Computational Bio-Modeling Lab

Researchers in Yongjie Jessica Zhang’s lab develop novel algorithms on biomodeling at molecular, cellular, tissue and organ scales, and explore applications in various application fields. The group is mainly focused on applications in biomedical fields, but is also working on projects in other fields including mechanical engineering, materials science, and electrical engineering.

Faculty

Yongjie Jessica Zhang

Yongjie Jessica Zhang

George Tallman Ladd and Florence Barrett Ladd Professor of Mechanical Engineering

Yongjie Jessica Zhang's research interests include computational geometry (especially mesh generation), computer graphics, visualization, finite element method, isogeometric analysis and their applications in computational biomedicine, computational biology and engineering. She joined Carnegie Mellon in 2007 as an assistant professor, was promoted to an associate professor in 2012, and became a full professor in 2016. She has co-authored over 170 publications in peer-reviewed international journals and conference proceedings.

Office
Scaife Hall 318
Phone
412-268-5332
Fax
412-268-3348
Email
jessicaz@andrew.cmu.edu
Google Scholar
Yongjie Jessica Zhang

Projects

The Computational Bio-Modeling Lab's research includes computational geometry (especially mesh generation), computer graphics, visualization, finite element method, isogeometric analysis and their applications in computational biomedicine, computational biology, and engineering. We are mainly focusing on applications in biomedical fields, but we are also working on projects in mechanical engineering, materials science, electrical engineering, civil engineering, architecture, geological engineering, and petroleum engineering.

Research team

Brian Coffin

Brian Coffin

Doctorate

Co-Advisor
Adam Feinberg
Research interests
additive manufacturing of soft materials; tissue engineering; vascular structure modeling
Email
bcoffin@andrew.cmu.edu
Xuan Liang

Xuan Liang

Post-Doctorate

Research interests
additive manufacturing, topology optimization, isogeometric analysis, machine learning
Email
xliang3@andrew.cmu.edu
Ashlee Liao

Ashlee Liao

Doctorate

Co-Advisor
Vickie Webster-Wood
Research interests
biorobotics, biomechanics, neural controls
Email
ashleel@andrew.cmu.edu
Angran Li

Angran Li

Doctorate

Research interests
neuron material transport, isogeometric analysis, spline modeling
Email
angranl@andrew.cmu.edu
Kuanren Qian

Kuanren Qian

Doctorate

Co-Advisor
Vickie Webster-Wood
Research interests
bioinspired robotics, neuron growth modeling
Email
kuanrenq@andrew.cmu.edu
Lisha White

Lisha White

Doctorate

Co-Advisor
Jon Cagan
Research interests
design, additive manufacturing, machine learning
Yuxuan Yu

Yuxuan Yu

Doctorate

Research interests
NURBS-based isogeometric analysis, fluid-structure interaction, mesh generation
Email
yuxuany1@andrew.cmu.edu
Marione Aluoch

Marione Aluoch

Undergraduate

Email
maluoch@andrew.cmu.edu
Sara Begane

Sara Begane

Undergraduate

Email
sbegane@andrew.cmu.edu
Marvin Bennett

Marvin Bennett

Undergraduate

Email
mcbennet@andrew.cmu.edu
Hyunji Kim

Hyunji Kim

Undergraduate

Email
hyunjik2@andrew.cmu.edu
Jialei Ginny Liu

Jialei Ginny Liu

Undergraduate

Email
jialeil@andrew.cmu.edu
Raaga Singireddy

Raaga Singireddy

Undergraduate

Email
rsingire@andrew.cmu.edu
Kyuwon Weon

Kyuwon Weon

Undergraduate

Email
kweon@andrew.cmu.edu
Visiting scholars and students
  • Yundong Gai, Ph.D. student in Dalian Institute of Technology, China
  • Yue Jia, Lecturer in Northwestern Polytechnic University, China
  • Yanyang Xiao, Ph.D. student in Xiamen University, China
 
