{"id":29,"date":"2023-11-02T11:40:17","date_gmt":"2023-11-02T11:40:17","guid":{"rendered":"https:\/\/www-cxcp1.tifrh.res.in\/~jmondal\/?page_id=29"},"modified":"2026-02-17T06:33:29","modified_gmt":"2026-02-17T06:33:29","slug":"publications","status":"publish","type":"page","link":"https:\/\/www.tifrh.res.in\/~jmondal\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"

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For Latest list of Publications visit Google Scholar<\/a><\/span><\/h3>\n

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  1. M. Sahil and J. Mondal* \u201cMachine Learning and Computer Simulation Disentangle the Fuzzy Inhibitor Binding by Hsp90\u201d<\/b><\/i>,J.Chem. Theory Comput. in press<\/a><\/li>\n

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  2. M. Sahil and J. Mondal* \u201cMultisubstrate Allostery with a Single Helical Switch in Cytochrome P450cam\u201d<\/b><\/i>,J. Phys. Chem. Lett. 17,314-324 (2026)<\/a><\/li>\n

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  3. P. Bera and J. Mondal* \u201cHow good is generative diffusion model for enhanced sampling of protein conformations across scales and in all-atom resolution\u201d<\/b><\/i>, J. Chem. Phys.163,114110 (2025)<\/a><\/li>\n

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  4. A. Krishna, N. Puthumadathil, D. K. Sarkar, B. B. Majumdar, D. Vikraman, J.Mondal and K. R. Mahendran \u201cControlling Nanopore Dynamics via Loop Stapling and Unstapling for Tunable Substrate Transport\u201d<\/b><\/i>, ACS Nano DOI: 10.1021\/acsnano.5c16470 (2025)<\/a><\/li>\n

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  5. M. Singh, A. Chatterjee, A. Nayak, P. Naskar, G. Kaur, J. Mondal, S. Dutta, K. Chattopadhyay \u201cCradle loop regulates -barrel pore-formation mechanism of Vibrio choleraecytolysin\u201d<\/b><\/i>,Structure DOI: 10.1016\/j.str.2025.10.013 (2025)<\/a><\/li>\n

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  6. A. K. Manna, S. Kundu, K. Jindal, D. Maity, S. Panda, P. Yadav, G. Mishra, S. Chatterjee, N. Sikdar, J. Mondal, S. Ghosh, T. N Narayanan, R. Haldar \u201cPhotochargeable Nanopores in Gas Permselective Membrane\u201d <\/b><\/i>,Angew. Chem. Int. Ed 64,e202513377 (2025)<\/a><\/li>\n

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  7. S. Sinha, A. Biswas, M. Sahil, J. Mondal, K. Mandal \u201cA Cryptic Loop that Modulates Protein-Protein Interaction: Implications in PfAMA1-PfRON2 Late-stage Binding Event\u201d<\/b><\/i>,ChemBioChem 26,e202400894 (2025)<\/a><\/li>\n

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  8. A. Mondal, S. N. Save, S. Sarkar, A. Kuttanamkuzhi, S. Bawari, T. Vijayakanth, U. Shivpuje, M. Lahiri, J. Mondal, S. Sharma, P. Talukdar \u201cPyrrole-Linked BenzimidazolylHydrazone Self-Assembly Forms HCl Channels and Induces Apoptosis in Cancer Cells\u201d<\/b><\/i>,Angew. Chem. Int. Ed 64,e202505019 (2025)<\/a><\/li>\n

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  9. A. Wasim, L. Schaefer and J. Mondal* \u201cEmploying Artificial Neural Networks for Optimal Storage and Facile Sharing of Molecular Dynamics Simulation Trajectories\u201d<\/b><\/i>,J. Chem. Information Model. 65,9022 (2025)<\/a><\/li>\n

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  10. S. Adhikari and J. Mondal* \u201cElucidating Protein Dynamics through the Optimal Annealing of Variational Autoencoders\u201d<\/b><\/i>, J. Chem. Theory Comput. 21,6367 (2025)<\/a><\/li>\n

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  11. P. Bera and J. Mondal* \u201cAccurate Prediction of the Kinetic Sequence of Physicochemical States Using Generative Artificial Intelligence<\/b><\/i>\u201d, Chemical Science (2025)<\/a> <\/li>\n

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  12. S. Ghosh, S. Roy, N. Baid, U. K. Das, S. Rakshit, P. Sanghavi, D. Hajra, S. Das, S. Menon, M. Sahil, S. Shaw, R. S Rajmani, H. Adicherla, S. Kaledhonkar, J. Mondal, D. Chakravortty, R. Mallik, A. Banerjee \u201cHost AAA-ATPase VCP\/p97 lyses ubiquitinated intracellular bacteria as an innate antimicrobial defence<\/b><\/i>\u201d, Nat Microbiol (2025)<\/a> <\/li>\n

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  13. U. Pramanik, A. Das, E. Brown, H. L Struckman, H. Wang, S. Stealey, M. L Sprunger, A. Wasim, J. Fascetti, J. Mondal, J. R. Silva, S. P. Zustiak, M. E Jackrel, J. S. Rudra \u201cHistidine-rich enantiomeric peptide coacervates enhance antigen sequestration and presentation to T cells<\/b><\/i>\u201d, Chemical Science (2025) DOI: 10.1039\/D5SC01163A<\/a> <\/li>\n

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  14. S. Sinha, A. Biswas, M. Sahil, J. Mondal*, K. Mandal* \u201cA Cryptic Loop that Modulates Protein-Protein Interaction: Implications in PfAMA1-PfRON2 Late-stage Binding Event<\/b><\/i>\u201d, ChemBioChem 2025, e202400894.<\/a> <\/li>\n

