Publications

A link to my Google Scholar, ResearchGate and LinkedIn along with my ORCID id profiles are given below :

• https://www.researchgate.net/profile/Srijit_Mukherjee2

• https://scholar.google.com/citations?user=rI7F2ewAAAAJ&hl=en

• https://www.linkedin.com/in/srijit-mukherjee-93449143/

• https://orcid.org/0000-0002-6439-9802

• My Stanford Profile: https://profiles.stanford.edu/srijit-mukherjee?tab=bio 

The last updated version of my can be found here as well: 

2025

14. Detection of Covalent Drug Binding In Live Cells Using A Quantum Cascade Laser and Nitrile Labeled Amino Acids
(In preparation for submission to Journal of American Chemical Society (ACS))
S. Mukherjee, S. D. E Fried, N.Y. Hong, N. Bagheri, J. Kirsh, I. I Mathews and S. G. Boxer.

13. Reaction Yield Detected Magnetic Resonance in a Transgenic Animal
(Under revisions in Nature (Springer))
S. C. Burd, N. Bagheri, M. Ingaramo, A. F. Condon, S. Mondal, D. P. Dowlatshahi, J. A. Summers, S. Mukherjee, A. York, S. Wakatsuki, S. G. Boxer, and M. Kasevich.

12. Disentangling Photobleaching Pathways in Red Fluorescent Proteins: Contributions of the mCherry Dark State to Photobleaching Pathways
(In preparation for submission to Journal of Physical Chemistry B (ACS))
P. Manna, S. Mukherjee, and R. Jimenez.

11. Electrostatic atlas of noncovalent interactions built in metal-organic frameworks
(Accepted in Nature Chemistry)
Z. Ji, S. Mukherjee, J. Andreo, S. Wuttke, and S. G. Boxer. (Joint First Author)

2024

10. Environment- and Conformation-Induced Frequency Shifts of C–D Vibrational Stark Probes in NAD(P)H Cofactors
Journal of Physical Chemistry Letters (ACS)
S. D. E. Fried, S. Mukherjee, Y. Mao, and S. G. Boxer
DOI: 10.1021/acs.jpclett.4c02497

9. Influence of Fluorescence Lifetime Selections and Conformational Flexibility on Brightness of FusionRed Variants
Journal of Physical Chemistry Letters (ACS)
S. Mukherjee, N. Douglas, and R. Jimenez
DOI: 10.1021/acs.jpclett.3c02765

2022

8. Conformational Dynamics of mCherry Variants: A Link Between Sidechain Motions and Fluorescence Brightness
Journal of Physical Chemistry - B (ACS)
S. Mukherjee, P. Manna, N. Douglas, P. P. Chapagain, and R. Jimenez
DOI: 10.1021/acs.jpcb.2c05584

7. Directed Evolution of a Bright Variant of mCherry: Suppression of Nonradiative Decay by Fluorescence Lifetime Selections
Journal of Physical Chemistry - B (ACS)
S. Mukherjee, P. Manna, S. T. Hung, F. Vietmeyer, P. Friis, A. Palmer, and R. Jimenez
DOI: 10.1021/acs.jpcb.2c01956

6. Characterizing Dark State Kinetics and Single Molecule Fluorescence of FusionRed and FusionRed-MQ at Low Irradiances
Physical Chemistry and Chemical Physics (RSC)
S. Mukherjee, C. Thomas, R. Wilson, E. Simmerman, S. T. Hung, and R. Jimenez
DOI: 10.1039/D2CP00889K

5. Photophysical Engineering of Fluorescent Proteins: Accomplishments and Challenges of Physical Chemistry Strategies
Journal of Physical Chemistry - B (ACS)
S. Mukherjee and R. Jimenez
DOI: 10.1021/acs.jpcb.1c05629

2020

4. Engineering of a Brighter Variant of the FusionRed Fluorescent Protein Using Lifetime Flow-Cytometry and Structure-Guided Mutations
Biochemistry (ACS)
S. Mukherjee, S. T. Hung, N. Douglas, P. Manna, C. Thomas, A. Ekrem, A. Palmer, and R. Jimenez
DOI: 10.1021/acs.biochem.0c00484

3. Enrichment of Rare Events Using a Multi-Parameter High Throughput Microfluidic Droplet Sorter
Lab on a Chip (RSC)
S. T. Hung, S. Mukherjee, and R. Jimenez
DOI: 10.1039/C9LC00790C

2018

2. Fluorescence Enhancement of Tb3+ in the Tb3+-Trimesic Acid-Gd3+ Complex: Role of Polynuclear Structures
Chemistry Select (Wiley)
P. Dubey, S. Mukherjee, A. R. Chowdhury, and K. S. Viswanathan
DOI: 10.1002/slct.201900035

1. Directed Evolution of Excited State Lifetime and Brightness in Red Fluorescent Proteins Using a Microfluidic Sorter
Integrative Biology (RSC)
P. Manna, S. T. Hung, S. Mukherjee, P. Friis, D. Simpson, M. Lo, A. E. Palmer, and R. Jimenez
DOI: 10.1039/c8ib00103k