arXiv subjects

Xiaoyu Song

Publications and source records attributed to Xiaoyu Song.

At least 37 records · Page 2Linked to original sources

arXiv2023

Nanoscale soil-water retention mechanism of unsaturated clay via MD and machine learning

In this article, we investigate the nanoscale soil-water retention mechanism of unsaturated clay through molecular dynamics and machine learning. Pyrophyllite was chosen due to its stable structure and as the precursor of other 2:1 clay minerals. A series of molecular dynamics simulations of clay at low degrees of saturation were conducted. Soil water was represented by a point cloud through the center-of-mass method. Water-air interface area was measured numerically by the alpha-shape method. The soil-water retention mechanism at the nanoscale was analyzed by distinguishing adsorptive pressure and capillary pressure at different mass water contents and considering the apparent capillary interface area (i.e., water-air interface area per unit water volume). The water number density profile was used to quantify the adsorption effect. A neural-network based machine learning technique was utilized to construct function relationships among matric suction, the mass water content, and the apparent water-air interface area. Our numerical results have demonstrated from a nanoscale perspective that the adsorption effect is dominated by the van der Waals force and hydroxyl hydration between the clay surface and water. As the mass water content increases, the adsorption pressure decreases, and capillarity plays a prominent role in the soil-water retention mechanism at the nanoscale.

cond-mat.mtrl-sci↗

arXiv2023

Visco-Cosserat periporomechanics for dynamic shear bands and crack branching in porous media

Periporomechanmics is a strong nonlocal framework for modeling the mechanics and physics of variably saturated porous media with evolving discontinuities. In periporomechanics, the horizon serves as a mathematical nonlocal parameter that lacks a precise physical meaning. In this article, as a new contribution we formulate a Cosserat periporomechanics paradigm for modeling dynamic shear banding and crack branching in dry porous media incorporating a micro-structure based length scale. In this micro-periporomechanics framework, each material point has both translational and rotational degrees of freedom in line with the Cosserat continuum theory. We formulate a stabilized Cosserat constitutive correspondence principle via the energy method through which classical viscous material models for porous media can be used in the proposed Cosserat periporomechanics. We have numerically implemented the micro-periporomechanics model through an explicit Lagrangian meshfree algorithm for dynamic problems. Two benchmark numerical examples are presented to test the computational micro-periporomechanics paradigm in modeling shear bands and mode-I cracks. We then present two numerical examples to show the efficacy of the proposed micro-periporomechanics for modeling the characteristics of shear banding bifurcation and dynamic crack branching in dry porous media.

math.NA↗

arXiv2023

Nanoscale creep mechanism of clay through MD modeling with hexagonal particles

In this article, we investigate the creep mechanism of clay at the nanoscale. We conduct the molecular dynamics (MD) modeling of clay samples consisting of hexagonal particles under compression and shear. The MD simulations include oedometer creep, shear creep, direct shear tests, and stress relaxation. The numerical results show that the nanoscale creep mechanism of clay is related to particle rotation, translation, and stacking under different loading conditions. The clay sample under creep shows two types of particle arrangements, i.e., the shifted face-to-face configuration and the face-to-edge configuration. The orientation angle of clay particles is computed to track the rotation of individual particles due to creep. The fabric variation of the clay under creep is characterized by the dihedral angle between the basal particle plane and the x-y plane and the order parameter. It is found that the factors affecting the microstructure variation of the clay aggregate include stress levels, loading rates, and particle sizes. In the nanoscale shear creep test, the creep process comprises three stages, i.e., primary, secondary, and tertiary. The microstructure change during creep depends on the initial alignment of clay particles. The clay creep under a more significant stress level results in a more considerable order parameter and a more orientated clay structure.

cond-mat.soft↗

arXiv2023

Towards reliable calcification detection: calibration of uncertainty in coronary optical coherence tomography images

