Macrodomain Structure Research Articles

Macrodomain structure formed in (Sr0.7Bi0.2□0.1)TiO3-modified Bi0.5Na0.4 K0.1TiO3 thin film

The performance of piezoelectric materials can often be improved near the morphotropic phase boundary (MPB), in this work, we introduced (Sr0.7Bi0.2□0.1)TiO3 into Bi0.5Na0.4 K0·1TiO3 thin films to regulate their properties. (1-x)BNKT–xSBT (x = 0.05, 0.10, 0.20, 0.30) lead free piezoelectric thin films were deposited on Pt(111)/Ti/SiO2/Si substrates by the sol–gel method, which was designed by the principle of optimal tolerance factor. The XRD and Raman spectra were investigated in detail to prove the formation of MPB in BNKT–0.10SBT thin films, and the most direct evidence is the movement of TF-R near room temperature. The rarest is the formation of macrodomain structure at MPB, which is especially beneficial to the improvement of piezoelectric property. There is no doubt that the most excellent ferroelectric (Pm = 59 μC cm−2, Pr = 13 μC cm−2 @700 kV/cm) and piezoelectric properties (72% higher than the initial component) can be obtained from the BNKT–0.10SBT thin film. The MPB formed when tolerance factor was adjusted to 0.9816, meanwhile macrodomain structure was observed under electric field, so that the ferroelectric and piezoelectric properties have been significantly improved at this point. This study provides a useful guide to research MPB in BNT-based thin films in order to improve ferroelectric and piezoelectric performances.

Ultrahigh pyroelectric effect and energy harvesting density of Pb(Lu1/2Nb1/2)O3–PbTiO3 crystals induced by FE-AFE phase transition

Large pyroelectric and energy harvesting properties have been attracting increasing attentions due to the practical applications in infrared detectors and energy harvesting technologies. Ferroelectric-antiferroelectric (FE-AFE) phase transitions are usually accompanied by a sharp drop in polarization, which will lead to excellent pyroelectric properties and energy harvesting density. Therefore, FE-AFE phase boundary design is an effective strategy to develop new pyroelectric materials. In this paper, Pb(Lu1/2Nb1/2)O3-PbTiO3 (PLN-PT) single crystals with FE-AFE phase transitions were obtained by molten salt growth method. The temperature-induced FE-AFE phase transition was verified by temperature-dependent macrodomain structure, DSC curves and dielectric properties. Obviously, PLN-PT crystals display excellent peak pyroelectric coefficient (∼6.8 μC/(cm2·K)) with a maximum depolarization temperature of 118 °C. Meanwhile, the pyroelectric energy harvesting density is as high as 2.62 J/cm3, which is much higher than other pyroelectric materials. The results reveal that the PLN-PT crystal is a promising candidate for infrared detectors and energy harvesting devices.

Targeting SARS-CoV-2 Nsp3 macrodomain structure with insights from human poly(ADP-ribose) glycohydrolase (PARG) structures with inhibitors

Arrival of the novel SARS-CoV-2 has launched a worldwide effort to identify both pre-approved and novel therapeutics targeting the viral proteome, highlighting the urgent need for efficient drug discovery strategies. Even with effective vaccines, infection is possible, and at-risk populations would benefit from effective drug compounds that reduce the lethality and lasting damage of COVID-19 infection. The CoV-2 MacroD-like macrodomain (Mac1) is implicated in viral pathogenicity by disrupting host innate immunity through its mono(ADP-ribosyl) hydrolase activity, making it a prime target for antiviral therapy. We therefore solved the structure of CoV-2 Mac1 from non-structural protein 3 (Nsp3) and applied structural and sequence-based genetic tracing, including newly determined A. pompejana MacroD2 and GDAP2 amino acid sequences, to compare and contrast CoV-2 Mac1 with the functionally related human DNA-damage signaling factor poly(ADP-ribose) glycohydrolase (PARG). Previously, identified targetable features of the PARG active site allowed us to develop a pharmacologically useful PARG inhibitor (PARGi). Here, we developed a focused chemical library and determined 6 novel PARGi X-ray crystal structures for comparative analysis. We applied this knowledge to discovery of CoV-2 Mac1 inhibitors by combining computation and structural analysis to identify PARGi fragments with potential to bind the distal ribose and adenosyl pockets of the CoV-2 Mac1 active site. Scaffold development of these PARGi fragments has yielded two novel compounds, PARG-345 and PARG-329, that crystallize within the Mac1 active site, providing critical structure-activity data and a pathway for inhibitor optimization. The reported structural findings demonstrate ways to harness our PARGi synthesis and characterization pipeline to develop CoV-2 Mac1 inhibitors targeting the ADP-ribose active site. Together, these structural and computational analyses reveal a path for accelerating development of antiviral therapeutics from pre-existing drug optimization pipelines.

