Publications

List of Publications     

ORCID

2024

• "Hydrogen-Bonded Network of Water in Phase-Separated Biomolecular Condensates" A. Joshi, A. Avni,* A, Walimbe, S. K. Rai, S. Sarkar, S. Mukhopadhyay*. J. Phys. Chem. Lett. 2024 https://pubs.acs.org/doi/10.1021/acs.jpclett.4c01153

• "Chaperone-mediated heterotypic phase separation regulates liquid-to-solid phase transitions into amyloid fibrils". S. K. Rai, R. Khanna, A. Sarbahi, A. Joshi, S. Mukhopadhyay*. bioRxiv 2024. https://doi.org/10.1101/2024.06.13.598862 

• “Ultrasensitive Detection of Lipid-Induced Misfolding of the Prion Protein at the Aqueous-Liquid Crystal Interface”. T. Gupta, L. Arora, S. Mukhopadhyay*, S.K.Pal*.  J. Phys. Chem. Lett. 2024. https://pubs.acs.org/doi/10.1021/acs.jpclett.3c02770

• "Intermolecular Energy Migration via HomoFRET Captures the Modulation in the Material Property of Phase-Separated Biomolecular Condensates" A. Joshi, A. Walimbe, S. Sarkar, L. Arora, G. Kaur, P. Jhandai, D. Chatterjee, I. Banerjee, S. Mukhopadhyay*. bioRxiv 2024. https://doi.org/10.1101/2024.02.12.579899

• “Illuminating the Interface: Protein aggregation at the condensate interface” P. Dogra* and S. Mukhopadhyay* Biophys. J. (New and Notable) 2024. https://doi.org/10.1016/j.bpj.2023.10.027

2023

• "Single-molecule FRET unmasks structural subpopulations and crucial molecular events during FUS low-complexity domain phase separation" A. Joshi, A. Walimbe, A. Avni, S. K. Rai, L. Arora, S. Sarkar & S. Mukhopadhyay* Nature Communications 2023, 14, 7331. www.nature.com/articles/s41467-023-43225-y 

• "Hydrogen–Deuterium Exchange Vibrational Raman Spectroscopy Distinguishes Distinct Amyloid Polymorphs Comprising Altered Core Architecture" A. Avni*, A. Joshi,  S Mukhopadhyay* J. Phys. Chem. Lett. 2023, 14, 24, 5592–5601.

https://doi.org/10.1021/acs.jpclett.3c01086

• "Liquid-Liquid Phase Separation of Intrinsically Disordered Proteins: A New Phase in Our Laboratory" A. Walimbe and S. Mukhopadhyay* ACM. 2023, 3(1):146-155. https://doi.org/10.51167/acm00049

• "ATP modulates self-perpetuating conformational conversion generating structurally distinct yeast prion amyloids that limit autocatalytic amplification" S. Mahapatra*, A. Sarbahi, N. Punia, A. Joshi, A. Avni, A. Walimbe, S. Mukhopadhyay*  J. Biol. Chem. 2023, 104654.  https://doi.org/10.1016/j.jbc.2023.104654

• "The bacterial nucleoid-associated proteins, HU, and Dps, condense DNA into context-dependent biphasic or multiphasic complex coacervates" A. Gupta*, A. Joshi, K. Arora, S. Mukhopadhyay and P. Guptasarma* J. Biol. Chem. 2023, 104637. https://doi.org/10.1016/j.jbc.2023.104637

• "Biophysics of biomolecular condensates" A. Joshi and S. Mukhopadhyay* Biophys. J. 2023. https://doi.org/10.1016/j.bpj.2023.02.002

• "Heterotypic electrostatic interactions control complex phase separation of tau and prion into multiphasic condensates and co-aggregates" S. K. Rai, R. Khanna, A. Avni & S. Mukhopadhyay* Proc. Natl. Acad. Sci. U. S. A. 2023, 120(2), e2216338120. https://doi.org/10.1073/pnas.2216338120 

