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Patents filed or granted

7. Sumaer Kamboj, Chase Harms, Lokender Kumar, Daniel Creamer, Colista West, Judith Klein-Seetharaman, and Susanta K. Sarkar. Purification of alpha-synuclein and preparing E. coli based Lewy body model leveraging amyloidogenic property. Patent filed, CSM, (2020).

6. Lokender Kumar, John Brice, Linda Toberer, Judith Klein-Seetharaman, Daniel Knauss, and Susanta K. Sarkar. Antimicrobial biopolymer formation from sodium alginate and algae extract using aminoglycosides. Patent filed, CSM, (2019).

5. Lokender Kumar and Susanta K. Sarkar. Matrix metalloprotease-1 as antibiofilm agent. Patent application: 16/355,090 (2018).

4. Lokender Kumar and Susanta K. Sarkar. Purification of active soluble recombinant matrix metalloproteinase-1 in Escherichia Coli. Patent application: 16/265,600 (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 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. Patent application: US20180356343A1 (2015).

1. Ambika Bumb, Susanta K. Sarkar, Martin W. Brechbiel, and Keir C.  Neuman. Method of preparing silica-coated nanodiamonds. Patent applications:CA2879407A1WO2014014970A1 (2014).

Publications

35. Sumaer Kamboj, Chase Harms, Derek Wright, Anthony Nash, Lokender Kumar, Judith Klein-Seetharaman, and Susanta K. Sarkar†, "Identification of substrate-specific allosteric fingerprints in matrix metalloprotease-1 on amyloid-beta peptide aggregates and drug screening with single molecule insights", Submitted, (2022).†Corresponding author.

34. Derek Wright, Chase Harms, and Susanta K. Sarkar†, "Identification of collagen-specific allosteric residues and changes at the catalytic site of matrix metalloprotease-1", Submitted, (2022).†Corresponding author.

33. Derek Wright, Roshan Klein-Seetharaman, and Susanta K. Sarkar†, "A stochastic approach to quantifying the recurrence time for different particle statistics and showing the emergence of the arrow of time", Submitted, (2022).†Corresponding author.

32. Sumaer Kamboj, Chase Harms, Derek Wright, Anthony Nash, Lokender Kumar, Judith Klein-Seetharaman, and Susanta K. Sarkar†, "Identification of allosteric fingerprints of alpha-synuclein aggregates in matrix metalloprotease-1 and substrate-specific virtual screening with single molecule insights", Scientific Reports, 12, (2022).†Corresponding author.

31. A. Michelle Lawing, Michael McCoy, Beth A. Reinke, Susanta K. Sarkar†, Felisa A. Smith, Derek Wright, "A framework for investigating rules of life by establishing zones of influence", Integrative and Comparative Biology, 61, 6, 2095–2108, 2021. †Corresponding author. NSF Integrating Biology Workshop.

30. Lokender Kumar, Nathanael Brenner, John Brice, Judith Klein-Seetharaman, and Susanta K. Sarkar†, “Cephalosporins target quorum sensing and suppress virulence of Pseudomonas aeruginosa in Caenorhabditis elegans infection model”, Frontiers in Microbiology, 12, 70, (2021).†Corresponding authors.

29. Sumaer Kamboj, Chase Harms, Lokender Kumar, Daniel Creamer, Colista West, Judith Klein-Seetharaman, and Susanta K. Sarkar†, “A method of purifying alpha-synuclein in E. coli without chromatography”, Heliyon, 7, 1, (2021).†Corresponding authors.

28. Lokender Kumar, Joan Planas-Iglesias, Chase Harms, Sumaer Kamboj, Derek Wright, Judith Klein-Seetharaman, and Susanta K. Sarkar†, “Activity-dependent interdomain dynamics of matrix metalloprotease-1 on fibrin”, Scientific Reports, 10, 1-14, (2020).†Corresponding author.

27. Lokender Kumar, Anthony Nash , Chase Harms , Joan Planas-Iglesias , Derek Wright , Judith Klein-Seetharaman, and Susanta K. Sarkar†, “Allosteric Communications between Domains Modulate the Activity of Matrix Metalloprotease-1”, Biophysical Journal, 119, 1-15, (2020).†Corresponding author. Selected for the cover page. Recommended in Faculty Opinions by Dr. Jean-Pierre Changeux, one of the pioneers of allostery in proteins, and by Dr. Greg Fields, one of the well-known experts in matrix metalloproteases.

26. Lokender Kumar, John Brice, Linda Toberer, Judith Klein-Seetharaman, Daniel Knauss, and Susanta K. Sarkar†, “Antimicrobial biopolymer formation from sodium alginate and algae extract using aminoglycosides”, PloS One, 14, 3,(2019).†Corresponding author.

25. Lokender Kumar, Christopher Cox, and Susanta K. Sarkar†, “Matrix metalloprotease-1 inhibits and disrupts Enterococcus faecalis biofilms”, PloS One,14,1,(2019).†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”, Protein Expression and Purification, 148, 59-67, (2018).†Corresponding author.

23. Warren Colomb, Matthew Osmond, Charles Durfee, Melissa D. Krebs, and Susanta K. Sarkar†, “Imaging and Analysis of Cellular Locations in Three-Dimensional Tissue Models”, Microscopy and Microanalysis, 25, 3, 753-761, (2019).†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, 270(3), 261-271, (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, 63-85, (2018).†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. One of the top 20 most read paper in Journal of Microscopy in 2018.

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 the cover page.

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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.