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Andrew J. Spakowitz, Ph.D. - Publications

Affiliations: 
2005 California Institute of Technology, Pasadena, CA 
Area:
Chemical Engineering, General Biophysics
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87 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Dutta S, Ghosh A, Spakowitz AJ. Effect of local active fluctuations on structure and dynamics of flexible biopolymers. Soft Matter. PMID 38226903 DOI: 10.1039/d3sm01491f  0.309
2022 Ghosh A, MacPherson Q, Wang ZG, Spakowitz AJ. Semiflexible polymer solutions. II. Fluctuations and Frank elastic constants. The Journal of Chemical Physics. 157: 154906. PMID 36272793 DOI: 10.1063/5.0120526  0.486
2020 Sandholtz SH, Kannan D, Beltran BG, Spakowitz AJ. Chromosome Structural Mechanics Dictates the Local Spreading of Epigenetic Marks. Biophysical Journal. 119: 1630-1639. PMID 33010237 DOI: 10.1016/J.Bpj.2020.08.039  0.355
2020 Cai PC, Krajina BA, Spakowitz AJ. Brachiation of a polymer chain in the presence of a dynamic network. Physical Review. E. 102: 020501. PMID 32942387 DOI: 10.1103/Physreve.102.020501  0.405
2020 Spakowitz AJ. Erratum: "Polymer physics across scales: Modeling the multiscale behavior of functional soft materials and biological systems" [J. Chem. Phys. 151, 230902 (2019)]. The Journal of Chemical Physics. 153: 099901. PMID 32891105 DOI: 10.1063/5.0023713  0.337
2020 Sandholtz SH, MacPherson Q, Spakowitz AJ. Physical modeling of the heritability and maintenance of epigenetic modifications. Proceedings of the National Academy of Sciences of the United States of America. PMID 32778583 DOI: 10.1073/Pnas.1920499117  0.301
2020 MacPherson Q, Beltran B, Spakowitz AJ. Chromatin Compaction Leads to a Preference for Peripheral Heterochromatin. Biophysical Journal. PMID 32097622 DOI: 10.1016/J.Bpj.2020.01.034  0.304
2020 Bucci G, Spakowitz AJ. Systematic Approach toward Accurate and Efficient DNA Sequencing via Nanoconfinement Acs Macro Letters. 9: 1184-1191. DOI: 10.1021/Acsmacrolett.0C00423  0.375
2020 Garner RM, Koslover EF, Spakowitz AJ, Theriot J. Leading Edge Maintenance in Migrating Neutrophil-Like HL-60 Cells is an Emergent Property of Branched Actin Growth Biophysical Journal. 118: 603a. DOI: 10.1016/J.Bpj.2019.11.3260  0.508
2019 Spakowitz AJ. Polymer physics across scales: Modeling the multiscale behavior of functional soft materials and biological systems. The Journal of Chemical Physics. 151: 230902. PMID 31864250 DOI: 10.1063/1.5126852  0.354
2019 Beltran B, Kannan D, MacPherson Q, Spakowitz AJ. Geometrical Heterogeneity Dominates Thermal Fluctuations in Facilitating Chromatin Contacts. Physical Review Letters. 123: 208103. PMID 31809067 DOI: 10.1103/Physrevlett.123.208103  0.367
2019 Sandholtz SH, Beltran BG, Spakowitz AJ. Physical modeling of the spreading of epigenetic modifications through transient DNA looping Journal of Physics a: Mathematical and Theoretical. 52: 434001. DOI: 10.1088/1751-8121/Ab41D2  0.331
2019 Rudnicki PE, MacPherson Q, Balhorn L, Feng B, Qin J, Salleo A, Spakowitz AJ. Impact of Liquid-Crystalline Chain Alignment on Charge Transport in Conducting Polymers Macromolecules. 52: 8932-8939. DOI: 10.1021/Acs.Macromol.9B01729  0.363
