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Daniel Einstein

Computational Biology


Dr. Einstein has nearly 15 years experience participating in multiple interdisciplinary research teams focused on the development of continuum and multiscale models of organ systems.

A recent focus area is the understanding and prediction of alveolar scale ventilator induced lung injury (VILI). This project combines the co-location of mass spectrometry imaging signals of inflammation biomarkers with imaging-based kinematic and multi scale modeling data. The underlying assumption is that extreme alveolar scale stresses produce well-characterized and well-understood inflammatory pathways. The research thrusts of this project are two fold. First, our work aims to measure and compute local ventilation from CT data from control and VILI subjects and correlate it with MSI data from the same subjects such that differences in the spectra between the two groups can be used to reveal spatial patterns of inflammation.

Second, we are developing a multiscale computational model of the entire rodent respiratory, integrated with a novel and focused imaging study of regional parenchymal strain and alveolar dynamics. Specifically, we will develop imaging-based multiscale computational models that connect airway mechanics with coupled, time-dependent parenchymal and alveolar scale mechanics. Parenchymal scale mechanics will be based on a novel implicit framework for lung parenchyma and will telescope to the alveolar scale, represented by stochastic populations of structural alveoli, articulated in terms of spatially arranged collagen, elastin and alveolar surfactant.

For the last 10 years, Dr. Einstein has lead the Computational Core of PNNL's Virtual Lung project, focusing on the development the open-source technologies that are the foundation for PNNLs organ-to-cell multi scale program. In addition, he provides bioengineering expertise and leadership to assure that simulations are faithful to the underlying biophysics, that models are accurate and well documented, that their predictions accord with experimental data, and that modeling efforts are responsive to the scope of each project. Recent contributions include: development of a novel, thermodynamically based framework for the nonlinear, implicit multi scale mechanics of tissues; the development with of a novel and efficient partitioned approach to multi scale coupling based on true mechanical, chemical and electrical equilibrium; the development of adaptive computational mesh dynamics algorithms for Lagrangian fluid-structure interaction in the heart; and numerous computational geometry and image processing algorithms.


Google Scholar:

Research Interests

  • Multiscale Mechanics and Thermodynamics of Tissues and Organs
  • Fluid-structure interactions
  • Extracting Mechanical Information from Images
  • Computational Geometry
  • Finite Element and Finite Volume Methods

Education and Credentials

  • B.S. Mechanical Engineering, University of Massachusetts
  • Ph.D. Bioengineering, University of Washington
  • Postdoctoral, Cleveland Clinic

Affiliations and Professional Service

  • University of Washington Department of Mechanical Engineering
  • NIH Interagency Modeling and Analysis Group
  • Northwest Institute for Advanced Computing (NIAC)

Awards and Recognitions

  • Tau Beta Pi
  • Professor Jon Kelly Memorial Prize for Outstanding Academic Performance

PNNL Publications


  • Dyedov V, N Ray, DR Einstein, X Jiao, and T Tautges. 2014. "AHF: Array-Based Half-Facet Data Structure for Mixed-Dimensional and Non-Manifold Meshes." In Proceedings of the 22nd International Meshing Roundtable, October 13-16, 2013, Orlando, Florida, ed. J Sarrate and M Staten, pp. 445-464.  Springer, Dordrecht, Netherlands.  doi:10.1007/978-3-319-02335-9
  • Freed AD, J Liao, and DR Einstein. 2014. "A Membrane Model from Implicit Elasticity Theory: Application to Visceral Pleura." Biomechanics and Modeling in Mechanobiology 13(4):871-881.  doi:10.1007/s10237-013-0542-8
  • Miller FJ, B Asgharian, JD Schroeter, O Price, RA Corley, DR Einstein, RE Jacob, TC Cox, S Kabilan, and T Bentley. 2014. "Respiratory tract lung geometry and dosimetry model for male Sprague-Dawley rats." Inhalation Toxicology 26(9):524-544.  doi:10.3109/08958378.2014.925991
  • Ray N, T Delaney, DR Einstein, and X Jiao. 2014. "Surface Remeshing with Robust High-Order Reconstruction." Engineering with Computers: An International Journal of Simulation-based Engineering 30(4):487-502.  doi:10.1007/s00366-014-0359-9