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  15. A. Mondal, G. K. Barik, S. Sarkar, U. Shivpuje, J. Mondal, M. K. Santra, P. Talukdar \u201cApoptosis-Inducing Activity of a 2-Hydroxyphenyl Benzamide-Based Self-Assembled Anion Channel<\/b><\/i>\u201d, Chem. Eur. J. 2025, 31, e202403252<\/a> <\/li>\n

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  16. Panda, S., Maity, T., Sarkar, A. K. Manna, J.Mondal and R. Halder \u201cDiffusion-programmed catalysis in nanoporous material<\/b><\/i>\u201d, Nat Commun 16, 1231 (2025)<\/a> <\/li>\n

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  17. M. Ahmed, S. Sarkar, R. Bhogade, A. Mondal, D. Mondal, J. Mondal and P. Talukdar\u201cDynamic regulation of ion transport through a bis(1,3-propanediol)-based channel via allosteric azobenzene photoswitching<\/b><\/i>\u201d, Nanoscale, DOI: 10.1039\/D4NR01711K (2025)<\/a> <\/li>\n

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  18. P. Bera, A. Wasim, S. Bakshi* and J. Mondal*\u201cProtein translation can fluidize bacterial cytoplasm <\/b><\/i>\u201d, PNAS Nexus, 3, pgae532 (2024)<\/a> <\/li>\n

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  19. T. Maity, S. Sarkar, S. Kundu, S. Panda, A. Sarkar, R. Hammad, K. Mandal, S. Ghosh*, J. Mondal* and R. Haldar*\u201cSteering Diffusion Selectivity of Chemical Isomers within alligned nano channels of metal-organic framework thin film <\/b><\/i>\u201d, Nature Communication, 15, 9636 (2024)<\/a> <\/li>\n

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  20. S. Sarkar and J. Mondal*\u201cHow Salt and Temperature Drive Reentrant Condensation of A\u03b240 <\/b><\/i>\u201d, Biochemistry, 62, 3030 (2024)<\/a> <\/li>\n

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  21. S. Sarkar, R. Sadhukhan, N. Mohandas, A. Ravi, T. N. Narayanan* and J. Mondal*\u201cAdenosine Triphosphate Inhibits Cold-Responsive Aggregation <\/b><\/i>\u201d, Langmuir, 40, 21587 (2024)<\/a> <\/li>\n

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  22. S. Menon, S. Adhikari and J. Mondal* \u201c An Integrated Machine Learning Approach Delineates Entropy-mediated Conformational Modulation of -synuclein by Small Molecule <\/b><\/i>\u201d, eLife 13,97709 (2024)<\/a> <\/li>\n

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  23. S. Sarkar, A. Guha, T. N. Narayanan*, J. Mondal* \u201c Osmolyte-Induced Modulation of Hofmeister Series <\/b><\/i>\u201d, J. Phys. Chem. B 128,9436 (2024)<\/a> <\/li>\n

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  24. S. Sarkar, S. Gupta, C. Mahato, D. Das and J. Mondal* \u201c Elucidating ATPs Role as Solubilizer of Biomolecular Aggregate<\/b><\/i>\u201d, eLife 13,RP99150 (2024)<\/a> <\/li>\n

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  25. P. Bera and J. Mondal* \u201c Machine learning unravels inherent structural patterns in Escherichia coli Hi-C matrices and predicts chromosome dynamics <\/b><\/i>\u201d, Nucleic Acids Research ,gkae749 (2024)<\/a> <\/li>\n

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  26. S. Menon and J. Mondal* \u201c Simulating the anti-aggregative effect of fasudil in early dimerisation process of alpha-synuclein <\/b><\/i>\u201d, Biophys. Chem. 314,107319 (2024)<\/a> <\/li>\n

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  27. A. Mondal, D. Mondal, S. Sarkar, U. Shivpuje, J. Mondal, P. Talukdar* \u201c Self-Assembled Hydrazide-Based Nanochannels: Efficient Water Translocation and Salt Rejection <\/b><\/i>\u201d, Angew Chem. Int. Ed. 63,e202415510 (2024)<\/a> <\/li>\n

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  28. R. Mehrani, J. Mondal, D. Ghazanfari, D. J. Goetz, K. D. McCall, S. Bergmeier, S. Sharma \u201c Capturing the Effects of Single Atom Substitutions on the Inhibition E\u000eciency of Glycogen Synthase Kinase-3beta Inhibitors via Markov State Modeling and Experiments<\/b><\/i>\u201d, J. Chem. Theo. Chem. 20,6278 (2024) <\/a> <\/li>\n

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  29. R. Sharma, S. Sarkar, S. Chattopadhyay, J. Mondal*, P. Talukdar* \u201c A Halogen-Bond-Driven Artificial Chloride-Selective Channel Constructed from 5-Iodoisophthalamide-based Molecules<\/b><\/i>\u201d, Angew Chem. Int. Ed. 63,e202319919 (2024) <\/a> <\/li>\n

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  30. A. Saroha, M. S. Bosco, S. Menon, P. Kumari, T. Maity, S. Rana, S. Kotak, J. Mondal, S. S. Agasti \u201cRegulation of microtubule dynamics and function in living cells via cucurbit[7]uril hostguest assembly<\/b><\/i>\u201d, Chemical Science 15,11981 (2024) <\/a> <\/li>\n

