Strong Negative Peak Research Articles

Collapses, Maxima, Multi‐Year Modulation and Trends of the Zapiola Anticyclonic Circulation: Insights From Mercator Reanalysis

AbstractThe Argentine Basin hosts a unique oceanic feature: the Zapiola Anticyclonic Circulation (ZAC) located above a sedimentary deposit. Taking advantage of a high‐resolution (1/12°) global ocean reanalysis (GLORYS12) we examine the ZAC over 27 years (1993–2019). The mean ZAC is bottom‐intensified with bottom currents reaching 0.10 ms−1. The ZAC volume transport ranges from −18.5 to 268 Sv with a mean of 122 Sv. The strong negative peaks correspond to occasional ZAC collapses. During large transport events (>195.4 Sv) the ZAC shows a well defined coherent gyre. Strong transport events are associated with high eddy kinetic energy (EKE) at the periphery of the ZAC (especially to the west and south). In contrast, during weak transport events (<49.8 Sv), EKE increases at the center of the ZAC and decreases at the ZAC periphery. A weak ZAC is more permeable to external mesoscale structures. Each weak event features a cyclonic eddy at the center of the ZAC carrying subantarctic cold and fresh waters. The ZAC exhibits a multi‐year modulation, with periods of 4–5 years (1993–1997, 1998–2003 and 2004–2009) of low salinity corresponding to low transport, and high salinity to high transport. Over the last 27 years, transport time series exhibit a significant negative trend of −15 Sv.decade−1 associated with a negative trend in EKE (−0.015 (m/s)2.decade−1) to the north west of the ZAC. Waters in the Zapiola region become warmer and saltier in the first 2,000 m of the water column because of the southward migration of the subtropical front.

Investigation of peak wind loading on a high-rise building in the atmospheric boundary layer using large-eddy simulations

Significant negative peak pressures have been observed in two recent wind tunnel experiments of a high-rise building for certain wind directions. This peak wind loading is crucial for the design of cladding systems. However, the governing flow physics is not well understood. In this study, large-eddy simulations with sufficient resolution are performed to capture and analyze these peak pressure phenomena. The atmospheric boundary layer flow is generated using a divergence free synthetic turbulence inflow generator before the high-rise building is placed in the flow at various wind directions. The mean, standard deviation, and peak pressure coefficients are shown to agree well with the experimental measurements. The strongest negative peak pressures near the top trailing corner on the leeward surface are captured by simulations with the resolved scale between the Taylor microscale and Kolmogorov scale. The probability density function of the pressure at the top trailing corner is well approximated using a log-normal distribution, which is a signature of the effect of small-scale turbulence intermittency. Flow visualization indicates that the strong negative peak values result from the interaction between small eddies shed from the separated flow region at the upwind roof edge and larger eddies downstream of the leeward roof edge.

Biophysical characterization of a recombinant lipase KV1 from Acinetobacter haemolyticus in relation to pH and temperature

Spectroscopic and calorimetric methods were employed to assess the stability and the folding aspect of a novel recombinant alkaline-stable lipase KV1 from Acinetobacter haemolyticus under varying pH and temperature. Data on far ultraviolet-circular dichroism of recombinant lipase KV1 under two alkaline conditions (pH 8.0 and 12.0) at 40 °C reveal strong negative ellipticities at 208, 217, 222 nm, implying its secondary structure belonging to a α + β class with 47.3 and 39.0% ellipticity, respectively. Results demonstrate that lipase KV1 adopts its most stable conformation at pH 8.0 and 40 °C. Conversely, the protein assumes a random coil structure at pH 4.0 and 80 °C, evident from a strong negative peak at ∼ 200 nm. This blue shift suggests a general decline in enzyme activity in conjunction with the partially or fully unfolded state that invariably exposed more hydrophobic surfaces of the lipase protein. The maximum emission at ∼335 nm for pH 8.0 and 40 °C indicates the adoption of a favorable protein conformation with a high number of buried tryptophan residues, reducing solvent exposure. Appearance of an intense Amide I absorption band at pH 8.0 corroborates an intact secondary structure. A lower enthalpy value for pH 4.0 over pH 8.0 and 12.0 in the differential scanning calorimetric data corroborates the stability of the lipase at alkaline conditions, while a low Km (0.68 ± 0.03 mM) for tributyrin verifies the high affinity of lipase KV1 for the substrate. The data, herein offer useful insights into future structure-based tunable catalytic activity of lipase KV1.

