Bulletin of the American Physical Society
APS March Meeting 2018
Volume 63, Number 1
Monday–Friday, March 5–9, 2018; Los Angeles, California
Session L02: Self-assembly of Nanomaterials: Supramolecular Self-assembly IFocus
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Sponsoring Units: DCP Chair: Nicholas Kotov, University of Michigan - Ann Arbor Room: LACC 150B |
Wednesday, March 7, 2018 11:15AM - 11:51AM |
L02.00001: How does a simple virus self-assemble? Invited Speaker: Vinothan Manoharan Simple RNA viruses consist of proteins that form a highly-ordered protective shell (called a capsid) around the viral RNA. Many such viruses are self-assembled: infectious viral particles form spontaneously in a mixture of RNA and coat protein. The yield and fidelity of the assembly is particularly remarkable in viruses with a triangulation number of 3 or higher, in which case some of the proteins must find their way to 5-fold-symmetry sites and others to 3-fold sites in the same shell. To understand how such systems assemble, we use interferometric techniques to measure the scattering of a single assembling viral particle (MS2 bacteriophage) as a function of time. By comparing the scattered intensity to that of the wild-type virus, we infer the mass of proteins that have attached to the central RNA on time scales ranging from milliseconds to minutes. We find that individual particles grow to nearly full size in a short time following a much longer delay period. The distribution of delay times suggests that the assembly follows a nucleation-and-growth pathway. |
Wednesday, March 7, 2018 11:51AM - 12:03PM |
L02.00002: Measurements of the Assembly of Individual HIV-1 Gag Protein Capsids Around Spherical Templates Aaron Goldfain, Rees Garmann, Pooja Saxena, Bogdan Dragnea, Vinothan Manoharan Despite the abundance of structural information about virus capsids, relatively little is known about how they assemble. The small sizes of the capsids and the wide range of timescales involved in the assembly process make it difficult to directly measure the assembly kinetics. We use a microscopy method based on interferometric scattering that addresses both of these challenges, allowing us to measure the the size of individual capsids as a function of time. We apply this method to study the self-assembly of the Gag protein of HIV-1 around a spherical template that is coated in nucleic acid. We find that a simple Langmuir adsorption model can describe the growth kinetics of each capsid. In addition, the assembly rate has a strong concentration dependence, and the binding of capsid proteins is reversible. |
Wednesday, March 7, 2018 12:03PM - 12:15PM |
L02.00003: Direct Measurements of the Assembly of Individual Viral Capsids Around Their RNA Genome Rees Garmann, Aaron Goldfain, Vinothan Manoharan Viral capsids are often constructed from many copies of a single protein subunit arranged with high symmetry into a closed shell. The architecture of these structures has been determined in exquisite detail using high-resolution structural techniques such as x-ray crystallography and cryo-electron microscopy. However, we do not yet understand how the capsids form. Kinetic measurements on bulk solutions of assembling capsids obscure the full pathways, because they measure the signal from viruses at different stages of growth. I will describe experiments in which we use interferometric scattering microscopy to monitor the assembly of single viral capsids from start to finish. In the experiments, we flow capsid proteins from bacteriophage MS2 into a sample chamber and monitor their binding to individual copies of the RNA genome that are tethered to the chamber surface. We find that the assembly kinetics are characterized by long delays preceding comparatively fast growth, suggesting a nucleation-and-growth assembly pathway. These findings should inform the construction of quantitative models of the assembly process. |
Wednesday, March 7, 2018 12:15PM - 12:27PM |
L02.00004: Encapsulation of cargo by protein shells with and without spontaneous curvature Farzaneh Mohajerani, Michael Hagan Bacterial microcompartments are large, roughly icosahedral protein shells that encase certain metabolic pathways in bacteria. Microcompartments form by assembling around a dense complex containing thousands of copies of enzymes and other components. How the formation of the microcompartment depends on the interplay between protein-protein interactions and the cargo is poorly understood. In this talk we present dynamical simulations and an equilibrium continuum theory exploring how microcompartment size and degree of shell completion depend on control parameters including interaction strengths, subunit and cargo stoichiometries, and the shell spontaneous curvature. Depending on these parameters, we find that the presence of a cargo can either increase or decrease the size of a shell, relative to the intrinsic protein spontaneous curvature. For example, even proteins without spontaneous curvature (which preferentially form flat sheets) exhibit a well-defined size distribution when assembling around stoichiometrically limiting cargo. These results may shed light on recent experimental observations – in some BMC systems, empty shells are smaller and more monodisperse than full shells, whereas in other systems empty shells are larger than full ones. |
