# life: it’s time to admit that ...

<< For too long, scientists have been content in espousing the lazy metaphor of living systems operating simply like machines, (..) Yet, it’s important to be open about the complexity of biology — including what we don’t know — because public understanding affects policy, health care and trust in science.  “So long as we insist that cells are computers and genes are their code,” writes Ball, life might as well be “sprinkled with invisible magic”. But, reality “is far more interesting and wonderful”, as he explains in this must-read user’s guide for biologists and non-biologists alike. >>️

Denis Noble. It’s time to admit that genes are not the blueprint for life. Nature. 626, 254-255 (2024). Feb 5,  2024. 

https://www.nature.com/articles/d41586-024-00327-x

Philip Ball. How Life Works: A User’s Guide to the New Biology. Pan Macmillan (2024). 

https://www.panmacmillan.com/authors/philip-ball/42387

Also: disorder, disorder & fluctuation, in https://www.inkgmr.net/kwrds.html  

Keywords: life, disorder, fluctuations

FonT: this point of view, published in the 70s-80s, would have made a damned impression. 

# gst: correlated noise and critical dimensions.

<< In equilibrium, the Mermin-Wagner theorem prohibits the continuous symmetry breaking for all dimensions d≤2. In this work, (AA) discuss that this limitation can be circumvented in nonequilibrium systems driven by the spatiotemporally long-range anticorrelated noise. >>

<< results suggest that the critical dimensions increase when the noise is positively correlated in space and time and decrease when anticorrelated. (AA)  also report that the spherical model with the correlated noise shows the hyperuniformity and giant number fluctuation even well above the critical point. >>️

Harukuni Ikeda. Correlated noise and critical dimensions. Phys. Rev. E 108, 064119. Dec 13, 2023.

https://journals.aps.org/pre/abstract/10.1103/PhysRevE.108.064119 

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

Keywords: gst, noise, fluctuations

# gst: rich behaviors from stochastic walking with variable long jumps.

AA << propose a generalized model where the random walker takes stochastic jumps of lengths proportional to its present position with certain probability, otherwise it makes forward and backward jumps of fixed (unit) length with given rates. The model exhibits a rich stochastic dynamic behavior.  (AA) obtain exact analytic results for the first two moments of the walker's displacement and show that a phase transition from a diffusive to superdiffusive regime occurs if the stochastic jumps of lengths that are twice (or more) of its present positions are allowed. This phase transition is accompanied by a reentrant diffusive behavior. >> 

Upendra Harbola. Stochastic walker with variable long jumps. Phys. Rev. E 108, 014135. July 28, 2023. 

https://journals.aps.org/pre/abstract/10.1103/PhysRevE.108.014135 

Also: walk, noise, fluctuations, dance,  in: https://www.inkgmr.net/kwrds.html

Keywords: gst, walks, random walks, noise, fluctuations

# 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: 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: apropos of transitions, perspectives on viscoelastic flow instabilities; the 'porous individualism'

<< given the observation that disorder can suppress the transition to elastic turbulence in 2D porous media (..), it has been unclear whether and how this transition manifests in disordered 3D media — though elastic turbulence has been speculated to underlie the long-standing observation that the macroscopic flow resistance of an injected polymer solution can abruptly increase above a threshold flow rate in a porous medium, but not in bulk solution >>️

AA << found that the transition to unstable flow in each pore is continuous, arising due to the increased persistence of discrete bursts of instability above a critical value of the characteristic (Weissenberg no.) Wi; however, the onset value varies from pore to pore. This observation that single pores exposed to the same macroscopic flow rate become unstable in different ways provides a fascinating pore-scale analog of “molecular individualism” [P.  De Gennes, Molecular individualism. Science 276, 1999–2000 (1997)], in which single polymers exposed to the same extensional flow elongate in different ways; the authors therefore termed it “porous individualism”, although it is important to note that here, this effect is still at the continuum (not molecular) scale. Thus, unstable flow is spatially heterogeneous across the different pores of the medium, with unstable and laminar regions coexisting >>

AA << quantitatively established that the energy dissipated by unstable pore-scale fluctuations generates an anomalous increase in flow resistance through the entire medium that agrees well with macroscopic pressure drop measurements. >>

Sujit S. Datta, Arezoo M. Ardekani, et al. Perspectives on viscoelastic flow instabilities and elastic turbulence. arXiv: 2108.09841v1 [physics.flu-dyn]. Aug 22, 2021. 

https://arxiv.org/abs/2108.09841

Also

keyword 'transition' | 'transitional' in FonT

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

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

keyword 'transition' | 'transizion*' in Notes (quasi-stochastic poetry)

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

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

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

keywords: gst, droplet, fluctuations, disorder, instability, viscoelastic flow instability, turbulence, elastic turbulence, individualism, porous individualism, transition

