Detection of underground mining induced land subsidence using Differential Interferometric SAR (D-InSAR) in Jharia coalfields

Mining induced land subsidence is very common in the areas of extensive underground coal mining which affects the overall geo-environmental scenario of the area. Jharia coalfields in Jharkhand has been experiencing land subsidence for several decades essentially due to underground mining and coal fire. Differential interferometric SAR (D-InSAR) technique has been used widely to identify and measure land subsidence. In this study, six ALOS PALSAR data pairs acquired during 2007-2008 were used to study land subsidence phenomenon in the Jharia coalfields. Two-pass D-InSAR was used in this study which uses two SAR images of the same area taken at different times to calculate the Line-of-Sight (LOS) path difference of a target point due to land displacement with the help of an external Digital Elevation Model (DEM). Well defined subsidence fringes were obtained in most of the differential interferogram pairs. The fringe areas were integrated to obtain the total subsidence affected areas during the observation period with rates of subsidence (in cm/year). The maximum subsidence rate calculated from D-InSAR processing is found to be 56.72 cm/yr and the minimum is 7.88 cm/yr. The total affected area in the study area is 7.2 sq kms. Field checks were done for confirmation of D-InSAR based subsidence results

Designed peptides with homochiral and heterochiral diproline templates as conformational constraints

Diproline segments have been advanced as templates for nucleation of folded structure in designed peptides. The conformational space available to homochiral and heterochiral diproline segments has been probed by crystallographic and NMR studies on model peptides containing L-Pro-L-Pro and D-Pro-L-Pro units. Four distinct classes of model peptides have been investigated: a) isolated D-Pro-L-Pro segments which form type II β-turn; b) D-Pro-L-Pro-L-Xxx sequences which form type II′-I (βII′-I′, consecutive β-turns) turns; c) D-Pro-L-Pro-D-Xxx sequences; d) L-Pro-L-Pro-L-Xxx sequences. A total of 17 peptide crystal structures containing diproline segments are reported. Peptides of the type Piv-D-Pro-L-Pro-L-Xxx-NHMe are conformationally homogeneous, adopting consecutive β-turn conformations. Peptides in the series Piv-D-Pro-L-Pro-D-Xxx-NHMe and Piv-L-Pro-L-Pro-L-Xxx-NHMe, display a heterogeneity of structures in crystals. A type VIa β-turn conformation is characterized in Piv-L-Pro-L-Pro-L-Phe-OMe (18), while an example of a 5→1 hydrogen bonded α-turn is observed in crystals of Piv-D-Pro-L-Pro-D-Ala-NHMe (11). An analysis of pyrrolidine conformations suggests a preferred proline puckering geometry is favored only in the case of heterochiral diproline segments. Solution NMR studies, reveal a strong conformational influence of the C-terminal Xxx residues on the structures of diproline segments. In L-Pro-L-Pro-L-Xxx sequences, the Xxx residues strongly determine the population of Pro-Pro cis conformers, with an overwhelming population of the trans form in L-Xxx = L-Ala (19)

Natural Abundant Solid State NMR Studies in Designed Tripeptides for Differentiation of Multiple Conformers

Solid state NMR (SSNMR) experiments on heteronuclei in natural abundance are described for three synthetically designed tripeptides Piv-(L)Pro_(L)Pro-(L)Phe-OMe (1), Piv-(D)Pro_(L)Pro_(L)Phe-OMe (2), and Piv-(D)Pro_(L)Pro_(L)Phe-NHMe (3). These peptides exist in different conformation as shown by solution state NMR and single crystal X-ray analysis (Chatterjee et al., Chem Eur J 2008, 14, 6192). In this study, SSNMR has been used to probe the conformations of these peptides in their powder form. The C-13 spectrum of peptide (1) showed doubling of resonances corresponding to cis/cis form, unlike in solution where the similar doubling is attributed to cis/trans form. This has been confirmed by the chemical shift differences of C-beta and C-gamma carbon of Proline in peptide (1) both in solution and SSNMR. Peptide (2) and (3) provided single set of resonances which represented all transform across the di-Proline segment. The results are In agreement with the X-ray analysis. Solid state N-15 resonances, especially from Proline residues provided additional information, which is normally not observable in solution state NMR. H-1 chemical shifts are also obtained from a two-dimensional heteronuclear correlation experiment between H-1-C-13. The results confirm the utility of NMR as a useful tool for identifying different conformers in peptides in the solid state. (C) 2009 Wiley Periodicals, Inc. Biopolymers 91: 851-860, 2009

