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Journal articles on the topic 'Atomistic and Mesoscale'

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Author: Grafiati

Published: 6 September 2023

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1

Wang, Yuying, Zhen Li, Junbo Xu, Chao Yang, and George Em Karniadakis. "Concurrent coupling of atomistic simulation and mesoscopic hydrodynamics for flows over soft multi-functional surfaces." Soft Matter 15, no. 8 (2019): 1747–57. http://dx.doi.org/10.1039/c8sm02170h.

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We develop an efficient parallel multiscale method that bridges the atomistic and mesoscale regimes, from nanometers to microns and beyond, via concurrent coupling of atomistic simulation and mesoscopic dynamics.

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2

Reith, Dirk, Mathias Pütz, and Florian Müller-Plathe. "Deriving effective mesoscale potentials from atomistic simulations." Journal of Computational Chemistry 24, no. 13 (August 12, 2003): 1624–36. http://dx.doi.org/10.1002/jcc.10307.

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3

Burbery, Nathaniel, Raj Das, W. George Ferguson, Giacomo Po, and Nasr Ghoniem. "Atomistic Activation Energy Criteria for Multi-Scale Modeling of Dislocation Nucleation in FCC Metals." International Journal of Computational Methods 13, no. 04 (July 4, 2016): 1641006. http://dx.doi.org/10.1142/s0219876216410061.

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This study contributes to the development of a ‘fundamental, atomistic basis’ to inform macro-scale models that can provide significant insights about the effect of dislocation microstructure evolution during plastic deformation. Within a mesoscale model, multi-dislocation interactions can be studied which are capable of driving high-stress effects such as dislocation nucleation under low applied stresses, due to stress-concentration in dislocation pile-ups at interfaces. This study establishes a methodology to evaluate a phenomenological model for atomic-scale crystal defect interactions from molecular dynamics simulations, which is a critical step for mesoscale studies of plastic deformation in metals. Dislocations are affected by thermally activated processes that become energetically favorable as the stress approaches a threshold value. The nudged elastic band technique is ideal for evaluating the energetic activation parameters from atomic simulations. With this method, the activation energy and volume were obtained for the process of homogeneous nucleation of a full dislocation loop in pure FCC aluminum. Using the (atomistic) activation parameters, a constitutive mathematical model is developed for simulations at the mesoscale, to evaluate the critical (local) shear stress threshold. The constitutive model is effective for extrapolating from an atomistic timeframe of femtoseconds to experimentally accessible timespans of seconds.

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4

Bulatov, Vasily, Farid F. Abraham, Ladislas Kubin, Benoit Devincre, and Sidney Yip. "Connecting atomistic and mesoscale simulations of crystal plasticity." Nature 391, no. 6668 (February 1998): 669–72. http://dx.doi.org/10.1038/35577.

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5

Kinjo, T., and S. Hyodo. "Linkage between atomistic and mesoscale coarse-grained simulation." Molecular Simulation 33, no. 4-5 (April 2007): 417–20. http://dx.doi.org/10.1080/08927020601155436.

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6

Unnikrishnan, V. U., G. U. Unnikrishnan, J. N. Reddy, and C. T. Lim. "Atomistic-mesoscale coupled mechanical analysis of polymeric nanofibers." Journal of Materials Science 42, no. 21 (July 14, 2007): 8844–52. http://dx.doi.org/10.1007/s10853-007-1820-6.

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7

Maurel, Gaëtan, Florent Goujon, Benoit Schnell, and Patrice Malfreyt. "Prediction of structural and thermomechanical properties of polymers from multiscale simulations." RSC Adv. 5, no. 19 (2015): 14065–73. http://dx.doi.org/10.1039/c4ra16417b.

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8

Maltsev, Ilya, Alexandr Mirzoev, Denis Danilov, and Britta Nestler. "Atomistic and mesoscale simulations of free solidification in comparison." Modelling and Simulation in Materials Science and Engineering 17, no. 5 (June 16, 2009): 055006. http://dx.doi.org/10.1088/0965-0393/17/5/055006.

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9

Noro, Massimo G., Prem K. C. Paul, and Patrick B. Warren. "Linking Atomistic and Mesoscale Simulations of Water-Soluble Polymers." Journal of the American Chemical Society 125, no. 24 (June 2003): 7190–91. http://dx.doi.org/10.1021/ja0343914.