Wednesday, March 7, 2018 12:27PM - 12:39PM |
L02.00005: Simulations on encapsulation of multiple cargoes in Bacterial Microcompartments Lev Tsidilkovski, Farzaneh Mohajerani, Michael Hagan Bacterial microcompartments are self-assembling protein shells that encapsulate enzymes to accelerate the rates of chemical reactions. Recent work has shown that encapsulation of multiple enzymes in microcompartments may increase the efficiency of multi-enzyme cascades by colocalizing the participating molecules. We will describe coarse-grained computational modeling of the colocalization and spatial organization of multiple cargo molecules within assembled shells. Our simulations show how modifying the interaction strengths of the particles involved changes relative quantities of the proteins contained within. We present analysis of simulation trajectories demonstrating the effects of assembly pathways, cargo-cargo interactions and shell-cargo interactions on the shell contents. Our results provide a basis for the future of re-engineering bacterial microcompartments as multienzyme nanoreactors. |
Wednesday, March 7, 2018 12:39PM - 12:51PM |
L02.00006: Effect of Polymer Chain Polydispersity on the Size of Spherical Micelles Formed in Solution Sriteja Mantha, Shuanhu Qi, Friederike Schmid Amphiphilic molecules in solution display a rich diversity of micellar morphologies. Micellar structures and their size distribution are expected to depend on molecular parameters like, chain length of amphiphilic molecules, the solvophobic to solvophilic ratio, the intermolecular interactions etc. In this work we investigate the effect of polymer length polydispersity on the size of spherical micelles formed by diblock copolymers in solution. Using self-consistent field theoretic simulations, we show that monodisperse polymers favor formation of micelles of different sizes, whereas polydisperse polymers favor the formation of micelles with monodisperse size distribution. Differences in the free energetic contributions associated with the chain stretching explains above differences in the size of micelles formed by monodisperse and polydisperse diblock copolymers in solution. In the micelles formed by monodisperse polymers, chains are stretched to different lengths to accommodate micelles of different sizes. On the other hand such a chain stretching is found to be very narrow in micelles formed by polydisperse polymers. |
Wednesday, March 7, 2018 12:51PM - 1:03PM |
L02.00007: Atomistic Simulations of Micellization and Adsorption of Imidazoline-Based Surfactants Near Metal-Water Interfaces Yathish Kurapati, Sumit Sharma Imidazoline-based surfactants are popular corrosion inhibitors in the oil and gas industry. These molecules are known to strongly adsorb onto the metal-water interfaces, as well as form micelles in the aqueous phase. High degree of corrosion inhibition is observed at concentrations close to critical micelle concentration (CMC). However, molecular underpinnings of the relationship between micellization and surface adsorption are not completely understood. By employing atomistic representation of imidazoline-based surfactants in explicit water, we have studied micellization and diffusion properties of these molecules as a function of micelle size and size of the alkyl tail. Furthermore, we have investigated the adsorption characteristics of these molecules at the metal-water interface and calculated free energy profiles of adsorption using umbrella sampling technique and weighted histogram analysis method (WHAM). We find that the micelle forming tendency and free energy of adsorption of these molecules depends strongly on the length of alkyl tail. The significance of inhibitor-inhibitor interactions on adsorption and micellization will be discussed. |
Wednesday, March 7, 2018 1:03PM - 1:15PM |
L02.00008: The Effect of Resins on the Aggregation Behavior of Asphaltenes Mortaza Derakhshani Molayousefi, Martin McCullagh Asphaltenes are macromolecules known to be responsible for forming deposits in pipelines and other petroleum industry equipment causing an annual expenditure of billions of dollars to clean up. Due to environmental disadvantages and tremendous cost of current cleaning methods, investigating alternative asphaltene precipitation alleviation strategies is necessary. Asphaltenes contain particular molecular features such as aromatic plains which facilitate their self-assembly in crude oil. However, the role of other components of crude oil such as resins is not transparent in the aggregation process due to the lack of a molecular-level insight. We conducted a molecular dynamics (MD) study to probe the role of resins in aggregation behavior of model asphaltenes at a molecular level. We classified asphaltenes to three categories of non-aggregating, mildly-aggregating, and readily-aggregating based on their aggregation propensity. We found either no or negative correlation between the presence of resin and the aggregation propensity of the asphaltenes. These findings will pave the road to modify oil production methods to minimize asphaltene deposition. |