Density Functional Study of Elastic Properties of Metallic Alloys

Special quasi-random structure (SQS) and coherent potential approximation (CPA) are techniques widely employed in the first-principles calculations of random alloys. The aim of the thesis is to study these approaches by focusing on the local lattice distortion (LLD) and the crystal symmetry effects. We compare the elastic parameters obtained from SQS and CPA calculations. For the CPA and SQS calculations, we employ the Exact Muffin-Tin Orbitals (EMTO) method and the pseudopotential method as implemented in the Vienna Ab initio Simulation Package (VASP), respectively. We compare the predicted trends of the VASP-SQS and EMTO-CPA parameters against composition. As a first case study, we investigate the elastic parameters of face centered cubic (fcc) Ti1−xAlx(0≤x≤100at.%) random solid solutions as a function of Al content (x). The EMTO-CPA and VASP-SQS results are in good agreement with each other. Comparing the lattice constants from SQS calculations with and without local lattice relaxations, we find that in Ti-rich (Al-rich) side the lattice constants remain almost unchanged (slightly increase) upon atomic relaxations. Taking local lattice distortions into consideration decreases the C11 and C44 elastic parameters, but their trends are not significantly affected. The C12 elastic constant, on the other hand, is almost unchanged when atomic relaxations are included. In general, the uncertainties in the elastic parameters associated with the symmetry lowering in supercell studies turn out to be superior to the differences between the two alloy techniques including the effect of LLD. We also investigate the elastic properties of random fcc Cu1−xAux(0≤x≤100 at.%) alloys as a function of Au content employing the CPA and SQS approaches. It is found that the CPA and SQS values forC11andC12 are consistent with each other no matter whether the atomic relaxations are taken into account or not. On the other hand, the EMTO-CPA values for C44 are slightly larger than those from SQS calculations especially for Cu-rich alloys which we ascribe to the differences in the DFT solvers rather than the differences between CPA and SQS. The Perdew-Burke-Ernzerhof (PBE) approximation to the exchange-correlation term in density functional theory (DFT) is a mature approach and have been adopted routinely to investigate the properties of metallic alloys. In most of the cases, PBE provides theoretical results in good agreement with experiments. However, the ordered Cu-Au system turned out to be a special case where large deviations between the PBE predictions and observations occur. In this work, we make use of a recently developed exchange-correlation functional, the so-called quasi-non-uniform exchange-correlation approximation (QNA), to calculate the lattice constants and formation energies for ordered Cu-Au alloys as a function of composition. The calculations are performed using the EMTO method. We find that the QNA functional leads to excellent agreement betweent heory and experiment. The PBE strongly overestimates the lattice constants for ordered Cu3Au, CuAu, CuAu3 compounds and also for the pure metals which is nicely corrected by the QNA approach. The errors in the formation energies of Cu3Au, CuAu, CuAu3relative to the experimental data decrease from 38-45% obtained with PBE to 5-9% calculated for QNA.  QC 20151216</p

Effects of hydrogen bonding on amide-proton chemical shift anisotropy in a proline-containing model peptide

