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1

High flexibility of DNA on short length scales probed by atomic force microscopy

Wiggins, Paul A., van der Heijden, Thijn, Moreno-Herrero, Fernando, Spakowitz, Andrew, Phillips, Rob, Widom, Jonathan, Dekker, Cees, Nelson, Philip C.

Journal:

Nature Nanotechnology

Year:

2006

Language:

english

File:

PDF, 276 KB

english, 2006

2

Bacterial Chromosomal Loci Move Subdiffusively through a Viscoelastic Cytoplasm

Weber, Stephanie C., Spakowitz, Andrew J., Theriot, Julie A.

Journal:

Physical Review Letters

Year:

2010

Language:

english

File:

PDF, 372 KB

english, 2010

3

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

Mollinger, Sonya A., Salleo, Alberto, Spakowitz, Andrew J.

Journal:

ACS Central Science

Year:

2016

Language:

english

File:

PDF, 3.05 MB

english, 2016

4

Fluctuation Effects in Semiflexible Diblock Copolymers

Mao, Shifan, MacPherson, Quinn, Spakowitz, Andrew J.

Journal:

ACS Macro Letters

Year:

2017

Language:

english

File:

PDF, 2.09 MB

english, 2017

5

Strong disorder leads to scale invariance in complex biological systems

Stylianidou, Stella, Lampo, Thomas J., Spakowitz, Andrew J., Wiggins, Paul A.

Journal:

Physical Review E

Year:

2018

Language:

english

File:

PDF, 933 KB

english, 2018

6

A Boltzmann-weighted hopping model of charge transport in organic semicrystalline films

Kwiatkowski, Joe J., Jimison, Leslie H., Salleo, Alberto, Spakowitz, Andrew J.

Journal:

Journal of Applied Physics

Year:

2011

Language:

english

File:

PDF, 1.46 MB

english, 2011

7

Three-dimensional architecture of the bacteriophage φ29 packaged genome and elucidation of its packaging process

Luis R. Comolli, Andrew J. Spakowitz, Cristina E. Siegerist, Paul J. Jardine, Shelley Grimes, Dwight L. Anderson, Carlos Bustamante, Kenneth H. Downing

Journal:

Year:

2008

Language:

english

File:

PDF, 2.15 MB

english, 2008

8

Systematic Coarse-Graining of Microscale Polymer Models as Effective Elastic Chains

Koslover, Elena F., Spakowitz, Andrew J.

Journal:

Year:

2013

Language:

english

File:

PDF, 1.02 MB

english, 2013

9

A Predictive Theoretical Model For Clathrin Self-Assembly

Mehraeen, Shafigh, Cordella, Nick, Spakowitz, Andrew J.

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 43 KB

english, 2010

10

Dynamic Strategies for Target-Site Search by DNA-Binding Proteins

Díaz de la Rosa, Mario A., Koslover, Elena F., Mulligan, Peter J., Spakowitz, Andrew J.

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 847 KB

english, 2010

11

Local Geometry and Elasticity in Compact Chromatin Structure

Koslover, Elena F., Fuller, Colin J., Straight, Aaron F., Spakowitz, Andrew J.

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 1.68 MB

english, 2010

12

Modeling the Effects of Structure and Epigenetic Modifications in Heterochromatin Condensation

Mulligan, Peter J., Koslover, Elena F., Spakowitz, Andrew J.

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 59 KB

english, 2011

13

Target Site Localization Dynamics of DNA-Binding Proteins in Vivo

Koslover, Elena F., de la Rose, Mario A. Diaz, Weber, Stephanie C., Spakowitz, Andrew J.

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 64 KB

english, 2011

14

Theoretical and Computational Modeling of Target-Site Search Kinetics In Vitro and In Vivo

Koslover, Elena F., Díaz de la Rosa, Mario A., Spakowitz, Andrew J.

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 1.10 MB

english, 2011

15

Analytical Tools To Distinguish the Effects of Localization Error, Confinement, and Medium Elasticity on the Velocity Autocorrelation Function

Weber, Stephanie C., Thompson, Michael A., Moerner, W.E., Spakowitz, Andrew J., Theriot, Julie A.

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 1.90 MB

english, 2012

16

DNA Packaging in Bacteriophage: Is Twist Important?

