Microstructural stability and superplasticity in an electrodeposited nanocrystalline Ni-P alloy

Stabilization of nanocrystalline grain sizes by second phase particles can facilitate superplasticity at high strain rates and/or low temperatures. A metastable single phase nano-Ni-P alloy prepared by electrodeposition, with a grain size of similar to 6 nm, transforms to a nanoduplex structure at T> 673 K, with similar to 4 vol.% Ni3P particles at triple junctions and within Ni grains. The nanoduplex microstructure is reasonably stable up to 777 K, and the growth of Ni grains occurs in a coupled manner with the growth of Ni3P particles such that the ratio of the two mean sizes (Z) is essentially constant. High temperature tests for a grain size of 290 nm reveal superplastic behavior with an optimum elongation to failure of 810% at a strain rate of 7 x 10(-4) s(-1) and a relatively low temperature of 777 K. Superplastic deformation enhances both grain growth and the ratio Z, implying that grain boundary sliding (GBS) significantly influences the microstructural dynamics. Analysis of the deformation processes suggests that superplasticity is associated with GBS controlled by the overcoming of intragranular particles by dislocations, so that deformation is independent of the grain size. The nano-Ni-P alloy exhibits lower ductility than nano-Ni due to concurrent cavitation caused by higher stresses. (C) 2011 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Interaction of A beta peptide (1-40) with amino acid aluminium complexes: relevance to Alzheimer's disease

A beta (39-43 aminoacid residues) is the principal peptide component of amyloid deposits in Alzheimer's disease (AD). A beta peptide is derived from the amyloid precursor protein (APP) in which mutations give rise to many forms of familial AD. Aluminium is reported to play a key role in inducing conformational change in the synthetic beta-amyloid peptide (1-40)from alpha-helix to beta-pleated sheet, leading to aggregation and fibrillar formation. We have studied the interaction of amino acid-Al complexes such as D-Asp-Al and L-Glu-Al with A beta(1-40) in TFE/buffer (70% TFE and 30% H2O v/v pH 6.7) mixture using CD spectroscopy. The interaction of either of these amino acid complexes with A beta(1-40) results in loss of alpha-helical content and the peptide is more unstructured compared to free Al3+ in the solution. Our data strongly support the idea, that the Al3+ in the form of aminoacid-Al complexes is more effective in inducing random coil conformation in the A beta peptide than the free Al3+ present in the solution.

Absolute Entropy and Energy of Carbon Dioxide Using the Two-Phase Thermodynamic Model

The two-phase thermodynamic (2PT) model is used to determine the absolute entropy and energy of carbon dioxide over a wide range of conditions from molecular dynamics trajectories. The 2PT method determines the thermodynamic properties by applying the proper statistical mechanical partition function to the normal modes of a fluid. The vibrational density of state (DoS), obtained from the Fourier transform of the velocity autocorrelation function, converges quickly, allowing the free energy, entropy, and other thermodynamic properties to be determined from short 20-ps MD trajectories. The anharmonic effects in the vibrations are accounted for by the broadening of the normal modes into bands from sampling the velocities over the trajectory. The low frequency diffusive modes, which lead to finite DoS at zero frequency, are accounted for by considering the DoS as a superposition of gas-phase and solid-phase components (two phases). The analytical decomposition of the DoS allows for an evaluation of properties contributed by different types of molecular motions. We show that this 2PT analysis leads to accurate predictions of entropy and energy of CO2 over a wide range of conditions (from the triple point to the critical point of both the vapor and the liquid phases along the saturation line). This allows the equation of state of CO2 to be determined, which is limited only by the accuracy of the force field. We also validated that the 2PT entropy agrees with that determined from thermodynamic integration, but 2PT requires only a fraction of the time. A complication for CO2 is that its equilibrium configuration is linear, which would have only two rotational modes, but during the dynamics it is never exactly linear, so that there is a third mode from rotational about the axis. In this work, we show how to treat such linear molecules in the 2PT framework.

