1
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Wu C. Temperature-Transferable Coarse-Grained Models for Volumetric Properties of Poly(lactic Acid). J Phys Chem B 2024; 128:358-370. [PMID: 38153413 DOI: 10.1021/acs.jpcb.3c07026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
A new coarse-grained (CG) model, for which each monomer is mapped as one bead at its center of mass, was developed for simulating the volumetric properties of the polylactide (PLA) bulk. The three bonded CG potentials are first parametrized against the strain energies of the dimer, trimer, and tetramer, and the nonbonded CG potentials are then optimized to match the melt densities of the decamer. With the derived CG potentials, molecular dynamics (MD) simulations are found to reproduce thermal expansion and glass transition. By rescaling the dihedral and nonbonded potentials with temperature-independent factors, the glass transition temperature (Tg) is also satisfactorily restored with little modifications on the volumetric expansive coefficients at both rubbery and glassy states. Therefore, the finally optimized CG potentials exhibit excellent temperature transferability, as rationalized by the Simha-Boyer relation. Furthermore, it is confirmed that the dihedral torsions and nonbonded interactions play key roles in glass transition. Also, the simulated bulk moduli and conformational properties in a wide temperature range compare well with the referenced data. The proposed multiscale scheme has great potential in simulating thermo-mechanical properties of PLA and other polymers.
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Affiliation(s)
- Chaofu Wu
- Hunan Provincial Key Laboratory of Fine Ceramics and Powder Materials, School of Materials and Environmental Engineering, Hunan University of Humanities, Science and Technology, Loudi 417000, Hunan, P. R. China
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2
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T A, Narayan R, Shenoy PA, Nayak UY. Computational modeling for the design and development of nano based drug delivery systems. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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3
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Zhu M, Ishaq MW, Li L. Advances in experimental studies of internal motions of non-linear macromolecular systems in solutions. POLYMER 2022. [DOI: 10.1016/j.polymer.2022.124966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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4
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Wu C, Li K, Ning X, Zhang L. An Enhanced Scheme for Multiscale Modeling of Thermomechanical Properties of Polymer Bulks. J Phys Chem B 2021; 125:8612-8626. [PMID: 34291641 DOI: 10.1021/acs.jpcb.1c02663] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While multiscale modeling significantly enhances the capability of molecular simulations of polymer systems, it is well realized that the systematically derived coarse-grained (CG) models generally underestimate the thermomechanical properties. In this work, a charge-based mapping scheme has been adopted to include explicit electrostatic interactions and benchmarked against two typical polymers, atactic poly(methyl methacrylate) (PMMA) and polystyrene (PS). The CG potentials are parameterized against the oligomer bulks of nine monomers per chain to match the essential structural features and the two basic pressure-volume-temperature (PVT) properties, which are obtained from the all-atomistic (AA) molecular dynamics (MD) simulations at a single elevated temperature. The so-parameterized CG potentials are extended with the MD method to simulate the two polymer bulks of one hundred monomers per chain over a wide temperature range. Without any scaling, all the simulated results, including mass densities and bulk moduli at room temperature, thermal expansion coefficients at rubbery and glassy states, and glass transition temperatures (Tg), compare well with the corresponding experimental data. The proposed scheme not only contributes to realistically simulating various thermomechanical properties of both apolar and polar polymers but also allows for directly simulating their electrical properties.
