See my google scholar page for an updated publication list.
Peer-Reviewed
- Wagoner JA and Dill KA, Evolution of mechanical cooperativity among myosin II motors. Proceedings of the National Academy of Sciences of the United States of America 118 (20), e2101871118, 2021 [doi]
- Cubik J, Alston JJ, et. al., The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA. Nature Communications 12 (1936), 1-17, 2021 [doi]
- Wagoner JA and Dill KA, Opposing pressures of speed and efficiency guide the evolution of molecular machines. Molecular Biology and Evolution 36 (12), 2813-2822, 2019 [doi]
- Wagoner JA and Dill KA, Mechanisms for achieving high speed and efficiency in biomolecular machines. Proceedings of the National Academy of Sciences of the United States of America 116 (13), 5902-5907, 2019 [doi]
- Wagoner JA and Pande VS, Communication: Adaptive boundaries in multiscale simulations. Journal of Chemical Physics 148 (14), 141104, 2018 [doi]
- Dixit P, Wagoner JA, Ghosh K, Weistuch C, Presse S, and Dill KA, Perspective: Maximum caliber is a general variational principle for dynamical systems. Journal of Chemical Physics 148 (1), 010901, 2018 [doi]
- Wagoner JA and Dill KA, Molecular Motors: Power Strokes Outperform Brownian Ratchets. Journal of Physical Chemistry B 120 (26), 6327-6336, 2016 [doi]
- Wagoner JA and Pande VS, Finite domain simulations with adaptive boundaries: accurate potentials and nonequilibrium movesets. Journal of Chemical Physics 139 (23), 234114, 2013 [doi]
- Wagoner JA and Pande VS, Reducing the effect of Metropolization on mixing times in molecular dynamics simulations. Journal of Chemical Physics 137 (21), 214103, 2012 [doi]
- Wagoner JA and Pande VS, A smoothly decoupled particle interface: New methods for coupling explicit and implicit solvent. Journal of Chemical Physics 134 (21), 214103, 2011 [doi]
- Dong F, Wagoner JA, and Baker NA, Assessing the performance of implicit solvation models at a nucleic acid surface. Physical Chemistry Chemical Physics 10, 4889-4902, 2008 [doi]
- Swanson JMJ, Wagoner JA, Baker NA, and McCammon JA, Optimizing the Poisson Dielectric Boundary with Explicit Solvent Forces and Energies: Lessons Learned with Atom-Centered Dielectric Functions. Journal of Chemical Theory and Computation 3, 170-184, 2007 [doi]
- Wagoner JA and Baker, NA, Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms. Proceedings of the National Academy of Sciences of the United States of America 103 (22), 8331-8336, 2006 [doi]
- Wagoner JA and Baker NA, Solvation forces on biomolecular structures: a comparison of explicit solvent and Poisson-Boltzmann models. Journal of Computational Chemistry 25 (13), 1623-1629, 2004 [doi]