Recent Publications (from 2022-2017)
56. Critical assessement of Self-Consistency Checks in the All-Atom Molecular Dynamics Simulation of Intrinsically Disordered Proteins. K. Gaalswyk, A. Haider and K. Ghosh Journal of Chemical Theory and Computation (2023). Manuscript Link
55. Rules of Physical Mathematics Govern Intrinsically Disordered Proteins. K. Ghosh, J. Huihui, A. Haider and M. Phillips Annual Review of Biophysics 51: 355-376 (2022). Manuscript Link
54. Stoichiometric versus stochastic interaction in models of liquid-liquid phase separation. K. Ghosh, Biophysical Journal 121:4-6 (2022). New and Notable Manuscript Link
53. Intra-chain interaction topology can identify functionally similar Intrinsically Disordered Proteins. J. Huihui and K. Ghosh, Biophysical Journal 120:1860-1868 (2021). Manuscript Link
52. Critical Comparison of MaxCal and Other Stochastic Modeling Approaches in Analysis of Gene Networks. T. Firman, J. Huihui, A. R. Clark and K. Ghosh, Entropy 23:357 (2021). Manuscript Link
51. (Almost) Everything in Cotranslational folding makes sense in the light of evolution. K. Ghosh, Biophysical Journal 119:1045 (2020). New and Notable Manuscript Link
50. An analytical theory to describe sequence-specific inter-residue distance profiles for Polyamphoyltes and Intrinsically Disordered Proteins. Jonathan Huihui and K. Ghosh, J. Chem. Phys. Communication 152:161102 (2020). Featured article Manuscript Link
49. A unified analytical theory of heteropolymers for sequence-specific phase behaviors of polyelectrolytes and polyampholytes. Yi-Hsuan Lin, J. Brady, H.S. Chan and K. Ghosh, J. Chem. Phys. 152:045102 (2020). Manuscript Link
48. The Maximum Caliber Variational Principle for Nonequilibria. K. Ghosh, P. Dixit, L. Agozzino, and K. A. Dill Annual Review of Physical Chemistry 71:213-238 (2020). Manuscript Link
47. The anti-aggregation holdase Hsp33 promotes the formation of folded protein structures. F. Moayed, S. Bezrukavnikov, M.N. Naqvi, B. Groitl, C.M. Cremers, G. Kramer, K. Ghosh, U. Jakob, and S.J. Tans Biophysical Journal 118:85-95 (2020). Manuscript Link
46. Maximum Caliber Can Build and Infer Models of Oscillation in a Three-Gene Feedback Network. T. Firman, A. Amgalan, and K. Ghosh J Phys Chem B 123:343-355 (2019). Manuscript Link
45. Kinetic vs. Thermodynamic Control of Mutational Effects on Protein Homeostasis: A Perspective from Computational Modeling and Experiment. K.F.R. Pobre, D.L. Powers, K. Ghosh, L.M. Gierasch, and E.T. Powers Protein Science 28:1324-1339 (2019) . Manuscript Link
44. Modulating charge patterning and ionic strength as a strategy to induce conformational changes in intrinsically disordered proteins. J. Huihui, T. Firman and K. Ghosh J. Chem. Phys. 149: 085101 (2018). Manuscript link
43. Sequence charge decoration dictates coil-globule transition in Intrinsically Disordered Proteins. T. Firman and K. Ghosh J. Chem. Phys. 148: 123305 (2018) Invited contribution. Manuscript link
42. Maximum Caliber Can Characterize Genetic Switches with Multiple Hidden Species. T. Firman, S. Wedekind, T.J. McMorrow and K. Ghosh J. Phys. Chem. B DOI: 10.1021/acs.jpcb.7b12251 (2018). Manuscript Link
41. Ancient Thioredoxins evolved to modern day Stability-Function requirement by altering Native State ensemble T. Modi, J. HuiHui, K. Ghosh and S. Ozkan Philosophical. Transactions of the Royal Society B. 373:1749 DOI: 10.1098/rstb.2017.0184 (2018). Manuscript link