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Affiliation(s)
- Chaofu Wu
- Hunan Provincial Key Laboratory of Fine Ceramics and Powder Materials, School of Materials and Environmental Engineering, Hunan University of Humanities, Science and Technology, Loudi, Hunan 417000, P. R. China
| | - Kewen Li
- Hunan Provincial Key Laboratory of Fine Ceramics and Powder Materials, School of Materials and Environmental Engineering, Hunan University of Humanities, Science and Technology, Loudi, Hunan 417000, P. R. China
| | - Xutao Ning
- Hunan Provincial Key Laboratory of Fine Ceramics and Powder Materials, School of Materials and Environmental Engineering, Hunan University of Humanities, Science and Technology, Loudi, Hunan 417000, P. R. China
| | - Lei Zhang
- Hunan Provincial Key Laboratory of Fine Ceramics and Powder Materials, School of Materials and Environmental Engineering, Hunan University of Humanities, Science and Technology, Loudi, Hunan 417000, P. R. China
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5
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Affiliation(s)
- Fang-Yi Lin
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
| | - Mengguo Yan
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
| | - Eric W. Cochran
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
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6
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Wu C. Multiscale Modeling Scheme for Simulating Polymeric Melts: Application to Poly(Ethylene Oxide). MACROMOL THEOR SIMUL 2017. [DOI: 10.1002/mats.201700066] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- C. Wu
- Hunan Provincial Key Laboratory of Fine Ceramics and Powder Materials; Hunan University of Humanities Science & Technology; Dixing Road 487, Louxing District Loudi 417000 Hunan Province P. R. China
- College of Materials and Environment Engineering; Hunan University of Humanities Science & Technology; Dixing Road 487, Louxing District Loudi 417000 Hunan Province P. R. China
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7
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Rai GJ, Biswas P. Topology driven structural transition of dendrimers with a dimensional cross-over. POLYMER 2017. [DOI: 10.1016/j.polymer.2017.03.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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8
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Filipe LCS, Machuqueiro M, Darbre T, Baptista AM. Exploring the Structural Properties of Positively Charged Peptide Dendrimers. J Phys Chem B 2016; 120:11323-11330. [PMID: 27739676 DOI: 10.1021/acs.jpcb.6b09156] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We report a combined experimental and computational approach to study the structural behavior of positively charged peptide dendrimers. Third-generation dendrimers containing combinations of positive/neutral amino acid residues in the different dendrimer generations were synthesized and their overall size evaluated using diffusion NMR. Molecular dynamics simulations were performed to obtain a comprehensive description of the molecular-level phenomena substantiating the structural differences observed. Comparison of the results presented with previous findings reveals a striking charge-dependent tendency in these systems, where the simple number and placement of charged amino acids in the sequence allows an extensive control over the exhibited structural features. Indeed, we observe that peptide dendrimers bearing progressively higher amounts of charged residues are characterized by an increasing structural plasticity, with a myriad of conformational states equally accessible to them. On the other hand, dendrimers containing only small amounts of charged residues evidence, to some extent, a characteristic structural rigidity.
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Affiliation(s)
- Luís C S Filipe
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa , Av. da República, EAN, 2780-157 Oeiras, Portugal
| | - Miguel Machuqueiro
- Centro de Química e Bioquímica and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa , 1749-016 Lisboa, Portugal
| | - Tamis Darbre
- Department of Chemistry and Biochemistry, University of Bern , Freiestrasse 3, 3012 Bern, Switzerland
| | - António M Baptista
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa , Av. da República, EAN, 2780-157 Oeiras, Portugal
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9
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Yu C, Ma L, Li S, Tan H, Zhou Y, Yan D. HBP Builder: A Tool to Generate Hyperbranched Polymers and Hyperbranched Multi-Arm Copolymers for Coarse-grained and Fully Atomistic Molecular Simulations. Sci Rep 2016; 6:26264. [PMID: 27188541 PMCID: PMC4870682 DOI: 10.1038/srep26264] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 04/28/2016] [Indexed: 12/31/2022] Open
Abstract
Computer simulation has been becoming a versatile tool that can investigate detailed information from the microscopic scale to the mesoscopic scale. However, the crucial first step of molecular simulation is model building, particularly for hyperbranched polymers (HBPs) and hyperbranched multi-arm copolymers (HBMCs) with complex and various topological structures. Unlike well-defined polymers, not only the molar weight of HBPs/HBMCs with polydispersity, but the HBPs/HBMCs with the same degree of polymerization (DP) and degree of branching (DB) also have many possible topological structures, thus making difficulties for user to build model in molecular simulation. In order to build a bridge between model building and molecular simulation of HBPs and HBMCs, we developed HBP Builder, a C language open source HBPs/HBMCs building toolkit. HBP Builder implements an automated protocol to build various coarse-grained and fully atomistic structures of HBPs/HBMCs according to user's specific requirements. Meanwhile, coarse-grained and fully atomistic output structures can be directly employed in popular simulation packages, including HOOMD, Tinker and Gromacs. Moreover, HBP Builder has an easy-to-use graphical user interface and the modular architecture, making it easy to extend and reuse it as a part of other program.
