E. Dodero-Rojas, J. N. Onuchic^, P. C. Whitford^. Sterically-confined rearrangements of SARS-CoV-2 spike protein control cell invasion. Submitted biorxiv
 D. I. Staquicini, F. H. F. Tang, C. Markosian, V. J. Yao, F. I. Staquicini, E. Dodero-Rojas, V. G. Contessoto, D. Davis, P. O’Brien, N. Habib, T. L.Smith, N. Bruiners, R. L. Sidman, M. L. Gennaro, E. C. Lattime, S. K. Libutti, P. C. Whitford, S. K. Burley, J. N. Onuchic, W. Arap, R. Pasqualini. Design and proof-of-concept for targeted phage-based COVID-19 vaccination strategies with a streamlined cold-fre supply chain. Submitted biorxiv
 F. Campos Freitas, G. Fuchs, R. J. de Oliveira, P. C. Whitford^. The dynamics of subunit rotation in a eukaryotic ribosome. Biophysica, 1, 204-221, 2021. manuscript
 M. Levi, K. Walak, A. Wang, U. Mohanty, P. C. Whitford^. A steric gate controls P/E hybrid formation of tRNA on the ribosome. Nature Communications 2020 manuscript
 P. C. Whitford^, W. Jiang, P. Serwer. Simulations of phage T7 capsid expansion reveal the role of molecular sterics on dynamics. Viruses 2020. manuscript
 E. Hoffer, S. Hong, S. Sunita, T. Maehigashi, R.L. Gonzalez Jr, P. C. Whitford, C.M. Dunham. Structural insights into mRNA reading frame regulation by tRNA modification and slippery codon-anticodon pairing. eLife 2020. manuscript
 P. Bandarkar, H. Yang, R. Y. Henley, M. Wanunu^, P. C. Whitford^. How nanopore translocation experiments can measure RNA unfolding. Biophysical Journal 2020. manuscript
 L. Ngu, J. N. Winters, K. Nguyen, K. E. Ramos, N. A. DeLateur, L. Makowski, P. C. Whitford, M. J. Ondrechen, P. J. Beuning. Probing remote residues important for catalysis in Escherichia coli ornithine transcarbamoylase. PLoS ONE. 15, e0228487, 2020. manuscript
 A. B. Oliveira Jr, H. Yang, P. C. Whitford, V. B. P. Leite. Distinguishing biomolecular pathways and mestable states. J. Chem. Theory Comput. 15, 6482-6490, 2019. manuscript
 F. C. Freitas, A. N. Lima, V. d.G. Contessoto, P. C. Whitford, R. J. de Oliveira. Drift-diffusion (DrDiff) framework determines kinetics and thermodynamics of two-state folding trajectories and tunes diffusive models. J. Chem. Phys. manuscript
 H. Yang, P. Bandarkar, R. Horne, V.B.P Leite, J. Chahine, P. C. Whitford^. Diffusion of tRNA inside the ribosome is position-dependent. J. Chem. Phys manuscript
 M. Levi, P. C. Whitford^. Dissecting the energetics of subunit rotation in the ribosome. J. Phys. Chem. B. DOI:10.1021/acs.jpcb.9b00178 manuscript
 H. Yang, J. Perrier, P. C. Whitford^. Disorder guides domain rearrangment in EF-Tu. Proteins: Structure, Function, Bioinformatics. 86, 1037-1046, 2018. manuscript
 M. Levi, K. Nguyen, L. Dukaye, P. C. Whitford^. Quantifying the relationship between single-molecule probes and subunit rotation in the ribosome. Biophysical Journal, 113, 2777-2786, 2017. manuscript
 H. Yang, J. K. Noel, P. C. Whitford^. Anisotropic Fluctuations in the Ribosome Determine tRNA kinetics. Journal of Physical Chemistry B, 121, 10593-10601, 2017. manuscript
 P. Waduge, R. Hu, P. Bandarkar, H. Yamazaki, B. Cressiot, Q. Zhao, P. C Whitford^ and M. Wanunu^. Nanopore-based measurements of protein size, fluctuations, and conformational changes. ACS Nano, 11, 5706-5716, 2017. manuscript
