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Optical matter (OM) systems consist of (nano-)particle constituents in solution that can self-organize into ordered arrays that are bound by electrodynamic interactions. They also manifest non-conservative forces, and the motions of the nano-particles are overdamped; i.e., they exhibit diffusive trajectories. We propose a data-driven approach based on principal components analysis (PCA) to determine the collective modes of non-conservative overdamped systems, such as OM structures, and harmonic linear discriminant analysis (HLDA) of time trajectories to estimate the reaction coordinate for structural transitions. We demonstrate the approach via electrodynamics-Langevin dynamics simulations of six electrodynamically-bound nanoparticles in an incident laser beam. The reaction coordinate we discover is in excellent accord with a rigorous committor analysis, and the identified mechanism for structural isomerization is in very good agreement with the experimental observations. The PCA-HLDA approach to data-driven discovery of reaction coordinates can aid in understanding and eventually controlling non-conservative and overdamped systems including optical and active matter systems., Optical matter consisting of nanoparticle constituents in solution is of key interest due to the exhibited self-assembling mechanisms. The authors propose a principal components analysis based data-driven approach to determine the collective modes of colloidal clusters mimicking optical binding used in colloidal self-assembly.

It is well-known that the interaction between passivated nanoparticles can be tuned by their complete immersion in a chosen solvent, such as water. What remains unclear on a molecular level is how nanoparticle interactions may be altered in the presence of solvent vapor where complete immersion is not achieved. In this paper, we report an all-atom molecular dynamics simulation study of the change in pair potential of mean force between dodecane thiol ligated gold nanoparticles (AuNPs) when exposed to water vapor. With the equilibrium vapor pressure of water at 25 \degree C, there is very rapid condensation of water molecules onto the surface of the AuNPs in the form of mobile clusters of 100-2000 molecules that eventually coalesce into a few large clusters. When the distance between two AuNPs decreases, a water cluster bridging them provides an adhesive force that increases the depth and alters the shape of the pair-potential of mean force. That change of shape includes a decreased curvature near the minimum, consistent with experimental data showing that cyclic exposure to water vapor and its removal reversibly decreases and increases the Young's modulus of a freely suspended self-assembled monolayer of these AuNPs., Comment: 26 pages, 11 figures. Accepted for publication in JCP

The search for local structures within a disordered medium has led to proposals of several methods for probing transient short-range symmetry in a homogeneous mono-atomic liquid. We offer a comparison of different characterizations of such local structure in an in-homogeneous liquid. We simulate the interfaces between a Lennard-Jones liquid and (i) a flat Lennard-Jones wall, (ii) a wall of face-centered cubic-packed Lennard-Jones particles, and (iii) a Lennard-Jones vapor. The interface density distributions in cases (i) and (ii) have oscillations extending several particle diameters into the bulk liquid, while that in case (iii) the interface density distribution monotonically decays from the bulk liquid to the vapor. We search for transient ordered fluctuations, which we identify with local ordered structures, using the Aperture Cross Correlation Function of the system. We find that only particles in the FCC-liquid interface that are in the two layers closest to the FCC surface exhibit preferred four-fold symmetry. Furthermore, the absence of three- or five-fold symmetry peaks in the Aperture Cross Correlation Function of the liquid-vapor interface yields a different picture of that interface than derived from the high density of bi-pyramidal clusters found in the Topological Cluster Classification study (Molecular Physics, 109 (7-10), 1393-1402 (2011)). While the Aperture Cross Correlation Function results need not be viewed as contradictory with the Topological Cluster Classification results, we argue the advantages of using the former to characterize transient ordered fluctuations as being both experimentally accessible in favorable cases and not reliant on a list of structures.

Supplemental Material

We report the structure of transient fluctuations in the liquid phase of a two-dimensional system that exhibits several ordered phases with different symmetries. The density-temperature phase diagram of the system studied, composed of particles with a repulsive shouldered soft-core pair interaction, has regions with stable liquid and hexatic phases, a square solid phase, two separate hexagonal solid phases and a quasi-crystalline phase with 12-fold symmetry. The structure of a fluctuation was determined by computing the same-time aperture cross correlation function of particle configurations. Along a low-temperature isotherm that intersects all the ordered phases we find that the liquid phase exhibits structured fluctuation with hexagonal symmetry near both liquid-hexatic transition lines. Along the same isotherm and in the stable liquid between the lower density hexatic-to-liquid and the higher density liquid-to-square solid transitions, we find that transient hexagonal ordered fluctuations dominate the liquid region near the hexatic-to-liquid transition and square ordered fluctuations dominate the liquid region near the liquid-to square solid transition, but that both structured fluctuations occur at all densities between these transition lines. At a higher temperature, at phase points in the liquid above but close to the density maximum of an underlying transition, there are ordered fluctuations that can be correlated with the structure of the lower temperature phase., Comment: 35 pages, 16 figures

We investigate the response of a dense monodisperse quasi-two-dimensional (q2D) colloid suspension when a particle is dragged by a constant velocity optical trap. Consistent with microrheological studies of other geometries, the perturbation induces a leading density wave and trailing wake, and we use Stokesian Dynamics (SD) simulations to parse direct colloid-colloid and hydrodynamic interactions. We go on to analyze the underlying individual particle-particle collisions in the experimental images. The displacements of particles form chains reminiscent of stress propagation in sheared granular materials. From these data, we can reconstruct steady-state dipolar flow patterns that were predicted for dilute suspensions and previously observed in granular analogs to our system. The decay of this field differs, however, from point Stokeslet calculations, indicating that the finite size of the colloids is important. Moreover, there is a pronounced angular dependence that corresponds to the surrounding colloid structure, which evolves in response to the perturbation. Put together, our results show that the response of the complex fluid is highly anisotropic owing to the fact that the effects of the perturbation propagate through the structured medium via chains of colloid-colloid collisions.