1. P. Jangid, S. Chaudhury*#, and A.B. Kolomeisky*#, Effect of Temperature in Dynamic Catalysis, J. Phys. Chem. C 2025, in press (# equal contribution)
2. A. Chauhan and S. Chaudhury*, Influence of Crowder Geometry and Flexibility on Polymer Translocation Dynamics, Chem. Asian J. 2025 , in press
3. A. Chauhan and S. Chaudhury*, Understanding Anti-Polyelectrolyte Effect in Polyzwitterions Using Coarse-Grained Molecular Dynamics Simulations, J. Phys. Chem. B 2025, 129, 3253–3262
4. P. Jangid and S. Chaudhury*, Transition Path Dynamics of Non-Markovian Systems across a Rough Potential Barrier, J. Phys. Chem. A 2024, 128, 10041–10052.
5. B. Punia and S. Chaudhury*# and A. B Kolomeisky* #, How Dynamic Surface Restructuring Impacts Intra-Particle Catalytic Cooperativity, J. Chem. Phys. 2024, 161, 194107. (# equal contribution).
6. P. Jangid, B. Punia and S. Chaudhury*, Stochastic dynamics of hairballs in single-polymer growth, Phys. Chem. Chem. Phys. 2024, 26, 29749- 29758
7. P. Jangid, S. Chaudhury*#, and A.B. Kolomeisky*#, Theoretical Understanding of Dynamic Catalysis, J. Phys. Chem. C 2024, 128, 9077- 9089 (# equal contribution)
8. A. Chauhan and S. Chaudhury*, Multivalent Salt-Induced Self-Assembly of Amphiphilic Polyelectrolytes of Different Charge Fractions: A Coarse-Grained Molecular Dynamics Simulation Study, J. Phys. Chem. B 2024, 128, 2037- 2044.
9. B. Punia and S. Chaudhury*, Macromolecular crowding facilitates ssDNA capture within biological nanopores: Role of size variation and solution heterogeneity, J. Phys. Chem. B 2024, 128, 1876- 1883.
10. P. Jangid and S. Chaudhury*, Exploring the role of heterogeneity in Quorum sensing cells: A discrete state stochastic approach, J. Sat. Mech: Theory and Experiment 2023, 093501.
11. B. Punia and S. Chaudhury* # and A. B Kolomeisky* #, How Heterogeneity Affects Cooperative Communications within Single Nanocatalysts, J. Phys. Chem. Lett. 2023, 14, 8227–8234. (# equal contribution)
12. B. Punia and S. Chaudhury*, Microscopic mechanism of Macromolecular Crowder-Assisted DNA Capture and Translocation through Biological Nanopores, J. Phys. Chem. B 2023, 127, 5850-5858. (cover page article)
13. S. Chaudhury*, P. Jangid and A.B. Kolomeisky*, Dynamics of chemical reactions on single nanocatalysts with heterogeneous active sites, J. Chem. Phys. 2023, 158, 074101.
14. D. Singh, B. Punia and S. Chaudhury*, Theoretical Tools to Quantify Stochastic Fluctuations in Single-Molecule Catalysis by Enzymes and Nanoparticles, ACS Omega 2022, 7, 47587- 47600. (invited mini review)
15. B. Punia and S. Chaudhury*, Theoretical Insights into the Full Description of DNA Target Search by Subdiffusing Proteins, Phys. Chem. Chem. Phys. 2022, 24, 29074 -29083.
16. A. Dabhade, A. Chauhan and S. Chaudhury*, Coupling Effects of Electrostatic Interactions and Salt Concentration Gradient in Polymer Translocation Through a Nanopore: A Coarse-Grained Molecular Dynamics Simulations Study, ChemPhysChem 2022, e202200666.
17. K. Mondal and S. Chaudhury*, Dynamics of the Protein Search for Targets on DNA in Quorum Sensing Cells, Biophys. J. 2022, 121, 2398-2410.
18. B. Punia and S. Chaudhury*, Influence of Nonspecific Interaction between Proteins and in vivo Cytoplasmic Crowders in Facilitated Diffusion of Proteins: Theoretical Insights, J. Phys. Chem. B 2022 126, 3037-3047.
