Journal Articles:
  1. Mukherjee, D., Jani, N.D., Narvid, J, and Shadden, S.C. (2018) The Role Of Circle Of Willis Anatomy Variations In cardio-embolic Stroke - A Patient-specific Simulation Based Study. Annals of Biomedical Engineering. 46(8):1128-1145. [bib | link][pre-print: bioRxiv-190579]- ​selected for journal cover feature
  2. Mukherjee, D., and Shadden, S.C. (2018). Modeling Thrombus-Hemodynamics Interactions Using A Hybrid Particle-Continuum Approach. Biomechanics and Modeling in Mechanobiology. 17(3):645-663. [bib | link]
  3. Mukherjee, D., and Shadden, S.C. (2017) Inertial Particle Dynamics In Large Artery Flows - Implications For Arterial Embolisms. Journal of Biomechanics. 52(8):155-164. [bib | link]
  4. Casas, G.*, Mukherjee, D.*, Celigueta, M.A., Zohdi, T.I., and Onate E. (2017). A Modular, Partitioned, Discrete Element Framework For Industrial Grain Distribution Systems With Rotating Machinery. Journal of Computational Particle Mechanics. 4(2):181-198. [bib | link]
  5. Mukherjee, D., Jani, N.D., Selvaganesan, K., Weng, C.L., and Shadden, S.C. (2016) Computational Assessment Of The Relation Between Embolism Source And Embolus Distribution To The Circle Of Willis For Improved Understanding Of Stroke Etiology. Journal of Biomechanical Engineering. 138(8):0810081-13. [bib | link]
  6. Mukherjee, D., Padilla, J., and Shadden, S.C. (2016). Numerical Investigation Of Fluid-Particle Interactions For Embolic Stroke. Theoretical and Computational Fluid Dynamics. 30(1):23-39 [bib | link]
  7. Mukherjee, D., and Zohdi, T.I. (2015). A Discrete Element Based Simulation Framework To Investigate Particulate Spray Deposition Processes. Journal of Computational Physics. 290:298-317. [bib | link]
  8. Mukherjee, D., and Zohdi, T.I. (2015). Computational Modeling Of The Dynamics & Interference Effects Of An Erosive Granular Jet Impacting A Porous, Compliant Surface. Granular Matter. 17(2):231-252. [bib | link]
  9. Mukherjee, D., Zaky, Z., Zohdi, T.I., Salama, A., and Sun, S. (2015). Investigation Of Guided Particle Transport For Noninvasive Healing Of Damaged Piping System Using Electro-Magneto-Mechanical Methods. Journal of Society of Petroleum Engineers. 20(4):872-883. [bib | link]
  10. Mukherjee, D., and Zohdi, T.I. (2014). Electromagnetic Control Of Charged Particulate Spray Systems - Models For Planning The Spray-gun Operations. Computer Aided Design. 46:211-215. [bib | link]

In Preparation:
  1. Mukherjee, D., Diamond, S.L., and Shadden, S.C. Modeling Flow-mediated Transport In The Neighborhood Of Blood Clots. 
  2. ​Mukherjee, D., and Zohdi, T.I. A Monte-Carlo Based Framework For Uncertainty Characterization And Durability Estimation For A Material Layer Impacted By A Particle.
  3. Mukherjee, D., and Zohdi, T.I. An Iterative Collide-And-stream Algorithm For Particle Ensembles With Non-Enduring Contacts. 

