# 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: 'transcriptional burst frequency' modulation (more or less noise) during gene regulation

<< In cells, genes are expressed through transcription, a process where genetic information encoded in DNA is copied into messenger RNA (mRNA). The mRNA is then translated to make protein molecules, the workhorses of cells. This entire process is subject to bursts of natural stochasticity—or randomness—which can impact the outcome of biological processes that proteins carry out. >>

<< This work for the first time identifies the role of randomness in altering the outcome of a developmental process.>> Madhav Mani. 

<< By analyzing experimental perturbations of Drosophila's senseless gene against mathematical models, the team determined the sources of the gene's stochasticity, and found that the randomness appears to be leveraged in order to accurately determine sensory neuron fates. >>

<< Let's say you are quickly flipping a light switch on and off, but you want more brightness out of your bulb. You could either get a brighter bulb that produced more photons per unit time, or you could leave the switch 'on' more than 'off,' (..) What we found is that organisms control the amount of gene expression by regulating how often the gene is permitted to switch on, rather than making more mRNAs when it is on. >> Madhav Mani. 

<< From these studies, we are learning rules for how genes can be made more or less noisy, (..) Sometimes cells want to harness the genetic noise—the level of variation in gene expression—to make randomized decisions. Other times cells want to suppress the noise because it makes cells too variable for the good of the organism. Intrinsic features of a gene can imbue them with more or less noise. >> Richard Carthew. 

Alex Gerage. Toward principles of gene regulation in multicellular systems. Northwestern University. Jul 1, 2020.

https://phys.org/news/2020-07-principles-gene-multicellular.html

Rachael Bakker, Madhav Mani, Richard W Carthew. The Wg and Dpp morphogens regulate gene expression by modulating the frequency of transcriptional bursts. eLife. doi: 10.7554/eLife.56076. Jun 22, 2020. 

https://elifesciences.org/articles/56076

# s-astro: exploring the sea of ‘noise’ to understand intricacies

<< Rather than trying to filter out the signal “noise” from stars around which exoplanets are orbiting, (AA) studied all of the signal information together to understand the intricacies within its structure >>

Jim Shelton. Searching a sea of ‘noise’ to find exoplanets — using only data as a guide.  Dec. 20, 2016

http://news.yale.edu/2016/12/20/searching-sea-noise-find-exoplanets-using-only-data-guide

Sahil Agarwal, Fabio Del Sordo and John S. Wettlaufer. Exoplanetary Detection by  multifractal spectral analysis. Publ. 2016  Dec.  20, 2016. The  Astronomical  Journal, Volume  153, Number  1;  doi 10.3847/1538-3881/153/1/12

http://iopscience.iop.org/article/10.3847/1538-3881/153/1/12

# gst: when randomly-timed external impulses can synchronize

<< Random perturbations applied in tandem to an ensemble of objects can synchronize their motion. (AA) study multiple copies of an object in periodic motion such as a firing neuron, each with an arbitrary phase. Randomly-timed external impulses can synchronize these phases. For impulses slightly too strong to synchronize, (they) find remarkable erratic synchronization, with stochastic fluctuations from near-perfect to more random synchronization. The sampled entropies of these phase distributions themselves form a steady-state ensemble. A stochastic dynamics model for the entropy's evolution accounts for the observed exponential distribution of entropies and the stochastic synchronization. >>

<< One general virtue of noise-induced synchronization is that one may use it to induce synchronization without

specific knowledge about the limit cycle being synchronized, such as the phase map function or the cycle time.(..) As noted in the Introduction, synchronization of a remote oscillator enables transmission of information.

