Добірка наукової літератури з теми "Non-canonical crack"

. Scientific hypothesis on moistening shrinkage mechanism for cement stone and concrete has been assumed as a basis for the present paper. Physical ideas on a mechanism for cracks volume increment in a concrete model presented as two-level structure have been accepted as a theoretical basis for a calculation method of crack resistance during capillary shrinkage. These ideas are the following: a matrix of hardening cement stone with inclusions and emptiness of various forms (cracks) as result of influences that change an intense deformed state in a point and a volume. The following assumptions have been accepted while making a theoretical justification for a calculation method of shrinkable concrete crack resistance. Following this methodology approaches of fracture mechanics according to a generalized criterion have been applied in the paper. Concrete is considered as an elastic quasi-homogeneous two-component medium which consists of the following parts:a) constructive part: a matrix – a cement stone with structural elements of crushed stone, sand; b) destructive part: emptiness – capillaries cracks and pores (cavities with initial cracks in walls). Emptiness in a matrix and contact zones are presented by a coordinated five-level system in the form and sizes which are multiple to a diameter due to impacts while reaching critical sizes. These critical sizes make it possible to pass from one level into another one according to the following scheme: size stabilization – accumulation delocalization – critical concentration in single volume – transition to the following level. Process of cracks formation and their growth are considered as a result of non-power influences on the basis of crack theory principles from a condition that fields of deformation and tension creating schemes of a normal separation and shift occur in the top part of each crack at its level in the initial concrete volume. Ксij(t) parameter as algebraic amount of critical values Kij in the whole system of all levels of cracks filling canonical volume up to critical concentration has been accepted as a generalized constant of property for concrete crack resistance in time, its resistance to formation, accumulation in volumes of micro-cracks and formation of trunk cracks with critical values. External temperature, moistening long influences create fields of tension in the top parts of cracks. Concrete destruction processes due to cracks are considered as generalized deformedintensed state in some initial volume having physical features which are inherent to a composite with strength and deformative properties. It is possible to realize analytical calculations for assessment of tension and crack resistance of concrete at early age on the basis of a generalized criterion in terms of stress intensity factor due to modern experimental data on capillary pressure value (70 kPa in 180 min after concrete placing). The developed algorithm of calculation allows to consider factors influencing on capillary pressure: type of cement, modifiers and mineral additives, concrete curing conditions.

Abstract NMR off-resonance R1ρ relaxation dispersion measurements on base carbon and nitrogen nuclei have revealed that wobble G·T/U mismatches in DNA and RNA duplexes exist in dynamic equilibrium with short-lived, low-abundance, and mutagenic Watson–Crick-like conformations. As Watson–Crick-like G·T mismatches have base pairing geometries similar to Watson–Crick base pairs, we hypothesized that they would mimic Watson–Crick base pairs with respect to the sugar-backbone conformation as well. Using off-resonance R1ρ measurements targeting the sugar C3′ and C4′ nuclei, a structure survey, and molecular dynamics simulations, we show that wobble G·T mismatches adopt sugar-backbone conformations that deviate from the canonical Watson–Crick conformation and that transitions toward tautomeric and anionic Watson–Crick-like G·T mismatches restore the canonical Watson–Crick sugar-backbone. These measurements also reveal kinetic isotope effects for tautomerization in D2O versus H2O, which provide experimental evidence in support of a transition state involving proton transfer. The results provide additional evidence in support of mutagenic Watson–Crick-like G·T mismatches, help rule out alternative inverted wobble conformations in the case of anionic G·T−, and also establish sugar carbons as new non-exchangeable probes of this exchange process.

As you know, the secondary structure of RNA molecules, unlike DNA, in addition to canonical or Watson-Crick pairs, non-canonical G-U pairs, this is guanine - uracil. The last pairs were established experimentally by X-ray diffraction analysis and are still a mystery to researchers. The fact is that such pairs are 5-10 times energetically weaker than the canonical pairs A-U, C-G. The question arises: why are such pairs needed? The study was carried out in the framework of the strict mathematical analogy established earlier by the authors of some cases of genetic overlaps and stems of the secondary structure of messenger RNAs. In this work, it is shown that due to the non-canonical G-U pair, using the new ambiguities found, it is possible to substantially “regulate” the stem free energy (even for small stems) - the most important biochemical characteristic. It turned out that the discovered effect for G-U pairs significantly exceeds a similar effect for canonical pairs A-U, C-G.