Optical coherence tomography (OCT) has become increasingly essential in assisting the treatment of coronary artery disease (CAD). Image-guided solutions such as Percutaneous Coronary Intervention (PCI) are extensively used during the treatment of CAD. However, unidentified calcified regions within a narrowed artery could impair the outcome of the PCI. Prior to treatments, object detection is paramount to automatically procure accurate readings on the location and thickness of calcifications within the artery. Deep learning-based object detection methods have been explored in a variety of applications. The quality of object detection predictions could lead to uncertain results, which are not desirable in safety-critical scenarios. In this work, we implement an object detection model, You-Only-Look-Once v5 (YOLO), on a calcification detection framework within coronary OCT images. We evaluate the uncertainty of predictions based on the expected calibration errors, thus assessing the certainty level of detection results. To calibrate confidence scores of predictions, we implement dependent logistic calibration using each detection result's confidence and center coordinates. With the calibrated confidence score of each prediction, we lower the uncertainty of predictions in calcification detection. Our results show that the YOLO achieves higher precision and recall in comparison with the other object detection model, meanwhile producing more reliable results. The calibrated confidence of prediction results in a confidence error of approximately 0.13, suggesting that the confidence calibration on calcification detection could provide a more trustworthy result, indicating a great potential to assist clinical evaluation of treating the CAD during the imaging-guided procedure.

eess.IV↗

arXiv2022

Structural constrained virtual histology staining for human coronary imaging using deep learning

Histopathological analysis is crucial in artery characterization for coronary artery disease (CAD). However, histology requires an invasive and time-consuming process. In this paper, we propose to generate virtual histology staining using Optical Coherence Tomography (OCT) images to enable real-time histological visualization. We develop a deep learning network, namely Coronary-GAN, to transfer coronary OCT images to virtual histology images. With a special consideration on the structural constraints in coronary OCT images, our method achieves better image generation performance than the conventional GAN-based method. The experimental results indicate that Coronary-GAN generates virtual histology images that are similar to real histology images, revealing the human coronary layers.

eess.IV↗

arXiv2022

Nanoscale crack propagation in clay with water adsorption through reactive MD modeling

The atomic-scale cracking mechanism in clay is vital in discovering the cracking mechanism of clay at the continuum scale in that clay is a nanomaterial. In this article, we investigate mechanisms of mode I and mode II crack propagations in pyrophyllite and Ca-montmorillonite with water adsorption through reactive molecular dynamics with a bond-order force field. Clay water adsorption is considered by adding water molecules to the clay surface. During the equilibration stage, water adsorption could cause bending deformation of the pre-defined edge crack region. The relatively small orientating angle of water molecules indicates the formation of hydrogen bonds in the crack propagation process. The peak number density of adsorbed water decreases with the increasing strains. The atomistic structure evolution of the crack tip under loading is analyzed to interpret the nanoscale crack propagation mechanism. The numerical results show that the crack tip first gets blunted with a significant increase in the radius of the curvature of the crack tip and a slight change in crack length. The crack tip blunting is studied by tracking the crack tip opening distance and O-Si-O angle in the tetrahedral Si-O cell in mode I and II cracks. We compare bond-breaking behaviors between Al-O and Si-O. It is found that Si-O bond breaking is primarily responsible for crack propagation. The critical stress intensity factor and critical energy release rate are determined from MD simulation results.

cond-mat.mtrl-sci↗

arXiv2022

Computational coupled large-deformation periporomechanics for dynamic failure and fracturing in variably saturated porous media

The large-deformation mechanics and multiphysics of continuous or fracturing partially saturated porous media under static and dynamic loads are significant in engineering and science. This article is devoted to a computational coupled large-deformation periporomechanics paradigm assuming passive air pressure for modeling dynamic failure and fracturing in variably saturated porous media. The coupled governing equations for bulk and fracture material points are formulated in the current/deformed configuration through the updated Lagrangian-Eulerian framework. It is hypothesized that the horizon of a mixed material point remains spherical, and its neighbor points are determined in the current configuration. As a significant contribution, the mixed interface/phreatic material points near the phreatic line are explicitly considered for modeling the transition from partial to full saturation (vice versa) through the mixed peridynamic state concept. We have formulated the coupled constitutive correspondence principle and stabilization scheme in the updated Lagrangian-Eulerian framework for bulk and interface points. We numerically implement the coupled large deformation periporomechanics through a fully implicit fractional-step algorithm in time and a hybrid updated Lagrangian-Eulerian meshfree method in space. Numerical examples are presented to validate the implemented stabilized computational coupled large deformation periporomechanics and demonstrate its efficacy and robustness in modeling dynamic failure and fracturing in variably saturated porous media.

