Global Optimization of Large Molecular Systems Using Rigid-Body Chain Stochastic Surface Walking
The global potential energy surface (PES) search of large molecular systems remains a significant challenge in chemistry due to “the curse of dimensionality”. To address this, here we develop a rigid-body chain method in the framework of a stochastic surface walking (SSW) global optimization method,...
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2025
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| _version_ | 1852020026260848640 |
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| author | Tong Guan (711702) |
| author2 | Xin-Tian Xie (19188391) Xiao-Jie Zhang (1512889) Cheng Shang (1333905) Zhi-Pan Liu (1335726) |
| author2_role | author author author author |
| author_facet | Tong Guan (711702) Xin-Tian Xie (19188391) Xiao-Jie Zhang (1512889) Cheng Shang (1333905) Zhi-Pan Liu (1335726) |
| author_role | author |
| dc.creator.none.fl_str_mv | Tong Guan (711702) Xin-Tian Xie (19188391) Xiao-Jie Zhang (1512889) Cheng Shang (1333905) Zhi-Pan Liu (1335726) |
| dc.date.none.fl_str_mv | 2025-05-27T11:38:45Z |
| dc.identifier.none.fl_str_mv | 10.1021/acs.jctc.5c00350.s003 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/dataset/Global_Optimization_of_Large_Molecular_Systems_Using_Rigid-Body_Chain_Stochastic_Surface_Walking/29154343 |
| dc.rights.none.fl_str_mv | CC BY-NC 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Biophysics Biochemistry Cell Biology Molecular Biology Neuroscience Biotechnology Computational Biology Chemical Sciences not elsewhere classified Physical Sciences not elsewhere classified unprecedentedly high efficiency stochastic surface walking low energy conformations body chain movement body chain method 172 atoms missed 10 times faster large molecular systems single rigid body body chain ssw global optimization method connected rigid bodies global optimization rigid bodies molecular dynamics molecular crystals termed rigid ssw ). significant challenge revealing many lattice variation generalized coordinate dimensionality ”. cooperative motion chemistry due algorithm realizes |
| dc.title.none.fl_str_mv | Global Optimization of Large Molecular Systems Using Rigid-Body Chain Stochastic Surface Walking |
| dc.type.none.fl_str_mv | Dataset info:eu-repo/semantics/publishedVersion dataset |
| description | The global potential energy surface (PES) search of large molecular systems remains a significant challenge in chemistry due to “the curse of dimensionality”. To address this, here we develop a rigid-body chain method in the framework of a stochastic surface walking (SSW) global optimization method, termed rigid-body chain SSW (RC-SSW). Based on the angle–axis representation for a single rigid body, our algorithm realizes the cooperative motion of connected rigid bodies and achieves the coupling between rigid-body chain movement and lattice variation in the generalized coordinate. By exploiting the numerical energy second derivative information on rigid bodies, RC-SSW can optimize the global PES of large molecular systems with an unprecedentedly high efficiency. We show that RC-SSW is more than 10 times faster in locating the model protein global minimum while revealing many more low energy conformations than molecular dynamics and can identify low energy phases of molecular crystals up to 172 atoms missed in the sixth CCDC blind test. |
| eu_rights_str_mv | openAccess |
| id | Manara_32a67bbd58d2076ccb3efa3af69a05ae |
| identifier_str_mv | 10.1021/acs.jctc.5c00350.s003 |
| network_acronym_str | Manara |
| network_name_str | ManaraRepo |
| oai_identifier_str | oai:figshare.com:article/29154343 |
| publishDate | 2025 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY-NC 4.0 |
