Articles

For a full list of publications, please see here.

  1. [PDF] Progressive Tree-Based Compression of Large-Scale Particle Data
    D Hoang, Harsh Bhatia, P Lindstrom, and V Pascucci.
    IEEE Transactions on Visualization and Computer Graphics (TVCG), vol. 30, issue 7, pp. 4321–4338, Mar 2023. doi:10.1109/TVCG.2023.3260628.

  2. [PDF] The Confluence of Machine Learning and Multiscale Simulations
    Harsh Bhatia, F Aydin, TS Carpenter, FC Lightstone, P-T Bremer, HI Ingólfsson, DV Nissley, and FH Streitz.
    Current Opinions in Structural Biology vol. 80, Jun 2023. doi:10.1016/j.sbi.2023.102569.

  3. Machine Learning-Driven Multiscale Modeling: Bridging the Scales with a Next-Generation Simulation Infrastructure
    HI Ingólfsson, Harsh Bhatia, F Aydin, T Oppelstrup, CA López, LG Stanton, TS Carpenter, S Wong, F Di Natale, X Zhang, JY Moon, CB Stanley, JR Chavez, K Nguyen, G Dharuman, V Burns, R Shrestha, D Goswami, G Gulten, QN Van, A Ramanathan, B Van Essen, NW Hengartner, AG Stephen, T Turbyville, P-T Bremer, S Gnanakaran, JN Glosli, FC Lightstone, DV Nissley, and FH Streitz.
    Journal of Chemical Theory & Computation vol. 19, issue 9, pp. 2658–2675, Apr 2023. doi:10.1021/acs.jctc.2c01018.

  4. Scalable Comparative Visualization of Ensembles of Call Graphs
    SP Kesavan, Harsh Bhatia, A Bhatele, S Brink, O Pearce, T Gamblin, P-T Bremer, and K-L Ma.
    IEEE Transactions on Visualization and Computer Graphics (TVCG), vol. 29, issue 3, 1691–1704, Nov, 2023. doi:10.1109/TVCG.2021.3129414.

  5. Data-driven Model for Divertor Plasma Detachment Prediction
    B Zhu, M Zhao, Harsh Bhatia, X Xu, P-T Bremer, W Meyer, N Li, and T Rognlien.
    Journal of Plasma Physics vol. 88, number 5, article: 895880504, Oct 2022. doi:10.1017/S002237782200085X.

  6. A Biology-Informed Similarity Metric for Simulated Patches of Human Cell Membrane
    Harsh Bhatia, JJ Thiagarajan, R Anirudh, TS Jayram, T Oppelstrup, HI Ingolfsson, FC Lightstone, and P-T Bremer.
    Machine Learning: Science and Technology, vol. 3, number 3, pp. 035010, Aug 2022. doi:10.1088/2632-2153/ac8523.

  7. Asynchronous Reciprocal Coupling of Martini 2.2 Coarse-Grained and CHARMM36 All-Atom Simulations in an Automated Multiscale Framework
    CA López, X Zhang, F Aydin, R Shrestha, QN Van, CB Stanley, TS Carpenter, K Nguyen, LA Patel, D Chen, V Burns, NW Hengartner, Tyler J.E. Reddy, Harsh Bhatia, F Di Natale, TH Tran, AH Chan, DK Simanshu, DV Nissley, FH Streitz, AG Stephen, TJ Turbyville, FC Lightstone, S Gnanakaran, HI Ingólfsson, C Neale.
    Journal of Computational and Theoretical Chemistry vol. 18, issue 8, pp. 5025–5045, Jul 2022. doi:10.1021/acs.jctc.2c00168.

  8. Exploring CRD Mobility during RAS/RAF Engagement at the Membrane
    K Nguyen, CA López, Chris Neale, QN Van, TS Carpenter, F Di Natale, T Travers, TH Tran, AH Chan, Harsh Bhatia, PH Frank, M Tonelli, X Zhang, G Gulten, T Reddy, V Burns, T Oppelstrup, NW Hengartner, DK Simanshu, P-T Bremer, De Chen, JN Glosli, R Shrestha, TJ Turbyville, FH Streitz, DV Nissley, HI Ingólfsson, AG Stephen, FC Lightstone, and S Gnanakaran.
    Biophysics Journal, vol. 121, issue 19, pp. 3630–3650, Oct 2022. doi:10.1016/j.bpj.2022.06.035.

