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Saurabh K, Dudenas PJ, Gann E, Reynolds VG, Mukherjee S, Sunday D, Martin TB, Beaucage PA, Chabinyc ML, DeLongchamp DM, Krishnamurthy A, Ganapathysubramanian B. CyRSoXS: a GPU-accelerated virtual instrument for polarized resonant soft X-ray scattering. J Appl Crystallogr 2023; 56:868-883. [PMID: 37284258 PMCID: PMC10241048 DOI: 10.1107/s1600576723002790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 03/24/2023] [Indexed: 06/08/2023] Open
Abstract
Polarized resonant soft X-ray scattering (P-RSoXS) has emerged as a powerful synchrotron-based tool that combines the principles of X-ray scattering and X-ray spectroscopy. P-RSoXS provides unique sensitivity to molecular orientation and chemical heterogeneity in soft materials such as polymers and biomaterials. Quantitative extraction of orientation information from P-RSoXS pattern data is challenging, however, because the scattering processes originate from sample properties that must be represented as energy-dependent three-dimensional tensors with heterogeneities at nanometre to sub-nanometre length scales. This challenge is overcome here by developing an open-source virtual instrument that uses graphical processing units (GPUs) to simulate P-RSoXS patterns from real-space material representations with nanoscale resolution. This computational framework - called CyRSoXS (https://github.com/usnistgov/cyrsoxs) - is designed to maximize GPU performance, including algorithms that minimize both communication and memory footprints. The accuracy and robustness of the approach are demonstrated by validating against an extensive set of test cases, which include both analytical solutions and numerical comparisons, demonstrating an acceleration of over three orders of magnitude relative to the current state-of-the-art P-RSoXS simulation software. Such fast simulations open up a variety of applications that were previously computationally unfeasible, including pattern fitting, co-simulation with the physical instrument for operando analytics, data exploration and decision support, data creation and integration into machine learning workflows, and utilization in multi-modal data assimilation approaches. Finally, the complexity of the computational framework is abstracted away from the end user by exposing CyRSoXS to Python using Pybind. This eliminates input/output requirements for large-scale parameter exploration and inverse design, and democratizes usage by enabling seamless integration with a Python ecosystem (https://github.com/usnistgov/nrss) that can include parametric morphology generation, simulation result reduction, comparison with experiment and data fitting approaches.
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Affiliation(s)
- Kumar Saurabh
- Department of Mechanical Engineering, Iowa State University, Ames, IA 50010, USA
| | - Peter J. Dudenas
- Material Measurement Laboratory, National Institute of Standards and Technology (NIST), Gaithersburg, MD 20899, USA
| | - Eliot Gann
- Material Measurement Laboratory, National Institute of Standards and Technology (NIST), Gaithersburg, MD 20899, USA
| | | | - Subhrangsu Mukherjee
- Material Measurement Laboratory, National Institute of Standards and Technology (NIST), Gaithersburg, MD 20899, USA
| | - Daniel Sunday
- Material Measurement Laboratory, National Institute of Standards and Technology (NIST), Gaithersburg, MD 20899, USA
| | - Tyler B. Martin
- Material Measurement Laboratory, National Institute of Standards and Technology (NIST), Gaithersburg, MD 20899, USA
| | - Peter A. Beaucage
- NIST Center for Neutron Research, National Institute of Standards and Technology (NIST), Gaithersburg, MD 20899, USA
| | - Michael L. Chabinyc
- Materials Department, University of California, Santa Barbara, CA 93106, USA
| | - Dean M. DeLongchamp
- Material Measurement Laboratory, National Institute of Standards and Technology (NIST), Gaithersburg, MD 20899, USA
| | - Adarsh Krishnamurthy
- Department of Mechanical Engineering, Iowa State University, Ames, IA 50010, USA
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Rongpipi S, Del Mundo JT, Gomez ED, Gomez EW. Extracting structural insights from soft X-ray scattering of biological assemblies. Methods Enzymol 2022; 678:121-144. [PMID: 36641206 DOI: 10.1016/bs.mie.2022.09.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Resonant soft X-ray scattering (RSoXS), a technique that combines X-ray absorption spectroscopy and X-ray scattering, can probe the nano- and meso-scale structure of biological assemblies with chemical specificity. RSoXS experiments yield scattering data collected at several photon energies, for example across an elemental absorption edge of interest. Collecting a near-edge X-ray absorption fine structure (NEXAFS) spectrum complements RSoXS experiments and determines X-ray energies that are best suited for RSoXS measurements. The analysis of RSoXS data is similar in many ways to analysis of small angle X-ray scattering using hard X-rays, with an added dimension that includes an X-ray energy dependence. This chapter discusses procedures for predicting scattering contrast and thereby identifying energies suitable for RSoXS measurements using NEXAFS spectra, analyses of 2D RSoXS images through integration into 1D profiles, and strategies for elucidating the origin of RSoXS scattering features. It also discusses existing and potential methods for interpretation of RSoXS data to gain detailed structural insights into biological systems.
