Publications

       
  1. D. Vikraman, B. B. Majumdar, S. K. Shravankumar, C. Weichbroadt, N. Fertig, M. Winterhalter J. Mondal and Mahendran, K. R.  “Conformational Flexibility driving charge-selective substrate location across bacterial transporter ”, Chemical Science, in press (2024)
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  2. A. Wasim, P. Bera and J. Mondal “Elucidation of Spatial Positioning of Ribosomes around Chromosome in Escherichia coli Cytoplasm via a Data-Informed Polymer-Based Model”, J. Phys. Chem. B 123,3368-3382 (2024)
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  3. A. Wasim, S. Menon and J. Mondal “Modulation of alpha-Synuclein Aggregation Amid Diverse Environmental Perturbation”, eLife 13, RP95180 (2024)
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  4. R. Sharma, S. Sarkar, S. Chattopadhyay, J. Mondal and P. Talukdar “A Halogen-Bond-Driven Artificial Chloride-Selective Channel Constructed from 5-Iodoisophthalamide-based Molecules”, Angew Chem. Int. edition 13, RP95180 (2024)
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  5. A. Wasim, P. Bera and J. Mondal “Development of a Data-Driven Integrative Model of a Bacterial Chromosome”, J. Chem. Theory Comput. 20, 1673 (2024)
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  6.   S. Sarkar, T. N. Narayanan and J. Mondal “A Synergistic View on Osmolyte’s Role Against Salt and Cold Stress in Bio-interfaces”, Langmuir,49, 17581 (2023)
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  7.   S. Adhikari and J. Mondal “Machine Learning Subtle Conformational Change due to Phosphorylation in Intrinsically Disordered Proteins”, J.Phys. Chem. B.,127, 9433 (2023)
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  8. M. Sahil,T. Singh, S. Ghosh and J. Mondal “3site Multisubstrate-Bound State of Cytochrome P450cam”, J.Am. Chem. Soc.,145, 23488 (2023)
  9. M. Sahil, J. Singh, S. Sahu, S. K. Pal, A. Yadav, R. Anand and J. Mondal “Identifying Selectivity Filters in Protein Biosensor for Ligand Screening”, JACS Au,3,2800 (2023)
  10. S. Sarkar, A. Guha, R. Sadhukhan, T. N. Narayanan and J. Mondal “Osmolytes as Cryoprotectants under Salt Stress”, ACS Biomater.Sci. Eng.,9, 5639 (2023)
  11. B. Dandekar, B. B. Majumdar and J. Mondal “Nonmonotonic Modulation of the Protein–Ligand Recognition Event by Inert Crowders”, J.Phys.Chem. B 127, 7449 (2023)
  12. C. Ghosh, S. Menon, S. Ball, S. Goswami, J. Mondal and D. Das “Emergence of Catalytic Triad by Short Peptide Based Nanofibrillar Assemblies”, Nano Lett.23, 5828 (2023)
  13. B. Dandekar, N. Ahalawat, S. Sinha and J. Mondal “Markov State Models Reconcile Conformational Plasticity of GTPase with Its Substrate Binding Event”, JACS Au 3, 1728 (2023)
  14. S. Bandyopadhyay and J. Mondal “A deep encoder–decoder framework for identifying distinct ligand binding pathways”, J.Chem.Phys. 158,194103 (2023)
  15. K. D. Tulsiyan, A. Mahalik, B. Dandekar, J. Mondal and H. S. Biswal “Enhancement of Peroxidase Activity in Magnetic Ionic Liquids”, ACS Sustainable Chem.Eng. 11, 8487 (2023)