  • Einstein DR, AP Kuprat, X Jiao, JP Carson, DM Einstein, RA Corley, and RE Jacob. 2013. "An Efficient Algorithm for Mapping Imaging Data to 3D Unstructured Grids in Computational Biomechanics." International Journal for Numerical Methods in Biomedical Engineering 29(1):1-16.  doi:10.1002/cnm.2489
  • Freed AD, and DR Einstein. 2013. "An Implicit Elastic Theory for Lung Parenchyma." International Journal of Engineering Science 62:31-47.  doi:10.1016/j.ijengsci.2012.08.003
  • Jacob RE, JP Carson, M Thomas, and DR Einstein. 2013. "Dynamic Multiscale Boundary Conditions for 4D CT Images of Healthy and Emphysematous Rat." PLoS One 8(6):Article No. e65874.  doi:10.1371/journal.pone.0065874
  • Jacob RE, SM Colby, S Kabilan, DR Einstein, and JP Carson. 2013. "In Situ Casting and Imaging of the Rat Airway Tree for Accurate 3D Reconstruction." Experimental Lung Research 39(6):249-257.  doi:10.3109/01902148.2013.801535
  • Kleese van Dam K, JP Carson, AL Corrigan, DR Einstein, ZC Guillen, BS Heath, AP Kuprat, IT Lanekoff, CS Lansing, J Laskin, D Li, Y Liu, MJ Marshall, EA Miller, G Orr, P Pinheiro da Silva, S Ryu, CJ Szymanski, and M Thomas. 2013. "Velo and REXAN - Integrated Data Management and High Speed Analysis for Experimental Facilities." In Proceedings of the IEEE 8th International Conference on EScience, October 8-12, 2012, Chicago, Illinois.  IEEE Press, Los Alamitos, CA.  doi: 10.1109/eScience.2012.6404463
  • Kuprat AP, S Kabilan, JP Carson, RA Corley, and DR Einstein. 2013. "A Bidirectional Coupling Procedure Applied to Multiscale Respiratory Modeling." Journal of Computational Physics 244:148-167.  doi:10.1016/


  • Corley RA, S Kabilan, AP Kuprat, JP Carson, KR Minard, RE Jacob, C Timchalk, RW Glenny, S Pipavath, TC Cox, C Wallis, R Larson, M Fanucchi, E Postlewait, and DR Einstein. 2012. "COMPARATIVE COMPUTATIONAL MODELING OF AIRFLOWS AND VAPOR DOSIMETY IN THE RESPIRATORY TRACTS OF RAT, MONKEY, AND HUMAN." Toxicological Sciences 128(2):500-516.  doi:10.1093/toxsci/kfs168
  • Asgharian B, O Price, G McClellan, RA Corley, DR Einstein, RE Jacob, JR Harkema, SA Carey, E Schelegle, D Hyde, J Kimbell, and FJ Miller. 2012. "Development of a Rhesus Monkey Lung Geometry Model and Application to Particle Deposition in Comparison to Humans." Inhalation Toxicology 24(13):869-899.  doi:10.3109/08958378.2012.725782
  • Freed AD, and DR Einstein. 2012. "Hypo-Elastic Model for Lung Parenchyma." Biomechanics and Modeling in Mechanobiology 11(3-4):557-573.  doi:10.1007/s10237-011-0333-z
  • Freed AD, DR Einstein, JP Carson, and RE Jacob. 2012. Viscoelastic Model for Lung Parenchyma for Multi-Scale Modeling of Respiratory System, Phase II: Dodecahedral Micro-ModelPNNL-21287, Pacific Northwest National Laboratory, Richland, WA. 
  • Minard KR, AP Kuprat, S Kabilan, RE Jacob, DR Einstein, JP Carson, and RA Corley. 2012. "Phase-Contrast MRI and CFD Modeling of Apparent 3He Gas Flow in Rat Pulmonary Airways." Journal of Magnetic Resonance 221:129-138.  doi:10.1016/j.jmr.2012.05.007
  • Neradilek MB, N Polissar, DR Einstein, RW Glenny, KR Minard, JP Carson, X Jiao, RE Jacob, TC Cox, E Postlewait, and RA Corley. 2012. "BRANCH-BASED MODEL FOR THE DIAMETERS OF THE PULMONARY AIRWAYS: ACCOUNTING FOR DEPARTURES FROM SELF-CONSISTENCY AND REGISTRATION ERRORS." The Anatomical Record 295(6):1027-1044.  doi:10.1002/ar.22476