Quasi-12 h inertia–gravity waves in the lower mesosphere observed by the PANSY radar at Syowa Station (39.6° E, 69.0° S)

Abstract. The first observations made by a complete PANSY radar system (Program of the Antarctic Syowa MST/IS Radar) installed at Syowa Station (39.6° E, 69.0° S) were successfully performed from 16 to 24 March 2015. Over this period, quasi-half-day period (12 h) disturbances in the lower mesosphere at heights of 70 to 80 km were observed. Estimated vertical wavelengths, wave periods and vertical phase velocities of the disturbances were approximately 13.7 km, 12.3 h and −0.3 m s−1, respectively. Under the working hypothesis that such disturbances are attributable to inertia–gravity waves, wave parameters are estimated using a hodograph analysis. The estimated horizontal wavelengths are longer than 1100 km, and the wavenumber vectors tend to point northeastward or southwestward. Using the nonhydrostatic numerical model with a model top of 87 km, quasi-12 h disturbances in the mesosphere were successfully simulated. We show that quasi-12 h disturbances are due to wave-like disturbances with horizontal wavelengths longer than 1400 km and are not due to semidiurnal migrating tides. Wave parameters, such as horizontal wavelengths, vertical wavelengths and wave periods, simulated by the model agree well with those estimated by the PANSY radar observations under the abovementioned assumption. The parameters of the simulated waves are consistent with the dispersion relationship of the inertia–gravity wave. These results indicate that the quasi-12 h disturbances observed by the PANSY radar are attributable to large-scale inertia–gravity waves. By examining a residual of the nonlinear balance equation, it is inferred that the inertia–gravity waves are likely generated by the spontaneous radiation mechanism of two different jet streams. One is the midlatitude tropospheric jet around the tropopause while the other is the polar night jet. Large vertical fluxes of zonal and meridional momentum associated with large-scale inertia–gravity waves are distributed across a slanted region from the midlatitude lower stratosphere to the polar mesosphere in the meridional cross section. Moreover, the vertical flux of the zonal momentum has a strong negative peak in the mesosphere, suggesting that some large-scale inertia–gravity waves originate in the upper stratosphere.

How planar are planar peptide bonds?

How planar are planar peptide bonds?

Estimation of glottal closure instants by considering speech signal as a spectrum

Close to glottal closure instants (GCIs), the speech signal is expected to change its amplitude rapidly and, at GCIs, it is expected to have strong negative peaks. A novel algorithm that exploits these two properties for the estimation of GCIs is presented. Here, a symmetrised speech segment is assumed to be a Fourier transform (FT) of an even function. In such a case, at the locations of the GCIs, the strong negative peaks in the symmetrised speech segment correspond to zeros that lie considerably outside the unit circle in the z-plane. The group delay spectrum of the time-domain signal derived by taking inverse FT of this assumed FT is expected to take a value close to −2π at the angular locations of these zeros. Mapping frequency scale to time scale, the frequency bins for which group delay reaches −2π correspond to the locations of GCIs. Theoretical justification for the proposed approach is also presented by defining a novel function called the conditional group delay function. Systematic evaluation is carried out on the CMU Arctic database and the performance of the proposed technique is better than that of the algorithms namely DYPSA, ZFF, YAGA and is close to that of SEDREAMS.

