Bulletin of the American Physical Society
APS March Meeting 2017
Volume 62, Number 4
Monday–Friday, March 13–17, 2017; New Orleans, Louisiana
Session X17: Self-Assembly III |
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Sponsoring Units: GSOFT Room: 276 |
Friday, March 17, 2017 8:00AM - 8:12AM |
X17.00001: Emulsion Droplets with DNA Origami Directed Patches: from Valence Control to Self-Assembly Yin Zhang, Xiaojin He, Rebecca Zhuo, Ruojie Sha, Jasna Brujic, Nadrian Seeman, Paul Chaikin Recently DNA-directed emulsion architectures have been explored. Building highly ordered structures requires strict valence control of the DNA binders on the droplet's surface. Here, we demonstrate such control using cross-like DNA origami [1] as building units to form functional patches on emulsion droplets. Our DNA origami crosses have three functional parts: vertical sticky ends on the bottom layer for attaching to emulsion droplets; horizontal sticky ends for tile-tile 2D-assembly; and vertical sticky ends on the top layer for droplet-droplet assembly. On the emulsion droplets the DNA origami tiles self-assemble into one large patch directed by the hybridization of the horizontal sticky ends. Complimentary patches on different droplets then lead to dimer formation. Another set of origami is designed with different horizontal sticky ends, which forms a second patch on the droplet surface.~ By using complementary vertical sticky ends modified patches, the linear chaining of these divalent emulsion droplets is achieved. Our work demonstrates a novel and versatile approach for the development of complex self-assembled materials. [Preview Abstract] |
Friday, March 17, 2017 8:12AM - 8:24AM |
X17.00002: DNA Origami Patterned Colloids for Programmed Design and Chirality Matan Yah Ben Zion, Xiaojin He, Corinna Maass, Ruojie Sha, Ned Seeman, Paul Chaikin Micron size colloidal particles are scientifically important as model systems for equilibrium and active systems in physics, chemistry and biology and for technologies ranging from catalysis to photonics. The past decade has seen development of new particles with directional patches, lock and key reactions and specific recognition that guide assembly of structures such as complex crystalline arrays. What remains lacking is the ability to self-assemble structures of arbitrary shape with specific chirality, placement and orientation of neighbors. Here we demonstrate the adaptation of DNA origami nanotechnology to the micron colloidal scale with designed control of neighbor type, placement and dihedral angle. We use DNA origami belts with programmed flexibility, and functionality to pattern colloidal surfaces and bind particles to specific sites at specific angles and make uniquely right handed or left handed structures. The hybrid DNA origami – colloid technology should allow the synthesis of designed functional structural and active materials. [Preview Abstract] |
Friday, March 17, 2017 8:24AM - 8:36AM |
X17.00003: Managing lifelike behavior in a dynamic self-assembled system Chad Ropp, Nicolas Bachelard, Yuan Wang, Xiang Zhang Self-organization can arise outside of thermodynamic equilibrium in a process of dynamic self-assembly. This is observed in nature, for example in flocking birds, but can also be created artificially with non-living entities. Such dynamic systems often display lifelike properties, including the ability to self-heal and adapt to environmental changes, which arise due to the collective and often complex interactions between the many individual elements. Such interactions are inherently difficult to predict and control, and limit the development of artificial systems. Here, we report a fundamentally new method to manage dynamic self-assembly through the direct external control of collective phenomena. Our system consists of a waveguide filled with mobile scattering particles. These particles spontaneously self-organize when driven by a coherent field, self-heal when mechanically perturbed, and adapt to changes in the drive wavelength. This behavior is governed by particle interactions that are completely mediated by coherent wave scattering. Compared to hydrodynamic interactions which lead to compact ordered structures, our system displays sinusoidal degeneracy and many different steady-state geometries that can be adjusted using the external field. [Preview Abstract] |
Friday, March 17, 2017 8:36AM - 8:48AM |
X17.00004: Improving Self-Assembly by Varying the Temperature Periodically with Time Oren Raz, Christopher Jarzynski Self-assembly (SA) is the process by which basic components organize into a larger structure without external guidance. These processes are common in Nature, and also have technological applications, e.g. growing a crystal with a specific structure. So far, artificial SA processes have been designed mostly using diffusive building blocks with high specificity and directionality. The formation of the self-assembled structures is then driven by free-energy minimization into a thermodynamically stable state. In an alternative approach to SA, macroscopic parameters such as temperature, pressure, pH, magnetic field etc., are varied periodically with time. In this case, the SA structures are the stable periodic states of the driven system. Currently there are no design principles for periodically driven SA, other than in the limits of fast or weak driving. We present guiding ideas for self-assembly under periodic driving. As an example, we show a particular case in which self-assembly errors can be dramatically reduced by varying a system's temperature periodically with time. [Preview Abstract] |
