Publications

2017
S. Wu, P. Angelikopoulos, C. Papadimitriou, and P. Koumoutsakos, “Bayesian Annealed Sequential Importance Sampling (BASIS): an unbiased version of Transitional Markov Chain Monte Carlo,” ASCE-ASME J. Risk Uncertain. Eng. Sys. B, 2017. Publisher's Version Bayesian Annealed Sequential Importance Sampling (BASIS): an unbiased version of Transitional Markov Chain Monte Carlo
N. Karathanasopoulos, P. Angelikopoulos, C. Papadimitriou, and P. Koumoutsakos, “Bayesian identification of the tendon fascicle's structural composition using finite element models for helical geometries,” Comput. Method. Appl. M. vol. 313, pp. 744–758, 2017. Publisher's Version
E. Oyarzua, J. H. Walther, C. M. Megaridis, P. Koumoutsakos, and H. A. Zambrano, “Carbon Nanotubes as Thermally Induced Water Pumps,” ACS Nano, vol. 11, no. 10, pp. 9997–10002, 2017. Publisher's Version
S. Verma, G. Abbati, G. Novati, and P. Koumoutsakos, “Computing the force distribution on the surface of complex, deforming geometries using vortex methods and Brinkman penalization,” Int. J. Numer. Meth. Fl. 2017. Publisher's Version
L. Kulakova, G. Arampatzis, P. Angelikopoulos, P. Hadjidoukas, C. Papadimitriou, and P. Koumoutsakos, “Data driven inference for the repulsive exponent of the Lennard-Jones potential in molecular dynamics simulations,” Sci. Rep.-UK, vol. 7, no. 1, pp. 16576, 2017. Publisher's VersionAbstract
The Lennard-Jones (LJ) potential is a cornerstone of Molecular Dynamics (MD) simulations and among the most widely used computational kernels in science. The LJ potential models atomistic attraction and repulsion with century old prescribed parameters ($q=6$, $p=12$ respectively), originally related by a factor of two for simplicity of calculations. We propose the inference of the repulsion exponent through Hierarchical Bayesian uncertainty quantification We use experimental data of the radial distribution function and dimer interaction energies from quantum mechanics simulations. We find that the repulsion exponent $p\approx6.5$ provides an excellent fit for the experimental data of liquid argon, for a range of thermodynamic conditions, as well as for saturated argon vapour. Calibration using the quantum simulation data did not provide a good fit in these cases. However, values $p\approx12.7$ obtained by dimer quantum simulations are preferred for the argon gas while lower values are promoted by experimental data. These results show that the proposed LJ 6-p potential applies to a wider range of thermodynamic conditions, than the classical LJ 6-12 potential. We suggest that calibration of the repulsive exponent in the LJ potential widens the range of applicability and accuracy of MD simulations.
E. R. Cruz-Chú, et al., “On phonons and water flow enhancement in carbon nanotubes,” Nat. Nanotechnol. vol. 12, no. 12, pp. 1106–1108, 2017. Publisher's Version
B. Mosimann, et al., “Reference Ranges for Fetal Atrioventricular and Ventriculoatrial Time Intervals and Their Ratios during Normal Pregnancy,” Fetal Diagn. Ther. 2017. Publisher's VersionAbstract
Background: The diagnostic assessment of fetal arrhythmias relies on the measurements of atrioventricular (AV) and ventriculoatrial (VA) time intervals. Pulsed Doppler over in- and outflow of the left ventricle and tissue Doppler imaging are well-described methods, while Doppler measurements between the left brachiocephalic vein and the aortic arch are less investigated. The aim of this study was to compare these methods of measurement, to find influencing factors on AV and VA times and their ratio, and to create reference ranges. Methods: Echocardiography was performed between 16 and 40 weeks of gestation in normal singleton pregnancies. Nomograms for the individual measurements were created using quantile regression with Matlab Data Analytics. Statistical analyses were performed with GraphPad version 5.0 for Windows. Results: A total of 329 pregnant women were en- rolled. A significant correlation exists between AV and VA times and gestational age (GA) (p = 0.0104 to <0.0001, σ = 0.1412 to 0.3632). No correlation was found between the AV:VA ratio and GA (p = 0.08 to 0.60). All measurements differed significantly amongst the studied methods (p < 0.0001). Conclusions: AV and VA intervals increase proportionally with GA; no other independent influencing factors could be identified. As significant differences exist between the three methods of assessment, it is crucial to use appropriate reference ranges to diagnose pathologies.
G. Novati, S. Verma, D. Alexeev, D. Rossinelli, W. M. Van Rees, and P. Koumoutsakos, “Synchronisation through learning for two self-propelled swimmers,” Bioinspir. Biomim. vol. 12, no. 3, pp. 036001, 2017. Publisher's VersionAbstract
The coordinated motion by multiple swimmers is a fundamental component in fish schooling. The flow field induced by the motion of each self-propelled swimmer implies non-linear hydrodynamic interactions among the members of a group. How do swimmers compensate for such hydrodynamic interactions in coordinated patterns? We provide an answer to this riddle though simulations of two, self-propelled, fish-like bodies that employ a learning algorithm to synchronise their swimming patterns. We distinguish between learned motion patterns and the commonly used a-priori specified movements, that are imposed on the swimmers without feedback from their hydrodynamic interactions. First, we demonstrate that two rigid bodies executing pre-specified motions, with an alternating leader and follower, can result in substantial drag-reduction and intermittent thrust generation. In turn, we study two self-propelled swimmers arranged in a leader-follower configuration, with a-priori specified body-deformations. These two self-propelled swimmers do not sustain their tandem configuration. The follower experiences either an increase or decrease in swimming speed, depending on the initial conditions, while the swimming of the leader remains largely unaffected. This indicates that a-priori specified patterns are not sufficient to sustain synchronised swimming. We then examine a tandem of swimmers where the leader has a steady gait and the follower learns to synchronize its motion, to overcome the forces induced by the leader’s vortex wake. The follower employs reinforcement learning to adapt its swimming-kinematics so as to minimize its lateral deviations from the leader’s path. Swimming in such a sustained synchronised tandem yields up to 30% reduction in energy expenditure for the follower, in addition to a 20% increase in its swimming-efficiency. The present results show that two self-propelled swimmers can be synchronised by adapting their motion patterns to compensate for flow-structure interactions. Moreover, swimmers can exploit the vortical structures of their flow field so that synchronised swimming is energetically beneficial.
E. Hovad, P. Larsen, J. Spangenberg, J. H. Walther, J. Thorborg, and J. H. Hattel, “Cavity prediction in sand mould production applying the DISAMATIC process,” Powder technology, vol. 321, pp. 204–217, 2017. Publisher's VersionAbstract

