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Chen, Si

Publications and source records attributed to Chen, Si.

At least 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

The Velociprobe: An ultrafast hard X-ray nanoprobe for high-resolution ptychographic imaging

Motivated by the advanced photon source upgrade, a new hard X-ray microscope called "Velociprobe" has been recently designed and built for fast ptychographic imaging with high spatial resolution. We are addressing the challenges of high-resolution and fast scanning with novel hardware designs, advanced motion controls, and new data acquisition strategies, including the use of high-bandwidth interferometric measurements. The use of granite, air-bearing-supported stages provides the necessary long travel ranges for coarse motion to accommodate real samples and variable energy operation while remaining highly stable during fine scanning. Scanning the low-mass zone plate enables high-speed and high-precision motion of the probe over the sample. With an advanced control algorithm implemented in a closed-loop feedback system, the setup achieves a position resolution (3σ) of 2 nm. The instrument performance is evaluated by 2D fly-scan ptychography with our developed data acquisition strategies. A spatial resolution of 8.8 nm has been demonstrated on a Au test sample with a detector continuous frame rate of 200 Hz. Using a higher flux X-ray source provided by double-multilayer monochromator, we achieve 10 nm resolution for an integrated circuit sample in an ultrafast scan with a detector's full continuous frame rate of 3000 Hz (0.33 ms per exposure), resulting in an outstanding imaging rate of 9 x 10 4 resolution elements per second

36 MATERIALS SCIENCE↗
DOE OSTI2019

Neuroprotective Role of Selected Antioxidant Agents in Preventing Cisplatin-Induced Damage of Human Neurons In Vitro

Chemotherapy-induced peripheral neuropathy (CIPN) is a side effect of platinum-based chemotherapy and decreases the quality of life of cancer patients. We compared neuroprotective properties of several agents using an in vitro model of terminally differentiated human cells NT2-N derived from cell line NT2/D1. Sodium azide and an active metabolite of amifostine (WR1065) increase cell viability in simultaneous treatment with cisplatin. In addition, WR1065 protects the non-dividing neurons by decreasing cisplatin caused oxidative stress and apoptosis. Accumulation of Pt in cisplatin-treated cells was heterogeneous, but the frequency and concentration of Pt in cells were lowered in the presence of WR1065 as shown by X-ray fluorescence microscopy (XFM). Transition metals accumulation accompanied Pt increase in cells; this effect was equally diminished in the presence of WR1065. To analyze possible chemical modulation of Pt-DNA bonds, we examined the platinum L III near edge spectrum by X-ray absorption spectroscopy. The spectrum found in cisplatin-DNA samples is altered differently by the addition of either WR1065 or sodium azide. Importantly, a similar change in Pt edge spectra was noted in cells treated with cisplatin and WR1065. Therefore, amifostine should be reconsidered as a candidate for treatments that reduce or prevent CIPN.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Disentangling the size-dependent geometric and electronic effects of palladium nanocatalysts beyond selectivity

The prominent size effect of metal nanoparticles shapes decisively nanocatalysis, but entanglement of the corresponding geometric and electronic effects prevents exploiting their distinct functionalities. In this work, we demonstrate that in palladium (Pd)–catalyzed aerobic oxidation of benzyl alcohol, the geometric and electronic effects interplay and compete so intensively that both activity and selectivity showed in volcano trends on the Pd particle size unprecedentedly. By developing a strategy of site-selective blocking via atomic layer deposition along with first principles calculations, we disentangle these two effects and unveil that the geometric effect dominates the right side of the volcano with larger-size Pd particles, whereas the electronic effect directs the left of the volcano with smaller-size Pd particles substantially. Selective blocking of the low-coordination sites prevents formation of the undesired by-product beyond the volcano relationship, achieving a remarkable benzaldehyde selectivity and activity at the same time for 4-nm Pd. Disentangling the geometric and electronic effects of metal nanoparticles opens a new dimension for rational design of catalysts.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2018

