# gst: a view of multi-system self-assembly

<< a team of scientists in Turkey has demonstrated the fundamental principles of a universal self-assembly process acting on a range of materials-starting from a few atoms-large quantum dots up to nearly 100 trillion atoms-large human cells. >>

AA << not only demonstrated the self-assembly of simple as well as complex structures that are more than four orders of magnitude different in size and mass. They all come together following a sigmoid function, also known as the S-curve. Curiously, they also observed that the individual deviations from the S-curves follow the statistics of the Tracy-Widom distribution, which manifests in diverse, social, economic, and physical systems.>>

<< To initiate self-assembly, either you force the system to deliver a specific outcome, or you use its inner dynamics to your advantage for universal outcomes. We followed the second approach, >> Serim Ilday.

Scientists uncover principles of universal self-assembly. Bilkent University. Apr 20, 2020.

https://phys.org/news/2020-04-scientists-uncover-principles-universal-self-assembly.html

Ghaith Makey, Sezin Galioglu, et al. Universality of dissipative self-assembly from quantum dots to human cells. Nat. Phys. doi: 10.1038/s41567-020-0879-8. Apr 20, 2020.

https://www.nature.com/articles/s41567-020-0879-8

Also

keyword 'self-assembly' in FonT

https://flashontrack.blogspot.com/search?q=self-assembly

keyword 'self' in Notes (quasi- stochastic poetry)

https://inkpi.blogspot.com/search?q=self

# s-nano: self-assembly, also in nanotech

<< some nanomaterials can be coaxed into snapping themselves into desired formations-a process called self-assembly >>

AA << have just developed a way to direct the self-assembly of multiple molecular patterns within a single material, producing new nanoscale architectures.  >>

Smarter  self-assembly  opens  new  pathways  for  nanotechnology. August  8,  2016.

http://m.phys.org/news/2016-08-smarter-self-assembly-pathways-nanotechnology.html

A. Stein, G. Wright, et al. Selective directed self-assembly of coexisting morphologies using block copolymer blends. Nature Communications 7, Article number: 12366 (2016) doi:10.1038/ncomms12366

http://www.nature.com/articles/ncomms12366

# gst: tuning of Janus particles under flows

<< Active colloidal systems with nonequilibrium self-organization constitute a long-standing, challenging area in material sciences and biology. To understand how hydrodynamic flow may be used to actively control self-assembly of Janus particles (JPs), (AA)  developed a model for the many-body hydrodynamics of amphiphilic JPs suspended in a viscous fluid with imposed far-field background flows. >>

They << alter the hydrophobic distribution on the JP-solvent interface to investigate the hydrodynamics that underlies the various morphologies and rheological properties of the JP assembly in the suspension. (They) find that JPs assemble into unilamellar, multilamellar, and striated structures. >>

AA << characterize the effective material properties of the JP structures and find that the unilamellar structure increases orientation order under shear flow, the multilamellar structure behaves as a shear thinning fluid, and the striated structure possesses a yield stress. >> ️

Szu-Pei Fu, Rolf Ryham, Bryan Quaife, and Y.-N. Young. Effects of tunable hydrophobicity on the collective hydrodynamics of Janus particles under flows. Phys. Rev. Fluids 8, 050501. May 11, 2023.

https://journals.aps.org/prfluids/abstract/10.1103/PhysRevFluids.8.050501

Also: Janus, in FonT:  https://flashontrack.blogspot.com/search?q=janus

Also: particle, self-assembly, in: https://www.inkgmr.net/kwrds.html

Keywords: particles, Janus, Janus particles, self-organization, self-assembly

# gst: intricate transitions in elastoactive structures.

<< The interplay between activity and elasticity often found in active and living systems triggers a plethora of autonomous behaviors ranging from self-assembly and collective motion to actuation. Among these, spontaneous self-oscillations of mechanical structures is perhaps the simplest and most widespread type of nonequilibrium phenomenon. >>️

<< Here, (AA) introduce a centimeter-sized model system for one-dimensional elastoactive structures. >>️

<< such structures exhibit flagellar motion when pinned at one end, self-snapping when pinned at two ends, and synchronization when coupled together with a sufficiently stiff link. (..) these transitions can be described quantitatively by simple models of coupled pendula with follower forces. >>️

