arXiv subjects

Petros Koumoutsakos

Publications and source records attributed to Petros Koumoutsakos.

At least 73 records · Page 4Linked to original sources

arXiv2020

A hybrid particle volume-of-fluid method for curvature estimation in multiphase flows

We present a particle method for estimating the curvature of interfaces in volume-of-fluid simulations of multiphase flows. The method is well suited for under-resolved interfaces, and it is shown to be more accurate than the parabolic fitting that is employed in such cases. The curvature is computed from the equilibrium positions of particles constrained to circular arcs and attracted to the interface. The proposed particle method is combined with the method of height functions at higher resolutions, and it is shown to outperform the current combinations of height functions and parabolic fitting. The algorithm is conceptually simple and straightforward to implement on new and existing software frameworks for multiphase flow simulations thus enhancing their capabilities in challenging flow problems. We evaluate the proposed hybrid method on a number of two- and three-dimensional benchmark flow problems and illustrate its capabilities on simulations of flows involving bubble coalescence and turbulent multiphase flows.

physics.comp-ph↗

arXiv2020

Machine Learning for Fluid Mechanics

The field of fluid mechanics is rapidly advancing, driven by unprecedented volumes of data from field measurements, experiments and large-scale simulations at multiple spatiotemporal scales. Machine learning offers a wealth of techniques to extract information from data that could be translated into knowledge about the underlying fluid mechanics. Moreover, machine learning algorithms can augment domain knowledge and automate tasks related to flow control and optimization. This article presents an overview of past history, current developments, and emerging opportunities of machine learning for fluid mechanics. It outlines fundamental machine learning methodologies and discusses their uses for understanding, modeling, optimizing, and controlling fluid flows. The strengths and limitations of these methods are addressed from the perspective of scientific inquiry that considers data as an inherent part of modeling, experimentation, and simulation. Machine learning provides a powerful information processing framework that can enrich, and possibly even transform, current lines of fluid mechanics research and industrial applications.

physics.flu-dyn↗

arXiv2019

Mirheo: High-Performance Mesoscale Simulations for Microfluidics

The transport and manipulation of particles and cells in microfluidic devices has become a core methodology in domains ranging from molecular biology to manufacturing and drug design. The rational design and operation of such devices can benefit from simulations that resolve flow-structure interactions at sub-micron resolution. We present a computational tool for large scale, efficient and high throughput mesoscale simulations of fluids and deformable objects at complex microscale geometries. The code employs Dissipative Particle Dynamics for the description of the flow coupled with visco-elastic membrane model for red blood cells and can also handle rigid bodies and complex geometries. The software (MiRheo) is deployed on hybrid GPU/CPU architectures exhibiting unprecedented time-to-solution performance and excellent weak and strong scaling for a number of benchmark problems. MiRheo exploits the capabilities of GPU clusters, leading to speedup of up to 10 in terms of time to solution as compared to state-of-the-art software packages and reaches 90 - 99 percent weak scaling efficiency on 512 nodes of the Piz Daint supercomputer. The software MiRheo, relies on a Python interface to facilitate the solution of complex problems and it is open source. We believe that MiRheo constitutes a potent computational tool that can greatly assist studies of microfluidics.

cs.CE↗

arXiv2019

Optimal sensing for fish school identification

Fish schooling implies an awareness of the swimmers for their companions. In flow mediated environments, in addition to visual cues, pressure and shear sensors on the fish body are critical for providing quantitative information that assists the quantification of proximity to other swimmers. Here we examine the distribution of sensors on the surface of an artificial swimmer so that it can optimally identify a leading group of swimmers. We employ Bayesian experimental design coupled with two-dimensional Navier Stokes equations for multiple self-propelled swimmers. The follower tracks the school using information from its own surface pressure and shear stress. We demonstrate that the optimal sensor distribution of the follower is qualitatively similar to the distribution of neuromasts on fish. Our results show that it is possible to identify accurately the center of mass and even the number of the leading swimmers using surface only information.

