Stringent Test Case Research Articles

Linear triglycerol-based fluorosurfactants show high potential for droplet-microfluidics-based biochemical assays.

Fluorosurfactants have expanded the landscape of high-value biochemical assays in microfluidic droplets, but little is known about how the spatial geometries and polarity of the head group contribute to the performance of fluorosurfactants. To decouple this, we design, synthesize, and characterize two linear and two dendritic glycerol- or tris-based surfactants with a common perfluoropolyether tail. To reveal the influence of spatial geometry, we choose inter-droplet cargo transport as a stringent test case. Using surfactants with linear di- and triglycerol, we show that the inter-droplet cargo transport is minimal compared with their dendritic counterparts. When we encapsulated a less-leaky sodium fluorescent dye into the droplets, quantitatively, we find that the mean fluorescence intensity of the PFPE-dTG stabilized PBS-only droplets after 72 h was ∼3 times that of the signal detected in PBS-only droplets stabilized by PFPE-lTG. We also demonstrate that the post-functionalization of PFPE-lTG having a linear geometry and four hydroxy groups enables the 'from-Droplet' fishing of the biotin-streptavidin protein complex without the trade-off between fishing efficiency and droplet stability. Thus, our approach to design user-friendly surfactants reveals the aspects of spatial geometry and facile tunability of the polar head groups that have not been captured or exploited before.

Absolute SiO concentration imaging in low-pressure nanoparticle-synthesis flames via laser-induced fluorescence

In this paper, we present a strategy for imaging measurements of absolute concentration values of gas-phase SiO in the combustion synthesis of silica, generated from the reaction of hexamethyldisiloxane (HMDSO) precursor in a lean (ϕ = 0.6) hydrogen/oxygen/argon flame. The method is based on laser-induced fluorescence (LIF) exciting the Q(42) rotational transition within the A1Π − X1Σ (1, 0) electronic band system of SiO at 231 nm. Corrections for temperature-dependent population of the related ground state are based on multi-line SiO–LIF thermometry utilizing transitions within the A1Π − X1Σ (0, 0) electronic band around 234 nm. Corrections for local collisional quenching are based on measured effective fluorescence lifetimes from the temporal signal decay using a short camera gate stepped with respect to the laser pulse. This fluorescence lifetime measurement was confirmed with additional measurements using a fast photomultiplier. The resulting semi-quantitative LIF signal was photometrically calibrated using Rayleigh scattering from known gas samples at various pressures and laser energies as well as with nitric oxide LIF. The obtained absolute SiO concentration values in the HMDSO-doped flames will serve as a stringent test case for recently developed flame kinetic mechanisms for this class of gas-borne silicon dioxide nanoparticle synthesis.

Molecular dynamics methods to predict peptide locations in membranes: LAH4 as a stringent test case

Determining the structure of membrane-active peptides inside lipid bilayers is essential to understand their mechanism of action. Molecular dynamics simulations can easily provide atomistic details, but need experimental validation. We assessed the reliability of self-assembling (or “minimum-bias”) and potential of mean force (PMF) approaches, using all-atom (AA) and coarse-grained (CG) force-fields. The LAH4 peptide was selected as a stringent test case, since it is known to attain different orientations depending on the protonation state of its four histidine residues.In all simulations the histidine side-chains inserted in the membrane when neutral, while they interacted with phospholipid headgroups in their charged state. This led to transmembrane orientations for neutral-His LAH4 in all minimum-bias AA simulations and in most CG trajectories. By contrast, the charged-His peptide stabilized membrane defects in AA simulations, whereas it was located at the membrane surface in some CG trajectories, and interacted with both lipid leaflets in others. This behavior is consistent with the higher antimicrobial activity and membrane-permeabilizing behavior of the charged-His LAH4. In addition, good agreement with solid-state NMR orientational data was observed in AA simulations.PMF calculations correctly predicted a higher membrane affinity for the neutral-His peptide. Interestingly, the structures and relative populations of PMF local free-energy minima corresponded to those determined in the less computationally demanding minimum-bias simulations.These data provide an indication about the possible membrane-perturbation mechanism of the charged-His LAH4 peptide: by interacting with lipid headgroups of both leaflets through its cationic side-chains, it could favor membrane defects and facilitate translocation across the bilayer.

Statistically accurate low-order models for uncertainty quantification in turbulent dynamical systems.