19. D. Singh and S. Chaudhury*, A single-molecule stochastic theory of protein-ligand binding in the presence of multiple unfolding/folding and ligand binding pathways, Biophysical Chemistry 2022, 285, 106803.
20. B. Punia and S. Chaudhury* # and A. B Kolomeisky* #, Microscopic mechanisms of cooperative communications within single nanocatalysts, Proc. Natl. Acad. Sci. USA 2022, 119, e2115135119. (# equal contribution)
21. B. Punia and S. Chaudhury* # and A. B Kolomeisky* #, Understanding the Reaction Dynamics on Heterogeneous Catalysts Using a Simple Stochastic Approach, J. Phys. Chem. Lett. 12 2021, 11802-11810. (# equal contribution)
22. A. Dabhade and S. Chaudhury*, Simulation Study of the Conformational Properties of Diblock Polyelectrolytes in Salt Solutions, Chem. Asian J. 2021, 16, 3354- 3362.
23. B. Punia and S. Chaudhury*, Theoretical study of the role of dynamic crowders in the protein search for targets on DNA, J. Stat. Mech: Theory and Experiment 2021, 073502
24. D. Singh, K. Mondal and S. Chaudhury*, Effect of Memory and Inertial Contribution on Transition Time Distributions: Theory and Simulation, J. Phys. Chem. B 2021,125, 4536–4545.
25. B. Ghosh, J. Sarabadani*, S. Chaudhury* and T. A- Nissila, 2021 Pulling a folded polymer through a nanopore, J. Phys. Condens. Matter 2021, 33, 015101.
26. K. Mondal and S. Chaudhury*, A theoretical study of the role of bulk crowders on target search dynamics of DNA binding proteins, J. Stat. Mech: Theory and Experiment 2020, 093204.
27. M. Samanta and S. Chaudhury*, Coarse-grained molecular dynamics simulations study of the conformational properties of single polyelectrolyte diblock copolymers, Biophysical Chemistry 2020, 266, 106437.
28. K. Mondal and S. Chaudhury*, Effect of DNA Conformation on the Protein Search for Targets on DNA: A Theoretical Perspective, J. Phys. Chem. B 2020,124, 3518- 3526.
29. S. Chaudhury*, D. Singh and A.B. Kolomeisky*, Theoretical Investigations of the Dynamics of Chemical Reactions on Nanocatalysts with Multiple Active Sites, J. Phys. Chem. Lett. 2020,11, 2330-2335.
30. D. Singh and S. Chaudhury*, Single-molecule kinetics of an enzyme in the phosphorylation- dephosphorylation cycle, J. Indian Chem. Soc. 2019, 96, 967 [Invited article in the Special Issue on Theoretical Chemistry]
31. D. Singh and S. Chaudhury*, Theoretical Study of the Conditional Non- Monotonic off Rate Dependence of Catalytic Reaction Rates in single enzymes in the Presence of Conformational Fluctuations, Chem. Phys. 2019, 523, 150-159.
32. B. Ghosh and S. Chaudhury*, Translocation Dynamics of an Asymmetrical Charged Polymer Though a Pore Under the Influence of Different pH Conditions, J. Phys. Chem. B 2019, 123, 4318-4323.
33. D. Singh and S. Chaudhury*, Effect of Substrate Number Fluctuations in Single Enzyme Kinetics, ACS Omega 2018, 3, 5574-5583 (by invitation)
34. D. Singh and S. Chaudhury*, Single-molecule kinetics of an enzyme in the presence of multiple substrates, ChemBioChem 2018, 19, 842-850.
35. B. Ghosh and S. Chaudhury*, Influence of the Location of Attractive Polymer-Pore Interactions on Translocation Dynamics, J. Phys. Chem. B 2018, 122, 360-368.
36. J. Sarabadani*, B. Ghosh, S. Chaudhury*, and T.A-Nissila, Dynamics of end-pulled polymer translocation through a nanopore, Euro. Phys. Lett. 2017, 120, 38004.
37. D. Singh and S. Chaudhury*, Statistical properties of fluctuating enzymes with dynamic cooperativity using a first passage time distribution formalism, J. Chem. Phys. 2017, 146, 145103.
