Publications
2024
24. Differential local ordering of mixed crowders determines effective size and stability of ss-DNA capped gold nanoparticle. S. Panigrahy and D. Nayar* J. Chem. Phys.,160, 014901 (2024) .Link
As part of special issue "2023 JCP Emerging Investigators Special Collection"
23. Plas-20k: Extended dataset of protein-ligand affinities from md simulations for machine learning applications. D. B. Korlepara, Vasavi C S, R. Srivastava, P. K. Pal, S. H. Raza, V. Kumar, S. Pandit, A. G. Nair, S. Pandey, S. Sharma, S. Jeurkar, K. Thakran, R. Jaglan, S. Verma, I. Ramachandran, P. Chatterjee, D. Nayar*, U. D. Priyakumar*; Scientific Data, 11, 180 (2024) .Link
2023
22. Molecular Crowders Can Induce Collapse in Hydrophilic Polymers via Soft Attractive Interactions. Divya Nayar* J. Phys. Chem. B, 127, 6265 (2023) .Link
As part of special issue "Early-Career and Emerging Researchers in Physical Chemistry 2023"
21. Ethylene glycol energetically disfavours oligomerization of pseudoisocyanine dyestuffs at crowded concentrations. S Rajput, R Pollak, K Huber, S Ebbinghaus, D Nayar. Soft Matter, 19, 6399-6413 Link
20. Structure, energetics and dynamics in crowded amino acid solutions: A molecular dynamics study. S. Panigrahy, R. Sahu, S. K. Reddy and D. Nayar* Phys. Chem. Chem. Phys. 25, 5430 (2023).Link
Selected as a 2023 HOT Article
19. Latent Biases in Machine Learning Models for Predicting Binding Affinities Using Popular Data Sets G.C. Kanakala, R. Aggarwal, D. Nayar, and U. D. Priyakumar* ACS Omega; 8, 2389-2397 (2023).Link
2022
18. PLAS-5k: Dataset of Protein-Ligand Affinities from Molecular Dynamics for Machine Learning Applications D. Korlepara, Vasavi C.S., S. Jeurkar, P. Pal, S. Roy, S. Mehta, S. Sharma, V. Kumar, C. Muvva, B. Sridharan, A. Garg, R. Modee, A. Bhati, D. Nayar,* and U. D. Priyakumar* Scientific Data (Nature); 9, 548 (2022).Link
2021
17. Current advances in bio-fabricated quantum dots emphasising the study of mechanisms to diversify their catalytic and biomedical applications R. Mahle, P. Kumbhakar, D. Nayar, T. N. Narayanan, K. K. Sadasivuni, C. S. Tiwary, R. Banerjee Dalton Transactions; 50, 14062-14080 (2021). Link
16. Crowding effects on water-mediated hydrophobic interactions R. Sahu and D. Nayar* J. Chem. Phys.; 155, 024903 (2021). Link
15. An interplay of excluded-volume and polymer–(co)solvent attractive interactions regulates polymer collapse in mixed solvents S. Bharadwaj, D. Nayar, C. Dalgicdir, N. F. A. van der Vegt J. Chem. Phys.; 154, 134903 (2021). Link
2020
14. A cosolvent surfactant mechanism affects polymer collapse in miscible good solvents S. Bharadwaj, D. Nayar, C. Dalgicdir, N. F. A. van der Vegt Commun. Chem. (Nature); 3, 165 (2020). Link
13. Small crowder interactions can drive hydrophobic polymer collapse as well as unfolding D. Nayar Phys. Chem. Chem. Phys.; 22; 18091-18101 (2020). Link
2018
12. Intrinsic conformational preferences and interactions in alpha-synuclein fibrils: Insights from MD simulations I. M. Ilie, D. Nayar , W. K. den Otter, N. F. A. van der Vegt, W. J. Briels J. Chem. Theory Comput.; 14; 3298-3310 (2018). link
11. Cosolvent Effects on Polymer Hydration Drive Hydrophobic Collapse D. Nayar, N. F. A. van der Vegt J. Phys. Chem. B; 122; 3587-3595 (2018). link
10. Convergence of Kirkwood Buff Integrals of Ideal and Non-ideal Aqueous Solutions Using Molecular Dynamics Simulations J. Milzetti, D. Nayar, N. F. A. van der Vegt J. Phys. Chem. B; 122; 5515-5526 (2018). link
2017
9. The Hydrophobic Effect and the Role of Cosolvents N. F. A. van der Vegt and D. Nayar J. Phys. Chem. B; 121, 9986-9998 (2017). link
8. Molecular origin of urea driven hydrophobic polymer collapse and unfolding depending on side chain chemistry D. Nayar, A. Folberth and N. F. A. van der Vegt Phys. Chem. Chem. Phys.; 19, 18156-18161 (2017). link
2016
7. Comparison of Hydration Behaviour and Conformational Preferences of Trp-Cage Miniprotein in Different Water Models M. Gupta, D. Nayar, C. Chakravarty and S. Bandyopadhyay; Phys. Chem. Chem. Phys.; 18, 32796-32813 (2016). link
2015
6. Free Energy Landscapes of Alanine Oligopeptides in Rigid-Body and Hybrid Water Models, D. Nayar and C. Chakravarty, J. Phys. Chem. B, 119, 11106- 11120 (2015). link
2014
5. Sensitivity of Local Hydration Behaviour and Conformational Preferences of Peptides to Choice of Water Model,D. Nayar and C. Chakravarty, Phys. Chem. Chem. Phys., 16, 10199-10213 (2014). link
2013
4. Water and Water-like Liquids: Relationships between Structure, Entropy and Mobility; D. Nayar and C. Chakravarty, Phys. Chem. Chem. Phys., 15, 14162-14177 (2013). link
2012
3. Relating Structure, Entropy and Energy of Solvation of Passivated Metal Nanoparticles; D. Nayar, H. O. S. Yadav, B. S. Jabes and C. Chakravarty, J. Phys. Chem. B. 116, 13124-13132 (2012). link
2. Water and other Tetrahedral Liquids: Order, Anomalies and Solvation; B. S. Jabes, D. Nayar, D. Dhabal, V. Molinero and C. Chakravarty, J. Phys.: Condens. Matter. 24, 284116 (2012). link
2011
1. Comparison of Tetrahedral Order, Liquid State Anomalies, and Hydration Behavior of mTIP3P and TIP4P Water Models; D. Nayar, M. Agarwal and C. Chakravarty; J. Chem. Theory Comput. 7, 3354-3367 (2011). link