# gst: apropos of disorder & fluctuations

a 'synthetic disorder & fluctuations' from these two blogs ... 

keyword 'disorder' in FonT 

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

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

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

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 

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

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

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

keyword 'waves' in FonT 

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

keyword 'onda' in Notes 

(quasi-stochastic poetry) 

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

keyword 'gst' (General Sistem Theory) in FonT 

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

# 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: density fluctuations may exist in an amorphous matrix

<< Silicon does not have to be crystalline, but can also be produced as an amorphous thin film. In such amorphous films, the atomic structure is disordered like in a liquid or glass. If additional hydrogen is incorporated during the production of these thin layers, so-called a-Si:H layers are formed. >>

<< With this study, we show that the a-Si:H is by no means a homogeneously amorphous material. The amorphous matrix is interspersed with nanometre-sized areas of varying local density, from cavities to areas of extremely high order, >> Klaus Lips

<< We find a nanoscopic order in the disorder of the a-Si:H layers by X-ray scattering measurements (..) We were then able to determine the distribution of the hydrogen atoms in the amorphous network by neutron scattering (..) We were able to discover nanometer-sized voids, which are created by slightly more than 10 missing atoms. These voids arrange themselves into clusters with a recurrent distance of about 1.6 nanometres to each other, >> Eike Gericke

Density fluctuations in amorphous silicon discovered. Helmholtz Association of German Research Centres. Oct 29, 2020. 

https://phys.org/news/2020-10-density-fluctuations-amorphous-silicon.html

Eike Gericke, Jimmy Melskens, et al. Quantification of Nanoscale Density Fluctuations in Hydrogenated Amorphous Silicon. Phys. Rev. Lett. 125, 185501. Oct 29,  2020. 

https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.125.185501

# gst: vacuum fluctuations (even in complete darkness)

<< physics is increasingly discovering how our universe is shaped by fluctuations of physical fields, which not only lead to tiny shifts of spectral lines of atoms, but moreover may cause the evaporation of black holes, and are ultimately responsible for the large-scale structure of our universe,  >>

AA  << have now made a large leap toward controlling strongly enhanced vacuum fluctuations much faster than typical timescales of virtual photons. To this end, they created a specialized semiconductor structure in which electrons are extremely strongly coupled to the light fields of tiny antennas designed for the so-called terahertz spectral range. As a result, vacuum fluctuations of light and matter fields participate in the interaction, strongly increasing the presence of virtual photons—even in complete darkness. >>

Understanding vacuum fluctuations in space. University of Regensburg. Aug 10, 2020.

https://phys.org/news/2020-08-vacuum-fluctuations-space.html 

<< The abrupt modification of the vacuum ground state causes spectrally broadband polarization oscillations confirmed by (AA) quantum model. In the future, this subcycle shaping of hybrid quantum states may trigger cavity-induced quantum chemistry, vacuum-modified transport or cavity-controlled superconductivity, opening new scenarios >>

M. Halbhuber, J. Mornhinweg, et al. Non-adiabatic stripping of a cavity field from electrons in the deep-strong coupling regime. Nat. Photonics. doi: 10.1038/ s41566-020-0673-2. Aug 10, 2020.

https://www.nature.com/articles/s41566-020-0673-2

# gst: apropos of strange fluctuations in oscillation and translation

<< The dynamical processes of the inner core rely significantly on the viscous strength of iron. Since plastic deformation of iron may produce crystallographic preferred orientations  (CPO), creep is commonly considered to be a potential source contributing to the seismic anisotropy observed in the inner core. The viscosity of the inner core also influences the rotational dynamics of the Earth. >>

AA << show  that  dislocation  creep  is  a key  mechanism driving  deformation  of  hcp (hexagonal  close  packed) iron  at  inner  core  conditions. The  associated  viscosity  agrees well  with  the  estimates  from  geophysical  observations  supporting  that  the  inner  core  is  significantly less  viscous  than  the  Earth’s  mantle. Such  low  viscosity  rules  out  inner  core  translation,  with  melting on one side  and  solidification  on  the  opposite,  but  allows  for  the  occurrence  of  the  seismically  observed fluctuations  in  inner  core  differential  rotation. >>

Sebastian Ritterbex & Taku Tsuchiya. Viscosity of hcp iron at Earth’s inner core conditions from density functional theory. Sci Rep 10, 6311 (2020). doi: 10.1038/s41598-020-63166-6. Apr 14, 2020.

https://www.nature.com/articles/s41598-020-63166-6

Is the Earth's inner core oscillating and translating anomalously? Ehime University.  Apr 14, 2020.

https://phys.org/news/2020-04-earth-core-oscillating-anomalously.html