STROBE Publications


Deep learning for single-shot autofocus microscopy

H. Pinkard, Z. Phillips, A. Babakhani, D.A. Fletcher, L. Waller, Optica 6, 794 (2019).

Direct observation of picosecond melting and disintegration of metallic nanoparticles

Y. Ihm, D.Hyung Cho, D. Sung, D. Nam, C. Jung, T. Sato, S. Kim, J. Park, S. Kim, M. Gallagher-Jones, Y. Kim, R. Xu, S. Owada, J.Hoon Shim, K. Tono, M. Yabashi, T. Ishikawa, J. Miao, D.Young Noh, C. Song, Nature Communications 10, (2019).

Cryo-EM structures of herpes simplex virus type 1 portal vertex and packaged genome

Y.T. Liu, J. Jih, X. Dai, G.Q. Bi, H. Zhou, Nature, (2019).

Advanced denoising for X-ray ptychography

H. Chang, P. Enfedaque, J. Zhang, J. Reinhardt, B. Enders, Y.S. Yu, D. Shapiro, C.G. Schroer, T. Zeng, S. Marchesini, Optics Express 27, 10395 (2019).

Infrared nanospectroscopic imaging in the rotating frame

S.C. Johnson, E.A. Muller, O. Khatib, E.A. Bonnin, A.C. Gagnon, M.B. Raschke, Optica 6, 424 (2019).

Recent advances in ultrafast X-ray sources

R. Schoenlein, T. Elsaesser, K. Holldack, Z. Huang, H. Kapteyn, M. Murnane, M. Woerner, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 377, (2019).

pH-dependent gating mechanism of the Helicobacter pylori urea channel revealed by cryo-EM

Y. Cui, K. Zhou, D. Strugatsky, Y. Wen, G. Sachs, H. Zhou, K. Munson, Science Advances 5, eaav8423 (2019).

Physics-based Learned Design: Optimized Coded-Illumination for Quantitative Phase Imaging

M. Kellman, E. Bostan, N. Repina, L. Waller, IEEE Transactions on Computational Imaging, 1 (2019).

Optical phantoms for biomedical polarimetry: a review

J. Chue-Sang, M. Gonzalez, A. Pierre, M. Laughrey, I. Saytashev, T. Novikova, J.C. Ramella-Roman, Journal of Biomedical Optics 24, 1 (2019).

Homochiral and racemic MicroED structures of a peptide repeat from the ice-nucleation protein InaZ

C. Zee, C. Glynn, M. Gallagher-Jones, J. Miao, C.G. Santiago, D. Cascio, T. Gonen, M.R. Sawaya, J.A. Rodriguez, IUCrJ 6, 197-205 (2019).

Atomic structures and deletion mutant reveal different capsid-binding patterns and functional significance of tegument protein pp150 in murine and human cytomegaloviruses with implications for therapeutic development

W. Liu, X. Dai, J. Jih, K. Chan, P. Trang, X. Yu, R. Balogun, Y. Mei, F. Liu, H. Zhou, PLOS Pathogens 15, e1007615 (2019).

Excitation and Emission Transition Dipoles of Type-II Semiconductor Nanorods

S. Ghosh, A.M. Chizhik, G. Yang, N. Karedla, I. Gregor, D. Oron, S. Weiss, J. Enderlein, A.I. Chizhik, Nano Letters, (2019).

Atomic structure of the translation regulatory protein NS1 of bluetongue virus

A. Kerviel, P. Ge, M. Lai, J. Jih, M. Boyce, X. Zhang, H. Zhou, P. Roy, Nature Microbiology, (2019).

Engineering Nanoscale Thermal Transport: Size- and Spacing-Dependent Cooling of Nanostructures

T.D. Frazer, J.L. Knobloch, K.M. Hoogeboom-Pot, D. Nardi, W. Chao, R.W. Falcone, M.M. Murnane, H.C. Kapteyn, J.N. Hernandez-Charpak, Physical Review Applied 11, (2019).

