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At least 127 records · Page 7

Numerical investigation of microbial quorum sensing under various flow conditions

Microorganisms efficiently coordinate phenotype expressions through a decision-making process known as quorum sensing (QS). We investigated QS amongst distinct, spatially distributed microbial aggregates under various flow conditions using a process-driven numerical model. Model simulations assess the conditions suitable for QS induction and quantify the importance of advective transport of signaling molecules. In addition, advection dilutes signaling molecules so that faster flow conditions require higher microbial densities, faster signal production rates, or higher sensitivities to signaling molecules to induce QS. However, autoinduction of signal production can substantially increase the transport distance of signaling molecules in both upstream and downstream directions. We present empirical approximations to the solutions of the advection–diffusion–reaction equation that describe the concentration profiles of signaling molecules for a wide range of flow and reaction rates. These empirical relationships, which predict the distribution of dissolved solutes along pore channels, allow to quantitatively estimate the effective communication distances amongst multiple microbial aggregates without further numerical simulations.

59 BASIC BIOLOGICAL SCIENCES↗

Turbulent Kinetic Energy Budgets over Gentle Topography Covered by Forests

Large-eddy simulations of flow over a “horizontally” uniform model forest are used to investigate the effects of gentle topography on the turbulent kinetic energy (TKE) budget within the canopy roughness sublayer. Despite significant differences between simulations using idealized sinusoidal topography and real topography of the Amazon forest, results indicate that the effects of topography are located predominantly in the upper canopy and above, and are mostly caused by mean advection of TKE. The “horizontally” averaged TKE budget from idealized and real gentle topographies are almost identical to that for flat terrain, including a clear inertial layer above the roughness sublayer in which shear production is balanced by local dissipation. At topography crests, where observational towers are usually located, mean vertical advection of TKE can be as important as horizontal advection. Here, we propose the use on an approximate TKE balance equation to estimate mean advection from single tower measurements, and introduce a new advection index that can be used as a proxy to quantify the importance of the topography on the TKE budget.

54 ENVIRONMENTAL SCIENCES↗

New insights into the flow dynamics of a deep freshwater aquifer in the semi-arid and saline Cuvelai-Etosha Basin, Northern Namibia: Results of a multi-environmental tracer study

Study region A paleo-megafan system of the Cubango River in the northern parts of the semi-arid Cuvelai-Etosha Basin, shared by Angola and Namibia. It hosts a deep freshwater aquifer, the so-called Kalahari-Ohangwena 2 (KOH-2), with the potential to resolve the imminent regional water supply shortages. Study focus Hydrogeochemical and multi-environmental tracer studies incorporating the use of age tracers 14 C, 36 Cl, 81 Kr and 4 He to determine the age of groundwater and provide insights into the flow dynamics of the KOH-2. New hydrological insights for the region Stable water isotopes and noble gas thermometry show that in a period with higher rainfall and recharge, temperatures were at least 3 – 4 °C lower than today. Several arguments led to the conclusion that younger groundwater, possibly of an age of 35,000 years, is mixed with ancient saline pore water. These include: 1) the correlation of measured 36 Cl and 81 Kr ratios, as well as 4 He concentrations, using a binary mixing model, and 2) the substantial variation in 81 Kr ages, ranging from 40,000 to 170,000 years, over relatively short distances—a phenomenon challenging to explain by advective groundwater flow equations. Consequently, the ages derived from 81 Kr measurements serve as indicators of the extent of freshening and therefore describe mixing ages rather than absolute travel times.

54 ENVIRONMENTAL SCIENCES↗

Observations of Offshore Internal Boundary Layers

The growth of the marine internal boundary layer (MIBL, height h i ) with the shore-normal distance x, is a topic of continuing interest because of its applications in coastal dispersion, offshore wind farm siting, coastal air-sea fluxes and in evaporative ducting. Available data on MIBL are only scarce, given its difficult to measure the variability of coastal winds. During Coupled Air-Sea Processes and Electromagnetic Research (CASPER) campaigns an array of instrumentation was deployed to measure offshore spatial variability and its effect on electromagnetic wave propagation. Meteorological sensors (flux towers and remote sensing) were deployed along the coast of Point Mugu, California, on a research vessel and FLoating Instrument Platform (FLIP) provided surface layer and boundary layer observations. In this article, measurements from multiple remote sensing instruments, such as synchronized triple Doppler lidars, small boat operations with tethered lifting system, and radiosondes provide a holistic view of the MIBL growth and its spatial variability from the coast. A convective and stable MIBL observed during two intensive operating period days showed distinct growth characteristics off the coast of Point-Mugu. During stable stratified atmospheric conditions, an MIBL was observed at least up to 47 km from the coast. The growth of the MIBL within the nearshore adjustment zone was influenced by surrounding atmospheric, oceanographic, and topographic conditions. A new parameterization scheme is developed based on advection-diffusion balance equations accounting for upstream turbulence and compared with h i observations from Doppler lidar and profiles from small boat. An evaluation of existing IBL theories was also conducted.

