Refereed Journal Articles
T. D. Lillian and N.C. Perkins. Electrostatics and self-contact in an ela stic rod approximation for DNA. J. Comput. Nonlinear Dyn., 6(1):0110086, 2011.
T. D. Lillian, S. Goyal, J. D. Kahn, E. Meyhöfer, and N. C. Perkins. Computational analysis of looping of a large family of highly bent DNA by lacI. Biophys. J., 95(12):5832–5842, 2008.
S. Goyal, T. Lillian, S. Blumberg, J.-C. Meiners, E. Meyhöfer, and N. C. Perkins. Intrinsic curvature of DNA influences LacR-mediated looping. Biophys. J., 93(12):4342–4359, 2007.
B. R. Cannon, T. D. Lillian, S. P. Magleby, L. L. Howell, and M. R. Linford. A compliant end-effector for microscribing. Precision Engineering, 29(1):86–94, 2005.
Conference Papers and Presentations
D. Wilson, T. Lillian, N. Perkins, S. Tkachenko, and J.-C. Meiners. 2010. A generalized theory of DNA looping and cyclization. 2010 APS March Meeting, Portland, Oregon. Abstract and presentation.
T. D. Lillian and N. C. Perkins. 2009. Electrostatics and self contact in an elastic rod approximation for DNA. IDETC/CIE 2009, San Diego, California. Paper and presentation.
N. C. Perkins, E. Meyhöfer, and T. D. Lillian. 2009. Computational analysis of DNA-LacI looping mechanics for a family of highly bent DNA molecules. Proceedings of 2009 NSF Engineering Research and Innovation Conference, Honolulu, Hawaii. Paper and poster.
N. C. Perkins, E. Meyhöfer, and T. D. Lillian. 2009. An electrostatic approximation for DNA self-contact applied to DNA supercoiling. Proceedings of 2009 NSF Engineering Research and Innovation Conference, Honolulu, Hawaii. Paper and poster.
T. D. Lillian and N. C. Perkins. 2009. Two parameter family of bent DNA and predicted DNA looping behaviors induced by the LacR protein. 2009 SIAM Conference on Dynamical Systems, Snowbird, Utah. Abstract and presentation.
D. Wilson, A. Tkachenko, T. Lillian, N. Perkins, and J. C. Meiners. 2009. The role of entropic effects on DNA loop formation. 2009 APS March Meeting, Pittsburgh, Pennsylvania. Abstract and presentation.
D. P. Wilson, J. C. Meiners, T. Lillian, A. Tkachenko, and N. C. Perkins. 2009. The role of sequence- dependent mechanics in DNA looping. Biophysical Society 53rd Annual Meeting, Boston, Massachusetts. Biophys. J., 96(3)20a. Abstract and presentation.
S. Goyal, T. Lillian, N. C. Perkins, and E. Meyhöfer. 2008. Mechanics of DNA looping by the lac repressor protein: How stress-free shape influences loop energetics and topology. International Union of Theoretical and Applied Mechanics Symposium on Cellular, Molecular and Tissue Mechanics, Woods Hole, Massachusetts. Abstract and presentation.
T. Lillian, N. C. Perkins, and S. Goyal. 2007. Computational elastic rod model applied to DNA looping. Proceedings of IDETC/CIE 2007, Las Vegas, Nevada. Paper and presentation.
D. P. Wilson, T. Lillian, S. Goyal, A. V. Tkachenko, N. C. Perkins, and J.-C. Meiners. 2007. Under- standing the role of thermal fluctuations in DNA looping. Proceedings of SPIE, Florence, Italy, Vol. 6602, pp. 660208. Paper.
D. P. Wilson, T. D. Lillian, S. Goyal, N. C. Perkins, A. Tkachenko, and J. C. Meiners. 2007. Modeling the entropic cost of DNA looping. Proceedings 51st Annual Meeting, Biophysical Society, Baltimore, Maryland. Abstract and presentation.
T. Lillian, S. Goyal, N. C. Perkins, and E. Meyhöfer. 2005. Modeling intrinsic curvature effects on LacR- DNA loop complexes. University of Michigan, Engineering Graduate Student Symposium, Ann Arbor, Michigan. Abstract, presentation and poster.
S. Goyal, T. Lillian, N. C. Perkins, and E. Meyhöfer. 2005. Cable dynamics applied to long-length scale mechanics of DNA. Proceedings of the Sixth International Symposium on Cable Dynamics, Charleston, South Carolina. Presentation and paper.
