EFFECT OF OFF-STOICHIOMETRY AND TERNARY ADDITIONS ON PLANAR FAULT ENERGIES IN Ni3Al

First principles calculations were done to evaluate the lattice parameter, cohesive energy and stacking fault energies of ordered gamma' (Ll(2)) precipitates in superalloys as a function of composition. It was found that addition of Ti and Ta lead to an increase in lattice parameter and decrease in cohesive energy, while Ni antisites had the opposite effect. Ta and Ti addition to stoichiometric Ni3Al resulted in an initial increase in the energies of APB((111)), CSF(111), APB((001)) and SISF(111). However, at higher concentrations, the fault energies decreased. Addition of Ni antisites decreased the energy of all four faults monotonically. A model based on nearest neighbor bonding was used for Ni-3(Al, Ta), Ni-3(Al, Ti) and Ni-3(Al, Ni) pseudo-binary systems and extended to pseudo- ternary Ni-3(Al, Ta, Ni) and Ni-3(Al, Ti, Ni) systems. Recipes were developed for predicting lattice parameters, cohesive energies and fault energies in pseudo- ternary systems on the basis of coefficients derived from simpler pseudobinary systems. The model predictions were found to be in good agreement with first principles calculations for lattice parameters, cohesive energies, and energies of APB((111)) and CSF(111).

Energy Hyperspace for Stacking Interaction in AU/AU Dinucleotide Step: Dispersion-Corrected Density Functional Theory Study

Double helical structures of DNA and RNA are mostly determined by base pair stacking interactions, which give them the base sequence-directed features, such as small roll values for the purine-pyrimidine steps. Earlier attempts to characterize stacking interactions were mostly restricted to calculations on fiber diffraction geometries or optimized structure using ab initio calculations lacking variation in geometry to comment on rather unusual large roll values observed in AU/AU base pair step in crystal structures of RNA double helices. We have generated stacking energy hyperspace by modeling geometries with variations along the important degrees of freedom, roll, and slide, which were chosen via statistical analysis as maximally sequence dependent. Corresponding energy contours were constructed by several quantum chemical methods including dispersion corrections. This analysis established the most suitable methods for stacked base pair systems despite the limitation imparted by number of atom in a base pair step to employ very high level of theory. All the methods predict negative roll value and near-zero slide to be most favorable for the purine-pyrimidine steps, in agreement with Calladine's steric clash based rule. Successive base pairs in RNA are always linked by sugar-phosphate backbone with C3-endo sugars and this demands C1-C1 distance of about 5.4 angstrom along the chains. Consideration of an energy penalty term for deviation of C1-C1 distance from the mean value, to the recent DFT-D functionals, specifically B97X-D appears to predict reliable energy contour for AU/AU step. Such distance-based penalty improves energy contours for the other purine-pyrimidine sequences also. (c) 2013 Wiley Periodicals, Inc. Biopolymers 101: 107-120, 2014.

Designing Ternary Co-crystals with Stacking Interactions and Weak Hydrogen Bonds. 4,4 `-Bis-hydroxyazobenzene

Three ternary co-crystals of the title compound are reported. The design strategy hinges on the identification of a robust synthon with O-H center dot center dot center dot N hydrogen bonds in a binary co-crystal. Construction of this module allows the tuning of pi center dot center dot center dot pi stacking interactions and weak hydrogen bonds to incorporate the third component into the crystal structure. Screening of various co-formers showed that a delicate balance of electrostatics is required for stacking to favor the formation of ternaries. A C-H center dot center dot center dot N hydrogen-bonded motif was also found to occur repetitively in the ternary co-crystals. The directional nature of weak hydrogen bonds allows them to be used effectively in this study.

Deformation of nanograined Ni-60Co alloy with low stacking fault energy

The evolution of deformation texture in a Ni-60Co alloy with low stacking fault energy and a grain size in the nanometre range has been investigated. The analyses of texture and microstructure suggest different mechanisms of deformation in nanocrystalline as compared to microcrystalline Ni-60Co alloy. In nanocrystalline material, the mechanism responsible for texture formation has been identified as partial slip, whereas in microcrystalline material, a characteristic texture forms due to twinning and shear banding.