1H, 13C, and 15N backbone chemical shift assignments of the apo and the ADP-ribose bound forms of the macrodomain of SARS-CoV-2 non-structural protein 3b

The SARS-CoV-2 genome encodes for approximately 30 proteins. Within the international project COVID19-NMR, we distribute the spectroscopic analysis of the viral proteins and RNA. Here, we report NMR chemical shift assignments for the protein Nsp3b, a domain of Nsp3. The 217-kDa large Nsp3 protein contains multiple structurally independent, yet functionally related domains including the viral papain-like protease and Nsp3b, a macrodomain (MD). In general, the MDs of SARS-CoV and MERS-CoV were suggested to play a key role in viral replication by modulating the immune response of the host. The MDs are structurally conserved. They most likely remove ADP-ribose, a common posttranslational modification, from protein side chains. This de-ADP ribosylating function has potentially evolved to protect the virus from the anti-viral ADP-ribosylation catalyzed by poly-ADP-ribose polymerases (PARPs), which in turn are triggered by pathogen-associated sensing of the host immune system. This renders the SARS-CoV-2 Nsp3b a highly relevant drug target in the viral replication process. We here report the near-complete NMR backbone resonance assignment (1H, 13C, 15N) of the putative Nsp3b MD in its apo form and in complex with ADP-ribose. Furthermore, we derive the secondary structure of Nsp3b in solution. In addition, 15N-relaxation data suggest an ordered, rigid core of the MD structure. These data will provide a basis for NMR investigations targeted at obtaining small-molecule inhibitors interfering with the catalytic activity of Nsp3b.

Low-frequency magnetic sensing by magnetoelectric metglas/bidomain LiNbO3 long bars

We present an investigation into the magnetic sensing performance of magnetoelectric bilayered metglas/bidomain LiNbO3 long thin bars operating in a cantilever or free vibrating regime and under quasi-static and low-frequency resonant conditions. Bidomain single crystals of Y + 128°-cut LiNbO3 were engineered by an improved diffusion annealing technique with a polarization macrodomain structure of the ‘head-to-head’ and ‘tail-to-tail’ type. Long composite bars with lengths of 30, 40 and 45 mm, as well as with and without attached small tip proof masses, were studied. ME coefficients as large as 550 V (cm · Oe)−1, corresponding to a conversion ratio of 27.5 V Oe−1, were obtained under resonance conditions at frequencies of the order of 100 Hz in magnetic bias fields as low as 2 Oe. Equivalent magnetic noise spectral densities down to 120 pT Hz−1/2 at 10 Hz and to 68 pT Hz−1/2 at a resonance frequency as low as 81 Hz were obtained for the 45 mm long cantilever bar with a tip proof mass of 1.2 g. In the same composite without any added mass the magnetic noise was shown to be as low as 37 pT Hz−1/2 at a resonance frequency of 244 Hz and 1.2 pT Hz−1/2 at 1335 Hz in a fixed cantilever and free vibrating regimes, respectively. A simple unidimensional dynamic model predicted the possibility to drop the low-frequency magnetic noise by more than one order of magnitude in case all the extrinsic noise sources are suppressed, especially those related to external vibrations, and the thickness ratio of the magnetic-to-piezoelectric phases is optimized. Thus, we have shown that such systems might find use in simple and sensitive room-temperature low-frequency magnetic sensors, e.g. for biomedical applications.

The study of dynamic characteristics during the vibration processing of parts

The results of theoretical studies on the dynamic characteristics of the process of vibroprocessing are presented, the essence of which is to create conservative zones limited by the current lines of a certain fixed vector field, which contributes to the formation of a macrodomain structure in the working medium. Domain structuring of the working tool reflects the configuration of the field grid of the external dynamic field and is the basis of the technology of vibration processing.

