Publications from Ph. D. and Postdoctoral Studies
1. “Nonideality in the Composition Dependence of Viscosity in Binary Mixtures”, Goundla Srinivas, Arnab Mukherjee, and Biman Bagchi, J. Chem. Phys. 114, 6220 (2001).
2. “Reentrant Behavior of Relaxation Time with Viscosity at Varying Composition in Binary ”, Arnab Mukherjee, Goundla Srinivas, and Biman Bagchi, Phys. Rev. Lett. 86, 5926 (2001).
3. “Nonideality in Binary Mixture: Correlation between Excess volume, Excess Viscosity and Diffusion Coefficients”, Arnab Mukherjee and Biman Bagchi, J. Phys Chem. B 105, 9581 (2001).
4. “Ionic Self-Diffusion in Concentrated Electrolyte Aqueous Solutions”, J.-F. Dufreche, O. Bernard and P. Turq, Arnab Mukherjee and Biman Bagchi, Phys. Rev. Lett. 88, 95902 (2002).
5. “Pressure and Temperature Dependence of Viscosity and Diffusion Coefficients in Glassy Binary Mixture”, Arnab Mukherjee, Sarika Bhattacharyya, and Biman Bagchi, J. Chem. Phys. 116, 4577 (2002).
6. “Correlated orientational and translational motions in supercooled liquids”, Sarika Bhattacharyya, Arnab Mukherjee, and Biman Bagchi, J. Chem. Phys. 117, 2741 (2002).
7. “Relaxation in binary mixtures: Non-ideality, heterogeneity and re-entrance”, Arnab Mukherjee, Goundla Srinivas, Sarika Bhattacharyya, and Biman Bagchi, Proc. Ind. Acad. Sci. (Chem. Sci.), 113, 393 (2001).
8. “Correlation between rate of folding, topology and energy landscape of a model protein HP-36”, Arnab Mukherjee and Biman Bagchi, J. Chem. Phys. 118, 4733 (2003).
9. “Origin of the sub-diffusivity behavior and crossover from sub-diffusive to super-diffusive dynamics near biological surface”, Arnab Mukherjee and Biman Bagchi, Phys. Chem. Comm. 6, 28 (2003).
10. “Fluorescence resonance energy transfer dynamics during protein folding: Evidence of multistage folding kinetics”, Arnab Mukherjee and Biman Bagchi, Curr. Sci., 85, 68 (2003).
11. “Probing folding free energy landscape of small proteins through minimalistic models: Folding of HP-36 and beta-amyloid”, Arnab Mukherjee and Biman Bagchi, Proc. Indian Acad. Sci. (Chem. Sci.), 115, 620 (2003).
12. “Contact pair dynamics during folding of two small proteins: Chicken villin head piece and the Alzheimer protein beta-amyloid”, Arnab Mukherjee and Biman Bagchi, J. Chem. Phys., 120, 1602 (2004).
13. “Rotational friction on globular proteins combining dielectric and hydrodynamic effects” Arnab Mukherjee and Biman Bagchi, Chem. Phys. Lett., 404, 409 (2005).
14. “Orientation-dependent potential of mean force for protein folding” Arnab Mukherjee, Prabhakar Bhimalapuram, and Biman Bagchi, J. Chem. Phys. 123, 014901 (2005).
15. “Fröster energy transfer in thin films of conjugated polymers and in solution, A. Mukherjee and B. Bagchi, J. Chin. Chem. Soc.” 53, 153 (2006).
16. “Anomalous orientation dependent effective pair interaction among histidine and other amino acid residues in metalloproteins: Breakdown of the hydropathy scale index” Arnab Mukherjee and Biman Bagchi, Biochemistry, 45, 5129 (2006).
17. "Solvent Frictional Forces in the rotational diffusion of proteins in water", Arnab Mukherjee and Biman Bagchi, Curr. Sci. 91, 1208 (2006).
18. “On the molecular mechanism of drug intercalation into DNA: A computer simulation study of the intercalation pathway, free energy and DNA structural changes”, Arnab Mukherjee*, Richard Lavery, Biman Bagchi, and James T. Hynes, J. Am. Chem. Soc. 130, 9747 (2008).
