Bulletin of the American Physical Society
APS March Meeting 2021
Volume 66, Number 1
Monday–Friday, March 15–19, 2021; Virtual; Time Zone: Central Daylight Time, USA
Session F07: Self-and Directed Assembly (Equilibrium and Non-equilibrium) IILive
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Sponsoring Units: DSOFT Chair: Agnese Curatolo, Harvard University Room: 07 |
Tuesday, March 16, 2021 11:30AM - 11:42AM Live |
F07.00001: Role of Interfacial Free Energy in Non-classical Nucleation of Polyhedral Nanoparticles Abhishek Sharma, Fernando A Escobedo Direct measurements of the interfacial free energy between disordered & ordered phases of hard nanoparticles were conducted via cleaving walls method with Monte Carlo simulations. At the disordered-ordered phase coexistence, hard cubes are found to have an unusually low interfacial free energy relative to other shapes. A law of mass action model is constructed to describe the relation between the concentration of ordered nuclei & interfacial free energy. For a low enough interfacial free energy, as in the case of hard cubes, the model predicts a high concentration of ordered nuclei in the disordered phase. This aligns with previous observations for hard cubes, where ripening among concentrated pre-critical nuclei leads to non-classical bulk phase transition. Simulations of hard truncated cubes reveal a similar phase transition, albeit with a much higher free energy barrier than hard cubes, a difference that can be ascribed to a higher interfacial free energy. Interfacial free energies were obtained for various crystal planes, which in case of hard gyrobifastigia accurately predict the shape & interfacial free energy of the nucleus via Wulff construction. Results indicate a general correlation of roughness of the interface with its interfacial free energy. |
Tuesday, March 16, 2021 11:42AM - 11:54AM Live |
F07.00002: A computational toolbox for heterogeneous self-assembly Agnese Curatolo, Carl Goodrich, Ofer Kimchi, Michael Brenner Self-assembly is a process in which small building blocks spontaneously form multimeric structures. This phenomenon is one of the hallmarks of soft matter, where it appears at all scales, from protein complexes, to lipid vesicles, to colloidal clusters. One of the hardest challenges in soft matter self-assembly is predicting the yield of a given structure from the properties of its building blocks and the conditions of the surrounding environment. In general, the parameter space is too large to be explored through experiments, which are often time-intensive and expensive. A more practical solution is to use analytical theories and simulations, which can improve our ability to engineer new materials with carefully designed properties. Previous efforts in this space have focused on the theoretical modeling of building blocks with simple geometry, such as spherical colloids. However, a theory for the self-assembly of building blocks with less trivial shapes, typical of, e.g. protein molecules, is still lacking. Here I will present an analytical/computational toolbox to compute the yield of structures whose building blocks can have arbitrary shape and interactions. |
Tuesday, March 16, 2021 11:54AM - 12:06PM Live |
F07.00003: The time complexity of self-assembly Florian Gartner, Isabella R Graf, Erwin Frey Time efficiency of self-assembly is crucial for many biological processes. Moreover, as larger and ever more complex nanostructures are to be realized for technological or medical applications, time efficiency in artificial self-assembly becomes vital. In computer science, the concept of time complexity is used to characterize the efficiency of an algorithm and to classify computational problems according to their degree of difficulty. This parameter describes how an algorithm’s runtime depends on the size of the input data. Here we characterize the time complexity of self-assembly processes by exploring how the time required to realize a certain, substantial yield of a given target structure scales with its size. We identify distinct classes of assembly scenarios, i.e. ‘algorithms’, to accomplish this task, and show that they exhibit drastically different degrees of complexity. Based on our analysis, we suggest a fully irreversible scheme for the artificial self-assembly of nanostructures, which complements the state-of-the-art approach using reversible binding reactions and requires no fine-tuning of binding energies. |
Tuesday, March 16, 2021 12:06PM - 12:18PM Live |
