# gst: movers and shaker, the dynamics of granular matter

 << Granular materials are disordered systems often found in a far-from-equilibrium state. >> 

 << You can think of it like a beaker filled with loose sand, (..) At first there are big holes between the grains. So initially, it's easy for a grain to shift position by falling into an empty space. But as these spaces start to get smaller, it becomes less likely that a grain can fall through one. As the taps continue, it takes increasingly cooperative events to create the space necessary for more compaction. >> Stefan Boettcher. 

<< Previous research has shown a similar statistical pattern for the behavior of amorphous solids that don't form ordered crystals when moving from a liquid to a solid state, such as glass and many polymers. >> 

Carol Clark. Movers and shakers: New evidence for a unifying theory of granular materials. Emory University. Jan 08, 2021. 

https://phys.org/news/2021-01-movers-shakers-evidence-theory-granular.html   

Paula A. Gago, Stefan Boettcher. 

Universal features of annealing and aging in compaction of granular piles. 

PNAS. 117 (52) 33072-33076. doi: 10.1073/ pnas.2012757117. Dec 14, 2020. 

https://www.pnas.org/content/117/52/33072

# gst: expanding 'bubbles' of distortion in the nano lattice of a material, a glimpse of polarons

 << Polarons are fleeting distortions in a material's atomic lattice that form around a moving electron in a few trillionths of a second, then quickly disappear. As ephemeral as they are, they affect a material's behavior, >> 

 << When you put a charge into a material by hitting it with light, like what happens in a solar cell, electrons are liberated, and those free electrons start to move around the material, (..) Soon they are surrounded and engulfed by a sort of bubble of local distortion—the polaron—that travels along with them, (..)  Some people have argued that this 'bubble' protects electrons from scattering off defects in the material, and helps explain why they travel so efficiently to the solar cell's contact to flow out as electricity. >> Burak Guzelturk.

<< The hybrid perovskite lattice structure is flexible and soft—like a strange combination of a solid and a liquid at the same time, (..) and this is what allows polarons to form and grow. >> Aaron Lindenberg.

Glennda Chui. First glimpse of polarons forming in a promising next-gen energy material. SLAC National Accelerator Laboratory. Jan 04, 2021.

https://phys.org/news/2021-01-glimpse-polarons-next-gen-energy-material.html

Burak Guzelturk, Thomas Winkler, et al.  Visualization of dynamic polaronic strain fields in hybrid lead halide perovskites. Nat. Mater. doi: 10.1038/ s41563-020-00865-5. 04 Jan 4, 2021.

https://www.nature.com/articles/s41563-020-00865-5   

# gst: apropos of 'strange' transitions to self-assemble into an egg; the coordinated elastic behavior to swirl in a vortex (D. melanogaster)

 << At the end of its first week of development, a striking change occurs in a fruit-fly egg cell. The cell’s internal fluid motion transitions from a disordered mix of small-scale flows to a single vortex that encompasses the entire cell. >> 

 << Given the fluid’s incompressibility, those forces can give rise to what the researchers call a  "swirling" instability, and the flow switches to a cell-spanning rotation. The threshold of molecular motor activity for the transition depends on the buckling of individual microtubules, which are treated as elastic rods. >> 

A Vortex in an Egg Cell. Physics 14, s1. Jan 13, 2021.  

https://physics.aps.org/articles/v14/s1

David B. Stein, Gabriele De Canio, et al. Swirling Instability of the Microtubule Cytoskeleton. Phys. Rev. Lett. 126, 028103.  doi: 10.1103/ PhysRevLett.126.028103. Jan 13, 2021.

https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.126.028103  

# gst: apropos of the structure of natural codes, a RNA folding knot (origami-style) dance

 << Every second, a myriad of shapeless strands of RNA fold, origami-style, into intricate structures inside living cells. Now, for the first time, researchers can watch a data-driven video of this folding as RNA molecules are made by the cellular machinery. >> 

<< as the RNA strand grows, it twists, forming knot-like structures. But as more RNA building blocks are added to the strand, the knots unravel, allowing the molecule’s structure to emerge. >> 

Ground-breaking films show RNA’s complex curves take shape. Experimental data and predictive algorithms combine to reveal the essential biomolecule’s shape-shifting.