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Affiliation(s)
- Sintu Rongpipi
- Advanced Light Source and Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Joshua T Del Mundo
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, United States
| | - Enrique D Gomez
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, United States; Department of Materials Science and Engineering and Materials Research Institute, The Pennsylvania State University, University Park, PA, United States.
| | - Esther W Gomez
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, United States; Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, United States.
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Chan JM, Wang M. Visualizing the Orientation of Single Polymers Induced by Spin-Coating. NANO LETTERS 2022; 22:5891-5897. [PMID: 35786930 DOI: 10.1021/acs.nanolett.2c01830] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The orientation of chains within polymeric materials influences their electrical, mechanical, and thermal properties. While many techniques can infer the orientation distribution of a bulk ensemble, it is challenging to determine this information at the single-chain level, particularly in an environment of otherwise identical polymers. Here, we use single-molecule localization microscopy (SMLM) to visualize the directions of chains within spin-coated polymer films. We find a strong relationship between shear force and the degree and direction of orientation, and additionally, we reveal the effects of chain length and solvent evaporation rate. This work utilizes single-chain resolution to observe the important, though often overlooked, property of chain orientation in the common fabrication process of spin-coating.
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Affiliation(s)
- Jonathan M Chan
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Muzhou Wang
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
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Del Mundo JT, Rongpipi S, Gomez ED, Gomez EW. Characterization of biological materials with soft X-ray scattering. Methods Enzymol 2022; 677:357-383. [DOI: 10.1016/bs.mie.2022.08.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Affiliation(s)
- Brian A. Collins
- Physics and Astronomy Washington State University Pullman Washington USA
| | - Eliot Gann
- Material Measurement Laboratory National Institute of Standards and Technology Gaithersburg Maryland USA
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Mukherjee S, Streit JK, Gann E, Saurabh K, Sunday DF, Krishnamurthy A, Ganapathysubramanian B, Richter LJ, Vaia RA, DeLongchamp DM. Polarized X-ray scattering measures molecular orientation in polymer-grafted nanoparticles. Nat Commun 2021; 12:4896. [PMID: 34385430 PMCID: PMC8361200 DOI: 10.1038/s41467-021-25176-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 07/08/2021] [Indexed: 11/08/2022] Open
Abstract
Polymer chains are attached to nanoparticle surfaces for many purposes, including altering solubility, influencing aggregation, dispersion, and even tailoring immune responses in drug delivery. The most unique structural motif of polymer-grafted nanoparticles (PGNs) is the high-density region in the corona where polymer chains are stretched under significant confinement, but orientation of these chains has never been measured because conventional nanoscale-resolved measurements lack sensitivity to polymer orientation in amorphous regions. Here, we directly measure local chain orientation in polystyrene grafted gold nanoparticles using polarized resonant soft X-ray scattering (P-RSoXS). Using a computational scattering pattern simulation approach, we measure the thickness of the anisotropic region of the corona and extent of chain orientation within it. These results demonstrate the power of P-RSoXS to discover and quantify orientational aspects of structure in amorphous soft materials and provide a framework for applying this emerging technique to more complex, chemically heterogeneous systems in the future.
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Affiliation(s)
- Subhrangsu Mukherjee
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Jason K Streit
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright Patterson Air Force Base, OH, USA
- UES, Inc., Dayton, OH, USA
| | - Eliot Gann
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Kumar Saurabh
- Department of Mechanical Engineering, Iowa State University, Ames, IA, USA
| | - Daniel F Sunday
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | | | | | - Lee J Richter
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Richard A Vaia
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright Patterson Air Force Base, OH, USA
| | - Dean M DeLongchamp
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA.