• "Guidelines for experimental characterization of liquid–liquid phase separation in vitro" S. G. Pattanashetty, A. Joshi, A. Walimbe, S. Mukhopadhyay in “Droplets of Life” 2023, chapter-8, pages 233-249. Vladimir N. Uversky, Academic Press. https://doi.org/10.1016/B978-0-12-823967-4.00012-9

2022

• "Molecular Origin of Internal Friction in Intrinsically Disordered Proteins" D. Das and S. Mukhopadhyay* Acc. Chem. Res. 2022, 55, 23, 3470–3480. https://doi.org/10.1021/acs.accounts.2c00528

• "Prying into biomolecular condensates using single-droplet surface-enhanced Raman spectroscopy" A. Avni https://t.co/s3zwqBx9Ai

Invitation from Nature Portfolio

• "Small molecules playing big roles: Tuning material properties of nucleolar condensates" S. K. Rai & S. Mukhopadhyay* Biophys. J. (New and Notable) 2022, ISSN 0006-3495 https://doi.org/10.1016/j.bpj.2022.08.043

• "Single-Droplet Surface-Enhanced Raman Scattering Decodes the Molecular Determinants of Liquid-Liquid Phase Separation" A. Avni, A. Joshi, A. Walimbe, S. G. Pattanashetty & S. Mukhopadhyay* Nat. Commun. 2022, 13, 4378. https://doi.org/10.1038/s41467-022-32143-0

• "Conformational Characteristics and Phase Behavior of Intrinsically Disordered Proteins─Where Physical Chemistry Meets Biology" L. Arora & S. Mukhopadhyay* J. Phys. Chem. B 2022, 126, 28, 5137–5139. https://doi.org/10.1021/acs.jpcb.2c04017 

• "Sub-stoichiometric Hsp104 regulates the genesis and persistence of self-replicable amyloid seeds of Sup35 prion domain" S. Mahapatra, A. Sarbahi, P. Madhu, H. M. Swasthi, A. Sharma, P. Singh, S. Mukhopadhyay* J. Biol. Chem. 2022, 14, 298(8):102143. https://doi.org/10.1016/j.jbc.2022.102143 

• "Spatiotemporal Modulations in Heterotypic Condensates of Prion and α-Synuclein Control Phase Transitions and Amyloid Conversion" A. Agarwal, L. Arora, S. K. Rai, A. Avni & S. Mukhopadhyay* Nature Commun. 2022 13, 1154. 

     https://www.nature.com/articles/s41467-022-28797-5

     This paper is also featured as an Editors' Highlight at Nature Communications.

• "Short-Range Backbone Dihedral Rotations Modulate Internal Friction in Intrinsically Disordered Proteins". D. Das, L. Arora &. S. Mukhopadhyay*. J. Am. Chem. Soc. 2022, 144, 4, 1739–1747. https://pubs.acs.org/doi/10.1021/jacs.1c11236

• "Conformational and Solvation Dynamics of an Amyloidogenic Intrinsically Disordered Domain of a Melanosomal Protein" P. Dogra*, S. Arya, A. K. Singh, A. Datta* & S. Mukhopadhyay* J. Phys. Chem. B. 2022, 126, 443–452. https://pubs.acs.org/doi/10.1021/acs.jpcb.1c09304

• "Prion Protein Biology Through the Lens of Liquid-Liquid Phase Separation". A. Agarwal* & S. Mukhopadhyay*.  J. Mol. Biol. 2022, 15, 434(1): 167368. https://doi.org/10.1016/j.jmb.2021.167368

2021

• "An intrinsically disordered pathological prion variant Y145Stop converts into self-seeding amyloids via liquid-liquid phase separation". A. Agarwal, S.K. Rai,  A. Avni  & S. Mukhopadhyay*. Proc. Natl. Acad. Sci. U. S. A. 2021, 118, 45, e2100968118. https://doi.org/10.1073/pnas.2100968118

• "Catalytic coacervate crucibles". S Mukhopadhyay* (News and Views) Nat. Chem. 2021, 13, 1028–1030. 

