Publications.

Journal Articles

  1. Laroche, A., Rovito, N., Liu, A., Allaeys, I., Adeoye, O., Heitsch, L., Pizella, S., Bark, D., Di Paola, J., Lee, J.M., Campbell, R., Mukherjee, D., Boilard, E., Denorme, F. Mechanisms Of Von Willebrand Factor Activation Driving No-Reflow In Ischemic Stroke. (submitted, under review).
  2. Teeraratkul, C., Krishnamurthy, A., and Mukherjee, D. Computational Modeling Of Immersed Non-spherical Bodies In Viscous Flows To Study Embolus-Hemodynamics Interactions In Large-Vessel Occlusion Stroke. (submitted, under review).  [bioRxiv] 
  3. Teeraratkul, C., Tomaiuolo, M., Stalker, T.J., and Mukherjee, D. A Stabilized Finite Element Technique For Transport Phenomena Within And Around Immersed Porous Bodies In Flow. Physics of Fluids. 37(10):101916. 2025. [doi]
  4. Roopnarinesingh, R., Jani, N.D., Leppert, M., and Mukherjee, D. Understanding Thromboembolus Transport Patterns In The Brain For Stroke In The Presence Of Carotid Artery Stenosis. PLoS Computational Biology. 21(9): e1013269. 2025. [medRxiv][doi]
  5. Majee, S., Sahni, A., Pal, J.D., McIntyre, E., and Mukherjee, D. Understanding Embolus Transport And Source To Destination Mapping Of Thromboemboli In Hemodynamics Driven By Left Ventricular Assist Device. Scientific Reports. 15:12150. 2025. [medRxiv] [doi]​
  6. Sahni, A., Majee, S., Pal, J.D., McIntyre, E.E., Cao, K., and Mukherjee, D. Hemodynamics Indicates Differences Between Patients With And Without A Stroke Outcome After Left Ventricular Assist Device Implantation. Computers in Biology and Medicine. 189:109877. 2025. [medRxiv] [doi]
  7. Venkatesh, S., Teeraratkul, C., Rovito, N., Mukherjee, D., and Lynch, M.E. High-Fidelity Computational Fluid Dynamics Model To Simulate Perfusion Through A Bone-Mimicking Scaffold. Computers in Biology and Medicine. 186:109637. 2025. [doi]
  8. Zablah, J.E., Shorofsky, M.J., Cao, K., and Mukherjee, D. Computational Fluid Dynamic Assessment Of Patients With Congenital Heart Disease From 3D Rotational Angiography. Pediatric Cardiology. 46:458-466. 2025. [doi]
  9. Mukherjee, D., Lai, V., Huang, Z., and Singh, A. The BIORES-21 Survey: Insights Into Remote And Online Education In Biomechanics And Mechanobiology. Journal of Biomechanical Engineering. 146(5):051006. 2024. [doi]
  10. Teeraratkul, C, Tomaiuolo, M., Stalker, T.J., and Mukherjee, D. Investigating Clot-flow Interactions by Integrating Intravital Imaging with In Silico Modeling for Analysis of Flow, Transport, and Hemodynamic Forces. Scientific Reports. 14(1):696. 2024. [bioRxiv]
  11. Gutierrez, N.J., Mukherjee, D., and Bark, D. Decoding Thrombosis Through Code: A Review Of Computational Models. Journal of Thrombosis and Haemostasis. 22(1):35-47. 2024. [doi open access]
  12. Roopnarinesingh, R., Leppert, M., and Mukherjee, D. Evidence And Mechanisms For Embolic Stroke In Contralateral Hemispheres From Carotid Artery Disease. Journal of the American Heart Association. 12(23):e-030792. 2023. [medRxiv] [doi open access]
  13. Sahni, A., McIntyre, E.E., Cao, K., Pal, J.D., and Mukherjee, D. The Relation Between Viscous Energy Dissipation And Pulsation For Aortic Hemodynamics Driven By A Left Ventricular Assist Device. Cardiovascular Engineering and Technology. 14:560-576. 2023. [medRxiv][doi]
  14. Sahni, A., McIntyre, E.E., Pal, J.D., and Mukherjee, D. Quantitative Assessment Of Aortic Hemodynamics For Varying Left Ventricular Assist Device Outflow Graft Angles And Flow Pulsation. Annals of Biomedical Engineering. 51(6):1226-1243. 2023. [doi] [medRxiv]
  15. Jung, H., Kang, T., Lee, C.H., Woo, S.Y., Yang, S.S., Mukherjee, D., Kim, D.I., and Ryu, J. Comparison Of Haemodynamics In Carotid Endarterectomy: Primary Closure Versus Patch Angioplasty. Engineering Applications of Computational Fluid Mechanics. 16(1):1601-1618. 2022. [open access manuscript].
