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Journal articles on the topic 'MARTINI model'

Author: Grafiati
Published: 6 September 2023

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1

Marrink, Siewert J., and D. Peter Tieleman. "Perspective on the Martini model." Chemical Society Reviews 42, no. 16 (2013): 6801. http://dx.doi.org/10.1039/c3cs60093a.

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2

Alessandri, Riccardo, Paulo C. T. Souza, Sebastian Thallmair, Manuel N. Melo, Alex H. de Vries, and Siewert J. Marrink. "Pitfalls of the Martini Model." Journal of Chemical Theory and Computation 15, no. 10 (September 9, 2019): 5448–60. http://dx.doi.org/10.1021/acs.jctc.9b00473.

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3

Alessandri, Riccardo, Fabian Grünewald, and Siewert J. Marrink. "The Martini Model in Materials Science." Advanced Materials 33, no. 24 (May 6, 2021): 2008635. http://dx.doi.org/10.1002/adma.202008635.

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4

Mahajan, Subhamoy, and Tian Tang. "Martini coarse-grained model for polyethylenimine." Journal of Computational Chemistry 40, no. 3 (November 10, 2018): 607–18. http://dx.doi.org/10.1002/jcc.25747.

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5

Grunewald, Fabian, Giulia Rossi, Alex H. de Vries, Siewert J. Marrink, and Luca Monticelli. "Transferable MARTINI Model of Poly(ethylene Oxide)." Journal of Physical Chemistry B 122, no. 29 (July 2, 2018): 7436–49. http://dx.doi.org/10.1021/acs.jpcb.8b04760.

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6

Grünewald, Fabian, Paulo C. T. Souza, Haleh Abdizadeh, Jonathan Barnoud, Alex H. de Vries, and Siewert J. Marrink. "Titratable Martini model for constant pH simulations." Journal of Chemical Physics 153, no. 2 (July 14, 2020): 024118. http://dx.doi.org/10.1063/5.0014258.

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7

Shang, Xu, Zhen Guan, Shuai Zhang, Lulin Shi, and Haihang You. "Predicting the aptamer SYL3C–EpCAM complex's structure with the Martini-based simulation protocol." Physical Chemistry Chemical Physics 23, no. 12 (2021): 7066–79. http://dx.doi.org/10.1039/d0cp05003b.

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The Martini-based aptamer–protein complex structure prediction protocol includes two major stages: (a) aptamer structure's 3D modeling and prediction and (b) the aptamer–protein complex structure prediction. We performed a MetaD simulation with an enhanced Martini model to predict the aptamer–protein complex structure.
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8

Vuong, P. N., S. Wanji, L. Sakka, S. Klager, and O. Bain. "The murid filariaMonanema martini: a model for onchocerciasis." Annales de Parasitologie Humaine et Comparée 66, no. 3 (1991): 109–20. http://dx.doi.org/10.1051/parasite/1991663109.

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9

Khan, Parvez, and Gaurav Goel. "Martini Coarse-Grained Model for Clay–Polymer Nanocomposites." Journal of Physical Chemistry B 123, no. 42 (October 2019): 9011–23. http://dx.doi.org/10.1021/acs.jpcb.9b06708.

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10

Falsafi, Ali, and Hossein Nejat Pishkenari. "MARTINI Coarse-Grained Model of Solid–Liquid Interface." Journal of Physical Chemistry C 120, no. 46 (November 10, 2016): 26259–69. http://dx.doi.org/10.1021/acs.jpcc.6b07159.

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11

Yesudasan, Sumith. "Extended MARTINI water model for heat transfer studies." Molecular Physics 118, no. 13 (November 21, 2019): e1692151. http://dx.doi.org/10.1080/00268976.2019.1692151.

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12

López, César A., Giovanni Bellesia, Antonio Redondo, Paul Langan, Shishir P. S. Chundawat, Bruce E. Dale, Siewert J. Marrink, and S. Gnanakaran. "MARTINI Coarse-Grained Model for Crystalline Cellulose Microfibers." Journal of Physical Chemistry B 119, no. 2 (January 6, 2015): 465–73. http://dx.doi.org/10.1021/jp5105938.

