The debate on whether an organic fluid nanoconfined by mica sheets will undergo a fluid-to-solid transition as the fluid film thickness is reduced below a critical value has lasted over two decades. Extensive experimental and simulation... more
The debate on whether an organic fluid nanoconfined by mica sheets will undergo a fluid-to-solid transition as the fluid film thickness is reduced below a critical value has lasted over two decades. Extensive experimental and simulation investigations have thus far left this question only partially addressed. In this work, we adapt and apply absolute free energy calculations to analyze the phase behavior of a simple model for nanoconfined fluids, consisting of spherical Lennard-Jones (LJ) molecules confined between LJ solid walls, which we use in combination with grand-canonical molecular dynamics simulations. Absolute Helmholtz free energy calculations of the simulated nanoconfined systems directly support the existence of order-disorder phase transition as a function of decreasing wall separation, providing results in close agreement with previous experiments and detailed atomistic simulations.
For many years, the drive towards computational physics studies that match the size and time-scales of experiment has been fueled by increases in processor and interconnect performance that could be exploited with relatively little... more
For many years, the drive towards computational physics studies that match the size and time-scales of experiment has been fueled by increases in processor and interconnect performance that could be exploited with relatively little modification to existing codes. Engineering and electrical power constraints have disrupted this trend, requiring more drastic changes to both hardware and software solutions. Here, we present details of the Cray XK6 architecture that achieves increased performance with the use of GPU accelerators. We review software development efforts in the LAMMPS molecular dynamics package that have been implemented in order to utilize hybrid high performance computers. We present benchmark results for solid-state, biological, and mesoscopic systems and discuss some challenges for utilizing hybrid systems. We present some early workin improving application performance on the XK6 and performance results for the simulation of liquid copper nanostructures with the embedded atom method.
Reconfigurability of two-dimensional colloidal crystal structures assembled by anisometric particles capable of changing their shape were studied by molecular dynamics computer simulation. We show that when particles change shape on cue,... more
Reconfigurability of two-dimensional colloidal crystal structures assembled by anisometric particles capable of changing their shape were studied by molecular dynamics computer simulation. We show that when particles change shape on cue, the assembled structures reconfigure into different ordered structures, structures with improved order, or more densely packed disordered structures, on faster time scales than can be achieved via self-assembly from an initially disordered arrangement. These results suggest that reconfigurable building blocks can be used to assemble reconfigurable materials, as well as to assemble structures not possible otherwise, and that shape shifting could be a promising mechanism to engineer assembly pathways to ordered and disordered structures.
Reconfigurable nanostructures represent an exciting new direction for materials. Applications of reversible transformations between nanostructures induced by molecular conformations under external fields can be found in a broad range of... more
Reconfigurable nanostructures represent an exciting new direction for materials. Applications of reversible transformations between nanostructures induced by molecular conformations under external fields can be found in a broad range of advanced technologies including smart materials, electromagnetic sensors, and drug delivery. With recent breakthroughs in synthesis and fabrication techniques, shape-changing nanoparticles are now possible. Such novel building blocks provide a conceptually new and exciting approach to self-assembly and phase transformations by providing tunable parameters fundamentally different from the usual thermodynamic parameters. Here we investigate via molecular simulation a transformation between two thermodynamically stable structures self-assembled by laterally tethered nanorods whose rod length is switched between two values. Building blocks with longer rods assemble into a square grid structure, while those with short rods form bilayer sheets with internal smectic A ordering at the same thermodynamic conditions. By shortening or lengthening the rods over a short time scale relative to the system equilibration time, we observe a transformation from the square grid structure into bilayer sheets, and vice versa. We also observe honeycomb grid and pentagonal grid structures for intermediate rod lengths. The reconfiguration between morphologically distinct nanostructures induced by dynamically switching the building block shape serves to motivate the fabrication of shape-changing nanoscale building blocks as a new approach to the self-assembly of reconfigurable materials.
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Molecular dynamics (MD) methods compute the trajectory of a system of point particles in response to a potential function by numerically integrating Newtonʼs equations of motion. Extending these basic methods with rigid body constraints... more
Molecular dynamics (MD) methods compute the trajectory of a system of point particles in response to a potential function by numerically integrating Newtonʼs equations of motion. Extending these basic methods with rigid body constraints enables composite particles with complex shapes such as anisotropic nanoparticles, grains, molecules, and rigid proteins to be modeled. Rigid body constraints are added to the GPU-accelerated MD package, HOOMD-blue, version 0.10.0. The software can now simulate systems of particles, rigid bodies, or mixed systems in microcanonical (NVE), canonical (NVT), and isothermal-isobaric (NPT) ensembles. It can also apply the FIRE energy minimization technique to these systems. In this paper, we detail the massively parallel scheme that implements these algorithms and discuss how our design is tuned for the maximum possible performance. Two different case studies are included to demonstrate the performance attained, patchy spheres and tethered nanorods. In typical cases, HOOMD-blue on a single GTX 480 executes 2.5–3.6 times faster than LAMMPS executing the same simulation on any number of CPU cores in parallel. Simulations with rigid bodies may now be run with larger systems and for longer time scales on a single workstation than was previously even possible on large clusters.
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The formation of helical scrolls formed by self-assembly of tethered nanorod amphiphiles and their molecular analogs are investigated. A model bilayer sheet assembled by laterally tethered nanorods is simulated and shown that it can fold... more
The formation of helical scrolls formed by self-assembly of tethered nanorod amphiphiles and their molecular analogs are investigated. A model bilayer sheet assembled by laterally tethered nanorods is simulated and shown that it can fold into distinct helical morphologies under different solvent conditions. The helices can reversibly transform from one morphology to another by dynamically changing the solvent condition. This model serves both to inspire the fabrication of laterally tethered nanorods for assembling helices at nanometer scales and as a proof-of-concept for engineering switchable nanomaterials via hierarchical self-assembly.
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Attachment of flexible coils to the middle of a rigid rod generates T-shaped rod–coil molecules that self-assemble into layers that roll up to form filled cylindrical and hollow tubular scrolls, depending on the coil length, in the solid... more
Attachment of flexible coils to the middle of a rigid rod generates T-shaped rod–coil molecules that self-assemble into layers that roll up to form filled cylindrical and hollow tubular scrolls, depending on the coil length, in the solid state (see picture); the rods are arranged parallel to the layer plane.
We use Brownian dynamics to investigate the self-assembly of single end tethered, laterally tethered, and double end tethered V-shaped nanoparticles. The simulation results are compared with model bent-core molecules without tethers and... more
We use Brownian dynamics to investigate the self-assembly of single end tethered, laterally tethered, and double end tethered V-shaped nanoparticles. The simulation results are compared with model bent-core molecules without tethers and polymer tethered nanorods to elucidate the combined effects of V-shaped geometry and the immiscibility between the V-shaped nanoparticles and the tethers on the self-assembled structures. We show that the V-shaped geometry significantly alters the phase diagram of tethered nanoparticles and further that the immiscibility between particles and tethers leads to structures not previously predicted for bent-core molecules. Examples of mesophases predicted include honeycomb, hexagonally packed cylinders, and perforated lamellar phases.