 K. Nguyen, H. Yang, P. C. Whitford^. How the ribosomal A-site finger can lead to tRNA species-dependent dynamics. Journal of Physical Chemistry B, 121, 2767-2775, 2017. manuscript
 J. K. Noel, P. C. Whitford^. How EF-Tu can contribute to efficient proofreading of aa-tRNA by the ribosome. Nature Communications. 7, 13314, 2016. manuscript
 K. Nguyen, P. C. Whitford^. Capturing transition states for tRNA hybrid-state formation in the ribosome. Journal of Physical Chemistry B. 120, 8768-8775, 2016. manuscript
 J. K. Noel^, M. Levi, M. Raghunathan, H. Lammert, R. L. Hayes, J. N. Onuchic^, P. C. Whitford^. SMOG 2: A versatile software package for generating structure-based models. PLOS Computational Biology. 12, e1004794, 2016. manuscript
 K. Nguyen, P. C. Whitford^. Steric interactions lead to collective tilting motion in the ribosome during mRNA-tRNA translocation. Nature Communications. 7, 10586, 2016. manuscript
 R. Hayes, J. K. Noel, A. Mandic, P. C. Whitford, K. Y. Sanbonmatsu, U. Mohanty, J. N. Onuchic. Generalized manning condensation model captures the RNA ion atmosphere. Phys. Rev. Lett. 114, 258105, 2015.
 J. Jackson, K. Nguyen, P. C. Whitford^. Exploring the balance between folding and function in proteins and RNA. Int. J. Mol. Sci. 16, 6868-6889, 2015. manuscript
 J. K. Noel, J. Chahine, V. B. P. Leite, P. C. Whitford^. Capturing transition paths and transition states for conformational rearrangements in the ribosome. Biophys. J. 107, 2881-2890, 2014. CORRECTION
 X. Lin, N. R. Eddy, J. K. Noel, P. C. Whitford, Q. Wang, J. Ma, J. N. Onuchic. Order and disorder control the functional rearrangement of influenza hemagglutinin. Proc. Nat. Acad. Sci. USA DOI: www.pnas.org/cgi/doi/10.1073/pnas.1412849111
 R. L. Hayes, J. K. Noel, P. C. Whitford, U. Mohanty, K. Y. Sanbonmatsu, J. N. Onuchic. Reduced model captures Mg2+-RNA interaction free energy of riboswitches. Biophysical Journal. 106, 1508, 2014.
 P. C. Whitford^, S. C. Blanchard, J. H. D. Cate, K. Y. Sanbonmatsu. Connecting the kinetics and energy landscape of tRNA translocation on the ribosome. PLoS Comp. Biol. 9, e1003003, 2013.
 P. C. Whitford^, K. Y. Sanbonmatsu^. Simulating movement of tRNA motion through the ribosome during hybrid-state formation. J. Chem. Phys. 139, 121919, 2013.
2012 (Joined NEU faculty 9/12)
 J. Wang, R. J. Oliveira, X. Chu, P. C. Whitford, J. Chahine, W. Han, E. Wang, J. N. Onuchic, V. B. P. Leite. Topopgraphy of funneled landscapes determines the thermodynamics and kinetics of protein folding. Proc. Nat. Acad. Sci. USA. 109, 15763-15768, 2012.
 R. L. Hayes, J. K. Noel, U. Mohanty, P. C. Whitford, S. P. Hennelly, J. N. Onuchic, K. Y. Sanbonmatsu. Magnesium fluctuations modulate RNA dynamics in the SAM-1 riboswitch. J. Amer. Chem. Soc. 134, 12043-12053, 2012.
 M. A. Jamros, L. C. deOliveira, P. C. Whitford, J. N. Onuchic, J. A. Adams, and P. A. Jennings. Substrate-specific reorganization of the conformational ensemble of CSK implicates novel modes of kinast function. PLoS Comp. Biol. 8, e1002695, 2012.
 J. K. Noel, P. C. Whitford and J. N. Onuchic. The shadow method: A Generally-Applicable contact definition for capturing the dynamics of biomolecular folding and function. J. Phys. Chem. 116, 8692-8702, 2012.
