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.     

Quantum Logic Gates and Nuclear Magnetic Resonance Pulse Sequences

There has recently been considerable interest in the use of nuclear magnetic resonance (NMR) as a technology for the implementation of small quantum computers. These computers operate by the laws of quantum mechanics, rather than classical mechanics and can be used to implement new quantum algorithms. Here we describe how NMR in principle can be used to implement all the elements required to build quantum computers, and draw comparisons between the pulse sequences involved and those of more conventional NMR experiments.     

Effects of experimental imperfections on a spin counting experiment

Spin counting NMR is an experimental technique that allows a determination of the size and time evolution of networks of dipolar coupled nuclear spins. This work reports on an average Hamiltonian treatment of two spin counting sequences and compares the efficiency of the two cycles in the presence of flip errors, RF inhomogeneity, phase transients, phase errors, and offset interactions commonly present in NMR experiments. Simulations on small quantum systems performed using the two cycles reveal the effects of pulse imperfections on the resulting multiple quantum spectra, in qualitative agreement with the average Hamiltonian calculations. Experimental results on adamantane are presented, demonstrating differences in the two sequences in the presence of pulse errors.     

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.     

液体多脉冲及二维FT-NMR实验的乘积算符描述的计算机模拟

本文报道了利用乘积算符方法分析多脉冲及二维FT-NMR实验的模拟程序PROPER-MT.该程序对分析弱耦合I_mS_n(I=1/2;S=(1)/2;1 ≤ m十n<4)自旋体系实验脉冲序列是普遍适用的;它可给出实验过程中体系任何时刻算符的解析表达式.用PROPER-MT程序对一些典型的多脉冲及二维FT-NMR实验进行了模拟,特别对多量子滤波及多自旋滤波脉冲序列进行了分析计算,得到了预期的结果.     

Clean TROSY: compensation for relaxation-induced artifacts

TROSY pulse sequences for recording, e.g., (1)H-(15)N chemical shift correlation spectra of proteins are designed to select only one of four two-dimensional multiplet components. However, all of the variants published so far are prone to relaxation-induced artifacts at the positions of two of the other multiplet components. This article introduces modifications to the two spin-state-selective coherence transfer building blocks of the TROSY mixing sequence resulting in a clean TROSY spectrum with the artifacts largely suppressed. It works by having the new mixing sequence generate peaks of opposite phase at the positions of the relaxation artifacts. The clean TROSY pulse sequence is marginally shorter than the original one and contains the same pulses. Experimental demonstration is presented for the (15)N-labeled proteins RAP 17-97 (N-terminal domain of alpha(2)-macroglobulin receptor associated protein) and EQT, equinatoxin II, from the Mediterranean anemone Actinia equina.     

组合脉冲宽带去耦

本文在理论分析的基础上,提出了一新的用于异核宽带去耦的组合脉冲:90°(X)150°(Y)70°(-Y)150°(Y)90°(X)。理论和实验表明,由此组合脉冲组成的去耦序列:NEW-16、NEW-32,去耦谱宽比常用的去耦序列:MLEV-16、WALTZ-16的去耦谱宽增加约30%。本文还提出了一种电路,使现已提出的大多数组合脉冲去耦序列,能在Varian XL-200 NMB谱仪上实现。     

Optimal control in NMR spectroscopy: Numerical implementation in SIMPSON

We present the implementation of optimal control into the open source simulation package SIMPSON for development and optimization of nuclear magnetic resonance experiments for a wide range of applications, including liquid- and solid-state NMR, magnetic resonance imaging, quantum computation, and combinations between NMR and other spectroscopies. Optimal control enables efficient optimization of NMR experiments in terms of amplitudes, phases, offsets etc. for hundreds-to-thousands of pulses to fully exploit the experimentally available high degree of freedom in pulse sequences to combat variations/limitations in experimental or spin system parameters or design experiments with specific properties typically not covered as easily by standard design procedures. This facilitates straightforward optimization of experiments under consideration of rf and static field inhomogeneities, limitations in available or desired rf field strengths (e.g., for reduction of sample heating), spread in resonance offsets or coupling parameters, variations in spin systems etc. to meet the actual experimental conditions as close as possible. The paper provides a brief account on the relevant theory and in particular the computational interface relevant for optimization of state-to-state transfer (on the density operator level) and the effective Hamiltonian on the level of propagators along with several representative examples within liquid- and solid-state NMR spectroscopy.     

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.     

Linking NMR pulse sequences: derivative relation between the responses of two pulse sequences

Examples are shown of how the derivative of the response of an NMR pulse sequence with respect to a variable in that pulse sequence can be obtained by another pulse sequence. This approach holds the potential of being a tool for discovery of new pulse sequences or a means of understanding how some pulse sequences are related to each other.     

Experimental realization of discrete fourier transformation on NMR quantum computers

We report the experimental implementation of discrete Fourier transformation (DFT) on a nuclear magnetic resonance (NMR) quantum computer. Experimental results agree well with the theoretical ones. With the pulse sequences that we propose and the refocusing pulse sequences that one uses to suppress unwanted one-spin and two-spin interactions, the DFT can, in principle, be realized on anyL-bit quantum number.     