54 ENVIRONMENTAL SCIENCES↗

Randomized Sketching Algorithms for Low-Memory Dynamic Optimization

This paper develops a novel limited-memory method to solve dynamic optimization problems. The memory requirements for such problems often present a major obstacle, particularly for problems with PDE constraints such as optimal flow control, full waveform inversion, and optical tomography. In these problems, PDE constraints uniquely determine the state of a physical system for a given control; the goal is to find the value of the control that minimizes an objective. While the control is often low dimensional, the state is typically more expensive to store. This paper suggests using randomized matrix approximation to compress the state as it is generated and shows how to use the compressed state to reliably solve the original dynamic optimization problem. Concretely, the compressed state is used to compute approximate gradients and to apply the Hessian to vectors. The approximation error in these quantities is controlled by the target rank of the sketch. This approximate first- and second-order information can readily be used in any optimization algorithm. As an example, we develop a sketched trust-region method that adaptively chooses the target rank using a posteriori error information and provably converges to a stationary point of the original problem. Numerical experiments with the sketched trust-region method show promising performance on challenging problems such as the optimal control of an advection-reaction-diffusion equation and the optimal control of fluid flow past a cylinder.

97 MATHEMATICS AND COMPUTING↗

Triangle based TVD schemes for hyperbolic conservation laws

A triangle based total variation diminishing (TVD) scheme for the numerical approximation of hyperbolic conservation laws in two space dimensions is constructed. The novelty of the scheme lies in the nature of the preprocessing of the cell averaged data, which is accomplished via a nearest neighbor linear interpolation followed by a slope limiting procedures. Two such limiting procedures are suggested. The resulting method is considerably more simple than other triangle based non-oscillatory approximations which, like this scheme, approximate the flux up to second order accuracy. Numerical results for linear advection and Burgers' equation are presented.

Durlofsky, Louis J.↗

Triangle based adaptive stencils for the solution of hyperbolic conservation laws

A triangle based total variation diminishing (TVD) scheme for the numerical approximation of hyperbolic conservation laws in two space dimensions is constructed. The novelty of the scheme lies in the nature of the preprocessing of the cell averaged data, which is accomplished via a nearest neighbor linear interpolation followed by a slope limiting procedures. Two such limiting procedures are suggested. The resulting method is considerably more simple than other triangle based non-oscillatory approximations which, like this scheme, approximate the flux up to second order accuracy. Numerical results for linear advection and Burgers' equation are presented.

Durlofsky, Louis J.↗

Evolution of a magnetic flux tube in two-dimensional penetrative convection

Highly supercritical compressible convection is simulated in a two-dimensional domain in which the upper half is unstable to convection while the lower half is stably stratified. This configuration is an idealization of the layers near the base of the solar convection zone. Once the turbulent flow is well developed, a toroidal magnetic field B sub tor is introduced to the stable layer. The field's evolution is governed by an advection-diffusion-type equation, and the Lorentz force does not significantly affect the flow. After many turnover times the field is stratified such that the absolute value of B sub tor/rho is approximately constant in the convective layer, where rho is density, while in the stable layer this ratio decreases linearly with depth. Consequently most of the magnetic flux is stored in the overshoot layer. The inclusion of rotation leads to travelling waves which transport magnetic flux latitudinally in a manner reminiscent of the migrations seen during the solar cycle.

