Publications

Articles
*Corresponding author. ^Equal contributions. Undergraduate co-authors are underlined.

Guarracino D, Baker JL, Gazley JL. (2023, accepted) Increasing undergraduate student-driven engagement with biochemical structures using visual molecular dynamics (VMD) and protein molecular modeling with real-world application in biochemistry class. Journal of College Science Teaching. 

Patkowski JB, Dahlberg T, Amin H, Gahlot DK, Vijayrajratnam S, Vogel JP, Francis MS, Baker JL,* Andersson M,* Costa TRD*. (2023) The F-pilus biomechanical adaptability accelerates conjugative dissemination of antimicrobial resistance and biofilm formation. Nature Communications 14, 1879 

Doran MH, Baker JL, Dahlberg T, Andersson A, Bullitt E. (2023) Three structural solutions for bacterial adhesion pilus stability and superelasticity. Structure S0969-2126(23)0081-3.

Dahlberg T,^ Baker JL,^ Bullitt E, Andersson M (2022). Unveiling molecular interactions that stabilize bacterial adhesion pili. Biophys J 121, 2096-2106. 

Felipe A, Lovenduski C, Baker JL, Lindberg GE (2022). Long-range heterogeneous structure in aqueous solutions of the deep eutectic solvent choline and geranate at the liquid-vapor interface. Phys Chem Chem Phys, 24, 13720-13729. 

Lindberg GE, Baker JL, Hanley J, Grundy WM, King C (2021). Density, Enthalpy of Vaporization and Local Structure of Neat n-Alkane Liquids. Liquids 1 (1), 47-59. 

Baker JL,* Dahlberg T, Bullitt E, Andersson M* (2021). Impact of an alpha helix and a cysteine-cysteine disulfide bond on the resistance of bacterial adhesion to stress. Proc. Natl. Acad. Sci. USA 118 (21) e2023595118 

Moreira, R.A., Guzman, H.V., Subramanian, B., Baker, J.L., Poma, A.B. (2020) Characterization of Structural and Energetic Differences between Conformations of the SARS-CoV-2 Spike Protein. Materials. 13(23), 5362. 

Chan, B. C.; Baker, J. L.; Bunagan, M. R.; Ekanger, L. A.; Gazley, J. L.; Hunter, R. A.; O’Connor, A. R.; Triano, R. M. (2020) Theory of Change to practice: How experimentalist teaching enabled faculty to navigate the COVID-19 disruption. J. Chem. Educ. 97, 2788–2792. 

Rodrigo A. Moreira, Mateusz Chwastyk, Joseph L. Baker, Horacio V. Guzman, Adolfo B. Poma. Quantitative determination of mechanical stability in the novel coronavirus spike protein. (2020) Nanoscale, 12(31), 16409-16413. 

Greene JR, Merrett KL, Heyert AJ, Simmons LF, Migliori CM, Vogt KC, Castro RS, Phillips PD, Baker JL, Lindberg GE, Fox DT, Del Sesto RE, Koppisch AT. (2019) Scope and Efficacy of the Broad-Spectrum Topical Antiseptic Choline Geranate. PLoS ONE 14(9): e0222211 

Carter EC, Heyert AJ, De Souza M, Baker JL, Lindberg GE. (2019) The ionic liquid [C4mpy][Tf2n] induces bound-like structure in the intrinsically disordered protein FlgM. Phys. Chem. Chem. Phys. 21:17950-17958 

Heyert AJ, Knox SL, Lindberg GE*, Baker JL*. (2017) Influence of an ionic liquid on the conformational sampling of Xaa-Pro dipeptides. J Mol Liq 227:66-75 

Baker JL,* Jafri H. (2016) Molecular simulations of lactose-bound and unbound forms of the FaeG adhesin reveal critical amino acids involved in sugar binding. J Mol Graph Model 70:100-108 

Hocky GM^, Baker JL^, Bradley MJ, Sinitskiy AV, De La Cruz EM, Voth GA. (2016) Cations stiffen actin filaments by adhering a key structural element to adjacent subunits. J Phys Chem B 12-:4558-4567 (*Equal authorship) 

Baker JL*, Furbish J, Lindberg GE*. (2015) Influence of the ionic liquid [C4mpy][Tf2n] on the structure of the miniprotein Trp-Cage. J Mol Graph Model 62:202-212 

Baker JL^, Courtemanche N^, Parton DL^, McCullagh M, Pollard TD, Voth GA. (2015) Electrostatic Interactions Between the Bni1p Formin FH2 Domain and Actin Influence Actin Filament Nucleation. Structure 23:68-79 

Baker JL, Voth GA. (2013) Effects of ATP and actin-filament binding on the dynamics of the myosin II S1 domain. Biophys J 105:1624-1634 

Ahlstrom LS^, Baker JL^, Ehrlich K, Campbell Z, Patel S, Vorontsov I, Tama F, and Miyashita O. (2013) Network Visualization of Conformational Sampling During Molecular Dynamics Simulation. J Mol Graph Model 46:140-149. 

Baker JL, Biais N, and Tama F (2013) Steered Molecular Dynamics Simulations of a Type IV Pilus Probe Initial Stages of a Force-Induced Conformational Transition. PLoS Comput Biol 9(4): e1003032

Zhang X, He X, Baker J, Tama F, Chang G, and Wright SH (2012) Twelve transmembrane helices form the functional core of mammalian multidrug and toxin extruder 1 (MATE1). J Biol Chem 287:27971-27982.

Baker J, Wright SH, and Tama F (2012) Simulations of substrate transport in the multidrug transporter EmrD. Proteins 80:1620-32 

Baker JL, Goldberg H, Perez G, and Sarcevic I (2007) Probing late neutrino mass properties with supernova neutrinos. Phys Rev D 76:063004 

Guillemin R, Hemmers O, Rolles D, Yu SW, Wolska A, Tran I, Hudson A, Baker J, and Lindle DW (2004) Nearest-Neighbor-Atom Core-Hole Transfer in Isolated Molecules. Phys Rev Lett 92, 223002 

Hemmers O, Guillemin R, Kanter EP, Krssig B, Lindle DW, Southworth SH, Wehlitz R, Baker J, Hudson A, Lotrakul M, Rolles D, Stolte WC, Tran IC, Wolska A, Yu SW, Amusia MY, Cheng KT, Chernysheva LV, Johnson WR, and Manson ST (2003) Dramatic Nondipole Effects in Low-Energy Photoionization: Experimental and Theoretical Study of Xe 5s. Phys Rev Lett 91, 053002 

Sapochak LS, Benincasa FE, Schofield RS, Baker JL, Riccio KK, Fogarty D, Kohlmann H, Ferris KF, and Burrows PE (2002) Electroluminescent zinc(II) bis(8-hydroxyquinoline): structural effects on electronic states and device performance. J Am Chem Soc, 124, 6119-25 

Book Chapters
*Corresponding author. ^Equal contributions. Undergraduate co-authors are underlined.

Moreira RA, Baker JL, Guzman HV, Poma AB. Assessing the stability of biological fibrils by molecular-scale simulations. In: Li, M.S., Kloczkowski, A., Cieplak, M., Kouza, M. (eds) Computer Simulations of Aggregation of Proteins and Peptides. Methods in Molecular Biology, vol 2340. Humana, New York, NY. 

Patents

Koppisch A, Del Sesto R, Fox D, Lindberg GE, Heyert A, Baker JL, Greene J. “Novel Antibiofilm Deep Eutectic Solvent Formulations.” (Int’l Application No. PCT/US2018/035475, US Application No. 16/307,347; Filing date: 12/5/2018; Issue Date: 1/4/2022).