An unstructured mesh convergent reaction–diffusion master equation for reversible reactions
The convergent reaction–diffusion master equation (CRDME) was recently developed to provide a lattice particle-based stochastic reaction–diffusion model that is a convergent approximation in the lattice spacing to an underlying spatially-continuous particle dynamics model. The CRDME was designed to...
Ausführliche Beschreibung
Gespeichert in:
| Autor*in: |
Isaacson, Samuel A. [verfasserIn] |
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| Format: |
E-Artikel |
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| Sprache: |
Englisch |
| Erschienen: |
2018transfer abstract |
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| Schlagwörter: |
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| Umfang: |
30 |
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| Übergeordnetes Werk: |
Enthalten in: Future-oriented repetitive thought, depressive symptoms, and suicide ideation severity: Role of future-event fluency and depressive predictive certainty - Miranda, Regina ELSEVIER, 2023, Amsterdam |
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| Übergeordnetes Werk: |
volume:374 ; year:2018 ; day:1 ; month:12 ; pages:954-983 ; extent:30 |
| Links: |
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| DOI / URN: |
10.1016/j.jcp.2018.07.036 |
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| 520 | |a The convergent reaction–diffusion master equation (CRDME) was recently developed to provide a lattice particle-based stochastic reaction–diffusion model that is a convergent approximation in the lattice spacing to an underlying spatially-continuous particle dynamics model. The CRDME was designed to be identical to the popular lattice reaction–diffusion master equation (RDME) model for systems with only linear reactions, while overcoming the RDME's loss of bimolecular reaction effects as the lattice spacing is taken to zero. In our original work we developed the CRDME to handle bimolecular association reactions on Cartesian grids. In this work we develop several extensions to the CRDME to facilitate the modeling of cellular processes within realistic biological domains. Foremost, we extend the CRDME to handle reversible bimolecular reactions on unstructured grids. Here we develop a generalized CRDME through discretization of the spatially continuous volume reactivity model, extending the CRDME to encompass a larger variety of particle–particle interactions. Finally, we conclude by examining several numerical examples to demonstrate the convergence and accuracy of the CRDME in approximating the volume reactivity model. | ||
| 520 | |a The convergent reaction–diffusion master equation (CRDME) was recently developed to provide a lattice particle-based stochastic reaction–diffusion model that is a convergent approximation in the lattice spacing to an underlying spatially-continuous particle dynamics model. The CRDME was designed to be identical to the popular lattice reaction–diffusion master equation (RDME) model for systems with only linear reactions, while overcoming the RDME's loss of bimolecular reaction effects as the lattice spacing is taken to zero. In our original work we developed the CRDME to handle bimolecular association reactions on Cartesian grids. In this work we develop several extensions to the CRDME to facilitate the modeling of cellular processes within realistic biological domains. Foremost, we extend the CRDME to handle reversible bimolecular reactions on unstructured grids. Here we develop a generalized CRDME through discretization of the spatially continuous volume reactivity model, extending the CRDME to encompass a larger variety of particle–particle interactions. Finally, we conclude by examining several numerical examples to demonstrate the convergence and accuracy of the CRDME in approximating the volume reactivity model. | ||
| 650 | 7 | |a Stochastic chemical kinetics |2 Elsevier | |