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13

Groń, Ryszard. "Wpływ "Vita Martini" Sulpicjusza Sewera na Vita Niniani Aelreda z Rievaulx." Vox Patrum 62 (September 4, 2014): 125–37. http://dx.doi.org/10.31743/vp.3582.

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The article was written to illustrate the possible impact of Vita Martini by Sulpicius Severus on Aelred of Rievaulx’s Vita Niniani. Both works are hagiogra­phies, thus were written as prime examples of faith and Christian virtues without excessive focus on biographical accuracy, as was common during the medieval period. The works were created in diverse cultural and historical settings: the for­mer portrays the life of Saint Martin of Tours, a very popular medieval bishop of Gaul, who was active during the 5th century; the hagiography was written by his disciple, Sulpicius Severus. The latter depicts the life of a missionary active in southern England, also in the 5th century, Saint Ninian of Whithorn. St. Ninian’s hagiography was, however, written seven centuries later by a well-known English abbot from Rievaulx, St. Aelred. The possible influence of Sulpicius Severus’ work on Vita Niniani by Aelred of Rievaulx can be concluded due to the similarities be­tween the two hagiographies, the popularity of Vita Martini in Cistercian circles and, simultaneously, an almost complete lack of historical information regarding St. Ninian’s life. The fact that Aelred quotes the Bede Venerable’ history note from the 8th century – which mentions that St. Martin was St. Ninian’s role model in the field of missionary care and pastoral work – as his chief resource, makes this influence is all the more probable. To carry out this article’s objective, the contents have been divided into three sections: the creation of Vita Niniani; a comparison of Bishop Ninian of Whithorn as a historical figure (based on contemporary his­torical and archeological research) with the portrait painted by Aelred (based on the Bede Venerable’ note and a piece of literature by an unknown writer); to final­ly show a comparison of Vita Niniani and Vita Martini.
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14

Javanainen, Matti, Hector Martinez-Seara, and Ilpo Vattulainen. "Excessive aggregation of membrane proteins in the Martini model." PLOS ONE 12, no. 11 (November 13, 2017): e0187936. http://dx.doi.org/10.1371/journal.pone.0187936.

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15

Campos-Villalobos, Gerardo, Flor R. Siperstein, and Alessandro Patti. "Transferable coarse-grained MARTINI model for methacrylate-based copolymers." Molecular Systems Design & Engineering 4, no. 1 (2019): 186–98. http://dx.doi.org/10.1039/c8me00064f.

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16

Gobbo, Cristian, Isabelle Beurroies, David de Ridder, Rienk Eelkema, Siewert J. Marrink, Steven De Feyter, Jan H. van Esch, and Alex H. de Vries. "MARTINI Model for Physisorption of Organic Molecules on Graphite." Journal of Physical Chemistry C 117, no. 30 (July 23, 2013): 15623–31. http://dx.doi.org/10.1021/jp402615p.

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17

Bennett, W. F. Drew, Alexander W. Chen, Serena Donnini, Gerrit Groenhof, and D. Peter Tieleman. "Constant pH simulations with the coarse-grained MARTINI model — Application to oleic acid aggregates." Canadian Journal of Chemistry 91, no. 9 (September 2013): 839–46. http://dx.doi.org/10.1139/cjc-2013-0010.

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Long chain fatty acids are biologically important molecules with complex and pH sensitive aggregation behavior. The carboxylic head group of oleic acid is ionizable, with the pKa shifting to larger values, even above a value of 7, in certain aggregate states. While experiments have determined the macroscopic phase behavior, we have yet to understand the molecular level details for this complex behavior. This level of detail is likely required to fully appreciate the role of fatty acids in biology and for nanoscale biotechnological and industrial applications. Here, we introduce the use of constant pH molecular dynamics (MD) simulations with the coarse-grained MARTINI model and apply the method to oleic acid aggregates and a model lipid bilayer. By running simulations at different constant pH values, we determined titration curves and the resulting pKa for oleic acid in different environments. The coarse-grained model predicts positive pKa shifts, with a shift from 4.8 in water to 6.5 in a small micelle, and 6.6 in a dioleoylphosphatidylcholine (DOPC) bilayer, similar to experimental estimates. The size of the micelles increased as the pH increased, and correlated with the fraction of deprotonated oleic acid. We show this combination of constant pH MD and the coarse-grained MARTINI model can be used to model pH-dependent surfactant phase behavior. This suggests a large number of potential new applications of large-scale MARTINI simulations in other biological systems with ionizable molecules.
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18

Mhashal, Anil R., and Sudip Roy. "Self-assembly of phospholipids on flat supports." Physical Chemistry Chemical Physics 17, no. 46 (2015): 31152–60. http://dx.doi.org/10.1039/c5cp03358f.