19. (invited Book Chapter): Simulation Study of Free Energy and Molecular Mechanism of Intercalation of the Anti-Cancer Drug Daunomycin into DNA, A. Mukherjee, R. Lavery, B. Bagchi, and James T. Hynes, in "Energy Transfer Dynamics in Biomaterial Systems", Eds. I. Burghardt, V. May, D. A. Micha, and E. R. Bittner, Springer Series in Chemical Physics, Vol. 93, 2009).
Publications after joining IISER Pune
20. “Entropy Balance in the Intercalation Process of an Anti-Cancer Drug Daunomycin” Arnab Mukherjee*, J. Phys. Chem. Lett. 2, 3021 (2011).
21. “Comparative Study of flavins’ binding with human serum albumin: a fluorometric, thermodynamic, and molecular dynamics approach“, Abhigyan Sengupta, D. S. Wilbee, Arnab Mukherjee*, Partha Hazra* Chem. Phys. Chem. 13, 2142 (2012).
22. “A multistep intercalation mechanism: molecular dynamics and free energy studies of the formation of a DNA-daunomycin complex”, M. Wilhelm, A. Mukherjee*, B. Bouvier, K. Zakrzewska, J.T. Hynes*, R. Lavery* J. Am. Chem. Soc. 134, 8588 (2012). (Received JACS spotlight: "A Computational Approach to Interpreting Intercalation" by E. J. Gordon. Link http://pubs.acs.org/doi/full/10.1021/ja305429h)
23. “Molecular Mechanism of Direct Proflavine-DNA Intercalation: Evidence for Drug-Induced Minimum Base-Stacking Penalty Pathway”, Wilbee D. S. and A. Mukherjee* J. Phys. Chem. B 116, 12208 (2012).
24. “Modulation of Excimer Formation of 9-(dicyano-vinyl)julolidine by the Macrocyclic Hosts”, Krishna Gavvala, Wilbee D Sasikala, Abhigyan Sengupta, Siddhi A Dalvi, Arnab Mukherjee, and Partha Hazra*, Phys. Chem. Chem. Phys., DOI:10.1039/C2CP43282J
25. “Intercalation and De-intercalation Pathway of Proflavine through the Minor and Major Grooves of DNA: Role of Water and Entropy”, Wilbee D Sasikala and Arnab Mukherjee*, Phys. Chem. Chem. Phys., DOI:10.1039/C3CP50501D
26. (invited book chapter) “ Drug-DNA Intercalation: From Discovery to the Molecular Mechanism ”, Arnab Mukherjee* and Wilbee D. Sasikala in Dynamics of Proteins and Nucleic Acids, Vol. 92, Series: Advances in Protein Chemistry and Structure Biology, Ed. Tatyana Karabencheva, UK: Academic Press, 2013, pp. 1-62.
27. “Sequence Dependent Free Energy Profiles of Localized B- to A-Form Transition of DNA in Water”, Mandar Kulkarni and Arnab Mukherjee* J. Chem. Phys. 139, 155102 (2013)
28. “Urea Induced Unfolding Dynamics of Flavin Adenine Dinucleotide (FAD): Spectroscopic and Molecular Dynamics Simulation Studies from Femto-Second to Nanosecond Regime”, Abhigyan Sengupta, Reman K. Singh, Krishna Gavvala, Raj Kumar Koninti, Arnab Mukherjee*, and Partha Hazra J. Phys. Chem. ,118, 1881 (2014)
29. “Single Water Entropy: Hydrophobic Crossover and Application to Drug Binding”, Wilbee D. Sasikala and Arnab Mukherjee* J. Phys. Chem. B B 118, 10553 (2014).
30. “Hopping Mediated Anion Transport through a Mannitol-Based Rosette Ion Channel”, Tanmoy Saha, Sathish Dasari, Debanjan Tewari, Annamalai Prathap, Kana M. Sureshan, Amal K. Bera*, Arnab Mukherjee*, and Pinaki Talukdar* J. Am. Chem. Soc. 136, 14128 (2014).
