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Stimuli-Responsive DNA-linked Nanoparticle Arrays as Programmable Surfaces Benjamin D. Myers, Edgar Palacios, Dorota Myers, Serkan Butun, Koray Aydin, and Vinayak P. Dravid Nano Lett., Just Accepted Manuscript • DOI: 10.1021/acs.nanolett.9b01340 • Publication Date (Web): 04 Jun 2019 Downloaded from http://pubs.acs.org on June 4, 2019

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Stimuli-Responsive DNA-linked Nanoparticle Arrays as Programmable Surfaces Benjamin D. Myers§~, Edgar Palacios‖, Dorota I. Myers^, Serkan Butun~, Koray Aydin‖, and Vinayak P. Dravid§~*

§ Department of Materials Science and Engineering, Northwestern University, Evanston, IL, 60208, USA ‖ Department of Electrical Engineering and Computer Science, Northwestern University, Evanston, IL, 60208, USA ^ Abbott Laboratories, Abbott Park, IL, 60064, USA ~ NUANCE Center, Northwestern University, Evanston, IL, 60208, USA

Keywords: directed assembly, DNA, nanoparticle, optical metasurface, dynamic responsive materials

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Abstract

Self- and directed-assembly approaches have enabled precise control over the composition and geometry of 2D and 3D nanoparticle constructs. However, the resulting structures are typically static, providing only a single structural arrangement of the nanoparticle building blocks. In this work, the power of DNA-linked nanoparticle assembly is coupled to a grayscale patterning technique to create programmable surfaces for assembly and thermally activated reorganization of gold nanoparticle arrays. Direct grayscale patterning of DNA monolayers by electron-beam lithography (DNA-EBL) enables the production of surfaces with nanometer-scale control over the density of functional DNA. This enables tuning of the particle-surface interactions with singlenanoparticle resolution and without the need for a physical template as employed in most directed assembly methods. This technique is applied on suspended membrane structures to achieve highresolution assembly of 2D nanoparticle arrays with highly mutable architectures. Gold nanorods assembled on grayscale-patterned surfaces exhibit temperature-dependent configurations and ordering behavior that result in tunable polarization-dependent optical properties. In addition, spherical gold particles assembled from a bimodal suspension produce arrays with temperaturedependent configurations of small and large particles. These results have important implications for the design and fabrication of reconfigurable nanoparticle arrays for application as structurally tunable optical metasurfaces.


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There is significant technological interest in nanoparticle-based devices for diverse applications in fields from optoelectronics1, 2 to energy harvesting3, 4 and medical diagnostics and therapeutics.57

Research exploring self-assembly of complex architectures from nanoscale building blocks is

helping define new ways to build materials with novel properties. A great deal of progress has been made in understanding and manipulating the fundamental forces8 responsible for governing these processes and a large number of different self-assembly strategies have been developed.9 Among these myriad assembly strategies, DNA-based assembly offers unrivaled flexibility in tuning the structure and properties in such nanoparticle superstructures.10-12 However, in applications such as the fabrication of optical metasurfaces, top-down lithographic approaches have dominated due to the ability to fabricate arbitrary structures with precise control over the short- and long-range order.13-16 The resulting structures, however, are typically polycrystalline with significant edge and surface roughness, which limit optical performance due to scattering losses.17, 18 In addition, they are usually planar, monolithic structures and strongly adhered to the substrate, which limit the range of optical properties and may preclude structural tunability, respectively. Directed assembly strategies make the large diversity of nanoparticle sizes, shapes and compositions available for fabrication of metasurfaces and other devices by utilizing the sitespecific positioning of a top-down process to define local forces that guide the assembly of individual nanoparticles. In particular, anisotropic nanoparticles such as gold nanorods hold interest due to their polarization-dependent optical properties19-22. Several directed assembly methods for oriented nanorod assembly have been developed, including nanoscale chemical patterning,23 capillary assembly in nanoscale trenches24-26 and block copolymer lithography.27 One of the most exciting advances in optical metasurfaces is the development of structurally reconfigurable systems that allow the tuning of optical properties based on a modification of the


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spatial organization and/or geometry of the optical elements.28 This has been achieved by a number of different approaches, including the use of MEMS-based devices that can change the distance between elements29-32 or their orientation33, 34. Other approaches include mechanical deformation of metasurfaces with flexible substrates,35-37 manipulation of multiple, stacked metasurfaces to change their relative in-plane38,