  16. S. Menon and J. Mondal “Conformational Plasticity in α-Synuclein and How Crowded Environment Modulates It”, J.Phys. Chem.B 127,4032 (2023)
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  17. T Maity, P Malik, S Bawari, S Ghosh, J Mondal, R Haldar “Chemically routed interpore molecular diffusion in metal-organic framework thin films”, Nature Comm.14,2212 (2023)
  18. N. Ahalawat, M. Sahil and J. Mondal “Resolving Protein Conformational Plasticity and Substrate Binding via Machine Learning”, J. Chem. Theory Comput. 19,2644 (2023)
  19. A Mondal, SN Save, S Sarkar, D Mondal, J Mondal, S Sharma, P Talukdar “A Benzohydrazide-Based Artificial Ion Channel that Modulates Chloride Ion Concentration in Cancer Cells and Induces Apoptosis by Disruption of Autophagy”, J. Am. Chem. Soc. 145,9737 (2023)
  20. M. Sahil, S. Sarkar and J. Mondal “Long-time-step molecular dynamics can retard simulation of protein-ligand recognition process”, Biophysical Journal 122, 802 (2023)
  21. N. Jamuna, A. Kamalakshan, B. Dandekar, A. Devassy, J. Mondal, and S. Mandal “Mechanistic Insight into the Amyloid Fibrillation Inhibition of Hen Egg White Lysozyme by Three Different Bile Acids”, J.Phys.Chem. B 127, 2198 (2023)
  22. S. Bawari, T. N. Narayanan and J. Mondal “Insights into the reaction pathways of platinum dissolution and oxidation during electrochemical processes”, Electrochem. Comm. 147, 107440 (2023)
  23. A Wasim, A Gupta, P Bera, J Mondal “Interpretation of organizational role of proteins on E. coli nucleoid via Hi-C integrated model”, Biophysical Journal 122, 63 (2023)
  24. S. Bawari, A. Guha, T. N. Narayanan and J. Mondal “Understanding Water Structure and Hydrogen Association on Platinum-Electrolyte Interface”, Oxford Open Materials Science 2, itac014 (2023)
  25. A. Mondal, G. K. Barik, S. Sarkar, D. Mondal, M. Ahmad, T. Vijayakanth, J. Mondal, M. K. Santra and P. Talukdar “Nontoxic Artificial Chloride Channel Formation in Epithelial Cells by Isophthalic Acid-Based Small Molecules”, Chem. Eur. J. 29,e202202887 (2022)
  26. 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 “Carbodicarbenes and Striking Redox Transitions of their Conjugate Acids: Influence of NHC versus CAAC as Donor Substituents”, Chem. Euro. J. 28,e202202888 (2022)
  27. J. Singh, M. Sahil, S. Ray, C. Dcosta, S. Panjikar,G. Krishnamoorthy, J. Mondal and R. Anand “Phenol sensing in nature modulated via a conformational switch governed by dynamic allostery”, J. Biol. Chem. 298,102399 (2022)
  28. C. Mahato, S. Menon, A. Singh, S. Afrose, J. Mondal and D. Das “Short Peptide-based Cross-β Amyloids Exploit Dual Residues for Phosphoesterase like Activity”, Chem. Sci. 13,9225-9231 (2022)
  29. D. Mondal, B. Dandekar, M. Ahmed, A. Mondal, J. Mondal and P. Talukdar “Selective and Rapid Water Translocation across Self-assembled Peptide-Diol Channel via the Formation of Dual Water Array”, Chem. Sci. 13,9614-9623 (2022)
  30. S. Pal, J. Koneru, C. Andreou, T. Rakhsit, V. K. Rajsekhar, M. Wlodaryczyk, J. Healy, M. F. Kircher and J. Mondal “DNA-Functionalized Gold Nanorods for Perioperative Optical Imaging and Photothermal Therapy of Triple-Negative Breast Cancer”, ACS Appl. Nano Mater.5, 9159-9169 (2022)