  9. [PDF] AMM: Adaptive Multilinear Meshes
    Harsh Bhatia, D Hoang, N Morrical, V Pascucci, P-T Bremer, and P Lindstrom.
    IEEE Transactions on Visualization and Computer Graphics (TVCG), vol. 28, issue 6, pp. 2350–3363, Jun 2022. doi:10.1109/TVCG.2022.3165392.
        Best Paper Award at IEEE Pacific Visualization Symposium.

  10. Machine Learning-driven Multiscale Modeling Reveals Lipid-Dependent Dynamics of RAS Signaling Protein
    HI Ingólfsson, C Neale, TS Carpenter, R Shrestha, CA Lopez, T Tran, T Oppelstrup, Harsh Bhatia, LG Stanton, X Zhang, S Sundram, F Di Natale, A Agarwal, G Dharuman, S Kokkila Schumacher, TJ Turbyville, G Gulten, Q Van, D Goswami, F Jean-Francios, C Agamasu, D Chen, J Hettige, T Travers, S Sarkar, M Surh, Y Yang, A Moody, S Liu, B Van Essen, A Voter, A Ramanathan, NW Hengartner, D Simanshu, A Stephen, P-T Bremer, S Gnanakaran, JN Glosli, FC Lightstone, F McCormick, D Nissley, and F Streitz.
    Proceedings of National Academy of Sciences (PNAS), vol. 119, issue 1, number e2113297119. 2022. doi:10.1073/pnas.2113297119.

  11. [PDF] Vector Field Decompositions using Multiscale Poisson Kernel
    Harsh Bhatia, RM Kirby, V Pascucci, and P-T Bremer.
    IEEE Transactions on Visualization and Computer Graphics (TVCG), vol. 27, issue 9, pp. 3781–3793, Sep 2021. doi:10.1109/TVCG.2020.2984413.

  12. [PDF] Leveraging Topological Events in Tracking Graphs for Understanding Particle Diffusion
    T McDonald, R Shrestha, X Yi, Harsh Bhatia, De Chen, D Goswami, V Pasucci, TJ Turbyville, and P-T Bremer.
    Computer Graphics Forum (Proceedings of EuroVis), vol. 40, issue 3, pp. 251–262, June 2021. doi:10.1111/cgf.14304.

  13. [PDF] Machine Learning Based Dynamic-Importance Sampling for Adaptive Multiscale Simulations
    Harsh Bhatia, TS Carpenter, HI Ingólfsson, Gautham Dharuman, P Karande, S Liu, T Oppelstrup, C Neale, FC Lightstone, B Van Essen, JN Glosli, and P-T Bremer.
    Nature Machine Intelligence, vol. 3, pp. 401–409, May 2021. doi:10.1038/s42256-021-00327-w.

  14. Visualizing Hierarchical Performance Profiles of Parallel Codes using CallFlow
    HT Nguyen, A Bhatele, N Jain, SP Kesavan, Harsh Bhatia, T Gamblin, K-L Ma, and P-T Bremer.
    IEEE Transactions on Visualization and Computer Graphics (TVCG), vol. 27, issue 4, pp. 2455–2468, Apr 2021. doi:10.1109/TVCG.2019.2953746.

  15. Efficient and Flexible Hierarchical Data Layouts for a Unified Encoding of Scalar Field Precision and Resolution
    D Hoang, B Summa, Harsh Bhatia, P Lindstrom, P Klacansky, W Usher, P-T Bremer, and V Pascucci.
    IEEE Transactions on Visualization and Computer Graphics (TVCG) (Proc. of IEEE VIS), vol. 27, issue 2, pp. 603–613, Feb 2021. doi:10.1109/TVCG.2020.3030381.

  16. Capturing Biologically Complex Tissue-Specific Membranes at Different Levels of Compositional Complexity
    HI Ingólfsson, Harsh Bhatia, T Zeppelin, WF Drew Bennett, K Carpenter, P-C Hsu, G Dharuman, P-T Bremer, B Schiøtt, FC Lightstone, and TS Carpenter.
    The Journal of Physical Chemistry B: Biophysics, Biomaterials, Liquids, Soft Matter, vol. 124, issue 36, pp. 7819–7829, Aug 2020. doi:10.1021/acs.jpcb.0c03368.