The sand shot in the DISAMATIC process is simulated by the discrete element method (DEM) taking into account the influence and coupling of the airflow with computational fluid dynamics (CFD). The DEM model is calibrated by a ring shear test, a sand pile experiment and a slump test. Subsequently, the DEM model is used to model the propagation of the green sand inside the mold chamber and the results are compared to experimental video footage. The chamber contains two cavities designed to quantify the deposited mass of green sand. The deposition of green sand in these two cavities is investigated with three cases of different air vent settings which control the ventilation of the chamber. These settings resulted in different air- and particle-velocities as well as different accumulated masses in the cavities, which were successfully simulated by the model.

C. K. Christiansen, J. H. Walther, P. Klit, and A. Vølund, “Investigation of journal orbit and flow pattern in a dynamically loaded journal bearing,” Tribology International, vol. 114, pp. 450–457, 2017. Publisher's VersionAbstract

A hydrodynamic journal bearing has been investigated using both the traditional two-dimensional (2D) Reynolds equation, and the full solution being the three-dimensional (3D) Navier-Stokes equations.

The two approaches are compared by performing an investigation of two inlet groove designs: the axial and the circumferential groove, respectively, on a bearing with length-to-diameter ratio of 0.5 exposed to a sinusoidal load pattern. Pressure distributions, journal orbits and frictional losses are compared. The modelling of grooves by pressure boundary conditions versus geometric conditions is examined. It is investigated if the presence of a groove increases frictional losses and the increase relates to groove dimensions. Furthermore, the influence of the groove design on the flow field is studied using the 3D solution.