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

Accurate knowledge of elemental distributions within biological organisms is critical for understanding their cellular roles. The ability to couple this knowledge with overall cellular architecture in three dimensions (3D) deepens our understanding of cellular chemistry. Using a whole, frozen-hydrated Chlamydomonas reinhardtii cell as an example, we report the development of 3D correlative microscopy through a combination of simultaneous cryogenic x-ray ptychography and x-ray fluorescence microscopy. By taking advantage of a recently developed tomographic reconstruction algorithm, termed GENeralized Fourier Iterative REconstruction (GENFIRE), we produce high-quality 3D maps of the unlabeled alga’s cellular ultrastructure and elemental distributions within the cell. We demonstrate GENFIRE’s ability to outperform conventional tomography algorithms and to further improve the reconstruction quality by refining the experimentally intended tomographic angles. As this method continues to advance with brighter coherent light sources and more efficient data handling, we expect correlative 3D x-ray fluorescence and ptychographic tomography to be a powerful tool for probing a wide range of frozen-hydrated biological specimens, ranging from small prokaryotes such as bacteria, algae, and parasites to large eukaryotes such as mammalian cells, with applications that include understanding cellular responses to environmental stimuli and cell-to-cell interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Rapid alignment of nanotomography data using joint iterative reconstruction and reprojection

As x-ray and electron tomography is pushed farther into the nanoscale, the limitations of rotation stages become more apparent leading to challenges in the alignment of the acquired projection images. Here we present an approach for rapid post-acquisition alignment of these projections to obtain high quality 3D images. Our approach is based on a joint estimation of alignment errors, and the object, using an iterative refinement procedure. We characterize convergence in simulations, and show its application in x-ray and electron nanotomography.

47 OTHER INSTRUMENTATION↗
DOE OSTI2017

Intracellular in situ labeling of TiO 2 nanoparticles for fluorescence microscopy detection

Titanium dioxide (TiO 2 ) nanoparticles are produced for many different purposes, including development of therapeutic and diagnostic nanoparticles for cancer detection and treatment, drug delivery, induction of DNA double-strand breaks, and imaging of specific cells and subcellular structures. Currently, the use of optical microscopy, an imaging technique most accessible to biology and medical pathology, to detect TiO 2 nanoparticles in cells and tissues ex vivo is limited with low detection limits, while more sensitive imaging methods (transmission electron microscopy, X-ray fluorescence microscopy, etc.) have low throughput and technical and operational complications. In this paper, we describe two in situ posttreatment labeling approaches to stain TiO 2 nanoparticles taken up by the cells. The first approach utilizes fluorescent biotin and fluorescent streptavidin to label the nanoparticles before and after cellular uptake; the second approach is based on the copper-catalyzed azide-alkyne cycloaddition, the so-called Click chemistry, for labeling and detection of azide-conjugated TiO 2 nanoparticles with alkyneconjugated fluorescent dyes such as Alexa Fluor 488. To confirm that optical fluorescence signals of these nanoparticles match the distribution of the Ti element, we used synchrotron X-ray fluorescence microscopy (XFM) at the Advanced Photon Source at Argonne National Laboratory. Titanium-specific XFM showed excellent overlap with the location of optical fluorescence detected by confocal microscopy. Finally and therefore, future experiments with TiO 2 nanoparticles may safely rely on confocal microscopy after in situ nanoparticle labeling using approaches described here.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2017

Effect of boron and carbon addition on microstructure and mechanical properties of the aged gamma-prime strengthened alumina-forming austenitic alloys [Effect of boron and carbon addition on microstructure and mechanical properties of the aged gamma-prime alumina-forming austenitic alloys]

