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Items: 41

1.

Active DNA Olympic Hydrogels Driven by Topoisomerase Activity.

Krajina BA, Zhu A, Heilshorn SC, Spakowitz AJ.

Phys Rev Lett. 2018 Oct 5;121(14):148001. doi: 10.1103/PhysRevLett.121.148001.

PMID:
30339454
2.

Strong disorder leads to scale invariance in complex biological systems.

Stylianidou S, Lampo TJ, Spakowitz AJ, Wiggins PA.

Phys Rev E. 2018 Jun;97(6-1):062410. doi: 10.1103/PhysRevE.97.062410.

PMID:
30011517
3.

Polymer Semiflexibility Induces Nonuniversal Phase Transitions in Diblock Copolymers.

Mao S, MacPherson Q, Spakowitz AJ.

Phys Rev Lett. 2018 Feb 9;120(6):067802. doi: 10.1103/PhysRevLett.120.067802.

PMID:
29481283
4.

Dynamic Light Scattering Microrheology Reveals Multiscale Viscoelasticity of Polymer Gels and Precious Biological Materials.

Krajina BA, Tropini C, Zhu A, DiGiacomo P, Sonnenburg JL, Heilshorn SC, Spakowitz AJ.

ACS Cent Sci. 2017 Dec 27;3(12):1294-1303. doi: 10.1021/acscentsci.7b00449. Epub 2017 Dec 15.

5.

Field-theoretic simulations of random copolymers with structural rigidity.

Mao S, MacPherson Q, Qin J, Spakowitz AJ.

Soft Matter. 2017 Apr 12;13(15):2760-2772. doi: 10.1039/c7sm00164a.

PMID:
28338151
6.

Cytoplasmic RNA-Protein Particles Exhibit Non-Gaussian Subdiffusive Behavior.

Lampo TJ, Stylianidou S, Backlund MP, Wiggins PA, Spakowitz AJ.

Biophys J. 2017 Feb 7;112(3):532-542. doi: 10.1016/j.bpj.2016.11.3208. Epub 2017 Jan 11.

7.

Anomalous Charge Transport in Conjugated Polymers Reveals Underlying Mechanisms of Trapping and Percolation.

Mollinger SA, Salleo A, Spakowitz AJ.

ACS Cent Sci. 2016 Dec 28;2(12):910-915. doi: 10.1021/acscentsci.6b00251. Epub 2016 Nov 10.

8.

Eliminating Fitting from the Modeling of Biological Processes.

Spakowitz AJ.

ACS Cent Sci. 2016 Sep 28;2(9):584-585. Epub 2016 Sep 12. No abstract available.

9.

Large-Scale Conformational Transitions in Supercoiled DNA Revealed by Coarse-Grained Simulation.

Krajina BA, Spakowitz AJ.

Biophys J. 2016 Oct 4;111(7):1339-1349. doi: 10.1016/j.bpj.2016.07.045.

10.

Physical Modeling of Dynamic Coupling between Chromosomal Loci.

Lampo TJ, Kennard AS, Spakowitz AJ.

Biophys J. 2016 Jan 19;110(2):338-347. doi: 10.1016/j.bpj.2015.11.3520.

11.

Interplay of Protein Binding Interactions, DNA Mechanics, and Entropy in DNA Looping Kinetics.

Mulligan PJ, Chen YJ, Phillips R, Spakowitz AJ.

Biophys J. 2015 Aug 4;109(3):618-29. doi: 10.1016/j.bpj.2015.06.054.

12.

Physical modeling of chromosome segregation in escherichia coli reveals impact of force and DNA relaxation.

Lampo TJ, Kuwada NJ, Wiggins PA, Spakowitz AJ.

Biophys J. 2015 Jan 6;108(1):146-53. doi: 10.1016/j.bpj.2014.10.074.

13.

Thermodynamic model of heterochromatin formation through epigenetic regulation.

Mulligan PJ, Koslover EF, Spakowitz AJ.

J Phys Condens Matter. 2015 Feb 18;27(6):064109. doi: 10.1088/0953-8984/27/6/064109. Epub 2015 Jan 7.

PMID:
25563699
14.