Friday, March 17, 2017 8:48AM - 9:00AM |
X17.00005: Assembly and disassembly kinetics of conical particles Stefan Paquay, Roya Zandi, Mike Hagan, Paul van der Schoot We investigate the assembly and disassembly of conical and rod-like particles on a spherical template by means of computer simulations. The shape of the particles provides a simple but more realistic model for virus capsomeres than spherical particles, and it allows us to qualitatively investigate the influence of the particle shape on the self-assembly. We vary the particle geometry, the inter-particle interaction strength and the particle-template interaction strength, and find four different regimes characterised by 1) no assembly at all, 2) assembly of a capsid exhibiting holes and tears, 3) assembly of a closed, almost defect-free capsid and 4) partial assembly of empty capsids in addition to a capsid forming around the nanoparticle. We also probe the assembly and disassembly rates, and find that the defective capsids disassemble much faster, hinting at the potential importance of holes and tears for the maturation of certain viruses including alphaviruses and HIV-1. [Preview Abstract] |
Friday, March 17, 2017 9:00AM - 9:12AM |
X17.00006: Equilibrium phase behavior and self-assembly dynamics of an SALR model of microphase formation Patrick Charbonneau, Yuan Zhuang Colloidal models with short-range attraction and long-range repulsion (SALR) assemble into a rich set of equilibrium periodic microphases, including cluster crystal, cylindrical, double gyroid and lamellar phases. We present the phase diagram of such an SALR system obtained using specialized Monte Carlo-based methods. Remarkably, we find that even in the disordered regime, the model exhibits rich structural crossovers, which gives rise to a complex sequence of dynamical regimes. The dynamics notably depends on the formation and percolation of mesoscale cavities. We also consider the ease with which periodic microphases self-assemble, which we use to provide guidance for the design of colloidal experiments to reliably obtain such structures. [Preview Abstract] |
Friday, March 17, 2017 9:12AM - 9:24AM |
X17.00007: Electrostatics of DNA-Functionalized Nanoparticles Kyle Hoffmann, Kurinji Krishnamoorthy, Sumit Kewalramani, Michael Bedzyk, Monica Olvera de la Cruz DNA-functionalized nanoparticles have applications in directed self-assembly and targeted cellular delivery of therapeutic proteins. In order to design specific systems, it is necessary to understand their self-assembly properties, of which the long-range electrostatic interactions are a critical component. We iteratively solved equations derived from classical density functional theory in order to predict the distribution of ions around DNA-functionalized Cg Catalase. We then compared estimates of the resonant intensity to those from SAXS measurements to estimate key features of DNA-functionalized proteins, such as the size of the region linking the protein and DNA and the extension of the single-stranded DNA. Using classical density functional theory and coarse-grained simulations, we are able to predict and understand these fundamental properties in order to rationally design new biomaterials. [Preview Abstract] |
Friday, March 17, 2017 9:24AM - 9:36AM |
X17.00008: Potential of mean force of DNA guided assemblies past Debye-Hückel regime Martin Girard, Soyoung Seo, Yaohua Li, Chad Mirkin, Monica Olvera de la Cruz Many of the bioinspired systems make use of biopolymers such as polypeptides or DNA. The latter is widely used in self-assembled systems, from colloidal crystals to origami construction. In these systems, salt is commonly required to screen the electrostatic repulsion between the strands. In the classical Debye-Hückel picture, salt ions are point particles and the screening distance is a decreasing monotonic function of salt concentration. This picture breaks down at moderate salt concentrations, where the behavior becomes non-monotonic. In this talk, we will show results for potential of mean force of DNA grafted colloids obtained through multiscale molecular dynamics. In this picture, the highly charged DNA causes non-trivial behavior at moderate salt concentrations ($c\sim 0.3 - 0.7$M), namely increase of repulsion for non-complementary DNA strands while repulsion decreases for complementary strands. We will show spatial cluster distribution as function of size and charge as well as implications for experimental systems. [Preview Abstract] |
Friday, March 17, 2017 9:36AM - 9:48AM |
X17.00009: Modelling of DNA-Mediated of Two- and --Three dimensional Protein-Protein and Protein-Nanoparticle Self-Assembly Jaime Millan, Janet McMillan, Jeff Brodin, Byeongdu Lee, Chad Mirkin, Monica Olvera de la Cruz Programmable DNA interactions represent a robust scheme to self-assemble a rich variety of tunable superlattices, where intrinsic and in some cases non-desirable nano-scale building blocks interactions are substituted for DNA hybridization events. Recent advances in synthesis has allowed the extension of this successful scheme to proteins, where DNA distribution can be tuned independently of protein shape by selectively addressing surface residues, giving rise to assembly properties in three dimensional protein-nanoparticle superlattices dependent on DNA distribution. In parallel to this advances, we introduced a scalable coarse-grained model that faithfully reproduces the previously observed co-assemblies from nanoparticles and proteins conjugates. Herein, we implement this numerical model to explain the stability of complex protein-nanoparticle binary superlattices and to elucidate experimentally inaccessible features such as protein orientation. Also, we will discuss systematic studies that highlight the role of DNA distribution and sequence on two-dimensional protein-protein and protein-nanoparticle superlattices. [Preview Abstract] |
