1. Shankha Narayan Chattopadhyaya, Inayat Ullah Irshad, Ajeet K. Sharma, Arvind Kumar Gupta, Parameter sensitivity and critical transition anticipation in bistable toxin-antitoxin dynamics, submitted to journal (2025)
2. Rupal Chauhan and Ajeet K. Sharma, Synergies and Trade-offs in the Heat Shock Response Mechanism, submitted to journal (2025)
3. Swayamshree Senapati, Ajeet K. Sharma, and Hemant Kumar, Kinetic model of E-P condensates dynamic reveals transcriptional speed, noise, energy trade-offs, submitted to journal (2025)
4. Biswajit Das, Jianhua Xing, Ajeet K. Sharma, and Hao Ge, The asymmetric torque-speed relationship reveal that the hook functions as a clutch for a bacterial flagellar motor, submitted to journal (2025)
5. Alfred M. Lentzsch, Ziyi Fan, Inayat U. Irshad, Edward P. O’Brien, Ajeet K. Sharma, Rachel Green, and Shu-ou Shan, HYPK promotes N-terminal acetylation through rapid ribosome exchange of NatA, Molecular Cell (2025)
6. Mahima, Anandamohan Ghosh, and Ajeet K. Sharma, The Dual Influence of Transcriptional and Translational Kinetics on Gene Expression Noise, Physical Review E, Vol. 112, 4 (2025).
7. Aneesa Manzoor, Mahima, Pushkin Kachroo, R. Uma Shankar, and Ajeet K. Sharma*, Stochastic dynamics in determining fertilization outcomes: effect of gamete number and travel path length, The European Physical Journal E, Vol. 48, 37 (2025)
8. Swayamshree Senapati, Inayat Ullah Irshad, Ajeet K. Sharma, Hemant Kumar, Predicting gene expression changes from chromatin structure modification, npj Systems Biology and Applications 11, 34 (2025).
9. Rupal Chauhan and Ajeet K. Sharma*, The speed-energy-efficiency trade-off in Hsp70 chaperone system, The Journal of Physical Chemistry B, Vol. 128, 49 (2024).
10. Inayat U. Irshad and Ajeet K. Sharma* Understanding the regulation of protein synthesis under stress conditions, Biophysical Journal, Volume 123, Issue 20, 3627 – 3639 (2024).
11. Sulagno Chakarborty, Inayat Ullah Irshad, Mahima, Ajeet K Sharma*, TIR predictor and optimizer: Web-tools for accurate prediction of translation initiation rate and precision gene design in Saccharomyces cerevisiae, Biotechnology Journal 19, e2400081 (2024).
12. Inayat U. Irshad and Ajeet K. Sharma*, Accurate estimation of translation rate parameters explains stoichiometric protein synthesis in E. coli, Biophysical Reports 3, 100131 (2023)
13. Swayamshree Senapati, Inayat U. Irshad, Ajeet K. Sharma and Hemant Kumar, Fundamental Insights into the Correlation between Chromosome Configuration and Transcription, Physical Biology, 20 051002 (2023)
14. Mahima and Ajeet K. Sharma, Optimization of ribosome utilization in Saccharomyces cerevisiae, PNAS Nexus 2, pgad074 (2023)
15. Ajeet K. Sharma, Johannes Venezian, Ayala Shiber, Günter Kramer, Bernd Bukau, and Edward P. O’Brien, Combinations of slow-translating codon clusters can increase mRNA half-life in Saccharomyces cerevisiae, Proceedings of the National Academy of Sciences of the United States of America 118, e2026362118 (2021)
16. Vandana Yadav#, Inayat Ullah Irshad#, Hemant Kumar and Ajeet K. Sharma*, Quantitative Modeling of protein Syntehsis using ribosome profiling data, Frontiers in Molecular Biosciences 8, 688700 (2021)
# Equal Contribution
* Corresponding Author
17. Ajeet K Sharma, Translational autoregulation of RF2 protein in E. coli through programmed frameshifting, Physical Review E 103, 062412 (2021).
