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Garduño-Juárez R, Tovar-Anaya DO, Perez-Aguilar JM, Lozano-Aguirre Beltran LF, Zubillaga RA, Alvarez-Perez MA, Villarreal-Ramirez E. Molecular Dynamic Simulations for Biopolymers with Biomedical Applications. Polymers (Basel) 2024; 16:1864. [PMID: 39000719 PMCID: PMC11244511 DOI: 10.3390/polym16131864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/13/2024] [Accepted: 04/13/2024] [Indexed: 07/17/2024] Open
Abstract
Computational modeling (CM) is a versatile scientific methodology used to examine the properties and behavior of complex systems, such as polymeric materials for biomedical bioengineering. CM has emerged as a primary tool for predicting, setting up, and interpreting experimental results. Integrating in silico and in vitro experiments accelerates scientific advancements, yielding quicker results at a reduced cost. While CM is a mature discipline, its use in biomedical engineering for biopolymer materials has only recently gained prominence. In biopolymer biomedical engineering, CM focuses on three key research areas: (A) Computer-aided design (CAD/CAM) utilizes specialized software to design and model biopolymers for various biomedical applications. This technology allows researchers to create precise three-dimensional models of biopolymers, taking into account their chemical, structural, and functional properties. These models can be used to enhance the structure of biopolymers and improve their effectiveness in specific medical applications. (B) Finite element analysis, a computational technique used to analyze and solve problems in engineering and physics. This approach divides the physical domain into small finite elements with simple geometric shapes. This computational technique enables the study and understanding of the mechanical and structural behavior of biopolymers in biomedical environments. (C) Molecular dynamics (MD) simulations involve using advanced computational techniques to study the behavior of biopolymers at the molecular and atomic levels. These simulations are fundamental for better understanding biological processes at the molecular level. Studying the wide-ranging uses of MD simulations in biopolymers involves examining the structural, functional, and evolutionary aspects of biomolecular systems over time. MD simulations solve Newton's equations of motion for all-atom systems, producing spatial trajectories for each atom. This provides valuable insights into properties such as water absorption on biopolymer surfaces and interactions with solid surfaces, which are crucial for assessing biomaterials. This review provides a comprehensive overview of the various applications of MD simulations in biopolymers. Additionally, it highlights the flexibility, robustness, and synergistic relationship between in silico and experimental techniques.
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Affiliation(s)
- Ramón Garduño-Juárez
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico
| | - David O Tovar-Anaya
- Laboratorio de Bioingeniería de Tejidos, División de Estudios de Posgrado e Investigación, Coyoacán 04510, Mexico
| | - Jose Manuel Perez-Aguilar
- School of Chemical Sciences, Meritorious Autonomous University of Puebla (BUAP), University City, Puebla 72570, Mexico
| | | | - Rafael A Zubillaga
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Mexico City 09340, Mexico
| | - Marco Antonio Alvarez-Perez
- Laboratorio de Bioingeniería de Tejidos, División de Estudios de Posgrado e Investigación, Coyoacán 04510, Mexico
| | - Eduardo Villarreal-Ramirez
- Laboratorio de Bioingeniería de Tejidos, División de Estudios de Posgrado e Investigación, Coyoacán 04510, Mexico
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Kiefer R, Le QB, Velmurugan BK, Otero TF. Artificial muscle like behavior of polypyrrole polyethylene oxide independent of applied potential ranges. J Appl Polym Sci 2021. [DOI: 10.1002/app.52039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Rudolf Kiefer
- Conducting Polymers in Composites and Applications Research Group, Faculty of Applied Sciences Ton Duc Thang University Ho Chi Minh City Vietnam
| | - Quoc Bao Le
- Conducting Polymers in Composites and Applications Research Group, Faculty of Applied Sciences Ton Duc Thang University Ho Chi Minh City Vietnam
| | | | - Toribio F. Otero
- Centre for Electrochemistry and Intelligent Materials (CEMI) Universidad Politécnica de Cartagena Murcia Spain
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3
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Li Y, Chen D, Cheng X, Gao F, Yang X, Mi Y, Zhou Q, Lan S, Cao Z. Mechanistic investigation on
moisture‐induced
softening of poly(vinyl acetate)‐stiffened polyester fabrics. J Appl Polym Sci 2020. [DOI: 10.1002/app.49316] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yongxiang Li
- Key Laboratory of Advanced Textile Materials and Manufacturing Technology and Engineering Research Center for Eco‐Dyeing & Finishing of Textiles, Ministry of EducationZhejiang Sci‐Tech University Hangzhou China
| | - Dongzhi Chen
- Key Laboratory of Advanced Textile Materials and Manufacturing Technology and Engineering Research Center for Eco‐Dyeing & Finishing of Textiles, Ministry of EducationZhejiang Sci‐Tech University Hangzhou China
| | | | - Feng Gao