J. Zavadlav and M. Praprotnik, “Adaptive resolution simulations coupling atomistic water to dissipative particle dynamics,” Journal of Chemical Physics, vol. 147, no. 11, pp. 114110, 2017. Publisher's VersionAbstract
Multiscale methods are the most efficient way to address the interlinked spatiotemporal scales encountered in soft matter and molecular liquids. In the literature reported hybrid approaches span from quantum to atomistic, coarse-grained, and continuum length scales. In this article, we present the hybrid coupling of the molecular dynamics (MD) and dissipative particle dynamics (DPD) methods, bridging the micro- and mesoscopic descriptions. The interfacing is performed within the adaptive resolution scheme (AdResS), which is a linear momentum conserving coupling technique. Our methodology is hence suitable to simulate fluids on the micro/mesoscopic scale, where hydrodynamics plays an important role. The presented approach is showcased for water at ambient conditions. The supramolecular coupling is enabled by a recently developed clustering algorithm SWINGER that assembles, disassembles, and reassembles clusters as needed during the course of the simulation. This allows for a seamless coupling between standard atomistic MD and DPD models. The developed framework can be readily applied to various applications in the fields of materials and life sciences, e.g., simulations of phospholipids and polymer melts, or to study the red blood cells behavior in normal and disease states.
I. Hanasaki and J. H. Walther, “Suspended particle transport through constriction channel with Brownian motion,” Physical Review E, vol. 96, no. 2, 2017. Publisher's VersionAbstract

It is well known that translocation events of a polymer or rod through pores or narrower parts of micro- and nanochannels have a stochastic nature due to the Brownian motion. However, it is not clear whether the objects of interest need to have a larger size than the entrance to exhibit the deviation from the dynamics of the surrounding fluid. We show by numerical analysis that the particle injection into the narrower part of the channel is affected by thermal fluctuation, where the particles have spherical symmetry and are smaller than the height of the constriction. The Péclet number (Pe) is the order parameter that governs the phenomena, which clarifies the spatio-temporal significance of Brownian motion compared to hydrodynamics. Furthermore, we find that there exists an optimal condition of Pe to attain the highest flow rate of particles relative to the dispersant fluid flow. Our finding is important in science and technology from nanopore DNA sequencers and lab-on-a-chip devices to filtration by porous materials and chromatography.

L. T. Nielsen, S. S. Asadzadeh, J. Dölger, J. H. Walther, T. Kiørboe, and A. Andersen, “Hydrodynamics of microbial filter feeding ,” Proceedings of the National Academy of Sciences (PNAS), vol. 114, no. 35, pp. 9373–9378, 2017. Publisher's VersionAbstract

Microbial filter feeders are an important group of grazers, significant to the microbial loop, aquatic food webs, and biogeochemical cycling. Our understanding of microbial filter feeding is poor, and, importantly, it is unknown what force microbial filter feeders must generate to process adequate amounts of water. Also, the trade-off in the filter spacing remains unexplored, despite its simple formulation: A filter too coarse will allow suitably sized prey to pass unintercepted, whereas a filter too fine will cause strong flow resistance. We quantify the feeding flow of the filter-feeding choanoflagellate Diaphanoeca grandis using particle tracking, and demonstrate that the current understanding of microbial filter feeding is inconsistent with computational fluid dynamics (CFD) and analytical estimates. Both approaches underestimate observed filtration rates by more than an order of magnitude; the beating flagellum is simply unable to draw enough water through the fine filter. We find similar discrepancies for other choanoflagellate species, highlighting an apparent paradox. Our observations motivate us to suggest a radically different filtration mechanism that requires a flagellar vane (sheet), something notoriously difficult to visualize but sporadically observed in the related choanocytes (sponges). A CFD model with a flagellar vane correctly predicts the filtration rate of D. grandis, and using a simple model we can account for the filtration rates of other microbial filter feeders. We finally predict how optimum filter mesh size increases with cell size in microbial filter feeders, a prediction that accords very well with observations. We expect our results to be of significance for small-scale biophysics and trait-based ecological modeling.

