# gst: apropos of avoidance, packing of stiff rods on ellipsoids; the effects of self-avoidance

AA << study the effects of geometry and self-avoidance on the ordering of slender filaments inside nonisotropic containers, considering cortical microtubules in plant cells, and packing of genetic material inside viral capsids as concrete examples. >>

<< Within a mean-field approximation, (AA) show analytically how the shape of the container, together with self-avoidance, affects the ordering of the stiff rods. (They)  find that the strength of the self-avoiding interaction plays a significant role in the preferred packing orientation, leading to a first-order transition for oblate cells, where the preferred orientation changes from azimuthal, along the equator, to a polar one, when self-avoidance is strong enough. >>

<< While for prolate spheroids the ground state is always a polar-like order, strong self-avoidance results with a deep metastable state along the equator. >>

<< the critical behavior of this system is in fact related to the butterfly catastrophe model. >>

Doron Grossman, Eytan Katzav. Effects of self-avoidance on the packing of stiff rods on ellipsoids. Phys. Rev. E 109, 054111. May 9, 2024. 

https://journals.aps.org/pre/abstract/10.1103/PhysRevE.109.054111

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

Keywords: gst, ellipsoids, spheroids,  oblate- prolate spheroids, avoidance, self-avoidance

# gst: quantum jamming on the macroscopic scale

 << In the presence of kinetic constraints, quasiparticles describing the behavior of an ordered arrangement of quantum spins can get “stuck” as their density increases. Because of its similarity to the formation of amorphous solids, this situation can be interpreted as the quantum analog of jamming. Jammed states are intrinsically unstable and small perturbations produce unusual nonequilibrium dynamics. >> 

 AA << show that quantum jamming is a mechanism to make microscopic phenomena visible at a macroscopic scale: A single impurity produces a permanent change in the state, and a few impurities leave an imprint of their scattering properties and bound states. >> 

Maurizio Fagotti. Quantum Jamming Brings Quantum Mechanics to Macroscopic Scales. Phys. Rev. X 14, 021015. Apr 23, 2024.

https://journals.aps.org/prx/abstract/10.1103/PhysRevX.14.021015

Also: particle, jamming, in https://www.inkgmr.net/kwrds.html 

Keywords: gst, particle, jamming

# gst: bubble phases sliding over periodically modulated substrates

AA << analyze a bubble-forming system composed of particles with competing long-range repulsive and short-range attractive interactions driven over a quasi-one-dimensional periodic substrate. >>️

They << find various pinned and sliding phases as a function of substrate strength and drive amplitude. When the substrate is weak, a pinned bubble phase appears that depins elastically into a sliding bubble lattice. For stronger substrates, (AA) find anisotropic bubbles, disordered bubbles, and stripe phases. Plastic depinning occurs via the hopping of individual particles from one bubble to the next in a pinned bubble lattice, and as the drive increases, there is a transition to a state where all of the bubbles are moving but are continuously shedding and absorbing individual particles. This is followed at high drives by a moving bubble lattice in which the particles can no longer escape their individual bubbles. >>️

<< When the bubbles shrink due to an increase in the attractive interaction term, they fit better inside the pinning troughs and become more strongly pinned, leading to a reentrant pinning phase. For weaker attractive terms, the size of the bubbles becomes greater than the width of the pinning troughs and the depinning becomes elastic with a reduced depinning threshold. >>

️

C. Reichhardt, C.J.O. Reichhardt. Sliding dynamics for bubble phases on periodic modulated substrates. Phys. Rev. Research 6, 023116. May 2, 2024.

https://journals.aps.org/prresearch/abstract/10.1103/PhysRevResearch.6.023116

Also: bubble, elastic, transition, in https://www.inkgmr.net/kwrds.html 

Keywords: gst, bubble, pinned bubble, elastic, transition

# gst: a case of noise-induced excitation wave (in coupled FH-N eq.)

<< There are various research topics such as stochastic resonance, coherent resonance, and neuroavalanche in excitable systems under external noises. >>️