Stacking Interactions in RNA and DNA: Roll-Slide Energy Hyperspace for Ten Unique Dinucleotide Steps

Understanding dinucleotide sequence directed structures of nuleic acids and their variability from experimental observation remained ineffective due to unavailability of statistically meaningful data. We have attempted to understand this from energy scan along twist, roll, and slide degrees of freedom which are mostly dependent on dinucleotide sequence using ab initio density functional theory. We have carried out stacking energy analysis in these dinucleotide parameter phase space for all ten unique dinucleotide steps in DNA and RNA using DFT-D by B97X-D/6-31G(2d,2p), which appears to satisfactorily explain conformational preferences for AU/AU step in our recent study. We show that values of roll, slide, and twist of most of the dinucleotide sequences in crystal structures fall in the low energy region. The minimum energy regions with large twist values are associated with the roll and slide values of B-DNA, whereas, smaller twist values correspond to higher stability to RNA and A-DNA like conformations. Incorporation of solvent effect by CPCM method could explain the preference shown by some sequences to occur in B-DNA or A-DNA conformations. Conformational preference of BII sub-state in B-DNA is preferentially displayed mainly by pyrimidine-purine steps and partly by purine-purine steps. The purine-pyrimidine steps show largest effect of 5-methyl group of thymine in stacking energy and the introduction of solvent reduces this effect significantly. These predicted structures and variabilities can explain the effect of sequence on DNA and RNA functionality. (c) 2014 Wiley Periodicals, Inc. Biopolymers 103: 134-147, 2015.

Role of synergistic pi-pi stacking and X-H center dot center dot center dot Cl (X = C, N, O) H-bonding interactions in gelation and gel phase crystallization

The self-assembly of p-pyridyl-ended oligo-p-phenylenevinylenes (OPVs) in ethanol leads to the formation of either hollow or solid microrods. The corresponding protonated OPVs with n-butyl chains induce transparent gelation and also gel phase crystallization owing to various synergistic noncovalent interactions. The chloride ion-selective gelation, AIEE and stimuli responsiveness of the gel are also observed.

Role of stacking fault energy on texture evolution revisited

Three materials, pure aluminium, Al-4 wt.% Mg, alpha-brass have been chosen to understand the evolution of texture and microstructure during rolling. Pure Al develops a strong copper-type rolling texture and the deformation is entirely slip dominated. In Al-4Mg alloy, texture is copper-type throughout the deformation. The advent of Cu-type shear bands in the later stages of deformation has a negligible effect on the final texture. alpha-brass shows a characteristic brass-type texture from the early stages of rolling. Extensive twinning in the intermediate stages of deformation (epsilon(t) similar to 0.5) causes significant texture reorientation towards alpha-fiber. Beyond 40% reduction, deformation is dominated by Bs-type shear bands, and the banding coincides with the evolution of <111>parallel to ND components. The crystallites within the bands preferentially show <110>parallel to ND components. The absence of the Cu component throughout the deformation process indicates that, for the evolution of brass-type texture, the presence of Cu component is not a necessary condition. The final rolling texture is a synergistic effect of deformation twinning and shear banding.

Protection of Digital Telecom Exchanges Against Lightning Surges and Earth Faults

Low-power electronic devices used in digital telecom exchanges are vulnerable to surge voltages and currents primarily originating from natural lightning or due to the direct interactions between electric power and telecommunication lines, etc., causing the earth/ground potential rise, neutral potential rise, and faults in the system. The fault currents may flow directly to telecom lines or through the equipment to the customer's premises, causing adequate damage to the equipment and personnel safety. In wireline applications, analog or digital, central office, exchanges, and subscriber sides have to be protected. Decisive protection and protective methods have to be employed for proper functioning of the equipment under overvoltage/overcurrent conditions. Current investigation reports some interesting results obtained on the recently developed high-voltage high-current protection cards used in digital telecom exchanges. The performances of protection cards both for the ring wave and hybrid wave surges are evaluated and presented. The surge generators required for the investigation are developed and fabricated in house as per the relevant telecom standards.

On the unstable stacking criterion for ideal and cracked copper-crystals

The unstable stacking criteria for an ideal copper crystal under homogeneous shearing and for a cracked copper crystal under pure mode II loading are analysed. For the ideal crystal under homogeneous shearing, the unstable stacking energy gamma(us) defined by Rice in 1992 results from shear with no relaxation in the direction normal to the slip plane. For the relaxed shear configuration, the critical condition for unstable stacking does not correspond to the relative displacement Delta = b(p)/2, where b(p) is the Burgers vector magnitude of the Shockley partial dislocation, but to the maximum shear stress. Based on this result, the unstable stacking energy Gamma(us) is defined for the relaxed lattice. For the cracked crystal under pure mode II loading, the dislocation configuration corresponding to Delta = b(p)/2 is a stable state and no instability occurs during the process of dislocation nucleation. The instability takes place at approximately Delta = 3b(p)/4. An unstable stacking energy Pi(us) is defined which corresponds to the unstable stacking state at which the dislocation emission takes place. A molecular dynamics method is applied to study this in an atomistic model and the results verify the analysis above.

Beyond Watson and Crick : programming the self-assembly and reconfiguration of DNA nanostructures based on stacking interactions

Life is the result of the execution of molecular programs: like how an embryo is fated to become a human or a whale, or how a person’s appearance is inherited from their parents, many biological phenomena are governed by genetic programs written in DNA molecules. At the core of such programs is the highly reliable base pairing interaction between nucleic acids. DNA nanotechnology exploits the programming power of DNA to build artificial nanostructures, molecular computers, and nanomachines. In particular, DNA origami—which is a simple yet versatile technique that allows one to create various nanoscale shapes and patterns—is at the heart of the technology. In this thesis, I describe the development of programmable self-assembly and reconfiguration of DNA origami nanostructures based on a unique strategy: rather than relying on Watson-Crick base pairing, we developed programmable bonds via the geometric arrangement of stacking interactions, which we termed stacking bonds. We further demonstrated that such bonds can be dynamically reconfigurable.

