Chimera Spectrum Diagnostics for Peptides Using Two-Dimensional Partial Covariance Mass Spectrometry

The rate of successful identification of peptide sequences by tandem mass spectrometry (MS/MS) is adversely affected by the common occurrence of co-isolation and co-fragmentation of two or more isobaric or isomeric parent ions. This results in so-called `chimera spectra’, which feature peaks of the fragment ions from more than a single precursor ion. The totality of the fragment ion peaks in chimera spectra cannot be assigned to a single peptide sequence, which contradicts a fundamental assumption of the standard automated MS/MS spectra analysis tools, such as protein database search engines. This calls for a diagnostic method able to identify chimera spectra to single out the cases where this assumption is not valid. Here, we demonstrate that, within the recently developed two-dimensional partial covariance mass spectrometry (2D-PC-MS), it is possible to reliably identify chimera spectra directly from the two-dimensional fragment ion spectrum, irrespective of whether the co-isolated peptide ions are isobaric up to a finite mass accuracy or isomeric. We introduce ‘3-57 chimera tag’ technique for chimera spectrum diagnostics based on 2D-PC-MS and perform numerical simulations to examine its efficiency. We experimentally demonstrate the detection of a mixture of two isomeric parent ions, even under conditions when one isomeric peptide is at one five-hundredth of the molar concentration of the second isomer.     

Effects of Periodic Excitation on the Flow Around a D-Shaped Cylinder at Low Reynolds Numbers

The baseline and forced flow around a bluff body with semi-elliptical D-shape was investigated by solving the 2D Navier–Stokes equations at low Reynolds numbers. A D-shape rather than the canonic circular-cylinder was selected due to the fixed separation points in the latter, enabling to study a pure wake rather than boundary-layer control. The correlation between Strouhal and Reynolds numbers, the mean drag, the lift and drag oscillations vs. the Reynolds number and wake structure were investigated and compared to experimental and numerical data. Effects of open-loop forcing, resulting from the influence of zero-mass-flux actuators located at the fixed separation points, were studied at a Reynolds number of 150. Fluidic rather than body motion or volume forcing was selected due to applicability considerations. The motivation for the study was to quantify the changes in the flow field features, as captured by Proper Orthogonal Decomposition (POD) analysis, due to open-loop forcing, inside and outside the “lock-in” regime. This is done in order to evaluate the suitability of low-order-models based on POD modes of this changing flow field, for future feed-back flow control studies. The evolution of the natural and the excited vortices in the Kármán wake were also investigated. The formation and convection regions of the vortex evolution were documented. It was found that the forcing causes an earlier detachment of the vortices from the boundary-layers, but does not affect their circulation or convection speeds. The results of the POD analysis of the near-wake flow show that the influence of the bluff body shape (“D”-shaped versus circular cylinder) on the baseline POD wake modes is small. It was found that the eigenfunctions (mode-shapes) of the POD velocity modes are less sensitive to slot excitation than the vorticity modes. As a result of the open-loop excitation, two types of mode-shape-change were observed: a mode can be exchanged with a lower-energy mode or shifted to a low energy level. In the latter case, the most energetic mode becomes the “actuator” mode. The evolution of one-slot excitation on still fluid (“Synthetic jet”) was studied and compared to published data and to “actuator” modes with external flow present. Based on the current findings, it is hypothesized that the cross-flow velocity POD modes are suitable for feedback control of wake flow using periodic excitation, due to their low sensitivity to the excitation as compared to the streamwise velocity or vorticity modes.     

DIOPTAS: a program for reduction of two-dimensional X-ray diffraction data and data exploration

The amount of data collected during synchrotron X-ray diffraction (XRD) experiments is constantly increasing. Most of the time, the data are collected with image detectors, which necessitates the use of image reduction/integration routines to extract structural information from measured XRD patterns. This step turns out to be a bottleneck in the data processing procedure due to a lack of suitable software packages. In particular, fast-running synchrotron experiments require online data reduction and analysis in real time so that experimental parameters can be adjusted interactively. Dioptas is a Python-based program for on-the-fly data processing and exploration of two-dimensional X-ray diffraction area detector data, specifically designed for the large amount of data collected at XRD beamlines at synchrotrons. Its fast data reduction algorithm and graphical data exploration capabilities make it ideal for online data processing during XRD experiments and batch post-processing of large numbers of images.     