AA << have studied the propagation of excitation waves in the coupled noisy FitzHugh-Nagumo equations with a one-dimensional pacemaker region and found that there is a phase-transition-like phenomenon from the short-range propagation to the whole-system propagation by changing the noise strength T.  >>️

Hidetsugu Sakaguchi. Noise-induced excitation wave and its size distribution in coupled FitzHugh-Nagumo equations on a square lattice. Phys. Rev. E 109, 044211. Apr 19, 2024.

https://journals.aps.org/pre/abstract/10.1103/PhysRevE.109.044211

Also: waves, noise, transition, in https://www.inkgmr.net/kwrds.html 

Keywords: gst, waves, noise, transition

# gst: random walk model for dual cascades in wave turbulence.

<< Dual cascades in turbulent systems with two conserved quadratic quantities famously arise in both two-dimensional hydrodynamic turbulence and also in wave turbulence based on four-wave interactions. >>

<< in wave turbulence the systematic spectral fluxes observed in a dual cascade do not require an irreversible dynamical mechanism, rather, they arise as the inevitable outcome of blind chance. >>️️

Oliver Bühler. Random walk model for dual cascades in wave turbulence. Phys. Rev. E 109, 055102. May 1, 2024. 

https://journals.aps.org/pre/abstract/10.1103/PhysRevE.109.055102

Also: waves, turbulence, random, weak, in https://www.inkgmr.net/kwrds.html 

Keywords: gst, waves, turbulence, weak turbulence, random, random walks

# gst: sudden noise-induced expansions beyond the onset of a steady symmetry-breaking bifurcation.

AA << consider fluid flows (..) subject to a steady symmetry-breaking bifurcation and forced by a weak noise acting on a slow timescale. >>

The validity of their proposed model << is tested on the flow past a sudden expansion for a given Reynolds number and different noise amplitudes. At a very low numerical cost, the statistics obtained from the amplitude equation accurately reproduce those of long-time direct numerical simulations. >>

Yves-Marie Ducimetière, Edouard Boujo, François Gallaire. Noise-induced transitions past the onset of a steady symmetry-breaking bifurcation: The case of the sudden expansion. Phys. Rev. Fluids 9, 053905. May 3, 2024. 

https://journals.aps.org/prfluids/abstract/10.1103/PhysRevFluids.9.053905

Also: transition, noise, in  https://www.inkgmr.net/kwrds.html 

Keywords: gst, transition, noise

# gst: apropos of uncertainty, notes on uncertainty, information, and classical dynamics.

<< Survival in this world is an adventure because we are so ignorant and everything around us seems so uncertain. In fact, it is hard to think of any realistic phenomenon that is completely free from one of the three kinds of uncertainty—deterministic (chaotic), stochastic, and quantum; more often than not, all of the three are present in various degrees. Thus, in order to gain any knowledge about any realistic system, one must understand how to characterize, quantify, and interpret these uncertainties. >>️

Sagar Chakraborty. Eclectic Notes on Uncertainty, Information, and Classical Dynamics. arXiv: 2404.13511v1 [physics.class-ph]. Apr 21, 2024.

https://arxiv.org/abs/2404.13511

Also: uncertainty, noise, error, in  https://www.inkgmr.net/kwrds.html 

Keywords: gst, information, uncertainty, ambiguity, noise, error 

# gst: inertia onset in disordered porous media flow.

AA << investigate the very onset of the inertial regime in pore-scale fluid flow in a three-dimensional, disordered porous media. >>️

Their << analysis shows that the onset of inertia observed in a standard way by computing the friction factor appears at a Reynolds number two orders of magnitude higher than indicated by analyzing tortuosity and spatial distribution of kinetic energy. >>️

Damian Sniezek, Sahrish B. Naqvi, Maciej Matyka. Inertia onset in disordered porous media flow. arXiv: 2403.00456v2 [physics.flu-dyn]. Mar 26, 2024. 

