Building the Microscopes of Tomorrow

The STROBE Science & Technology Center brings together imaging science experts from seven universities and partners with national labs, industry and academe to push the boundaries of imaging science capabilities and technologies, while building a diverse workforce that is prepared for 21st century careers in science and technology.

RESEARCH HIGHLIGHTS

MRS PREM Research Scholars Symposium

STROBE Director of Outreach and Broadening Participation, Dr. Sarah Schreiner, worked with the NSF and other PREM (NSF Partnership . . .

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Predicting heat flow in 3D semiconductor nanosystems

McBennett, A. et al., Nano Letters 23, 2129 (2023).

Nanostructuring on length scales corresponding to phonon mean free paths provides control over heat flow in semiconductors and makes . . .

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STROBE IN THE NEWS

CU Students Become Solar Scientists

July 25, 2023|9news|

An unusual research project at the University of Colorado turned more than a thousand . . .

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Turning Up the Heat in Quantum Materials

June 12, 2023|JILA, CU Boulder|

Quantum materials, a fascinating class of materials that harness the power of quantum mechanics, are . . .

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STROBE AWARDS

Margaret Murnane is Awarded a Honorary Doctorate from the University of Salamanca

June 20, 2023|University of Salamanca, JILA|

Renowned scientist, JILA Fellow, and University of Colorado Boulder professor Margaret Murnane has been granted . . .

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Congrats to Dr. Rachael Merritt for Receiving an NSF Mathematical and Physical Sciences Ascending Postdoctoral Research Fellowship

June 1, 2023|National Science Foundation|

The NSF Mathematical and Physical Sciences Ascending Postdoctoral Research Fellowships (MPS-Ascend) supports postdoctoral fellows performing . . .

Continue Reading

STROBE IN THE NEWS

CU Students Become Solar Scientists

July 25, 2023|9news|

An unusual research project at the University of Colorado turned more than a thousand . . .

Continue Reading

Turning Up the Heat in Quantum Materials

June 12, 2023|JILA, CU Boulder|

Quantum materials, a fascinating class of materials that harness the power of quantum mechanics, are . . .

Continue Reading

STROBE AWARDS

Margaret Murnane is Awarded a Honorary Doctorate from the University of Salamanca

June 20, 2023|University of Salamanca, JILA|

Renowned scientist, JILA Fellow, and University of Colorado Boulder professor Margaret Murnane has been granted . . .

Continue Reading

Congrats to Dr. Rachael Merritt for Receiving an NSF Mathematical and Physical Sciences Ascending Postdoctoral Research Fellowship

June 1, 2023|National Science Foundation|

The NSF Mathematical and Physical Sciences Ascending Postdoctoral Research Fellowships (MPS-Ascend) supports postdoctoral fellows performing . . .

Continue Reading

Two-color high-harmonic generation from relativist

Two-color high-harmonic generation from relativistic plasma mirrors

N. F. Beier, F. F. Dollar, Physical Review E, 108, 015201, (2023).

DOI: 10.1103/physreve.108.015201

High-intensity laser solid interactions are capable of generating attosecond light bursts via high-harmonic generation—most work focuses on single beam interactions. In this paper, we perform a numerical investigation on the role of wavelength and polarization in relativistic, high-harmonic generation from normal-incidence, two-beam interactions off plasma mirrors. We find that the two-beam harmonic-generation mechanism is a robust process described by a set of well-defined selection rules. We demonstrate that the emitted harmonics from normal-incidence interactions exhibit an intensity optimization when the incident fields are of equal intensity for two-color circularly polarized fields.

Protein target highlights in CASP15: Analysis of m

Protein target highlights in CASP15: Analysis of models by structure providers

L. T. Alexander, J. Durairaj, A. Kryshtafovych, L. A. Abriata, Y. Bayo, G. Bhabha, C. Breyton, S. G. Caulton, J. Chen, S. Degroux, D. C. Ekiert, B. S. Erlandsen, P. L. Freddolino, D. Gilzer, C. Greening, J. M. Grimes, R. Grinter, M. Gurusaran, M. D. Hartmann, C. J. Hitchman, J. R. Keown, A. Kropp, P. Kursula, A. L. Lovering, B. Lemaitre, A. Lia, S. Liu, M. Logotheti, S. Lu, S. Markússon, M. D. Miller, G. Minasov, H. H. Niemann, F. Opazo, G. N. Phillips, O. R. Davies, S. Rommelaere, M. Rosas‐Lemus, P. Roversi, K. Satchell, N. Smith, M. A. Wilson, K. Wu, X. Xia, H. Xiao, W. Zhang, Z. ng Zhou, K. Fidelis, M. Topf, J. Moult, T. Schwede, Proteins: Structure, Function, and Bioinformatics, 1-29, (2023).