Peer-reviewed Proceedings:
  1. Mukherjee, D., and Shadden, S.C. (2017). Fictitious Domain Particle-based Modeling for Thrombosis. Proceedings of the 2017 Summer Biomechanics, Bioengineering and Biotransport Conference. [bib|link**]
  2. Mukherjee, D., Jani, N.D., and Shadden, S.C. (2017). Discrete Particle Modeling For Thrombotic And Embolic Phenomena In Arteries. Proceedings of the 5th International Conference On Computational And Mathematical Biomedical Engineering. [bib | link**]
  3. Mukherjee, D., and Shadden, S.C. (2016). Towards Non-invasive, Computational Modeling Of The Transport Of Thrombo-Emboli And Athero-Emboli Along Arteries. Proceedings of the 2016 Summer Biomechanics, Bioengineering and Biotransport Conference (SB3C 2016). DOI: 10.13140/RG.2.1.4656.3445. [bib | link**] 
  4. Mukherjee, D., and Shadden, S.C. (2015). Insights Into The Hemodynamic Factors Affecting Embolus Transport For Stroke. Proceedings of the 2015 Summer Biomechanics, Bioengineering and Biotransport Conference (SB3C 2015). DOI: 10.13140/RG.2.1.2415.3048.  [bib | link**]
  5. Mukherjee, D., and Zohdi, T.I. (2013). Computer Modeling And Simulation Framework For Particulate Spray Based Manufacturing Processes. Proceedings of the ASME International Mechanical Engineering Congress & Exposition (IMECE 2013). [bib | link]
  6. Mukherjee, D., and Mansour, A.E. (2010). Preliminary Concept And Feasibility Studies On Ocean Energy Device Design From Used Ships. Proceedings of the 29th International Conference on Ocean & Offshore, and Arctic Engineering (OMAE 2010) - best paper award [bib | link]
**DOI and download available through Researchgate

Conference Presentations:
  1. Computational Investigations On Flow-mediated Transport Processes At The Blood-thrombus Interface. Mukherjee, D. 72nd Annual Meeting of the American Physical Society Division of Fluid Dynamics, Seattle, Washington. November 2019.
  2. Developing A New CFD Course Based On Open Source Tools: Design Experience And Student Outcomes. Mukherjee, D. 72nd Annual Meeting of the American Physical Society Division of Fluid Dynamics, Seattle, Washington. November 2019.
  3. Computational Analysis Of Interstitial Fluid Flow Through The Lacunar-canalicular System With Morphological Variations. Khadangale, S., Hajebrahimi, S., Lynch, M.E., and Mukherjee, D. 72nd Annual Meeting of the American Physical Society Division of Fluid Dynamics, Seattle, Washington. November 2019.
  4. ​Computational Study Of Hemodynamic Nature In Patient-specic Cerebrovasculature With Lenticulostriate Artery Under ICA Stenosis Conditions. Kang, T., Mukherjee, D., Kim, J.M., Park, K.Y., and Ryu, J.  72nd Annual Meeting of the American Physical Society Division of Fluid Dynamics, Seattle, Washington. November 2019.
  5. Image-driven Particle-based Methods For Stroke And Thrombosis. Mukherjee, D. VI International Conference On Particle-based Methods. Fundamentals And Applications, Barcelona, Spain. October, 2019.
  6. Computational Investigations On Cerebral Vasculature Anatomy And Its Role In Embolic Stroke. Mukherjee, D., Jani, N.D., Narvid, J., and Shadden, S.C.  The 15th United States National Congress on Computational Mechanics, Austin, Texas. July 2019.
  7. Towards Developing Hybrid Particle-continuum Frameworks For Thrombosis And Embolization Biomechanics In Large Arteries. Mukherjee, D., Diamond, S.L., and Shadden, S.C. The 8'th World Congress Of Biomechanics, Dublin, Ireland. July 2018.
  8. Hybrid Particle-continuum Computational Models For Thrombus Biomechanics.  Mukherjee, D., and Shadden, S.C. The 13'th World Congress On Computational Mechanics, New York City, New York. July 2018.
  9. Computational Quantification Of Cerebrovascular Flow During A Trans-catheter Aortic Valve Implantation. Pyne, J., Mukherjee, D., Ryu, J., Narvid, J., and Shadden, S.C. The Heart And Brain Symposium, Chicago, Illinois. June 2018.
  10. The Role Of Hemodynamics In Organizing Transport In Thrombus Neighborhood. Mukherjee, D., and Shadden, S.C., 2018 Cellular and Molecular Bioengineering Conference, Biomedical Engineering Society, Key Largo, Florida. January, 2018.
