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Staff information


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








  • 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/



  • 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. 


  • 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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