  17. Scalable Topological Data Analysis and Visualization for Evaluating Data-Driven Models in Scientific Applications
    S Liu, D Wang, D Maljovec, R Anirudh, JJ Thiagarajan, SA Jacobs, B Van Essen, D Hysom, J-S Yeom, J Gaffney, L Peterson, PB Robinson, Harsh Bhatia, V Pascucci, BK Spears, and P-T Bremer.
    IEEE Transactions on Visualization and Computer Graphics (TVCG) (Proc. of IEEE VIS), vol. 26, issue 1, pp. 291–300, Jan. 2020. doi:10.1109/TVCG.2019.2934594.

  18. MemSurfer: A Tool for Robust Computation and Characterization of Curved Membranes
    Harsh Bhatia, HI Ingólfsson, TS Carpenter, FC Lightstone, and P-T Bremer.
    Journal of Chemtical Theory and Computation, vol. 15, issue 11, pp 6411–6421, November 2019. doi:10.1021/acs.jctc.9b00453.

  19. [PDF] A Study of the Trade-off between Reducing Precision and Reducing Resolution for Data Analysis and Visualization
    D Hoang, P Klacansky, Harsh Bhatia, P-T Bremer, P Lindstrom, and V Pascucci.
    IEEE Transactions on Visualization and Computer Graphics (TVCG) (Proc. of IEEE VIS), vol. 25, issue 1, pp 1193–1203, August 2018. doi:10.1109/TVCG.2018.2864853.

  20. [PDF] Interactive Investigation of Traffic Congestion on Fat-Tree Networks Using TreeScope
    Harsh Bhatia, N Jain, A Bhatele, Y Livnat, J Domke, V Pascucci, and P-T Bremer.
    Computer Graphics Forum (Proceedings of EuroVis), vol. 33, issue 3, pp. 561–572, June 2018. doi:10.1111/cgf.13442.

  21. [PDF] TopoMS: Comprehensive Topological Exploration for Molecular and Condensed-Matter Systems
    Harsh Bhatia, AG Gyulassy, V Lordi, JE Pask, V Pascucci, and P-T Bremer.
    Journal of Computational Chemistry, vol. 39, issue 16, pp 936–952, June 2018. doi:10.1002/jcc.25181.
        Appeared as the cover image of Journal of Computational Chemistry.

  22. Computational Lipidomics of the Neuronal Plasma Membrane
    HI Ingólfsson, TS Carpenter, Harsh Bhatia, P-T Bremer, SJ Marrink, and FC Lightstone.
    Biophysical Journal, vol. 113, issue 10, pp 2271–2280, November 2017. doi:10.1016/j.bpj.2017.10.017.
        Appeared as the cover image of Biophysics Journal, and appeared in the Best of 2017 collection.

  23. Complex Ion Dynamics in Carbonate Lithium-Ion Battery Electrolytes
    MT Ong, Harsh Bhatia, AG Gyulassy, EW Draeger, V Pascucci, P-T Bremer, V Lordi, and JE Pask.
    The Journal of Physical Chemistry C, vol. 121, no. 12, pp 6589–6595, March 2017. doi:10.1021/acs.jpcc.7b02006.

  24. [PDF] Enabling Discovery Through Visual Exploration: An Introduction to Data Visualization & Its Applications
    Harsh Bhatia.
    ACM SIGCAS Computer Society, vol. 46, no. 3, Nov. 2016. doi:10.1145/3024949.3024952.

  25. [PDF] Critical Point Cancellation in 3D Vector Fields: Robustness and Discussion
    P Skraba, P Rosen, B Wang, G Chen, Harsh Bhatia, and V Pascucci.
    IEEE Transactions on Visualization and Computer Graphics (TVCG), vol. 22, no. 6, pp. 1683–1693, Jun. 2016. doi:10.1109/TVCG.2016.2534538.
        Won the Best Paper Award at IEEE Pacific Visualization Symposium, 2016.

  26. [PDF] Local, Smooth, and Consistent Jacobi Set Simplification.
    Harsh Bhatia, B Wang, G Norgard, V Pascucci, and P-T Bremer
    Computational Geometry — Theory and Applications, vol. 48, issue 5, pp. 311–332, May 2015. doi:10.1016/j.comgeo.2014.10.009.

  27. [PDF] The Natural Helmholtz-Hodge Decomposition for Open-Boundary Flow Analysis
    Harsh Bhatia, V Pascucci, and P-T Bremer.
    IEEE Transactions on Visualization and Computer Graphics (TVCG), vol. 20, no. 11, pp. 1566–1578, Nov. 2014. doi:10.1109/TVCG.2014.2312012.

