arXiv subjects

Rui Sun

Publications and source records attributed to Rui Sun.

At least 163 records · Page 9Linked to original sources

arXiv2017

Representation of Reynolds Stress Perturbations with Application in Machine-Learning-Assisted Turbulence Modeling

Numerical simulations based on Reynolds-Averaged Navier--Stokes (RANS) equations are widely used in engineering design and analysis involving turbulent flows. However, RANS simulations are known to be unreliable in many flows of engineering relevance, which is largely caused by model-form uncertainties associated with the Reynolds stresses. Recently, a machine-learning approach has been proposed to assist RANS modeling by building a functional mapping from mean flow features to discrepancies in RANS modeled Reynolds stresses as compared to high-fidelity data. However, it remains a challenge to represent discrepancies in the Reynolds stress eigenvectors in machine learning due to the requirements of spatial smoothness, frame-independence, and realizability. In this work, we propose three schemes for representing perturbations to the eigenvectors of RANS modeled Reynolds stresses: (1) discrepancy-based Euler angles, (2) direct-rotation-based Euler angles, and (3) unit quaternions. We compare these metrics by performing a priori and a posteriori tests on two canonical flows: fully developed turbulent flows in a square duct and massively separated flows over periodic hills. The results demonstrate that the direct-rotation-based Euler angles representation lacks spatial smoothness while the discrepancy-based Euler angles representation lacks frame-independence, making them unsuitable for being used in machine-learning-assisted turbulence modeling. In contrast, the representation based on unit quaternion satisfies all the requirements stated above, and thus it is an ideal choice in representing the perturbations associated with the eigenvectors of Reynolds stress tensors. This finding has clear importance for uncertainty quantification and machine learning in turbulence modeling and for data-driven computational mechanics in general.

physics.flu-dyn↗

arXiv2017

Measurement of magic-wavelength optical dipole trap by using the laser-induced fluorescence spectra of trapped single cesium atoms

Based on the multi-level model, we have calculated light shifts for Zeeman states of hyperfine levels of cesium (Cs) 6S1/2 ground state and 6P3/2 excited state.The magic-wavelength linearly-polarized optical dipole trap (ODT) for Cs 6S1/2 F=4, mF=+4 - 6P3/2 F'=5, mF=+5 transition is experimentally constructed and characterized by using the laser-induced fluorescence spectra of trapped single Cs atoms. The magic wavelength is 937.7 nm which produces almost the same light shift for 6S1/2 F=4, mF=+4 ground state and 6P3/2 F'=5, mF=+5 excited state with linearly-polarized ODT laser beam. Compared to undisturbed Cs 6S1/2 F=4, mF=+4 - 6P3/2 F'=5, mF=+5 transition frequency in free space, the differential light shift is less than 0.7 MHz in a linearly-polarized 937.7 nm ODT, which is less than 1.2% of the trap depth. We also discussed influence of the trap depth and the bias magnetic field on the measurement results.

physics.atom-ph↗

arXiv2017

Investigating the Settling Dynamics of Cohesive Silt Particles With Particle-Resolving Simulations

The settling of cohesive sediment is ubiquitous in aquatic environments. In the settling process, the silt particles show behaviors that are different from non-cohesive particles due to the influence of inter-particle cohesive force. While it is a consensus that cohesive behaviors depend on the characteristics of sediment particles (e.g., Bond number, particle size distribution), little is known about the exact influence of these characteristics on the cohesive behaviors. In the present work, three-dimensional settling process is investigated numerically by using CFD--DEM (Computational Fluid Dynamics--Discrete Element Method). The inter-particle collision force, the van der Waals force, and the fluid--particle interaction forces are considered. The numerical model is used to simulate the hindered settling process of silt based on the experimental setup in the literature. The results obtained in the simulations, including the structural densities of the beds, the characteristic lines, and the particle terminal velocity, are in good agreement with the experimental observations in the literature. To the authors' knowledge, this is the first time that the influences of non-dimensional Bond number and particle polydispersity on the structural densities of silt beds have been investigated separately. The results demonstrate that the cohesive behavior of silt in the settling process is attributed to both the cohesion among silt particles themselves and the particle polydispersity. To guide to the macro-scale modeling of cohesive silt sedimentation, the collision frequency functions obtained in the numerical simulations are also presented based on the micromechanics of particles. The results obtained by using CFD--DEM indicate that the binary collision theory over-estimated the particle collision frequency in the flocculation process at high solid volume fraction.