Ellen Zheng, Martin Brandenbourger, et al. Self-Oscillation and Synchronization Transitions in Elastoactive Structures. Phys. Rev. Lett. 130, 178202. April 25, 2023. 

https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.130.178202

Also:  transition, particle, self-assembly, elastic, pendulum in https://www.inkgmr.net/kwrds.html

Keywords: gst, transition, particle, self-assembly, elastic, pendulum

# chem: spontaneous reconfiguration of deformable nanoparticles (in response to environmental cues)

<< Deformable nanoparticles (NPs) offer unprecedented opportunities as dynamic building blocks that can spontaneously reconfigure during assembly in response to environmental cues. >>

<< deformable spherical NPs of radius 50 nm whose surface is tailored with octahedrally distributed charged patches and double-cap charged patches adapt their shape differently in response to changes in surface charge coverage and ionic strength. >>

AA << find shape transitions to rounded octahedra, faceted octahedra, faceted bowls, oblate spheroids, spherocylinders, dented beans, and dimpled rounded bowls. >>

AA << demonstrate that similar shape transitions can be achieved in deformable NPs of different sizes. >>️

Fanbo Sun, Nicholas E. Brunk, Vikram Jadhao. Shape control of deformable charge-patterned nanoparticles. Phys. Rev. E 107, 014502. Jan 10, 2023.

https://journals.aps.org/pre/abstract/10.1103/PhysRevE.107.014502

Img https://twitter.com/PhysRevE/status/1613183219377086468

Also

keyword 'self-assembly' in FonT

https://flashontrack.blogspot.com/search?q=self-assembly

keyword 'nano' in FonT

https://flashontrack.blogspot.com/search?q=nano

keyword 'nano' in Notes 

(quasi-stochastic poetry)

https://inkpi.blogspot.com/search?q=nano

Keywords: chem, nano, nanoparticles,  NPs, self-assembly, colloids, polymers, vesicle structures.

# gst: self-repelling species could self-organize.

<< Catalytically active particles form clusters when they respond not only to their own chemical targets but to those of other catalysts, too. >>️

AA  << show that the phenomenon of self-organization depends strongly on the network topology. >>️

They << modeled a three-species system (..) systems where each species responds chemotactically only to its own substrate cannot self-organize unless one species is self-attracting. >>️

<< Next, they developed a model that allowed species to respond to both their substrates and their products. Pair interactions between different species in this more complex model drove an instability that spread throughout the three-species system, causing the catalysts to clump together. Surprisingly, this self-organization process occurred even among particles that were individually self-repelling. >>️

Rachel Berkowitz. Self-Repelling Species Still Self-Organize. Physics 16, s128. Sept 19, 2023. 

https://physics.aps.org/articles/v16/s128

Vincent Ouazan-Reboul, Ramin Golestanian, Jaime Agudo-Canalejo. Network effects lead to self-organization in metabolic cycles of self-repelling catalysts. Phys. Rev. Lett. 131, 128301. Sep 19, 2023. 

http://dx.doi.org/10.1103/PhysRevLett.131.128301

Also: self-assembly, network, in https://www.inkgmr.net/kwrds.html 

Keywords: gst, self-assembly, network,  topology.

# evol: spontaneous, immediate asymmetry, the chiral twist

<< When holding a right hand in front of a mirror, one can see a reflected image of a left hand and vice versa. In 1848, Louis Pasteur discovered that organic molecules are much like our hands: they come in mirror-image pairs of left- and right-handed variants. Nowadays, we know that this handedness or chirality (from the Greek word for "hand") is a hallmark of organic molecules. >>

<< Organic molecules are rich in carbon atoms, which form bonds to create either a right or a left "nano-hand." Yet, puzzlingly, life almost always selects to exclusively use one of the two mirror-image twins—a phenomenon called homochirality. For example, terrestrial life is based on left-handed amino acids and right-handed sugars. >>️️

<< A model now proposes a novel explanation for the emergence of homochirality in life—a longstanding puzzle about the origin of life on Earth. >>️