physics.flu-dyn↗

arXiv2019

Bubbles in Turbulent Flows: Data-driven, kinematic models with memory terms

We present data driven kinematic models for the motion of bubbles in high-Re turbulent fluid flows based on recurrent neural networks with long-short term memory enhancements. The models extend empirical relations, such as Maxey-Riley (MR) and its variants, whose applicability is limited when either the bubble size is large or the flow is very complex. The recurrent neural networks are trained on the trajectories of bubbles obtained by Direct Numerical Simulations (DNS) of the Navier Stokes equations for a two-component incompressible flow model. Long short term memory components exploit the time history of the flow field that the bubbles have encountered along their trajectories and the networks are further augmented by imposing rotational invariance to their structure. We first train and validate the formulated model using DNS data for a turbulent Taylor-Green vortex. Then we examine the model predictive capabilities and its generalization to Reynolds numbers that are different from those of the training data on benchmark problems, including a steady (Hill's spherical vortex) and an unsteady (Gaussian vortex ring) flow field. We find that the predictions of the developed model are significantly improved compared with those obtained by the MR equation. Our results indicate that data-driven models with history terms are well suited in capturing the trajectories of bubbles in turbulent flows.

physics.flu-dyn↗

arXiv2019

Data-Driven Forecasting of High-Dimensional Chaotic Systems with Long Short-Term Memory Networks

We introduce a data-driven forecasting method for high-dimensional chaotic systems using long short-term memory (LSTM) recurrent neural networks. The proposed LSTM neural networks perform inference of high-dimensional dynamical systems in their reduced order space and are shown to be an effective set of nonlinear approximators of their attractor. We demonstrate the forecasting performance of the LSTM and compare it with Gaussian processes (GPs) in time series obtained from the Lorenz 96 system, the Kuramoto-Sivashinsky equation and a prototype climate model. The LSTM networks outperform the GPs in short-term forecasting accuracy in all applications considered. A hybrid architecture, extending the LSTM with a mean stochastic model (MSM-LSTM), is proposed to ensure convergence to the invariant measure. This novel hybrid method is fully data-driven and extends the forecasting capabilities of LSTM networks.

physics.comp-ph↗

arXiv2019

Optimal sensor placement for artificial swimmers

Natural swimmers rely for their survival on sensors that gather information from the environment and guide their actions. The spatial organization of these sensors, such as the visual fish system and lateral line, suggests evolutionary selection, but their optimality remains an open question. Here, we identify sensor configurations that enable swimmers to maximize the information gathered from their surrounding flow field. We examine two-dimensional, self-propelled and stationary swimmers that are exposed to disturbances generated by oscillating, rotating and D-shaped cylinders. We combine simulations of the Navier-Stokes equations with Bayesian experimental design to determine the optimal arrangements of shear and pressure sensors that best identify the locations of the disturbance-generating sources. We find a marked tendency for shear stress sensors to be located in the head and the tail of the swimmer, while they are absent from the midsection. In turn, we find a high density of pressure sensors in the head along with a uniform distribution along the entire body. The resulting optimal sensor arrangements resemble neuromast distributions observed in fish and provide evidence for optimality in sensor distribution for natural swimmers.

physics.flu-dyn↗

arXiv2019

Remember and Forget for Experience Replay

Experience replay (ER) is a fundamental component of off-policy deep reinforcement learning (RL). ER recalls experiences from past iterations to compute gradient estimates for the current policy, increasing data-efficiency. However, the accuracy of such updates may deteriorate when the policy diverges from past behaviors and can undermine the performance of ER. Many algorithms mitigate this issue by tuning hyper-parameters to slow down policy changes. An alternative is to actively enforce the similarity between policy and the experiences in the replay memory. We introduce Remember and Forget Experience Replay (ReF-ER), a novel method that can enhance RL algorithms with parameterized policies. ReF-ER (1) skips gradients computed from experiences that are too unlikely with the current policy and (2) regulates policy changes within a trust region of the replayed behaviors. We couple ReF-ER with Q-learning, deterministic policy gradient and off-policy gradient methods. We find that ReF-ER consistently improves the performance of continuous-action, off-policy RL on fully observable benchmarks and partially observable flow control problems.