Spakowitz, Andrew James, Wang, Zhen-Gang

Journal:

Biophysical Journal

Year:

2005

Language:

english

File:

PDF, 291 KB

english, 2005

17

Optical Measurement of Mechanical Forces Inside Short DNA Loops

Shroff, Hari, Sivak, David, Siegel, Jake J., McEvoy, A.L., Siu, Merek, Spakowitz, Andrew, Geissler, Phillip L., Liphardt, Jan

Journal:

Biophysical Journal

Year:

2008

Language:

english

File:

PDF, 341 KB

english, 2008

18

Selective dispersion of high purity semiconducting single-walled carbon nanotubes with regioregular poly(3-alkylthiophene)s

Lee, Hang Woo, Yoon, Yeohoon, Park, Steve, Oh, Joon Hak, Hong, Sanghyun, Liyanage, Luckshitha S., Wang, Huiliang, Morishita, Satoshi, Patil, Nishant, Park, Young Jun, Park, Jong Jin, Spakowitz, Andrew

Journal:

Nature Communications

Year:

2011

Language:

english

File:

PDF, 1.13 MB

english, 2011

19

Target Site Search Strategy Of Gene Regulatory Proteins

de la Rosa, Mario Diaz, Spakowitz, Andrew J.

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 61 KB

english, 2009

20

Target-Site Search of DNA-Binding Proteins

de la Rosa, Mario A. Diaz, Koslover, Elena F., Mulligan, Peter J., Spakowitz, Andrew J.

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 53 KB

english, 2010

21

Table of Contents

de la Rosa, Mario A. Diaz, Koslover, Elena F., Mulligan, Peter J., Spakowitz, Andrew J.

Journal:

Surgery for Obesity and Related Diseases

Year:

2010

Language:

english

File:

PDF, 130 KB

english, 2010

22

Theoretical Design of Model Nanoparticles for Targeted Cell-Surface Binding

Cordella, Nicholas, Mehraeen, Shafigh, Spakowitz, Andrew J.

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 39 KB

english, 2010

23

Theoretical Modeling of Protein Accessibility to the Chromatin Fiber

Koslover, Elena F., de la Rosa, Mario Diaz, Mulligan, Peter J., Spakowitz, Andrew J.

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 37 KB

english, 2010

24

Role of DNA Fluctuations in RNA Polymerase Translocation through a Single Nucleosome

Sudhanshu, Bariz, Koslover, Elena F., Mihardja, Shirley, Spakowitz, Andrew J.

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 54 KB

english, 2010

25

Chromosomal Loci Move Subdiffusively Through a Viscoelastic Cytoplasm

Weber, Stephanie C., Theriot, Julie A., Spakowitz, Andrew J.

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 45 KB

english, 2010

26

Role of DNA Elasticity and Nucleosome Geometry in Hierarchical Packaging of Chromatin

Koslover, Elena F., Fuller, Colin, Straight, Aaron F., Spakowitz, Andrew J.

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 39 KB

english, 2010

27

Theoretical Modeling of the Weaving of Clathrin into Nanoscale Baskets

Mehraeen, Shafigh, Cordella, Nicholas, Yoo, Jee Soo, Spakowitz, Andrew J.

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 119 KB

english, 2011

28

Structure and Dynamics of Supercoiled DNA in Confinement

Diaz de la Rosa, Mario A., Spakowitz, Andrew J.

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 35 KB

english, 2012

29

Single Molecule Analysis of Substeps in the Mechanochemical Cycle of DNA Gyrase

Basu, Aakash, Koslover, Lena, Schoeffler, Allyn, Tretter, Elsa, Berger, James M., Spakowitz, Andrew J., Bryant, Zev D.

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 53 KB

english, 2010

30

Twist and Tension-mediated Elastic Coupling between DNA-Bending Proteins

Koslover, Elena F., Spakowitz, Andrew J.

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 39 KB

english, 2009

31

Theoretical Model of HP1-Induced Heterochromatin Formation

Mulligan, Peter J., Koslover, Elena F., Spakowitz, Andrew J.

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 39 KB

english, 2010

32

Membrane Fluctuations Destabilize Clathrin Protein Lattice Order

Cordella, Nicholas, Lampo, Thomas J., Mehraeen, Shafigh, Spakowitz, Andrew J.

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 2.63 MB

english, 2014

33

Physical Modeling of Chromosome Segregation in E. Coli Reveals Impact of Force and DNA Relaxation

Lampo, Thomas J., Kuwada, Nathan J., Wiggins, Paul A., Spakowitz, Andrew J.

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 42 KB

english, 2014

34

Force Fluctuations Impact Genome Processing Kinetics

Koslover, Elena F., Spakowitz, Andrew J.

