Modelling of the nanoscale

While all matter is composed of atoms, the organisation of those atoms may differ on the nanoscale. The application of extraordinary experimental tools with remarkable precision has demonstrated this, and highlighted the need for greater quantitative understanding of matter at the nanoscale.

Over the past century advances in computer science have spurred advances in fundamental theoretical techniques, mathematical modelling, and numerical simulation, giving rise to a revolution with extraordinary impact for nanoscience and nanoengineering. In this simulation and modelling themed issue, the development of ab initio methods, density functional algorithms, molecular dynamics, Monte Carlo techniques, and multigrid, multiscale methods are presented. Depending upon the scientific objectives, molecular dynamics and ab initio methods are the prevailing techniques. For large systems, such as DNA and proteins, molecular dynamics is a useful tool for investigating atomic motion. The trajectories of molecules and atoms can be determined empirically using a force field, or one may analyze properties. On the other hand, ab initio quantum mechanical methods are useful in the investigation of the electronic structure of smaller nanoscale materials, by solving Schrödinger equations with the appropriate Hamitonian.¹

In this issue, several important methods for modelling nanoscale matter are reviewed, and new studies are introduced, in the following areas: 1) the interaction between inorganic nanostructures and soft matter, including carbon nanotubes (CNTs) and proteins;^2,3 2) CNT–water interactions;^4–6 3) confinement and catalysis; 4) DNA–nanopore interactions and sequencing;^7,8 5) nanomaterial–environmental interactions; 6) the structure of nanoparticles, and nanomaterials; 7) nucleation, growth and transformation; and 8) the optical properties of nanostructures.^9–13 The aim of the issue is to provide some perspective for the latest developments, and to identify the most promising routes which could lead to a deeper understanding of nanoscale modelling. Our authors have contributed to many of these (aforementioned) areas, and offer both experimental and theoretical points of view.

Sloan and coworkers (DOI: 10.1039/C2NR11621A) have studied the discrete Lindqvist ion [W₆O₁₉]²⁻ encapsulated in a double walled carbon nanotube (DWNT), using both low-voltage aberration-corrected transmission electron microscopy (AC-TEM) and density functional theory (DFT). The DFT calculations on [W₆O₁₉]²⁻ are in very good agreement with experimental measurements of W separations obtained during the high precision imaging. Luan et al. (DOI: 10.1039/C1NR11201E) have reviewed both their experimental and computational efforts on DNA sequencing using a solid state nanopore. Nanopore-based DNA sequencing is a promising candidate for low-cost and high-throughput genome sequencing and personal medicine. In this review, they show how to slow down and control the DNA translocation through the pore.

Li and Mu (DOI: 10.1039/C1NR11108F) have addressed a long standing problem, exploring why guanidinium chloride (GdmCl) has a stronger denaturing power for proteins than urea, using molecular dynamics simulations. They find, for both hydrophobic and charged nanoparticles, 4 M GdmCl shows stronger dissociation capability than 7 M urea, which provides a new and powerful explanation. Lai and Barnard (DOI: 10.1039/C1NR11102G) have examined another important problem, the design of carbon-based nanomaterials for hydrogen storage. They propose that diamond nanoparticles may provide a new promising high temperature candidate with moderate storage capacity, but good potential for recyclability, through extensive electronic structure simulations.

Meanwhile, Fortunelli and coworkers (DOI: 10.1039/C1NR11051A) have studied the propylene partial oxidation by an Ag₃ supported MgO(100) surface, using first principles DFT calculations coupled with reactive global optimization. They find that the presence of an oxide support drastically changes the potential energy landscape of the system, favoring configurations interacting positively with the electrostatic field from the surface, and that the reaction energy barriers are crucial in the competition between thermodynamically and kinetically favored reaction products. Pugno and coworkers (DOI: 10.1039/C2NR11664B) propose an analytical multiscale method based on a fiber bundle model to evaluate the role of hierarchy on structural strength of natural and bio-inspired materials. They find that an increase in the number of hierarchy levels leads to a decrease in the strength of material, while mixing different types of fibers often enhances the strength. Ding and Ma (DOI: 10.1039/C1NR11425E), on the other hand, have investigated interactions between Janus particles and membranes, which are of great importance in drug/gene delivery, using coarse grained dissipative particle dynamics (DPD). Interestingly, they find that there exist two different modes: insertion and engulfment. When the hydrophilic part of the particle is close to the membrane, or the particle has a larger section area and higher hydrophilic coverage, the particle is more likely to be engulfed than inserted. These studies provide significant insight to the design of better nanoparticles for drug delivery.^2–8

In addition, some important topics in nanotechnology have attracted less attention by the modelling community, such as the hazards responsible for nanotoxicity. More than twenty pivotal factors¹⁴ can influence the toxic responses¹⁵ and biomedical functions¹⁶ of a nanomaterial, so a purely experimental approach is both time-consuming and costly. Moreover, combined and synergetic effects of many factors typically render experimental observations inclusive or lead to inconsistent conclusions. Accordingly, theoretical modelling capable of quantitatively understanding, quantitatively analyzing,¹⁷ and predicting nanotoxicity is both a significant challenge and future opportunity.