<< Homochirality emerges spontaneously in prebiotic chemical networks that adapt to optimize energy harvesting from the environment. Previously, it was believed that chiral symmetry breaking requires multiple loops of auto-catalysis, which increasingly produces one enantiomer of a molecule while inhibiting the formation of the other. However, the IBS team's results showed that the underlying mechanism of symmetry breaking is very general, as it can occur in large reaction systems with many random molecules and does not require sophisticated network architectures. It was found that this sharp transition to homochirality stems from the self-configuration of the reaction network in order to achieve more efficient harvesting of energy from the environment. >>️

Learning chemical networks give life a chiral twist. Institute for Basic Science. Apr 26, 2022. 

https://phys.org/news/2022-04-chemical-networks-life-chiral.html

William D. Pineros, Tsvi Tlusty. Spontaneous chiral symmetry breaking in a random driven chemical system. Nat Commun 13, 2244. doi: 10.1038/ s41467-022-29952-8. Apr 26, 2022.

https://www.nature.com/articles/s41467-022-29952-8

Also

keyword 'chiral' in FonT

https://flashontrack.blogspot.com/search?q=chiral

keyword 'self-assembly' in FonT

https://flashontrack.blogspot.com/search?q=self-assembly

Keywords: evolution, gst, randomness, self-assembly, self-configuration, break symmetry, asymmetry, chiral, chirality  

# gst: how a synchronization could emerge from chaotic activities

<< Can we find order in chaos? Physicists have shown, for the first time that chaotic systems can synchronize due to stable structures that emerge from chaotic activity. These structures are known as fractals, shapes with patterns which repeat over and over again in different scales of the shape. As chaotic systems are being coupled, the fractal structures of the different systems will start to assimilate with each other, taking the same form, causing the systems to synchronize. >>️

<< If the systems are strongly coupled, the fractal structures of the two systems will eventually become identical, causing complete synchronization between the systems. These findings help us understand how synchronization and self-organization can emerge from systems that didn't have these properties to begin with, like chaotic systems and biological systems. >>️

Topological synchronization of chaotic systems. Bar-Ilan University. Apr 22, 2022. 

https://phys.org/news/2022-04-topological-synchronization-chaotic.html

<< chaotic synchronization has a specific trait in various systems, from continuous systems and discrete maps to high dimensional systems: synchronization initiates from the sparse areas of the attractor, and it creates what (AA) termed as the ‘zipper effect’, a distinctive pattern in the multifractal structure of the system that reveals the microscopic buildup of the synchronization process. >>️

Lahav, N., Sendina-Nadal, I., et al. Topological synchronization of chaotic systems. Sci Rep 12, 2508. doi: 10.1038/ s41598-022-06262-z. Feb 15, 2022. 

https://www.nature.com/articles/s41598-022-06262-z

Also

keyword 'self-assembly' in FonT

https://flashontrack.blogspot.com/search?q=self-assembly

Keywords: gst, self-assembly, self-organization, fractals, topological synchronization, zipper effect, chaos, chaotic systems

# gst: packing in slender structures, the geometry of squeezed elastic beams

<< The behavior of a collection of squeezed elastic beams is determined by geometry, not by complex forces. >>️

Dan Garisto. How Order Emerges in Bendy Beam Bunches. Physics 16, 54. Apr 3, 2023.

https://physics.aps.org/articles/v16/54

<< A collection of thin structures buckle, bend, and bump into each other when confined. This contact can lead to the formation of patterns: hair will self-organize in curls; DNA strands will layer into cell nuclei; paper, when crumpled, will fold in on itself, forming a maze of interleaved sheets. This pattern formation changes how densely the structures can pack, as well as the mechanical properties of the system. >>️

<< Here (AA) study the emergence of order in a canonical example of packing in slender structures, i.e., a system of parallel confined elastic beams. >>️

They << find that the compressive stiffness and stored bending energy of this metamaterial are directly proportional to the number of beams that are geometrically frustrated at any given point.  >>

️

Arman Guerra, Anja C. Slim, et al. Self-Ordering of Buckling, Bending, and Bumping Beams. Phys. Rev. Lett. 130, 148201. Apr 3, 2023.

