Loomis Laboratory of Physics
1110 West Green Street
Urbana, IL 61801-3080
David Winogradoff earned his B.S. in Mathematics in 2009 from Haverford College, and his PhD in Chemical Physics in 2015 from the University of Maryland, College Park under the direction of Prof. Garegin Papoian. He is currently a postdoctoral fellow working with Prof. Aleksei Aksimentiev at the Center for the Physics of Living Cells in the Physics Department at the University of Illinois, Urbana-Champaign.
He specializes in computational biophysics, including atomistic and coarse-grained molecular dynamics simulations. In particular, he focuses on modelling chromatin, detergent-induced protein unfolding, selective transport across the nuclear pore complex, viruses, and the crowded environment inside a living cell. These efforts are essential to the goal of building a complete, computational model of an entire cell.
He also contributes to outreach efforts of the Aksimentiev group and the Center for the Physics of Living Cells, including the annual CPLC summer school and the development of an image-making tutorial (http://www.ks.uiuc.edu/Training/Workshop/Urbana2018c/tutorials/dna-nanostructure-visualization.pdf), the live demonstration of which has been viewed over 1,000 times on YouTube (https://www.youtube.com/watch?v=jySOUCZqq-M).
See his profiles on Google Scholar (https://scholar.google.com/citations?hl=en&user=D7vMTnoAAAAJ), and ResearchGate (https://www.researchgate.net/profile/David_Winogradoff).
- The acetylation landscape of the H4 histone tail: disentangling the interplay between the specific and cumulative effects." J Am Chem Soc 137:6245-6253 (2015). "
- Shearing of the CENP-A dimerization interface mediates plasticity in the octameric centromeric nucleosome." Scientific reports 5 (2015). "
- Promiscuous histone mis-assembly is actively prevented by chaperones." Journal of the American Chemical Society 138:13207-13218 (2016). "
- Molecular Mechanism of Spontaneous Nucleosome Unraveling." Journal of Molecular Biology 431:323-335 (2019). "
- The Oligomerization Landscape of Histones." Biophysical Journal 116:1845-1855 (2019). "
- Protein unfolding by SDS: the microscopic mechanisms and the properties of the SDS-protein assembly." Nanoscale 12:5422-5434 (2020). "
- Molecular dynamics simulations of DNA--DNA and DNA--protein interactions." Current Opinion in Structural Biology 64:88-96 (2020). "