https://arxiv.org/abs/2403.00456

Also: inertia, disorder, in FonT 

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

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

Keywords: gst, inertia, disorder

# gst: Lévy flights and Lévy walks under stochastic resetting.

<< Stochastic resetting is a protocol of starting anew, which can be used to facilitate the escape kinetics. (AA)  demonstrate that restarting can accelerate the escape kinetics from a finite interval restricted by two absorbing boundaries also in the presence of heavy-tailed, Lévy-type, α

-stable noise. However, the width of the domain where resetting is beneficial depends on the value of the stability index α determining the power-law decay of the jump length distribution. For heavier (smaller α) distributions, the domain becomes narrower in comparison to lighter tails. >>

<< Additionally, (AA) explore connections between Lévy flights (LFs) and Lévy walks (LWs) in the presence of stochastic resetting. First of all, (They) show that for Lévy walks, the stochastic resetting can also be beneficial in the domain where the coefficient of variation is smaller than 1. Moreover, (They) demonstrate that in the domain where LWs are characterized by a finite mean jump duration (length), with the increasing width of the interval, the LWs start to share similarities with LFs under stochastic resetting. >>️

Bartosz Żbik, Bartłomiej Dybiec. Lévy flights and Lévy walks under stochastic resetting. Phys. Rev. E 109, 044147. April 22, 2024.

https://journals.aps.org/pre/abstract/10.1103/PhysRevE.109.044147

Also: keyword Lévy in FonT

https://flashontrack.blogspot.com/search?q=Lévy&m=1

Also: escape, noise, in https://www.inkgmr.net/kwrds.html 

Keywords: gst, escape, noise, stochastic resetting, Lévy

# gst: apropos of synchronization of large bubble clouds, self-oscillating acoustic bubbles that bounce

<< Self-oscillations underlie many natural phenomena such as heartbeat, ocean waves, and the pulsation of variable stars. (..) In this study, (AA) consider two closely spaced bubbles pulsating in the kHz range in response to ultrasonic excitation. A translational bouncing motion emerges from their interaction with a much lower frequency than the bubble pulsation frequency. >>

Their analysis << reveals that the observed bubble bouncing exhibits the main features of self-oscillation, such as negative damping and the emergence of a limit cycle. These results highlight unexpected nonlinear effects in the field of microbubbles and give insights into the understanding of synchronization in large bubble clouds. >>️

Gabriel Regnault, Alexander A Doinikov, et al. Phenomenon of self-oscillation in bubble dynamics: Bouncing acoustic bubbles. arXiv: 2404.05822v1 [physics.flu-dyn]. Apr 8, 2024.

https://arxiv.org/abs/2404.05822

Also: bubble, bouncing, behav, in https://www.inkgmr.net/kwrds.html 

Keywords: gst, bubble, self-oscillation, bouncing, behavior, collective behavior, bouncing motion, synchronization

# life: oops! AI - artificial intelligence - now beats humans at basic tasks.

<< Artificial intelligence (AI) systems, such as the chatbot ChatGPT, have become so advanced that they now very nearly match or exceed human performance in tasks including reading comprehension, image classification and competition-level mathematics, according to a new report. >>️

Nicola Jones. AI now beats humans at basic tasks — new benchmarks are needed, says major report. Stanford University’s 2024 AI Index charts the meteoric rise of artificial-intelligence tools. Nature. doi: 10.1038/ d41586-024-01087-4. Apr 15, 2024. 

https://www.nature.com/articles/d41586-024-01087-4

<< Welcome to the seventh edition of the AI Index report. The 2024 Index is our most comprehensive to date and arrives at an important moment when AI’s influence on society has never been more pronounced. >>

️

THE AI INDEX REPORT. Measuring trends in AI. 

https://aiindex.stanford.edu/report/

Also:  "qui non e' impossibile immaginare ..." (here it is not impossible to imagine ... ). In: FonT. Dec 31, 2015. 

https://flashontrack.blogspot.com/2015/12/rmx-s-gst-anomalous-formation-of.html

Also:  artificial intell, analogy, nfulaw,  oops, in https://www.inkgmr.net/kwrds.html 