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Affiliation(s)
- Chunyang Yu
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Li Ma
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Shanlong Li
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Haina Tan
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Yongfeng Zhou
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Deyue Yan
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, P. R. China
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10
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Wu C. Phase Morphologies of Binary Polymer Blends Predicted by Systematically Coarse-Grained Models. MACROMOL THEOR SIMUL 2016. [DOI: 10.1002/mats.201500087] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Chaofu Wu
- College of Materials and Environment Engineering; Hunan University of Humanities Science & Technology; Dixing Road 487 Louxing DistrictLoudi 417000 Hunan Province P. R. China
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11
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Freire JJ, Rubio AM, McBride C. Calculation of Conformational Properties and Rouse Relaxation Times of PAMAM-EDA Dendrimers under Different pH Conditions. MACROMOL THEOR SIMUL 2016. [DOI: 10.1002/mats.201600012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Juan J. Freire
- Departamento de Ciencias y Técnicas Fisicoquímicas; Facultad de Ciencias; Universidad Nacional de Educación a Distancia (UNED); Paseo Senda del Rey 9 28040 Madrid Spain
| | - Ana M. Rubio
- Departamento de Química Física; Facultad de Ciencias Químicas; Universidad Complutense; Ciudad Universitaria; 28040 Madrid Spain
| | - Carl McBride
- Departamento de Ciencias y Técnicas Fisicoquímicas; Facultad de Ciencias; Universidad Nacional de Educación a Distancia (UNED); Paseo Senda del Rey 9 28040 Madrid Spain
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12
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Liang J, Chen P, Dong B, Huang Z, Zhao K, Yan LT. Ligand-Receptor Interaction-Mediated Transmembrane Transport of Dendrimer-like Soft Nanoparticles: Mechanisms and Complicated Diffusive Dynamics. Biomacromolecules 2016; 17:1834-44. [PMID: 27049403 DOI: 10.1021/acs.biomac.6b00241] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nearly all nanomedical applications of dendrimer-like soft nanoparticles rely on the functionality of attached ligands. Understanding how the ligands interact with the receptors in cell membrane and its further effect on the cellular uptake of dendrimer-like soft nanoparticles is thereby a key issue for their better application in nanomedicine. However, the essential mechanism and detailed kinetics for the ligand-receptor interaction-mediated transmembrane transport of such unconventional nanoparticles remain poorly elucidated. Here, using coarse-grained simulations, we present the very first study of molecular mechanism and kinetics behaviors for the transmembrane transport of dendrimer-like soft nanoparticles conjugated with ligands. A phase diagram of interaction states is constructed through examining ligand densities and membrane tensions that allows us to identify novel endocytosis mechanisms featured by the direct wrapping and the penetration-extraction vesiculation. The results provide an in-depth insight into the diffusivity of receptors and dendrimer in the membrane plane and demonstrate how the ligand density influences receptor diffusion and uptake kinetics. It is interesting to find that the ligand-conjugated dendrimers present superdiffusive behaviors on a membrane, which is revealed to be driven by the random fluctuation dynamics of the membrane. The findings facilitate our understanding of some recent experimental observations and could establish fundamental principles for the future development of such important nanomaterials for widespread nanomedical applications.