F07.00004: 3D self-replication of DNA nanostructures Feng Zhou, Heng Ni, Guolong Zhu, Ruojie Sha, Nadrian Seeman, Paul M Chaikin Self-replication is a natural process that can generate materials and pass along information. We have seen several examples of artificial self-replication in which the template assembles, organizes and directs formation of the target nanostructure. However, the self-assembly procedure generally requires an assembly space of higher dimensionality than that of the template. This makes it challenging to template and replicate a 3D object. Here, we report the direct self-replication of a 3D object. First, we fabricate a three face cube corner as our template. The replication proceeds by self-assembling three daughter origami tiles to three edges of the cube corner. DNA single strands on each cube face and daughter tile hybridize to fold the tiles inward and complete the cubic box. The daughter tiles are then cross-linked into a new cube corner. Heating releases the two complementary cube corners. This method provides a general approach for conducting high-order self-replication by organizing the materials via folding. Considering that the 3D DNA nanostructure is a functional platform, this type of 3D self-replication can produce new materials, such as chiral plasmonic nanomaterials, by passing the steric information through successive generations. |
Tuesday, March 16, 2021 12:18PM - 12:30PM Live |
F07.00005: A Coarse-Grained Simulation Model for Self-Assembly of DNA-Coated Emulsion Droplets Gaurav Mitra, Chuan Chang, Angus McMullen, Daniela Puchall, Jasna Brujic, Glen Hocky DNA-coated emulsion droplets constitute a promising experimental platform for self-assembly because of thermo-reversible binding interactions between the complementary strands of sticky DNA on adjacent droplets. The DNA are mobile and can freely diffuse on the surface of these droplets and the valence of the droplets naturally emerges as a consequence of the concentration of DNA on the surface as well as the strength of the binding or unbinding interactions. We have designed a coarse-grained molecular dynamics simulation model to study the self-assembly of these DNA-coated emulsion droplets. Using this model we show, in accordance with experiment, that ‘colloidomer’ chains can be formed under conditions where the preferred valence is two. We also study the behavior of these colloidomers in solution. The crucial element of our simulation model is temperature-dependent dynamic binding and unbinding between beads representing the DNA-coated droplets. This dynamic binding is implemented as a custom plugin to HOOMD-Blue which allows us to incorporate and study its effect on the self-assembly process. This platform opens the path for the study of thermodynamic valence control and folding of emulsion droplets. |
Tuesday, March 16, 2021 12:30PM - 12:42PM Live |
F07.00006: Aggregation of amyloid beta protein under different shearing conditions: Experiments and modelling Sriram Krishnamurthy, Swathi Sudhakar, Ethayaraja Mani Amyloid proteins are prone to form insoluble fibrillar aggregates, which have implications in various neurodegenerative diseases. While the monomers themselves are not toxic, their assembly into oligomers and fibrillar forms are harmful. There is a multi-fold increase in the fibrillation rate when the peptide solution is stirred, shaken, or agitated. In this work, steady and unsteady shear experiments are performed on Aβ40 solution using a Couette cell and orbital shaker, respectively. Under steady shear, there is an increase in both the mass of fibrils and aggregation rate with the shear rate. When shaken, the lag time decreases with an increase in the rotational speed of the shaker. A population balance model is developed to account for the effect of steady and unsteady shear on the aggregation of Aβ40 to explain these contrasting mechanisms of aggregation kinetics. The kinetic model includes the primary nucleation, elongation, fragmentation, and depolymerization steps. The effect of steady shear is captured by the depolymerization rate constant (kd). It is observed that the kd decreases with shear rate initially and saturates at high shear rates. The population balance model results agree quantitatively well with the experimental data. |
Tuesday, March 16, 2021 12:42PM - 12:54PM Live |
F07.00007: Elastic Frustration In Self-Assembly M. Mert Terzi, Hugo Le Roy, Martin Lenz Self-assembly of identical particles, if the particles fit together, leads to space filling aggregates. However, in the case of misfitting particles, the resulting aggregates may have limiting sizes due to the frustration. One of the ways of the frustration occurs is the shape misfit of building blocks such that particles need to deform elastically in order to fit each other. The energy cost of elastic deformation competes with a surface tension which drives the particle into assembly. In the regime in which these two energies are comparable, it is very little known about what type of structures and shapes the aggregates have due to the elastic frustration. We tackle the frustrated self-assembly using a coarse grained, continuum model. We determine a phase diagram which shows favorable shapes of aggregates for given parameters. The phase diagram shows us that incompressibility and existence of soft modes favors the fibrillar structures for aggregates. |
Tuesday, March 16, 2021 12:54PM - 1:06PM Live |
F07.00008: Renormalization group analysis of frustrated self-assembly Lara Koehler, Pierre Ronceray, Martin Lenz The self-assembly of shapes that do not fit exactly together can lead to geometrical frustration, and previous numerical simulations have shown that this frustration tend to favor slender self-assembled structures. However, the relationship between the microscopic shape, and the size, structure and dimensionality of the emerging aggregate have yet to be understood. |
