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The open port interface (OPI) coupled to an atmospheric pressure ion source is used to capture, dilute, focus, and transport nanoliter volume sample droplets for high-speed mass spectrometric analysis. For typical applications, the system has been optimized to achieve 1 Hz nanoliter volume sample transfer rates while simultaneously diluting the sample >1000-fold to minimize sample matrix-induced ionization suppression. Geometric, flow, and dispensing alterations to the system presented here demonstrate that sample transfer rates for the OPI of at least 15 Hz are possible. The fluid dynamic processes that enable sampling rates of 1 Hz and greater are examined in detail by correlating computational fluid dynamics simulations, analytic calculations, experimental data, photographic footage, and reference to the fluid dynamics literature. The resulting models and experimental results provide the rationale underlying the design and tuning of the system as well as information for developing optimized analytical methods. In combination with acoustic droplet dispensing, referred to as acoustic ejection mass spectrometry (AEMS), this system can be considered to be a special case of flow injection analysis with unique features that control the peak width, symmetry, and segregation of the samples transported in a fluid while simultaneously enabling their mixing and dilution with carrier fluids. In addition, conditions are established to prevent direct contact of the sample with a surface enabling, in combination with a contact-free dispenser like acoustic ejection, a dramatic reduction in sample-to-sample carry-over.

The Oriented-Eddy Collision (OEC) model treats turbulent flow as a non-Newtonian fluid where the average behavior of turbulence is modeled as a collection of interacting fluid particles which have inherent orientation. The model is derived from the two-point velocity correlation transport equation, and has the form of a collection of Reynolds-stress transport equations, with one set of transport equations for each representative eddy direction. The addition of eddy orientation information adds important physics to the model and allows the model to represent structural (two-point) information about the turbulence. This structural information is sufficient to allow the model to capture the effect of external forces and imposed mean strains (such as rapid distortion theory) exactly. The only physical effects that must be empirically modeled are those that are due to turbulence-turbulence interactions, referred to as eddy collisions. The performance of the model in a number of canonical flow situations is presented.

Numerical methods with discrete conservation statements are useful because they cannot produce solutions that violate important physical constraints. A large number of numerical methods used in computational fluid dynamics (CFD) have either global or local conservation statements for some of the primary unknowns of the method. This review suggests that local conservation of primary unknowns often follows from global conservation of those quantities. Secondary conservation involves the conservation of derived quantities, such as kinetic energy, entropy, and vorticity, which are not directly unknowns of the numerical system. Secondary conservation can further improve physical fidelity of a numerical solution, but it is typically much harder to achieve. We consider current approaches to secondary conservation and techniques used outside of CFD that are potentially related. Finally, the review concludes with a discussion of how secondary conservation properties might be included automatically.

Prior work has demonstrated the effectiveness of using two-equation closures as the basis for universal, self-adapting turbulence models that are effective at any mesh resolution (Perot and Gadebusch in Phys. Fluids 19:115105, 2007). In order to demonstrate the broad applicability of the fundamental approach, the same behavior is now demonstrated for a second-moment closure (SMC). The SMC has the advantage over the earlier two-equation universal closure of being more accurate in the coarse mesh limit and of having a natural mechanism for backscattering energy from the modeled to the resolved turbulent fluctuations. The mathematical explanation for why Reynolds averaged (RANS) transport equation closures are applicable at any mesh resolution, including the large eddy simulation (LES) regime, is reviewed. It is demonstrated that for the problem of isotropic decaying turbulence, the SMC model produces good predictions at any mesh resolution and with arbitrary initial conditions. In addition, it is shown that the proposed model automatically adapts to the mesh resolution provided. The self-adaptive nature of the method is clearly observed when different initial conditions are used. It is shown that classic RANS models (often thought to produce steady and smooth solutions) can produce three-dimensional, unsteady, and chaotic solutions when generalized correctly and when provided with sufficient mesh resolution. The implications of these observations on the fundamental theories of RANS and LES turbulence modeling are discussed.

Direct numerical simulations (DNSs) are used to investigate the drag-reducing performance of superhydrophobic surfaces (SHSs) in turbulent channel flow. SHSs combine surface roughness with hydrophobicity and can, in some cases, support a shear-free air–water interface. Slip velocities, wall shear stresses and Reynolds stresses are considered for a variety of SHS microfeature geometry configurations at a friction Reynolds number of Reτ ≈ 180. For the largest microfeature spacing studied, an average slip velocity over 75% of the bulk velocity is obtained, and the wall shear stress reduction is found to be nearly 40%. The simulation results suggest that the mean velocity profile near the superhydrophobic wall continues to scale with the wall shear stress but is offset by a slip velocity that increases with increasing microfeature spacing.