Here, the goal of this work was to understand the effects of aging at 800 °C on the microstructures and mechanical properties of two recently-developed AFA stainless steels based on Fe-14Cr-32Ni-3Nb-3Al-2Ti (wt.%), one of which contained small additions of boron and carbon. To that end both the size distributions and growth kinetics of the B2, Laves phase, L1 2 precipitates present were quantified. While the lattice parameter, morphology, size and coarsening behavior of the L1 2 precipitates was the same in both AFA alloys, the B and C enhanced the grain boundary coverage by both Laves phase and B2-NiAl precipitates, but suppressed their coarsening. These interstitial additions also suppressed the formation of twins and discontinuous precipitation, which were observed in the B and C-free material. It is shown that the yield strength at 700 °C is largely controlled by the size of the L1 2 precipitates, with the largest strengthening effect obtained after aging for 2.4 h for both AFA alloys. Longer aging time led to a loss of strength mainly due to the coarsening of the L1 2 precipitates.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Joint reconstruction of x-ray fluorescence and transmission tomography

X-ray fluorescence tomography is based on the detection of fluorescence x-ray photons produced following x-ray absorption while a specimen is rotated; it provides information on the 3D distribution of selected elements within a sample. One limitation in the quality of sample recovery is the separation of elemental signals due to the finite energy resolution of the detector. Another limitation is the effect of self-absorption, which can lead to inaccurate results with dense samples. To recover a higher quality elemental map, we combine x-ray fluorescence detection with a second data modality: conventional x-ray transmission tomography using absorption. By using these combined signals in a nonlinear optimization-based approach, we demonstrate the benefit of our algorithm on real experimental data and obtain an improved quantitative reconstruction of the spatial distribution of dominant elements in the sample. Furthermore, compared with single-modality inversion based on x-ray fluorescence alone, this joint inversion approach reduces ill-posedness and should result in improved elemental quantification and better correction of self-absorption.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2017

Multifunctional Biomedical Imaging in Physiological and Pathological Conditions Using a NIR-II Probe

Contrasted with imaging in the visible (400–650 nm) and near-infrared window I (NIR-I, 650–900 nm) regions, imaging in near-infrared window II (NIR-II, 1000–1700 nm) is a highly promising in vivo imaging modality with improved resolution and deeper tissue penetration. Here, a small molecule NIR-II dye,5,5'-(1H,5H-benzo[1,2-c:4,5-c'] bis[1,2,5]thiadiazole)-4,8-diyl)bis(N,N-bis(4-(3-((tert-butyldimethylsilyl)oxy)propyl)phenyl) thiophen-2-amine), is successfully encapsulated into phospholipid vesicles to prepare a probe CQS1000. The novel NIR-II probe is studied for in vivo multifunctional biological imaging. The results of this study indicate that the NIR-II vesicle CQS1000 can noninvasively and dynamically visualize and monitor many physiological and pathological conditions of circulatory systems, including lymphatic drainage and routing, angiogenesis of tumor, and vascular deformity such as arterial thrombus formation and ischemia with high spatial and temporal resolution. More importantly, by virtue of the favorable half-life of blood circulation of CQS1000, NIR-II imaging is capable of aiding precise resection of tumor such as osteosarcoma and accelerating the process of lymph node dissection to complete sentinel lymph node biopsy for better decision making during the tumor surgery. Overall, CQS1000 is a highly promising NIR-II probe for multifunctional biomedical imaging in physiological and pathological conditions, surpassing traditional NIR-I imaging modality and pathologic assessments for clinical diagnosis and treatment.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Trace Metal Imaging of Sulfate-Reducing Bacteria and Methanogenic Archaea at Single-Cell Resolution by Synchrotron X-Ray Fluorescence Imaging

Metal cofactors are required for many enzymes in anaerobic microbial respiration. This paper examined iron, cobalt, nickel, copper, and zinc in cellular and abiotic phases at the single-cell scale for a sulfate-reducing bacterium (Desulfococcus multivorans) and a methanogenic archaeon (Methanosarcina acetivorans) using synchrotron X-ray fluorescence microscopy. Relative abundances of cellular metals were also measured by inductively coupled plasma mass spectrometry. Finally, for both species, zinc and iron were consistently the most abundant cellular metals. M. acetivorans contained higher nickel and cobalt content than D. multivorans, likely due to elevated metal requirements for methylotrophic methanogenesis. Cocultures contained spheroid zinc sulfides and cobalt/copper sulfides.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

