Mass Flux Schemes and Connection to Shock Instability

We analyze numerical mass fluxes with an emphasis on their capability for accurately capturing shock and contact discontinuities. The study of mass flux is useful because it is the term common to all conservation equations and the numerical diffusivity introduced in it bears a direct consequence to the prediction of contact (stationary and moving) discontinuities, which are considered to be the limiting case of the boundary layer. We examine several prominent numerical flux schemes and analyze the structure of numerical diffusivity. This leads to a detailed investigation into the cause of certain catastrophic breakdowns by some numerical flux schemes. In particular, we identify the dissipative terms that are responsible for shock instabilities, such as the odd–even decoupling and the so-called “carbuncle phenomenon”. As a result, we propose a conjecture stating the connection of the pressure difference term to these multidimensional shock instabilities and hence a cure to those difficulties. The validity of this conjecture has been confirmed by examining a wide class of upwind schemes. The conjecture is useful to the flux function development, for it indicates whether the flux scheme under consideration will be afflicted with these kinds of failings. Thus, a class of shock-stable schemes can be identified. Interestingly, a shock-stable scheme's self-correcting capability is demonstrated with respect to carbuncle-contaminated profiles for flows at both low supersonic and high Mach numbers.     

Non-CPMG Fast Spin Echo with full signal

The standard Fast Spin Echo sequence used in MR imaging relies on the CPMG condition. A consequence of this condition is that only one component of the transverse magnetization can be measured. To counter this, some phase modulation schemes (XY, MLEV.) for the pulse train have been proposed, but they are useful only over a very restricted range, close to pi, of the refocusing pulse rotation angle. Some other solutions not relying on phase modulation have also been suggested, but they destroy one half the available signal. Revisiting the phase modulation approach, J. Murdoch ("Second SMR Scientific Meeting," p. 1145, 1994) suggested that a quadratic phase modulation could generate a train of classical echoes. We show here that indeed a quadratic phase modulation has a very suitable property: after an adequate change of frame, the dynamic of the system composed of all the protons situated in one pixel can be seen as stationary. If the parameter of the quadratic phase modulation is well chosen, it is then possible to put the dynamic system in a combination of two suitable states and obtain a signal identical to the signal of a classical spin echo, at least for nutation of the refocusing pulse higher than, approximately, two radians.     

Time-optimal coherence-order-selective transfer of in-phase coherence in heteronuclear IS spin systems

Based on principles of geometric optimal control theory, coherence transfer building blocks can be derived which achieve optimal sensitivity. Here, experimental pulse sequences are presented that achieve the best possible coherence-order-selective in-phase transfer (S(-)-->I(-)) for a heteronuclear 2-spin system for any given mixing time in the absence of relaxation. For short mixing times, the optimal experiment improves the sensitivity of isotropic mixing by up to 12.5%.     

A New Two-Dimensional Pulse Sequence for T2* Measurements of Protons in C Isotopomers

A new two-dimensional pulse sequence for T₂* measurement of protons directly coupled to ¹³C spins is proposed. The sequence measures the tranverse relaxation time of heteronuclear proton single-quantum coherence under conditions of free precession and is therefore well suited to evaluate relaxation losses of proton magnetization during preparation delays of heteronuclear pulse experiments in analytical NMR. The relevant part of the pulse sequence can be inserted as a “building block” into any direct or inverse detecting H,C correlation pulse sequence if proton spin–spin relaxation is to be investigated. In this contribution, the building block is inserted into a HETCOR as well as into a HMQC pulse sequence. Experimental results for the HETCOR-based sequence are given.     

H Spectroscopy without Solvent Suppression: Characterization of Signal Modulations at Short Echo Times

While most proton (¹H) spectra acquired in vivo utilize selective suppression of the solvent signal for more sensitive detection of signals from the dilute metabolites, recent reports have demonstrated the feasibility and advantages of collecting in vivo data without solvent attenuation. When these acquisitions are performed at short echo times, the presence of frequency modulations of the water resonance may become an obstacle to the identification and quantitation of metabolite resonances. The present report addresses the characteristics, origin, and elimination of these sidebands. Sideband amplitudes were measured as a function of delay time between gradient pulse and data collection, as a function of gradient pulse amplitude, and as a function of spatial location of the sample for each of the three orthogonal gradient sets. Acoustic acquisitions were performed to demonstrate the correlation between mechanical vibration resonances and the frequencies of MR sidebands. A mathematical framework is developed and compared with the experimental results. This derivation is based on the theory that these frequency modulations are induced by magnetic field fluctuations generated by the transient oscillations of gradient coils.     

