基于Eclipse图形建模框架的图形化脉冲序列设计软件的实现

采用Eclipse图形建模框架（Graphical Modeling Framework,GMF）技术构建了一个图形化磁共振脉冲序列设计软件．软件具备所见即所得的特点,用户使用拖放方式所画出的脉冲序列与教科书和参考文献上的脉冲序列几乎一样．软件支持核磁共振（Nuclear Magnetic Resonance,NMR）波谱和磁共振成像（Magnetic Resonance Imaging,MRI）的脉冲序列设计,同时提供实验参数管理模块,实现脉冲序列基础上的NMR实验设计和执行预览．得益于GMF完善的模型-视图-控制器模式和强大的代码生成能力,软件开发周期大幅度缩短、扩展能力大幅度提高．     

The virtual NMR spectrometer: a computer program for efficient simulation of NMR experiments involving pulsed field gradients

This paper presents a software program, the Virtual NMR Spectrometer, for computer simulation of multichannel, multidimensional NMR experiments on user-defined spin systems. The program is capable of reproducing most features of the modern NMR experiment, including homo- and heteronuclear pulse sequences, phase cycling, pulsed field gradients, and shaped pulses. Two different approaches are implemented to simulate the effect of pulsed field gradients on coherence selection, an explicit calculation of all coherence transfer pathways, and an effective approximate method using integration over multiple positions in the sample. The applications of the Virtual NMR Spectrometer are illustrated using homonuclear COSY and DQF COSY experiments with gradient selection, heteronuclear HSQC, and TROSY. The program uses an intuitive graphical user interface, which resembles the appearance and operation of a real spectrometer. A translator is used to allow the user to design pulse sequences with the same programming language used in the actual experiment on a real spectrometer. The Virtual NMR Spectrometer is designed as a useful tool for developing new NMR experiments and for tuning and adjusting the experimental setup for existing ones prior to running costly NMR experiments, in order to reduce the setup time on a real spectrometer. It will also be a useful aid for learning the general principles of magnetic resonance and contemporary innovations in NMR pulse sequence design.     

Real-time imaging of the spatial distribution of rf-heating in NMR samples during broadband decoupling

Continuous radio-frequency (rf) irradiation during decoupling and spin-lock periods in NMR pulse sequences may lead to undesired sample heating. Heat-sensitive samples can suffer damage from the sudden temperature rise which cannot be adequately compensated by the temperature control system. Moreover, as the heating is spatially inhomogeneous, higher temperature increases can arise locally than are indicated by the average increase detected by the temperature controller. In this work we present a technique that allows measurement of a real-time 2D-image of the temperature distribution inside an NMR sample during an experiment involving rf-heating. NMR imaging methods have previously been used to project the temperature distribution inside an NMR sample onto a single spatial axis or to acquire steady-state 2D- temperature distributions. The real-time 2D-temperature profiles obtained with our procedure provide much more detailed data. Our results show, that not only inhomogeneous heating but also inhomogeneous sample cooling contribute to the build-up of temperature gradients across the sample. The technique can be used to visualize rf-heating in order to protect sensitive samples and to experimentally test new coil geometries or to guide probehead design.     

配备于自旋回波仪的计算机系统

本文介绍配备在自旋回波仪中的计算机系统,由TP-801计算机、外围设备、接口电路和一套应用软件组成。该系统可以产生自旋回波实验所需要的多种脉冲序列,包括90°-90°、90°-180°、180°-90°、Carr-Purcell序列等。同时,计算机采集回波信号或FID,并进行数据处理,其结果可以直接由计算机或示波器、绘图仪显示,也可以存入磁带。仪器可以快速准确地测量弛豫时间T₁、T₂,也适用于核磁共振自旋回波方面的教学。在本文结束部分给出了一些样品的测量结果。本文介绍的计算机系统可以和普通的CW-NMR谱仪结合,使之增加自旋回波测量功能。     

syris: a flexible and efficient framework for X‐ray imaging experiments simulation