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19

Marrink, Siewert J., H. Jelger Risselada, Serge Yefimov, D. Peter Tieleman, and Alex H. de Vries. "The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations." Journal of Physical Chemistry B 111, no. 27 (July 2007): 7812–24. http://dx.doi.org/10.1021/jp071097f.

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20

Michalowsky, Julian, Johannes Zeman, Christian Holm, and Jens Smiatek. "A polarizable MARTINI model for monovalent ions in aqueous solution." Journal of Chemical Physics 149, no. 16 (October 28, 2018): 163319. http://dx.doi.org/10.1063/1.5028354.

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21

Yesylevskyy, Semen O., Lars V. Schäfer, Durba Sengupta, and Siewert J. Marrink. "Polarizable Water Model for the Coarse-Grained MARTINI Force Field." PLoS Computational Biology 6, no. 6 (June 10, 2010): e1000810. http://dx.doi.org/10.1371/journal.pcbi.1000810.

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22

Salassi, S., F. Simonelli, A. Bartocci, and G. Rossi. "A Martini coarse-grained model of the calcein fluorescent dye." Journal of Physics D: Applied Physics 51, no. 38 (August 9, 2018): 384002. http://dx.doi.org/10.1088/1361-6463/aad4b8.

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23

Rossi, Giulia, Ioannis Giannakopoulos, Luca Monticelli, Niko K. J. Rostedt, Sakari R. Puisto, Chris Lowe, Ambrose C. Taylor, Ilpo Vattulainen, and Tapio Ala-Nissila. "A MARTINI Coarse-Grained Model of a Thermoset Polyester Coating." Macromolecules 44, no. 15 (August 9, 2011): 6198–208. http://dx.doi.org/10.1021/ma200788a.

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24

Akhshi, Parisa, Jaakko Uusitalo, Helgi Ingolfsson, Siewert-Jan Marrink, and D. Peter Tieleman. "Development of Coarse-Grained Martini Model for Nucleic Acid Structures." Biophysical Journal 106, no. 2 (January 2014): 704a. http://dx.doi.org/10.1016/j.bpj.2013.11.3896.

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25

Shen, Zhiqiang, William Baker, Huilin Ye, and Ying Li. "pH-Dependent aggregation and pH-independent cell membrane adhesion of monolayer-protected mixed charged gold nanoparticles." Nanoscale 11, no. 15 (2019): 7371–85. http://dx.doi.org/10.1039/c8nr09617a.

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26

Majumder, Ayan, and John E. Straub. "Addressing the Excessive Aggregation of Membrane Proteins in the MARTINI Model." Journal of Chemical Theory and Computation 17, no. 4 (March 15, 2021): 2513–21. http://dx.doi.org/10.1021/acs.jctc.0c01253.

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27

Zhao, Mingfei, Janani Sampath, Sarah Alamdari, Gillian Shen, Chun-Long Chen, Christopher J. Mundy, Jim Pfaendtner, and Andrew L. Ferguson. "MARTINI-Compatible Coarse-Grained Model for the Mesoscale Simulation of Peptoids." Journal of Physical Chemistry B 124, no. 36 (August 10, 2020): 7745–64. http://dx.doi.org/10.1021/acs.jpcb.0c04567.

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28

Webb, Alexis, Clement Arnarez, and Edward Lyman. "Hysteresis and the Cholesterol-Dependent Melting Transition of the Martini Model." Biophysical Journal 112, no. 3 (February 2017): 384a. http://dx.doi.org/10.1016/j.bpj.2016.11.2088.