Electrostatics inside the SecY Translocon

SecY constitutes the core of the highly conserved SecYEG translocon complex that governs the translocation or integration of proteins across or into cytoplasmic membranes. Besides its role of guiding nascent membrane protein chains into the lipid bilayer, it also plays an important role in determining transmembrane topology via the so-called positive-inside rule. Site-directed mutations of translocons are known to modify the topology of nascent α-helical segments [1]. We performed molecular dynamics simulations of SecYE from Pyrococcus furiosus [2] embedded in a POPC bilayer. In this structure, SecY is in a partially open ‘primed’ state. It conveniently remained open over the course of a 450 ns simulation due to the presence of lipids wedged between helices TM2b and TM7 (the lateral gate), thus allowing close examination of the electrostatics within the translocon. Within the channel, water dipoles exhibit a preferred orientation, which affects the electrostatic (ES) potential. Time-averaged ES maps reveal a largely positive potential relative to the bulk aqueous phase within the channel except for a strong negative peak at the N-terminus of TM2b. This has implications for the entry of signal sequences into the translocon channel.Research supported by NIH grants RO1 GM74637 and PO1 GM86685.

Characteristic Raman Optical Activity Signatures of Protein β-Sheets

In this study, we compute and analyze theoretical Raman optical activity spectra of large model β-sheets in order to identify reliable signatures for this important secondary structure element. We first review signatures that have already been proposed to be indicative of β-sheets. From these signatures, we find that only the couplet in the amide I region can be regarded as a truly reliable signature. In addition, we propose a strong negative peak at ∼1350 cm(-1) to be another good signature for parallel as well as antiparallel β-sheets. We study the robustness of these signatures with respect to perturbations induced by the amino acid side chains, the overall conformation of the sheet structure, and microsolvation. It is found that the latter effects can be very well understood and separated employing the concept of localized modes. Finally, we investigate whether Raman optical activity is capable of discriminating between parallel and antiparallel β-sheets. The amide III region turns out to be most promising for this purpose.

Optical thickness determination of hexagonal boron nitride flakes

Optical reflectivity contrast provides a simple, fast, and noninvasive method for characterization of few monolayer samples of two-dimensional materials. Here, we apply this technique to measure the thickness of thin flakes of hexagonal Boron Nitride (hBN), which is a material of increasing interest in nanodevice fabrication. The optical contrast shows a strong negative peak at short wavelengths and zero contrast at a thickness dependent wavelength. The optical contrast varies linearly for 1-80 layers of hBN, which permits easy calibration of thickness. We demonstrate the applicability of this quick characterization method by comparing atomic force microscopy and optical contrast results.

Study of sodium tellurite glass using the thermally stimulated depolarization current technique (TSDC)

In order to have a better understanding of the role of the structure and the defects involved in the polarization processes in an 85TeO 2–15Na 2O mol% glass, we used the thermally stimulated depolarization currents (TSDC technique). The TSDC of the non-irradiated sample presented a strong negative peak of current at the temperature of 340 K, preceded by a relatively weak positive peak at about 300 K, after different d.c. voltages of 1200, 1500 and 2000 V were applied. No response was obtained with 1000 V, but the peak intensity increased considerably for voltages above 1200 V. After γ-irradiation of 25 and 50 KGy doses, a depolarization of the negative peak was observed in the sample submitted to25 KGy, whereas for the sample irradiated with 50 KGy, six TSDC peaks appeared at regular intervals of 5 KGy, in the temperature range of 100 and 300 K.

