Literature DB >> 22891294

Application of compressed sensing to the simulation of atomic systems.

Xavier Andrade1, Jacob N Sanders, Alán Aspuru-Guzik.   

Abstract

Compressed sensing is a method that allows a significant reduction in the number of samples required for accurate measurements in many applications in experimental sciences and engineering. In this work, we show that compressed sensing can also be used to speed up numerical simulations. We apply compressed sensing to extract information from the real-time simulation of atomic and molecular systems, including electronic and nuclear dynamics. We find that, compared to the standard discrete Fourier transform approach, for the calculation of vibrational and optical spectra the total propagation time, and hence the computational cost, can be reduced by approximately a factor of five.

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Year:  2012        PMID: 22891294      PMCID: PMC3435224          DOI: 10.1073/pnas.1209890109

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  17 in total

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Authors: 
Journal:  Phys Rev Lett       Date:  1996-10-28       Impact factor: 9.161

2.  Modified Ehrenfest Formalism for Efficient Large-Scale ab initio Molecular Dynamics.

Authors:  Xavier Andrade; Alberto Castro; David Zueco; J L Alonso; Pablo Echenique; Fernando Falceto; Ángel Rubio
Journal:  J Chem Theory Comput       Date:  2009-04-14       Impact factor: 6.006

3.  Sparse MRI: The application of compressed sensing for rapid MR imaging.

Authors:  Michael Lustig; David Donoho; John M Pauly
Journal:  Magn Reson Med       Date:  2007-12       Impact factor: 4.668

4.  Real-time time-dependent density functional theory approach for frequency-dependent nonlinear optical response in photonic molecules.

Authors:  Y Takimoto; F D Vila; J J Rehr
Journal:  J Chem Phys       Date:  2007-10-21       Impact factor: 3.488

5.  Time-dependent density functional theory scheme for efficient calculations of dynamic (hyper)polarizabilities.

Authors:  Xavier Andrade; Silvana Botti; Miguel A L Marques; Angel Rubio
Journal:  J Chem Phys       Date:  2007-05-14       Impact factor: 3.488

6.  Efficient formalism for large-scale ab initio molecular dynamics based on time-dependent density functional theory.

Authors:  J L Alonso; X Andrade; P Echenique; F Falceto; D Prada-Gracia; A Rubio
Journal:  Phys Rev Lett       Date:  2008-08-28       Impact factor: 9.161

7.  Time-dependent density-functional theory in massively parallel computer architectures: the OCTOPUS project.

Authors:  Xavier Andrade; Joseba Alberdi-Rodriguez; David A Strubbe; Micael J T Oliveira; Fernando Nogueira; Alberto Castro; Javier Muguerza; Agustin Arruabarrena; Steven G Louie; Alán Aspuru-Guzik; Angel Rubio; Miguel A L Marques
Journal:  J Phys Condens Matter       Date:  2012-05-04       Impact factor: 2.333

8.  Magnetic circular dichroism in real-time time-dependent density functional theory.

Authors:  K-M Lee; K Yabana; G F Bertsch
Journal:  J Chem Phys       Date:  2011-04-14       Impact factor: 3.488

9.  Direct inference of protein-DNA interactions using compressed sensing methods.

Authors:  Mohammed AlQuraishi; Harley H McAdams
Journal:  Proc Natl Acad Sci U S A       Date:  2011-08-08       Impact factor: 11.205

10.  Faster STORM using compressed sensing.

Authors:  Lei Zhu; Wei Zhang; Daniel Elnatan; Bo Huang
Journal:  Nat Methods       Date:  2012-04-22       Impact factor: 28.547

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  7 in total

1.  Compressed Sensing for the Fast Computation of Matrices: Application to Molecular Vibrations.

Authors:  Jacob N Sanders; Xavier Andrade; Alán Aspuru-Guzik
Journal:  ACS Cent Sci       Date:  2015-03-23       Impact factor: 14.553

2.  Compressive Sensing in Quantum Chemistry: A Little Computation Goes a Long Way.

Authors:  Gregory J O Beran
Journal:  ACS Cent Sci       Date:  2015-03-23       Impact factor: 14.553

3.  Continuous Compressed Sensing for Surface Dynamical Processes with Helium Atom Scattering.

Authors:  Alex Jones; Anton Tamtögl; Irene Calvo-Almazán; Anders Hansen
Journal:  Sci Rep       Date:  2016-06-15       Impact factor: 4.379

4.  Machine learning molecular dynamics for the simulation of infrared spectra.

Authors:  Michael Gastegger; Jörg Behler; Philipp Marquetand
Journal:  Chem Sci       Date:  2017-08-10       Impact factor: 9.825

5.  Efficient route to high-bandwidth nanoscale magnetometry using single spins in diamond.

Authors:  Graciana Puentes; Gerald Waldherr; Philipp Neumann; Gopalakrishnan Balasubramanian; Jörg Wrachtrup
Journal:  Sci Rep       Date:  2014-04-14       Impact factor: 4.379

6.  Mapping multidimensional electronic structure and ultrafast dynamics with single-element detection and compressive sensing.

Authors:  Austin P Spencer; Boris Spokoyny; Supratim Ray; Fahad Sarvari; Elad Harel
Journal:  Nat Commun       Date:  2016-01-25       Impact factor: 14.919

7.  Revealing true coupling strengths in two-dimensional spectroscopy with sparsity-based signal recovery.

Authors:  Hadas Frostig; Tim Bayer; Yonina C Eldar; Yaron Silberberg
Journal:  Light Sci Appl       Date:  2017-12-29       Impact factor: 17.782

  7 in total

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