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29

Modarresi, Mohsen, Juan Felipe Franco-Gonzalez, and Igor Zozoulenko. "Morphology and ion diffusion in PEDOT:Tos. A coarse grained molecular dynamics simulation." Physical Chemistry Chemical Physics 20, no. 25 (2018): 17188–98. http://dx.doi.org/10.1039/c8cp02902d.

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A Martini coarse-grained Molecular Dynamics (MD) model for the doped conducting polymer poly(3,4-ethylenedioxythiophene) (PEDOT) is developed. It is shown that the diffusion coefficients decrease exponentially as the hydration level is reduced.
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30

Gautieri, Alfonso, Antonio Russo, Simone Vesentini, Alberto Redaelli, and Markus J. Buehler. "Coarse-Grained Model of Collagen Molecules Using an Extended MARTINI Force Field." Journal of Chemical Theory and Computation 6, no. 4 (March 24, 2010): 1210–18. http://dx.doi.org/10.1021/ct100015v.

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31

Han, Rui. "Dry Ten Martini problem for the non-self-dual extended Harper’s model." Transactions of the American Mathematical Society 370, no. 1 (July 7, 2017): 197–217. http://dx.doi.org/10.1090/tran/6989.

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32

Lavino, Alessio D., Paola Carbone, and Daniele Marchisio. "MARTINI coarse‐grained model for poly‐ε‐caprolactone in acetone‐water mixtures." Canadian Journal of Chemical Engineering 98, no. 9 (May 8, 2020): 1868–79. http://dx.doi.org/10.1002/cjce.23761.

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33

Moreira, Rodrigo A., Stefan A. L. Weber, and Adolfo B. Poma. "Martini 3 Model of Cellulose Microfibrils: On the Route to Capture Large Conformational Changes of Polysaccharides." Molecules 27, no. 3 (February 1, 2022): 976. http://dx.doi.org/10.3390/molecules27030976.

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High resolution data from all-atom molecular simulations is used to parameterize a Martini 3 coarse-grained (CG) model of cellulose I allomorphs and cellulose type-II fibrils. In this case, elementary molecules are represented by four effective beads centred in the positions of O2, O3, C6, and O6 atoms in the D-glucose cellulose subunit. Non-bonded interactions between CG beads are tuned according to a low statistical criterion of structural deviation using the Martini 3 type of interactions and are capable of being indistinguishable for all studied cases. To maintain the crystalline structure of each single cellulose chain in the microfibrils, elastic potentials are employed to retain the ribbon-like structure in each chain. We find that our model is capable of describing different fibril-twist angles associated with each type of cellulose fibril in close agreement with atomistic simulation. Furthermore, our CG model poses a very small deviation from the native-like structure, making it appropriate to capture large conformational changes such as those that occur during the self-assembly process. We expect to provide a computational model suitable for several new applications such as cellulose self-assembly in different aqueous solutions and the thermal treatment of fibrils of great importance in bioindustrial applications.
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34

Tseng, Sei Wo Winger, Teng Wen Chang, and Ji Hong Lin. "Form Generation Model of Two Thinking Paths." Advanced Materials Research 201-203 (February 2011): 1177–80. http://dx.doi.org/10.4028/www.scientific.net/amr.201-203.1177.

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A model of two thinking paths is developed in this article. Early researchers of computer aided for product design focused their attention on sensation of consumers on product appearance to meet the consumer need. However, these generative rules of digital form did not consider the thinking process during design concept development. The experiment was designed to explore the concept transformation of two thinking patterns, and the shape generation in design thinking developing. The martini wine cup had been selected as a design target to collect the data. The model of two thinking paths was then developed based on results of the design thinking experiment. An experimental system, called thinking pattern-based generation system, a.l.a. ThinkGen, was then implemented to test the model.
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35

Fang, Mingjia. "Application of molecular dynamics simulation in self-assembly." Journal of Physics: Conference Series 2108, no. 1 (November 1, 2021): 012085. http://dx.doi.org/10.1088/1742-6596/2108/1/012085.