DOI: 10.1002/prot.26545

We present an in-depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the submitted predictions. While the overall ability to predict three-dimensional protein structures continues to impress, reproducing uncommon features not previously observed in experimental structures is still a challenge. Furthermore, instances with conformational flexibility and large multimeric complexes highlight the need for novel scoring strategies to better emphasize biologically relevant structural regions. Looking ahead, closer integration of computational and experimental techniques will play a key role in determining the next challenges to be unraveled in the field of structural molecular biology.

Scanning transmission X-ray microscopy at the Adva

Scanning transmission X-ray microscopy at the Advanced Light Source

T. Feggeler, A. Levitan, M. A. Marcus, H. Ohldag, D. A. Shapiro, Journal of Electron Spectroscopy and Related Phenomena, 267, 147381, (2023).

DOI: 10.1016/j.elspec.2023.147381

Over 50 years of development, synchrotron based X-ray microscopy has become a routine and powerful tool for the analysis of nanoscale structure and chemistry in many areas of science. Scanning X-ray microscopy is particularly well suited to the study of chemical and magnetic states of matter and has become available at most synchrotron light sources using a variety of optical schemes, detectors and sample environments. The Advanced Light Source at Lawrence Berkeley National Laboratory has an extensive program of soft X-ray scanning microscopy which supports a broad range of scientific research using a suite of advanced tools for high spatio-temporal resolution and control of active materials. Instruments operating within an energy range between 200–2500 eV with spatial resolution down to 7 nm and sub 20 picosecond time resolution are available. These capabilities can be routinely used in combination with a variety of sample stimuli, including gas or fluid flow, temperature control from 100 to 1200 K, DC bias and pulsed or continuous microwave excitation. We present here a complete survey of our instruments, their most advanced capabilities and a perspective on how they complement each other to solve complex problems in energy, materials and environmental science.

Accurate real space iterative reconstruction (RESI

Accurate real space iterative reconstruction (RESIRE) algorithm for tomography

M. Pham, Y. Yuan, A. Rana, S. Osher, J. Miao, Scientific Reports, 13, (2023).

DOI: 10.1038/s41598-023-31124-7

Tomography has made a revolutionary impact on the physical, biological and medical sciences. The mathematical foundation of tomography is to reconstruct a three-dimensional (3D) object from a set of two-dimensional (2D) projections. As the number of projections that can be measured from a sample is usually limited by the tolerable radiation dose and/or the geometric constraint on the tilt range, a main challenge in tomography is to achieve the best possible 3D reconstruction from a limited number of projections with noise. Over the years, a number of tomographic reconstruction methods have been developed including direct inversion, real-space, and Fourier-based iterative algorithms. Here, we report the development of a real-space iterative reconstruction (RESIRE) algorithm for accurate tomographic reconstruction. RESIRE iterates between the update of a reconstructed 3D object and the measured projections using a forward and back projection step. The forward projection step is implemented by the Fourier slice theorem or the Radon transform, and the back projection step by a linear transformation. Our numerical and experimental results demonstrate that RESIRE performs more accurate 3D reconstructions than other existing tomographic algorithms, when there are a limited number of projections with noise. Furthermore, RESIRE can be used to reconstruct the 3D structure of extended objects as demonstrated by the determination of the 3D atomic structure of an amorphous Ta thin film. We expect that RESIRE can be widely employed in the tomography applications in different fields. Finally, to make the method accessible to the general user community, the MATLAB source code of RESIRE and all the simulated and experimental data are available at https://zenodo.org/record/7273314.

In Situ and Emerging Transmission Electron Microsc

In Situ and Emerging Transmission Electron Microscopy for Catalysis Research

H. Chao, K. Venkatraman, S. Moniri, Y. Jiang, X. Tang, S. Dai, W. Gao, J. Miao, M. Chi, Chemical Reviews, 123, 8347-8394, (2023).

DOI: 10.1021/acs.chemrev.2c00880

Catalysts are the primary facilitator in many dynamic processes. Therefore, a thorough understanding of these processes has vast implications for a myriad of energy systems. The scanning/transmission electron microscope (S/TEM) is a powerful tool not only for atomic-scale characterization but also in situ catalytic experimentation. Techniques such as liquid and gas phase electron microscopy allow the observation of catalysts in an environment conducive to catalytic reactions. Correlated algorithms can greatly improve microscopy data processing and expand multidimensional data handling. Furthermore, new techniques including 4D-STEM, atomic electron tomography, cryogenic electron microscopy, and monochromated electron energy loss spectroscopy (EELS) push the boundaries of our comprehension of catalyst behavior. In this review, we discuss the existing and emergent techniques for observing catalysts using S/TEM. Challenges and opportunities highlighted aim to inspire and accelerate the use of electron microscopy to further investigate the complex interplay of catalytic systems.