Nature. Jan 19, 2021. 

https://www.nature.com/articles/d41586-021-00126-8

AA << model the folding of an RNA called SRP, an ancient RNA found in all kingdoms of life. The molecule is well-known for its signature hairpin shape. When watching the videos, the researchers discovered that the molecule ties itself into a knot and unties itself very quickly. Then it suddenly flips into the correct hairpin-like structure using an elegant folding pathway called toehold mediated strand displacement. >>

<< To the best of our knowledge, this has never been seen in nature, (..) We think the RNA has evolved to untie itself from knots because if knots persist, it can render the RNA nonfunctional. The structure is so essential to life that it had to evolve to find a way to get out of a knot. >> Julius Lucks. 

Amanda Morris. New Videos Show RNA as it's Never Been Seen. First-ever data-driven movies illuminate RNA's mysterious folding process.  McCormick School of Engineering. Jan 15, 2021.

https://www.mccormick.northwestern.edu/news/articles/2021/01/new-videos-show-rna-as-its-never-been-seen.html 

https://youtu.be/2XTi9LG9NnU

Angela M Yu, Paul M. Gasper, et al. Computationally reconstructing cotranscriptional RNA folding from experimental data reveals rearrangement of non-native folding intermediates. Molecular Cell. doi: 10.1016/ j.molcel.2020.12.017

Jan 15, 2021. 

https://www.cell.com/molecular-cell/fulltext/S1097-2765(20)30936-9

# gst: apropos of waves perturbed by weak turbulences

<< Wave phenomena are ubiquitous at all scales throughout the Universe, and where there are waves, there’s the potential for wave turbulence. Wave turbulence is the physical state that arises in a continuous medium when a large number of wave modes interact with each other randomly. >>

<< A specific case of wave turbulence in which weakly nonlinear waves propagate in an unbounded space is described by weak turbulence theory. Capturing the dynamics of this regime will be helpful to accurately model large fluid systems. >>

<< In a rotating fluid, the predicted wave spectrum for interacting weakly nonlinear inertial waves is perturbed by the formation of geostrophic modes—columnar vortices aligned with the rotation axis (..) (AA) successfully suppress geostrophic modes with the addition of two honeycomb-patterned plates, allowing them to confirm the predictions of weak turbulence theory. >>

Sergey Nazarenko. Verifying Weak Turbulence Theory.  Physics 13, 194. Dec 14, 2020. 

https://physics.aps.org/articles/v13/194

Eduardo Monsalve, Maxime Brunet, et al. Quantitative Experimental Observation of Weak Inertial-Wave Turbulence. Phys. Rev. Lett. 125, 254502. Dec 14, 2020.

https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.125.254502

# gst: the strong impact on nanosheets by the weak van der Waals force

<< Van der Waals is a weak force that allows neutral molecules to attract one another through randomly fluctuating dipoles, depending on distance. Though small, its effects can be seen in the macro world, like when geckos walk up walls. >> 

<< Van der Waals forces are everywhere and, essentially, at the nanoscale everything is sticky, (..) When you put a large, flat particle on a large, flat surface, there's a lot of contact, and it's enough to permanently deform a particle that's really thin and flexible. >> 

Matt Jones. 

<< the ubiquitous, "weak" van der Waals force was sufficient to indent a rigid silver nanosheet. The phenomenon suggests possible applications in nanoscale optics or catalytic systems. >>

<< In further experiments, (..) nanospheres could be used to control the shape of the deformation, from single ridges when two spheres are close, to saddle shapes or isolated bumps when the spheres are farther apart. >> 

Mike Williams. Weak force has strong impact on nanosheets. Rice University. Dec 15, 2020. 

https://phys.org/news/2020-12-weak-strong-impact-nanosheets.html

Sarah M. Rehn, Theodor M. Gerrard-Anderson, et al. Mechanical Reshaping of Inorganic Nanostructures with Weak Nanoscale Forces. Nano Lett. doi: 10.1021/ acs.nanolett.0c03383. Dec 10, 2020. 

https://pubs.acs.org/doi/10.1021/acs.nanolett.0c03383  

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