| spelling | Global Optimization of Large Molecular Systems Using Rigid-Body Chain Stochastic Surface WalkingTong Guan (711702)Xin-Tian Xie (19188391)Xiao-Jie Zhang (1512889)Cheng Shang (1333905)Zhi-Pan Liu (1335726)BiophysicsBiochemistryCell BiologyMolecular BiologyNeuroscienceBiotechnologyComputational BiologyChemical Sciences not elsewhere classifiedPhysical Sciences not elsewhere classifiedunprecedentedly high efficiencystochastic surface walkinglow energy conformationsbody chain movementbody chain method172 atoms missed10 times fasterlarge molecular systemssingle rigid bodybody chain sswglobal optimization methodconnected rigid bodiesglobal optimizationrigid bodiesmolecular dynamicsmolecular crystalstermed rigidssw ).significant challengerevealing manylattice variationgeneralized coordinatedimensionality ”.cooperative motionchemistry duealgorithm realizesThe global potential energy surface (PES) search of large molecular systems remains a significant challenge in chemistry due to “the curse of dimensionality”. To address this, here we develop a rigid-body chain method in the framework of a stochastic surface walking (SSW) global optimization method, termed rigid-body chain SSW (RC-SSW). Based on the angle–axis representation for a single rigid body, our algorithm realizes the cooperative motion of connected rigid bodies and achieves the coupling between rigid-body chain movement and lattice variation in the generalized coordinate. By exploiting the numerical energy second derivative information on rigid bodies, RC-SSW can optimize the global PES of large molecular systems with an unprecedentedly high efficiency. We show that RC-SSW is more than 10 times faster in locating the model protein global minimum while revealing many more low energy conformations than molecular dynamics and can identify low energy phases of molecular crystals up to 172 atoms missed in the sixth CCDC blind test.2025-05-27T11:38:45ZDatasetinfo:eu-repo/semantics/publishedVersiondataset10.1021/acs.jctc.5c00350.s003https://figshare.com/articles/dataset/Global_Optimization_of_Large_Molecular_Systems_Using_Rigid-Body_Chain_Stochastic_Surface_Walking/29154343CC BY-NC 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/291543432025-05-27T11:38:45Z |
| spellingShingle | Global Optimization of Large Molecular Systems Using Rigid-Body Chain Stochastic Surface Walking Tong Guan (711702) Biophysics Biochemistry Cell Biology Molecular Biology Neuroscience Biotechnology Computational Biology Chemical Sciences not elsewhere classified Physical Sciences not elsewhere classified unprecedentedly high efficiency stochastic surface walking low energy conformations body chain movement body chain method 172 atoms missed 10 times faster large molecular systems single rigid body body chain ssw global optimization method connected rigid bodies global optimization rigid bodies molecular dynamics molecular crystals termed rigid ssw ). significant challenge revealing many lattice variation generalized coordinate dimensionality ”. cooperative motion chemistry due algorithm realizes |
| status_str | publishedVersion |
| title | Global Optimization of Large Molecular Systems Using Rigid-Body Chain Stochastic Surface Walking |
| title_full | Global Optimization of Large Molecular Systems Using Rigid-Body Chain Stochastic Surface Walking |
| title_fullStr | Global Optimization of Large Molecular Systems Using Rigid-Body Chain Stochastic Surface Walking |
| title_full_unstemmed | Global Optimization of Large Molecular Systems Using Rigid-Body Chain Stochastic Surface Walking |
| title_short | Global Optimization of Large Molecular Systems Using Rigid-Body Chain Stochastic Surface Walking |
| title_sort | Global Optimization of Large Molecular Systems Using Rigid-Body Chain Stochastic Surface Walking |
| topic | Biophysics Biochemistry Cell Biology Molecular Biology Neuroscience Biotechnology Computational Biology Chemical Sciences not elsewhere classified Physical Sciences not elsewhere classified unprecedentedly high efficiency stochastic surface walking low energy conformations body chain movement body chain method 172 atoms missed 10 times faster large molecular systems single rigid body body chain ssw global optimization method connected rigid bodies global optimization rigid bodies molecular dynamics molecular crystals termed rigid ssw ). significant challenge revealing many lattice variation generalized coordinate dimensionality ”. cooperative motion chemistry due algorithm realizes |