https://doi.org/10.1038/s41557-021-00815-x

• "Distinct types of amyloid‐β oligomers displaying diverse neurotoxicity mechanisms in Alzheimer's disease". P. Madhu, & S. Mukhopadhyay*. J. Cell Biochem. 2021, 122, 11, 1594-1608. 
  https://doi.org/10.1002/jcb.30141

• "Fluorescence Depolarization Kinetics Captures Short-Range Backbone Dihedral Rotations and Long-Range Correlated Dynamics of an Intrinsically Disordered Protein". D. Das, L. Arora, & S. Mukhopadhyay*. J. Phys. Chem. B.  2021, 125, 34, 9708–9718. https://doi.org/10.1021/acs.jpcb.1c04426

• "Liquid–liquid phase separation of tau: From molecular biophysics to physiology and disease". S.K. Rai, A. Savastano, P. Singh, S. Mukhopadhyay*, & M. Zweckstetter*. Protein Sci. 2021, 30, 7, 1294-1314. 

https://doi.org/10.1002/pro.4093

• "Ultrasensitive Characterization of the Prion Protein by Surface-Enhanced Raman Scattering: Selective Enhancement via Electrostatic Tethering of the Intrinsically Disordered …". S. Singh, A. Agarwal, A. Avni, & S. Mukhopadhyay*. J. Phys. Chem. Lett. 2021, 12, 12, 3187–3194.

https://doi.org/10.1021/acs.jpclett.1c00240

• "Conformation-specific perturbation of membrane dynamics by structurally distinct oligomers of Alzheimer's amyloid-β peptide". P. Madhu, D. Das, & S. Mukhopadhyay*. Phys. Chem. Chem. Phys., 2021,23, 9686-9694. https://doi.org/10.1039/D0CP06456D

2020

• "Hofmeister Ions Modulate the Autocatalytic Amyloidogenesis of an Intrinsically Disordered Functional Amyloid Domain via Unusual Biphasic Kinetics" P. Dogra, S.S. Roy, A. Joshi & S. Mukhopadhyay*. J. Mol. Biol. 2020, 432, 23, 6173-6186. https://doi.org/10.1016/j.jmb.2020.10.015

• "The Dynamism of Intrinsically Disordered Proteins: Binding-Induced Folding, Amyloid Formation, and Phase Separation" S. Mukhopadhyay*. J. Phys. Chem. B. 2020, 124, 51, 11541–11560 (Invited Feature Article). 

      https://doi.org/10.1021/acs.jpcb.0c07598

• "Differentiating Conformationally Distinct Alzheimer’s Amyloid-β Oligomers Using Liquid Crystals" I. Pani, P. Madhu, N. Najiya, A. Aayush, S. Mukhopadhyay* & S.K. Pal* J. Phys. Chem. Lett. 2020,  2020, 11, 21, 9012–9018.

       https://doi.org/10.1021/acs.jpclett.0c01867

• "Excitation Energy Migration Unveils Fuzzy Interfaces within the Amyloid Architecture" A. Majumdar, D. Das, P. Madhu, A. Avni & S. Mukhopadhyay*.  Biophys. J. 2020, 118, 2621-2626. 

   https://doi.org/10.1016/j.bpj.2020.04.015

• "Discerning Dynamic Signatures of Membrane-Bound α-Synuclein Using Site-Specific Fluorescence Depolarization Kinetics" K. Bhasne, N. Jain, R. Karnawat, S. Arya, A. Majumdar, A. Singh & S. Mukhopadhyay*.  J. Phys. Chem. B. 2020, 124, 708-717.         https://doi.org/10.1021/acs.jpcb.9b09118

• "Energy Migration Captures Membrane-Induced Oligomerization of the Prion Protein" A. Agarwal, D. Das, T. Banerjee & S. Mukhopadhyay*. BBA - Proteins and Proteomics, 2020, 1868, 2, 140324. 

https://doi.org/10.1016/j.bbapap.2019.140324

• "Preferential Recruitment of Conformationally Distinct Amyloid-β Oligomers by the Intrinsically Disordered Region of the Human Prion Protein" P. Madhu & S. Mukhopadhyay*. ACS Chem. Neurosci. 2020, 11, 1, 86–98. 