cs.LG↗

arXiv2019

Bending models of lipid bilayer membranes: spontaneous curvature and area-difference elasticity

We preset a computational study of bending models for the curvature elasticity of lipid bilayer membranes that are relevant for simulations of vesicles and red blood cells. We compute bending energy and forces on triangulated meshes and evaluate and extend four well established schemes for their approximation: Kantor and Nelson 1987, Phys. Rev. A 36, 4020, Jülicher 1996, J. Phys. II France 6, 1797, Gompper and Kroll 1996, J. Phys. I France 6, 1305, and Meyer et. al. 2003 in Visualization and Mathematics III, Springer, p35, termed A, B, C, D. We present a comparative study of these four schemes on the minimal bending model and propose extensions for schemes B, C and D. These extensions incorporate the reference state and non-local energy to account for the spontaneous curvature, bilayer coupling, and area-difference elasticity models. Our results indicate that the proposed extensions enhance the models to account for shape transformation including budding/vesiculation as well as for non-axisymmetric shapes. We find that the extended scheme B is superior to the rest in terms of accuracy, and robustness as well as simplicity of implementation. We demonstrate the capabilities of this scheme on several benchmark problems including the budding-vesiculating process and the reproduction of the phase diagram of vesicles.

cs.CE↗

arXiv2019

Personalized Radiotherapy Design for Glioblastoma: Integrating Mathematical Tumor Models, Multimodal Scans and Bayesian Inference

Glioblastoma is a highly invasive brain tumor, whose cells infiltrate surrounding normal brain tissue beyond the lesion outlines visible in the current medical scans. These infiltrative cells are treated mainly by radiotherapy. Existing radiotherapy plans for brain tumors derive from population studies and scarcely account for patient-specific conditions. Here we provide a Bayesian machine learning framework for the rational design of improved, personalized radiotherapy plans using mathematical modeling and patient multimodal medical scans. Our method, for the first time, integrates complementary information from high resolution MRI scans and highly specific FET-PET metabolic maps to infer tumor cell density in glioblastoma patients. The Bayesian framework quantifies imaging and modeling uncertainties and predicts patient-specific tumor cell density with confidence intervals. The proposed methodology relies only on data acquired at a single time point and thus is applicable to standard clinical settings. An initial clinical population study shows that the radiotherapy plans generated from the inferred tumor cell infiltration maps spare more healthy tissue thereby reducing radiation toxicity while yielding comparable accuracy with standard radiotherapy protocols. Moreover, the inferred regions of high tumor cell densities coincide with the tumor radioresistant areas, providing guidance for personalized dose-escalation. The proposed integration of multimodal scans and mathematical modeling provides a robust, non-invasive tool to assist personalized radiotherapy design.

cs.CE↗

arXiv2018

Bayesian selection for coarse-grained models of liquid water

The necessity for accurate and computationally efficient representations of water in atomistic simulations that can span biologically relevant timescales has born the necessity of coarse-grained (CG) modeling. Despite numerous advances, CG water models rely mostly on a-priori specified assumptions. How these assumptions affect the model accuracy, efficiency, and in particular transferability, has not been systematically investigated. Here we propose a data driven, comparison and selection for CG water models through a Hierarchical Bayesian framework. We examine CG water models that differ in their level of coarse-graining, structure, and number of interaction sites. We find that the importance of electrostatic interactions for the physical system under consideration is a dominant criterion for the model selection. Multi-site models are favored, unless the effects of water in electrostatic screening are not relevant, in which case the single site model is preferred due to its computational savings. The charge distribution is found to play an important role in the multi-site model's accuracy while the flexibility of the bonds/angles may only slightly improve the models. Furthermore, we find significant variations in the computational cost of these models. We present a data informed rationale for the selection of CG water models and provide guidance for future water model designs.