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or out-of-plane40 positions and the use of phase-change

materials.41-43 However, most of these approaches have only been demonstrated in the GHz and low-THz regimes, while systems that operate at visible frequencies do so by controlling the surrounding materials (e.g. substrate stretching), rather than the individual elements.35-37 Thus, there remains an interesting challenge to develop methodologies that enable structurally tunable and reconfigurable optical metasurfaces through manipulation of the position and orientation of the individual nanoscale elements. Such an approach is challenging as many of the aforementioned directed assembly strategies rely on strong particle-surface interactions to achieve high pattern fidelity, which may preclude the ability to reposition the particles in response to external stimuli. Directed assembly of nanoparticles by combining DNA-based assembly with top-down lithographic patterning offers an opportunity to address this challenge. Such an approach can take advantage of the tunable and reversible binding afforded by the polyvalent DNA interactions, while relying on patterning tools to define the particle positions. Recently, a directed assembly approach combining EBL and DNA-based assembly was applied to fabricate arrays of stacked nanoparticles with tunable interparticle and particle-substrate distances.44 This work demonstrates one type of structural reconfigurability for dynamic modulation of optical properties by changing the nanoparticle-substrate distance. However, as with most top-down fabrication processes, the position of each stack of particles remains fixed according to the 2D lattice prescribed by the EBL patterning step. Recently, we demonstrated the use of direct electron-beam patterning of DNA


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(DNA-EBL) to modulate substrate DNA density and thereby control particle-substrate interactions to drive size-selective assembly.45 Briefly, the DNA-EBL process involves electron beam exposure of a substrate densely functionalized with ssDNA “anchor” strands, damaging a fraction of the DNA proportional to the electron dose. A second ssDNA “linker” strand is then hybridized to the undamaged anchor strands, resulting in a linker density that is inversely proportional to the electron dose. This variation in linker density modulates the interactions between nanoparticles functionalized with DNA complimentary and the linker strands, driving the size-selective assembly behavior. Here, we first demonstrate a modified DNA-EBL process for directed assembly with control over nanoparticle position and orientation by high-dose (i.e. binary) patterning on DNAfunctionalized suspended silicon nitride membranes as shown schematically in Figure 1a-b. We then show the capabilities of gray-scale patterning to drive reorganization of these nanoparticle arrays based on temperature-dependent interactions between the nanoparticles and local gradations in linker density as shown schematically in Figure 1c-f. The lack of a physical template in this approach allows the particles to interact with the entire chemically-patterned surface. This results in temperature-dependent particle arrangements informed by the rich thermodynamics and kinetics of the polyvalent DNA binding coupled with the geometric influence of the grayscale DNA patterns. The effects of nanoparticle geometry, pattern geometry, electron dose and assembly temperature on the nanoparticle arrangement are studied. We find that patterning of 2D rectangular arrays (Figure 1g) results in gold nanorods assemblies that exhibit temperature-controlled ordering behavior with a transition from a more disordered state at low temperature to a more ordered state at high temperature. The ordering behavior is manifested as a combination of translational alignment to a 2D lattice and orientational alignment to rectangular regions of high DNA density


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Figure 1. Schematic illustration (showing only linker strands for clarity) of a) high-dose DNAEBL-patterned substrate with linker strands attached and subsequent b) directed assembly of DNA-functionalized nanorods, c) two-tone grayscale-patterned substrate with linker strands attached and subsequent assembly and reorganization showing temperature-dependent ordering at d) low, e) moderate and f) high temperature. Schematic illustrations of the three patterning schemes in this work: g) rectangular, h) square grid and i) circle arrays with color key to illustrate dose variation (pattern dimensions vary with experiments).


