Journal Publications

1. Masud, N., Tang, J., Hasib, H. H., Jubery, T. Z., Lee, X. X., Guo, H., & Sarkar, A. (2024). Correlating macroscopic plant growth parameters to nanomechanical properties of cellulose microfibrils. Current Plant Biology, 38, 100345.

2. Koep, A., Masud, N., Van't Hul, J., Stanley, C., Nilsen-Hamilton, M., Sarkar, A., & Schneider, I. C. (2024). Design and Assembly of a Cargo-agnostic Hollow Two-lidded DNA Box for Drug Delivery. bioRxiv, 2024-03.

3. Masud, N., Rade, J., Hasib, M. H. H., Krishnamurthy, A., & Sarkar, A. (2024). Machine learning approaches for improving atomic force microscopy instrumentation and data analytics. Frontiers in Physics, 12, 1347648.

4. Sarkar, A., Niraula, G., LeVine, D., Zhao, Y., Tu, Y., Mollaeian, K., ... & Wang, X. (2023). Development of a ratiometric tension sensor exclusively responding to integrin tension magnitude in live cells. ACS sensors, 8(10), 3701-3712. 

5. Cutshaw, G., Hassan, N., Uthaman, S., Wen, X., Singh, B., Sarkar, A., & Bardhan, R. (2023). Monitoring metabolic changes in response to chemotherapies in cancer with Raman spectroscopy and metabolomics. Analytical Chemistry, 95(35), 13172-13184. 

6. Waite, J. R., Tan, S. Y., Saha, H., Sarkar, S., & Sarkar, A. (2023). Few-shot deep learning for AFM force curve characterization of single-molecule interactions. Patterns, 4(1).

7. Rade, J., Zhang, J., Sarkar, S., Krishnamurthy, A., Ren, J., & Sarkar, A. (2022). Deep Learning for Live Cell Shape Detection and Automated AFM Navigation. Bioengineering, 9(10), 522.

8.  Sarkar, A. (December 2021). Biosensing, characterization of biosensors, and improved drug delivery approaches using Atomic Force Microscopy: A review. Frontiers in Nanotechnology

9.  Sarkar, A*., Mao, S.*, Wang, Y., Song, C., LeVine, D., Wang, X., and Que, L. (2021). Microfluidic chip grafted with integrin tension sensors for evaluating the effects of flowing shear force and ROCK inhibitor on platelets. Lab on a chip, (* made equal contribution and they share the first authorship)

10. Sarkar, A., LeVine, D. N., Kuzmina, N., Zhao, Y., & Wang, X. (2020). Cell migration driven by self-generated integrin ligand gradient on ligand-labile surfaces. Current Biology, 30(20), 4022-4032. doi: https://doi.org/10.1016/j.cub.2020.08.020

11. Sarkar, A., LeVine, D., Zhao, Y., Mollaeian, K., Ren, J., & Wang, X. (2020). Tandem tension sensor reveals substrate rigidity-dependence of integrin molecular tensions in live cells. bioRxiv. doi: https://doi.org/10.1101/2020.01.24.918946

12. Zhao, Y., Sarkar, A., & Wang, X. (2020). Peptide nucleic acid based tension sensor for cellular force imaging with strong DNase resistance. Biosensors and Bioelectronics, 150, 111959. doi: https://doi.org/10.1016/j.bios.2019.111959

13. Wang, Y., Zhao, Y., Sarkar, A., & Wang, X. (2019). Optical sensor revealed abnormal nuclease spatial activity on cancer cell membrane. Journal of biophotonics, 12(5), e201800351. DOI: 10.1002/jbio.201800351

14. Sarkar, A., Zhao, Y., Wang, Y., & Wang, X. (2018). Force-activatable coating enables high-resolution cellular force imaging directly on regular cell culture surfaces. Physical biology, 15(6), 065002. doi: 10.1088/1478-3975/aac69d

15. Wang, Y., LeVine, D. N., Gannon, M., Zhao, Y., Sarkar, A., Hoch, B., & Wang, X. (2018). Force-activatable biosensor enables single platelet force mapping directly by fluorescence imaging. Biosensors and Bioelectronics, 100, 192-200. DOI: 10.1016/j.bios.2017.09.007

16.  Zhao, Y., Wang, Y., Sarkar, A., & Wang, X. (2018). Keratocytes generate high integrin tension at the trailing edge to mediate rear De-adhesion during rapid cell migration. Iscience, 9, 502-512. doi: https://doi.org/10.1016/j.isci.2018.11.016

17. Sarkar, A.#, Sohail, A., Dong, J., Prunotto, M., Shinki, K., Fridman, R., & Hoffmann, P. M. (2019). Live cell measurements of interaction forces and binding kinetics between Discoidin Domain Receptor 1 (DDR1) and collagen I with atomic force microscopy. Biochimica et Biophysica Acta (BBA)-General Subjects, 1863(11), 129402. DOI: 10.1016/j.bbagen.2019.07.011

18. Jones, S. K., Sarkar, A.#, Feldmann, D. P., Hoffmann, P., & Merkel, O. M. (2017). Revisiting the value of competition assays in folate receptor-mediated drug delivery. Biomaterials, 138, 35-45. doi: https://doi.org/10.1016/j.biomaterials.2017.05.034

Conference Publications

1. Masud, N., Faivre, N., Lee, X. X., Ekpenyong, A. E., & Sarkar, A. (2024). Understanding the effects of radioimmunotherapy on nanomechanical, viscoelastic properties of live glioblastoma cells using atomic force microscopy. Biophysical Journal, 123(3), 408a.

