Publications
From IISER Pune
2024
51. Theoretical Understanding of Dynamic Catalysis, P. Jangid, S. Chaudhury*# and A. B Kolomeisky*#, J. Phys. Chem. C 128, 9077 (2024) (#equal contribution)
50. Macromolecular crowding facilitates ssDNA capture within biological nanopores: Role of size variation and solution heterogeneity, B. Punia and S. Chaudhury*, J. Phys. Chem. B. 128, 1876 (2024)
49. Multivalent Salt-Induced Self-Assembly of Amphiphilic Polyelectrolytes of Different Charge Fractions: A Coarse-Grained Molecular Dynamics Simulation Study, A. Chauhan and S. Chaudhury*, J. Phys. Chem. B. 128, 2037 (2024)
2023
48. How Heterogeneity Affects Cooperative Communications within Single Nanocatalysts, B. Punia and S. Chaudhury*# and A. B Kolomeisky*#, J. Phys. Chem. Lett 14, 8227 (2023) (#equal contribution)
47. Exploring the role of heterogeneity in Quorum sensing cells: A discrete state stochastic approach, P. Jangid and S. Chaudhury*, J. Sat. Mech: Theory and Experiment, 093501 (2023)
46. Microscopic Mechanism of Macromolecular Crowder-Assisted DNA Capture and Translocation through Biological Nanopores, B. Punia and S. Chaudhury*, J. Phys. Chem. B. 127, 5850 (2023)
45. Dynamics of chemical reactions on single nanocatalysts with heterogeneous active sites, S. Chaudhury*#, P. Jangid and A.B. Kolomeisky*#, J. Chem. Phys. 158, 074101 (2023) (#equal contribution)
2022
44. Theoretical Tools to Quantify Stochastic Fluctuations in Single-Molecule Catalysis by Enzymes and Nanoparticles, D. Singh, B. Punia and S. Chaudhury*, ACS Omega, 7, 47587 (2022) (invited review)
43. Theoretical Insights into the Full Description of DNA Target Search by Subdiffusing Proteins, B. Punia and S. Chaudhury*, Phys. Chem. Chem. Phys. 24, 29074 (2022).
42. Coupling Effects of Electrostatic Interactions and Salt Concentration Gradient in Polymer Translocation Through a Nanopore: A Coarse-Grained Molecular Dynamics Simulations Study, A. Dabhade, A. Chauhan and S. Chaudhury*, ChemPhysChem, e202200666 (2022).
41. Dynamics of the Protein Search for Targets on DNA in Quorum Sensing Cells, K. Mondal and S. Chaudhury*, Biophysical Journal, 121, 2398 (2022).
40. Influence of Nonspecific Interaction between Proteins and in vivo Cytoplasmic Crowders in Facilitated Diffusion of Proteins: Theoretical Insights, B. Punia and S. Chaudhury*, J. Phys. Chem. B, 126, 3037 (2022).
39. A single-molecule stochastic theory of protein- ligand binding in the presence of multiple unfolding/folding and ligand binding pathways, D. Singh and S. Chaudhury*, Biophysical Chemistry, 285, 106803 (2022).
38. Microscopic mechanisms of cooperative communications within single nanocatalysts, B. Punia and S. Chaudhury*# and A. B Kolomeisky*#, Proc. Natl. Acad. Sci. USA, 119, e2115135119 (2022). (#equal contribution)
2021
37. Understanding the Reaction Dynamics on Heterogeneous Catalysts Using a Simple Stochastic Approach, B. Punia and S. Chaudhury*# and A. B Kolomeisky*#, J. Phys. Chem. Lett. 12, 11802 (2021). (#equal contribution)
36. Simulation Study of the Conformational Properties of Diblock Polyelectrolytes in Salt Solutions, A. Dabhade and S. Chaudhury*, Chem Asian J. 16, 3354 (2021)
35. Theoretical study of the role of dynamic crowders in the protein search for targets on DNA, B. Punia and S. Chaudhury*, J. Sat. Mech: Theory and Experiment 073502 (2021).
34. Effect of Memory and Inertial contribution on Transition Time Distributions: Theory and Simulation, D. Singh, K. Mondal and S. Chaudhury*, J. Phys. Chem. B 125, 4536 (2021).
2020
33. Pulling a folded polymer through a nanopore, B. Ghosh, J. Sarabadani*, S. Chaudhury* and T. A- Nissila, J. Phys. Condes. Matter 33, 015101 (2021).
32. A theoretical study of the role of bulk crowders on target search dynamics of DNA binding proteins, K. Mondal and S. Chaudhury*, J. Sat. Mech: Theory and Experiment 093204 (2020).
31. Coarse-grained molecular dynamics simulations study of the conformational properties of single polyelectrolyte diblock copolymers, M. Samanta and S. Chaudhury*, Biophysical Chemistry, 266, 106437 (2020).
30. Effect of DNA Conformation on the Protein Search for Targets on DNA: A Theoretical Perspective, K. Mondal and S. Chaudhury*, J. Phys. Chem. B 124, 3518 (2020)
29. Theoretical Investigations of the Dynamics of Chemical Reactions on Nanocatalysts with Multiple Active Sites, S. Chaudhury*#, D. Singh and A.B. Kolomeisky*#, J. Phys. Chem. Lett. 11, 2330 (2020). (#equal contribution)
2019
28. Single-molecule kinetics of an enzyme in the phosphorylation- dephosphorylation cycle, D. Singh and S. Chaudhury*, J. India Chem. Soc. 96, 967 (2019) [invited article in a Special Issue on "Theoretical Chemistry"].