  31. S. Sarkar, A. Guha, T. N. Narayanan and J. Mondal “Zwitterionic Osmolytes Revive Surface Charges under Salt Stress via Dual Mechanisms”, J.Phys. Chem. Lett. 13,5660 (2022)
  32. B. Majumdar and J. Mondal “Impact of Inert Crowders on Host–Guest Recognition Process”, J.Phys. Chem. B 126,4200 (2022)
  33. P. Bera, A. Wasim and J. Mondal “Hi-C embedded polymer model of Escherichia coli reveals the origin of heterogeneous subdiffusion in chromosomal loci”, Phys. Rev. E. 105,064402 (2022)
  34. S. Bandyopadhyay, B. Majumdar and J. Mondal “Solvent’s Role in Cavity–Ligand Recognition Would Depend on the Mode of Ligand Diffusion”, J.Phys. Chem. B 126,2952 (2022)
  35. N. Sharma, S. Singh, A. S. Tanwar, J. Mondal and R. Anand “Mechanism of Coordinated Gating and Signal Transduction in Purine Biosynthetic Enzyme Formylglycinamidine Synthetase”, ACS Catalysis 12,1930 (2022)
  36. B. Dandekar, S. Sinha and J. Mondal “Role of molecular dynamics in optimising ligand discovery: Case study with novel inhibitor search for peptidyl t-RNA hydrolase”, Chem. Phys. Impact. 3,100048 (2021)
  37. J. Koneru, S. Sinha and J. Mondal “Molecular Dynamics Simulations Elucidate Oligosaccharide Recognition Pathways by Galectin-3 at Atomic Resolution”, J. Biol. Chem., 297,101271(2021)
  38. S.Bawari,M. N. Nair, J. Mondal and T. N. Narayanan “Elucidating the Mechanism of Nitrogen Doping in Graphene Oxide: Structural Evolution of Dopants and the Role of Oxygen”, J. Phys. Chem. C, 125, 22547 (2021)
  39. J. Koneru, P. Dheeraj, N. Dube,P. Ghosh and J. Mondal “Spontaneous transmembrane pore formation by short-chain synthetic peptide”, Biophysical Journal,120, 4557-4574(2021)
  40. S. Bandyopadhyay and J. Mondal “A deep autoencoder framework for discovery of metastable ensembles in biomacromolecules”, J. Chem. Phys.155,114106 (2021)
  41. P. Bera, A. Wasim, J Mondal and P. Ghosh “Mechanistic underpinning of cell aspect ratio-dependent emergent collective motions in swarming bacteria”, Soft Matter,17,7322-7331 (2021)
  42. S. Sarkar and J Mondal “Mechanistic Insights on ATP™’s Role as a Hydrotrope”, J.Phys. Chem. B,125,7717-7731(2021)
  43. D. Prakaschand and J Mondal “Conformational Reorganization of Apolipoprotein E Triggered by Phospholipid Assembly”, J.Phys. Chem. B,125,5285-5295(2021)
  44. B. Dandekar, N. Ahalawat and J Mondal “Reconciling conformational heterogeneity and substrate recognition in cytochrome P450”, Biophysical Journal,120,1732-1745(2021)
  45. A. Wasim, A. Gupta and J Mondal “A Hi–C data-integrated model elucidates E. coli chromosome’s multiscale organization at various replication stages”, Nucleic Acids Research, 49,3077-3091 (2021)
  46. A. Som, M. Pahwa, S. Bawari, N. Das Saha, R. Sasmal, M. S. Bosco, J. Mondal and S. S. Agasti “Multiplexed optical barcoding of cells via photochemical programming of bioorthogonal host–guest recognition”, Chemical Science, 12,5484-5494 (2021)
  47. N. Ahalawat and J Mondal “An Appraisal of Computer Simulation Approaches in Elucidating Biomolecular Recognition Pathways”, J.Phys. Chem. Letters, 12, 633-641 (2021)