Two-photon PSF-engineered image scanning microscopy

O. Tzang, D. Feldkhun, A. Agrawal, A. Jesacher, R. Piestun, Optics Letters 44, 895 (2019).

Focusability of laser pulses at petawatt transport intensities in thin-film compression

D.M. Farinella, J. Wheeler, A.E. Hussein, J. Nees, M. Stanfield, N. Beier, Y. Ma, G. Cojocaru, R. Ungureanu, M. Pittman, J. Demailly, E. Baynard, R. Fabbri, M. Masruri, R. Secareanu, A. Naziru, R. Dabu, A. Maksimchuk, K. Krushelnick, D. Ros, G. Mourou, T. Tajima, F. Dollar, Journal of the Optical Society of America B 36, A28 (2019).

Generalized proximal smoothing (GPS) for phase retrieval

M. Pham, P. Yin, A. Rana, S. Osher, J. Miao, Optics Express 27, 2792-2808 (2019).

Temporal magnification for streaked ultrafast electron diffraction and microscopy

D. Cesar, P. Musumeci, Ultramicroscopy 199, 1 - 6 (2019).

Nanoscale mosaicity revealed in peptide microcrystals by scanning electron nanodiffraction

M. Gallagher-Jones, C. Ophus, K.C. Bustillo, D.R. Boyer, O. Panova, C. Glynn, C.T. Zee, J. Ciston, K.Canton Mancia, A.M. Minor, J.A. Rodriguez, Communications Biology 2, (2019).

Focusing and scanning through scattering media in microseconds

D. Feldkhun, O. Tzang, K.H. Wagner, R. Piestun, Optica 6, 72 (2019).

Blended coarse gradient descent for full quantization of deep neural networks

P. Yin, S. Zhang, J. Lyu, S. Osher, Y. Qi, J. Xin, Research in the Mathematical Sciences 6, (2019).

Atomic structures of enterovirus D68 in complex with two monoclonal antibodies define distinct mechanisms of viral neutralization

Q. Zheng, R. Zhu, L. Xu, M. He, X. Yan, D. Liu, Z. Yin, Y. Wu, Y. Li, L. Yang, W. Hou, S. Li, Z. Li, Z. Chen, Z. Li, H. Yu, Y. Gu, J. Zhang, T.S. Baker, H. Zhou, B.S. Graham, T. Cheng, S. Li, N. Xia, Nature Microbiology 4, 124 - 133 (2019).

Block Matching Local SVD Operator Based Sparsity and TV Regularization for Image Denoising

J. Liu, S. Osher, Journal of Scientific Computing 78, 607 - 624 (2019).


Ptychographic amplitude and phase reconstruction of bichromatic vortex beams

Y. Esashi, C.T. Liao, B. Wang, N. Brooks, K.M. Dorney, C. Hernández-García, H. Kapteyn, D. Adams, M. Murnane, Optics Express 26, 34007 (2018).

Quantitative differential phase contrast (DPC) microscopy with computational aberration correction

M. Chen, Z.F. Phillips, L. Waller, Optics Express 26, 32888-32899 (2018).

Different functional states of fusion protein gB revealed on human cytomegalovirus by cryo electron tomography with Volta phase plate

Z. Si, J. Zhang, S. Shivakoti, I. Atanasov, C.L. Tao, W.H. Hui, K. Zhou, X. Yu, W. Li, M. Luo, G.Q. Bi, H. Zhou, PLOS Pathogens 14, e1007452 (2018).

Atomic-Scale Structure and Stress Release Mechanism in Core–Shell Nanoparticles

M. Nathanson, K. Kanhaiya, A. Pryor, J. Miao, H. Heinz, ACS Nano 12, 12296 - 12304 (2018).

Correlative 3D x-ray fluorescence and ptychographic tomography of frozen-hydrated green algae

J. Deng, Y.Hung Lo, M. Gallagher-Jones, S. Chen, A. Pryor, Q. Jin, Y.Pyo Hong, Y.S.G. Nashed, S. Vogt, J. Miao, C. Jacobsen, Science Advances 4, eaau4548 (2018).

STEM Imaging with Beam-Induced Hole and Secondary Electron Currents

W.A. Hubbard, M. Mecklenburg, H.Leung Chan, B.C. Regan, Physical Review Applied 10, (2018).

