Yongjie Jessica Zhang

Carnegie Mellon University | CMU · Department of Mechanical Engineering

Reduced order modeling lowers the computational cost of solving PDEs by learning a low-order spatial representation from data and dynamically evolving these representations using manifold projections of the governing equations. While commonly used, linear subspace reduced-order models (ROMs) are often suboptimal for problems with a slow decay of Ko...

When designed effectively, support structures for Laser Powder Bed Fusion (LPBF) quickly dissipate heat and mitigate part distortion without driving up excessive costs. Lattices, composed of individual unit cells strategically arranged to achieve a desired function, are a promising solution as support structure. Prior research utilizing gradient-ba...

Automatic rib labeling and anatomical centerline extraction are common prerequisites for various clinical applications. Prior studies either use in-house datasets that are inaccessible to communities, or focus on rib segmentation that neglects the clinical significance of rib labeling. To address these issues, we extend our prior dataset ( RibSeg...

Current biological neural controllers in biohybrid robotics rely on networks of self-assembled neurons. However, to be able to reproducibly create neuron circuits optimized for specific functions, the connections that the neurons form need to be controlled. Towards addressing this need, we have developed a tool for the Generation of Automatic Neuro...

The intracellular material transport plays a crucial role in supporting a neuron cell’s survival and function. The disruption of transport may lead to the onset of various neurodegenerative diseases. Therefore, it is essential to study how neurons regulate the material transport process and have a better understanding of the traffic jam formation....

Mesh-based image warping techniques typically represent image deformation using linear functions on triangular meshes or bilinear functions on rectangular meshes. This enables simple and efficient implementation, but in turn, restricts the representation capability of the deformation, often leading to unsatisfactory warping results. We present a no...

High-quality mesh generation is the foundation of accurate finite element analysis. Due to the vast interior vertices search space and complex initial boundaries, mesh generation for complicated domains requires substantial manual processing and has long been considered the most challenging and time-consuming bottleneck of the entire modeling and a...

Neuron growth is a complex, multi-stage process that develops sophisticated morphologies and interwoven neurite networks. Recent advances have enabled us to examine the effects of neuron growth factors and seek causes for neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. A computational...

This paper presents the application of triangle configuration B-splines (TCB-splines) for representing and analyzing the Kirchhoff-Love shell in the context of isogeometric analysis (IGA). The Kirchhoff-Love shell formulation requires global $C^1$-continuous basis functions. The nonuniform rational B-spline (NURBS)-based IGA has been extensively us...

We present an efficient fully discrete algorithm for solving the Allen–Cahn and Cahn–Hilliard equations on complex curved surfaces. The spatial discretization employs the recently developed IGA (isogeometric analysis) framework, where we adopt the strategy of Loop subdivision with the superior adaptability of any topological structure, and the basi...

The motor-driven intracellular transport plays a crucial role in supporting a neuron cell’s survival and function, with motor proteins and microtubule (MT) structures collaborating to promptly deliver the essential materials to the right location in neuron. The disruption of transport may lead to the onset of various neurodegenerative diseases. The...

The nervous system serves as an inspiration for control and processing systems but can be difficult to replicate or directly implement using biological neurons in bioinspired and biohybrid systems. An alternative path is to use synthetic biomolecular neuristors that are inspired by biological neurons and can closely mimic their spiking behavior. A...

The structural design and additive manufacturing (AM) of cross-flow heat exchangers (HXs) are studied. A unit-based design framework is proposed to optimize the channel configuration in order to improve heat exchange performance (HXP) and meanwhile control pressure drop (PD) between the fluid inlet and outlet. A gradient-based optimization methodol...

Predicting pediatric spinal deformity (PSD) from X-ray images collected on the patient’s initial visit is a challenging task. This work builds on our previous method and provides a novel bio-informed framework based on a mechanistic machine learning technique with dynamic patient-specific parameters to predict PSD. We provide a geometry-based bone...

Machine learning (ML) and artificial intelligence (AI) are reshaping the way we model biomechanics systems. This special issue gathers together original articles at the forefront of data-driven methods in biomechanics. Specifically, the articles in this issue cover physics-informed ML methods for partial differential equations (PDE) and ordinary di...

