Publications 2021

In situ spectroscopy

Schematic showing the electrochemical cell used for the operando measurements, and how the EXAFS data can be used to deduce the chemistry happening during this reaction. "
ACS Omega (2021); 
https://pubs.acs.org/doi/10.1021/acsomega.1c00792

  1. Ando N., Barquera B., Bartlett D.H., Boyd E., Burnim A.A., Byer A.S., Colman D., Gillilan R.E., Gruebele M., Makhatadze G., Royer C.A., Shock E., Wand A.J. and Watkins M.B. "The Molecular Basis for Life in Extreme Environments". Annu. Rev. Biophys, 50:343-372. 2021. DOI: 10.1146/annurev-biophys-100120-072804. Instrument: ID7A1 (HP BioSAXS & BioSAXS)

  2. Antonio D.J., Weiss J.T., Shanks K.S., Ruff J.P.C., Jaime M., Saul A., Swinburne T., Salamon M., Shrestha K., Lavina B., Koury D., Gruner S.M., Andersson D.A., Stanek S.R., Durakiewicz T., Smith J.L., Islam Z., & Gofryk K. "Piezomagnetic switching and complex phase equilibria in uranium dioxide." Communications Materials, 2, 1, 1-6. 2021.
    doi:     10.1038/s43246-021-00121-6 Instrument: ID4B (QM2)

  3. Beaucage P.A., Van Dover R.B., DiSalvo F.J., Gruner S.M., Wiesner U. "Superconducting Quantum Metamaterials from Convergence of Soft and Hard Condensed Matter Science." Adv Mater, 33, 26, 2021.
    doi: 10.1002/adma.202006975 Instrument: G1

  4. Bhattacharyya J.J., Nair S., Pagan D.C., Tari V.,  Lebensohn R.A., Rollett A.D., and Agnew S.R. "Elastoplastic transition in a metastable β-Titanium alloy, Timetal-18–An in-situ synchrotron X-ray diffraction study." International Journal of Plasticity, 139, 102947, 2021. doi: 10.1016/j.ijplas.2021.102947 Instrument: ID3A (FAST)

  5. Brown D.W., Anghel V., Balogh L., Clausen B., Johnson N.S., Martinez R.M., Pagan D.C., Rafailov G., Ravkov L., Strantza M., & Zepeda-Alarcon E. "Evolution of the Microstructure of Laser Powder Bed Fusion Ti-6Al-4V During Post-Build Heat Treatment". Metallurgical and Materials Transactions, A, 52, 5165–5181, 2021). doi: 10.1007/s11661-021-06455-7 Instrument: ID3A (FAST)

  6. ChangX., Fan Y., Zhao K., Fang J., Liu D., Tang M-C., Barrit D., Smilgies D-F., Li R., Lu J., Li J., Yang T., Amassian A., Ding Z., Chen Y., Liu S.F., Huang W. "Perovskite Solar Cells toward Eco-Friendly Printing". 2021. doi: org/10.34133/2021/9671892 

  7. Chen X., He Y., Wu S., Song Y., Yuan D., Bourret-Courchesne E., Ruff J.P.C., Islam Z., Frano A., and Birgeneau R.J. "Structural and magnetic transitions in the planar antiferromagnet Ba4Ir3O10." Physical Review B, 103, 22, 224420. 2021. doi: 10.1103/PhysRevB.103.224420 Instrument: ID4B (QM2)

  8. Cho E-A., Zhang P., Kumar V., Huang Q., Duncan J.S., Wu J. "Phosphorylation of RIAM by src promotes integrin activation by unmasking the PH domain of RIAM. Structure." 29, 4, 320-329, E4, 2021. doi: 10.1016/j.str.2020.11.011 Instrument: ID7B2

