Local Structural Stability Research Articles

A hybrid density functional study of silicon and phosphorus doped hexagonal boron nitride monolayer

We present a hybrid density functional study of silicon (Si) and phosphorus (P) doped hexagonal boron nitride (h-BN). The local geometry, electronic structure and thermodynamic stability of SiB, SiN, PB and PN are examined using hybrid Heyd-Scuseria- Ernzerhof (HSE) functional. The defect induced buckling and the local bond distances around the defect are sensitive to charge state modulation q = -2, -1, 0, +1 and +2. The +1 charge state is found to be the most energetically stable state and significantly reduces the buckling. Based on the charge state thermodynamic transition levels, we noted that the SiN, SiN and PB defects are too deep to be ionized, and can alter the optical properties of h-BN material.

The similar and different evolutionary trends of MATE family occurred between rice and Arabidopsis thaliana.

BackgroundMultidrug and toxic compound extrusion (MATE) transporter proteins are present in all organisms. Although the functions of some MATE gene family members have been studied in plants, few studies have investigated the gene expansion patterns, functional divergence, or the effects of positive selection.ResultsForty-five MATE genes from rice and 56 from Arabidopsis were identified and grouped into four subfamilies. MATE family genes have similar exon-intron structures in rice and Arabidopsis; MATE gene structures are conserved in each subfamily but differ among subfamilies. In both species, the MATE gene family has expanded mainly through tandem and segmental duplications. A transcriptome atlas showed considerable differences in expression among the genes, in terms of transcript abundance and expression patterns under normal growth conditions, indicating wide functional divergence in this family. In both rice and Arabidopsis, the MATE genes showed consistent functional divergence trends, with highly significant Type-I divergence in each subfamily, while Type-II divergence mainly occurred in subfamily III. The Type-II coefficients between rice subfamilies I/III, II/III, and IV/III were all significantly greater than zero, while only the Type-II coefficient between Arabidopsis IV/III subfamilies was significantly greater than zero.A site-specific model analysis indicated that MATE genes have relatively conserved evolutionary trends. A branch-site model suggested that the extent of positive selection on each subfamily of rice and Arabidopsis was different: subfamily II of Arabidopsis showed higher positive selection than other subfamilies, whereas in rice, positive selection was highest in subfamily III. In addition, the analyses identified 18 rice sites and 7 Arabidopsis sites that were responsible for positive selection and for Type-I and Type-II functional divergence; there were no common sites between rice and Arabidopsis. Five coevolving amino acid sites were identified in rice and three in Arabidopsis; these sites might have important roles in maintaining local structural stability and protein functional domains.ConclusionsWe demonstrate that the MATE gene family expanded through tandem and segmental duplication in both rice and Arabidopsis. Overall, the results of our analyses contribute to improved understanding of the molecular evolution and functions of the MATE gene family in plants.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0895-0) contains supplementary material, which is available to authorized users.

An atomic-scale insight into the effects of hydrogen microalloying on the glass-forming ability and ductility of Zr-based bulk metallic glasses

Notable improvements in both the glass-forming ability (GFA) and ambient temperature compressive ductility of Zr-based metallic glasses due to hydrogen microalloying have been reported by Granata et al. [1]. These two aspects of amorphous materials are considered to be mutually opposing properties in a metallic glass-forming system, usually explained via structural short-range order, local symmetry, structural free-volume and bonding character. To fundamentally understand why hydrogen simultaneously enhances GFA and ductility, ab initio molecular dynamic simulations were carried out on a Zr64Cu22Al12 alloy to assess how this element affects the local atomic configuration, electronic structure, chemical bonding and atomic transport processes. It is revealed that, while the addition of 1.5at.% H decreases the icosahedral order of the supercooled liquid over the entire temperature range studied, it decreases the diffusivity of the metallic constituents over the temperature range where heterogeneous nucleation is expected to occur. In this tradeoff between local structural stability and depressed crystal nucleation dynamics, the latter dominates in the H-containing alloy and the capacity for glass formation is enhanced. In addition, H was found to increase iconicity of the base glassy alloy, promote heterogeneity in the local structure and increase metallicity. In the competition between these opposing tendencies of chemical bonding and local structure to determine mechanical properties, the latter prevails and explains the experimentally-observed improvement in compressive ductility.

