Eric Rawdon's Publications Page


Below are links to my papers. If you do not have access to these journals, please email me at ejrawdon [at] stthomas.edu and I will get you a PDF.


Published Papers

  1. LinkProt: A database collecting information about biological links
    Pawel Dabrowski-Tumanski, Aleksandra Jarmolinska, Wanda Niemyska, Eric Rawdon, Kenneth Millett, and Joanna Sulkowska
    Nucleic Acids Res., 45(D1): D243-D249, 2016.
    doi:10.1093/nar/gkw976

  2. How topoisomerase IV can efficiently unknot and decatenate negatively supercoiled DNA molecules without causing their torsional relaxation
    Eric J. Rawdon, Julien Dorier, Dusan Racko, Kenneth C. and Millett, and Andrzej Stasiak
    Nucleic Acids Res., 44(10): 4528-4538, 2016.
    doi:10.1093/nar/gkw311

  3. Knotting fingerprints resolve knot complexity and knotting pathways in ideal knots
    David A. B. Hyde, Joshua Henrich, Eric J. Rawdon, and Kenneth C. Millett
    J. Phys.: Condens. Matter, 27: 354112, 2015.
    doi:10.1088/0953-8984/27/35/354112

  4. Subknots in ideal knots, random knots, and knotted proteins
    Eric J. Rawdon, Kenneth C. Millett, and Andrzej Stasiak
    Sci. Rep., 5: 8928, 2015.
    doi:10.1038/srep08928

  5. Link lengths and their growth powers
    Youngsik Huh, Sungjong No, Seungsang Oh, and Eric J. Rawdon
    Journal of Physics A: Mathematical and Theoretical, 48(3): 035202, 2015.
    doi:10.1088/1751-8113/48/3/035202

  6. KnotProt: a database of proteins with knots and slipknots
    Michal Jamroz, Wanda Niemyska, Eric J. Rawdon, Andrzej Stasiak, Kenneth C. Millett, Piotr Sulkowski, and Joanna I. Sulkowska
    Nucleic Acids Res. , 43 (D1 ): D306-D314 , 2015 .
    doi:10.1093/nar/gku1059

  7. The spectrum of tightly knotted flux tubes in QCD
    Roman V. Buniy, Jason Cantarella, Thomas W. Kephart, and Eric J. Rawdon
    Journal of Physics: Conference Series, 544(1): 012025, 2014.
    doi:10.1088/1742-6596/544/1/012025

  8. The knot spectrum of confined random equilateral polygons
    Yuanan Diao, Claus Ernst, Anthony Montemayor, Eric J. Rawdon, and Uta Ziegler
    Molecularly Based Mathematical Biology, 2: 19-33, 2014.
    doi:10.2478/mlbmb-2014-0002

  9. The tight knot spectrum in QCD
    Roman V. Buniy, Jason Cantarella, Thomas W. Kephart, and Eric J. Rawdon
    Phys. Rev. D, 89: 054513, 2014.
    doi:10.1103/PhysRevD.89.054513

  10. Knotted arcs in open chains, closed chains, and proteins
    Eric J. Rawdon
    Oberwolfach Reports, 22: 31-32, 2013.
    doi:10.4171/OWR/2013/22

  11. Knot localization in proteins
    Eric J. Rawdon, Kenneth C. Millett, Joanna I. Sulkowska, and Andrzej Stasiak
    Biochem. Soc. Trans., 41(2): 538-541, 2013.
    doi:10.1042/BST20120329

  12. Identifying knots in proteins
    Kenneth C. Millett, Eric J. Rawdon, Andrzej Stasiak, and Joanna I. Sulkowska
    Biochem. Soc. Trans., 41(2): 533-537, 2013.
    doi:10.1042/BST20120339

  13. Knotting pathways in proteins
    Joanna I. Sulkowska, Jeffrey K. Noel, Cesar A. Ramirez-Sarmiento, Eric J. Rawdon, Kenneth C. Millett, and Jose N. Onuchic
    Biochem. Soc. Trans., 41(2): 523-527, 2013.
    doi:10.1042/BST20120342

  14. All monofilament knots assume sliding conformation in vivo
    Daniel A. Davis, Donna M. Pellowski, and Eric J. Rawdon
    Dermatol. Surg., 39(5): 729-733, 2013.
    doi:10.1111/dsu.12112