Dynamic 2D implementation of 3D diffractive optics

H. Wang, R. Piestun, Optica 5, 1220 (2018).

Full-field imaging of thermal and acoustic dynamics in an individual nanostructure using tabletop high harmonic beams

R.M. Karl, G.F. Mancini, J.L. Knobloch, T.D. Frazer, J.N. Hernandez-Charpak, ña Abad, D.F. Gardner, E.R. Shanblatt, M. Tanksalvala, C.L. Porter, C.S. Bevis, D.E. Adams, H.C. Kapteyn, M.M. Murnane, Science Advances 4, eaau4295 (2018).

Characterizing the Quantum-Confined Stark Effect in Semiconductor Quantum Dots and Nanorods for Single-Molecule Electrophysiology

Y. Kuo, J. Li, X. Michalet, A. Chizhik, N. Meir, O. Bar-Elli, E. Chan, D. Oron, J. Enderlein, S. Weiss, ACS Photonics 5, 4788 - 4800 (2018).

Motion-resolved quantitative phase imaging

M. Kellman, M. Chen, Z.F. Phillips, M. Lustig, L. Waller, Biomedical Optics Express 9, 5456-5466 (2018).

Structural insights on TRPV5 gating by endogenous modulators

T.E.T. Hughes, R.A. Pumroy, A.Torun Yazici, M.A. Kasimova, E.C. Fluck, K.W. Huynh, A. Samanta, S.K. Molugu, H. Zhou, V. Carnevale, T. Rohacs, V.Y. Moiseenkova-Bell, Nature Communications 9, (2018).

Discovery and structural characterization of a therapeutic antibody against coxsackievirus A10

R. Zhu, L. Xu, Q. Zheng, Y. Cui, S. Li, M. He, Z. Yin, D. Liu, S. Li, Z. Li, Z. Chen, H. Yu, Y. Que, C. Liu, Z. Kong, J. Zhang, T.S. Baker, X. Yan, H. Zhou, T. Cheng, N. Xia, Science Advances 4, eaat7459 (2018).

Cryo-EM of full-length α-synuclein reveals fibril polymorphs with a common structural kernel

B. Li, P. Ge, K.A. Murray, P. Sheth, M. Zhang, G. Nair, M.R. Sawaya, W.Shik Shin, D.R. Boyer, S. Ye, D.S. Eisenberg, H. Zhou, L. Jiang, Nature Communications 9, (2018).

Malaria parasite translocon structure and mechanism of effector export

C.M. Ho, J.R. Beck, M. Lai, Y. Cui, D.E. Goldberg, P.F. Egea, H. Zhou, Nature 561, 70 - 75 (2018).

Phase-transition–induced p-n junction in single halide perovskite nanowire

Q. Kong, W. Lee, M. Lai, C.G. Bischak, G. Gao, A.B. Wong, T. Lei, Y. Yu, L.W. Wang, N.S. Ginsberg, P. Yang, Proceedings of the National Academy of Sciences 115, 8889 - 8894 (2018).

Electron Ghost Imaging

S. Li, F. Cropp, K. Kabra, J. Lane, G. Wetzstein, P. Musumeci, D. Ratner, Physical Review Letters 121, 114801 (2018).

Cryo-EM structure of the human α5β3 GABAA receptor

S. Liu, L. Xu, F. Guan, Y.T. Liu, Y. Cui, Q. Zhang, X. Zheng, G.Q. Bi, H. Zhou, X. Zhang, S. Ye, Cell Research 28, 958 - 961 (2018).

Building atomic models based on near atomic resolution cryoEM maps with existing tools

I. Yu, L. Nguyen, J. Avaylon, K. Wang, M. Lai, H. Zhou, Journal of Structural Biology 204, 313 - 318 (2018).

Nanoimaging and Control of Molecular Vibrations through Electromagnetically Induced Scattering Reaching the Strong Coupling Regime

E.A. Muller, B. Pollard, H.A. Bechtel, R. Adato, D. Etezadi, H. Altug, M.B. Raschke, ACS Photonics 5, 3594 - 3600 (2018).

