Spakowitz Research Group

Theory and Computation of Biological Processes and Soft Materials

Publications

  1. Q. MacPherson, B. Beltran, and A. J. Spakowitz. "Bottom–up modeling of chromatin segregation due to epigenetic modifications,” PNAS, www.pnas.org/cgi/doi/10.1073/pnas.1812268115 (2018).
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  2. B. A. Krajina, A. Zhu, S. C. Heilshorn, and A. J. Spakowitz. "Active DNA Olympic Hydrogels Driven by Topoisomerase Activity,” Physical Review Letters, 121, 148001 (2018).
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  3. S. Stylianidou, T. J. Lampo, A. J. Spakowitz, and P. A. Wiggins. "Strong disorder leads to scale invariance in complex biological systems," Phys. Rev. E, 97, 062410 (2018).
  4. S. Mao, Q. J. MacPherson, C. Liu, and A. J. Spakowitz. "Thermodynamic Model of Solvent Effects in Semiflexible Diblock and Random Copolymer Assembly,” Macromolecules, DOI: 10.1021/acs.macromol.8b00172 (2018).
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  5. S. Mao, Q. J. MacPherson, and A. J. Spakowitz. "Polymer semiflexibility induces nonuniversal phase transitions in diblock copolymers,” Physical Review Letters, 120, 067802 (2018).
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  6. S. Mao, Q. J. MacPherson, and A. J. Spakowitz. "Fluctuation Effects in Semiflexible Diblock Copolymers,” Macro Letters, 7, 59, DOI: 10.1021/acsmacrolett.7b00638 (2017).
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  7. B. A. Krajina, C. Tropini, A. Zhu, P. DiGiacomo, J. L. Sonnenburg, S. C. Heilshorn, and A. J. Spakowitz. "Dynamic Light Scattering Microrheology Reveals Multiscale Viscoelasticity of Polymer Gels and Precious Biological Materials,” ACS Central Science, doi:10.1021/acscentsci.7b00449 (2017).
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  8. S. Mao, Q. J. MacPherson, J. Qin, and A. J. Spakowitz. "Field-theoretic simulations of random copolymers with structural rigidity,” Soft Matter, doi: 10.1039/c7sm00164a (2017).
    pdf supplemental materials
  9. E. Pilyugina, B. Krajina, A. J. Spakowitz, J. D. Schieber. "Buckling a Semiflexible Polymer Chain under Compression,” Polymers, 9, 99, doi:10.3390 (2017).
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  10. T. J. Lampo, S. Stylianidou, M. P. Backlund, P. A. Wiggins, and A. J. Spakowitz. "Cytoplasmic RNA-Protein Particles Exhibit Non-Gaussian Subdiffusive Behavior,” Biophysical Journal, 112, 1 (2017).
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  11. E. F. Koslover, M. A. Díaz de la Rosa, and A. J. Spakowitz. "Crowding and hopping in a protein's diffusive transport on DNA,” Journal of Physics A: Mathematical and Theoretical, 50, 074005 (2017).
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  12. S. M. Mollinger, A. Salleo, and A. J. Spakowitz. "Anomalous Charge Transport in Conjugated Polymers Reveals Underlying Mechanisms of Trapping and Percolation,” ACS Central Science (2016).
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  13. B. A. Krajina and A. J. Spakowitz. "Large-Scale Conformational Transitions in Supercoiled DNA Revealed by Coarse-Grained Simulation," Biophysical Journal, 111, 1339 (2016).
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  14. A. J. Spakowitz. "Eliminating Fitting from the Modeling of Biological Processes," ACS Central Science, DOI: 10.1021/acscentsci.6b00263 (2016).
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  15. A. J. Spakowitz. “Complex Biological Systems,” 2016, pp. 239-252 in: Handbook of Science and Technology Convergence, edited by W. S. Bainbridge and M. C. Roco. Springer Reference, Switzerland.
  16. S. Mao, Q. J. MacPherson, S. S. He, E. Coletta, and A. J. Spakowitz. "Impact of Conformational and Chemical Correlations on Microphase Segregation in Random Copolymers," Macromolecules, DOI: 10.1021 (2016).
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  17. T. J. Lampo, A. S. Kennard, A. J. Spakowitz. "Physical modeling of dynamic coupling of chromosomal loci," Biophysical Journal, 110, 1, 338 (2016).
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  18. P. Mulligan, Y.-J. Chen, R. Phillips, A. J. Spakowitz. "Interplay of Protein Binding Interactions, DNA Mechanics, and Entropy in DNA Looping Kinetics," Biophysical Journal, 109, 3, 618 (2015).
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  19. S. A. Mollinger, B. A. Krajina, R. Noriega, A. Salleo, and A. J. Spakowitz. “Percolation, tie-molecules, and the microstructural determinants of charge transport in semicrystalline conjugated polymers,” Macro Letters, 4, 708 (2015).
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  20. P. Mulligan, L. Koslover, A. J. Spakowitz. "Thermodynamic model of heterochromatin formation through epigenetic regulation," Journal of Physics: Condensed Matter, 27, 064109 (2015).
