Literature DB >> 25093693

Computer-intensive simulation of solid-state NMR experiments using SIMPSON.

Zdeněk Tošner1, Rasmus Andersen2, Baltzar Stevensson3, Mattias Edén3, Niels Chr Nielsen4, Thomas Vosegaard5.   

Abstract

Conducting large-scale solid-state NMR simulations requires fast computer software potentially in combination with efficient computational resources to complete within a reasonable time frame. Such simulations may involve large spin systems, multiple-parameter fitting of experimental spectra, or multiple-pulse experiment design using parameter scan, non-linear optimization, or optimal control procedures. To efficiently accommodate such simulations, we here present an improved version of the widely distributed open-source SIMPSON NMR simulation software package adapted to contemporary high performance hardware setups. The software is optimized for fast performance on standard stand-alone computers, multi-core processors, and large clusters of identical nodes. We describe the novel features for fast computation including internal matrix manipulations, propagator setups and acquisition strategies. For efficient calculation of powder averages, we implemented interpolation method of Alderman, Solum, and Grant, as well as recently introduced fast Wigner transform interpolation technique. The potential of the optimal control toolbox is greatly enhanced by higher precision gradients in combination with the efficient optimization algorithm known as limited memory Broyden-Fletcher-Goldfarb-Shanno. In addition, advanced parallelization can be used in all types of calculations, providing significant time reductions. SIMPSON is thus reflecting current knowledge in the field of numerical simulations of solid-state NMR experiments. The efficiency and novel features are demonstrated on the representative simulations.
Copyright © 2014 Elsevier Inc. All rights reserved.

Keywords:  Cloud computing; Fast powder averaging; Optimal control pulse sequence optimization; SIMPSON; Simulation of solid-state NMR experiments

Year:  2014        PMID: 25093693     DOI: 10.1016/j.jmr.2014.07.002

Source DB:  PubMed          Journal:  J Magn Reson        ISSN: 1090-7807            Impact factor:   2.229


  17 in total

1.  Selective excitation enables assignment of proton resonances and (1)H-(1)H distance measurement in ultrafast magic angle spinning solid state NMR spectroscopy.

Authors:  Rongchun Zhang; Ayyalusamy Ramamoorthy
Journal:  J Chem Phys       Date:  2015-07-21       Impact factor: 3.488

2.  Field-stepped ultra-wideline NMR at up to 36 T: On the inequivalence between field and frequency stepping.

Authors:  Ivan Hung; Adam R Altenhof; Robert W Schurko; David L Bryce; Oc Hee Han; Zhehong Gan
Journal:  Magn Reson Chem       Date:  2020-12-29       Impact factor: 2.447

3.  Proton chemical shift tensors determined by 3D ultrafast MAS double-quantum NMR spectroscopy.

Authors:  Rongchun Zhang; Kamal H Mroue; Ayyalusamy Ramamoorthy
Journal:  J Chem Phys       Date:  2015-10-14       Impact factor: 3.488

4.  B-MWW Zeolite: The Case Against Single-Site Catalysis.

Authors:  Natalie R Altvater; Rick W Dorn; Melissa C Cendejas; William P McDermott; Brijith Thomas; Aaron J Rossini; Ive Hermans
Journal:  Angew Chem Int Ed Engl       Date:  2020-02-28       Impact factor: 15.336

5.  Application of the limited-memory quasi-Newton algorithm for multi-dimensional, large flip-angle RF pulses at 7T.

Authors:  Mads S Vinding; Daniel Brenner; Desmond H Y Tse; Sebastian Vellmer; Thomas Vosegaard; Dieter Suter; Tony Stöcker; Ivan I Maximov
Journal:  MAGMA       Date:  2016-08-02       Impact factor: 2.310

6.  MAS dependent sensitivity of different isotopomers in selectively methyl protonated protein samples in solid state NMR.

Authors:  Kai Xue; Riddhiman Sarkar; Zdenek Tosner; Daniela Lalli; Carina Motz; Benita Koch; Guido Pintacuda; Bernd Reif
Journal:  J Biomol NMR       Date:  2019-09-12       Impact factor: 2.835

7.  Proton-Assisted Recoupling (PAR) in Peptides and Proteins.

Authors:  Kevin J Donovan; Sheetal K Jain; Robert Silvers; Sara Linse; Robert G Griffin
Journal:  J Phys Chem B       Date:  2017-11-27       Impact factor: 2.991

8.  Phase cycling schemes for finite-pulse-RFDR MAS solid state NMR experiments.

Authors:  Rongchun Zhang; Yusuke Nishiyama; Pingchuan Sun; Ayyalusamy Ramamoorthy
Journal:  J Magn Reson       Date:  2015-01-06       Impact factor: 2.229

9.  A cross-polarization based rotating-frame separated-local-field NMR experiment under ultrafast MAS conditions.

Authors:  Rongchun Zhang; Joshua Damron; Thomas Vosegaard; Ayyalusamy Ramamoorthy
Journal:  J Magn Reson       Date:  2014-11-15       Impact factor: 2.229

10.  1020MHz single-channel proton fast magic angle spinning solid-state NMR spectroscopy.

Authors:  Manoj Kumar Pandey; Rongchun Zhang; Kenjiro Hashi; Shinobu Ohki; Gen Nishijima; Shinji Matsumoto; Takashi Noguchi; Kenzo Deguchi; Atsushi Goto; Tadashi Shimizu; Hideaki Maeda; Masato Takahashi; Yoshinori Yanagisawa; Toshio Yamazaki; Seiya Iguchi; Ryoji Tanaka; Takahiro Nemoto; Tetsuo Miyamoto; Hiroto Suematsu; Kazuyoshi Saito; Takashi Miki; Ayyalusamy Ramamoorthy; Yusuke Nishiyama
Journal:  J Magn Reson       Date:  2015-10-17       Impact factor: 2.229

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