math.NA↗

arXiv2022

Synthesis of an aqueous, air-stable, superconducting 1T'-WS$_2$ monolayer-ink

Liquid-phase chemical exfoliation is ideal to achieve industry scale production of two-dimensional (2D) materials for a wide range of application such as printable electronics, catalysis and energy storage. However, many impactful 2D materials with potentials in quantum technologies can only be studied in lab settings due to their air-sensitivity, and loss of physical performance after chemical processing. Here, we report a simple chemical exfoliation method to create a stable, aqueous, surfactant-free, superconducting ink containing phase-pure 1T'-WS$_2$ monolayers that are isotructural to the air-sensitive topological insulator 1T'-WTe$_2$. We demonstrate that thin films can be cast on both hard and flexible substrates. The printed film is metallic at room temperature and superconducting below 7.3 K, shows strong anisotropic unconventional superconducting behavior with an in-plane and out-of-plane upper critical magnetic field of 30.1 T and 5.3 T, has a critical current of 44 mA, and is stable at ambient conditions for at least 30 days. Our results show that chemical processing can provide an engineering solution, which makes non-trivial 2D materials that used to be only studied in laboratories commercially accessible.

cond-mat.mtrl-sci↗

arXiv2022

A Class of Magnetic Topological Material Candidates with Hypervalent Bi Chains

The link between crystal and electronic structure is crucial for understanding structure-property relations in solid-state chemistry. In particular, it has been instrumental in understanding topological materials, where electrons behave differently than they would in conventional solids. Herein, we identify 1D Bi chains as a structural motif of interest for topological materials. We focus on Sm$_3$ZrBi$_5$, a new quasi-one-dimensional (1D) compound in the Ln$_3$MPn$_5$ (Ln = lanthanide; M = metal; Pn = pnictide) family that crystallizes in the P$6_{3}$/mcm space group. Density functional theory calculations indicate a complex, topologically non-trivial electronic structure that changes significantly in the presence of spin-orbit coupling. Magnetic measurements show a quasi-1D antiferromagnetic structure with two magnetic transitions at 11.7 and 10.7 K that are invariant to applied field up to 9 T, indicating magnetically frustrated spins. Heat capacity, electrical, and thermal transport measurements support this claim and suggest complex scattering behavior in Sm$_3$ZrBi$_5$. This work highlights 1D chains as an unexplored structural motif for identifying topological materials, as well as the potential for rich physical phenomena in the Ln$_3$MPn$_5$ family.

cond-mat.mtrl-sci↗

arXiv2022

Automatic Block-wise Pruning with Auxiliary Gating Structures for Deep Convolutional Neural Networks

Convolutional neural networks are prevailing in deep learning tasks. However, they suffer from massive cost issues when working on mobile devices. Network pruning is an effective method of model compression to handle such problems. This paper presents a novel structured network pruning method with auxiliary gating structures which assigns importance marks to blocks in backbone network as a criterion when pruning. Block-wise pruning is then realized by proposed voting strategy, which is different from prevailing methods who prune a model in small granularity like channel-wise. We further develop a three-stage training scheduling for the proposed architecture incorporating knowledge distillation for better performance. Our experiments demonstrate that our method can achieve state-of-the-arts compression performance for the classification tasks. In addition, our approach can integrate synergistically with other pruning methods by providing pretrained models, thus achieving a better performance than the unpruned model with over 93\% FLOPs reduced.

cs.CV↗

arXiv2022

Multi-scale reconstruction of undersampled spectral-spatial OCT data for coronary imaging using deep learning

