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1. Orientational phase behavior of polymer-grafted nanocubes

   https://doi.org/10.1039/c9nr04859f  

   Lee, Brian Hyun-jong ; Arya, Gaurav ( August 2019 , Nanoscale)

   Surface functionalization of nanoparticles with polymer grafts was recently shown to be a viable strategy for controlling the relative orientation of shaped nanoparticles in their higher-order assemblies. In this study, we investigated in silico the orientational phase behavior of coplanar polymer-grafted nanocubes confined in a thin film. We first used Monte Carlo simulations to compute the two-particle interaction free-energy landscape of the nanocubes and identify their globally stable configurations. The nanocubes were found to exhibit four stable phases: those with edge–edge and face–face orientations, and those exhibiting partially overlapped slanted and parallel faces previously assumed to be metastable. Moreover, the edge–edge configuration originally thought to involve kissing edges instead displayed partly overlapping edges, where the extent of the overlap depends on the attachment positions of the grafts. We next formulated analytical scaling expressions for the free energies of the identified configurations, which were used for constructing a comprehensive phase diagram of nanocube orientation in a multidimensional parameter space comprising of the size and interaction strength of the nanocubes and the Kuhn length and surface density of the grafts. The morphology of the phase diagram was shown to arise from an interplay between polymer- and surface-mediated interactions, especially differences in theirmore »scalings with respect to nanocube size and grafting density across the four phases. The phase diagram provided insights into tuning these interactions through the various parameters of the system for achieving target configurations. Overall, this work provides a framework for predicting and engineering interparticle configurations, with possible applications in plasmonic nanocomposites where control over particle orientation is critical.« less
2. Following the microscopic pathway to adsorption through chemisorption and physisorption wells

   https://doi.org/10.1126/science.abc9581  

   Borodin, Dmitriy ; Rahinov, Igor ; Shirhatti, Pranav R. ; Huang, Meng ; Kandratsenka, Alexander ; Auerbach, Daniel J. ; Zhong, Tianli ; Guo, Hua ; Schwarzer, Dirk ; Kitsopoulos, Theofanis N. ; et al ( September 2020 , Science)

   Adsorption involves molecules colliding at the surface of a solid and losing their incidence energy by traversing a dynamical pathway to equilibrium. The interactions responsible for energy loss generally include both chemical bond formation (chemisorption) and nonbonding interactions (physisorption). In this work, we present experiments that revealed a quantitative energy landscape and the microscopic pathways underlying a molecule’s equilibration with a surface in a prototypical system: CO adsorption on Au(111). Although the minimum energy state was physisorbed, initial capture of the gas-phase molecule, dosed with an energetic molecular beam, was into a metastable chemisorption state. Subsequent thermal decay of the chemisorbed state led molecules to the physisorption minimum. We found, through detailed balance, that thermal adsorption into both binding states was important at all temperatures.
3. Two-step crystallization and solid–solid transitions in binary colloidal mixtures

   https://doi.org/10.1073/pnas.2008561117  

   Fang, Huang ; Hagan, Michael F. ; Rogers, W. Benjamin ( November 2020 , Proceedings of the National Academy of Sciences)

   Crystallization is fundamental to materials science and is central to a variety of applications, ranging from the fabrication of silicon wafers for microelectronics to the determination of protein structures. The basic picture is that a crystal nucleates from a homogeneous fluid by a spontaneous fluctuation that kicks the system over a single free-energy barrier. However, it is becoming apparent that nucleation is often more complicated than this simple picture and, instead, can proceed via multiple transformations of metastable structures along the pathway to the thermodynamic minimum. In this article, we observe, characterize, and model crystallization pathways using DNA-coated colloids. We use optical microscopy to investigate the crystallization of a binary colloidal mixture with single-particle resolution. We observe classical one-step pathways and nonclassical two-step pathways that proceed via a solid–solid transformation of a crystal intermediate. We also use enhanced sampling to compute the free-energy landscapes corresponding to our experiments and show that both one- and two-step pathways are driven by thermodynamics alone. Specifically, the two-step solid–solid transition is governed by a competition between two different crystal phases with free energies that depend on the crystal size. These results extend our understanding of available pathways to crystallization, by showing that size-dependent thermodynamicmore »forces can produce pathways with multiple crystal phases that interconvert without free-energy barriers and could provide approaches to controlling the self-assembly of materials made from colloids.« less
4. Kinetic control of stationary flux ratios for a wide range of biochemical processes

   https://doi.org/10.1073/pnas.1920873117  

   Mallory, Joel D. ; Kolomeisky, Anatoly B. ; Igoshin, Oleg A. ( April 2020 , Proceedings of the National Academy of Sciences)

   One of the most intriguing features of biological systems is their ability to regulate the steady-state fluxes of the underlying biochemical reactions; however, the regulatory mechanisms and their physicochemical properties are not fully understood. Fundamentally, flux regulation can be explained with a chemical kinetic formalism describing the transitions between discrete states, with the reaction rates defined by an underlying free energy landscape. Which features of the energy landscape affect the flux distribution? Here we prove that the ratios of the steady-state fluxes of quasi–first-order biochemical processes are invariant to energy perturbations of the discrete states and are only affected by the energy barriers. In other words, the nonequilibrium flux distribution is under kinetic and not thermodynamic control. We illustrate the generality of this result for three biological processes. For the network describing protein folding along competing pathways, the probabilities of proceeding via these pathways are shown to be invariant to the stability of the intermediates or to the presence of additional misfolded states. For the network describing protein synthesis, the error rate and the energy expenditure per peptide bond is proven to be independent of the stability of the intermediate states. For molecular motors such as myosin-V, the ratio ofmore »forward to backward steps and the number of adenosine 5′-triphosphate (ATP) molecules hydrolyzed per step is demonstrated to be invariant to energy perturbations of the intermediate states. These findings place important constraints on the ability of mutations and drug perturbations to affect the steady-state flux distribution for a wide class of biological processes.

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5. Tunable Orientation and Assembly of Polymer-Grafted Nanocubes at Fluid–Fluid Interfaces

   https://doi.org/10.1021/acsnano.1c10416  

   Zhou, Yilong ; Tang, Tsung-Yeh ; Lee, Brian Hyun-jong ; Arya, Gaurav ( April 2022 , ACS Nano)

   Self-assembly of faceted nanoparticles is a promising route for fabricating nanomaterials; however, achieving low-dimensional assemblies of particles with tunable orientations is challenging. Here, we demonstrate that trapping surface-functionalized faceted nanoparticles at fluid–fluid interfaces is a viable approach for controlling particle orientation and facilitating their assembly into unique one- and two-dimensional superstructures. Using molecular dynamics simulations of polymer-grafted nanocubes in a polymer bilayer along with a particle-orientation classification method we developed, we show that the nanocubes can be induced into face-up, edge-up, or vertex-up orientations by tuning the graft density and differences in their miscibility with the two polymer layers. The orientational preference of the nanocubes is found to be governed by an interplay between the interfacial area occluded by the particle, the difference in interactions of the grafts with the two layers, and the stretching and intercalation of grafts at the interface. The resulting orientationally constrained nanocubes are then shown to assemble into a variety of unusual architectures, such as rectilinear strings, close-packed sheets, bilayer ribbons, and perforated sheets, which are difficult to obtain using other assembly methods. Our work thus demonstrates a versatile strategy for assembling freestanding arrays of faceted nanoparticles with possible applications in plasmonics, optics, catalysis, andmore »membranes, where precise control over particle orientation and position is required.« less