  9. Clinger J.A., Moreau D.W., McLeod M.J., Holyoak T., Thorne R.E. "Millisecond Mix-and-Quench Crystallography (MMQX) Enables Time-Resolved Studies of PEPCK With Remote Data Collection". bioRxiv. 2021. doi: 10.1101/2021.04.06.438620 Instrument: ID7B2 (HPBio MX & FlexX)

  10. Crittenden J.A. "Quantitative assessment of finite-element models for magnetostatic field calculations." Nuclear Instruments and Methods in Physics Research, Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, 1005, 165370, 2021. doi: 10.1016/j.nima.2021.165370

  11. Cunci L., González-Colón V., Vargas-Pérez B.L., Ortiz-Santiago J., Pagán M., Carrion P., Cruz J., Molina-Ontoria A., Martinez N., Silva W., Echegoyen L. and Cabrera C.R. "Multicolor Fluorescent Graphene Oxide Quantum Dots for Sensing Cancer Cell Biomarkers." ACS Appl. Nano Mater., 4, 1, 211–219, 2021. DOI: 10.1021/acsanm.0c02526 Instrument: F2

  12. Dagenais P., Desjardins G., Legault P. "An integrative NMR-SAXS approach for structural determination of large RNAs defines the substrate-free state of a trans-cleaving Neurospora Varkud Satellite ribozyme." Nucleic Acids Research, 49, 20, 11959–11973, 2021. doi: 10.1093/nar/gkab963. Instrument: ID7A1 (HP BioSAXS & BioSAXS)

  13. Dawson P. R., Miller M.P., Pollock T.M., Wendorf J., Mills L.H., Stinville J.C., Charpagne M.A., and Echlin M.P. "Mechanical Metrics of Virtual Polycrystals (MechMet)." Integrating Materials and Manufacturing Innovation, 1-21, 2021. doi: 10.1007/s40192-021-00206-7 Instrument: ID3A (FAST)

  14. Debefve L. M, Pollock C. J. "Systematic assessment of DFT methods for geometry optimization of mononuclear platinum-containing complexes". Phys. Chem. Chem. Phys. 10, 23(43):24780-24788, 2021. doi: 10.1039/d1cp01851e. Instrument: ID2A (PIPOXS)

  15. Echlin M.P., Kasemer M., Chatterjee K., Boyce D., Stinville J.C., Callahan P.G., Wielewski E., Park J-S., Williams J.C., Suter R.M., Pollock T.M., Miller M.P., & Dawson P.R. "Microstructure-Based Estimation of Strength and Ductility Distributions for α+ β Titanium Alloys." Metallurgical and Materials Transactions A, 52, 6, 2411-2434. 2021. doi: https://doi.org/10.1007/s11661-021-06233-5 Instrument: ID3A (FAST)

  16. Fisher C.R. Nygren K.E., Beaudoin A.J. "Validation of materials-informed digital twin: Mapping residual strains in HSLA steel weldment using high energy X-rays". Journal of Manufacturing Processes, 74, 75-87, 2022. doi: 10.1016/j.jmapro.2021.11.057 

  17. Ghale P. "Energy of non-relativistic many-particle quantum states from non-commuting Coulomb field and momentum operators." 2021.  https://arxiv.org/abs/2010.01656 Instrument: ID4B (QM2)

  18. Gibson J.M., Cui H., Ali M.Y., Zhao X., Debler E.W., Zhao J., Trybus K.M., Solmaz S.R., and Wang C. "Coil-to-Helix Transition at the Nup358-BicD2 Interface for Dynein Recruitment and Activation." bioRxiv, 2021. doi: 10.1101/2021.05.06.443034 Instrument: ID7A1 (HP BioSAXS & BioSAXS)

  19. Gordon J.V., Lim R.E., Wilkin M.J., Pagan D.C., Lebensohn R.A., and Rollett A.D. "Evaluating the grain-scale deformation behavior of a single-phase FCC high entropy alloy using synchrotron high energy diffraction microscopy." Acta Materialia, 215, 117120, 2021. doi:10.1016/j.actamat.2021.117120 Instrument: ID3A (FAST)

