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## Publications & |
## Research |
## Molecular |

* | S. Stanhope, J.E. Rubin, & D. Swigon, Robustness of solutions of the inverse problem for linear dynamical system with uncertain data, SIAM/ASA J, Uncertainty Quantification, 5, 572–597 (2017). |

* | S. Stanhope, J.E. Rubin, & D. Swigon, Identifiability of linear dynamical systems from a single trajectory, SIADS, 13, 1729–1815 (2014). |

* | D. Swigon, Ensemble modeling of biological systems, in Mathematics and Life Sciences, Eds. A.V. Antoniouk and R.V.N. Melnik, De Gruyter (2012). |

* | H. Bulut, H. Merdan, & D. Swigon, A Novel Mathematical Model for Asset Pricing, submitted to Chaos , . |

* | M. DeSantis & D. Swigon, Dynamics of wealth in a multi-group asset flow model, submitted to PLoS ONE, , . |

* | M. DeSantis, D. Swigon, & G. Caginalp, Nonlinear dynamics and stability in a multi-group asset flow model, SIADS, 11, 1114–1148 (2012). |

* | I. Ramirez Zuniga, J.E. Rubin, D. Swigon, & G. Clermont, Mathematical Modeling of Energy Consumption in the Acute Inflammatory Response, accepted in Journal of Theoretical Biology, , (2018). |

* | L.-A. Zhang, A. Urbano, R.S. Parker, D. Swigon, I. Banerjee, & G. Clermont, Endophenotypes Defined by Heat Map Clustering, submitted to Intensive Care Medicine, , . |

* | L.-A. Zhang, G. Clermont, A. Urbano, D. Swigon, I. Banerjee, & R.S. Parker, APT-MCMC, a C++/Python implementation of Markov Chain Monte Carlo for parameter identification, Comp. and Chem. Eng., 110, 1-12 (2018). |

* | E. Mochan-Keef, L.-A. Zhang, D. Swigon, A. Urbano, G.B. Ermentrout, M. Matuszewski, F.R. Toapanta, T.M. Ross, R.S. Parker, & G. Clermont, Discrete dynamical modeling of influenza infection suggests age-dependent differences in immunity, J. Virol., 91, e00395-17 (2017). |

* | L.-A. Zhang, R.S. Parker, D. Swigon, I. Banerjee, S. Bahrami, H. Redl, & G. Clermont, A one-nearest-neighbor approach to identify the original time of infection using censored baboon sepsis data, CCM Journal, 44, e432-e442 (2016). |

* | I. Price, E. Mochan-Keef, D. Swigon, G.B. Ermentrout, S. Lukens, F.R. Toapanta, T.M. Ross, & G. Clermont, The inflammatory response to influenza A Virus H1N1: an experimental and mathematical study, J. Theor. Biol, 374, 83-93 (2015).PDF and Supplements |

* | E. Mochan, D. Swigon, G.B. Ermentrout, & G. Clermont, A three-tiered study of differences in murine intrahost immune response to multiple pneumococcal strains, PlOS ONE, 10(8):e134012 (2015). |

* | Lukens, S. R., DePasse, J., Rosenfeld, R., Ghedin, E., Mochan, E., Brown, S.T., Grefenstette, J., Burke, D.S., Swigon, D., G.B. Ermentrout, & G. Clermont, A large-scale immuno-epidemiological simulation of influenza A epidemics, BMC Public Health, 14, 1019 (2014). |

* | E. Mochan, D. Swigon, G.B. Ermentrout, S. Lukens, & G. Clermont, A mathematical model of intrahost pneumococcal pneumonia infection dynamics in murine strains, J. Theor. Biol., 353, 44–54 (2014). |

* | 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). |

* | 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). |

* | T. Stepien & D. Swigon, Traveling waves in one-dimensional elastic continuum model of cell layer migration with stretch-dependent proliferation, SIADS, 13, 1489–1516 (2014). |

* | J. Arciero, & D. Swigon, Equation-based models of wound healing and collective cell migration, in Complex Systems and Computational Biology Approaches to Acute Inflammation, Eds. G. An and Y. Vodovotz (2013) 185–207. |

* | J.C. Arciero, Q. Mi, M.F. Branca, D. Hackam, & D. Swigon, Using a continuum model to predict closure time of gaps in intestinal epithelial cell layers, accepted in Wound Repair and Regeneration, 21, 256–265 (2013) |

* | K. Penner, B. Ermentrout, & D. Swigon, Pattern formation in a model of acute inflammation, SIADS, 11, 629–660 (2012).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). |

* | 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). |

* | J. Wei, L. Czapla, M.A. Grosner, & W.K. Olson, DNA topology confers sequence specificity to non-specific architectural proteins, PNAS (2014). |

* | Y.Y. Biton, S. Kumar, D. Dunlop, & D. Swigon, Lac-repressor mediated DNA looping: Monte Carlo simulation of constrained DNA molecules complemented with current experimental results, PLoS ONE, 9, e92475 (2014). |

* | W.K. Olson, M.A. Grosner, L. Czapla, & D. Swigon, Structural insights into the looping of protein-decorated DNA from computer simulations, Biochem. Soc. Trans. 41, 559–564 (2013). |

* | D. Swigon, S. Lim, & Y. Kim, Dynamical simulations of DNA supercoiling and compression, Biochem. Soc. Trans. 41, 554–558 (2013). |

* | L. Czapla, M.A. Grosner, D. Swigon, & W.K. Olson, Interplay of protein and DNA structure revealed in simulations of the lac operon, PLoS One, 8, e56548 (2013). |

* | A. Kocsis & D. Swigon, DNA stretching modeled at the base pair level: overtwisting and shear instability in elastic linkages, Int. J. Nonlin. Mech, 47, 639–654 (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). |

* | W.K. Olson, A.R. Srinivasan, A.V. Colasanti, G. Zheng, & D. Swigon, DNA Biomechanics, Handbook of Molecular Biophysics, 359–382 (2009). |

* | D. Swigon, The Mathematics of DNA Structure, Mechanics, and Dynamics, IMA Volumes in Mathematics and Its Applications, 150, 293–320 (2009). |

* | 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). |

* | 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). |

* | 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). |

* | 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). |

* | L. Czapla, D. Swigon, & W.K. Olson, Sequence-dependent Effects in the Cyclization of Short DNA, J. Chem. Theory Comput., 2, 685–695 (2006). |

* | 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). |

* | 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). |

* | B.D. Coleman, W.K. Olson, & D. Swigon, Theory of sequence-dependent DNA elasticity, J. Chem. Phys., 118, 7127–7140 (2003). |

* | 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). |

* | D. Keller, D. Swigon, & C. Bustamante, Relating single molecule measurements to thermodynamics, Biophys. J, 84,733–738 (2003). |

* |
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(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). |

* | 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). |

* | I. Tobias, D. Swigon, & B. D. Coleman, Elastic stability of DNA configurations: I. General theory, Phys. Rev. E 61, 747–758 (2000). |

* | Configurations with Self-Contact in the Theory of the Elastic Rod Model for DNA, Doctoral Dissertation, Rutgers University, January 1999. |

* | 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). |

* | 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). |

* | 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).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. |