David Winogradoff

e-mail: 
dwinogra@illinois.edu
phone: 
(301) 529-6494
office: 
261 LLP

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). 

 

Publications

  1. David Winogradoff, Ignacia Echeverria, Davit A. Potoyan, and Garegin A. Papoian. "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).
  2. David Winogradoff, Haiqing Zhao, Yamini Dalal, and Garegin A. Papoian. "Shearing of the CENP-A dimerization interface mediates plasticity in the octameric centromeric nucleosome." Scientific reports 5 (2015).
  3. Haiqing Zhao*, David Winogradoff*, Minh Bui, Yamini Dalal, and Garegin Papoian. "Promiscuous histone mis-assembly is actively prevented by chaperones." Journal of the American Chemical Society 138:13207-13218 (2016). PDF icon The cover image on JACS (2.25 MB)PDF icon SI for the paper (33.5 MB)
  4. David Winogradoff, and Aleksei Aksimentiev. "Molecular Mechanism of Spontaneous Nucleosome Unraveling." Journal of Molecular Biology 431:323-335 (2019). PDF icon supplementary_information.pdf (28.94 MB)
  5. Haiqing Zhao, David Winogradoff, Yamini Dalal, and Garegin A. Papoian. "The Oligomerization Landscape of Histones." Biophysical Journal 116:1845-1855 (2019).
  6. David Winogradoff, Shalini John, and Aleksei Aksimentiev. "Protein unfolding by SDS: the microscopic mechanisms and the properties of the SDS-protein assembly." Nanoscale 12:5422-5434 (2020). PDF icon supplement.pdf (6.71 MB)