physics.comp-ph↗

arXiv2018

ContextVP: Fully Context-Aware Video Prediction

Video prediction models based on convolutional networks, recurrent networks, and their combinations often result in blurry predictions. We identify an important contributing factor for imprecise predictions that has not been studied adequately in the literature: blind spots, i.e., lack of access to all relevant past information for accurately predicting the future. To address this issue, we introduce a fully context-aware architecture that captures the entire available past context for each pixel using Parallel Multi-Dimensional LSTM units and aggregates it using blending units. Our model outperforms a strong baseline network of 20 recurrent convolutional layers and yields state-of-the-art performance for next step prediction on three challenging real-world video datasets: Human 3.6M, Caltech Pedestrian, and UCF-101. Moreover, it does so with fewer parameters than several recently proposed models, and does not rely on deep convolutional networks, multi-scale architectures, separation of background and foreground modeling, motion flow learning, or adversarial training. These results highlight that full awareness of past context is of crucial importance for video prediction.

cs.CV↗

arXiv2018

Deep-Reinforcement-Learning for Gliding and Perching Bodies

Controlled gliding is one of the most energetically efficient modes of transportation for natural and human powered fliers. Here we demonstrate that gliding and landing strategies with different optimality criteria can be identified through deep reinforcement learning without explicit knowledge of the underlying physics. We combine a two dimensional model of a controlled elliptical body with deep reinforcement learning (D-RL) to achieve gliding with either minimum energy expenditure, or fastest time of arrival, at a predetermined location. In both cases the gliding trajectories are smooth, although energy/time optimal strategies are distinguished by small/high frequency actuations. We examine the effects of the ellipse's shape and weight on the optimal policies for controlled gliding. Surprisingly, we find that the model-free reinforcement learning leads to more robust gliding than model-based optimal control strategies with a modest additional computational cost. We also demonstrate that the gliders with D-RL can generalize their strategies to reach the target location from previously unseen starting positions. The model-free character and robustness of D-RL suggests a promising framework for developing mechanical devices capable of exploiting complex flow environments.

cs.RO↗

arXiv2018

$S$-Leaping: An adaptive, accelerated stochastic simulation algorithm, bridging $τ$-leaping and $R$-leaping

We propose the $S$-leaping algorithm for the acceleration of Gillespie's stochastic simulation algorithm that combines the advantages of the two main accelerated methods; the $τ$-leaping and $R$-leaping algorithms. These algorithms are known to be efficient under different conditions; the $τ$-leaping is efficient for non-stiff systems or systems with partial equilibrium, while the $R$-leaping performs better in stiff system thanks to an efficient sampling procedure. However, even a small change in a system's set up can critically affect the nature of the simulated system and thus reduce the efficiency of an accelerated algorithm. The proposed algorithm combines the efficient time step selection from the $τ$-leaping with the effective sampling procedure from the $R$-leaping algorithm. The $S$-leaping is shown to maintain its efficiency under different conditions and in the case of large and stiff systems or systems with fast dynamics, the $S$-leaping outperforms both methods. We demonstrate the performance and the accuracy of the $S$-leaping in comparison with the $τ$-leaping and $R$-leaping on a number of benchmark systems involving biological reaction networks.

math.PR↗

arXiv2018

A Computational Study of the Collapse of a Cloud with 12500 Gas Bubbles in a Liquid