      https://doi.org/10.1021/acschemneuro.9b00646

2019

• "Intermolecular Charge-Transfer Modulates Liquid–Liquid Phase Separation and Liquid-to-Solid Maturation of an Intrinsically Disordered pH-Responsive Domain" P. Dogra, A. Joshi, A. Majumdar, & S. Mukhopadhyay*. J. Am. Chem. Soc. 2019, 141, 51, 20380-20389. https://doi.org/10.1021/jacs.9b10892

• "Liquid-Liquid Phase Separation is Driven by Large-Scale Conformational Unwinding and Fluctuations of Intrinsically Disordered Protein Molecules" A. Majumdar, P. Dogra, S. Maity & S. Mukhopadhyay*. J. Phys. Chem. Lett. 2019, 10, 3929−3936. https://doi.org/10.1021/acs.jpclett.9b01731

• "Design of Aqueous-Liquid Crystal Interfaces to Monitor Protein Aggregation at Nanomolar Concentrations" I. Pani, H.M. Swasthi, & S. Mukhopadhyay* & S.K. Pal*. J. Phys. Chem. C. 2019, 123, 1305-1312. https://doi.org/10.1021/acs.jpcc.8b10863

• "Intrinsically disordered proteins in the formation of functional amyloids from bacteria to humans." A. Avni, H. M. Swasthi, A. Majumdar, & S. Mukhopadhyay*. Prog Mol Biol Transl Sci. 2019, 166, 109-143. https://doi.org/10.1016/bs.pmbts.2019.05.005

• "Editorial on intrinsically disordered proteins: Amyloid formation and phase separation." S. Mukhopadhyay* Biochim. Biophys. Acta. Proteins Proteom. 2019, 1867 (10), 868–869. https://doi.org/10.1016/j.bbapap.2019.06.011 

2018

• "Fluorescence Depolarization Kinetics to Study the Conformational Preference, Structural Plasticity, Binding, and Assembly of Intrinsically Disordered Proteins" A. Majumdar & S. Mukhopadhyay*. Methods in Enzymology 2018, 611, 347-381. https://doi.org/10.1016/bs.mie.2018.09.031

• "Human Fibrinogen Inhibits Amyloid Assembly of Biofilm-Forming CsgA" H.M. Swasthi, K. Bhasne, S. Mahapatra, & S. Mukhopadhyay*. Biochemistry 2018, 57, 44, 6270–6273.                                                                                                          https://doi.org/10.1021/acs.biochem.8b00841

• "Femtosecond Hydration Map of Intrinsically Disordered α-Synuclein" S. Arya, A. Singh, K. Bhasne, P. Dogra, A. Datta,* P. Das,* & S. Mukhopadhyay*. Biophys. J. 2018, 114, 2540–2551.                                                                                                                                       

          https://doi.org/10.1016/j.bpj.2018.04.028

• "Synergistic Amyloid Switch Triggered by Early Heterotypic Oligomerization of Intrinsically Disordered α-Synuclein and Tau" K. Bhasne, S. Sebastian, N. Jain, & S. Mukhopadhyay*. J. Mol. Biol. 2018, 430, 16, 2508-2520.

   https://doi.org/10.1016/j.jmb.2018.04.020

• "Formation of Heterotypic Amyloids: α-Synuclein in Co-Aggregation" K. Bhasne, & S. Mukhopadhyay. Proteomics. 2018, 18, 21-22, e1800059. 

     https://doi.org/10.1002/pmic.201800059

• "Studying backbone torsional dynamics of intrinsically disordered proteins using fluorescence depolarization kinetics." D. Das, & S. Mukhopadhyay*. J. Biosci. 2018, 43, 455–462. 

 https://doi.org/10.1007/s12038-018-9766-1

2017

• "Electrostatic lipid-protein interactions sequester the curli amyloid fold on the lipopolysaccharide membrane surface" H.M. Swasthi & S. Mukhopadhyay*. J. Biol. Chem. 2017, 292, 19861-19872.

https://doi.org/10.1074/jbc.M117.815522  Featured in a virtual special issue.

