# evol: flip of the script when an entity invert code sequences

<< Jekyll and Hyde flip of the script when bacteria invert gene sequences. If a cell can diversify its own genome, this can be advantageous in the face of changing environmental conditions. Bacteria have been found that can alter encoded proteins by using the trick of sequence inversion inside genes. >>️

Chia-Chi Chang, Robert R. Jenq. Jekyll and Hyde flip of the script when bacteria invert gene sequences. Nature 634, 42-43. Sep 25, 2024. 

https://www.nature.com/articles/d41586-024-02807-6

Chia-Chi Chang, Robert R. Jenq. Bacteria invert gene sequences to flip the script. Nature. Vol 634. Oct 3, 2024 (pdf)  https://media.nature.com/original/magazine-assets/d41586-024-02807-6/d41586-024-02807-6.pdf

Chanin RB, West PT, et al. Intragenic DNA inversions expand bacterial coding capacity. Nature. 2024 Oct; 634 (8032): 234-242. doi: 10.1038/s41586-024-07970-4. Sep 25, 2024. 

https://pubmed.ncbi.nlm.nih.gov/39322669/

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

Also: 

DNA https://flashontrack.blogspot.com/search?q=dna 

RNA https://flashontrack.blogspot.com/search?q=rna 

CODES https://flashontrack.blogspot.com/search?q=codes

Also (quasi-stochastic poetry): 

DNA  https://inkpi.blogspot.com/search?q=dna 

RNA https://inkpi.blogspot.com/search?q=rna 

CODICE https://inkpi.blogspot.com/search?q=codice

Keywords: evolution, codes, DNA, RNA

# gst: apropos of breaking mechanisms, crack of a floating particle raft caused by waves.

<< When particles of a few tens of microns are spread on the surface of water, they aggregate under the action of capillary forces and form a thin floating membrane, a particle raft. >>

<< For a sufficiently strong wave amplitude, the raft breaks up progressively by developing cracks and producing fragments whose sizes decrease on a timescale long compared to the period of the wave. (AA)  characterize the breaking mechanisms.  >>️️

<< The visual appearance of the fragments distributed in size and surrounded by open water bears a notable resemblance to the floes produced by the fracturing of sea ice by waves in the polar oceans. Fragmentation concepts and morphological tools built for sea ice floes can be applied to (AA) macroscopic analog, on which the entire dynamic evolution is accessible. However, the mechanics of the two systems differ, as (AA) particle raft breaks due to the viscous stresses, whereas the sea ice fractures due to its bending by the waves. >>️

Louis Saddier, Ambre Palotai, et al. Breaking of a floating particle raft by water waves. Phys. Rev. Fluids 9, 094302. Sep 27, 2024.

https://journals.aps.org/prfluids/abstract/10.1103/PhysRevFluids.9.094302 

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

Also: 'break' in  https://flashontrack.blogspot.com/search?q=break

Also: 'raft' in  https://flashontrack.blogspot.com/search?q=raft

Also: 'zattera' (quasi-stochastic poetry) in  https://inkpi.blogspot.com/search?q=zattera  'randa' (quasi-stochastic poetry) in https://inkpi.blogspot.com/search?q=randa

Keywords: gst, crack, break, particle, raft, particle raft

# gst: apropos of inertial particles, they dispersion in turbulent canopy flows with buoyant and nonbuoyant plumes.

<< In an idealized “wind-driven” model system, (AA) consider the impact of plume buoyancy, plume momentum, and canopy turbulence on the downstream transport of particles in the wake of a canopy, and in particular the mean and standard deviation of the distribution of landing sites. >>

<< In a first set of experiments, particles were released with a fixed starting elevation above the plumes' upper boundaries, such that the particles were not lofted by the plume. In these cases, observations suggest that plumes have a role in extending particles' streamwise transport by delaying their downward transport. The plumes also have a strong role in increasing absolute dispersion of the particles, although less so when dispersion is normalized by distance traveled. While canopy turbulence alone significantly increases particle dispersion, in the presence of the plume its impact is more limited. Canopy turbulence was also found to cause shorter mean landing positions. >>

<< In a second set of experiments, particles were released at the plume source/outlet such that their initial vertical momentum was provided by the plume's momentum and buoyancy. In these cases, the impact of canopy turbulence on particle transport is observed more distinctly. The canopy coherent structures introduce a mechanical instability to the plume, which manifests as vertical oscillatory motions that lead to variability in the particles' initial conditions and, therefore, trajectories. This leads to particles settling at both shorter and longer downstream distances. >>