Protein folding intermediates of invasin protein IbeA from Escherichia coli

IbeA of Escherichia coli K1 was cloned, expressed and purified as a His(6)-tag fusion protein. The purified fusion protein inhibited E. coli K1 invasion of human brain microvascular endothelial cells and was heat-modifiable. The structural and functional aspects, along with equilibrium unfolding of IbeA, were studied in solution. The far-UV CD spectrum of IbeA at pH 7.0 has a strong negative peak at 215 nm, indicating the existence of beta-sheet-like structure. The acidic unfolding curve of IbeA at pH 2.0 shows the existence of a partially unfolded molecule (molten globule-like structure) with beta-sheet-like structure and displays strong 8-anilino-2-naphthyl sulfonic acid (ANS) binding. The pH dependent intrinsic fluorescence of IbeA was biphasic. At pH 2.0, IbeA exists in a partially unfolded state with characteristics of a molten globule-like state, and the protein is in extended beta-sheet conformation and exhibits strong ANS binding. Guanidine hydrochloride denaturation of IbeA in the molten globule-like state is noncooperative, contrary to the cooperativity seen with the native protein, suggesting the presence of two domains (possibly) in the molecular structure of IbeA, with differential unfolding stabilities. Furthermore, tryptophan quenching studies suggested the exposure of aromatic residues to solvent in this state. Acid denatured unfolding of IbeA monitored by far-UV CD is non-cooperative with two transitions at pH 3.0-1.5 and 1.5-0.5. At lower pH, IbeA unfolds to the acid-unfolded state, and a further decrease in pH to 2.0 drives the protein to the A state. The presence of 0.5 m KCl in the solvent composition directs the transition to the A state by bypassing the acid-unfolded state. Additional guanidine hydrochloride induced conformational changes in IbeA from the native to the A-state, as monitored by near- and far-UV CD and ANS-fluorescence.

Pathway of Information Transmission from Heme to Protein upon Ligand Binding/Dissociation in Myoglobin Revealed by UV Resonance Raman Spectroscopy

Gas sensory heme proteins respond to their environment by binding a specific gas molecule to heme and transmitting this primary binding signal to the protein. How the binding signal is transmitted from the heme to the protein remains to be clarified. Using UV resonance Raman (UVRR) spectroscopy, we investigated this pathway in sperm whale myoglobin as a model gas sensory heme protein. Based on the UVRR data and the effects of deleting one of three important pathways (His-93, 6-propionate, or 7-propionate), we determined the changes in the conformation of globin that occur upon binding of CO, nitric oxide (NO), or O(2) to heme and how they are transmitted from heme to globin. The UVRR results show that heme discriminates different ligands, resulting in different conformations in the globin protein. Specifically, NO induces changes in the spectrum of Trp residues in the A-helix that are significantly different from those induced by O(2) or CO binding. On the other hand, binding of O(2) to heme produces changes in the Tyr residues of the H-helix that are different from those induced by CO or NO binding. Furthermore, we found that cleavage of the Fe-His-93 covalent bond eliminates communication to the terminal region of the H-helix and that the 7-propionate hydrogen-bonding network is essential for transmitting the CO or NO binding signal to the N and C termini. Finally, the 6-propionate is important only for NO binding. Thus, the hydrogen-bonding network in the protein appears to be critical for intramolecular signal transduction in gas sensory heme proteins.

Comparison of the Vibration Mode of Metals in HNO3by a Partial Least-Squares Regression Analysis of Near-Infrared Spectra

The near-infrared (NIR) spectra of such metals as Cu(II), Mn(II), Zn(II) and Fe(III) in HNO(3) in the 700-1,860 nm region were subjected to a partial least-squares regression analysis and leave-out cross-validation to develop chemometric models. The models yielded a coefficient of determination in cross validation of 0.9744 [Cu(II)], 0.9631 [Mn(II)], 0.9154 [Zn(II)] and 0.741 [Fe(III)]. The regression coefficients for Cu(II), Mn(II) and Zn(II), but not for Fe(III), showed strong negative peaks at around 1,050-1,200 nm, a zone where spectral bands have been reported to decrease with increasing pH value. A positive peak at around 710-750 nm, which may have been due to water absorption, was observed in regression coefficients of Cu(II), Mn(II) and Zn(II) but not in Fe(III), while a negative peak was observed in that for Fe(III) at around 710-750 nm. These results indicate that the divalent cations [Cu(II), Mn(II) and Zn(II)] showed different absorption in the NIR region from the trivalent cation [Fe(III)], suggesting that the vibration mode of water, which mirrors the interaction between cations and water, may be influenced by valency.