Past students

Postdocs

  • Hugo Casquero, 2017-2020 (now an Assistant Professor at University of Michigan, Dearborn)
  • Xiaodong Wei, 2017-2018, Postdoc in Mechanical Engineering (now at EPFL, Switzerland)
  • Hong Zhang, Postdoc in Mechanical Engineering, 2011-2013 (now at Indiana University-Purdue University Indianapolis)
  • Mohamed Ebeida, Postdoc in Mechanical Engineering, 2008-2010 (now at Sandia National Laboratory)

  

Ph.D. students

  • Aishwarya Pawar, Ph.D. student in Mechanical Engineering, 2016-2020 (now a postdoc at Purdue University)
  • Xiaodong Wei, Ph.D. student in Mechanical Engineering, 2013-2017 (now at EPFL, Switzerland)
  • Arjun Kumar, Ph.D. student in Mechanical Engineering, 2013-2016 (now at Carl Zeiss X-ray Microscopy Inc.)
  • Kangkang Hu, Ph.D. student in Mechanical Engineering, 2012-2016 (now at Alibaba Cloud, Hangzhou, China)
  • Tao Liao, Ph.D. Student in Mechanical Engineering, 2011-2015 (now at Google, Boston)
  • Lei Liu, Ph.D. Student in Mechanical Engineering, 2011-2015 (now at Google, Pittsburgh)
  • Jin Qian, Ph.D. Student in Mechanical Engineering, 2008-2013 (now at Huatai Ruilian Fund, Beijing)
  • Xinghua Liang, Ph.D. Student in Mechanical Engineering, 2008-2013 (now at ANSYS Chicago Office)
  • Wenyan Wang, Ph.D. Student in Mechanical Engineering, 2008-2012 (now at ANSYS Chicago Office)
  • Erick Johnson, Ph.D. Student in Mechanical Engineering, 2009-2010 (now Assistant Professor at Montana State University)

 

Masters students

  • Brian Heecheon Kang, MS-P student in Mechanical Engineering, 2019-2020
  • Max Farfel, MS Student in Materials Science and Engineering (co-advised with Prof. Anthony Rollett), 2019-2020
  • Kuanren Qian, MS-P Student in Mechanical Engineering, 2018-2020
  • Haolin Liu, MS-P Student in Mechanical Engineering, 2019
  • Jingru Wu, MS Student in Biomedical Engineering, 2019
  • Yile Feng, MS-P Student in Biomedical Engineering, 2019
  • Zilu Wang, MS Student in Mechanical Engineering, 2018-2019
  • Zisheng Ye, MS-P student in Mechanical Engineering, Fall 2017
  • Lichengxi Huang, MS Student in Civil Engineering, Fall 2016
  • Shuo Li, MS Student in Civil Engineering, Fall 2016
  • Yicong Lai, MS-P Student in Mechanical Engineering, 2014-2016
  • Aishwarya Pawar, MS-P Student in Mechanical Engineering, 2014-2015
  • Shuai Cui, MS-P Student in Mechanical Engineering, 2015 Fall
  • Charles Scott Gerfen, MS-P Student in Mechanical Engineering, 2015 Summer
  • Joshua Chen, MS-P Student in School of Architecture, 2014-2015
  • Yang Gao, MS-P Student in Biomedical Engineering, 2014-2015
  • Chiyu Dong, MS-P Student in Mechanical Engineering, 2012-2014
  • Suyue Han, MS-P Student in Mechanical Engineering, 2012-2014
  • Ruitian Liu, MS-P Student in Mechanical Engineering, 2012-2014
  • You Zhou, MS-P Student in Mechanical Engineering, 2013-2014
  • Ling Zhan, MS-P Student in Mechanical Engineering, 2012-2014
  • Xiaoyi Fu, MS-P Student in Mechanical Engineering, 2011-2013
  • Yuanfeng Jiao, MS-P Student in Biomedical Engineering, 2010-2012
  • Kibaek Lee, MS-P Student in Mechanical Engineering, 2011-2012
  • Yiming Jing, MS-P Student in Mechanical Engineering, 2009-2011
  • Jun Ma, MS-P Student in Mechanical Engineering, 2009-2011
  • Rong Li, MS-P Student in Mechanical Engineering, 2007-2008

