disLocate: tools to rapidly quantify local intermolecular structure to assess two-dimensional order in self-assembled systems

Abstract

Order classification is particularly important in photonics, optoelectronics, nanotechnology, biology, and biomedicine, as self-assembled and living systems tend to be ordered well but not perfectly. Engineering sets of experimental protocols that can accurately reproduce specific desired patterns can be a challenge when (dis)ordered outcomes look visually similar. Robust comparisons between similar samples, especially with limited data sets, need a finely tuned ensemble of accurate analysis tools. Here we introduce our numerical Mathematica package disLocate, a suite of tools to rapidly quantify the spatial structure of a two-dimensional dispersion of objects. The full range of tools available in disLocate give different insights into the quality and type of order present in a given dispersion, accessing the translational, orientational and entropic order. The utility of this package allows for researchers to extract the variation and confidence range within finite sets of data (single images) using different structure metrics to quantify local variation in disorder. Containing all metrics within one package allows for researchers to easily and rapidly extract many different parameters simultaneously, allowing robust conclusions to be drawn on the order of a given system. Quantifying the experimental trends which produce desired morphologies enables engineering of novel methods to direct self-assembly.

Universal Transfer Printing of Micelle-Templated Nanoparticles Using Plasma-Functionalized Graphene

“… 2 , 6 , 12 , 43 , 44 The other advantage of reverse micelle deposition (RMD) is the control over the 2D dispersion: highly ordered periodic arrays with varying spacing and organization are achieved with the simple tuning of deposition parameters. 10 , 12 To produce RMD nanoparticles, poly(styrene- b -2-vinyl pyridine) (PS- b -P2VP) diblock copolymer reverse micelles are formed in a nonpolar solvent. To introduce these nanoparticles on to the organic surface, we utilized a transfer method based on a modified graphene layer acting as a mechanical support.…”

“… 2 , 3 , 6 , 8 Reverse micelle templates formed by diblock copolymers offer a high degree of nanoparticle size control with 2D dispersion tuning, for a wide variety of materials. 10 − 13 However, processes for preparing such arrays of colloidal nanoparticles tend not to be universally suitable across the variety of substrates used in electronic devices. In particular, there is a need to use an oxygen or inert gas plasma to remove the polymer shell from around the nanoparticle.…”

Simu-D: A Simulator-Descriptor Suite for Polymer-Based Systems under Extreme Conditions

“…This step can include visualization, including 3-D representation and animation, of the computergenerated system configurations and calculation of relevant quantities through proper interpretation of the raw simulation data. Corresponding suites also exist for interactive visualization, description, and analysis including, among others, ParaView [53], VMD [54], disLocate [55], UCSF chimera [56], OVITO [57], and i-Rheo GT [58].…”

Identification of Local Structure in 2-D and 3-D Atomic Systems through Crystallographic Analysis

“…Significant advances have been made in numerical methods and algorithms enhancing simulation aspects like speed, accuracy, general applicability, user friendliness and robustness. In parallel, advanced software packages are now available that allow efficient atomic/molecular visualization and/or analysis of the computer-generated structures including animation of the corresponding trajectories [5][6][7][8][9]. For crystallization and phase transitions visual inspection is vital as it allows a better understanding of structural changes and provides a preliminary identification of the established ordered morphologies.…”