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Affiliation(s)
- Junshi Liang
- Key Laboratory of Advanced Materials (MOE), Department of Chemical Engineering, Tsinghua University , Beijing 100084, P. R. China
| | - Pengyu Chen
- Key Laboratory of Advanced Materials (MOE), Department of Chemical Engineering, Tsinghua University , Beijing 100084, P. R. China
| | - Bojun Dong
- Key Laboratory of Advanced Materials (MOE), Department of Chemical Engineering, Tsinghua University , Beijing 100084, P. R. China
| | - Zihan Huang
- Key Laboratory of Advanced Materials (MOE), Department of Chemical Engineering, Tsinghua University , Beijing 100084, P. R. China
| | - Kongyin Zhao
- State Key Laboratory of Separation Membranes and Membrane Processes, Tianjin Polytechnic University , Tianjin 300387, China
| | - Li-Tang Yan
- Key Laboratory of Advanced Materials (MOE), Department of Chemical Engineering, Tsinghua University , Beijing 100084, P. R. China
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13
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Ortiz AM, Sánchez-Méndez A, de Jesús E, Flores JC, Gómez-Sal P, Mendicuti F. Poly(benzyl ether) Dendrimers Functionalized at the Core with Palladium Bis(N-Heterocyclic Carbene) Complexes as Catalysts for the Heck Coupling Reaction. Inorg Chem 2016; 55:1304-14. [DOI: 10.1021/acs.inorgchem.5b02629] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Alba M. Ortiz
- Departamento de Química Orgánica
y Química Inorgánica, Universidad de Alcalá, Edificio de Farmacia, Campus Universitario, E28871 Alcalá
de Henares, Madrid, Spain
| | - Alberto Sánchez-Méndez
- Departamento de Química Orgánica
y Química Inorgánica, Universidad de Alcalá, Edificio de Farmacia, Campus Universitario, E28871 Alcalá
de Henares, Madrid, Spain
| | - Ernesto de Jesús
- Departamento de Química Orgánica
y Química Inorgánica, Universidad de Alcalá, Edificio de Farmacia, Campus Universitario, E28871 Alcalá
de Henares, Madrid, Spain
| | - Juan C. Flores
- Departamento de Química Orgánica
y Química Inorgánica, Universidad de Alcalá, Edificio de Farmacia, Campus Universitario, E28871 Alcalá
de Henares, Madrid, Spain
| | - Pilar Gómez-Sal
- Departamento de Química Orgánica
y Química Inorgánica, Universidad de Alcalá, Edificio de Farmacia, Campus Universitario, E28871 Alcalá
de Henares, Madrid, Spain
| | - Francisco Mendicuti
- Departamento de Química Analítica, Química Física e Ingeniería Química, Universidad de Alcalá, E28871 Alcalá de Henares, Madrid, Spain
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14
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Yu C, Ma L, Li K, Li S, Liu Y, Zhou Y, Yan D. Molecular dynamics simulation studies of hyperbranched polyglycerols and their encapsulation behaviors of small drug molecules. Phys Chem Chem Phys 2016; 18:22446-57. [DOI: 10.1039/c6cp03726g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Computer simulation could disclose more details about the conformations of HPGs and their encapsulation behaviors of guest molecules.
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Affiliation(s)
- Chunyang Yu
- School of Chemistry & Chemical Engineering
- State Key Laboratory of Metal Matrix Composites
- Shanghai Jiao Tong University
- Shanghai
- P. R. China
| | - Li Ma
- School of Chemistry & Chemical Engineering
- State Key Laboratory of Metal Matrix Composites
- Shanghai Jiao Tong University
- Shanghai
- P. R. China
| | - Ke Li
- School of Chemistry & Chemical Engineering
- State Key Laboratory of Metal Matrix Composites
- Shanghai Jiao Tong University
- Shanghai
- P. R. China
| | - Shanlong Li
- School of Chemistry & Chemical Engineering
- State Key Laboratory of Metal Matrix Composites
- Shanghai Jiao Tong University
- Shanghai
- P. R. China
| | - Yannan Liu
- School of Chemistry & Chemical Engineering
- State Key Laboratory of Metal Matrix Composites
- Shanghai Jiao Tong University
- Shanghai
- P. R. China
| | - Yongfeng Zhou
- School of Chemistry & Chemical Engineering
- State Key Laboratory of Metal Matrix Composites
- Shanghai Jiao Tong University
- Shanghai
- P. R. China
| | - Deyue Yan
- School of Chemistry & Chemical Engineering
- State Key Laboratory of Metal Matrix Composites
- Shanghai Jiao Tong University
- Shanghai
- P. R. China
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15