Pattern pulses: design of arbitrary excitation profiles as a function of pulse amplitude and offset

A novel class of pulses is presented which can be regarded as a generalization of both frequency-selective pulses and B1-selective pulses. The excitation profile of these pulses forms a pre-defined pattern in two dimensions, which are spanned by pulse offset and radio-frequency (RF) amplitude. The presented pulses were designed numerically based on principles of optimal control theory. For simple test patterns, we demonstrate the flexibility of this approach by simulations and experiments. This previously unknown flexibility may trigger novel applications in NMR spectroscopy and imaging. As a first practical application, we demonstrate a direct approach for calibrating RF pulses.     

Gradient hysteresis in MRI and NMR experiments

In this paper, we describe a gradient hysteresis effect that can modulate the current in gradient coils during MRI and NMR experiments. A simple pulse sequence is presented for the purpose of evaluating the resulting changes in the accumulated phase. Additionally, the nature of the gradient pulse shape changes is described. These experiments will be of interest to MRI and NMR scientists who are developing pulse sequences requiring precision gradient performance or who are currently seeking the source of unexplained NMR artifacts.     

Efficient measurement of (3)J(N,Cgamma) and (3)J(C',Cgamma) coupling constants of aromatic residues in (13)C, (15)N-labeled proteins

An NMR pulse sequence is proposed for the simultaneous determination of side chain chi1 torsion-angle related (3)J(N,Cgamma) and (3)J(C', Cgamma) couplings in aromatic amino acid spin systems. The method is of the quantitative J correlation type and takes advantage of attenuated (15)N and (1)H transverse relaxation by means of the TROSY principle. Unlike previously developed schemes for the measurement of either of the two coupling types, spectra contain internal reference peaks that are usually recorded in separate experiments. Therefore, the desired information is extracted from a single rather than four data sets. The new method is demonstrated with uniformly (13)C/(15)N labeled Desulfovibrio vulgaris flavodoxin, which contains 14 aromatic out of 147 total amino acid residues.     

ODIN-object-oriented development interface for NMR

A cross-platform development environment for nuclear magnetic resonance (NMR) experiments is presented. It allows rapid prototyping of new pulse sequences and provides a common programming interface for different system types. With this object-oriented interface implemented in C++, the programmer is capable of writing applications to control an experiment that can be executed on different measurement devices, even from different manufacturers, without the need to modify the source code. Due to the clear design of the software, new pulse sequences can be created, tested, and executed within a short time. To post-process the acquired data, an interface to well-known numerical libraries is part of the framework. This allows a transparent integration of the data processing instructions into the measurement module. The software focuses mainly on NMR imaging, but can also be used with limitations for spectroscopic experiments. To demonstrate the capabilities of the framework, results of the same experiment, carried out on two NMR imaging systems from different manufacturers are shown and compared with the results of a simulation.     

Diffusion in porous building materials with high internal magnetic field gradients

An algorithm to calculate NMR signals of a multi-echo pulse sequence with arbitrary position dependent B0 and B1 fields taking into account relaxation and spin-diffusion is presented. The multi-echo pulse sequence consists of an initial RF pulse ("90 degrees " RF pulse) and a series of L refocusing RF pulses with arbitrary phases and flip-angles. The calculation is exact and takes into account all the magnetization pathways that contribute to the signal on a predefined spatial grid. The theoretical prediction is verified experimentally using a high field NMR microscopy system. The algorithm was implemented in a simulation program in order to optimize the design of an inside-out MR intra-vascular catheter that is used for characterization of vessel wall tissue. Measured data obtained with the catheter are in good agreement with the theoretical prediction of the simulation.     

Field propagation phenomena in ultra high field NMR: a Maxwell-Bloch formulation

The principal advantage of NMR at high field is the concomitant increase in signal-to-noise ratio (SNR). This can be traded for improved spatial resolution and combined with parallel imaging to achieve higher temporal resolution. At high field strength, the RF-wavelength and the dimension of the human body complicate the development of NMR coils. For example, at 7 T, the wavelength in free space corresponds to about 1m. The dielectric constant in tissue with a high water content can be as high as 70 and at a larmor frequency of 300 MHz, this corresponds to a wavelength inside tissue of less than 15 cm. The operating wavelength is thus comparable to the diameter of most body parts. To this end, both temporal and spatial variations of the excitation field must be taken into account in addition to the expected increase in conductivity. For all these reasons, we find the propagation of radiation at ultra high fields (>4 T) new phenomena commonly observed in quantum optics but traditionally negligible in NMR such as phase modulation of the excitation field such that the identity between pulse area and flip angle is no longer valid. In this paper, the emergence of field propagation phenomena in NMR experiments is analytically and numerically demonstrated. It is shown that in addition to the well-studied dielectric resonance phenomena at high magnetic fields (>4 T), field propagation effects transform the excitation pulse into an adiabatic excitation. The high field strength also mean that nonlinear effects such as self-induced transparency are now possible in NMR experiments.     

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.     

GAVA: spectral simulation for in vivo MRS applications

An application that provides a flexible and easy to use interface to the GAMMA spectral simulation package is described that is targeted at investigations using in vivo MR spectroscopic methods. The program makes available a number of widely used spatially localized MRS pulse sequences and NMR parameters for commonly observed tissue metabolites, enabling spectra to be simulated for any pulse sequence parameter and viewed in an integrated display. The application is interfaced with a database for storage of all simulation parameters and results of the simulations. This application provides a convenient method for generating a priori spectral information used in parametric spectral analyses and for visual examination of the effects of difference pulse sequences and parameter settings.