Bulletin of the American Physical Society
APS March Meeting 2022
Volume 67, Number 3
Monday–Friday, March 14–18, 2022; Chicago
Session K25: Self- and Directed Assembly IRecordings Available
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Sponsoring Units: DSOFT Chair: Chrisy Du, Harvard Room: McCormick Place W-187A |
Tuesday, March 15, 2022 3:00PM - 3:12PM |
K25.00001: Computational Reverse-Engineering Analysis for Scattering Experiments of Assembled Mixtures of Nanoparticles Christian M Heil, Arthi Jayaraman Nanoparticle assembly is a common route to generate materials with specific properties. The assembled material must undergo characterization at multiple length scales to link the structural features with the macroscopic properties. Small angle scattering (SAS) is a useful method to characterize nanoparticles’ assembled structure. The output of SAS experiments is the averaged intensity at various wave vectors, I(q) vs. q, whose interpretation often relies on fitting with analytical models. This model selection can be a limitation when appropriate analytical models do not exist. We present a computational method, CREASE, to analyze the scattering results from spherical nanoparticle mixtures assembled in various confinement geometries. We test the strengths and limitations of our method by using a variety of in silico I(q) obtained from simulations of binary nanoparticle assemblies with varying mixture composition and nanoparticle size dispersity that exhibit varying degrees of mixing/demixing within a confined spherical or thin-film geometry. We will also present extensions of this method for systems (e.g., concentrated solution of micelles) where the form factor of the particle (i.e., micelle) is unknown, and CREASE analyzes both structure and form factor in the assembled mixture. |
Tuesday, March 15, 2022 3:12PM - 3:24PM |
K25.00002: Particle Design Rules for Size Control of Frustrated Assembly : Role of Interaction Range Douglas M Hall, Mark J Stevens, Gregory M Grason Recent developments in the precise tuning of soft particle geometry and interactions provide new opportunities to design functional nanostructures with equilibrium size control by geometric frustration. A current theoretical challenge is to understand the role of discrete particles, and how limitations apparent in discrete particle design connect to limits in the achievable size control as consequences of various modes of frustration escape, such as defect formation and morphology transitions. |
Tuesday, March 15, 2022 3:24PM - 3:36PM |
K25.00003: Decoding the growth kinetics of complex crystals via local structural analysis Maya Martirossyan, Julia Dshemuchadse The growth kinetics of materials with complex crystal structures, such as clathrates and Frank Kasper phases, are poorly described by the standard attachment-based models used for simple, close-packed structures. We can bridge this gap by simulating the self-assembly of identical particles that interact via isotropic pair potentials [1], and study how particles take on different “roles” as they settle into different crystal sites, or local environments. Identical particles that occupy distinct crystal sites exhibit different kinetic behaviors, which we observe via a machine-learning powered order parameter [2] that classifies particles into different local environments during the self-assembly process. This analysis is performed and compared for a variety of structures with different complexities and coordination numbers, and can provide insight for the design and assembly of materials with desired structures and functionalities. |
Tuesday, March 15, 2022 3:36PM - 3:48PM |
K25.00004: Non-equilibrium capillary self-assembly Stuart J Thomson, Daniel M Harris Existing, well-established principles of interfacial capillary self-assembly focus on the behavior of such systems at equilibrium, wherein the resultant self-assembled structures reside in a local minimum of a free-energy landscape. Inspired by recent experiments involving overdamped, microscopic colloids, we herein study experimentally and theoretically the structural rearrangements between ground states of clusters of millimetric spheres bound by capillary attractions. The structural rearrangements are driven by chaotic Faraday waves, which in turn play the role of an active bath. In contrast to colloids, inertial effects are non-negligible in our macroscopic system, prompting the development of a Langevin model of the particle dynamics, informed by the fundamental aspects of the fluid system. Our highly tunable experimental system addresses the relative paucity of model systems for studying inertial active and driven matter and informs new directions for non-invasive, directed self-assembly at the macroscale. |
Tuesday, March 15, 2022 3:48PM - 4:00PM |
K25.00005: Order originating from disorder with intrinsically disordered peptide amphiphiles Roy Beck Amphiphilic molecules and their self-assembled structures have long been the target of extensive research due to their potential applications in fields ranging from materials design to biomedical. An emerging class of molecules, namely, peptide amphiphiles, combines key advantages and circumvents some disadvantages of conventional phospholipids and block copolymers. In this talk, I present new peptide amphiphiles composed of an intrinsically disordered peptide conjugated to variants of hydrophobic domains. These molecules termed intrinsically disordered peptide amphiphiles, exhibit a sharp pH-induced micellar phase-transition from low-dispersity spheres to extremely elongated worm-like micelles. I will present an experimental characterization of the transition and propose a theoretical model to describe the pH response. We also show the potential of the shape transition to serve as a mechanism for the design of a cargo hold-and-release application. Such amphiphilic systems demonstrate the power of tailoring the interactions between disordered peptides for various stimuli-responsive biomedical applications. |