- Key Laboratory of Advanced Textile Materials and Manufacturing Technology and Engineering Research Center for Eco‐Dyeing & Finishing of Textiles, Ministry of EducationZhejiang Sci‐Tech University Hangzhou China
| | | | - Yifang Mi
- Key Laboratory of Advanced Textile Materials and Manufacturing Technology and Engineering Research Center for Eco‐Dyeing & Finishing of Textiles, Ministry of EducationZhejiang Sci‐Tech University Hangzhou China
| | - Qiubao Zhou
- Key Laboratory of Advanced Textile Materials and Manufacturing Technology and Engineering Research Center for Eco‐Dyeing & Finishing of Textiles, Ministry of EducationZhejiang Sci‐Tech University Hangzhou China
| | | | - Zhihai Cao
- Key Laboratory of Advanced Textile Materials and Manufacturing Technology and Engineering Research Center for Eco‐Dyeing & Finishing of Textiles, Ministry of EducationZhejiang Sci‐Tech University Hangzhou China
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Zhang D, Li K, Li Y, Sun H, Cheng J, Zhang J. Characteristics of water absorption in amine-cured epoxy networks: a molecular simulation and experimental study. SOFT MATTER 2018; 14:8740-8749. [PMID: 30357239 DOI: 10.1039/c8sm01516c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Moisture corrosion of cured epoxy resins seriously affects the durability of epoxy products and has been a serious issue in scientific and engineering fields. In this study, a series of cured epoxy resins with different structures were prepared by tuning their curing conversion in both experimental and simulation methods. In experiments, the equilibrium water content and the diffusion coefficient of amine-cured epoxy resins were measured by gravimetric measurement. The interaction between water molecules and epoxy network was investigated by time-resolved FTIR, difference spectroscopy and 2D correlation spectroscopy. In simulation, the hydrogen bonds, the mobility of hydroxypropyl ether groups and water molecules, and the free volume with its distributions were analyzed. Five types of water molecules were intuitively observed in this study; free volume had a stronger influence on equilibrium water content than polarity in the bifunctional epoxy/amine system, and the increase in the diffusion coefficient was considered as the result of reduction in motion resistance and an increase in channels for the motion of water molecules.
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Affiliation(s)
- Dujuan Zhang
- Key Laboratory of Carbon Fiber and Functional Polymers, Ministry of Education, Beijing University of Chemical Technology, Beijing 100029, P. R. China.
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5
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Tam LH, Lau D, Wu C. Understanding interaction and dynamics of water molecules in the epoxy via molecular dynamics simulation. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1540869] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Lik-ho Tam
- School of Transportation Science and Engineering, Beihang University, Beijing, People’s Republic of China
| | - Denvid Lau
- Department of Architecture and Civil Engineering, City University of Hong Kong, Hong Kong, People’s Republic of China
| | - Chao Wu
- School of Transportation Science and Engineering, Beihang University, Beijing, People’s Republic of China
- Department of Civil and Natural Resources Engineering, University of Canterbury, Christchurch, New Zealand
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6
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Tam LH, Wu C. Molecular Mechanics of the Moisture Effect on Epoxy/Carbon Nanotube Nanocomposites. NANOMATERIALS 2017; 7:nano7100324. [PMID: 29027979 PMCID: PMC5666489 DOI: 10.3390/nano7100324] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 10/08/2017] [Accepted: 10/09/2017] [Indexed: 01/19/2023]
Abstract
The strong structural integrity of polymer nanocomposite is influenced in the moist environment; but the fundamental mechanism is unclear, including the basis for the interactions between the absorbed water molecules and the structure, which prevents us from predicting the durability of its applications across multiple scales. In this research, a molecular dynamics model of the epoxy/single-walled carbon nanotube (SWCNT) nanocomposite is constructed to explore the mechanism of the moisture effect, and an analysis of the molecular interactions is provided by focusing on the hydrogen bond (H-bond) network inside the nanocomposite structure. The simulations show that at low moisture concentration, the water molecules affect the molecular interactions by favorably forming the water-nanocomposite H-bonds and the small cluster, while at high concentration the water molecules predominantly form the water-water H-bonds and the large cluster. The water molecules in the epoxy matrix and the epoxy-SWCNT interface disrupt the molecular interactions and deteriorate the mechanical properties. Through identifying the link between the water molecules and the nanocomposite structure and properties, it is shown that the free volume in the nanocomposite is crucial for its structural integrity, which facilitates the moisture accumulation and the distinct material deteriorations. This study provides insights into the moisture-affected structure and properties of the nanocomposite from the nanoscale perspective, which contributes to the understanding of the nanocomposite long-term performance under the moisture effect.
