Publications: IIT Bombay
Submitted but unpublished
68. Mechanism of Deamination of Mycobacterial Deaminase Selectively Targeting Mutagenic Bases - Sini Porathoor, Asha Rani Choudhury, Rajarshi Chakrabarti and Ruchi Anand (submitted).
67. Exploring the Effect of Hydrocarbon Crosslinkers on the Structure and Binding of Stapled p53 Peptide - Asha Rani Choudhury, Vikram Gaikwad, Atanu Maity and Rajarshi Chakrabarti (submitted) (bioRxiv).
2024
66. Osmolyte-induced Conformational Stabilization of a Hydrophobic Polymer - Pooja Nanavare, Soham Sarkar, Abhijit Bijay Jena, and Rajarshi Chakrabarti Phys. Chem. Chem. Phys. 26, 24021 (2024).
65. Compound Giant Unilamellar Vesicle as a Model for Electrohydrodynamics of Artificial Nucleate Cell - Rupesh Kumar, Rajarshi Chakrabarti and Rochish M. Thaokar Soft Matter 20, 6995 (2024).
64. A Passive Star Polymer in a Dense Active Bath: Insights from Computer Simulations - Ramanand Singh Yadav, Sanaa Sharma, Ralf Metzler and Rajarshi Chakrabarti Soft Matter 20, 3910 (2024). (This article has appeared as the outside back cover of the Journal). (Correction: Soft Matter, 20, 5258 (2024)).
63. Decoding the Dynamics of BCL9 Triazole Stapled Peptide - Vikram Gaikwad, Asha Rani Choudhury and Rajarshi Chakrabarti Biophys. Chem. 307, 107197 (2024).
62. Dynamic Clustering of Active Rings - Ligesh Theeyancheri, Subhasish Chaki, Tapomoy Bhattacharjee and Rajarshi Chakrabarti Phys. Rev. Res. 6, L012038 (2024).
2023
61. Escape dynamics of a self-propelled nanorod from circular confinements with narrow openings - Praveen Kumar and Rajarshi Chakrabarti Soft Matter 19, 6743 (2023).
60. Structure and dynamics of an active polymer chain inside a nanochannel grafted with polymers - Rajiblochan Sahoo and Rajarshi Chakrabarti Soft Matter 19, 5978 (2023).
59. Active Dynamics of Linear Chains and Rings in Porous Media - Ligesh Theeyancheri, Subhasish Chaki, Tapomoy Bhattacharjee and Rajarshi Chakrabarti J. Chem. Phys. 159, 014902 (2023).
58. Dynamics of a Methane Hydrophobe in Aqueous Choline Chloride Solution: Insights from Molecular Dynamics Simulations - Pooja Nanavare, Ligesh Theyancheri, Soham Sarkar and Rajarshi Chakrabarti, Chem. Phys. Impact 6, 100223 (2023).
57. A Polymer Chain with Dipolar Active Forces in Connection to Spatial Organization of Chromatin - Subhasish Chaki, Ligesh Theeyancheri and Rajarshi Chakrabarti, Soft Matter 19, 1348 (2023).
56. Dynamics of a spherical self-propelled tracer in a polymeric medium: interplay of self-propulsion, stickiness, and crowding - Ramanand Singh Yadav, Chintu Das and Rajarshi Chakrabarti, Soft Matter 19, 689 (2023).
55. Dynamics of self-propelled tracer particles inside a polymer network - Praveen Kumar and Rajarshi Chakrabarti, Phys. Chem. Chem. Phys. 25, 1937 (2023).
54. Shear viscosity for finitely extensible chains with fluctuating internal friction and hydrodynamic interactions - R. Kailasham, Rajarshi Chakrabarti and J. Ravi Prakash, J. Rheology 67, 105 (2023).
2022
53. Reconfiguration, swelling and tagged monomer dynamics of a single polymer chain in Gaussian and non-Gaussian active baths - Koushik Goswami, Subhasish Chaki and Rajarshi Chakrabarti, J. Phys. A: Math & Theo. 55, 423002 (2022). (Invited Topical Review).
52. In Silico Studies of Active Probe Dynamics in Crowded Media - Ligesh Theeyancheri, Rajiblochan Sahoo, Praveen Kumar and Rajarshi Chakrabarti, ACS Omega 7, 33637 (2022). (Invited Mini-Review).
