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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 critical biological processes. Members of 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 for our collective development. The philosophy of our laboratory will be demanding with clear expectations and fairness.

  PI: Susanta K. Sarkar (CV)  

We aspire to be ourselves

  Assistant Professor
  Department of Physics
  Colorado School of Mines
  Research Directions:
1. Collagen degradation by matrix metalloproteases (MMPs).
2. Allosteric communications and promiscuity of MMPs.

Funding: NIH, NSF, COEDIT.


Multidisciplinary Research

INTEGRATIVE BIOPHYSICS Our multidisciplinary research laboratory allows for exploring transformative research ideas because we do core sample preparations, experiments, and analyses ourselves.

Lokender Kumar et al. Activity-dependent interdomain dynamics of matrix metalloprotease-1 on fibrin. (Scientific Reports, 10, 1-14, 2020).

Lokender Kumar et al. Allosteric Communications between Domains Modulate the Activity of Matrix Metalloprotease-1. (Biophysical Journal, 119, 1-15, 2020). 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.

Lokender Kumar et al. Antimicrobial biopolymer formation from sodium alginate and algae extract using aminoglycosides. (PLOS ONE, 14, 3, 2019).

Lokender Kumar et al. Matrix metalloproteases-1 inhibits and eradicates Enterococcus faecalis biofilms. (PLOS ONE, 14, 1, 2019).

MICROSCOPY We build our 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. Imaging and Analysis of Cellular Locations in Three-Dimensional Tissue Models. (Microscopy and Microanalysis, 25, 3, 753-761, 2019).

John Czerski et al. Spectroscopic identification of fluorophores at single molecule level using photoluminescence excitation spectra. (Journal of Microscopy, The Royal Microscopical Society, 270(3), 261-271,  2018).

Warren Colomb et al. Estimation of microscope drift using fluorescent nanodiamonds as fiducial markers. (Journal of Microscopy, The Royal Microscopical Society, 266(3), 298-306, 2017). One of the top 20 most read paper in Journal of Microscopy in 2018.

MOLECULAR BIOLOGY We purify and characterize our proteins! We have a complete facility for E. coli-based molecular biology and protein purification, including an 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.

Sumaer Kamboj et al. A method of purifying alpha-synuclein in E. coli without chromatography. (Heliyon, 7, 1, 2021). Patent Filed.

Lokender Kumar et al. Efficient protease based purification of recombinant matrix metalloproteinase-1 in E. coli. (Protein Expression and Purification, 148, 59-67, 2018). Patent Filed.

COMPUTATION We develop our analyses and simulations! We have multiple high-end computers for data analysis and simulations.

Warren Colomb et al. Extracting Physics of Life at the Molecular Level: A Review of Single-molecule Data Analyses. (Physics of Life Reviews, Jun 13:153-154, 2015).

Updates

September 20 2022 Susanta receives a $1.14 million single-PI NIH R01 grant on collagen fibril degradation by matrix metalloproteases.

August 17 2022 Chase successfully defended his Ph.D. thesis proposal. Congratulations!

July 14 2022 Susanta receives a $50,000 NIH supplement grant on MMP1 interactions with amyloid-beta aggregates.

March 23 2022 Sumaer's paper on MMP1 interactions with alpha-synuclein aggregates has been accepted by Scientific Reports. Congratulations!

November 18 2021 Susanta receives a $150,000 COEDIT grant for commercialization of inexpensive recombinant alpha-synuclein and amyloid-beta peptide.

July 26 2021 Sumaer has successfully defended his Ph.D. thesis. Congratulations!

January 29 2021 Susanta receives an NSF STTR grant to commercialize MMPs.

December 24 2020 Sumaer's paper on alpha-synuclein paper has been accepted by Heliyon. Congratulations!

November 15 2020 Lokender's paper on activity-dependent dynamics of MMP1 on fibrin has been accepted by Scientific Reports. Congratulations!

July 01 2020 Lokender's artistic drawing related to the paper on allosteric communications in MMP1 has been accepted as the cover page by Biophysical Journal. Congratulations!

June 09 2020 Lokender's paper on allosteric communications in MMP1 has been accepted by the Biophysical Journal. Congratulations!

March 24 2020 Susanta receives an NIH R15 grant on the fibrinolytic activity of MMP1.

November 08 2019 Congratulations to Derek for successfully defending his MS thesis.

July 26 2019 Congratulations to John Brice for getting his dream job as a patent geek! Multidisciplinary training at our laboratory along with his chosen coursework makes him unique. A combined BS(Physics)/MS(Electrical) background with extensive training in alginate biopolymer and pathogens!

June 06 2019 Warren's paper on estimation of microscope drift was among the top 20 downloaded papers in Journal of Microscopy. Congratulations!

March 18 2019 Lokender, John, and Linda's paper on antimicrobial alginate biopolymer has been accepted. Congratulations!

January 02 2019 Warren's paper on modeling cellular locations as Poisson process and Lokender's paper on MMP1 as antibiofilm agent have been accepted during the holiday break. Congratulations!

April 03 2018 Lokender's paper on MMP1 purification has been accepted by Protein Purification and Expression. Congratulations!

March 19 2018 Warren successfully defended his PhD thesis. Congratulations Dr. Colomb! Moving on to his full time job that leverages his 3D computational imaging training.

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!

Positions Available

CSM students - Please contact me for senior design projects and/or research opportunities at ssarkar@mines.edu. Due to COVID-19, senior design project will be computational.