Aberration recovery by imaging a weak diffuser

G. Gunjala, S. Sherwin, A. Shanker, L. Waller, Optics Express 26, 21054 (2018).

In Situ Structures of the Polymerase Complex and RNA Genome Show How Aquareovirus Transcription Machineries Respond to UncoatingABSTRACT

K. Ding, L. Nguyen, H. Zhou, Journal of Virology 92, (2018).

Quantitative characterization of high temperature oxidation using electron tomography and energy-dispersive X-ray spectroscopy

J. Zhou, M. Taylor, G.A. Melinte, A.J. Shahani, C.C. Dharmawardhana, H. Heinz, P.W. Voorhees, J.H. Perepezko, K. Bustillo, P. Ercius, J. Miao, Scientific Reports, (2018).

Compressed sensing FTIR nano-spectroscopy and nano-imaging

B. ästner, F. ähling, A. Hornemann, G. Ulrich, A. Hoehl, M. Kruskopf, K. Pierz, M.B. Raschke, G. übbeler, C. Elster, Optics Express 26, 18115 (2018).

Super-Resolution Imaging of Clickable Graphene Nanoribbons Decorated with Fluorescent Dyes

D. Joshi, M. Hauser, G. Veber, A. Berl, K. Xu, F.R. Fischer, Journal of the American Chemical Society 140, 9574 - 9580 (2018).

Tunable Polaron Distortions Control the Extent of Halide Demixing in Lead Halide Perovskites

C.G. Bischak, A.B. Wong, E. Lin, D.T. Limmer, P. Yang, N.S. Ginsberg, The Journal of Physical Chemistry Letters 9, 3998 - 4005 (2018).

Accumulation of Dense Core Vesicles in Hippocampal Synapses Following Chronic Inactivity

C.L. Tao, Y.T. Liu, H. Zhou, P.M. Lau, G.Q. Bi, Frontiers in Neuroanatomy 12, (2018).

Adaptive wavefront shaping for controlling nonlinear multimode interactions in optical fibres

O. Tzang, A.M. Caravaca-Aguirre, K. Wagner, R. Piestun, Nature Photonics 12, 368 - 374 (2018).

Understanding Chemical Bonding in Alloys and the Representation in Atomistic Simulations

J. Liu, E. Tennessen, J. Miao, Y. Huang, J.M. Rondinelli, H. Heinz, The Journal of Physical Chemistry C 122, 14996 - 15009 (2018).

Single-shot 3D coherent diffractive imaging of core-shell nanoparticles with elemental specificity

A. Pryor, A. Rana, R. Xu, J.A. Rodriguez, Y. Yang, M. Gallagher-Jones, H. Jiang, K. Kanhaiya, M. Nathanson, J. Park, S. Kim, S. Kim, D. Nam, Y. Yue, J. Fan, Z. Sun, B. Zhang, D.F. Gardner, C.Sato Baral Dias, Y. Joti, T. Hatsui, T. Kameshima, Y. Inubushi, K. Tono, J.Yang Lee, M. Yabashi, C. Song, T. Ishikawa, H.C. Kapteyn, M.M. Murnane, H. Heinz, J. Miao, Scientific Reports 8, (2018).

Structure of Telomerase with Telomeric DNA

J. Jiang, Y. Wang, L. šac, H. Chan, R. Basu, H. Zhou, J. Feigon, Cell 173, 1179 - 1190.e13 (2018).

In situ coherent diffractive imaging

Y.Hung Lo, L. Zhao, M. Gallagher-Jones, A. Rana, J.J. Lodico, W. Xiao, B.C. Regan, J. Miao, Nature Communications 9, (2018).

Analysis of Global and Site-Specific Radiation Damage in Cryo-EM

J. Hattne, D. Shi, C. Glynn, C.T. Zee, M. Gallagher-Jones, M.W. Martynowycz, J.A. Rodriguez, T. Gonen, Structure 26, 759 - 766.e4 (2018).

Far Infrared Synchrotron Near-Field Nanoimaging and Nanospectroscopy

O. Khatib, H.A. Bechtel, M.C. Martin, M.B. Raschke, L. Carr, ACS Photonics 5, 2773 - 2779 (2018).

Students’ flexible use of ontologies and the value of tentative reasoning: Examples of conceptual understanding in three canonical topics of quantum mechanics

J.R. Hoehn, N.D. Finkelstein, Physical Review Physics Education Research 14, (2018).

