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. Proteins containing 6-crossing knot types and their folding pathways
    Maciej Sikora, Erica Flapan, Helen Wong, Pawel Rubach, Wojciech Garstka, Szymon Niewieczerzal, Eric J Rawdon, and Joanna I Sulkowska.
    Submitted, 2023.

  2. An introduction to KnotPlot
    Robert G. Scharein and Eric J. Rawdon.
    Submitted, 2023.

  3. Using the HOMFLY-PT polynomial to compute knot types
    Eric J. Rawdon and Robert G. Scharein.
    Submitted, 2023.

  4. AlphaKnot: server to analyze entanglement in structures predicted by AlphaFold methods
    Wanda Niemyska, Pawel Rubach, Bartosz A. Gren, Mai Lan Nguyen, Wojciech Garstka, Fernando Bruno da Silva, Eric J. Rawdon, and Joanna I. Sulkowska.
    Nucleic Acids Res., 50: W44-W50, 2022.
    doi:10.1093/nar/gkac388

  5. RiFNet: Automated rib fraction detection in postmortem computed tomography
    Victor Ibanez, Samuel Gunz, Svenja Erne, Eric J. Rawdon, Garyfalia Ampanozi, Sabine Franckenberg, Till Sieberth, Raffael Affolter, Lars C. Ebert, and Akos Dobay.
    Forensic Sci. Med. Pathol., 18: 20-29, 2022.
    doi:10.1007/s12024-021-00431-8

  6. Knotting spectrum of polygonal knots in extreme confinement
    Claus Ernst, Eric J. Rawdon, and Uta Ziegler.
    J. Phys. A: Math. Theor., 54: 235202, 2021.
    doi:10.1088/1751-8121/abf8e8

  7. Open knots
    Julien Dorier, Dimos Goundaroulis, Eric J. Rawdon, and Andrzej Stasiak.
    In Colin Adam, Erica Flapan, Allison Henrich, Louis H. Kauffman, Lewis D. Ludwig, and Sam Nelson., editors
    Encyclopedia of Knot Theory
    pages 859-874, Boca Raton, FL, USA, 2021. Chapman and Hall/CRC.
    doi:10.1201/9781138298217

  8. KnotProt 2.0: a database of proteins with knots and other entangled structures
    Pawel Dabrowski-Tumanski, Pawel Rubach, Dimos Goundaroulis, Julien Dorier, Piotr Sulkowski, Kenneth C. Millett, Eric J. Rawdon, Andrzej Stasiak, and Joanna I. Sulkowska.
    Nucleic Acids Res., 47(D1): D367-D375, 2019.
    doi:10.1093/nar/gky1140

  9. Open knotting
    Erin Brine-Doyle, Madeline Shogren, Emily Vecchia, and Eric J. Rawdon.
    In New Directions in Geometric and Applied Knot Theory
    pages 176-204, Berlin, 2018. De Gruyter.
    doi:10.1515/9783110571493-009

  10. The knot spectrum of random knot spaces
    Yuanan Diao, Claus Ernst, Eric J. Rawdon, and Uta Ziegler.
    In New Directions in Geometric and Applied Knot Theory
    pages 205-237, Berlin, 2018. De Gruyter.
    doi:10.1515/9783110571493-010

  11. Average crossing number and writhe of knotted random polygons in confinement
    Yuanan Diao, Claus Ernst, Eric J. Rawdon, and Uta Ziegler.
    React. Funct. Polym., 131: 430-444, 2018.
    doi:10.1016/j.reactfunctpolym.2018.07.028

  12. Total curvature and total torsion of knotted random polygons in confinement
    Yuanan Diao, Claus Ernst, Eric J. Rawdon, and Uta Ziegler.
    J. Phys. A: Math. Theor., 51: 154002, 2018.
    doi:10.1088/1751-8121/aab1ed

  13. Knot fertility and lineage
    Jason Cantarella, Allison Henrich, Elsa Magness, Oliver O'Keefe, Kayla Perez, Eric J. Rawdon, and Briana Zimmer.
    J. Knot Theory Ramifications, 26(13): 1750093, 2017.
    doi:10.1142/S0218216517500936

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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

  23. Knotted arcs in open chains, closed chains, and proteins
    Eric J. Rawdon.
    Oberwolfach Reports, 22: 31-32, 2013.
    doi:10.14760/OWR-2013-22

  24. 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

  25. 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

  26. 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

  27. 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

  28. 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

  29. 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

  30. 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

  31. 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

  32. 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

  33. 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

  34. 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

  35. 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

  36. 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

  37. 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.
    http://ci.nii.ac.jp/naid/110007230476/en

  38. 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

  39. 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

  40. 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

  41. 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

  42. 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

  43. 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

  44. 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

  45. 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

  46. 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

  47. 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

  48. 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

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

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

  51. 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

  52. 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

  53. 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

  54. 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

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

  56. 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

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