X-ray ptychographic and fluorescence microscopy of frozen-hydrated cells using continuous scanning

X-ray microscopy can be used to image whole, unsectioned cells in their native hydrated state. It complements the higher resolution of electron microscopy for submicrometer thick specimens, and the molecule-specific imaging capabilites of fluorescence light microscopy. We describe here the first use of fast, continuous x-ray scanning of frozen hydrated cells for simultaneous sub-20 nm resolution ptychographic transmission imaging with high contrast, and sub-100 nm resolution deconvolved x-ray fluorescence imaging of diffusible and bound ions at native concentrations, without the need to add specific labels. Here, by working with cells that have been rapidly frozen without the use of chemical fixatives, and imaging them under cryogenic conditions, we are able to obtain images with well preserved structural and chemical composition, and sufficient stability against radiation damage to allow for multiple images to be obtained with no observable change.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2017

Nanoscale x-ray imaging of circuit features without wafer etching

Modern integrated circuits (ICs) employ a myriad of materials organized at nanoscale dimensions, and certain critical tolerances must be met for them to function. To understand departures from intended functionality, it is essential to examine ICs as manufactured so as to adjust design rules ideally in a nondestructive way so that imaged structures can be correlated with electrical performance. Electron microscopes can do this on thin regions or on exposed surfaces, but the required processing alters or even destroys functionality. Microscopy with multi-keV x-rays provides an alternative approach with greater penetration, but the spatial resolution of x-ray imaging lenses has not allowed one to see the required detail in the latest generation of ICs. X-ray ptychography provides a way to obtain images of ICs without lens-imposed resolution limits with past work delivering 20–40-nm resolution on thinned ICs. We describe a simple model for estimating the required exposure and use it to estimate the future potential for this technique. Here we show that this approach can be used to image circuit detail through an unprocessed 300-μm-thick silicon wafer with sub-20-nm detail clearly resolved after mechanical polishing to 240-μm thickness was used to eliminate image contrast caused by Si wafer surface scratches. Here, by using continuous x-ray scanning, massively parallel computation, and a new generation of synchrotron light sources, this should enable entire nonetched ICs to be imaged to 10-nm resolution or better while maintaining their ability to function in electrical tests.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Synchrotron-based X-ray fluorescence microscopy enables multiscale spatial visualization of ions involved in fungal lignocellulose deconstruction

Ions play an important role in the growth and development of filamentous fungi, particularly in the fungal decay process of lignocellulose materials. The role of ions in wood degradation, and more broadly fungal metabolism, have implications for diverse research disciplines ranging from plant pathology and forest ecology, to wood protection. Despite the importance of ions in both enzymatic and non-enzymatic fungal decay mechanisms, the spatial distribution of ions in wood and fungal hyphae during decay is not known. Here we employ synchrotron based X-ray fluorescence microscopy (XFM) to map physiologically relevant ions, such as K, Ca, Mn, Fe, and Zn, in wood being decayed by the model brown rot fungus Serpula lacrymans . Two-dimensional XFM maps were obtained to study the ion spatial distributions from mm to submicron length scales in wood and hyphae. Three-dimensional ion volume reconstructions with submicron spatial resolution were also acquired of wood cell walls and fungal hyphae, and an estimation of oxalate concentration at the microscale was made. Results show that the fungus actively transports some ions, such as Fe, into the wood and controls the distribution of ions at both the bulk wood and cellular length scales. Within the fungal hyphae, ion volume reconstructions show inhomogeneous ion distributions at the micron length scale and this localization may be indicative of both physiological status and requirements or in some cases, potentially sites associated with the initiation of metal-catalyzed wood degradation. Finally, these measurements illustrate how synchrotron based XFM is uniquely qualified for probing the role of ions in the growth and metabolic processes of filamentous fungi.

59 BASIC BIOLOGICAL SCIENCES↗