Stochastic synchronization appears to have comparable ability, potentially useable by technology or biology. >>️

<< The stochastic synchronization phenomenon explored above seems to be a distinctive mode of organization. It can be produced via broad classes of driving, and creates striking fluctuations of randomness. This model may aid understanding of other puzzling systems showing erratic fluctuations, such as strong turbulence. >>️

️

Yunxiang Song, Thomas A. Witten. Stochastic synchronization induced by noise. arXiv:2108.13172v1 [cond-mat.stat-mech]. Aug 16, 2021.

https://arxiv.org/abs/2108.13172

Also

<< stabilizzare il volo del fascio di aquiloni  >> in: ️2149 - onda di predazione (to knock seals off the ice).  Notes. Dec 17, 2007. (quasi-stochastic poetry)

https://inkpi.blogspot.com/2007/12/2149-onda-di-predazione-to-knock-seals.html

keyword 'noise' | 'fuzzy' in FonT

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

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

# game: low-cooperativity feedbacks in burst size could be preferable for noisy proteins

AA << consider a specific kind of negative feedback, which makes bursts smaller in the excess of protein >>

<< Increasing the strength of the feedback may lead to dramatically different outcomes depending on a key parameter, the noise load >>

<< for noise loads smaller than critical, the coefficient of variation remains bounded with increasing feedback strength; contrastingly, if the noise load is larger than critical, the coefficient of variation diverges to infinity in the limit of ever greater feedback strengths >>

<< Interestingly, high-cooperativity feedbacks have lower critical noise loads, implying that low-cooperativity feedbacks in burst size can be preferable for noisy proteins >>

Pavol Bokes, Abhyudai Singh, Yen Ting Lin. High Cooperativity In Negative Feedback Can Amplify Noisy Gene Expression. biorxiv sysbio. doi: 10.1101/125914  April 10, 2017.

http://www.biorxiv.org/content/early/2017/04/10/125914

# rmx-s-brain: entities who know how to manage noise

<< pale spear-nosed bats (Phyllostomus discolor) (..) adapts its echolocation calls to the surrounding noise level >>

http://m.phys.org/news/2016-01-echolocation-noise.html

Jinhong Luo, Holger R. Goerlitz  et al. Linking the sender to the receiver: vocal adjustments by bats to maintain signal detection in noise. Scientific Reports 5, Article number: 18556 (2015)
doi:10.1038/srep18556

http://www.nature.com/articles/srep18556

# gst: stochastic resonance mediated by optimal noise level values; transport of colloidal particles induced by substrate concentration oscillations.

AA << show the existence of a  stochastic resonant regime in the transport of active colloidal particles under confinement. The periodic addition of substrate to the system causes the spectral amplification to exhibit a maximum for an optimal noise level value. The consequence of this is that particles can travel longer distances with lower fuel consumption. The stochastic resonance phenomenon found allows the identification of optimal scenarios for the transport of active particles, enabling them to reach regions that are otherwise difficult to access, and may therefore find applications in transport. >>️

J. D. Torrenegra-Rico, A. Arango-Restrepo, J. M. Rubi. Optimal transport of active particles induced by substrate concentration oscillations. Phys. Rev. E 108, 014134. July 28, 2023.

https://journals.aps.org/pre/abstract/10.1103/PhysRevE.108.014134

Img: https://twitter.com/PhysRevE/status/1687119409096089602

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

Keywords: gst, particle, colloids, noise, stochastic resonance, substrate oscillation

# gst: approaching chaotic dynamics to trace the complexity of rough nanostructured surfaces

AA << use the basic ingredients of chaotic dynamics (stretching and folding of phase space points) for the characterization of the complexity of microscopy images of rough surfaces. The key idea is to use an image as the initial condition of a chaotic discrete dynamical system, such as the Arnold cat map, and track its transformations during the first iterations of the map. Since the basic effects of the Arnold map are the stretching and folding of image texture, the application of the map leads to an enhancement of the high frequency content of images along with an increase of discontinuities in pixel intensities. (AA) exploit these effects to quantify the complexity of S type (lying between homogeneity and randomness) of the image texture since the first (enhancement of high frequencies) can be used to quantify the distance of texture from randomness and noise and the second (the proliferation of discontinuities) the distance from order and homogeneity. The method is validated in synthetic images which are generated from computer generated surfaces with controlled correlation length and fractal dimension and it is applied in real images of nanostructured surfaces obtained from a scanning electron microscope with very interesting results. >>️

A. Kondi, V. Constantoudis, P. Sarkiris, K. Ellinas, and E. Gogolides. Using chaotic dynamics to characterize the complexity of rough surfaces. Phys. Rev. E 107, 014206. Jan 11, 2023. 

https://journals.aps.org/pre/abstract/10.1103/PhysRevE.107.014206

https://twitter.com/PhysRevE/status/1613569770338533376

Also

Able to track changes in noise. 

