Theory and Computation of Biological Processes and Complex Materials
The Spakowitz lab is engaged in projects that address fundamental chemical and physical phenomena underlying a range of biological processes and soft-material applications. Current research in our lab focuses on four main research themes: chromosomal organization and dynamics, protein self-assembly, polymer membranes, and charge transport in conducting polymers. These broad research areas offer complementary perspectives on chemical and physical processes, and we leverage this complementarity throughout our research. Our approach draws from a diverse range of theoretical and computational methods, including analytical theory of semiflexible polymers, polymer field theory, continuum elastic mechanics, Brownian dynamics simulation, equilibrium and dynamic Monte Carlo simulations, and analytical theory and numerical simulations of reaction-diffusion phenomena. A common thread in our work is the need to capture phenomena over many length and time scales, and our flexibility in research methodologies provides us with the critical tools to address these complex multidisciplinary problems.
Weber, S. C., Spakowitz, A. J., & Theriot, J. A. (2010). Bacterial Chromosomal Loci Move Subdiffusively through a Viscoelastic Cytoplasm. PHYSICAL REVIEW LETTERS, 104(23).
MacPherson, Q., Beltran, B., & Spakowitz, A. J. (2018). Bottom-up modeling of chromatin segregation due to epigenetic modifications. Proceedings of the National Academy of Sciences of the United States of America.
Hong, S.-H., Toro, E., Mortensen, K. I., de la Rosa, M. A. D., Doniach, S., Shapiro, L., … McAdams, H. H. (2013). Caulobacter chromosome in vivo configuration matches model predictions for a supercoiled polymer in a cell-like confinement. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 110(5), 1674–79.
Noriega, R., Salleo, A., & Spakowitz, A. J. (2013). Chain conformations dictate multiscale charge transport phenomena in disordered semiconducting polymers. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 110(41), 16315–20.
Beltran, B., Kannan, D., MacPherson, Q., & Spakowitz, A. J. (2019). Geometrical Heterogeneity Dominates Thermal Fluctuations in Facilitating Chromatin Contacts. PHYSICAL REVIEW LETTERS, 123(20).
Mulligan, P. J., Chen, Y.-J., Phillips, R., & Spakowitz, A. J. (2015). Interplay of Protein Binding Interactions, DNA Mechanics, and Entropy in DNA Looping Kinetics. BIOPHYSICAL JOURNAL, 109(3), 618–29.
Cordella, N., Lampo, T. J., Mehraeen, S., & Spakowitz, A. J. (2014). Membrane fluctuations destabilize clathrin protein lattice order. Biophysical Journal, 106(7), 1476–88.
Cordella, N., Lampo, T. J., Melosh, N., & Spakowitz, A. J. (2015). Membrane indentation triggers clathrin lattice reorganization and fluidization. SOFT MATTER, 11(3), 439–48.
Chen, Y.-J., Johnson, S., Mulligan, P., Spakowitz, A. J., & Phillips, R. (2014). Modulation of DNA loop lifetimes by the free energy of loop formation. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111(49), 17396–401.
Koslover, E. F., & Spakowitz, A. J. (2014). Multiscale dynamics of semiflexible polymers from a universal coarse-graining procedure. PHYSICAL REVIEW E, 90(1).