Membrane indentation triggers clathrin lattice reorganization and fluidization.

Cordella N, Lampo TJ, Melosh N, Spakowitz AJ.

Soft Matter. 2015 Jan 21;11(3):439-48. doi: 10.1039/c4sm01650e.

PMID:
25412023
15.

Modulation of DNA loop lifetimes by the free energy of loop formation.

Chen YJ, Johnson S, Mulligan P, Spakowitz AJ, Phillips R.

Proc Natl Acad Sci U S A. 2014 Dec 9;111(49):17396-401. doi: 10.1073/pnas.1415685111. Epub 2014 Nov 19.

16.

Multiscale dynamics of semiflexible polymers from a universal coarse-graining procedure.

Koslover EF, Spakowitz AJ.

Phys Rev E Stat Nonlin Soft Matter Phys. 2014 Jul;90(1):013304. Epub 2014 Jul 14.

PMID:
25122407
17.

Rheology and simulation of 2-dimensional clathrin protein network assembly.

VanDersarl JJ, Mehraeen S, Schoen AP, Heilshorn SC, Spakowitz AJ, Melosh NA.

Soft Matter. 2014 Sep 7;10(33):6219-27. doi: 10.1039/c4sm00025k.

PMID:
25012232
18.

Membrane fluctuations destabilize clathrin protein lattice order.

Cordella N, Lampo TJ, Mehraeen S, Spakowitz AJ.

Biophys J. 2014 Apr 1;106(7):1476-88. doi: 10.1016/j.bpj.2013.11.4505. Erratum in: Biophys J. 2014 Jul 15;107(2):539.

19.

An in vitro assay for entry into cilia reveals unique properties of the soluble diffusion barrier.

Breslow DK, Koslover EF, Seydel F, Spakowitz AJ, Nachury MV.

J Cell Biol. 2013 Oct 14;203(1):129-47. doi: 10.1083/jcb.201212024. Epub 2013 Oct 7.

20.

Chain conformations dictate multiscale charge transport phenomena in disordered semiconducting polymers.

Noriega R, Salleo A, Spakowitz AJ.

Proc Natl Acad Sci U S A. 2013 Oct 8;110(41):16315-20. doi: 10.1073/pnas.1307158110. Epub 2013 Sep 23.

21.

Single molecule imaging reveals a major role for diffusion in the exploration of ciliary space by signaling receptors.

Ye F, Breslow DK, Koslover EF, Spakowitz AJ, Nelson WJ, Nachury MV.

Elife. 2013 Aug 6;2:e00654. doi: 10.7554/eLife.00654.

22.

Caulobacter chromosome in vivo configuration matches model predictions for a supercoiled polymer in a cell-like confinement.

Hong SH, Toro E, Mortensen KI, de la Rosa MA, Doniach S, Shapiro L, Spakowitz AJ, McAdams HH.

Proc Natl Acad Sci U S A. 2013 Jan 29;110(5):1674-9. doi: 10.1073/pnas.1220824110. Epub 2013 Jan 14.

23.

Intrinsic fluctuations lead to broad range of transduced forces in tethered-bead single-molecule experiments.

Mehraeen S, Spakowitz AJ.

Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Aug;86(2 Pt 1):021902. Epub 2012 Aug 2.

PMID:
23005780
24.

Force fluctuations impact kinetics of biomolecular systems.

Koslover EF, Spakowitz AJ.

Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Jul;86(1 Pt 1):011906. Epub 2012 Jul 10.

PMID:
23005451
25.

Analytical tools to distinguish the effects of localization error, confinement, and medium elasticity on the velocity autocorrelation function.

Weber SC, Thompson MA, Moerner WE, Spakowitz AJ, Theriot JA.

Biophys J. 2012 Jun 6;102(11):2443-50. doi: 10.1016/j.bpj.2012.03.062. Epub 2012 Jun 5.

26.

Nonthermal ATP-dependent fluctuations contribute to the in vivo motion of chromosomal loci.

Weber SC, Spakowitz AJ, Theriot JA.

Proc Natl Acad Sci U S A. 2012 May 8;109(19):7338-43. doi: 10.1073/pnas.1119505109. Epub 2012 Apr 19.