Friday, March 17, 2017 9:48AM - 10:00AM |
X17.00010: The role of shape vs. patches in protein crystallization Jens Glaser, Sharon C Glotzer Proteins fold into a multitude of three-dimensional native structures. The structures of over 100,000 known proteins are deposited in the protein data bank, and most of them have been determined through X-ray crystallography. We ask the question if the role of shape in protein crystallization can be isolated using simulation. Current computational studies show that patchy complementary contacts stabilize experimentally observed P212121 crystal structures for relatively globular protein using spherical protein models. Here we study an anisotropic rigid shape model of green fluorescent protein based on a coarse-grained representation of the atomic coordinates. Using GPU-accelerated molecular dynamics simulations, we find that the experimentally found crystal structure can be stabilized in self-assembly by using complementary attractive patches, confirming the earlier findings. However, we discuss the additional roles of solvent mediated and electrostatic interactions, depletion effects and the self-assembly properties of a purely hard shape model in stabilizing different assemblies. Our findings shed light on fundamental assembly mechanisms in colloidal systems with many competing interactions. [Preview Abstract] |
Friday, March 17, 2017 10:00AM - 10:12AM |
X17.00011: Emergence of Life-Like Properties from Dissipative Self-Assembly of Nanoparticles Serim Ilday, Ghaith Makey, Gursoy B. Akguc, Ozgun Yavuz, Onur Tokel, Ihor Pavlov, Oguz Gulseren, F. Omer Ilday A profoundly fundamental question at the interface between physics and biology remains open: What are the minimum requirements for emergence of life-like properties from non-living systems? Here, we address this question and report emergent complex behavior of tens to thousands of colloidal nanoparticles in a system designed to be as plain as possible: The system is driven far from equilibrium by ultrafast laser pulses, which create spatiotemporal temperature gradients, inducing Marangoni-type flow that drags the particles towards aggregation; strong Brownian motion, used as source of fluctuations, opposes aggregation. Nonlinear feedback mechanisms naturally arise between the flow, the aggregate, and Brownian motion, allowing fast external control with minimal intervention. Consequently, complex behavior, analogous to those commonly seen in living organisms, emerges, whereby the aggregates can self-sustain, self-regulate, self-replicate, self-heal and can be transferred from one location to another, all within seconds. Aggregates can comprise of only one pattern or bifurcated patterns can co-exist, compete, survive or die. [Preview Abstract] |
Friday, March 17, 2017 10:12AM - 10:24AM |
X17.00012: Enhanced self-assembly of actin encapsulated in polypeptide coacervates Patrick M. McCall, Samanvaya Srivastava, Sarah L. Perry, David R. Kovar, Margaret L. Gardel, Matthew V. Tirrell Proteins typically exist and do the work of the cell in crowded environments, in stark contrast to the dilute solution limit traditionally used to study biomolecular properties and interactions. This begs the question of how crowded environments with plentiful weak interactions impact biologically important molecular reactions. Building on recent success encapsulating the model protein bovine serum albumin (BSA) in the crowded interior of liquid polyelectrolyte-complex coacervates, we use polypeptide coacervates as a platform to examine the electrostatically-driven self-assembly of the ubiquitous protein actin into linear filaments. Remarkably, in spite of the high concentration of strongly charged molecules in the coacervate interior, we observe that actin is still capable of assembling into micron-long filaments. In contrast to the uniform distribution of the non-reactive BSA inside coacervates, we find the F-actin is strongly peripherally localized, perhaps owing to depletion interactions. Additionally, we observe that the rate of actin self-assembly is enhanced \textgreater 50-fold inside coacervates. Consistent with an increase in the local protein concentration in coacervates, encapsulated actin assembles below the critical concentration of bulk solution. [Preview Abstract] |
Friday, March 17, 2017 10:24AM - 10:36AM |
X17.00013: Watching Nanoscale Self-Assembly Kinetics of Gold Prisms in Liquids Juyeong Kim, Zihao Ou, Matthew R. Jones, Qian Chen We use liquid-phase transmission electron microscopy to watch self-assembly of gold triangular prisms into polymer-like structures. The in situ dynamics monitoring enabled by liquid-phase transmission electron microscopy, single nanoparticle tracking, and the marked conceptual similarity between molecular reactions and nanoparticle self-assembly combined elucidate the following mechanistic understanding: a step-growth polymerization based assembly statistics, kinetic pathways sampling particle curvature dependent energy minima and their interconversions, and directed assembly into polymorphs (linear or cyclic chains) through in situ modulation of the prism bonding geometry. Our study bridges the constituent kinetics on the molecular and nanoparticle length scales, which enriches the design rules in directed self-assembly of anisotropic nanoparticles. [Preview Abstract] |
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