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  31. D. Vikraman,B. B. Majumdar, Sharavankumar S.K, C. Weichbrodt, N. Fertig, M. Winterhalter, J.Mondal*, K. R. Mahendran* \u201cConformational Flexibility drivingCharge-selective Substrate Translocation across a Bacterial Transporter<\/b><\/i>\u201d, Chemical Science15,9333 (2024) <\/a> <\/li>\n

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  32. N. Mohandas, S. Bawari, J J.T. Shibuya, S. Ghosh, J.Mondal, T. N. Narayanan, A. Cuesta* \u201cUnderstanding electrochemical interfaces through comparing experimental and computational charge densitypotential curves<\/b><\/i>\u201d, Chemical Science 15,6643 (2024) <\/a> <\/li>\n

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  33. A. Wasim, P. Bera and J. Mondal \u201cElucidation of Spatial Positioning of Ribosomes around Chromosome in Escherichia coli Cytoplasm via a Data-Informed Polymer-Based Model<\/b><\/i>\u201d, J. Phys. Chem. B 123,3368-3382 (2024) <\/a> <\/li>\n

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  34. A. Wasim, S. Menon and J. Mondal \u201cModulation of alpha-Synuclein Aggregation Amid Diverse Environmental Perturbation<\/b><\/i>\u201d, eLife 13, RP95180 (2024) <\/a> <\/li>\n

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  35. R. Sharma, S. Sarkar, S. Chattopadhyay, J. Mondal and P. Talukdar \u201cA Halogen-Bond-Driven Artificial Chloride-Selective Channel Constructed from 5-Iodoisophthalamide-based Molecules<\/b><\/i>\u201d, Angew Chem. Int. edition 13, RP95180 (2024) <\/a> <\/li>\n

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  36. A. Wasim, P. Bera and J. Mondal \u201cDevelopment of a Data-Driven Integrative Model of a Bacterial Chromosome<\/b><\/i>\u201d, J. Chem. Theory Comput. 20, 1673 (2024) <\/a> <\/li>\n

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  37. \u00a0 S. Sarkar, T. N. Narayanan and J. Mondal \u201cA Synergistic View on Osmolyte\u2019s Role Against Salt and Cold Stress in Bio-interfaces<\/b><\/i>\u201d, Langmuir,49, 17581 (2023) <\/a> <\/li>\n

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  38. \u00a0S. Adhikari and J. Mondal \u201cMachine Learning Subtle Conformational Change due to Phosphorylation in Intrinsically Disordered Proteins<\/b><\/i>\u201d, J.Phys. Chem. B.,127, 9433 (2023) <\/a> <\/li>\n

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  39. M. Sahil,T. Singh, S. Ghosh and J. Mondal \u201c3site Multisubstrate-Bound State of Cytochrome P450cam<\/b><\/i>\u201d, J.Am. Chem. Soc.,145, 23488 (2023) <\/a><\/li>\n

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  40. M. Sahil, J. Singh, S. Sahu, S. K. Pal, A. Yadav, R. Anand and J. Mondal \u201cIdentifying Selectivity Filters in Protein Biosensor for Ligand Screening<\/b><\/i>\u201d, JACS Au,3,2800 (2023) <\/a><\/li>\n

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  41. S. Sarkar, A. Guha, R. Sadhukhan, T. N. Narayanan and J. Mondal \u201cOsmolytes as Cryoprotectants under Salt Stress<\/b><\/i>\u201d, ACS Biomater.Sci. Eng.,9, 5639 (2023) <\/a><\/li>\n

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  42. B. Dandekar, B. B. Majumdar and J. Mondal \u201cNonmonotonic Modulation of the Protein\u2013Ligand Recognition Event by Inert Crowders<\/b><\/i>\u201d, J.Phys.Chem. B 127, 7449 (2023) <\/a><\/li>\n

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  43. C. Ghosh, S. Menon, S. Ball, S. Goswami, J. Mondal and D. Das \u201cEmergence of Catalytic Triad by Short Peptide Based Nanofibrillar Assemblies<\/b><\/i>\u201d, Nano Lett.23, 5828 (2023) <\/a><\/li>\n

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  44. B. Dandekar, N. Ahalawat, S. Sinha and J. Mondal \u201cMarkov State Models Reconcile Conformational Plasticity of GTPase with Its Substrate Binding Event<\/b><\/i>\u201d, JACS Au 3, 1728 (2023) <\/a><\/li>\n

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  45. S. Bandyopadhyay and J. Mondal \u201cA deep encoder\u2013decoder framework for identifying distinct ligand binding pathways<\/b><\/i>\u201d, J.Chem.Phys. 158,194103 (2023) <\/a><\/li>\n

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  46. K. D. Tulsiyan, A. Mahalik, B. Dandekar, J. Mondal and H. S. Biswal \u201cEnhancement of Peroxidase Activity in Magnetic Ionic Liquids<\/b><\/i>\u201d, ACS Sustainable Chem.Eng. 11, 8487 (2023) <\/a><\/li>\n

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  47. S. Menon and J. Mondal \u201cConformational Plasticity in \u03b1-Synuclein and How Crowded Environment Modulates It<\/b><\/i>\u201d, J.Phys. Chem.B 127,4032 (2023) <\/a><\/li>\n

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  48. T Maity, P Malik, S Bawari, S Ghosh, J Mondal, R Haldar \u201cChemically routed interpore molecular diffusion in metal-organic framework thin films<\/b><\/i>\u201d, Nature Comm.14,2212 (2023) <\/a><\/li>\n

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  49. N. Ahalawat, M. Sahil and J. Mondal \u201cResolving Protein Conformational Plasticity and Substrate Binding via Machine Learning<\/b><\/i>\u201d, J. Chem. Theory Comput. 19,2644 (2023) <\/a><\/li>\n

