LAUSR.org creates dashboard-style pages of related content for over 1.5 million academic articles. Sign Up to like articles & get recommendations!

Rapid Calculation of Molecular Kinetics Using Compressed Sensing.

Photo by sarahdorweiler from unsplash

Recent methods for the analysis of molecular kinetics from massive molecular dynamics (MD) data rely on the solution of very large eigenvalue problems. Here we build upon recent results from… Click to show full abstract

Recent methods for the analysis of molecular kinetics from massive molecular dynamics (MD) data rely on the solution of very large eigenvalue problems. Here we build upon recent results from the field of compressed sensing and develop the spectral oASIS method, a highly efficient approach to approximate the leading eigenvalues and eigenvectors of large generalized eigenvalue problems without ever having to evaluate the full matrices. The approach is demonstrated to reduce the dimensionality of the problem by 1 or 2 orders of magnitude, directly leading to corresponding savings in the computation and storage of the necessary matrices and a speedup of 2 to 4 orders of magnitude in solving the eigenvalue problem. We demonstrate the method on extensive data sets of protein conformational changes and protein-ligand binding using the variational approach to conformation dynamics (VAC) and time-lagged independent component analysis (TICA). Our approach can also be applied to kernel formulations of VAC, TICA, and extended dynamic mode decomposition (EDMD).

Keywords: calculation molecular; compressed sensing; using compressed; molecular kinetics; rapid calculation; kinetics using

Journal Title: Journal of chemical theory and computation
Year Published: 2018

Link to full text (if available)


Share on Social Media:                               Sign Up to like & get
recommendations!

Related content

More Information              News              Social Media              Video              Recommended



                Click one of the above tabs to view related content.