Spakowitz Research Group

Theory and Computation of Biological Processes and Soft Materials

Publications

  • M. Beckinghausen and A. J. Spakowitz "Exploration of Phase Behavior in Asymmetric Semiflexible Polyelectrolyte Mixtures Using Polymer Field Theory," Macromolecules 57, 5, 2505 (2024).
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  • S. Dutta, A. Ghosh, and A. J. Spakowitz "Effect of local active fluctuations on structure and dynamics of flexible biopolymers," Soft Matter 20, 1694 (2024).
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  • W. Michaels, A. J. Spakowitz, and J. Qin. "Conformational Statistics of Ribbon-like Chains," Macromolecules 56, 20, 8359 (2023).
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  • S. Dutta, A. Ghosh, A. N. Boettiger, and A. J. Spakowitz. "Leveraging polymer modeling to reconstruct chromatin connectivity from live images," Biophysical Journal 122, 3532 (2023).
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  • M. Beckinghausen and A. J. Spakowitz. "Interplay of Polymer Structure, Solvent Ordering, and Charge Fluctuations in Polyelectrolyte Solution Thermodynamics," Macromolecules 56, 1, 136 (2022).
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  • L. Balhorn, Q. MacPherson, K. C. Bustillo, C. J. Takacs, A. J. Spakowitz, and A. Salleo. "Closing the loop between microstructure and charge transport in conjugated polymers by combining microscopy and simulation," PNAS 119, 46, e2204346119 (2022).
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  • A. Ghosh, Q. MacPherson, Z.-G. Wang, A. J. Spakowitz. "Semiflexible polymer solutions. II. Fluctuations and Frank elastic constants," Journal of Chemical Physics https://aip.scitation.org/doi/10.1063/5.0120526 (2022).
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  • P. C. Cai, B. Su, L. Zou, M. J. Webber, S. C. Heilshorn, A. J. Spakowitz. "Rheological Characterization and Theoretical Modeling Establish Molecular Design Rules for Tailored Dynamically Associating Polymers," ACS Central Science https://doi.org/10.1021/acscentsci.2c00432 (2022).
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  • M. J. Kratochvil, G. Kaber, S. Demirdjian, P. C. Cai, E. B. Burgener, N. Nagy, G. L. Barlow, M. Popescu, M. R. Nicolls, M. G. Ozawa, D. P. Regula, A. E. Pacheco-Navarro, S. Yang, V. A. de Jesus Perez, H. Karmouty-Quintana, A. M. Peters, B. Zhao, M. L. Buja, P. Y. Johnson, R. B. Vernon, T. N. Wight, Stanford COVID-19 Biobank Study Group, C. E. Milla, A. J. Rogers, A. J. Spakowitz, S. C. Heilshorn, and P. L. Bollyky. "Biochemical, biophysical, and immunological characterization of respiratory secretions in severe SARS-CoV-2 infections," JCI Insight 7, 12, e152629 (2022).
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  • Q. Chen, T. Dharmaraj, P. C. Cai, E. B. Burgener, N. L. Haddock, A. J. Spakowitz, and P. L. Bollyky. "Bacteriophage and Bacterial Susceptibility, Resistance, and Tolerance to Antibiotics," Pharmaceutics 14, 7, 1425 (2022).
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  • A. Ghosh and A. J. Spakowitz. "Active and thermal fluctuations in multi-scale polymer structure and dynamics," Soft Matter https://doi.org/10.1039/d2sm00593j (2022).
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  • C. H. Starr, Z. Bryant, and A. J. Spakowitz. "Coarse-Grained Modeling Reveals the Impact of Supercoiling and Loop Length in DNA Looping Kinetics," Biophysical Journal https://doi.org/10.1016/j.bpj.2022.04.009 (2022).
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  • T. A. C. Newman, B. Beltran, J. M. McGehee, D. Elnatana, C. K. Cahoon, M. R. Paddy, D. B. Chua, A. J. Spakowitz, and S. M. Burgess. "Diffusion and distal linkages govern interchromosomal dynamics during meiotic prophase," PNAS https://doi.org/10.1073/pnas.2115883119 (2022).
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  • A. Ghosh and A. J. Spakowitz. "Statistical behavior of nonequilibrium and living biological systems subjected to active and thermal fluctuations," Phys. Rev. E 105, 014415 (2022).
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  • J. G. Wakim, S. H. Sandholtz, and A. J. Spakowitz. "Impact of chromosomal organization on epigenetic drift and domain stability revealed by physics-based simulations," Biophysical Journal 120, 22, 4932-4943 (2021).