  15. Sedimentation of macroscopic rigid knots and its relation to gel electrophoretic mobility of DNA knots
    Cedric Weber, Mathias Carlen, Giovanni Dietler, Eric J. Rawdon, and Andrzej Stasiak
    Sci. Rep., 3: 1091, 2013.
    doi:10.1038/srep01091

  16. Conservation of complex knotting and slipknotting patterns in proteins
    Joanna I. Sulkowska, Eric J. Rawdon, Kenneth C. Millett, Jose N. Onuchic, and Andrzej Stasiak
    Proc. Natl. Acad. Sci. USA , 109 (26 ): E1715-E1723 , 2012 .
    doi:10.1073/pnas.1205918109

  17. Shapes of tight composite knots
    Jason Cantarella, Al LaPointe, and Eric J. Rawdon
    J. Phys. A, 45(22): 225202, 2012.
    doi:10.1088/1751-8113/45/22/225202

  18. Cumulative shapes of knotted polymers
    Eric J. Rawdon, Kenneth C. Millett, Vy T. Tran, and Andrzej Stasiak
    Prog. Theor. Phys. Suppl., 191: 165-171, 2011.
    doi:10.1143/PTPS.191.165

  19. Physical knot theory: the study of sizes and shapes of polymers
    Eric J. Rawdon
    In Louis H. Kauffman, Sofia Lambropoulou, Slavik Jablan, and Jozef H. Prztycki, editors
    Introductory Lectures on Knot Theory
    volume 46 of Ser. Knots Everything, pages 457-481, Singapore, 2011. World Sci. Publishing.
    doi:10.1142/7784

  20. Knot tightening by constrained gradient descent
    Ted Ashton, Jason Cantarella, Michael Piatek, and Eric J. Rawdon
    Experiment. Math., 20(1): 57-90, 2011.
    doi:10.1080/10586458.2011.544581

  21. Symmetry-breaking in cumulative measures of shapes of polymer models
    Kenneth C. Millett, Eric J. Rawdon, Vy T. Tran, and Andrzej Stasiak
    J. Chem. Phys., 133: 154113, 2010.
    doi:10.1063/1.3495482

  22. Error analysis of the Minimum Distance Energy of a polygonal knot and the Moebius Energy of an approximating curve
    Eric J. Rawdon and Joseph Worthington
    J. Knot Theory Ramifications, 19(8): 975-1000, 2010.
    doi:10.1142/S0218216510008303

  23. Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles
    Davide Demurtas, Arnaud Amzallag, Eric J. Rawdon, John H. Maddocks, Jacques Dubochet, and Andrzej Stasiak
    Nucl. Acids Res, 37(9): 2882-2893, 2009.
    doi:10.1093/nar/gkp137

  24. Shapes of knotted cyclic polymers
    Eric J. Rawdon, John C. Kern, Michael Piatek, Patrick Plunkett, Andrzej Stasiak, and Kenneth C. Millett
    Bussei Kenkyu, 92(1): 32-37, 2009.
    doi:10.1093/nar/gkp137

  25. Effect of knotting on polymer shapes and their enveloping ellipsoids
    Kenneth C. Millett, Patrick Plunkett, Michael Piatek, Eric J. Rawdon, and Andrzej Stasiak
    J. Chem. Phys., 130(16): 165104, 2009.
    doi:10.1063/1.3117923

  26. Effect of knotting on the shape of polymers
    Eric J. Rawdon, John C. Kern, Michael Piatek, Patrick Plunkett, Andrzej Stasiak, and Kenneth C. Millett
    Macromolecules, 41(21): 8281-8287, 2008.
    doi:10.1021/ma801389c

  27. Scaling behavior and equilibrium lengths of knotted polymers
    Eric Rawdon, Akos Dobay, John C. Kern, Kenneth C. Millett, Michael Piatek, Patrick Plunkett, and Andrzej Stasiak
    Macromolecules, 41(12): 4444-4451, 2008.
    doi:10.1021/ma8000803

  28. Polygonal knot space near ropelength-minimized knots
    Kenneth C. Millett, Michael Piatek, and Eric J. Rawdon
    J. Knot Theory Ramifications, 17(5): 601-631, 2008.
    doi:10.1142/S0218216508006282