Jennings, R. L.↗

Some Experiences with Nonoverlapping Schur Complement Parallel Preconditioning for CFD Calculations

In this work we consider solving matrices which arise from the discretization of advection-diffusion field equations on arbitrary triangulated domains using stabilized numerical methods. The talk will discuss several candidate matrix preconditioning algorithms based on the 2 x 2 block factorization induced by an apriori partitioning of the triangulated domain. Application of the 2 x 2 block preconditioner requires the formation and inversion of the Schur complement submatrix. We consider several strategies for simplifying this task: incomplete Schur complement factorizations, drop tolerance element filling, Schur complement probing, and localized Schur complement inversion. Numerical results will be shown comparing performance and efficiency of these approximations. The matrix preconditioner has also been embedded into a Newton algorithm for solving the nonlinear Euler and Navier-Stokes equations governing compressible flow. The remainder of the talk will show numerous examples in CFD to demonstrate the efficiency and robustness of the techniques.

Barth, Timothy J.↗

Shock Capturing via Limiting for High-Order Methods including Discontinuous Galerkin

High-order methods, such as discontinuous Galerkin (DG), spectral, and flux reconstruction (FR), are prone to generating unwanted oscillations near shocks and discontinuities. Conventional limiting techniques, while effective in suppressing oscillations near shocks, often compromise accuracy near extrema, where the solution is only first-order accurate. This paper introduces a novel limiting technique for these high-order schemes, aimed at effectively managing shocks while preserving accuracy. The key idea is to expand the standard monotonicity limits to provide “room” near smooth extrema, ensuring that limiting has no effect and thus preserving accuracy. Near a discontinuity, these expanded limits effectively reduce to the original monotonicity limits, suppressing oscillations. Additional motivation is drawn from a formula for the derivative of Radau polynomials, which depicts the behavior of oscillations resulting from discontinuities. This behavior leads to a simplification by applying the limits to the sum of magnitudes of all modes, linear and higher degree. Unlike typical approaches, which rely on successful detection to activate limiting, our limiter depends continuously on the data, there by avoiding potential issues if detection fails. To reduce computing time, efficient criteria for detecting smooth regions where limiting is unnecessary are presented. Combined with detection, the continuous dependence on the data is lost, but the method is more economical. A notable characteristic of the entire process is its simplicity in both concept and implementation. Numerical tests for advection and Euler equations are conducted to demonstrate the effectiveness of the proposed method.

numerical methods↗

Shock Capturing via Limiting for High-Order Methods including Discontinuous Galerkin

High-order methods, such as discontinuous Galerkin (DG), spectral, and flux reconstruction (FR), are prone to generating unwanted oscillations near shocks and discontinuities. Conventional limiting techniques, while effective in suppressing oscillations near shocks, often compromise accuracy near extrema, where the solution is only first-order accurate. This paper introduces a novel limiting technique for these high-order schemes, aimed at effectively managing shocks while preserving accuracy. The key idea is to expand the standard monotonicity limits to provide “room” near smooth extrema, ensuring that limiting has no effect and thus preserving accuracy. Near a discontinuity, these expanded limits effectively reduce to the original monotonicity limits, suppressing oscillations. Additional motivation is drawn from a formula for the derivative of Radau polynomials, which depicts the behavior of oscillations resulting from discontinuities. This behavior leads to a simplification by applying the limits to the sum of magnitudes of all modes, linear and higher degree. Unlike typical approaches, which rely on successful detection to activate limiting, our limiter depends continuously on the data, there by avoiding potential issues if detection fails. To reduce computing time, efficient criteria for detecting smooth regions where limiting is unnecessary are presented. Combined with detection, the continuous dependence on the data is lost, but the method is more economical. A notable characteristic of the entire process is its simplicity in both concept and implementation. Numerical tests for advection and Euler equations are conducted to demonstrate the effectiveness of the proposed method.

numerical methods↗

High-order limiting methods using maximum principle bounds derived from the Boltzmann equation I: Euler equations

The use of limiting methods for high-order numerical approximations of hyperbolic conservation laws generally requires defining an admissible region/bounds for the solution. In this work, we present a novel approach for computing solution bounds and limiting for the Euler equations through the kinetic representation provided by the Boltzmann equation, which allows for extending limiters designed for linear advection directly to the Euler equations. Given an arbitrary set of solution values to compute bounds over (e.g., numerical stencil) and a desired linear advection limiter, the proposed approach yields an analytic expression for the admissible region of particle distribution function values, which may be numerically integrated to yield a set of bounds for the density, momentum, and total energy. Further, these solution bounds are shown to preserve positivity of density/pressure/internal energy and, when paired with a limiting technique, can robustly resolve strong discontinuities while recovering high-order accuracy in smooth regions without any ad hoc corrections (e.g., relaxing the bounds). This approach is demonstrated in the context of an explicit unstructured high-order discontinuous Galerkin/flux reconstruction scheme for a variety of difficult problems in gas dynamics, including cases with extreme shocks and shock-vortex interactions. Furthermore, this work presents a foundation for limiting techniques for more complex macroscopic governing equations that can be derived from an underlying kinetic representation for which admissible solution bounds are not well-understood.