Abstract Canonical eukaryotic mRNA translation requires 5′cap recognition by initiation factor 4E (eIF4E). In contrast, many positive-strand RNA virus genomes lack a 5′cap and promote translation by non-canonical mechanisms. Among plant viruses, PTEs are a major class of cap-independent translation enhancers located in/near the 3′UTR that recruit eIF4E to greatly enhance viral translation. Previous work proposed a single form of PTE characterized by a Y-shaped secondary structure with two terminal stem-loops (SL1 and SL2) atop a supporting stem containing a large, G-rich asymmetric loop that forms an essential pseudoknot (PK) involving C/U residues located between SL1 and SL2. We found that PTEs with less than three consecutive cytidylates available for PK formation have an upstream stem-loop that forms a kissing loop interaction with the apical loop of SL2, important for formation/stabilization of PK. PKs found in both subclasses of PTE assume a specific conformation with a hyperreactive guanylate (G*) in SHAPE structure probing, previously found critical for binding eIF4E. While PTE PKs were proposed to be formed by Watson–Crick base-pairing, alternative chemical probing and 3D modeling indicate that the Watson–Crick faces of G* and an adjacent guanylate have high solvent accessibilities. Thus, PTE PKs are likely composed primarily of non-canonical interactions.

1. INTRODUCTION 3992. DEFINITIONS 4013. CIS BASEPAIRS 4103.1 Cis Watson–Crick/Watson–Crick 4103.2 Wobble pairings 4113.3 Cis Watson–Crick/Hoogsteen pairings 4163.4 Bifurcated pairings 4173.5 Cis open and water-inserted 4214. TRANS BASEPAIRS 4234.1 Trans Watson–Crick/Watson–Crick 4234.2 Trans wobble pairs 4244.3 Trans Watson–Crick/Hoogsteen pairs 4244.4 Trans Hoogsteen/Hoogsteen pairs 4304.5 Trans bifurcated pairings 4325. SHALLOW-GROOVE PAIRINGS 4325.1 Hoogsteen/Shallow-groove pairs 4335.2 Watson–Crick/Shallow-groove pairings 4385.3 Shallow-groove/Shallow-groove pairings 4406. SIDE-BY-SIDE BASES 4467. DEFINING A LIBRARY OF ISOSTERIC PAIRINGS 4468. CONCLUSIONS 4519. ACKNOWLEDGEMENTS 45210. REFERENCES 452RNA molecules fold into a bewildering variety of complex 3D structures. Almost every new RNA structure obtained at high resolution reveals new, unanticipated structural motifs, which we are rarely able to predict at the current stage of our theoretical understanding. Even at the most basic level of specific RNA interactions – base-to-base pairing – new interactions continue to be uncovered as new structures appear. Compilations of possible non-canonical base-pairing geometries have been presented in previous reviews and monographs (Saenger, 1984; Tinoco, 1993). In these compilations, the guiding principle applied was the optimization of hydrogen-bonding. All possible pairs with two standard H-bonds were presented and these were organized according to symmetry or base type. However, many of the features of RNA base-pairing interactions that have been revealed by high-resolution crystallographic analysis could not have been anticipated and, therefore were not incorporated into these compilations. These will be described and classified in the present review. A recently presented approach for inferring basepair geometry from patterns of sequence variation (Gautheret & Gutell, 1997) relied on the 1984 compilation of basepairs (Saenger, 1984), and was extended to include all possible single H-bond combinations not subject to steric clashes. Another recent review may be consulted for a discussion of the NMR spectroscopy and thermodynamic effects of non-canonical (‘mismatched’) RNA basepairs on duplex stability (Limmer, 1997).

AbstractThe article traces the interpretation of the flood story in children's literature, from the apparently literal versions, in which imaginative reinterpretation is transferred to the illustrations, to the non-verbal crowded scenes of Peter Spier, the Midrashic retellings of Scholem Asch and Marc Gellman, feminist readings, like those of Bach and Exum, Madeleine L'Engle's teen novel, and versions which stress the annihilatory implications, including Janisch and Zwerger's Noah's Ark. It concludes with a discussion of Ruth Kerr's How Mrs. Monkey Missed the Ark, in which the canonical text is virtually eliminated, and only appears through the cracks.