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10

Mo, Zunli, Lijun Qiao, Yaling Sun, and Hejun Li. "Atomistic and mesoscale interface simulation of graphite nanosheet/AgCl/polypyrrole composite." Computational Materials Science 45, no. 4 (June 2009): 981–85. http://dx.doi.org/10.1016/j.commatsci.2008.12.020.

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11

Unnikrishnan, V. U., D. Banerjee, and J. N. Reddy. "Atomistic-mesoscale interfacial resistance based thermal analysis of carbon nanotube systems." International Journal of Thermal Sciences 47, no. 12 (December 2008): 1602–9. http://dx.doi.org/10.1016/j.ijthermalsci.2007.10.012.

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12

Shea, Joan-Emma. "Aggregation of the TAU Protein: Insights from Atomistic and Mesoscale Simulations." Biophysical Journal 114, no. 3 (February 2018): 185a. http://dx.doi.org/10.1016/j.bpj.2017.11.1032.

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13

Shenogin, Sergei, and Rahmi Ozisik. "Simulation of plastic deformation in glassy polymers: Atomistic and mesoscale approaches." Journal of Polymer Science Part B: Polymer Physics 43, no. 8 (2005): 994–1004. http://dx.doi.org/10.1002/polb.20389.

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14

Jhon, Myung S., Pil Seung Chung, Robert L. Smith, and Lorenz T. Biegler. "A Description of Multiscale Modeling for the Head-Disk Interface Focusing on Bottom-Level Lubricant and Carbon Overcoat Models." Advances in Tribology 2013 (2013): 1–27. http://dx.doi.org/10.1155/2013/794151.

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The challenges in designing future head disk interface (HDI) demand efficient theoretical modeling tools with flexibility in investigating various combinations of perfluoropolyether (PFPE) and carbon overcoat (COC) materials. For broad range of time and length scales, we developed multiscale/multiphysical modeling approach, which can bring paradigm-shifting improvements in advanced HDI design. In this paper, we introduce our multiscale modeling methodology with an effective strategic framework for the HDI system. Our multiscale methodology in this paper adopts a bottom to top approach beginning with the high-resolution modeling, which describes the intramolecular/intermolecular PFPE-COC degrees of freedom governing the functional oligomeric molecular conformations on the carbon surfaces. By introducing methodology for integrating atomistic/molecular/mesoscale levels via coarse-graining procedures, we investigated static and dynamic properties of PFPE-COC combinations with various molecular architectures. By bridging the atomistic and molecular scales, we are able to systematically incorporate first-principle physics into molecular models, thereby demonstrating a pathway for designing materials based on molecular architecture. We also discussed future materials (e.g., graphene for COC, star-like PFPEs) and systems (e.g., heat-assisted magnetic recording (HAMR)) with higher scale modeling methodology, which enables the incorporation of molecular/mesoscale information into the continuum scale models.

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15

PEREIRA, SIMÃO PEDRO, GIULIO SCOCCHI, RADOVAN TOTH, PAOLA POSOCCO, DANIEL R. NIETO, SABRINA PRICL, and MAURIZIO FERMEGLIA. "MULTISCALE MODELING OF POLYMER/CLAY NANOCOMPOSITES." Journal of Multiscale Modelling 03, no. 03 (September 2011): 151–76. http://dx.doi.org/10.1142/s1756973711000467.

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Multiscale molecular modeling (M3) is applied in many fields of material science, but it is particularly important in the polymer science, due to the wide range of phenomena occurring at different scales which influence the ultimate properties of the materials. In this context, M3 plays a crucial role in the design of new materials whose properties are infiuenced by the structure at nanoscale. In this work we present the application of a multiscale molecular modeling procedure to characterize polymer/clay nanocomposites obtained with full/partial dispersion of nanofillers in a polymer. This approach relies on a step-by step message-passing technique from atomistic to mesoscale to finite element level; thus, computer simulations at all scales are completely integrated and the calculated results are compared to available experimental evidences. In details, nine polymer nanocomposite systems have been studied by different molecular modeling methods, such as atomistic Molecular Mechanics and Molecular Dynamics, the mesoscale Dissipative Particles Dynamics and the macroscale Finite Element Method. The entire computational procedure has been applied to a number of diverse polymer nanocomposite systems based on montmorillonite as clay and different clay surface modifiers, and their mechanical, thermal and barrier properties have been predicted in agreement with the available experimental data.