A framework for low-order predictive statistical modeling and uncertainty quantification in turbulent dynamical systems is developed here. These reduced-order, modified quasilinear Gaussian (ROMQG) algorithms apply to turbulent dynamical systems in which there is significant linear instability or linear nonnormal dynamics in the unperturbed system and energy-conserving nonlinear interactions that transfer energy from the unstable modes to the stable modes where dissipation occurs, resulting in a statistical steady state; such turbulent dynamical systems are ubiquitous in geophysical and engineering turbulence. The ROMQG method involves constructing a low-order, nonlinear, dynamical system for the mean and covariance statistics in the reduced subspace that has the unperturbed statistics as a stable fixed point and optimally incorporates the indirect effect of non-Gaussian third-order statistics for the unperturbed system in a systematic calibration stage. This calibration procedure is achieved through information involving only the mean and covariance statistics for the unperturbed equilibrium. The performance of the ROMQG algorithm is assessed on two stringent test cases: the 40-mode Lorenz 96 model mimicking midlatitude atmospheric turbulence and two-layer baroclinic models for high-latitude ocean turbulence with over 125,000 degrees of freedom. In the Lorenz 96 model, the ROMQG algorithm with just a single mode captures the transient response to random or deterministic forcing. For the baroclinic ocean turbulence models, the inexpensive ROMQG algorithm with 252 modes, less than 0.2% of the total, captures the nonlinear response of the energy, the heat flux, and even the one-dimensional energy and heat flux spectra.

Energetic and environmental benefits of co-digestion of food waste and cattle slurry: A preliminary assessment

The research evaluated the feasibility of centralised pre-processing and pasteurisation of source-separated domestic food waste followed by transport to farms for anaerobic co-digestion with dairy cattle slurry. Data from long-term experiments on the co-digestion of these two substrates was used to predict gross energy yields; net yields were then derived from full system analysis using an energy modelling tool. The ratio of cattle slurry to food waste in the co-digestion was based on the nutrient requirements of the dairy farm and was modelled using both nitrogen and phosphorous as the limiting factor. The model was run for both medium-size and large farms in which the cattle were housed either all year round or for only 50% of the year. The results showed that the addition of food waste improved energy yields per digester unit volume, with a corresponding increased potential for improving farm income by as much as 50%. Data for dairy farms in the county of Hampshire UK, which has a low density of dairy cattle and a large population, was used as a stringent test case to verify the applicability of the concept. In this particular case the nutrient requirements of the larger farms could be satisfied, and further benefits were gained from the reduction in greenhouse gas emissions avoided through improved manure management and fertiliser imports. The results indicated that this approach offered major advantages in terms of resource conservation and pollution abatement when compared to either centralised anaerobic digestion of food waste or energy recovery from thermal treatment.

Time-dependent density functional theory versus Bethe–Salpeter equation: an all-electron study

We perform first-principle calculations for the macroscopic dielectric function within an all-electron full-potential framework, i.e., the linearized augmented planewave (LAPW) method. To this extent we pursue two different routes, which are, on the one hand, many-body perturbation theory (MBPT) by solving the Bethe-Salpeter equation (BSE), and time-dependent density functional theory (TDDFT), on the other hand. The implementation into one program package, i.e., the EXC!TiNG code, allows a direct comparison of these approaches, in terms of accuracy as well as efficiency. We briefly review the theory, and describe in detail the quantities specific to the LAPW method. As an example we show the results for GaAs which is well-investigated in the literature, and hence serves as a stringent test case.

FASTDXL: A Generalized Screen to Trap Disulfide-Stabilized Complexes for Use in Structural Studies

Structural studies of macromolecular complexes have produced extraordinary insights into a wide variety of biological processes. Unfortunately, as structural biologists pursue larger and more challenging assemblies, weakly stable and/or nonspecific interactions can become significant roadblocks to structure determination. We have developed a rapid and effective pool-based screen, termed FASTDXL (focused array screening technique for disulfide X-linking), to produce and identify disulfide-stabilized protein-nucleic acid assemblies. A significant strength of FASTDXL is that it can take advantage of prior structural knowledge about molecular interactions, but does not necessarily rely upon it. A detailed application of the approach to the difficult problem of trapping a bacterial primase-ssDNA complex is described, validating the method as a route toward obtaining diffracting crystals suitable for structure determination.

