I22-Small angle scattering & Diffraction
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Diamond Proposal Number(s):
[14217, 14792]
Abstract: The enzyme sphingomyelinase (SMase) is an important biomarker for several diseases such as Niemann Pick’s, atherosclerosis, multiple sclerosis, and HIV. We present a two-component colorimetric SMase activity assay that is more sensitive and much faster than currently available commercial assays. Herein, SMase-triggered release of cysteine from a sphingomyelin (SM)-based liposome formulation with 60 mol % cholesterol causes gold nanoparticle (AuNP) aggregation, enabling colorimetric detection of SMase activities as low as 0.02 mU/mL, corresponding to 1.4 pM concentration. While the lipid composition offers a stable, nonleaky liposome platform with minimal background signal, high specificity toward SMase avoids cross-reactivity of other similar phospholipases. Notably, use of an SM-based liposome formulation accurately mimics the natural in vivo substrate: the cell membrane. We studied the physical rearrangement process of the lipid membrane during SMase-mediated hydrolysis of SM to ceramide using small- and wide-angle X-ray scattering. A change in lipid phase from a liquid to gel state bilayer with increasing concentration of ceramide accounts for the observed increase in membrane permeability and consequent release of encapsulated cysteine. We further demonstrated the effectiveness of the sensor in colorimetric screening of small-molecule drug candidates, paving the way for the identification of novel SMase inhibitors in minutes. Taken together, the simplicity, speed, sensitivity, and naked-eye readout of this assay offer huge potential in point-of-care diagnostics and high-throughput drug screening.
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Aug 2018
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E02-JEM ARM 300CF
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Diamond Proposal Number(s):
[16854]
Abstract: High-energy irradiation of materials can lead to void formation due to the aggregation of vacancies, reducing the local stress in the system. Studying void formation and its interplay with vacancy clusters in bulk materials at the atomic level has been challenging due to the thick volume of 3D materials, which generally limits high-resolution transmission electron microscopy. The thin nature of 2D materials is ideal for studying fundamental material defects such as dislocations and crack tips and has potential to reveal void formation by vacancy aggregation in detail. Here, using atomic-resolution in situ transmission electron microscopy of 2D monolayer MoS2, we capture rapid thermal diffusion of S vacancies into ultralong (∼60 nm) 1D S vacancy channels that initiate void formation at high vacancy densities. Strong interactions are observed between the 1D channels and void growth, whereby Mo and S atoms are funneled back and forth between the void edge and the crystal surface to enable void enlargement. Preferential void growth up to 100 nm is shown to occur by rapid digestion of 1D S vacancy channels as they make contact. These results reveal the atomistic mechanisms behind void enlargement in 2D materials under intense high-energy irradiation at high temperatures and the existence of ultralong 1D vacancy channels. This knowledge may also help improve the understanding of void formation in other systems such as nuclear materials, where direct visualization is challenging due to 3D bulk volume.
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Aug 2018
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I05-ARPES
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Boris V.
Senkovskiy
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Dmitry Yu.
Usachov
,
Alexander V.
Fedorov
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Tomas
Marangoni
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Danny
Haberer
,
Cesare
Tresca
,
Gianni
Profeta
,
Vasile
Caciuc
,
Shigeru
Tsukamoto
,
Nicolae
Atodiresei
,
Niels
Ehlen
,
Chaoyu
Chen
,
José
Avila
,
Maria C.
Asensio
,
Andrei Yu.
Varykhalov
,
Alexei
Nefedov
,
Christof
Wöll
,
Timur K.
Kim
,
Moritz
Hoesch
,
Felix R.