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Abstract During the past few years, numerous studies have been done in self-assembly. Among most of these studies, Molecular Dynamic Simulation is widely used to construct the experiment model. This work firstly introduced three practical applications of MD simulation in self-assembly. Then, two main kinds of simulation are discussed including all-atom simulation and coarse-grained simulation, together with the way of thoughts before the simulation start. It is found that researchers always start with the whole analysis of the substances that need to be studied. It helps to confirm the appropriate model that can apply in the simulation naturally. Besides, depended on the principles that need to be studied, the way of establishing the simulation system varies, ranging from separation experiment in both types of simulation to the change of essential parameters. Furthermore, the adoption of L-J potential in MD simulation proves to be a wise option on account of its convenient and simple model. It is remarkable that, considering some small details like the differences between implicit and explicit solution, classical Martini force field is replaced by Dry Martini force field.
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36

Maftouni, N., M. Amininassab, M. N. Mello, and S. Marink. "Nanocomputation of Mechanical Properties in Nanobio Membrane." Applied Mechanics and Materials 110-116 (October 2011): 3883–87. http://dx.doi.org/10.4028/www.scientific.net/amm.110-116.3883.

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It is very essential to know mechanical properties in different regions of nanobio membrane as one of the most important parts of living systems. Here the coarse-grained (CG) simulations method have been used to study the pressure profile in a system including nanobio membrane and water. CG simulations have become an important tool to study many biomolecular processes, exploring scales inaccessible to traditional models of atomistic resolution. One of the major simplifications of CG models is the representation of the solvent, which is either implicit or modeled explicitly as a van der Waals particle. The effect of polarization has been ignored in the initial CG water molecules model. Given the important role of water as a solvent in biological systems, its treatment is very important to the properties derived from simulation studies. Till now two models have been parameterized to simulate water: i) standard MARTINI water and ii) polarizable coarse-grained water model. Both of mentioned water models are proper to be used in combination with the CG MARTINI force field. In this work both of these models have been used for simulation. One micro second CG molecular dynamics simulation has been done for two separate systems. Each system includes water and hydrated 1-palmitoyl-2-oleoyl-1-sn-3-phosphatidylcholine (POPC) lipid nanobio membrane. The difference between two systems is in simulated water models that one system has standard MARTINI water and the other one has polarizable water. In each case pressure profile calculation has been done via Virial pressure theorem. Results indicate that using polarizable water model leads to higher picks in pressure profile in water region near surface of nanobio membrane. This can be related to density of polarizable water and also may play role as a small barrier.
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37

Kumar, Raj, Young Kyu Lee, and Yong Seok Jho. "Martini Coarse-Grained Model of Hyaluronic Acid for the Structural Change of Its Gel in the Presence of Monovalent and Divalent Salts." International Journal of Molecular Sciences 21, no. 13 (June 29, 2020): 4602. http://dx.doi.org/10.3390/ijms21134602.

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Hyaluronic acid (HA) has a wide range of biomedical applications including the formation of hydrogels, microspheres, sponges, and films. The modeling of HA to understand its behavior and interaction with other biomolecules at the atomic level is of considerable interest. The atomistic representation of long HA polymers for the study of the macroscopic structural formation and its interactions with other polyelectrolytes is computationally demanding. To overcome this limitation, we developed a coarse grained (CG) model for HA adapting the Martini scheme. A very good agreement was observed between the CG model and all-atom simulations for both local (bonded interactions) and global properties (end-to-end distance, a radius of gyration, RMSD). Our CG model successfully demonstrated the formation of HA gel and its structural changes at high salt concentrations. We found that the main role of CaCl2 is screening the electrostatic repulsion between chains. HA gel did not collapse even at high CaCl2 concentrations, and the osmotic pressure decreased, which agrees well with the experimental results. This is a distinct property of HA from other proteins or polynucleic acids which ensures the validity of our CG model. Our HA CG model is compatible with other CG biomolecular models developed under the Martini scheme, which allows for large-scale simulations of various HA-based complex systems.
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38

Schwammle, Donnalee. "Occupational Competence Explored." Canadian Journal of Occupational Therapy 63, no. 5 (December 1996): 323–30. http://dx.doi.org/10.1177/000841749606300508.