L. Fu, S. Litvinov, X. Y. Hu, and N. A. Adams, “A novel partitioning method for block-structured adaptive meshes,” Journal of Computational Physics, vol. 341, pp. 447–473, 2017. Publisher's VersionAbstract

We propose a novel partitioning method for block-structured adaptive meshes utilizing the meshless Lagrangian particle concept. With the observation that an optimum partitioning has high analogy to the relaxation of a multi-phase fluid to steady state, physically motivated model equations are developed to characterize the background mesh topology and are solved by multi-phase smoothed-particle hydrodynamics. In contrast to well established partitioning approaches, all optimization objectives are implicitly incorporated and achieved during the particle relaxation to stationary state. Distinct partitioning sub-domains are represented by colored particles and separated by a sharp interface with a surface tension model. In order to obtain the particle relaxation, special viscous and skin friction models, coupled with a tailored time integration algorithm are proposed. Numerical experiments show that the present method has several important properties: generation of approximately equal-sized partitions without dependence on the mesh-element type, optimized interface communication between distinct partitioning sub-domains, continuous domain decomposition which is physically localized and implicitly incremental. Therefore it is particularly suitable for load-balancing of high-performance CFD simulations.

    A. Economides, et al., “Towards the Virtual Rheometer,” in Proceedings of the Platform for Advanced Scientific Computing - PASC \textquotesingle17, 2017. Publisher's VersionAbstract
    Recent advances in medical research and bio-engineering have led to the development of devices capable of handling fluids and biological matter at the microscale. The operating conditions of medical devices are constrained to ensure that characteristic properties of blood flow, such as mechanical properties and local hemodynamics, are not altered during operation. These properties are a consequence of the red blood cell (RBC) microstructure, which changes dynamically according to the device geometry. The understanding of the mechanics and dynamics that govern the interactions between the RBCs is crucial for the quantitative characterization of blood flow, a stepping stone towards the design of medical devices specialized to the patient, in the context of personalized medicine. This can be achieved by analyzing the microstructural characteristics of the RBCs and study their dynamics. In this work we focus on the quantification of the microstructure of high and low hematocrit blood flows, in wall bounded geometries. We present distributions of the RBCs according to selected deformation criteria and dynamic characteristics, and elaborate on mechanisms that control their collective behavior, focusing on the interplay between cells and shear induced effects.
    Towards the Virtual Rheometer: High Performance Computing for the Red Blood Cell Microstructure
    N. Ramos-García, M. M. Hejlesen, J. N. Sørensen, and J. H. Walther, “Hybrid vortex simulations of wind turbines using a three-dimensional viscous-inviscid panel method,” Wind Energy, vol. 20, no. 11, pp. 1871–1889, 2017. Publisher's VersionAbstract
    A hybrid filament-mesh vortex method is proposed and validated to predict the aerodynamic performance of wind turbine rotors and to simulate the resulting wake. Its novelty consists of using a hybrid method to accurately simulate the wake down stream of the wind turbine while reducing the computational time used by the method. The proposed method uses a hybrid approach, where the near wake is resolved by using vortex filaments, which carry the vorticity shed by the trailing edge of the blades. The interaction of the vortex filaments in the near vicinity of the wind turbine is evaluated using a direct calculation, whereas the contribution from the large downstream wake is calculated using a mesh-based method. The hybrid method is first validated in detail against the well-known MEXICO experiment, using the direct filament method asa comparison. The second part of the validation includes a study of the influence of the time-integration scheme used for evolving the wake in time, aeroelastic simulations of the National Renewable Energy Laboratory 5 MW wind turbine and an analysis of the central processing unit time showing the gains of using the hybrid filament-mesh method. Copyright ©2017 John Wiley & Sons, Ltd.
    H. J. Spietz, M. M. Hejlesen, and J. H. Walther, “Iterative Brinkman penalization for simulation of impulsively started flow past a sphere and a circular disc,” Journal of Computational Physics, vol. 336, pp. 261–274, 2017. Publisher's VersionAbstract
    We present a Brinkman penalization method for three-dimensional (3D) flows using particle vortex methods, improving the existing technique by means of an iterative process. We perform simulations to study the impulsively started flow past a sphere at Re = 1000 and normal to a circular disc at Re = 500. The simulation results obtained for the flow past a sphere are found in qualitative good agreement with previously published results obtained using respectively a 3D vortex penalization method and a 3D vortex method combined with an accurate boundary element method. From the results obtained for the flow normal to a circular disc it is found that the iterative method enables the use of a time step that is one order of magnitude larger than required by the standard non-iterative Brinkman penalization method.
    K. M. Pang, N. Karvounis, J. H. Walther, J. Schramm, P. Glarborg, and S. Mayer, “Modelling of temporal and spatial evolution of sulphur oxides and sulphuric acid under large, two-stroke marine engine-like conditions using integrated CFD-chemical kinetics ,” Applied Energy, vol. 193, pp. 60–73, 2017. Publisher's VersionAbstract