Improved Spin-Echo-Edited NMR Diffusion Measurements

The need for simple and robust schemes for the analysis of ligand-protein binding has resulted in the development of diffusion-based NMR techniques that can be used to assay binding in protein solutions containing a mixture of several ligands. As a means of gaining spectral selectivity in NMR diffusion measurements, a simple experiment, the gradient modified spin-echo (GOSE), has been developed to reject the resonances of coupled spins and detect only the singlets in the (1)H NMR spectrum. This is accomplished by first using a spin echo to null the resonances of the coupled spins. Following the spin echo, the singlet magnetization is flipped out of the transverse plane and a dephasing gradient is applied to reduce the spectral artifacts resulting from incomplete cancellation of the J-coupled resonances. The resulting modular sequence is combined here with the BPPSTE pulse sequence; however, it could be easily incorporated into any pulse sequence where additional spectral selectivity is desired. Results obtained with the GOSE-BPPSTE pulse sequence are compared with those obtained with the BPPSTE and CPMG-BPPSTE experiments for a mixture containing the ligands resorcinol and tryptophan in a solution of human serum albumin.     

Monotonicity Preserving Weighted Essentially Non-oscillatory Schemes with Increasingly High Order of Accuracy

In this paper we design a class of numerical schemes that are higher-order extensions of the weighted essentially non-oscillatory (WENO) schemes of G.-S. Jiang and C.-W. Shu (1996) and X.-D. Liu, S. Osher, and T. Chan (1994). Used by themselves, the schemes may not always be monotonicity preserving but coupled with the monotonicity preserving bounds of A. Suresh and H. T. Huynh (1997) they perform very well. The resulting monotonicity preserving weighted essentially non-oscillatory (MPWENO) schemes have high phase accuracy and high order of accuracy. The higher-order members of this family are almost spectrally accurate for smooth problems. Nevertheless, they, have robust shock capturing ability. The schemes are stable under normal CFL numbers. They are also efficient and do not have a computational complexity that is substantially greater than that of the lower-order members of this same family of schemes. The higher accuracy that these schemes offer coupled with their relatively low computational complexity makes them viable competitors to lower-order schemes, such as the older total variation diminishing schemes, for problems containing both discontinuities and rich smooth region structure. We describe the MPWENO schemes here as well as show their ability to reach their designed accuracies for smooth flow. We also examine the role of steepening algorithms such as the artificial compression method in the design of very high order schemes. Several test problems in one and two dimensions are presented. For multidimensional problems where the flow is not aligned with any of the grid directions it is shown that the present schemes have a substantial advantage over lower-order schemes. It is argued that the methods designed here have great utility for direct numerical simulations and large eddy simulations of compressible turbulence. The methodology developed here is applicable to other hyperbolic systems, which is demonstrated by showing that the MPWENO schemes also work very well on magnetohydrodynamical test problems.     

Numerical simulation of one- and two-dimensional ESEEM experiments

Numerical simulation has become an indispensable tool for the interpretation of pulse EPR experiments. In this work it is shown how automatic orientation selection, grouping of operator factors, and direct selection and elimination of coherences can be used to improve the efficiency of time-domain simulations of one- and two-dimensional electron spin echo envelope modulation (ESEEM) spectra. The program allows for the computation of magnetic interactions of any symmetry and can be used to simulate spin systems with an arbitrary number of nuclei with any spin quantum number. Experimental restrictions due to finite microwave pulse lengths are addressed and the enhancement of forbidden coherences by microwave pulse matching is illustrated. A comparison of simulated and experimental HYSCORE (hyperfine sublevel correlation) spectra of ordered and disordered systems with varying complexity shows good qualitative agreement.     