  16. Mukherjee, D., and Wadhwa, G. A Mesoscale Agent Based Modeling Framework For Flow-mediated Infection Transmission In Indoor Occupied Spaces. Computer Methods in Applied Mechanics and Engineering. 401(A): 115485. 2022. [medRxiv] 
  17. Kang T., Mukherjee, D., and Ryu, J. Hemodynamic Flow Characteristics At Stenosed Artery: Computational Analysis Of Progressive Unilateral Carotid Stenosis In Three-dimensional Patient-specific Aortic-cerebral Vasculature. Physics of Fluids. 34(6):061902-19. 2022. [doi]
  18. Mukherjee, D., and Barker, A. Using Simulation Based Active Learning Strategies For Teaching Biofluids Concepts. Journal of  Biomechanical Engineering. 143(12):121011-6. 2021. [doi]
  19. Wilson, J., Miller, S., and Mukherjee, D. A Lagrangian Approach Towards Quantitative Analysis Of Flow-mediated Infection Transmission In Indoor Spaces With Applications To SARS-CoV-2. International Journal of Computational Fluid Dynamics. 35(9):727-742. 2021. [medRxiv] [doi]
  20. Kang, T., Mukherjee, D., and Ryu, J. Numerical investigation of carotid stenosis in three-dimensional aortic-cerebral vasculature: Pulsatility index, resistive index, time-to-peak velocity, and flow characteristics. Engineering Applications of Computational Fluid Mechanics. 15(1):1645-1665. 2021. [open access manuscript]
  21. ​Teeraratkul, C., and Mukherjee, D. Microstructure Aware Modeling Of Biochemical Transport In Arterial Blood Clots. Journal of Biomechanics. 127:110692. 2021. [bioRxiv]
  22. Kang, T., Mukherjee, D., Kim, J.M., Park, K.Y., and Ryu, J. Effects Of Progressive Carotid Stenosis On The Hemodynamics Of The Circle of Willis: Aorta-to-Cerebral 3D Patient-specific Simulation. Engineering Applications of Computational Fluid Mechanics. 15(1):830-847.  2021. [open-access manuscript]
  23. Teeraratkul, C., Irwin, Z., Shadden, S.C., and Mukherjee, D. Computational Investigation Of Blood Flow And Flow-mediated Transport In Arterial Thrombus Neighborhood. Biomechanics and Modeling in Mechanobiology. 20:701-715. ​​​2021. ​[bioRxiv]
  24. Mukherjee, D. Developing Effective Screencast Modules For Teaching Computational Techniques In Remote Modalities. Biomedical Engineering Education. 1(2):307-311. 2021. [author-manuscript]
  25. Miller, S., Mukherjee, D., Wilson, J., Clements, N., and Steiner, C. Implementing A Negative-Pressure Isolation Space Within A Skilled Nursing Facility To Control SARS-CoV-2 Transmission. American Journal of Infection Control. 49(4):438-446. 2020. [medRxiv]
  26. Mukherjee, D., Jani, N.D., Narvid, J., and Shadden, S.C. The Role Of Circle of Willis Anatomy In Cardio-embolic Stroke - A Patient-specific Simulation Based Study. Annals of Biomedical Engineering. 46(8):1128-1145. 2018. [bioRxiv] [doi]
  27. Mukherjee, D., and Shadden, S.C. Modeling Blood Flow Around A Thrombus Using A Hybrid Particle-Continuum Approach. Biomechanics and Modeling in Mechanobiology. 17(3):645-663. 2018. [doi]
  28. Mukherjee, D., and Shadden, S.C. Inertial Particle Dynamics In Large Artery Flows - Implications For Modeling Arterial Embolisms. Journal of Biomechanics. 52(8):155-164. 2017. [doi]
  29. Casas, G., Mukherjee, D., Celigueta, M.A., Zohdi, T.I., and Onate, E. A Modular, Partitioned, Discrete Element Framework For Industrial Grain Distribution Systems With Rotating Machinery. Journal of Computational Particle Mechanics. 4(2):181-198. 2017. [doi]