An open‐source framework for conducting a broad range of virtual X‐ray imaging experiments, syris, is presented. The simulated wavefield created by a source propagates through an arbitrary number of objects until it reaches a detector. The objects in the light path and the source are time‐dependent, which enables simulations of dynamic experiments, e.g. four‐dimensional time‐resolved tomography and laminography. The high‐level interface of syris is written in Python and its modularity makes the framework very flexible. The computationally demanding parts behind this interface are implemented in OpenCL, which enables fast calculations on modern graphics processing units. The combination of flexibility and speed opens new possibilities for studying novel imaging methods and systematic search of optimal combinations of measurement conditions and data processing parameters. This can help to increase the success rates and efficiency of valuable synchrotron beam time. To demonstrate the capabilities of the framework, various experiments have been simulated and compared with real data. To show the use case of measurement and data processing parameter optimization based on simulation, a virtual counterpart of a high‐speed radiography experiment was created and the simulated data were used to select a suitable motion estimation algorithm; one of its parameters was optimized in order to achieve the best motion estimation accuracy when applied on the real data. syris was also used to simulate tomographic data sets under various imaging conditions which impact the tomographic reconstruction accuracy, and it is shown how the accuracy may guide the selection of imaging conditions for particular use cases.     

Correspondence between spin-dynamic phases and pulse program phases of NMR spectrometers

Spin state selective experiments have become very useful tools in solution NMR spectroscopy, particularly in the context of TROSY line narrowing. However, the practical implementation of such pulse sequences is frequently complicated by unexpected instrument behavior. Furthermore, a literal theoretical analysis of sequences published with specific phase settings can fail to rationalize such experiments and can seemingly contradict experimental findings. In this communication, we develop a practical approach to this ostensible paradox. Spin-dynamic design, rationalization, and simulation of NMR pulse sequences, as well as their confident and reliable implementation across current spectrometer hardware platforms, require precise understanding of the underlying nutation axis conventions. While currently often approached empirically, we demonstrate with a simple but general pulse program how to uncover these correspondences a priori in the general case. From this, we deduce a correspondence table between the spin-dynamic phases used in NMR theory and simulation on the one hand and pulse program phases of current commercial spectrometers on the other. As a practical application of these results, we analyze implementations of the original (1)H-(15)N TROSY experiment and illustrate how steady-state magnetization can be predictably, rather than empirically, added to a desired component. We show why and under which circumstances a literal adoption of phases from published sequences can lead to incorrect results. We suggest that pulse sequences should be consistently given with spin-dynamically correct (physical) phases, rather than in spectrometer-specific (software) syntax.     

SPINEVOLUTION: a powerful tool for the simulation of solid and liquid state NMR experiments

Exact numerical simulations of NMR experiments are often required for the development of new techniques and for the extraction of structural and dynamic information from the spectra. Simulations of solid-state magic angle spinning (MAS) experiments can be particularly demanding both computationally and in terms of the programming required to carry them out, even if special simulation software is used. We recently developed a number of approaches that dramatically improve the efficiency and allow a high degree of automation of these computations. In the present paper, we describe SPINEVOLUTION, a highly optimized computer program that implements the new methodology. The algorithms used in the program will be described separately. Although particularly efficient for the simulation of experiments with complex pulse sequences and multi-spin systems in solids, SPINEVOLUTION is a versatile and easy to use tool for the simulation and optimization of virtually any NMR experiment. The performance of SPINEVOLUTION was compared with that of another recently developed NMR simulation package, SIMPSON. Benchmarked on a series of examples, SPINEVOLUTION was consistently found to be orders of magnitude faster. At the time of publication, the program is available gratis for non-commercial use.     

