I developed a nonequilibrium mathematical theoretical model for torque and twist dynamics of DNA in the geometry of typical single-molecule experiments. See our PRE paper for details.
I have also studied a phenomenon that we call “facilitated dissociation.” My collaborators in the Marko lab experimentally observe that the kinetics of proteins unbinding from DNA are enhanced by the presence of competitor species (such as other proteins or DNA molecules). I have developed some theoretical methods and models to understand how this works.
References
- EJ Banigan and JF Marko (2014) Torque correlation length and stochastic twist dynamics of DNA. Phys. Rev. E 89: 062706.
- RD Giuntoli, NB Linzer, EJ Banigan, CE Sing, M Olvera de la Cruz, JS Graham, RC Johnson, and JF Marko (2015) DNA-segment-facilitated dissociation of Fis and NHP6A from DNA detected via single-molecule mechanical response. J. Mol. Biol., 427: 3123-3136.
- RI Kamar, EJ Banigan, A Erbas, RD Giuntoli, M Olvera de la Cruz, RC Johnson, and JF Marko (2017) Facilitated dissociation of transcription factors from single DNA binding sites. Proc. Natl. Acad. Sci. USA 114: E3251.