(quasi-stochastic poetry) 

Notes. Sep 13, 2007. 

https://inkpi.blogspot.com/2007/09/2147-able-to-track-changes-in-noise.html

Also

keyword 'chaos' | 'chaotic' in Font

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

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

keyword 'caos' | 'caotico' in Notes (quasi-stochastic poetry)

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

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

Keywords: gst, chaos, chaotic, nano, roughness, wetting, surfaces, etching scanning 

# music: masters of noise, Frank Zappa plays bicycles

Frank Zappa teaches Steve Allen to play The Bicycle (aired March 3, 1963).

https://youtu.be/QF0PYQ8IOL4

<< This televisual gem inspired me follow along which got me into endless trouble at family picnics and barbecues for playing my own symphonic masterpieces which, for some strange reason, nobody else seemed to enjoy. I extended Frank's genius to my exploration of the vacuum cleaner, ping pong balls and paddles, (..)  The next time you're out in a forest I challenge you to explore the musical nature of nature for yourself. Trees make great drums and often ring with higher tones - not to mention the musical benefits of rocks and stones. >>️️

That Hairy Canadian. Jun 21, 2014. 

https://m.youtube.com/@ThatHairyCanadian

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

Keywords: music, jazz, noise, error

# gst: cooperating vs self-serving bacteria in transitional (noise) scenarios

AA << study a well-mixed, finite population consisting of two strains competing for the limited resources provided by an environment that randomly switches between states of abundance and scarcity >>

AA << consider two scenarios—one of pure resource competition, and one in which one strain provides a public good—and investigate how environmental randomness (external noise) coupled to demographic (internal) noise determines the population’s fixation properties and size distribution >>

Karl Wienand, Erwin Frey, Mauro Mobilia. Evolution of a Fluctuating Population in a Randomly Switching Environment. Phys. Rev. Lett. 119, 158301 Oct 11, 2017

https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.119.158301

AA << showed that a randomly changing environment can create a level playing field between self-serving bacteria and bacteria that work together >>

<< Cooperating bacterial populations are more likely to survive in changing habitats >>

Fluctuating environments can help cooperating bacteria. Oct 12, 2017

https://m.phys.org/news/2017-10-fluctuating-environments-cooperating-bacteria.html

# phys: it could be used to completely remove all noise from a noisy channel

AA << have proposed a second level of quantization, in which both the information carriers and the channels can be in quantum superposition. In this new paradigm of communication, the information carriers can travel through multiple channels simultaneously. >>

AA << formulated a quantum communications model that can be used to compute the amount of information that can be reliably transmitted when using a given number of channels in a quantum superposition. (..) for certain types of noise, the superposition of channels, along with the ability to switch a channel with itself, could be used to completely remove all noise. This opens up the possibility of obtaining perfect quantum communication in a noisy channel. >>

Lisa Zyga. Physicists propose a second level of quantization for quantum Shannon theory. Phys.org  May 22, 2019.

https://m.phys.org/news/2019-05-physicists-quantization-quantum-shannon-theory.html  

Giulio Chiribella, Hler Kristjansson.
Quantum Shannon theory with superpositions of trajectories. Proceedings of the Royal Society A.   doi: 10.1098/rspa.2018.0903  May 8, 2019.

https://royalsocietypublishing.org/doi/full/10.1098/rspa.2018.0903  

# s-evol: a noise effect inside: new species pulsating by chance instead of ...

<< W. Andrew Barr, a visiting assistant professor of anthropology, published a report that says it's possible the pulse of new species could have occurred by chance and might not be directly related to climate change >>

