Flat-Histogram Monte Carlo as an Efficient Tool To Evaluate Adsorption Processes Involving Rigid and Deformable Molecules

Monte Carlo simulations are the foundational technique for predicting thermodynamic properties of open systems where the process of interest involves the exchange of particles. Thus, they have been used extensively to computationally evaluate the adsorption properties of nanoporous materials and are critical for the in silico identification of promising materials for a variety of gas storage and chemical separation applications. In this work we demonstrate that a well-known biasing technique, known as "flat-histogram" sampling, can be combined with temperature extrapolation of the free energy landscape to efficiently provide significantly more useful thermodynamic information than standard open ensemble MC simulations. Namely, we can accurately compute the isosteric heat of adsorption and number of particles adsorbed for various adsorbates over an extremely wide range of temperatures and pressures from a set of simulations at just one temperature. We extend this derivation of the temperature extrapolation to adsorbates with intramolecular degrees of freedom when Rosenbluth sampling is employed. Consequently, the working capacity and isosteric heat can be computed for any given combined temperature/pressure swing adsorption process for a large range of operating conditions with both rigid and deformable adsorbates. Continuous thermodynamic properties can be computed with this technique at very moderate computational cost, thereby providing a strong case for its application to the in silico identification of promising nanoporous adsorbents

mahynski/FHMCSimulation: Bugfix for Z-matrix loop

Fixed accelerated Z-matrix loop so all entries are properly recorded

mahynski/DEVProject v1.0.0

Simple project manager script to setup standardized file tree for new revision-controlled projects

Programming Interfacial Porosity and Symmetry with Escherized Colloids

We simultaneously designed the porosity and plane symmetry of self-assembling colloidal films by using isohedral tiles to determine the location and shape of enthalpically interacting surface patches on motifs being functionalized. The symmetries of both the tile and motif determine the plane symmetry group of the final assembly. Previous work has either ignored symmetry considerations altogether or accounted for only the tile’s properties, applicable only when the motif is asymmetric; this approach provides a complete account and enables the design of symmetric colloids using this tile-based approach, which are often more practical to manufacture. We present the methodology, based on the type of the tile, and provide computational tools that enable the automatic classification of all tiles for a given motif and the optimization of the tile to fit the motif, sometimes referred to as “Escherization”

Monte Carlo simulation of cylinders with short-range attractions

Cylindrical or rod-like particles are promising materials for the applications of fillers in nanocomposite materials and additives to control rheological properties of colloidal suspensions. Recent advances in particle synthesis allows for cylinders to be manufactured with short-ranged attractions to study the gelation as a function of packing fraction, aspect ratio and attraction strength. In order to aid in the analysis of small-angle scattering experiments of rod-like particles, computer simulation methods were used to model these particles with specialized Monte Carlo algorithms and tabular superquadric potentials. The attractive interaction between neighboring rods increases with the amount of locally-accessible surface area, thus leading to patchy-like interactions. We characterize the clustering and percolation of cylinders as the attractive interaction increases from the homogenous fluid at relatively low attraction strength, for a variety of aspect ratios and packing fractions. Comparisons with the experimental scattering results are also presented, which are in agreement

Bottom-Up Colloidal Crystal Assembly with a Twist

Globally ordered colloidal crystal lattices have broad utility in a wide range of optical and catalytic devices, for example, as photonic band gap materials. However, the self-assembly of stereospecific structures is often confounded by polymorphism. Small free-energy differences often characterize ensembles of different structures, making it difficult to produce a single morphology at will. Current techniques to handle this problem adopt one of two approaches: that of the “top-down” or “bottom-up” methodology, whereby structures are engineered starting from the largest or smallest relevant length scales, respectively. However, recently, a third approach for directing high fidelity assembly of colloidal crystals has been suggested which relies on the introduction of polymer cosolutes into the crystal phase [Mahynski, N.; Panagiotopoulos, A. Z.; Meng, D.; Kumar, S. K. <i>Nat. Commun.</i> <b>2014</b>, <i>5</i>, 4472]. By tuning the polymer’s morphology to interact uniquely with the void symmetry of a single desired crystal, the entropy loss associated with polymer confinement has been shown to strongly bias the formation of that phase. However, previously, this approach has only been demonstrated in the limiting case of close-packed crystals. Here, we show how this approach may be generalized and extended to complex open crystals, illustrating the utility of this “structure-directing agent” paradigm in engineering the nanoscale structure of ordered colloidal materials. The high degree of transferability of this paradigm’s basic principles between relatively simple crystals and more complex ones suggests that this represents a valuable addition to presently known self-assembly techniques

Directionally Interacting Spheres and Rods Form Ordered Phases

The structures formed by mixtures of dissimilarly shaped nanoscale objects can significantly enhance our ability to produce nanoscale architectures. However, understanding their formation is a complex problem due to the interplay of geometric effects (entropy) and energetic interactions at the nanoscale. Spheres and rods are perhaps the most basic geometrical shapes and serve as convenient models of such dissimilar objects. The ordered phases formed by each of these individual shapes have already been explored, however, when mixed, spheres and rods have demonstrated only limited structural organization to date. Here, we show using experiments and theory that the introduction of directional attractions between rod ends and isotropically interacting spherical nanoparticles (NPs) through DNA base pairing leads to the formation of ordered three-dimensional lattices. The spheres and rods arrange themselves in a complex alternating manner, where the spheres can form either a face-centered cubic (FCC) or hexagonal close-packed (HCP) lattice, or a disordered phase, as observed by <i>in situ</i> X-ray scattering. Increasing NP diameter at fixed rod length yields an initial transition from a disordered phase to the HCP crystal, energetically stabilized by rod-rod attraction across alternating crystal layers, as revealed by theory. In the limit of large NPs, the FCC structure is instead stabilized over the HCP by rod entropy. We, therefore, propose that directionally specific attractions in mixtures of anisotropic and isotropic objects offer insight into unexplored self-assembly behavior of noncomplementary shaped particles