Measurement of Small One-Bond Proton–Carbon Residual Dipolar Coupling Constants in Partially Oriented C Natural Abundance Oligosaccharide Samples: Analysis of Heteronuclear JCH-Modulated Spectra with the BIRD Inversion Pulse

Two 2D J-modulated HSQC-based experiments were designed for precise determination of small residual dipolar one-bond carbon–proton coupling constants in ¹³C natural abundance carbohydrates. Crucial to the precision of a few hundredths of Hz achieved by these methods was the use of long modulation intervals and BIRD pulses, which acted as semiselective inversion pulses. The BIRD pulses eliminated effective evolution of all but ¹J_CH couplings, resulting in signal modulation that can be described by simple modulation functions. A thorough analysis of such modulation functions for a typical four-spin carbohydrate spin system was performed for both experiments. The results showed that the evolution of the ¹H–¹H and long-range ¹H–¹³C couplings during the BIRD pulses did not necessitate the introduction of more complicated modulation functions. The effects of pulse imperfections were also inspected. While weakly coupled spin systems can be analyzed by simple fitting of cross peak intensities, in strongly coupled spin systems the evolution of the density matrix needs to be considered in order to analyse data accurately. However, if strong coupling effects are modest the errors in coupling constants determined by the “weak coupling” analysis are of similar magnitudes in oriented and isotropic samples and are partially cancelled during dipolar coupling calculation. Simple criteria have been established as to when the strong coupling treatment needs to be invoked.     

2D(13)C-(13)C MAS NMR correlation spectroscopy with mixing by true (1)H spin diffusion reveals long-range intermolecular distance restraints in ultra high magnetic field

An improved 2D (13)C-(13)C CP(3) MAS NMR correlation experiment with mixing by true (1)H spin diffusion is presented. With CP(3), correlations can be detected over a much longer range than with direct (1)H-(13)C or (13)C-(13)C dipolar recoupling. The experiment employs a (1)H spin diffusion mixing period tau(m) sandwiched between two cross-polarization periods. An optimized CP(3) sequence for measuring polarization transfer on a length scale between 0.3 and 1.0 nm using short mixing times of 0.1 ms < tau(m) < 1 ms is presented. For such a short tau(m), cross talk from residual transverse magnetization of the donating nuclear species after a CP can be suppressed by extended phase cycling. The utility of the experiment for genuine structure determination is demonstrated using a self-aggregated Chl a/H(2)O sample. The number of intramolecular cross-peaks increases for longer mixing times and this obscures the intermolecular transfer events. Hence, the experiment will be useful for short mixing times only. For a short tau(m) = 0.1 ms, intermolecular correlations are detected between the ends of phytyl tails and ring carbons of neighboring Chl a molecules in the aggregate. In this way the model for the structure, with stacks of Chl a that are arranged back to back with interdigitating phytyl chains stretched between two bilayers, is validated.     

Convection-Diffusion Lattice Boltzmann Scheme for Irregular Lattices

In this paper, a lattice Boltzmann (LB) scheme for convection diffusion on irregular lattices is presented, which is free of any interpolation or coarse graining step. The scheme is derived using the axioma that the velocity moments of the equilibrium distribution equal those of the Maxwell–Boltzmann distribution. The axioma holds for both Bravais and irregular lattices, implying a single framework for LB schemes for all lattice types. By solving benchmark problems we have shown that the scheme is indeed consistent with convection diffusion. Furthermore, we have compared the performance of the LB schemes with that of finite difference and finite element schemes. The comparison shows that the LB scheme has a similar performance as the one-step second-order Lax–Wendroff scheme: it has little numerical diffusion, but has a slight dispersion error. By changing the relaxation parameter ω the dispersion error can be balanced by a small increase of the numerical diffusion.     

Cogwheel phase cycling

A new method for constructing phase cycles is described. The new schemes apply to experiments involving several consecutive coherence transfer steps. The radiofrequency phases of two or more irradiation blocks are incremented simultaneously, as opposed to the traditional "nested" scheme, in which the block phases are incremented independently. In many cases, the "cogwheel" phase cycles achieve the same selectivity as traditional phase cycles, using fewer steps. Significant time savings are achievable in a wide range of NMR experiments.     