We investigate the process of cloud cavitation collapse through large-scale simulation of a cloud composed of 12500 gas bubbles. A finite volume scheme is used on a structured Cartesian grid to solve the Euler equations, and the bubbles are discretized by a diffuse interface method. We investigate the propagation of the collapse wave front through the cloud and provide comparisons to simplified models. We analyze the flow field to identify each bubble of the cloud and its associated microjet. We find that the oscillation frequency of the bubbles and the velocity magnitude of the microjets depend on the local strength of the collapse wave and hence on the radial position of the bubbles in the cloud. At the same time, the direction of the microjets is influenced by the distribution of the bubbles in its vicinity. Finally, an analysis of the pressure pulse spectrum shows that the pressure pulse rate is well captured by an exponential law.

physics.comp-ph↗

arXiv2018

Data-assisted reduced-order modeling of extreme events in complex dynamical systems

Dynamical systems with high intrinsic dimensionality are often characterized by extreme events having the form of rare transitions several standard deviations away from the mean. For such systems, order-reduction methods through projection of the governing equations have limited applicability due to the large intrinsic dimensionality of the underlying attractor but also the complexity of the transient events. An alternative approach is data-driven techniques that aim to quantify the dynamics of specific modes utilizing data-streams. Several of these approaches have improved performance by expanding the state representation using delayed coordinates. However, such strategies are limited in regions of the phase space where there is a small amount of data available, as is the case for extreme events. In this work, we develop a blended framework that integrates an imperfect model, obtained from projecting equations into a subspace that still contains crucial dynamical information, with data-streams through a recurrent neural network (RNN) architecture. In particular, we employ the long-short-term memory (LSTM), to model portions of the dynamics which cannot be accounted by the equations. The RNN is trained by analyzing the mismatch between the imperfect model and the data-streams, projected in the reduced-order space. In this way, the data-driven model improves the imperfect model in regions where data is available, while for locations where data is sparse the imperfect model still provides a baseline for the prediction of the system dynamics. We assess the developed framework on two challenging prototype systems exhibiting extreme events and show that the blended approach has improved performance compared with methods that use either data streams or the imperfect model alone. The improvement is more significant in regions associated with extreme events, where data is sparse.

nlin.CD↗

arXiv2018

Langevin Diffusion for Population Based Sampling with an Application in Bayesian Inference for Pharmacodynamics

We propose an algorithm for the efficient and robust sampling of the posterior probability distribution in Bayesian inference problems. The algorithm combines the local search capabilities of the Manifold Metropolis Adjusted Langevin transition kernels with the advantages of global exploration by a population based sampling algorithm, the Transitional Markov Chain Monte Carlo (TMCMC). The Langevin diffusion process is determined by either the Hessian or the Fisher Information of the target distribution with appropriate modifications for non positive definiteness. The present methods is shown to be superior over other population based algorithms, in sampling probability distributions for which gradients are available and is shown to handle otherwise unidentifiable models. We demonstrate the capabilities and advantages of the method in computing the posterior distribution of the parameters in a Pharmacodynamics model, for glioma growth and its drug induced inhibition, using clinical data.

stat.CO↗

arXiv2018

Efficient collective swimming by harnessing vortices through deep reinforcement learning

Fish in schooling formations navigate complex flow-fields replete with mechanical energy in the vortex wakes of their companions. Their schooling behaviour has been associated with evolutionary advantages including collective energy savings. How fish harvest energy from their complex fluid environment and the underlying physical mechanisms governing energy-extraction during collective swimming, is still unknown. Here we show that fish can improve their sustained propulsive efficiency by actively following, and judiciously intercepting, vortices in the wake of other swimmers. This swimming strategy leads to collective energy-savings and is revealed through the first ever combination of deep reinforcement learning with high-fidelity flow simulations. We find that a `smart-swimmer' can adapt its position and body deformation to synchronise with the momentum of the oncoming vortices, improving its average swimming-efficiency at no cost to the leader. The results show that fish may harvest energy deposited in vortices produced by their peers, and support the conjecture that swimming in formation is energetically advantageous. Moreover, this study demonstrates that deep reinforcement learning can produce navigation algorithms for complex flow-fields, with promising implications for energy savings in autonomous robotic swarms.

physics.flu-dyn↗