  30. Mukherjee, D., Jani, N., Selvaganesan, K., Weng, C.L., and Shadden, S.C. 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):081008-081008-13. 2016. [doi]
  31. Mukherjee, D., Padilla, J., and Shadden, S.C. Numerical Investigation Of Fluid-particle Interactions For Embolic Stroke. Theoretical and Computational Fluid Dynamics. 30(1):23-39. 2015. [doi]
  32. Mukherjee, D., and Zohdi, T.I. A Discrete Element Based Simulation Framework To Investigate Particulate Spray Deposition Processes. Journal of Computational Physics. 290:298-317. 2015. [doi]
  33. Mukherjee, D., and Zohdi, T. I. Computational Modeling Of The Dynamics & Interference Effects Of An Erosive Granular Jet Impacting A Porous, Compliant Surface. Granular Matter. 17(2):231-252. 2015. [doi]
  34. Mukherjee, D., Zaky, Z., Zohdi, T.I., Salama, A., and Sun, S. 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. 2015. [doi]
  35. Mukherjee, D., and Zohdi, T. I. Electromagnetic Control Of Charged Particulate Spray Systems - Models For Planning The Spray-gun Operations. Computer-Aided Design. 46:211-215. 2014. [doi]

Conference Proceedings

  1. Tucker, A., Ashrafee, A., and Mukherjee, D. An In Vitro Benchtop Model For Cerebral Circulation And Drug Transport. In: Proceedings of the ASME SB3C Summer Bioengineering Conference. Santa Ana Pueblo, New Mexico. June 2025.
  2. Roopnarinesingh, R., Majee, S., Rinkel, L., Coutinho, J., Cao, K., and Mukherjee, D. An In Silico Methodology For Discerning Etiology For Embolic Stroke Of Undetermined Source. In: Proceedings of the ASME SB3C Summer Bioengineering Conference. Santa Ana Pueblo, New Mexico. June 2025.
  3. Roopnarinesingh, R., Mukherjee, D., Majee, S., Cao, K., Rinkel, L., and Coutinho, J. Integrating Standard-of-care Clinical Stroke Workup Within In Silico Embolic Stroke Models For Etiology Disambiguation. Stroke. 56: Suppl_1: TP228. Abstract published for the 2025 American Heart Association International Stroke Conference. 2025.
  4. Rovito, N., and Mukherjee, D. In Silico Analysis Of Flow-mediated Drug Transport For Thrombolytic Therapy In Acute Ischemic Stroke. In: ASME International Mechanical Engineering Congress and Exposition, Vol. 88667, pp. V008T10A026. 2025.
  5. Chauhan, A., Tucker, A., and Mukherjee D. Development Of A Benchtop Model For Cerebral Collateral Circulation. In: Proceedings of the Summer Biomechanics, Bioengineering, and Biotransport Conference, Lake Geneva, Wisconsin, June 2024.
  6. Teeraratkul, C., and Mukherjee, D. A Micromechanics Based Multiscale Model For Platelet-driven Clot Contraction. In: Proceedings of the Summer Biomechanics, Bioengineering, and Biotransport Conference, Lake Geneva, Wisconsin, June 2024.
  7. Majee, S., Sahni, A., McIntyre, E.E., Pal, J.D., and Mukherjee, D. In Silico Investigation On Stroke Risks From Left Ventricular Assist Device. In: Proceedings of the Summer Biomechanics, Bioengineering, and Biotransport Conference, Vail, Colorado. June 2023.
  8. Roopnarinesingh, R., Jani, N.D., Leppert, M., and Mukherjee, D. Quantification Of Embolus Transport To The Brain From Carotid Stenosis Sites. In: Proceedings of the Summer Biomechanics, Bioengineering, and Biotransport Conference, Vail, Colorado. June 2023.
  9. Teeraratkul, C., Stalker, T.J., Tomaiuolo, M., and Mukherjee, D. Image Driven Simulation Of Hemodynamics Around A Dynamic Clot In Vivo. In: Proceedings of the Summer Biomechanics, Bioengineering, and Biotransport Conference, Vail, Colorado. June 2023.