cond-mat.soft↗

arXiv2017

Correlation, Breit and Quantum Electrodynamics effects on energy level and transition properties of W$^{54+}$ ion

The electron correlation effects and Breit interaction as well as Quantum Electro-Dynamics (QED) effects were expected to have important contribution to the energy level and transition properties of heavy highly charged ions. The ground states [Ne]$3s^{2}3p^{6}3d^{2}$ and first excited states [Ne]3s$^{2}3p^{5}3d^{3}$ of W$^{54+}$ ion have been studied by using Multi-Configuration Dirac-Fock method with the implementation of Grasp2K package. A restricted active space was employed to investigate the correlation contribution from different models. The Breit interaction and QED effects were taken into account in the relativistic configuration interaction calculation with the converged wavefunction. It is found that the correlation contribution from 3s and 3p orbital have important contribution to the energy level, transition wavelength and probability of the ground and the first excited state of W$^{54+}$ ion.

physics.atom-ph↗

arXiv2016

E1, M1, E2 transition energies and probabilities of W$^{54+}$ ions

A comprehensive theoretical study of the E1, M1, E2 transitions of Ca-like tungsten ions is presented. Using multi-configuration Dirac-Fock (MCDF) method with a restricted active space treatment, the wavelengths and probabilities of the M1 and E2 transitions between the multiplets of the ground state configuration ([Ne]3s$^{2}$3p$^{6}$3d$^{2}$) and of the E1 transitions between [Ne]3s$^{2}$3p$^{5}$3d$^{3}$ and [Ne]3s$^{2}$3p$^{6}$3d$^{2}$ have been calculated. The results are in reasonable agreement with available experimental data. The present E1 and M1 calculations are compared with previous theoretical values. For E2 transitions, the importance of electron correlation from 3s and 3p orbitals is pointed out. Several strong E1 transitions are predicted, which have potential advantage for plasma diagnostics.

physics.atom-ph↗

arXiv2016

wtest: an R Package for Testing Main and Interaction Effect in Genotype Data with Binary Traits

This R package evaluates main and pair-wise interaction effect of single nucleotide polymorphisms (SNPs) via the W-test, scalable to whole genome-wide data sets. The package provides fast and accurate p-value estimation of genetic markers, as well as diagnostic checking on the probability distributions. It allows flexible stage-wise or exhaustive association testing in a user-friendly interface. Availability: The package is available in CRAN, or from website: http://www2.ccrb.cuhk.edu.hk/wtest

stat.CO↗

arXiv2016

Realistic Representation of Grain Shapes in CFD--DEM Simulations of Sediment Transport: A Bonded-Sphere Approach

Development of algorithms and growth of computational resources in the past decades have enabled simulations of sediment transport processes with unprecedented fidelities. The Computational Fluid Dynamics--Discrete Element Method (CFD--DEM) is one of the high-fidelity approaches, where the motions of and collisions among the sediment grains as well as their interactions with surrounding fluids are resolved. In most DEM solvers the particles are modeled as soft spheres due to computational efficiency and implementation complexity considerations, although natural sediments are usually mixture of non-spherical particles. Previous attempts to extend sphere-based DEM to treat irregular particles neglected fluid-induced torques on particles, and the method lacked flexibility to handle sediments with an arbitrary mixture of particle shapes. In this contribution we proposed a simple, efficient approach to represent common sediment grain shapes with bonded spheres, where the fluid forces are computed and applied on each sphere. The proposed approach overcomes the aforementioned limitations of existing methods and has improved efficiency and flexibility over existing approaches. We use numerical simulations to demonstrate the merits and capability of the proposed method in predicting the falling characteristics, terminal velocity, threshold of incipient motion, and transport rate of natural sediments. The simulations show that the proposed method is a promising approach for faithful representation of natural sediment, which leads to accurate simulations of their transport dynamics. The proposed method also opens the possibility for first-principle-based simulations of the flocculation and sedimentation dynamics of cohesive sediments. Elucidation of these physical mechanisms can provide much needed improvement on the prediction capability and physical understanding of muddy coast dynamics.

physics.comp-ph↗

arXiv2016

A W-test collapsing method for rare variant testing with applications to exome sequencing data of hypertensive disorder