The structural design and additive manufacturing (AM) of cross-flow heat exchangers (HXs) are studied. A unit-based design framework is proposed to optimize the channel configuration in order to improve heat exchange performance (HXP) and meanwhile control pressure drop (PD) between the fluid inlet and outlet. A gradient-based optimization methodol...

Neuron morphology gives rise to distinct axons and dendrites and plays an essential role in neuronal functionality and circuit dynamics. In rat hippocampal neurons, morphological development occurs over roughly one week in vitro. This development has been qualitatively described as occurring in 5 stages. Still, there is a need to quantify cell grow...

Heat exchangers (HXs) have gained increasing attention due to the intensive demand of performance improving and energy saving for various equipment and machines. As a natural application, topology optimization has been involved in the structural design of HXs aiming at improving heat exchange performance (HXP) and meanwhile controlling pressure dro...

We present a new computational framework of neuron growth based on the phase field method and develop an open-source software package called “NeuronGrowth_IGAcollocation”. Neurons consist of a cell body, dendrites, and axons. Axons and dendrites are long processes extending from the cell body and enabling information transfer to and from other neur...

Vector image representation methods that can faithfully reconstruct objects and color variations in a raster image are desired in many practical applications. This paper presents triangular configuration B-spline (referred to as TCB-spline)-based vector graphics for raster image vectorization. Based on this new representation, an automatic raster i...

Neuron morphology gives rise to distinct axons and dendrites and plays an essential role in neuronal functionality and circuit dynamics. In rat hippocampal neurons, morphological development occurs over roughly one week in vitro. This development has been qualitatively described as occurring in 5 stages. Still, there is a need to quantify cell grow...

Isogeometric analysis (IGA) was introduced to integrate methods for analysis and computer-aided design (CAD) into a unified process. High-quality parameterization of a physical domain plays a crucial role in IGA. However, obtaining high-quality parameterizations for complex geometries retains a challenge. Triangle configuration based bivariate simp...

The intracellular transport process plays an important role in delivering essential materials throughout branched geometries of neurons for their survival and function. Many neurodegenerative diseases have been associated with the disruption of transport. Therefore, it is essential to study how neurons control the transport process to localize mate...

The intracellular transport process plays an important role in delivering essential materials throughout branched geometries of neurons for their survival and function. Many neurodegenerative diseases have been associated with the disruption of transport. Therefore, it is essential to study how neurons control the transport process to localize mate...

Analysis-suitable T-splines (AST-splines) are a promising candidate to achieve a seamless integration between the design and the analysis of thin-walled structures in industrial settings. In this work, we allow multiple extraordinary points per face, i.e., we remove the restriction of preceding works that required extraordinary points to be at leas...

This paper proposes a method for the construction of quadratic serendipity element (QSE) shape functions on planar convex and concave polygons. Existing approaches for constructing QSE shape functions are linear combinations of the pair-wise products of generalized barycentric coordinates with linear precision, restricted to the convex polygonal do...

In this paper, we extend our earlier polycube-based all-hexahedral mesh generation method to hexahedral-dominant mesh generation, and present the HexDom software package. Given the boundary representation of a solid model, HexDom creates a hex-dominant mesh by using a semi-automated polycube-based mesh generation method. The resulting hexahedral do...

Fused deposition modeling (FDM)-based 4D printing uses thermoplastics to produce artifacts and requires computational analysis to assist its design processes of complex geometries. Previously, finite element analysis (FEA) has been used to simulate 4D printing deformations, and its accuracy has been computationally and experimentally verified. Howe...

In this paper, we present two software packages, HexGen and Hex2Spline, that seamlessly integrate geometry design with isogeometric analysis (IGA) in LS-DYNA. Given a boundary representation of a solid model, HexGen creates a hexahedral mesh by utilizing a semi-automatic polycube-based mesh generation method. Hex2Spline takes the output hexahedral...

The intracellular transport process plays an important role in delivering essential materials throughout branched geometries of neurons for their survival and function. Many neurodegenerative diseases have been associated with the disruption of transport. Therefore, it is essential to study how neurons control the transport process to localize mate...

Neurons exhibit complex geometry in their branched networks of neurites which is essential to the function of individual neuron but also brings challenges to transport a wide variety of essential materials throughout their neurite networks for their survival and function. While numerical methods like isogeometric analysis (IGA) have been used for m...