A C-H center dot center dot center dot O hydrogen bond stabilized polypeptide chain reversal motif at the C terminus of helices in proteins

The serendipitous observation of a C-H...O hydrogen bond mediated polypeptide chain reversal in synthetic peptide helices has led to a search for the occurrence of a similar motif in protein structures. From a dataset of 634 proteins, 1304 helices terminating in a Schellman motif have been examined. The C-H...O interaction between the T - 4 (CH)-H-alpha and T + 1 C=O group (C...O 3.5 Angstrom) becomes possible only when the T + 1 residue adopts an extended beta conformation (T is defined as the helix terminating residue adopting an alpha(L) conformation). In all, 111 examples of this chain reversal motif have been identified and the compositional and conformational. preferences at positions T - 4, T, and T + 1 determined. A marked preference for residues like Set, Glu and Gln is observed at T - 4 position with the motif being further stabilized by the formation of a side-chain-backbone O...H-N hydrogen bond involving the side-chain of residue T - 4 and the N-H group of residue T + 3. In as many as 57 examples, the segment following the helix was extended with three to four successive residues in beta conformation. In a majority of these cases, the succeeding beta strand lies approximately antiparallel with the helix, suggesting that the backbone C-H...O interactions may provide a means of registering helices and strands in an antiparallel orientation. Two examples were identified in which extended registry was detected with two sets of C-H...O hydrogen bonds between (T - 4) (CH)-H-alpha...C=O (T + 1) and (T - 8) (CH)-H-alpha...C=O (T + 3). 0 2002 Published by Elsevier Science Ltd.

Mutagenicity associated with O6-methylguanine-DNA damage and mechanism of nucleotide flipping by AGT during repair

Methylated guanine damage at O6 position (i.e. O6MG) is dangerous due to its mutagenic and carcinogenic character that often gives rise to G:C-A:T mutation. However, the reason for this mutagenicity is not known precisely and has been a matter of controversy. Further, although it is known that O6-alkylguanine-DNA alkyltransferase (AGT) repairs O6MG paired with cytosine in DNA, the complete mechanism of target recognition and repair is not known completely. All these aspects of DNA damage and repair have been addressed here by employing high level density functional theory in gas phase and aqueous medium. It is found that the actual cause of O6MG mediated mutation may arise due to the fact that DNA polymerases incorporate thymine opposite to O6MG, misreading the resulting O6MG:T complex as an A:T base pair due to their analogous binding energies and structural alignments. It is further revealed that AGT mediated nucleotide flipping occurs in two successive steps. The intercalation of the finger residue Arg 128 into the DNA double helix and its interaction with the O6MG: C base pair followed by rotation of the O6MG nucleotide are found to be crucial for the damage recognition and nucleotide flipping.

Densification and microstructure development in spark plasma sintered WC–6 wt% ZrO2 nanocomposites

In this paper, we report the results of a transmission electron microscopy investigation on WC–6 wt% ZrO2nanocomposite, spark plasma sintered at 1300 °C, for varying times of up to 20 min. The primary aim of this work was to understand the evolution of microstructure during such a sintering process. The investigation revealed the presence of nanocrystalline ZrO2particles (30–50 nm) entrapped within submicron WC grains. In addition, relatively coarser ZrO2(60–100 nm) particles were observed to be either attached to WC grain boundaries or located at WC triple grain junctions. The evidence of the presence of a small amount of W2C, supposed to have been formed due to sintering reaction between WC and ZrO2, is presented here. Detailed structural investigation indicated that ZrO2in the spark plasma sintered nanocomposite adopted an orthorhombic crystal structure, and the possible reasons for o-ZrO2formation are explained. The increase in kinetics of densification due to the addition of ZrO2is believed to be caused by the enhanced diffusion kinetics in the presence of nonstoichiometric nanocrystalline ZrO2.

Theory of Gas Hydrates: Effect of the Approximation of Rigid Water Lattice

One of the assumptions of the van der Waals and Platteeuw theory for gas hydrates is that the host water lattice is rigid and not distorted by the presence of guest molecules. In this work, we study the effect of this approximation on the triple-point lines of the gas hydrates. We calculate the triple-point lines of methane and ethane hydrates via Monte Carlo molecular simulations and compare the simulation results with the predictions of van der Waals and Platteeuw theory. Our study shows that even if the exact intermolecular potential between the guest molecules and water is known, the dissociation temperatures predicted by the theory are significantly higher. This has serious implications to the modeling of gas hydrate thermodynamics, and in spite of the several impressive efforts made toward obtaining an accurate description of intermolecular interactions in gas hydrates, the theory will suffer from the problem of robustness if the issue of movement of water molecules is not adequately addressed.