Topochemical Speciation of Intercalated Palladium in Graphite by Valence Band X-ray Spectrometry in the Electron Microprobe

The binding state of palladium was studied within the frame of an investigation on the mechanism of analyte fixation during the pyrolysis step in graphite furnace atomic spectrometry. One approach was the determination of the palladium intercalated in the pyrolytic coating of the graphite tube. Due to the low concentrations of intercalated palladium in the pyrolytic coating, precise determination of the shift of certain X-ray lines was chosen. From several investigated valence state sensitive X-ray transitions, the Pd Lbeta2/15 (L3-N4,5) line shift was the one best determinable. The measured line shifts are in the range of -0.14 to 0.71 eV at line widths of 13 eV (fwhm) and a line energy of 3.1729 keV. These very small line shifts were determined by electron probe microanalysis. The detection of the small line shifts was performed with a new method-by evaluation of the change of the intensity in the flanks of the X-ray line. The measurements yielded the following results: inside the pyrolytic graphite, the palladium is distributed inhomogeneously in the form of clusters or islands and in the form of particles on the surface of the pyrolytic graphite. The differentiation between particles and clusters is a very practical one: as long as a particle can be seen in the SEM we talk of particles. Often, however, Pd is detected in an area on the tube or platform surface without detection of a particle. Hence, it can be assumed that the Pd is present in the form of clusters which might even be intercalated in the uppermost graphite layers. The valence state inside these clusters does not appear to be uniform. It can be interpreted as a mixture of Pd with PdO in the center of the clusters or particles (positive peak shift) and of Pd bound to the graphite (strong negative peak shift). On the basis of these observations, a way is proposed to determine how activated Pd atoms in intercalated Pd domains are forming strong covalent bonds to analytes. These bonds are responsible for the analyte fixation of even very volatile analytes.

Time-resolved reflectance difference spectroscopy study of Sb- and As-terminated InP(1 0 0) surfaces

Using time-resolved reflectance difference spectroscopy (RDS) we studied the formation of Sb and As overlayers on InP(1 0 0) under real-time metalorganic vapour-phase epitaxy conditions at 560°C. Exposure of a clean P-rich InP surface to TBAs vapour caused a (2×4)-like RDS spectrum similar to previous reports for bulk InAs. This (2×4)-like surface evolved to a (4×2)-like In-rich surface with a strong negative minimum at 2.0 eV after a 2 s H 2 purge. The RDS spectrum then recovered very rapidly to the InP(2×4)-like surface after only a few monolayers of InP growth. Exposure of the P-rich InP surface to TMSb vapour resulted in the formation of a new RDS spectrum with a strong negative peak at 1.9 eV and a positive feature at 3.7 eV which is attributed to surface–surface transitions. Sb surface layers were found to be much more stable and persistent than As layers, and RDS data indicate significant Sb after as much as 200 Å of subsequent InP growth.

Magnetooptical Effects of Room Temperature Molecular-Based Magnetic Films Composed of Vanadium Hexacyanochromates

We electrochemically synthesized film-type vanadium hexacyanochromate-based magnets with high critical temperatures (Tc): KI0.31VII0.49VIII0.51[CrIII(CN)6]0.94·6.5H2O (1) (Tc = 310 K) and KI0.61VII0.97VIII0.03[CrIII(CN)6]0.88·7.2H2O·0.4C2H5OH (2) (Tc = 345 K). The colors of these films were blue and dark blue. For film 1, the Faraday ellipticity (FE) spectra showed a weak negative peak (A) and a strong negative peak (B) around 550 nm (−640 deg cm-1 at 50 K) and 660 nm (−2300 deg cm-1 at 50 K), respectively. In the Faraday rotation (FR) spectra, two dispersive-shaped lines were observed at the same wavelength. Simulation of these spectra showed that the observed spectra can be classified as the paramagnetic type of Faraday effects. For film 2, the Faraday effect was observed even above room temperature. In its FE spectra, two negative peaks were observed around 530 nm (−850 deg cm-1 at 50 K) and 660 nm (−300 deg cm-1 at 50 K), respectively. These FE peak positions are close to the peak positions of A and ...

