Automated data reduction for hydrogen/deuterium exchange experiments,enabled by high-resolution fourier transform ion cyclotron resonance mass spectrometry

Mass analysis of proteolytic fragment peptides following hydrogen/deuterium exchange offers a general measure of solvent accessibility/hydrogen bonding (and thus conformation) of solution-phase proteins and their complexes. The primary problem in such mass analyses is reliable and rapid assignment of mass spectral peaks to the correct charge state and degree of deuteration of each fragment peptide, in the presence of substantial overlap between isotopic distributions of target peptides, autolysis products, and other interferant species. Here, we show that at sufficiently high mass resolving power (m/Δm_50% ≥ 100,000), it becomes possible to resolve enough of those overlaps so that automated data reduction becomes possible, based on the actual elemental composition of each peptide without the need to deconvolve isotopic distributions. We demonstrate automated, rapid, reliable assignment of peptide masses from H/D exchange experiments, based on electrospray ionization FT-ICR mass spectra from H/D exchange of solution-phase myoglobin. Combined with previously demonstrated automated data acquisition for such experiments, the present data reduction algorithm enhances automation (and thus expands generality and applicability) for high-resolution mass spectrometry-based analysis of H/D exchange of solution-phase proteins.     

Dynamical energy analysis for built-up acoustic systems at high frequencies

Standard methods for describing the intensity distribution of mechanical and acoustic wave fields in the high frequency asymptotic limit are often based on flow transport equations. Common techniques are statistical energy analysis, employed mostly in the context of vibro-acoustics, and ray tracing, a popular tool in architectural acoustics. Dynamical energy analysis makes it possible to interpolate between standard statistical energy analysis and full ray tracing, containing both of these methods as limiting cases. In this work a version of dynamical energy analysis based on a Chebyshev basis expansion of the Perron-Frobenius operator governing the ray dynamics is introduced. It is shown that the technique can efficiently deal with multi-component systems overcoming typical geometrical limitations present in statistical energy analysis. Results are compared with state-of-the-art hp-adaptive discontinuous Galerkin finite element simulations.     

Preserving the activity of cellulase in a batch foam fractionation process

Foam fractionation isone of the low operating-cost techniques for removing proteins from a dilute solution. The initial bulk solution pH and air superficial velocity play an importantrole in the foam-fractionation process. Denaturation of proteins (enzymes) can occur, however, during the foamfractionation process from the shear forces resulting from bursting air bubbles. At the extreme bulk solution pHs (lower than 3.0 and higher than 10.0), the en zymatic activity of cellulase in the foamate phase drops significantly. Within these two pH boundsan increase in the air superficial velocity, V_o, and a decrease in the bulk solution pH leads to a decrease in the separation ratio (SR), defined as theratio of the protein concentration in the foamate to the protein concentration in the residue. On the other hand, an increase in V_o provides a higher foamate-protein recovery. The process efficiency is defined as the product of foamate-protein recovery times the SR times the cellulase activity. The optimal operating condition of the cellulase foamfractionation process is taken into account at the maximum value of the processefficiency. In this study, that optimal condition is atan air superficial velocity of 32 cm/min and a bulk-solution pH of 10.0. At this condition, the recovered foamate is about 80% of the original protein mass, the SR is about 12, and the en zymatic activity is about 60% of the original cellulase activity.     

Bread dough rheology: an improved damage function model

We describe an improved damage function model for bread dough rheology. The model has relatively few parameters, all of which can easily be found from simple experiments as discussed in this paper. Small deformations in the linear region are described by a gel-like power-law memory function. Then, we consider a set of large non-reversing deformations—stress relaxation after a step of shear, steady shearing and elongation beginning from rest and biaxial stretching. With the introduction of a revised strain measure which includes a Mooney–Rivlin term, all of these motions can be well described by the damage function described previously. For reversing step strains, larger amplitude oscillatory shearing and recoil we present a discussion which shows how the damage function model can be applied in these cases.     