ZrO2-Supported Fe2O3 for Chemical-Looping-Based Hydrogen Production: Effect of pH on Its Structure and Performance As Probed by X-ray Absorption Spectroscopy and Electrical Conductivity Measurements

Chemical looping is a promising process to produce high purity H2 while simultaneously capturing CO2. The key requirement for this process is the availability of oxygen carriers that possess a high cyclic redox stability, resistance to carbon deposition, and thermal sintering. In this study, ZrO2-supported Fe2O3-based oxygen carriers were developed using a coprecipitation technique. We assess in detail the influence of the key synthesis parameter, i.e., the pH value at which the precipitation was performed, on the morphological properties, chemical composition, local structure, and cyclic redox stability. The performance of the new oxygen carriers was compared to unsupported Fe2O3 and Al2O3-supported Fe2O3. A higher degree of disorder in the local structure of oxygen carriers precipitated at low pH values was confirmed by X-ray absorption spectroscopy (XAS) measurements. Electrical conductivity measurements showed that supporting Fe2O3 on ZrO2 lowered significantly the activation energy for charge transpo...

Concurrent Increases and Decreases in Local Stability and Conformational Heterogeneity in Cu, Zn Superoxide Dismutase Variants Revealed by Temperature-Dependence of Amide Chemical Shifts.

The chemical shifts of backbone amide protons in proteins are sensitive reporters of local structural stability and conformational heterogeneity, which can be determined from their readily measured linear and nonlinear temperature-dependences, respectively. Here we report analyses of amide proton temperature-dependences for native dimeric Cu, Zn superoxide dismutase (holo pWT SOD1) and structurally diverse mutant SOD1s associated with amyotrophic lateral sclerosis (ALS). Holo pWT SOD1 loses structure with temperature first at its periphery and, while having extremely high global stability, nevertheless exhibits extensive conformational heterogeneity, with ∼1 in 5 residues showing evidence for population of low energy alternative states. The holo G93A and E100G ALS mutants have moderately decreased global stability, whereas V148I is slightly stabilized. Comparison of the holo mutants as well as the marginally stable immature monomeric unmetalated and disulfide-reduced (apo(2SH)) pWT with holo pWT shows that changes in the local structural stability of individual amides vary greatly, with average changes corresponding to differences in global protein stability measured by differential scanning calorimetry. Mutants also exhibit altered conformational heterogeneity compared to pWT. Strikingly, substantial increases as well as decreases in local stability and conformational heterogeneity occur, in particular upon maturation and for G93A. Thus, the temperature-dependence of amide shifts for SOD1 variants is a rich source of information on the location and extent of perturbation of structure upon covalent changes and ligand binding. The implications for potential mechanisms of toxic misfolding of SOD1 in disease and for general aspects of protein energetics, including entropy-enthalpy compensation, are discussed.

Prediction of the structures of the plant-specific regions of vascular plant cellulose synthases and correlated functional analysis

Seed plants express cellulose synthase (CESA) protein isoforms with non-redundant functions, but how the isoforms function differently is unknown. Compared to bacterial cellulose synthases, CESAs have two insertions in the large cytosolic loop: the relatively well-conserved Plant Conserved Region (P-CR) and a Class Specific Region (CSR) that varies between CESAs. Absent any atomic structure of a plant CESA, we used ab initio protein structure prediction and molecular modeling to explore how these plant-specific regions may modulate CESA function. We modeled P-CR and CSR peptides from Arabidopsis thaliana CESAs representing the six clades of seed plant CESAs. As expected, the predicted wild type P-CR structures were similar. Modeling of the mutant P-CR of Atcesa8 R362K (fra6) suggested that changes in local structural stability and surface electrostatics may cause the mutant phenotype. Among CSRs within CESAs required for primary wall cellulose synthesis, the amino sequence and the modeled arrangement of helices was most similar in AtCESA1 and AtCESA3. Genetic complementation of known Arabidopsis mutants showed that the CSRs of AtCESA1 and AtCESA3 can function interchangeably in vivo. Analysis of protein surface electrostatics led to ideas about how the surface charges on CSRs may mediate protein–protein interactions. Refined modeling of the P-CR and CSR regions of GhCESA1 from cotton modified their tertiary structures, spatial relationships to the catalytic domain, and preliminary predictions about CESA oligomer formation. Cumulatively, the results provide structural clues about the function of plant-specific regions of CESA.