• "Site-Specific Fluorescence Depolarization Kinetics Distinguishes the Amyloid Folds Responsible for Distinct Yeast Prion Strains" D. Narang, H.M. Swasthi, S. Mahapatra & S. Mukhopadhyay*. J. Phys. Chem. B. 2017, 121, 8447-8453. 

https://doi.org/10.1021/acs.jpcb.7b05550

• "Detergent-induced Aggregation of an Amyloidogenic Intrinsically Disordered Protein" S. Arya, P. Dogra, N. Jain & S. Mukhopadhyay*. J. Chem. Sci. 2017, 129, 1817–1827. 

https://doi.org/10.1007/s12039-017-1386-z

• "pH-Responsive Mechanistic Switch Regulates the Formation of Dendritic and Fibrillar Nanostructures of a Functional Amyloid" P. Dogra, M. Bhattacharya & S. Mukhopadhyay*. J. Phys. Chem. B. 2017, 121, 412-419.

 https://doi.org/10.1021/acs.jpcb.6b11281

• "Stepwise unfolding of human β2‑microglobulin into a disordered amyloidogenic precursor at low pH" D. Narang, A. Singh & S. Mukhopadhyay*. Eur. Biophys. J. 2017, 46, 65–76. 

https://doi.org/10.1007/s00249-016-1138-x

2016

• "Water Rearrangements upon Disorder-to-Order Amyloid Transition" S. Arya, A. K. Singh, T. Khan, M. Bhattacharya, A. Datta,* & S. Mukhopadhyay*. J. Phys. Chem. Lett. 2016, 7, 4105−4110. 

 https://doi.org/10.1021/acs.jpclett.6b02088

      Click here to play the presentation!

• "Direct Observation of the Intrinsic Backbone Torsional Mobility of Disordered Proteins" N. Jain, & S. Mukhopadhyay*. Biophys. J. 2016, 111, 768-774.

https://doi.org/10.1016/j.bpj.2016.07.023

• "Characterization of Salt-Induced Oligomerization of Human β2-Microglobulin at Low pH" D. Narang, A. Singh, H.M. Swasthi & S. Mukhopadhyay*. J. Phys. Chem. B.  2016, 120, 32, 7815–7823. 

https://doi.org/10.1021/acs.jpcb.6b05619

• "Confined Water in Amyloid-competent Oligomers of the Prion Protein" V. Dalal, S. Arya & S. Mukhopadhyay*. ChemPhysChem. 2016, 17, 2804.

https://doi.org/10.1002/cphc.201600440

2015

• Book Review on "Madness and Memory: The Discovery of Prions - A New Biological Principle of Disease" by Stanley Prusiner. S. Mukhopadhyay. Curr. Sci. 2015, 109, 1737. https://www.currentscience.ac.in/Volumes/109/09/1737.pdf 

• "Studying Protein Misfolding and Aggregation using Fluorescence Spectroscopy" M. Bhattacharya & S.Mukhopadhyay*. Reviews in Fluorescence, 8. Springer. 2015  

https://doi.org/10.1007/978-3-319-24609-3_1

• "Conformational Switching and Nanoscale Assembly of Human Prion Protein into Polymorphic Amyloids via Structurally Labile Oligomers" V. Dalal, S. Arya, M. Bhattacharya & S. Mukhopadhyay*.  Biochemistry, 2015, 54, 7505-13. 

https://doi.org/10.1021/acs.biochem.5b01110

• "Appearance of Annular Ring-like Intermediates during Amyloid Fibril Formation from Human Serum Albumin" S. Arya, A. Kumari, V. Dalal, M. hattacharya & S. Mukhopadhyay*. Phys. Chem. Chem. Phys. 2015, 17, 22862-22871.

https://doi.org/10.1039/C5CP03782D

• "Applications of Fluorescence Anisotropy in Understanding Protein Conformational Disorder and Aggregation" N. Jain, S. Mukhopadhyay*. Applied Spectroscopy and the Science of Nanomaterials. Progress in Optical Science and Photonics Springer, Singapore, 2015, 2. 