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at each lattice site. This transition results in a modification of the optical properties with the more ordered structures providing stronger polarization-dependent light scattering. We also investigate the assembly of gold nanorods on a patterned square grid (Figure 1h) where the preferred nanorod orientation (vertical, horizontal, diagonal and out-of-plane) is strongly temperature-dependent. Finally, we extend the technique to the assembly of arrays spherical particles from a mixed suspension containing a bimodal distribution of particles, which display temperature-dependent lattice configurations on circle array patterns (Figure 1i). These results demonstrate the use of grayscale DNA-EBL to modulate local particle-substrate interactions and drive high-fidelity nanoparticle assembly with temperature-controlled in-plane reorganization toward the fabrication of structurally reconfigurable metasurfaces. The effects of electron scattering in bulk substrates preclude their use for high-density, highresolution patterning of DNA due to proximity effects. To achieve high-resolution patterning by DNA-EBL, suspended silicon nitride membranes were used as substrates in order to minimize these proximity effects. In comparison to bulk substrates, electron scattering in the suspended silicon nitride membranes is significantly reduced (as shown in Figure S.3 in the Supporting Information), which allows for high spatial resolution patterning and a large degree of control over the local DNA density for gray-scale patterning. To demonstrate the high fidelity of this technique, high-dose (4,333 µC cm-2) exposures with a large duty cycle (95%) were used to create binary patterns with rectangular landing sites. These patterns were used to direct the assembly of gold nanorods functionalized with DNA complementary to the substrate linker DNA with control over position and orientation as shown in Figure 2 through DNA-EBL with suspended membranes. Temperature-controlled reorganization in the nanoparticle arrays is enabled by grayscale patterning. As proof-of-concept, a simple grayscale patterning approach was applied, as shown


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Figure 2. High resolution patterning of Au nanorods (NR2) by high-dose (4333 µC cm-2) binary patterning with 20 nm-wide landing sites showing a) 2D arrays with 200 × 300 nm periodicity, b) split-ring design and c) twisting orientations with d-f) corresponding FFTfiltered images (Scale bars are 1 µm). schematically in Figure 1g, which produces three gradations in DNA density: 1) high density on the rectangular landing sites, 2) intermediate density in the orthogonal interstitial regions and 3) low density in the diagonal interstitial regions. In contrast to the binary patterning, the presence of linker strands in the interstitial regions modifies the assembly behavior such that different nanoparticle arrangements are achieved as a function of assembly temperature. While the parameter space for these experiments is potentially quite large (nanorod geometry, DNA sequence, patterning parameters and various assembly conditions), this work is focused on nanorod size (and, indirectly, nanorod end-curvature), patterning conditions (geometry, dose) and assembly temperature. Two batches of nanorods were selected with nominal lengths of 148 and 124 nm, both with nominal widths of 40 nm (NR1 and NR2, respectively). The nanorods with


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higher aspect ratio (NR1) were hypothesized to demonstrate improved orientation control, however, the longitudinal plasmon resonance of the shorter rods (NR2) is blue-shifted (from 850 nm to 780 nm), which is within a reasonable range for optical measurements. In addition to the different aspect ratio, the two batch of particles also exhibit different end-curvature radii (RNR1 >> RNR2) as shown in the Figure S.1 in the Supporting Information. The pattern geometry was fixed to provide landing sites with a pitch in both transverse and longitudinal directions such that there would be a nominal 60 nm spacing between particles in both directions (NR1: 100 × 210 nm, NR2: 100 × 190 nm). This pitch was chosen intentionally to provide a small enough spacing between lattice sites such that particles could interact with more than one site. This is in contrast to the binary patterned surface in Figure 2a, where the pitch was specifically controlled to avoid particles interacting with multiple sites. To analyze the nanoparticle configurations as a function of temperature, it is necessary to lock the particles in position by silica embedding.46 While this procedure is irreversible, it allows a snapshot of the dynamic assembly process at each assembly temperature. Multiple substrates with identical patterning conditions were used to assess temperature dependence of the assembly process. Thus, the transitions between the different configurations are inferred from these snapshots as the DNA-nanoparticle-substrate system needs to be solvated in buffer to remain active and techniques to image directly, such as in situ electron microscopy, are still under development.47 As shown in Figure 3, the degree of ordering in the nanorod arrays increases with assembly temperature. At low temperatures, the nanorod arrays exhibit more disordered arrangements with higher instances of random orientation. At higher assembly temperatures, the films are less dense and nanorods assume a preferred orientation along the rectangular landing sites. There are distinct