An adaptive viscoelastic stress splitting scheme and its applications: AVSS/SI and AVSS/SUPG

We report an adaptive viscoelastic stress splitting (AVSS) scheme, which was found to be extremely robust in the numerical simulation of viscoelastic flow involving steep stress boundary layers. The scheme is different from the elastic viscous split stress (EVSS) in that the local Newtonian component is allowed to depend adaptively on the magnitude of the local elastic stress. Two decoupled versions of the scheme were implemented for the Upper Convected Maxwell (UCM) model: the streamline integration (AVSS/SI), and the streamline upwind Petrov-Galerkin (AVSS/SUPG) methods of integrating the stress. The implementations were benchmarked against the known analytic Poiseuille solution, and no upper limiting Weissenberg number was found (the computation was stopped at Weissenberg number of O(10⁴)). The flow past a sphere in a tube was solved next, giving convergent results up to a Weissenberg number of 3.2 with the AVSS/SI and 1.55 with the AVSS/SUPG (both were decoupled schemes; without the adaptive scheme, the limiting Weissenberg number for the decoupled streamline integration method was about 0.3). These results show that the decoupled AVSS is more stable than the corresponding EVSS, and the SI is more robust than SUPG in solving the constitutive equation of hyperbolic type. In addition, we found a very long stress wake behind the sphere, and a weak vortex in the rear stagnation region at a Weissenberg number above W_i of about 1.6, which does not seem to increase in size or strength with increasing W_i.     

β-Octafluorinated tetrakis(ethoxycarbonyl)porphyrin

Tetrakis(alloxycarbonyl)porphyrin and its β-octafluoro-substituted derivatives were synthesized via Lindsey method and transformed to their zinc complexes.Single crystal X-ray structures of corresponding Zn(Ⅱ) porphyrins revealed that β-octafluorination will give more compactness of porphyrin moieties in the crystal structure owing to the hydrogen bonding interactions involving β-fluorine atoms.An unusual six-coordinated Zn(Ⅱ) was found via intramolecular coordination of oxygen atom of meso-substituents with central Zn(Ⅱ).     

Microviscoelasticity of soft repulsive sphere dispersions: tracer particle microrheology of triblock copolymer micellar liquids and soft crystals

Tracer particle microrheology using diffusing wave spectroscopy-based microrheology is demonstrated to be a useful method to study the dynamics of aqueous Pluronic? F108 solutions, which are viewed as solutions of repulsive soft spheres. The measured zero-shear microviscosity of noncrystallizing micellar dispersions indicates micelle corona dehydration upon increasing temperature. Colloidal sphere thermal motion is shown to be exquisitely sensitive to the onset of crystallization in these micellar dispersions. High temperature dynamics are dominated by an apparent soft repulsive micelle-micelle interaction potential indicating the important role played by lubrication forces and ultimately micelle corona interpenetration and compression at sufficiently high concentrations. The measured microscopic viscoelastic storage and loss moduli are qualitatively similar to those experimentally observed in mechanical measurements on colloidal dispersions and crystals, and calculated from mode coupling theory of colloidal suspensions. The observation of subdiffusive colloidal sphere thermal motion at short time-scales is strong evidence that the observed microscopic viscoelastic properties reflect the dynamics of individual micelles rather than a dispersion of micellar crystallites.     

Measurement and Prediction of Machining Induced Redistribution of Residual Stress in the Aluminium Alloy 7449

The residual stress distributions in two 7449 aluminium alloy rectilinear blocks have been determined using neutron diffraction. Heat treatment included cold water immersion quenching and a period of precipitation hardening. Quenching induced very high magnitude residual stresses into the two blocks. One block was measured in this condition while the other was incrementally machined by milling to half thickness. Neutron diffraction measurements were made on the milled half thickness block at equivalent locations to the unmachined block. This permitted through thickness measurements from both blocks to be compared, revealing the redistribution of residual stresses induced by machining. A square cross section post in the centre of the machined face was left to act as a stress free reference sample. The distortions arising on the face opposite to that being milled were measured using a co-ordinate measuring machine. The residual stresses and distortion arising in the blocks have been compared to finite element analysis prediction and found to generally agree. Material removal only caused distortion and the residual stresses to redistribute; there was no stress relaxation evident.     

Construction of fiber-optic bundle light-collection systems and calculations of collection efficiency

This paper describes the position-sensitive light-collection system that we use in our fast-beam laser experiments. The collection system consists of fiber-optic bundles whose facets are arranged to accept light emitted from a beam of fluorescent atoms. The flexibility of the fiber bundles allows their use in scanning collection systems with precise position sensitivity. We describe calculations of geometrical collection efficiency using a numerical integration scheme and compare the results with measurements. We also compare the collection efficiencies of the different fiber bundle arrangements that we used as our apparatus evolved with the implementation of various improvements.