    In this work, three-dimensional computational fluid dynamics (CFD) studies of sulphur oxides (SOx) and sulphuric acid (H2SO4) formation processes in a large, low speed two-stroke marine diesel engine are carried out. The current numerical study aims to investigate the conversion of sulphuric dioxide (SO2) to sulphuric trioxide (SO3) and the possibility of H2SO4 condensation which are the prerequisites to better understand the corrosion-induced wear phenomenon. This is achieved with the aid of the implementation of a multicomponent surrogate model, which comprises a skeletal n-heptane mechanism and a reduced sulphur subset mechanism. In the present work, performance of the coupled CFD-chemical kinetic model is evaluated using both qualitative and quantitative methods. The modelling results show that the temporal and spatial evolutions of SOx predicted by the skeletal model are similar to those by the base mechanism. Predictions of the variations of SOx and the associated SO2 to SO3 conversion in response to the change of fuel sulphur content, swirl velocity, start of injection, scavenge pressure and humidity qualitatively agree with numerical and experimental results from the literature. The model is further evaluated using the measured SO2 to SO3 conversion levels in a low load, low scavenge pressure case and a low load, high scavenge pressure case. The absolute values of simulated and measured conversion levels are close, although the former appear to be higher. The current results show that the flame impinges at the cylinder liner near top dead centre. The gas is cooled rapidly by the wall temperature and H2SO4 is produced in the region where the local temperature is less than 600 K. Based on the flue gas correlation, the acid dew point temperature is higher than the wall temperature, suggesting that acid condensation may begin early at the top part of the cylinder liner. The predicted distribution corresponds well with the distribution of corroded parts observed in service engines. The model is expected to serve as an important tool to simulate the rates of SO2 absorption into lubricating oil film and H2SO4 condensation in this combustion system.

    Y. Yang, J. H. Walther, Y. Yan, and C. Wen, “CFD modeling of condensation process of water vapor in supersonic flows,” Applied Thermal Engineering, vol. 115, pp. 1357–1362, 2017. Publisher's VersionAbstract

    The condensation phenomenon of vapor plays an important role in various industries, such as the steam flow in turbines and refrigeration system. A mathematical model is developed to predict the spontaneous condensing phenomenon in the supersonic flows using the nucleation and droplet growth theories. The numerical approach is validated with the experimental data, which shows a good agreement between them. The condensation characteristics of water vapor in the Laval nozzle are described in detail. The results show that the condensation process is a rapid variation of the vapor-liquid phase change both in the space and in time. The spontaneous condensation of water vapor will not appear immediately when the steam reaches the saturation state. Instead, it occurs further downstream the nozzle throat, where the steam is in the state of supersaturation.

    E. Wagemann, E. Oyarzua, J. H. Walther, and H. A. Zambrano, “Slip divergence of water flow in graphene nanochannels: the role of chirality,” Physical Chemistry Chemical Physics, vol. 19, no. 13, pp. 8646–8652, 2017. Publisher's VersionAbstract

    Graphene has attracted considerable attention due to its characteristics as a 2D material and its fascinating properties, providing a potential building block for nanofabrication. In nanochannels the solid–liquid interface plays a non-negligible role in determining the fluid dynamics. Therefore, for an optimal design of nanofluidic devices, a comprehensive understanding of the slippage in a water flow confined between graphene walls is important. In nanoconfinement, experimental and computational studies have found the slip length to increase nonlinearly when the shear rate is larger than a critical value. Here, by conducting molecular dynamics simulations, we study the influence of the graphene crystallographic orientation on the slip boundary conditions inside a nanoslit channel. The flow in channels with heights of 2.0, 2.4 and 2.8 nm is driven parallel to the zig-zag and arm-chair crystallographic directions. We extract flow rates, velocity profiles, slip velocities and slip lengths. The slip velocity displays a linear relationship to the shear stress up to a critical value, which is not size dependent. Moreover, the slip length is found to be shear stress dependent above a critical shear stress value of 0.4 MPa. Furthermore, our results indicate that after this critical shear stress is reached, the flow rates are significantly influenced (up to 10%) by the particular orientation of the graphene topology.

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