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  21. T. Lampo, N. Kuwada, P. Wiggins, A. J. Spakowitz. "Physical Modeling of Chromosome Segregation in Escherichia coli Reveals Impact of Force and DNA Relaxation," Biophysical Journal, 108, 146 (2015).
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  22. N. Cordella, T. Lampo, N. Melosh, A. J. Spakowitz. "Membrane indentation triggers clathrin lattice reorganization and fluidization," Soft Matter, 11, 439 (2015).
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  23. Y.-J. Chen, S. Johnson, P. Mulligan, A. J. Spakowitz, R. Phillips. "Modulation of DNA loop lifetimes by the free energy of loop formation," PNAS, DOI: 10.1073/pnas.1415685111 (2015).
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  24. E. F. Koslover and A. J. Spakowitz. "Multiscale dynamics of semiflexible polymers from a universal coarse-graining procedure," Physical Review E, 90, 013304 (2014).
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  25. J. VanDersarl, S. Mehraeen, A. Schoen, S. Heilshorn, A. J. Spakowitz, N. Melosh. "Rheology and simulation of 2-dimensional clathrin protein network assembly," Soft Matter, 10, 6219 (2014).
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  26. N. Cordella, T. J. Lampo, S. Mehraeen, A. J. Spakowitz. "Membrane Fluctuations Destabilize Clathrin Protein Lattice Order," Biophysical Journal, 106, 7, 1476 (2014).
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  27. A. P. Schoen, N. Cordella, S. Mehraeen, M. A. Arunagirinathan, A. J. Spakowitz, S. C. Heilshorn. "Dynamic remodelling of disordered protein aggregates is an alternative pathway to achieve robust self-assembly of nanostructures," Soft Matter, 9, 38, 9137 (2013).
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  28. R. Noriega, A. Salleo, and A. J. Spakowitz. "Chain conformations dictate multiscale charge transport phenomena in disordered semiconducting polymers," PNAS, 10.1073, 1307158110 (2013).
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  29. F. Ye, D. K. Breslow, E. F. Koslover, A. J. Spakowitz, W. J. Nelson, and M. V. Nachury. "Single molecule imaging reveals a major role for diffusion in the exploration of ciliary space by signaling receptors," eLIFE, 2, e00654 (2013).
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  30. E. F. Koslover and A. J. Spakowitz. "Discretizing elastic chains for coarse-grained polymer models," Soft Matter, 9, 7016 (2013).
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  31. E. F. Koslover and A. J. Spakowitz. "Systemic Coarse-Graining of Microscale Polymer Models as Effective Elastic Chains," Macromolecules, 46, 5, 2003 (2013).
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  32. S. H. Hong, E. Toro, K. I. Mortensen, M. A. Díaz de la Rosa, S. Doniach, L. Shapiro, A. J. Spakowitz and H. H. McAdams. "Caulobacter chromosome in vivo configuration matches model predictions for a supercoiled polymer in a cell-like confinement," PNAS, 10.1073, 1220824110 (2012).
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  33. A. J. Spakowitz and M. Muthukumar. Chapter 9.13: “Viral Packaging of Nucleic Acids,” 2012, pp. 231-245 in: Polymer Science: A Comprehensive Reference, edited by M. Möller and K. Matyjaszewski. Elsevier Academic Press, San Diego, CA.
  34. S. Mehraeen and A. J. Spakowitz. "Intrinsic fluctuations lead to broad range of transduced forces in tethered-bead single-molecule experiments," Physical Review E, 86, 021902 (2012).
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  35. S. C. Weber, M. S. Thompson, W. E. Moerner, A. J. Spakowitz, and J. A. Theriot. "Analytical Tools To Distinguish the Effects of Localization Error, Confinement, and Medium Elasticity on the Velocity Autocorrelation Function," Biophys. J., 102, 2443-2450 (2012).
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  36. E. F. Koslover and A. J. Spakowitz. "Force fluctuations impact kinetics of biomolecular systems," Physical Review E, 86, 011906 (2012).
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  37. S. C. Weber, A. J. Spakowitz, and J. A. Theriot. "Nonthermal ATP-dependent fluctuations contribute to the in vivo motion of chromosomal loci," PNAS, 109, 19, 7338-7343 (2012).
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  38. H. W. Lee, Y. Yoon, S. Park, J. H. Oh, S. Hong, L. S. Liyanage, H. Wang, S. Morishita, N. Patil, Y. J. Park, A. J. Spakowitz, G. Galli, F. Gygi, P. H. S. Wong, J. B. H. Tok, J. M. Kim, and Z. Bao. "Selective dispersion of high purity semiconducting single-walled carbon nanotubes with regioregular poly(3-alkylthiophene)s," Nature Communications, 2, 541 (2011).
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  39. E. F. Koslover, M. A. Díaz de la Rosa, and A. J. Spakowitz. "Theoretical and Computational Modeling of Target-Site Search Kinetics in Vitro and in Vivo," Biophys. J., 101, 4, 856 (2011).
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  40. S. Mehraeen, N. Cordella, J. S. Yoo, and A. J. Spakowitz. "Impact of defect creation and motion on the thermodynamics and large-scale reorganization of self-assembled clathrin lattices," Soft Matter, 7, 8789 (2011).