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16

KIM, J. H., S. H. CHOI, D. H. JUNG, C. S. CHO, and Y. J. CHOI. "A COARSE-GRAINED MODEL OF MONOOLEIN: COMPARISON WITH THE ATOMISTIC MODEL." International Journal of Nanoscience 08, no. 01n02 (February 2009): 169–73. http://dx.doi.org/10.1142/s0219581x09005918.

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Monoolein (2,3-dihydroxypropyl (Z)-octadec-9-enoate) is one of the monoacylglycerol and has been studied for various applications in food, pharmaceutical, and cosmetic industry. Those applications make use of the phase behavior of monoolein. In order to understand the lipid bilayer phase of monoolein in mesoscale, a coarse-grained model has been built and tested in this work. The monoolein molecule was represented by two hydrophilic heads and six hydrophobic tails. The three water molecules were also represented as one bead. For comparison, the atomistic model has also been used for molecular dynamics simulation on the lipid bilayer phase in isothermal-isobaric (NPT) ensemble. The interaction and bond bending potential parameters for dissipative particle dynamics (DPD) were obtained with molecular dynamics simulations on lipid bilayer in water. And we also obtained the interaction parameters of the coarse-grained model, which agree well with the atomistic model. We compared the simulated phases using the coarse-grained model with using the atomistic model. With these parameters, we successfully reproduced the lamella phase of monoolein in DPD simulations.

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17

Ioannidou, Katerina, Konrad J. Krakowiak, Mathieu Bauchy, Christian G. Hoover, Enrico Masoero, Sidney Yip, Franz-Josef Ulm, Pierre Levitz, Roland J. M. Pellenq, and Emanuela Del Gado. "Mesoscale texture of cement hydrates." Proceedings of the National Academy of Sciences 113, no. 8 (February 8, 2016): 2029–34. http://dx.doi.org/10.1073/pnas.1520487113.

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Strength and other mechanical properties of cement and concrete rely upon the formation of calcium–silicate–hydrates (C–S–H) during cement hydration. Controlling structure and properties of the C–S–H phase is a challenge, due to the complexity of this hydration product and of the mechanisms that drive its precipitation from the ionic solution upon dissolution of cement grains in water. Departing from traditional models mostly focused on length scales above the micrometer, recent research addressed the molecular structure of C–S–H. However, small-angle neutron scattering, electron-microscopy imaging, and nanoindentation experiments suggest that its mesoscale organization, extending over hundreds of nanometers, may be more important. Here we unveil the C–S–H mesoscale texture, a crucial step to connect the fundamental scales to the macroscale of engineering properties. We use simulations that combine information of the nanoscale building units of C–S–H and their effective interactions, obtained from atomistic simulations and experiments, into a statistical physics framework for aggregating nanoparticles. We compute small-angle scattering intensities, pore size distributions, specific surface area, local densities, indentation modulus, and hardness of the material, providing quantitative understanding of different experimental investigations. Our results provide insight into how the heterogeneities developed during the early stages of hydration persist in the structure of C–S–H and impact the mechanical performance of the hardened cement paste. Unraveling such links in cement hydrates can be groundbreaking and controlling them can be the key to smarter mix designs of cementitious materials.

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18

Dufresne, Alice, Jack Arayro, Tingtao Zhou, Katerina Ioannidou, Franz-Josef Ulm, Roland Pellenq, and Laurent Karim Béland. "Atomistic and mesoscale simulation of sodium and potassium adsorption in cement paste." Journal of Chemical Physics 149, no. 7 (August 21, 2018): 074705. http://dx.doi.org/10.1063/1.5042755.

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19

Lininger, Christianna N., Nicholas W. Brady, and Alan C. West. "Equilibria and Rate Phenomena from Atomistic to Mesoscale: Simulation Studies of Magnetite." Accounts of Chemical Research 51, no. 3 (March 2, 2018): 583–90. http://dx.doi.org/10.1021/acs.accounts.7b00531.

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20

Haslam, A. J., D. Moldovan, S. R. Phillpot, D. Wolf, and H. Gleiter. "Combined atomistic and mesoscale simulation of grain growth in nanocrystalline thin films." Computational Materials Science 23, no. 1-4 (April 2002): 15–32. http://dx.doi.org/10.1016/s0927-0256(01)00218-x.