42 ENGINEERING↗

Efficient Multigrid Reduction-in-Time for Method-of-Lines Discretizations of Linear Advection

Parallel-in-time methods for partial differential equations (PDEs) have been the subject of intense development over recent decades, particularly for diffusion-dominated problems. It has been widely reported in the literature, however, that many of these methods perform quite poorly for advection-dominated problems. In this report we analyze the particular iterative parallel-in-time algorithm of multigrid reduction-in-time (MGRIT) for discretizations of constant-wave-speed linear advection problems. We focus on common method-of-lines discretizations that employ upwind finite differences in space and Runge-Kutta methods in time. Using a convergence framework we developed in previous work, we prove for a subclass of these discretizations that, if using the standard approach of rediscretizing the fine-grid problem on the coarse grid, robust MGRIT convergence with respect to CFL number and coarsening factor is not possible. This poor convergence and non-robustness is caused, at least in part, by an inadequate coarse-grid correction for smooth Fourier modes in space-time known as characteristic components. We propose an alternative coarse-grid operator that provides a better correction of these modes. This coarse-grid operator is related to previous work and uses a semi-Lagrangian discretization combined with an implicitly treated truncation error correction. Theory and numerical experiments show the proposed coarse-grid operator yields fast MGRIT convergence for many of the method-of-lines discretizations considered, including for both implicit and explicit discretizations of high order. Parallel results demonstrate speed-up over sequential time-stepping.

97 MATHEMATICS AND COMPUTING↗

Equivalence of Fluctuation Splitting and Finite Volume for One-Dimensional Gas Dynamics

The equivalence of the discretized equations resulting from both fluctuation splitting and finite volume schemes is demonstrated in one dimension. Scalar equations are considered for advection, diffusion, and combined advection/diffusion. Analysis of systems is performed for the Euler and Navier-Stokes equations of gas dynamics. Non-uniform mesh-point distributions are included in the analyses.

Wood, William A.↗

Experiments on a round turbulent buoyant plume

This paper reports a comprehensive set of hot-wire measurements of a round buoyant plume which was generated by forcing a jet of hot air vertically up into quiescent environment. The boundary conditions of the experiment were measured, and are documented in the present paper in an attempt to sort out the contradictory mean flow results from the earlier studies. The ambient temperature was monitored to insure that the facility was not stratified and that the experiment was conducted in a neutral environment. The axisymmetry of the flow was checked by using a planar array of sixteen thermocouples and the mean temperature measurements from these are used to supplement the hot-wire measurements. The source flow conditions were measured so as to ascertain the rate at which the buoyancy was added to the flow. The measurements conserve buoyancy within 10 percent. The results are used to carry out the balances of the mean energy and momentum differential equations. In the mean energy equation it is found that the vertical advection of the energy is primarily balanced by the radial turbulent transport. In the mean momentum equation the vertical advection of momentum and the buoyancy force balance the radial turbulent transport. The buoyancy force is the second largest term in this balance and is responsible for the wider (and higher) velocity profiles in plumes as compared to jets. Budgets of the temperature variance and turbulence kinetic energy are also carried out in which thermal and mechanical dissipation rates are obtained as the closing terms. Similarities and differences between the two balances are discussed. It is found that even though the direct affect of buoyancy on turbulence, as evidenced by the buoyancy production term, is substantial, most of the turbulence is produced by shear. This is in contrast to the mean velocity field where the affect of buoyancy force is quite strong. Therefore, it is concluded that in a buoyant plume the primary affect of buoyancy on turbulence is indirect, and enters through the mean velocity field (giving larger shear production).

