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Research Philosophy and Directions

   


We are a multidisciplinary research group. Our vision is to develop better imaging and analysis tools to understand important biological processes. Members in our group will learn independent thinking, single-molecule instrumentation, rigorous data analysis, simulation, molecular biology, and cutting edge imaging for biomedical applications. Soft skills such as grant writing, multi-tasking, presentation, and interpersonal communications will be necessary part of our collective development. Philosophy of our laboratory will be demanding with clear expectations and fairness.

We don't do everything, but we do well whatever we do!

  PI: Susanta K. Sarkar (CV)  

We aspire to be ourselves

  Assistant Professor
  Department of Physics
  Colorado School of Mines
  Research Directions:
1. Collagen fibril degradation by matrix metalloproteases
2. Applications of matrix metalloproteases beyond collagen

Multidisciplinary Research

MICROSCOPY We build our own microscopes! We have three highly modular microscopes with extensive experimental capabilities: a Total Internal Reflection Fluorescence Microscope (TIRFM) for single molecule studies, a light sheet microscope to image 5 mm or more thick samples, and a multiphoton microscope for time resolved two-photon imaging.

Warren Colomb et al. Quantification of cellular distribution as Poisson process in 3D matrix using a multiview light-sheet microscope. (Scientific Reports, Submitted 2017).

John Czerski et al. Spectroscopic identification of fluorophores at single molecule level using photoluminescence excitation spectra. (Journal of Microscopy, Accepted 2017).

Warren Colomb et al. Estimation of microscope drift using fluorescent nanodiamonds as fiducial markers. (Journal of Microscopy, Accepted 2017).

MOLECULAR BIOLOGY We purify and characterize our own proteins! We have complete facility for E. coli based molecular biology and protein purification including autoclave, shaker, AKTA FPLC, SORVALL centrifuge, -80 freezer, -20 freezer, 4 degree refrigerator, cell disruptor, micro-centrifuge, fumehood, two-stage water deionizer, PCR, nanodrop, and ice maker.

Lokender Kumar et al. Efficient protease based purification of recombinant matrix metalloproteinase-1 in E. coli. (Scientific Reports, Submitted 2017). Patent Filed.

COMPUTATION We develop our own analyses and simulations! We have multiple high end computers for data analysis and simulations (12 core/24 thread, 512 MB SSD, 64 GB RAM).

Warren Colomb et al. Extracting Physics of Life at the Molecular Level: A Review of Single-molecule Data Analyses. (Physics of Life Reviews, Accepted 2015).

BEYOND COLLAGEN DEGRADATION Our multidisciplinary research laboratory allows for exploration of transformative research ideas beyond our comfort zone because we do core sample preparations, experiments, and analyses ourselves. Stay tuned to be surprised soon!

Updates

January 15 2018 John and Warren's paper on spectroscopic identification of single molecules has been accepted by the Journal of Microscopy. Congratulations!

January 05 2018 Lokender has been accepted by the New Antibacterial Discovery and Development Gordon Research Conference. Congratulations!

November 08 2017 Susanta has been awarded the Outstanding Basic Science Award at the 2017 NHLBI Director's Awards Ceremony.

December 22 2017 Warren has signed a job offer that is very relevant to his PhD training. On his way to graduate in May 2018 as planned in 4 years! Congratulations!

January 25 2017 Warren and John's paper on microscope drift estimation has been accepted by the Journal of Microscopy. Congratulations!

June 02 2016 Dr. Lokender Kumar will join us as a postdoctoral fellow. Welcome!

March 10 2016 Postdoctoral position with strong background in molecular biology and MMP/collagen biochemistry is available for single molecule study of collagen degradation. Very competitive salary and career building opportunity.

May 04 2015 Frank Cannataro defended his MS thesis successfully. Warren Colomb wins the best poster award. We have published our first paper on single molecule data analysis.

March 24 2014 Single Molecule Biophysics goes online!

January 07 2014 Single Molecule Biophysics Laboratory starts at Colorado School of Mines!

Patents

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 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:US 20170046823 A1CA2879407A1EP2874943A1EP2874943A4WO2014014970A1 (2014).

Publications

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”, Submitted (2017).†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.

Positions Available

CSM students - Please contact me for senior design projects and/or research opportunities at ssarkar@mines.edu.