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21

Hüter, Claas, Chi-Dzu Nguyen, Robert Spatschek, and Jörg Neugebauer. "Scale bridging between atomistic and mesoscale modelling: applications of amplitude equation descriptions." Modelling and Simulation in Materials Science and Engineering 22, no. 3 (April 1, 2014): 034001. http://dx.doi.org/10.1088/0965-0393/22/3/034001.

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22

Sun, Tiedong, Alexander Mirzoev, Vishal Minhas, Nikolay Korolev, Alexander P. Lyubartsev, and Lars Nordenskiöld. "A multiscale analysis of DNA phase separation: from atomistic to mesoscale level." Nucleic Acids Research 47, no. 11 (May 20, 2019): 5550–62. http://dx.doi.org/10.1093/nar/gkz377.

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23

Beyerlein, I. J., and A. Hunter. "Understanding dislocation mechanics at the mesoscale using phase field dislocation dynamics." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 374, no. 2066 (April 28, 2016): 20150166. http://dx.doi.org/10.1098/rsta.2015.0166.

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In this paper, we discuss the formulation, recent developments and findings obtained from a mesoscale mechanics technique called phase field dislocation dynamics (PFDD). We begin by presenting recent advancements made in modelling face-centred cubic materials, such as integration with atomic-scale simulations to account for partial dislocations. We discuss calculations that help in understanding grain size effects on transitions from full to partial dislocation-mediated slip behaviour and deformation twinning. Finally, we present recent extensions of the PFDD framework to alternative crystal structures, such as body-centred cubic metals, and two-phase materials, including free surfaces, voids and bi-metallic crystals. With several examples we demonstrate that the PFDD model is a powerful and versatile method that can bridge the length and time scales between atomistic and continuum-scale methods, providing a much needed understanding of deformation mechanisms in the mesoscale regime.

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24

Iwamoto, Nancy. "Studies of Mesoscale Models Parameterized by Molecular Models for Interface Failure in Epoxy Molding Compounds." International Symposium on Microelectronics 2011, no. 1 (January 1, 2011): 000657–64. http://dx.doi.org/10.4071/isom-2011-wp1-paper1.

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Deeper understanding of material failure must include consideration of contributions from the molecular and atomistic scales from which a more complete root cause picture may be constructed. The current study, supported by an international consortium effort (NanoInterface) [1], reports efforts to bridge the gap between molecular models and macroscale models by use of a mesoscale discrete particle method. Both the initial stress-strain curve and the latter part of the stress strain curve has been developed for perfect (flat) interfaces as well as simulated rough interfaces, using a saw-tooth configuration.

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25

García-Negrón, Valerie, Akinola D. Oyedele, Eduardo Ponce, Orlando Rios, David P. Harper, and David J. Keffer. "Evaluation of nano- and mesoscale structural features in composite materials through hierarchical decomposition of the radial distribution function." Journal of Applied Crystallography 51, no. 1 (February 1, 2018): 76–86. http://dx.doi.org/10.1107/s1600576717016843.

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Composite materials possessing both crystalline and amorphous domains, when subjected to X-ray and neutron scattering, generate diffraction patterns that are often difficult to interpret. One approach is to perform atomistic simulations of a proposed structure, from which the analogous diffraction pattern can be obtained for validation. The structure can be iteratively refined until simulation and experiment agree. The practical drawback to this approach is the significant computational resources required for the simulations. In this work, an alternative approach based on a hierarchical decomposition of the radial distribution function is used to generate a physics-based model allowing rapid interpretation of scattering data. In order to demonstrate the breadth of this approach, it is applied to a series of carbon composites. The model is compared with atomistic simulation results in order to demonstrate that the contributions of the crystalline and amorphous domains, as well as their interfaces, are correctly captured. Because the model is more efficient, additional structural refinement is performed to increase the agreement of the simulation result with the experimental data. The model achieves a reduction in computational effort of six orders of magnitude relative to simulation. The model can be generally extended to other composite materials.

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26

Silbermann, Jörg R., Sabine H. L. Klapp, Martin Schoen, Naresh Chennamsetty, Henry Bock, and Keith E. Gubbins. "Mesoscale modeling of complex binary fluid mixtures: Towards an atomistic foundation of effective potentials." Journal of Chemical Physics 124, no. 7 (February 21, 2006): 074105. http://dx.doi.org/10.1063/1.2161207.