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Smeijers A, Markvoort A, Pieterse K, Hilbers P. Coarse-grained modelling of urea-adamantyl functionalised poly(propylene imine) dendrimers. MOLECULAR SIMULATION 2015. [DOI: 10.1080/08927022.2015.1096359] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- A.F. Smeijers
- Computational Biology, Department of Biomedical Engineering, Technische Universiteit Eindhoven, Eindhoven, the Netherlands
| | - A.J. Markvoort
- Computational Biology, Department of Biomedical Engineering, Technische Universiteit Eindhoven, Eindhoven, the Netherlands
- Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Eindhoven, the Netherlands
| | - K. Pieterse
- Computational Biology, Department of Biomedical Engineering, Technische Universiteit Eindhoven, Eindhoven, the Netherlands
- Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Eindhoven, the Netherlands
| | - P.A.J. Hilbers
- Computational Biology, Department of Biomedical Engineering, Technische Universiteit Eindhoven, Eindhoven, the Netherlands
- Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Eindhoven, the Netherlands
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16
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Freire JJ, Rubio AM, McBride C. Coarse-Grained and Atomistic Simulations for theG = 4 PAMAM-EDA Dendrimer. MACROMOL THEOR SIMUL 2015. [DOI: 10.1002/mats.201500028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Juan J. Freire
- Departamento de Ciencias y Técnicas Fisicoquímicas, Facultad de Ciencias; Universidad Nacional de Educación a Distancia; Paseo Senda del Rey 9 28040 Madrid Spain
| | - Ana M. Rubio
- Departamento de Química Física, Facultad de Ciencias Químicas; Universidad Complutense; 28040 Madrid Spain
| | - Carl McBride
- Departamento de Ciencias y Técnicas Fisicoquímicas, Facultad de Ciencias; Universidad Nacional de Educación a Distancia; Paseo Senda del Rey 9 28040 Madrid Spain
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17
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18
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Rubio AM, McBride C, Freire JJ. Binary Interactions between Dendrimer Molecules. A Simulation Study. Macromolecules 2014. [DOI: 10.1021/ma501127f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ana M. Rubio
- Departamento
de Química Física, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, Spain
| | - Carl McBride
- Departamento
de Ciencias y Técnicas Fisicoquímicas, Facultad de Ciencias, Universidad Nacional de Educación a Distancia (UNED), Paseo Senda del
Rey 9, 28040 Madrid, Spain
| | - Juan J. Freire
- Departamento
de Ciencias y Técnicas Fisicoquímicas, Facultad de Ciencias, Universidad Nacional de Educación a Distancia (UNED), Paseo Senda del
Rey 9, 28040 Madrid, Spain
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19
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Guo R, Mao J, Yan LT. Unique dynamical approach of fully wrapping dendrimer-like soft nanoparticles by lipid bilayer membrane. ACS NANO 2013; 7:10646-10653. [PMID: 24255955 DOI: 10.1021/nn4033344] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Wrapping dendrimer-like soft nanoparticles by cell membrane is an essential event in their endocytosis in drug and gene delivery, but this process remains poorly elucidated. Using computer simulations and theoretical analysis, we report the detailed dynamics of the process in which a lipid bilayer membrane fully wraps a dendrimer-like soft nanoparticle. By constructing a phase diagram, we firstly demonstrate that there exist three states in the interaction between a dendrimer and a lipid bilayer membrane, i.e., penetration, penetration and partial wrapping, and full wrapping states. The wrapping process of dendrimer-like nanoparticles is found to take a unique approach where the penetration of the dendrimer into the membrane plays a significant role. The analysis of various energies within the system provides a theoretical justification to the state transition observed from simulations. The findings also support recent experimental results and provide a theoretical explanation for them. We expect that these findings are of immediate interest to the study of the cellular uptake of dendrimer-like soft nanoparticles and can prompt the further application of this class of nanoparticles in nanomedicine.
