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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. (Microscopy and Microanalysis, Accepted, 2018).

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).

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. (Protein Expression and Purification, 148, 59-67, 2018). 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, Jun 13:153-154, 2015).

BEYOND COLLAGEN DEGRADATION Our multidisciplinary research laboratory allows for exploration of transformative research ideas because we do core sample preparations, experiments, and analyses ourselves.

Lokender Kumar et al. Antimicrobial biopolymer formation from sodium alginate and algae extract using aminoglycosides.(PLOS ONE, Accepted, 2018).

Lokender Kumar et al. Matrix metalloproteases-1 inhibits and eradicates Enterococcus faecalis biofilms. (PLOS ONE, Accepted, 2018).

Updates

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.