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27

Markutsya, Sergiy, Rodney O. Fox, and Shankar Subramaniam. "Coarse-Graining Approach to Infer Mesoscale Interaction Potentials from Atomistic Interactions for Aggregating Systems." Industrial & Engineering Chemistry Research 51, no. 49 (November 27, 2012): 16116–34. http://dx.doi.org/10.1021/ie3013715.

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28

Gao, Jing, Jingyuan Yan, Beikai Zhao, Ze Zhang, and Qian Yu. "In situ observation of temperature-dependent atomistic and mesoscale oxidation mechanisms of aluminum nanoparticles." Nano Research 13, no. 1 (December 18, 2019): 183–87. http://dx.doi.org/10.1007/s12274-019-2593-3.

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29

RAHMAN, R., and A. HAQUE. "A PERIDYNAMICS FORMULATION BASED HIERARCHICAL MULTISCALE MODELING APPROACH BETWEEN CONTINUUM SCALE AND ATOMISTIC SCALE." International Journal of Computational Materials Science and Engineering 01, no. 03 (September 2012): 1250029. http://dx.doi.org/10.1142/s2047684112500297.

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In this paper, a multiscale modeling framework has been established between peridynamics and atomistic models. Peridynamics (PD) formulation is based on continuum theory implying nonlocal force based interactions. Peridynamics (PD) and molecular dynamics (MD) have similarities since both use nonlocal force based interaction. It means continuum points in PD and MD atoms are separated by finite distance and exert force upon each other. In this work PD based continuum model of epoxy polymer is defined by meshless Lagrangian particles. MD is coupled with PD based continuum model through a hierarchical multiscale modeling framework. In this framework, PD particles at coarse scale interact with fine scale PD particles by transferring pressure, displacements and velocities among each other. Based on the same hierarchical coupling method, fine scale PD model is seamlessly interfaced with molecular model through an intermediate mesoscale region i.e. coarse-grain atomic model. At the end of this hierarchical downscaling, the information — such as deformation, energy and other important parameters — were captured in the atomistic region under the applied force at micro and macro regions. A two-dimensional plate of neat epoxy was considered for demonstration of such multiscale simulation platform. The region of interest in the 2D plate was interfaced with atomistic model by applying the proposed hierarchical coupling method. The results show reasonable consistency between PD and MD simulations.

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30

Buehler, Markus J. "Mesoscale modeling of mechanics of carbon nanotubes: Self-assembly, self-folding, and fracture." Journal of Materials Research 21, no. 11 (November 2006): 2855–69. http://dx.doi.org/10.1557/jmr.2006.0347.

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Using concepts of hierarchical multiscale modeling, we report development of a mesoscopic model for single-wall carbon nanotubes with parameters completely derived from full atomistic simulations. The parameters in the mesoscopic model are fit to reproduce elastic, fracture, and adhesion properties of carbon nanotubes, in this article demonstrated for (5,5) carbon nanotubes. The mesoscale model enables modeling of the dynamics of systems with hundreds of ultralong carbon nanotubes over time scales approaching microseconds. We apply our mesoscopic model to study self-assembly processes, including self-folding, bundle formation, as well as the response of bundles of carbon nanotubes to severe mechanical stimulation under compression, bending, and tension. Our results with mesoscale modeling corroborate earlier results, suggesting a novel self-folding mechanism, leading to creation of racket-shaped carbon nanotube structures, provided that the aspect ratio of the carbon nanotube is sufficiently large. We find that the persistence length of the (5,5) carbon nanotube is on the order of a few micrometers in the temperature regime from 300 to 1000 K.

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31

CHAN, ELAINE R., LIN C. HO, and SHARON C. GLOTZER. "MESOSCALE COMPUTER SIMULATIONS OF POLYMER-TETHERED ORGANIC/INORGANIC NANOCUBE SELF-ASSEMBLY." International Journal of Modern Physics C 20, no. 09 (September 2009): 1443–56. http://dx.doi.org/10.1142/s0129183109014503.

