Bulletin of the American Physical Society
APS March Meeting 2020
Volume 65, Number 1
Monday–Friday, March 2–6, 2020; Denver, Colorado
Session F30: Self-Limiting Assemblies II: Programmable AssembliesFocus
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Sponsoring Units: DSOFT DPOLY DBIO Chair: Efi Efrati, Weizmann Institute of Science Room: 502 |
Tuesday, March 3, 2020 8:00AM - 8:12AM |
F30.00001: Finite-Size Colloidal Constructs Designed through Self-Assembly of Defective Colloidal Molecules Nishan Parvez, Mehdi Zanjani Engineering various types of structures through self-assembly of colloidal particles is a powerful approach in material design and processing. While simple colloidal building blocks provide a number of well-known structures, more complex building blocks, such as colloidal molecules, are needed to create novel structures with desired functionalities and tunable properties. |
Tuesday, March 3, 2020 8:12AM - 8:24AM |
F30.00002: Self-assembly of protein-made structures Agnese Curatolo, Carl Goodrich, Ofer Kimchi, Michael Phillip Brenner, Yang Hsia, Zibo Chen, Scott Boyken, David Baker Living organisms create complex protein based materials with remarkable properties. Inspired by those, one could ask if it would be possible to design protein-based materials from scratch for specific human uses, with applications ranging from medicine to biomaterials. |
Tuesday, March 3, 2020 8:24AM - 9:00AM |
F30.00003: Programmable self-assembly of DNA origami capsids based on the principles of virus structure. Invited Speaker: Seth Fraden We provide a general and modular solution for building synthetic icosahedral shells on the scale of 100 nm, motivated by the 1962 Caspar and Klug theory of virus structure. Strategies were explored for controlling the pathways, kinetics, and the yield by which subunits arrange themselves into icosahedral symmetry. The methods of DNA origami were employed to produce accurately-designed and rigid building blocks. We created multiple large virus-like capsids and validated the structures using cryo electron microscopy and studied the capsid assembly process experimentally and with a computational model to elucidate how the kinetics and yield of target structures depends on control parameters. Our capsid building blocks represent a near-ideal manifestation of patchy particles whose geometry and interactions can be designed with sub-nanometer and kBT precision, thus achieving a long sought after goal in soft matter physics. |
Tuesday, March 3, 2020 9:00AM - 9:12AM |
F30.00004: Functionalized DNA origami shells for cargo encapsulation S.Ali Aghvami, Chris SIgl, Elena Willner, Hendrik Dietz, Seth Fraden Inspired by the efficient design of virus particles, we develop self-assembling DNA origami icosahedral nanostructures for cargo encapsulation and delivery. Our design is based on the Casper and Klug (CK) geometric principles of virus structure. We demonstrate a robust method for self-assembly of virus like DNA origami capsids of various sizes by designing specific capsomers with programmable shape complementary lock and key interactions. The building blocks are designed and constructed according to the CK symmetry principles that dictate the minimal number of distinct bonds per capsid. These DNA nanostructures are highly modular, allowing us to successfully functionalize them for encapsulation of organic and non-organic cargo particles. We study self-assembly of capsid and encapsulation of different types of particles with TEM and electrophoretic mobility assays to elucidate different aspects of assembly pathways and encapsulation yield. These DNA origami structures are biocompatible and have highly controllable size and shape, making them candidates for biomaterial engineering purposes such as drug delivery and gene therapy. |
Tuesday, March 3, 2020 9:12AM - 9:24AM |
F30.00005: Structural and mechanical properties of nucleic acid nanotubes: A combined all-atom and coarse-grained molecular dynamics study Supriyo Naskar, Himanshu Joshi, Mounika Gosika, Banani Chakraborty, Nadrian C Seeman, Prabal K Maiti In this work, we introduce a computational framework to model nucleic acid nanotubes and estimate their mechanical properties using various levels of theory. Using atomistic molecular dynamics (MD) simulations, we report the enhancement of the structural and mechanical stability of DNA nanotube (DNT) by changing the salt concentrations. The calculated persistence length (Lp) of the DNTs is ~1-2 μm which is an order of magnitude higher than that of a single dsDNA. DNTs have stretch modulus (γ) value in the range of ~6-8 nN. We find that, with the gradual increment of salt concentration, an increase in Lp and γ which reaffirms the structural and mechanical stability of the DNT at higher salt concentrations. We also model DNT using two widely used coarse-grain (CG) models – namely Martini and oxDNA. We compare and contrast the all-atom MD and experimental results with the results obtained using these CG models. We also propose a model of hexagonal nanotubes made of dsRNA connected by double crossover at different positions. The calculated γ and Lp of the in silico modeled RNTs are in the same range of values as in the case of DNTs. Using helicoidal parameters of individual base pairs, we explain the relative flexibility and rigidity of the RNTs having different sequences. |