40. Perspective: Maximum Caliber is a general variational principle for dynamical systems. P.D. Dixit, J.A. Wagoner, C. Weistuch, S. Presse, K. Ghosh and K.A. Dill J. Chem. Phys. 148: 010901 (2018). Manuscript link
39. All-atom simulations reveal protein charge decoration in the folded and unfolded ensemble is key in thermophilic adaptation. L. Sawle, J. HuiHui and K. Ghosh J. Chem. Theor. Comp. DOI 10.1021/acs.jctc.7b00545 (2017). Manuscript link
38. Building predictive models of genetic circuits using the principle of Maximum Caliber. T. Firman, G. Balazsi and K. Ghosh Biophysical Journal 113(9):2121-2130 (2017). Manuscript link
Publications (from 2016 - 2009)
37. Role of Proteome Physical Chemistry in Cell Behavior. K. Ghosh, A. M.R. de Graff, L. Sawle and K.A. Dill J Phys Chem B (2016) (Feature article). Manuscript link
36. Convergence of molecular dynamics simulation of protein native states: feasibility vs self-consistency dilemma. L. Sawle and K. Ghosh J. Chem. Theor. Comp (2016). Manuscript link
35. A theoretical method to compute sequence dependent configurational properties in charged polymers and proteins. L. Sawle and K. Ghosh J. Chem. Phys. 143, 085101 (2015). Manuscript link
34. Reply to C. Tsallis `Conceptual Inadequacy of the Shore and Johnson Axioms for Wide Classes of Complex Systems S Pressé, K. Ghosh, J Lee and Ken A. Dill Entropy, 17, 5043-5046 (2015). Manuscript link
33. Proteome folding kinetics is limited by protein halflife. T. Zou, N. Williams, S.B. Ozkan and K. Ghosh PLOS ONE: DOI: 10.1371/journal.pone.0112701 (2014). Manuscript link
32. Nonadditive Entropies Yield Probability Distributions with Biases not Warranted by the Data. S Presse, K. Ghosh, J. Lee and K.A. Dill Phys. Rev. Lett. 111: 180604 (2013). Manuscript link
31. Competition enhances stochasticity in biochemical reactions. T Firman and K. Ghosh J. Chem. Phys. 139: 121915 (2013) (invited contribution). Manuscript link
30. Principles of maximum entropy and maximum caliber. S. Presse, K. Ghosh, J. Lee and K.A Dill Rev. Mod. Phys. 85: 1115-1141 (2013) (invited contribution). Manuscript link
29. Inhrent properties of adenylosuccinate lyase could explain S-Ado/SAICAr ratio due to homozygous R426H and R303C mutations S.P. Ray, N. Duval, T.G. Wilkinson II, S.E. Shaheen, K. Ghosh and D. Patterson Biochemica et Biophysica Acta Proteins and Proteomics 1834: 1510 (2013). Manuscript link
28. Why and how does native topology dictate the folding speed of a protein? M. Rustad and K. Ghosh J. Chem. Phys. 137:205104 (2012). Manuscript link
27. Structural and Biochemical Characterization of Human Adenylosuccinate Lyase (ADSL) and the R303C ADSL Deficiency-Associated Mutation. S. P. Ray, M. K. Deaton, G. C. Capodagli, L.A.F. Calkins, L. Sawle, K. Ghosh, D. Patterson, and S. D. Pegan Biochemistry 51: 6731 (2012). Manuscript link
26. Markov processes follow from the principle of Maximum Caliber. H. Ge, S Presse, K. Ghosh and K. Dill J. Chem. Phys. 136: 064108 (2012). Manuscript link
25. Evidence of Multiple Folding Pathways for the Villin Headpiece Subdomain. L. Zhu, K. Ghosh, M. King, T. Cellmer, O. Bakajin, L. Lapidus J. Phys. Chem B 115:12632 (2011). Manuscript link
