1. Transcription-translation coupling shapes global resource allocation in gene expression
Mahima, Ajeet K. Sharma
Submitted to journal (2026)
2. Synergies and Trade-offs in the Heat Shock Response Mechanism
Rupal Chauhan, Biswajit Das and Ajeet K. Sharma
PLOS Computational Biology (2026)
https://doi.org/10.1371/journal.pcbi.1014729
3. Hook stiffness as a mechanical switch for torque regulation in the bacterial flagellar motor.
Biswajit Das, Jianhua Xing, Ajeet K. Sharma, and Hao Ge
Biophysical Journal (2026).
https://doi.org/10.1016/j.bpj.2026.02.018
4. Parameter sensitivity and critical transition anticipation in bistable toxin-antitoxin dynamics
Shankha Narayan Chattopadhyaya, Inayat Ullah Irshad, Ajeet K. Sharma, Arvind Kumar Gupta
Computers in Biology and Medicine, Vol. 204, 111535 (2026).
https://doi.org/10.1016/j.compbiomed.2026.111535
5. Kinetic model of E-P condensates dynamic reveals transcriptional speed, noise, energy trade-offs
Swayamshree Senapati, Ajeet K. Sharma, and Hemant Kumar
Biophysical Journal, Vol. 125(6), 1543-1559.(2026)
https://doi.org/10.1016/j.bpj.2026.02.015
6. HYPK promotes N-terminal acetylation through rapid ribosome exchange of NatA
Alfred M. Lentzsch, Ziyi Fan, Inayat U. Irshad, Edward P. O’Brien, Ajeet K. Sharma, Rachel Green, and Shu-ou Shan
Molecular cell, Vol. 85(24), 4562-4574 (2025)
https://doi.org/10.1016/j.molcel.2025.11.017
7. The Dual Influence of Transcriptional and Translational Kinetics on Gene Expression Noise
Mahima, Anandamohan Ghosh, and Ajeet K. Sharma
Physical Review E, Vol. 112, 4 (2025).
https://doi.org/10.1103/sc8f-7ldc
8. Stochastic dynamics in determining fertilization outcomes: effect of gamete number and travel path length
Aneesa Manzoor, Mahima, Pushkin Kachroo, R. Uma Shankar, and Ajeet K. Sharma*
The European Physical Journal E, Vol. 48, 37 (2025)
10.1140/epje/s10189-025-00501-7
9. Predicting gene expression changes from chromatin structure modification
Swayamshree Senapati, Inayat Ullah Irshad, Ajeet K. Sharma, Hemant Kumar
npj Systems Biology and Applications 11, 34 (2025).
10.1038/s41540-025-00510-4
10. The speed-energy-efficiency trade-off in Hsp70 chaperone system,
Rupal Chauhan and Ajeet K. Sharma*
The Journal of Physical Chemistry B, Vol. 128, 49 (2024).
https://doi.org/10.1021/acs.jpcb.4c06594
11. Understanding the regulation of protein synthesis under stress conditions
Inayat U. Irshad and Ajeet K. Sharma*
Biophysical Journal, Volume 123, Issue 20, 3627 – 3639 (2024).
https://doi.org/10.1016/j.bpj.2024.09.014
12. TIR predictor and optimizer: Web-tools for accurate prediction of translation initiation rate and precision gene design in Saccharomyces cerevisiae
Sulagno Chakarborty, Inayat Ullah Irshad, Mahima, Ajeet K Sharma*,
Biotechnology Journal 19, e2400081 (2024).
10.1002/biot.202400081
13. Decoding stoichiometric protein synthesis in E. coli through translation rate parametersß
Inayat U. Irshad and Ajeet K. Sharma*
Biophysical Reports 3, 100131 (2023)
10.1016/j.bpr.2023.100131
14. Fundamental Insights into the Correlation between Chromosome Configuration and Transcription
Swayamshree Senapati, Inayat U. Irshad, Ajeet K. Sharma and Hemant Kumar
Physical Biology, 20 051002 (2023)
10.1088/1478-3975/ace8e5
15. Optimization of ribosome utilization in Saccharomyces cerevisiae,
Mahima and Ajeet K. Sharma
PNAS Nexus 2, pgad074 (2023)
PMC10053027
16. Combinations of slow-translating codon clusters can increase mRNA half-life in Saccharomyces cerevisiae
Ajeet K. Sharma, Johannes Venezian, Ayala Shiber, Günter Kramer, Bernd Bukau, and Edward P. O’Brien
Proceedings of the National Academy of Sciences of the United States of America 118, e2026362118 (2021)
10.1073/pnas.2026362118
17. Quantitative Modeling of Protein Synthesis Using Ribosome Profiling Data
Vandana Yadav, Inayat Ullah Irshad, Hemandt Kumar and Ajeet K. Sharma
Frontiers in Molecular Biosciences 8, 688700 (2021)
10.3389/fmolb.2021.688700
# Equal Contribution
* Corresponding Author
18. Translational autoregulation of RF2 protein in E.coli through progammed frameshifting
Ajeet K. Sharma
Physical Review E 103, 062412 (2021)
10.1103/PhysRevE.103.062412
19. Hierarchical Markov State Model Building to Describe Molecular Processes
David K Wolfe, Joseph R Persichetti, Ajeet K Sharma, Phillip S Hudson, H Lee Woodcock, Edward P O’Brien
Journal of Chemical Theory and Computation 16, 1816 (2020)
10.1021/acs.jctc.9b00955
20. A chemical kinetic basis for measuring translation initiation and elongation rates from ribosome profiling data
Ajeet K. Sharma, Pietro Sormanni, Nabeel Ahmed, Prajwal Ciryam, Ulrike Friedrich, Guenter Kramer and Edward P. O’Brien
PLoS computational Biology 15, e1007070 (2019)
10.1371/journal.pcbi.1007070
21. Kinetic and structural comparison of a protein’s cotranslational folding and refolding pathways
Avi J. Samelson, Eric Bolin, Shawn M. Costello, Ajeet K. Sharma, Edward P. O’Brien and Susan Marqusee
Science Advances 4, eaas9098 (2018).