2. Hasib, M.H.H., Masud, N., Hejazi, S. S., Reuel, N., & Sarkar, A. (2024). Characterization of biomolecule-attached single-walled carbon nanotubes (SWCNTs) using Atomic Force Microscopy. Institute of Biological Engineering Annual Meeting 2024, Atlanta, GA (also accepted and presented in Nanovax conference 2024 conference, Ames, IA).

3. Masud, N., Faivre, N., Lee, X. X., Ekpenyong, A. E., & Sarkar, A. (2024). Exploring cellular mechanics in glioblastoma and the effects of Radioimmunotherapy: An Atomic Force Microscopy Investigation. Institute of Biological Engineering Annual Meeting 2024, Atlanta, GA (also accepted and presented in Nanovax conference 2024 conference, Ames, IA).

4. Masud, N., Fonder, C., Hasib, M.H.H., Sakaguchi, D., Bentil, S., Sarkar, A. (2024). The effects of blast-induced traumatic brain injury on brain cellular mechanics. Biomedical Engineering Society Annual Meeting 2024, Baltimore, MD.

5. J. Rade, E. Herron, M. H. H. Hasib, N. Masud, S. Sarkar, A. Sarkar, A.  Krishnamurthy, Deep learning for 3D Protein Structure Prediction from AFM images, Biomedical Engineering Society Annual Meeting 2024, Baltimore, MD.

6. J. Rade, E. Herron, S. Sarkar, A. Sarkar, A.  Krishnamurthy, 3D Reconstruction of Protein Structures from Multi-view AFM Images using

7. Neural Radiance Fields (NeRFs). Computer Vision and Pattern Recognition Conference (CVPR) 2024, Seattle, WA.

8. N. Masud, A. Pulickal Mathew, R. Bardhan, A. Sarkar, Characterization of mechanically tuned liposomal nanocarriers for cell and phenotype-specific endocytosis using Atomic Force Microscopy, accepted to be presented as a poster in Biomedical Engineering Society (BMES) Annual meeting, Seattle, WA, 2023.

9. A. Koep, N. Masud, A. Sarkar, M. Nilsen-Hamilton, and I. Schneider, Collagen Localized Nanoscale Drug Delivery System, accepted to be presented as a poster and a flash talk in Biomedical Engineering Society (BMES) Annual meeting, Seattle, WA, 2023.

10. N. Masud, A. Pulickal Mathew, R. Bardhan, A. Sarkar, Tuning of Young’s modulus and surface ligand density of liposomal nanocarriers for cell and phenotype-specific endocytosis, Institute of Biological Engineering (IBE) annual conference, April 2023.

11. C. Stanley, A. Ananya, B. Narasimhan, M. Kohut, A. Sarkar, Studying the nanomechanical properties of aging on mice bone marrow derived cells using atomic force microscopy (AFM), NCUR , Wisconsin 2023 (poster).

12. C. Stanley, A. Ananya, B. Narasimhan, M. Kohut, A. Sarkar, Effects of aging on nanomechanical properties of mice bone marrow derived cells using atomic force microscopy (AFM), Biophysical Society 67th Annual Meeting, San Diego, CA 2023.

13. J. Rade, S. Sarkar, A. Krishnamurthy, A. Sarkar, Virtual AFM: Generating Synthetic 2D Multi-view Images from 3D Protein Structure, Biomedical Engineering Society (BMES) Annual meeting, San Antonio, TX, 2022.

14. 13. A. Koep, A. Sarkar, S. Alam, T. Prozorov, I. Schneider, Actuatable Hollow DNA Origami Drug Delivery Constructs, Biomedical Engineering Society (BMES) Annual meeting, presented as a poster and a flash talk, San Antonio, TX, 2022.

15. J. Rade, S. Sarkar, A. Krishnamurthy, A. Sarkar, Virtual AFM: Generating Synthetic 2D Multi-view Images from 3D Protein Structure, Biomedical Engineering Society (BMES) Annual meeting, San Antonio, TX, 2022.

16. A. Koep, A. Sarkar, S. Alam, T. Prozorov, I. Schneider, Actuatable Hollow DNA Origami Drug Delivery Constructs, Biomedical Engineering Society (BMES) Annual meeting, San Antonio, TX, 2022.

17. J. Rade, S. Sarkar, A. Sarkar, A. Krishnamurthy, 3D Reconstruction of Protein Complex Structures Using Synthesized Multi-View AFM Images, Machine Learning in Structural Biology (MLSB) Workshop at the 36th Conference on Neural Information Processing Systems (NeurIPS), New Orleans, LA, 2022.

