arXiv subjects

Xiaojing Zheng

Publications and source records attributed to Xiaojing Zheng.

9 recordsLinked to original sources

arXiv2026

Erodible bed turbulence modulation driven by transition between longitudinal and transverse bedforms at varying Shields numbers

The mechanism of turbulence modulation in particle-laden flow over erodible beds remains an open question. Using particle-resolved direct numerical simulations, this study realises a longitudinal-to-transverse bedform transition by varying the Shields number, revealing non-monotonic modulation of near-wall turbulence. At low Shields numbers, streamwise sediment ridges generate form-induced streaks that produce a distinct secondary peak in the premultiplied energy spectra, exceeding the conventional near-wall turbulent peak and enhancing the turbulent kinetic energy. As the Shields number increases, saltation intensifies and disrupts these structures, causing the secondary peak to vanish in the streamwise direction and weaken in the spanwise direction, thereby suppressing turbulence. Proper orthogonal decomposition of the bed surface reveals a redistribution of modal contribution from a single dominant mode to higher-order modes, with longitudinal features persisting as remnants, directly linking bedform evolution to turbulence modulation.

physics.flu-dyn↗

arXiv2026

LoopPerm-CPD: A Robust Loop Permutation Framework for Automatic Multiple Change-Point Detection in Longitudinal Data

Human viral challenge studies, in which participants are deliberately inoculated with influenza strains such as H1N1 or H3N2 and monitored through longitudinal transcriptomic profiling before and after inoculation, are critical for characterizing dynamic biological immune responses to viral infection. A key analytical goal in such settings is to detect critical transition times, or change points, at which an underlying trajectory shifts direction or rate, indicating events such as the onset of an immune response or recovery. However, change-point detection in these longitudinal data is fundamentally challenging because observations are often sparse and irregularly spaced, sample sizes are small, outliers are common, and the number of change points is unknown in advance. To address these challenges, we propose LoopPerm-CPD, a robust change-point detection approach with a built-in loop permutation procedure for automatic multiple change-point detection. The method evaluates candidate slope change points and assesses their significance using within-subject circular permutation combined with binary segmentation, jointly estimating both the number and locations of change points. The accompanying R package, LoopPerm-CPD, implements this framework and flexibly accommodates generalized least squares, quantile regression, and quantile rank-score statistics for different types of longitudinal outcomes. The proposed approach is evaluated through simulations, demonstrating Type I error control and improved power compared with competing methods. Applied to real data, the framework identifies interpretable transition points in multiple human respiratory viral inoculation studies. Together, these results establish LoopPerm-CPD and its companion software as a robust and user-friendly tool for change-point detection in complex human longitudinal cohort data.

stat.ME↗

arXiv2026

HR-VILAGE-3K3M: A Human Respiratory Viral Immunization Longitudinal Gene Expression Dataset for Systems Immunity

Respiratory viral infections pose a global health burden, yet the cellular immune mechanisms underlying protection and pathology remain unclear. Natural infection cohorts often lack pre-exposure baselines and time-controlled sampling, whereas inoculation and vaccination trials generate well-structured longitudinal transcriptomic data. However, these datasets are scattered across repositories and processed inconsistently, hindering integrative and AI-driven analyses. To address these challenges, we developed the Human Respiratory Viral Immunization LongitudinAl Gene Expression (HR-VILAGE-3K3M) repository: an AI-ready resource integrating bulk and single-cell transcriptomic profiles from 3,178 subjects across 66 studies. The dataset spans vaccination, inoculation, and mixed exposures, with samples from blood and nasal swabs collected from public repositories including GEO, ImmPort, and ArrayExpress. We curated and harmonized subject-level metadata, standardized outcome measures, and applied unified preprocessing with rigorous quality control. We further provide benchmark analyses illustrating its utility. This resource supports discovery of biomarkers, immune mechanisms, and methodological development. As one of the largest longitudinal transcriptomic resources for human respiratory viral immunization, HR-VILAGE-3K3M enables reproducible and scalable analyses to accelerate vaccine and antiviral research.

q-bio.GN↗

arXiv2024

Multi-range fractional model for convective atmospheric surface-layer turbulence

We develop a multi-range fractional (MRF) model to capture the turbulent spectrum consisting of multiple self-similar ranges impacted by multiple effects. The MRF model is validated using long-term observational atmospheric surface layer data from Qingtu lake with extreme Reynolds numbers up to Re$_τ\sim O(10^6)$. The spectral exponent in each range and the transition scales between different ranges are solo parameters in the MRF model and are identified for streamwise velocity, vertical velocity, and temperature, and they update the quantifications in the multi-point Monin-Obukhov theory. Therefore, based on the MRF model and considering the consistency between the turbulent spectrum and variance, we propose an expression for the vertical dependence of the streamwise velocity variance that is inadequately described by the Monin-Obukhov similarity theory. The MRF model provides a new method to analyze and quantify turbulent data, and as a time-series model, it enables the generation of synthetic turbulent data.

physics.flu-dyn↗

arXiv2023

A multiple-time-step integration algorithm for particle-resolved simulation with physical collision time

