@article{THESIS,
      recid = {10148},
      author = {Coraor, Aria Eesti},
      title = {Chemically-Specific Molecular Simulation of  Oligonucleosomal Chromatin Structure},
      publisher = {University of Chicago},
      school = {Ph.D.},
      address = {2023-12},
      number = {THESIS},
      pages = {139},
      abstract = {The manner in which nucleosomes stack to form higher order  chromatin is critical to biological regulation of gene  expression, but remains poorly understood. Throughout this  work, we utilize multiple coarse-grained models to  characterize chromatin structure across length-scales, and  lend physical interpretation to experimental results. Our  simulations reveal that classical, ideal models for  chromatin structure are not thermodynamically stable, and  that chromatin displays a wide range of heteromorphic  structures at equilibrium which span the range between  these ideal models. We combine these simulation results  with Bayesian maximum a-posteriori estimation to augment  the interpretability of related cryo-electron microscopy  techniques which have heretofore been used to characterize  chromatin fiber structure. We further extend these  simulations to fibers of chromatin bearing H4K16  acylations, which are epigenetic marks understood to drive  increases in gene expression in vivo. Our results  demonstrate that, although all H4K16 acylations  significantly alter chromatin fiber structure, the  resulting structural variation is small compared to the  natural heterogeneity present in each fiber at  equilibrium.Lastly, we develop and validate a novel method  to directly compare and contrast chromatin structural  measurements obtained by complementary Hi-C and IF-sSMLM  measurements, and demonstrate this method's utility on  simulated chromatin structures. In total, our work both  adds considerable detail to the field of chromatin folding,  and provides clear avenues for future developments of  combined computational and experimental techniques.},
      url = {http://knowledge.uchicago.edu/record/10148},
      doi = {https://doi.org/10.6082/uchicago.10148},
}