 

Undergraduate students

  • Kyle Wagner, Undergraduate student in Statistics and Machine Learning, Summer 2020
  • Jeffrey He, Undergraduate Student in Northwestern University, Summer 2019 and 2020
  • David Oh, Undergraduate Student in Mechanical Engineering, Summer 2019
  • Brian Kang, Undergraduate Student in Mechanical Engineering, Summer 2019
  • Gregory Miller, Undergraduate Student in Mechanical Engineering, Summer 2017
  • Qingyuan Wu, Undergraduate Student in Mechanical Engineering, Summer 2017
  • Brandon Xu, Undergraduate Student in Mechanical Engineering, Summer 2017
  • Diana Li, Undergraduate Student in Mechanical Engineering, Fall 2016
  • Robert Macedo, Undergraduate Student in Physics, Fall 2014
  • Conor Fitzgerald, Undergraduate Student in Mechanical Engineering and Biomedical Engineering, Summer 2013
  • Kyung Jae Lee, Undergraduate Student in Mechanical Engineering, Summer 2012 (SURF)
  • Mark Erazo, Undergraduate Student in Mechanical Engineering, Fall 2011
  • Huan (Steve) Qin, Undergraduate Student in Mechanical Engineering, Fall 2011
  • Ojas Mainkar, Undergraduate Student in Mechanical Engineering and Biomedical Engineering, Summer 2011 (SURF)
  • Deborah Gruner, Undergraduate Student in Mathematical Sciences, 2010
  • Indira Biswas, Undergraduate Student in Mechanical Engineering, 2009
  • Mikhail F. Lara, Undergraduate Student in Mechanical Engineering and Biomedical Engineering, 2008 (SURG)
  • Julie Hoi Yan Ng, Undergraduate Student in Mechanical Engineering, 2008
  • Changho Oh, Undergraduate Student in Mechanical Engineering, 2007-2008 (SURF)

 

Visiting scholars and students

  • Yundong Gai, PhD Student in Dalian Institute of Technology, China, 2018-2019
  • Yanyang Xiao, PhD Student in Xiamen University, China, 2018-2019
  • Juan Cao, Associate Professor in Xiamen University, China, 2017-2018
  • Zhonggui Chen, Associate Professor in Xiamen University, China, 2017-2018
  • Bin Li, Ph.D. Student in Zhejiang University, China, 2017-2018
  • Lifeng Zhu, Associate Professor in Southeast University, China, 2017-2018
  • Adam Robert Updegrove, Visiting Ph.D. Student from University of California, Berkeley, May-June, 2017
  • Hugo Casquero Penelas, Visiting Ph.D. Student from University of A Coruna, Spain, 2014-2015, 2016
  • Onofre Marco Alacid, Visiting Ph.D. Student from Polytechnic University of Valencia, Spain, 2014
  • Xinge Li, Visiting Ph.D. Student from Chinese Academy of Sciences, China, 2014, 2016
  • Onofre Marco Alacid, Visiting Ph.D. Student from Polytechnic University of Valencia, Spain, 2013
  • Yue Jia, Visiting Ph.D. Student from Bauhaus-University Weimar, Germany, 2013-2014 (Now at Northwestern Polytechnic University, Xi'an, China)
  • Juelin Leng, Ph.D. Student in Chinese Academy of Sciences (Visiting Student), 2012
  • Rui Zhang, Ph.D. Student in School of Architecture (Summer Intern), 2008

Courses

Current courses

Course Course Name Location Units Semester Offered
24-311 Numerical Methods Pittsburgh 12 Spring

Publications

Publication lists

For a list of Jessica Zhang’s publications, please see the following: 