51. Distinct mode of membrane interaction and disintegration by diverse class of Antimicrobial peptides - Nutan Agadi, Atanu Maity, Akash Kumar Jha, Rajarshi Chakrabarti and Ashutosh Kumar BBA - Biomembranes 1864, 184047 (2022).
50. Structure and Orientation of Water and Choline Chloride Molecules Around a Methane Hydrophobe: A Computer Simulation Study - Pooja Nanavare, Asha Rani Choudhury, Soham Sarkar, Atanu Maity and Rajarshi Chakrabarti ChemPhysChem 23, e202200446 (2022). (Special Collection Issue: Theoretical Chemistry Symposium 2021). This article has appeared as a Cover Feature of the Journal.
49. Migration of active rings in porous media - Ligesh Theeyancheri, Subhasish Chaki, Tapomoy Bhattacharjee and Rajarshi Chakrabarti, Phys. Rev. E 106, 014504 (2022).
48. Computational design of stapled peptide inhibitor against SARS CoV-2 receptor binding domain - Asha Rani Choudhury, Atanu Maity, Sayantani Chakraborty and Rajarshi Chakrabarti Peptide Science e24267 (2022).
47. Chemically symmetric and asymmetric self-driven dumbbells in 2D polymer gel - Praveen Kumar, Ligesh Theeyancheri, and Rajarshi Chakrabarti Soft Matter 18, 2663 (2022).
46. Motion of an active particle with dynamical disorder - Koushik Goswami and Rajarshi Chakrabarti Soft Matter 18, 2332 (2022).
45. Transport of a self-propelled tracer through a hairy cylindrical channel: interplay of stickiness and activity - Rajiblochan Sahoo, Ligesh Theeyancheri and Rajarshi Chakrabarti, Soft Matter 18, 1310 (2022).
2021
44. In silico Elucidation of Molecular Picture of Water-Choline Chloride Mixture - Soham Sarkar, Atanu Maity and Rajarshi Chakrabarti, J. Phys. Chem. B, 125, 13212 (2021).
43. Stochastic resetting and first arrival subjected to Gaussian noise and Poisson white noise - Koushik Goswami and Rajarshi Chakrabarti, Phys. Rev. E 104, 034113 (2021).
42. How important are fluctuations in the treatment of internal friction in polymers? - R. Kailasham, Rajarshi Chakrabarti and J. Ravi Prakash, Soft Matter 17, 7133 (2021).
41. Rouse model with fluctuating internal friction - R. Kailasham, Rajarshi Chakrabarti and J. Ravi Prakash - J. Rheol. 65, 903 (2021).
40. Effect of Stapling on the Thermodynamics of mdm2-p53 Binding - Atanu Maity, Asha Rani Choudhury and Rajarshi Chakrabarti, J. Chem. Inf. Model 61, 1989 (2021).
30. Microscopic Structural Features of Water in Aqueous-Reline Mixture of varying Compositions - Soham Sarkar, Atanu Maity and Rajarshi Chakrabarti, Phys. Chem. Chem. Phys. 23, 3779 (2021).
2020
38. Directing the diffusion of a non-magnetic nanosized active particle with external magnetic fields - Martin Kaiser, Pedro A. Sanchez, Nairhita Samanta, Rajarshi Chakrabarti and Sofia S. Kantorovich, J. Phys. Chem. B 124, 8188 (2020).
37. Translational and rotational dynamics of a self-propelled Janus probe in crowded environments - Ligesh Theeyancheri, Subhasish Chaki, Nairhita Samanta, Rohit Goswami, Raghunath Chelakkot and Rajarshi Chakrabarti, Soft Matter 16, 8482 (2020).
36. Escape of a passive particle from activity-induced energy landscape: Emergence of slow and fast effective diffusion - Subhasish Chaki and Rajarshi Chakrabarti, Soft Matter 16, 7103 (2020). (This article has been featured in an online themed collection: Soft Matter Most Popular 2020).
35. Wet and dry internal friction can be measured with the Jarzynski equality - R. Kailasham, Rajarshi Chakrabarti and J. Ravi Prakash, Phys. Rev. Res. 2, 013331 (2020).
34. Choline chloride as a nano-crowder protects HP-36 from urea-induced denaturation: Insights from Solvent Dynamics and Protein-Solvent interaction - Atanu Maity, Soham Sarkar, Ligesh Theeyancheri and Rajarshi Chakrabarti, ChemPhysChem 21, 552 (2020).
