Due to their unique geometry complex, self-assembled nanoporous 2D molecular crystals offer a broad landscape of potential applications, ranging from adsorption and catalysis to optoelectronics, substrate processes, and future nanomachine applications. Here we report and discuss the results of extensive all-atom Molecular Dynamics (MD) investigations of self-assembled organic monolayers (SAOM) of interdigitated 1,3,5-tristyrilbenzene (TSB) molecules terminated by alkoxy peripheral chains Cn containing n carbon atoms (TSB3,5-Cn) deposited onto highly ordered pyrolytic graphite (HOPG). In vacuo structural and electronic properties of the TSB3,5-Cn molecules were initially determined using ab initio second order Moller-Plesset (MP2) calculations. The MD simulations were then used to analyze the behavior of the self-assembled superlattices, including relaxed lattice geometry (in good agreement with experimental results) and stability at ambient temperatures. We show that the intermolecular disordering of the TSB3,5-Cn monolayers arises from competition between decreased rigidity of the alkoxy chains (loss of intramolecular order) and increased stabilization with increasing chain length (afforded by interdigitation). We show that the inclusion of guest organic molecules (e.g., benzene, pyrene, coronene, hexabenzocoronene) into the nanopores (voids formed by interdigitated alkoxy chains) of the TSB3,5-Cn superlattices stabilizes the superstructure, and we highlight the importance of alkoxy chain mobility and available pore space in the dynamics of the systems and their potential application in selective adsorption.

Nano-porous two-dimensional molecular crystals, self-assembled on atomically flat host surfaces offer a broad range of possible applications, from molecular electronics to future nano-machines. Computer-assisted designing of such complex structures requires numerically intensive modeling methods. Here we present the results of extensive, fully atomistic simulations of self-assembled monolayers of interdigitated molecules of 1,3,5-tristyrilbenzene substituted by C6 alkoxy peripheral chains (TSB3,5-C6), deposited onto highly-ordered pyrolytic graphite. Structural and electronic properties of the TSB3,5-C6 molecules were determined from ab initio calculations, then used in Molecular Dynamics simulations to analyze the mechanism of formation, epitaxy, and stability of the TSB3,5-C6 nanoporous superlattice. We show that the monolayer disordering results from the competition between flexibility of the C6 chains and their stabilization by interdigitation. The inclusion of guest molecules (benzene and pyrene) into superlattice nanopores stabilizes the monolayer. The alkoxy chain mobility and available pore space defines the systems dynamics, essential for potential application.

We present the results of extensive Monte Carlo simulations of intercalated manganese-titanium (Mn-Ti) layered TiS2 crystals. The computational model involves mixtures of Mn and Ti in various percentages placed on a triangular lattice with fixed lattice sites and up to five layers. The range of concentrations of intercalated Mn studied was 5%  ⩽  X Mn  ⩽  33% and for Ti, 0%  ⩽  X Ti  ⩽  15%, where X A denotes the percentage of the total number of lattice sites occupied by species A. The species are allowed to interact spatially through a screened Coulomb potential and magnetically with external and RKKY field terms. Structurally, the pure Mn systems present as disordered at very low densities and evolve through a 2  ×  2 structure (perfect at X Mn  =  25%) up to a [Formula: see text]  ×  [Formula: see text] lattice (perfect at X Mn  =  33%), with variations of the two 'perfect' lattice structures depending on density. Changes in density for pure Mn systems as well as those intercalated with both Mn and Ti dramatically affects the system's structural and magnetic properties, and the magnetic behavior of various morphological features present in the system are discussed. The RKKY interaction is adjusted based on the intercalant compositions and is very sensitive to structural variations in the intercalant layers. The composition ranges studied here encompass and exceed those that are experimentally accessible, which helps place experimentally relevant densities in perspective.