Tuesday, March 15, 2022 4:00PM - 4:12PM |
K25.00006: Programmable self-assembly of nanotubes using DNA origami nanoparticles Daichi Hayakawa, Thomas E Videbaek, Huang Fang, Douglas M Hall, Michael F Hagan, Gregory M Grason, William B Rogers Many proteins and RNA molecules use shape-specific interactions to assemble functional structures in biological systems. The intricate folds and complex interactions between such biomolecules endow them with tunable valence, specificity, and prescribed local curvature, which are all crucial for assembling complicated structures. However, designing and producing synthetic particles with a similar level of structural information is difficult. In this talk, I will show that such geometrical features can be programmed into nanometer-scale synthetic particles using DNA origami. More specifically, we design and synthesize triangular subunits which are roughly 50 nanometers in size and can assemble into rigid tubules of a user-prescribed width, reaching a few micrometers in length. Because the binding angles at the interaction sites can be independently tuned, we can assemble a variety of tubules with widths between 100 to 400 nm. Interestingly, we find that there is a distribution in the width and the chirality of the assembled tubes, suggesting that our DNA origami colloids are flexible. Finally, we introduce a possible route to limit unwanted tubule structures by increasing the number of particle types used in the assembly. |
Tuesday, March 15, 2022 4:12PM - 4:24PM |
K25.00007: Understanding the mechanism of self-limited assembly of tubules using Monte Carlo simulations Huang Fang, Botond Tyukodi, Michael F Hagan, William B Rogers Self-assembly of biomacromolecules is an important approach that nature uses to build biological structures, such as ribosomes, microtubules and viral capsids. Unlike the self-assembly of most synthetic materials, which grow in an unbounded manner, many biological structures undergo self-limited assembly: The assembled structures have at least one finite dimension. An essential question is how such assemblies terminate their growth to select a well-controlled size. To answer this question, we use Monte Carlo simulations to study the kinetic pathways of a class of self-limited structures: cylindrical tubules that are assembled from triangular monomers. In addition to assembly of the target geometry, we observe that the same monomers also assemble into tubules with different widths and chiralities, due to thermal fluctuations and assembly-pathway-dependent kinetic effects. We show that the width distribution is determined by a competition between the monomer insertion rate and the structure closure rate, as well as the underlying free energy landscape. These results elucidate design principles for assembling self-limited structures from synthetic components, such as artificial microtubules that have a desired width and chirality. |
Tuesday, March 15, 2022 4:24PM - 4:36PM |
K25.00008: Effect of Force-dependent Unbinding Kinetics on the Self-Assembly of DNA-Coated Emulsion Droplets Gaurav Mitra, Glen M Hocky Micron-sized emulsion droplets coated with mobile DNA linkers can self-organize into predetermined structures by appropriate control of the droplet valence. Our coarse-grained molecular dynamics simulation model is designed to study the phenomenon of self-assembly of these droplets. A crucial piece of our model is specific one-to-one dynamic bonding between coarse-grained beads representing DNA. We previously designed the model so that the kinetics includes temperature-dependent rates, in order to appropriately represent DNA melting. But we also know that mechanical forces can play a role in governing the lifetime of molecular interactions. Here, we introduce different models of force dependent kinetics into our dynamic bonding model. We then explore how the force-dependent unbinding rates affects the valence of these emulsion droplets. Also, we show how the force-dependent unbinding governs the kinetics of growth of the "adhesion patch" formed between two droplets (by recruitment of the DNA linkers) as well as the size of the adhesion patch. |
Tuesday, March 15, 2022 4:36PM - 4:48PM |
K25.00009: Closed vesicle formation through the spontaneous curvature of flat colloidal membranes Raymond Adkins, Zvonimir Dogic, Leroy Jia, Robert Pelcovits, Thomas Powers, Yuefeng Yang Edgeless vesicles serve many functions in biology, including storage and transport. Many of these functions require shape transformation, where vesicles spontaneously bud off and fuse with one another. However, the length and time scales associated with these processes do not permit visualization of these shape changes in real time with molecular details. We study the dynamics of vesicle formation using a model system of micron-thick colloidal membranes. While colloidal membranes displays similar physics to biological membranes, the dynamics occur at length and time scales that are several orders of magnitude larger than typical cellular vesicles. We describe the observed dynamics of initially flat sheets that undergo curving, budding and fracturing to form closed colloidal vesicles. |
Tuesday, March 15, 2022 4:48PM - 5:00PM |