Structure of the herpes simplex virus 1 capsid with associated tegument protein complexes

X. Dai, H. Zhou, Science 360, eaao7298 (2018).

Multi-model imaging of the interaction of nanomaterials with cells

J. Miao, IUCrJ 5, 122 - 123 (2018).

Long-Lived Correlated Triplet Pairs in a π-Stacked Crystalline Pentacene Derivative

B.D. Folie, J.B. Haber, S. Refaely-Abramson, J.B. Neaton, N.S. Ginsberg, Journal of the American Chemical Society 140, 2326 - 2335 (2018).

Spectrally Resolved and Functional Super-resolution Microscopy via Ultrahigh-Throughput Single-Molecule Spectroscopy

R. Yan, S. Moon, S.J. Kenny, K. Xu, Accounts of Chemical Research, (2018).

Sub-ångström cryo-EM structure of a prion protofibril reveals a polar clasp

M. Gallagher-Jones, C. Glynn, D.R. Boyer, M.W. Martynowycz, E. Hernandez, J. Miao, C.T. Zee, I.V. Novikova, L. Goldschmidt, H.T. McFarlane, G.F. Helguera, J.E. Evans, M.R. Sawaya, D. Cascio, D.S. Eisenberg, T. Gonen, J.A. Rodriguez, Nature Structural & Molecular Biology 25, 131 - 134 (2018).

Membrane insertion of—and membrane potential sensing by—semiconductor voltage nanosensors: Feasibility demonstration

K. Park, Y. Kuo, V. Shvadchak, A. Ingargiola, X. Dai, L. Hsiung, W. Kim, Z.H. Zhou, P. Zou, A.J. Levine, J. Li, S. Weiss, Science Advances 4, e1601453 (2018).

Structure and mutagenesis reveal essential capsid protein interactions for KSHV replication

X. Dai, D. Gong, H. Lim, J. Jih, T.T. Wu, R. Sun, H. Zhou, Nature 553, 521 - 525 (2018).

Thermometry of Silicon Nanoparticles

M. Mecklenburg, B. Zutter, C. Regan, Physical Review Applied 9, (2018).


Intercalation events visualized in single microcrystals of graphite

E.R. White, J.J. Lodico, B.C. Regan, Nature Communications, (2017).

Multiple beam ptychography for large field-of-view, high throughput, quantitative phase contrast imaging

C. Bevis, R. Karl, J. Reichanadter, D.F. Gardner, C. Porter, E. Shanblatt, M. Tanksalvala, G.F. Mancini, H. Kapteyn, M. Murnane, D. Adams, Ultramicroscopy 184, 164 - 171 (2017).

Nanoimaging of Electronic Heterogeneity in Bi2Se3 and Sb2Te3 Nanocrystals

X. Lu, O. Khatib, X. Du, J. Duan, W. Wei, X. Liu, H.A. Bechtel, F. D'Apuzzo, M. Yan, A. Buyanin, Q. Fu, J. Chen, M. Salmeron, J. Zeng, M.B. Raschke, P. Jiang, X. Bao, Advanced Electronic Materials, 1700377 (2017).

Catastrophic disassembly of actin filaments via Mical-mediated oxidation

E.E. Grintsevich, P. Ge, M.R. Sawaya, H.Gizem Yesilyurt, J.R. Terman, H. Zhou, E. Reisler, Nature Communications 8, (2017).

General-purpose, wide field-of-view reflection imaging with a tabletop 13  nm light source

C.L. Porter, M. Tanksalvala, M. Gerrity, G. Miley, X. Zhang, C. Bevis, E. Shanblatt, R. Karl, M.M. Murnane, D.E. Adams, H.C. Kapteyn, Optica 4, 1552 (2017).

Structure of the yeast spliceosomal postcatalytic P complex

S. Liu, X. Li, L. Zhang, J. Jiang, R.C. Hill, Y. Cui, K.C. Hansen, H. Zhou, R. Zhao, Science 358, 1278 - 1283 (2017).

3D image scanning microscopy with engineered excitation and detection

C. Roider, R. Piestun, A. Jesacher, Optica 4, 1373 (2017).

Low Dimensional Manifold Model for Image Processing

S. Osher, Z. Shi, W. Zhu, SIAM Journal on Imaging Sciences 10, 1669 - 1690 (2017).

Conformation-Directed Formation of Self-Healing Diblock Copolypeptide Hydrogels via Polyion Complexation

Y. Sun, A.L. Wollenberg, T.Mark ’ Shea, Y. Cui, H. Zhou, M.V. Sofroniew, T.J. Deming, Journal of the American Chemical Society 139, 15114 - 15121 (2017).