In this paper, we present a multiple-time-step integration algorithm (MTSA) for particle collisions in particle-resolved simulations. Since the time step required for resolving a collision process is much smaller than that for a fluid flow, the computational cost of the traditional soft-sphere model by reducing the time step is quite high in particle-resolved simulations. In one state-of-the-art methodology, collision time is stretched to several times the flow solver time step for the fluid to adapt to the sudden change in particle motion. However, the stretched collision time is not physical, the hydrodynamic force may be severely underestimated during a stretched collision, and the simulation of sediment transport may be sensitive to the stretched collision time. The proposed MTSA adopts different time steps to resolve fluid flow, fluid-particle interaction, and particle collision. We assessed the MTSA for particle-wall collisions as well as particle-particle collisions, determined the optimal iteration number in the algorithm, and obtained excellent agreements with experimental measurements and reference simulations. The computational cost of the MTSA can be reduced to about one order of magnitude less than that using the traditional soft-sphere model with almost the same accuracy. The MTSA was then implemented in a particle-resolved simulation of sediment transport with thousands of particles. {By comparing the results obtained using the MTSA and a version of the stretching collision time algorithm similar to Costa et al.(2015), we found that stretching the collision time reduced particle stiffness, weakened particle entrainment, and affected some turbulence and particle statistics.

physics.flu-dyn↗

arXiv2022

Particle resolved simulation of sediment transport by a hybrid parallel approach

Sediment transport over an erodible sediment bed is studied by particle resolved simulations with a hybrid parallel approach. To overcome the challenges of load imbalance in the traditional domain decomposition method when encountering highly uneven distributions of particles in sediment transport, the parallel approach of Darmana et al.(2006) originally developed for point particle simulations is modified and implemented into particle resolved simulations. A novel memory optimization technique is proposed to reduce the memory requirement of the hybrid approach for spherical particles with equal size. The present hybrid parallel approach shows good scalability and high parallel efficiency in a challenging sediment transport test case with more than a million spherical particles. Our code is validated by several benchmark cases, and the results show good agreement with experimental and computational data in the literature. Furthermore, a turbulent flow over an erodible sediment bed is simulated. An extraction method is proposed to distinguish the saltating and rolling particles and extract impact and rebound information of the particle-mobile bed interaction. The probability distribution functions (PDF) of several saltation parameters such as velocity, angle, and spanwise angular velocity of impact and rebound events are presented. Splash functions are established for the particle-mobile bed interaction in the turbulent flow, which was rarely investigated in the experiments and is helpful to model the complex particle-bed interactions in turbulent flow.

physics.flu-dyn↗

arXiv2021

Scale-dependent inclination angle of turbulent structures in stratified atmospheric surface layers

A large-scale spanwise and wall-normal array of sonic anemometers in the atmospheric surface layer is used to acquire all three components of instantaneous fluctuating velocity as well as temperature in a range of stability conditions. These data permit investigation of the three-dimensional statistical structure of turbulence structures. The present work extends the view of a self-similar range of wall-attached turbulence structures to the atmospheric surface layer under unstable and near-neutral stability conditions, and includes the statistical structure in both the wall-normal and spanwise directions in relation to the streamwise wavelength. Results suggest that the self-similar wall-attached structures have similar aspect ratios between streamwise/wall-normal scales and streamwise/spanwise scales such that $λ_x/Δz : λ_x/Δy \approx 1$ for both near-neutral and unstable conditions. By analysing the phase shift between synchronized measurements, in the spectral domain, it is quantified how the structure inclination angle varies with stability. Under the most unstable conditions, coherent structures of $λ_x/δ= 1$ are inclined at angles as high as $65^\circ$ relative to the solid boundary, while larger scales of $λ_x/δ= 6$ exhibit inclination angles of approximately $35^\circ$. For near-neutral stability conditions, the angle tends towards $12^\circ$ for all scales. It is noted that in the near-neutral condition, the structure inclination angle and the aspect ratio -- and thus the statistical modeling of coherent structures in the ASL -- are highly sensitive to the value of the stability parameter.

physics.flu-dyn↗

arXiv2021

A scaling improved inner-outer decomposition of near-wall turbulent motions

Near-wall turbulent velocities in turbulent channel flows are decomposed into small-scale and large-scale components at $y^+<100$ by improving the predictive inner-outer model of Baars et al. [Phys. Rev. Fluids 1, 054406 (2016)], where $y^+$ is the viscous-normalized wall-normal height. The small-scale one is obtained by reducing the outer reference height (a parameter in the model) from the center of the logarithmic layer to $y^+=100$, which can fully remove outer influences. On the other hand, the large-scale one represents the near-wall footprints of outer energy-containing motions. We present plenty of evidences that demonstrate that the small-scale motions are Reynolds-number invariant with the viscous scaling, at friction Reynolds numbers between 1000 and 5200. At lower Reynolds numbers from 180 to 600, the small scales can not be scaled by the viscous units, and the vortical structures are progressively strengthened as Reynolds number increases, which is proposed as a possible mechanism responsible for the anomalous scaling behavior. Finally, it is found that a small-scale part of the outer large-scale footprint can be well scaled by the viscous units.

physics.flu-dyn↗

arXiv2016

Physical model for turbulent friction on rough surfaces

We present a physical model for turbulent friction on rough surfaces with regularly distributed roughness elements. Wall shear stresses are expressed as functions of physical quantities. Surfaces with varying roughness densities and roughness elements with different aspect ratios are considered. We propose a straight forward method based on the conservation of momentum to deduce the drag on elements by expressing it as functions of the maximum drag and drag reductions ratios, as the drag on individual elements decreases as packing density increases. A drag reduction effect of momentum redistribution is proposed and the mutual sheltering effect is studied. These two drag reduction mechanisms for individual elements are significant for sparse and dense surfaces, respectively. Reduction ratios for redistribution effect and mutual sheltering effect are deduced, for the two different types of rough surfaces. The shear stress on elements and the total wall shear stress are obtained as the result of the drag analysis. The estimated wall shear stresses of the proposed model are consistent with classical experimental measurements.

physics.flu-dyn↗