  11. Flow-mediated Transport Around A Macroscopic Arterial Thrombus. Mukherjee, D., Garduono, J., and Shadden, S.C., 70'th Annual Meeting Of The American Physical Society Division Of Fluid Dynamics, Denver, Colorado, November 2017.
  12. Approximating Ischemic Stroke Location And Abnormal Tissue Regions Through Subtracting NCCT and CTA Scans. Pyne, J., Mukherjee, D., Narvid, J., Bowen, M., Dehkhargani, S., and Shadden, S.C., The 14th Annual UCSF Imaging Research Symposium, San Francisco, California, October 2017.
  13. Discrete Particle Techniques For Modeling Fragmentation Of Blood Clots. Mukherjee, D., and Shadden, S.C., 14th United States National Congress On Computational Mechanics, Montreal, Canada, July 2017.
  14. Particle-based Computational Techniques For Stroke And Thrombosis. Mukherjee, D., and Shadden, S.C., Berkeley/Stanford Computational Mechanics Festival, Berkeley, California, April 2017.
  15. Fictitious Domain Based Models For Resolving Interaction Of A Clot With Blood Flow. Mukherjee, D., and Shadden, S.C., 69th Annual Meeting Of The American Physical Society Division Of Fluid Dynamics, Portland, Oregon, November 2016.
  16. Evaluating Blood Flow And Embolus Distribution In The Brain As A Function Of The Anatomy Of The Circle Of Willis. Jani, N.D., Mukherjee, D., Shadden, S.C., 69th Annual Meeting Of The American Physical Society Division Of Fluid Dynamics, Portland, Oregon, November 2016.
  17. Influence Of Variations In Circle Of Willis Anatomy On Cerebral Circulation & Embolus Distribution. Jani, N.D., Mukherjee, D., and Shadden, S.C., Annual Meeting Of The Biomedical Engineering Society, Minneapolis, Minnesota, October 2016. 
  18. Thrombus Hemodynamics Interactions: From Intra-Thrombus Transport To Macro-Scale Flow Structures. Mukherjee, D. and Shadden, S.C., Mechbio Symposium: Putting Together The Cell Mechanome, San Diego, California, August 2016.
  19. Modeling Embolus Transport & Thrombus Interaction With Arterial Hemodynamics & Its Relevance To Improving Treatment Procedures. Mukherjee, D., and Shadden, S.C., 5th International Conference On Engineering Frontiers In Pediatric And Congenital Heart Disease, Orlando, Florida, June 2016. - ​best poster award
  20. Characterizing Embolus Transport To The Circle Of Willis. Mukherjee, D., Jani, N., and Shadden, S.C., The 8th International Bio-Fluids Symposium, Pasadena, California, February 2016.
  21. Modeling And Simulation Of Cardiogenic Embolic Particle Transport To The Brain. Mukherjee, D., Jani, N., and Shadden, S.C., 68th Annual Meeting Of The American Physical Society Division Of Fluid Dynamics, Boston, Massachusetts, November 2015.
  22. Large-Scale Grain Distribution Simulations With Rotating Machinery Using Efficient Discrete Element Models. Casas, G., Mukherjee, D., Celigueta, M.A., Zohdi, T.I., and Onate, E., Particles 2015 - IV International Conference On Particle-Based Methods: Fundamentals And Applications, Barcelona, Spain, September, 2015.
  23. Embolus Interactions With Blood Flow And Its Role In Stroke. Mukherjee, D., and Shadden, S.C., 13th United States National Congress On Computational Mechanics, San Diego, California, July 2015.
  24. A Patient-Specific CFD-Based Study Of Embolic Particle Transport For Stroke. Mukherjee, D., and Shadden, S.C., 67th Annual Meeting Of The American Physical Society Division Of Fluid Dynamics, San Francisco, California, November 2014.