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 35 KB

english, 2012

35

Dynamic Re-Discretization Allows Simulation of Biopolymers Across Length-Scales

Mulligan, Peter, Koslover, Elena F., Spakowitz, Andrew J.

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 42 KB

english, 2014

36

Subdiffusive motion of a polymer composed of subdiffusive monomers

Weber, Stephanie C., Theriot, Julie A., Spakowitz, Andrew J.

Journal:

Physical Review E

Year:

2010

Language:

english

File:

PDF, 612 KB

english, 2010

37

Biocompatible Force Sensor with Optical Readout and Dimensions of 6 nm 3

Shroff, Hari, Reinhard, Björn M., Siu, Merek, Agarwal, Harish, Spakowitz, Andrew, Liphardt, Jan

Journal:

Year:

2005

Language:

english

File:

PDF, 203 KB

english, 2005

38

Exact Results for a Semiflexible Polymer Chain in an Aligning Field

Spakowitz, Andrew J., Wang, Zhen-Gang

Journal:

Year:

2004

Language:

english

File:

PDF, 138 KB

english, 2004

39

Discretizing elastic chains for coarse-grained polymer models

Koslover, Elena F., Spakowitz, Andrew J.

Journal:

Year:

2013

Language:

english

File:

PDF, 848 KB

english, 2013

40

Impact of defect creation and motion on the thermodynamics and large-scale reorganization of self-assembled clathrin lattices

Mehraeen, Shafigh, Cordella, Nicholas, Yoo, Jee Soo, Spakowitz, Andrew J.

Journal:

Year:

2011

Language:

english

File:

PDF, 1.38 MB

english, 2011

41

Rheology and simulation of 2-dimensional clathrin protein network assembly

VanDersarl, Jules J., Mehraeen, Shafigh, Schoen, Alia P., Heilshorn, Sarah C., Spakowitz, Andrew J., Melosh, Nicholas A.

Journal:

Year:

2014

Language:

english

File:

PDF, 1.04 MB

english, 2014

42

Dynamic remodelling of disordered protein aggregates is an alternative pathway to achieve robust self-assembly of nanostructures

Schoen, Alia P., Cordella, Nicholas, Mehraeen, Shafigh, Arunagirinathan, Manickam Adhimoolam, Spakowitz, Andrew J., Heilshorn, Sarah C.

Journal:

Year:

2013

Language:

english

File:

PDF, 619 KB

english, 2013

43

Membrane indentation triggers clathrin lattice reorganization and fluidization

Cordella, Nicholas, Lampo, Thomas J., Melosh, Nicholas, Spakowitz, Andrew J.

Journal:

Year:

2015

Language:

english

File:

PDF, 2.71 MB

english, 2015

44

Semiflexible polymer solutions. I. Phase behavior and single-chain statistics

Spakowitz, Andrew J., Wang, Zhen-Gang

Journal:

The Journal of Chemical Physics

Year:

2003

Language:

english

File:

PDF, 427 KB

english, 2003

45

Semiflexible Polymer Confined to a Spherical Surface

Spakowitz, Andrew J., Wang, Zhen-Gang

Journal:

Physical Review Letters

Year:

2003

Language:

english

File:

PDF, 207 KB

english, 2003

46

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

Mehraeen, Shafigh, Sudhanshu, Bariz, Koslover, Elena F., Spakowitz, Andrew J.

Journal:

Physical Review E

Year:

2008

Language:

english

File:

PDF, 572 KB

english, 2008

47

Twist- and Tension-Mediated Elastic Coupling between DNA-Binding Proteins

Koslover, Elena F., Spakowitz, Andrew J.

Journal:

Physical Review Letters

Year:

2009

Language:

english

File:

PDF, 480 KB

english, 2009

48

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

Mehraeen, Shafigh, Spakowitz, Andrew J.

Journal:

Physical Review E

Year:

2012

Language:

english

File:

PDF, 1.15 MB

english, 2012

49

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

Chen, Yi-Ju, Johnson, Stephanie, Mulligan, Peter, Spakowitz, Andrew J., Phillips, Rob

Journal:

Proceedings of the National Academy of Sciences

Year:

2014

Language:

english

File:

PDF, 1.26 MB

english, 2014

50

Force fluctuations impact kinetics of biomolecular systems

Koslover, Elena F., Spakowitz, Andrew J.

Journal:

Physical Review E

Year:

2012

Language:

english

File:

PDF, 1.16 MB

english, 2012