Interaction of Protein Occupancy, Chromosome Structure, and Gene Regulation in E. coli

Chromosome structure facilitates coordinated regulation of related genes as well as controlling the access of transcription machinery to DNA. In human cells, the control of a chromosome's location within the nucleus, its contacts with other sections of DNA, and its individual collection of DNA binding proteins is a well‐established method of regulation. In the simpler bacterial cell, with no nuclear membrane and with genetic information contained in a circular chromosome, initial hypotheses were that the DNA does not have a controlling architecture. However, studies by Valens et al. (EMBO 2004) and Cagliero et al. (Nucleic Acids Research 2013) in Escherichia coli and Umbarger et al. (Mol. Cell 2011) in Caulobacter crescentus illustrated that the genetic material of bacteria also appears to follow some structural rules. From these studies, researchers hypothesized that the E. coli chromosome follows a macrodomain structure, with nearby segments forming clusters distinct from neighboring DNA. In contrast, the Caulobacter chromosome appeared to twist on itself, producing interactions between points halfway across the genome. Independently, Vora et al. (Mol. Cell 2009) observed that the E. coli chromosome contains regions of very high protein occupancy, termed EPODs, many of which are transcriptionally silent and which are enriched for nucleoid protein binding sites.To unify these observations, we have performed experiments to characterize the conformation of E. coli genomes at different stages of growth and to analyze the interaction of protein occupancy with genome structure and gene transcription. Our genome conformation capture studies revealed no signs of higher order structure in either logarithmic or stationary E. coli. However, we do see correlations between methylation, recombination hot spots and regions of high DNA‐DNA interaction. In addition, studies of genome wide protein occupancy reveal an anti‐correlation between extended protein occupancy domains (EPODs) and DNA accessibility; i.e., EPODs are usually found in regions of DNA with low interaction frequencies. EPODs appear to result from the cooperative activity of several nucleoid associated proteins including Fis and Hfq, so it is unsurprising that they appear to have a connection with chromosome structure. The presence of such EPODs would be presumed to affect the likelihood of gene expression just as heterochromatic regions of eukaryotic DNA are known to repress transcription. To assess the effect of EPOD occupancy on gene expression, we have inserted a uniform construct into various locations on the E. coli chromosome and measured expression, identifying a crucial role for EPODs in modulating transcription rates. These studies provide a global picture of the fundamental role of chromosome organization in E. coli.Support or Funding InformationSupport from the Cellular Biotechnology Training Program (GMK), R00 GM097033 (PLF) and University of Michigan startup funding (PLF)

The Adaptation of Temperate Bacteriophages to Their Host Genomes

Rapid turnover of mobile elements drives the plasticity of bacterial genomes. Integrated bacteriophages (prophages) encode host-adaptive traits and represent a sizable fraction of bacterial chromosomes. We hypothesized that natural selection shapes prophage integration patterns relative to the host genome organization. We tested this idea by detecting and studying 500 prophages of 69 strains of Escherichia and Salmonella. Phage integrases often target not only conserved genes but also intergenic positions, suggesting purifying selection for integration sites. Furthermore, most integration hotspots are conserved between the two host genera. Integration sites seem also selected at the large chromosomal scale, as they are nonrandomly organized in terms of the origin–terminus axis and the macrodomain structure. The genes of lambdoid prophages are systematically co-oriented with the bacterial replication fork and display the host high frequency of polarized FtsK-orienting polar sequences motifs required for chromosome segregation. matS motifs are strongly avoided by prophages suggesting counter selection of motifs disrupting macrodomains. These results show how natural selection for seamless integration of prophages in the chromosome shapes the evolution of the bacterium and the phage. First, integration sites are highly conserved for many millions of years favoring lysogeny over the lytic cycle for temperate phages. Second, the global distribution of prophages is intimately associated with the chromosome structure and the patterns of gene expression. Third, the phage endures selection for DNA motifs that pertain exclusively to the biology of the prophage in the bacterial chromosome. Understanding prophage genetic adaptation sheds new lights on the coexistence of horizontal transfer and organized bacterial genomes.

Fabrication of PMN–PZT Transparent Ceramics by Two‐Stage Sintering

Highly optically transparent ceramics of (1−x) Pb ( Mg 1/3 Nb 2/3) O 3–x Pb ( Zr 0.53, Ti 0.47) O 3 ( PMN – PZT ) were fabricated by a two‐stage sintering method without La‐modification. The ceramics exhibited high optical transparency (64% at 1500 nm) for visible and near infrared wavelength. The ferroelectric domain and microstructure of PMN – PZT transparent ceramics prepared were also investigated. Fully dense microstructure was observed in all PMN – PZT transparent ceramic samples. Higher PMN containing compositions exhibited pyrochlore phase and relatively lower transparency for near infrared wavelengths. Fine and irregular fingerprint ferroelectric domains were observed in all PMN – PZT compositions except in the PMN – PZT 67/33 composition that had dense microstructure and pure perovskite phase. This PMN – PZT 67/33 composition exhibited the lowest transparency (40% at 1500 nm) with large‐scale macrodomain structure.