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  50. A Mondal, SN Save, S Sarkar, D Mondal, J Mondal, S Sharma, P Talukdar \u201cA Benzohydrazide-Based Artificial Ion Channel that Modulates Chloride Ion Concentration in Cancer Cells and Induces Apoptosis by Disruption of Autophagy<\/b><\/i>\u201d, J. Am. Chem. Soc. 145,9737 (2023) <\/a><\/li>\n

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  51. M. Sahil, S. Sarkar and J. Mondal \u201cLong-time-step molecular dynamics can retard simulation of protein-ligand recognition process<\/b><\/i>\u201d, Biophysical Journal 122, 802 (2023) <\/a><\/li>\n

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  52. N. Jamuna, A. Kamalakshan, B. Dandekar, A. Devassy, J. Mondal, and S. Mandal \u201cMechanistic Insight into the Amyloid Fibrillation Inhibition of Hen Egg White Lysozyme by Three Different Bile Acids<\/b><\/i>\u201d, J.Phys.Chem. B 127, 2198 (2023) <\/a><\/li>\n

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  53. S. Bawari, T. N. Narayanan and J. Mondal \u201cInsights into the reaction pathways of platinum dissolution and oxidation during electrochemical processes<\/b><\/i>\u201d, Electrochem. Comm. 147, 107440 (2023) <\/a><\/li>\n

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  54. A Wasim, A Gupta, P Bera, J Mondal \u201cInterpretation of organizational role of proteins on E. coli nucleoid via Hi-C integrated model<\/b><\/i>\u201d, Biophysical Journal 122, 63 (2023) <\/a><\/li>\n

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  55. S. Bawari, A. Guha, T. N. Narayanan and J. Mondal \u201cUnderstanding Water Structure and Hydrogen Association on Platinum-Electrolyte Interface<\/b><\/i>\u201d, Oxford Open Materials Science 2, itac014 (2023) <\/a><\/li>\n

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  56. A. Mondal, G. K. Barik, S. Sarkar, D. Mondal, M. Ahmad, T. Vijayakanth, J. Mondal, M. K. Santra and P. Talukdar \u201cNontoxic Artificial Chloride Channel Formation in Epithelial Cells by Isophthalic Acid-Based Small Molecules<\/b><\/i>\u201d, Chem. Eur. J. 29,e202202887 (2022) <\/a><\/li>\n

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  57. R. Dolai, R. Kumar, B. Elvers, P. Pal, B. Joseph,R. Sikari, M. Nayak, A. Maiti, T. Singh, N. Chryochos, A. Jayaraman, I. Krummernacher, J. Mondal, U. Deva Priyakumar, H. Braunschweig, C. B. Yilidiz, C. Schulzke, A. Jana \u201cCarbodicarbenes and Striking Redox Transitions of their Conjugate Acids: Influence of NHC versus CAAC as Donor Substituents<\/b><\/I>\u201d, Chem. Euro. J. 28,e202202888 (2022) <\/a><\/li>\n

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  58. J. Singh, M. Sahil, S. Ray, C. Dcosta, S. Panjikar,G. Krishnamoorthy, J. Mondal and R. Anand \u201cPhenol sensing in nature modulated via a conformational switch governed by dynamic allostery<\/b><\/I>\u201d, J. Biol. Chem. 298,102399 (2022) <\/a><\/li>\n

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  59. C. Mahato, S. Menon, A. Singh, S. Afrose, J. Mondal and D. Das \u201cShort Peptide-based Cross-\u03b2 Amyloids Exploit Dual Residues for Phosphoesterase like Activity<\/b><\/i>\u201d, Chem. Sci. 13,9225-9231 (2022) <\/a><\/li>\n

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  60. D. Mondal, B. Dandekar, M. Ahmed, A. Mondal, J. Mondal and P. Talukdar \u201cSelective and Rapid Water Translocation across Self-assembled Peptide-Diol Channel via the Formation of Dual Water Array<\/b><\/i>\u201d, Chem. Sci. 13,9614-9623 (2022) <\/a><\/li>\n

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  61. S. Pal, J. Koneru, C. Andreou, T. Rakhsit, V. K. Rajsekhar, M. Wlodaryczyk, J. Healy, M. F. Kircher and J. Mondal \u201cDNA-Functionalized Gold Nanorods for Perioperative Optical Imaging and Photothermal Therapy of Triple-Negative Breast Cancer<\/b><\/i>\u201d, ACS Appl. Nano Mater.5, 9159-9169 (2022) <\/a><\/li>\n

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  62. S. Sarkar, A. Guha, T. N. Narayanan and J. Mondal \u201cZwitterionic Osmolytes Revive Surface Charges under Salt Stress via Dual Mechanisms<\/b><\/i>\u201d, J.Phys. Chem. Lett. 13,5660 (2022) <\/a><\/li>\n

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  63. B. Majumdar and J. Mondal \u201cImpact of Inert Crowders on Host\u2013Guest Recognition Process<\/b><\/i>\u201d, J.Phys. Chem. B 126,4200 (2022) <\/a><\/li>\n

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  64. P. Bera, A. Wasim and J. Mondal \u201cHi-C embedded polymer model of Escherichia coli reveals the origin of heterogeneous subdiffusion in chromosomal loci<\/b><\/i>\u201d, Phys. Rev. E. 105,064402 (2022) <\/a><\/li>\n

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  65. S. Bandyopadhyay, B. Majumdar and J. Mondal \u201cSolvent\u2019s Role in Cavity\u2013Ligand Recognition Would Depend on the Mode of Ligand Diffusion<\/b><\/i>\u201d, J.Phys. Chem. B 126,2952 (2022) <\/a><\/li>\n

