Publications: IIT Bombay
2023
57. 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).
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).