  20. Gustafson S.E., Pagan D.C., Shade P.A., and Sangid M.D. "Dynamic recovery observed in distinct grains within a polycrystalline nickel-based superalloy during cyclic high temperature fatigue via high energy X-ray diffraction microscopy." Scripta Materialia,192, 37-42, 2021. doi: 10.1016/j.scriptamat.2020.10.004 Instrument: ID3A (FAST)

  21. Han H., Yao Y., and Robinson R.D. "Interplay between Chemical Transformations and Atomic Structure in Nanocrystals and Nanoclusters." Accounts of Chemical Research, 54, 3, 509-519. 2021. doi: 10.1021/acs.accounts.0c00704 Instrument: ID2A (PIPOXS)

  22. Harish B., Gillilan R.E., Zou J., Wang J., Raleigh D.P., and Royer C.A. "Protein unfolded states populated at high and ambient pressure are similarly compact." Biophysical Journal, 2021. doi: 10.1016/j.bpj.2021.04.031 Instrument: ID7A1 (HP BioSAXS & BioSAXS)

  23. Harrison J.J.E.K., Tuske S., Das K., Ruiz F.X., Bauman J.D., Boyer P.L., DeStefano J.J., Hughes S.H., and Arnold E. "Crystal Structure of a Retroviral Polyprotein: Prototype Foamy Virus Protease-Reverse Transcriptase (PR-RT)." Viruses, 13(8), 1495, 2021. doi: 10.3390/v13081495. Instrument: F1.

  24. He L., Pagan D.C., Nardi A., and Hassani M. "Synchrotron X-ray diffraction studies of the phase-specific deformation in additively manufactured Ni–CrC composites". Composites Part B: Engineering. 109086, 2021. doi: 10.1016/j.compositesb.2021.109086. Instrument: ID3A (FAST)

  25. Huang H., Zhu J., Ge B., Gerdes F., Klinke C., Wang Z. "In Situ Constructing the Kinetic Roadmap of Octahedral Nanocrystal Assembly Toward Controlled Superlattice Fabrication". J. Am. Chem. Soc., 143, 11, 4234-4243, 2021. doi: 10.1021/jacs.0c12087 Instrument: B1

  26. Jiang Y-X., Yin J-X., Denner M.M., Shumiya N., Ortiz B.R., Xu G., Guguchia Z., He J., Hossain M.S., Liu X., Ruff J., Kautzsch L., Zhang S.S., Chang G., Belopolski I., Zhang Q., Cochran T.A., Multer D., Litskevich M., Cheng Z-J., Yang X.P., Wang Z., Thomale R., Neupert T., Wilson S.D., Hasan M.Z. "Unconventional chiral charge order in kagome superconductor KV3Sb5".  Nat Mater., 2021. doi: 10.1038/s41563-021-01034-y

  27. Kim L.R., Tucker A.E., Clyne M., Castellano C., Kim A., Chung D.D., DaVeiga C.T., Parsons E.M., Vatamaniuk O.K., Jeong J. "Ferroportin 3 is a dual-targeted mitochondrial/chloroplast iron exporter necessary for iron homeostasis in Arabidopsis". The Plant Journal. 2021.doiI: 10.1111/tpj.15286 Instrument: F3

  28. Li Y., Gillilan R., and Abbaspourrad A. "Tuning C-Phycocyanin Photoactivity via pH-Mediated Assembly–Disassembly". Biomacromolecules, 22, 12, 5128–5138, 2021. DOI: 10.1021/acs.biomac.1c01095 Instrument: ID7A1 (HP BioSAXS & BioSAXS)

  29. Liu Y., Moural T., Koirala BK S., Hernandez J., Shen Z., Alyokhin A., Zhu F. "Structure and function of one unclassified-class glutathione S-transferase in Leptinotarsa decemlineata." Int. J. Mol. Sci., 22, 21, 11921, 2021. doi: 10.3390/ijms222111921. Instrument: ID 7B2 (HPBio MX & FlexX)