  48. M. Mukherjee and J Mondal “Bottom-Up View of the Mechanism of Action of Protein-Stabilizing Osmolytes”, J.Phys. Chem. B, 124, 11316 (2020)
  49. M. Mukherjee and J Mondal “Unifying the Contrasting Mechanisms of Protein-Stabilising Osmolytes”, J.Phys. Chem. B, 124, 6565 (2020)
  50. B. R. Dandekar and J Mondal “Capturing Protein-Ligand Recognition Pathways in Coarse-grained Simulation”, J.Phys. Chem. Letters, 11, 5302 (2020)
  51. N. Sharma, N. Ahalawat, P. Sandhu, E. Strauss, J Mondal and R. Anand “Role of allosteric switches and adaptor domains in long-distance cross-talk and transient tunnel formation”, Sci. Advances, 6, eaay7919 (2020)
  52. P. D. Dheeraj, N. Ahalawat, S. Bandyopadhyay, S. Sengupta and J Mondal “Nonaffine Displacements Encode Collective Conformational Fluctuations in Proteins”, J. Chem. Theory Comput., 16, 2508 (2020)
  53. S. Bawari,K. Sharma,G. Kalita, P. K. Madhu, TN Narayanan and J. Mondal “Structural Evolution of BCN Systems from Graphene Oxide Towards Electrocatalytically Active Atomic Layers”, Mater. Chem. Front., 4, 2330 (2020), (Hot article)
  54. A. Guha, NM Kaley, J Mondal and TN Narayanan “Engineering the hydrogen evolution reaction of transition metals: effect of Li ions”, J. Mater. Chem. A, 8, 15795 (2020)
  55. N. Ahalawat, S. Bandyopadhyay and J Mondal “On the role of solvent in hydrophobic cavity–ligand recognition kinetics”, J. Chem. Phys., 152, 074104 (2020)
  56. A. Guha, S Narayanaru, NM Kaley,DK Rao,J Mondal and TN Narayanan “Mechanistic insight into high yield electrochemical nitrogen reduction to ammonia using lithium ions”, Materials Today Communications,21, 100700 (2019)
  57. J. K. Koneru, X. Zhu and J. Mondal “A Quantitative Assessment of the Conformational Heterogeneity in Amylose across Force Fields”, J. Chem.Theory Comput.,15, 6203 (2019)
  58. M. Mukherjee and J. Mondal “Osmolyte-Induced Macromolecular Aggregation Is Length-Scale Dependent”, J. Phys.Chem. B,123, 8697 (2019)
  59. 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 “Membrane-Disrupting Nanofibrous Peptide Hydrogels”, ACS Biomater. Sci. Eng, 5,4657 (2019)
  60. J. K. Koneru, S. Sinha* and J. Mondal* “In Silico Re-Optimization of Binding Affinity and Drug-Resistance Circumvention Ability in Kinase Inhibitors:Case study with RL-45 and Src kinase”, J. Phys. Chem. B, 123, 6664 (2019)
  61. J. K. Koneru and J. Mondal “Quantitative assessment of amylose dimerization process across force fields”, J. Indian Chem. Soc.,96, 949 (2019)
  62. S Bawari, S. Pal, S. Pal, J. Mondal* and T N Narayanan* “Enhanced Photo-Electrocatalytic Hydrogen Generation in Graphene/hBN van der Waals Structures”, J. Phys. Chem. C, 123,17249(2019)
  63. M Mukherjee and J. Mondal* “Osmolyte-Induced Collapse of a Charged Macromolecule”, J. Phys. Chem. B, 123,4636(2019)
  64. 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 “DNA-enabled rational design of fluorescence-Raman bimodal nanoprobes for cancer imaging and therapy””, Nature Comm. ,10,1926(2019)
  65. M Mukherjee, J Mondal, S Karmakar* “Role of α and β relaxations in collapsing dynamics of a polymer chain in supercooled glass-forming liquid””, J. Chem. Phys.,150,114503(2019)