The morphology of the nasal cavity in mammals with a good sense of smell includes features that are thought to improve olfactory airflow, such as a dorsal conduit that delivers odours quickly to the olfactory mucosa, an enlarged olfactory recess at the back of the airway, and a clear separation of the olfactory and respiratory regions of the nose. The link between these features and having a good sense of smell has been established by functional examinations of a handful of distantly related mammalian species. In this paper, we provide the first detailed examination of olfactory airflow in a group of closely related species that nevertheless vary in their sense of smell. We study six species of phyllostomid bats that have different airway morphologies and foraging ecologies, which have been linked to differences in olfactory ability or reliance. We hypothesize that differences in morphology correlate with differences in the patterns and rates of airflow, which in turn are consistent with dietary differences. To compare species, we make qualitative and quantitative comparisons of the patterns and rates of airflow through the olfactory region during both inhalation and exhalation across the six species. Contrary to our expectations, we find no clear differences among species in either the patterns of airflow through the airway or in rates of flow through the olfactory region. By and large, olfactory airflow seems to be conserved across species, suggesting that morphological differences appear to be driven by other mechanical demands on the snout, such as breathing and feeding. Olfactory ability may depend on other aspects of the system, such as the neurobiological processing of odours that work within the existing morphology imposed by other functional demands on the nasal cavity.

The olfactory recess-a blind pocket at the back of the nasal airway-is thought to play an important role in mammalian olfaction by sequestering air outside of the main airstream, thus giving odorants time to re-circulate. Several studies have shown that species with large olfactory recesses tend to have a well-developed sense of smell. However, no study has investigated how the size of the olfactory recess relates to air circulation near the olfactory epithelium. Here we used a computer model of the nasal cavity from a bat to test the hypothesis that a larger olfactory recess improves olfactory airflow. We predicted that during inhalation, models with an enlarged olfactory recess would have slower rates of flow through the olfactory region (i.e. the olfactory recess plus airspace around the olfactory epithelium), while during exhalation these models would have little to no flow through the olfactory recess. To test these predictions we experimentally modified the size of the olfactory recess while holding the rest of the morphology constant. During inhalation we found that an enlarged olfactory recess resulted in lower rates of flow in the olfactory region. Upon exhalation, air flowed through the olfactory recess at a lower rate in the model with an enlarged olfactory recess. Taken together, these results indicate that an enlarged olfactory recess improves olfactory airflow during both inhalation and exhalation. These findings add to our growing understanding of how the morphology of the nasal cavity may relate to function in this understudied region of the skull.

Publisher Summary This chapter describes the solution of a single very large pattern-matching search using a supercomputing cluster of GPUs. The objective is to compare a query sequence that has a length on the order of 102 – 106 with a “database” sequence that has a size on the order of roughly 108, and find the locations where the test sequence best matches parts of the database sequence. This study examines how to achieve efficient parallelism for this problem on a single GPU and between the GPUs when they have a relatively slow interconnect. Pattern matching in the presence of noise and uncertainty is an important computational problem in a variety of fields. It is widely used in computational biology and bioinformatics. The Smith–Waterman (SW) algorithm is a dynamic programming algorithm for finding the optimal alignment between two sequences once the relative penalty for mismatches and gaps in the sequences is specified. The optimal match between these two sequences is eight items long and requires the insertion of one gap in the database and the toleration of one mismatch (the third-to-last character in the match) as well as a shifting of the starting point of the query sequence. The SW algorithm determines the optimal alignment by constructing a table that involves an entry for the combination of every item of the query sequence and in the database sequence. The current implementation keeps track of the location of the highest 200 alignment scores on each GPU. This list changes dynamically as the algorithm processes the rows of the table. One way to optimize this algorithm further is to combine the three steps into a single GPU call. The key to this approach is being able to synchronize the threads within the kernel, because each step of the algorithm must be entirely completed (for all threads) before the next step can be executed.

The fractional step method for solving the incompressible Navier-Stokes equations in primitive variables is analyzed as a block LU decomposition. In this formulation the issues involving boundary conditions for the intermediate velocity variables and the pressure are clearly resolved. In addition, it is shown that poor temporal accuracy (first-order) is not due to boundary conditions, but due to the method itself. A generalized block LU decomposition that overcomes this difficulty is presented, allowing arbitrarily high temporal order of accuracy. The generalized decomposition is shown to be useful for a wide range of problems including steady problems. Technical issues, such as stability and the appropriate pressure update scheme, are also addressed. Numerical simulations of the steady, incompressible Navier-Stokes equations in a square domain confirm the theoretical results. 18 refs., 4 figs.