Characterizing Methyl‐Bearing Side Chain Contacts and Dynamics Mediating Amyloid β Protofibril Interactions Using 13Cmethyl‐DEST and Lifetime Line Broadening

Many details pertaining to the formation and interactions of protein aggregates associated with neurodegenerative diseases are invisible to conventional biophysical techniques. We recently introduced ¹⁵N dark‐state exchange saturation transfer (DEST) and ¹⁵N lifetime line‐broadening to study solution backbone dynamics and position‐specific binding probabilities for amyloid β (Aβ) monomers in exchange with large (2–80 MDa) protofibrillar Aβ aggregates. Here we use ¹³C_methyl DEST and lifetime line‐broadening to probe the interactions and dynamics of methyl‐bearing side chains in the Aβ‐protofibril‐bound state. We show that all methyl groups of Aβ40 populate direct‐contact bound states with a very fast effective transverse relaxation rate, indicative of side‐chain‐mediated direct binding to the protofibril surface. The data are consistent with position‐specific enhancements of ¹³C_methyl‐${R{{{\rm tethered}\hfill \atop 2\hfill}}}$ values in tethered states, providing further insights into the structural ensemble of the protofibril‐bound state.     

A characterization of duality through section/projection correspondence in the finite dimensional setting

In this paper, we show that the well-known duality operation in the context of convex bodies in Rn is completely characterized by its property of interchanging sections with projections. Our results are compared to results by Böröczky-Schneider and Artstein-Milman, who showed that in many cases, the property of order reversing is sufficient to determine a duality operation, up to obvious linear modifications. In fact, we provide another result that recovers a known characterization of duality by the property of order reversing, and up to a mild condition, also a characterization of duality by interchanging sections by projections.     

Anisotropic Electron Conductance Driven by Reaction Byproducts on a Porous Network of Dibromobenzothiadiazole on Cu(110)

Efficiency in charge‐transport is a fundamental but demanding prerequisite to allow better exploitation of molecular functionalities in organic electronics and energy‐conversion systems. Here, we report on a mechanism that enables a one‐dimensional conductance structure by connecting discrete molecular states at 2.1 eV through the pores of a metal–organic network on Cu(110). Two adjacent, periodic and isoenergetic contributions, namely a molecular resonance and the confined surface‐state, add‐up leading to anisotropic structures, as channels, observable in real‐space conductance images. The adsorption configurations of Br atoms, inorganic byproduct of the redox‐reacted 4,7‐dibromobenzo[c]‐1,2,5‐thiadiazole (2Br‐BTD) molecules on the copper surface, drive the confinement of the Cu surface state within the pores and critically control the channel continuity. Small displacements of the Br atoms change the local surface potential misaligning the energy levels. This work visualizes the effect of order‐disorder transitions caused by the movement of single atoms in the electronic properties of two‐dimensional organic networks.     

Harnack inequality and continuity of solutions to quasi-linear degenerate parabolic equations with coefficients from Kato-type classes

For a general class of divergence type quasi-linear degenerate parabolic equations with measurable coefficients and lower order terms from nonlinear Kato-type classes, we prove local boundedness and continuity of solutions, and the intrinsic Harnack inequality for positive solutions.     

Markov chains on $${{\mathbb {Z}}^+}$$ Z + : analysis of stationary measure via harmonic functions approach

Queueing Systems - We suggest a method for constructing a positive harmonic function for a wide class of transition kernels on $${{\mathbb {Z}}^+}$$ . We also find natural conditions under which...     

Quantitative Estimates on the Binding Energy for Hydrogen in Non-Relativistic QED

In this paper, we determine the exact expression for the hydrogen binding energy in the Pauli–Fierz model up to the order α ⁵ log α ⁻¹, where α denotes the fine structure constant, and prove rigorous bounds on the remainder term of the order o(α ⁵ log α ⁻¹). As a consequence, we prove that the binding energy is not a real analytic function of α, and verify the existence of logarithmic corrections to the expansion of the ground state energy in powers of α, as conjectured in the recent literature.