  28. [PDF] Extracting Features from Time-Dependent Vector Fields Using Internal Reference Frames
    Harsh Bhatia, V Pascucci, RM Kirby, and P-T Bremer.
    Computer Graphics Forum (Proceedings of EuroVis), vol. 33, issue 3, pp. 21–39, Jun. 2014. doi:10.1111/cgf.12358.

  29. [PDF] The Helmholtz-Hodge Decomposition — A Survey
    Harsh Bhatia, G Norgard, V Pascucci, and P-T Bremer.
    IEEE Transactions on Visualization and Computer Graphics (TVCG), vol. 19, no. 8, pp. 1386–1404, Aug. 2013. doi:10.1109/TVCG.2012.316.
        Appeared as the IEEE TVCG spotlight of the month.

  30. [PDF] Visualizing Robustness of Critical Points for 2D Time-Varying Vector Fields
    B Wang, P Rosen, P Skraba, Harsh Bhatia, and V Pascucci.
    Computer Graphics Forum (Proceedings of EuroVis), vol. 32, issue 3pt 2, pp. 221–230, Jun. 2013. doi:10.1111/cgf.12109.

  31. [PDF] Comments on the "Meshless Helmholtz-Hodge decomposition"
    Harsh Bhatia, G Norgard, V Pascucci, and P-T Bremer.
    IEEE Transactions on Visualization and Computer Graphics (TVCG), vol. 19, no. 3, pp. 527–528, Mar. 2013. doi:10.1109/TVCG.2012.62.

  32. [PDF] Flow Visualization with Quantified Spatial and Temporal Errors using Edge Maps
    Harsh Bhatia, S Jadhav, P-T Bremer, G Chen, JA Levine, LG Nonato, and V Pascucci.
    IEEE Transactions on Visualization and Computer Graphics (TVCG), vol. 18, no. 9, pp. 1383–1396, Sept. 2012. doi:10.1109/TVCG.2011.265.

  33. [PDF] A Quantized boundary representation of 2D Flow
    JA Levine, S Jadhav, Harsh Bhatia, V Pascucci, and P-T Bremer.
    Computer Graphics Forum (Proceedings of EuroVis), vol. 31, issue 3pt1, pp. 945–954, Jun. 2012. doi:10.1111/j.1467-8659.2012.03087.x.

Conference Proceedings

  1. Data Movement Visualized: A Unified Framework for Tracking and Visualizing Data Movements in Heterogeneous Architectures
    SP Kesavan, Harsh Bhatia, K Dasu, O Pearce, and K-L Ma. In Proceedings of the IEEE Pacific Visualization Conference, Apr. 2024.

  2. [PDF] Generalizable Coordination of Large Multiscale Ensembles: Challenges and Learnings at Scale
    Harsh Bhatia, F Di Natale, JY Moon, X Zhang, JR Chavez, F Aydin, CB Stanley, T Oppelstrup, C Neale, S Kokkila Schumacher, D Ahn, S Herbein, TS Carpenter, S Gnanakaran, P-T Bremer, JN Glosli, FC Lightstone, and HI Ingólfsson. In Proceedings of the ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis, SC '21, Article No. 10, Nov 2021. doi:10.1145/3458817.3476210.

  3. [PDF] Data-Driven Estimation of Temporal-Sampling Errors in Unsteady Flows
    Harsh Bhatia, SN Petruzza, R Anirudh, AG Gyulassy, RM Kirby, V Pascucci, and P-T Bremer.</br> In: Bebis G. et al. (eds) Advances in Visual Computing. ISVC 2021. Lecture Notes in Computer Science, vol 13017. Springer, Cham. doi:03010.1007/978-3-030-90439-5_19.

  4. [PDF] High-quality and Low-memory-footprint Progressive Decoding of Large-scale Particle Data
    D Hoang, Harsh Bhatia, P Lindstrom, and V Pascucci.</br> The 11th IEEE Symposium on Large Data Analysis and Visualization (LDAV), 32–42, 2021. doi:10.1109/LDAV53230.2021.00011.
    Honorable Mention.

  5. [PDF] A Massively Parallel Infrastructure for Adaptive Multiscale Simulations: Modeling RAS Initiation Pathway for Cancer
    F Di Natale, Harsh Bhatia, TS Carpenter, C Neale, S Kokkila Schumacher, T Oppelstrup, LG Stanton, X Zhang, S Sundram, TRW Scogland, G Dharuman, MP Surh, Y Yang, C Misale, L Schneidenbach, C Costa, C Kim, B D'Amora, S Gnanakaran, DV Nissley, FH Streitz, FC Lightstone, P-T Bremer, JN Glosli, and HI Ingólfsson. In Proceedings of the ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis, SC '19, Article No. 57, November 2019. doi:10.1145/3295500.3356197.
        Best Paper at SC 2019.