18. David K Wolfe, Joseph R Persichetti, Ajeet K Sharma, Phillip S Hudson, H Lee Woodcock, Edward P O’Brien, Hierarchical Markov State Model Building to Describe Molecular Processes, Journal of Chemical Theory and Computation 16, 1816 (2020).
19. Ajeet K. Sharma, Pietro Sormanni, Nabeel Ahmed, Prajwal Ciryam, Ulrike Friedrich, Guenter Kramer and Edward P. O’Brien, A chemical kinetic basis for measuring translation initiation and elongation rates from ribosome profiling data, PLoS computational Biology 15, e1007070 (2019).
20. Avi J. Samelson, Eric Bolin, Shawn M. Costello, Ajeet K. Sharma, Edward P. O’Brien and Susan Marqusee, The ribosome tunes nascent chain folding away from aggregation-prone folding intermediates, Science Advances 4, eaas9098 (2018).
21. Ajeet K. Sharma, Nabeel Ahmed and Edward P. O’Brien, Determinants of translation speed are randomly distributed across transcripts resulting in a universal scaling of protein synthesis times, Phys. Rev. E 97, 022409 (2018).
22. Ajeet K. Sharma and Edward P. O’Brien, Non-equilibrium coupling of protein structure and function to translation-elongation kinetics, Current Opinion in Structural Biology 49, 94 (2018).
23. Ajeet K. Sharma and Edward P. O’Brien, Increasing protein production rates can decrease the rate at which functional protein is produced and their steady-state levels, The Journal of Physical Chemistry B 121, 6775 (2017)
24. Ajeet K. Sharma, Bernd Bukau and Edward P. O’Brien, Physical origins of codon positions that strongly influence cotranslational folding: A framework for controlling nascent-protein folding, J. Am. Chem. Soc. 138, 1180 (2016).
25. Daniel A. Nissley, Ajeet K. Sharma, Nabeel Ahmed, Ulrike A. Friedrich, Gunter Kramer, Bernd Bukau and Edward P. O’Brien, Accurate prediction of cellular co-translational folding indicates proteins can switch from post- to co-translational folding, Nature Communications 7, 10341 (2016).
26. Colin D. Kinz-Thompson#, Ajeet K. Sharma#, Joachim Frank, Ruben L. Gonzalez Jr. and Debashish Chowdhury, Quantitative connection between ensemble thermodynamics and single- molecule kinetics: A case study using cryogenic electron microscopy and single-molecule fluorescence resonance energy transfer investigations of the ribosome, The Journal of Physical Chemistry B 119, 10888 (2015).
# Equal Contribution
27. Ajeet K. Sharma#, Blerta Shtylla# and Debashish Chowdhury, Distribution of lifetimes of kinetochore-microtubule attachments:interplay of energy landscape, molecular motors and mi crotubule (de-) polymerization, Phys. Biol. 11, 036004 (2014).
# Equal Contribution
28. Ajeet K. Sharma and Debashish Chowdhury, First-passage problems in DNA replication: effects of template tension on stepping and exonuclease activities of a DNA polymerase motor, J. Phys.: Condens. Matter 25, 374105 (2013).
29. Ajeet K. Sharma and Debashish Chowdhury, Template-directed biopolymerization: tape-
copying turing machine, Biophysical Reviews and Letters 7, 135 (2012)
30. Ajeet K. Sharma and Debashish Chowdhury, Error correction during DNA replication, Phys. Rev. E 86, 011913 (2012).
31. Ajeet K. Sharma and Debashish Chowdhury, Stochastic theory of protein synthesis and polysome: ribosome profiling on a single mRNA transcript, J. Theor. Biol. 289, 36-46 (2011)
32. Ajeet K. Sharma and Debashish Chowdhury, Distribution of dwell times of a ribosome: effects of infidelity, kinetic proofreading and ribosome crowding, Physical Biology 8, 026005 (2011).
33. Ajeet K. Sharma and Debashish Chowdhury, Quality control by a mobile molecular workshop: quality versus quantity Phys. Rev. E 82, 031912 (2010) (Selected for the October 1, 2010, issue of the Virtual Journal of Biological Physics Research)
Computational Biology and Biophysics Lab 