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Farokh Payam A, Passian A. Imaging beyond the surface region: Probing hidden materials via atomic force microscopy. SCIENCE ADVANCES 2023; 9:eadg8292. [PMID: 37379392 DOI: 10.1126/sciadv.adg8292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 05/24/2023] [Indexed: 06/30/2023]
Abstract
Probing material properties at surfaces down to the single-particle scale of atoms and molecules has been achieved, but high-resolution subsurface imaging remains a nanometrology challenge due to electromagnetic and acoustic dispersion and diffraction. The atomically sharp probe used in scanning probe microscopy (SPM) has broken these limits at surfaces. Subsurface imaging is possible under certain physical, chemical, electrical, and thermal gradients present in the material. Of all the SPM techniques, atomic force microscopy has entertained unique opportunities for nondestructive and label-free measurements. Here, we explore the physics of the subsurface imaging problem and the emerging solutions that offer exceptional potential for visualization. We discuss materials science, electronics, biology, polymer and composite sciences, and emerging quantum sensing and quantum bio-imaging applications. The perspectives and prospects of subsurface techniques are presented to stimulate further work toward enabling noninvasive high spatial and spectral resolution investigation of materials including meta- and quantum materials.
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Affiliation(s)
- Amir Farokh Payam
- Nanotechnology and Integrated Bioengineering Centre, School of Engineering, Ulster University, Belfast, UK
| | - Ali Passian
- Quantum Computing and Sensing, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
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Bilkey N, Li H, Borodinov N, Ievlev AV, Ovchinnikova OS, Dixit R, Foston M. Correlated mechanochemical maps of Arabidopsis thaliana primary cell walls using atomic force microscope infrared spectroscopy. QUANTITATIVE PLANT BIOLOGY 2022; 3:e31. [PMID: 37077971 PMCID: PMC10095902 DOI: 10.1017/qpb.2022.20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 09/11/2022] [Accepted: 10/07/2022] [Indexed: 05/03/2023]
Abstract
Spatial heterogeneity in composition and organisation of the primary cell wall affects the mechanics of cellular morphogenesis. However, directly correlating cell wall composition, organisation and mechanics has been challenging. To overcome this barrier, we applied atomic force microscopy coupled with infrared (AFM-IR) spectroscopy to generate spatially correlated maps of chemical and mechanical properties for paraformaldehyde-fixed, intact Arabidopsis thaliana epidermal cell walls. AFM-IR spectra were deconvoluted by non-negative matrix factorisation (NMF) into a linear combination of IR spectral factors representing sets of chemical groups comprising different cell wall components. This approach enables quantification of chemical composition from IR spectral signatures and visualisation of chemical heterogeneity at nanometer resolution. Cross-correlation analysis of the spatial distribution of NMFs and mechanical properties suggests that the carbohydrate composition of cell wall junctions correlates with increased local stiffness. Together, our work establishes new methodology to use AFM-IR for the mechanochemical analysis of intact plant primary cell walls.
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Affiliation(s)
- Natasha Bilkey
- Department of Biology, Center for Engineering Mechanobiology, Washington University in St. Louis, St. Louis, Missouri63130, USA
| | - Huiyong Li
- Department of Energy, Environmental and Chemical Engineering, Center for Engineering Mechanobiology, Washington University in St. Louis, St. Louis, Missouri63130, USA
| | - Nikolay Borodinov
- Center for Nanophase Materials Science, Oak Ridge National Laboratory, Oak Ridge, Tennessee37831, USA
| | - Anton V. Ievlev
- Center for Nanophase Materials Science, Oak Ridge National Laboratory, Oak Ridge, Tennessee37831, USA
| | - Olga S. Ovchinnikova
- Center for Nanophase Materials Science, Oak Ridge National Laboratory, Oak Ridge, Tennessee37831, USA
| | - Ram Dixit
- Department of Biology, Center for Engineering Mechanobiology, Washington University in St. Louis, St. Louis, Missouri63130, USA
| | - Marcus Foston
- Department of Energy, Environmental and Chemical Engineering, Center for Engineering Mechanobiology, Washington University in St. Louis, St. Louis, Missouri63130, USA
- Author for correspondence: M. Foston, E-mail:
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Action of lytic polysaccharide monooxygenase on plant tissue is governed by cellular type. Sci Rep 2017; 7:17792. [PMID: 29259205 PMCID: PMC5736606 DOI: 10.1038/s41598-017-17938-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 11/28/2017] [Indexed: 11/08/2022] Open
Abstract
Lignocellulosic biomass bioconversion is hampered by the structural and chemical complexity of the network created by cellulose, hemicellulose and lignin. Biological conversion of lignocellulose involves synergistic action of a large array of enzymes including the recently discovered lytic polysaccharide monooxygenases (LPMOs) that perform oxidative cleavage of cellulose. Using in situ imaging by synchrotron UV fluorescence, we have shown that the addition of AA9 LPMO (from Podospora anserina) to cellulases cocktail improves the progression of enzymes in delignified Miscanthus x giganteus as observed at tissular levels. In situ chemical monitoring of cell wall modifications performed by synchrotron infrared spectroscopy during enzymatic hydrolysis demonstrated that the boosting effect of the AA9 LPMO was dependent on the cellular type indicating contrasted recalcitrance levels in plant tissues. Our study provides a useful strategy for investigating enzyme dynamics and activity in plant cell wall to improve enzymatic cocktails aimed at expanding lignocelluloses biorefinery.