Structural Rigidity of Paranemic Crossover and Juxtapose DNA Nanostructures

Crossover motifs are integral components for designing DNA-based nanostructures and nanomechanical devices due to their enhanced rigidity compared to the normal B-DNA. Although the structural rigidity of the double helix B-DNA has been investigated extensively using both experimental and theoretical tools, to date there is no quantitative information about structural rigidity and the mechanical strength of parallel crossover DNA motifs. We have used fully atomistic molecular dynamics simulations in explicit solvent to get the force-extension curve of parallel DNA nanostructures to characterize their mechanical rigidity. In the presence of monovalent Na(+) ions, we find that the stretch modulus (gamma(1)) of the paranemic crossover and its topoisomer JX DNA structure is significantly higher (similar to 30%) compared to normal B-DNA of the same sequence and length. However, this is in contrast to the original expectation that these motifs are almost twice as rigid compared to the double-stranded B-DNA. When the DNA motif is surrounded by a solvent with Mg(2+) counterions, we find an enhanced rigidity compared to Na(+) environment due to the electrostatic screening effects arising from the divalent nature of Mg(2+) ions. To our knowledge, this is the first direct determination of the mechanical strength of these crossover motifs, which can be useful for the design of suitable DNA for DNA-based nanostructures and nanomechanical devices with improved structural rigidity.

Dynamic and thermodynamic anomalies of water at low temperatures: from bulk water to reverse micelles and DNA hydration layer

Liquid water is known to exhibit remarkable thermodynamic and dynamic anomalies, ranging from solvation properties in supercritical state to an apparent divergence of the linear response functions at a low temperature. Anomalies in various dynamic properties of water have also been observed in the hydration layer of proteins, DNA grooves and inside the nanocavity, such as reverse micelles and nanotubes. Here we report studies on the molecular origin of these anomalies in supercooled water, in the grooves of DNA double helix and reverse micelles. The anomalies have been discussed in terms of growing correlation length and intermittent population fluctuation of 4- and 5-coordinated species. We establish correlation between thermodynamic response functions and mean squared species number fluctuation. Lifetime analysis of 4- and 5-coordinated species reveals interesting differences between the role of the two species in supercooled and constrained water. The nature and manifestations of the apparent and much discussed liquid-liquid transition under confinement are found to be markedly different from that in the bulk. We find an interesting `faster than bulk' relaxation in reverse micelles which we attribute to frustration effects created by competition between the correlations imposed by surface interactions and that imposed by hydrogen bond network of water.

Allosteric Communication in Cysteinyl tRNA Synthetase A NETWORK OF DIRECT AND INDIRECT READOUT

Protein structure networks are constructed for the identification of long-range signaling pathways in cysteinyl tRNA synthetase (CysRS). Molecular dynamics simulation trajectory of CysRS-ligand complexes were used to determine conformational ensembles in order to gain insight into the allosteric signaling paths. Communication paths between the anticodon binding region and the aminoacylation region have been identified. Extensive interaction between the helix bundle domain and the anticodon binding domain, resulting in structural rigidity in the presence of tRNA, has been detected. Based on the predicted model, six residues along the communication paths have been examined by mutations (single and double) and shown to mediate a coordinated coupling between anticodon recognition and activation of amino acid at the active site. This study on CysRS clearly shows that specific key residues, which are involved in communication between distal sites in allosteric proteins but may be elusive in direct structure analysis, can be identified from dynamics of protein structure networks.