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  66. N. Sharma, S. Singh, A. S. Tanwar, J. Mondal and R. Anand \u201cMechanism of Coordinated Gating and Signal Transduction in Purine Biosynthetic Enzyme Formylglycinamidine Synthetase<\/b><\/i>\u201d, ACS Catalysis 12,1930 (2022) <\/a><\/li>\n

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  67. B. Dandekar, S. Sinha and J. Mondal \u201cRole of molecular dynamics in optimising ligand discovery: Case study with novel inhibitor search for peptidyl t-RNA hydrolase<\/b><\/i>\u201d, Chem. Phys. Impact. 3,100048 (2021) <\/a><\/li>\n

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  68. J. Koneru, S. Sinha and J. Mondal \u201cMolecular Dynamics Simulations Elucidate Oligosaccharide Recognition Pathways by Galectin-3 at Atomic Resolution<\/b><\/i>\u201d, J. Biol. Chem., 297,101271(2021) <\/a><\/li>\n

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  69. S.Bawari,M. N. Nair, J. Mondal and T. N. Narayanan \u201cElucidating the Mechanism of Nitrogen Doping in Graphene Oxide: Structural Evolution of Dopants and the Role of Oxygen<\/b><\/i>\u201d, J. Phys. Chem. C, 125, 22547 (2021) <\/a><\/li>\n

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  70. J. Koneru, P. Dheeraj, N. Dube,P. Ghosh and J. Mondal \u201cSpontaneous transmembrane pore formation by short-chain synthetic peptide<\/b><\/i>\u201d, Biophysical Journal,120, 4557-4574(2021) <\/a><\/li>\n

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  71. S. Bandyopadhyay and J. Mondal \u201cA deep autoencoder framework for discovery of metastable ensembles in biomacromolecules<\/b><\/i>\u201d, J. Chem. Phys.155,114106 (2021) <\/a><\/li>\n

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  72. P. Bera, A. Wasim, J Mondal and P. Ghosh \u201cMechanistic underpinning of cell aspect \tratio-dependent emergent collective motions in swarming bacteria<\/b><\/i>\u201d, Soft Matter,17,7322-7331 (2021) <\/a><\/li>\n

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  73. S. Sarkar and J Mondal \u201cMechanistic Insights on ATP\u0099\u2019s Role as a Hydrotrope<\/b><\/i>\u201d, J.Phys. Chem. B,125,7717-7731(2021) <\/a><\/li>\n

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  74. D. Prakaschand and J Mondal \u201cConformational Reorganization of Apolipoprotein E Triggered by Phospholipid Assembly<\/b><\/i>\u201d, J.Phys. Chem. B,125,5285-5295(2021) <\/a><\/li>\n

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  75. B. Dandekar, N. Ahalawat and J Mondal \u201cReconciling conformational heterogeneity and substrate recognition in cytochrome P450<\/b><\/i>\u201d, Biophysical Journal,120,1732-1745(2021) <\/a><\/li>\n

    <\/p>\n

  76. A. Wasim, A. Gupta and J Mondal \u201cA Hi\u2013C data-integrated model elucidates E. coli chromosome\u2019s multiscale organization at various replication stages<\/b><\/i>\u201d, Nucleic Acids Research, 49,3077-3091 (2021) <\/a><\/li>\n

    <\/p>\n

  77. A. Som, M. Pahwa, S. Bawari, N. Das Saha, R. Sasmal, M. S. Bosco, J. Mondal and S. S. Agasti \u201cMultiplexed optical barcoding of cells via photochemical programming of bioorthogonal host\u2013guest recognition<\/b><\/i>\u201d, Chemical Science, 12,5484-5494 (2021) <\/a><\/li>\n

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  78. N. Ahalawat and J Mondal \u201cAn Appraisal of Computer Simulation Approaches in Elucidating Biomolecular Recognition Pathways<\/b><\/i>\u201d, J.Phys. Chem. Letters, 12, 633-641 (2021) <\/a><\/li>\n

    <\/p>\n

  79. M. Mukherjee and J Mondal \u201cBottom-Up View of the Mechanism of Action of Protein-Stabilizing Osmolytes<\/b><\/i>\u201d, J.Phys. Chem. B, 124, 11316 (2020) <\/a><\/li>\n

    <\/p>\n

  80. M. Mukherjee and J Mondal \u201cUnifying the Contrasting Mechanisms of Protein-Stabilising Osmolytes<\/b><\/i>\u201d, J.Phys. Chem. B, 124, 6565 (2020) <\/a><\/li>\n

    <\/p>\n

  81. B. R. Dandekar and J Mondal \u201cCapturing Protein-Ligand Recognition Pathways in Coarse-grained Simulation<\/b><\/i>\u201d, J.Phys. Chem. Letters, 11, 5302 (2020) <\/a><\/li>\n

    <\/p>\n

  82. N. Sharma, N. Ahalawat, P. Sandhu, E. Strauss, J Mondal and R. Anand \u201cRole of allosteric switches and adaptor domains in long-distance cross-talk and transient tunnel formation<\/b><\/i>\u201d, Sci. Advances, 6, eaay7919 (2020) <\/a><\/li>\n

    <\/p>\n

  83. P. D. Dheeraj, N. Ahalawat, S. Bandyopadhyay, S. Sengupta and J Mondal \u201cNonaffine Displacements Encode Collective Conformational Fluctuations in Proteins<\/b><\/i>\u201d, J. Chem. Theory Comput., 16, 2508 (2020) <\/a><\/li>\n

