Publications

1

Spectral DefocusCam: Super-Resolved Hyperspectral Imaging Through Defocus

C. Foley, E. Markley, K. Yanny, L. Waller, K. Monakhova, 2025 IEEE International Conference on Computational Photography (ICCP), 1-12, (2025).

10.1109/iccp64821.2025.11143845

2

Structural basis for L-isoaspartyl-containing protein recognition by the human PCMTD1 cullin-RING E3 ubiquitin ligase

E. Z. Pang, B. Zhao, C. Flowers, E. Oroudjeva, J. B. Winter, V. Pandey, M. R. Sawaya, J. Wohlschlegel, J. A. Loo, J. A. Rodriguez, S. G. Clarke, Journal of Biological Chemistry, 301, 110735, (2025).

10.1016/j.jbc.2025.110735

3

Cooling-Rate-Driven Polymorphism and Vacancy Ordering in Ce2MnGe6 Intergrowth Phases

M. E. Raines, G. T. McCandless, B. C. Schundelmier, S. Cetin, T. G. Spencer, M. C. Scott, K. Wei, J. Y. Chan, Crystal Growth & Design, 25, 9405-9415, (2025).

10.1021/acs.cgd.5c01182

4

Measuring Chemical Shifts with Energy-Dispersive X-Ray Spectroscopy

Y. Chen, R. Jin, Y. Heffes, B. Zutter, T. P. O’Neill, J. J. Lodico, B. C. Regan, M. Mecklenburg, Physical Review Letters, 135, 157002, (2025).

10.1103/t1rs-7kr2

5

Multi-element tomography: leveraging absorption and phase contrast in soft x-ray ptychography

J. Plumb, A. Ditter, D. Kim, K. Lee, Y. Yu, D. Shapiro, X-Ray Nanoimaging: Instruments and Methods VII, 13622, 4, (2025).

10.1117/12.3063920

6

Leveraging structure-informed machine learning for fast steric zipper propensity prediction across whole proteomes

S. Zink, S. Qu, T. Holton, E. Shankar, P. Stanley, D. S. Eisenberg, M. R. Sawaya, J. A. Rodriguez, PLOS Computational Biology, 21, e1013395, (2025).

10.1371/journal.pcbi.1013395

7

Focusing of relativistic electron beams with permanent magnetic solenoid

T. T. Xu, C. R. Duncan, P. P. Denham, B. H. Schaap, A. A. Kulkarni, D. D. Garcia, S. D. Anderson, P. P. Musumeci, R. J. England, Physical Review Accelerators and Beams, 28, 082401, (2025).

10.1103/phhz-fgnl

8

Point Defect Induced Potential Wells across the m-Plane of Core/Shell GaN Nanowires

S. Rezaie, G. Kusch, L. Samuelson, J. B. Wagner, S. Yazdi, physica status solidi (RRL) – Rapid Research Letters, 2500145, (2025).

10.1002/pssr.202500145

9

Structural insights into functional regulation of the human CPEB3 prion by an amyloid-forming segment

M. D. Flores, M. R. Sawaya, D. R. Boyer, S. Zink, S. Tovmasyan, A. Saucedo, L. S. Richards, C. Zee, J. Cardenas, L. Fioriti, J. A. Rodriguez, Structure, 33, 1314-1324.e5, (2025).

10.1016/j.str.2025.05.007

10

Combining MicroED and native mass spectrometry for structural discovery of enzyme-small molecule complexes

N. W. Vlahakis, C. W. Flowers, M. Liu, M. P. Agdanowski, S. Johnson, J. A. Summers, L. C. Jacobs, C. Keyser, P. Russell, S. L. Rose, J. Orlans, N. Adhami, Y. Chen, M. R. Sawaya, S. Basu, D. de Sanctis, Y. Chen, S. Wakatsuki, H. M. Nelson, J. A. Loo, Y. Tang, J. A. Rodriguez, Proceedings of the National Academy of Sciences, 122, e2503780122, (2025).

10.1073/pnas.2503780122

11

The Effect of Electrode Structure on Ferroelectric Domains in Hf0.5Zr0.5O2

T. O'Neill, Y. Chen, H. Chan, M. Lenox, W. Hubbard, J. Ihlefeld, B. Regan, Microscopy & Microanalysis, 31, ozaf048.567, (2025).

