Publications

27. Gendreizig, D.; Kalarikkal, A.; Holtbrügge, S. L.; Mukherjee, S.; Galazzo, L.; Kucher, S.; Rosspeintner, A.; Schäfer, L. V.; Bordignon, E. A combined approach to extract rotational dynamics of globular proteins undergoing liquid-liquid phase separation. J. Phys. Chem. B 2025, 129, 1185–1196. DOI: 10.1021/acs.jpcb.4c06259

26. Liu, Y.; Karmakar, R.; Steinchen, W.; Mukherjee, S.; Bange, G.; Schäfer, L. V.; Thanbichler, M. Membrane binding properties of the cytoskeletal protein bactofilin eLife, 2024, 13, RP100749 (reviewed preprint). DOI: 10.7554/eLife.100749.1

25. Mukherjee, S.;  Schäfer, L. V. Heterogeneous Slowdown of Dynamics in the Condensate of an Intrinsically Disordered Protein. J. Phys. Chem. Lett. 2024, 15, 11244−11251. DOI: 10.1021/acs.jpclett.4c02142

24. Mukherjee, S.; Ramos, S.; Pezzotti, S.; Kalarikkal, A.; Prass, T. M.; Galazzo, L.; Gendreizig, D.; Barbosa, N.; Bordignon, E.; Havenith, M.; Schäfer, L. V. Entropy Tug-of-War Determines Solvent Effects in the Liquid–Liquid Phase Separation of a Globular Protein. J. Phys. Chem. Lett. 2024, 15, 4047−4055. DOI: 10.1021/acs.jpclett.3c03421

23. Mondal, S.#; Mukherjee, S.#; Bagchi, B. Melting and Bubble Formation in a Double-Stranded DNA: Microscopic Aspects of Early Base Pair Opening Events and the Role of Water. J. Phys. Chem. B 2024, 128, 2076–2086. DOI: 10.1021/acs.jpcb.3c06519

(#Equal contribution; Gregory A. Voth Festschrift Virtual Special Issue)

22. Mukherjee, S.; Schäfer, L. V. Thermodynamic Forces from Protein and Water Govern Condensate Formation of an Intrinsically Disordered Protein Domain. Nat. Commun. 2023, 14, 5892. DOI: 10.1038/s41467-023-41586-y

(Featured on RUB website; Covered by multiple news outlets)

21. Mukherjee, S.; Mondal, S.; Bagchi, B. Bimodal 1/f Noise and Anticorrelation between DNA-Water and DNA-Ion Energy Fluctuations. J. Phys. Chem. B 2023, 127, 1965–1975. DOI: 10.1021/acs.jpcb.2c08402 

(Xiaoliang Sunney Xie Festschrift Virtual Special Issue)

20. Mukherjee, S.*; Schäfer, L. V.* Spatially Resolved Hydration Thermodynamics in Biomolecular Systems. J. Phys. Chem. B 2022, 126, 3619–3631. DOI: 10.1021/acs.jpcb.2c01088 

(*Corresponding author; Perspective article; Journal front cover)

19. Venkatesha, A.; Gomes, R.; Nair, A. S.; Mukherjee, S.; Bagchi, B.; Bhattacharyya, A. J. A Redox-Active 2-D Covalent Organic Framework as a Cathode in an Aqueous Mixed-Ion Electrolyte Zn-Ion Battery: Experimental and Theoretical Investigations. ACS Sustainable Chem. Eng. 2022, 10, 6205–6216. DOI: 10.1021/acssuschemeng.1c08678

18. Mukherjee, S.; Mondal, S.; Acharya, S.; Bagchi, B. Tug-of-War between Internal and External Frictions and Viscosity Dependence of Rate in Biological Reactions. Phys. Rev. Lett. 2022, 128, 108101. DOI: 10.1103/PhysRevLett.128.108101 

(Featured on IISc website; Covered by The Times of India)

17. Mukherjee, S.; Acharya, S.; Mondal, S.; Banerjee, P.; Bagchi, B. Structural Stability of Insulin Oligomers and Protein Association−Dissociation Processes: Free Energy Landscape and Universal Role of Water. J. Phys. Chem. B 2021, 125, 11793−11811. DOI: 10.1021/acs.jpcb.1c05811 

(Feature Article: 125 Years of The Journal of Physical Chemistry Virtual Special Issue)

16. Acharya, S.; Mondal, S.; Mukherjee, S.; Bagchi, B. Rate of Insulin Dimer Dissociation: Interplay between Memory Effects and Higher Dimensionality. J. Phys. Chem. B 2021, 125, 9678−9691. DOI: 10.1021/acs.jpcb.1c03779 

(Yoshitaka Tanimura Festschrift Virtual Special Issue)