Researcher's paper challenges the claim that the genus Homo originated in response to environmental changes. Aug 4, 2017

https://m.phys.org/news/2017-08-paper-genus-homo-response-environmental.html

W. Andrew Barr. Signal or noise? A null model method for evaluating the significance of turnover pulses. Paleobiology 2017 doi: 10.1017/pab.2017.21 Publ. online: 31 July 2017

https://www.cambridge.org/core/journals/paleobiology/article/signal-or-noise-a-null-model-method-for-evaluating-the-significance-of-turnover-pulses/17FBC5F2A96CA2BA0657A2E411170EAB#

also

<< "Nell' Arte tutto e', o dovrebbe essere, un esperimento". Gill Evans. >>

2127 - enigmistiche tonalita'. March 23, 2007

http://inkpi.blogspot.it/2007/03/2127-enigmistiche-tonalita.html

# brain: related noise in perception, like a type of "groupthink"

<< The findings, (..) offer new insights into the limits of perception and could aid in the design of so-called neuroprosthetics-devices that enable people to regain some lost sensory capabilities. >>

<< because neurons are highly interconnected, when one randomly responds incorrectly and misidentifies an image, it can influence other neurons to make the same mistake. >>

<< You can think of correlated noise like a type of 'groupthink,' in which neurons can act like lemmings, with one heedlessly following another into making a mistake, >> Surya Ganguli

<< Remarkably, the visual system is able to cut through about 90% of this neuronal noise, but the remaining 10% places a limit on how finely we can discern between two images that look very similar. >>

<< With this study, we've helped resolve a puzzle that's been around for over 30 years about what limits mammals-and by extension humans-when it comes to sensory perception, >> Mark Schnitzer

Adam Hadhazy. Misfiring from jittery neurons sets fundamental limit on perception.  Stanford University. Apr 9, 2020.

https://medicalxpress.com/news/2020-04-misfiring-jittery-neurons-fundamental-limit.html

Rumyantsev OI, Lecoq JA, et al. Fundamental bounds on the fidelity of sensory cortical coding. Nature 580, 100–105 doi:.10.1038/ s41586-020-2130-2. Mar 18, 2020.

https://www.nature.com/articles/s41586-020-2130-2

# gst: behavior of microswimmers in a vortex with translational and rotational noise

AA << propose a theoretical model to investigate the dynamics of elongated microswimmers in elementary vortices, namely active particles in two- and three-dimensional rotlets. A deterministic model first reveals the existence of bounded orbits near the centre of the vortex and unbounded orbits elsewhere. (AA) further discover a conserved quantity of motion that allows (..) to map the phase space according to the type of the orbit (bounded vs unbounded). (They) next introduce translational and rotational noise into the system. Using a Fokker--Planck formalism, (AA) quantify the quality of trapping near the centre of the vortex by examining the probability of escape and the mean time of escape from the region of deterministically bounded orbits. (AA) finally show how to use these findings to formulate a prediction for the radius of the depletion zone, which compares favourably with the experiments of Sokolov and Aranson (2016). >>

Ivan Tanasijevic, Eric Lauga. Microswimmers in vortices: Dynamics and trapping. arXiv: 2211.05866v1 [physics.bio-ph].  Nov 10, 2022. 

https://arxiv.org/abs/2211.05866

Also

'microswimmers' in FonT 

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

Keywords: gst, behav, translation,  rotation, trapping, noise, swimmer, swimming,  microswimmers, fluid dynamics, vortex, vortices, vortexes, vorticity

# brain: to consider neurons driven by a shot noise

<< Individual presynaptic spikes can have a significant effect on a neuron's dynamics. It is thus desirable to explicitly account for the pulse-like nature of neural input, i.e. consider neurons driven by a shot noise >>

Droste F, Lindner B. Exact analytical results for integrate-and-fire neurons driven by excitatory shot noise. J Comput Neurosci. 2017 Aug;43(1):81-91. doi: 10.1007/s10827-017-0649-5. Epub 2017 Jun 6.

