Publications⌗

  1. Christina H. McCulley and Alice R. Walker. Dimer interface destabilization of photodissociative Dronpa driven by asymmetric monomer dynamics. J. Phys. Chem. B. 2023, 127(43), 9248-9257. https://doi.org/10.1021/acs.jpcb.3c03798 Preprint: https://chemrxiv.org/engage/chemrxiv/article-details/6478e79be64f843f412a424a

  2. Yasmin Shamsudin, Alice R. Walker, Chey M. Jones, Todd J. Martínez, and Steven G. Boxer. Simulation-guided engineering of split GFPs with efficient beta-strand photodissociation. Nat. Commun. 2023, 14, 7401. https://doi.org/10.1038/s41467-023-42954-4 Preprint: https://chemrxiv.org/engage/chemrxiv/article-details/63f8e46832cd591f126c248e

  3. Mark A. Hix and Alice R. Walker. AutoParams: An automated web-based tool to generate force field parameters for molecular dynamics simulations. J. Chem. Inf. Model. 2023, 63, 20, 6293-6301. https://doi.org/10.1021/acs.jcim.3c01049 Preprint: https://chemrxiv.org/engage/chemrxiv/article-details/64a35d1d9ea64cc167645740 Source code: https://github.com/arwalkerlab/AutoParams

  4. Abigail Cousino, Lanka Wickramasinghe, Widana Kaushalya, Samarage Perera, Habib Baydoun, Alice R. Walker, and Claudio Verani. Studies on monolayer formation and electron transport in Au|LB|Au junctions containing 3d4 MnIII metallosurfactants. J. Phys. Chem. C 2023, 127, 33, 16654-16667. https://doi.org/10.1021/acs.jpcc.3c03616

  5. Joseph Wakpal, Vishaka Pathiranage, Alice R. Walker, and Hien M. Nguyen. Rational design and expedient synthesis of heparan sulfate mimetics from natural aminoglycosides for structure and activity relationship studies. Angew. Chem. Int. Ed. 2023, 62, e202304325. https://doi.org/10.1002/anie.202304325

  6. Whitney S.Y. Ong*, Ke Ji*, Vishaka Pathiranage*, Caden Maydew, Kiheon Baek, Rhiza Lyne E. Villones, Gabriele Meloni, Alice R. Walker, and Sheel Dodani. Angew. Chem. Int. Ed. 2023, e202302304. https://doi.org/10.1002/anie.202302304 Preprint: https://chemrxiv.org/engage/chemrxiv/article-details/63a223bab9c5f65de5da502f

  7. Ashlyn R. Murphy, Mark A. Hix, and Alice R. Walker. Exploring the effects of mutagenesis on FusionRed using excited state QM/MM dynamics and classical force field simulations. ChemBioChem 2023, e202200799. https://doi.org/10.1002/cbic.202200799 Featured on the front cover of ChemBioChem and as VIP: https://chemistry-europe.onlinelibrary.wiley.com/doi/epdf/10.1002/cbic.202300300 Preprint: https://chemrxiv.org/engage/chemrxiv/article-details/63ae991fa53ea645b35c5dac

  8. Solomon Yamoah Effah*, W. K. D. N. Kaushalya*, Mark A. Hix, and Alice R. Walker. Computational investigations of the excited state dynamics and quenching mechanisms of polycyclic aromatic hydrocarbon DNA adducts in solution. Electron. Struct. 2022, 4, 044003. https://doi.org/10.1088/2516-1075/aca4ff Preprint: https://chemrxiv.org/engage/chemrxiv/article-details/63127a9f5351a31eefed04dc

  9. Alice R. Walker, Boning Wu, Jan Meisner, Michael D. Fayer, and Todd J. Martínez. Proton transfer from a photoacid to a water wire: first principles simulations and fast fluorescence spectroscopy. J. Phys. Chem. B 2021, 125, 45, 12539–12551 https://doi.org/10.1021/acs.jpcb.1c07254 Featured on supplementary cover. https://pubs.acs.org/toc/jpcbfk/125/45 Preprint: https://chemrxiv.org/engage/chemrxiv/article-details/61400bf68e38a349cb525743

  10. Madison B. Berger, Alice R. Walker, Erik Antonio Vázquez-Montelongo and G. Andrés Cisneros. Computational investigations of two iron and a-ketoglutarate-dependent family enzymes: structural and electronic level insights. Phys. Chem. Chem. Phys. 2021, 23, 22227-22240 https://doi.org/10.1039/D1CP03800A

#Preprints

#Prior to faculty appointment:

  1. Joseph E. Thomaz*, Alice R. Walker*, Stephen J. Van Wyck, Jan Meisner, Todd J. Martínez, and Michael D. Fayer. Proton transfer dynamics in the aprotic proton accepting solvent 1-methylimidazole. The Journal of Physical Chemistry B, 2020.

  2. Alice R. Walker, Nikhil Baddam, and G. Andrés Cisneros. Unfolding pathways of hen egg-white lysozyme in ethanol. The Journal of Physical Chemistry B, 123(15):3267–3271, 2019

  3. Hailey L. Gahlon, Alice R. Walker, G. Andrés Cisneros, Meindert H. Lamers, and David S. Rueda. Reduced structural flexibility for an exonuclease deficient DNA polymerase III mutant. Physical Chemistry Chemical Physics, 20(40):26892–26902, 2018

  4. Nicole Antczak, Alice R. Walker, Hannah R. Stern, Emmett M. Leddin, Carl Palad, Timothy A. Coulther, Rebecca J. Swett, G. Andrés Cisneros, and Penny J. Beuning. Characterization of nine cancer-associated variants in human DNA polymerase κ. Chemical Research in Toxicology, 31(8):697–711, 8 2018

  5. Pramodha S. Liyanage, Alice R. Walker, Alfonso Brenlla, G. Andrés Cisneros, Louis J. Romano, and David Rueda. Bulky lesion bypass requires Dpo4 binding in distinct conformations. Scientific Reports, 7(1):17383–, 2017

  6. Alice R. Walker and G. Andrés Cisneros. Computational simulations of DNA polymerases: Detailed insights on structure/function/mechanism from native proteins to cancer variants. Chemical Research in Toxicology, 30(11):1922–1935, 11 2017

  7. Alice R. Walker, Pavel Silvestrov, Tina A. Müller, Robert H. Podolsky, Gregory Dyson, Robert P. Hausinger, and G. Andrés Cisneros. ALKBH7 variant related to prostate cancer exhibits altered substrate binding. PLOS Computational Biology, 13(2):1–13, 2 2017

  8. Alice R. Walker, Robin Bonomi, Vadim Popov, Juri G. Gelovani, and G. Andrés Cisneros. Investigating carbohydrate based ligands for galectin-3 with docking and molecular dynamics studies. Journal of Molecular Graphics and Modelling, 71:211 – 217, 2017

  9. Eric G. Kratz, Alice R. Walker, Louis Lagardére, Filippo Lipparini, Jean Philip Piquemal, and G. Andrés Cisneros. LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields. Journal of Computational Chemistry, 37(11):1019–29, 1 2016

  10. Daniel B. Lawson and Alice Walker. Cycloaddition of ethene on a series of single-walled carbon nanotubes. Computational and Theoretical Chemistry, 981:31 – 37, 2012

*indicates that these authors contributed equally.