Literature DB >> 21261335

A new Lanczos-based algorithm for simulating high-frequency two-dimensional electron spin resonance spectra.

Yun-Wei Chiang1, Jack H Freed.   

Abstract

The Lanczos algorithm (LA) is a useful iterative method for the reduction of a large matrix to tridiagonal form. It is a storage efficient procedure requiring only the preceding two Lanczos vectors to compute the next. The quasi-minimal residual (QMR) method is a powerful method for the solution of linear equation systems, Ax = b. In this report we provide another application of the QMR method: we incorporate QMR into the LA to monitor the convergence of the Lanczos projections in the reduction of large sparse matrices. We demonstrate that the combined approach of the LA and QMR can be utilized efficiently for the orthogonal transformation of large, but sparse, complex, symmetric matrices, such as are encountered in the simulation of slow-motional 1D- and 2D-electron spin resonance (ESR) spectra. Especially in the 2D-ESR simulations, it is essential that we store all of the Lanczos vectors obtained in the course of the LA recursions and maintain their orthogonality. In the LA-QMR application, the QMR weight matrix mitigates the problem that the Lanczos vectors lose orthogonality after many LA projections. This enables substantially more Lanczos projections, as required to achieve convergence for the more challenging ESR simulations. It, therefore, provides better accuracy for the eigenvectors and the eigenvalues of the large sparse matrices originating in 2D-ESR simulations than does the previously employed method, which is a combined approach of the LA and the conjugate-gradient (CG) methods, as evidenced by the quality and convergence of the 2D-ESR simulations. Our results show that very slow-motional 2D-ESR spectra at W-band (95 GHz) can be reliably simulated using the LA-QMR method, whereas the LA-CG consistently fails. The improvements due to the LA-QMR are of critical importance in enabling the simulation of high-frequency 2D-ESR spectra, which are characterized by their very high resolution to molecular orientation.

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Year:  2011        PMID: 21261335      PMCID: PMC3041155          DOI: 10.1063/1.3523576

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  11 in total

Review 1.  Electron spin resonance in studies of membranes and proteins.

Authors:  P P Borbat; A J Costa-Filho; K A Earle; J K Moscicki; J H Freed
Journal:  Science       Date:  2001-01-12       Impact factor: 47.728

Review 2.  Rhodopsin structure, dynamics, and activation: a perspective from crystallography, site-directed spin labeling, sulfhydryl reactivity, and disulfide cross-linking.

Authors:  Wayne L Hubbell; Christian Altenbach; Cheryl M Hubbell; H Gobind Khorana
Journal:  Adv Protein Chem       Date:  2003

3.  A 2D-ELDOR study of the liquid ordered phase in multilamellar vesicle membranes.

Authors:  Antonio J Costa-Filho; Yuhei Shimoyama; Jack H Freed
Journal:  Biophys J       Date:  2003-04       Impact factor: 4.033

4.  High-frequency ESR at ACERT.

Authors:  Keith A Earle; Boris Dzikovski; Wulf Hofbauer; Jozef K Moscicki; Jack H Freed
Journal:  Magn Reson Chem       Date:  2005-11       Impact factor: 2.447

Review 5.  Recent advances and applications of site-directed spin labeling.

Authors:  Gail E Fanucci; David S Cafiso
Journal:  Curr Opin Struct Biol       Date:  2006-09-01       Impact factor: 6.809

6.  Simulating electron spin resonance spectra of nitroxide spin labels from molecular dynamics and stochastic trajectories.

Authors:  Deniz Sezer; Jack H Freed; Benoît Roux
Journal:  J Chem Phys       Date:  2008-04-28       Impact factor: 3.488

7.  Coexisting domains in the plasma membranes of live cells characterized by spin-label ESR spectroscopy.

Authors:  Musti J Swamy; Laura Ciani; Mingtao Ge; Andrew K Smith; David Holowka; Barbara Baird; Jack H Freed
Journal:  Biophys J       Date:  2006-03-24       Impact factor: 4.033

8.  Dynamic molecular structure and phase diagram of DPPC-cholesterol binary mixtures: a 2D-ELDOR study.

Authors:  Yun-Wei Chiang; Antonio J Costa-Filho; Jack H Freed
Journal:  J Phys Chem B       Date:  2007-08-31       Impact factor: 2.991

9.  Using Markov models to simulate electron spin resonance spectra from molecular dynamics trajectories.

Authors:  Deniz Sezer; Jack H Freed; Benoit Roux
Journal:  J Phys Chem B       Date:  2008-08-12       Impact factor: 2.991

10.  Parametrization, molecular dynamics simulation, and calculation of electron spin resonance spectra of a nitroxide spin label on a polyalanine alpha-helix.

Authors:  Deniz Sezer; Jack H Freed; Benoît Roux
Journal:  J Phys Chem B       Date:  2008-04-16       Impact factor: 2.991

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  2 in total

1.  Focus: Two-dimensional electron-electron double resonance and molecular motions: The challenge of higher frequencies.

Authors:  John M Franck; Siddarth Chandrasekaran; Boris Dzikovski; Curt R Dunnam; Jack H Freed
Journal:  J Chem Phys       Date:  2015-06-07       Impact factor: 3.488

2.  Microsecond dynamics in proteins by two-dimensional ESR: Predictions.

Authors:  Pranav Gupta; Zhichun Liang; Jack H Freed
Journal:  J Chem Phys       Date:  2020-06-07       Impact factor: 3.488

  2 in total

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