 J. Singh, P. C. Whitford, N. Hayre, J. N. Onuchic and D. Cox. Massive conformation change in the prion protein: Using dual-basin structure-based models to find misfolding pathways. Proteins: Struct. Func. Bioinfo. 80, 1299-1307, 2012.
 A. Ahmed, P. C. Whitford, K. Y. Sanbonmatsu and F. Tama. Consensus between flexible fitting computational methods to interpret cryo-EM data. J. Struct. Biol. 177, 561-570, 2012.
 P. C. Whitford, A. Ahmed, Y. Yu, S. P. Hennelly, F. Tama, C. M. T. Spahn, J. N. Onuchic and K. Y. Sanbonmatsu. Excited states of ribosome translocation revealed through integrative molecular modeling. Proc. Nat. Acad. Sci. USA. 108, 18943-18948, 2011.
 R. Nechushtai, H. Lammert, D. Michaeli, Y. Eizenberg-Domovish, J. A. Zuris, M. A. Luca, D. T. Capraro, A. Fish, O. Shimshon, M. Roy, A. Schug, P. C. Whitford, O. Livnah, J. N. Onuchic and P. A. Jennings. Allostery in the ferredoxin protein motif does not involve a conformational switch. Proc. Nat. Acad. Sci. USA. 108, 2240-2245, 2011.
 P. C. Whitford^, J. N. Onuchic and K. Y. Sanbonmatsu. Connecting energy landscapes and experimental rates for aminoacyl-tRNA accommodation in the ribosome. J. Amer. Chem. Soc. 132, 13170-13171, 2010. (communication)
 A. H. Ratje, J. Loerke, A. Mikolajka, M. Brünner, P. W. Hildebrand, A. Starosta, A. Doenhoefer, S. R. Connell, P. Fucini, T. Mielke, P. C. Whitford, J. N. Onuchic, Y. Yanan, K. Y. Sanbonmatsu, R. K. Hartmann, P. A. Penczek, D. N. Wilson and C. M. T. Spahn. Head swivel on the ribosome facilitates translocation via intra-subunit tRNA hybrid sites. Nature 468, 713-716, 2010.
 M. A. Jamros, L. C. deOliveira, P. C. Whitford, J. N. Onuchic, J. A. Adams, D. K. Blumenthal and P. A. Jennings. Proteins at work: A combined SAXS and theoretical determination of the multiple structures involved on the protein kinase functional landscape. J. Biol. Chem. 285, 36121-36128, 2010.
 J. K. Noel, P. C. Whitford, K. Y. Sanbonmatsu, and J. N. Onuchic. SMOG@ctbp: Simplified deployment of structure-based models in GROMACS. Nucleic Acid Research 38(suppl. 2), W657-W661, 2010.
 P. C. Whitford, P. Geggier, R. Altman, S. C. Blanchard, J. N. Onuchic, and K. Y. Sanbonmatsu. Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways. RNA. 16, 1196-1204, 2010.
 R. J. Oliveira*, P. C. Whitford*^, J. Chahine, J. Wang, J. N. Onuchic, and V. B. P. Leite^. Exploring the origin of non-monotonic complex behavior and the effects of non-native interactions on the diffusive properties of protein folding. Biophys. J. 99, 600-608, 2010.
 P. C. Whitford, A. Schug, J. Saunders, S. P. Hennelly, J. N. Onuchic, and K. Y. Sanbonmatsu. Nonlocal helix formation is key to understanding S-adenosylmethionine riboswitch function. Biophys. J. 96, L7-9, 2009. (On cover).
 P. C. Whitford, J. K. Noel, S. Gosavi, A. Schug, K. Y. Sanbonmatsu, and J. N. Onuchic. An all-atom structure-based potential for proteins: Bridging minimal models with all-atom empirical forcefields. Prot. Struct. Func. Bioinfo. 75, 430-441, 2009.
 S. Gosavi, P. C. Whitford, P. A. Jennings, and J. N. Onuchic. Extracting function from a b-trefoil folding motif. Proc. Nat. Acad. Sci. 105, 10384–10389, 2008.