2018 MacPherson Q, Beltran B, Spakowitz AJ. Bottom-up modeling of chromatin segregation due to epigenetic modifications. Proceedings of the National Academy of Sciences of the United States of America. 115: 12739-12744. PMID 30478042 DOI: 10.1073/Pnas.1812268115  0.314
2018 Krajina BA, Zhu A, Heilshorn SC, Spakowitz AJ. Active DNA Olympic Hydrogels Driven by Topoisomerase Activity. Physical Review Letters. 121: 148001. PMID 30339454 DOI: 10.1103/Physrevlett.121.148001  0.376
2018 Stylianidou S, Lampo TJ, Spakowitz AJ, Wiggins PA. Strong disorder leads to scale invariance in complex biological systems. Physical Review. E. 97: 062410. PMID 30011517 DOI: 10.1103/Physreve.97.062410  0.31
2018 Mao S, MacPherson Q, Spakowitz AJ. Polymer Semiflexibility Induces Nonuniversal Phase Transitions in Diblock Copolymers. Physical Review Letters. 120: 067802. PMID 29481283 DOI: 10.1103/Physrevlett.120.067802  0.339
2018 Mao S, MacPherson Q, Liu C, Spakowitz AJ. Thermodynamic Model of Solvent Effects in Semiflexible Diblock and Random Copolymer Assembly Macromolecules. 51: 4167-4177. DOI: 10.1021/Acs.Macromol.8B00172  0.365
2018 Garner RM, Koslover E, Spakowitz AJ, Theriot JA. Stability on the Edge: Probing the Biophysical Mechanisms of Polarity Maintenance in Motile Cells Biophysical Journal. 114: 648a-649a. DOI: 10.1016/J.Bpj.2017.11.3502  0.507
2018 Sandholtz S, MacPherson Q, Spakowitz A. Physical Modeling of the Spreading and Maintenance of Epigenetic Modifications through DNA Looping and Condensation Biophysical Journal. 114: 583a. DOI: 10.1016/J.Bpj.2017.11.3191  0.33
2018 MacPherson Q, Sandholtz S, Spakowitz A. A Polymer Physics Model for Epigenetic Control of Chromatin Compaction Biophysical Journal. 114: 563a. DOI: 10.1016/J.Bpj.2017.11.3080  0.34
2018 Newman T, Beltran BG, McGehee J, Cahoon C, Elnatan D, Chu D, Burgess S, Spakowitz A. Long-Range Structural Changes in the Meiotic Nucleus Revealed by Changes in Stress Communication Along the Chromosome Biophysical Journal. 114: 30a. DOI: 10.1016/J.Bpj.2017.11.212  0.398
2017 Pilyugina E, Krajina B, Spakowitz AJ, Schieber JD. Buckling a Semiflexible Polymer Chain under Compression. Polymers. 9. PMID 30970780 DOI: 10.3390/Polym9030099  0.39
2017 Krajina BA, Tropini C, Zhu A, DiGiacomo P, Sonnenburg JL, Heilshorn SC, Spakowitz AJ. Dynamic Light Scattering Microrheology Reveals Multiscale Viscoelasticity of Polymer Gels and Precious Biological Materials. Acs Central Science. 3: 1294-1303. PMID 29296670 DOI: 10.1021/Acscentsci.7B00449  0.366
2017 Mao S, MacPherson Q, Qin J, Spakowitz AJ. Field-theoretic simulations of random copolymers with structural rigidity. Soft Matter. PMID 28338151 DOI: 10.1039/C7Sm00164A  0.366
2017 Lampo TJ, Stylianidou S, Backlund MP, Wiggins PA, Spakowitz AJ. Cytoplasmic RNA-Protein Particles Exhibit Non-Gaussian Subdiffusive Behavior. Biophysical Journal. PMID 28088300 DOI: 10.1016/J.Bpj.2016.11.3208  0.31
2017 Koslover EF, Díaz de la Rosa M, Spakowitz AJ. Crowding and hopping in a protein’s diffusive transport on DNA Journal of Physics a: Mathematical and Theoretical. 50: 074005. DOI: 10.1088/1751-8121/Aa53Ee  0.382