Textbook

Edited books

Book chapters

  • Y. Lai, L. Liu, Y. J. Zhang, J. Chen, E. Fang, J. Lua. Rhino 3D to Abaqus: A T-spline Based Isogeometric Analysis Software Platform. The edited volume of the Modeling and Simulation in Science, Engineering and Technology Book Series devoted to AFSI 2014 - a birthday celebration conference for Tayfun Tezduyar. Springer Publisher. Editors: Yuri Bazilevs and Kenji Takizawa. Part IV:271-281, 2016. 
  • Y. Zhang. Challenges and Advances in Image-Based Geometric Modeling and Mesh Generation. Image-Based Geometric Modeling and Mesh Generation. Springer Publisher. Editor: Yongjie (Jessica) Zhang, 2013. (Review Article) 
  • J. Leng, G. Xu, Y. Zhang, J. Qian. Quality Improvement of Segmented Hexahedral Meshes using Geometric Flows. Image-Based Geometric Modeling and Mesh Generation. Springer Publisher. Editor: Yongjie (Jessica) Zhang, 2013. 
  • S. S. Hossain, Y. Zhang. Application of Isogeometric Analysis to Simulate Local Nanoparticulate Drug Delivery in Patient-Specific Coronary Arteries. Multiscale Simulations and Mechanics of Biological Materials: Wing Liu's 60 Anniversary Volume. John Wiley & Sons Lt. Publisher. Editors: Shaofan Li and Dong Qian, 2012. 
  • S. S. Hossain, A. M. Kopacz, Y. Zhang, S.-Y. Lee, T.-R. Lee, M. Ferrari, T. J.R. Hughes, W. K. Liu, P. Decuzzi. Multiscale Modeling for the Vascular Transport of Nanoparticles. Nano and Cell Mechanics. Wiley Series in Micro and Nano Technologies. Editors: Gang Bao and Horacio Espinosa, 2012 (Review Article) 

