B-spline tight frame based force matching method
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...
| Main Authors: | , , , , |
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| Other Authors: | |
| Format: | Journal Article |
| Language: | English |
| Published: |
2018
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| Online Access: | https://hdl.handle.net/10356/87036 http://hdl.handle.net/10220/45216 |
| _version_ | 1811697632113852416 |
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| author | Yang, Jianbin Zhu, Guanhua Tong, Dudu Lu, Lanyuan Shen, Zuowei |
| author2 | School of Biological Sciences |
| author_facet | School of Biological Sciences Yang, Jianbin Zhu, Guanhua Tong, Dudu Lu, Lanyuan Shen, Zuowei |
| author_sort | Yang, Jianbin |
| collection | NTU |
| description | 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. |
| first_indexed | 2024-10-01T07:58:20Z |
| format | Journal Article |
| id | ntu-10356/87036 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T07:58:20Z |
| publishDate | 2018 |
| record_format | dspace |
| spelling | ntu-10356/870362023-02-28T17:02:13Z B-spline tight frame based force matching method Yang, Jianbin Zhu, Guanhua Tong, Dudu Lu, Lanyuan Shen, Zuowei School of Biological Sciences Force Matching Coarse-grained Methods 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. MOE (Min. of Education, S’pore) Accepted version 2018-07-25T02:10:48Z 2019-12-06T16:33:39Z 2018-07-25T02:10:48Z 2019-12-06T16:33:39Z 2018 Journal Article 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 0021-9991 https://hdl.handle.net/10356/87036 http://hdl.handle.net/10220/45216 10.1016/j.jcp.2018.02.024 en Journal of Computational Physics © 2018 Elsevier Inc. All rights reserved. This paper was published in Journal of Computational Physics and is made available with permission of Elsevier Inc. 26 p. application/pdf |
| spellingShingle | Force Matching Coarse-grained Methods Yang, Jianbin Zhu, Guanhua Tong, Dudu Lu, Lanyuan Shen, Zuowei B-spline tight frame based force matching method |
| title | B-spline tight frame based force matching method |
| title_full | B-spline tight frame based force matching method |
| title_fullStr | B-spline tight frame based force matching method |
| title_full_unstemmed | B-spline tight frame based force matching method |
| title_short | B-spline tight frame based force matching method |
| title_sort | b spline tight frame based force matching method |
| topic | Force Matching Coarse-grained Methods |
| url | https://hdl.handle.net/10356/87036 http://hdl.handle.net/10220/45216 |
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