https://doi.org/10.1007/978-981-287-242-5_3

2014

• "Ordered Water within the Collapsed Globules of an Amyloidogenic Intrinsically Disordered Protein" S. Arya & S. Mukhopadhyay*. J. Phys. Chem. B. 2014, 118, 9191–9198. 

https://doi.org/10.1021/jp504076a

• "Nanophotonics of Protein Amyloids" M. Bhattacharya & S. Mukhopadhyay*. Nanophotonics 2014, 3, 51-59.           https://doi.org/10.1515/nanoph-2013-0045

• "Nanoscale Optical Imaging of Amyloid Fibrils" V. Dalal, S. Arya & S. Mukhopadhyay*. 'Bionanoimaging: Protein Misfolding & Aggregation' (Elsevier 2013 Editors: Y. Lyubchenko & V. Uversky), 2014, 409-428.

https://doi.org/10.1016/B978-0-12-394431-3.00037-7

2013

• "Structural and Dynamical Insights into the Membrane-bound α-Synuclein" N. Jain, K. Bhasne, H.M. Swasthi & S. Mukhopadhyay*. PLoS ONE 2013, 8, 12, e83752. 

 https://doi.org/10.1371/journal.pone.0083752

• "Dynamics and Dimension of an Amyloidogenic Disordered State of Human β2-Microglobulin" D. Narang, P.K. Sharma & S. Mukhopadhyay*. Eur. Biophys. J. 2013, 42, 767-76. 

https://doi.org/10.1007/s00249-013-0923-z

• "Nanoscopic Amyloid Pores Formed via Stepwise Protein Assembly" M. Bhattacharya, N. Jain, P. Dogra, S. Samai & S. Mukhopadhyay*. J. Phys. Chem. Lett. 2013, 4, 480-85. 

http://dx.doi.org/10.1021/jz3019786

2012

• "Nanoscale Fluorescence Imaging of Single Amyloid Fibrils" V. Dalal, M. Bhattacharya, D. Narang, P.K. Sharma & S. Mukhopadhyay*. J. Phys. Chem. Lett. 2012, 3, 1783-1787. 

https://doi.org/10.1021/jz300687f

Click here for the video slide share! 

• "Structural and Dynmical Insights into the Molten-Globule form of Ovalbumin" M. Bhattacharya and S. Mukhopadhyay*. J. Phys. Chem. B. 2012, 116, 520-531. 

https://doi.org/10.1021/jp208416d

2011

• "Chain Collapse of an Amyloidogenic Intrinsically Disordered Protein" N. Jain, M. Bhattacharya and S. Mukhopadhyay*. Biophys. J. 2011, 101, 1720-1729. 

https://doi.org/10.1016/j.bpj.2011.08.024

• "Insights into the Mechanism of Aggregation and Fibril Formation from Bovine Serum Albumin" M. Bhattacharya, N. Jain and S. Mukhopadhyay*. J. Phys. Chem. B. 2011, 115, 4195–4205.

https://doi.org/10.1021/jp111528c

• "pH-induced Conformational Isomerization of Bovine Serum Albumin Studied by Extrinsic and Intrinsic Protein Fluorescence" M. Bhattacharya, N. Jain, K. Bhasne, V. Kumari, & S. Mukhopadhyay*. Journal of Fluorescence. 2011, 21, 1083-1090.  https://doi.org/10.1007/s10895-010-0781-3

• "Kinetics of Surfactant-induced Aggregation of Lysozyme Studied by Fluorescence Spectroscopy" N. Jain, M. Bhattacharya, & S. Mukhopadhyay*. Journal of Fluorescence 2011, 21, 615-625. 

https://doi.org/10.1007/s10895-010-0749-3

Publications from Samrat Mukhopadhyay's PhD and postdoctoral work

• "Conserved features of intermediates in amyloid assembly determine their benign or toxic states" R. Krishnan,† J.L. Goodman,† S. Mukhopadhyay,† C.D. Pacheco, E.A. Lemke, A.A. Deniz & S. Lindquist. Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 28, 11172-11177. (†These authors contributed equally to this work.) 