Gene clusters reflecting macrodomain structure respond to nucleoid perturbations

Focusing on the DNA-bridging nucleoid proteins Fis and H-NS, and integrating several independent experimental and bioinformatic data sources, we investigate the links between chromosomal spatial organization and global transcriptional regulation. By means of a novel multi-scale spatial aggregation analysis, we uncover the existence of contiguous clusters of nucleoid-perturbation sensitive genes along the genome, whose expression is affected by a combination of topological DNA state and nucleoid-shaping protein occupancy. The clusters correlate well with the macrodomain structure of the genome. The most significant of them lay symmetrically at the edges of the ter macrodomain and involve all of the flagellar and chemotaxis machinery, in addition to key regulators of biofilm formation, suggesting that the regulation of the physical state of the chromosome by the nucleoid proteins plays an important role in coordinating the transcriptional response leading to the switch between a motile and a biofilm lifestyle.

Evidence of 90° polarization switching in polycrystalline macro-domains of self-supported BaTiO3 films

It was shown previously that the self-supported films of nanocrystalline (30–80 nm) BaTiO3 spontaneously split into regions, within which the direction of spontaneous polarization of each grain is aligned as closely as possible to some average direction. These regions, called polycrystalline macro-domains, may be of two types: (1) those with out-of-plane polarization and (2) those with in-plane polarization. In-plane macro-domains exhibit in-plane optical anisotropy which can be monitored using cross-polarized transmitted light. This property was utilized in the current work to study the influence of temperature variation on macro-domains. According to the temperature dependence of the intensity of cross-polarized transmitted light, the films could be divided into three groups: (group 1) those films that did not exhibit strong changes in intensity; (group 2) those that exhibited a strong and abrupt change at a temperature between 20 and 120 °C; and (group 3) those that upon heating exhibited a gradual increase in the intensity of the cross-polarized transmitted light. The observed changes were reversible and consistent with a 90° rotation of the c-axis of some grains, which caused reversible changes in the macro-domain structure.

In situ TEM Investigations of the High‐Temperature Relaxor Ferroelectric BiScO3–Pb(Mg1/3Nb2/3)O3–PbTiO3 Ternary Solid Solution

Compositions near the morphotropic phase boundary (MPB) of the BiScO3–Pb(Mg1/3Nb2/3)O3–PbTiO3 ternary system showed high‐temperature relaxor properties (1 kHz) of Tmax∼250°C and a permittivity maximum of ∼16 000. Transmission electron microscopy (TEM) was used to investigate the nature of the microstructure under ambient conditions and with in situ heating studies for samples with different composition and electric field‐temperature histories. A mottled domain structure was observed with diffraction contrast TEM techniques and associated with frozen in polar micro‐domains. These observations are consistent with the low field permittivity temperature measurements made under various frequencies (100 Hz–100 kHz) with a freezing temperature, Tf∼160°C. Field‐cooled (FC) samples exhibited a macro‐domain structure similar to normal ferroelectric behavior. On heating the FC samples to approximately the Tmax and above, the domain contrast was no longer apparent. When subsequently cooled to room temperature conditions, a micro‐domain structure was observed, similar to the zero FC samples. The results are discussed with respect to permittivity measurements and phenomenological mechanisms contributing to the dispersion in the permittivity below the Curie maximum.

Disintegration of the Prolamellar Body Structure at High Concentrations of Hg2+

The effects of high concentrations of Hg (2+) (10 (-2) M and 10 (-3) M) were investigated on the ultrastructure and on the light-induced transformation of isolated prolamellar bodies (PLBs) of dark-grown wheat leaves. Our earlier work on wheat leaf homogenates ( , Plant Biology 6, 358 - 368) showed that, depending on the concentration, Hg (2+) reacts with protochlorophyllide, NADPH and the NADPH : protochlorophyllide oxidoreductase (POR, EC 1.3.1.33) enzyme and induces disaggregation of the macrodomain structure of this latter. Spectroscopic analyses confirmed that 15 min incubation with 10 (-2) M Hg (2+) at 4 degrees Celsius completely inhibited the activity of POR also in isolated PLBs. Ultrastructural investigations revealed the loosening of the PLB structure in the Hg (2+)-treated sample, i.e., intensive vesicle formation on the surface of the PLB membranes. The hexagonal geometry of the inner lattice was not disturbed, however, the unit cell size significantly increased. The disruption of the PLB membranes upon irradiation was studied after 40 min incubation with 10 (-3) M Hg (2+) at 4 degrees Celsius and a subsequent irradiation for 40 min at 20 degrees Celsius. Equimolar concentrations (10 (-3) M) of NADPH and Hg (2+) were added to the samples 10 min prior or after the addition of Hg (2+). Our results suggest that Hg (2+) accelerates the disruption of the PLB membranes and that NADPH can only partially prevent this process. These membrane transformations were similar to those observed in the initial steps of the Shibata shift of control samples.