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10.1016/j.jcp.2018.07.036 doi /cbs_pica/cbs_olc/import_discovery/elsevier/einzuspielen/GBV00000000000981.pica (DE-627)ELV044439741 (ELSEVIER)S0021-9991(18)30497-2 DE-627 ger DE-627 rakwb eng 610 VZ 44.91 bkl Isaacson, Samuel A. verfasserin aut An unstructured mesh convergent reaction–diffusion master equation for reversible reactions 2018transfer abstract 30 nicht spezifiziert zzz rdacontent nicht spezifiziert z rdamedia nicht spezifiziert zu rdacarrier The convergent reaction–diffusion master equation (CRDME) was recently developed to provide a lattice particle-based stochastic reaction–diffusion model that is a convergent approximation in the lattice spacing to an underlying spatially-continuous particle dynamics model. The CRDME was designed to be identical to the popular lattice reaction–diffusion master equation (RDME) model for systems with only linear reactions, while overcoming the RDME's loss of bimolecular reaction effects as the lattice spacing is taken to zero. In our original work we developed the CRDME to handle bimolecular association reactions on Cartesian grids. In this work we develop several extensions to the CRDME to facilitate the modeling of cellular processes within realistic biological domains. Foremost, we extend the CRDME to handle reversible bimolecular reactions on unstructured grids. Here we develop a generalized CRDME through discretization of the spatially continuous volume reactivity model, extending the CRDME to encompass a larger variety of particle–particle interactions. Finally, we conclude by examining several numerical examples to demonstrate the convergence and accuracy of the CRDME in approximating the volume reactivity model. The convergent reaction–diffusion master equation (CRDME) was recently developed to provide a lattice particle-based stochastic reaction–diffusion model that is a convergent approximation in the lattice spacing to an underlying spatially-continuous particle dynamics model. The CRDME was designed to be identical to the popular lattice reaction–diffusion master equation (RDME) model for systems with only linear reactions, while overcoming the RDME's loss of bimolecular reaction effects as the lattice spacing is taken to zero. In our original work we developed the CRDME to handle bimolecular association reactions on Cartesian grids. In this work we develop several extensions to the CRDME to facilitate the modeling of cellular processes within realistic biological domains. Foremost, we extend the CRDME to handle reversible bimolecular reactions on unstructured grids. Here we develop a generalized CRDME through discretization of the spatially continuous volume reactivity model, extending the CRDME to encompass a larger variety of particle–particle interactions. Finally, we conclude by examining several numerical examples to demonstrate the convergence and accuracy of the CRDME in approximating the volume reactivity model. Stochastic chemical kinetics Elsevier Volume reactivity model Elsevier Stochastic reaction–diffusion Elsevier Reaction–diffusion master equation Elsevier Doi model Elsevier Zhang, Ying oth Enthalten in Elsevier Miranda, Regina ELSEVIER Future-oriented repetitive thought, depressive symptoms, and suicide ideation severity: Role of future-event fluency and depressive predictive certainty 2023 Amsterdam (DE-627)ELV010178430 volume:374 year:2018 day:1 month:12 pages:954-983 extent:30 https://doi.org/10.1016/j.jcp.2018.07.036 Volltext GBV_USEFLAG_U GBV_ELV SYSFLAG_U SSG-OLC-PHA GBV_ILN_24 GBV_ILN_90 44.91 Psychiatrie Psychopathologie VZ AR 374 2018 1 1201 954-983 30 |
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10.1016/j.jcp.2018.07.036 doi /cbs_pica/cbs_olc/import_discovery/elsevier/einzuspielen/GBV00000000000981.pica (DE-627)ELV044439741 (ELSEVIER)S0021-9991(18)30497-2 DE-627 ger DE-627 rakwb eng 610 VZ 44.91 bkl Isaacson, Samuel A. verfasserin aut An unstructured mesh convergent reaction–diffusion master equation for reversible reactions 2018transfer abstract 30 nicht spezifiziert zzz rdacontent nicht spezifiziert z rdamedia nicht spezifiziert zu rdacarrier The convergent reaction–diffusion master equation (CRDME) was recently developed to provide a lattice particle-based stochastic reaction–diffusion model that is a convergent approximation in the lattice spacing to an underlying spatially-continuous particle dynamics model. The CRDME was designed to be identical to the popular lattice reaction–diffusion master equation (RDME) model for systems with only linear reactions, while overcoming the RDME's loss of bimolecular reaction effects as the lattice spacing is taken to zero. In our original work we developed the CRDME to handle bimolecular association reactions on Cartesian grids. In this work we develop several extensions to the CRDME to facilitate the modeling of cellular processes within realistic biological domains. Foremost, we extend the CRDME to handle reversible bimolecular reactions on unstructured