Picoliter (1)H NMR spectroscopy

In this study, a 267-microm-diameter solenoid transceiver is used to acquire localized (1)H NMR spectra and the measured signal-to-noise ratio (SNR) at 500 MHz is shown to be within 20--30% of theoretical limits formulated by considering only its resistive losses. This is illustrated using a 100-microm-diameter globule of triacylglycerols (approximately 900mM) that may be an oocyte precursor in young Xenopus laevis frogs and a water sample containing choline at a concentration often found in live mammalian cells (approximately 33 mM). In chemical shift imaging (CSI) experiments performed using a few thousand total scans, the choline methyl line is shown to have an acceptable SNR in resolved volume elements containing only 50 pL of sample, and localized spectra are resolved from just 5 pL in the Xenopus globule. These findings demonstrate the feasibility of performing (1)H NMR on picoliter-scale sample volumes in biological cells and tissues and illustrate how the achieved SNR in spectroscopic images can be predicted with reasonable accuracy at microscopic spatial resolutions.     

Separating Structure and Dynamics in CSA/DD Cross-Correlated Relaxation: A Case Study on Trehalose and Ubiquitin

We present two new sensitivity enhanced gradient NMR experiments for measuring interference effects between chemical shift anisotropy (CSA) and dipolar coupling interactions in a scalar coupled two-spin system in both the laboratory and rotating frames. We apply these methods for quantitative measurement of longitudinal and transverse cross-correlation rates involving interference of ¹³C CSA and ¹³C–¹H dipolar coupling in a disaccharide, α,α- -trehalose, at natural abundance of ¹³C as well as interference of amide ¹⁵N CSA and ¹⁵N–¹H dipolar coupling in uniformly ¹⁵N-labeled ubiquitin. We demonstrate that the standard heteronuclear T₁, T₂, and steady-state NOE autocorrelation experiments augmented by cross-correlation measurements provide sufficient experimental data to quantitatively separate the structural and dynamic contributions to these relaxation rates when the simplifying assumptions of isotropic overall tumbling and an axially symmetric chemical shift tensor are valid.     

Improved narrowband dipolar recoupling for homonuclear distance measurements in rotating solids

Recovery of the magnetic dipolar interaction between nuclei bearing the same gyromagnetic ratio in rotating solids can be promoted by synchronous rf irradiation. Determination of the dipolar interaction strength can serve as a tool for structural elucidation in polycrystalline powders. Spinning frequency dependent narrow-band (nb) RFDR and SEDRA experiments are utilized as simple techniques for the determination of dipolar interactions between the nuclei in coupled homonuclear spin pairs. The magnetization exchange and coherence dephasing due to a fixed number of rotor-synchronously applied pi-pulses is monitored at spinning frequencies in the vicinity of the rotational resonance (R(2)) conditions. The powder nbRFDR and nbSEDRA decay curves of spin magnetizations and coherences, respectively, as a function of the spinning frequency can be measured and analyzed using simple rate equations providing a quantitative measure of the dipolar coupling. The effects of the phenomenological relaxation parameters in these rate equations are discussed and an improved methodology is suggested for analyzing nbRFDR data for small dipolar couplings. The distance between the labeled nuclei in the 1,3-(13)C(2)-hydroxybutyric acid molecule is rederived using existing nbRFDR results and the new simulation procedure. A nbSEDRA experiment has been performed successfully on a powder sample of singly labeled 1-(13)C-L-leucine measuring the dipolar interaction between the labeled carboxyl carbon and the natural abundant beta-carbon. Both narrowband techniques are employed for the determination of the nuclear distances between the side-chain carbons of leucine and its carbonyl carbon in a tripeptide Leu-Gly-Phe that is singly (13)C-labeled at the leucine carbonyl carbon position.     

Divergence- and Curl-Preserving Prolongation and Restriction Formulas

We present new second-order prolongation and restriction formulas which preserve the divergence and, in some cases, the curl of a discretized vector field. The formulas are suitable for adaptive and hierarchical mesh algorithms with a factor-of-2 linear resolution change. We examine both staggered and collocated discretizations for the vector field on two- and three-dimensional Cartesian grids. The new formulas can be used in combination with numerical schemes that require a divergence-free solution in some discrete sense, such as the constrained transport schemes of computational magnetohydrodynamics. We also obtain divergence-preserving interpolation functions which may be used for streamline or field line tracing.     