Phononic crystals (PnCs) have seen increasing popularity due to band gap property for sound wave propagation. As a natural bridge, topology optimization has been applied to the design of PnCs. However, thus far most of the existent works on topological design of PnCs have been focused on single micro-scale topology optimization of a periodical unit...

Neurons exhibit complex geometry in their branched networks of neurites which is essential to the function of individual neuron but also brings challenges to transport a wide variety of essential materials throughout their neurite networks for their survival and function. While numerical methods like isogeometric analysis (IGA) have been used for m...

Analysis-suitable T-splines (AST-splines) are a promising candidate to achieve a seamless integration between the design and the analysis of thin-walled structures in industrial settings. In this work, we generalize AST-splines to allow multiple extraordinary points within the same face. This generalization drastically increases the flexibility to...

In this paper, we extend our earlier polycube-based all-hexahedral mesh generation method to hexahedral-dominant mesh generation, and present the HexDom software package. Given the boundary representation of a solid model, HexDom creates a hex-dominant mesh by using a semi-automated polycube-based mesh generation method. The resulting hexahedral do...

We extend the recently introduced divergence-conforming immersed boundary (DCIB) method [1] to fluid-structure interaction (FSI) problems involving closed co-dimension one solids. We focus on capsules and vesicles, whose discretization is particularly challenging due to the higher-order derivatives that appear in their formulations. In two-dimensio...

In this paper, we propose an improved singularity structure simplification method for hexahedral (hex) meshes using a weighted ranking approach. In previous work, the selection of to-be-collapsed base complex sheets/chords is only based on their thickness, which will introduce a few closed-loops and cause an early termination of simplification and...

This paper presents an enhanced version of our previous work, hybrid non‐uniform subdivision (HNUS) surfaces1, to achieve optimal convergence rates in isogeometric analysis. We introduce a parameter λ (1/4 < λ <1) to control the rate of shrinkage of irregular regions, so the method is called tuned hybrid non‐uniform subdivision (tHNUS). Thus, HUNS...

Scoliosis, an abnormal curvature of the human spinal column, is characterized by a lateral deviation of the spine, accompanied by axial rotation of the vertebrae. Adolescent Idiopathic Scoliosis (AIS) is the most common type, affecting children between ages 8 to 18 when bone growth is at its maximum rate. We propose a mechanistic machine learning a...

Manufacturing nonplanar electronics often requires the integration of functions and forms through embedding circuit boards into three-dimensional (3D) shapes. While most popular solutions rely on cavities where electronics reside in forms of rigid circuit boards, other alternative approaches leverage 3D printing or layer lamination to create 3D ele...

Prediction of the likely evolution of traffic scenes is a challenging task because of high uncertainties from sensing technology and the dynamic environment. It leads to failure of motion planning for intelligent agents like autonomous vehicles. In this paper, we propose a fluid-inspired model to estimate collision risk in road scenes. Multi-object...

In this paper, we present two software packages, HexGen and Hex2Spline, that seamlessly integrate geometry design with isogeometric analysis (IGA) in LS-DYNA. Given a boundary representation of a solid model, HexGen creates a hexahedral mesh by utilizing a semi-automatic polycube-based mesh generation method. Hex2Spline takes the output hexahedral...

We present an algorithm for curve skeleton extraction from unstructured points using visibility as a guide. We introduce visible cells inside the point samples. By locating a viewpoint in the space, visible points from the viewpoint are connected to indicate the visible region, which locally captures the interior structure of the points and is call...

In this article, we present a survey on surface remeshing techniques, classifying all collected articles in different categories and analyzing specific methods with their advantages, disadvantages, and possible future improvements. Following the systematic literature review methodology, we define step-by-step guidelines throughout the review proces...

Morphing materials allow us to create new modalities of interaction and fabrication by leveraging dynamic behaviors of materials. Yet, despite the ongoing rapid growth of computational tools within this realm, current developments are bottlenecked by the lack of an effective simulation method. As a result, existing design tools must trade-off betwe...

Four-dimensional (4D) printing, a new technology emerged from additive manufacturing (3D printing), is widely known for its capability of programming post-fabrication shape-changing into artifacts. Fused deposition modeling (FDM)-based 4D printing, in particular, uses thermoplastics to produce artifacts and requires computational analysis to assist...

