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Patents

5. Lokender Kumar and Susanta K. Sarkar. Matrix metalloprotease-1 as antibiofilm agent. Patent filed, CSM, (2018).

4. Lokender Kumar and Susanta K. Sarkar. Purification of active soluble recombinant matrix metalloproteinase-1 in Escherichia Coli. Patent filed, CSM, U.S. Provisional Application Number 62625141 (2017).

3. Susanta K. Sarkar, Ambika Bumb, and Keir C.  Neuman. Imaging methods and computer-readable media. This patent is on background-free imaging by selective modulation of nanodiamond fluorescence using a magnetic field. US 20170046823 A1US Patent 9449377 (2016).

2. Keir Cajal Neuman, Han Wen, Jennifer Hong, Chang Kuyn Yi, Ambika Bumb, Susanta Kumar Sarkar, A.K. Manna, L.E. Samelson. Fluorescent nanodiamonds for use as fiducial markers for microscopy and fluorescence imaging. U.S. Provisional Application Number 62/262,058 (2015).

1. Ambika Bumb, Susanta K. Sarkar, Martin W. Brechbiel, and Keir C.  Neuman. Method of preparing silica-coated nanodiamonds. Patent applications:CA2879407A1, EP2874943A1EP2874943A4WO2014014970A1 (2014).

Publications

25. Lokender Kumar, Christopher Cox, Reuben Collins, and Susanta K. Sarkar†, “Matrix metalloprotease-1 inhibits and disrupts Enterococcus faecalis biofilms”, Submitted (2018).†Corresponding author.

24. Lokender Kumar, Warren Colomb, John Czerski, Christopher Cox, and Susanta K. Sarkar†, “Efficient protease based purification of recombinant matrix metalloproteinase-1 in E. coli”, Accepted (2018).†Corresponding author.

23. Warren Colomb, Matthew Osmond, Charles Durfee, Melissa D. Krebs, and Susanta K. Sarkar†, “Quantification of cellular distribution as Poisson process in 3D matrix using a multiview light-sheet microscope”, Submitted (2017).†Corresponding author.

22. John Czerski, Warren Colomb, Frank Cannataro, and Susanta K. Sarkar†, “Spectroscopic identification of fluorophores at single molecule level using photoluminescence excitation spectra”, doi:10.1111/jmi.12679, Journal of Microscopy, The Royal Microscopical Society, (2018).†Corresponding author.

21. John Czerski and S. K. Sarkar†, “High-resolution and high-contrast fluorescence imaging with carbon nanomaterials for pre-clinical and clinical applications”, Invited book chapter, Carbon Nanomaterials for Bioimaging, Bioanalysis and Therapy, Wiley, (2017).†Corresponding author.

20. Warren Colomb, John Czerski, Jaydeep Sau, and Susanta K. Sarkar†, “Estimation of microscope drift using fluorescent nanodiamonds as fiducial markers”, Journal of Microscopy, The Royal Microscopical Society, 266(3), 298-306, (2017).†Corresponding author. CODES

19. Andrew Dittmore, Jonathan Silver, Susanta K. Sarkar, Barry Marmer, Gregory Goldberg, and Keir C. Neuman, “Internal Strain Drives Spontaneous Periodic Buckling in Collagen and Regulates Remodeling”, PNAS, Vol 113, No 30, 8436-8441, (2016).

18. Proudian, Andrew P., and Susanta K. Sarkar†, "Modeling the effect of transient violations of the second law of thermodynamics on heat transfer in silicon nanowire." arXiv preprint arXiv:1606.01997 (2016).†Corresponding author.

17. Susanta K. Sarkar†. Single Molecule Biophysics and Poisson Process Approach to
Statistical Mechanics. Institute of Physics, UK/ Morgan-Claypool, Concise Physics Series. Book. (2016).†Corresponding author.

16. Kristina M. Herbert, Susanta K. Sarkar, Maria Mills, Hilda C. Delgado De la Herran, Keir C. Neuman, and Joan A. Steitz, “A heterotrimer model of the complete Microprocessor complex revealed by single-molecule subunit counting”, RNA, 22: 175-183, (2016).

15. Kelsie Merchant and Susanta K. Sarkar†, Fluorescent nanodiamonds for molecular and cellular bioimaging.The IEEE Journal of Selected Topics in Quantum Electronics (IEEE JSTQE, accepted). Invited Review. (2015). †Corresponding author.

14. W. Colomb and Susanta K. Sarkar†, “Digging deeper into noise. Reply to comment on" Extracting physics of life at the molecular level: A review of single-molecule data analyses”, Physics of Life Reviews, Jun 13:153-154, (2015). Commentary. (2015). †Corresponding author.