A computer algorithm for the simulation of any nuclear magnetic resonance (NMR) imaging method

More than a dozen Nuclear Magnetic Resonance (NMR) imaging methods have been described using different radio-frequency pulse sequences, magnetic field gradient variations, and data processing. In order to have a theoretical understanding in the most general case, we have conceived a computer program for the simulation of NMR imaging techniques. The algorithm uses the solution of the Bloch equations at each point of a simulated object. The direction of every elementary magnetic moment is computed at each instant, and stored in an array giving the global signal to be processed, whatever the pulse and gradient sequence. To test the validity of this program, we have simulated some well-known experimental results. Some applications are presented which contribute to the understanding of image distortions and to techniques such as selective radio-frequency pulse or oscillating gradients. This program can be used to unravel physical and technological causes of image distortions, to have a "microscopic" look at any parameter of an experiment, and to study the contrast given by various NMR imaging techniques as a function of the three NMR parameters, i.e., the hydrogen nuclei density rho and the relaxation times T1 and T2.     

Simultaneous acquisition of pulse EPR orientation selective spectra

High resolution pulse EPR methods are usually applied to resolve weak magnetic electron-nuclear or electron-electron interactions that are otherwise unresolved in the EPR spectrum. Complete information regarding different magnetic interactions, namely, principal components and orientation of principal axis system with respect to the molecular frame, can be derived from orientation selective pulsed EPR measurements that are performed at different magnetic field positions within the inhomogeneously broadened EPR spectrum. These experiments are usually carried out consecutively, namely a particular field position is chosen, data are accumulated until the signal to noise ratio is satisfactory, and then the next field position is chosen and data are accumulated. Here we present a new approach for data acquisition of pulsed EPR experiments referred to as parallel acquisition. It is applicable when the spectral width is much broader than the excitation bandwidth of the applied pulse sequence and it is particularly useful for orientation selective pulse EPR experiments. In this approach several pulse EPR measurements are performed within the waiting (repetition) time between consecutive pulse sequences during which spin lattice relaxation takes place. This is achieved by rapidly changing the main magnetic field, B(0), to different values within the EPR spectrum, performing the same experiment on the otherwise idle spins. This scheme represents an efficient utilization of the spectrometer and provides the same spectral information in a shorter time. This approach is demonstrated on W-band orientation selective electron-nuclear double resonance (ENDOR), electron spin echo envelope modulation (ESEEM), electron-electron double resonance (ELDOR)--detected NMR and double electron-electron resonance (DEER) measurements on frozen solutions of nitroxides. We show that a factors of 3-6 reduction in total acquisition time can be obtained, depending on the experiment applied.     

A rapid measurement of flow propagators in porous rocks

NMR flow propagators have been obtained for brine flowing through Bentheimer sandstone using the rapid DiffTrain pulse sequence. In this way, 8 flow propagators at different observation times Delta were acquired in 67 mins, compared to 7 h for the same measurements implemented with conventional pulsed field gradient (PFG) sequences. DiffTrain allows this time saving to be achieved through the acquisition of multiple displacement probability distributions over a range of Delta in a single measurement. If only the propagator moments are required, this experiment time can be further reduced to 9 mins through appropriate sparse sampling at low q values. The propagator moments obtained from DiffTrain measurements with dense and sparse q-space sampling are shown to be equivalent to those obtained from conventional PFG measurements.     

Direct measurement of dipole-dipole/CSA cross-correlated relaxation by a constant-time experiment

Relaxation rates in NMR are usually measured by intensity modulation as a function of a relaxation delay during which the relaxation mechanism of interest is effective. Other mechanisms are often suppressed during the relaxation delay by pulse sequences which eliminate their effects, or cancel their effects when two data sets with appropriate combinations of relaxation rate effects are added. Cross-correlated relaxation (CCR) involving dipole-dipole and CSA interactions differ from auto-correlated relaxation (ACR) in that the signs of contributions can be changed by inverting the state of one spin involved in the dipole-dipole interaction. This property has been exploited previously using CPMG sequences to refocus CCR while ACR evolves. Here we report a new pulse scheme that instead eliminates intensity modulation by ACR and thus allows direct measurement of CCR. The sequence uses a constant time relaxation period for which the contribution of ACR does not change. An inversion pulse is applied at various points in the sequence to effect a decay that depends on CCR only. A 2-D experiment is also described in which chemical shift evolution in the indirect dimension can share the same constant period. This improves sensitivity by avoiding the addition of a separate indirect dimension acquisition time. We illustrate the measurement of residue specific CCR rates on the non-myristoylated yeast ARF1 protein and compare the results to those obtained following the conventional method of measuring the decay rates of the slow and fast-relaxing (15)N doublets. The performances of the two methods are also quantitatively evaluated by simulation. The analysis shows that the shared constant-time CCR (SCT-CCR) method significantly improves sensitivity.     