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Affiliation(s)
- Ruohai Guo
- Key Laboratory of Advanced Materials (MOE), Department of Chemical Engineering, Tsinghua University , Beijing 100084, P. R. China
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20
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Freire JJ, Ahmadi A, McBride C. Molecular Dynamics Simulations of the Protonated G4 PAMAM Dendrimer in an Ionic Liquid System. J Phys Chem B 2013; 117:15157-64. [DOI: 10.1021/jp402586s] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Juan J. Freire
- Departamento
de Ciencias y Técnicas Fisicoquímicas, Facultad de Ciencias, Universidad Nacional de Educación a Distancia (UNED), Paseo Senda del
Rey 9, 28040 Madrid, Spain
| | - Amirhossein Ahmadi
- Departamento
de Ciencias y Técnicas Fisicoquímicas, Facultad de Ciencias, Universidad Nacional de Educación a Distancia (UNED), Paseo Senda del
Rey 9, 28040 Madrid, Spain
| | - Carl McBride
- Departamento
de Ciencias y Técnicas Fisicoquímicas, Facultad de Ciencias, Universidad Nacional de Educación a Distancia (UNED), Paseo Senda del
Rey 9, 28040 Madrid, Spain
- Instituto de Química Física Rocasolano (CSIC), Serrano 119, 28006 Madrid, Spain
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21
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Lu Y, An L, Wang ZG. Intrinsic Viscosity of Polymers: General Theory Based on a Partially Permeable Sphere Model. Macromolecules 2013. [DOI: 10.1021/ma400872s] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yuyuan Lu
- State Key Laboratory of Polymer
Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R.China
| | - Lijia An
- State Key Laboratory of Polymer
Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R.China
| | - Zhen-Gang Wang
- Division of Chemistry and Chemical
Engineering, California Institute of Technology, Pasadena, California 91125, United States
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22
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Wu C. A Combined Scheme for Systematically Coarse-Graining of Stereoregular Polymer Blends. Macromolecules 2013. [DOI: 10.1021/ma400572f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Chaofu Wu
- Department of Chemistry and Materials
Science, Hunan University of Humanities, Science and Technology, Loudi 417000, People’s Republic of
China
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23
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Tian WD, Ma YQ. Theoretical and computational studies of dendrimers as delivery vectors. Chem Soc Rev 2013; 42:705-27. [PMID: 23114420 DOI: 10.1039/c2cs35306g] [Citation(s) in RCA: 179] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
It is a great challenge for nanomedicine to develop novel dendrimers with maximum therapeutic potential and minimum side-effects for drug and gene delivery. As delivery vectors, dendrimers must overcome lots of barriers before delivering the bio-agents to the target in the cell. Extensive experimental investigations have been carried out to elucidate the physical and chemical properties of dendrimers and explore their behaviors when interacting with biomolecules, such as gene materials, proteins, and lipid membranes. As a supplement of the experimental techniques, it has been proved that computer simulations could facilitate the progress in understanding the delivery process of bioactive molecules. The structures of dendrimers in dilute solutions have been intensively investigated by monomer-resolved simulations, coarse-grained simulations, and atom-resolved simulations. Atomistic simulations have manifested that the hydrophobic interactions, hydrogen-bond interactions, and electrostatic attraction play critical roles in the formation of dendrimer-drug complexes. Multiscale simulations and statistical field theories have uncovered some physical mechanisms involved in the dendrimer-based gene delivery systems. This review will focus on the current status and perspective of theoretical and computational contributions in this field in recent years. (275 references).
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Affiliation(s)
- Wen-de Tian
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, Soochow University, Suzhou 215006, China
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Amorós D, Ortega A, García de la Torre J. Prediction of Hydrodynamic and Other Solution Properties of Partially Disordered Proteins with a Simple, Coarse-Grained Model. J Chem Theory Comput 2013; 9:1678-85. [DOI: 10.1021/ct300948u] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- D. Amorós
- Departamento de Química Física,
Facultad
de Química, Universidad de Murcia, 30071 Murcia, Spain
| | - A. Ortega
- Departamento de Química Física,
Facultad
de Química, Universidad de Murcia, 30071 Murcia, Spain
| | - J. García de la Torre
- Departamento de Química Física,
Facultad
de Química, Universidad de Murcia, 30071 Murcia, Spain
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25
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Svaneborg C, Pedersen JS. A formalism for scattering of complex composite structures. I. Applications to branched structures of asymmetric sub-units. J Chem Phys 2012; 136:104105. [PMID: 22423826 DOI: 10.1063/1.3682778] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Carsten Svaneborg
- Center for Fundamental Living Technology, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5320 Odense, Denmark.
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26
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Konkolewicz D, Perrier S, Stapleton D, Gray-Weale A. Modeling highly branched structures: Description of the solution structures of dendrimers, polyglycerol, and glycogen. ACTA ACUST UNITED AC 2011. [DOI: 10.1002/polb.22340] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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27
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Długosz M, Zieliński P, Trylska J. Brownian dynamics simulations on CPU and GPU with BD_BOX. J Comput Chem 2011; 32:2734-44. [PMID: 21638295 DOI: 10.1002/jcc.21847] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Revised: 04/27/2011] [Accepted: 04/30/2011] [Indexed: 11/07/2022]
Abstract
There has been growing interest in simulating biological processes under in vivo conditions due to recent advances in experimental techniques dedicated to study single particle behavior in crowded environments. We have developed a software package, BD_BOX, for multiscale Brownian dynamics simulations. BD_BOX can simulate either single molecules or multicomponent systems of diverse, interacting molecular species using flexible, coarse-grained bead models. BD_BOX is written in C and employs modern computer architectures and technologies; these include MPI for distributed-memory architectures, OpenMP for shared-memory platforms, NVIDIA CUDA framework for GPGPU, and SSE vectorization for CPU.