Dielectric properties of Pb (Zn1/3Nb2/3)O3-PbZrO3-PbTiO3 solid solution near morphotropic phase boundary

The dielectric properties of Pb(Zn1/3Nb2/3) O3-PbZrO3−PbTiO3 (PZN-PZ-PT) system near the rhombohedral/tetragonal morphotropic phase boundary (MPB) are carefully studied in this paper. It is found that, for all samples, the curves around the temperatures of dielectric permittivity peak show the characteristics of diffuse phase transition. The change in PbZrO3/PbTiO3 ratio has much influence on the dielectric properties of the samples. The extent of diffuse phase transition increases with the increasing Zr/Ti ratio. The samples in rhombohedral region have typical diffuse phase transition in the temperature range measured. However, for the samples with tetragonal symmetry, a spontaneous normal ferroelectric-relaxor phase transition exists at temperature lower than that of permittivity peak. This normal ferroelectric-relaxor phase transition is confirmed by the experiment of thermally driven current. The analysis of TEM reveals that the samples in tetragonal region show a 90% macrodomain structure, while the samples in rhombohedral region have the configuration of microdomain structure.

Induced magnetic superstructure in the FeBO3: Mg weak ferromagnet

The domain structure of a FeBO3: Mg single crystal was studied with a polarizing microscope. It was found that application of a magnetic field along the hard axis in the basal plane of this weak ferromagnet gives rise, within a certain field-strength interval, to a magnetic superstructure observed against the background of the macrodomain structure of the sample. The magnetic superstructure is visually represented as a quasi-periodic system of bands oriented perpendicular to the applied field, with an alternating magneto-optic image contrast along an axis coinciding with the magnetic-field direction. The absence of sharp changes in the contrast of the magnetic superstructure image along this axis is explained as being due to the smooth variation of the sublattice magnetic-moment azimuth with spatial coordinates. The results obtained are discussed within the parameters of the instability of a uniform magnetic state of a system in the random field induced by a magnetic field.

Spatially resolved heat conduction in polar perhydrotriphenylene inclusion compounds studied by means of thermal waves

Scanning pyroelectric microscopy was applied to study the local thermal diffusivity in polar perhydrotriphenylene (PHTP) inclusion compounds. A thermal wave technique with special heat flow and pyroelectric detection principles was used to measure the longitudinal (K∥) and transversal (K⊥) thermal diffusivity of needle shaped crystals. As expected, we have found a higher thermal conductivity along the channel direction: K∥>K⊥. K∥ also showed a variation along the needle axis, the K∥ values near the capping faces being higher than in the center region. Based on these observations we suggest a relation between the longitudinal thermal conductivity and the local density of orientational defects of the dipolar guest molecules which reaches a maximum in the area around the seed. These findings are in agreement with previous pyroelectric studies, revealing a macrodomain structure and a spatially dependent pyroelectric activity for two different PHTP inclusion compounds.

Macrodomain structure related to the electric field-induced phase transition in Pb(Mg1/3Nb2/3)O3

Abstract The first-order electric field-induced phase transition in Pb(Mg1/3Nb2/3)O3, [PMN] single crystals, from the average cubic phase to a macroscopically polar 3m phase, was studied more specifically by the optical domain examinations with polarized light microscopy. Different aspects of induced macrodomain structure and phase boundary related to the establishment, decay and reversal of the induced polarization were presented. The mechanism of the induced phase transition was described, from the domain point of view, as a transformation from polar nanodomains to polar macrodomain states resulting in a trigonal distortion with symmetry breaking.

A crystallographic analysis of the macrodomain structure in Pb(Mg1/3Nb2/3)O3

A crystallographic analysis of the ferroelectric/ferroelastic domains and phase boundaries in thin platelets of Pb(Mg1/3Nb2/3)O3, associated with the electric-field-induced phase transition from the disordered cubic phase to the induced 3m phase, is reported. Calculations have been performed by taking into account the internal stresses and their relation to the unit cell parameters. The results have permitted us to interpret the experimentally observed polar macrodomain structure, phase boundary and switching of the induced polarization. A diagram connecting the possible domain types and the shapes of the m3m from or to 3m phase boundaries has been proposed. The role of the several domain types and features of their elastic matching have also been analysed.