Ribonucleic acids (RNA) and RNA−protein complexes are essential components of biological information transfer, catalytic processes and are associated with regulatory functions. This broad range of biological functions is paralleled at the conformational level by a large number of non-canonical structural elements or sequences with non-standard backbone conformations, e.g., loops, bulges, pseudo-knots and complex tertiary folds. NMR spectroscopy has evolved to a powerful tool for the determination of ribonucleic acid structures of up to 20 kDa. Uniform or selective stable isotope labelling aids in solving assignment problems arising from the inherently limited chemical shift dispersion and overlap of resonances for larger nucleotide sequences. Recent developments of multi-dimensional heteronuclear NMR pulse sequences allow e.g., to directly observe the hydrogen bonding pattern of canonical Watson−Crick base pairs as well as of unusual types of base pairs, thereby opening up a fast access to secondary structure screening of RNA. Detailed conformational descriptions are obtained using conventional NOE andJcoupling-derived data, nowadays supplemented by information from residual dipolar couplings. The latter method also provides a new means for the probing of dynamical features of ribonucleic acids.

Polynucleotide chains obeying Watson-Crick pairing are apt to form non-canonical complexes such as triple-helical nucleic acids. From early characterization in vitro, their occurrence in vivo has been strengthened by increasing evidence, although most remain circumstantial particularly for triplex DNA. Here, different approaches were employed to specify triple-stranded DNA sequences in the Drosophila melanogaster chromosomes. Antibodies to triplex nucleic acids, previously characterized, bind to centromeric regions of mitotic chromosomes and also to the polytene section 59E of mutant strains carrying the brown dominant allele, indicating that AAGAG tandem satellite repeats are triplex-forming sequences. The satellite probe hybridized to AAGAG-containing regions omitting chromosomal DNA denaturation, as expected, for the intra-molecular triplex DNA formation model in which single-stranded DNA coexists with triplexes. In addition, Thiazole Orange, previously described as capable of reproducing results obtained by antibodies to triple-helical DNA, binds to AAGAG repeats in situ thus validating both detection methods. Unusual phenotype and nuclear structure exhibited by Drosophila correlate with the non-canonical conformation of tandem satellite arrays. From the approaches that lead to the identification of triple-helical DNA in chromosomes, facilities particularly provided by Thiazole Orange use may broaden the investigation on the occurrence of triplex DNA in eukaryotic genomes.

Abstract Human telomeres are composed of GGGTTA repeats and interspersed with variant repeats. The GGGCTA variant motif was identified in the proximal regions of human telomeres about 10 years ago and was shown to display a length-dependent instability. In parallel, a structural study showed that four GGGCTA repeats folded into a non-canonical G-quadruplex (G4) comprising a Watson–Crick GCGC tetrad. It was proposed that this non-canonical G4 might be an additional obstacle for telomere replication. In the present study, we demonstrate that longer GGGCTA arrays fold into G4 and into hairpins. We also demonstrate that replication protein A (RPA) efficiently binds to GGGCTA repeats structured into G4 but poorly binds to GGGCTA repeats structured into hairpins. Our results (along with results obtained with a more stable variant motif) suggest that GGGCTA hairpins are at the origin of GGGCTA length-dependent instability. They also suggest, as working hypothesis, that failure of efficient binding of RPA to GGGCTA structured into hairpins might be involved in the mechanism of GGGCTA array instability. On the basis of our present and past studies about telomeric G4 and their interaction with RPA, we propose an original point of view about telomeric G4 and the evolution of telomeric motifs.