The first part of this thesis describes the design and implementation of stacking bonds. Our work addresses the fundamental question of whether one can create diverse bond types out of a single kind of attractive interaction—a question first posed implicitly by Francis Crick while seeking a deeper understanding of the origin of life and primitive genetic code. For the creation of multiple specific bonds, we used two different approaches: binary coding and shape coding of geometric arrangement of stacking interaction units, which are called blunt ends. To construct a bond space for each approach, we performed a systematic search using a computer algorithm. We used orthogonal bonds to experimentally implement the connection of five distinct DNA origami nanostructures. We also programmed the bonds to control cis/trans configuration between asymmetric nanostructures.

The second part of this thesis describes the large-scale self-assembly of DNA origami into two-dimensional checkerboard-pattern crystals via surface diffusion. We developed a protocol where the diffusion of DNA origami occurs on a substrate and is dynamically controlled by changing the cationic condition of the system. We used stacking interactions to mediate connections between the origami, because of their potential for reconfiguring during the assembly process. Assembling DNA nanostructures directly on substrate surfaces can benefit nano/microfabrication processes by eliminating a pattern transfer step. At the same time, the use of DNA origami allows high complexity and unique addressability with six-nanometer resolution within each structural unit.

The third part of this thesis describes the use of stacking bonds as dynamically breakable bonds. To break the bonds, we used biological machinery called the ParMRC system extracted from bacteria. The system ensures that, when a cell divides, each daughter cell gets one copy of the cell’s DNA by actively pushing each copy to the opposite poles of the cell. We demonstrate dynamically expandable nanostructures, which makes stacking bonds a promising candidate for reconfigurable connectors for nanoscale machine parts.

Frictional properties of faults : from observation on the Longitudinal Valley Fault, Taiwan, to dynamic simulations

Faults can slip either aseismically or through episodic seismic ruptures, but we still do not understand the factors which determine the partitioning between these two modes of slip. This challenge can now be addressed thanks to the dense set of geodetic and seismological networks that have been deployed in various areas with active tectonics. The data from such networks, as well as modern remote sensing techniques, indeed allow documenting of the spatial and temporal variability of slip mode and give some insight. This is the approach taken in this study, which is focused on the Longitudinal Valley Fault (LVF) in Eastern Taiwan. This fault is particularly appropriate since the very fast slip rate (about 5 cm/yr) is accommodated by both seismic and aseismic slip. Deformation of anthropogenic features shows that aseismic creep accounts for a significant fraction of fault slip near the surface, but this fault also released energy seismically, since it has produced five M_w>6.8 earthquakes in 1951 and 2003. Moreover, owing to the thrust component of slip, the fault zone is exhumed which allows investigation of deformation mechanisms. In order to put constraint on the factors that control the mode of slip, we apply a multidisciplinary approach that combines modeling of geodetic observations, structural analysis and numerical simulation of the "seismic cycle". Analyzing a dense set of geodetic and seismological data across the Longitudinal Valley, including campaign-mode GPS, continuous GPS (cGPS), leveling, accelerometric, and InSAR data, we document the partitioning between seismic and aseismic slip on the fault. For the time period 1992 to 2011, we found that about 80-90% of slip on the LVF in the 0-26 km seismogenic depth range is actually aseismic. The clay-rich Lichi M\'elange is identified as the key factor promoting creep at shallow depth. Microstructural investigations show that deformation within the fault zone must have resulted from a combination of frictional sliding at grain boundaries, cataclasis and pressure solution creep. Numerical modeling of earthquake sequences have been performed to investigate the possibility of reproducing the results from the kinematic inversion of geodetic and seismological data on the LVF. We first investigate the different modeling strategy that was developed to explore the role and relative importance of different factors on the manner in which slip accumulates on faults. We compare the results of quasi dynamic simulations and fully dynamic ones, and we conclude that ignoring the transient wave-mediated stress transfers would be inappropriate. We therefore carry on fully dynamic simulations and succeed in qualitatively reproducing the wide range of observations for the southern segment of the LVF. We conclude that the spatio-temporal evolution of fault slip on the Longitudinal Valley Fault over 1997-2011 is consistent to first order with prediction from a simple model in which a velocity-weakening patch is embedded in a velocity-strengthening area.

Fe−TPP Coordination Network with Metalloporphyrinic Neutral Radicals and Face-to-Face and Edge-to-Face π−π Stacking

Artículo científico Inorg. Chem. 2013, 52, 8074−8081