grids. Here we develop a generalized CRDME through discretization of the spatially continuous volume reactivity model, extending the CRDME to encompass a larger variety of particle–particle interactions. Finally, we conclude by examining several numerical examples to demonstrate the convergence and accuracy of the CRDME in approximating the volume reactivity model. The convergent reaction–diffusion master equation (CRDME) was recently developed to provide a lattice particle-based stochastic reaction–diffusion model that is a convergent approximation in the lattice spacing to an underlying spatially-continuous particle dynamics model. The CRDME was designed to be identical to the popular lattice reaction–diffusion master equation (RDME) model for systems with only linear reactions, while overcoming the RDME's loss of bimolecular reaction effects as the lattice spacing is taken to zero. In our original work we developed the CRDME to handle bimolecular association reactions on Cartesian grids. In this work we develop several extensions to the CRDME to facilitate the modeling of cellular processes within realistic biological domains. Foremost, we extend the CRDME to handle reversible bimolecular reactions on unstructured grids. Here we develop a generalized CRDME through discretization of the spatially continuous volume reactivity model, extending the CRDME to encompass a larger variety of particle–particle interactions. Finally, we conclude by examining several numerical examples to demonstrate the convergence and accuracy of the CRDME in approximating the volume reactivity model. Stochastic chemical kinetics Elsevier Volume reactivity model Elsevier Stochastic reaction–diffusion Elsevier Reaction–diffusion master equation Elsevier Doi model Elsevier Zhang, Ying oth Enthalten in Elsevier Miranda, Regina ELSEVIER Future-oriented repetitive thought, depressive symptoms, and suicide ideation severity: Role of future-event fluency and depressive predictive certainty 2023 Amsterdam (DE-627)ELV010178430 volume:374 year:2018 day:1 month:12 pages:954-983 extent:30 https://doi.org/10.1016/j.jcp.2018.07.036 Volltext GBV_USEFLAG_U GBV_ELV SYSFLAG_U SSG-OLC-PHA GBV_ILN_24 GBV_ILN_90 44.91 Psychiatrie Psychopathologie VZ AR 374 2018 1 1201 954-983 30 |
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10.1016/j.jcp.2018.07.036 doi /cbs_pica/cbs_olc/import_discovery/elsevier/einzuspielen/GBV00000000000981.pica (DE-627)ELV044439741 (ELSEVIER)S0021-9991(18)30497-2 DE-627 ger DE-627 rakwb eng 610 VZ 44.91 bkl Isaacson, Samuel A. verfasserin aut An unstructured mesh convergent reaction–diffusion master equation for reversible reactions 2018transfer abstract 30 nicht spezifiziert zzz rdacontent nicht spezifiziert z rdamedia nicht spezifiziert zu rdacarrier The convergent reaction–diffusion master equation (CRDME) was recently developed to provide a lattice particle-based stochastic reaction–diffusion model that is a convergent approximation in the lattice spacing to an underlying spatially-continuous particle dynamics model. The CRDME was designed to be identical to the popular lattice reaction–diffusion master equation (RDME) model for systems with only linear reactions, while overcoming the RDME's loss of bimolecular reaction effects as the lattice spacing is taken to zero. In our original work we developed the CRDME to handle bimolecular association reactions on Cartesian grids. In this work we develop several extensions to the CRDME to facilitate the modeling of cellular processes within realistic biological domains. Foremost, we extend the CRDME to handle reversible bimolecular reactions on unstructured grids. Here we develop a generalized CRDME through discretization of the spatially continuous volume reactivity model, extending the CRDME to encompass a larger variety of particle–particle interactions. Finally, we conclude by examining several numerical examples to demonstrate the convergence and accuracy of the CRDME in approximating the volume reactivity model. The convergent reaction–diffusion master equation (CRDME) was recently developed to provide a lattice particle-based stochastic reaction–diffusion model that is a convergent approximation in the lattice spacing to an underlying spatially-continuous particle dynamics model. The CRDME was designed to be identical to the popular lattice reaction–diffusion master equation (RDME) model for systems with only linear reactions, while overcoming the RDME's loss of bimolecular reaction effects