2017 Mao S, MacPherson Q, Spakowitz AJ. Fluctuation Effects in Semiflexible Diblock Copolymers Acs Macro Letters. 7: 59-64. DOI: 10.1021/Acsmacrolett.7B00638  0.373
2017 Spakowitz AJ. Multi-Scale Modeling of Chromosomal DNA in Prokaryotic and Eukaryotic Cells Biophysical Journal. 112: 180a. DOI: 10.1016/J.Bpj.2016.11.1001  0.398
2016 Mollinger SA, Salleo A, Spakowitz AJ. Anomalous Charge Transport in Conjugated Polymers Reveals Underlying Mechanisms of Trapping and Percolation. Acs Central Science. 2: 910-915. PMID 28058280 DOI: 10.1021/Acscentsci.6B00251  0.368
2016 Krajina BA, Spakowitz AJ. Large-Scale Conformational Transitions in Supercoiled DNA Revealed by Coarse-Grained Simulation. Biophysical Journal. 111: 1339-1349. PMID 27705758 DOI: 10.1016/J.Bpj.2016.07.045  0.384
2016 Schenk G, Krajina B, Spakowitz A, Doniach S. Potential for measurement of the distribution of DNA folds in complex environments using Correlated X-ray Scattering. Modern Physics Letters. B, Condensed Matter Physics, Statistical Physics, Applied Physics. 30. PMID 27127310 DOI: 10.1142/S0217984916501177  0.338
2016 Lampo TJ, Kennard AS, Spakowitz AJ. Physical Modeling of Dynamic Coupling between Chromosomal Loci. Biophysical Journal. 110: 338-47. PMID 26789757 DOI: 10.1016/J.Bpj.2015.11.3520  0.367
2016 Mao S, Macpherson QJ, He SS, Coletta E, Spakowitz AJ. Impact of Conformational and Chemical Correlations on Microphase Segregation in Random Copolymers Macromolecules. 49: 4358-4368. DOI: 10.1021/Acs.Macromol.5B02639  0.407
2016 Lampo TJ, Kennard AS, Spakowitz AJ. Physical Modeling of Stress Communication between Chromosome Loci Biophysical Journal. 110: 66a-67a. DOI: 10.1016/J.Bpj.2015.11.425  0.38
2015 Mulligan PJ, Chen YJ, Phillips R, Spakowitz AJ. Interplay of Protein Binding Interactions, DNA Mechanics, and Entropy in DNA Looping Kinetics. Biophysical Journal. 109: 618-29. PMID 26244743 DOI: 10.1016/J.Bpj.2015.06.054  0.393
2015 Lampo TJ, Kuwada NJ, Wiggins PA, Spakowitz AJ. Physical modeling of chromosome segregation in escherichia coli reveals impact of force and DNA relaxation. Biophysical Journal. 108: 146-53. PMID 25564861 DOI: 10.1016/J.Bpj.2014.10.074  0.42
2015 Mulligan PJ, Koslover EF, Spakowitz AJ. Thermodynamic model of heterochromatin formation through epigenetic regulation. Journal of Physics. Condensed Matter : An Institute of Physics Journal. 27: 064109. PMID 25563699 DOI: 10.1088/0953-8984/27/6/064109  0.317
2015 Mollinger SA, Krajina BA, Noriega R, Salleo A, Spakowitz AJ. Percolation, Tie-Molecules, and the Microstructural Determinants of Charge Transport in Semicrystalline Conjugated Polymers Acs Macro Letters. 4: 708-712. DOI: 10.1021/Acsmacrolett.5B00314  0.342
2014 Chen YJ, Johnson S, Mulligan P, Spakowitz AJ, Phillips R. 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: 17396-401. PMID 25411314 DOI: 10.1073/Pnas.1415685111  0.412
2014 Koslover EF, Spakowitz AJ. Multiscale dynamics of semiflexible polymers from a universal coarse-graining procedure. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 90: 013304. PMID 25122407 DOI: 10.1103/Physreve.90.013304  0.41
2014 VanDersarl JJ, Mehraeen S, Schoen AP, Heilshorn SC, Spakowitz AJ, Melosh NA. Rheology and simulation of 2-dimensional clathrin protein network assembly. Soft Matter. 10: 6219-27. PMID 25012232 DOI: 10.1039/C4Sm00025K  0.312