  30. Lormand J.D., Kim S-K., Walters-Marrah G.A., Brownfield B.A., Fromme J.C., Winkler W.C., Goodson J.R., Lee V.T., Sondermann H. "Structural characterization of NrnC identifies unifying features of dinucleases." 2021. doi:  10.7554/eLife.70146. Instrument: ID 7B2 (HPBio MX & FlexX) 

  31. Losada N., Ruiz F.X., Curreli F., Gruber K., Pilch A., Das K., Debnath A.K., and Arnold E. "HIV-1 gp120 Antagonists Also Inhibit HIV-1 Reverse Transcriptase by Bridging the NNRTI and NRTI Sites." J. Med. Chem., 64, 22, 16530–16540, 2021. doi: 10.1021/acs.jmedchem.1c01104. Instrument: ID 7B2 (HPBio MX & FlexX)

  32. Lv B.Q., Zong A., Wu D., Rozhkov A.V., Fine B.V., Chen S-D., Hashimoto M., Lu D-H., Li M., Huang Y-B., Ruff J.P.C., Walko D.A., Chen Z.H., Hwang I., Su Y., Shen X., Wang X., Han F., Po H.C., Wang Y., Jarillo-Herrero P., Wang X., Zhou H., Sun C-J., Wen H., Shen Z-X., Wang N.L., Gedik N. "Unconventional hysteretic transition in a charge density wave." 2021. https://arxiv.org/abs/2106.09774 Instrument: ID4B (QM2)

  33. Mäkinen J.J., Shin Y., Vieras E., Virta E.P., Metsä-Ketelä M., Murakami K.S. & Belogurov G.A. "The mechanism of the nucleo-sugar selection by multi-subunit RNA polymerases." Nat Commun., 12, 796, 2021. doi: 10.1038/s41467-021-21005-w. Instrument: F1

  34. Mboge M.Y., Combs J., Singh S., Andring J., Wolff A., Tu C., Zhang Z., McKenna R., and Frost S.C. "Inhibition of Carbonic Anhydrase Using SLC-149: Support for a Noncatalytic Function of CAIX in Breast Cancer." J. Med. Chem., 64, 3, 1713–1724, 2021. doi: 10.1021/acs.jmedchem.0c02077. Instrument: F1

  35. Moreau D.W., Atakisi H., and Thorne R.E. "Ice in biomolecular cryocrystallography." Acta Cryst., 77, 540-554, 2021. doi: 10.1107/S2059798321001170. Instrument: F1

  36. Murphy-Leonard A.D., Pagan D.C., Callahan P.G., Heinkel Z.K., Jasien C.E., and Rowenhorst D.J. "Investigation of porosity, texture, and deformation behavior using high energy X-rays during in-situ tensile loading in additively manufactured 316L stainless steel." Materials Science and Engineering, A, 810, 141034. 2021. doi: 10.1016/j.msea.2021.141034 Instrument: ID3A (FAST)

  37. Musinski W.D., Shade P.A., Pagan D.C., and Bernier J.V. "Statistical aspects of grain-level strain evolution and reorientation during the heating and elastic-plastic loading of a Ni-base superalloy at elevated temperature." Materialia, 16, 101063. 2021. doi: 10.1016/j.mtla.2021.101063 Instrument: ID3A (FAST)

  38. Nagaoka Y., Suda M., Yoon I., Chen N., Yang H., Liu Y., Anzures B.A., Parman S.W., Wang Z.,  Grünwald M., Yamamoto H.M., Chen O. "Bulk grain-boundary materials from nanocrystals." Chem., 7, 2, 509-525. 2021. doi: 10.1016/j.chempr.2020.12.026