as the lattice spacing is taken to zero. In our original work we developed the CRDME to handle bimolecular association reactions on Cartesian grids. In this work we develop several extensions to the CRDME to facilitate the modeling of cellular processes within realistic biological domains. Foremost, we extend the CRDME to handle reversible bimolecular reactions on unstructured grids. Here we develop a generalized CRDME through discretization of the spatially continuous volume reactivity model, extending the CRDME to encompass a larger variety of particle–particle interactions. Finally, we conclude by examining several numerical examples to demonstrate the convergence and accuracy of the CRDME in approximating the volume reactivity model. Stochastic chemical kinetics Elsevier Volume reactivity model Elsevier Stochastic reaction–diffusion Elsevier Reaction–diffusion master equation Elsevier Doi model Elsevier Zhang, Ying oth Enthalten in Elsevier Miranda, Regina ELSEVIER Future-oriented repetitive thought, depressive symptoms, and suicide ideation severity: Role of future-event fluency and depressive predictive certainty 2023 Amsterdam (DE-627)ELV010178430 volume:374 year:2018 day:1 month:12 pages:954-983 extent:30 https://doi.org/10.1016/j.jcp.2018.07.036 Volltext GBV_USEFLAG_U GBV_ELV SYSFLAG_U SSG-OLC-PHA GBV_ILN_24 GBV_ILN_90 44.91 Psychiatrie Psychopathologie VZ AR 374 2018 1 1201 954-983 30 |
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10.1016/j.jcp.2018.07.036 doi /cbs_pica/cbs_olc/import_discovery/elsevier/einzuspielen/GBV00000000000981.pica (DE-627)ELV044439741 (ELSEVIER)S0021-9991(18)30497-2 DE-627 ger DE-627 rakwb eng 610 VZ 44.91 bkl Isaacson, Samuel A. verfasserin aut An unstructured mesh convergent reaction–diffusion master equation for reversible reactions 2018transfer abstract 30 nicht spezifiziert zzz rdacontent nicht spezifiziert z rdamedia nicht spezifiziert zu rdacarrier The convergent reaction–diffusion master equation (CRDME) was recently developed to provide a lattice particle-based stochastic reaction–diffusion model that is a convergent approximation in the lattice spacing to an underlying spatially-continuous particle dynamics model. The CRDME was designed to be identical to the popular lattice reaction–diffusion master equation (RDME) model for systems with only linear reactions, while overcoming the RDME's loss of bimolecular reaction effects as the lattice spacing is taken to zero. In our original work we developed the CRDME to handle bimolecular association reactions on Cartesian grids. In this work we develop several extensions to the CRDME to facilitate the modeling of cellular processes within realistic biological domains. Foremost, we extend the CRDME to handle reversible bimolecular reactions on unstructured grids. Here we develop a generalized CRDME through discretization of the spatially continuous volume reactivity model, extending the CRDME to encompass a larger variety of particle–particle interactions. Finally, we conclude by examining several numerical examples to demonstrate the convergence and accuracy of the CRDME in approximating the volume reactivity model. The convergent reaction–diffusion master equation (CRDME) was recently developed to provide a lattice particle-based stochastic reaction–diffusion model that is a convergent approximation in the lattice spacing to an underlying spatially-continuous particle dynamics model. The CRDME was designed to be identical to the popular lattice reaction–diffusion master equation (RDME) model for systems with only linear reactions, while overcoming the RDME's loss of bimolecular reaction effects as the lattice spacing is taken to zero. In our original work we developed the CRDME to handle bimolecular association reactions on Cartesian grids. In this work we develop several extensions to the CRDME to facilitate the modeling of cellular processes within realistic biological domains. Foremost, we extend the CRDME to handle reversible bimolecular reactions on unstructured grids. Here we develop a generalized CRDME through discretization of the spatially continuous volume reactivity model, extending the CRDME to encompass a larger variety of particle–particle interactions. Finally, we conclude by examining several numerical examples to demonstrate the convergence and accuracy of the CRDME in approximating the volume reactivity model. Stochastic chemical kinetics Elsevier Volume reactivity model Elsevier Stochastic reaction–diffusion Elsevier Reaction–diffusion master equation Elsevier Doi model Elsevier Zhang, Ying oth Enthalten in Elsevier Miranda, Regina ELSEVIER Future-oriented repetitive thought, depressive symptoms, and suicide ideation severity: Role of future-event fluency and depressive predictive certainty 2023 Amsterdam (DE-627)ELV010178430 volume:374 year:2018 day:1 month:12 pages:954-983 extent:30 https://doi.org/10.1016/j.jcp.2018.07.036 Volltext GBV_USEFLAG_U GBV_ELV SYSFLAG_U SSG-OLC-PHA GBV_ILN_24 GBV_ILN_90 44.91 Psychiatrie Psychopathologie VZ AR 374 2018 1 1201 954-983 30 |