Stable local structure in LSMCO system and its relationship with pseudogap

Pseudogap is a unique property of high-[Formula: see text] superconductors. However, it was also found that there is a similar pseudogap in giant magnetoresistive La–Sr–Mn–O materials, which are not superconductors. In our previous research, we suggested that the origin of the pseudogap is correlated with the stability of [Formula: see text] plane. We call it a steady “fixed triangle” local structure. If our assumption is correct, it will be expected to find a similar stable local structure in the La–Sr–Mn–O system, which is similar to the [Formula: see text] plane in cuprates. We synthesized Co-doped [Formula: see text] (LSMCO) materials and investigated them. Based on the detailed analysis of the crystalline structure, it is found that there indeed exists a stable local triangles in [Formula: see text] plane. Comparing this similarity with the fixed triangles in the cuprate superconductors, it shows that the origin of the pseudogap may possibly be correlated with the stability of the local structure.

Structure Stabilization by Mixed Anions in Oxyfluoride Cathodes for High-Energy Lithium Batteries.

Mixed-anion oxyfluorides (i.e., FeOxF2-x) are an appealing alternative to pure fluorides as high-capacity cathodes in lithium batteries, with enhanced cyclability via oxygen substitution. However, it is still unclear how the mixed anions impact the local phase transformation and structural stability of oxyfluorides during cycling due to the complexity of electrochemical reactions, involving both lithium intercalation and conversion. Herein, we investigated the local chemical and structural ordering in FeO0.7F1.3 at length scales spanning from single particles to the bulk electrode, via a combination of electron spectrum-imaging, magnetization, electrochemistry, and synchrotron X-ray measurements. The FeO0.7F1.3 nanoparticles retain a FeF2-like rutile structure but chemically heterogeneous, with an F-rich core covered by thin O-rich shell. Upon lithiation the O-rich rutile phase is transformed into Li-Fe-O(-F) rocksalt that has high lattice coherency with converted metallic Fe, a feature that may facilitate the local electronic and ionic transport. The O-rich rocksalt is highly stable over lithiation/delithiation and thus advantageous to maintain the integrity of the particle, and due to its predominant distribution on the surface, it is expected to prevent the catalytic interaction of Fe with electrolyte. Our findings of the structural origin of cycling stability in oxyfluorides may provide insights into developing viable high-energy electrodes for lithium batteries.

Ab initio simulation: The correlation between the local melt structure and segregation behavior of Fe, V, Ti and Si in liquid Al

In this study, the elements Fe, Si, V and Ti, which exhibit typical segregation behavior in Al, were chosen as solute atoms to be analyzed. The structure of molten Al, the local structure around solute atoms and the diffusion of the solute atoms were studied using ab initio molecular dynamics simulations. The results showed that the minimum addition of a solute (1 atom) does not significantly influence the structure of liquid Al as a whole. However, the local structure around foreign atoms varies dramatically for the different solute species. The local structure around Fe was the most compact and stable among the four types of solute atoms, leading to its lower diffusion coefficient. Conversely, the local structure around Si was the most relaxed structure. For the transition metal elements (Fe, V and Ti), there was a correlation between the equilibrium partition coefficients and local structures around these solutes in the molten Al. This simple relationship between the solute atmosphere, chemistry and temperature, requires further study. In summary, the close packing and stable local structure around the solute atoms can affect both their diffusion and segregation behavior in the melt. In addition, we suggest that more transition metal elements should be investigated to corroborate the results of this study.