The efficient storage and transportation of natural gas is one of the most important enabling technologies for use in energy applications. Adsorption in porous systems, which will allow the transportation of high-density fuel under low pressure, is one of the possible solutions. We present and discuss extensive grand canonical Monte Carlo (GCMC) simulation results of the adsorption of methane into slit-shaped graphitic pores of various widths (between 7 angstrom and 50 angstrom), and at pressures P between 0 bar and 360 bar. Our results shed light on the dependence of film structure on pore width and pressure. For large widths, we observe multi-layer adsorption at supercritical conditions, with excess amounts even at large distances from the pore walls originating from the attractive interaction exerted by a very high-density film in the first layer. We are also able to successfully model the experimental adsorption isotherms of heterogeneous activated carbon samples by means of an ensemble average of the pore widths, based exclusively on the pore-size distributions (PSD) calculated from subcritical nitrogen adsorption isotherms. Finally, we propose a new formula, based on the PSD ensemble averages, to calculate the isosteric heat of adsorption of heterogeneous systems from singlepore-width calculations. The methods proposed here will contribute to the rational design and optimization of future adsorption-based storage tanks.

We present the results of extensive fully atomistic molecular dynamics (MD) simulations of tetracosane (C24H50) bilayer and trilayer systems adsorbed onto the basal plane of graphite. At low temperature, both layers of the bilayer exist in well-defined solid phases. With increasing temperature, the system exhibits separated smectic phases that eventually lead to melting. During this process, we observed a strong interlayer translational correlation and mobility between layers; however, the upper layer presents more intra- (chain) and intermolecular disorder because of a lack of confinement and a greater distance to the graphite substrate. Simulations of the perpendicular trilayer patch show that gauche defects provide the main mechanism for spreading of the bottom and outer perimeter of the patch in the solid, leading to the ultimate collapse of the patch with increasing temperature and formation of a flat (parallel) trilayer that melts at a higher temperature than the bilayer structure. The wide variety ...

Heterogeneity in dopant concentration has long been important to the electronic properties in chemically doped materials. In this work, we experimentally demonstrate that during the chemical vapor deposition process, in contrast to three-dimensional polycrystals, the substitutional nitrogen atoms avoid crystal grain boundaries and edges over micron length scales while distributing uniformly in the interior of each grain. This phenomenon is universally observed independent of the details of the growth procedure such as temperature, pressure, substrate, and growth precursor.

We have investigated the low-temperature spin-glasslike phase in the intercalated transition-metal dichalcogenide Mn${}_{0.09}$Ti${}_{1.1}$S${}_{2}$. A departure from Curie--Weiss behavior in the paramagnetic regime indicated the formation of small ferromagnetically correlated clusters. The Vogel--Fulcher law provided an excellent description of relaxation times in the vicinity of the transition, showing that the glasslike phase occurs due to interaction between the clusters. Cole--Cole plots for data close to the transition were linear, which is consistent with a simple exponential distribution of cluster sizes. A Monte Carlo simulation of the dichalcogenide system, including excess self-intercalated Ti ions, gave an exponential cluster-size distribution for a relatively narrow range of concentration values of Mn and Ti ions, values that were consistent with those of the Mn${}_{0.09}$Ti${}_{1.1}$S${}_{2}$ sample. Strong commonality in the relaxation behavior with certain ferroelectric relaxor systems suggests underlying similarity in the microscopic structure of the clusters in both systems, which may be chainlike or quasi-one-dimensional.

Graphene single layers grown by chemical vapor deposition on single crystal Cu substrates are subject to nonuniform physisorption strains that depend on the orientation of the Cu surface. The strains are revealed in Raman spectra and quantitatively interpreted by molecular dynamics (MD) simulations. An average compressive strain on the order of 0.5% is determined in graphene on Cu(111). In graphene on Cu (100), MD simulations interpret the observed highly nonuniform strains.