Дисертаційна робота присвячена розробці чисельних і аналітичних методів розрахунку коефіцієнта інтенсивності напружень, (КІН) для некласичних проблем механіки руйнування, зокрема, для тріщин складної форми та для тріщин в тонкостінних конструкціях з врахуванням геометричної нелінійності, (ГН). Представлена модифікація методу Вільямса, що враховує затухаючі на нескінченності члени. Досліджено межі та надані рекомендації щодо застосування даного методу. Розроблено аналітичний метод розрахунку КІН в трубах з довгими осьовими поверхневими тріщинами з врахуванням ГН в залежності від внутрішнього тиску. Наведено результати верифікації величин КІН з отриманими в роботі чисельними розв’язками МСЕ. Побудовані чисельні моделі для розрахунку КІН та розкриття берегів тріщин в ГН постановці для наскрізних тріщин в залежності від змінної величини осьової сили. Побудована апроксимаційна формула, що описує вплив ГН ефекту для узагальненої осьової сили та безрозмірної довжини тріщини. Показана значимість ефекту для реальних лабораторних експериментів. Розроблено універсальний напіваналітичний метод розв’язку інтегро-диференційного рівняння теорії пружності для плоских тріщин нормального відриву довільної форми. Для перевірки аналітичних результатів побудовані чисельні моделі МСЕ для тріщин різної форми, наприклад, для прямокутної, внутрішньої півелітичної тріщини, тощо, та проведено співставлення результатів. Проведені практичні розрахунки КІН в часі для елементів конструкцій АЕС для різних сценаріїв протікання аварійних ситуацій. Створено ряд імітаційних моделей з вбудованою тріщиною, для якої розрахунки КІН проводилися методами нелінійної механіки руйнування. Для тріщин, що проходять через наплавлений матеріал, де відбувається стрибки напружень, обґрунтовано застосування методу функцій впливу, для чого розроблено аналітико-чисельну процедуру, що використовує частково неперервні базові закони навантаження.
The dissertation is dedicated to the development of numerical and analytical methods for calculating the stress intensity factor (SIF) for nonclassical problems of fracture mechanics, in particular, for cracks of complex shape and for cracks in thin structures with taking into account geometric nonlinearity (GN) and their applications in various industries, in particular, for nuclear power plants, for calculation of the elements of the reactor unit. A modification of Williams's method is presented, which describes the stress state in the crack tip. For modification of the classical approach in the considered method the additional members were presented, which are infinite in the crack tip, but attenuate at infinity. The main idea of the method is to divide the whole area of the body into two separate parts – internal one, which embraces the tip of the crack, and the external one. In the inner area, only the classic Williams functions are used, and in the outer area both the classical members and additional ones are used. At the boundary between the selected subdomains, the conjugation conditions are to be fulfilled, the essence of which is to equalize here the stresses and displacements. The very high efficiency of this method is shown for bodies that have the shape of a circle, or are infinite, where almost exact values (up to 6-7 digits) are achieved when using no more than 12-16 members of the expansion. However, for a very elongated rectangular body the method gives much worse results, and the error can reach up to 2%. The practical significance of the proposed approach consists in the obtaining the simple and effective tool for testing the capabilities of commercial packages for calculating the parameters of fracture mechanics, which, as we know, do not always provide the correct results for case when load is applied on the crack surfaces. A thin-walled pipe with a long surface crack is considered. The pipe, surface of which may contain the initial deviation form ideal circle, is loaded by inner pressure. In first time the problem of determining the SIF was considered in a geometrically nonlinear formulation, when changes in the geometry of the body in the process of deformation are accounted for linear material behavior. Based on the Chen-Finnie method, which considers the crack as concentrated compliance, and on original solution for geometrically nonlinear behavior of curved initially distorted beam, the compact analytical formulas are obtained, which gives the value of SIF for each value of inner pressure. Comparison of the analytical results with those obtained by careful numerical FEM analysis, on the one hand, showed their good correspondence, and therefore the accuracy and efficiency of both the analytical and numerical procedures are confirmed. On the other hand, for the first time in the scientific literature, the value of SIF in a geometrically nonlinear formulation are obtained for surface cracks in slightly distorted cylindrical shell with surface long crack. It was shown that even for perfectly circular pipes having the cracks with depth up to half of the thickness of pipe walls, loaded by moderate level of inner pressure, the geometrical nonlinear values of SIF can be 10-15% less than those at linear approach application. This is very significant practical result. Another geometrically nonlinear problem is numerically investigated by known commercial FEM software for the through crack, which is loaded by a significant value of additional longitudinal force (the main factor of geometric nonlinearity considered) and small value of internal pressure (linear consideration). This statement distinguished this task from research conducted at NASA (USA), where the pressure and axial force were proportional as to pipe with closed ends. The geometric nonlinearity of the study is investigated through an