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10.1016/j.jcp.2018.07.036 doi /cbs_pica/cbs_olc/import_discovery/elsevier/einzuspielen/GBV00000000000981.pica (DE-627)ELV044439741 (ELSEVIER)S0021-9991(18)30497-2 DE-627 ger DE-627 rakwb eng 610 VZ 44.91 bkl Isaacson, Samuel A. verfasserin aut An unstructured mesh convergent reaction–diffusion master equation for reversible reactions 2018transfer abstract 30 nicht spezifiziert zzz rdacontent nicht spezifiziert z rdamedia nicht spezifiziert zu rdacarrier The convergent reaction–diffusion master equation (CRDME) was recently developed to provide a lattice particle-based stochastic reaction–diffusion model that is a convergent approximation in the lattice spacing to an underlying spatially-continuous particle dynamics model. The CRDME was designed to be identical to the popular lattice reaction–diffusion master equation (RDME) model for systems with only linear reactions, while overcoming the RDME's loss of bimolecular reaction effects as the lattice spacing is taken to zero. In our original work we developed the CRDME to handle bimolecular association reactions on Cartesian grids. In this work we develop several extensions to the CRDME to facilitate the modeling of cellular processes within realistic biological domains. Foremost, we extend the CRDME to handle reversible bimolecular reactions on unstructured grids. Here we develop a generalized CRDME through discretization of the spatially continuous volume reactivity model, extending the CRDME to encompass a larger variety of particle–particle interactions. Finally, we conclude by examining several numerical examples to demonstrate the convergence and accuracy of the CRDME in approximating the volume reactivity model. The convergent reaction–diffusion master equation (CRDME) was recently developed to provide a lattice particle-based stochastic reaction–diffusion model that is a convergent approximation in the lattice spacing to an underlying spatially-continuous particle dynamics model. The CRDME was designed to be identical to the popular lattice reaction–diffusion master equation (RDME) model for systems with only linear reactions, while overcoming the RDME's loss of bimolecular reaction effects as the lattice spacing is taken to zero. In our original work we developed the CRDME to handle bimolecular association reactions on Cartesian grids. In this work we develop several extensions to the CRDME to facilitate the modeling of cellular processes within realistic biological domains. Foremost, we extend the CRDME to handle reversible bimolecular reactions on unstructured grids. Here we develop a generalized CRDME through discretization of the spatially continuous volume reactivity model, extending the CRDME to encompass a larger variety of particle–particle interactions. Finally, we conclude by examining several numerical examples to demonstrate the convergence and accuracy of the CRDME in approximating the volume reactivity model. Stochastic chemical kinetics Elsevier Volume reactivity model Elsevier Stochastic reaction–diffusion Elsevier Reaction–diffusion master equation Elsevier Doi model Elsevier Zhang, Ying oth Enthalten in Elsevier Miranda, Regina ELSEVIER Future-oriented repetitive thought, depressive symptoms, and suicide ideation severity: Role of future-event fluency and depressive predictive certainty 2023 Amsterdam (DE-627)ELV010178430 volume:374 year:2018 day:1 month:12 pages:954-983 extent:30 https://doi.org/10.1016/j.jcp.2018.07.036 Volltext GBV_USEFLAG_U GBV_ELV SYSFLAG_U SSG-OLC-PHA GBV_ILN_24 GBV_ILN_90 44.91 Psychiatrie Psychopathologie VZ AR 374 2018 1 1201 954-983 30 |
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Enthalten in Future-oriented repetitive thought, depressive symptoms, and suicide ideation severity: Role of future-event fluency and depressive predictive certainty Amsterdam volume:374 year:2018 day:1 month:12 pages:954-983 extent:30 |