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Occupational competence is an important construct in occupational therapy but how well do we really understand it? This article reviews White's 1959 theory of competence motivation to facilitate a deeper understanding of the various factors involved in competence. In light of these ideas, the Occupational Competence Model (Polatajko, 1992) and The Enablement Model (Martini, Polatajko & Wilcox, 1995) are revisited and revisions are suggested. Finally, the role of occupational therapy in the promotion of competence is discussed.
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39

Barbosa, Gabriel D., and C. Heath Turner. "Martini Coarse-Grained Model for Poly(alkylimidazolium) Ionenes and Applications in Aromatic Compound Extraction." Macromolecules 55, no. 1 (December 29, 2021): 26–34. http://dx.doi.org/10.1021/acs.macromol.1c01932.

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40

Rossi, G., P. F. J. Fuchs, J. Barnoud, and L. Monticelli. "A Coarse-Grained MARTINI Model of Polyethylene Glycol and of Polyoxyethylene Alkyl Ether Surfactants." Journal of Physical Chemistry B 116, no. 49 (November 29, 2012): 14353–62. http://dx.doi.org/10.1021/jp3095165.

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41

Vögele, Martin, Christian Holm, and Jens Smiatek. "Properties of the polarizable MARTINI water model: A comparative study for aqueous electrolyte solutions." Journal of Molecular Liquids 212 (December 2015): 103–10. http://dx.doi.org/10.1016/j.molliq.2015.08.062.

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42

Seo, Mikyung, and Peter Tieleman. "Improving Internal Peptide Dynamics in the Coarse-Grained Martini Model: Application to Amyloid Peptides." Biophysical Journal 98, no. 3 (January 2010): 569a—570a. http://dx.doi.org/10.1016/j.bpj.2009.12.3090.

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43

Kitjanon, Jiramate, Wasinee Khuntawee, Saree Phongphanphanee, Thana Sutthibutpong, Nattaporn Chattham, Mikko Karttunen, and Jirasak Wong-ekkabut. "Nanocomposite of Fullerenes and Natural Rubbers: MARTINI Force Field Molecular Dynamics Simulations." Polymers 13, no. 22 (November 22, 2021): 4044. http://dx.doi.org/10.3390/polym13224044.

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The mechanical properties of natural rubber (NR) composites depend on many factors, including the filler loading, filler size, filler dispersion, and filler-rubber interfacial interactions. Thus, NR composites with nano-sized fillers have attracted a great deal of attention for improving properties such as stiffness, chemical resistance, and high wear resistance. Here, a coarse-grained (CG) model based on the MARTINI force field version 2.1 has been developed and deployed for simulations of cis-1,4-polyisoprene (cis-PI). The model shows qualitative and quantitative agreement with the experiments and atomistic simulations. Interestingly, only a 0.5% difference with respect to the experimental result of the glass transition temperature (Tg) of the cis-PI in the melts was observed. In addition, the mechanical and thermodynamical properties of the cis-PI-fullerene(C60) composites were investigated. Coarse-grained molecular dynamics (MD) simulations of cis-PI-C60 composites with varying fullerene concentrations (0–32 parts per hundred of rubber; phr) were performed over 200 microseconds. The structural, mechanical, and thermal properties of the composites were determined. The density, bulk modulus, thermal expansion, heat capacity, and Tg of the NR composites were found to increase with increasing C60 concentration. The presence of C60 resulted in a slight increasing of the end-to-end distance and radius of the gyration of the cis-PI chains. The contribution of C60 and cis-PI interfacial interactions led to an enhancement of the bulk moduli of the composites. This model should be helpful in the investigations and design of effective fillers of NR-C60 composites for improving their properties.
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44

Srinivasan, Sriraksha, Valeria Zoni, and Stefano Vanni. "Estimating the Accuracy of the Martini Model Towards the Investigation of Peripheral Protein - Membrane Interactions." Biophysical Journal 120, no. 3 (February 2021): 232a. http://dx.doi.org/10.1016/j.bpj.2020.11.1540.

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45

Arnarez, Clement, Alexis Webb, Eric Rouvière, and Edward Lyman. "Hysteresis and the Cholesterol Dependent Phase Transition in Binary Lipid Mixtures with the Martini Model." Journal of Physical Chemistry B 120, no. 51 (December 15, 2016): 13086–93. http://dx.doi.org/10.1021/acs.jpcb.6b09728.