 P. C. Whitford, S. Gosavi, and J. N. Onuchic. Conformational transitions in adenylate kinase – Allosteric communication reduces misligation. J. Biol. Chem. 283, 2042–2048, 2008.
 A. Schug, P. C. Whitford, Y. Levy, and J. N. Onuchic. Mutations as trapdoors to two competing native conformations of the rop-dimer. Proc. Nat. Acad. Sci. 104, 17674–17679, 2007.
 P. C. Whitford, O. Miyashita, Y. Levy, and J. N. Onuchic. Conformational transitions of adenylate kinase: Switching by cracking. J. Mol. Biol. 366, 1661–1671, 2007.
 J. E. Mills, P. C. Whitford, J. Shaffer, J. N. Onuchic, J. A. Adams, and P. A. Jennings. A novel disulfide bond in the SH2 domain of the C-terminal Src kinase controls catalytic activity. J. Mol. Biol. 365, 1460–1468, 2007.
 P. C. Whitford, and G. D. J. Phillies. Enhanced septahedral ordering in cold Lennard-Jones fluids. Phys. Rev. E 72, 021203, 2005.
 P. C. Whitford, and G. D. J. Phillies. Extended-range order, diverging static length scales, and local structure formation in cold Lennard-Jones fluids . J. Chem. Phys. 122, 044508, 2005.
 G. D. J. Phillies, R. O’Connell, P. Whitford, and K. A. Streletzky. Mode structure of diffusive transport in hydroxypropylcellulose:water. J. Chem. Phys. 119, 9903–9913, 2003.
 M. Levi, J. K. Noel, P. C. Whitford. Studying ribosome dynamics with simplified models. Methods. 2019. manuscript
 P. C. Whitford. The ribosome’s energy landscape: Recent insights from computation. Biophys. Rev. 7, 301-310, 2015. DOI: 10.1007/s12551-014-0155-1
 P. C. Whitford^, J. N. Onuchic^. What protein folding teaches us about biological function and molecular machines. Curr. Opin. Struct. Biol. 30, 57-62, 2015.
 J. K. Noel, P. C. Whitford^. How simulations reveal dynamics, disorder and the energy landscapes of biomolecular function. Israel J. Chem. DOI: 10.1002/ijch.201400018, 2014.
 P. C. Whitford, K. Y. Sanbonmastu, J. N. Onuchic. Biomolecular dynamics: Order-disorder transitions and energy landscapes. Rep. Prog. Phys. 75, 076601, 2012.
 R. J. Oliveira, P. C. Whitford, J. Chahine, V. B. P. Leite and J. Wang. Coordinate and time dependent diffusion dynamics in protein folding. Methods 52, 91-98, 2010.
 P. C. Whitford. Disorder guides protein function. Proc. Nat. Acad. Sci. USA. 110, 7114-7115, 2013.
 P. C. Whitford, J. N. Onuchic, and P. G. Wolynes. Energy landscape along an enzymatic reaction trajectory: hinges or cracks? HFSP J. 2, 61–64, 2008.
 K. Nguyen, P. C. Whitford. Challenges in describing ribosome dynamics. Phys. Biol. 14, 023001, 2017. manuscript
 M. Levi, P. Bandarkar, H. Yang, A. Wang, U. Mohanty, J. K. Noel, P. C. Whitford. Using SMOG 2 to simulate complex biomolecular assemblies.
 K. Y. Sanbonmatsu, S. C. Blanchard and P. C. Whitford. Molecular dynamics simulations of the ribosome. Biophysical approaches to translational control of gene expression. 2012. ISBN: 978-1-4614-3990-5
 P. C. Whitford, R. B. Altman, P. Geggier, D. Terry, J. B. Munro, J. N. Onuchic, C. M. T. Spahn, K. Y. Sanbonmatsu, S. C. Blanchard. Chapter 24: Dynamic views of ribosome function: energy landscapes and ensembles. The Ribosome: Structure, Function, and Dynamics. 2011. ISBN: 978-3-7091-0214-5.
 K. Y. Sanbonmatsu, S. C. Blanchard and P. C. Whitford. Chapter 4: Information processing by nanomachines: decoding by the ribosome. Molecular Machines. 2011. ISBN-13: 978-98143442