Fischer
,
Alexander
Gruneis
Diamond Proposal Number(s):
[17064]
Abstract: We investigate the electronic and vibrational properties of bottom-up synthesized aligned armchair graphene nanoribbons of N=7 carbon atoms width periodically doped by substitutional boron atoms (B-7AGNRs). Using angle-resolved photoemission spectroscopy (ARPES), we find that the dopant-derived valence and conduction band states are notably hybridized with electronic states of Au substrate and spread in energy. The interaction with the substrate leaves the bands with pure carbon character rather unperturbed. This results in an identical effective mass of ~0.2 m0 for the next highest valence band compared to pristine 7AGNRs. We probe the phonons of B-7AGNRs by ultra-high vacuum (UHV) Raman spectroscopy and reveal the existence of characteristic splittings and red-shifts of Raman modes due to the presence of substitutional boron atoms. Comparing the Raman spectra for three visible lasers (red, green and blue) we find that interaction with gold suppresses the Raman signal from B-7AGNRs and the energy of a green laser (2.33 eV) is closer to the resonant E22 transition. The hybridized electronic structure of the B-7AGNR/Au interface is expected to improve electrical characteristics of contacts between graphene nanoribbon and Au. The Raman fingerprint allows easy identification of B-7AGNRs, that is particularly useful for device fabrication.
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Jul 2018
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E02-JEM ARM 300CF
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Abstract: We show that Pt nanoclusters preferentially nucleate along the grain boundaries (GBs) in polycrystalline MoS2 monolayer films, with dislocations acting as the seed site. Atomic resolution studies by aberration-corrected annular dark-field scanning transmission electron microscopy reveal periodic spacing of Pt nanoclusters with dependence on GB tilt angles and random spacings for the antiphase boundaries (i.e., 60°). Individual Pt atoms are imaged within the dislocation core sections of the GB region, with various positions observed, including both the substitutional sites of Mo and the hollow center of the octahedral ring. The evolution from single atoms or small few atom clusters to nanosized particles of Pt is examined at the atomic level to gain a deep understanding of the pathways of Pt seed nucleation and growth at the GB. Density functional theory calculations confirm the energetic advantage of trapping Pt at dislocations on both the antiphase boundary and the small-angle GB rather than on the pristine lattice. The selective decoration of GBs by Pt nanoparticles also has a beneficial use to easily identify GB areas during microscopic-scale observations and track long-range nanoscale variances of GBs with spatial detail not easy to achieve using other methods. We show that GBs have nanoscale meandering across micron-scale distances with no strong preference for specific lattice directions across macroscopic ranges.
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May 2018
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I18-Microfocus Spectroscopy
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Abstract: Techniques to analyse human telomeres are imperative in studying the molecular mechanism of ageing and related diseases. Two important aspects of telomeres are their length in DNA base pairs (bps), and their biophysical nanometer dimensions. However, there are currently no techniques that can simultaneously measure these quantities in individual cell nuclei. Here, we develop and evaluate a telomere “dual” gold nanoparticle-fluorescent probe simultaneously compatible with both X-ray fluorescence (XRF) and super resolution microscopy. We used silver enhancement to independently visualise the spatial locations of gold nanoparticles inside nuclei, comparing to a standard QFISH (quantitative fluorescence in-situ hybridisation) probe, and showed good specificity at ~90%. For sensitivity, we calculated telomere length based on a DNA:gold binding ratio using XRF, and compared to quantitative polymerase chain reaction (qPCR) measurements. The sensitivity was low (~10%), probably because of steric interference prohibiting the relatively large 10 nm gold nanoparticles access to DNA space. We then measured the biophysical characteristics of individual telomeres using super resolution microscopy. Telomeres that have an average length of ~10 kbps, have diameters ranging between ~60-300 nm. Further, we treated cells with a telomere-shortening drug, and showed there was a small but significant difference in telomere diameter in drug-treated vs control cells. We discuss our results in relation to the current debate surrounding telomere compaction.
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Nov 2017
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I24-Microfocus Macromolecular Crystallography
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Benjamin
Cressiot
,
Sandra J.
Greive
,
Wei
Si
,
Tomas
Pascoa
,
Mehrnaz
Mojtabavi
,
Maria
Chechik
,
Huw T.
Jenkins
,
Xueguang
Lu
,
Ke
Zhang
,
Aleksei
Aksimentiev
,
Alfred A.