Advancement in sequencing technology enables the study of association between complex disorders and rare variants with low minor allele frequencies. One of the major challenges in rare variant testing is lack of statistical power of traditional testing methods due to extremely low variances of single nucleotide polymorphisms. In this paper, we introduce a W-test collapsing method that evaluates the distributional differences in cases and controls using a combined log of odds ratio. The proposed method is compared with the Weighted-Sum Statistic and Sequence Kernel Association Test using simulation data sets and showed better performances and faster computing speed. In the study of real next generation sequencing data set of hypertensive disorder, we identified genes of interesting biological functions that are associated to metabolism disorder and inflammation, which include the MACROD1, NLRP7, AGK, PAK6 and APBB1. The W-test collapsing method offers a fast, effective and alternative way for rare variants association analysis.

q-bio.QM↗

arXiv2016

Enhancing power of rare variant association test by Zoom-Focus Algorithm (ZFA) to locate optimal testing region

Motivation: Exome or targeted sequencing data exerts analytical challenge to test single nucleotide polymorphisms (SNPs) with extremely small minor allele frequency (MAF). Various rare variant tests were proposed to increase power by aggregating SNPs within a fixed genomic region, such as a gene or pathway. However, a gene could contain from several to thousands of markers, and not all of them may be related to the phenotype. Combining functional and non-functional SNPs in arbitrary genomic region could impair the testing power. Results: We propose a Zoom-Focus algorithm (ZFA) to locate the optimal testing region within a given genomic region, as a wrapper function to be applied in conjunction with rare variant association tests. In the first Zooming step, a given genomic region is partitioned by order of two, and the best partition is located within all partition levels. In the next Focusing step, boundaries of the zoomed region are refined. Simulation studies showed that ZFA substantially enhanced the statistical power of rare variant tests by over 10 folds, including the WSS, SKAT and W-test. The algorithm is applied on real exome sequencing data of hypertensive disorder, and identified biologically relevant genetic markers to metabolic disorder that are undiscoverable by testing using full gene. The proposed algorithm is an efficient and powerful tool to increase the effectiveness of rare variant association tests for exome sequencing datasets of complex disorder.

q-bio.GN↗

arXiv2016

Sediment Micromechanics in Sheet Flows Induced by Asymmetric Waves: A CFD-DEM Study

Understanding the sediment transport in oscillatory flows is essential to the investigation of the overall sediment budget for coastal regions. This overall budget is crucial for the prediction of the morphological change of coastline in engineering applications. Since the sediment transport in oscillatory flows is dense particle-laden flow, appropriate modeling of the particle interaction is critical. Although traditional two-fluid approaches have been applied to the study of sediment transport in oscillatory flows, the approaches do not resolve the interaction of the particles. Particle-resolved modeling of sediment transport in oscillatory flows and the study of micromechanics of sediment particles are still lacking. In this work, a parallel CFD-DEM solver that can resolve the inter-particle collision is applied to study the granular micromechanics of sediment particles in oscillatory flows. The results obtained from the CFD-DEM solver are validated by using the experimental data of coarse and medium sands. The comparison with experimental results suggests that the flow velocity, the sediment flux and the net sediment transport rate predicted by are satisfactory. Moreover, the micromechanic quantities of the sediment bed are presented in detail, including Voronoi concentration, coordination number, and particle interaction force. It is demonstrated that variation of these micromechanic quantities at different phases in the oscillatory cycle is significant, which is due to different responses of the sediment bed. To investigate the structural properties of the sediment bed, the correlation of the Voronoi volume fraction and coordination number are compared to the results from the fluidized bed simulations. The consistency in the comparison indicates the structural micromechanics of sediment transport and fluidized bed are similar despite the differences in flow patterns.

physics.comp-ph↗

arXiv2016

CFD-DEM Simulations of Current-Induced Dune Formation and Morphological Evolution