Key points to consider when studying RNA remodeling by proteins.

Cellular RNAs depend on proteins for efficient folding to specific functional structures and for transitions between functional structures. This dependence arises from intrinsic properties of RNA structure. Specifically, RNAs possess stable local structure, largely in the form of helices, and they have abundant opportunities to form alternative helices and tertiary contacts and therefore to populate alternative structures. Proteins with RNA chaperone activity, either ATP-dependent or ATP-independent, can promote structural transitions by interacting with single-stranded RNA (ssRNA) to compete away partner interactions and then release ssRNA so that it can form new interactions. In this chapter we review the basic properties of RNA and the proteins that function as chaperones and remodelers. We then use these properties as a foundation to explore key points for the design and interpretation of experiments that probe RNA rearrangements and their acceleration by proteins.

On local structural stability of one-dimensional shocks in radiation hydrodynamics

In this paper, we are concerned with the local structural stability of one-dimensional shock waves in radiation hydrodynamics described by the isentropic Euler-Boltzmann equations. Even though in this radiation hydrodynamics model, the radiative effects can be understood as source terms to the isentropic Euler equations of hydrodynamics, in general the radiation field has singularities propagated in an angular domain issuing from the initial point across which the density is discontinuous. This is the major difficulty in the stability analysis of shocks. Under certain assumptions on the radiation parameters, we show there exists a local weak solution to the initial value problem of the one dimensional Euler-Boltzmann equations, in which the radiation intensity is continuous, while the density and velocity are piecewise Lipschitz continuous with a strong discontinuity representing the shock-front. The existence of such a solution indicates that shock waves are structurally stable, at least local in time, in radiation hydrodynamics.

First-Principles Study of Structure, Vibrational, and Elastic Properties of Stoichiometric and Calcium-Deficient Hydroxyapatite

Hydroxyapatite (HAp), a primary constituent of human bone, is usually nonstoichiometric with varying Ca/P molar ratios, with the well-known fact that Ca deficiency can cause marked reductions in its mechanical properties. To gain insights into the mechanism of this degradation, we employ first-principles calculations based on density functional theory and determine the effects of Ca deficiency on structure, vibrational, and elastic properties of HAp. Our simulation results confirm a considerable reduction in the elastic constants of HAp due to Ca deficiency, which was experimentally reported earlier. Stress-induced transformation of the Ca-deficient defected structure into a metastable state upon the application of stress could be a reason for this. Local structural stability of HAp and Ca-deficient HAp structures is assessed with full phonon dispersion studies. Further, specific signatures in the computed vibrational spectra for Ca deficiency in HAp can be utilized in experimental characterization of different types of defected HAp.

Magnetic and local structure analysis for Fe/Cr multilayer films

XMCD of Fe L2,3-edge and EXAFS of Fe and Cr K-edge measurements were carried out for Fe/Cr multilayer films which were deposited with several conditions. Magnetic moment of Fe was weakly depending on the film thickness. Relation between the disorder of the local structure and the coercivity was investigated. From EXAFS Debye-Waller analysis, it was found that the thinner films show the smaller Debye-Waller factor, or the more stable local structure. The stable local structure presents large coercivity.

Investigating the Conformational Dynamics of DNA with Lesions through Fluorescence-Based Technniques and Computer Simulations

