Addressing the Folding of Intermolecular Springs in Particle Simulations: Fixed Image Convention
Mesoscopic simulations of long polymer chains and soft matter systems are conducted routinely in the literature in order to assess the long-lived relaxation processes manifested in these systems. Coarse-grained chains are, however, prone to unphysical intercrossing due to their inherent softness. Th...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-05-01
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| Series: | Computation |
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| Online Access: | https://www.mdpi.com/2079-3197/11/6/106 |
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| author | Aristotelis P. Sgouros Doros N. Theodorou |
| author_facet | Aristotelis P. Sgouros Doros N. Theodorou |
| author_sort | Aristotelis P. Sgouros |
| collection | DOAJ |
| description | Mesoscopic simulations of long polymer chains and soft matter systems are conducted routinely in the literature in order to assess the long-lived relaxation processes manifested in these systems. Coarse-grained chains are, however, prone to unphysical intercrossing due to their inherent softness. This issue can be resolved by introducing long intermolecular bonds (the so-called slip-springs) which restore these topological constraints. The separation vector of intermolecular bonds can be determined by enforcing the commonly adopted minimum image convention (MIC). Because these bonds are soft and long (ca 3–20 nm), subjecting the samples to extreme deformations can lead to topology violations when enforcing the MIC. We propose the fixed image convention (FIC) for determining the separation vectors of overextended bonds, which is more stable than the MIC and applicable to extreme deformations. The FIC is simple to implement and, in general, more efficient than the MIC. Side-by-side comparisons between the MIC and FIC demonstrate that, when using the FIC, the topology remains intact even in situations with extreme particle displacement and nonaffine deformation. The accuracy of these conventions is the same when applying affine deformation. The article is accompanied by the corresponding code for implementing the FIC. |
| first_indexed | 2024-03-11T02:36:36Z |
| format | Article |
| id | doaj.art-3486fdb5345646f188d9b8907838a329 |
| institution | Directory Open Access Journal |
| issn | 2079-3197 |
| language | English |
| last_indexed | 2024-03-11T02:36:36Z |
| publishDate | 2023-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Computation |
| spelling | doaj.art-3486fdb5345646f188d9b8907838a3292023-11-18T09:53:58ZengMDPI AGComputation2079-31972023-05-0111610610.3390/computation11060106Addressing the Folding of Intermolecular Springs in Particle Simulations: Fixed Image ConventionAristotelis P. Sgouros0Doros N. Theodorou1School of Chemical Engineering, National Technical University of Athens (NTUA), GR-15780 Athens, GreeceSchool of Chemical Engineering, National Technical University of Athens (NTUA), GR-15780 Athens, GreeceMesoscopic simulations of long polymer chains and soft matter systems are conducted routinely in the literature in order to assess the long-lived relaxation processes manifested in these systems. Coarse-grained chains are, however, prone to unphysical intercrossing due to their inherent softness. This issue can be resolved by introducing long intermolecular bonds (the so-called slip-springs) which restore these topological constraints. The separation vector of intermolecular bonds can be determined by enforcing the commonly adopted minimum image convention (MIC). Because these bonds are soft and long (ca 3–20 nm), subjecting the samples to extreme deformations can lead to topology violations when enforcing the MIC. We propose the fixed image convention (FIC) for determining the separation vectors of overextended bonds, which is more stable than the MIC and applicable to extreme deformations. The FIC is simple to implement and, in general, more efficient than the MIC. Side-by-side comparisons between the MIC and FIC demonstrate that, when using the FIC, the topology remains intact even in situations with extreme particle displacement and nonaffine deformation. The accuracy of these conventions is the same when applying affine deformation. The article is accompanied by the corresponding code for implementing the FIC.https://www.mdpi.com/2079-3197/11/6/106minimum imageslip-springmesoscopicBrownian dynamicsdeformation |
| spellingShingle | Aristotelis P. Sgouros Doros N. Theodorou Addressing the Folding of Intermolecular Springs in Particle Simulations: Fixed Image Convention Computation minimum image slip-spring mesoscopic Brownian dynamics deformation |
| title | Addressing the Folding of Intermolecular Springs in Particle Simulations: Fixed Image Convention |
| title_full | Addressing the Folding of Intermolecular Springs in Particle Simulations: Fixed Image Convention |
| title_fullStr | Addressing the Folding of Intermolecular Springs in Particle Simulations: Fixed Image Convention |
| title_full_unstemmed | Addressing the Folding of Intermolecular Springs in Particle Simulations: Fixed Image Convention |
| title_short | Addressing the Folding of Intermolecular Springs in Particle Simulations: Fixed Image Convention |
| title_sort | addressing the folding of intermolecular springs in particle simulations fixed image convention |
| topic | minimum image slip-spring mesoscopic Brownian dynamics deformation |
| url | https://www.mdpi.com/2079-3197/11/6/106 |
| work_keys_str_mv | AT aristotelispsgouros addressingthefoldingofintermolecularspringsinparticlesimulationsfixedimageconvention AT dorosntheodorou addressingthefoldingofintermolecularspringsinparticlesimulationsfixedimageconvention |