Understanding the fundamental mechanisms of sediment transport, particularly those during the formation and evolution of bedforms, is of critical scientific importance and has engineering relevance. Traditional approaches of sediment transport simulations heavily rely on empirical models, which are not able to capture the physics-rich, regime-dependent behaviors of the process. With the increase of available computational resources in the past decade, CFD-DEM (computational fluid dynamics-discrete element method) has emerged as a viable high-fidelity method for the study of sediment transport. However, a comprehensive, quantitative study of the generation and migration of different sediment bed patterns using CFD-DEM is still lacking. In this work, current-induced sediment transport problems in a wide range of regimes are simulated, including 'flat bed in motion', `small dune', `vortex dune' and suspended transport. Simulations are performed by using SediFoam, an open-source, massively parallel CFD-DEM solver developed by the authors. This is a general-purpose solver for particle-laden flows tailed for particle transport problems. Validation tests are performed to demonstrate the capability of CFD-DEM in the full range of sediment transport regimes. Comparison of simulation results with experimental and numerical benchmark data demonstrates the merits of CFD-DEM approach. In addition, the improvements of the present simulations over existing studies using CFD-DEM are presented. The present solver gives more accurate prediction of sediment transport rate by properly accounting for the influence of particle volume fraction on the fluid flow. In summary, this work demonstrates that CFD-DEM is a promising particle-resolving approach for probing the physics of current-induced sediment transport.

physics.flu-dyn↗

arXiv2016

Quantification of Uncertainties in Turbulence Modeling: A Comparison of Physics-Based and Random Matrix Theoretic Approaches

Numerical models based on Reynolds-Averaged Navier-Stokes (RANS) equations are widely used in engineering turbulence modeling. However, the RANS predictions have large model-form uncertainties for many complex flows. Quantification of these large uncertainties originating from the modeled Reynolds stresses has attracted attention in turbulence modeling community. Recently, a physics-based Bayesian framework for quantifying model-form uncertainties has been proposed with successful applications to several flows. Nonetheless, how to specify proper priors without introducing unwarranted, artificial information remains challenging to the current form of the physics-based approach. Another recently proposed method based on random matrix theory provides the prior distributions with the maximum entropy, which is an alternative for model-form uncertainty quantification in RANS simulations. In this work, we utilize the random matrix theoretic approach to assess and possibly improve the specification of priors used in the physics-based approach. The numerical results show that, to achieve maximum entropy in the prior of Reynolds stresses, the perturbations of shape parameters in Barycentric coordinates are normally distributed. Moreover, the perturbations of the turbulence kinetic energy should conform to log-normal distributions. Finally, it sheds light on how large the variance of each physical variable should be compared with each other to achieve the approximate maximum entropy prior. The conclusion can be used as a guidance for specifying proper priors in the physics-based, Bayesian uncertainty quantification framework.

physics.comp-ph↗

arXiv2016

The Flux-Scaling Scenario: De Sitter Uplift and Axion Inflation

Non-geometric flux-scaling vacua provide promising starting points to realize axion monodromy inflation via the F-term scalar potential. We show that these vacua can be uplifted to Minkowski and de Sitter by adding an anti D3-brane or a D-term containing geometric and non-geometric fluxes. These uplifted non-supersymmetric models are analyzed with respect to their potential to realize axion monodromy inflation self-consistently. Admitting rational values of the fluxes, we construct examples with the required hierarchy of mass scales.

hep-th↗

arXiv2016

SediFoam: A general-purpose, open-source CFD-DEM solver for particle-laden flow with emphasis on sediment transport

With the growth of available computational resource, CFD-DEM (computational fluid dynamics-discrete element method) becomes an increasingly promising and feasible approach for the study of sediment transport. Several existing CFD-DEM solvers are applied in chemical engineering and mining industry. However, a robust CFD-DEM solver for the simulation of sediment transport is still desirable. In this work, the development of a three-dimensional, massively parallel, and open-source CFD-DEM solver SediFoam is detailed. This solver is built based on open-source solvers OpenFOAM and LAMMPS. OpenFOAM is a CFD toolbox that can perform three-dimensional fluid flow simulations on unstructured meshes; LAMMPS is a massively parallel DEM solver for molecular dynamics. Several validation tests of SediFoam are performed using cases of a wide range of complexities. The results obtained in the present simulations are consistent with those in the literature, which demonstrates the capability of SediFoam for sediment transport applications. In addition to the validation test, the parallel efficiency of SediFoam is studied to test the performance of the code for large-scale and complex simulations. The parallel efficiency tests show that the scalability of SediFoam is satisfactory in the simulations using up to O(10^7) particles.

physics.flu-dyn↗

arXiv2015

Diffusion-Based Coarse Graining in Hybrid Continuum-Discrete Solvers: Theoretical Formulation and A Priori Tests