Accurate propagation of genetic material is essential for life. Yet, DNA is constantly being bombarded by various external factors resulting in millions of lesions per day. Lesions include modified bases, backbone nicks, and single stranded gaps. The presence of such lesions could lead to differences in the conformational dynamics of DNA, suggesting a potential mechanism for DNA repair enzymes to locate damages. To investigate how the presence of lesions affects the conformational dynamics of DNA, Forster resonance energy transfer (FRET) was used. The DNA samples contained internally modified Cy3/Cy5 dyes. Each DNA sample was designed to have a different lesion such as a nick or abasic site. Higher FRET efficiencies were expected if the DNA was more dynamic. However, only small differences in the FRET efficiency were found. Therefore, time-resolved anisotropy was used in combination with FRET, where faster acceptor emission depolarization is indicative of more dynamic DNA. To gain an understanding of the atomistic details, molecular dynamics (MD) simulations were performed and MD trajectories analyzed in terms of global and local structural quantities such as bending angle and helicoidal parameters. Both experiments and simulations showed that nicked DNA behaves similarly to intact DNA. However, the introduction of a single stranded gap of nucleotides increases the dynamic behavior of the DNA. While a nick alone did not change the conformational dynamics of the DNA, the introduction of a mismatch base or abasic site increased conformational dynamics by weakening the hydrogen bonding and stacking interactions around the nick. The combination of experimental and computational results suggests that the disruption of local structural stability leads to global conformational changes.

Cerium Substitution in Yttrium Iron Garnet: Valence State, Structure, and Energetics

The garnet structure is a promising nuclear waste form because it can accommodate various actinide elements. Yttrium iron garnet, Y3Fe5O12 (YIG), is a model composition for such substitutions. Since cerium (Ce) can be considered an analogue of actinide elements such as thorium (Th), plutonium (Pu), and uranium (U), studying the local structure and thermodynamic stability of Ce-substituted YIG (Ce:YIG) can provide insights into the structural and energetic aspects of large ion substitution in garnets. Single phases of YIG with Ce substitution up to 20 mol % (Y3–xCexFe5O12 with 0 ≤ x ≤ 0.2) were synthesized through a citrate–nitrate combustion method. The oxidation state of Ce was examined by X-ray absorption near edge structure spectroscopy (XANES); the oxidation state and site occupancy of iron (Fe) as a function of Ce loading also was monitored by 57Fe–Mossbauer spectroscopy. These measurements establish that Ce is predominantly in the trivalent state at low substitution levels, while a mixture of trival...

An alignment-free fingerprint bio-cryptosystem based on modified Voronoi neighbor structures

Bio-cryptography is an emerging security technology which combines cryptography with biometrics. A good bio-cryptosystem is required to protect the privacy of the relevant biometric data as well as achieving high recognition accuracy. Fingerprints have been widely used in bio-cryptosystem design. However, fingerprint uncertainty caused by distortion and rotation during the image capturing process makes it difficult to achieve a high recognition rate in most bio-cryptographic systems. Moreover, most existing bio-cryptosystems rely on the accurate detection of singular points for fingerprint image pre-alignment, which is very hard to achieve, and the image rotation transformation during the alignment process can cause significant singular point deviation and minutiae changes. In this paper, by taking full advantage of local Voronoi neighbor structures (VNSs), e.g. local structural stability and distortion insensitivity, we propose an alignment-free bio-cryptosystem based on fixed-length bit-string representations extracted from modified VNSs, which are rotation- and translation-invariant and distortion robust. The proposed alignment-free bio-cryptosystem is able to provide strong security while achieving good recognition performance. Experimental results in comparison with most existing alignment-free bio-cryptosystems using the publicly-available databases show the validity of the proposed scheme.

Effects of Oscillatory Flow on Fertilization in the Green Sea Urchin Strongylocentrotus droebachiensis

Broadcast spawning invertebrates that live in shallow, high-energy coastal habitats are subjected to oscillatory water motion that creates unsteady flow fields above the surface of animals. The frequency of the oscillatory fluctuations is driven by the wave period, which will influence the stability of local flow structures and may affect fertilization processes. Using an oscillatory water tunnel, we quantified the percentage of eggs fertilized on or near spawning green sea urchins, Strongylocentrotus droebachiensis. Eggs were sampled in the water column, wake eddy, substratum and aboral surface under a range of different periods (T = 4.5 – 12.7 s) and velocities of oscillatory flow. The root-mean-square wave velocity (rms(u w)) was a good predictor of fertilization in oscillatory flow, although the root-mean-square of total velocity (rms(u)), which incorporates all the components of flow (current, wave and turbulence), also provided significant predictions. The percentage of eggs fertilized varied between 50 – 85% at low flows (rms(u w) <0.02 m s−1), depending on the location sampled, but declined to below 10% for most locations at higher rms(u w). The water column was an important location for fertilization with a relative contribution greater than that of the aboral surface, especially at medium and high rms(u w) categories. We conclude that gametes can be successfully fertilized on or near the parent under a range of oscillatory flow conditions.