Hayoon Chung, Laura K. C. Sunberg, et al. Dispersion of inertial particles in turbulent canopy flows with buoyant and nonbuoyant plumes. Phys. Rev. Fluids 9, 093801. Sept 25, 2024.

https://journals.aps.org/prfluids/abstract/10.1103/PhysRevFluids.9.093801  

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

Keywords: gst, particle, turbulence

# brain: time delay in 'reservoir brain' as a reservoir network, a hypothesis

<< Both the predictive power and the memory storage capability of an artificial neural network called a reservoir computer increase when time delays are added into how the network processes signals, according to a new model. >>️

<< They also suggest that incorporating time delays could offer advantages to living neural networks (such as those found in human and animal brains). Such a finding would be tantalizing, as time delays are known to decrease performance in living systems. For example, for a baseball player facing an oncoming ball, a longer time delay between perception and action (which is learned from experience) will decrease the likelihood they hit a home run. Are there instead cases in which time delays increase an organism’s ability to perform some task? Has evolution shaped our brains, which could perhaps be thought of as a collection of reservoir computers, so that the time delay between one neuron sending a signal and a second receiving it is exactly the right length for understanding the visual and audio that constantly impinge upon our eyes and ears? Does adding time delays impact the number of neurons the brain needs to operate correctly? Further work is needed to answer these questions, but such work could lead to a new understanding of how biological organism’s function.  >>️

Sarah Marzen. Time Delays Improve Performance of Certain Neural Networks. Physics 17, 111. July 22, 2024. 

https://physics.aps.org/articles/v17/111 

Also: pause, silence, jazz, network, brain, ai (artificial intell), in https://www.inkgmr.net/kwrds.html 

Keywords: gst, brain, network, neural network, reservoir network, reservoir computer, time delay, ai, artificial intelligence

# gst: extreme events in two-coupled chaotic oscillators.

This AA study << focuses on the emergence of extreme events in a system of diffusively and bidirectionally two coupled Rössler oscillators and unraveling the mechanism behind the genesis of extreme events. (AA) find the appearance of extreme events in three different observables: average velocity, synchronization error, and one transverse directional variable to the synchronization manifold. >>

<< The emergence of extreme events in average velocity variables happens due to the occasional in-phase synchronization. The on-off intermittency plays for the crucial role in the genesis of extreme events in the synchronization error dynamics and in the transverse directional variable to the synchronization manifold. The bubble transition of the chaotic attractor due to the on-off intermittency is illustrated for the transverse directional variable. >>

S. Sudharsan, Tapas Kumar Pal, et al. Extreme events in two-coupled chaotic oscillators. arXiv: 2409.15855v1 [nlin.CD]. Sep 24, 2024. 

https://arxiv.org/abs/2409.15855

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

Keywords: gst, transition, bubble transition, extreme events

# gst: dynamics of pulsating spheres orbiting black holes.

AA << study the chaotic dynamics of spinless extended bodies in a wide class of spherically symmetric spacetimes, which encompasses black-hole scenarios in many modified theories of gravity. (They) show that a spherically symmetric pulsating ball may have chaotic motion in this class of spacetimes. >>

AA << use Melnikov's method to show the presence of homoclinic intersections, which imply chaotic behavior, as a consequence of (their)  assumption that the test body has an oscillating radius. >>

Fernanda de F. Rodrigues, Ricardo A. Mosna, Ronaldo S. S. Vieira. Chaotic dynamics of pulsating spheres orbiting black holes. arXiv: 2409.14667v1 [gr-qc]. Sep 23, 2024.

https://arxiv.org/abs/2409.14667

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

Keywords: gst, black hole, homoclinic orbit, chaos, transition

# gst: complexity of a flat-foldings random origami

AA << give the result of approximate enumeration of the total number of flat-foldings of single-vertex origami diagram with random width of angles gathering around the central vertex, and obtain its size dependence for an asymptotic prediction towards the limit of infinite size. >>️

<< In addition, an outlook with respect to the chained determination of local stacking orders of facets caused by the constraint that prohibits the penetration of them is also provided from the viewpoint of organizing the terms included in the physical model. A method to efficiently solve the problem of the determination or enumeration of flat-foldings is discussed based on the above perspectives. >>️

Chihiro Nakajima. An Efficient Enumeration of Flat-Foldings : Study on Random Single Vertex Origami. arXiv: 2409.03240v1 [cond-mat.stat-mech]. Sep 5, 2024.

https://arxiv.org/abs/2409.03240

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

Keywords: gst, origami, kirigami