Coronary artery disease (CAD) is a cardiovascular condition with high morbidity and mortality. Intravascular optical coherence tomography (IVOCT) has been considered as an optimal imagining system for the diagnosis and treatment of CAD. Constrained by Nyquist theorem, dense sampling in IVOCT attains high resolving power to delineate cellular structures/ features. There is a trade-off between high spatial resolution and fast scanning rate for coronary imaging. In this paper, we propose a viable spectral-spatial acquisition method that down-scales the sampling process in both spectral and spatial domain while maintaining high quality in image reconstruction. The down-scaling schedule boosts data acquisition speed without any hardware modifications. Additionally, we propose a unified multi-scale reconstruction framework, namely Multiscale- Spectral-Spatial-Magnification Network (MSSMN), to resolve highly down-scaled (compressed) OCT images with flexible magnification factors. We incorporate the proposed methods into Spectral Domain OCT (SD-OCT) imaging of human coronary samples with clinical features such as stent and calcified lesions. Our experimental results demonstrate that spectral-spatial downscaled data can be better reconstructed than data that is downscaled solely in either spectral or spatial domain. Moreover, we observe better reconstruction performance using MSSMN than using existing reconstruction methods. Our acquisition method and multi-scale reconstruction framework, in combination, may allow faster SD-OCT inspection with high resolution during coronary intervention.

eess.IV↗

arXiv2022

Modeling and Validating Temporal Rules with Semantic Petri-Net for Digital Twins

Semantic rule checking on RDFS/OWL data has been widely used in the construction industry. At present, semantic rule checking is mainly performed on static models. There are still challenges in integrating temporal models and semantic models for combined rule checking. In this paper, Semantic Petri-Net (SPN) is proposed as a novel temporal modeling and validating method, which implements the states and transitions of the Colored Petri-Net directly based on RDFS and SPARQL, and realizes two-way sharing of knowledge between domain semantic webs and temporal models in the runtime. Several cases are provided to demonstrate the possible applications in digital twins with concurrent state changes and dependencies.

cs.AI↗

arXiv2022

Updated Lagrangian unsaturated periporomechanics for extreme large deformation in unsaturated porous media

Unsaturated periporomechanics is a strong nonlocal poromechanics based on peridynamic state and effective force concept. In the previous periporomechnics the total Lagrangian formulation is adopted for the solid skeleton of porous media. In this article as a new contribution we formulate and implement an updated Lagrangian unsaturated periporomechanics framework for modeling extreme large deformation in unsaturated soils under drained condition, e.g., soil column collapse. In this new framework the so-called bond-associated sub-horizon concept is utilized to enhance the stability and accuracy at extreme large deformation of solid skeleton. The stabilized nonlocal velocity gradient in the deformed configuration is used to update the effective force state from a critical state based visco-plastic model for unsaturated soils. The updated Lagrangian periporomechanics is implemented numerically through an explicit Newmark scheme for high-performance computing. Numerical examples are presented to demonstrate the efficacy of the updated Lagrangian periporomechanics and its robustness in modeling unsaturated soil column collapse under drained condition.

physics.geo-ph↗

arXiv2022

MD modeling of cracks in clay at the nanoscale

Cracks in clay are significant in geotechnical and geoenvironmental engineering (e.g., embankment erosion and stability of landfill cover systems). This article studies the mechanism of nucleation and growth of cracks in clay at the nanoscale through full-scale molecular dynamics simulations. The clay adopted is pyrophyllite, and the force field is CLAYFF. The crack formation in a pyrophyllite clay layer is evaluated under uniaxial tension and simple shear. The numerical results show that cracks in the nanoscale pyrophyllite clay layer are brittle and strain-rate dependent. Small strain rate results in low ultimate tensile/shear strength. As strain rate increases, clay crack shifts from a single-crack pattern to a multiple-crack one. The cracking mechanism is investigated from bond breakage analysis at the atomic scale. It is found that the first bond breakage occurs in the silicon-surface oxygen bond. As a crack propagates, the relative percentage of broken silicon-surface oxygen bonds is the smallest compared to other types of metal-oxygen interactions, demonstrating that the atomic interaction between silicon and surface oxygen atoms is the strongest. To understand the propagation of cracks, we also study the stress intensity factor and energy release rate of pyrophyllite and their size dependence at the atomic scale.

cond-mat.mtrl-sci↗

arXiv2021

NEMD modeling of nanoscale hydrodynamics of clay-water system at elevated temperature