31. “Theoretical Study of Structural Changes in DNA under High External Hydrostatic Pressure”, P. Sudheer Kumar, Arnab Mukherjee*, and Anirban Hazra* J. Phys. Chem. B 119, 3348 (2015).
32. “Distribution of Residence time of water around DNA Base Pairs: Governing Factors and the Origin of Heterogeneity”, Debasis Saha, Shreyas Supekar, and Arnab Mukherjee* J. Phys. Chem. B 119, 11371 (2015). Biman Bagchi Festschrift
33. “Molecular Origin of DNA Kinking by Transcription Factors”, Reman K. Singh, Wilbee D. Sasikala, and Arnab Mukherjee*, J. Phys. Chem. B 119, 11590 (2015).
34. “Computational Approach to Explore B/A Junction Free Energy in DNA”, Mandar Kulkarni and Arnab Mukherjee*, Chem. Phys. Chem. 17, 147 (2016). (DOI: 10.1002/cphc.201500690).
35. “Structure and Dynamics of Proflavine Association around DNA", Wilbee D. Sasikala and Arnab Mukherjee* , Phys. Chem. Chem. Phys. 18, 10383 (2016).
36. “Ionic Liquid Prolongs DNA Translocation through Graphene Nanopore", Mandar Kulkarni* and Arnab Mukherjee*, RSC Advances, 6, 46019 (2016).
37. "An Ultrahydrophobic Fluorous Metal-organic Framework Derived Recyclable Composite As A Promising Platform to Tackle Marine Oil Spills", Soumya Mukherjee, Ankit M. Kansara, Debasis Saha, Rajesh Gonnade, Dinesh Mullangi, Biplab Manna, Aamod V. Desai, Arnab Mukherjee, and Sujit K. Ghosh, Chemistry - A European Journal, 22, 10937 (2016).
38. "Impact of Ions on Invidial Water Entropy" Debasis Saha and Arnab Mukherjee*, J. Phys. Chem. B 120, 7471 (2016).
39. "Ionic Liquid Induced G-quadruplex Formation and Stablization: Spectroscopic and Simulation Studies" Sagar Satpati, Mandar Kulkarni, Arnab Mukherjee*, Partha Hazra*, Phys. Chem. Chem. Phys., 18, 29740 (2016).
40. "One-pot Synthesis and Transmembrane Chloride Transport Properties of C3-Symmetric Benzoxazine Urea" Arundhati Roy, Debasis Saha, Arnab Mukherjee, Pinaki Talukdar, Org. Lett., 18, 5864 (2016).
41. "Water modulates the ultraslow dynamics of hydrated ionic liquids near CG rich DNA: consequence to DNA stability " Debasis Saha*, Mandar Kulkarni, and Arnab Mukherjee*, Phys. Chem. Chem. Phys. 18, 32107 (2016).
42. "pH-Gated Chloride Transport by Triazine-based Tripodal Semicage", Arundhati Roy, Debasis Saha, Prashant Sahebrao Mandal, Arnab Mukherjee, and Pinaki Talukdar*, Chemistry - A European Journal, 23, 1241 (2017).
43. "Chloride Transport through Supramolecular Barrel-Rosette Ion Channels: Lipophilic Control and Apoptosis-Inducing Activity", Tanmoy Saha, Amitosh Gautam, Arnab Mukherjee, Mayurika Lahiri, Pinaki Talukdar*, J. Am. Chem. Soc., 138, 16443 (2017).
44. "Mechanism of Unfolding of Human Prion Protein", Reman K. Singh, Neharika G. Chamachi, Suman Chakrabarty*, and Arnab Mukherjee*, J. Phys. Chem. B, 121, 550 (2017).
45. "Broadband Terahertz Dielectric Spectroscopy of Alcohols " Sohini Sarkar, Debasis Saha, Sneha Banerjee, Arnab Mukherjee, and Pankaj Mondal*, Chem. Phys. Lett., 678, 65 (2017).
46. "Connecting Diffusion and Entropy of Bulk Water at the Single Particle Level", Debasis Saha and Arnab Mukherjee*, J. Chem. Sci. 129, 825 (2017). [Special Issue dedicated to the Memory of Prof. Charusita Chakraborty]
47. "Understanding B-DNA to A-DNA transition in the right-handed DNA helix: Perspective from a local to global transition ", Mandar Kulkarni and Arnab Mukherjee*, Prog. Biophys. Mol. Biol. 128, 63 (2017).