Antson
,
Meni
Wanunu
Diamond Proposal Number(s):
[13587]
Abstract: Nanopore-based sensors for nucleic acid sequencing and single-molecule detection typically employ pore-forming membrane proteins with hydrophobic external surfaces, suitable for insertion into a lipid bilayer. In contrast, hydrophilic pore-containing molecules such as DNA origami, have been shown to require chemical modification to favor insertion into a lipid environment. In this work, we describe a strategy for inserting polar proteins with an inner pore into lipid membranes, focusing here on a circular 12-subunit assembly of the thermophage G20c portal protein. X-ray crystallography, electron microscopy, molecular dynamics and thermal/chaotrope denaturation experiments all find the G20c portal protein to have a highly stable structure, favorable for nanopore sensing applications. Porphyrin conjugation to a cysteine mutant in the protein facilitates the protein’s insertion into lipid bilayers, allowing us to probe ion transport through the pore. Finally, we probed the portal interior size and shape using a series of cyclodextrins of varying sizes, revealing asymmetric transport that possibly originates from the portal’s DNA-ratchet function.
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Nov 2017
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I09-Surface and Interface Structural Analysis
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Martin
Schwarz
,
Alexander
Riss
,
Manuela
Garnica
,
Jacob
Ducke
,
Peter S.
Deimel
,
David A.
Duncan
,
Pardeep
Kumar Thakur
,
Tien-lin
Lee
,
Ari Paavo
Seitsonen
,
Johannes V.
Barth
,
Francesco
Allegretti
,
Willi
Auwärter
Diamond Proposal Number(s):
[14624]
Abstract: Atomically thin hexagonal boron nitride (h-BN) layers on metallic supports represent a promising platform for the selective adsorption of atoms, clusters, and molecular nanostructures. Specifically, scanning tunneling microscopy (STM) studies revealed an electronic corrugation of h-BN/Cu(111), guiding the self-assembly of molecules and their energy level alignment. A detailed characterization of the h-BN/Cu(111) interface including the spacing between the h-BN sheet and its support—elusive to STM measurements—is crucial to rationalize the interfacial interactions within these systems. To this end, we employ complementary techniques including high-resolution noncontact atomic force microscopy, STM, low-energy electron diffraction, X-ray photoelectron spectroscopy, the X-ray standing wave method, and density functional theory. Our multimethod study yields a comprehensive, quantitative structure determination including the adsorption height and the corrugation of the sp2 bonded h-BN layer on Cu(111). Based on the atomic contrast in atomic force microscopy measurements, we derive a measurable–hitherto unrecognized–geometric corrugation of the h-BN monolayer. This experimental approach allows us to spatially resolve minute height variations in low-dimensional nanostructures, thus providing a benchmark for theoretical modeling. Regarding potential applications, e.g., as a template or catalytically active support, the recognition of h-BN on Cu(111) as a weakly bonded and moderately corrugated overlayer is highly relevant.