  39. Namitz K.E.W., Zheng T., Canning A.J., Alicea-Velazquez N.L., Castañeda C.A., Cosgrove M.S., & Hanes S.D. "Structure analysis suggests Ess1 isomerizes the carboxy-terminal domain of RNA polymerase II via a bivalent anchoring mechanism." Commun Biol., 4, 398, 2021. doi: 10.1038/s42003-021-01906-8. Instrument: F1

  40. Neding B., Pagan D. C., Hektor J., Hedström P. "Formation of Dislocations and Stacking Faults in Embedded Individual Grains during In Situ Tensile Loading of an Austenitic Stainless Steel". Materials, 14, 20, 5919, 2021. doi:10.3390/ma14205919 Instrument: ID3A (FAST)

  41. Ortiz B.R., Teicher S.M.L, Kautzsch L., Sarte P.M., Ruff J.P.C., Seshadri R., and Wilson S.D. "Fermi surface mapping and the nature of charge density wave order in the kagome superconductor CsV3Sb5". 2021.  https://arxiv.org/abs/2104.07230  Instrument: ID4B (QM2)

  42. Pagan D.C., Nygren K.E., and Miller M.P. "Analysis of a Three-Dimensional Slip Field in a Hexagonal Ti Alloy from in-situ High-Energy X-ray Diffraction Microscopy Data." Acta Materialia. Volume 221. 117372, 2021. doi: 10.1016/j.actamat.2021.117372 Instrument: ID3A (FAST)

  43. Patterson D.C., Ruiz M.P., Hyerin Yoon H., Walker J.A., Armache J-P., Yennawar N.H., and Weinert E.E. "Differential ligand-selective control of opposing enzymatic activities within a bifunctional c-di-GMP enzyme." PNAS, 2021. doi: 10.1073/pnas.210065711. Instrument: ID7A1 (HP BioSAXS & BioSAXS) 

  44. Pudasaini A., Green R., Song Y.H., Blumenfeld A., Karki N., Imaizumi T. and Zoltowski B.D. "Steric and Electronic Interactions at Gln154 in ZEITLUPE Induce Reorganization of the LOV Domain Dimer Interface." Biochemistry, 60, 2, 95–103, 2021. doi: 10.1021/acs.biochem.0c00819 Instrument: F1

  45. Rai D.K., Gillilan R.E., Huang Q., Miller R., Ting E., Lazarev A., Tate M.W.. and Gruner S.M. "High-pressure small-angle X-ray scattering cell for biological solutions and soft materials." J. Appl. Cryst., 54, 1, 111-122, 2021. doi: 10.1107/S1600576720014752  Instrument: ID7A1 (HP BioSAXS & BioSAXS)

  46. Sheng H., Jiang Y., Ishka M.R., Chia J.C., Dokuchayeva T., Kavulych Y., Zavodna T.O., Mendoza P.N., Huang R., Smieshka L.M., Miller J., Woll A.R., Terek O.I., Romanyuk N.D., Piñeros M., Zhou Y., Vatamaniuk O.K. "YSL3-mediated copper distribution is required for fertility, seed size and protein accumulation in Brachypodium." Plant Physiol., 86, 1, 655-676, 2021. DOI: 10.1093/plphys/kiab054. Instrument: F3

  47. Shin Y., Murakami K.S. "Watching the bacterial RNA polymerase transcription reaction by time-dependent soak-trigger-freeze X-ray crystallography." The Enzymes, 49, 305-314, 2021. doi: 10.1016/bs.enz.2021.06.009. Instrument: F1.