Multiple microscopic techniques have been employed to study Mn-intercalated Ti1+delta S2 at different length scales. The introduction of Mn intercalates resulted in the formation of two distinct types of one-dimensional structures; both exhibited extremely high aspect ratios, with lengths exceeding hundreds of micrometers. The smaller of the two features were only a few nanometers wide, while the larger one-dimensional structures had widths on the order of magnitude of one hundred nanometers. The one-dimensional structures were detected on samples with a range of Mn-doping levels but were especially common in samples with a 15% Mn-doping concentration. In these samples, a high density of parallel linear structures could be found at lengths ranging from the nanometer to micrometer scale. One-dimensional structures were never found in Ti1+delta S2 samples without Mn dopants. We utilized Monte Carlo simulations to better understand these structures, which arise from interactions between the two species of intercalates in the system: Mn ions and excess Ti ions bound to intercalation sites. While the arrangement of intercalated ions has no long-range order, interactions between various nanoscale domains leads to the formation of domain-wall-like structures extending over macroscopic distances.

We present a versatile three – dimensional two – phase model for simulating snow drift relocation around buildings utilizing deflection fins of various shapes and sizes. The first phase involves numerically obtaining the air velocity profile around the building and fin using a velocity – pressure Navier – Stokes algorithm, while the second phase involves direct classical simulation of snowfall with particle – particle, particle – surface and one – way particle – gusting wind interactions introduced to control accumulation, erosion, clumping and drifting. Because the simulation technique is direct, it is potentially useful for storms and surfaces with widely varying conditions. We are also able to consider the effect of crosswinds.

The results of extensive molecular dynamics simulations and theoretical considerations of the adsorption of methane–methyl mercaptan mixtures in slit-shaped carbon nanopores are presented. We observe significant mobility of both methane and mercaptan molecules within the pore volume, between pores, and between adsorbed and gas phases for a wide range of temperatures and pressures. Although mercaptans adsorb preferentially relative to methane, the process remains reversible, provided non-oxidizing conditions are maintained. A mercaptan/methane ratio of the order of 200ppm in the adsorbed phase is sufficient for the gas phase to have a mercaptan concentration above the human threshold for detection. The reversibility of the adsorption process and low concentration of mercaptans makes it unlikely that these would be harmful for adsorbed natural gas storage systems.

All-atom molecular dynamics (MD) computer simulations of C-60 fullerene patches adsorbed onto graphite are conducted at various coverages for very low temperatures. There appears to be a hindered tumbling rotational transition through T <= 20 K seen in the simulations that accompanies dramatic lattice expansion and configurational energy change with temperature in the adlayer. Moreover, the transition is unique in that it appears to be continuous and understandable on the basis of very simple dynamical arguments. The results suggest that such behavior could be present and influential in a wide range of molecules whose dynamical (time averaged) shapes are very close to their static symmetry, in contrast to surface systems with lower symmetry constituents and sharp rotational transitions. The transition is also observed in annealed, percolating adlayers and its dependence on lattice topology is discussed.

We present results of molecular dynamics computer simulations of hexane (C6H14 or C6) and pentane (C5H12 or C5) adlayers physisorbed onto a graphite substrate, for various submonolayer coverages. The hexane and pentane molecules incorporate explicit hydrogens and the graphite is modelled as a six-layer all-atom structure. Even though C6 and C5 have different structures at monolayer completion, both systems generally behave similarly in the submonolayer regime and results are in reasonable agreement with experiment for both systems. Specifically, there are four distinct topological regimes involving empty space: at densities closest to full coverage, there are large domains with individual vacancies, then with decreasing density, large vacancy patches appear first, followed by the formation of connected networks of smaller domains with multiple orientations that ultimately separate into individual patches. The energetics and melting behaviour of all systems are readily understood within the framework of the topology presented at various densities.

The two-dimensional Material Point Method (MPM) algorithm outlined by Chen and Brannon has been extended to three dimensions. The development of the code is discussed as well as applications for simulating bullet impact on biological and non-biological systems.