48. "Self-assembly of small-molecule fumaramides allows transmembrane chloride channel formation " Arundhati Roy, Amitosh Gautam, Javid Ahmad Malla, Sohini Sarkar, Arnab Mukherjee and Pinaki Talukdar, Chem. Comm. (doi: 10.1039/C7CC08693H)
49. "Effect of Water and Ionic Liquids on Biomolecules" Debasis Saha and Arnab Mukherjee ;*, Biophys. Rev. (in press).
50. "Controlling an Anticancer Drug Mediated G-quadruplex Formation and Stabilization by a Molecular Container" Sagar Satpathi, Reman K. Singh, Arnab Mukherjee*, and Partha Hazra*, Phys. Chem. Chem. Phys. (in press).
51. "Design of Bivalent Nucleic Acid Ligands for Recognition of RNA2 Repeated Expansion Associated with Huntington’s Disease" Shivaji A. Thadke, J. Dinithi R. Perera, V. M. Hridya, Kirti Bhatt, Ashif Y. Shaikh, Wei-Che Hsieh, Mengshen Chen, Chakicherla Gayathri, Roberto R. Gil, Gordon S. Rule, Arnab Mukherjee, Charles A. Thornton, and Danith H. Ly*, Biochemistry, 57, 2094 (2018).
52. "Probing the Viscosity Dependence of Rate: Internal Friction or the Lack of Friction?" V. M. Hridya and Arnab Mukherjee, J. Phys. Chem. B 122, 9081 (2018)
53. "Shape-Selective Bifacial Recognition of Double Helical B-DNA" Shivaji A. Thadke, J. Dinithi R. Perera, V. M. Hridya, Roberto R. Gil, Arnab Mukherjee, and Danith H. Ly*, Commun Chem 1, 79 (2018).
54. "Dynamical Recrossing in the Intercalation Process of the Anticancer Agent Proflavine into DNA" V. M. Hridya, James T. Hynes*, Arnab Mukherjee*, J. Phys. Chem. B 123, 51, 10904-10914 (2019).
55. "Arresting an Unusual Amide Tautomer Using Divalent Cations "J. Phys. Chem. B 123, 40, 8419-8424
Somnath M. Kashid Reman K. Singh Hyojin Kwon Young Sam Kim* Arnab Mukherjee* Sayan Bagchi*
J. Phys. Chem. B 123, 40, 8419-8424 (2019).
56. "Apoptosis-inducing activity of a fluorescent barrel-rosette M+/Cl− channel " Javid Ahmad Malla, Rintu M. Umesh, Amal Vijay, Arnab Mukherjee, Mayurika Lahiri, Pinaki Talukdar Chem. Sci. 11, 2420-2428 (2020).
57. "Arresting an Unusual Amide Tautomer Using Divalent Cations’”, 8424, Somnath M. Kashid Reman K. Singh Hyojin Kwon Young Sam Kim*, Arnab Mukherjee*, and Sayan Bagchi*, J. Phys. Chem. B, 125, 1, 479–483 (2021).
58. "Molecular Mechanism of Intercalation of SOX-4 Protein into DNA Inducing Bends and Kinks" Reman Kumar Singh and Arnab Mukherjee*, J. Phys. Chem. B, 125, 3752-3762 (2021) .
59. "Atomistic de-novo inhibitor generation guided drug repurposing for SARS-CoV-2 spike protein with free energy validation by well-tempered metadynamics" Rituparno Chowdhury†, Venkata Sai Sreyas Adury, Amal Vijay, Reman K. Singh, and Arnab Mukherjee* ,Chemistry, an Asian journal, 16, 1634-1642 (2021).
60. “Accurate Prediction of B-form/A-form DNA Conformation Propensity from Primary Sequence: A Machine Learning and Free energy Handshake”, Abhijit Gupta, Mandar Kulkarni, and Arnab Mukherjee* ,Patterns, 2, 100329 (2021).