  • Carson JP, AP Kuprat, X Jiao, F del Pin, and DR Einstein. 2010. "An Anisotropic Fluid-Solid Model of the Mouse Heart." In Computers in Cardiology 2009, Park City, Utah September 13-16, 2009, vol. 36, pp. 377-380.  Computers in Cardiology and IEEE, Piscataway, NJ. 
  • Carson JP, AP Kuprat, X Jiao, V Dyedov, F del Pin, JM Guccione, MB Ratcliffe, and DR Einstein. 2010. "Adaptive Generation of Multimaterial Grids from imaging data for Biomedical Lagrangian Fluid-Structure Simulations." Biomechanics and Modeling in Mechanobiology 9(2):187-201.  doi:10.1007/S10237-009-0170-5
  • Carson JP, DR Einstein, KR Minard, M Fanucchi, C Wallis, and RA Corley. 2010. "High resolution lung airway cast segmentation with proper topology suitable for computational fluid dynamic simulations." Computerized Medical Imaging and Graphics 34(7):572-857.  doi:10.1016/j.compmedimag.2010.03.001
  • Freed AD, DR Einstein, and MS Sacks. 2010. "Hypoelastic Soft Tissues Part II: In-Plane Biaxial Experiments." Acta Mechanica 213(1-2):205-222.  doi:10.1007/d00707-010-0357-y
  • Hsu EW, LJ Healy, DR Einstein, and AP Kuprat. 2010. "Imaging-Based Assessment and Modeling of the Structures of the Myocardium." Chapter 2 in Computational Cardiovascular Mechanics: Modeling and Applications in Heart Failure, pp. 23-29.  Springer, New York, NY. 
  • Jiao X, DR Einstein, and V Dyedov. 2010. "Local Orthogonal Cutting Method for Computing Medial Curves and Its Biomedical Applications." SIAM Journal on Scientific Computing 32(2):947-969.  doi:10.1137/090767170
  • Sun K, Z Zhang, T Suzuki, JF Wenk, N Stander, DR Einstein, D Saloner, AW Wallace, JM Guccione, and MB Ratcliffe. 2010. "Dor procedure for dyskinetic anteroapical myocardial infarction fails to improve contractility in the borderzone." Journal of Thoracic and Cardiovascular Surgery 140(1):233-239.  doi:10.1016/j.jtcvs.2009.11.055
  • Wenk JF, CS Jhun, Z Zhang, K Sun, M Burger, DR Einstein, MB Ratcliffe, and JM Guccione. 2010. "In Vivo Left Ventricular Geometry and Boundary Conditions." Chapter 1 in In Computational Cardiovascular Mechanics: Modeling and Applications in Heart Failure, ed. Guccione, JM, GS Kassak and MB Ratcliffe, pp. 3-21.  Springer US, New York, NY. 
  • Wischgoll T, DR Einstein, AP Kuprat, X Jiao, and GS Kassab. 2010. "Vascular Geometry Reconstruction and Grid Generation." Chapter 7 in Computational Cardiovascular Mechanics: Modeling and Applications in Heart Failure, pp. 103-119.  Springer, New York, NY. 