Keywords: life, ai, artificial intelligence, analogy, nfulaw

# gst: apropos of collective behaviors, a visual model to reproduces swarming, schooling, and milling.

<< Animal collective behavior is often modeled with self-propelled particles, assuming each individual has “omniscient” knowledge of its neighbors. Yet, neighbors may be hidden from view and we do not know the effect of this information loss. To address this question, (AA) propose a visual model of collective behavior where each particle moves according to bioplausible visual cues, in particular the optic flow. This visual model successfully reproduces three classical collective behaviors: swarming (no orientational order), schooling (high orientational order), and milling (the group coordinately swirls in a circular pattern). >>️

Diego Castro, Franck Ruffier, Christophe Eloy. Modeling collective behaviors from optic flow and retinal cues. Phys. Rev. Research 6, 023016. Apr 4, 2024. 

https://journals.aps.org/prresearch/abstract/10.1103/PhysRevResearch.6.023016

Also: swarm, flock, behav, particle, in https://www.inkgmr.net/kwrds.html 

Keywords: gst, swarming, flocking, behavior, particle, self-propelled particles

# gst: evolving disorder and chaos induces acceleration of elastic waves.

<< Static or frozen disorder, characterised by spatial heterogeneities, influences diverse complex systems, encompassing many-body systems, equilibrium and nonequilibrium states of matter, intricate network topologies, biological systems, and wave-matter interactions. >>

AA << investigate elastic wave propagation in a one-dimensional heterogeneous medium with diagonal disorder. (They) examine two types of complex elastic materials: one with static disorder, where mass density randomly varies in space, and the other with evolving disorder, featuring random variations in both space and time. (AA) results indicate that evolving disorder enhances the propagation speed of Gaussian pulses compared to static disorder. Additionally, (They) demonstrate that the acceleration effect also occurs when the medium evolves chaotically rather than randomly over time. The latter establishes that evolving randomness is not a unique prerequisite for observing wavefront acceleration, introducing the concept of chaotic acceleration in complex media. >>️

M. Ahumada, L. Trujillo, J. F. Marín. Evolving disorder and chaos induces acceleration of elastic waves. arXiv: 2403.02113v1 [cond-mat.dis-nn]. Mar 4, 2024. 

https://arxiv.org/abs/2403.02113

Also: waves, elastic, chaos, transition, in https://www.inkgmr.net/kwrds.html 

Keywords: gst, waves, elastic, chaos, transition

# gst: exploring the on-demand dynamical generation of a plethora of dispersive shock waves arising in attractive one-dimensional droplet-bearing environment.

AA << demonstrate the controllable generation of distinct types of dispersive shock-waves emerging in a quantum droplet bearing environment with the aid of step-like initial conditions. Dispersive regularization of the ensuing hydrodynamic singularities occurs due to the competition between meanfield repulsion and attractive quantum fluctuations. This interplay delineates the dominance of defocusing (hyperbolic) and focusing (elliptic) hydrodynamic phenomena respectively being designated by real and imaginary speed of sound. >>

<< Surprisingly, dispersive shock waves persist across the hyperbolic-to-elliptic threshold, while a plethora of additional wave patterns arise, such as rarefaction waves, traveling dispersive shock waves, (anti)kinks and droplet wavetrains. >>

AA << results pave the way for unveiling a multitude of unexplored coherently propagating waveforms in such attractively interacting mixtures. >>

Sathyanarayanan Chandramouli, Simeon I. Mistakidis, Garyfallia C. Katsimiga, Panayotis G. Kevrekidis. 