Imaging the electron charge density in monolayer M

Imaging the electron charge density in monolayer MoS2 at the Ångstrom scale

J. Martis, S. Susarla, A. Rayabharam, C. Su, T. Paule, P. Pelz, C. Huff, X. Xu, H. Li, M. Jaikissoon, V. Chen, E. Pop, K. Saraswat, A. Zettl, N. R. Aluru, R. Ramesh, P. Ercius, A. Majumdar, Nature Communications, 14, 4363, (2023).

DOI: 10.1038/s41467-023-39304-9

Four-dimensional scanning transmission electron microscopy (4D-STEM) has recently gained widespread attention for its ability to image atomic electric fields with sub-Ångstrom spatial resolution. These electric field maps represent the integrated effect of the nucleus, core electrons and valence electrons, and separating their contributions is non-trivial. In this paper, we utilized simultaneously acquired 4D-STEM center of mass (CoM) images and annular dark field (ADF) images to determine the projected electron charge density in monolayer MoS2. We evaluate the contributions of both the core electrons and the valence electrons to the derived electron charge density; however, due to blurring by the probe shape, the valence electron contribution forms a nearly featureless background while most of the spatial modulation comes from the core electrons. Our findings highlight the importance of probe shape in interpreting charge densities derived from 4D-STEM and the need for smaller electron probes.

Exceeding the limits of algorithmic self-calibrate

Exceeding the limits of algorithmic self-calibrated aberration recovery in Fourier ptychography

E. Li, S. Sherwin, G. Gunjala, L. Waller, Optics Continuum, 2, 119, (2023).

DOI: 10.1364/optcon.475990

Fourier ptychographic microscopy is a computational imaging technique that provides quantitative phase information and high resolution over a large field-of-view. Although the technique presents numerous advantages over conventional microscopy, model mismatch due to unknown optical aberrations can significantly limit reconstruction quality. A practical way of correcting for aberrations without additional data capture is through algorithmic self-calibration, in which a pupil recovery step is embedded into the reconstruction algorithm. However, software-only aberration correction is limited in accuracy. Here, we evaluate the merits of implementing a simple, dedicated calibration procedure for applications requiring high accuracy. In simulations, we find that for a target sample reconstruction error, we can image without any aberration corrections only up to a maximum aberration magnitude of λ/40. When we use algorithmic self-calibration, we can tolerate an aberration magnitude up to λ/10 and with our proposed diffuser calibration technique, this working range is extended further to λ/3. Hence, one can trade off complexity for accuracy by using a separate calibration process, which is particularly useful for larger aberrations.

Native structure of mosquito salivary protein unco

Native structure of mosquito salivary protein uncovers domains relevant to pathogen transmission

S. Liu, X. Xia, E. Calvo, Z. ng Zhou, Nature Communications, 14, 899, (2023).

DOI: 10.1038/s41467-023-36577-y

Female mosquitoes inject saliva into vertebrate hosts during blood feeding. This process transmits mosquito-borne human pathogens that collectively cause ~1,000,000 deaths/year. Among the most abundant and conserved proteins secreted by female salivary glands is a high-molecular weight protein called salivary gland surface protein 1 (SGS1) that facilitates pathogen transmission, but its mechanism remains elusive. Here, we determine the native structure of SGS1 by the cryoID approach, showing that the 3364 amino-acid protein has a Tc toxin-like Rhs/YD shell, four receptor domains, and a set of C-terminal daisy-chained helices. These helices are partially shielded inside the Rhs/YD shell and poised to transform into predicted transmembrane helices. This transformation, and the numerous receptor domains on the surface of SGS1, are likely key in facilitating sporozoite/arbovirus invasion into the salivary glands and manipulating the host’s immune response.

Cryo-EM structure of amyloid fibril formed by α-s

Cryo-EM structure of amyloid fibril formed by α-synuclein hereditary A53E mutation reveals a distinct protofilament interface

C. Sun, K. Zhou, P. DePaola, W. Shin, T. Hillyer, M. R. Sawaya, R. Zhu, C. Peng, Z. ng Zhou, L. Jiang, Journal of Biological Chemistry, 299, 104566, (2023).

