Rock climbing: A local-global algorithm to compute minimum energy and minimum free energy pathways
The calculation of minimum energy or minimum free energy paths is an important step in the quantitative and qualitative studies of chemical and physical processes. The computations of these coordinates present a significant challenge and have attracted considerable theoretical and computational inte...
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| Published in | The Journal of chemical physics Vol. 147; no. 15; pp. 152718 - 152727 |
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| Main Authors | , , , |
| Format | Journal Article |
| Language | English |
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American Institute of Physics
21.10.2017
AIP Publishing LLC |
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| Abstract | The calculation of minimum energy or minimum free energy paths is an important step in the quantitative and qualitative studies of chemical and physical processes. The computations of these coordinates present a significant challenge and have attracted considerable theoretical and computational interest. Here we present a new local-global approach to study reaction coordinates, based on a gradual optimization of an action. Like other global algorithms, it provides a path between known reactants and products, but it uses a local algorithm to extend the current path in small steps. The local-global approach does not require an initial guess to the path, a major challenge for global pathway finders. Finally, it provides an exact answer (the steepest descent path) at the end of the calculations. Numerical examples are provided for the Mueller potential and for a conformational transition in a solvated ring system. |
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| AbstractList | The calculation of minimum energy or minimum free energy paths is an important step in the quantitative and qualitative studies of chemical and physical processes. The computations of these coordinates present a significant challenge and have attracted considerable theoretical and computational interest. Here we present a new local-global approach to study reaction coordinates, based on a gradual optimization of an action. Like other global algorithms, it provides a path between known reactants and products, but it uses a local algorithm to extend the current path in small steps. The local-global approach does not require an initial guess to the path, a major challenge for global pathway finders. Finally, it provides an exact answer (the steepest descent path) at the end of the calculations. Numerical examples are provided for the Mueller potential and for a conformational transition in a solvated ring system. The calculation of minimum energy or minimum free energy paths is an important step in the quantitative and qualitative studies of chemical and physical processes. The computations of these coordinates present a significant challenge and have attracted considerable theoretical and computational interest. Here we present a new local-global approach to study reaction coordinates, based on a gradual optimization of an action. Like other global algorithms, it provides a path between known reactants and products, but it uses a local algorithm to extend the current path in small steps. The local-global approach does not require an initial guess to the path, a major challenge for global pathway finders. Finally, it provides an exact answer (the steepest descent path) at the end of the calculations. Numerical examples are provided for the Mueller potential and for a conformational transition in a solvated ring system.The calculation of minimum energy or minimum free energy paths is an important step in the quantitative and qualitative studies of chemical and physical processes. The computations of these coordinates present a significant challenge and have attracted considerable theoretical and computational interest. Here we present a new local-global approach to study reaction coordinates, based on a gradual optimization of an action. Like other global algorithms, it provides a path between known reactants and products, but it uses a local algorithm to extend the current path in small steps. The local-global approach does not require an initial guess to the path, a major challenge for global pathway finders. Finally, it provides an exact answer (the steepest descent path) at the end of the calculations. Numerical examples are provided for the Mueller potential and for a conformational transition in a solvated ring system. |
| Author | Chen, Szu-Hua Elber, Ron Fathizadeh, Arman Templeton, Clark |
| Author_xml | – sequence: 1 givenname: Clark surname: Templeton fullname: Templeton, Clark organization: Department of Chemical Engineering, University of Texas at Austin – sequence: 2 givenname: Szu-Hua surname: Chen fullname: Chen, Szu-Hua organization: Computational Biology Center, IBM Thomas J. Watson Research Center – sequence: 3 givenname: Arman surname: Fathizadeh fullname: Fathizadeh, Arman organization: Institute for Computational Engineering and Sciences, University of Texas at Austin – sequence: 4 givenname: Ron surname: Elber fullname: Elber, Ron organization: 4 Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, USA |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/29055297$$D View this record in MEDLINE/PubMed |
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| Cites_doi | 10.1063/1.2212942 10.1073/pnas.0909636107 10.1063/1.458112 10.1063/1.4935110 10.1088/1749-4699/4/1/015002 10.1016/j.str.2012.02.018 10.1016/s0166-1280(97)00038-9 10.1103/physrevlett.97.108101 10.1021/jp045546c 10.3390/e19050219 10.1063/1.4827495 10.1016/0263-7855(96)00018-5 10.1063/1.2748396 10.1103/physrevlett.96.090601 10.1529/biophysj.106.101899 10.1137/070699500 10.1002/qua.560382419 10.1002/jcc.20289 10.1063/1.451695 10.1021/ja00372a029 10.1146/annurev.physchem.040808.090412 10.1016/0263-7855(94)80072-3 10.1063/1.442352 10.1021/jp0777059 10.1063/1.1691018 10.1063/1.445675 10.1016/0009-2614(87)80576-6 10.1107/s0567739478001680 10.1142/3816 10.1103/PhysRevB.66.052301 10.1007/bf00547608 10.1080/00268978100100861 10.1007/s008940050065 |
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| SubjectTerms | Algorithms Free energy Mathematical analysis Organic chemistry Physics Special Topic: Reaction Pathways |
| Title | Rock climbing: A local-global algorithm to compute minimum energy and minimum free energy pathways |
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