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Figure 3. Temperature-controlled ordering in gold nanorod arrays via grayscale DNA-EBL patterning and directed assembly. SEM images with FFT inset showing NR1 films with 40 × 150 nm landing sites on 100 × 210 nm pitch grid spacing assembled at a) 25, b) 32.5, c) 40 and d) 47.5 °C and corresponding NR2 films with 40 × 130 nm landing sites on 100 × 190 nm pitch grid spacing (e-h). Both are patterned on suspended substrates with 1000 μC cm-2 nominal electron dose in interstitial regions (Scale bars are 1 μm). ACS Paragon Plus Environment

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differences observed between arrays of NR1 and NR2 rods, with the NR1 rods exhibiting a larger ordering transition in addition to showing some nanorods with out-of-plane orientation at low temperature. Optical spectroscopy and finite-difference time-domain (FDTD) simulations were applied to investigate the effects of nanorod ordering and alignment on the optical properties of these arrays. The NR2 samples with 100 × 190 nm pitch were used for these studies, as the longitudinal plasmon resonance is blue-shifted to approximately 780 nm, which is within range of the spectrometer. Specifically, the polarization dependence of the reflectance was measured for the nanorod arrays assembled at low and high temperatures to assess the impact of ordering on the optical properties. The data shown in Figure 4a highlight the impact of the thermally activated reorganization on the optical properties. First, the data show a significant increase in reflectance with polarization along the longitudinal axis (PL) of the nanorods compared to the transverse direction (PT) accompanied by a change in spectral shape. While arrays at both high and low temperature show some polarization-dependence, the magnitude is significantly larger for the high temperature case due to a greater degree of nanorod alignment. For example, there are two broad peaks near 540 nm and 650 nm in the reflectance spectra and the change in reflectance with polarization (PL vs PT) is about 89% larger at 540 nm and about 61% larger at 650 nm for the high temperature case. FDTD simulations of the NR2 nanorods with geometry matching the ideal experimental configuration (perfect arrays of 40 × 130 nm rods with 100 × 190 nm pitch) are shown in Figure 4b and illustrate a polarization-dependent reflectance that corresponds well to the experimental data. Differences between the simulation and experiment are likely due to the assembly defects in the experimental samples, compared to the perfect arrays used in simulation. Light scattering by broadband reflection dominates the change in optical properties, while changes in absorption are relatively


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small and correspond to the transverse (520 nm) and longitudinal (780) SPR modes of individual particles.

Figure 4. a) Optical measurement data from gold nanorod (NR2) arrays with 100 × 190 nm pitch and 1000 μC cm-2 electron dose showing large shift in polarization-dependent reflectance as a function of assembly temperature due to increased ordering at high temperature. Inset shows polarization-dependent optical microscopy (reflection) images of NR2 assembled at 40 °C (scale is 30 μm) b) Optical simulation data from nanorods arrays with same dimensions showing strong polarization-dependent optical scattering and weaker absorption effects for aligned nanorod arrays. c) ACF data showing ΔξT and ΔξL as a function of landing-site width and electron dose for NR1 arrays. d) Violin plots showing the distribution of nanorod (NR1) orientations as measured by particle detection indicating the shift from a bimodal to a skewed unimodal distribution as a function of temperature (40 nm landing sites and 1000 μC cm-2). The degree of ordering in these experiments was quantified by the application of two different image analysis tools. First, a 2D autocorrelation function (ACF) approach (described in the Supporting Information) was applied to produce ordering parameters, ξT and ξL, that describe the


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degree of ordering in the transverse and longitudinal directions, respectively. Second, a particle detection method (described in the Supporting Information) was used to measure the orientation (θ) of each nanorod. The ACF method is useful for assessing overall ordering, including both positional and orientational components, while the particle detection method provides a more direct measure of nanoparticle alignment. In general, both analytical methods show that ordering in the arrays increases with decreasing landing-site width, increasing electron dose and increasing temperature. These data indicate that the best ordering is achieved by high contrast exposure, which produces in large differences in DNA density in exposed and unexposed regions, coupled with high assembly temperatures, which prevent adsorption in the lower density regions. In addition, the patterning of smaller landing sites improves the precision of particle position and orientation control by geometric confinement. To assess the largest degree of reorganization, these metrics are evaluated at low (25 °C) and high (47.5 °C) to calculate a change in ordering (ΔξT and ΔξL), which is plotted in Figure 4c as a function of the landing-site width and electron dose for the NR2 arrays. These data illustrate that the largest degree of reorganization occurs with smaller landing sites, presumably due to greater geometric confinement. In addition, the change in ordering generally increases with increasing electron dose, however, for the 40 nm landing sites, the greatest reorganization occurs with moderate electron doses (near 1000 µC cm-2) and decreases with higher dose. Violin plots from the condition with the largest change in ordering (as measured by Δθ and Δξ) are shown in Figure 4d and clearly illustrate this large change in orientational ordering with increasing temperature. The thermally activated reorganization in these systems can be described by considering how the polyvalent binding of the DNA-linked nanoparticles is modified by the local gradations in DNA density. As shown previously, the equilibrium surface density of particles45 and melting (i.e.