Journal publications

  • Y. Xiao, Z. Chen, J. Cao, Y. J. Zhang, C. Wang. Optimal Power Diagrams via Function Approximation. The Special Issue of Solid and Physical Modeling in Computer-Aided Design, 102:52-60, 2018. 
  • Z. Chen, T. Zhang, J. Cao, Y. J. Zhang, C. Wang. Point Cloud Resampling Using Centroid Voronoi Tessellation Methods. The Special Issue of Solid and Physical Modeling in Computer-Aided Design, 102:12-21, 2018. 
  • Z. Chen, W. Chen, J. Guo, J. Cao, Y. J. Zhang. Orientation Field Guided Line Abstraction for 3D Printing. The Special Issue of Geometric Modeling and Processing in Computer Aided Geometric Design, 62:253-262, 2018. 
  • Y. Jia, C. Anitesuc, Y. J. Zhang, G. Xu, C. Li, T. Rabczuk. PHT-Spline-Based Enhanced Isogeometric Collocation Method. Journal of Computer-Aided Design & Computer Graphics (China), 30(4):702-706, 2018. 
  • B. Urick, T. M. Sanders, S. S. Hossain, Y. Zhang, T. J. R. Hughes. Review of Patient-Specific Vascular Modeling: Template-Based Isogeometric Framework and the Case for CAD. Archives of Computational Methods in Engineering, 2017. DOI: https://doi.org/10.1007/s11831-017-9246-z 
  • A. Pawar, Y. J. Zhang, C. Anitescu, Y. Jia, T. Rabczuk. DTHB3D_Reg: Dynamic Truncated Hierarchical B-Spline Based 3D Nonrigid Image Registration. Communications in Computational Physics, 23(3):877-898, 2018. 
  • K. Hu, Y. J. Zhang, G. Xu. CVT-based 3D Image Segmentation and Quality Improvement of Tetrahedral/Hexahedral Meshes Using Anisotropic Giaquinta-Hildebrandt Operator. Computer Methods in Biomechanics and Biomedical Engineering: Imaging & Visualization, 6(3):331-342, 2018. 
  • X. Wei, Y. J. Zhang, T. J. R. Hughes. Truncated Hierarchical Tricubic C0 Spline Construction on Unstructured Hexahedral Meshes for Isogeometric Analysis Applications. A Special Issue of Advances in Mathematics of Finite Elements in Honor of Ivo Babuska in Computers and Mathematics with Applications, 74(9):2203-2220, 2017. 
  • Y. Lai, Y. J. Zhang, L. Liu, X. Wei, E. Fang, J. Lua. Integrating CAD with Abaqus: A Practical Isogeometric Analysis Software Platform for Industrial Applications. A Special Issue of HOFEIM 2016 in Computers and Mathematics with Applications, 74(7):1648-1660, 2017. 
  • X. Wei, Y. J. Zhang, L. Liu, T. J. R. Hughes. Truncated T-splines: Fundamentals and Methods. Computer Methods in Applied Mechanics and Engineering Special Issue on Isogeometric Analysis, 316:349-372, 2017. 
  • K. Hu, Y. J. Zhang, T. Liao. Surface Segmentation for Polycube Construction Based on Generalized Centroidal Voronoi Tessellation. Computer Methods in Applied Mechanics and Engineering Special Issue on Isogeometric Analysis, 316:280-296, 2017. 
  • C. L. Chan, C. Anitescu, Y. Zhang, T. Rabczuk. Two and Three Dimensional Image Registration Based on B-spline Composition and Level Sets. Communications in Computational Physics, 21(2):600-622, 2017. 
  • G. Lorenzo, M. A. Scott, K. B. Tew, T. J. R. Hughes, Y. J. Zhang, L. Liu, G. Vilanova, H. Gomez. Tissue Scale, Personalized Modeling and Simulation of Prostate Cancer Growth. PNAS, 113(48):E7663-E7671, 2016. 
  • H. Casquero, L. Liu, Y. Zhang, A. Reali, J. Kiendl, H. Gomez. Arbitrary-Degree T-splines for Isogeometric Analysis of Fully Nonlinear Kirchhoff-Love Shells. Computer-Aided Design Special Issue on Isogeometric Design and Analysis, 82C:140-153, 2016. 
  • L. Liu, H. Casquero, H. Gomez, Y. Zhang. Hybrid-Degree Weighted T-splines and Their Application in Isogeometric Analysis. A Special Issue of AFSI 2014 in Computers and Fluids, 141:42-53, 2016. 
  • A. Pawar, Y. Zhang, Y. Jia, X. Wei, T. Rabczuk, C. L. Chan, C. Anitescu. Adaptive FEM-based Nonrigid Image Registration Using Truncated Hierarchical B-splines. A Special Issue of FEF 2015 in Computers and Mathematics with Applications, 72:2028-2040, 2016. 
  • D. T. O'Connor, K. I. Elkhodary, Y. Fouad, M. S. Greene, F. Sabet, J. Qian, Y. Zhang, W. K. Liu, I. Jasiuk. Modeling Orthotropic Elasticity, Localized Plasticity and Fracture in Trabecular Bone.Computational Mechanics, 58(3):423-439, 2016. 
  • K. Hu, Y. Zhang. Centroidal Voronoi Tessellation Based Polycube Construction for Adaptive All-Hexahedral Mesh Generation. Computer Methods in Applied Mechanics and Engineering, 305:405-421, 2016. 
  • H. Casquero, L. Liu, Y. Zhang, A. Reali, H. Gomez. Isogeometric Collocation Using Analysis-Suitable T-splines of Arbitrary Degree. Computer Methods in Applied Mechanics and Engineering, 301:164-186, 2016. 
  • Q. Pan, G. Xu, G. Xu, Y. Zhang. Isogeometric Analysis Based on Extended Catmull-Clark Subdivision. Computers and Mathematics with Applications, 71(1):105-119, 2016. 
  • X. Wei, Y. J. Zhang, M. A. Scott, T. J. R. Hughes. Extended Truncated Hierarchical Catmull-Clark Subdivision. Computer Methods in Applied Mechanics and Engineering, 299:316-336, 2016. 
  • H-C Lee, T. Liao, Y. J. Zhang, G. Yang. Shape Component Analysis: Structure-Preserving Dimension Reduction on Biological Shape Spaces. Bioinformatics, 32(5):755-763, 2016. 
  • H. Casquero, L. Liu, C. Bona-Casas, Y. Zhang, H. Gomez. A Hybrid Variational-Collocation Immersed Method for Fluid-Structure Interaction Using Unstructured T-splines. International Journal for Numerical Methods in Engineering, 105:855-880, 2016. 
  • Y. Gao, Y. Zhang, P. Menon. 3D Shape Comparison Using a Laplace Spectral Shape Matching Approach. The Special Issue of CompIMAGE'14 in Computer Methods in Biomechanics and Biomedical Engineering: Imaging & Visualization, 4(2):86-97, 2016. 
  • K. Hu, Y. Zhang. Image Segmentation and Adaptive Superpixel Generation Based on Harmonic Edge-Weighted Centroidal Voronoi Tessellation. The Special Issue of CompIMAGE'14 in Computer Methods in Biomechanics and Biomedical Engineering: Imaging & Visualization, 4(2):46-60, 2016. 
  • T. Liao, X. Li, G. Xu, Y. Zhang. Secondary Laplace Operator and Generalized Giaquinta-Hildebrandt Operator with Applications on Surface Segmentation and Smoothing. A Special Issue of SIAM Conference on Geometric & Physical Modeling 2015 in Computer Aided Design, 70:56-66, 2016. Autodesk Best Paper Award 1st Place 