Coarse graining is an important ingredient in many multi-scale continuum-discrete solvers such as CFD--DEM (computational fluid dynamics--discrete element method) solvers for dense particle-laden flows. Although CFD--DEM solvers have become a mature technique that is widely used in multiphase flow research and industrial flow simulations, a flexible and easy-to-implement coarse graining algorithm that can work with CFD solvers of arbitrary meshes is still lacking. In this work, we proposed a new coarse graining algorithm for continuum--discrete solvers for dense particle-laden flows based on solving a transient diffusion equation. Via theoretical analysis we demonstrated that the proposed method is equivalent to the statistical kernel method with a Gaussian kernel, but the current method is much more straightforward to implement in CFD--DEM solvers. \textit{A priori} numerical tests were performed to obtain the solid volume fraction fields based on given particle distributions, the results obtained by using the proposed algorithm were compared with those from other coarse graining methods in the literature (e.g., the particle centroid method, the divided particle volume method, and the two-grid formulation). The numerical tests demonstrated that the proposed coarse graining procedure based on solving diffusion equations is theoretically sound, easy to implement and parallelize in general CFD solvers, and has improved mesh-convergence characteristics compared with existing coarse graining methods. The diffusion-based coarse graining method has been implemented into a CFD--DEM solver, the results of which are presented in a separate work (R. Sun and H. Xiao, Diffusion-based coarse graining in hybrid continuum-discrete solvers: Application in CFD-DEM solvers for particle laden flows).

physics.comp-ph↗

arXiv2015

Diffusion-Based Coarse Graining in Hybrid Continuum-Discrete Solvers: Applications in CFD-DEM

In this work, a coarse-graining method previously proposed by the authors in a companion paper based on solving diffusion equations is applied to CFD-DEM simulations, where coarse graining is used to obtain solid volume fraction, particle phase velocity, and fluid-particle interaction forces. By examining the conservation requirements, the variables to solve diffusion equations for in CFD-DEM simulations are identified. The algorithm is then implemented into a CFD-DEM solver based on OpenFOAM and LAMMPS, the former being a general-purpose, three-dimensional CFD solver based on unstructured meshes. Numerical simulations are performed for a fluidized bed by using the CFD-DEM solver with the diffusion-based coarse-graining algorithm. Converged results are obtained on successively refined meshes, even for meshes with cell sizes comparable to or smaller than the particle diameter. This is a critical advantage of the proposed method over many existing coarse-graining methods, and would be particularly valuable when small cells are required in part of the CFD mesh to resolve certain flow features such as boundary layers in wall bounded flows and shear layers in jets and wakes. Moreover, we demonstrate that the overhead computational costs incurred by the proposed coarse-graining procedure are a small portion of the total costs in typical CFD-DEM simulations as long as the number of particles per cell is reasonably large, although admittedly the computational overhead of the coarse graining often exceeds that of the CFD solver. Other advantages of the present algorithm include more robust and physically realistic results, flexibility and easy implementation in almost any CFD solvers, and clear physical interpretation of the computational parameter needed in the algorithm. In summary, the diffusion-based method is a theoretically elegant and practically viable option for CFD-DEM simulations.

physics.comp-ph↗

arXiv2014

T-duality, Non-geometry and Lie Algebroids in Heterotic Double Field Theory

A number of issues in heterotic double field theory are studied. This includes the analysis of the T-dual configurations of a flat constant gauge flux background, which turn out to be non-geometric. Performing a field redefinition to a non-geometric frame, these T-duals take a very simple form reminiscent of the constant Q- and R-flux backgrounds. In addition, it is shown how the analysis of arXiv:1304.2784 generalizes to heterotic generalized geometry. For every field redefinition specified by an O(D,D+n) transformation, the structure of the resulting supergravity action is governed by the differential geometry of a corresponding Lie algebroid.

hep-th↗

arXiv2014

Non-associative Deformations of Geometry in Double Field Theory

Non-geometric string backgrounds were proposed to be related to a non-associative deformation of the space-time geometry. In the flux formulation of double field theory (DFT), the structure of mathematically possible non-associative deformations is analyzed in detail. It is argued that on-shell there should not be any violation of associativity in the effective DFT action. For imposing either the strong or the weaker closure constraint we discuss two possible non-associative deformations of DFT featuring two different ways how on-shell associativity can still be kept.

hep-th↗