27. Theoretical Study of the Conditional Non-Monotonic off rate dependence of catalytic reaction rates in single enzymes in the Presence of Conformational Fluctuations, D. Singh and S. Chaudhury*, Chem. Phys. 523, 150 (2019).
26. Translocation Dynamics of an Asymmetrically charged polymer through a Pore under the influence of different pH conditions, B. Ghosh and S. Chaudhury*, J. Phys. Chem. B 123, 4318 (2019).
2018
25. Effect of Substrate Number Fluctuations in Stochastic Enzyme Kinetics, D. Singh and S. Chaudhury*, ACS Omega 3, 5574 (2018).
24. Single-Molecule Kinetics of an Enzyme in the Presence of Multiple Substrates, D. Singh and S. Chaudhury*, ChemBioChem 18, 842 (2018).
23. Influence of the Location of Attractive Polymer-Pore Interactions on Translocation Dynamics, B. Ghosh and S. Chaudhury*, J. Phys. Chem. B 122, 360 (2018).
2017
22. Dynamics of end-pulled polymer translocation through a nanopore, J. Sarabadani*, B.Ghosh, S. Chaudhury* and T.A-Nissila, Euro Phys. Lett. 120, 38004 (2017).
21. Statistical properties of fluctuating enzymes with dynamic cooperativity using a first passage time distribution formalism, D. Singh and S. Chaudhury*, J. Chem. Phys. 146, 145103 (2017).
20. A stochastic theoretical approach to study the size-dependent catalytic activity of a metal nanoparticle at the single- molecule level, D. Singh and S. Chaudhury*, Phys. Chem. Chem. Phys. 19, 8889- 8895 (2017).
2016
19. Fluctuation theorems for total entropy production in generalized Langevin systems, B. Ghosh and S. Chaudhury*, Physica A: Statistical Mechanics and its Applications (2016).
2015
18. Modeling the heterogeneous catalytic activity of a single nanoparticle using a first passage time distribution formalism, A. Das and S. Chaudhury*, Chem. Phys. Lett. 641, 193-198 (2015).
17. Modeling the effect of transcriptional noise on switching in gene networks in a genetic bistable switch, S. Chaudhury*, J. Biol. Phys. 41, 235 (2015).
2014
16. Poisson indicator and Fano Factor for probing dynamic disorder in single molecule enzyme inhibition kinetics, S. Chaudhury*, J. Phys. Chem. B, 118, 10405 (2014).
Before joining IISER Pune
15. Universality of Poisson indicator and Fano factor of transport event statistics in ion channels and enzyme kinetics, S. Chaudhury*, J. Cao and N. A. Sinitsyn, J. Phys. Chem. B, 117, 503 (2013).
14. Spontaneous clearance of viral infections by mesoscopic fluctuations, S. Chaudhury*, A. S. Perelson, and N. A. Sinitsyn, PLoS ONE, 7, e38549 (2012).
13. Dynamic disorder in quasi- equilibrium enzymatic systems, S. Chaudhury and O. A. Igoshin, PLoS ONE, 5, e12364(2010).
12. A harmonic transition state approximation for the duration of reactive events in complex molecular rearrangements, S. Chaudhury and D. E. Makarov, J. Chem. Phys, 133, 034118 (2010).
11. Dynamic-disorder driven substrate inhibition and bistability in simple enzymatic reaction, S. Chaudhury and O. A. Igoshin, J. Phys. Chem. B 113, 13421(2009).
10. A re-examination of non-equilibrium work relations for forced harmonic oscillators in non-Markovian heat baths, S. Chaudhury, D. Chatterjee and B. J. Cherayil, J. Stat. Mech. P10006 (2008).
9. The dynamics of single enzyme reactions: A reconsideration of the Kramers model for colored noise processes, S. Chaudhury, D. Chatterjee and B. J. Cherayil, J. Chem. Phys. 129, 075104 (2008).
8. A model of anomalous chain translocation dynamics, S. Chaudhury and B. J. Cherayil, J. Phys. Chem. B, 112, 15973 (2008) (Part of the “Karl Freed Festschrift”).
7. The dynamics of intermittent strand separation in double-stranded DNA, D. Chatterjee, S. Chaudhury and B. J. Cherayil, J. Chem. Phys. 127, 155104 (2007).
6. Modulation of electron transfer kinetics by protein conformational fluctuations during early-stage photosynthesis, S. Chaudhury and B. J. Cherayil, J. Chem. Phys. 127, 145103 (2007).
5. Dynamic disorder in single-molecule Michaelis-Menten kinetics: The reaction-diffusion formalism in the Wilemski-Fixman approximation, S. Chaudhury and B. J. Cherayil, J. Chem. Phys. 127, 1051034 (2007).
4. A model of fluorescence intermittency in single enzymes, S. Chaudhury, S.C. Kou and B. J. Cherayil, J. Phys. Chem. B 111, 2377 (2007).
3. Structural relaxation in complex liquids: Non-Markovian dynamics in a bistable potential, S. Chaudhury and B. J. Cherayil, J. Chem. Phys. 125, 184505 (2006).
2. First passage time distribution for barrier crossing in a double well under fractional Gaussian noise, S. Chaudhury and B. J. Cherayil, J. Chem. Phys. 125, 114106 (2006).
1.Complex chemical kinetics in single enzyme molecules: Kramers model with fractional Gaussian noise, S. Chaudhury and B. J. Cherayil, J. Chem. Phys. 125, 024904 (2006).