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  • G. Bucci, K. Gadelrab, and A. J. Spakowitz. "Free Energy and Dynamics of Annihilation of Topological Defects in Nanoconfined DNA," Macromolecules 54, 20, 9268–9279 (2021).
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  • P. C. Cai, B. A. Krajina, M. J. Kratochvil, L. Zou, A. Zhu, E. B. Burgener, P. L. Bollyky, C. E. Milla, M. J. Webber, A. J. Spakowitz, S. C. Heilshorn. "Dynamic light scattering microrheology for soft and living materials," Soft Matter DOI: 10.1039/d0sm01597k (2021).
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  • B. A. Krajina, B. L. LeSavage, J. G. Roth, A. W. Zhu, P. C. Cai, A. J. Spakowitz, and S. C. Heilshorn. "Microrheology reveals simultaneous cell-mediated matrix stiffening and fluidization that underlie breast cancer invasion," Science Advances 7, 8, eabe1969 (2021).
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  • S. H. Sandholtz, D. Kannan, B. G. Beltran, A. J. Spakowitz. "Chromosome Structural Mechanics Dictates the Local Spreading of Epigenetic Marks," Biophysical Journal DOI:https://doi-org.stanford.idm.oclc.org/10.1016/j.bpj.2020.08.039 (2020).
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  • S. H. Sandholtz, Q. MacPherson, A. J. Spakowitz. "Physical Modeling of the Heritability and Maintenance of Epigenetic Modifications," PNAS doi: 10.1073/pnas.1920499117 (2020).
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  • P. C. Cai, B. A. Krajina, A. J. Spakowitz. "Brachiation of a polymer chain in the presence of a dynamic network," Rapid Communication in Physical Review E 102, 020501(R) (2020).
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  • G. Bucci and A. J. Spakowitz. "Systematic Approach toward Accurate and Efficient DNA Sequencing via Nanoconfinement," Macro Letters 9, 8, 1184–1191 (2020).
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  • Q. MacPherson, B. Beltran, A. J. Spakowitz. "Chromatin Compaction Leads to a Preference for Peripheral Heterochromatin," Biophys. J. 188, 6 (2020).
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  • R. P. Ghosh, J. M. Franklin, W. E. Draper, Q. Shi, B. G. Beltran, A. J. Spakowitz, J. T. Liphardt. "A fluorogenic array for temporally unlimited single-molecule tracking," Nature chemical biology 15, 4, 401-409 (2019).
  • A. J. Spakowitz. "Polymer physics across scales: Modeling the multiscale behavior of functional soft materials and biological systems,” J. Chem. Phys. 151, 230902 (2019).
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  • B. Beltran, D. Kannan, Q. MacPherson, and A. J. Spakowitz. "Geometrical heterogeneity dominates thermal fluctuations in facilitating chromatin contacts,” Physical Review Letters 123, 208103 (2019).
  • P. E. Rudnicki, Q. MacPherson, L. Belhorn, B. Feng, J. Qin, A. Salleo, and A. J. Spakowitz. "Impact of liquid-crystalline chain alignment on charge transport in conducting polymers,” Macromolecules doi: 10.1021/acs.macromol.9b01729 (2019).
  • S. H. Sandholtz, B. Beltran, A. J. Spakowitz. "Physical modeling of the spreading of epigenetic modifications through transient DNA looping,” J. Phys. A: Math. Theor. 52, 434001 (2019).
  • A. J. Spakowitz. "Transient Anomalous Diffusion in a Heterogeneous Environment,” Frontiers in Physics, doi: 10.3389/fphy.2019.00119 (2019).
  • 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).
  • 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).
  • 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).
  • B. A. Krajina, A. C. Proctor, A. P. Schoen, A. J. Spakowitz, S. C. Heilshorn "Biotemplated synthesis of inorganic materials: An emerging paradigm for nanomaterial synthesis inspired by nature," Progress in Materials Science, 91, 1 (2018).
  • 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).
  • S. Mao, Q. J. MacPherson, and A. J. Spakowitz. "Polymer semiflexibility induces nonuniversal phase transitions in diblock copolymers,” Physical Review Letters, 120, 067802 (2018).
  • 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).
  • 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).
  • 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).
  • E. Pilyugina, B. Krajina, A. J. Spakowitz, J. D. Schieber. "Buckling a Semiflexible Polymer Chain under Compression,” Polymers, 9, 99, doi:10.3390 (2017).
  • 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).
  • 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).