10.1093/mam/ozaf048.567

12

Structure of a new capsid form and comparison with A-, B-, and C-capsids clarify herpesvirus assembly

A. Stevens, S. Kashyap, E. Crofut, A. Alvarez-Cabrera, J. Jih, Y. Liu, Z. ng Zhou, Journal of Virology, 99, 7, (2025).

10.1128/jvi.00504-25

13

A Gaussian Parameterization for Direct Atomic Structure Identification in Electron Tomography

N. M. Singh, T. Chien, A. C. McCray, C. Ophus, L. Waller, 2025 IEEE International Conference on Computational Photography (ICCP), 1-10, (2025).

10.1109/iccp64821.2025.11143828

14

Curvature Generation and Engineering Principles from Shewanella oneidensis Multi-flagellin Flagellum

Q. Lou, H. Fan, Y. Liu, J. F. Miller, Y. Huang, Z. ng Zhou, ACS Nano, 19, 25682-25696, (2025).

10.1021/acsnano.5c02744

15

In situ insights into antibody-mediated neutralization of a pre-fusion Junin virus glycoprotein complex

L. J. Taylor, M. R. Sawaya, J. B. Westover, C. Wang, F. Jimenez, A. J. Muñoz, J. Whitelegge, B. B. Gowen, G. F. Helguera, R. Castells-Graells, J. A. Rodriguez, Cell Reports, 44, 115971, (2025).

10.1016/j.celrep.2025.115971

16

Crystal Nucleation and Growth in High-Entropy Alloys Revealed by Atomic Electron Tomography

J. Miao, Y. Yuan, S. Moniri, Y. Yang, J. Zhou, A. Yuan, D. Kim, Y. Yang, C. Li, W. Chen, P. Ercius, Microscopy and Microanalysis, 31, ozaf048.792, (2025).

10.1093/mam/ozaf048.792

17

Annealing Optimization for HZO Thin Films with In-Situ STEM EBIC Characterization

Y. Chen, H. Chan, T. O’Neill, M. Lenox, W. Hubbard, J. Ihlefeld, B. Regan, Microscopy and Microanalysis, 31, ozaf048.574, (2025).

10.1093/mam/ozaf048.574

18

Chemical Shifts Observed Using Energy Dispersive Spectroscopy

M. Mecklenburg, R. Jin, Y. Heffes, B. Zutter, T. O’Neill, J. Lodico, B. Regan, Y. Chen, Microscopy and Microanalysis, 31, ozaf048.825, (2025).

10.1093/mam/ozaf048.825

19

Secondary electron emission current mapping for nanoscale thermometry

W. Hubbard, M. Mecklenburg, H. Chan, B. Regan, Nanotechnology, 36, 265704, (2025).

10.1088/1361-6528/ade445

20

Fabrication of a novel porous silicon biomembrane for applications in organ-on-chip technology

M. C. Williams, C. Wiens, S. Genc, S. Thompson, L. Gislason, D. Blake, J. Jessing, Biomedical Microdevices, 27, 32, (2025).

10.1007/s10544-025-00760-3

21

Sample motion for structured illumination fluorescence microscopy

R. Cao, G. Meng, L. Waller, Optics Letters, 50, 4074, (2025).

10.1364/ol.560873

22

Nanoscale confinement of phonon flow and heat transport

A. Beardo, W. Chen, B. McBennett, T. Karimzadeh Sabet, E. E. Nelson, T. H. Culman, H. C. Kapteyn, J. L. Knobloch, M. M. Murnane, I. Dabo, npj Computational Materials, 11, 172, (2025).

10.1038/s41524-025-01593-7

23

Structure, identification, and characterization of the RibD-enolase complex in Francisella

X. Liu, D. Clemens, B. Lee, R. Aguirre, M. Horwitz, Z. Zhou, Protein & Cell, pwaf045, 1-6, (2025).

10.1093/procel/pwaf045

24

Demonstration and structural basis of a therapeutic DNA aptamer for SARS-CoV-2 spike protein detection

Y. Liu, K. Wang, W. Wang, S. Kashyap, J. Jih, A. Imani, T. Hsiai, Z. ng Zhou, Biosensors and Bioelectronics, 287, 117691, (2025).