2014 Cordella N, Lampo TJ, Mehraeen S, Spakowitz AJ. Membrane fluctuations destabilize clathrin protein lattice order. Biophysical Journal. 106: 1476-88. PMID 24703309 DOI: 10.1016/J.Bpj.2013.11.4505  0.331
2014 Mulligan P, Koslover EF, Spakowitz AJ. Dynamic Re-Discretization Allows Simulation of Biopolymers Across Length-Scales Biophysical Journal. 106: 250a. DOI: 10.1016/J.Bpj.2013.11.1466  0.447
2013 Noriega R, Salleo A, Spakowitz AJ. 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: 16315-20. PMID 24062459 DOI: 10.1073/Pnas.1307158110  0.366
2013 Hong SH, Toro E, Mortensen KI, de la Rosa MA, Doniach S, Shapiro L, Spakowitz AJ, McAdams HH. 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: 1674-9. PMID 23319648 DOI: 10.1073/Pnas.1220824110  0.411
2013 Schoen AP, Cordella N, Mehraeen S, Arunagirinathan MA, Spakowitz AJ, Heilshorn SC. Dynamic remodelling of disordered protein aggregates is an alternative pathway to achieve robust self-assembly of nanostructures Soft Matter. 9: 9137-9145. DOI: 10.1039/C3Sm50830G  0.311
2013 Koslover EF, Spakowitz AJ. Discretizing elastic chains for coarse-grained polymer models Soft Matter. 9: 7016-7027. DOI: 10.1039/C3Sm50311A  0.413
2013 Koslover EF, Spakowitz AJ. Systematic coarse-graining of microscale polymer models as effective elastic chains Macromolecules. 46: 2003-2014. DOI: 10.1021/Ma302056V  0.404
2012 Mehraeen S, Spakowitz AJ. Intrinsic fluctuations lead to broad range of transduced forces in tethered-bead single-molecule experiments. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 86: 021902. PMID 23005780 DOI: 10.1103/Physreve.86.021902  0.309
2012 Koslover EF, Spakowitz AJ. Force fluctuations impact kinetics of biomolecular systems. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 86: 011906. PMID 23005451 DOI: 10.1103/Physreve.86.011906  0.329
2012 Weber SC, Thompson MA, Moerner WE, Spakowitz AJ, Theriot JA. Analytical tools to distinguish the effects of localization error, confinement, and medium elasticity on the velocity autocorrelation function. Biophysical Journal. 102: 2443-50. PMID 22713559 DOI: 10.1016/J.Bpj.2012.03.062  0.537
2012 Weber SC, Spakowitz AJ, Theriot JA. Nonthermal ATP-dependent fluctuations contribute to the in vivo motion of chromosomal loci. Proceedings of the National Academy of Sciences of the United States of America. 109: 7338-43. PMID 22517744 DOI: 10.1073/Pnas.1119505109  0.542
2012 Koslover EF, Spakowitz AJ. Force Fluctuations Impact Genome Processing Kinetics Biophysical Journal. 102: 279a. DOI: 10.1016/J.Bpj.2011.11.1542  0.357
2012 Diaz de la Rosa MA, Spakowitz AJ. Structure and Dynamics of Supercoiled DNA in Confinement Biophysical Journal. 102: 279a. DOI: 10.1016/J.Bpj.2011.11.1541  0.411
2011 Koslover EF, Díaz de la Rosa MA, Spakowitz AJ. Theoretical and computational modeling of target-site search kinetics in vitro and in vivo. Biophysical Journal. 101: 856-65. PMID 21843476 DOI: 10.1016/J.Bpj.2011.06.066  0.351