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Volumetric modeling is an important topic for material modeling and isogeometric simulation. In this paper, two kinds of interpolatory Catmull-Clark volumetric subdivision approaches over unstructured hexahedral meshes are proposed based on the limit point formula of Catmull-Clark subdivision volume. The basic idea of the first method is to constru...

This paper presents an enhanced version of our previous work, hybrid non-uniform subdivision surfaces [19], to achieve optimal convergence rates in isogeometric analysis. We introduce a parameter $\lambda$ ($\frac{1}{4}<\lambda<1$) to control the rate of shrinkage of irregular regions, so the method is called tuned hybrid non-uniform subdivision (t...

The reaction-diffusion system is naturally used in chemistry to represent substances reacting and diffusing over the spatial domain. Its solution illustrates the underlying process of a chemical reaction and displays diverse spatial patterns of the substances. Numerical methods like finite element method (FEM) are widely used to derive the approxim...

In this paper, we propose an explicit isogeometric topology optimization approach based on moving morphable voids (MMVs) with closed B-spline boundary curves, named TOP-IGA-MMV in short. We model the design domain by a NURBS patch, and then employ the NURBS-based isogeometric analysis (IGA) for structural response and the well-established adjoint a...

Analysis-suitable T-splines (ASTS) including both extraordinary points and T-junctions are used to solve Kirchhoff–Love shell problems. Extraordinary points are required to represent surfaces with arbitrary topological genus. T-junctions enable local refinement of regions where increased resolution is needed. The benefits of using ASTS to define sh...

Surpervoxels are becoming increasingly popular in many point cloud processing applications. However, few methods have been devised specifically for generating compact supervoxels from unstructured three-dimensional (3D) point clouds. In this study, we aimed to generate high quality over-segmentation of point clouds. We propose a merge-swap optimiza...

Patient-specific computational flow analysis of coronary arteries with time-dependent medical-image data can provide valuable information to doctors making treatment decisions. Reliable computational analysis requires a good core method, high-fidelity space and time discretizations, and an anatomically realistic representation of the lumen motion....

We extend the recently introduced divergence-conforming immersed boundary (DCIB) method [1] to fluid-structure interaction (FSI) problems involving closed co-dimension one solids. We focus on capsules and vesicles, whose discretization is particularly challenging due to the higher-order derivatives that appear in their formulations. In two-dimensio...

Recently, triangle configuration based bivariate simplex splines (referred to as TCB-spline) have been introduced to the geometric computing community. TCB-splines retain many attractive theoretic properties of classical B-splines, such as partition of unity, local support, polynomial reproduction and automatic inbuilt high-order smoothness. In thi...

Purpose Majority of the existing direct slicing methods have generated precise slicing contours from different surface representations, they do not carry any interior information. Whereas, heterogeneous solids are highly preferable for designing and manufacturing sophisticated models. To directly slice heterogeneous solids for additive manufacturin...

Four-dimensional (4D) printing, a new technology emerged from additive manufacturing (3D printing), is widely known for its capability of programming post-fabrication shape-changing into artifacts. Fused deposition modeling (FDM)-based 4D printing, in particular, uses thermoplastics to produce artifacts and requires computational analysis to assist...

This paper introduces a new non-uniform subdivision surface representation, called hybrid non-uniform subdivision surface (for short, HNUSS). The subdivision scheme is constructed through two steps. The first step inserts a set of edges and converts a valence-n extraordinary point into a valence-n face. The second step combines both primal and dual...

We present a novel approach for joint image segmentation and nonrigid registration using bidirectional composition based level set formulation. This efficient framework incorporates automatic structural analysis from image segmentation into the registration framework. This method has shown an improved performance as compared to carrying out segment...

In curve modeling, interpolation allows users to directly control the location of curve features. While previous literatures have focused on generating interpolatory curves with properties of smoothness and locality, they usually have difficulty in controlling over geometric feature points (e.g., cusps, loops, and inflection points) that mark salie...

Cartons are commonly used in the packaging industry, and standard carton patterns are broadly used in mass production. However, their designs may not fit different containees or specific fabrication requirements well. Taking the dimensions of the containees as input, we study the patterns of cartons and propose a system named “Cartonist” to efficie...

Thermoplastic and Fused Deposition Modeling (FDM) based 4D printing are rapidly expanding to allow for space- and material-saving 2D printed sheets morphing into 3D shapes when heated. However, to our knowledge, all the known examples are either origami-based models with obvious folding hinges, or beam-based models with holes on the morphing surfac...