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Affiliation(s)
- Lik-Ho Tam
- School of Transportation Science and Engineering, Beihang University, 37 Xueyuan Road, Beijing 100191, China.
| | - Chao Wu
- School of Transportation Science and Engineering, Beihang University, 37 Xueyuan Road, Beijing 100191, China.
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7
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Iwata S. Molecular dynamics simulation of effect of glycerol monostearate on amorphous polyethylene in the presence of water. J Mol Model 2017; 23:115. [PMID: 28289957 DOI: 10.1007/s00894-017-3297-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 02/27/2017] [Indexed: 10/20/2022]
Abstract
Polyethylene (PE) is used widely as an electrical insulating material. However, the deterioration of its insulating ability is accelerated by exposure to a humid environment. To prevent the influence of water molecules, mixing 2,3-dihydroxypropyl octadecanoate-known as glycerol monostearate (GMS)-into PE has been proposed. However, the physical mechanism underlying the effect of GMS remains unclear. In the present study, the behavior of water molecules in amorphous PE with and without GMS molecule(s) was investigated in terms of diffusion and clustering using molecular dynamics (MD) simulations. Analyzing the mean square displacement (MSD), diffusion coefficient and radial distribution function (RDF) of the water molecules revealed that GMS contributed to suppressing the diffusion and dispersion of water molecules. Furthermore, it was demonstrated that, in the case of 4 wt% GMS and less than 2 wt% water, GMS contributes to reducing the diffusion coefficient of water molecules but does not change the glass transition temperature (T g) of the system drastically.
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Affiliation(s)
- Shinya Iwata
- Technology Research Institute of Osaka Prefecture, 7-1, Ayumino-2, Izumi-shi, Osaka, 5941157, Japan.
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8
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Adeleke OA, Monama NO, Tsai PC, Sithole HM, Michniak-Kohn BB. Combined Atomistic Molecular Calculations and Experimental Investigations for the Architecture, Screening, Optimization, and Characterization of Pyrazinamide Containing Oral Film Formulations for Tuberculosis Management. Mol Pharm 2015; 13:456-71. [DOI: 10.1021/acs.molpharmaceut.5b00698] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Oluwatoyin A. Adeleke
- Centre
for High Performance Computing, Council for Scientific and Industrial Research, Pretoria, South Africa, 0001
- Centre
for Dermal Research—New Jersey Centre for Biomaterials, Rutgers—The State University of New Jersey, Piscataway, New Jersey 08854, United States
- Department
of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers—The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Nkwe O. Monama
- Centre
for High Performance Computing, Council for Scientific and Industrial Research, Pretoria, South Africa, 0001
| | - Pei-Chin Tsai
- Centre
for Dermal Research—New Jersey Centre for Biomaterials, Rutgers—The State University of New Jersey, Piscataway, New Jersey 08854, United States
- Department
of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers—The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Happy M. Sithole
- Centre
for High Performance Computing, Council for Scientific and Industrial Research, Pretoria, South Africa, 0001
| | - Bozena B. Michniak-Kohn
- Centre
for Dermal Research—New Jersey Centre for Biomaterials, Rutgers—The State University of New Jersey, Piscataway, New Jersey 08854, United States
- Department
of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers—The State University of New Jersey, Piscataway, New Jersey 08854, United States
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