10.1016/j.bios.2025.117691

25

Scattering-based super-resolution optical fluctuation imaging

S. Yudovich, G. Posnjak, L. Shani, E. Teblum, T. Liedl, J. Enderlein, S. Weiss, Optics Express, 33, 18824, (2025).

10.1364/oe.541324

26

Infectivity and structure of SARS-CoV-2 after hydrogen peroxide treatment

S. R. Aliyari, G. Xie, X. Xia, L. Wang, Z. ng Zhou, G. Cheng, mBio, 16, e03994-24, (2025).

10.1128/mbio.03994-24

27

Fast partial Fourier transforms for large-scale ptychography

R. Parada, S. Wu Fung, S. Osher, Inverse Problems and Imaging, 0-0, (2025).

10.3934/ipi.2025019

28

Ring deconvolution microscopy: exploiting symmetry for efficient spatially varying aberration correction

A. Kohli, A. N. Angelopoulos, D. McAllister, E. Whang, S. You, K. Yanny, F. M. Gasparoli, B. Chang, R. Fiolka, L. Waller, Nature Methods, (2025).

10.1038/s41592-025-02684-5

29

Structures of Native Doublet Microtubules from Trichomonas vaginalis Reveal Parasite-Specific Proteins

A. Stevens, S. Kashyap, E. H. Crofut, S. E. Wang, K. A. Muratore, P. J. Johnson, Z. ng Zhou, Nature Communications, 16, 3996, (2025).

10.1038/s41467-025-59369-y

30

Optimized EUV Scatterometry Measurements with Tunable High Harmonic Generation and the Fisher Information Matrix

C. Klein, N. W. Jenkins, Y. Shao, Y. Li, S. Park, W. Kim, H. C. Kapteyn, M. M. Murnane, Metrology, Inspection, and Process Control XXXIX, 1342607, 5, (2025).

10.1117/12.3051113

31

Lab-based multi-wavelength EUV diffractometry for critical dimensions

B. M. Barnes, A. Chew, N. W. Jenkins, Y. Shao, M. Y. Sohn, R. ph Kline, D. F. Sunday, P. P. Balakrishnan, T. A. Germer, S. Grantham, C. Klein, S. L. Moffitt, E. L. Shirley, H. C. Kapteyn, M. M. Murnane, Metrology, Inspection, and Process Control XXXIX, 134261V, 63, (2025).

10.1117/12.3050342

32

Enhanced EUV mask imaging using Fourier ptychographic microscopy

C. Gu, A. Islegen-Wojdyla, M. P. Benk, K. A. Goldberg, L. Waller, Optical and EUV Nanolithography XXXVIII, 13424, 40, (2025).

10.1117/12.3051223

33

Interferometric scattering microscopy

N. S. Ginsberg, C. Hsieh, P. Kukura, M. Piliarik, V. Sandoghdar, Nature Reviews Methods Primers, 5, 23, (2025).

10.1038/s43586-025-00391-1

34

Self-Assembled Magnetic Nanoparticle Layers: Structural Control for Reconfigurable Magnetism and Functional Applications

X. Lu, J. Zou, M. Pham, A. Rana, C. Liao, E. Cating Subramanian, X. Wu, Y. Lo, C. S. Bevis, R. M. Karl, S. Lepadatu, Y. Yu, Y. Tserkovnyak, T. P. Russell, D. A. Shapiro, H. Kapteyn, M. Murnane, R. Streubel, J. Miao, ACS Applied Nano Materials, 8, 6643-6650, (2025).

10.1021/acsanm.5c00461

35

Trypanosome doublet microtubule structures reveal flagellum assembly and motility mechanisms

X. Xia, M. M. Shimogawa, H. Wang, S. Liu, A. Wijono, G. Langousis, A. M. Kassem, J. A. Wohlschlegel, K. L. Hill, Z. ng Zhou, Science, 387, 1162, (2025).