2019
33. Transport of probe particles in polymer network: effects of probe size, network rigidity and probe-polymer interaction - Praveen Kumar, Ligesh Theeyancheri, Subhasish Chaki and Rajarshi Chakrabarti, Soft Matter 15, 8992 (2019). (This article has appeared as the inside back cover of the Journal).
32. Effects of active fluctuations on energetics of a colloidal particle: superdiffusion, dissipation and entropy production - Subhasish Chaki and Rajarshi Chakrabarti, Physica A: Statistical Mechanics and its Applications 530, 121574 (2019).
31. Enhanced diffusion, swelling and slow reconfiguration of a single chain in non-Gaussian active bath - Subhasish Chaki and Rajarshi Chakrabarti, J. Chem. Phys. 150, 094902 (2019).
30. Azadirachtin inhibits amyloid formation, disaggregates pre-formed fibrils, and protects pancreatic β-cells from human islet amyloid polypeptide (hIAPP) induced cytotoxicity - Richa Dubey, Ketaki Patil, Sarath Chandra Dantu, Parnika Bhatia, Nikita Malik, Jhankar D. Acharya, Soham Sarkar, Soumadwip Ghosh, Rajarshi Chakrabarti, Shilpy Sharma, Ashutosh Kumar, Biochemical Journal 476, 889-907 (2019).
29. Salt Induced Structural Collapse, Swelling and Signature of Aggregation of Two ssDNA Strands: Insights from Molecular Dynamics Simulation - Soham Sarkar, Atanu Maity, Aditya Sarma Phukon, Soumadwip Ghosh and Rajarshi Chakrabarti, J. Phys. Chem. B 123, 47 (2019).
2018
28. Rheological consequences of wet and dry friction in a dumbbell model with hydrodynamic interactions and internal viscosity - R. Kailasham, Rajarshi Chakrabarti and J. Ravi Prakash, J. Chem. Phys. 149, 094903 (2018). (This article has been selected as a 2018 Editors' Choice article).
27. Entropy production and work fluctuation relations for a single particle in active bath - Subhasish Chaki and Rajarshi Chakrabarti, Physica A: Statistical Mechanics and its Applications, 511, 302 (2018).
2017
26. Ammonium-based stabilizers effectively counteract the Urea-conferred denaturation in a small protein: Insights from molecular dynamics simulations - Soham Sarkar, Soumadwip Ghosh and Rajarshi Chakrabarti, RSC Adv., 7, 52888 (2017).
25. Can ammonium-based room temperature ionic liquid counteract the urea-induced denaturation of a small peptide? - Soumadwip Ghosh, Souvik Dey, Mahendra Patel and Rajarshi Chakrabarti, Phys. Chem. Chem. Phys., 19, 7772 (2017). (This article has been featured in an online themed collection: New Frontiers in Indian Research).
2016
24. Molecular Dynamics Simulation Elucidates the Preferential Binding Affinity of Sodium and Tetramethylammonium Ions for Tetrameric Nafion Unit under Aqueous Conditions - Soumadwip Ghosh and Rajarshi Chakrabarti, RSC Adv., 6, 97961 (2016).
23. Tracer Diffusion in a sea of polymers with binding zones: Mobile vs frozen traps - Nairhita Samanta and Rajarshi Chakrabarti, Soft Matter, 12, 8554 (2016). (This article has been featured in an online themed collection: New Frontiers in Indian Research).
22. Unzipping of Double-Stranded Ribonucleic Acids by Graphene and Single-Walled Carbon Nanotube: Helix Geometry versus Surface Curvature - Soumadwip Ghosh and Rajarshi Chakrabarti, J. Phys. Chem. C, 120, 22681 (2016).
21. Spontaneous unzipping of Xylonucleic acid on Single-walled carbon nanotube: a computational study - Soumadwip Ghosh and Rajarshi Chakrabarti, J. Phys. Chem. B, 120, 3642 (2016).
20. Chain reconfiguration in active noise - Nairhita Samanta and Rajarshi Chakrabarti, J. Phys. A: Math & Theo. 49, 195601 (2016). (This article has received the top cited author award in Mathematics from India).
19. Probing the salt concentration dependent nucleobase distributions in a single stranded DNA-single walled nanotube hybrid with molecular dynamics - Soumadwip Ghosh, Nisheet Patel and Rajarshi Chakrabarti, J. Phys. Chem. B, 120, 455 (2016). (Correction (spelling): J. Phys. Chem. B, 120, 2868 (2016)).
