Large-scale atomistic simulations, which we define as containing more than 100 000 atoms, are becoming more commonplace as computational resources increase and efficient classical molecular dynamics algorithms are developed. With the advent of grid-computing methods, it is now possible to simulate even larger systems efficiently. Using this new technology, we have simulated montmorillonite clay systems containing up to approximately ten million atoms whose dimensions approach those of a realistic clay platelet. This considerably extends the spatial dimensions of microscopic simulation into a domain normally encountered in mesoscopic simulation. The simulations exhibit emergent behavior with increasing size, manifesting collective thermal motion of clay sheet atoms over lengths greater than 150 Å. This motion produces low-amplitude, long-wavelength undulations of the clay sheets, implicitly inhibited by the small system sizes normally encountered in atomistic simulation. The thermal bending fluctuations allow us to calculate material properties, which are hard to obtain experimentally due to the small size of clay platelets. Montmorillonite is commonly used as a filler in clay−polymer nanocomposites, and estimation of the elastic properties of the composite requires accurate knowledge of the elastic moduli of the components. We estimate the bending modulus to be 1.6 × 10-17 J, corresponding to an in-plane Young's modulus of 230 GPa. We encounter a clay sheet persistence length of approximately 1400 Å, which dampens the undulations at long wavelengths for the largest system in our study.

The intercalation of DNA into layered double hydroxides (LDHs) has various applications, including drug delivery for gene therapy and origins of life studies. The nanoscale dimensions of the interlayer region make the exact conformation of the intercalated DNA difficult to elucidate experimentally. We use molecular dynamics techniques, performed on high performance supercomputing grids, to carry out large-scale simulations of double stranded, linear and plasmid DNA up to 480 base pairs in length intercalated within a magnesium-aluminum LDH. Currently only limited experimental data have been reported for these systems. Our models are found to be in agreement with experimental observations, according to which hydration is a crucial factor in determining the structural stability of DNA. Phosphate backbone groups are found to align with aluminum lattice positions. At elevated temperatures and pressures, relevant to origins of life studies which maintain that the earliest life forms originated around deep ocean hydrothermal vents, the structural stability of LDH-intercalated DNA is substantially enhanced as compared to DNA in bulk water. We also discuss how the materials properties of the LDH are modified due to DNA intercalation.

Layered double hydroxides (LDHs) have generated a large amount of interest in recent years because of their ability to intercalate a multitude of anionic species. Atomistic simulation techniques such as molecular dynamics have provided considerable insight into the behavior of these materials. The advent of supercomputing grids allows us to explore larger-scale models with considerable ease. Here, we present our findings from large-scale molecular dynamics simulations of Mg 2 Al-LDHs intercalated with chloride ions. The largest studied system size consists of one million atoms with lateral dimensions of 588 Å × 678 Å. The system exhibits emergent properties, which are suppressed in smaller-scale simulations. Undulatory modes are caused by the collective thermal motion of atoms in the LDH layers. At length scales larger than 20.7 Å, these thermal undulations cause the LDH sheets to interact and the oscillations are damped. The thermal undulations provide information about the materials properties of the system. In this way, we obtain values for the bending modulus of 8.3 ( 0.4 × 10 -19 J with in-plane Young's moduli of 63.4 ( 0.5 GPa for a hydrated system and 139 ( 1 GPa for the LDH sheets alone.

Layered double hydroxides (LDHs) have been shown to form staged intermediate structures in experimental studies of intercalation. However, the mechanism by which staged structures are produced remains undetermined. Using molecular dynamics simulations, we show that LDHs are flexible enough to deform around bulky intercalants such as deoxyribonucleic acid (DNA). The flexibility of layered materials has previously been shown to affect the pathway by which staging occurs. We explore three possible intermediate structures which may form during intercalation of DNA into Mg2Al LDHs and study how the models differ energetically. When DNA strands are stacked directly on top of each other, the LDH system has a higher potential energy than when they are stacked in a staggered or interstratified structure. It is generally thought that staged intercalation occurs through a Daumas-Herold or a Rudorff model. We find, on average, greater diffusion coefficients for DNA strands in a Daumas-Herold configuration compared to a Rudorff model and a stage-1 structure. Our simulations provide evidence for the presence of peristaltic modes of motion within Daumas-Herold configurations. This is confirmed by spectral analysis of the thickness variation of the basal spacing. Peristaltic modes are more prominent in the Daumas-Herold structure compared to the Rudorff and stage-1 structures and support a mechanism by means of which bulky intercalated molecules such as DNA rapidly diffuse within an LDH interlayer.

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