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Enthalten in Future-oriented repetitive thought, depressive symptoms, and suicide ideation severity: Role of future-event fluency and depressive predictive certainty Amsterdam volume:374 year:2018 day:1 month:12 pages:954-983 extent:30 |
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an unstructured mesh convergent reaction–diffusion master equation for reversible reactions |
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An unstructured mesh convergent reaction–diffusion master equation for reversible reactions |
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The convergent reaction–diffusion master equation (CRDME) was recently developed to provide a lattice particle-based stochastic reaction–diffusion model that is a convergent approximation in the lattice spacing to an underlying spatially-continuous particle dynamics model. The CRDME was designed to be identical to the popular lattice reaction–diffusion master equation (RDME) model for systems with only linear reactions, while overcoming the RDME's loss of bimolecular reaction effects as the lattice spacing is taken to zero. In our original work we developed the CRDME to handle bimolecular association reactions on Cartesian grids. In this work we develop several extensions to the CRDME to facilitate the modeling of cellular processes within realistic biological domains. Foremost, we extend the CRDME to handle reversible bimolecular reactions on unstructured grids. Here we develop a generalized CRDME through discretization of the spatially continuous volume reactivity model, extending the CRDME to encompass a larger variety of particle–particle interactions. Finally, we conclude by examining several numerical examples to demonstrate the convergence and accuracy of the CRDME in approximating the volume reactivity model. |
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The convergent reaction–diffusion master equation (CRDME) was recently developed to provide a lattice particle-based stochastic reaction–diffusion model that is a convergent approximation in the lattice spacing to an underlying spatially-continuous particle dynamics model. The CRDME was designed to be identical to the popular lattice reaction–diffusion master equation (RDME) model for systems with only linear reactions, while overcoming the RDME's loss of bimolecular reaction effects as the lattice spacing is taken to zero. In our original work we developed the CRDME to handle bimolecular association reactions on Cartesian grids. In this work we develop several extensions to the CRDME to facilitate the modeling of cellular processes within realistic biological domains. Foremost, we extend the CRDME to handle reversible bimolecular reactions on unstructured grids. Here we develop a generalized CRDME through discretization of the spatially continuous volume reactivity model, extending the CRDME to encompass a larger variety of particle–particle interactions. Finally, we conclude by examining several numerical examples to demonstrate the convergence and accuracy of the CRDME in approximating the volume reactivity model. |
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The convergent reaction–diffusion master equation (CRDME) was recently developed to provide a lattice particle-based stochastic reaction–diffusion model that is a convergent approximation in the lattice spacing to an underlying spatially-continuous particle dynamics model. The CRDME was designed to be identical to the popular lattice reaction–diffusion master equation (RDME) model for systems with only linear reactions, while overcoming the RDME's loss of bimolecular reaction effects as the lattice spacing is taken to zero. In our original work we developed the CRDME to handle bimolecular association reactions on Cartesian grids. In this work we develop several extensions to the CRDME to facilitate the modeling of cellular processes within realistic biological domains. Foremost, we extend the CRDME to handle reversible bimolecular reactions on unstructured grids. Here we develop a generalized CRDME through discretization of the spatially continuous volume reactivity model, extending the CRDME to encompass a larger variety of particle–particle interactions. Finally, we conclude by examining several numerical examples to demonstrate the convergence and accuracy of the CRDME in approximating the volume reactivity model. |
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