Causal viscous hydrodynamics for central heavy-ion collisions

We study causal viscous hydrodynamics in the context of central relativistic heavy-ion collisions and provide details of a straightforward numerical algorithm to solve the hydrodynamic equations. It is shown that correlation functions of fluctuations provide stringent test cases for any such numerical algorithm. Passing these tests, we study the effects of viscosity on the temperature profile in central heavy-ion collisions. Also, we find that it is possible to counter-act the effects of viscosity to some extent by re-adjusting the initial conditions. However, viscous corrections are strongest for high-mass particles, signaling the breakdown of hydrodynamic descriptions for large eta/s.

Relaxation of open crystal structures with a density functional tight-binding scheme: Illustration in the case of the acetonitrile crystal

In view of its interest for high pressure simulations of molecular crystals, the self-consistent field density functional tight-binding model is coupled to a symmetry-constrained optimization routine and applied to a stringent test case: the open structure of the acetonitrile crystal. The symmetry-constrained relaxation is compared with two symmetry-unconstrained relaxations, one starting from the observed X-ray structure and the other one from a structure obtained after a optimization of the atoms positions within the observed unit cell. According to the procedure employed for the crystal relaxation, three different energy minima with similar energies are found.

Accuracy of the Induced Velocity from Helicoidal Wake Vortices Using Straight-Line Segmentation

The accuracy of a straight-line segmentation approximation to a series of helicoidal vortices is considered. The problem is examined for different values of the helical pitch, the number of wake turns, and the wake skew angle. Results documenting both the accuracy and the relative errors of the discretized helical vortex and a vortex ring are compared. It is found that with sufficiently small segments, straight-line segmentation of both the vortex ring and of the helical vortex give at least a second-order accurate reconstruction of the induced velocity field. It is shown that the vortex ring can be viewed as a special case of a helical vortex as its pitch tends to zero. Based on the magnitude of the errors found for the two cases, a vortex ring is shown to be a more stringent test case than a helical vortex when the straight-line segmentation approach is used. The accuracy of the induced velocity field when a skewed helix is represented by straight-line segmentation is shown to be second-order accurate for various combinations of helical pitch and wake skew angle. A comparison with the unskewed helical vortex reveals that the errors in the induced velocity field are almost the same in the two cases. Nomenclature a = empirical constant for wake expansion E =L egendre’s elliptic integral of the second kind K =L egendre’s elliptic integral of the first kind L 2 norm = second norm of the error vector M = number of divisions per revolution of helical wake N = number of turns in the helix N f = number of vortex filaments in the helix p = helical pitch (distance between adjacent filaments normalized by radius) R = rotor radius or radius of vortex ring, m

Bulk Band Gaps in Divalent Hexaborides

Complementary angle-resolved photoemission and bulk-sensitive k-resolved resonant inelastic x-ray scattering of divalent hexaborides reveal a >1 eV X-point gap between the valence and conduction bands, in contradiction to the band overlap assumed in several models of their novel ferromagnetism. This semiconducting gap implies that carriers detected in transport measurements arise from defects, and the measured location of the bulk Fermi level at the bottom of the conduction band implicates boron vacancies as the origin of the excess electrons. The measured band structure and X-point gap in CaB6 additionally provide a stringent test case for many-body quasiparticle band calculations.

RecA-promoted sliding of base pairs within DNA repeats: quantitative analysis by a slippage assay

RecA that catalyses efficient homology search and exchange of DNA bases has to effect major transitions in the structure as well as the dynamics of bases within RecA–DNA filament. RecA induces slippage of paired strands in poly(dA)–poly(dT) duplex using the energy of ATP hydrolysis. Here, we have adopted the targeted ligation assay and quantified the strand slippage within a short central cassette of (dA) 4–(dT) 4 duplex. The design offers a stringent test case for scoring a cross-talk between A residues with those of T that are diagonally placed on the opposite strand at either −3, −2, −1, +1, +2, or +3 pairing frames. As expected, the cross-talk levels in RecA mediated as well as thermally annealed duplexes were maximal in non-diagonal pairing frame (i.e., 0-frame), the levels of which fell off gradually as the frames became more diagonal, i.e., −3<−2<−1 or +3<+2<+1. Interestingly, the level of cross-talk in naked duplexes was intrinsically less efficient in minus frames than their plus frame counterparts. The asymmetry created in naked duplexes by such a disparity between minus versus plus frames was partially obviated by RecA. Moreover, RecA promoted a significantly higher level of cross-talk selectively in −2 and −1 frames, as compared to that in naked DNA, which suggests a model that the elevated cross-talk in RecA filament may be limited to base pairs housed within the same rather than adjacent RecA monomers.