18. Reconfiguration Dynamics in folded and intrinsically disordered protein with internal friction: Effect of solvent quality and denaturant - Nairhita Samanta and Rajarshi Chakrabarti, Physica A: Statistical Mechanics and its Applications, 450, 165 (2016).
17. Thermodynamics of site specific small molecular ion interaction with DNA duplex : a molecular dynamics study - Soumadwip Ghosh, Mayank K Dixit and Rajarshi Chakrabarti, Mole. Simul., 42, 715 (2016).
2015
16. Ion assisted structural collapse of a single stranded DNA: a molecular dynamics approach - Soumadwip Ghosh, Himanshu Dixit and Rajarshi Chakrabarti, Chem. Phys., 459, 137 (2015).
15. Looping Dynamics of a flexible chain with internal friction at different degrees of compactness - Nairhita Samanta and Rajarshi Chakrabarti, Physica A: Statistical Mechanics and its Applications, 436, 377 (2015).
2014
14. Looping and reconfiguration dynamics of a flexible chain with internal friction - Nairhita Samanta, Jayanta Ghosh and Rajarshi Chakrabarti, AIP Adv., 4, 067102 (2014).
13. Diffusion in an elastic medium: A model for macromolecule transport across the nuclear pore complex - Rajarshi Chakrabarti, Ananya Debnath and K. L. Sebastian, Physica A: Statistical Mechanics and its Applications, 404, 65 (2014).
2013
12. End to end loop formation in a single polymer chain with internal friction - Nairhita Samanta and Rajarshi Chakrabarti, Chem. Phys. Letts., 582, 71 (2013).
11. Tracer diffusion in crowded cylindrical channel - Rajarshi Chakrabarti, Stefan Kesselheim, Peter Košovan and Christian Holm, Phys. Rev. E, 87, 062709 (2013).
Publications: Pre IIT Bombay
10. Dynamics of end-to-end loop formation for an isolated chain in viscoelastic fluid - Rajarshi Chakrabarti, Physica A: Statistical Mechanics and its Applications, 391, 5326 (2012).
9. Dynamics of end-to-end loop formation: A flexible chain in the presence of hydrodynamic interaction – Rajarshi Chakrabarti, Physica A: Statistical Mechanics and its Applications, 391, 4081 (2012).
8. Packing Correlations, Collective Scattering and Compressibility of Fractal-like Aggregates in Polymer Nanocomposites and Suspensions – Rajarshi Chakrabarti, Jean-Yves Delannoy, Marc Couty and Kenneth S Schweizer, Soft Matter, 7, 5397 (2011).
7. Bubble dynamics in double stranded DNA: A Rouse chain based approach – Rajarshi Chakrabarti, Chem. Phys. Letts., 502, 107 (2011).
6. Polymer mediated structure of nanoparticles in dense melts: transferability and effective one component approach - Rajarshi Chakrabarti and Kenneth S. Schweizer, J. Chem. Phys. 133, 144905 (2010).
5. Dynamic disorder with exponential sink – Rajarshi Chakrabarti, Chem. Phys. Letts., 495, 60 (2010).
4. A lower bound to the survival probability and an approximate first passage time distribution for Markovian and non-Markovian dynamics in phase space - Rajarshi Chakrabarti and K. L. Sebastian, J. Chem. Phys. 131, 224504 (2009).
3. Transient state work fluctuation theorem for a classical harmonic oscillator linearly coupled to a harmonic bath - Rajarshi Chakrabarti, Pramana – J. Phys., 72(4), 665, (2009).
2. Exact Analytical Evaluation of Time Dependent Transmission Coefficient from the method of reactive flux for an inverted parabolic barrier- Rajarshi Chakrabarti, J. Chem. Phys., 126 (13), 134106 (2007).
1. Rate Processes with Dynamical Disorder: A Direct Variational Approach - Ananya Debnath, Rajarshi Chakrabarti and K. L. Sebastian, J. Chem. Phys., 124 (20), 204111 (2006).
Conference Proceedings:
1. How does the tail length and separation between the tagged monomers influence the reconfiguration of a chain with internal friction for different solvent-quality? - Nairhita Samanta and Rajarshi Chakrabarti, J. Phys : Conf. Ser, 759, 012014 (2016).