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46

Pizzirusso, Antonio, Antonio De Nicola, and Giuseppe Milano. "MARTINI Coarse-Grained Model of Triton TX-100 in Pure DPPC Monolayer and Bilayer Interfaces." Journal of Physical Chemistry B 120, no. 16 (April 14, 2016): 3821–32. http://dx.doi.org/10.1021/acs.jpcb.6b00646.

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47

Seo, Mikyung, and Peter Tieleman. "Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model: Application in Amyloid Peptide Aggregation." Biophysical Journal 100, no. 3 (February 2011): 148a. http://dx.doi.org/10.1016/j.bpj.2010.12.1016.

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Herzog, Florian A., Lukas Braun, Ingmar Schoen, and Viola Vogel. "Introducing Improved Protein Side Chain Dynamics in the MARTINI Model to Simulate Protein-Membrane Interactions." Biophysical Journal 110, no. 3 (February 2016): 575a—576a. http://dx.doi.org/10.1016/j.bpj.2015.11.3078.

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SCHENKE, BJÖRN, SANGYONG JEON, and CHARLES GALE. "MONTE-CARLO SIMULATION OF HEAVY-ION COLLISIONS." International Journal of Modern Physics E 20, no. 07 (July 2011): 1588–93. http://dx.doi.org/10.1142/s0218301311019921.

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Results from the Modular Algorithm for Relativistic Treatment of heavy IoN Interactions (MARTINI) are presented. This comprehensive event generator for the hard and penetrating probes in high energy nucleus-nucleus collisions employs a time evolution model for the soft background, PYTHIA 8.1 and the McGill-AMY parton evolution scheme including radiative as well as elastic processes. It generates full event configurations in the high pT region, allowing to perform the same processing as with experimental data, such as multi-particle correlation analyses and full jet reconstruction.
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50

Krishnaveni, K., M. Sabitha, M. Murugan, C. Kandeepan, S. Ramya, T. Loganathan, and R. Jayakumararaj. "vNN model cross validation towards Accuracy, Sensitivity, Specificity and kappa performance measures of β-caryophyllene using a restricted-unrestricted applicability domain on Artificial Intelligence & Machine Learning approach based in-silico prediction." Journal of Drug Delivery and Therapeutics 12, no. 1-S (February 22, 2022): 123–31. http://dx.doi.org/10.22270/jddt.v12i1-s.5222.

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Wide-reaching interest in use of plant derived secondary metabolites (PDSMs) has been growing world over. This implies that the beneficial effects of plant based natural products (PBNPs) being rediscovered and harnessed for the development of novel drugs; drug-leads and structural background for drug design. Survey of literature on the indigenous use of traditional medicinal knowledge bestows ethnopharmacological potentials of PBNPs that has inspired drug design and development through research in drug discovery; PBNPs provide baseline for the development of drug leads against various pharmacological targets. Studies indicate that Cymbopogon martini Essential Oil (CMEO) exhibits a wide range of biological activities (anticancer, antidiabetic, antibacterial, antifungal, antioxidant, hepatoprotective and insecticide) attributed to the presence of bio-active secondary metabolites (BASM). However, wide-spread application of CMEO is limited because of typical odor, color and taste. In the present study, In-silico Absorption, Distribution, Metabolism, Elimination, Toxicity (ADMET) studies of β-caryophyllene (BCP) from Cymbopogon martinii is envisaged. β-caryophyllene enhances wound healing through multiple routes therefore, Non AMES toxic, Non-carcinogens, and biodegradable nature of β-caryophyllene prospects this compound as considered as an apt lead for the development of drugs for the treatment of cuts and wounds besides other diseases viz., diabetics, cancer, metabolic inflammation and other long term complications associated with these diseases. In particular, BCP inhibits cytochrome P450 isoforms (CYP3A4) that metabolize xenobiotics and results in adverse effects. Pharmacokinetic properties and predicted score values of β-caryophyllene have highlighted that both pharmacological and toxicological aspects need to be further investigated before put to clinical trials. Keywords: ADMET; β-caryophyllene; Cymbopogon martinii; Cardiotoxicity; Cytotoxicity; Drugability; Pharmacokinetics; Bioactivity; Essential Oil;
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