There are many other interesting works in this special themed issue on nanoscale modelling, which provide new clarity regarding the structure and properties of molecules and materials at nanoscale. We strongly encourage readers to read through all of them. We would like to thank all the authors for their excellent contributions, as well as the referees for their tremendous effort in helping the present guest editors to select these papers, and to improve their final quality.

References

1. S. G. Louie, Conceptual Foundations of Materials: A Standard Model for Ground- and Excited-State Properties; Contemporary Concepts of Condensed Matter Science, Elsevier, New York, 2006.
2. G. Zuo, Q. Huang, G. Wei, R. Zhou and H. Fang, Plugging into proteins: poisoning protein function by a hydrophobic nanoparticle, ACS Nano, 2010, 4, 7508–7514.
3. C. Ge, J. Du, L. Zhao, L. Wang, Y. Liu, D. Li, Y. Yang, R. Zhou, Y. Zhao, Z. Chai and C. Chen, Binding of blood proteins to carbon nanotubes reduces cytotoxicity, Proc. Natl. Acad. Sci. U. S. A., 2011, 108, 16968–16973.
4. J. Li, X. Gong, H. Lu, D. Li, H. Fang and R. Zhou, Electrostatic gating of a nanometer water channel, Proc. Natl. Acad. Sci. U. S. A., 2007, 104, 3687–3692.
5. Y. Tu, P. Xiu, R. Wan, J. Hu, R. Zhou and H. Fang, Water-mediated signal multiplication with Y-shaped carbon nanotubes, Proc. Natl. Acad. Sci. U. S. A., 2009, 106, 18120–18124.
6. Y. Tu, R. Zhou and H. Fang, Signal transmission, conversion and multiplication by polar molecules confined in nanochannels, Nanoscale, 2010, 2, 1976–1983.
7. B. Luan, G. Martyna and G. Stolovitzky, Characterizing and controlling the motion of ssDNA in a solid-state nanopore, Biophys. J., 2011, 101, 2214–2222.
8. B. Luan, H. Peng, S. Polonsky, S. Rossnagel, G. Stolovitzky and G. Martyna, Base-by-base ratcheting of single stranded DNA through a solid-state nanopore, Phys. Rev. Lett., 2010, 104, 238103.
9. Y. W. Son, M. L. Cohen and S. G. Louie, Phys. Rev. Lett., 2006, 97, 216803.
10. X. Zhu and H. B. Su, J. Phys. Chem. C, 2010, 114, 17257.
11. L. Yang, C.-H. Park, Y.-W. Son, M. L. Cohen and S. G. Louie, Phys. Rev. Lett., 2007, 99, 186801.
12. M. Wang and C. M. Li, Nanoscale, 2011, 3, 2324.
13. C. A. Rozzi, D. Varsano, A. Marini, E. K. U. Gross and A. Rubio, Phys. Rev. B: Condens. Matter Mater. Phys., 2006, 73, 205119.
14. Nanotoxicology, ed. Y. Zhao and S. Nalwa, American Scientific Publishers, LA, USA, 2007.
15. X.-J. Liang, H. Meng, Y. Wang, H. He, J. Meng, J. Lu, P. C. Wang, Y. Zhao, X. Gao, B. Sun, C. Chen, G. Xing, D. Shen, M. M. Gottesman, Y. Wu, J.-j. Yin and L. Jia, Metallofullerene nanoparticles circumvent tumor resistance to cisplatin by reactivating endocytosis, Proc. Natl. Acad. Sci. U. S. A., 2010, 107, 7449–7454.
16. Y. Zhao, G. Xing and Z. Chai, Nanotoxicology: Are Carbon Nanotubes Safe?, Nat. Nanotechnol., 2008, 3, 191–192.
17. X. He, Z. Zhang, J. Liu, Y. Ma, P. Zhang, Y. Li, Z. Wu, Y. Zhao and Z. Chai, Quantifying the biodistribution of nanoparticles, Nat. Nanotechnol., 2011, 6, 755.

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