A streaming multi-GPU implementation of image simulation algorithms for scanning transmission electron microscopy

A. Pryor, C. Ophus, J. Miao, Advanced Structural and Chemical Imaging 3:15, (2017).

Noninvasive Cathodoluminescence-Activated Nanoimaging of Dynamic Processes in Liquids

C.G. Bischak, R.B. Wai, C. Cherqui, J.A. Busche, S.C. Quillin, C.L. Hetherington, Z. Wang, C.D. Aiello, D.G. Schlom, S. Aloni, F. Ogletree, D.J. Masiello, N.S. Ginsberg, ACS Nano 11, 10583 - 10590 (2017).

Resolving ultrafast exciton migration in organic solids at the nanoscale

S.B. Penwell, L.D.S. Ginsberg, R. Noriega, N.S. Ginsberg, Nature Materials 16, 1136 - 1141 (2017).

Atomic structure of the human cytomegalovirus capsid with its securing tegument layer of pp150

X. Yu, J. Jih, J. Jiang, Z.H. Zhou, Science 35673, eaam6892 (2017).

Correlative cellular ptychography with functionalized nanoparticles at the Fe L-edge

M. Gallagher-Jones, C.Sato Baral Dias, A. Pryor, K. Bouchmella, L. Zhao, Y.Hung Lo, M.Borba Cardoso, D. Shapiro, J. Rodriguez, J. Miao, Scientific Reports 7, 4757, (2017).

Reliable computational design of biological-inorganic materials to the large nanometer scale using Interface-FF

C.C. Dharmawardhana, K. Kanhaiya, T.J. Lin, A. Garley, M.R. Knecht, J. Zhou, J. Miao, H. Heinz, Molecular Simulation 43, 1394–1405 (2017).

GENFIRE: A generalized Fourier iterative reconstruction algorithm for high-resolution 3D imaging

A. Pryor, Y. Yang, A. Rana, M. Gallagher-Jones, J. Zhou, Y.Hung Lo, G. Melinte, W. Chiu, J.A. Rodriguez, J. Miao, Scientific Reports 7, 23: S1, (2017).

Sub-wavelength coherent imaging of periodic samples using a 13.5 nm tabletop high harmonic light source

D. Gardner, M. Tanksalvala, E. Shanblatt, X. Zhang, B. Galloway, C. Porter, R. Karl, C. Bevis, D. Adams, H. Kapteyn, M. Murnane, G. Mancini, Nature Photonics 11, 259–263 (2017).

Deciphering chemical order/disorder and material properties at the single-atom level

C.C. Yang, M.C. Chen, C. Scott, O. R., A. Xu, P. Jr., F. Wu, W. Sun, J. Theis, M. Zhou, P.R.C. Eisenbach, R.F. Kent, H. Sabirianov, E. Zeng, J. Miao, Nature 542, 75-79 (2017).

Double-shot MeV electron diffraction and microscopy

P. Musumeci, D. Cesar, J. Maxson, Structural Dynamics 4, 044025, (2017).


Corrigendum: CryoEM structure of the Methanospirillum hungatei archaellum reveals structural features distinct from the bacterial flagellum and type IV pilus

N. Poweleit, P. Ge, H.H. Nguyen, R.R.Ogorzal Loo, R.P. Gunsalus, Z.H. Zhou, Nature Microbiology 2, 16264 (2016).

Frontier methods in coherent X-ray diffraction for high-resolution structure determination

M. Gallagher-Jones, J.A. Rodriguez, J. Miao, Quarterly Reviews of Biophysics 49, (2016).

In situ structures of the genome and genome-delivery apparatus in a single-stranded RNA virus

X. Dai, Z. Li, M. Lai, S. Shu, Y. Du, Z.H. Zhou, R. Sun, Nature 541, 112 - 116 (2016).

Infrared vibrational nanocrystallography and nanoimaging

E.A. Muller, B. Pollard, H.A. Bechtel, P. van Blerkom, M.B. Raschke, Science Advances 2, e1601006 - e1601006 (2016).