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A molecular simulation study of the mesoscale self-assembly of tethered nanoparticles having a cubic geometry is presented. Minimal models of the tethered nanocubes are developed to represent a polyhedral oligomeric silsesquioxane (POSS) molecule with polymeric substituents. The models incorporate some of the essential structural features and interaction specificity of POSS molecules, and facilitate access to the long length and timescales pertinent to the assembly process while foregoing atomistic detail. The types of self-assembled nanostructures formed by the tethered nanocubes in solution are explored via Brownian dynamics simulations using these minimal models. The influence of various parameters, including the conditions of the surrounding medium, the molecular weight and chemical composition of the tether functionalities, and the number of tethers on the nanocube, on the formation of specific structures is demonstrated. The role of cubic nanoparticle geometry on self-assembly is also assessed by comparing the types of structures formed by tethered nanocubes and by their flexible coil triblock copolymer and tethered nanosphere counterparts. Morphological phase diagrams are proposed to describe the behavior of the tethered nanocubes.

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32

Root, Seth, Thomas A. Haill, J. Matthew D. Lane, Aidan P. Thompson, Gary S. Grest, Diana G. Schroen, and Thomas R. Mattsson. "Shock compression of hydrocarbon foam to 200 GPa: Experiments, atomistic simulations, and mesoscale hydrodynamic modeling." Journal of Applied Physics 114, no. 10 (September 14, 2013): 103502. http://dx.doi.org/10.1063/1.4821109.

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33

Santangelo, Giuseppe, Andrea Di Matteo, Florian Müller-Plathe, and Giuseppe Milano. "From Mesoscale Back to Atomistic Models: A Fast Reverse-Mapping Procedure for Vinyl Polymer Chains." Journal of Physical Chemistry B 111, no. 11 (March 2007): 2765–73. http://dx.doi.org/10.1021/jp066212l.

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Komarov, P. V., I. N. Veselov, P. P. Chu, P. G. Khalatur, and A. R. Khokhlov. "Atomistic and mesoscale simulation of polymer electrolyte membranes based on sulfonated poly(ether ether ketone)." Chemical Physics Letters 487, no. 4-6 (March 2010): 291–96. http://dx.doi.org/10.1016/j.cplett.2010.01.049.

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35

Karatrantos, Argyrios, Nigel Clarke, and Martin Kröger. "Modeling of Polymer Structure and Conformations in Polymer Nanocomposites from Atomistic to Mesoscale: A Review." Polymer Reviews 56, no. 3 (January 8, 2016): 385–428. http://dx.doi.org/10.1080/15583724.2015.1090450.

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36

Domain, Christophe. "Multiscale Modelling of Microstructure Evolution under Radiation Damage of Steels Based on Atomistic to Mesoscale Methods." EPJ Web of Conferences 51 (2013): 02004. http://dx.doi.org/10.1051/epjconf/20135102004.

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37

Moldovan†, Dorel, Dieter Wolf‡, and Simon R. Phillpot. "Linking atomistic and mesoscale simulations of nanocrystalline materials: quantitative validation for the case of grain growth." Philosophical Magazine 83, no. 31-34 (October 2003): 3643–59. http://dx.doi.org/10.1080/14786430310001603382.

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38

Baimova, Julia A., and Sergey V. Dmitriev. "High-energy mesoscale strips observed in two-dimensional atomistic modeling of plastic deformation of nano-polycrystal." Computational Materials Science 50, no. 4 (February 2011): 1414–17. http://dx.doi.org/10.1016/j.commatsci.2010.11.024.

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39

Peter, Christine, Luigi Delle Site, and Kurt Kremer. "Classical simulations from the atomistic to the mesoscale and back: coarse graining an azobenzene liquid crystal." Soft Matter 4, no. 4 (2008): 859. http://dx.doi.org/10.1039/b717324e.

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40

Berthonneau, Jeremie, Amaël Obliger, Pierre-Louis Valdenaire, Olivier Grauby, Daniel Ferry, Damien Chaudanson, Pierre Levitz, Jae Jin Kim, Franz-Josef Ulm, and Roland J. M. Pellenq. "Mesoscale structure, mechanics, and transport properties of source rocks’ organic pore networks." Proceedings of the National Academy of Sciences 115, no. 49 (November 15, 2018): 12365–70. http://dx.doi.org/10.1073/pnas.1808402115.