    <\/p>\n

  84. S. Bawari,K. Sharma,G. Kalita, P. K. Madhu, TN Narayanan and J. Mondal \u201cStructural Evolution of BCN Systems from Graphene Oxide Towards Electrocatalytically Active Atomic Layers<\/b><\/i>\u201d, Mater. Chem. Front., 4, 2330 (2020), (Hot article) <\/a><\/li>\n

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  85. A. Guha, NM Kaley, J Mondal and TN Narayanan \u201cEngineering the hydrogen evolution reaction of transition metals: effect of Li ions<\/b><\/i>\u201d, J. Mater. Chem. A, 8, 15795 (2020) <\/a><\/li>\n

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  86. N. Ahalawat, S. Bandyopadhyay and J Mondal \u201cOn the role of solvent in hydrophobic cavity\u2013ligand recognition kinetics<\/b><\/i>\u201d, J. Chem. Phys., 152, 074104 (2020) <\/a><\/li>\n

    <\/p>\n

  87. A. Guha, S Narayanaru, NM Kaley,DK Rao,J Mondal and TN Narayanan \u201cMechanistic insight into high yield electrochemical nitrogen reduction to ammonia using lithium ions<\/b><\/i>\u201d, Materials Today Communications,21, 100700 (2019) <\/a><\/li>\n

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  88. J. K. Koneru, X. Zhu and J. Mondal \u201cA Quantitative Assessment of the Conformational Heterogeneity in Amylose across Force Fields<\/b><\/i>\u201d, J. Chem.Theory Comput.,15, 6203 (2019) <\/a><\/li>\n

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  89. M. Mukherjee and J. Mondal \u201cOsmolyte-Induced Macromolecular Aggregation Is Length-Scale Dependent<\/b><\/i>\u201d, J. Phys.Chem. B,123, 8697 (2019) <\/a><\/li>\n

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  90. B. Sarkar, Z. Siddiqui, P. K. Nguyen, N. Dube, W. Fu, S. Park, S. Jaisinghani, R. Paul, S. D. Kozuch, D. Deng, P. Montoro,M. Li, D. Sabatino,D. S. Perlin,W. Zhang, J. Mondal and V. A. Kumar \u201cMembrane-Disrupting Nanofibrous Peptide Hydrogels<\/b><\/i>\u201d, ACS Biomater. Sci. Eng, 5,4657 (2019)<\/a><\/li>\n

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  91. J. K. Koneru, S. Sinha* and J. Mondal* \u201cIn Silico Re-Optimization of Binding Affinity and Drug-Resistance Circumvention Ability in Kinase Inhibitors:Case study with RL-45 and Src kinase<\/b><\/i>\u201d, J. Phys. Chem. B, 123, 6664 (2019)<\/a><\/li>\n

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  92. J. K. Koneru and J. Mondal \u201cQuantitative assessment of amylose dimerization process across force fields<\/b><\/i>\u201d, J. Indian Chem. Soc.,96, 949 (2019) <\/a><\/li>\n

    <\/p>\n

  93. S Bawari, S. Pal, S. Pal, J. Mondal* and T N Narayanan* \u201cEnhanced Photo-Electrocatalytic Hydrogen Generation in Graphene\/hBN van der Waals Structures<\/b><\/i>\u201d, J. Phys. Chem. C, 123,17249(2019)<\/a><\/li>\n

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  94. M Mukherjee and J. Mondal* \u201cOsmolyte-Induced Collapse of a Charged Macromolecule<\/b><\/i>\u201d, J. Phys. Chem. B, 123,4636(2019)<\/a><\/li>\n

    <\/p>\n

  95. S. Pal, A. Ray, C. Andreou, Y. Zhou, T. Rakshit, M. Wlodarczyk, M. Maeda, R. Toledo-Crow, N. Berisha, J. Yang, H. Hsu, A. Oseledchyk, J. Mondal, S. Zou and M. F. Kircher \u201cDNA-enabled rational design of fluorescence-Raman bimodal nanoprobes for cancer imaging and therapy\u201d<\/b><\/i>\u201d, Nature Comm. ,10,1926(2019)<\/a><\/li>\n

    <\/p>\n

  96. M Mukherjee, J Mondal, S Karmakar* \u201cRole of \u03b1 and \u03b2 relaxations in collapsing dynamics of a polymer chain in supercooled glass-forming liquid\u201d<\/b><\/i>\u201d, J. Chem. Phys.,150,114503(2019)<\/a><\/li>\n

    <\/p>\n

  97. J.Mondal \u201cA brief appraisal of computational modeling of antimicrobial peptides\u2019 activity\u201d<\/b><\/i>\u201d, Drug development research,80,28(2019)<\/a><\/li>\n

    <\/p>\n

  98. D. Dube, N. Ahalawat, H. Khandelia, J.Mondal* and S. Sengupta* \u201cOn identifying collective displacements in apo-proteins that reveal eventual binding pathways\u201d<\/b><\/i>\u201d, PLOS Comput. Biol.,15, e1006665(2019)<\/a><\/li>\n

    <\/p>\n

  99. N. Ahalawat and J. Mondal* \u201cMapping the Substrate Recognition in Cytochrome P450<\/b><\/i>\u201d, J. Am. Chem. Soc.,140,17743(2018)<\/a><\/li>\n

    <\/p>\n

  100. N. Ahalawat and J. Mondal* \u201cAssessment and optimization of collective variables for protein conformational landscape: GB1 \u03b2-hairpin as a case study,<\/b><\/i>\u201d, J. Chem. Phys.,149,094101(2018) (Featured Article)<\/a> (Highlighted in AIP)<\/a><\/li>\n

