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Icosahedral capsids are ubiquitous among spherical viruses, yet their assem- bly pathways and governing interactions remain elusive. We present a molecular dynamics model that incorporates essential physical and biological interactions, including protein diffusion, genome flexibility, and a conformational switch that mimics allostery and activates the elastic properties of proteins upon binding. This switch makes the simulations computationally feasible and enables the assembly of icosahedral capsids around a flexible genome—overcoming long-standing lim- itations in previous models. Using this framework, we successfully reproduce the self-assembly of subunits around a flexible genome into icosahedral shells with numbers greater than one – most notably 3, the most common structure in na- ture – a feat that rigid-body models have so far failed to achieve. We systematically explore the range of morphologies formed with different genome architectures, in line with in vitro experiments using cowpea chlorotic mottle virus capsid proteins: viral RNAs with more complex structure form more complete and stable capsids than linear ones. These results provide a predictive framework for genome-guided assembly and capsid design. 

Aerodynamic shape optimization is very useful for enhancing the performance of wind-sensitive structures. However, shape parameterization, as the first step in the pipeline of aerodynamic shape optimization, still heavily depends on empirical judgment. If not done properly, the resulting small design space may fail to cover many promising shapes, and hence hinder realizing the full potential of aerodynamic shape optimization. To this end, developing a novel shape parameterization scheme that can reflect real-world complexities while being simple enough for the subsequent optimization process is important. This study proposes a machine learning-based scheme that can automatically learn a low-dimensional latent representation of complex aerodynamic shapes for bluff-body wind-sensitive structures. The resulting latent representation (as design variables for aerodynamic shape optimization) is composed of both discrete and continuous variables, which are embedded in a hierarchy structure. In addition to being intuitive and interpretable, the mixed discrete and continuous variables with the hierarchy structure allow stakeholders to narrow the search space selectively based on their interests. As a proof-of-concept study, shape parameterization examples of tall building cross sections are used to demonstrate the promising features of the proposed scheme and guide future investigations on data-driven parameterization for aerodynamic shape optimization of wind-sensitive structures. 

Aerodynamic shape optimization is very useful for enhancing the performance of wind-sensitive structures. However, shape parameterization, as the first step in the pipeline of aerodynamic shape optimization, still heavily depends on empirical judgment. If not done properly, the resulting small design space may fail to cover many promising shapes, and hence hinder realizing the full potential of aerodynamic shape optimization. To this end, developing a novel shape parameterization scheme that can reflect real-world complexities while being simple enough for the subsequent optimization process is important. This study proposes a machine learning-based scheme that can automatically learn a low-dimensional latent representation of complex aerodynamic shapes for bluff-body wind-sensitive structures. The resulting latent representation (as design variables for aerodynamic shape optimization) is composed of both discrete and continuous variables, which are embedded in a hierarchy structure. In addition to being intuitive and interpretable, the mixed discrete and continuous variables with the hierarchy structure allow stakeholders to narrow the search space selectively based on their interests. As a proof-of-concept study, shape parameterization examples of tall building cross sections are used to demonstrate the promising features of the proposed scheme and guide future investigations on data-driven parameterization for aerodynamic shape optimization of wind-sensitive structures 

The paper presents a new Yoshimura origami that exhibits flat foldability. 

Oxidation of the sub-arc mantle driven by slab-derived fluids has been hypothesized to contribute to the formation of gold deposits in magmatic arc environments that host the majority of metal resources on Earth. However, the mechanism by which the infiltration of slab-derived fluids into the mantle wedge changes its oxidation state and affects Au enrichment remains poorly understood. Here, we present the results of a numerical model that demonstrates that slab-derived fluids introduce large amounts of sulfate (S6+) into the overlying mantle wedge that increase its oxygen fugacity by up to 3 to 4 log units relative to the pristine mantle. Our model predicts that as much as 1 wt.% of the total dissolved sulfur in slab-derived fluids reacting with mantle rocks is present as the trisulfur radical ion, S3–. This sulfur ligand stabilizes the aqueous Au(HS)S3– complex, which can transport Au concentrations of several grams per cubic meter of fluid. Such concentrations are more than three orders of magnitude higher than the average abundance of Au in the mantle. Our data thus demonstrate that an aqueous fluid phase can extract 10 to 100 times more Au than in a fluid-absent rock-melt system during mantle partial melting at redox conditions close to the sulfide-sulfate boundary. We conclude that oxidation by slab-derived fluids is the primary cause of Au mobility and enrichment in the mantle wedge and that aqueous fluid-assisted mantle melting is a prerequisite for formation of Au-rich magmatic hydrothermal and orogenic gold systems in subduction zone settings.