https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.130.148201

Also

keyword 'self-assembly' in FonT

https://flashontrack.blogspot.com/search?q=self-assembly

keyword 'elastic' in FonT

https://flashontrack.blogspot.com/search?q=elastic

keyword 'elastico' in Notes

(quasi-stochastic poetry)

https://inkpi.blogspot.com/search?q=elastico

Keywords: gst, self-assembly, beams, buckling, bending, bumping, elasticity

# evol: life as a product of molecular self-assembly

<< There are currently two main schools of thought regarding the origins of RNA. In one school, RNA is considered to be a product of nonenzymatic, prebiotic reactions. In the other, RNA is considered to be a product of chemical and/or biological evolution. >>

AA << report progress toward finding a proto-RNA that is the product of molecular self-assembly. >>

Cafferty B.J., Fialho D.M., Hud N.V. (2018) Searching for Possible Ancestors of RNA: The Self-Assembly Hypothesis for the Origin of Proto-RNA. In: Menor-Salvan C. (eds) Prebiotic Chemistry and Chemical Evolution of Nucleic Acids. Nucleic Acids and Molecular Biology, vol 35. Springer, Cham. doi: 10.1007/978-3-319-93584-3_5

https://link.springer.com/chapter/10.1007%2F978-3-319-93584-3_5

Joelle Renstrom. New study identifies possible ancestors of RNA. Astrobiol  Mag. Sep 17, 2018.

https://m.phys.org/news/2018-09-ancestors-rna.html 

# gst: emergent organization and polarization due to active fluctuations.

AA << introduce and study a model of active Brownian motion with multiplicative noise describing fluctuations in the self-propulsion or activity. (They) find that the standard picture of density accumulation in slow regions is qualitatively modified by active fluctuations, as stationary density profiles are generally not determined only by the mean self-propulsion speed landscape. As a result, activity gradients generically correlate the particle self-propulsion speed and orientation, leading to emergent polarization at interfaces pointing either towards dense or dilute regions depending on the amount of noise in the system.  >>

️

Benoit Mahault, Prakhar Godara, Ramin Golestanian. Emergent organization and polarization due to active fluctuations. Phys. Rev. Research 5, L022012. April 12, 2023. 

https://journals.aps.org/prresearch/abstract/10.1103/PhysRevResearch.5.L022012

Also: 'particle', 'fluctuations', 'noise', 'self-assembly' in https://www.inkgmr.net/kwrds.html

Keywords: gst, particle, organization, polarization, fluctuations, noise, self-propulsion, self-assembly 

# gst: emergence of self-organizing zigzag patterns among (magnetic) particles suspended in a liquid

<< When molecules or bacteria organize into a long-range pattern, researchers want to understand how the microscopic interactions lead to the macroscopic order. (AA) observed such self-organization in magnetic particles suspended in a liquid and subjected to an oscillating magnetic field. Through experiments and simulations, the team showed that the resulting zigzag pattern is explained by the fluid flow generated around the oscillating particles, not by any details of the particles or the applied field. Similar zigzag patterns have also been seen in charged colloids subjected to oscillating electric fields, so the explanation may cover a range of particle systems. The researchers also believe that understanding and controlling the effect could lead to useful applications in microfluidics devices. >>️

David Ehrenstein. Self-Organized Zigzags from Fluid Flow. Physics 16, 138. Aug 11, 2023.

https://physics.aps.org/articles/v16/138

Gaspard Junot, Marco De Corato, Pietro Tierno. Large Scale Zigzag Pattern Emerging from Circulating Active Shakers. Phys. Rev. Lett. 131, 068301. Aug 11, 2023. 

https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.131.068301

Also: particle, self-assembly, chiral, behav, in: https://www.inkgmr.net/kwrds.html  

Keywords: gst, behavior, particle, self-assembly, self-organization, chiral, active shakers, squirmers, alternating chirality

# gst: pseudo epileptic seizures in self-organized bistability

<< Self-organized bistability (SOB) stands as a critical behavior for the systems delicately adjusting themselves to the brink of bistability, characterized by a first-order transition. >>️

(AA) << embark on a theoretical exploration that extends the boundaries of the SOB concept on a higher-order network (implicitly embedded microscopically within a simplicial complex) while considering the limitations imposed by coupling constraints. >>️

AA << use continuous synchronization diagrams and statistical data from spontaneous synchronized events to demonstrate the crucial role SOB plays in initiating and terminating temporary synchronized events. (They) show that under weak coupling consumption, these spontaneous occurrences closely resemble the statistical traits of the epileptic brain functioning. >>