https://www.ncbi.nlm.nih.gov/m/pubmed/28585050/

# s-gst-brain: trigger creativity also by noise in neural forecasting phenomena

<< The theory also posits a role for noise or variability in neural activity to explore different possible interpretations, even when the sensory input and prediction are the same >>

<< This noise-driven process of exploration may be the neural basis of creativity >>

How does the brain make perceptual predictions over time? Feb. 6, 2017

https://m.medicalxpress.com/news/2017-02-brain-perceptual.html

David J. Heeger. Theory of cortical function. PNAS. Feb. 3, 2017. doi: 10.1073/pnas.1619788114

http://m.pnas.org/content/early/2017/02/03/1619788114

# life: mimesis, ambiguity, noise, when an entity is master of disguise.

<< At every stage in their lives, from egg to adult, leaf and stick insects prove to be prey that can trick their predators. >>️

Allie Yang. These insects are masters of disguise—even before hatching. nationalgeographic.com. Oct 17, 2023.

https://www.nationalgeographic.com/animals/article/phasmids-stick-leaf-insects-eggs-camouflouge

Also: mimesis, in Notes (quasi-stochastic poetry)

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

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

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

Keywords: mimesis, disguise, ambiguity, noise, metamorphosis, two-faced Janus

# gst: like steering a marble through a tilting labyrinth, randomness seems to quickly deliver specific outcomes.

<< According to the infinite monkey theorem, a monkey randomly hitting the keys of a typewriter will eventually write something worth reading—but it might take a few trillion years of trying. For those lacking the patience to wait, (AA)  now show that randomness can deliver specific outcomes much more quickly.  Simulating a 2D nanocluster of a dozen particles, (they) determine the temperature at which thermal fluctuations can most quickly rearrange those particles into a predetermined shape. They find that this time can be dramatically cut by applying an appropriate macroscopic force to the particles. >>

<< The duo also simulated nanoclusters that were subject to a macroscopic force field, for example, metallic nanoparticles in an electric field. Like steering a marble through a tilting labyrinth, they found the optimal global force to apply at each iteration such that the nanocluster navigated the space of possible configurations several orders of magnitude more quickly. >>️️

Marric Stephens. Rearranging Nanoclusters Using Randomness. Physics 15, s83. Jun 22, 2022. 

https://physics.aps.org/articles/v15/s83

Francesco Boccardo, Olivier Pierre-Louis. Controlling the Shape of Small Clusters with and without Macroscopic Fields. Phys. Rev. Lett. 128, 256102. Jun 22, 2022.  

https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.128.256102

Also

keyword 'random' in FonT:

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

keyword 'error' | 'fuzzy' | 'noise'  in FonT 

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

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

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

keywords 'errore' | 'errori' in Notes (quasi-stochastic poetry)

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

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

keywords 'jelly roll' in FonT

https://flashontrack.blogspot.com/search?q=jelly+roll

Keywords: gst, nano, nanocluster, fluctuations, randomness, noise

# 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: the effects of order- disorder on a system of swarmalators that move on a one-dimensional ring.

<< Swarmalators are phase oscillators that cluster in space, like fireflies flashing on a swarm to attract mates. >>

<< In this work, (AA) explore the effects of disorder induced by phase frustration on a system of Swarmalators that move on a one-dimensional ring. >>

They find << numerically and analytically, the ordered and disordered states that emerge in the system. The active states, not present in the model without disorder, resemble states found previously in numerical studies for the 2D Swarmalators system. One of these states, in particular, shows similarities to turbulence generated in a flattened media. (AA) show that all ordered states can be generated for any values of the coupling constants by tuning the phase frustration parameters only. Moreover, many of these combinations display multi-stability. >>️

Joao U.F. Lizarraga, Marcus A.M. de Aguiar. Sakaguchi Swarmalators. arXiv: 2305.08615v1 [nlin.PS]. May 15, 2023. 

https://arxiv.org/abs/2305.08615

Also:  'swarm', 'turbulence', 'noise', 'particle' in: https://www.inkgmr.net/kwrds.html

Keywords: gst, swarm, turbulence, noise, particle