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Organic matter is responsible for the generation of hydrocarbons during the thermal maturation of source rock formation. This geochemical process engenders a network of organic hosted pores that governs the flow of hydrocarbons from the organic matter to fractures created during the stimulation of production wells. Therefore, it can be reasonably assumed that predictions of potentially recoverable confined hydrocarbons depend on the geometry of this pore network. Here, we analyze mesoscale structures of three organic porous networks at different thermal maturities. We use electron tomography with subnanometric resolution to characterize their morphology and topology. Our 3D reconstructions confirm the formation of nanopores and reveal increasingly tortuous and connected pore networks in the process of thermal maturation. We then turn the binarized reconstructions into lattice models including information from atomistic simulations to derive mechanical and confined fluid transport properties. Specifically, we highlight the influence of adsorbed fluids on the elastic response. The resulting elastic energy concentrations are localized at the vicinity of macropores at low maturity whereas these concentrations present more homogeneous distributions at higher thermal maturities, due to pores’ topology. The lattice models finally allow us to capture the effect of sorption on diffusion mechanisms with a sole input of network geometry. Eventually, we corroborate the dominant impact of diffusion occurring within the connected nanopores, which constitute the limiting factor of confined hydrocarbon transport in source rocks.

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41

Kravchyk, Kostiantyn V., Laura Piveteau, Riccarda Caputo, Meng He, Nicholas P. Stadie, Maryna I. Bodnarchuk, Rainer T. Lechner, and Maksym V. Kovalenko. "Colloidal Bismuth Nanocrystals as a Model Anode Material for Rechargeable Mg-Ion Batteries: Atomistic and Mesoscale Insights." ACS Nano 12, no. 8 (August 7, 2018): 8297–307. http://dx.doi.org/10.1021/acsnano.8b03572.

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42

Hanson, D. E. "A mesoscale strength model for silica-filled polydimethylsiloxane based on atomistic forces obtained from molecular dynamics simulations." Journal of Chemical Physics 113, no. 17 (November 2000): 7656–62. http://dx.doi.org/10.1063/1.1313536.

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43

Gabriel, Joshua J., Noah H. Paulson, Thien C. Duong, Francesca Tavazza, Chandler A. Becker, Santanu Chaudhuri, and Marius Stan. "Uncertainty Quantification in Atomistic Modeling of Metals and Its Effect on Mesoscale and Continuum Modeling: A Review." JOM 73, no. 1 (October 26, 2020): 149–63. http://dx.doi.org/10.1007/s11837-020-04436-6.

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Reina, C., L. Sandoval, and J. Marian. "Mesoscale computational study of the nanocrystallization of amorphous Ge via a self-consistent atomistic phase-field model." Acta Materialia 77 (September 2014): 335–51. http://dx.doi.org/10.1016/j.actamat.2014.06.009.

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Rabias, Ioannis, Cyril Langlois, Astero Provata, Brendan J. Howlin, and Doros N. Theodorou. "Linking the atomistic scale and the mesoscale: molecular orbital and solid state packing calculations on poly(p-phenylene)." Polymer 43, no. 1 (January 2002): 185–93. http://dx.doi.org/10.1016/s0032-3861(01)00587-0.

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De Nicola, Antonio, Toshihiro Kawakatsu, Camillo Rosano, Massimo Celino, Mattia Rocco, and Giuseppe Milano. "Self-Assembly of Triton X-100 in Water Solutions: A Multiscale Simulation Study Linking Mesoscale to Atomistic Models." Journal of Chemical Theory and Computation 11, no. 10 (August 28, 2015): 4959–71. http://dx.doi.org/10.1021/acs.jctc.5b00485.

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Laurini, Erik, Domenico Marson, Maurizio Fermeglia, and Sabrina Pricl. "In silico design of self-assembly nanostructured polymer systems by multiscale molecular modeling." Science, Technology and Innovation 6, no. 3 (September 17, 2019): 1–10. http://dx.doi.org/10.5604/01.3001.0013.4795.

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The fast development of digitalization and computational science is opening new possibilities for a rapid design of new materials. Computational tools coupled with focused experiments can be successfully used for the design of new nanostructured materials in different sectors, particularly in the area of biomedical applications. This paper starts with a general introduction on the future of computational tools for the design of new materials and introduces the paradigm of multiscale molecular modeling. It then continues with the description of the multiscale (i.e., atomistic, mesoscale and finite element calculations) computational recipe for the prediction of novel materials and structures for biomedical applications. Finally, the comparison of in silico and experimental results on selected systems of interest in the area of life sciences is reported and discussed. The quality of the agreement obtained between virtual and real data for such complex systems indeed confirms the validity of computational tools for the design of nanostructured polymer systems for biomedical applications.