2011 Sudhanshu B, Mihardja S, Koslover EF, Mehraeen S, Bustamante C, Spakowitz AJ. Tension-dependent structural deformation alters single-molecule transition kinetics Proceedings of the National Academy of Sciences of the United States of America. 108: 1885-1890. PMID 21245354 DOI: 10.1073/Pnas.1010047108  0.361
2011 Mehraeen S, Cordella N, Yoo JS, Spakowitz AJ. Impact of defect creation and motion on the thermodynamics and large-scale reorganization of self-assembled clathrin lattices Soft Matter. 7: 8789-8799. DOI: 10.1039/C1Sm05053B  0.357
2011 Koslover EF, de la Rose MAD, Weber SC, Spakowitz A. Target Site Localization Dynamics of DNA-Binding Proteins in Vivo Biophysical Journal. 100: 70a. DOI: 10.1016/J.Bpj.2010.12.582  0.377
2011 Mulligan PJ, Koslover EF, Spakowitz AJ. Modeling the Effects of Structure and Epigenetic Modifications in Heterochromatin Condensation Biophysical Journal. 100: 67a. DOI: 10.1016/J.Bpj.2010.12.566  0.307
2011 Mehraeen S, Cordella N, Yoo JS, Spakowitz AJ. Theoretical Modeling of the Weaving of Clathrin into Nanoscale Baskets Biophysical Journal. 100: 405a. DOI: 10.1016/J.Bpj.2010.12.2406  0.387
2010 Koslover EF, Fuller CJ, Straight AF, Spakowitz AJ. Local geometry and elasticity in compact chromatin structure. Biophysical Journal. 99: 3941-50. PMID 21156136 DOI: 10.1016/J.Bpj.2010.10.024  0.369
2010 Weber SC, Spakowitz AJ, Theriot JA. Bacterial chromosomal loci move subdiffusively through a viscoelastic cytoplasm. Physical Review Letters. 104: 238102. PMID 20867274 DOI: 10.1103/Physrevlett.104.238102  0.573
2010 Weber SC, Theriot JA, Spakowitz AJ. Subdiffusive motion of a polymer composed of subdiffusive monomers. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 82: 011913. PMID 20866654 DOI: 10.1103/Physreve.82.011913  0.6
2010 de la Rosa MA, Koslover EF, Mulligan PJ, Spakowitz AJ. Dynamic strategies for target-site search by DNA-binding proteins. Biophysical Journal. 98: 2943-53. PMID 20550907 DOI: 10.1016/J.Bpj.2010.02.055  0.331
2010 Weber SC, Theriot JA, Spakowitz AJ. Chromosomal Loci Move Subdiffusively Through a Viscoelastic Cytoplasm Biophysical Journal. 98. DOI: 10.1016/J.Bpj.2009.12.3615  0.43
2010 Sudhanshu B, Koslover EF, Mihardja S, Spakowitz AJ. Role of DNA Fluctuations in RNA Polymerase Translocation through a Single Nucleosome Biophysical Journal. 98: 476a-477a. DOI: 10.1016/J.Bpj.2009.12.2596  0.378
2010 Koslover EF, de la Rosa MD, Mulligan PJ, Spakowitz A. Theoretical Modeling of Protein Accessibility to the Chromatin Fiber Biophysical Journal. 98: 476a. DOI: 10.1016/J.Bpj.2009.12.2591  0.336
2010 Koslover EF, Fuller C, Straight AF, Spakowitz AJ. Role of DNA Elasticity and Nucleosome Geometry in Hierarchical Packaging of Chromatin Biophysical Journal. 98: 474a. DOI: 10.1016/J.Bpj.2009.12.2584  0.372
2010 de la Rosa MAD, Koslover EF, Mulligan PJ, Spakowitz AJ. Target-Site Search of DNA-Binding Proteins Biophysical Journal. 98: 221a. DOI: 10.1016/J.Bpj.2009.12.1194  0.345
2010 Basu A, Koslover L, Schoeffler A, Tretter E, Berger J, Spakowitz AJ, Bryant ZD. Single Molecule Analysis of Substeps in the Mechanochemical Cycle of DNA Gyrase Biophysical Journal. 98: 221a. DOI: 10.1016/J.Bpj.2009.12.1192  0.372
2010 Mehraeen S, Cordella N, Spakowitz AJ. A Predictive Theoretical Model For Clathrin Self-Assembly Biophysical Journal. 98: 10a. DOI: 10.1016/J.Bpj.2009.12.059  0.388