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Affiliation(s)
- Maciej Długosz
- Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Warsaw, Poland.
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28
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de la Torre JG, Ortega Á, Amorós D, Schmidt RR, Cifre JGH. Methods and Tools for the Prediction of Hydrodynamic Coefficients and Other Solution Properties of Flexible Macromolecules in Solution. A Tutorial Minireview. Macromol Biosci 2010; 10:721-30. [DOI: 10.1002/mabi.200900464] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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29
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de la Torre JG, Hernández Cifre JG, Ortega Á, Schmidt RR, Fernandes MX, Pérez Sánchez HE, Pamies R. SIMUFLEX: Algorithms and Tools for Simulation of the Conformation and Dynamics of Flexible Molecules and Nanoparticles in Dilute Solution. J Chem Theory Comput 2009; 5:2606-18. [DOI: 10.1021/ct900269n] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- José García de la Torre
- Departamento de Química Física, Facultad de Química Universidad de Murcia, 30071 Murcia, Spain, Centro de Química da Madeira, Universidade da Madeira, 9000-390 Funchal, Portugal, Forschungszentrum Karlsruhe GmbH, Institut für Nanotechnologie, D-76021 Karlsruhe, Germany, and Department of Physical Chemistry, University of Oslo, Oslo, Norway
| | - José G. Hernández Cifre
- Departamento de Química Física, Facultad de Química Universidad de Murcia, 30071 Murcia, Spain, Centro de Química da Madeira, Universidade da Madeira, 9000-390 Funchal, Portugal, Forschungszentrum Karlsruhe GmbH, Institut für Nanotechnologie, D-76021 Karlsruhe, Germany, and Department of Physical Chemistry, University of Oslo, Oslo, Norway
| | - Álvaro Ortega
- Departamento de Química Física, Facultad de Química Universidad de Murcia, 30071 Murcia, Spain, Centro de Química da Madeira, Universidade da Madeira, 9000-390 Funchal, Portugal, Forschungszentrum Karlsruhe GmbH, Institut für Nanotechnologie, D-76021 Karlsruhe, Germany, and Department of Physical Chemistry, University of Oslo, Oslo, Norway
| | - Ricardo Rodríguez Schmidt
- Departamento de Química Física, Facultad de Química Universidad de Murcia, 30071 Murcia, Spain, Centro de Química da Madeira, Universidade da Madeira, 9000-390 Funchal, Portugal, Forschungszentrum Karlsruhe GmbH, Institut für Nanotechnologie, D-76021 Karlsruhe, Germany, and Department of Physical Chemistry, University of Oslo, Oslo, Norway
| | - Miguel X. Fernandes
- Departamento de Química Física, Facultad de Química Universidad de Murcia, 30071 Murcia, Spain, Centro de Química da Madeira, Universidade da Madeira, 9000-390 Funchal, Portugal, Forschungszentrum Karlsruhe GmbH, Institut für Nanotechnologie, D-76021 Karlsruhe, Germany, and Department of Physical Chemistry, University of Oslo, Oslo, Norway
| | - Horacio E. Pérez Sánchez
- Departamento de Química Física, Facultad de Química Universidad de Murcia, 30071 Murcia, Spain, Centro de Química da Madeira, Universidade da Madeira, 9000-390 Funchal, Portugal, Forschungszentrum Karlsruhe GmbH, Institut für Nanotechnologie, D-76021 Karlsruhe, Germany, and Department of Physical Chemistry, University of Oslo, Oslo, Norway
| | - R. Pamies
- Departamento de Química Física, Facultad de Química Universidad de Murcia, 30071 Murcia, Spain, Centro de Química da Madeira, Universidade da Madeira, 9000-390 Funchal, Portugal, Forschungszentrum Karlsruhe GmbH, Institut für Nanotechnologie, D-76021 Karlsruhe, Germany, and Department of Physical Chemistry, University of Oslo, Oslo, Norway
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