obtained by Reinforcement Learning (RL) algorithms. We show that Actor-Critic RL algorithms are able to find quasi-optimal solutions in the presence of either time-independent or chaotically evolving flow configurations. For our application, ON solutions develop unstable behavior within the typical duration of the navigation process, and are therefore not useful in practice. We first explore navigation of turbulent flow using a constant propulsion speed. Based on a discretized phase-space, the propulsion direction is adjusted with the aim to minimize the time spent to reach the target. Further, we explore a case where additional control is obtained by allowing the engine to power off. Exploiting advection of the underlying flow, allows the target to be reached with less energy consumption. In this case, we optimize a linear combination between the total navigation time and the total time the engine is switched off. Our approach can be generalized to other setups, for example, navigation under imperfect environmental forecast or with different models for the moving vessel.

eess.SY↗

arXiv2021

Microscale modelling of dielectrophoresis assembly processes

This work presents a microscale approach for simulating the dielectrophoresis (DEP) assembly of polarizable particles under an external electric field. The model is shown to capture interesting dynamical and topological features, such as the formation of chains of particles and their incipient aggregation into hierarchical structures. A quantitative characterization in terms of the number and size of these structures is also discussed. This computational model could represent a viable numerical tool to study the mechanical properties of particle-based hierarchical materials and suggest new strategies for enhancing their design and manufacture.

physics.comp-ph↗

arXiv2021

Wet to dry self-transitions in dense emulsions: from order to disorder and back

One of the most distinctive hallmarks of many-body systems far from equilibrium is the spontaneous emergence of order under conditions where disorder would be plausibly expected. Here, we report on the self-transition between ordered and disordered emulsions in divergent microfluidic channels, i.e. from monodisperse assemblies to heterogeneous polydisperse foam-like structures, and back again to ordered ones. The transition is driven by the nonlinear competition between viscous dissipation and surface tension forces as controlled by the device geometry, particularly the aperture angle of the divergent microfluidic channel. An unexpected route back to order is observed in the regime of large opening angles, where a trend towards increasing disorder would be intuitively expected.

cond-mat.soft↗

arXiv2020

LBsoft: a parallel open-source software for simulation of colloidal systems

We present LBsoft, an open-source software developed mainly to simulate the hydro-dynamics of colloidal systems based on the concurrent coupling between lattice Boltzmann methods for the fluid and discrete particle dynamics for the colloids. Such coupling has been developed before, but, to the best of our knowledge, no detailed discussion of the programming issues to be faced in order to attain efficient implementation on parallel architectures, has ever been presented to date. In this paper, we describe in detail the underlying multi-scale models, their coupling procedure, along side with a description of the relevant input variables, to facilitate third-parties usage. The code is designed to exploit parallel computing platforms, taking advantage also of the recent AVX-512 instruction set. We focus on LBsoft structure, functionality, parallel implementation, performance and availability, so as to facilitate the access to this computational tool to the research community in the field. The capabilities of LBsoft are highlighted for a number of prototypical case studies, such as pickering emulsions, bicontinuous systems, as well as an original study of the coarsening process in confined bijels under shear.

physics.comp-ph↗

arXiv2020

A Multiresolution Mesoscale Approach for Microscale Hydrodynamics

A new class of multiscale scheme is presented for micro-hydrodynamic problems based on a dual representation of the fluid observables. The hybrid model is first tested against the classical flow between two parallel plates and then applied to a plug flow within a micrometer-sized striction and a shear flow within a microcavity. Both cases demonstrate the capability of the multiscale approach to reproduce the correct macroscopic hydrodynamics also in the presence of refined grids (one and two levels), while retaining the correct thermal fluctuations, embedded in the multiparticle collision method. This provides the first step toward a novel class of fully mesoscale hybrid approaches able to capture the physics of fluids at the micro- and nanoscales whenever a continuum representation of the fluid falls short of providing the complete physical information, due to a lack of resolution and thermal fluctuations.

physics.comp-ph↗

arXiv2020

Towards Exascale Design of Soft Mesoscale Materials

We provide a brief survey of our current developments in the simulation-based design of novel families of mesoscale porous materials using computational kinetic theory. Prospective applications on exascale computers are also briefly discussed and commented on, with reference to two specific examples of soft mesoscale materials: microfluid crystals and bi-continuous jels

physics.comp-ph↗

arXiv2020

Multiparticle collision dynamics for fluid interfaces with near-contact interactions

We present an extension of the multiparticle collision dynamics method for flows with complex interfaces, including supramolecular near-contact interactions mimicking the effect of surfactants. The new method is demonstrated for the case of (i) short range repulsion of droplets in close contact, (ii) arrested phase separation and (iii) different pattern formation during spinodal decomposition of binary mixtures.

cond-mat.soft↗

arXiv2020

Lattice Boltzmann simulations capture the multiscale physics of soft flowing crystals

The study of the underlying physics of soft flowing materials depends heavily on numerical simulations, due to the complex structure of the governing equations reflecting the competition of concurrent mechanisms acting at widely disparate scales in space and time. A full-scale computational modelling remains a formidable challenge since it amounts to simultaneously handle six or more spatial decades in space and twice as many in time. Coarse-grained methods often provide a viable strategy to significantly mitigate this issue, through the implementation of mesoscale supramolecular forces designed to capture the essential physics at a fraction of the computational cost of a full-detail description. Here, we review some recent advances in the design of a lattice Boltzmann mesoscale approach for soft flowing materials, inclusive of near-contact interactions (NCI) between dynamic interfaces, as they occur in high packing-fraction soft flowing crystals. The method proves capable of capturing several aspects of the rheology of soft flowing crystals, namely, i) a 3/2 power-law dependence of the dispersed phase flow rate on the applied pressure gradient, ii) the structural transition between an ex-two and ex-one (bamboo) configurations with the associated drop of the flow rate, iii) the onset of interfacial waves once NCI is sufficiently intense.

physics.comp-ph↗

arXiv2019

Zermelo's problem: Optimal point-to-point navigation in 2D turbulent flows using Reinforcement Learning

To find the path that minimizes the time to navigate between two given points in a fluid flow is known as Zermelo's problem. Here, we investigate it by using a Reinforcement Learning (RL) approach for the case of a vessel which has a slip velocity with fixed intensity, Vs , but variable direction and navigating in a 2D turbulent sea. We show that an Actor-Critic RL algorithm is able to find quasi-optimal solutions for both time-independent and chaotically evolving flow configurations. For the frozen case, we also compared the results with strategies obtained analytically from continuous Optimal Navigation (ON) protocols. We show that for our application, ON solutions are unstable for the typical duration of the navigation process, and are therefore not useful in practice. On the other hand, RL solutions are much more robust with respect to small changes in the initial conditions and to external noise, even when V s is much smaller than the maximum flow velocity. Furthermore, we show how the RL approach is able to take advantage of the flow properties in order to reach the target, especially when the steering speed is small.

nlin.CD↗

arXiv2019

Self-similar Subgrid-scale Models for Inertial Range Turbulence and Accurate Measurements of Intermittency

A class of spectral subgrid models based on a self-similar and reversible closure is studied with the aim to minimize the impact of subgrid scales on the inertial range of fully developed turbulence. In this manner, we improve the scale extension where anomalous exponents are measured by roughly one order of magnitude, when compared to direct numerical simulations or to other popular subgrid closures at the same resolution. We found a first indication that intermittency for high order moments is not captured by many of the popular phenomenological models developed so far.

physics.flu-dyn↗