https://doi.org/10.1073/pnas.1209527109

• "Direct and Selective Elimination of Specific Prions and Amyloids by 4,5-Dianilinophthalimide and Analogs" H. Wang, M.L. Duennwald, B.E. Roberts, L.M. Rozeboom, Y.L. Zhang, A.D. Steele, R. Krishnan, L.J. Su, D. Griffin, S. Mukhopadhyay, E.J. Hennessy, P. Weigele, B.J. Blanchard, J. King, A.A. Deniz, S.L. Buchwald, V.M. Ingram, S. Lindquist, & J. Shorter. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 7159-7164.  https://doi.org/10.1073/pnas.0801934105

• "Single-Molecule Biophysics: At the Interface of Biology, Physics and Chemistry" A.A. Deniz, & S. Mukhopadhyay and E.A. Lemke. J. R. Soc. Interface 2008, 5, 15-45.  https://doi.org/10.1098/rsif.2007.1021

• "A natively unfolded yeast prion monomer adopts an ensemble of collapsed and rapidly fluctuating structures" S. Mukhopadhyay, R. Krishnan, E. A. Lemke, S. Lindquist & A.A. Deniz. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 2649-2654.  https://doi.org/10.1073/pnas.0611503104 

• "Biomolecular structure and dynamics using fluorescence from single diffusing molecules" S. Mukhopadhyay & A.A. Deniz. J. Fluorescence 2007, 17, 775-783. https://doi.org/10.1007/s10895-007-0214-0

• "Characterization of amyloid fibril formation by mapping residue-specific fluorescence dynamics" S. Mukhopadhyay, P. Nayak, J. B. Udgaonkar and G. Krishnamoorthy. J. Mol. Biol. 2006, 358, 935-942. 

https://doi.org/10.1016/j.jmb.2006.02.006

• "Advances in Molecular Hydrogels" S. Bhattacharya, U. Maitra, S. Mukhopadhyay, & A. Srivastava in "Molecular Gels" 2006. P. Terech, R.G. Weiss (Eds.) Kluwer Academic Publishers, The Netherlands. https://link.springer.com/chapter/10.1007/1-4020-3689-2_18

• "Structure and Dynamics of a Molecular Hydrogel" S. Mukhopadhyay, Uday Maitra, Ira, G. Krishnamoorthy, J. Scmidt & Y. Talmon.  J. Am. Chem. Soc. 2004, 126, 15905-15914.  https://doi.org/10.1021/ja046788t

• "Facile Synthesis, Aggregation Behavior, and Cholesterol Solubilization of Avicholic Acid" S. Mukhopadhyay & U. Maitra. Organic Lett. 2004, 6, 31-34.  https://doi.org/10.1021/ol036073f

• "Chemistry and Biology of Bile Acids: A Review" S. Mukhopadhyay  & U. Maitra.  Curr. Sci. 2004, 87, 1666-1683.  http://www.jstor.org/stable/24109764

• "Dynamics of Bound Dyes in a Non-polymeric Aqueous Gel Derived from a Tripodal Bile Salt" S. Mukhopadhyay, Ira, G. Krishnamoorthy & U. Maitra. J. Phys. Chem. B. 2003, 107, 2189-2192. 

https://doi.org/10.1021/jp027079+

• "Hydrogel Route to Nanotubes of Metal Oxides and Sulfates" G. Gundiah, S. Mukhopadhyay, U.G. Tumkurkar, A. Govindaraj, U. Maitra & C.N.R. Rao. J. Mater. Chem. 2003, 13, 2118-2122.

https://doi.org/10.1039/B304007K

• "Hydrophobic Pockets in a Non-polymeric Aqueous Gel: Observation of such a Gelation Process by Color Change" U. Maitra, S. Mukhopadhyay, A. Sarkar, P. Rao & S.S. Indi. Angew. Chem. Int. Ed. 2001, 40, 2281-2283. 

https://doi.org/10.1002/1521-3773(20010618)40:12%3C2281::AID-ANIE2281%3E3.0.CO;2-L