15. Mondal, S.; Mukherjee, S.; Acharya, S.; Bagchi, B. Unfolding of Dynamical Events in the Early Stage of Insulin Dimer Dissociation. J. Phys. Chem. B 2021, 125, 7958−7966. DOI: 10.1021/acs.jpcb.1c03104 

(Dave Thirumalai Festschrift Virtual Special Issue)

14. Mukherjee, S.; Mondal, S.; Bagchi, B. Stochastic Formulation of Multiwave Pandemic: Decomposition of Growth into Inherent Susceptibility and External Infectivity Distributions. J. Chem. Sci. 2021, 133, 1-18. DOI: 10.1007/s12039-021-01981-8

13. Mukherjee, S.; Bagchi, B. Theoretical analyses of pressure-induced glass transition in water: Signatures of surprising diffusion-entropy scaling across the transition. Mol. Phys. 2021, 119, e1930222. DOI: 10.1080/00268976.2021.1930222 

(Klein Special Issue)

12. Mondal, S.; Mukherjee, S.; Bagchi, B. Mathematical Modeling and Cellular Automata Simulation of Infectious Disease Dynamics: Applications to the Understanding of Herd Immunity. J. Chem. Phys. 2020, 153, 114119. DOI: 10.1063/5.0018807

11. Mukherjee, S.; Mondal, S.; Bagchi, B. Dynamical Theory and Cellular Automata Simulations of Pandemic Spread: Understanding Different Temporal Patterns of Infections. arXiv, 2020. arXiv:2004.14787

10. Mukherjee, S.; Bagchi, B. Entropic Origin of the Attenuated Width of the Ice-Water Interface. J. Phys. Chem. C 2020, 124, 7334−7340. DOI: 10.1021/acs.jpcc.0c02030

9. Mukherjee, S.; Deshmukh, A. A.; Mondal, S.; Gopal, B.; Bagchi, B. Destabilization of Insulin Hexamer in Water-Ethanol Binary Mixture. J. Phys. Chem. B 2019, 123, 10365−10375. DOI: 10.1021/acs.jpcb.9b07689

8. Mukherjee, S.; Mondal, S.; Bagchi, B. Mechanism of Solvent Control of Protein Dynamics. Phys. Rev. Lett. 2019, 122, 058101. DOI: 10.1103/PhysRevLett.122.058101 

(Featured on IISc website)

7. Mukherjee, S.; Mondal, S.; Acharya, S.; Bagchi, B. DNA Solvation Dynamics. J. Phys. Chem. B 2018, 122, 11743−11761. DOI: 10.1021/acs.jpcb.8b08140 

(William A. Eaton Festschrift Special Issue)

6. Mondal, S.; Samajdar, R. N.; Mukherjee, S.; Bhattacharyya, A. J.; Bagchi, B. Unique Features of Metformin: A Combined Experimental, Theoretical, and Simulation Study of Its Structure, Dynamics, and Interaction Energetics with DNA Grooves. J. Phys. Chem. B 2018, 122, 2227−2242. DOI: 10.1021/acs.jpcb.7b11928 

5. Mukherjee, S.; Mondal, S.; Deshmukh, A. A.; Gopal, B.; Bagchi, B. What Gives an Insulin Hexamer Its Unique Shape and Stability? Role of Ten Confined Water Molecules. J. Phys. Chem. B 2018, 122, 1631–1637. DOI: 10.1021/acs.jpcb.8b00453 

(C&EN News coverage; Featured on IISc website)

4. Mondal, S.; Mukherjee, S.; Bagchi, B. Origin of Diverse Time Scales in the Protein Hydration Layer Solvation Dynamics: A Simulation Study. J. Chem. Phys. 2017, 147, 154901. DOI: 10.1063/1.4995420

3. Mondal, S.; Mukherjee, S.; Bagchi, B. Protein Hydration Dynamics: Much Ado about Nothing? J. Phys. Chem. Lett. 2017, 8, 4878–4882. DOI: 10.1021/acs.jpclett.7b02324 

(Viewpoint article)

2. Mukherjee, S.; Mondal, S.; Bagchi, B. Distinguishing Dynamical Features of Water inside Protein Hydration Layer: Distribution Reveals what is Hidden Behind the Average. J. Chem. Phys. 2017, 147, 024901. DOI: 10.1063/1.4990693

1. Mondal, S.; Mukherjee, S.; Bagchi, B. Decomposition of Total Solvation Energy into Core, Side-chains and Water Contributions: Role of Cross Correlations and Protein Conformational Fluctuations in Dynamics of Hydration Layer. Chem. Phys. Lett. 2017, 683, 29-37. DOI: 10.1016/j.cplett.2017.05.001 

(Ahmed Zewail Commemoration Issue)