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Gilna P, Lynd LR, Mohnen D, Davis MF, Davison BH. Progress in understanding and overcoming biomass recalcitrance: a BioEnergy Science Center (BESC) perspective. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:285. [PMID: 29213324 PMCID: PMC5707806 DOI: 10.1186/s13068-017-0971-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 11/15/2017] [Indexed: 06/07/2023]
Abstract
The DOE BioEnergy Science Center has operated as a virtual center with multiple partners for a decade targeting overcoming biomass recalcitrance. BESC has redefined biomass recalcitrance from an observable phenotype to a better understood and manipulatable fundamental and operational property. These manipulations are the result of deeper biological understanding and can be combined with other advanced biotechnology improvements in biomass conversion to improve bioenergy processes and markets. This article provides an overview of key accomplishments in overcoming recalcitrance via better plants, better microbes, and better tools and combinations. A perspective on the aspects of successful center operation is presented.
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Affiliation(s)
- Paul Gilna
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Bldg. 1505, Rm. 100A, Oak Ridge, TN 37831-6037 USA
| | - Lee R. Lynd
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Bldg. 1505, Rm. 100A, Oak Ridge, TN 37831-6037 USA
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755 USA
| | - Debra Mohnen
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Bldg. 1505, Rm. 100A, Oak Ridge, TN 37831-6037 USA
- Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602 USA
| | - Mark F. Davis
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Bldg. 1505, Rm. 100A, Oak Ridge, TN 37831-6037 USA
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Brian H. Davison
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Bldg. 1505, Rm. 100A, Oak Ridge, TN 37831-6037 USA
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Soliman M, Ding Y, Tetard L. Nanoscale subsurface imaging. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:173001. [PMID: 28140334 DOI: 10.1088/1361-648x/aa5b4a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The ability to probe structures and functional properties of complex systems at the nanoscale, both at their surface and in their volume, has drawn substantial attention in recent years. Besides detecting heterogeneities, cracks and defects below the surface, more advanced explorations of chemical or electrical properties are of great interest. In this article, we review some approaches developed to explore heterogeneities below the surface, including recent progress in the different aspects of metrology in optics, electron microscopy, and scanning probe microscopy. We discuss the principle and mechanisms of image formation associated with each technique, including data acquisition, data analysis and modeling for nanoscale structural and functional imaging. We highlight the advances based on atomic force microscopy (AFM). Our discussion first introduces methods providing structural information of the buried structures, such as position in the volume and geometry. Next we present how functional properties including conductivity, capacitance, and composition can be extracted from the modalities available to date and how they could eventually enable tomography reconstructions of systems such as overlay structures in transistors or living systems. Finally we propose a perspective regarding the outstanding challenges and needs to push the field forward.
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Affiliation(s)
- M Soliman
- NanoScience Technology Center, 12424 Research Parkway, University of Central Florida, Orlando, FL, 32826, United States of America. Materials Science and Engineering, 12760 Pegasus Drive, University of Central Florida, Orlando, FL, 32816, United States of America
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Šimkovic I, Kelnar I, Mendichi R, Bertok T, Filip J. Composite films prepared from agricultural by-products. Carbohydr Polym 2017; 156:77-85. [DOI: 10.1016/j.carbpol.2016.09.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 07/14/2016] [Accepted: 09/05/2016] [Indexed: 11/30/2022]
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Zhang S, Aslan H, Besenbacher F, Dong M. Quantitative biomolecular imaging by dynamic nanomechanical mapping. Chem Soc Rev 2014; 43:7412-29. [DOI: 10.1039/c4cs00176a] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Comments on the paper “A comprehensive modeling and vibration analysis of AFM microcantilevers subjected to nonlinear tip-sample interaction forces” by Sohrab Eslami and Nader Jalili. Ultramicroscopy 2013; 131:92-3. [DOI: 10.1016/j.ultramic.2013.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Revised: 10/18/2012] [Accepted: 03/22/2013] [Indexed: 11/19/2022]
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Tetard L, Passian A, Jung S, Ragauskas AJ, Davison BH. Development of New Methods in Scanning Probe Microscopy for Lignocellulosic Biomass Characterization. Ind Biotechnol (New Rochelle N Y) 2012. [DOI: 10.1089/ind.2012.0017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Laurene Tetard
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN
- Measurement Science and Systems Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN
| | - Ali Passian
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN
- Department of Physics, University of Tennessee, Knoxville, TN
| | - Seokwon Jung
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA
| | - Art J. Ragauskas
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA
| | - Brian H. Davison
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN
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Foston M, Ragauskas AJ. Biomass Characterization: Recent Progress in Understanding Biomass Recalcitrance. Ind Biotechnol (New Rochelle N Y) 2012. [DOI: 10.1089/ind.2012.0015] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Marcus Foston
- BioEnergy Science Center, School of Chemistry and Biochemistry, Institute of Paper Science and Technology, Georgia Institute of Technology, Atlanta, GA
| | - Arthur J. Ragauskas
- BioEnergy Science Center, School of Chemistry and Biochemistry, Institute of Paper Science and Technology, Georgia Institute of Technology, Atlanta, GA
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