  25. Investigation Of Noninvasive Healing Of Damaged Piping System Using Electro-Magneto-Mechanical Methods. Mukherjee, D., Zaky, Z., Zohdi, T.I., Salama, A., and Sun, S., Society Of Petroleum Engineers International Oilfield Corrosion Conference And Exhibition, Aberdeen, United Kingdom, May 2014. - best poster award
  26. Collision Driven Particle Dynamics Simulations For Analyzing Flows Of Particulate Sprays And Jets. Mukherjee, D., and Zohdi, T.I., 66th Annual Meeting Of The American Physical Society Division of Fluid Dynamics, Pittsburgh, Pennsylvania, November 2013.
  27. Electromagnetic Control Of Charged Particulate Spray Systems - Planning The Spray-Gun Operations. Mukherjee, D., and Zohdi, T.I., SIAM Conference on Geometrical and Physical Modeling, Denver, Colorado, November 2013.
  28. Discrete Particle Simulation For The Analysis Of Colliding And Flowing Particulate Media. Mukherjee, D., and Zohdi, T.I., Berkeley/Stanford Computational Mechanics Festival (CompFest), Berkeley, California, October 2013.
  29. Development Of A Computer Simulation Tool For Discrete Element Method And Collision Driven Particle Dynamics Simulations. Mukherjee, D., and Zohdi, T.I., 12th United States National Congress on Computational Mechanics, Raleigh, North Carolina, July 2013.

Invited Presentations:

  1. Computational Investigations On Unravelling The Hemodynamic Underpinnings Of Cardiovascular Diseases - invited talk at the Department of Mechanical Engineering, the University of Colorado, Boulder, March 2018. 
  2. Particles In Flow: Computational Insights Into The Rich Dynamics Of Particle Systems With Applications In Manufacturing And Biomechanics - invited talk at the Department of Mechanical and Aerospace Engineering, the University at Buffalo, February 2018.
  3. Insights Into Developing Patient-specific Computational Fluid Dynamics Models For Cardiovascular Diseases - invited talk at the Department of Mechanical Engineering, Villanova University, February 2018.
  4. Computational Investigations On The Hemodynamic Underpinnings Of Cardiovascular Diseases - invited talk at the Department of Mechanical Engineering, University of Nevada, Reno, January 2018. 
  5. Understanding Blood Flow And Flow Mediated Transport Around Arterial Blood Clots - invited talk at the Berkeley Fluids Seminar Series, U.C. Berkeley, October 2017.
  6. Discrete Particle Based Computational Techniques For Investigating The Role Of Hemodynamics In Stroke And Thrombosis - invited talk at the Department of Mathematics, University of Houston, October 2017.
  7. Exploring The Hemodynamic Underpinnings Of Stroke, Thrombosis, And Embolisms - invited talk at the Auburn University Seminar Series, September 2017. 
  8. Hybrid Particle-continuum Modeling For Thrombosis And Embolism - An Overview - invited talk at the Diamond Lab, Institute for Medicine and Engineering, University of Pennsylvania, August 2017.
  9. Collective Dynamics And Flow Of Particle Systems - Applications In Industry And Healthcare - invited talk at the Department of Mechanical Engineering, Stony Brook University, April 2017. 
  10. Image-driven, Particle Based Computational Models For Thrombotic And Embolic Phenomena In Large Arteries - invited talk for the Berkeley Fluids Seminar series, University of California, Berkeley, October 2016.
  11. Image-based Computational Modeling Of Thrombotic And Embolic Phenomena In Large Arteries - invited talk at the Medtronic Technical Forum, Medtronic, Irvine, California, June, 2016
  12. ​Discrete Particle Simulations For The Analysis Of Colliding And Flowing Particulate Media - invited talk for the Berkeley Fluids Seminar series, University of California, Berkeley, October, 2013.
  13. Discrete Element And Collision Driven Particle Dynamics Simulations For Manufacturing - invited talk for Siemens Energy, Orlando, Florida, April, 2013.
  14. The Story Of Sprays, Grains, And Computers - An Overview Of Probing Granular & Particulate Material Using Computer Simulations - invited talk at the Department of Physics, Indian Institute of Science Education & Research, Bhopal, India, January 2013.