Modeling and analysis of ensemble average solvation energy and solute–solvent interfacial fluctuations
Variational implicit solvation models (VISMs) have gained extensive popularity in the molecular-level solvation analysis of biological systems due to their cost-effectiveness and satisfactory accuracy. Central in the construction of VISM is an interface separating the solute and the solvent. However...
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| Language: | English |
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De Gruyter
2024-12-01
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| Series: | Computational and Mathematical Biophysics |
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| Online Access: | https://doi.org/10.1515/cmb-2024-0017 |
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| author | Shao Yuanzhen Chen Zhan Zhao Shan |
| author_facet | Shao Yuanzhen Chen Zhan Zhao Shan |
| author_sort | Shao Yuanzhen |
| collection | DOAJ |
| description | Variational implicit solvation models (VISMs) have gained extensive popularity in the molecular-level solvation analysis of biological systems due to their cost-effectiveness and satisfactory accuracy. Central in the construction of VISM is an interface separating the solute and the solvent. However, traditional sharp-interface VISMs fall short in adequately representing the inherent randomness of the solute–solvent interface, a consequence of thermodynamic fluctuations within the solute–solvent system. Given that experimentally observable quantities are ensemble averaged, the computation of the ensemble average solvation energy (EASE)–the averaged solvation energy across all thermodynamic microscopic states–emerges as a key metric for reflecting thermodynamic fluctuations during solvation processes. This study introduces a novel approach to calculating the EASE. We devise two diffuse-interface VISMs: one within the classic Poisson–Boltzmann (PB) framework and another within the framework of size-modified PB theory, accounting for the finite-size effects. The construction of these models relies on a new diffuse interface definition u(x)u\left(x), which represents the probability of a point xx found in the solute phase among all microstates. Drawing upon principles of statistical mechanics and geometric measure theory, we rigorously demonstrate that the proposed models effectively capture EASE during the solvation process. Moreover, preliminary analyses indicate that the size-modified EASE functional surpasses its counterpart based on the classic PB theory across various analytic aspects. Our work is the first step toward calculating EASE through the utilization of diffuse-interface VISM. |
| format | Article |
| id | doaj-art-21d8c32e7ea64026b3e16dcf55f9a131 |
| institution | Kabale University |
| issn | 2544-7297 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | De Gruyter |
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| series | Computational and Mathematical Biophysics |
| spelling | doaj-art-21d8c32e7ea64026b3e16dcf55f9a1312025-01-20T11:08:25ZengDe GruyterComputational and Mathematical Biophysics2544-72972024-12-011211374310.1515/cmb-2024-0017Modeling and analysis of ensemble average solvation energy and solute–solvent interfacial fluctuationsShao Yuanzhen0Chen Zhan1Zhao Shan2Department of Mathematics, The University of Alabama, Tuscaloosa, AL, 35401, United States of AmericaDepartment of Mathematical Sciences, Georgia Southern University, GA, 30458, United States of AmericaDepartment of Mathematics, The University of Alabama, Tuscaloosa, AL, 35401, United States of AmericaVariational implicit solvation models (VISMs) have gained extensive popularity in the molecular-level solvation analysis of biological systems due to their cost-effectiveness and satisfactory accuracy. Central in the construction of VISM is an interface separating the solute and the solvent. However, traditional sharp-interface VISMs fall short in adequately representing the inherent randomness of the solute–solvent interface, a consequence of thermodynamic fluctuations within the solute–solvent system. Given that experimentally observable quantities are ensemble averaged, the computation of the ensemble average solvation energy (EASE)–the averaged solvation energy across all thermodynamic microscopic states–emerges as a key metric for reflecting thermodynamic fluctuations during solvation processes. This study introduces a novel approach to calculating the EASE. We devise two diffuse-interface VISMs: one within the classic Poisson–Boltzmann (PB) framework and another within the framework of size-modified PB theory, accounting for the finite-size effects. The construction of these models relies on a new diffuse interface definition u(x)u\left(x), which represents the probability of a point xx found in the solute phase among all microstates. Drawing upon principles of statistical mechanics and geometric measure theory, we rigorously demonstrate that the proposed models effectively capture EASE during the solvation process. Moreover, preliminary analyses indicate that the size-modified EASE functional surpasses its counterpart based on the classic PB theory across various analytic aspects. Our work is the first step toward calculating EASE through the utilization of diffuse-interface VISM.https://doi.org/10.1515/cmb-2024-0017biomolecule solvationpoisson–boltzmannvariational implicit solvation modelensemble average solvation energyfinite size effectprimary: 49q10secondary: 35j2092c40 |
| spellingShingle | Shao Yuanzhen Chen Zhan Zhao Shan Modeling and analysis of ensemble average solvation energy and solute–solvent interfacial fluctuations Computational and Mathematical Biophysics biomolecule solvation poisson–boltzmann variational implicit solvation model ensemble average solvation energy finite size effect primary: 49q10 secondary: 35j20 92c40 |
| title | Modeling and analysis of ensemble average solvation energy and solute–solvent interfacial fluctuations |
| title_full | Modeling and analysis of ensemble average solvation energy and solute–solvent interfacial fluctuations |
| title_fullStr | Modeling and analysis of ensemble average solvation energy and solute–solvent interfacial fluctuations |
| title_full_unstemmed | Modeling and analysis of ensemble average solvation energy and solute–solvent interfacial fluctuations |
| title_short | Modeling and analysis of ensemble average solvation energy and solute–solvent interfacial fluctuations |
| title_sort | modeling and analysis of ensemble average solvation energy and solute solvent interfacial fluctuations |
| topic | biomolecule solvation poisson–boltzmann variational implicit solvation model ensemble average solvation energy finite size effect primary: 49q10 secondary: 35j20 92c40 |
| url | https://doi.org/10.1515/cmb-2024-0017 |
| work_keys_str_mv | AT shaoyuanzhen modelingandanalysisofensembleaveragesolvationenergyandsolutesolventinterfacialfluctuations AT chenzhan modelingandanalysisofensembleaveragesolvationenergyandsolutesolventinterfacialfluctuations AT zhaoshan modelingandanalysisofensembleaveragesolvationenergyandsolutesolventinterfacialfluctuations |