David Swigon's Publications

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Mathematical immunology, cell migration, and other topics

*	M. DeSantis, D. Swigon, and G. Caginalp, Nonlinear dynamics and stability in a multi-group asset flow model, submitted (2012).
*	D. Swigon, Ensemble modeling of biological systems, accepted (2011). PDF
*	K. Penner, B. Ermentrout, & D. Swigon, Pattern formation in a model of acute inflammation, revised (2011). PDF and supplementary movies Figure 4.2, Figure 7.1, Figure 7.2, Figure 7.3, Figure 7.4, Figure 7.5
*	J.C. Arciero, Q. Mi, M.F. Branca, D. Hackam, & D. Swigon, Continuum model of collective cell migration in wound healing and colony expansion, Biophys. J., 100, 535–543 (2011). PDF
*	B. Riviere, Y. Epshteyn, D. Swigon & Y. Vodovotz, A simple mathematical model of signaling resulting from the binding of lipopolysaccharide with Toll-like receptor 4 demonstrates inherent preconditioning behavior Math. Biosc., 217, 19–26 (2008). PDF
*	Q. Mi, D. Swigon, B. Riviere, S. Cetin, Y. Vodovotz, & D. Hackam, One-dimensional elastic continuum model of enterocyte layer migration, Biohys. J., 93, 3745–3752 (2007). PDF
*	B. Hancioglu, D. Swigon, & G. Clermont, A dynamical model of human immune response to influenza A virus infection, J. Theor. Biol., 246, 70–86 (2007). PDF

Sequence-dependent DNA elasticity and biological applications

*	A. Kocsis & D. Swigon, DNA stretching modeled at the base pair level: overtwisting and shear instability in elastic linkages, accepted (2011). PDF and supplement
*	S. Lim, Y. Kim & D. Swigon, Dynamics of an electrostatically charged rod in fluid, Proc. R. Soc. A, 467, 569–590 (2010). PDF
*	W.K. Olson, A.R. Srinivasan, A.V. Colasanti, G. Zheng, & D. Swigon, DNA Biomechanics, Handbook of Molecular Biophysics, 359–382 (2009). PDF
*	D. Swigon, The Mathematics of DNA Structure, Mechanics, and Dynamics, IMA Volumes in Mathematics and Its Applications, 150, 293–320 (2009). PDF
*	L. Czapla, D. Swigon, & W.K. Olson, Effects of the Nucleoid Protein HU on the Structure, Flexibility, and Ring-Closure Properties of DNA deduced from Monte Carlo Simulations, J. Mol. Biol, 382, 353–370 (2008). PDF
*	D. Swigon, & W.K. Olson, Mesoscale modeling of multi-protein-DNA assemblies: The role of the catabolic activator protein in Lac-repressor-mediated DNA looping, Int. J. Non-linear Mech., 43, 1082–1093 (2008). PDF
*	Y. Biton, B.D. Coleman, & D. Swigon, On bifurcations of equilibria of intrinsically curved electrically charged, rod-like structures that model DNA in solution, J. Elasticity, 87, 187–210 (2007). PDF
*	D. Swigon, B.D. Coleman, & W.K. Olson, Modeling the Lac repressor-operator assembly. I. The influence of DNA looping on Lac repressor conformation, Proc. Natl. Acad. Sci. USA, 103, 9879–9884 (2006). PDF
*	L. Czapla, D. Swigon, & W.K. Olson, Sequence-dependent Effects in the Cyclization of Short DNA, J. Chem. Theory Comput., 2, 685–695 (2006). PDF
*	C.L. Lawson, D. Swigon, K. Murakami, S.A. Darst, H.M. Ebright, & R.H. Ebright, Catabolite activator protein (CAP): DNA binding and transcription activation, Curr. Opin. Struct. Bio., 14, 1–11 (2004). PDF
*	W.K. Olson, D. Swigon, & B.D. Coleman, Implications of the dependence of the elastic properties of DNA on nucleotide sequence, Phil. Trans. Roy. Soc. Lond. A, 362, 1403-1422 (2004). PDF
*	B.D. Coleman, W.K. Olson, & D. Swigon, Theory of sequence-dependent DNA elasticity, J. Chem. Phys., 118, 7127–7140 (2003). PDF

Elastic rod model for DNA

*	B.D. Coleman & D. Swigon, Theory of self-contact in Kirchhoff rods with applications to supercoiling of knotted and unknotted DNA plasmids, Phil. Trans. Roy. Soc. Lond. A, 362, 1281-1299 (2004). PDF
*	D. Keller, D. Swigon, & C. Bustamante, Relating single molecule measurements to thermodynamics, Biophys. J, 84,733–738 (2003). PDF
*	B.D. Coleman & D. Swigon, Theory of Self-Contact in DNA Molecules Modeled as Elastic Rods. In: Nuovi progressi nella fisica matematica dall'eredità di Dario Graffi, pp. 281-295, Atti dei Convegni Lincei, Vol. 177, Accademia Nazionale dei Lincei, Rome, 2002. PDF PDF(Grayscale reprint)
*	B. D. Coleman & D. Swigon, Theory of supercoiled elastic rings with self-contact and its application to DNA plasmids, J. Elasticity, 60, 171–221 (2000). PDF
*	B. D. Coleman, D. Swigon, & I. Tobias, Elastic stability of DNA configurations: II. Supercoiled plasmids with self-contact, Phys. Rev. E 61, 759–770 (2000). PDF
*	I. Tobias, D. Swigon, & B. D. Coleman, Elastic stability of DNA configurations: I. General theory, Phys. Rev. E 61, 747–758 (2000). PDF
*	Configurations with Self-Contact in the Theory of the Elastic Rod Model for DNA, Doctoral Dissertation, Rutgers University, January 1999. PDF
*	D. Swigon, B. D. Coleman, & I. Tobias, The elastic rod model for DNA and its application to the tertiary structure of DNA minicircles in mononucleosomes, Biophys. J. 74, 2515–2530 (1998). PDF
*	B. D. Coleman, I. Tobias, & D. Swigon, Theory of influence of end conditions on self-contact in DNA loops, J. Chem. Phys. 103, 9101–9019 (1995). PDF
*	B. D. Coleman, E. Dill, & D. Swigon, On the dynamics of flexure and stretch in the theory of elastic rods, Arch. Rational Mech. Anal. 129, 147–174 (1995). PDF Reprinted with a commentary in Localization and Solitary Waves in Solid Mechanics, A. R. Champneys, G. W. Hunt, and J. M. T. Thompson (eds.), Advanced Series in Nonlinear Dynamics, Vol. 12, World Scientific, Singapore, 1999.