  66. J.Mondal “A brief appraisal of computational modeling of antimicrobial peptides’ activity””, Drug development research,80,28(2019)
  67. D. Dube, N. Ahalawat, H. Khandelia, J.Mondal* and S. Sengupta* “On identifying collective displacements in apo-proteins that reveal eventual binding pathways””, PLOS Comput. Biol.,15, e1006665(2019)
  68. N. Ahalawat and J. Mondal* “Mapping the Substrate Recognition in Cytochrome P450”, J. Am. Chem. Soc.,140,17743(2018)
  69. N. Ahalawat and J. Mondal* “Assessment and optimization of collective variables for protein conformational landscape: GB1 β-hairpin as a case study,”, J. Chem. Phys.,149,094101(2018) (Featured Article) (Highlighted in AIP)
  70. M Mukherjee and J. Mondal* “Heterogeneous Impacts of Protein-Stabilizing Osmolytes on Hydrophobic Interaction”, J. Phys. Chem. B,122,6922(2018)
  71. J Mondal*, N. Ahalawat, S. Pandit, L. Kay and P. Vallurupalli “Atomic resolution mechanism of ligand binding to a solvent inaccessible cavity in T4 lysozyme”, PLOS Computational Biology,14,5,e1006180(2018)
  72. S Bawari,T N. Narayanan and J Mondal* “Atomistic Elucidation of Sorption Processes in Hydrogen Evolution Reaction on a van der Waals Heterostructure”, Journal Physical Chemistry C,122,10034(2018)
  73. S Bawari, N M. Kaley, S Pal, T V Vineesh, S Ghosh, J Mondal* and T N. Narayanan “On the hydrogen evolution reaction activity of graphene–hBN van der Waals heterostructures”, Physical Chemistry Chemical Physics,20,15007(2018)
  74. Y Lyu, N Xiang, J Mondal, X Zhu, G Narsimhan, “Characterization of Interactions between Curcumin and Different Types of Lipid Bilayers by Molecular Dynamics Simulation”, Journal of Physical Chemistry B, 122,2341 (2018)
  75. A Ray, N Ahalawat, J Mondal*, “Atomistic Insights into Structural Differences between E3 and E4 Isoforms of Apolipoprotein E”, Biophysical Journal, 113,2682 (2017)
  76. S Ray, A Maitra, A Biswas, S Panjikar, J Mondal, R Anand, “Functional Insights into the Mode of DNA and Ligand Binding of the TetR Family Regulator TylP from Streptomyces fradiae”, Journal of Biological Chemistry, 292, 15301 (2017)
  77. P. Tiwary, J. Mondal and B. J. Berne, “How and when does an anticancer drug leave its binding site?”, Science Advances, 3, e1700014 (2017)
  78. R. Berkovich*, J. Mondal*,I. Paster and B. J. Berne, “Simulated Force quench Dynamics shows GB1 protein is not a two-state folder”, J.Phys.Chem. B,121, 5162 (2017)
  79. I. Tah and J. Mondal*, “How does a hydrophobic macromolecule respond to a mixed osmolyte environment?”, J. Phys.Chem. B., 120, 10969 (2016)
  80. J. Mondal*, P. Tiwary and B. J. Berne, “How a kinase inhibitor withstands gatekeeper residue mutation”, J. Am. Chem. Soc., 138, 4608 (2016)
  81. S. Roy, D. Skoff, D. Perroni, J. Mondal, A. Yethiraj, M. K. Mahanthappa, M. T. Zanni and J. L. Skinner, “Water Dynamics in the gyroid phases of self-assembled gemini surfactants”, J. Am. Chem. Soc., 138,2472(2016)
  82. P. Tiwary, J. Mondal, J. A. Morrone and B. J. Berne, “Role of Water and steric constraints in the kinetics of ligand-cavity unbinding”, Proc. Natl. Acad. Sci. USA,112, 12015 (2015)