In the process of surface modeling from scanned point data, a segmentation that partitions a point cloud into meaningful regions or extracts important features from the 3D point data plays an important role in compressing the scanned data and fitting surface patches. In this paper, a new spectral point cloud surface segmentation method is proposed...

We present a novel blended B-spline method to construct bicubic/tricubic splines over unstructured quadrilateral and hexahedral meshes for isogeometric analysis. C^1 and (truncated) C^2 B-spline functions are used in regular elements, whereas C^0 and (truncated) C^1 B-spline functions are adopted in boundary elements and interior irregular elements...

In this paper, we propose an enhanced isogeometric analysis (IGA) collocation method. It is well known that the location of the collocation points plays an important role in the accuracy and stability of IGA collocation methods. This is particularly true for non-uniform meshes and domains generated from multi-patch geometries. We present an enhance...

Immersed boundary (IB) methods deal with incompressible visco-elastic solids interacting with incompressible viscous fluids. A long-standing issue of IB methods is the challenge of accurately imposing the incompressibility constraint at the discrete level. We present the divergence-conforming immersed boundary (DCIB) method to tackle this issue. Th...

In this paper, we present a novel method for generating cell complexes with anisotropy conforming to the Hessian of an arbitrary given function. This is done by variationally optimizing the discontinuous piecewise linear approximation of the given functions over power diagrams. The resulting cell complexes corresponding to the approximations are re...

This paper presents a novel technique for resampling point clouds of a smooth surface. The key contribution of this paper is the generalization of centroidal Voronoi tessellation (CVT) to point cloud datasets to make point resampling practical and efficient. In particular, the CVT on a point cloud is efficiently computed by restricting the Voronoi...

The current work presents an enhanced isogeometric analysis (IGA) collocation method by combining the traditional IGA collocation method and the Galerkin IGA method. The traditional IGA collocation method exhibits high computational efficiency when solving partial differential equations (PDEs) problems. But the method may produce unstable results a...

This paper focuses on printing a 2D color image by using a desktop fused deposition modeling (FDM) 3D printer. A fully automatic framework is presented to convert a 2D image into a non-photorealistic line drawing which is suitable for 3D printing. Firstly, an image is partitioned into a moderate number of regions, and contours of these regions are...

We review the literature on patient-specific vascular modeling, with particular attention paid to three-dimensional arterial networks. Patient-specific vascular modeling typically involves three main steps: image processing, analysis suitable model generation, and computational analysis. Analysis suitable model generation techniques that are curren...

We present a new method for truncated hierarchical tricubic spline (TH-spline3D) construction to enable adaptive isogeometric analysis on unstructured hexahedral meshes. Taking the input unstructured hexahedral mesh as the control mesh, we first develop blending functions with the aid of tricubic Bernstein polynomials. This development is an extens...

The present work carries out molecular dynamics simulations to compute the thermal conductivity of the borophene nanoribbon and the borophene nanotube using the Muller-Plathe approach. We investigate the thermal conductivity of the armchair and zigzag borophenes, and show the strong anisotropic thermal conductivity property of borophene. We compare...

Isogeometric analysis (IGA) has been developed for more than a decade. However, the usage of IGA is by far limited mostly within academic community. The lack of automatic or semi-automatic software platform of IGA is one of the main bottlenecks that prevent IGA from wide applications in industry. In this paper, we present a comprehensive IGA softwa...

Given an input 3D image, in this paper we first segment it into several clusters by extending the 2D harmonic edge-weighted centroidal Voronoi tessellation (HEWCVT) method to the 3D image domain. The Dual Contouring method is then applied to construct tetrahedral meshes by analyzing both material change edges and interior edges. An anisotropic Giaq...

Amethod for non-rigid image registration that is suitable for large deformations is presented. Conventional registration methods embed the image in a B-spline object, and the image is evolved by deforming the B-spline object. In this work, we represent the image using B-spline and deform the image using a composition approach. We also derive a comp...

Given an input three-dimensional (3D) image in this paper, we first segment it into several clusters by extending the two-dimensional harmonic edge-weighted centroidal Voronoi tessellation method to the 3D image domain. The dual contouring method is then applied to construct tetrahedral meshes by analysing both material change edges and interior ed...