Origin and Prediction of Highly Specific Bond Cleavage Sites in the Thermal Activation of Intact Protein Ions

Predicting the fragmentation patterns of proteins would be beneficial for the reliable identification of intact proteins by mass spectrometry. However, the ability to accurately make such predictions remains elusive. An approach to predict the specific cleavage sites in whole proteins resulting from collision-induced dissociation by use of an improved electrostatic model for calculating the proton configurations of highly-charged protein ions is reported. Using ubiquitin, cytochrome c, lysozyme and β-lactoglobulin as prototypical proteins, this approach can be used to predict the fragmentation patterns of intact proteins. For sufficiently highly charged proteins, specific cleavages occur near the first low-basicity amino acid residues that are protonated with increasing charge state. Hybrid QM/QM′ (QM=quantum mechanics) and molecular dynamics (MD) simulations and energy-resolved collision-induced dissociation measurements indicated that the barrier to the specific dissociation of the protonated amide backbone bond is significantly lower than competitive charge remote fragmentation. Unlike highly charged peptides, the protons at low-basicity sites in highly charged protein ions can be confined to a limited sequence of low-basicity amino acid residues by electrostatic repulsion, which results in highly specific fragmentation near the site of protonation. This research suggests that the optimal charge states to form specific sequence ions of intact proteins in higher abundances than the use of less specific ion dissociation methods can be predicted a priori.     

NIFTy 3 – Numerical Information Field Theory: A Python Framework for Multicomponent Signal Inference on HPC Clusters

NIFTy , “Numerical Information Field Theory,” is a software framework designed to ease the development and implementation of field inference algorithms. Field equations are formulated independently of the underlying spatial geometry allowing the user to focus on the algorithmic design. Under the hood, NIFTy ensures that the discretization of the implemented equations is consistent. This enables the user to prototype an algorithm rapidly in 1D and then apply it to high‐dimensional real‐world problems. This paper introduces NIFTy  3, a major upgrade to the original NIFTy  framework. NIFTy  3 allows the user to run inference algorithms on massively parallel high performance computing clusters without changing the implementation of the field equations. It supports n‐dimensional Cartesian spaces, spherical spaces, power spaces, and product spaces as well as transforms to their harmonic counterparts. Furthermore, NIFTy  3 is able to handle non‐scalar fields, such as vector or tensor fields. The functionality and performance of the software package is demonstrated with example code, which implements a mock inference inspired by a real‐world algorithm from the realm of information field theory. NIFTy  3 is open‐source software available under the GNU General Public License v3 (GPL‐3) at https://gitlab.mpcdf.mpg.de/ift/NIFTy/tree/NIFTy_3 .     

Development and validation of an ultra‐high‐performance liquid chromatography–tandem mass spectrometry method to determine the bioavailability of warfarin and its major metabolite 7‐hydroxy warfarin in rats dosed with oral formulations containing different polymorphic forms

A simple, sensitive and rapid ultra‐high‐performance liquid chromatography–electrospray ionization–tandem mass spectrometry method was developed and validated for the quantification of warfarin and 7‐hydroxy warfarin in Sprague Dawley (SD) rats. Animals were administered a single dose of warfarin sodium formulations (crystalline and amorphous) at 12 mg/kg via oral gavage and blood was drawn over a 96‐h time course. Sample process recoveries, matrix effect and analyte stability were determined. The linearity for warfarin and 7‐hydroxy warfarin was from 5 to 2000 ng/mL in blank SD rat plasma. Correlation coefficients (r²) for standard calibration curves were >.98 and analytes quantified within ±15% of target at all calibrator concentrations. The average percent accuracy and precision for intra‐ and inter‐day were 93.7%–113.8% and ≤12.1%, respectively, for warfarin and 7‐hydroxy warfarin, across the quality control standards (5, 10, 500, 1800 and 2000 ng/mL). Acceptable analytical recovery (>55%) was achieved with process efficiencies >41.5% and matrix effects <139.9% over the analytical range. Both analytes were stable in stock solution, autosampler, benchtop and three cycles of freeze–thaw with percent accuracy ≥90.2% and precision (percent relative standard deviation) ≤14%. The validated method was successfully applied to a pre‐clinical bioavailability study of crystalline and amorphous warfarin sodium formulations in SD rats.     