Sigma Coordinate Pressure Gradient Errors and the Seamount Problem

In a recent paper by Mellor et al., it was found that, in two-dimensional ( x, z) applications with finite horizontal viscosity and zero diffusivity, the velocity error, associated with the evaluation of horizontal density or pressure gradients on a sigma coordinate grid, prognostically disappeared, leaving behind a small and physically insignificant distortion in the density field. The initial error is numerically consistent in that it decreases as the square of the grid increment size. In this paper, we label this error as a sigma error of the first kind. In three-dimensional applications, the authors have encountered an error that did not disappear and that has not been understood by us or, apparently, others. This is a vorticity error that is labeled a sigma error of the second kind and is a subject of this paper. Although it does not prognostically disappear, it seems to be tolerably small. To evaluate these numerical errors, the authors have adopted the seamount problem initiated by Beckman and Haidvogel. It represents a stringent test case, as evidenced by their paper, wherein the model is initialized with horizontal isopycnals, zero velocity, and no forcing; then, any velocities that develop must be considered errors. Two appendices are important adjuncts to the paper, the first providing theoretical confirmation and understanding of the numerical results, and the second delving into additional errors related to horizontal or isosigma diffusion. It is, however, shown that satisfactory numerical solutions are obtained with zero diffusivity.

Transition states for hydrogen radical reactions: LiFH as a stringent test case for density functional methods

The Becke three-parameter Lee–Yang–Parr (B3LYP) density functional method is applied to the study of the reaction Li + HF → H + LiF; the results obtained are compared with experiment and previous multireference singles and doubles configuration interaction (MRDCI) calculations, and with singles and doubles quadratic configuration interaction (QCISD) and Gaussian 2 (G2) model chemistry calculations performed also in this paper. It is found that, using an extended 6-311 + + G(3df,3pd) basis set, the predicted stabilization enthalpy of the initial LiFH complex (–34•6 kJ mo1-1) and the exoergicity of the reaction (–7•3 kJ mo1-1) are predicted in agreement with experiment (∼ – 31 kJ mo1-1 and – 4•8 ± 8 kJ mo1-1, respectively). These results are also in agreement with the MRDCI calculations (∼ – 31•5 kJ mo1-1 and – 9 kJ mo1-1, respectively). However, the energy of the transition state with respect to the reactants at the B3LYP level is about 25 kJ mo1-1 lower than the MRDCI result (which agrees with the QCISD a...

Transition states for hydrogen radical reactions: LiFH as a stringent test case for density functional methods

Transition states for hydrogen radical reactions: LiFH as a stringent test case for density functional methods

Redundancy analysis and the evolutionary learning algorithm as complementary processing tools for dendrochronological data

To process dendrochronological data sets, mathematical techniques that can handle complexity are needed. Two methods from the field of numerial ecology are introduced in tree ring analysis: redundancy analysis (an eigenvector method) and the evolutionary learning algorithm (a machine learning tool). Both methods show to be appropriate for a stringent test case. Redundancy analysis explains variance in tree ring data by environmental date revealing main trends. The evolutionary learning algorithm can be applied to look for unexpected strong environmental signals possibly departing from main trends.

Test of high-angular-resolution X-ray photoelectron diffraction and holographic imaging for c(2 × 2)S on Ni(001)