Asp-170 Is Crucial for the Redox Properties of Vanillyl-alcohol Oxidase

Vanillyl-alcohol oxidase is a flavoprotein containing a covalent flavin that catalyzes the oxidation of 4-(methoxymethyl)phenol to 4-hydroxybenzaldehyde. The reaction proceeds through the formation of a p-quinone methide intermediate, after which, water addition takes place. Asp-170, located near the N5-atom of the flavin, has been proposed to act as an active site base. To test this hypothesis, we have addressed the properties of D170E, D170S, D170A, and D170N variants. Spectral and fluorescence analysis, together with the crystal structure of D170S, suggests that the Asp-170 replacements do not induce major structural changes. However, in D170A and D170N, 50 and 100%, respectively, of the flavin is non-covalently bound. Kinetic characterization of the vanillyl-alcohol oxidase variants revealed that Asp-170 is required for catalysis. D170E is 50-fold less active, and the other Asp-170 variants are about 10(3)-fold less active than wild type enzyme. Impaired catalysis of the Asp-170 variants is caused by slow flavin reduction. Furthermore, the mutant proteins have lost the capability of forming a stable complex between reduced enzyme and the p-quinone methide intermediate. The redox midpoint potentials in D170E (+6 mV) and D170S (-91 mV) are considerably decreased compared with wild type vanillyl-alcohol oxidase (+55 mV). This supports the idea that Asp-170 interacts with the protonated N5-atom of the reduced cofactor, thus increasing the FAD redox potential. Taken together, we conclude that Asp-170 is involved in the process of autocatalytic flavinylation and is crucial for efficient redox catalysis.

Analysis of the interface in ferromagnet/insulator junctions by inelastic-electron-tunneling-spectroscopy

Inelastic-electron-tunneling-spectroscopy (IETS) has been applied to investigate the electron states of the interface of Al/Al 2O 3/Co( d Co=0∼50 Å)/Al and Al/Al 2O 3/Ni( d Ni=0∼50 Å)/Al tunneling junctions. A positive zero-bias anomaly was observed in the conductance curve of the junction with d Co⩽20 Å. Correspondingly, the IET spectra showed a strong negative peak at 4 mV, while another broad peak was observed for the junctions with d Co⩾10 Å. These results were discussed in terms of the paramagnetic impurity and magnon assisted tunneling processes. On the other hand, a positive peak was observed in the IET curves for the junction with Ni. The possibility of formation of an Ni–Al alloy was considered to explain this result.

Analysis of the Interlayer in Al/Al2O3/Co/Al Junctions by Inelastic-Electron Tunneling-Spectroscopy

Inelastic-Electron-Tunneling-Spectroscopy (IETS) has been applied to investigate the electron states of the interface of Al/Al2O3/Co(dCo)/Al tunneling junctions. A zero-bias anomaly was observed in the conductance curve of the junction with dCo of 2 A and decreased with increasing dCo. The IET spectra of these junctions showed a strong negative peak at 4 mV, corresponding to the zero- bias anomaly, while the another broad peak was observed for the junctions with dCo ≥10&Aring. The peak was different in the position from that assigned to the Al-O LO phonon mode observed for Al/Al2O3/Al junction. From the magnetization measurement, it is confirmed that the ferromagnetic layer was formed for the junctions with dCo ≥10 &Aring These results were discussed with the paramagnetic impurity and magnon assisted tunneling process.

Analysis of the Interlayers in a Ferromagnet/Insulator Junction by Inelastic Electron-Tunneling Spectroscopy

Inelastic electron-tunneling spectroscopy (IETS) has been used to investigate the vibrational spectrum in Al/Al2O3/CO/AI tunneling junctions with various Co thicknesses (d Co). A zero-bias anomaly was observed in the conductance curve of the junction with dCo of 2A, and decreased with increasing dCo. The IET spectra of these junctions showed strong negative peaks at 4 mV, corresponding to the zero-bias anomaly, while phonon spectra were observed for the junction with dCo ≥ 10A. The peak position was different from that of Al/Al2O3/Al. After annealing of the junction with dCo of 2A at 250°C for one hour, the zero-bias anomaly decreased and the phonon spectrum appeared.