    <\/p>\n

  101. M Mukherjee and J. Mondal* \u201cHeterogeneous Impacts of Protein-Stabilizing Osmolytes on Hydrophobic Interaction<\/b><\/i>\u201d, J. Phys. Chem. B,122,6922(2018)<\/a><\/li>\n

    <\/p>\n

  102. J Mondal*, N. Ahalawat, S. Pandit, L. Kay and P. Vallurupalli \u201cAtomic resolution mechanism of ligand binding to a solvent inaccessible cavity in T4 lysozyme<\/b><\/i>\u201d, PLOS Computational Biology,14,5,e1006180(2018)<\/a><\/li>\n

    <\/p>\n

  103. S Bawari,T N. Narayanan and J Mondal* \u201cAtomistic Elucidation of Sorption Processes in Hydrogen Evolution Reaction on a van der Waals Heterostructure<\/b><\/i>\u201d, Journal Physical Chemistry C,122,10034(2018) <\/a><\/li>\n

    <\/p>\n

  104. S Bawari, N M. Kaley, S Pal, T V Vineesh, S Ghosh, J Mondal* and T N. Narayanan \u201cOn the hydrogen evolution reaction activity of graphene\u2013hBN van der Waals heterostructures<\/b><\/i>\u201d, Physical Chemistry Chemical Physics,20,15007(2018)<\/a><\/li>\n

    <\/p>\n

  105. Y Lyu, N Xiang, J Mondal, X Zhu, G Narsimhan, \u201cCharacterization of Interactions between Curcumin and Different Types of Lipid Bilayers by Molecular Dynamics Simulation<\/b><\/i>\u201d, Journal of Physical Chemistry B, 122,2341 (2018)<\/a><\/li>\n

    <\/p>\n

  106. A Ray, N Ahalawat, J Mondal*, \u201cAtomistic Insights into Structural Differences between E3 and E4 Isoforms of Apolipoprotein E<\/b><\/i>\u201d, Biophysical Journal, 113,2682 (2017)<\/a><\/li>\n

    <\/p>\n

  107. S Ray, A Maitra, A Biswas, S Panjikar, J Mondal, R Anand, \u201cFunctional Insights into the Mode of DNA and Ligand Binding of the TetR Family Regulator TylP from Streptomyces fradiae<\/b><\/i>\u201d, Journal of Biological Chemistry, 292, 15301 (2017)<\/a><\/li>\n

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  108. P. Tiwary, J. Mondal and B. J. Berne, \u201cHow and when does an anticancer drug leave its binding site?<\/b><\/i>\u201d, Science Advances, 3, e1700014 (2017)<\/a><\/li>\n

    <\/p>\n

  109. R. Berkovich*, J. Mondal*,I. Paster and B. J. Berne, \u201cSimulated Force quench Dynamics shows GB1 protein is not a two-state folder<\/b><\/i>\u201d, J.Phys.Chem. B,121, 5162 (2017)<\/a><\/li>\n

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  110. I. Tah and J. Mondal*, \u201cHow does a hydrophobic macromolecule respond to a mixed osmolyte environment?<\/b><\/i>\u201d, J. Phys.Chem. B., 120, 10969 (2016)<\/a><\/li>\n

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  111. J. Mondal*, P. Tiwary and B. J. Berne, \u201cHow a kinase inhibitor withstands gatekeeper residue mutation<\/b><\/i>\u201d, J. Am. Chem. Soc., 138, 4608 (2016)<\/a><\/li>\n

    <\/p>\n

  112. S. Roy, D. Skoff, D. Perroni, J. Mondal, A. Yethiraj, M. K. Mahanthappa, M. T. Zanni and J. L. Skinner, \u201cWater Dynamics in the gyroid phases of self-assembled gemini surfactants<\/b><\/i>\u201d, J. Am. Chem. Soc., 138,2472(2016)<\/a><\/li>\n

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  113. P. Tiwary, J. Mondal, J. A. Morrone and B. J. Berne, \u201cRole of Water and steric constraints in the kinetics of ligand-cavity unbinding<\/b><\/i>\u201d, Proc. Natl. Acad. Sci. USA,112, 12015 (2015)<\/a><\/li>\n

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  114. J. Mondal, D. Halverson, I.T.S. Li, G. Stirnemann, G. C. Walker and B. J. Berne, \u201cHow osmolytes influence hydrophobic polymer conformations: A unified view from experiment and theory<\/b><\/i>\u201d, Proc. Natl. Acad. Sci. USA,112,9270 (2015)<\/a><\/li>\n

    <\/p>\n

  115. P. Ghosh, J. Mondal, E. Ben-Jacob and H. Levine, \u201c Mechanically driven phase-separation in a growing bacterial colony<\/b><\/i>\u201d, Proc. Natl. Acad. Sci. USA, 112,E2166 (2015)<\/a><\/li>\n

    <\/p>\n

  116. J. Mondal, R.A. Friesner and B.J. Berne , \u201cRole of Desolvation in Thermodynamics and Kinetics of Ligand Binding to a Kinase<\/b><\/i>\u201d, J.Chem.Theory Comput.,10, 5696 ( 2014)<\/a><\/li>\n

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  117. S. Baksi,H. Choi, J. Mondal, J.C. Weisshaar , \u201cTime-dependent effects of transcription and translation-halting drugs on the spatial distributions of the Escherichia coli chromosome and ribosomes<\/b><\/i>\u201d, Mol. Micro.,94,871 ( 2014 )<\/a><\/li>\n

    <\/p>\n

  118. E.Choi, J. Mondal and A. Yethiraj , \u201cCoarse-grained models for aquous Poly-ethylene Oxide solutions<\/b><\/i>\u201d, J. Phys. Chem. B, 118,323 ( 2014 )<\/a><\/li>\n