We have obtained azimuthal X-ray photoelectron diffraction (XPD) data with a high angular resolution of ± 1.5° for S2p emission from the well-defined surface structure of c(2 × 2)S on Ni(001). The relatively high position of the adsorbate with respect to the substrate makes this a stringent test case of the structural sensitivity of forward-scattering-dominated XPD. With this higher resolution, the data are nonetheless found to be sensitive to atomic structure, including in particular both the vertical height of S above Ni ( z) and the first-to-second layer Ni interplanar spacing ( d 12). A single scattering cluster (SSC) theoretical analysis using R-factors to judge goodness of fit yields z = 1.39 ± 0.05 A ̊ and d 12 = 1.86 ± 0.05 A ̊ , in excellent agreement with other recent experimental and theoretical studies. This analysis also indicates that clusters of up to at least 25 Å in radius (200–250 atoms) are needed to accurately describe all of the diffraction fine structure observed; thus, although XPD is primarily a short-range order probe, high-resolution data provides sensitivity to order that may go out as far as 10–15 neighbor shells. For takeoff angles with respect to the surface of less than about 10°, multiple scattering effects appear to become more important, as verified by fully converged multiple scattering cluster (MSC) calculations; however, for takeoff angles larger than 10°, these effects fall away rapidly, making a single-scattering analysis of such data still a useful approach. Finally, we have analyzed our experimental data and SSC simulations of it using recently suggested Fourier-transform holographic inversion methods. Although our data are too limited to permit fully accurate holographic imaging, features associated with the nearest neighbor S atoms in the adsorbate overlayer are seen in both experimental and theoretical images. In addition, the theoretical calculations indicate that the atomic images can be improved if: the solid angle of the hologram is limited so as to exclude the strong forward scattering features at low takeoff angles; effects due to non-constant scattering factor amplitudes and phases are corrected out using the scattered-wave-included Fourier-transform method of Saldin et al., and/or the hologram range is further limited so as to avoid the overlap of twin and real images. Several interesting directions for further study with such high-resolution data, SSC R-factor analyses, and holographic imaging, are thus suggested.

Microscopic models for quantum mechanical calculations of chemical processes in solutions: LD/AMPAC and SCAAS/AMPAC calculations of solvation energies

AbstractOur previously developed approaches for integrating quantum mechanical molecular orbital methods with microscopic solvent models are refined and examined. These approaches consider the nonlinear solute–solvent coupling in a self‐consistent way by incorporating the potential from the solvent dipoles in the solute Hamiltonian, while considering the polarization of the solvent by the potential from the solute charges. The solvent models used include the simplified Langevin Dipoles (LD) model and the much more expensive surface constrained All Atom Solvent (SCAAS) model, which is combined with a free energy pertubation (FEP) approach. Both methods are effectively integrated with the quantum mechanical AMPAC package and can be easily combined with other quantum mechanical programs. The advantages of the present approaches and their earlier versions over macroscopic reaction field models and supermolecular approaches are considered. A LD/MNDO study of solvated organic ions demonstrates that this model can yield reliable solvation energies, provided the quantum mechanical charges are scaled to have similar magnitudes to those obtained by high level ab initio methods. The incorporation of a field‐dependent hydrophobic term in the LD free energy makes the present approach capable of evaluating the free energy of transfer of polar molecules from non polar solvents to aqueous solutions. The reliability of the LD approach is examined not only by evaluating a rather standard set of solvation energies of organic ions and polar molecules, but also by considering the stringent test case of sterically hindered hydrophobic ions. In this case, we compare the LD/MNDO solvation energies to the more rigorous FEP/SCAAS/MNDO solvation energies. Both methods are found to give similar results even in this challenging test case. The FEP/SCAAS/AMPAC method is incorporated into the current version of the program ENZYMIX. This option allows one to study chemical reactions in enzymes and in solutions using the MNDO and AM1 approximations. A special procedure that uses the EVB method as a reference potential for SCF MO calculations should help in improving the reliability of such studies.

Determination of the chemical environment of sulphur in petroleum asphaltenes by X-ray absorption spectroscopy

Sulphur K-edge X-ray absorption spectra are analysed for a diverse series of petroleum asphaltenes. The spectra of the asphaltenes are interpreted by fitting with a linear superposition of model compound spectra. This analysis procedure is shown to work quite well in a stringent test case. The reduced forms of sulphur, thiophenes and sulphides dominate in all of the asphaltenes. Generally, the sulphoxide group is the most dominant form of the oxidized sulphur. Comparison of the X-ray data with the elemental composition of the asphaltenes shows that the sulphur and oxygen are preferentially bonded to each other. The inverse dependence of the oxygen-sulphur correlation with the fraction of sulphur which is sulphide suggests that oxidation of sulphur occurs preferentially at the sulphide group.

Calculation of radial couplings in the model-potential and pseudopotential approaches: The NaH quasimolecule.

We present an extension of the analytical method of Macias and Riera to calculate radial couplings, to include model potentials or (local and nonlocal) pseudopotentials, in the Hamiltonian. As an illustration, energies, couplings, and momentum matrix elements are presented and discussed for the two-effective-electron NaH quasimolecule, as a stringent test case.