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Sep 2017
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I09-Surface and Interface Structural Analysis
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Anu
Baby
,
Marco
Gruenewald
,
Christian
Zwick
,
Felix
Otto
,
Roman
Forker
,
Gerben
Van Straaten
,
Markus
Franke
,
Benjamin
Stadtmueller
,
Christian
Kumpf
,
Gian Paolo
Brivio
,
Guido
Fratesi
,
Torsten
Fritz
,
Egbert
Zojer
Diamond Proposal Number(s):
[10370]
Abstract: The current study generates profound atomistic insights into doping-induced changes of the optical and electronic properties of the prototypical PTCDA/Ag(111) interface. For doping K atoms are used, as KxPTCDA/Ag(111) has the distinct advantage of forming well-defined stoichiometric phases. To arrive at a conclusive, unambiguous, and fully atomistic understanding of the interface properties, we combine state-of-the-art density-functional theory calculations with optical differential reflectance data, photoelectron spectra, and X-ray standing wave measurements. In combination with the full structural characterization of the KxPTCDA/Ag(111) interface by low-energy electron diffraction and scanning tunneling microscopy experiments (ACS Nano 2016, 10, 2365–2374), the present comprehensive study provides access to a fully characterized reference system for a well-defined metal–organic interface in the presence of dopant atoms, which can serve as an ideal benchmark for future research and applications. The combination of the employed complementary techniques allows us to understand the peculiarities of the optical spectra of K2PTCDA/Ag(111) and their counterintuitive similarity to those of neutral PTCDA layers. They also clearly describe the transition from a metallic character of the (pristine) adsorbed PTCDA layer on Ag(111) to a semiconducting state upon doping, which is the opposite of the effect (degenerate) doping usually has on semiconducting materials. All experimental and theoretical efforts also unanimously reveal a reduced electronic coupling between the adsorbate and the substrate, which goes hand in hand with an increasing adsorption distance of the PTCDA molecules caused by a bending of their carboxylic oxygens away from the substrate and toward the potassium atoms.
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Sep 2017
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I22-Small angle scattering & Diffraction
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Diamond Proposal Number(s):
[10311]
Abstract: Articular cartilage is a natural biomaterial whose structure at the micro- and nanoscale is critical for healthy joint function and where degeneration is associated with widespread disorders such as osteoarthritis. At the nanoscale, cartilage mechanical functionality is dependent on the collagen fibrils and hydrated proteoglycans that form the extracellular matrix. The dynamic response of these ultrastructural building blocks at the nanoscale, however, remains unclear. Here we measure time-resolved changes in collagen fibril strain, using small angle X-ray diffraction during compression of bovine and human cartilage explants. We demonstrate the existence of a collagen fibril tensile pre-strain, estimated from the D-period at approximately 1-2%, due to osmotic swelling pressure from the proteoglycan. We reveal for the first time, a rapid reduction and recovery of this pre-strain which occurs during stress relaxation, approximately 60 seconds after the onset of peak load. Furthermore, we show that this reduction in pre-strain is linked to disordering in the intrafibrillar molecular packing, alongside changes in the axial overlapping of tropocollagen molecules within the fibril. Tissue degradation in the form of selective proteoglycan removal disrupts both the collagen fibril pre-strain and the transient response during stress relaxation. This study bridges a fundamental gap in the knowledge describing time-dependent changes in collagen pre-strain and molecular organisation that occur during physiological loading of articular cartilage. This previously unknown transient response is likely to transform our understanding of the role of collagen fibril nano-mechanics in the biomechanics of cartilage and other hydrated soft tissues.
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Aug 2017
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E02-JEM ARM 300CF
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Abstract: Pt-nanocrystal:MoS2 hybrid materials have promising catalytic properties for hydrogen evolution, and understanding their detailed structures at the atomic scale is crucial to further development. Here, we use an in situ heating holder in an aberration-corrected transmission electron microscope to study the formation of Pt nanocrystals directly on the surface of monolayer MoS2 from a precursor on heating to 800 °C. Isolated single Pt atoms and small nanoclusters are observed after in situ heating, with two types of preferential alignment between the Pt nanocrystals and the underlying monolayer MoS2. Strain effects and thickness variations of the ultrasmall Pt nanocrystal supported on MoS2 are studied, revealing that single atomic planes are formed from a nonlayered face-centered cubic bulk Pt configuration with a lattice expansion of 7–10% compared to that of bulk Pt. The Pt nanocrystals are surrounded by an amorphous carbon layer and in some cases have etched the local surrounding MoS2 material after heating. Electron beam irradiation also initiates Pt nanocrystal etching of the local MoS2, and we study this process in real time at atomic resolution. These results show that the presence of carbon around the Pt nanocrystals does not affect their epitaxial relationship with the MoS2 lattice. Single Pt atoms within the carbon layer are also immobilized at high temperature. These results provide important insights into the formation of Pt:MoS2 hybrid materials.
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Aug 2017
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