2009 Koslover EF, Spakowitz AJ. Twist and Tension-mediated Elastic Coupling between DNA-Bending Proteins Biophysical Journal. 96: 178102. DOI: 10.1016/J.Bpj.2008.12.3015  0.373
2009 de la Rosa MD, Spakowitz AJ. Target Site Search Strategy Of Gene Regulatory Proteins Biophysical Journal. 96: 366a. DOI: 10.1016/J.Bpj.2008.12.1972  0.34
2008 Mehraeen S, Sudhanshu B, Koslover EF, Spakowitz AJ. End-to-end distribution for a wormlike chain in arbitrary dimensions. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 77: 061803. PMID 18643291 DOI: 10.1103/Physreve.77.061803  0.336
2008 Shroff H, Sivak D, Siegel JJ, McEvoy AL, Siu M, Spakowitz A, Geissler PL, Liphardt J. Optical measurement of mechanical forces inside short DNA loops. Biophysical Journal. 94: 2179-86. PMID 18065484 DOI: 10.1529/Biophysj.107.114413  0.342
2008 Comolli LR, Spakowitz AJ, Siegerist CE, Jardine PJ, Grimes S, Anderson DL, Bustamante C, Downing KH. Three-dimensional architecture of the bacteriophage phi29 packaged genome and elucidation of its packaging process. Virology. 371: 267-77. PMID 18001811 DOI: 10.1016/J.Virol.2007.07.035  0.349
2006 Wiggins PA, van der Heijden T, Moreno-Herrero F, Spakowitz A, Phillips R, Widom J, Dekker C, Nelson PC. High flexibility of DNA on short length scales probed by atomic force microscopy. Nature Nanotechnology. 1: 137-41. PMID 18654166 DOI: 10.1038/Nnano.2006.63  0.39
2006 Mihardja S, Spakowitz AJ, Zhang Y, Bustamante C. Effect of force on mononucleosomal dynamics Proceedings of the National Academy of Sciences of the United States of America. 103: 15871-15876. PMID 17043216 DOI: 10.1073/Pnas.0607526103  0.355
2006 Spakowitz AJ. Wormlike chain statistics with twist and fixed ends Europhysics Letters. 73: 684-690. DOI: 10.1209/Epl/I2005-10447-9  0.363
2005 Spakowitz AJ, Wang ZG. End-to-end distance vector distribution with fixed end orientations for the wormlike chain model. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 72: 041802. PMID 16383410 DOI: 10.1103/Physreve.72.041802  0.513
2005 Bois JS, Venkataraman S, Choi HM, Spakowitz AJ, Wang ZG, Pierce NA. Topological constraints in nucleic acid hybridization kinetics. Nucleic Acids Research. 33: 4090-5. PMID 16043632 DOI: 10.1093/Nar/Gki721  0.483
2005 Spakowitz AJ, Wang ZG. DNA packaging in bacteriophage: is twist important? Biophysical Journal. 88: 3912-23. PMID 15805174 DOI: 10.1529/Biophysj.104.052738  0.553
2004 Spakowitz AJ, Wang ZG. Exact results for a semiflexible polymer chain in an aligning field Macromolecules. 37: 5814-5823. DOI: 10.1021/Ma049958V  0.519
2003 Spakowitz AJ, Wang ZG. Semiflexible polymer confined to a spherical surface. Physical Review Letters. 91: 166102. PMID 14611419 DOI: 10.1103/Physrevlett.91.166102  0.488
2003 Spakowitz AJ, Wang ZG. Semiflexible polymer solutions. I. Phase behavior and single-chain statistics Journal of Chemical Physics. 119: 13113-13128. DOI: 10.1063/1.1628669  0.508
2001 Spakowitz AJ, Wang ZG. Free expansion of elastic filaments. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 64: 061802. PMID 11736202 DOI: 10.1103/Physreve.64.061802  0.545
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