K25.00010: Multispecies tilings increase the accuracy in assembly of self-limited structures Thomas E Videbaek, Huang Fang, Daichi Hayakawa, Michael F Hagan, William B Rogers The ability to design more complicated subunits for self-assembly, as seen with patchy particles or DNA origami, has opened a large space of complex structures that can be made. One subset of these structures are those with a self-limited length scale, such as spherical shells or cylinders. An interesting consequence of introducing a self-limited length scale larger than the constituent subunits is that the system becomes sensitive to thermal fluctuations, leading to nearby, off-target states in assembly outcomes. We investigate strategies for limiting off-target states from assembly by using multiple types of subunits. To study this assembly strategy we consider tubules composed of triangular monomers. Tube assembly needs at minimum a single type of subunit, where each edge of a triangular monomer has a specific binding angle with another monomer. Tubes with similar widths only differ by slight changes in these binding angles, which are accessible by thermal fluctuations. Using simulations and energetics calculations, we study how multiple species of triangular subunits increases specificity of tubule assembly. We find that the minimum number of subunits needed to achieve full specificity scales with the bending rigidity of the binding sites and the target width of the tube. |
Tuesday, March 15, 2022 5:00PM - 5:12PM |
K25.00011: Temperature protocols for selective self-assembly of competing structures Srikanth Sastry, Arunkumar Bupathy, Daan Frenkel Multi-component self-assembly mixtures offer the ability to encode multiple target structures. Earlier theoretical work have focussed on selective retrieval via changes to the composition of the mixture, seeding or choice of specific interactions, which are target specific. In this work, we show the design of multi-component self-assembly system that can form one of two pre-defined structures through simple temperature protocols. Surprisingly, our observations show that to avoid spurious aggregation, the different components should preferrable have different bonding neighbors in the two target structures. At the same time, our results indicate that the component libary itself should be shared by the two structures, in order to improve selective retrieval. We demonstrate one possible way in which selectivity can be improved, for one of the design targets, through secondary aggregates which we term vestigial aggregates. |
Tuesday, March 15, 2022 5:12PM - 5:24PM Withdrawn |
K25.00012: Liquid phase separation out of thermodynamical equilibrium Alexandra Tayar, Fernando Caballero, Omar A Saleh, Cristina Marchetti, Zvonimir Dogic Living cells contain millions of enzymes and proteins, which carry out multiple reactions simultaneously. To optimize these processes, cells compartmentalize reactions in membraneless liquid condensates. Certain features of cellular condensates can be explained by principles of liquid-liquid phase separation studied in material science. However, biological condensates exist in the inherently out of equilibrium environment of a living cell, being driven by force-generating microscopic processes. These cellular conditions are fundamentally different than the equilibrium conditions of liquid-liquid phase separation studied in materials science and physics. Currently, we lack model systems that enable rigorous studies of these processes. Living cells are too complex for quantitative analysis, while reconstituted equilibrium condensates fail to capture the non-equilibrium environment of biological cells. To bridge this gap, we reconstituted DNA-based membraneless condensates in an active environment that mimics the conditions of a living cell. We combine condensates with a reconstituted network of cytoskeletal filaments and molecular motors and study how the mechanical interactions change the phase behavior and dynamics of membraneless structures. Studying these composite materials elucidates the fundamental physics rules that govern the behavior of liquid-liquid phase separation away from equilibrium while providing insight into the mechanism of condensate phase separation in cellular environments. |
Tuesday, March 15, 2022 5:24PM - 5:36PM |
K25.00013: How the genome modifies the stability and morphology of viral shells Sanaz Panahandeh, Siyu Li, Roya Zandi Simple RNA viruses self-assemble spontaneously and encapsulate their genome into a shell called the capsid. This process is mainly driven by the attractive electrostatics interaction between the positive charges on capsid proteins and the negative charges on the genome. Despite its importance and many decades of intense research, how the virus selects and packages its native RNA inside the crowded environment of a host cell cytoplasm in the presence of an abundance of non-viral RNA and other anionic polymers, it has remained a mystery. In this research, we perform a series of simulations using coarse-grained models to monitor the growth of a viral shell andround a cargo. We find that RNA can completely modify the structure and stability of the capsid. The work suggests that capsid can assemble around non-viral RNA but forming non-icosahedral virion. We show that these structures are strained and can be split into fragments along the stress lines. These fragments can later be assembled into the stable native icosahedral structure if the viral genome becomes available, suggesting a new pathway for the formation of virion in the cell in the presence of other polyanionic species. |
Tuesday, March 15, 2022 5:36PM - 5:48PM |
K25.00014: Self-assembly of retroviral shells and the role of line tension. Yinan Dong, Alex Travesset, Roya Zandi We use continuum elasticity theory to investigate the dynamics of assembly of viral shells. The focus of our study is on the spherical, conical, and spherocylindical structures pertinent to the capsids of retroviruses such as HIV. Within continuum elasticity formalism almost all available results on curved topographies to date are obtained within either a small curvature expansion or an empirical covariant generalization that accounts for screening between Gaussian curvature and disclinations. In this talk, we present a formulation of elasticity theory in curved geometries that allows us to solve the exact elasticity equations for completely general geometries including those relevant to the structure of retroviruses. I also present how our formalism allows us to include the effect of line tension when a viral shell grows. |
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