incremental increase in loads and the corresponding recalculation of the SIF for the already taken into account changes in the deformed geometry (curvature). A number of tasks for determining the SIF for different pipe radii and dimensionless force values were calculated. Dimensionless parameters, which characterize the deviation of the values of SIF from the linear one, are numerically determined. Application of least square method allowed to suggest the simplified analytical formula for calculation of these deviations. These results are of great theoretical and practical importance. In particular, it is shown that for real pipes the neglecting by influence of axial force in usual approach may lead to 4-6% error of SIF determination. It is noted that additional account for large values of pressure, possible plastic deformations, may further reduce the actual values of SIF. Thus, the significance of the problems and the need for further research in this direction are shown. The necessity of analysis of flat cracks of non-canonical shape in three-dimensional bodies is noted. This is due to the fact that almost all existing solutions in the literature and reference results in normative documents are given for cracks that have shape of an ellipse or its part. However, real cracks detected by non-destructive testing are irregularly shaped cracks. Therefore, it is necessary to create the analytical methods that would allow to assess the impact of the crack shape, and to verify them with careful numerical procedures by FEM. For this purpose, flat internal cracks in infinite 3D body are considered. The formulation of problems for them is reduced to well-known integro-differential equation of the theory of elasticity. Note, that exact fundamental analytical solutions of which exist only for a circular crack and only for some simple laws of loading for an elliptic crack. A universal semi-analytical method for solving the integro-differential equation of the theory of elasticity for plane cracks of normal separation of arbitrary shape has been developed. It is proposed to consider the displacement of the crack edges as a product of a certain function of the crack shape, which satisfy to known asymptotic behavior of the displacement field near the crack front, and a certain polynomial series. As for the functions of the form, three variants of their choice were investigated - a) classical, which depends on the squares of ratio of radial coordinate of the considered point, and the corresponding coordinate of contour point; b) multiplicative, based on the product of equations describing the straight sections of the crack contour, and c) the original Oore-Burns function, which is an integral of the crack contour from the inverse square of the distance of the considered point to each point of the contour. The results showed that the greatest accuracy is achieved by application of hypersingular approach with Oore-Burns function of form. The verification of results was performed for elliptic crack, semielliptic inner crack, rectangular crack. The results were compared with numerical ones calculated by FEM. Practical calculations of SIF dependance with time for NPP reactor ant its elements for different scenarios of emergency situations are carried out. A number of simulation models with a built-in crack have been created, for which SIF calculations were performed by nonlinear FEM analysis. For cracks going through the cladding, where stress jumps occur, the method of influence functions is elaborated, and analytical-numerical procedure used piece-wise continuous basic laws of loading. Practical calculations were performed for the nozzle of reactor vessel, the cylindrical part of vessel, the core barrel and core baffle. These calculations were used to justify the extension of the service life of several units of Ukrainian NPPs.
Диссертационная работа посвящена разработке численных и аналитических методов расчета коэффициента интенсивности напряжений, (КИН) для неклассических проблем механики разрушения, в частности, для трещин сложной формы и для трещин в тонкостенных конструкциях с учетом геометрической нелинейности, (ГН). Представлена модификация метода Вильямса, что учитывает затухающие на бесконечности члены. Исследованы границы и даны рекомендации о применении данного метода. Разработан аналитический метод расчета КИН в трубах с длинными осевыми поверхностными трещинами с учетом ГН в зависимости от внутреннего давления. Результаты хорошо коррелируют с полученными в роботе численными решениями МКЭ. Построены численные модели для расчета КИН и раскрытия берегов трещин в ГН постановке для сквозных трещин в зависимости от переменной величины осевой силы. Построена апроксимационная формула, что описывает влияние ГН эффекта для обобщенной осевой силы и безразмерной длины трещины. Показана значимость эффекта для реальных лабораторных экспериментов. Разработан универсальный полуаналитический метод решения интегро-дифференциального уравнения теории упругости для плоских трещин нормального отрыва произвольной формы. Для проверки аналитических результатов построены численные модели МКЭ для трещин разной формы, например, для прямоугольной, внутренней полуэллиптической трещины, и др., и проведено сопоставление результатов. Проведены практические расчеты КИН во времени для элементов конструкций АЭС для разных сценариев прохождения аварийных ситуаций. Для этого создан ряд имитационных моделей со встроенной трещиной, для которой расчеты КИН проводили методами нелинейной механики разрушения. Для трещин, что проходят через наплавленный материал, где происходят скачки напряжений, обосновано применение метода функций влияния, для чего разработано аналитико-численную процедуру, что использует частично непрерывные базовые законы нагружения.