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desorption) temperature48 is directly dependent on the surface DNA density. At low temperatures, the binding strength of each individual DNA linkage is higher, which results in a densely packed nanoparticle film that less sensitive to the surface patterning. As the temperature is increased, the nanorods preferentially bind to the unexposed landing sites where DNA density is high enough to provide a sufficient number of DNA linkages. This provides a driving force that has a direct influence on both the position and orientation of the adsorbed particles. The largest changes in ordering with increasing temperature are observed with an optimum dose near 1000 µC cm-2. At higher electron doses, the DNA density between landing sites is very low, which produces strong ordering even at low temperatures, resulting in smaller Δθ and Δξ. The moderate electron dose of 1000 µC cm-2 provides sufficient contrast for oriented assembly at high temperature, but still allows the relatively disordered low temperature configuration. In effect, the grayscale patterning by DNA-EBL creates a programmable surface with a thermodynamic landscape that changes with temperature. This can be illustrated by close examination of the NR1 nanorod assembly. At low temperature (Figure 3a), there are three distinct nanoparticle orientations: vertical, horizontal and out-of-plane. The out-of-plane orientation is related to the higher bond strength at low temperature and the large radius of curvature on the NR1 nanorod ends, which provides a relatively large surface area for binding. The horizontally oriented particles bridge neighboring landing sites and result in the bimodal distribution at low temperature shown in the violin plots in Figure 4d. As the temperature is increased, both of these configurations become energetically unfavorable due to the lower DNA density between landing sites and the lower bond strength. This results in a preference for the vertical orientation and a skewed unimodal distribution. In comparison, the assemblies of the shorter NR2 nanorods in Figure 3e-h exhibit neither the out-of-plane assembly, nor the bimodal distribution due to horizontal alignment at low temperature. This is likely due to the shorter


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nanorod length and higher end-curvature, resulting in a more gradual increase in ordering and alignment. The optimization of patterning conditions achieved by these experiments indicates that small landing-site widths are favorable for better overall orientation control (Figure S.6 and S.7) as well as a larger ordering effect (Figure 4c). However, while this work provides some guidance for general application, even in the simple case of a rectangular grid of oriented nanorods, the optimum pattern parameters will depend on several factors including the nanorod size (and size distribution), aspect ratio, DNA length and the desired periodicity. The magnitude of the electron dose primarily sets the relative difference in DNA density between the landing sites and the interstices, but also has an indirect influence on the landing-site size due to proximity effects. While patterning on the suspended silicon nitride membranes reduce proximity effects, there is still some electron scattering, which results in an increased width of the exposed lines with increasing dose, which causes a decrease in the landing site width. This explains the general trend of increased ordering with electron dose for the larger landing sites (50 – 60 nm) as the landingsite size is effectively decreasing with increasing dose (Figure 4c). However, for the smallest landing sites, the effect of grayscale patterning can clearly be seen as the change in ordering (both by Δξ and Δθ) decreases at higher doses as the patterns become more binary and highly ordered assemblies are generated even at lower temperatures. The temperature-dependent ordering behavior seen in nanorod assembly on rectangular grids patterns provides a starting point to explore alternative patterning geometries and nanoparticle shapes. The rich interplay of assembly thermodynamics, kinetics and geometric confinement through patterning is explored in two additional schemes: 1) nanorod assembly on a square grid pattern and 2) assembly of a mixed suspension of small (30 nm) and large (80 nm) spherical


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nanoparticles on circle array patterns. In the first scheme, the patterning and assembly methodology is essentially the same as for the rectangular grid described above, but the geometry is modified to allow particle interactions with both nearest neighbor and next-nearest neighbor sites. The results of these experiments are shown in Figure 5a-d and show that the nanoparticle