Conference publications

  • Y. Xiao, Z. Chen, J. Cao, Y. J. Zhang, C. Wang. Optimal Power Diagrams via Function Approximation. The Special Issue of Solid and Physical Modeling in Computer-Aided Design. Bilbao, Spain. June 11-13, 2018. 
  • Z. Chen, T. Zhang, J. Cao, Y. J. Zhang, C. Wang. Point Cloud Resampling Using Centroid Voronoi Tessellation Methods. Solid and Physical Modeling. Bilbao, Spain. June 11-13, 2018. 
  • L. Zhu, X. Li, W. Lu, Y. J. Zhang. A Field-Based Representation of Surrounding Vehicle Motion from a Monocular Camera. The 29th IEEE Intelligence Vehicle Symposium. Changshu, Suzhou, China. June 26-30, 2018. 
  • Z. Chen, W. Chen, J. Guo, J. Cao, Y. J. Zhang. Orientation Field Guided Line Abstraction for 3D Printing. The 12th International Conference on Geometric Modeling and Processing. Aachen, Germany. April 9-11, 2018. 
  • X. Chai, D. Qian, Q. Ba, A. Li, Y. J. Zhang, G. Yang. Image-Based Measurement of Cargo Traffic Flow in Complex Neurite Networks. IEEE International Conference on Image Processing. Beijing, China. September 17-20, 2017. 
  • A. Pawar, Y. Zhang, Y. Jia, C. Anitescu, T. Rabczuk. 3D Nonrigid Image Registration Using Truncated Hierarchical B-splines. 5th International Conference on Computational and Mathematical Biomedical Engineering. Pittsburgh, PA. April 10-12, 2017. 
  • H. Casquero, C. Bona-Casas, Y. Zhang, H. Gomez. Dynamics and Rheology of Biological Cells in Flow. 5th International Conference on Computational and Mathematical Biomedical Engineering. Pittsburgh, PA. April 10-12, 2017. 
  • K. Hu, Y. J. Zhang, X. Li, G. Xu. Feature-Aligned Surface Parameterization Using Secondary Laplace Operator and Loop Subdivision. 25th International Meshing Roundtable. Washington, DC. Sept. 27-30, 2016. Procedia Engineering, 163:186-198, 2016. 
  • K. Hu, Y. Zhang, G. Xu. CVT-based 3D Image Segmentation for Quality Tetrahedral Meshing. CompIMAGE (Computer Modeling of Objects Presented in Images: Fundamentals, Methods, and Applications). Niagara Falls, USA. Sept. 21-23, 2016. Best Paper Award 
  • E. Fang, Y. Lai, J. Lua, Y. J. Zhang, N. D. Phan. Isogeometric Analysis based Finite Element Approach for Ductile Failure Prediction of the Second Sandia Fracture Challenge Problem. AHS International's 72nd Annual Forum and Technology Display Conference. West Palm Beach, FL. May 17-19, 2016.