Genome-Wide Analysis of Selective Constraints on High Stability Regions of mRNA Reveals Multiple Compensatory Mutations in Escherichia coli

Message RNA (mRNA) carries a large number of local secondary structures, with structural stability to participate in the regulations of gene expression. A worthy question is how the local structural stability is maintained under the constraint that multiple selective pressures are imposed on mRNA local regions. Here, we performed the first genome-wide study of natural selection operating on high structural stability regions (HSRs) of mRNAs in Escherichia coli. We found that HSR tends to adjust the folded conformation to reduce the harm of mutations, showing a high level of mutational robustness. Moreover, guanine preference in HSR was observed, supporting the hypothesis that the selective constraint for high structural stability may partly account for the high percentage of G content in Escherichia coli genome. Notably, we found a substantially reduced synonymous substitution rate in HSRs compared with that in their adjacent regions. Surprisingly and interestingly, the non-key sites in HSRs, which have slight effect on structural stability, have synonymous substitution rate equivalent to background regions. To explain this result, we identified compensatory mutations in HSRs based on structural stability, and found that a considerable number of synonymous mutations occur to restore the structural stability decreased heavily by the mutations on key sites. Overall, these results suggest a significant role of local structural stability as a selective force operating on mRNA, which furthers our understanding of the constraints imposed on protein-coding RNAs.

Fine Modulation of the Respiratory Syncytial Virus M2–1 Protein Quaternary Structure by Reversible Zinc Removal from Its Cys3-His1 Motif

Human respiratory syncytial virus (hRSV) is a worldwide distributed pathogen that causes respiratory disease mostly in infants and the elderly. The M2-1 protein of hRSV functions as a transcription antiterminator and partakes in virus particle budding. It is present only in Pneumovirinae, namely, Pneumovirus (RSV) and Metapneumovirus, making it an interesting target for specific antivirals. hRSV M2-1 is a tight tetramer bearing a Cys3-His1 zinc-binding motif, present in Ebola VP30 protein and some eukaryotic proteins, whose integrity was shown to be essential for protein function but without a biochemical mechanistic basis. We showed that removal of the zinc atom causes dissociation to a monomeric apo-M2-1 species. Surprisingly, the secondary structure and stability of the apo-monomer is indistinguishable from that of the M2-1 tetramer. Dissociation reported by a highly sensitive tryptophan residue is much increased at pH 5.0 compared to pH 7.0, suggesting a histidine protonation cooperating in zinc removal. The monomeric apo form binds RNA at least as well as the tetramer, and this interaction is outcompeted by the phosphoprotein P, the RNA polymerase cofactor. The role of zinc goes beyond stabilization of local structure, finely tuning dissociation to a fully folded and binding competent monomer. Removal of zinc is equivalent to the disruption of the motif by mutation, only that the former is potentially reversible in the cellular context. Thus, this process could be triggered by a natural chelator such as glutathione or thioneins, where reversibility strongly suggests a modulatory role in the participation of M2-1 in the assembly of the polymerase complex or in virion budding.

Historical crane on the redesigned original trestle bridge as a memorial of Gdansk Shipyard

The paper includes selected aspects of the study, whose goal is to hold the historical crane 642-24 in its current location after the modification of trestle bridge static scheme. The scope of the paper includes the assessment of current technical condition of the object, a presentation of FEM analyses, a description of the assumed load cases, results of the static calculations, checking the effort of construction elements, global and local structure stability and its dynamic characteristics.