24. Physical limits of cells and proteomes. K. A. Dill, K. Ghosh, J. Schmit Proc. Natl. Acad. Sci. 108: 17876 (2011).
23. How do thermophilic proteins and proteomes withstand high temperature ? L. Sawle, K. Ghosh Biophys J 101, 217 (2011). Manuscript link
22. Stochastic dynamics of complexation reaction in the limit of small numbers. K. Ghosh J. Chem. Phys. 134, 195101 (2011). Manuscript link
21. Modeling Stochastic Dynamics in Biochemical Systems with Feedback using Maximum Caliber: S. Presse, K. Ghosh, K.A. Dill J Phys Chem B 115, 6202-6212 (2011). Manuscript link
20. What drives amyloid molecules to assemble into oligomers and fibrils ? J. Schmit, K. Ghosh and K. A. Dill Biophys J 100, 450-458 (2011). Manuscript link
19. Cellular proteomes have broad distributions of protein stability: K. Ghosh and K.A. Dill Biophys J 99, 3996-4002 (2010). Manuscript link
18. Dynamical fluctuations in biochemical reactions and cycles: S. Presse, K. Ghosh, R. Phillips and K. A. Dill. Phys Rev E 82, 031905 (2010). Manuscript link
17. Trajectory approach to two-state kinetics of single particles on sculpted energy landscapes: D. Wu, K. Ghosh, M. Inamdar, H. J. Lee, S. Fraser, K. A. Dill and R. Phillips. Phys. Rev. Lett. 103, 050603 (2009). Manuscript link
16. Computing protein stabilities from their chain lengths: K. Ghosh and K. A. Dill. Proc. Natl. Acad. Sci. 106(26), 10649-10654 (2009).
15. Theory for protein folding cooperativity: helix-bundles. K. Ghosh and K. A. Dill, J. Am. Chem. Soc. 131(6), 2306 (2009). Manuscript link
Publications (from 2008 - 1997)
14. Maximum caliber: A variational approach applied to two-state dynamics. G Stock, K. Ghosh and K. A. Dill, J. Chem. Phys., 128 (19), 194102 (2008). Manuscript link
13. The ultimate speed limit to protein folding is conformational searching. K. Ghosh, S. B. Ozkan and K. A. Dill, J. Am. Chem. Soc., 129, 11920 (2007)
12. Measuring Flux Distribution in the Small-Numbers Limit. E. Seitaridou, M. M. Inamdar, R. Phillips, K. Ghosh and K. A. Dill, J. Phys. Chem B, 111, 2288 (2007).
11. Teaching the Principles of Statistical Dynamics. K. Ghosh, K. Dill, M. N. Inamdar, E. Seitaridou and R. Phillips, Am. J. Phys., 74, 123-133 (2006).
10. Triple Points in Solutions of Polydisperse Semiflexible Polymers. K. Ghosh and M. Muthukumar, Phys. Rev. Lett., 91, 158303 (2003).
9. Polyelectrolyte solutions with added salt: A simulation study. S. Liu, K. Ghosh and M. Muthukumar, J. Chem. Phys., 119, 1813 (2003).
8. Phase Transitions in Solutions of Semiflexible Polyelectrolytes. K. Ghosh, Gustavo A. Carri and M. Muthukumar, J. Chem. Phys., 116, 5299 (2002).
7. Scattering Properties of a Single Semiflexible Polyelectrolyte. K. Ghosh, M. Muthukumar, J. Polym. Sci. B. Polymer Physics, 39, 2644 (2001).
6. Configurational properties of a single semiflexiblepolyelectrolyte. K. Ghosh, Gustavo A. Carri and M. Muthukumar, J. Chem Phys., 115, 4367 (2001).
5. The random field Ising model In a transverse field: multicritical point. K. Ghosh, J. K. Bhattacharjee, Phys Lett A, 238, 203 (1998).
4. Field theoretical calculation of the specific heat exponent for a classical N-vector model in a random external field. K. Ghosh, A. Dutta, J.K. Bhattacharjee, Eur. Phys. J. B, 4, 219 (1998).
3. Saha Ionization Equation. K. Ghosh and G. Ghosh , Eur. J. Phys., 19, 7 (1998).
2. Distributions of time-headways in a particle-hopping model of vehicular traffic. K. Ghosh, A. Majumdar, D. Chowdhury, Phys. Rev. E, 58, 4012 (1998).
1. Particle-hopping models of vehicular traffic: Distributions of distance headways and distance between jams. D. Chowdhury, K. Ghosh, A. Majumdar, S. Sinha, R.B. Stinchcombe , Physica A, 246, 471 (1997).