10.1126/sciadv.aas9098
22. Determinants of translation speed are randomly distributed across transcripts resulting in a universal scaling of protein synthesis times
Ajeet K. Sharma, Nabeel Ahmed and Edward P. O’Brien
Phys. Rev. E 97, 022409 (2018)
https://doi.org/10.1103/PhysRevE.97.022409
23. Non-equilibrium coupling of protein structure and function to translation–elongation kinetics
Ajeet K. Sharma and Edward P. O’Brien
Current Opinion in Structural Biology 49, 94 (2018).
https://doi.org/10.1016/j.sbi.2018.01.005
24. Increasing Protein Production Rates Can Decrease the Rate at Which Functional Protein Is Produced and Their Steady-State Level
Ajeet K. Sharma and Edward P. O’Brien
The Journal of Physical Chemistry B 121, 6775 (2017)
https://doi.org/10.1021/acs.jpcb.7b01700
25. Physical Origins of Codon Positions That Strongly Influence Cotranslational Folding: A Framework for Controlling Nascent-Protein Folding
Ajeet K. Sharma, Bernd Bukau and Edward P. O’Brien
J. Am. Chem. Soc. 138, 1180 (2016)
https://doi.org/10.1021/jacs.5b08145
26. Accurate prediction of cellular co-translational folding indicates protein can switch from post-to co-translational folding
Daniel A. Nissley, Ajeet K. Sharma, Nabeel Ahmed, Ulrike A. Friedrich, Gunter Kramer, Bernd Bukau and Edward P. O’Brien
Nature Communications 7, 10341 (2016)
https://doi.org/10.1038/ncomms10341
27. 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
Colin D. Kinz-Thompson#, Ajeet K. Sharma#, Joachim Frank, Ruben L. Gonzalez Jr. and Debashish Chowdhury
The Journal of Physical Chemistry B 119, 10888 (2015).
https://doi.org/10.1021/jp5128805
28. Distribution of lifetimes of kinetochore–microtubule attachments: interplay of energy landscape, molecular motors and microtubule (de-)polymerization
Ajeet K. Sharma#, Blerta Shtylla# and Debashish Chowdhury
Phys. Biol. 11, 036004 (2014).
10.1088/1478-3975/11/3/036004
29. First-passage problems in DNA replication: effects of template tension on stepping and exonuclease activities of a DNA polymerase motor
Ajeet K. Sharma, and Debashish Chowdhury
J. Phys.: Condens. Matter 25, 374105 (2013).
10.1088/0953-8984/25/37/374105
30. Template-directed biopolymerization: tape-copying turing machine
Ajeet K. Sharma, and Debashish Chowdhury
Biophysical Reviews and Letters 7, 135 (2012)
https://doi.org/10.1142/S1793048012300083
31. Error correction during DNA replication
Ajeet K. Sharma, and Debashish Chowdhury
Phys. Rev. E 86, 011913 (2012)
10.1103/PhysRevE.86.011913
32. Stochastic theory of protein synthesis and polysome: Ribosome profile on a single mRNA transcript
Ajeet K. Sharma, and Debashish Chowdhury
J. Theor. Biol. 289, 36-46 (2011)
https://doi.org/10.1016/j.jtbi.2011.08.023
33. Distribution of dwell times of a ribosome: effects of infidelity, kinetic proofreading and ribosome crowding
Ajeet K. Sharma, and Debashish Chowdhury
Physical Biology 8, 026005 (2011)
10.1088/1478-3975/8/2/026005
34. Quality control by a mobile molecular workshop: Quality versus quantity
Ajeet K. Sharma, and Debashish Chowdhury
Phys. Rev. E 82, 031912 (2010) (Selected for the October 1, 2010, issue of the Virtual Journal of Biological Physics Research)
10.1103/PhysRevE.82.031912