Figure 5. SEM images with FFT inset for assembly and temperature-controlled reorganization of nanoparticles on surfaces patterned by DNA-EBL at temperatures (left-right) of 25, 32.5, 40 and 47.5 °C for a-d) NR1 nanorods on a square grid with 40 nm landing sites, x/y pitch of 80 nm and 1000 μC cm-2 electron dose showing change in preferred nanorod orientation, e-h) bimodal suspension of spherical nanoparticles on a circle array pattern with 220 nm diameter, x/y pitch of 400 nm and 900 μC cm-2 electron dose, i-l) bimodal suspension of spherical nanoparticles on a circle array pattern with circle diameter and x/y pitch of 200 nm and 1000 μC cm-2 electron dose (Scale bars are 1μm).


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films are highly ordered even at low temperature, but the preferred orientation is strongly temperature-dependent. This temperature-dependent reorganization results in a mixture of out-ofplane, diagonal and orthogonal at low temperature with orthogonal orientation dominating at higher temperatures. The reduction in the number of out-of-plane nanorods at high temperature is due to the lower surface area and concomitant reduction in binding strength. The reduction in the number of diagonal particles is due to the patterning strategy, which relied on overlapping exposures such that the interstitial regions between next-nearest neighbor sites received twice the electron dose as that between nearest neighbor sites. Finally, the same grayscale patterning strategy is applied to a bimodal suspension of small and large nanoparticles. In these experiments, a combination of geometric confinement and the sizeselective assembly behavior previously observed45 results in strongly temperature-dependent configurations. In the first example (Figure 5e-h), an array of 220 nm diameter circles was patterned with a pitch of 400 nm. This results in a relatively disordered small-particle dominated film at low temperature, which transitions to a hole array surrounded by small particles, then an array of large particles surrounded by small particles and finally a hole array surrounded by a mixture of small and large particles. By changing the patterning scheme to a 200 nm circle with 200 nm pitch, the resulting nanoparticle configuration is similar at low temperature, but results in a disordered mixture of small and large particles at intermediate temperature and a well-defined array of large particles positioned on interstitial sites at high temperature as shown in Figure 5i-l. In summary, this work demonstrates the use of DNA-EBL to create programmable surfaces for nanoparticle assembly and thermally activated reorganization by grayscale patterning. The three different patterning strategies serve as a proof-of-concept to illustrate the power and potential of this method for creating nanoparticle assemblies that can undergo structural reorganization with


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changes in temperature and we demonstrate the concomitant changes in optical properties. The grayscale patterning capability of the DNA-EBL process is critical to exploit the thermodynamics of DNA-linked nanoparticle assembly to realize structural transformations, which would not be possible with traditional directed assembly techniques based on binary patterning. Such structural tunability based on the reorganization of the individual nanoparticle elements provides a mechanism for dynamic modification of optical properties in these metasurfaces. Further, while this work utilized gold nanoparticles and DNA interactions, it may be possible to generalize this approach to take advantage of the range of existing nanoparticle morphologies and compositions in addition to different assembly strategies.

ASSOCIATED CONTENT Supporting Information. Nanoparticle functionalization and assembly methods, substrate preparation, electron beam patterning details, optical measurement and simulation methods, electron and optical microscopy methods, STEM images of NR1/NR2 nanorods, polarized light optical microscopy, simulation results for electron scattering in the silicon nitride membranes, image analysis procedures and results. This material is available free of charge via the Internet at http://pubs.acs.org. AUTHOR INFORMATION Corresponding Author * Email: [email protected]


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Author Contributions The manuscript was written through contributions of all authors. All authors have given approval to the final version of the manuscript.

ACKNOWLEDGMENT This work was primarily supported by the Air Force Office of Scientific Research under Award Number FA9550-17-1-0348. The methodology and approach developed in this work are partially supported by the Air Force Research Laboratory under agreement number FA8650-15-2-5518. This work made use of the EPIC and NUFAB facilities of Northwestern University’s NUANCE Center, which has received support from the Soft and Hybrid Nanotechnology Experimental (SHyNE) Resource (NSF NNCI-1542205); the MRSEC program (NSF DMR-1720139) at the Materials Research Center; the International Institute for Nanotechnology (IIN); the Keck Foundation; and the State of Illinois, through the IIN.

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