  48. Soto-Pérez J., Betancourt L.E., Trinidad P., Larios E., Rojas-Pérez A., Quintana G., Sasaki K., Pollock C.J., Debefve L.M., and Cabrera C.R. "In Situ X-ray Absorption Spectroscopy of PtNi-Nanowire/Vulcan XC-72R under Oxygen Reduction Reaction in Alkaline Media." ACS omega, 2021. doi: 10.1021/acsomega.1c00792 Instrument: ID2A (PIPOXS)

  49. Srivastava Y., Bonn-Breach R., Chavali S.S., Lippa G.M., Jenkins J.L. and Wedekind J.E. "Affinity and Structural Analysis of the U1A RNA Recognition Motif with Engineered Methionines to Improve Experimental Phasing." Crystals, 11, 3, 2021. doi: 10.3390/cryst11030273. Instrument: G1

  50. Stoupin S.,  KrawczykT., Sagan D., Temnykh A., Smieska L., Woll A., Ruff J., Lyndaker A., Pauling A., Croom B.P., Trigg E.B. "Side-bounce beamlines using single-reflection diamond monochromators at Cornell High Energy Synchrotron Source". J. Synchrotron Radiat., 28, 2, 429-438. 2021. doi: 10.1107/S160057752100120X Instrument: ID3B (FMB)

  51. Thedford P.R., Beaucage P.A., Susca E.M., Chao C.A.,  Nowack K.C., Van Dover R.B., Gruner S.M., and Wiesner U. "Superconducting Quantum Metamaterials from High Pressure Melt Infiltration of Metals into Block Copolymer Double Gyroid Derived Ceramic Templates." Advanced Functional Materials, 31, 23, 2100469. 2021. doi: 10.1002/adfm.202100469 Instrument: ID4B (QM2)

  52. Torabi S-F., Chen Y-L., Zhang K., Wang J.,  DeGregorio S.J., Vaidya A.T., Su Z., Pabit S.A., Chiu W., Pollack L., and Steitz J.A. "Structural analyses of an RNA stability element interacting with poly (A)." Proceedings of the National Academy of Sciences 118, 14, 2021. doi: 10.1073/pnas.2026656118 Instrument: ID7A1 (HP BioSAXS & BioSAXS)

  53. Turk L.S., Kuang X., Dal Pozzo V., Patel K., Chen M.,  Huynh K., Currie M.J., Mitchell D., Dobson R.C.J., D'Arcangelo G., Dai W., Comoletti D. "The structure-function relationship of a signaling-competent, dimeric Reelin fragment." Structure, 29, 10, 1156-1170, 2021. doi: 10.1016/j.str.2021.05.012 Instrument: ID7A1 (HP BioSAXS & BioSAXS)

  54. Venderley J., Matty M., Mallayya K., Krogstad M., Ruff J., Pleiss G., Mandrus V.K.D., Phelan D., Poudel L., Wilson A.G., Weinberger K, Upreti P., Norman M.R., Rosenkranz S., Osborn R., Kim E-A. "Harnessing Interpretable and Unsupervised Machine Learning to Address Big Data from Modern X-ray Diffraction." 2021. https://arxiv.org/abs/2008.03275 Instrument: ID4B (QM2)

  55. Werner J.G., Lee H., Wiesner U., and Weitz D.A. "Ordered Mesoporous Microcapsules from Double Emulsion Confined Block Copolymer Self-Assembly." ACS Nano, 15, 2, 3490–3499, 2021. doi: 10.1021/acsnano.1c00068. Instrument: G1

  56. Yuan Y., Bhargava A., and Robinson R.D. "Fe Cations Control the Plasmon Evolution in CuFeS2 Nanocrystals." Chemistry of Materials, 33, 2, 608-615. 2021. doi: 10.1021/acs.chemmater.0c03829  Instrument: ID2A (PIPOXS)

  57. Zhao J., Blayney A., Liu X., Gandy L., Jin W., Yan L., Ha J-H., Canning A.J., Connelly M., Yang C., Liu X., Xiao Y., Cosgrove M.S., Solmaz S.R., Zhang Y., Ban D., Chen J., Loh S.N., Wang C. "EGCG binds intrinsically disordered N-terminal domain of p53 and disrupts p53-MDM2 interaction". Nature Communications., 12, 986. Published online 2021. doi: 10.1038/s41467-021-21258-5 Instrument: ID7A1 (HP BioSAXS & BioSAXS)