DOI: 10.1016/j.jbc.2023.104566

Synucleinopathies like Parkinson's disease (PD), dementia with Lewy bodies (DLB), and multiple systems atrophy (MSA), have the same pathologic feature of misfolded α-synuclein protein (α-syn) accumulation in the brain. PD patients who carry α-syn hereditary mutations tend to have earlier onset and more severe clinical symptoms than sporadic PD patients. Therefore, revealing the effect of hereditary mutations to the α-syn fibril structure can help us understand these synucleinopathies’ structural basis. Here, we present a 3.38 Å cryo-electron microscopy structure of α-synuclein fibrils containing the hereditary A53E mutation. The A53E fibril is symmetrically composed of two protofilaments, similar to other fibril structures of WT and mutant α-synuclein. The new structure is distinct from all other synuclein fibrils, not only at the interface between proto-filaments, but also between residues packed within the same proto-filament. A53E has the smallest interface with the least buried surface area among all α-syn fibrils, consisting of only two contacting residues. Within the same protofilament, A53E reveals distinct residue re-arrangement and structural variation at a cavity near its fibril core. Moreover, the A53E fibrils exhibit slower fibril formation and lower stability compared to WT and other mutants like A53T and H50Q, while also demonstrate strong cellular seeding in α-synuclein biosensor cells and primary neurons. In summary, our study aims to highlight structural differences – both within and between the protofilaments of A53E fibrils – and interpret fibril formation and cellular seeding of α-synuclein pathology in disease, which could further our understanding of the structure-activity relationship of α-synuclein mutants.

Evaluation protocol for revealing magnonic contras

Evaluation protocol for revealing magnonic contrast in TR-STXM measurements

B. Zingsem, T. Feggeler, R. Meckenstock, D. Spoddig, T. Schaffers, S. Pile, H. Ohldag, M. Farle, H. Wende, A. Ney, K. Ollefs, AIP Advances, 13, 045020, (2023).

DOI: 10.1063/5.0145753

We present a statistically motivated method to extract magnonic contrast from time-resolved scanning transmission x-ray microscopy (TR-STXM) measurements. TR-STXM is an element-specific method for resolving spin-dynamics in space and time. It offers nanometer spatial resolution and picosecond temporal resolution. The presented method makes it possible to obtain phase and amplitude profiles of spin-waves from STXM measurements. Furthermore, it allows for a rigorous transformation to reciprocal magnon k⃗-space, revealing k⃗-dependent magnon properties such as the magnon dispersion in three dimensions and for all directions of the magnetic anisotropy. We demonstrate our method using X-band ferromagnetic resonance on a micrometer-sized permalloy assembly.

Structural basis of gRNA stabilization and mRNA re

Structural basis of gRNA stabilization and mRNA recognition in trypanosomal RNA editing

S. Liu, H. Wang, X. Li, F. Zhang, J. J. Lee, Z. Li, C. Yu, J. J. Hu, X. Zhao, T. Suematsu, A. L. Alvarez-Cabrera, Q. Liu, L. Zhang, L. Huang, I. Aphasizheva, R. Aphasizhev, Z. Hong Zhou, Science, 381, eadg4725, (2023).

DOI: 10.1126/science.adg4725

The architectures of distinct RESC states reveal a diversity of protein folds that have been co-opted into the RNA editing machinery. We have discovered how common gRNA elements function in stabilizing this short molecule and engaging mRNA. Our results show that gRNA-mRNA recognition emanates from ribonucleoprotein complex remodeling rather than initiating base pairing of the anchor sequence with the mRNA target. Last, structural information on essential functional features, such as the RESC2 triphosphate binding site, may facilitate development of new trypanocides.

Graphics-processing-unit-accelerated Monte Carlo s

Graphics-processing-unit-accelerated Monte Carlo simulation of polarized light in complex three-dimensional media

S. Yan, S. L. Jacques, J. C. Ramella-Roman, Q. Fang, Journal of Biomedical Optics, 27, 083015-1, (2022).

DOI: 10.1117/1.jbo.27.8.083015

Significance: Monte Carlo (MC) methods have been applied for studying interactions between polarized light and biological tissues, but most existing MC codes supporting polarization modeling can only simulate homogeneous or multi-layered domains, resulting in approximations when handling realistic tissue structures.

Aim: Over the past decade, the speed of MC simulations has seen dramatic improvement with massively parallel computing techniques. Developing hardware-accelerated MC simulation algorithms that can accurately model polarized light inside three-dimensional (3D) heterogeneous tissues can greatly expand the utility of polarization in biophotonics applications.

Approach: Here, we report a highly efficient polarized MC algorithm capable of modeling arbitrarily complex media defined over a voxelated domain. Each voxel of the domain can be associated with spherical scatters of various radii and densities. The Stokes vector of each simulated photon packet is updated through photon propagation, creating spatially resolved polarization measurements over the detectors or domain surface.

Results: We have implemented this algorithm in our widely disseminated MC simulator, Monte Carlo eXtreme (MCX). It is validated by comparing with a reference central-processing-unit-based simulator in both homogeneous and layered domains, showing excellent agreement and a 931-fold speedup.

Conclusion: The polarization-enabled MCX offers biophotonics community an efficient tool to explore polarized light in bio-tissues, and is freely available at http://mcx.space/.

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