  83. J. Mondal, D. Halverson, I.T.S. Li, G. Stirnemann, G. C. Walker and B. J. Berne, “How osmolytes influence hydrophobic polymer conformations: A unified view from experiment and theory”, Proc. Natl. Acad. Sci. USA,112,9270 (2015)
  84. P. Ghosh, J. Mondal, E. Ben-Jacob and H. Levine, “ Mechanically driven phase-separation in a growing bacterial colony”, Proc. Natl. Acad. Sci. USA, 112,E2166 (2015)
  85. J. Mondal, R.A. Friesner and B.J. Berne , “Role of Desolvation in Thermodynamics and Kinetics of Ligand Binding to a Kinase”, J.Chem.Theory Comput.,10, 5696 ( 2014)
  86. S. Baksi,H. Choi, J. Mondal, J.C. Weisshaar , “Time-dependent effects of transcription and translation-halting drugs on the spatial distributions of the Escherichia coli chromosome and ribosomes”, Mol. Micro.,94,871 ( 2014 )
  87. E.Choi, J. Mondal and A. Yethiraj , “Coarse-grained models for aquous Poly-ethylene Oxide solutions”, J. Phys. Chem. B, 118,323 ( 2014 )
  88. J. Mondal, E. Choi and A. Yethiraj , “Computer Simulation of Poly-ethylene Oxide in Ionic Liquid”, Macromolecules 47,438 ( 2014 )
  89. J. Mondal, J.A.Morrone and B.J. Berne , “How hydrophobic drying forces impact the kinetics of molecular recognition”, Proc. Natl. Acad. Sci. USA ,110,13277 (2013).
  90. J. Mondal, G. Stirnemann and B.J. Berne , “When does Trimethylamine N-oxide fold a polymer chain and urea unfold it?”, J. Phys. Chem. B ,117,8723 (2013).
  91. J. Mondal, M. Mahanthappa and A. Yethiraj, “Self-assembly of gemini surfactants: A computer simulation study.”, J. Phys. Chem. B, 117,4254 (2013)
  92. J. Mondal and A. Yethiraj, “Effect of secondary structure on self-assembly of amphiphilic molecules: A multiscale simulation study”, J. Chem. Phys., 136, 084902 (2012).
  93. J. Mondal, X. Zhu,Q. Cui and A. Yethiraj, “Insights on sequence-dependent pKa-shift in catalytic reactions of beta-peptide foldamers”, J. Phys. Chem. B, 116, 491 (2012).
  94. J. Mondal and A. Yethiraj, “The driving force for the association of amphiphilic molecules”, J. Phys. Chem. Lett. 2, 2391 (2011).
  95. J. Mondal, B. P. Bratton, Y. Li, A. Yethiraj and J. C. Weisshaar, “Entropy-based mechanism of ribosomic nucleoid segregation in E.Coli cells”, Biophys. J., 100, 2605 (2011).
  96. J. Mondal, X. Zhu, Q. Cui and A. Yethiraj, “Sequence-dependent interaction of beta-peptides with membrane”, J. Phys. Chem. B, 114,13585 (2010).
  97. J. Mondal, X. Zhu, Q. Cui and A. Yethiraj, “Self-assembly of beta-peptides:Insights from pair and many-body free energy of association”, J. Phys. Chem. C,114,13551 (2010).
  98. J. Mondal, B. J. Sung and A. Yethiraj, “Sequence-dependent self-assembly of beta-peptides: Insights from coarse-grained model”, J. Chem. Phys., 132, 065103 (2010).
  99. J. Mondal, B. J. Sung and A. Yethiraj, “Sequence-dependent organization of beta-peptides in self-assembled monolayers.”, J. Phys. Chem. B, 113, 9379 (2009).
  100. V. Sharma, B. Bapat, J. Mondal, M. Hochlaf, K. Giri and N. Sathyamurthy, “Dissociative double ionization of CO2: Dynamics,energy levels and lifetimes.”, J. Phys. Chem. A, 111, 10205 (2007).