  29. Total curvature and total torsion of knotted polymers
    Patrick Plunkett, Michael Piatek, Akos Dobay, John C. Kern, Kenneth C. Millett, Andrzej Stasiak, and Eric J. Rawdon
    Macromolecules, 40(10): 3860-3867, 2007.
    doi:10.1021/ma0627673

  30. Polygonal approximation and energy of smooth knots
    Eric J. Rawdon and Jonathan K. Simon
    J. Knot Theory Ramifications, 15(4): 429-451, 2006.
    doi:10.1142/S0218216506004543

  31. Visualizing the tightening of knots
    Jason Cantarella, Michael Piatek, and Eric Rawdon
    In VIS'05: Proceedings of the 16th IEEE Visualization 2005 (VIS'05)
    pages 575-582, Washington, DC, USA, 2005. IEEE Computer Society.
    doi:10.1109/VISUAL.2005.1532844

  32. Physical and Numerical Models in Knot Theory
    Jorge Alberto Calvo, Kenneth C. Millett, Eric J. Rawdon, and Andrzej Stasiak, editors volume 36 of Ser. Knots Everything, Singapore, 2005.
    doi:10.1142/5766

  33. Ropelength of tight polygonal knots
    Kenneth C. Millett and Eric J. Rawdon
    In Physical and Numerical Models in Knot Theory
    volume 36 of Ser. Knots Everything, pages 247-274, Singapore, 2005. World Sci. Publishing.
    doi:10.1142/5766

  34. Ropelength of tight polygonal knots
    Justyna Baranska, Piotr Pieranski, and Eric J. Rawdon
    In Physical and Numerical Models in Knot Theory
    volume 36 of Ser. Knots Everything, pages 293-321, Singapore, 2005. World Sci. Publishing.
    doi:10.1142/5766

  35. Length of the tightest trefoil knot
    Justyna Baranska, Piotr Pieranski, Sylwester Przybyl, and Eric J. Rawdon
    Phys. Rev. E, 70(5): 051810, 2004.
    doi:10.1103/PhysRevE.70.051810

  36. Role of flexibility in entanglement
    Gregory Buck and Eric J. Rawdon
    Phys. Rev. E, 70(1): 011803, 2004.
    doi:10.1103/PhysRevE.70.011803

  37. Can computers discover ideal knots?
    Eric J. Rawdon
    Experiment. Math., 12(3): 287-302, 2003.
    doi:10.1080/10586458.2003.10504499

  38. Energy, ropelength, and other physical aspects of equilateral knots
    Kenneth C. Millett and Eric J. Rawdon
    J. Comput. Phys., 186(2): 426-456, 2003.
    doi:10.1016/S0021-9991(03)00026-3

  39. Upper bounds for equilateral stick numbers
    Eric J. Rawdon and Robert G. Scharein
    In Physical knots: knotting, linking, and folding geometric
    volume 304 of Contemp. Math., pages 55-75, Providence, RI, 2002. Amer. Math. Soc..
    doi:10.1090/conm/304

  40. Physical knots: knotting, linking, and folding geometric
    Jorge Alberto Calvo, Kenneth C. Millett, and Eric J. Rawdon, editors volume 304 of Contemporary Mathematics, Providence, RI, 2002.
    Papers from the AMS Special Session on Physical Knotting and.
    doi:10.1090/conm/304

  41. Moebius energy of thick knots
    Eric J. Rawdon and Jonathan K. Simon
    Topology Appl., 125(1): 97-109, 2002.
    doi:10.1016/S0166-8641(01)00263-2

  42. Approximating smooth thickness
    Eric J. Rawdon
    J. Knot Theory Ramifications, 9(1): 113-145, 2000.
    doi:10.1142/S0218216500000062

  43. Thickness of knots
    Richard A. Litherland, Jonathan Simon, Oguz Durumeric, and Eric Rawdon
    Topology Appl., 91(3): 233-244, 1999.
    doi:10.1016/S0166-8641(97)00210-1

  44. Approximating the thickness of a knot
    Eric J. Rawdon
    In Ideal knots
    pages 143-150, Singapore, 1998. World Sci. Publishing.
    doi:10.1142/3843