Tuesday, March 3, 2020 9:24AM - 9:36AM |
F30.00006: Self-assembly of DNA origami particles into self-limited surfaces Daichi Hayakawa, Douglas Hall, Chris SIgl, Gregory Grason, William Rogers The combination of proteins’ unique folded shapes and specific interactions enable them to self-assemble into functional, nanostructured materials, such as viral capsids and microtubules. In this talk, I will present experimental results showing that we can mimic these features using DNA origami. We devise a scheme for designing synthetic building blocks with prescribed shapes and specific interactions. Our building blocks are DNA origami triangles, which bind via DNA base stacking interactions between shape-complementary edges. The dihedral angles between neighboring building blocks can be tuned independently by designing the building-block geometry. We illustrate our design approach by making triangular building blocks that assemble into self-limited structures, like a zigzag nanotube which is limited in size along one dimension. Molecular dynamics simulations, gel electrophoresis, and electron microscopy verify the three-dimensional structures of the individual building blocks as well as their assemblies. Going forward, our design method will enable us to create other building blocks that self-assemble into surfaces with user-prescribed curvatures. |
Tuesday, March 3, 2020 9:36AM - 9:48AM |
F30.00007: Frustration in the absence of Gaussian Curvature: what we learned from colloidal crystallization on a cylinder Nabila Tanjeem, William H Wilkin, Christopher Rycroft, Vinothan Manoharan We demonstrate the effects of a closure constraint on a crystal in the absence of Gaussian curvature. Most studies on closure constraints have focused on crystals on the surface of a sphere, in which case both Gaussian curvature and topology affect the crystallization dynamics. To separate the effects of topology from Gaussian curvature, we study crystallization of colloidal spheres on the surface of a cylinder experimentally, because a cylinder has zero Gaussian curvature, but has a surface that loops back on itself. We find that chiral structures and line-slip defects emerge owing to the closure constraint. We also find that owing to anisotropic crystal growth on a thin and long cylinder, line-slip defects with smaller chiral angles become frustrated, incorporating kinks and fractional vacancies that do not relax in experimental timescale. We show a connection between crystal morphology and growth dynamics, which may elucidate the assembly mechanism of tubular crystalline materials, such as rod-like viruses, bacterial S-layers, and nanotubes. |
Tuesday, March 3, 2020 9:48AM - 10:00AM |
F30.00008: Self-Assembly of Triply-Periodic Minimal Surfaces, An “Inverted” Caspar-Klug Approach Carlos Duque, Douglas Hall, Botond Tyukodi, Michael Hagan, Gregory Grason, Christian Santangelo The seminal work of Caspar and Klug paved the way to deepen our understanding of the formation of viral shells. Since then, many efforts have been put into understanding the structural properties of a wide variety of viruses. Recently, with the development of DNA nanotechnology, it has been possible to program DNA nanoparticles to self-assemble into intricate shapes by carefully designing some elemental building blocks. In this work, we are interested in studying an “inverted” Caspar-Klug problem, focussed primarily on structures with negative Gaussian curvature. More specifically, we study a family of surfaces called triply periodic minimal surfaces (TPMS). During this talk I’ll describe our efforts to discretize these surfaces using a Caspar-Klug approach. Furthermore, I’ll discuss how we can encode some simple rules on the programable matter in order to self-assemble into the desired structures. We perform Monte Carlo simulations to test the validity of the matching rules and finally touch upon the robustness of the assembled structures with the introduction of imperfections in the assembly process. |
Tuesday, March 3, 2020 10:00AM - 10:12AM |