13. W. Colomb and Susanta K. Sarkar†, “Extracting Physics of Life at the Molecular Level: A Review of Single-molecule Data Analyses”, Physics of Life Reviews, Jun 13:107-37, (2015). Invited Review. (2015). †Corresponding author.

12. Susanta K. Sarkar†, Ambika Bumb†, Xufeng S. Wu, Kem A. Sochacki, Peter Kellman, Martin W. Brechbiel, and Keir C. Neuman. Wide-field in vivo background free imaging by selective magnetic modulation of nanodiamond fluorescence. Biomedical Optics Express 5(4), 1190–1202 (2014). †Equal contributions. US Patent US 20140099007 A1. Selected for cover page illustration.

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11. Susanta K. Sarkar, Ambika Bumb, Maria Mills, and Keir C. Neuman. Single-Molecule Fluorescence. Cell 153(6):1408-1408.e1 (2013).

10. Ambika Bumb†, Susanta K. Sarkar†, Martin W. Brechbiel, and Keir C.  Neuman. Silica encapsulation of fluorescent nanodiamonds for colloidal stability and facile surface functionalization. J. Am. Chem. Soc. 135 (21), 7815–7818 (2013). †Equal contributions. Selected for cover page illustration.Highlighted in Nature Methods. Spotlighted in JACS. Patent WO 2014014970 A1.

9. Arthur Z. Eisen, Susanta K. Sarkar, Keir C. Neuman, Gregory A. Bannikov, and Gregory I. Goldberg. Matrix metallopeptidase 9 / gelatinase B. Invited book chapter in the Handbook of Proteolytic Enzymes, 3rd Edition, Neil D. Rawlings, Editor (2012). Importance of MMP9 in collagen degradation.

8. Susanta K. Sarkar, Barry Marmer, Gregory Goldberg, and Keir C. Neuman. Single-molecule tracking of collagenase on native type I collagen fibrils reveals degradation mechanism. Current Biology, 22, 1-10, June 19, (2012). Mechanistic details of collagen fibril degradation. Selected for cover page illustration. Commentary in Current Biology. Selected by Faculty of 1000 twice.

7. Ambika Bumb, Susanta K. Sarkar, Xufeng S. Wu, Martin W. Brechbiel, and Keir C.  Neuman. Quantitative characterization of fluorophores in multi-component nanoprobes by single-molecule fluorescence. Biomedical Optics Express, 10, 2762-2769 (2011). New high-throughput method to accurately characterize dyes using single-molecule counting.

6. Ashley H. Hardin, Susanta K. Sarkar, Yeonee Seol, Grace F. Liou, Neil Osheroff, and Keir C. Neuman. Direct measurement of DNA bending by type IIA topoisomerases: implications for non-equilibrium topology simplification. Nucleic Acid Research, 1-15, (2011). Disproved one of the most accepted models in the field. Selected by Faculty of 1000.

5. Nesha May Andoy, Susanta K. Sarkar, Qi Wang, Jaime J. Benitez, Aleksandr Kalininskiy, and Peng Chen. Single-Molecule Study of Metalloregulator CueR-DNA Interactions Using Engineered Holliday Junctions. Biophysical Journal, 97, 844–852  (2009).

4. Susanta K. Sarkar, Nesha May Andoy, Jaime J. Benitez, Peng R. Chen, Jason S. Kong, Chuan He, and Peng Chen. Engineered Holliday junctions as single molecule reporters for protein-DNA interactions with application to a MerR-family regulator. J. Am. Chem. Soc. 129, 12461-12467 (2007). New method to study protein-DNA interactions at single-molecule level.

3. Yan Guo, Susanta K. Sarkar, and Hailin Wang. Pulse propagation near exciton resonance:   Anomalous transition between slow and fast light. Conference paper, Slow and fast light, Salt Lake City, Utah (2007). Velocity of light and propagation of optical pulses.

2. Susanta K. Sarkar, Yan Guo, and Hailin Wang. Tunable optical delay via carrier induced exciton dephasing in semiconductor quantum wells. Optics Express 14 (7), 2845 (2006). First tunable velocity of light using incoherent optical process.

1. Susanta K. Sarkar, Phedon Palinginis, Hailin Wang, Pei-Cheng Ku, Connie J. Chang-Hasnain, N.H. Kwong, and R. Binder. Inducing electron spin coherence in GaAs quantum well waveguides: Spin coherence without spin precession. Physical Review B 72, 035343 (2005). First electron spin coherence without magnetic field in a quantum well waveguide.