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Sunday DF, Dolejsi M, Chang AB, Richter LJ, Li R, Kline RJ, Nealey PF, Grubbs RH. Confinement and Processing Can Alter the Morphology and Periodicity of Bottlebrush Block Copolymers in Thin Films. ACS NANO 2020; 14:17476-17486. [PMID: 33225683 DOI: 10.1021/acsnano.0c07777] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Bottlebrush block copolymers (BBCPs) are intriguing architectural variations on linear BCPs with highly tunable structure. Confinement can have a significant impact on polymer assembly, giving rise to changes in morphology, assembly kinetics, and properties like the glass transition. Given that confinement leads to significant changes in the persistence length of bottlebrush homopolymers, it is reasonable to expect that BBCPs will see significant changes in their structure and periodicity relative to the bulk morphology. Understanding how confinement influences assembly will be important for designing BBCPs for thin film applications including membranes, integrated photonic structures, and potentially BCP lithography. In order to study the effects of confinement on BBCP conformation and morphology, a blade coating was used to prepare films with continuous variation in film thickness. Unlike thin films of linear BCPs, islands/holes were not observed, and instead mixtures of parallel and perpendicular morphologies emerge after annealing. The lamellar periodicity (L0) of the morphologies is found to be thickness dependent, increasing L0 with decreasing film thickness for blade coated films. Films coated out of tetrahydrofuran (THF) resulted in a single well-defined lamellar periodicity, verified through atomic force microscopy (AFM) and grazing incidence small-angle X-ray scattering (GISAXS), which increases dramatically from the bulk value (30.6 nm) and continues to increase as the film thickness decreases. The largest observed L0 was 65.5 nm, and this closely approaches the estimated upper limit of 67 nm corresponding to a fully extended backbone in a bilayer arrangement. Films coated out of propylene glycol methyl ether acetate (PGMEA) resulted in a mixture of perpendicular lamellae and a smaller, likely cylindrical morphology. The lamellar portion of the film shows the same thickness dependence as the lamellae observed in the THF coated films. The scaling of the lamellar L0 with respect to film thickness follows predictions for confined semiflexible polymers with weak excluded volume interactions and can be related to models for confinement of DNA. Spin coated films shows the same reduction in periodicity, although at very different film thicknesses. This result suggests that the material has shallow free-energy barriers to transitioning between different L0 and morphologies, a property that could be taken advantage of for patterning diverse structures with a single material.
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Affiliation(s)
- Daniel F Sunday
- Materials Science and Engineering Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Moshe Dolejsi
- Institute for Molecular Engineering, University of Chicago, 5801 S Ellis Ave, Chicago, Illinois 60637, United States
| | - Alice B Chang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Lee J Richter
- Materials Science and Engineering Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Ruipeng Li
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - R Joseph Kline
- Materials Science and Engineering Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Paul F Nealey
- Institute for Molecular Engineering, University of Chicago, 5801 S Ellis Ave, Chicago, Illinois 60637, United States
| | - Robert H Grubbs
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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Su GM, Cordova IA, Wang C. New Insights into Water Treatment Materials with Chemically Sensitive Soft and Tender X-rays. ACTA ACUST UNITED AC 2020. [DOI: 10.1080/08940886.2020.1784695] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Gregory M. Su
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Isvar A. Cordova
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Cheng Wang
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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Su GM, White W, Renna LA, Feng J, Ardo S, Wang C. Photoacid-Modified Nafion Membrane Morphology Determined by Resonant X-ray Scattering and Spectroscopy. ACS Macro Lett 2019; 8:1353-1359. [PMID: 35651146 DOI: 10.1021/acsmacrolett.9b00622] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Covalent attachment of photoacid dye molecules to perfluorinated sulfonic acid membranes is a promising route to enable active light-driven ion pumps, but the complex relationship between chemical modification and morphology is not well understood in this class of functional materials. In this study we demonstrate the effect of bound photoacid dyes on phase-segregated membrane morphology. Resonant X-ray scattering near the sulfur K-edge reveals that introduction of photoacid dyes to the end of the ionomer side chains enhances phase segregation among ionomer domains, and the ionomer domain spacing increases with increasing amount of bound dye. Furthermore, relative crystallinity is marginally enhanced within semicrystalline domains composed of the perfluorinated backbone. X-ray absorption spectroscopy coupled with first-principles density functional theory calculations suggest that above a critical concentration, the multiple hydrophilic groups on the attached photoacid dye may help increase residual water content and promote hydration of adjacent sulfonic acid side chains under dry or ambient conditions.
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Affiliation(s)
- Gregory M. Su
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - William White
- Department of Chemistry, University of California Irvine, Irvine, California 92697, United States
| | - Lawrence A. Renna
- Department of Chemistry, University of California Irvine, Irvine, California 92697, United States
| | - Jun Feng
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Shane Ardo
- Department of Chemistry, University of California Irvine, Irvine, California 92697, United States
- Department of Chemical Engineering & Biomolecular Engineering, University of California Irvine, Irvine, California 92697, United States
- Department of Materials Science & Engineering, University of California Irvine, Irvine, California 92697, United States
| | - Cheng Wang
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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Su GM, Cordova IA, Yandrasits MA, Lindell M, Feng J, Wang C, Kusoglu A. Chemical and Morphological Origins of Improved Ion Conductivity in Perfluoro Ionene Chain Extended Ionomers. J Am Chem Soc 2019; 141:13547-13561. [DOI: 10.1021/jacs.9b05322] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Gregory M. Su
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Isvar A. Cordova
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | | | | | - Jun Feng
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Cheng Wang
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Ahmet Kusoglu
- Energy Conversion Group, Energy Technologies Area, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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