The engineering problems involving clay under non-isothermal conditions (e.g., geothermal energy harvest, landfill cover system, and nuclear waste disposal) are multiscale and multiphysics by nature. The nanoscale hydrodynamics of clay at elevated temperature is essential in developing a physics-based multiscale model for clay under non-isothermal conditions. The nonequilibrium molecular dynamics (NEMD) is a useful tool to study the nanoscale hydrodyndamics of clay. This article presents an NEMD modeling of hydrodynamics of clay nanopores at elevated temperatures. Water flow confined in pyrophyllite and montmorillonite clay nanopores is investigated. The nonequilibrium state is maintained by uniformly exerting an external force on each water molecule. The NEMD simulations have provided a molecular-scale perspective of temperature effect on clay-water density, water flow velocity, shear viscosity, clay-water slip length, hydraulic conductivity, and clay-water friction coefficient. The numerical results have shown a strong temperature dependence of fluid flow velocity, shear viscosity, clay-water slip length, and hydraulic conductivity at the nanoscale. We have validated the applicability of cubic law in determining hydraulic conductivity at the nanopore scale under at elevated temperature. It is found from our numerical results that slip clay-water boundary condition is an essential factor in properly determining nanoscale fluid flow velocity. By numerical examples, we also study the impact of nanopore size and clay layer thickness on the hydrodynamics of the clay-water system.

physics.flu-dyn↗

arXiv2021

Computational multiphase periporomechanics for unguided cracking in unsaturated porous media

In this article we formulate and implement a computational multiphase periporomechanics model for unguided fracturing in unsaturated porous media. The same governing equation for the solid phase applies on and off cracks. Crack formation in this framework is autonomous, requiring no prior estimates of crack topology. As a new contribution, an energy-based criterion for arbitrary crack formation is formulated using the peridynamic effective force state for unsaturated porous media. Unsaturated fluid flow in the fracture space is modeled in a simplified way in line with the nonlocal formulation of unsaturated fluid flow in bulk. The formulated unsaturated fracturing periporomechanics is numerically implemented through a fractional step algorithm in time and a two-phase mixed meshless method in space. The two-stage operator split converts the coupled periporomechanics problem into an undrained deformation and fracture problem and an unsaturated fluid flow in the deformed skeleton configuration. Numerical simulations of in-plane open and shear cracking are conducted to validate the accuracy and robustness of the fracturing unsaturated periporomechanics model. Then numerical examples of wing cracking and non-planar cracking in unsaturated soil specimens are presented to demonstrate the efficacy of the proposed multiphase periporomechanics model for unguided cracking in unsaturated porous media.

math.NA↗

arXiv2021

A stabilized computational nonlocal poromechanics model for dynamic analysis of saturated porous media

In this article we formulate a stable computational nonlocal poromechanics model for dynamic analysis of saturated porous media. As a novelty, the stabilization formulation eliminates zero-energy modes associated with the original multiphase correspondence constitutive models in the coupled nonlocal poromechanics model. The two-phase stabilization scheme is formulated based on an energy method that incorporates inhomogeneous solid deformation and fluid flow. In this method, the nonlocal formulations of skeleton strain energy and fluid flow dissipation energy equate to their local formulations. The stable coupled nonlocal poromechanics model is solved for dynamic analysis by an implicit time integration scheme. As a new contribution, we validate the coupled stabilization formulation by comparing numerical results with analytical and finite element solutions for one-dimensional and two-dimensional dynamic problems in saturated porous media. Numerical examples of dynamic strain localization in saturated porous media are presented to demonstrate the efficacy of the stable coupled poromechanics framework for localized failure under dynamic loads.

math.NA↗

arXiv2020

A computational periporomechanics model for localized failure in unsaturated porous media

We implement a computational periporomechanics model for simulating localized failure in unsaturated porous media. The coupled periporomechanics model is based on the peridynamic state concept and the effective force state concept. The coupled governing equations are integral-differential equations without assuming the continuity of solid displacement and fluid pressures. The fluid flow and effective force states are determined by nonlocal fluid pressure and deformation gradients through the recently formulated multiphase constitutive correspondence principle. The coupled peri-poromechanics is implemented numerically for high-performance computing by an implicit multiphase meshfree method utilizing the message passing interface. The numerical implementation is validated by simulating classical poromechanics problems and comparing the numerical results with analytical solutions and experimental data. Numerical examples are presented to demonstrate the robustness of the fully coupled peri-poromechanics in modeling localized failures in unsaturated porous media.

math.NA↗