Dispersive shock waves in a one-dimensional droplet-bearing environment. arXiv: 2404.02998v2 [nlin.PS]. Apr 5, 2024. 

https://arxiv.org/abs/2404.02998

Also: waves, drop, in https://www.inkgmr.net/kwrds.html 

Keywords: gst, waves, drops 

# gst: apropos of evaporation, puncturing of active drops

<< By virtue of self-propulsion, active particles impart intricate stresses to the background fluids. (..) this active stress can be utilized to greatly control evaporation dynamics of active drops. >>

AA << discover a new phenomenon of puncturing of the active drops, where the air-liquid interface of the drop undergoes spontaneous tearing and there occurs a formation of a new three-phase contact line due to the liquid-air interface hitting the liquid-solid interface through evaporation-driven mass loss. Post puncturing, (AA) see an inside-out evaporation of the drop, where the new contact line sweeps towards the pinned outer contact line of the drops, contrasting regular drops that straightaway shrink to zero volume with self-similar shape. >>

<< Furthermore, (..) the activity inside the drops can manipulate the three-phase contact-line dynamics, which for contractile drops can result in an up to 50% enhanced lifetime of the drop and 33% quicker evaporation for extensile drops. By analyzing the flux distribution inside the drop, (AA) gain insights on nonintuitive deposition patterns (e.g., ring galaxy type deposits that demonstrate controllable spatial gradients in the concentrations of the deposited particles) of active particles, which are oftentimes biological substances or bimetallic nanoparticles of interest. >>

Ghansham Rajendrasingh Chandel, Vishal Sankar Sivasankar, Siddhartha Das. Evaporation of active drops: Puncturing drops and particle deposits of ring galaxy patterns. Phys. Rev. Fluids 9, 033603. Mar 27, 2024. 

https://journals.aps.org/prfluids/abstract/10.1103/PhysRevFluids.9.033603

Also: drop, particle, evaporation, transition, in https://www.inkgmr.net/kwrds.html 

Keywords: gst, drop, particle, evaporation, transition, drop interactions, droplet, droploid

# gst: creating topological vortex rings (on demand)

<< Vortex rings are ubiquitous topological structures in nature. In solid magnetic systems, their formation leads to intriguing physical phenomena and potential device applications. >>

 Here, AA << theoretically show that topological vortex rings can be created by a current pulse in a chiral magnetic nanocylinder with a trench structure. The creation process involves the formation of a vortex ring street, i.e., a chain of magnetic vortex rings with an alternative linking manner. The created vortex rings can be bounded with monopole-antimonopole pairs and possess a rich and controllable linking topology (..) which is determined by the duration and amplitude of the current pulse. >>

Yizhou Liu, Naoto Nagaosa. Current-Induced Creation of Topological Vortex Rings in a Magnetic Nanocylinder. Phys. Rev. Lett. 132, 126701. Mar 19, 2024. 

https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.132.126701

Ryan Wilkinson. Magnetic Vortex Rings on Demand. Physics 17, s29. Mar 19,  2024. 

https://physics.aps.org/articles/v17/s29

Also: vortex, in https://www.inkgmr.net/kwrds.html 

Keywords: vortex, vortices, vortexes, vorticity, spin dynamics, spin texture, chiral magnets

# gst: elastomers fail from the edge.

<< The performance of soft devices is limited by the fracture resistance of elastomers. (..) A key observation is that thicker elastomers can be significantly tougher than thinner ones. (AA) show that this surprising toughness enhancement in thick samples emerges from the 3D geometry of the fracture process. In contrast to the classical picture of a 2D crack, failure is driven by the growth of two separate “edge” cracks that nucleate early on at a sample’s sides. As loading is increased, these cracks propagate in towards the sample midplane. When they merge, samples reach their ultimate failure strength. In thicker samples, edge cracks need to propagate farther before meeting, resulting in increased sample toughness. (AA) demonstrate that edge-crack growth is controlled by the elastomer’s strain-stiffening properties. >>

️

Nan Xue, Rong Long, Eric R. Dufresne, Robert W. Style. Elastomers Fail from the Edge. Phys. Rev. X 14, 011054. March 22, 2024. 