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Chiu, Ming, Tak W. Kee, and David M. Huang. "Coarse-Grained Simulations of the Effects of Chain Length, Solvent Quality, and Chemical Defects on the Solution-Phase Morphology of MEH-PPV Conjugated Polymers." Australian Journal of Chemistry 65, no. 5 (2012): 463. http://dx.doi.org/10.1071/ch12029.

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A mesoscale coarse-grained model of the conjugated polymer poly(2-methoxy-5-(2′-ethylhexyloxy)-1,4-phenylenevinylene) (MEH-PPV) in implicit solvent is developed. The model is parametrized to reproduce the local structure and dynamics of an atomistic simulation model and accounts for the effects of solvent quality and saturation chemical defects on the polymer structure. Polymers with defect concentrations of 0 to 10 % are simulated using Langevin dynamics in tetrahydrofuran (THF) and in a model poor solvent for chain lengths and solution concentrations used experimentally. The polymer chains are extended in THF and collapse into compact structures in the poor solvent. The radius of gyration decreases with defect content in THF and agrees quantitatively with experiment. The structures formed in poor solvent by chains with 300 monomer units change from toroidal to cylindrical with increasing defect content, while chains containing 1000 monomers form cylinders regardless of defect content. These results have implications for energy transfer in MEH-PPV.

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Chiu, Ming, Tak W. Kee, and David M. Huang. "Corrigendum to: Coarse-Grained Simulations of the Effects of Chain Length, Solvent Quality, and Chemical Defects on the Solution-Phase Morphology of MEH-PPV Conjugated Polymers." Australian Journal of Chemistry 66, no. 4 (2013): 505. http://dx.doi.org/10.1071/ch12029_co.

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Abstract:

A mesoscale coarse-grained model of the conjugated polymer poly(2-methoxy-5-(2'-ethylhexyloxy)-1,4-phenylenevinylene) (MEH-PPV) in implicit solvent is developed. The model is parametrized to reproduce the local structure and dynamics of an atomistic simulation model and accounts for the effects of solvent quality and saturation chemical defects on the polymer structure. Polymers with defect concentrations of 0 to 10 % are simulated using Langevin dynamics in tetrahydrofuran (THF) and in a model poor solvent for chain lengths and solution concentrations used experimentally. The polymer chains are extended in THF and collapse into compact structures in the poor solvent. The radius of gyration decreases with defect content in THF and agrees quantitatively with experiment. The structures formed in poor solvent by chains with 300 monomer units change from toroidal to cylindrical with increasing defect content, while chains containing 1000 monomers form cylinders regardless of defect content. These results have implications for energy transfer in MEH-PPV.

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Truszkowska, A., and M. Porfiri. "Molecular dynamics of ionic polymer-metal composites." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 379, no. 2208 (August 30, 2021): 20200408. http://dx.doi.org/10.1098/rsta.2020.0408.

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Ionic polymer-metal composites (IPMCs) constitute a promising class of soft, active materials with potentially ubiquitous use in science and engineering. Realizing the full potential of IPMCs calls for a deeper understanding of the mechanisms underpinning their most intriguing characteristics: the ability to deform under an electric field and the generation of a voltage upon mechanical deformation. These behaviours are tightly linked to physical phenomena at the level of atoms, including rearrangements of ions and molecules, along with the formation of sub-nanometre thick double layers on the surface of the metal electrodes. Several continuum theories have been developed to describe these phenomena, but their experimental and theoretical validation remains incomplete. IPMC modelling at the atomistic scale could beget valuable support for these efforts, by affording granular analysis of individual atoms. Here, we present a simplified atomistic model of IPMCs based on classical molecular dynamics. The three-dimensional IPMC membrane is constrained by two smooth walls, a simplified analogue of metal electrodes, impermeable only to counterions. The electric field is applied as an additional force acting on all the atoms. We demonstrate the feasibility of simulating counterions’ migration and pile-up upon the application of an electric field, similar to experimental observations. By analysing the spatial configuration of atoms and stress distribution, we identify two mechanisms for stress generation. The presented model offers new insight into the physical underpinnings of actuation and sensing in IPMCs. This article is part of the theme issue ‘Progress in mesoscale methods for fluid dynamics simulation’.

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