F30.00009: Colloidal crystallization on a cone Jessica Sun, Nabila Tanjeem, Vinothan Manoharan We study the self-assembly of colloidal spheres on the surface of a cone, which has zero Gaussian curvature but varying mean curvature. Therefore, we expect that a colloidal crystal growing on a cone must self-intersect at an angle and is limited to a finite size. In our experimental system, colloidal particles assemble by short-ranged depletion interactions onto a pulled microcapillary tube. For a cylindrical tube of constant mean curvature, defects form where the crystalline grain self-intersects. These defects, called line-slip defects, consist of particle pairs with five-fold coordination along the defect line. However, as we increase the cone angle of the tube, a gap opens up along the defect line. This gap, or fractional vacancy, has varying width along the length of the defect. We show that the varying width of the fractional vacancy corresponds with the cone angle. When we increase the cone angle to a critical value, the system reaches a jammed state. |
Tuesday, March 3, 2020 10:12AM - 10:24AM |
F30.00010: Programming extrinsic geometry to control membrane self-assembly Douglas Hall, Mark Stevens, Gregory Grason Advancements in nanotechnology have furthered the ability for tailoring shape of building blocks for self-assembly. A current challenge is to develop theories of self-limiting assembly of distinct superstructures, e.g. to create ribbons with robustly self-regulating and finite dimensions that are much larger than the building block dimensions. Previous work successfully describes helical nanoribbon assembly and how molecular shape is related to the programmed intrinsic geometry of the assembly (i.e. the preferred Gaussian curvature), resulting in self-limitation via frustration-induced stresses. |
Tuesday, March 3, 2020 10:24AM - 10:36AM |
F30.00011: Dynamical and equilibrium calculations of self-limited assembly through geometric frustration Botond Tyukodi, Farzaneh Mohajerani, Gregory Grason, Michael Hagan The self-assembly of subunits into large structures with well-defined finite sizes is ubiquitous in biology. Understanding how to engineer self-assembling structures that exhibit such self-limiting assembly would have important applications in developing functional materials. Recent theoretical arguments have proposed a broad mechanism for self-limiting, geometrically frustrated assembly, in which the preferred local packing of subunits is frustrated by an incompatibility with the preferred global order of the assembly process. |
Tuesday, March 3, 2020 10:36AM - 10:48AM |
F30.00012: Emergence of fiber in frustrated self assembly Hugo Le Roy, Martin Lenz, Mert Terzi Self-organization is an essential characteristic of life at all scales. Mistakes in self-organization at the protein level can lead to severe diseases such as Alzheimer’s, in which normally soluble proteins aggregate into fibril structures that interfere with the protein’s initial biological role. We try to understand the general mechanism behind these aggregation phenomena, which are exhibited by a wide variety of proteins. If surface tension energy would drive aggregation, it would do so at the cost of elastic energy due to protein deformation from there ill-fitting shape. Previous studies have found that fiber-like aggregates can have an energetic benefit over other shapes, representing a trade-off between surface tension and elastic energies. In this work, we use statistical physics tools to investigate the thermodynamic stability of such fibers in more realistic conditions |
Tuesday, March 3, 2020 10:48AM - 11:00AM |
F30.00013: Role of Geometrical Frustration in Self-limiting Enantioselective Synthesis of Chiroptical Helices prashant kumar, Jiao Yan, Alexander F Simon, Daniel Katz, Douglas Hall, Gregory Grason, Nicholas Kotov Tunable rotation of light polarization across a wide wavelength spectrum is a desired property for optoelectronic materials. Nanoscale helices and their segments (bow-ties) are expected to exhibit some of the strongest chiroptical activity among nanoscale structures with mirror asymmetry. Successful efforts for fabrication of helices with desired geometry (pitch, length, width, twist angle and thickness) have been focused on top-down approaches such as ion-beam lithography. However, lithographic methods are limited by the fabrication efficiency of the instrumentation involved, thereby hindering bulk production. Herein, we present a colloidal synthesis route for enantiopure bow-ties by guiding the electrostatic and coordination interactions between cadmium ions and chiral amino acid cysteine (Cys). Cd-Cys bow-ties are self-assembled from sheet-like monomeric units, with individually controllable length, width and pitch, leading to tunable chiroptical activity across 500 nm to 3 μm wavelength range. This self-limiting structure of bow-ties can be described within the theoretical framework of geometrical frustration and provide chemical design rules for controlling the interaction and bending energy of monomeric units. |
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