James L. Suter

Computer simulation study of the structural stability and materials properties of DNA-intercalated layered double hydroxides

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.

Recent advances in large-scale atomistic and coarse-grained molecular dynamics simulation of clay minerals

We review the recent advances in large-scale and coarse-grained molecular dynamics applied to clay minerals. Recent advances in local and distributed high performance computational resources together with the development of efficient parallelized algorithms has enabled the simulation of increasingly realistic large-scale models of clay mineral systems. Using this improved technology, it is becoming possible to simulate realistic clay platelet sizes at an atomistic level. This has considerably extended the spatial dimensions of microscopic simulation into a domain normally encountered in mesoscopic simulation. The simulation of large-scale model systems is important to further study complex phenomena, such as the structural and mechanical properties of disordered layered materials such as clays. In order to achieve even larger length and longer time-scales coarse-grained methods are increasingly employed, capturing phenomena such as composite failure modes and intercalation.

Role of Host Layer Flexibility in DNA Guest Intercalation Revealed by Computer Simulation of Layered Nanomaterials

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.

Chemically Specific Multiscale Modeling of Clay–Polymer Nanocomposites Reveals Intercalation Dynamics, Tactoid Self‐Assembly and Emergent Materials Properties

A quantitative description is presented of the dynamical process of polymer intercalation into clay tactoids and the ensuing aggregation of polymer-entangled tactoids into larger structures, obtaining various characteristics of these nanocomposites, including clay-layer spacings, out-of-plane clay-sheet bending energies, X-ray diffractograms, and materials properties. This model of clay–polymer interactions is based on a three-level approach, which uses quantum mechanical and atomistic descriptions to derive a coarse-grained yet chemically specific representation that can resolve processes on hitherto inaccessible length and time scales. The approach is applied to study collections of clay mineral tactoids interacting with two synthetic polymers, poly(ethylene glycol) and poly(vinyl alcohol). The controlled behavior of layered materials in a polymer matrix is centrally important for many engineering and manufacturing applications. This approach opens up a route to computing the properties of complex soft materials based on knowledge of their chemical composition, molecular structure, and processing conditions.

Computer simulation study of the materials properties of intercalated and exfoliated poly(ethylene)glycol clay nanocomposites

Very large-scale molecular dynamics simulations are performed to investigate the effects of montmorillonite clay filler on poly(ethylene) glycol in the formation of clay-polymer nanocomposites. We present the results of MD simulations of intercalated and exfoliated nanocomposites at sizes which approach those of a realistic clay platelet. The simulations allow us to determine the difference between polymer adsorbed on the surface of the clay and that more remote from it. All polymers arrange themselves in layers parallel to the surface, each layer being approximately 4 A thick. We find the polymer conformation of the inner-most layer is distinct, due to complexation with the counterions found near the charged clay surface. The diffusion of polymer within this layer is much lower than that of others layers, which effectively increases the size of the nanofiller and makes gas permeation more tortuous. We perform non-equilibrium molecular dynamics simulations by imposing a strain on the model and analysing the stress response. By partitioning the stress response into clay and different polymer layers, we find that the inner-most polymer layer has a much higher Youngs modulus than the remaining layers in the direction of the polymer chains.

Rule based design of clay-swelling inhibitors

In oil and gas drilling operations, drilling fluids perform essential tasks such as lubricating the drill bit, providing hydrostatic pressure and removing drill cuttings. One important function of the drilling fluid is to stop compacted clay minerals, commonly encountered in drilling operations, from taking up water from the drilling fluids and consequently swelling. Such a scenario can have an adverse impact on drilling operations and may lead to significantly increased oil well construction costs. With increasingly stringent environmental guidelines determining which swelling inhibitors are available for use in the oilfield as drilling fluid additives, there is a need to fully understand the mechanisms of clay hydration in order to design new swelling inhibitors which conform to evolving regulations. Using a range of computational techniques and analysis, combined with known experimental results, we have devised a set of “rule-based” design criteria for clay-swelling inhibitors. To achieve this, we have formulated a hydration energy parameter, which assesses the changes in energy during the step-wise progression from mono- to bi- to trilayers of water in the clay sheet galleries. This parameter can be used to rationalise and predict the swelling profiles for clays containing both cationic and neutral clay swelling inhibitors. The rules we have devised are as follows: (i) Cationic inhibitors should be able to replace sodium ions in the interlayer. (ii) Cationic inhibitors should possess a water soluble, hydrophobic backbone. (iii) Cationic inhibitors should have primary di-amine or mono-quaternary amine functionality. (iv) Cationic inhibitors should have little alcohol functionality. (v) The hydrophobic backbone of the cationic inhibitor should be long enough to form a dense monolayer in the interlayer. (vi) For neutral inhibitors, the inhibitor should be a water soluble organic molecule of low molecular weight with well defined domains of relatively high hydrophobicity and small domains of hydrophobicity. Our “rule-based” criteria will facilitate the rational design of improved—and more environmentally acceptable—clay swelling inhibitors for oilfield drilling operations.