38. D. Singh and S. Chaudhury*, A stochastic theoretical approach to study the size-dependent catalytic activity of a metal nanoparticle at the single-molecule level, Phys. Chem. Chem. Phys. 2017, 19, 8889-8895.
39. B. Ghosh and S. Chaudhury*, Fluctuation theorems for total entropy production in generalized Langevin systems, Physica A: Statistical Mechanics and its Applications 2017, 466, 133-139.
40. A. Das and S. Chaudhury*, Modeling the heterogeneous catalytic activity of a single nanoparticle using a first passage time distribution formalism, Chem. Phys. Lett. 2015, 641,193-198.
41. S. Chaudhury*, Modeling the effect of transcriptional noise on switching in gene networks in a genetic bistable switch, J. Biol. Phys. 2015, 41, 235-246.
42. S. Chaudhury*, Poisson Indicator and Fano Factor for Probing Dynamic Disorder in Single-Molecule Enzyme Inhibition Kinetics, S. Chaudhury*, J. Phys. Chem. B 2014, 118, 10405- 10412.
43. S. Chaudhury*, J. Cao and N. A. Sinitsyn, Universality of Poisson indicator and Fano factor transport event statistics in ion channels and enzyme kinetics, J. Phys. Chem. B 2013, 117, 503-509.
44. S. Chaudhury*, A. S. Perelson and N. A. Sinitsyn, Spontaneous Clearance of Viral Infections by Mesoscopic Fluctuations, PLoS ONE 2012, 7, e38549.
45. S. Chaudhury and D. E. Makarov, A harmonic transition state approximation for the duration of reactive events in complex molecular rearrangements, J. Chem. Phys. 2010, 133, 034118.
46. S. Chaudhury and O. A. Igoshin, Dynamic disorder in quasi-equilibrium enzymatic systems, PLoS ONE 2010, 5, e12364.
47. S. Chaudhury and O. A. Igoshin, Dynamic-disorder driven substrate inhibition and bistability in simple enzymatic reaction, J. Phys. Chem. B 2009, 113, 13421-13428.
48. S. Chaudhury, D. Chatterjee and B. J. Cherayil, A re-examination of non-equilibrium work relations for forced harmonic oscillators in non- Markovian heat baths, J. Stat. Mech: Theory and Experiment 2008, P10006.
49. S. Chaudhury, D. Chatterjee and B. J. Cherayil, The dynamics of single enzyme reactions: A reconsideration of the Kramers model for colored noise processes, J. Chem. Phys. 2008, 129, 075104.
50. S. Chaudhury and B. J. Cherayil, A model of anomalous chain translocation dynamics, J. Phys. Chem. B 2008, 112, 15973-15979 (Part of the “Karl Freed Festschrift”).
51. D. Chatterjee, S. Chaudhury and B. J. Cherayil, The dynamics of intermittent strand separation in double-stranded DNA, J. Chem. Phys. 2007, 127, 155104.
52. S. Chaudhury and B. J. Cherayil, Modulation of electron transfer kinetics by protein conformational fluctuations during early-stage photosynthesis, J. Chem. Phys. 2007, 127, 145103.
53. S. Chaudhury and B. J. Cherayil, Dynamic disorder in single-molecule Michaelis-Menten kinetics: The reaction-diffusion formalism in the Wilemski- Fixman approximation, J. Chem. Phys. 2007, 127, 1051034.
54. S. Chaudhury, S.C. Kou and B. J. Cherayil, A model of fluorescence intermittency in single enzymes, J. Phys. Chem. B 2007, 111, 2377-2384.
55. S. Chaudhury and B. J. Cherayil, Structural relaxation in complex liquids: Non-Markovian dynamics in a bistable potential, J. Chem. Phys. 2006, 125, 184505.
56. S. Chaudhury and B. J. Cherayil, First passage time distribution for barrier crossing in a double well under fractional Gaussian noise, J. Chem. Phys. 2006, 125, 114106.
57. S. Chaudhury and B. J. Cherayil, 2006 Complex chemical kinetics in single enzyme molecules: Kramers model with fractional Gaussian noise, J. Chem. Phys. 2006, 125, 02490.