Dan was raised in a suburb of Seattle, Washington, where he was an avid runner. He attended Brigham Young University where he studied chemical engineering and competed on the university’s cross country and track teams. After spending a year performing CFD calculations with Professor Phil Smith at the University of Utah, he enrolled in the chemical and biological PhD program at the University of Wisconsin, Madison. His interests include running and cycling. When he is not at working or performing these activities, he enjoys being a father and performing service in the local community.
Coarse-grained models offer access to length and time scales not attainable with traditional all-atom simulation. However, the coarse-grained models alone do not enable the sampling of rare events. Dan couples coarse-grained models with enhanced sampling techniques such as metadynamics, forward flux sampling, and transition path sampling to sample rare events and obtain free energies.
His current work focuses on mechanisms of DNA hybridization. He is also interested in the development of improved DNA models incorporating sequence-dependent properties and more rigorous thermodynamics. These models would be applied to provide new insight into the role of DNA mechanical properties in gene expression and DNA compaction.
Córdoba, Andrés, et al. "A molecular view of the dynamics of dsDNA packing inside viral capsids in the presence of ions." Biophysical journal 112.7 (2017): 1302-1315.
Lequieu, Joshua, et al. "Mechanical response of dna–nanoparticle crystals to controlled deformation." ACS central science 2.9 (2016): 614-620.
Hinckley, Daniel M., and Juan J. de Pablo. "Coarse-grained ions for nucleic acid modeling." Journal of chemical theory and computation 11.11 (2015): 5436-5446.
Lequieu, Joshua P., Daniel M. Hinckley, and Juan J. de Pablo. "A molecular view of DNA-conjugated nanoparticle association energies." Soft Matter 11.10 (2015): 1919-1929.
G. S. Freeman, D. M. Hinckley, J. P. Lequieu, J. K. Whitmer, and J. J. de Pablo. Coarse-grained modeling of DNA curvature. JCP. 2014. Vol. 141, Pg. 165103.
Freeman, Gordon S., et al. "DNA shape dominates sequence affinity in nucleosome formation." Physical review letters 113.16 (2014): 168101.
D. M. Hinckley, J. P. Lequieu, and J. J. de Pablo . Coarse-grained modeling of DNA oligomer hybridization: Length, sequence, and salt effects. JCP . 2014. Vol. 141.
An experimentally-informed coarse-grained 3-site-per-nucleotide model of DNA: Structure, thermodynamics, and dynamics of hybridization
Hinckley, Daniel M., et al. "An experimentally-informed coarse-grained 3-site-per-nucleotide model of DNA: Structure, thermodynamics, and dynamics of hybridization." The Journal of chemical physics 139.14 (2013): 10B604_1.