Performance of distributed multiscale simulations

Multiscale simulations model phenomena across natural scales using monolithic or component-based code, running on local or distributed resources. In this work, we investigate the performance of distributed multiscale computing of component-based models, guided by six multiscale applications with different characteristics and from several disciplines. Three modes of distributed multiscale computing are identified: supplementing local dependencies with large-scale resources, load distribution over multiple resources, and load balancing of small- and large-scale resources. We find that the first mode has the apparent benefit of increasing simulation speed, and the second mode can increase simulation speed if local resources are limited. Depending on resource reservation and model coupling topology, the third mode may result in a reduction of resource consumption.

Influence of surface chemistry and charge on mineral-RNA interactions.

We present the results of large-scale molecular simulations, run over several tens of nanoseconds, of 25-mer sequences of single-stranded ribonucleic acid (RNA) in bulk water and at the surface of three hydrated positively charged MgAl layered double hydroxide (LDH) minerals. The three LDHs differ in surface charge density, through varying the number of isomorphic Al substitutions. Over the course of the simulations, RNA adsorbs tightly to the LDH surface through electrostatic interactions between the charged RNA phosphate groups and the alumina charge sites present in the LDH sheet. The RNA strands arrange parallel to the surface with the base groups aligning normal to the surface and exposed to the bulk aqueous region. This templating effect makes LDH a candidate for amplifying the population of a known RNA sequence from a small number of RNAs. The structure and interactions of RNA at a positively charged, hydroxylated LDH surface were compared with those of RNA at a positively charged calcium montmorillonite surface, allowing us to establish the comparative effect of complexation and water structure at hydroxide and silicate surfaces. The systems were studied by computing radial distribution functions, atom density plots, and radii of gyration, as well as visualization. An observation pertinent to the role of these minerals in prebiotic chemistry is that, for a given charge density on the mineral surface, different genetic sequences of RNA adopt different configurations.

Real science at the petascale

We describe computational science research that uses petascale resources to achieve scientific results at unprecedented scales and resolution. The applications span a wide range of domains, from investigation of fundamental problems in turbulence through computational materials science research to biomedical applications at the forefront of HIV/AIDS research and cerebrovascular haemodynamics. This work was mainly performed on the US TeraGrid ‘petascale’ resource, Ranger, at Texas Advanced Computing Center, in the first half of 2008 when it was the largest computing system in the world available for open scientific research. We have sought to use this petascale supercomputer optimally across application domains and scales, exploiting the excellent parallel scaling performance found on up to at least 32 768 cores for certain of our codes in the so-called ‘capability computing’ category as well as high-throughput intermediate-scale jobs for ensemble simulations in the 32–512 core range. Furthermore, this activity provides evidence that conventional parallel programming with MPI should be successful at the petascale in the short to medium term. We also report on the parallel performance of some of our codes on up to 65 636 cores on the IBM Blue Gene/P system at the Argonne Leadership Computing Facility, which has recently been named the fastest supercomputer in the world for open science.

Determining materials properties of natural composites using molecular simulation

Layered double hydroxides (LDHs) have a wide range of potential uses due to their ability to intercalate anionic species, including poly-anionic biopolymers. Atomistic simulations can provide considerable insight into these nano-structured materials, particularly given the recent advance in high-performance computing facilities and scalable simulation codes that has enabled simulations virtually free of finite size effects. In this work we present our findings of large-scale (>100 000 atoms) molecular dynamics simulations of Mg–Al LDHs intercalated with alginate oligomers. We have investigated the effect of two different alginate oligomer chain lengths upon the materials properties of these LDH composites. In addition to this we have explored finite size effects through the use of three different system sizes for each alginate oligomer, the largest of which contains ∼240 000 atoms. We estimate the average bending modulus of the systems to be 3 × 10−19 J. However, we find the smallest alginate oligomer in our study dampens the undulations of the LDH sheets at long wavelengths, which confers a greater interlayer compressibility due to the small alginate molecules bridging the interlayer spacing. The initial orientation of larger alginate oligomers is found to have an impact on the Youngs moduli of the composite materials over the timescales considered in this work. We find the average in-plane Youngs modulus to be approximately 40 GPa for the total composite materials and 135 GPa for the LDH sheets alone.