  • Corley RA, KR Minard, S Kabilan, DR Einstein, AP Kuprat, JR harkema, J Kimbell, ML Gargas, and JH Kinzell. 2009. "Magnetic resonance imaging and computational fluid dynamics (CFD) simulations of rabbit nasal airflows for the development of hybrid CFD/PBPK models ." Inhalation Toxicology 21(5-7):512-518. 
  • Corley RA, KR Minard, S Kabilan, DR Einstein, AP Kuprat, JR Harkema, J Kimbell, ML Gargas, and JH Kinzell. 2009. "Magnetic Resonance Imaging and Computational Fluid Dynamics (CFD) Simulations of Rabbit Nasal Airflows for the Development of Hybrid CFD/PBPK Models." Inhalation Toxicology 21(6):512-518. 
  • Dyedov V, DR Einstein, X Jiao, AP Kuprat, JP Carson, and F del Pin. 2009. "Variational Generation of Prismatic Boundary-Layer Meshes for Biomedical Computing." International Journal for Numerical Methods in Engineering 79(8):907-945.  doi:10.1002/nme.2583
  • Einstein DR, F del Pin, X Jiao, AP Kuprat, JP Carson, K Kunzelman, RP Cochran, JM Guccione, and MB Ratcliffe. 2009. "Fluid-Structure Interactions of the Mitral Valve and Left Heart: Comprehensive Strategies, Past, Present and Future." International Journal for Numerical Methods in Biomedical Engineering 26(3-4):348-380.  doi:10.1002/cnm.1280
  • Jiao X, DR Einstein, V Dyedov, and JP Carson. 2009. "Automatic Identification and Truncation of Boundary Outlets in Complex Imaging-Derived Biomedical Geometries." Medical & Biological Engineering & Computing 47(9):989-999.  doi:10.1007/s11517-009-0501-9
  • Kuprat AP, and DR Einstein. 2009. "An Anisotropic Scale-Invariant Unstructured Mesh Generator Auitable for Volumetric Imaging Data." Journal of Computational Physics 228(3):619-640.  doi:10.1016/
  • Schievano S, K Kunzelman, M Nicosia, RP Cochran, DR Einstein, S Khambadkone, and P Bonheoffer. 2009. "Percutaneous Mitral Valve Dilatation: Single Balloon versus Double Balloon - A Finite Element Study." Journal of Heart Valve Disease 18:28-34. 
  • Sun K, N Stander, CS Jhun, Z Zhang, T suzuki, GY Wang, M Saeed, AW wallace, E Tseng, AJ Baker, D Saloner, DR Einstein, MB Ratcliffe, and JM Guccione. 2009. "A Computationally Efficient Formal Optimization of Regional Myocardial Contractility in a Sheep with Left Ventricular Aneurysm." Journal of Biomechanical Engineering 131(11):Article Number: 111001.  doi:10.1115/1.3148464
  • Tawhai M, J Bischoff, DR Einstein, A Erdemir, T Guess, and J Reinbolt. 2009. "Multiscale Modeling in Computational Biomechanics: Determining Computational Priorities and Addressing Current Challenges." IEEE Engineering in Medicine and Biology Magazine 28(3):41-9. 


  • Einstein DR, B Neradilak, N Pollisar, KR Minard, C Wallis, M Fanucchi, JP Carson, AP Kuprat, S Kabilan, R Jacob, and R Corley. 2008. "An Automated Self-similarity Analysis of the Pulmonary Tree of the Sprague-Dawley Rat." The Anatomical Record 291(12):1628-1648.  doi:10.1002/ar.20771
  • Kinon C, B Fata, and DR Einstein. 2008. "Characterization of Highly Nonlinear and Anisotropic Vascular Tissues from Experimental Inflation Data: a Validation Study Towards the Use of Clinical Data for In-vivo Modeling and Analysis." Annals of Biomedical Engineering 36(10):1668-1680.  doi:10.1007/s10439-008-9541-9
  • Minard KR, RE Jacob, G Laicher, DR Einstein, AP Kuprat, and RA Corley. 2008. "MR Imaging of Apparent 3He Gas Transport in Narrow Pipes and Rodent Airways ." Journal of Magnetic Resonance 194(2):182-191.  doi:10.1016/j.jmr.2008.07.006


  • Kunzelman KS, DR Einstein, and RP Cochran. 2007. "FLUID-STRUCTURE INTERACTION MODELS OF THE MITRAL VALVE: FUNCTION IN NORMAL AND PATHOLOGIC STATES." Philosophical Transactions of the Royal Society of London Series B, Biological Sciences 362(1484):1393-1406. 


  • Einstein DR, AD Freed, and I Vesely. 2006. "Invariant Formulation for Dispersed Transverse Isotropy in Tissues of the Aortic Outflow Tract." In Mechanics of Biological Tissue, pp. 355-368.  Springer, Secaucus, NJ. 
  • Minard KR, DR Einstein, RE Jacob, S Kabilan, AP Kuprat, C Timchalk, LL Trease, and RA Corley. 2006. "Application of Magnetic Resonance (MR) Imaging for the Development and Validation of Computational Fluid Dynamic (CFD) Models of the Rat Respiratory System." Inhalation Toxicology 18(10):787-794.  doi: 10.1080/08958370600748729


  • Einstein DR, AD Freed, N Stander, B Fata, and I Vesely. 2005. "Inverse Parameter Fitting of Biological Tissues: A Response Surface Approach." Annals of Biomedical Engineering 33(12):1819-1830. 
  • Freed AD, DR Einstein, and I Vesely. 2005. "Invariant formulation for dispersed transverse isotropy in aortic heart valves: An efficient means for modeling fiber splay." Biomechanics and Modeling in Mechanobiology 4(2-3):100-117. 

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