Tuesday, March 16, 2021 1:06PM - 1:18PM Live |
F07.00009: Anyonic defect braiding and spontaneous chiral symmetry breaking in dihedral liquid crystals Alexander Mietke, Jorn Dunkel Dihedral liquid crystals (DLCs) are assemblies of microscopic constituent particles that exhibit k-fold discrete rotational and reflection symmetries. Generalizing the half-integer defects in nematic liquid crystals, two-dimensional DLCs can host point defects of fractional topological charge ±m/k. Starting from a generic microscopic model, we derive a unified hydrodynamic description of DLCs with aligning and anti-aligning interactions in terms of Ginzburg-Landau and Swift-Hohenberg theories for a universal complex order-parameter field. Using this, we demonstrate in both continuum and particle simulations how braiding protocols, implemented through a suitable boundary anchoring, can realize classical counterparts of anyonic exchange symmetries. The theory further predicts a novel spontaneous chiral symmetry breaking transition in anti-aligning DLCs, in quantitative agreement with particle simulations. In view of recent advances in the design and assembly of dihedral colloids, we expect that these theoretical predictions can be realized with currently available technology, promising a path to fractional topological information storage in soft matter systems. |
Tuesday, March 16, 2021 1:18PM - 1:30PM Live |
F07.00010: Domain-wall networks rule the ordering dynamics of flocking matter. Amelie Chardac, Ludwig Hoffmann, Yoann Poupart, Luca Giomi, Denis Bartolo We address the ordering dynamics of flocking matter. |
Tuesday, March 16, 2021 1:30PM - 1:42PM Live |
F07.00011: Complex and Stable Capillary Origami Structures through Adhesion Timothy Twohig, Andrew Croll Capillary origami has had great success in offering a solution to nondestructively create bends, folds, and wrinkles in even the thinnest of polymer films. However, to achieve the full potential of origami designs with capillary-driven assembly, methods to create stable and multi-step structures need to be explored. Our research incorporates adhesion into the existing methods for capillary origami to give the researcher the opportunity to bend, crease, and unfold thin films in a manner similar to the multi-step procedures needed to create classic origami models. Tuning film-film and film-substrate adhesion values creates a versatile handle that can be used to precisely place desired features in a thin film system. Bending plays an integral role in the peeling process, which we map out in an experimental state diagram which highlights how ‘directional’ adhesion allows more precise peeling control. Capillary origami techniques can then be used to physically move the film to the desired position, facilitating both the folding and unfolding processes. Repetition of this process allows for the creation of multi-step, folded designs that are not otherwise possible. |
Tuesday, March 16, 2021 1:42PM - 1:54PM Live |
F07.00012: Harnessing the Bacterial Bath for Self-Assembly Dan Grober, Jeremie Palacci
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Tuesday, March 16, 2021 1:54PM - 2:06PM Live |
F07.00013: Machines made of Machines: Design and mechanical study of an active polymer Quentin Martinet, Antoine Aubret, Jeremie Palacci It has been previously demonstrated that Janus particles can be optically controlled to self-assemble into micro-gears [Aubret et al., Nature Physics 2018]. By using a spatial light modulator (SLM), we have been able to construct a great number of more complex micro-machines. With a light pattern, it is then possible to configure the dynamical behavior of a structure, such as a translation movement with an arrow’s shape. |
Tuesday, March 16, 2021 2:06PM - 2:18PM Live |
F07.00014: Characterizing the routes to nonequilibrium morphologies in two dimensional microphase formers Bijoy Daga, Patrick Charbonneau
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Tuesday, March 16, 2021 2:18PM - 2:30PM Live |
F07.00015: Nonequilibrium speed-up of multi-target self-assembly Gili Bisker, Jeremy England Many biological systems rely on the ability to self-assemble different target structures using the same set of components. Equilibrium self-assembly suffers from a limited capacity in this case, due to increasing number of decoy states with increasing number of targets encoded. Moreover, increasing the kinetic stability of a target comes at a price of introducing kinetic traps, leading to slower assembly. Using a toy physical model of interacting particles, we demonstrate that local driving can improve both the assembly times and kinetic stability of multi-target self-assembly. Our results illustrate the role that nonequilibrium drive plays in overcoming trade-offs that are inherent to equilibrium assemblies. |
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