Longitudinal relaxation due to cross-correlation between dipolar ((HN-1H alpha)-H-1) and amide-proton chemical shift anisotropy (H-1(N) CSA) has been measured in a model tripeptide Piv-(L)Pro-(L)Pro-(L)Phe-OMe. The peptide bond across diproline segment is known to undergo cis/trans isomerization and only in the cis form does the lone Phe amide-proton become involved in intramolecular hydrogen bonding. The strength of the cross correlated relaxation interference is found to be significantly different between cis and trans forms, and this difference is shown as an influence of intramolecular hydrogen bonding on the amide-proton CSA. (C) 2015 Elsevier B.V. All rights reserved

Simultaneous Occurrence of Nanospheres and Nanofibers Self‐Assembled from Achiral Tripeptides

Abstract The achiral tripeptide Boc‐Aib‐MABA‐Aib‐OMe has the ability to co‐exist as nanospheres and as a network of nanofibers in methanol. Furthermore, AFM and TEM images show the presence of bulges in the network of nanofibers. Interestingly, the formation of nanofibers is seen to emerge from the outer boundary of the spherical structures. Some of the nanofibers curl up at the tip and later result in the formation of hollow nanospheres with thick boundaries. The presence of β‐turn‐like structures with hydrogen bonding is observed using FT‐IR studies. The presence of hydrogen bonding is also demonstrated by using NMR studies

Entrapment of a water wire in a hydrophobic peptide channel with an aromatic lining

A one-dimensional water wire has been characterized by X-ray diffraction in single crystals of the tripeptide Ac-Phe-Pro-Trp-OMe. Crystals in the hexagonal space group P65 reveal a central hydrophobic channel lined by aromatic residues which entraps an approximately linear array of hydrogen bonded water molecules. The absence of any significant van der Waals contact with the channel walls suggests that the dominant interaction between the "water wire" and "peptide nanotube" is electrostatic in origin. An energy difference of 16 kJmol-1 is estimated for the distinct orientations of the water wire dipole with respect to the macrodipole of the peptide nanotube. The structural model suggests that Grotthuss type proton conduction may, through constricted hydrophobic channels, be facilitated by concerted, rotational reorientation of water molecules

Designed Peptides with Homochiral and Heterochiral Diproline Templates as Conformational Constraints

Diproline segments have been advanced as templates for nucleation of folded structure in designed peptides. The conformational space available to homochiral and heterochiral diproline segments has been probed by crystallographic and NMR studies on model peptides containing L-Pro-L-Pro and D-Pro-L-Pro units. Four distinct classes of model peptides have been investigated: a)isolated D-Pro-L-Pro segments which form type II' \beta -turn; b) D-Pro-L-Pro-L-Xxx sequences which form type II'-I $(\beta_{II'-I}$, consecutive \beta -turns) turns; c) D-Pro-L-Pro-D-Xxx sequences; d) L-Pro-L-Pro-L-Xxx sequences. A total of 17 peptide crystal structures containing diproline segments are reported. Peptides of the type Piv-D-Pro-L-Pro-L-Xxx-NHMe are conformationally homogeneous, adopting consecutive \beta-turn conformations. Peptides in the series Piv-D-Pro-L-Pro-D-Xxx-NHMe and Piv-L-Pro-L-Pro-L-Xxx-NHMe, display a heterogeneity of structures in crystals. A type VIa \beta -turn conformation is characterized in Piv-L-Pro-L-Pro-L-Phe-OMe (18), while an example of a 5\rightarrow 1 hydrogen bonded \alpha-turn is observed in crystals of Piv-D-Pro-L-Pro-D-Ala-NHMe (11). An analysis of pyrrolidine conformations suggests a preferred proline puckering geometry is favored only in the case of heterochiral diproline segments. Solution NMR studies, reveal a strong conformational influence of the C-terminal Xxx residues on the structures of diproline segments. In L-Pro-L-Pro-L-Xxx sequences, the Xxx residues strongly determine the population of Pro-Pro cis conformers, with an overwhelming population of the trans form in L-Xxx = L-Ala (19)