Convection-compensating PGSE experiment incorporating excitation-sculpting water suppression (CONVEX)

We present a new diffusion experiment which provides simultaneous suppression of an on-resonance solvent peak and compensation for convection. The experiment, which we name CONVEX, exploits similarities between two functionally different pulse sequences to enable the same sequence to be used simultaneously for two different purposes. The CONVEX pulse sequence combines a double-echo PGSE with double excitation-sculpting water suppression, using unequal gradient pulse-pair amplitudes (g1 and g2) and unequal diffusion intervals (Delta1 and Delta2). Convection compensation is achieved by setting g1:g2 = Delta2:Delta1. The new experiment provides the spectral quality, flat baseline, and water-suppression power characteristic of excitation-sculpting experiments, combined with excellent compensation for convection. The resulting Stejskal-Tanner plots are linear over a greater range of signal attenuation than in the absence of water suppression. Possible applications include protein NMR; NMR of cellular or colloidal systems; and the monitoring of technological processes.     

The use of sample rotation for minimizing convection effects in self-diffusion NMR measurements.

Undesirable temperature gradients in a NMR sample tube are usually generated by an inappropriate temperature regulation system. We have shown that such convection effects can greatly distort the measurement of translational self-diffusion coefficients. The use of sample spinning helps to minimize such undesirable effects by disruption of convection fluxes due to resulting Coriolis forces that have a strongly stabilizing effect on the conducting state of the system (J. Lounila et al., J. Magn. Reson. A 118, 50 (1996)). This simple trick allows the accurate measurement of diffusion coefficients for a wide range of temperatures and solvents without the need for a convection-compensated NMR pulse sequences or more sophisticated temperature control units. Experimental data obtained for some target compounds dissolved in several common deuterated solvents at different temperatures are reported and discussed.     

Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing 2D NMR with reduced radiofrequency load

The SOFAST-HMQC experiment [P. Schanda, B. Brutscher, Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds, J. Am. Chem. Soc. 127 (2005) 8014-8015] allows recording two-dimensional correlation spectra of macromolecules such as proteins in only a few seconds acquisition time. To achieve the highest possible sensitivity, SOFAST-HMQC experiments are preferably performed on high-field NMR spectrometers equipped with cryogenically cooled probes. The duty cycle of over 80% in fast-pulsing SOFAST-HMQC experiments, however, may cause problems when using a cryogenic probe. Here we introduce SE-IPAP-SOFAST-HMQC, a new pulse sequence that provides comparable sensitivity to standard SOFAST-HMQC, while avoiding heteronuclear decoupling during (1)H detection, and thus significantly reducing the radiofrequency load of the probe during the experiment. The experiment is also attractive for fast and sensitive measurement of heteronuclear one-bond spin coupling constants.     

Selective time-reversal pulses for NMR imaging

Using a nonlinear systems approach, a selective time-reversal pulse for multiple-slice-multiple-echo NMR imaging sequences has been developed. The results of both computer simulation and experiments on a 1.5 T imaging system demonstrate the markedly improved selectivity of the pulse compared to conventional time-reversal pulses.     

13C PGSE NMR experiment with heteronuclear dipolar decoupling to measure diffusion in liquid crystals and solids

A new PGSE NMR experiment, designed to measure molecular diffusion coefficients in systems with nonvanishing static dipolar coupling, is described. The fast static dipolar dephasing of the single-quantum (13)C coherences is removed by multiple-pulse heteronuclear decoupling. The resulting slow dephasing of the (13)C coherences allows for inserting appropriate gradient pulses into the pulse sequence. The presence of the large magnetic field gradient reduces the efficiency of the decoupling sequences which is compensated for by introducing a scheme of sequential slice selection across the sample. The method is demonstrated by (19)F-decoupled (13)C PGSE NMR experiments in a lyotropic nematic and lamellar liquid crystal.     