Completely Conservative and Oscillationless Semi-Lagrangian Schemes for Advection Transportation

In this paper, we present a new type of semi-Lagrangian scheme for advection transportation equation. The interpolation function is based on a cubic polynomial and is constructed under the constraints of conservation of cell-integrated average and the slope modification. The cell-integrated average is defined via the spatial integration of the interpolation function over a single grid cell and is advanced using a flux form. Nonoscillatory interpolation is constructed by choosing proper approximation to the cell-center values of the first derivative of the interpolation function, which appears to be a free parameter in the present formulation. The resulting scheme is exactly conservative regarding the cell average of the advected quantity and does not produce any spurious oscillation. Oscillationless solutions to linear transportation problems were obtained. Incorporated with an entropy-enforcing numerical flux, the presented schemes can accurately compute shocks and sonic rarefaction waves when applied to nonlinear problems.     

The Lattice Solid Model to Simulate the Physics of Rocks and Earthquakes: Incorporation of Friction

The particle-based lattice solid model developed to study the physics of rocks and the nonlinear dynamics of earthquakes is refined by incorporating intrinsic friction between particles. The model provides a means for studying the causes of seismic wave attenuation, as well as frictional heat generation, fault zone evolution, and localisation phenomena. A modified velocity–Verlat scheme that allows friction to be precisely modelled is developed. This is a difficult computational problem given that a discontinuity must be accurately simulated by the numerical approach (i.e., the transition from static to dynamical frictional behaviour). This is achieved using a half time step integration scheme. At each half time step, a nonlinear system is solved to compute the static frictional forces and states of touching particle-pairs. Improved efficiency is achieved by adaptively adjusting the time step increment, depending on the particle velocities in the system. The total energy is calculated and verified to remain constant to a high precision during simulations. Numerical experiments show that the model can be applied to the study of earthquake dynamics, the stick–slip instability, heat generation, and fault zone evolution. Such experiments may lead to a conclusive resolution of the heat flow paradox and improved understanding of earthquake precursory phenomena and dynamics.     

On Performance of Methods with Third- and Fifth-Order Compact Upwind Differencing

The difference schemes for fluid dynamics type of equations based on third- and fifth-order Compact Upwind Differencing (CUD) are considered. To validate their properties following from a linear analysis, calculations were carried out using the inviscid and viscous Burgers' equation as well as the compressible Navier–Stokes equation written in the conservative form for curvilinear coordinates. In the latter case, transonic cascade flow was chosen as a representative example. The performance of the CUD methods was estimated by investigating mesh convergence of the solutions and comparing with the results of second-order schemes. It is demonstrated that the oscillation-free steep gradients solutions obtained without using smoothing techniques can provide considerable increase of accuracy even when exploiting coarse meshes.     

A High-Order WENO Finite Difference Scheme for the Equations of Ideal Magnetohydrodynamics

We present a high-order accurate weighted essentially non-oscillatory (WENO) finite difference scheme for solving the equations of ideal magnetohydrodynamics (MHD). This scheme is a direct extension of a WENO scheme, which has been successfully applied to hydrodynamic problems. The WENO scheme follows the same idea of an essentially non-oscillatory (ENO) scheme with an advantage of achieving higher-order accuracy with fewer computations. Both ENO and WENO can be easily applied to two and three spatial dimensions by evaluating the fluxes dimension-by-dimension. Details of the WENO scheme as well as the construction of a suitable eigen-system, which can properly decompose various families of MHD waves and handle the degenerate situations, are presented. Numerical results are shown to perform well for the one-dimensional Brio–Wu Riemann problems, the two-dimensional Kelvin–Helmholtz instability problems, and the two-dimensional Orszag–Tang MHD vortex system. They also demonstrate the importance of maintaining the divergence free condition for the magnetic field in achieving numerical stability. The tests also show the advantages of using the higher-order scheme. The new 5th-order WENO MHD code can attain an accuracy comparable with that of the second-order schemes with many fewer grid points.