https://journals.aps.org/prx/abstract/10.1103/PhysRevX.14.011054

Also: elastic, crack, in https://www.inkgmr.net/kwrds.html 

Keywords: gst, elastic, crack, elastomers, fracture

# evol: emergence of single vs. multi-state allostery

      FIG. 1. The elastic network model

<< Allostery, the change of activity of a  macromolecule in response to a perturbation at a distance from its active site, is thought to be a ubiquitous feature of proteins. Initially described in the context of multimeric proteins, it is now understood to underlie the regulation of proteins with diverse structural architectures, from receptors to signaling proteins and metabolic enzymes. >>️

<< Here, (AA) analyze a simplified model of protein allostery under a range of physical and evolutionary constraints. (They) find that a continuum of mechanisms between two archetypes emerges through evolution. In one limit, a single-state mechanism exists where ligand binding induces a displacement along a single normal mode, and in the other limit, a multi-state mechanism exists where ligand binding induces a switch across an energy barrier to a different stable state. Importantly, whenever the two mechanisms are possible, the multi-state mechanism confers a stronger allosteric effect and thus a selective advantage. >>

️

Eric Rouviere, Rama Ranganathan, Olivier Rivoire. Emergence of Single- versus Multi-State Allostery. PRX Life 1, 023004. Nov 9, 2023.

https://journals.aps.org/prxlife/abstract/10.1103/PRXLife.1.023004

Also: allostery in FonT https://flashontrack.blogspot.com/search?q=allostery

Also: allosterico in Notes 

(quasi-stochastic poetry)

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

Keywords: gst, allostery, elastic, evolution

# gst: rearrangements of a jammed 2-D emulsion (during slow compression).

<< As amorphous materials get jammed, both geometric and dynamic heterogeneity are observed. (AA)  investigate the correlation between the local geometric heterogeneity and local rearrangements in a slowly compressed bidisperse quasi-two-dimensional emulsion system. The compression is driven by evaporation of the continuous phase. >>

<< droplets in heterogeneous local regions are more likely to have local rearrangements. These rearrangements are generally T1 events where two droplets converge toward a void, and two droplets move away from the void to make room for the converging droplets. Thus, the presence of the voids tends to orient the T1 events. >>️

<< The presence of a correlation between the structural quantities and the rearrangement dynamics remains qualitatively unchanged over the entire range of packing fractions observed. >>️

Xin Du, Eric R. Weeks. Rearrangements during slow compression of a jammed  two-dimensional emulsion. Phys. Rev. E 109, 034605. Mar 20,  2024.

https://journals.aps.org/pre/abstract/10.1103/PhysRevE.109.034605

Also: drop, in https://www.inkgmr.net/kwrds.html 

Keywords: drops, droplets, droploids 

# gst: near the Hopf boundary, Intermittency and chimera states.

AA << study collective dynamics of networks of mutually coupled identical Lorenz oscillators near a subcritical Hopf bifurcation. Such systems exhibit induced multistable behavior with interesting spatiotemporal dynamics including synchronization, desynchronization, and chimera states. >>️

<< For analysis, (AA) first consider a ring topology with nearest-neighbor coupling and find that the system may exhibit intermittent behavior due to the complex basin structures and dynamical frustration, where temporal dynamics of the oscillators in the ensemble switches between different attractors. Consequently, different oscillators may show a dynamics that is intermittently synchronized (or desynchronized), giving rise to intermittent chimera states. The behavior of the intermittent laminar phases is characterized by the characteristic time spent in the synchronization manifold, which decays as a power law. >>

<< Such intermittent dynamics is quite general and is also observed in an ensemble of a large number of oscillators arranged in variety of network topologies including nonlocal, scale-free, random, and small-world networks. >>️

Anjuman Ara Khatun, Yusra Ahmed Muthanna, et al. Collective dynamics of coupled Lorenz oscillators near the Hopf boundary: Intermittency and chimera states. Phys. Rev. E 109, 034208. March 15, 2024.

https://journals.aps.org/pre/abstract/10.1103/PhysRevE.109.034208

Also: transition, intermittency, chaos, chimera, network, in https://www.inkgmr.net/kwrds.html

Keywords: gst, transition, intermittency, chaos, chimera, network