Shabbir, Aamir↗

Comments on the Diffusive Behavior of Two Upwind Schemes

The diffusive characteristics of two upwind schemes, multi-dimensional fluctuation splitting and locally one-dimensional finite volume, are compared for scalar advection-diffusion problems. Algorithms for the two schemes are developed for node-based data representation on median-dual meshes associated with unstructured triangulations in two spatial dimensions. Four model equations are considered: linear advection, non-linear advection, diffusion, and advection-diffusion. Modular coding is employed to isolate the effects of the two approaches for upwind flux evaluation, allowing for head-to-head accuracy and efficiency comparisons. Both the stability of compressive limiters and the amount of artificial diffusion generated by the schemes is found to be grid-orientation dependent, with the fluctuation splitting scheme producing less artificial diffusion than the finite volume scheme. Convergence rates are compared for the combined advection-diffusion problem, with a speedup of 2.5 seen for fluctuation splitting versus finite volume when solved on the same mesh. However, accurate solutions to problems with small diffusion coefficients can be achieved on coarser meshes using fluctuation splitting rather than finite volume, so that when comparing convergence rates to reach a given accuracy, fluctuation splitting shows a speedup of 29 over finite volume.

Wood, William A.↗

Diffusion Characteristics of Upwind Schemes on Unstructured Triangulations

The diffusive characteristics of two upwind schemes, multi-dimensional fluctuation splitting and dimensionally-split finite volume, are compared for scalar advection-diffusion problems. Algorithms for the two schemes are developed for node-based data representation on median-dual meshes associated with unstructured triangulations in two spatial dimensions. Four model equations are considered: linear advection, non-linear advection, diffusion, and advection-diffusion. Modular coding is employed to isolate the effects of the two approaches for upwind flux evaluation, allowing for head-to-head accuracy and efficiency comparisons. Both the stability of compressive limiters and the amount of artificial diffusion generated by the schemes is found to be grid-orientation dependent, with the fluctuation splitting scheme producing less artificial diffusion than the dimensionally-split finite volume scheme. Convergence rates are compared for the combined advection-diffusion problem, with a speedup of 2-3 seen for fluctuation splitting versus finite volume when solved on the same mesh. However, accurate solutions to problems with small diffusion coefficients can be achieved on coarser meshes using fluctuation splitting rather than finite volume, so that when comparing convergence rates to reach a given accuracy, fluctuation splitting shows a 20-25 speedup over finite volume.

Wood, William A.↗

Explicit Discontinuous Galerkin Methods for Conservation Laws

The two explicit DG methods in this study are based on a ‘predictor-corrector’ formulation, the first introduced by Lörcher, Gassner, and Munz (2007, 2008) called space–time expansion discontinuous Galerkin or STE-DG scheme, and the second, introduced independently by the author (Huynh 2006, 2013) called the upwind moment scheme. The predictor step of the two methods is essentially identical using a Cauchy-Kovalevsky (CK) procedure, which involves no interaction of the data among neighboring cells. The corrector step also shares the same space-time integration formulation and is where interaction of the data among neighboring cells takes place; the difference, however, is in how the resulting space-time volume integral is estimated. As a consequence of the different estimates, for the case of advection in one spatial dimension (1D), the moment scheme has a CFL (Courant-Friedrichs-Lewy) condition of 1 for all p and is accurate to order 2p+1, i.e., it possesses the super accuracy property, whereas the STE-DG method has a more restrictive CFL condition and is accurate to the expected order of p+1. For 1D advection, compared with the CFL conditions of 1/(2p+1) of standard RK-DG (Runge-Kutta) scheme where space and time discretization are of the same order, the moment scheme allows a significantly larger time step size. It also turns out that the scheme yields a result identical to Van Leer’s scheme III (1977), which amounts to shifting the data a distance of advection corresponding to the time step and projecting the result onto the space of polynomial solutions. Contrary to Van Leer’s approach, however, the space-time ‘predictor-corrector’ formulation facilitates extensions to the case of systems of equations. Concerning 2D extensions, in the case of advection, when the flow is along the diagonal direction, the CFL conditions for the moment schemes become restrictive as will be shown by Fourier (Von Neumann) stability and accuracy analyses. Since the moment scheme employs the right Radau points as collocation points in time, the method is closely related to the implicit Radau IIA scheme, which is stable for any time step size. The role of Radau IIA in relieving stability restriction for these explicit DG schemes remains to be explored

Discontinuous Galerkin↗