️

Md Sayeed Anwar, Nikita Frolov, Alexander E. Hramov, Dibakar Ghosh. Self-organized bistability on globally coupled higher-order networks. arXiv: 2401.02825v1 [nlin.AO]. Jan 5, 2024.

https://arxiv.org/abs/2401.02825

Also: transition, self-assembly, brain, in: https://www.inkgmr.net/kwrds.html

Keywords: gst, transition, self-assembly, bistability, self-organized bistability, brain, epileptic seizure

# s-chem: self-assembled also into cuboids

<< Phospholipid liposomes are archetypical self-assembled structures. To minimize the surface tension, the vesicles typically are spherical >>

<< A 1,2-diamidophospholipid is presented that self-assembles into a cuboid structure. Owing to intermolecular hydrogen bonding, the bilayer membranes form an exceptionally tight subgel packing, leading to a maximization of flat structural elements and a minimization of any edges. These conditions are optimized in the geometrical structure of a cube >>

Frederik  Neuhaus, Dennis  Mueller, et al. Vesicle  Origami:  Cuboid  Phospholipid  Vesicles  Formed  by Template-Free  Self-Assembly. Angewandte  Chemie  International  Edition.  Vol. 56,  Issue 23, June  1,  2017. Pages  6515–6518. doi: 10.1002/anie.201701634

http://onlinelibrary.wiley.com/doi/10.1002/anie.201701634/abstract

Phosphorus-containing lipid  molecule self-assembles into a cuboid structure. June  5,  2017

https://m.phys.org/news/2017-06-phosphorus-containing-lipid-molecule-self-assembles-cuboid.html

# bots: tiny machinery, nanobots (molecule-sized bots) from 1k to millions swarming together to perform tasks

<< Multi-disciplinary research has led to the innovative fabrication of molecule-sized robots. Scientists are now advancing their efforts to make these robots interact and work together in the millions. >>

AA << have made molecular robots with three key components: microtubules, single-stranded DNA, and a light-sensing chemical compound. The microtubules act as the molecular robot's motor, converting chemical energy into mechanical work. The DNA strands act as the information processor due to its incredible ability to store data and perform multiple functions simultaneously. The chemical compound, azobenzene derivative, is able to sense light, acting as the molecular robot's on/off switch. (..) (They) have successfully controlled the shape of those swarms by tuning the length and rigidity of the microtubules. Relatively stiff robots swarm in uni-directional, linear bundles, while more flexible ones form rotating, ring-shaped swarms.>>

<< A continuing challenge, though, is making separate groups of robots swarm at the same time, but in different patterns. This is needed to perform multiple tasks simultaneously. >>

Scientists working to make molecule-sized robots swarm together to perform tasks. National Institute for Materials Science. Jun 18, 2020.

https://phys.org/news/2020-06-scientists-molecule-sized-robots-swarm-tasks.html   

Arif Md. Rashedul Kabir, Daisuke Inoue,  Akira Kakugo. Molecular swarm robots: recent progress and future challenges.  Science and Technology of Advanced Materials. 21:1, 323-332. doi: 10.1080/ 14686996.2020.1761761. Jun 16, 2020. 

https://www.tandfonline.com/doi/full/10.1080/14686996.2020.1761761 

Also

keyword 'bot' in FonT

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keyword 'self-assembly' in FonT

https://flashontrack.blogspot.com/search?q=self-assembly

# s-chem: weak van der Waals' bonds to self-assembly

Gecko Hamaker, a  open source << software to calculate van der Waals forces between molecules and meso/nanoscale units, predict molecular organization and evaluate whether new combinations of materials will stick together, thereby facilitating the design of meso/nanoscale self-assembly >>

http://m.phys.org/news/2015-09-open-science-van-der-waals-interaction.html

# s-chem: self-assembly of smallest nanocubes

<< Induced by an external magnetic field, nanocubes spontaneously assemble into 1D chains, 2D monolayer sheets, and large 3D cuboids with almost perfect internal ordering. >>

Sara Mehdizadeh Taheria, Maria Michaelisa, et al. Self-assembly of smallest magnetic particles. PNAS 2015, vol. 112, no. 47, 14484–14489.