N. Babbel, B. Despain, T. Lillian, D. Olson, R. Painter, and M. Sedas. 2004. Micro ornithopter design at Brigham Young University. Proceedings of the 8th International Micro Air Vehicle Competition, Tucson, Arizona. Paper.
Conference Papers and Presentations
T. D. Lillian, M. Taranova, I. Andricioaei and N. C. Perkins. 2010. Simulating the relaxation of DNA supercoils by topoisomerase I. Biophysical Society 54th Annual Meeting, San Francisco, California. Abstract and poster.
T. A. Lionberger, D. Demurtas, T. Lillian, J. Dorier, N. Perkins, and A. Stasiak. 2010. A direct observation of DNA flexibility at the single molecule level. Biophysical Society 54th Annual Meeting, San Francisco, California. Abstract submitted.
D. P. Wilson, T. Lillian, A. Tkachenko, N. Perkins, and J-C. Meiners. 2010. A generalized theory of DNA cyclization and loop formation considering the effects of binding topology and sequence-dependent curvature. Biophysical Society 54th Annual Meeting, San Francisco, California. Abstract and poster.
A. Hirsh, T. D. Lillian, and N. C. Perkins. 2010. Investigating classic lac repressor-DNA looping experiments using a computational rod model. Biophysical Society 54th Annual Meeting, San Francisco, California. Abstract and poster.
T. D. Lillian, and N. C. Perkins. 2009. Re–interpretation of Müller-Hill experiments on the LacR-DNA complex using a computational model. Biophysical Society 53rd Annual Meeting, Boston, Massachusetts. Biophys. J., 96(3)576a. Abstract and poster.
T. D. Lillian, S. Goyal, E. Meyhöfer, and N. C. Perkins. 2008. Elastic rod model for protein mediated DNA looping. North American Congress on Biomechanics, Ann Arbor, Michigan. Abstract and poster.
T. D. Lillian, S. Goyal, E. Meyhöfer, J. D. Kahn, and N. C. Perkins. 2008. Computational elastic rod theory captures DNA and protein flexibility in the lac-repressor complex. Proceedings 52nd Annual Meeting, Biophysical Society, Long Beach, California. Abstract and poster.
D. P. Wilson, T. D. Lillian, S. Goyal, N. C. Perkins, A. V. Tkachenko, and J.-C. Meiners. 2008. Modeling the free energy cost of DNA loop formation. Proceedings 52nd Annual Meeting, Biophysical Society, Long Beach, California. Abstract and poster.
T. D. Lillian, S. Goyal, N. C. Perkins, J. C. Meiners, and J. D. Kahn. 2007. Computational rod theory predicts experimental characteristics of DNA looping by the lac repressor. Proceedings 51st Annual Meeting, Biophysical Society, Baltimore, Maryland. Abstract and poster.
S. Goyal, T. Lillian, D. Wilson, E. Meyhöfer, J. C. Meiners, and N. C. Perkins. 2007. Sensitivity of DNA looping to sequence-dependent stiffness. Proceedings 51st Annual Meeting, Biophysical Society, Baltimore, Maryland. Abstract and poster.
T. Lillian, S. Goyal, E. Meyöfer, J.-C. Meiners, and N. C. Perkins. 2006. Inter-operator phasing affects DNA looping: Computational study. Single Molecule Symposium, Ann Arbor, Michigan. Abstract and poster.
D. Oros, T. Lillian, S. Goyal, N. C. Perkins, A. Tkachenko, and J.-C. Meiners. 2006. Modeling entropic cost of DNA looping. Single Molecule Symposium, Ann Arbor, Michigan. Abstract and poster.
S. Goyal, T. Lillian, E. Meyöfer, C. Meiners, and N. Perkins. 2006. A computational rod model to simulate the structural mechanics of DNA. Single Molecule Symposium, Ann Arbor, Michigan. Abstract and poster.
T. D. Lillian, S. Goyal, S. Blumberg, N. C. Perkins, and J. C. Meiners. 2006. Computational predictions of optimal inter-operator A-tract phasing for dna looping. Proceedings 50th Annual Meeting, Biophysical Society, Salt Lake City, Utah. Abstract and poster.
D. Wilson, T. D. Lillian, S. Goyal, N. C. Perkins, A. Tkachenko, and J. C. Meiners. 2006. Modeling the entropic cost of DNA looping. Proceedings 50th Annual Meeting (late abstract), Biophysical Society, Salt Lake City, Utah. Abstract and poster.