Wednesday, March 7, 2018 1:15PM - 1:27PM |
L02.00009: Understanding the Mechanism behind Polymorphism and Phase Transitions in p-Type Small Organic Semiconductor Nikita Sengar, Paulette Clancy Small organic semiconductors (OSs) have a predilection to pack into multiple, structurally distinct, crystal structures (polymorphism) with differing ability to transport charge. Controlling polymorphism is critically important since any slight variation in π-orbital overlap can lead to orders of magnitude difference in charge carrier mobility. In order to understand the origin behind polymorphism in single crystals of a high performing p-type OS, di-tertiary butyl benzothiophene (ditBu-BTBT), we conducted a detailed Molecular Dynamics (MD) study to predict the structures of stable and metastable polymorphs, and find ways to control inter-polymorph phase transitions in ditBu-BTBT systems. We used a combination of MD and advanced Bayesian optimization to accelerate the pace of finding the best combinations of candidate polymorphs (optimizing six dimensions of unit cell lengths and angles) and temperature that leads to the lowest energy structure. Next, we calculated the free energy barrier associated with the rotation of side-chains around the central core of ditBu-BTBT. We hypothesize that these calculations explain what triggers, or offsets, phase transitions in molecular crystals. The insight gained by this novel approach can be used to design next-generation materials. |
Wednesday, March 7, 2018 1:27PM - 1:39PM |
L02.00010: Quantitative description of segregation degree in holographic nanocomposites Guannan Chen, Mingli Ni, Haiyan Peng, Xiaolin Xie Holographic nanocomposites have been broadly used in photonic crystals, 3D display, data storage and so forth. They are formed via holographic photopolymerization induced phase separation with photoinitiating system, monomer and nanoparticles. During the formation of holographic nanocomposites, it is crucial to control the photopolymerization kinetics and gelation, and thus to achieve predesigned grating features with desirable size and morphology. Toward this end, a photoinitibitor with concurrent photoinitiation and photoinhibition functions is proposed to exert the precise spatiotemporal control on the grating structures. In addition, a correlation between the segregation degree, SD, and the ratio of gelation time to viscosity of mixture for holography is deduced. The function provides theoretical guidance to control the morphology and performance of holograms. |
Wednesday, March 7, 2018 1:39PM - 1:51PM |
L02.00011: Two-dimensional bilayer ice structure on Au(111) probed by noncontact atomic force microscope. Runze Ma, Duanyun Cao, Jinbo Peng, Ying Jiang The initial stages of heterogeneous ice nucleation at surfaces are relevant to many fields as diverse as atmospheric chemistry, astrophysics and biology. To date, scanning tunneling microscope (STM) has been ideal to provide molecular-scale description of water-solid interaction. However, a majority of the STM works have been done focused on hydrophilic surfaces, such as Pt, Ru, Pd, NaCl, MgO etc. The atomic–scale structures of ice overlayers on hydrophobic surfaces are still lacking. The main difficulty lies in the perturbation of the probe on the fragile water structures on the hydrophobic surfaces because of the weak water-surface interaction. |
Wednesday, March 7, 2018 1:51PM - 2:03PM |
L02.00012: Glassy Dynamics at Pre-melted Grain Boundaries in Ice Ih Maurice De Koning, Pedro Moreira, Roberto Gomes de Aguiar Veiga, Ingrid de Almeida Ribeiro, Rodrigo Moura Freitas, Julian Helfferich Using first-principles and classical molecular dynamics simulations, we study pre-melting phenomena in pristine coincident-site-lattice grain boundaries in proton-disordered hexagonal ice Ih at temperatures just below the melting point Tm. The results are consistent with experimental estimates for the pre-melt layer thickness of low-disorder impurity-free GBs and provide key insight into the mobility of water molecules in the pre-melted layers. In particular, the translational motion of the water molecules is found to be subdiffusive for time scales longer than 10 ns. Furthermore, it is well-described by a continuous-time random walk model characterized by a waiting-time distribution with a power-law decay, suggesting that the dynamics in the pre-melt layers at GBs in ice Ih is glassy in nature, even at temperatures close to Tm. |
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