The effect of droplet oscillation on internal heat transfer was investigated using a transient, three-dimensional Navier-Stokes solver for free-surface flows. The code solves conservation of momentum and energy on a three-dimensional deforming domain. The investigation sought to explore the effect that oscillations might have on temperature non-uniformity within droplets. Biot numbers of 0.1 and 0.25 were investigated for three different degrees of distortion: no perturbation, 13% and 35%. The droplets were given an initial perturbation and allowed to relax back to a spherical shape. The results show that the effect of the oscillation is minimal. As expected, the effect was greatest at large distortion and large Biot number. However, it appears that distortion does not contribute much to heat transfer within droplets.Copyright © 2002 by ASME

The effect of axisymmetric contraction and expansion on isotropic turbulence and its subsequent decay are evaluated by way of direct numerical simulation. Low, moderate, and high rates of contraction and expansion are evaluated at a moderate Reynolds number using two different sets of initial conditions of isotropic turbulence. The initial turbulence is generated via mechanical mixing so that the large scales of the turbulence develop naturally. Length scales, decay rates, anisotropy, and two-point correlations are investigated both during and after the straining process, with the goal of quantifying how anisotropic turbulence behaves during return-to-isotropy.

Direct numerical simulation is used to evaluate the effect of plane strain on isotropic homogeneous turbulence. The subsequent return to isotropy after the removal of the strain is also investigated. Large, moderate, and small strain rates are computed at moderate turbulence Reynolds numbers. The initial turbulence is generated via mechanical mixing so that the large scale turbulence develops relatively naturally. Turbulence length scales, Reynolds numbers, decay rates, and anisotropy are computed over the range of the simulations, with the goal of quantifying how anisotropic decay behaves. The simulations indicate that large scale anisotropy may not decay to zero at very large times. In agreement with experimental data, the presence of a recovery region is discerned before the return process is observed. Trajectory crossing is observed on the anisotropy invariant map indicating that anisotropy itself is not sufficient to determine its time evolution. Model constants for classic return-to-isotropy models are determined from the data and shown to vary with time. The oriented-eddy collision model [M. B. Martell and J. B. Perot, “The oriented-eddy collision turbulence model,” Flow, Turbul. Combust. 89(3), 335 (2012)], which includes turbulent structure information, is shown to predict the salient structure of the straining and return process.

These surfaces have been shown to provide drag reduction in laminar and turbulent flows. In this work, direct numerical simulation is used to investigate the drag reducing performance of superhydrophobic surfaces in turbulent channel flow. Slip velocities, wall shear stresses, and Reynolds stresses are determined for a variety of superhydrophobic surface microfeature geometry configurations at friction Reynolds numbers of Re180, Re395, and Re590. This work provides evidence that superhydrophobic surfaces are capable of reducing drag in turbulent flow situations by manipulating the laminar sublayer. For the largest microfeature spacing, an average slip velocity over 80% of the bulk velocity is obtained, and the wall shear stress reduction is found to be greater than 50%. The simulation results suggest that the mean velocity profile near the superhydrophobic wall continues to scale with the wall shear stress and the log layer is still present, but both are offset by a slip velocity that is primarily dependent on the microfeature spacing. © 2010 American Institute of Physics. doi:10.1063/1.3432514

A two-equation transport model is used to model turbulence at any mesh resolution, from Reynolds-averaged Navier–Stokes (RANS), to large eddy simulations (LES), to direct numerical simulations. The two-equation model used is a slight modification of the standard k∕e model that allows the backscatter of energy to resolved scales. A mathematical explanation is provided for why RANS models (such as this two-equation model) are applicable to LES. The model automatically adapts to the mesh resolution provided and no interaction from the user is necessary. This approach is tested on the problem of moderately high Reynolds number isotropic decaying turbulence and gives good predictions at any mesh resolution and with different initial conditions. A detailed analysis shows that at LES resolutions the solution remains fully unsteady and three-dimensional and does not approach a RANS-like solution.

From simulation data it is shown that the difference between the true rate of dissipation of turbulent kinetic energy and the ‘‘isotropic dissipation’’ used by Reynolds‐averaged modelers is less than 2% in a conventional viscous wall region, and negligible elsewhere. The difference is a contribution to viscous diffusion which is a small fraction of the total.