  10. Jenkins, T.D., Santo, B.A., Ciecierska, S.K., Patel, T.R., Mukherjee, D., Siddiqui, A.H., and Tutino, V.M. The Association Between Clot Presentation On CT, Biological Composition, And Material Properties: Implications For Pre-treatment Imaging Biomarkers. In: Proceedings of the Summer Biomechanics, Bioengineering, and Biotransport Conference, Vail, Colorado. June 2023.
  11. Sahni, A., McIntyre, E., Pal, J.D., and Mukherjee, D. Stroke Risk Quantification For Patients With A Left Ventricular Assist Device. Stroke. 54: Suppl_1: AWP228. Abstract published for the 2023 American Heart Association International Stroke Conference. 2023.
  12. Shorofsky, M.J., Mukherjee, D., Cao, K., Morgan, G.J., and Zablah, J.E., Feasibility Of Performing Computational Fluid Dynamic Assessment Of A Patient With Congenital Heart Disease From 3D Rotational Angiography. In: Proceedins Of CSI Frankfurt Congress 2022. Journal of Echocardiography. 39:859-876. 2022.
  13. Roopnarinesingh, R., and Mukherjee, D. In Silico Investigation Of Contralateral Embolic Stroke Risks From Carotid Artery Disease. Proceedings of the Summer Biomechanics, Bioengineering, and Biotransport Conference, Eastern Shore, Maryland, USA. June 2022. 
  14. Andrews, S., Trivedi, P., and Mukherjee, D. An Iterative Approach To Assign Tumor Specific Flow Boundary Conditions For Liver Cancer Using Multi-modal Image Analysis. Proceedings of the Summer Biomechanics, Bioengineering, and Biotransport Conference, Eastern Shore, Maryland, USA. June 2022. 
  15. Sahni, A., Pal, J., and Mukherjee, D. Assessing The Hemodynamic Influence Of Pulse Flow Modulation For Left Ventricular Assist Devices. Proceedings of the Summer Biomechanics, Bioengineering, and Biotransport Conference, Virtual. June 2021.  
  16. Zemlicka, A., Beiter, A., Trivedi, P., and Mukherjee, D. In Silico Modeling Of Embolic Particle Drug Delivery For Liver Cancer. Proceedings of the Summer Biomechanics, Bioengineering, and Biotransport Conference, Virtual. June 2021.  
  17. Teeraratkul, C., and Mukherjee, D. Parallel Implementation Of A Hybrid Particle-continuum Finite Element Framework For Blood Clot Biomechanics. Proceedings of the International Conference for High Performance Computing, Networking, Storage, and Analysis. ACM-SC20. November 2020. 
  18. Khadangale, S.B., Hajebrahimi, S., Ferguson, V.L., Lynch, M.E., and Mukherjee, D. Fluid-Structure Interaction Framework For Fluid Flow Through The Bone Lacunar-Canalicular System With Morphological Variations. Proceedings of the Summer Biomechanics, Bioengineering, and Biotransport Conference, Virtual. June 2020. 
  19. Mukherjee, D., and Shadden, S.C. Fictitious Domain Particle-Based Modeling For Thrombosis. Proceedings of the Summer Biomechanics, Bioengineering, and Biotransport Conference, Tucson, Arizona, USA. June 2017.
  20. Mukherjee, D., Jani, N.D., and Shadden, S.C. Discrete Particle Modeling For Thrombotic And Embolic Phenomena In Arteries. Proceedings of the 5th International Conference on Computational and Mathematical Biomedical Engineering, Pittsburgh, Pennsylvania, USA. April 2017.
  21. Mukherjee, D., and Shadden, S.C. Towards Non-invasive, Computational Modeling Of The Transport Of Thrombo-Emboli And Athero-Emboli Along Arteries. Proceedings of the Summer Biomechanics, Bioengineering and Biotransport Conference, National Harbor, Maryland, USA. June 2016.
  22. Mukherjee, D., and Shadden, S.C. Insights Into The Hemodynamic Factors Affecting Embolus Transport For Stroke. Proceedings of the Summer Biomechanics, Bioengineering and Biotransport Conference, Snowbird, Utah, USA. June 2015.
  23. Mukherjee, D., and Zohdi, T.I. Computer Modeling and Simulation Framework for Particulate Spray Based Manufacturing Processes. Proceedings of the ASME International Mechanical Engineering Congress & Exposition, San Diego, California, USA.
  24. Mukherjee, D., and Mansour, A.E. 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, Shanghai, China. - [best paper award]
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