  • 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, 2, 12, 910 (2016).
  • B. A. Krajina and A. J. Spakowitz. "Large-Scale Conformational Transitions in Supercoiled DNA Revealed by Coarse-Grained Simulation," Biophysical Journal, 111, 1339 (2016).
  • A. J. Spakowitz. "Eliminating Fitting from the Modeling of Biological Processes," ACS Central Science, doi: 10.1021/acscentsci.6b00263 (2016).
  • 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.
  • 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).
  • T. J. Lampo, A. S. Kennard, A. J. Spakowitz. "Physical modeling of dynamic coupling of chromosomal loci," Biophysical Journal, 110, 1, 338 (2016).
  • 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).
  • 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).
  • P. Mulligan, L. Koslover, A. J. Spakowitz. "Thermodynamic model of heterochromatin formation through epigenetic regulation," Journal of Physics: Condensed Matter, 27, 064109 (2015).
  • 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).
  • N. Cordella, T. Lampo, N. Melosh, A. J. Spakowitz. "Membrane indentation triggers clathrin lattice reorganization and fluidization," Soft Matter, 11, 439 (2015).
  • 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).
  • E. F. Koslover and A. J. Spakowitz. "Multiscale dynamics of semiflexible polymers from a universal coarse-graining procedure," Physical Review E, 90, 013304 (2014).
  • 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).
  • N. Cordella, T. J. Lampo, S. Mehraeen, A. J. Spakowitz. "Membrane Fluctuations Destabilize Clathrin Protein Lattice Order," Biophysical Journal, 106, 7, 1476 (2014).
  • 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).
  • R. Noriega, A. Salleo, and A. J. Spakowitz. "Chain conformations dictate multiscale charge transport phenomena in disordered semiconducting polymers," PNAS, 10.1073, 1307158110 (2013).
  • 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).
  • E. F. Koslover and A. J. Spakowitz. "Discretizing elastic chains for coarse-grained polymer models," Soft Matter, 9, 7016 (2013).
  • E. F. Koslover and A. J. Spakowitz. "Systemic Coarse-Graining of Microscale Polymer Models as Effective Elastic Chains," Macromolecules, 46, 5, 2003 (2013).
  • 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).
  • 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.
  • 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).
  • 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).
  • E. F. Koslover and A. J. Spakowitz. "Force fluctuations impact kinetics of biomolecular systems," Physical Review E, 86, 011906 (2012).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • S. C. Weber, J. A. Theriot, A. J. Spakowitz. "Subdiffusive motion of a polymer composed of subdiffusive monomers," Phys. Rev. E, 82, 011913 (2010).
  • 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).
  • S. C. Weber, A. J. Spakowitz, J. A. Theriot. "Bacterial Chromosomal Loci Move Subdiffusively through a Viscoelastic Cytoplasm," Phys. Rev. Lett., 104, 238102 (2010).
  • E. F. Koslover, A. J. Spakowitz. "Twist and tension-mediated elastic coupling between DNA-binding proteins," Phys. Rev. Lett., 102, 178102 (2009).
  • 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).
  • 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).
  • 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).
  • 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).
  • S. Mihardja, A. J. Spakowitz, Y. L. Zhang, C. Bustamante. "Effect of force on mononucleosomal dynamics," PNAS, 103, 15871 (2006).
  • A. J. Spakowitz. "Wormlike chain statistics with twist and fixed ends," Europhys. Lett., 73, 684 (2006).
  • 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).
  • 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).
  • 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).
  • A. J. Spakowitz and Z.-G. Wang. "DNA Packaging in Bacteriophage: Is Twist Important?," Biophys. J., 88, 3912 (2005).
  • A. J. Spakowitz. "Semiflexible Polymers: Fundamental Theory and Applications in DNA Packaging," Ph.D. Thesis, 2004.
  • A. J. Spakowitz and Z.-G. Wang. "Exact results for a semiflexible polymer chain in an aligning field," Macromolecules, 37, 15, 5814 (2004).
  • A. J. Spakowitz and Z.-G. Wang. "Semiflexible polymer solutions. I. phase behavior and single-chain statistics," J. Chem. Phys., 119, 24, 13113 (2003).
  • A. J. Spakowitz and Z.-G. Wang. "Semiflexible polymer confined to a spherical surface," Phys. Rev. Lett., 91, 16, 166102 (2003).
  • A. J. Spakowitz and Z.-G. Wang. "Free expansion of elastic filaments," Phys. Rev. E, 6406, 6, 061802 (2001).