http://m.pnas.org/content/112/47/14484

# gst: critical points seem to act behind the complex behavior of collectives.

<< Current experiments support the controversial hypothesis that a well-known concept in physics—a critical point—is behind the striking behavior of collective animal systems. >>

AA << showed that light-controlled microswimming particles can be made to organize into collective states such as swarms and swirls. By studying the particles fluctuating between these states, they provide evidence for critical behavior—and support for a physical principle underlying the complex behavior of collectives.>>

<< What we observed is that the system can make sudden transitions from one state to the other, which demonstrates the flexibility needed to react to an external perturbation like a predator, (..) and provides clear evidence for a critical behavior. >> Clemens Bechinger

<< Through very simple interactions, they have shown that you can tune a physical system to a collective state - criticality - of balance between order and disorder. >> Iain Couzin

Physics principle explains order and disorder of swarms. University of Konstanz. Jun 11, 2020.

https://phys.org/news/2020-06-physics-principle-disorder-swarms.html

Bauerle T., Loffler R.C., Bechinger C. Formation of stable and responsive collective states in suspensions of active colloids. Nat Commun 11, 2547. doi: 10.1038/ s41467-020-16161-4. May 21, 2020.

https://www.nature.com/articles/s41467-020-16161-4

Also 

keyword 'self-assembly' in FonT

https://flashontrack.blogspot.com/search?q=self-assembly

# s-gst-chem: weak long-range van der Waals interactions in self-assembly

<< The researchers found that weak long-range van der Waals (attractive or repulsive forces between molecules or atomic groups that do not arise from interactions due to a covalent bond or electrostatic force) yielded the largest contribution to the molecule-surface interaction >>

A self-assembling molecular nanoswitch
A possible future molecular memory device. January 18, 2016

http://www.kurzweilai.net/a-self-assembling-molecular-nanoswitch

<< We find that on both substrates, the adsorbate-substrate interaction is dominated by attractive van der Waals forces >>

Moritz Müller, Katharina Diller, et al. Interfacial charge rearrangement and intermolecular interactions: Density-functional theory study of free-base porphine adsorbed on Ag(111) and Cu(111). The Journal of Chemical Physics, 2016; 144 (2): 024701 DOI: 10.1063/1.4938259 (open access)

http://scitation.aip.org/content/aip/journal/jcp/144/2/10.1063/1.4938259

# life: apropos of transitions, a leap from chemistry to biology, the hypothesis of self-assembling droplets, the 'droplet world'.

AA << identify conditions suitable for concurrent peptide generation and self-assembly, and (..) show how a proliferating peptide-based droplet could be created by using synthesised amino acid thioesters as prebiotic monomers. Oligopeptides generated from the monomers spontaneously formed droplets through liquid–liquid phase separation in water. The droplets underwent a steady growth–division cycle by periodic addition of monomers through autocatalytic self-reproduction. Heterogeneous enrichment of RNA and lipids within droplets enabled RNA to protect the droplet from dissolution by lipids. >>

Matsuo, M., Kurihara, K. Proliferating coacervate droplets as the missing link between chemistry and biology in the origins of life. Nat Commun 12, 5487. doi: 10.1038/ s41467-021-25530-6. Sep 24,  2021.

https://www.nature.com/articles/s41467-021-25530-6

<< By constructing peptide droplets that proliferate with feeding on novel amino acid derivatives, we have experimentally elucidated the long-standing mystery of how prebiotic ancestors were able to proliferate and survive by selectively concentrating prebiotic chemicals, (..) Rather than an RNA world, we found that 'droplet world' may be a more accurate description, as our results suggest that droplets became evolvable molecular aggregates—one of which became our common ancestor. >> Muneyuki Matsuo.

Answering a century-old question on the origins of life. Hiroshima University. Sep 27, 2021. 

https://phys.org/news/2021-09-century-old-life.html

Also

keyword 'drop' | 'droplet' in FonT

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https://flashontrack.blogspot.com/search?q=droplet

keyword 'transition' in FonT

https://flashontrack.blogspot.com/search?q=transition

keyword 'transizione' in Notes (quasi-stochastic poetry): 

https://inkpi.blogspot.com/search?q=transizione

keywords: life, originsoflife, transitions, drop, droplet