Improving pulse sequences for 3D DOSY: convection compensation

Signal overlap in the NMR dimension significantly complicates the construction and analysis of 2D diffusion-ordered (DOSY) spectra. Such problems can often be reduced or even eliminated by extending the NMR domain of a DOSY experiment into two dimensions, giving a 3D-DOSY spectrum. To date such experiments have generally sacrificed some signal-to-noise ratio and have required extensive and time-consuming phase cycling. A new family of pulse sequences with internal diffusion encoding (IDOSY) has been introduced which avoids both of these problems. It is often straightforward to incorporate convection compensation in such sequences at no cost in signal-to-noise ratio. Here, some of the problems caused by convection in DOSY are described and illustrated, and the efficacy of convection compensation in the 2DJ-IDOSY and COSY-IDOSY experiments is demonstrated.     

Multiecho sequence for velocity imaging in inhomogeneous rf fields

The unambiguous determination of velocities with spatial resolution in a multiecho PFG NMR sequence strongly depends on the homogeneity of the B1 field. This affects, in particular, the use of surface coils that bear considerable potential for on-line flow monitoring where a fast-imaging sequence can become vital. However, even with most rf coils dedicated for imaging applications, B1 inhomogeneities are sufficiently large to generate severe problems in performing velocity-imaging experiments. In this paper, the use of a combination of different phase cycles in Carr-Purcell sequences is discussed. The suggested phase cycling scheme tolerates large flip angle imperfections arising in inhomogeneous B1 fields, and thus allows acquisition of a maximum number of echoes within a pulse train. The performance of the velocity-imaging sequence is proven by using phantom samples developing known laminar flow patterns.     

A multinuclear magnetic resonance imaging technique--simultaneous proton and sodium imaging

Simultaneous imaging of proton and sodium is achieved using a new two coil system and a time-multiplexing technique with a 1.5 T NMR imaging system. Distinctly different NMR parameters of protons and sodium, such as resonant frequencies and T1 relaxation rates, are incorporated in the imaging with a new dual coil arrangement. Since the T1 relaxation time of sodium is substantially shorter than that of protons, a set of fast repeating sodium pulse sequences is inserted between the proton pulse repetition intervals. The different resonant frequencies of the nuclei provide good isolation between the two RF coils. In this paper, the system configuration and the pulse sequence employed for the proposed simultaneous multinuclear imaging of protons and sodium are presented along with some preliminary results.     

A Q-band pulse EPR/ENDOR spectrometer and the implementation of advanced one- and two-dimensional pulse EPR methodology

A versatile high-power pulse Q-band EPR spectrometer operating at 34.5--35.5 GHz and in a temperature range of 4--300 K is described. The spectrometer allows one to perform one- and two-dimensional multifrequency pulse EPR and pulse ENDOR experiments, as well as continuous wave experiments. It is equipped with two microwave sources and four microwave channels to generate pulse sequences with different amplitudes, phases, and carrier frequencies. A microwave pulse power of up to 100 W is available. Two channels form radiofrequency pulses with adjustable phases for ENDOR experiments. The spectrometer performance is demonstrated by single crystal pulse ENDOR experiments on a copper complex. A HYSCORE experiment demonstrates that the advantages of high-field EPR and correlation spectroscopy can be combined and exploited at Q-band. Furthermore, we illustrate how this combination can be used in cases where the HYSCORE experiment is no longer effective at 35 GHz because of the shallow modulation depth. Even in cases where the echo modulation is virtually absent in the HYSCORE experiment at Q-band, matched microwave pulses allow one to get HYSCORE spectra with a signal-to-noise ratio as good as at X-band. Finally, it is shown that the high microwave power, the short pulses, and the broad resonator bandwidth make the spectrometer well suited to Fourier transform EPR experiments.