    <\/p>\n

  119. J. Mondal, E. Choi and A. Yethiraj , \u201cComputer Simulation of Poly-ethylene Oxide in Ionic Liquid<\/b><\/i>\u201d, Macromolecules 47,438 ( 2014 )<\/a><\/li>\n

    <\/p>\n

  120. J. Mondal, J.A.Morrone and B.J. Berne , \u201cHow hydrophobic drying forces impact the kinetics of molecular recognition<\/b><\/i>\u201d, Proc. Natl. Acad. Sci. USA ,110,13277 (2013).<\/a><\/li>\n

    <\/p>\n

  121. J. Mondal, G. Stirnemann and B.J. Berne , \u201cWhen does Trimethylamine N-oxide fold a polymer chain and urea unfold it?<\/b><\/i>\u201d, J. Phys. Chem. B ,117,8723 (2013).<\/a><\/li>\n

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  122. J. Mondal, M. Mahanthappa and A. Yethiraj, \u201cSelf-assembly of gemini surfactants: A computer simulation study.<\/b><\/i>\u201d, J. Phys. Chem. B, 117,4254 (2013)<\/a><\/li>\n

    <\/p>\n

  123. J. Mondal and A. Yethiraj, \u201cEffect of secondary structure on self-assembly of amphiphilic molecules: A multiscale simulation study<\/b><\/i>\u201d, J. Chem. Phys., 136, 084902 (2012).<\/a><\/li>\n

    <\/p>\n

  124. J. Mondal, X. Zhu,Q. Cui and A. Yethiraj, \u201cInsights on sequence-dependent pKa-shift in catalytic reactions of beta-peptide foldamers<\/b><\/i>\u201d, J. Phys. Chem. B, 116, 491 (2012).<\/a><\/li>\n

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  125. J. Mondal and A. Yethiraj, \u201cThe driving force for the association of amphiphilic molecules<\/b><\/i>\u201d, J. Phys. Chem. Lett. 2, 2391 (2011).<\/a><\/li>\n

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  126. J. Mondal, B. P. Bratton, Y. Li, A. Yethiraj and J. C. Weisshaar, \u201cEntropy-based mechanism of ribosomic nucleoid segregation in E.Coli cells<\/b><\/i>\u201d, Biophys. J., 100, 2605 (2011).<\/a><\/li>\n

    <\/p>\n

  127. J. Mondal, X. Zhu, Q. Cui and A. Yethiraj, \u201cSequence-dependent interaction of beta-peptides with membrane<\/b><\/i>\u201d, J. Phys. Chem. B, 114,13585 (2010).<\/a><\/li>\n

    <\/p>\n

  128. J. Mondal, X. Zhu, Q. Cui and A. Yethiraj, \u201cSelf-assembly of beta-peptides:Insights from pair and many-body free energy of association<\/b><\/i>\u201d, J. Phys. Chem. C,114,13551 (2010).<\/a><\/li>\n

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  129. J. Mondal, B. J. Sung and A. Yethiraj, \u201cSequence-dependent self-assembly of beta-peptides: Insights from coarse-grained model<\/b><\/i>\u201d, J. Chem. Phys., 132, 065103 (2010).<\/a><\/li>\n

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  130. J. Mondal, B. J. Sung and A. Yethiraj, \u201cSequence-dependent organization of beta-peptides in self-assembled monolayers.<\/b><\/i>\u201d, J. Phys. Chem. B, 113, 9379 (2009).<\/a><\/li>\n

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  131. V. Sharma, B. Bapat, J. Mondal, M. Hochlaf, K. Giri and N. Sathyamurthy, \u201cDissociative double ionization of CO2: Dynamics,energy levels and lifetimes.<\/b><\/i>\u201d, J. Phys. Chem. A, 111, 10205 (2007).<\/a><\/li>\n<\/ol>\n

    <\/ol>\n

    [\/et_pb_code][\/et_pb_column][\/et_pb_row][\/et_pb_section]<\/p>\n","protected":false},"excerpt":{"rendered":"

    For Latest list of Publications visit Google Scholar M. Sahil and J. Mondal* \u201cMachine Learning and Computer Simulation Disentangle the Fuzzy Inhibitor Binding by Hsp90\u201d,J.Chem. Theory Comput. in press M. Sahil and J. Mondal* \u201cMultisubstrate Allostery with a Single Helical Switch in Cytochrome P450cam\u201d,J. Phys. Chem. Lett. 17,314-324 (2026)P. Bera and J. Mondal* \u201cHow good […]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_et_pb_use_builder":"on","_et_pb_old_content":"","_et_gb_content_width":"","footnotes":""},"class_list":["post-29","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.tifrh.res.in\/~jmondal\/wp-json\/wp\/v2\/pages\/29","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.tifrh.res.in\/~jmondal\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.tifrh.res.in\/~jmondal\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.tifrh.res.in\/~jmondal\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.tifrh.res.in\/~jmondal\/wp-json\/wp\/v2\/comments?post=29"}],"version-history":[{"count":28,"href":"https:\/\/www.tifrh.res.in\/~jmondal\/wp-json\/wp\/v2\/pages\/29\/revisions"}],"predecessor-version":[{"id":218,"href":"https:\/\/www.tifrh.res.in\/~jmondal\/wp-json\/wp\/v2\/pages\/29\/revisions\/218"}],"wp:attachment":[{"href":"https:\/\/www.tifrh.res.in\/~jmondal\/wp-json\/wp\/v2\/media?parent=29"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}