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  41. J. J. Kwiatkowski, L. H. Jimison, A. Salleo, and A. J. Spakowitz. "A Boltzmann-weighted hopping model of charge transport in organic semicrystalline films," Journal of Applied Physics, 109, 113720 (2011).
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  42. B. Sudhanshu, S. Mihardja, E. F. Koslover, S. Mehraeen, C. Bustamante, and A. J. Spakowitz. "Tension-dependent structural deformation alters single-molecule transition kinetics," PNAS, 108, 5, 1885 (2011).
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  43. E. F. Koslover, C. J. Fuller, A. F. Straight, and A. J. Spakowitz. "Local Geometry and Elasticity in Compact Chromatin Structure," Biophys. J., 99, 3941 (2010).
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  44. S. C. Weber, J. A. Theriot, A. J. Spakowitz. "Subdiffusive motion of a polymer composed of subdiffusive monomers," Phys. Rev. E, 82, 011913 (2010).
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  45. M. A. Díaz de la Rosa, E. F. Koslover, P. J. Mulligan, A. J. Spakowitz. "Dynamic Strategies for Target-Site Search by DNA-Binding Proteins," Biophys. J., 98, 2943 (2010).
    pdf supplemental material
  46. S. C. Weber, A. J. Spakowitz, J. A. Theriot. "Bacterial Chromosomal Loci Move Subdiffusively through a Viscoelastic Cytoplasm," Phys. Rev. Lett., 104, 238102 (2010).
    pdf supplemental material featured synopsis in Physics
  47. E. F. Koslover, A. J. Spakowitz. "Twist and tension-mediated elastic coupling between DNA-binding proteins," Phys. Rev. Lett., 102, 178102 (2009).
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  48. S. Mehraeen, B. Sudhanshu, E. F. Koslover, A. J. Spakowitz. "End-to-end distribution for a wormlike chain in arbitrary dimensions," Phys. Rev. E, 77, 061803 (2008).
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  49. H. Shroff, D. Sivak, J. J. Siegel, A. L. McEvoy, M. Siu, A. J. Spakowitz, P. L. Geissler, J. Liphardt. "Optical measurement of mechanical forces inside short DNA loops," Biophys. J., 94, 6, 2179 (2008).
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  50. L. R. Comolli, A. J. Spakowitz, C. E. Siegerist, P. J. Jardine, S. Grimes, D. L. Anderson, B. Bustamante, K. H. Downing. "Three-dimensional architecture of the bacteriophage phi 29 packaged genome and elucidation of its packaging process," Virology, 371, 2, 267 (2008).
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  51. P. A. Wiggins, T. Van der Heijden, F. Moreno-Herrero, A. J. Spakowitz, R. Phillips, J. Widom, C. Dekker, P. C. Nelson. "High flexibility of DNA on short length scales probed by atomic force microscopy," Nature Nanotechnology, 1, 2, 137 (2006).
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  52. S. Mihardja, A. J. Spakowitz, Y. L. Zhang, C. Bustamante. "Effect of force on mononucleosomal dynamics," PNAS, 103, 15871 (2006).
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  53. A. J. Spakowitz. "Wormlike chain statistics with twist and fixed ends," Europhys. Lett., 73, 684 (2006).
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  54. A. J. Spakowitz and Z.-G. Wang. "End-to-end distance vector distribution with fixed end orientations for the wormlike chain model," Phys. Rev. E, 72, 041802 (2005).
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  55. J. S. Bois, S. Venkataraman, H. M. T. Choi, A. J. Spakowitz, Z.-G. Wang and N. A. Pierce. "Topological constraints in nucleic acid hybridization kinetics," NAR, 33, 13, 4090 (2005).
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  56. H. Shroff, B. M. Reinhard, M. Siu, H. Agarwal, A. Spakowitz, J. Liphardt. "Biocompatible Force Sensor with Optical Readout and Dimensions of 6 nm3," Nano Letters, 5, 7, 1509 (2005).
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  57. A. J. Spakowitz and Z.-G. Wang. "DNA Packaging in Bacteriophage: Is Twist Important?," Biophys. J., 88, 3912 (2005).
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  58. A. J. Spakowitz. "Semiflexible Polymers: Fundamental Theory and Applications in DNA Packaging," Ph.D. Thesis, 2004.
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  59. A. J. Spakowitz and Z.-G. Wang. "Exact results for a semiflexible polymer chain in an aligning field," Macromolecules, 37, 15, 5814 (2004).
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  60. A. J. Spakowitz and Z.-G. Wang. "Semiflexible polymer solutions. I. phase behavior and single-chain statistics," J. Chem. Phys., 119, 24, 13113 (2003).
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  61. A. J. Spakowitz and Z.-G. Wang. "Semiflexible polymer confined to a spherical surface," Phys. Rev. Lett., 91, 16, 166102 (2003).
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  62. A. J. Spakowitz and Z.-G. Wang. "Free expansion of elastic filaments," Phys. Rev. E, 6406, 6, 061802 (2001).
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