  6. Comparing GPU Power and Frequency Capping: A Case Study with the MuMMI Workflow
    T Patki, Z Frye, Harsh Bhatia, F Di Natale, JN Glosli, HI Ingolfsson and B Rountree. In 2019 IEEE/ACM Workflows in Support of Large-Scale Science (WORKS), 31–39, November 2019. doi:10.1109/WORKS49585.2019.00009.

  7. Interpreting Galilean Invariant Vector Field Analysis via Extended Robustness
    B Wang, R Bujack, P Rosen, P Skraba, Harsh Bhatia, and H Hagen.
    In Topological Methods in Data Analysis and Visualization V, 221–235, 2020 doi:10.1007/978-3-030-43036-8_14.

  8. [PDF] Interactive Exploration of Atomic Trajectories Through Relative-Angle Distribution and Associated Uncertainties
    Harsh Bhatia, AG Gyulassy, V Pascucci, M Bremer, MT Ong, V Lordi, EW Draeger, JE Pask, and P-T Bremer.
    In Proceedings of the 9th IEEE Pacific Visualization Symposium, pp. 120–127, Taipei, Taiwan. Apr. 19–22, 2016. doi:10.1109/PACIFICVIS.2016.7465259.

  9. [PDF] Computing Accurate Morse-Smale Complexes from Gradient Vector Fields
    AG Gyulassy, Harsh Bhatia, P-T Bremer, and V Pascucci.
    In Topological and Statistical Methods for Complex Data — Tackling Large-Scale, High-Dimensional, and Multivariate Data Sets, Mathematics and Visualization, pp. 205–218, J Bennett, F Vivodtzev, V Pascucci (Eds.), Springer Berlin Heidelberg, 2015. doi:10.1007/978-3-662-44900-4_12.

  10. [PDF] Robust Detection of Singularities in Vector Fields
    Harsh Bhatia, AG Gyulassy, H Wang, P-T Bremer, and V Pascucci.
    In Topological Methods in Data Analysis and Visualization III - Theory, Algorithms, and Applications, Mathematics and Visualization, pp. 3–18, P-T Bremer, I Hotz, V Pascucci, R Peikert (Eds.), Springer Berlin Heidelberg, 2014. doi:10.1007/978-3-319-04099-8_1.

  11. [PDF] Consistent Approximation of Local Flow Behavior for 2D Vector Fields
    S Jadhav, Harsh Bhatia, P-T Bremer, JA Levine, LG Nonato, and V Pascucci.
    In Topological Methods in Data Analysis and Visualization II — Theory, Algorithms, and Applications, Mathematics and Visualization, pp. 141–159, R Peikert, H Hauser, H Carr, R Fuchs (Eds.), Springer Berlin Heidelberg, 2012. doi:10.1007/978-3-642-23175-9_10.

  12. [PDF] Edge Maps: Representing Flow with Bounded Error
    Harsh Bhatia, S Jadhav, P-T Bremer, G Chen, JA Levine, LG Nonato, and V Pascucci.
    In Proceedings of the 4th IEEE Pacific Visualization Symposium, pp. 75–82, Hong Kong, China, Mar. 1–4, 2011. doi:10.1109/PACIFICVIS.2011.5742375.
        Appeared on the cover of the Proceedings, and won the Best Paper Award.

  13. [PDF] A Queuing-Theoretic Framework for Modeling and Analysis of Mobility in WSNs
    Harsh Bhatia, RB Lenin, A Munjal, S Ramaswamy, and S Srivastava.
    In Proceedings of the 8th Workshop on Performance Metrics for Intelligent Systems (PerMIS), 248–253, Gaithersburg, Maryland, USA, Aug. 19–21, 2008. doi:10.1145/1774674.1774713.

Dissertations

  • Consistent Feature Extraction From Vector Fields: Combinatorial Representations and Analysis Under Local Reference Frames
    Harsh Bhatia.
    Ph.D. Dissertation, The University of Utah, USA. May 2015.

  • Application of QNA to analyze the 'Queueing Network Mobility Model' of Mobile Ad-hoc Networks
    Harsh Bhatia.
    B.Tech. Project Report, Dhirubhai Ambani Institute of Information and Communication Technology, India. Jun 2007.