18. A. Sarkar, N. Hassan, R. Bardhan, Multimodal characterization of live cancer cells using Atomic Force Microscopy and Raman spectroscopy, presented as a poster, Biophysical Society 66th Annual Meeting, San Francisco, CA 2022.

19. A. Sarkar, S. Yang, B. Chen, High Resolution Single Molecule Imaging of WRC-Rac1 Protein Complex with Atomic Force Microscopy, Biomedical Engineering Society (BMES) Annual meeting, Orlando, Fl 2021.

20.  J. Rade, S. Sarkar, A. Krishnamurthy, J. Ren, A. Sarkar, AI Guided Measurement of Live Cells Using AFM, Modelling, Estimation and Control Conference (MECC), Austin, TX 2021.

21.  A. Sarkar, J. Waite, S. Sarkar, Deep learning for fast Atomic Force Microscopy data analytics, selected for platform presentation and presented as a talk, Biophysical Society 65th Annual Meeting (virtual) 2021.

22. S. Mao~ , A. Sarkar ~, D. LeVine, X. Wang, L. Que, Studies of the drug treatment effects on platelets using integrative tension sensors embedded in a microfuidic chip, Microfluidics for Hematology, presented as talk, Chicago, IL 2020 (~ made equal contribution and share the first authorship)

23. A. Sarkar, Y. Wang, X. Wang, Determining Integrin Molecular Tension for the Recruitment and the activation of Focal Adhesion Kinase, Biophysical Society (BPS), 63rd Annual meeting, presented as poster, Baltimore, MD 2019.

24.  A. Sarkar, X. Wang, Integrin molecular tensions in live cells are altered by substrate rigidity, Biophysical Society (BPS), 62nd Annual meeting, presented as a talk and poster, San Francisco, CA 2018 [the work was also presented as a talk and poster in the ISU Research Day, Iowa State University, 2018]

25. A. Sarkar, R. Fridman, A. Sohail and P. M. Hoffmann, Measurement of DDR-Collagen interaction Forces with Atomic force Microscopy, American Physical Society (APS) March Meeting, San Antonio, TX 2015

26.  A. Sarkar, E. Mayyas and P. M. Hofmann, Effect of Surface Density of Active sites on Rupture Force Distributions of Single Molecule Interactions, Biophysical Society (BPS), 59th Annual Meeting, Baltimore, MD 2015

27.  A. Sarkar and P. M. Hoffmann, Effect of active site density on rupture force distributions in ligand-protein force measurements, American Physical Society (APS) Ohio-Region Section Meeting, April 2014, Youngstown, OH (presented as poster) [the work was also presented during the Physics Graduate Research Day, Wayne State University, April 2014]

28.  A. Sarkar, E. Kramkowski, E. Mayyas and P. M. Hoffmann, Multiple attachments, heterogeneous binding and the high force tail in protein-protein binding force histograms, American Physical Society (APS) March Meeting, March 2013, Baltimore, MD (presented as poster) [the work was also presented during the Physics Graduate Research Day, Wayne State University, April 2013]

29.  A. Sarkar, E. Kramkowski and P. M. Hoffmann, Live cell imaging and determination of protein-protein rupture force with AFM, American Physical Society (APS) Ohio-Region Section Meeting, October 2012, Detroit, MI (presented as poster) [the work was also presented in Michigan Microscopy and Microanalysis Society Fall 2012 Meeting]

Invited Talks

1. A. Sarkar, Single molecule interaction forces and reaction kinetics of ligand-receptor systems using AFM on live cells and  fast data analytics, Biomedical Engineering Society at Iowa State University, November 2022.

2. A. Sarkar, Force activatable biosensors and fast Atomic Force Microscopy data analytics using machine learning approaches, Department of Physics, Wayne State University, March 2022.

3. A. Sarkar, High resolution imaging, nanomechanical characterization, and measurement of interaction forces and binding kinetics of protein-protein interactions with AFM, Nanovaccine Institute, Iowa State University, December 2021 (2021 Fall Seminars).

4. A. Sarkar, S. Yang and B. Chen, High Resolution Single Molecule Imaging of WRC-Rac1 Protein Complex with Atomic Force Microscopy, 2021 Biomedical Engineering Society (BMES) Annual meeting, October 2021, Orlando, FL.

5. A. Sarkar, Measurement of interaction forces and binding kinetics of protein-protein interactions with AFM, Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, March 2021 (2021 Spring Seminars).

6. A. Sarkar, J. Waite, S. Sarkar, Deep learning for fast Atomic Force Microscopy data analytics, selected for platform presentation and presented as a talk, Biophysical Society 65th Annual Meeting (virtual) 2021.

7. A. Sarkar, Single molecule force measurements on live cells with Atomic Force Microscopy (AFM) and force activatable biosensors at Department of Electrical and Computer Engineering, Iowa State University, March 2020.

8. A. Sarkar, X. Wang, Integrin molecular tensions in live cells are altered by substrate rigidity, Biophysical Society (BPS), 62nd Annual meeting, presented as a talk, San Francisco, CA, 2018.

9. A. Sarkar, Interaction forces and reaction kinetics of ligand-cell receptor systems using Atomic Force Microscopy (AFM) at Department of Physics, Iowa State University, October 2015.