DNA interaction,cytotoxicity and molecular structure of cobalt complex of 4‐amino‐N‐(6‐chloropyridazin‐3‐yl)benzene sulfonamide in the presence of secondary ligand pyridine

Novel cobalt complex of 4‐amino‐N‐(6‐chloropyridazin‐3‐yl)benzene sulfonamide (sulfachloropyridazine) has been synthesized and characterized by elemental analysis, FT‐IR spectroscopy and magnetic susceptibility (VSM). Cobalt complex of Sulfachloropyridazine (Co‐SCP) crystallized in monoclinic space group P2₁/n with Z = 4. The structure is solved by direct method and refined to R = 0.099 for 4720 reflections with I ?4σ(I). The results of FT‐IR spectra suggest the binding of cobalt atom to the sulfonamide ligand which is in agreement with the crystal structure determination. In crystal structure, molecule is linked via, C‐H … π, C‐Cl … π and π … π intermolecular interactions. The computational studies like the optimization energy and root means square deviation compare with single crystal structure, frontier molecular orbital (Homo‐Lumo energy) and binding energy of the Co‐SCP has been carried out using DFT/B3LYP level of theory in gaseous phase. Hirshfeld surfaces and the 2D‐fingerprint analysis are performed to study the nature of interactions and their measurable contributions towards crystal packing. The interaction of the complex with DNA is investigated using viscosity measurement and absorption titration studies. The result shows the complex bind to DNA with intercalative mode with high DNA‐binding constant (K_b). Also, in vivo and in vitro cytotoxic studies are performed using S. pombe cells and brine shrimp lethality bioassay. DNA‐cleavage study shows better cleaving ability of the complex.     

Growth and characterization of two-dimensional crystals for communication and energy applications

This review article covers the growth and characterization of two-dimensional (2D) crystals of transition metal chalcogenides, h-BN, graphene, etc. The chemical vapor transport method for bulk single crystal growth is discussed in detail. Top-down methods like mechanical and liquid exfoliation and bottom-up methods like chemical vapor deposition and molecular beam epitaxy for mono/few-layer growth are described. The optimal characterization techniques such as optical, atomic force, scanning electron, and Raman spectroscopy for identification of mono/few-layer(s) of the 2D crystals are discussed. In addition, a survey was done for the application of 2D crystals for both creation and deterministic transfer of single-photon sources and photovoltaic systems. Finally, the application of plasmonic nanoantenna was proposed for enhanced solar-to-electrical energy conversion and faster/brighter quantum communication devices.     

Validation of quartz crystal rheometry in the megahertz frequency regime

The utility of the quartz crystal microbalance (QCM) as a high‐frequency rheometer operating at 15 MHz was demonstrated. High‐frequency data obtained from a series of rubbery materials were compared with results obtained from traditional dynamic mechanical analysis (DMA) at much lower frequencies. The high‐frequency data enable meaningful shift factors to be obtained at temperatures much further above glass‐transition temperature (T _g) than would otherwise be possible, giving a more complete picture of the temperature dependence of the viscoelastic properties. The QCM can also be used to quantify mass uptake and changes in viscoelastic properties during sample oxidation. The viscoelastic response spanning the full range of behaviors from the rubber to glassy regimes was found to fit well with a six‐element model consisting of three power‐law springpot elements. One of these elements is particularly sensitive to the behavior in the transition regime where the phase angle is maximized. The value of this quantity is obtained from the maximum phase angle, which can be obtained from a temperature sweep at fixed frequency, proving a means for more detailed frequency‐dependent rheometric information to be obtained from a fixed‐frequency measurement at a range of temperatures. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2019 , 57, 1246–1254     

A dynamic free-entry oligopoly with sluggish entry and exit adjustments

We study a dynamic free-entry oligopoly with sluggish entry and exit of firms under general demand and cost functions. We show that the number of firms in a steady-state open-loop solution for a dynamic free-entry oligopoly is smaller than that at static equilibrium and that the number of firms in a steady-state memoryless closed-loop solution is larger than that in an open-loop solution.     

Multiple positive solutions for Schrödinger‐Poisson system involving singularity and critical exponent

In this paper, the existence and multiplicity of positive solutions is established for Schrödinger‐Poisson system of the form where 0 ∈ Ω is a smooth bounded domain in , , and λ > 0 is a real parameter. Combining with the variational method and Nehari manifold method, two positive solutions of the system are obtained.     

Unconditionally Superclose Analysis of a New Mixed Finite Element Method for Nonlinear Parabolic Equation

This paper develops a framework to deal with the unconditional superclose analysis of nonlinear parabolic equation. Taking the finite element pair $Q_{11}/Q_{01} × Q_{10}$ as an example, a new mixed finite element method (FEM) is established and the $τ$ -independent superclose results of the original variable $u$ in $H^1$-norm and the flux variable $\mathop{q} \limits ^{\rightarrow}= −a(u)∇u$ in $L^2$-norm are deduced ($τ$ is the temporal partition parameter). A key to our analysis is an error splitting technique, with which the time-discrete and the spatial-discrete systems are constructed, respectively. For the first system, the boundedness of the temporal errors is obtained. For the second system, the spatial superclose results are presented unconditionally, while the previous literature always only obtain the convergent estimates or require certain time step conditions. Finally, some numerical results are provided to confirm the theoretical analysis, and show the efficiency of the proposed method.