Dynamic Supply and Threshold Voltage Scaling for CMOS Digital Circuits Using In-Situ Power Monitor

A generalized power tracking algorithm that minimizes power consumption of digital circuits by dynamic control of supply voltage and the body bias is proposed. A direct power monitoring scheme is proposed that does not need any replica and hence can sense total power consumed by load circuit across process, voltage, and temperature corners. Design details and performance of power monitor and tracking algorithm are examined by a simulation framework developed using UMC 90-nm CMOS triple well process. The proposed algorithm with direct power monitor achieves a power savings of 42.2% for activity of 0.02 and 22.4% for activity of 0.04. Experimental results from test chip fabricated in AMS 350 nm process shows power savings of 46.3% and 65% for load circuit operating in super threshold and near sub-threshold region, respectively. Measured resolution of power monitor is around 0.25 mV and it has a power overhead of 2.2% of die power. Issues with loop convergence and design tradeoff for power monitor are also discussed in this paper.

Role of Nonplanar Peptide Unit in Regular Polypeptide Helices - New Model for Pply-Beta-Benzyl-L-Aspartate

The effect of non-planarity of the peptide unit on helical structures stabilized by intrachain hydrogen bonds is discussed. While the present calculations generally agree with those already reported in the literature for right-handed helical structures, it is found that the most stable left-handed structure is a novel helix, called the delta-helix. Its helical parameters are close to these reported for poly-beta-benzyl-L -aspartate. Conformational energy calculations show that poly-beta-benzyl-L -aspartate with the delta-helical structure is considerably more stable than the structure it is generally believed to take up (the omega-helix) by about 15 kcal/mol-residue.

Studies on hydrogen-bonds .4. proposed working criteria for assessing qualitative strength of hydrogen-bonds

The data obtained in the earlier parts of this series for the donor and acceptor end parameters of N-H. O and O-H. O hydrogen bonds have been utilised to obtain a qualitative working criterion to classify the hydrogen bonds into three categories: “very good” (VG), “moderately good” (MG) and weak (W). The general distribution curves for all the four parameters are found to be nearly of the Gaussian type. Assuming that the VG hydrogen bonds lie between 0 and ± la, MG hydrogen bonds between ± 1s̀ and ± 2s̀, W hydrogen bonds beyond ± 2s̀ (where s̀ is the standard deviation), suitable cut-off limits for classifying the hydrogen bonds in the three categories have been derived. These limits are used to get VG and MG ranges for the four parameters 1 and θ (at the donor end) and ± and ± (at the acceptor end). The qualitative strength of a hydrogen bond is decided by the cumulative application of the criteria to all the four parameters. The criterion has been further applied to some practical examples in conformational studies such as α-helix and can be used for obtaining suitable location of hydrogen atoms to form good hydrogen bonds. An empirical approach to the energy of hydrogen bonds in the three categories has also been presented.

Free Energy Barriers for Escape of Water Molecules from Protein Hydration Layer

Free energy barriers separating interfacial water molecules from the hydration layer at the surface of a protein to the bulk are obtained by using the umbrella sampling method of free energy calculation. We consider hydration layer of chicken villin head piece (HP-36) which has been studied extensively by molecular dynamics simulations. The free energy calculations reveal a strong sensitivity to the secondary structure. In particular, we find a region near the junction of first and second helix that contains a cluster of water molecules which are slow in motion, characterized by long residence times (of the order of 100 ps or more) and separated by a large free energy barrier from the bulk water. However, these ``slow'' water molecules constitute only about 5-10% of the total number of hydration layer water molecules. Nevertheless, they play an important role in stabilizing the protein conformation. Water molecules near the third helix (which is the important helix for biological function) are enthalpically least stable and exhibit the fastest dynamics. Interestingly, barrier height distributions of interfacial water are quite broad for water surrounding all the three helices (and the three coils), with the smallest barriers found for those near the helix-3. For the quasi-bound water molecules near the first and second helices, we use well-known Kramers' theory to estimate the residence time from the free energy surface, by estimating the friction along the reaction coordinate from the diffusion coefficient by using Einstein relation. The agreement found is satisfactory. We discuss the possible biological function of these slow, quasi-bound (but transient) water molecules on the surface.

A non-metal catalysed oxidation of primary azides to nitriles at ambient temperature

A novel non-metal catalyzed oxidation of organic azides to nitriles under solvent-free conditions is presented employing catalytic amounts of KI, and DABCO in aq. TBHP at room temperature. This nonmetal catalyzed oxidation of azides provides good selectivity as double and triple bonds were not oxidized under the present reaction conditions.