10.1126/science.adr3314

36

Accounting for electron-beam-induced warping of molecular nanocrystals in MicroED structure determination

N. Vlahakis, A. Clauss, J. A. Rodriguez, IUCrJ, 12, 223-238, (2025).

10.1107/s2052252524012132

37

A Liquid-Core Fiber Platform for Classical and Entangled Two-Photon Absorption Measurements

K. M. Parzuchowski, M. D. Mazurek, C. H. Camp, M. J. Stevens, R. Jimenez, ACS Photonics, 4C02076, (2025).

10.1021/acsphotonics.4c02076

38

Correlated nanoimaging of structure and dynamics of cation-polaron coupling in hybrid perovskites

R. Wilcken, B. L. Esses, R. S. Nithyananda Kumar, L. A. Hurley, S. E. Shaheen, M. B. Raschke, Science Advances, 11, eads3706, (2025).

10.1126/sciadv.ads3706

39

Near-Field Thermal Radiation as a Probe of Nanoscale Hot Electron and Phonon Transport

M. Habibi, A. Beardo, L. Cui, ACS Nano, 19, 6033-6043, (2025).

10.1021/acsnano.4c11893

40

Self-Heating Conductive Ceramic Composites for High Temperature Thermal Energy Storage

L. Yang, P. Peng, N. Weger, S. Mills, C. Messeri, A. K. Menon, S. Zeltmann, F. Babbe, Q. Zheng, C. Dun, C. Zhang, J. J. Urban, A. M. Minor, R. Prasher, H. Breunig, S. Lubner, ACS Energy Letters, 10, 1002-1012, (2025).

10.1021/acsenergylett.4c03270

41

Computational microscopy with coherent diffractive imaging and ptychography

J. Miao, Nature, 637, 281-295, (2025).

10.1038/s41586-024-08278-z

42

Robust broadband ptychography algorithms for high-harmonic soft X-ray supercontinua

B. Shearer, H. Kapteyn, I. Binnie, N. W. Jenkins, M. Murnane, Optics Express, 33, 717, (2025).

10.1364/oe.541675

43

Perturbative Fourier ptychographic microscopy for fast quantitative phase imaging

M. Zach, K. Shen, R. Cao, M. Unser, L. Waller, J. Dong, Optics Express, 33, 38984, (2025).

10.1364/oe.560811

44

Dynamics and structure of the B2→B19’ phase transformation in NiTi revealed through in situ 4D-STEM

J. Donohue, S. H. Mills, B. H. Savitzky, S. E. Zeltmann, C. Ophus, A. M. Minor, Materials Science and Engineering: A, 926, 147951, (2025).

10.1016/j.msea.2025.147951

45

Multi-slice electron ptychographic tomography for three-dimensional phase-contrast microscopy beyond the depth of focus limits

A. Romanov, M. Cho, M. Scott, P. Pelz, Journal of Physics: Materials, 8, 015005, (2024).

10.1088/2515-7639/ad9ad2

46

Composition and in situ structure of the Methanospirillum hungatei cell envelope and surface layer

H. Wang, J. Zhang, S. Liao, A. M. Henstra, D. Leon, J. Erde, J. A. Loo, R. R. Ogorzalek Loo, Z. ng Zhou, R. P. Gunsalus, Science Advances, 10, eadr8596, (2024).

10.1126/sciadv.adr8596

47

Native DGC structure rationalizes muscular dystrophy-causing mutations

S. Liu, T. Su, X. Xia, Z. ng Zhou, Nature, 637, 1261-1271, (2024).

10.1038/s41586-024-08324-w

48

Single-shot ionization-based monitor for pulsed electron beams

P. P. Denham, A. A. Ody, P. P. Musumeci, N. N. Burger, N. N. Cook, G. G. Andonian, Physical Review Applied, 22, 064033, (2024).

10.1103/physrevapplied.22.064033

49

Molecular sociology of virus-induced cellular condensates supporting reovirus assembly and replication

X. Liu, X. Xia, M. W. Martynowycz, T. Gonen, Z. ng Zhou, Nature Communications, 15, 10638, (2024).

10.1038/s41467-024-54968-7

50

From Beam Damage to Massive Reaction Amplification under the Electron Microscope: An Ionization-Induced Chain Reaction in Crystals of a Dewar Benzene

K. A. Konieczny, I. Paul, J. A. Rodriguez, M. A. Garcia-Garibay, ACS Central Science, 10, 2346-2352, (2024).

10.1021/acscentsci.4c01429

STROBE Publications

2025