27.

Theoretical and computational modeling of target-site search kinetics in vitro and in vivo.

Koslover EF, Díaz de la Rosa MA, Spakowitz AJ.

Biophys J. 2011 Aug 17;101(4):856-65. doi: 10.1016/j.bpj.2011.06.066.

28.

Tension-dependent structural deformation alters single-molecule transition kinetics.

Sudhanshu B, Mihardja S, Koslover EF, Mehraeen S, Bustamante C, Spakowitz AJ.

Proc Natl Acad Sci U S A. 2011 Feb 1;108(5):1885-90. doi: 10.1073/pnas.1010047108. Epub 2011 Jan 18.

29.

Local geometry and elasticity in compact chromatin structure.

Koslover EF, Fuller CJ, Straight AF, Spakowitz AJ.

Biophys J. 2010 Dec 15;99(12):3941-50. doi: 10.1016/j.bpj.2010.10.024.

30.

Bacterial chromosomal loci move subdiffusively through a viscoelastic cytoplasm.

Weber SC, Spakowitz AJ, Theriot JA.

Phys Rev Lett. 2010 Jun 11;104(23):238102. Epub 2010 Jun 8.

31.

Subdiffusive motion of a polymer composed of subdiffusive monomers.

Weber SC, Theriot JA, Spakowitz AJ.

Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Jul;82(1 Pt 1):011913. Epub 2010 Jul 19.

32.

Dynamic strategies for target-site search by DNA-binding proteins.

de la Rosa MA, Koslover EF, Mulligan PJ, Spakowitz AJ.

Biophys J. 2010 Jun 16;98(12):2943-53. doi: 10.1016/j.bpj.2010.02.055.

33.

Twist- and tension-mediated elastic coupling between DNA-binding proteins.

Koslover EF, Spakowitz AJ.

Phys Rev Lett. 2009 May 1;102(17):178102. Epub 2009 Apr 30.

PMID:
19518837
34.

End-to-end distribution for a wormlike chain in arbitrary dimensions.

Mehraeen S, Sudhanshu B, Koslover EF, Spakowitz AJ.

Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Jun;77(6 Pt 1):061803. Epub 2008 Jun 9.

PMID:
18643291
35.

Three-dimensional architecture of the bacteriophage phi29 packaged genome and elucidation of its packaging process.

Comolli LR, Spakowitz AJ, Siegerist CE, Jardine PJ, Grimes S, Anderson DL, Bustamante C, Downing KH.

Virology. 2008 Feb 20;371(2):267-77. Epub 2007 Nov 14.

36.

Effect of force on mononucleosomal dynamics.

Mihardja S, Spakowitz AJ, Zhang Y, Bustamante C.

Proc Natl Acad Sci U S A. 2006 Oct 24;103(43):15871-6. Epub 2006 Oct 16.

37.

End-to-end distance vector distribution with fixed end orientations for the wormlike chain model.

Spakowitz AJ, Wang ZG.

Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Oct;72(4 Pt 1):041802. Epub 2005 Oct 7.

PMID:
16383410
38.

Topological constraints in nucleic acid hybridization kinetics.

Bois JS, Venkataraman S, Choi HM, Spakowitz AJ, Wang ZG, Pierce NA.

Nucleic Acids Res. 2005 Jul 25;33(13):4090-5. Print 2005.

39.

DNA packaging in bacteriophage: is twist important?

Spakowitz AJ, Wang ZG.

Biophys J. 2005 Jun;88(6):3912-23. Epub 2005 Apr 1.

40.

Semiflexible polymer confined to a spherical surface.

Spakowitz AJ, Wang ZG.

Phys Rev Lett. 2003 Oct 17;91(16):166102. Epub 2003 Oct 16.

PMID:
14611419
41.

Free expansion of elastic filaments.

Spakowitz AJ, Wang ZG.

Phys Rev E Stat Nonlin Soft Matter Phys. 2001 Dec;64(6 Pt 1):061802. Epub 2001 Nov 27. Erratum in: Phys Rev E Stat Nonlin Soft Matter Phys. 2005 May;71(5 Pt 2):059902.

PMID:
11736202

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