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https://hdl.handle.net/10356/87036| Title: | B-spline tight frame based force matching method |
| Authors: | Yang, Jianbin Zhu, Guanhua Tong, Dudu Lu, Lanyuan Shen, Zuowei |
| Keywords: | Force Matching Coarse-grained Methods |
| Issue Date: | 2018 |
| Source: | Yang, J., Zhu, G., Tong, D., Lu, L., & Shen, Z. (2018). B-spline tight frame based force matching method. Journal of Computational Physics, 362, 208-219. doi:10.1016/j.jcp.2018.02.024 |
| Series/Report no.: | Journal of Computational Physics |
| Abstract: | In molecular dynamics simulations, compared with popular all-atom force field approaches, coarse-grained (CG) methods are frequently used for the rapid investigations of long time- and length-scale processes in many important biological and soft matter studies. The typical task in coarse-graining is to derive interaction force functions between different CG site types in terms of their distance, bond angle or dihedral angle. In this paper, an L1-regularized least squares model is applied to form the force functions, which makes additional use of the B-spline wavelet frame transform in order to preserve the important features of force functions. The B-spline tight frames system has a simple explicit expression which is useful for representing our force functions. Moreover, the redundancy of the system offers more resilience to the effects of noise and is useful in the case of lossy data. Numerical results for molecular systems involving pairwise non-bonded, three and four-body bonded interactions are obtained to demonstrate the effectiveness of our approach. |
| URI: | https://hdl.handle.net/10356/87036 http://hdl.handle.net/10220/45216 |
| ISSN: | 0021-9991 |
| DOI: | 10.1016/j.jcp.2018.02.024 |
| Schools: | School of Biological Sciences |
| Rights: | © 2018 Elsevier Inc. All rights reserved. This paper was published in Journal of Computational Physics and is made available with permission of Elsevier Inc. |
| Fulltext Permission: | open |
| Fulltext Availability: | With Fulltext |
| Appears in Collections: | SBS Journal Articles |
Files in This Item:
| File | Description | Size | Format | |
|---|---|---|---|---|
| B-spline tight frame based force matching method.pdf | 2.64 MB | Adobe PDF |  View/Open |
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