# gst: distance to criticality in unknown noise

<< real-world systems are often corrupted by unknown levels of noise that can distort (..) temporal signatures. Here (AA) aim to develop noise-robust indicators of the distance to criticality (DTC) for systems affected by dynamical noise in two cases: when the noise amplitude is either fixed or is unknown and variable across recordings. >>️

<< in the variable-noise setting, where (..) conventional indicators perform poorly, (AA) highlight new types of high-performing time-series features and show that their success is accomplished by capturing the shape of the invariant density (which depends on both the DTC and the noise amplitude) relative to the spread of fast fluctuations (which depends on the noise amplitude). (AA) introduce a new high-performing time-series statistic, the rescaled autodensity (RAD). >>️

Brendan Harris, Leonardo L. Gollo, Ben D. Fulcher. Tracking the Distance to Criticality in Systems with Unknown Noise. Phys. Rev. X 14, 031021. Aug 8, 2024.

https://journals.aps.org/prx/abstract/10.1103/PhysRevX.14.031021

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

Keywords: gst, criticality, bifurcation, noise, transition

# gst: existence of hidden metastable states, bifurcations of inflating balloons and interacting hysterons.

AA << consider a system of connected rubber balloons that can be described by a Preisach model of noninteracting hysterons under pressure control but for which the hysterons become coupled under volume control. >>

<< Changes in the transition graphs turn out to be related to changes in the topology of the configuration space of the balloons, providing a particularly geometric view of how transition graphs can be designed, as well as additional information on the existence of hidden metastable states. This class of systems is more general than just balloons. >>️

Gentian Muhaxheri and Christian D. Santangelo. Bifurcations of inflating balloons and interacting hysterons. Phys. Rev. E 110, 024209. Aug 16, 2024.

https://journals.aps.org/pre/abstract/10.1103/PhysRevE.110.024209

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

Keywords: gst, balloons, bifurcations, hysteresis, hysterons, transition

# gst: spontaneous bouncing, trampolining, and hovering behaviors of a levitating water droplet without constraints.

<< The levitating Leidenfrost (LF) state of a droplet on a heated substrate is often accompanied by fascinating behaviors such as star-shaped deformations, self-propulsion, bouncing, and trampolining. These behaviors arise due to the vapor flow instabilities at the liquid-vapor interface beneath the droplet at sizes typically comparable to the capillary length scale of the liquid. >>

AA << report on the spontaneous bouncing, trampolining, and hovering behavior of an unconstrained LF water droplet. (..) the water droplet exhibits an increase in bouncing height at specific radii with intermittent reduction in the height of bounce leading to a quiescent LF state. The reemergence of the trampolining behavior from the quiescent hovering state without any external forcing is observed at sizes as low as 0.1 times the capillary length. (AA) attribute the droplet bouncing behavior to the dynamics of vapor flow beneath the LF droplet. >>

AA << propose that the trampolining behavior of the droplet at specific radii is triggered by harmonic and subharmonic resonance between the natural frequency of the vapor layer and Rayleigh frequency of the droplet. This proposed mechanism of resonance-driven trampolining of LF droplets is observed to be applicable for different liquids irrespective of the initial volume and substrate temperatures, thus indicating a universality of the behavior. (AA) attribute the intermittent trampolining events to the change in the natural frequency of the droplet and the vapor layer due to evaporative mass loss. >>

Pranjal Agrawal, Susmita Dash. Reemergence of Trampolining in a Leidenfrost Droplet. arXiv: 2408.02335v1 [physics.flu-dyn]. Aug 5, 2024. 

https://arxiv.org/abs/2408.02335

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

Keywords: gst, drop, droplet, droploid, behav, behaviour

# gst: apropos of 'normal' (jazzy?) codes, bacteria encode hidden, free-floating genes outside their genome.

AA << show that bacteria break that rule and can create free-floating and ephemeral genes, raising the possibility that similar genes exist outside of our own genome. >>️

<< What this discovery upends is the notion that the chromosome has the complete set of instructions that cells use to produce proteins, (..) We now know that, at least in bacteria, there can be other instructions not preserved in the genome that are nonetheless essential for cell survival. (..) The DNA molecule is a fully functioning, free-floating, transient gene. >> Samuel Sternberg. 

Bacteria Encode Hidden Genes Outside Their Genome—Do We? Columbia University Irving Medical Center. Aug 8, 2024. 

https://www.cuimc.columbia.edu/news/bacteria-encode-hidden-genes-outside-their-genome-do-we   

Stephen Tang, Valentin Conte, et al. De novo gene synthesis by an antiviral reverse transcriptase. Science. doi: 10.1126/ science.adq0876. Aug 8, 2024. 

https://www.science.org/doi/10.1126/science.adq0876

Also: 

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

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

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

CRISPR  https://flashontrack.blogspot.com/search?q=crispr

normal, jazz, in https://www.inkgmr.net/kwrds.html 

Keywords: gst, codes, dna, rna, crispr, normal, jazz

# gst: networks of pendula with diffusive interactions, chaotic regime seems to emerge at low energies.

AA << study a system of coupled pendula with diffusive interactions, which could depend both on positions and on momenta. The coupling structure is defined by an undirected network, while the dynamic equations are derived from a Hamiltonian; as such, the energy is conserved. >>️

<< The behaviour observed showcases a mechanism for the appearance of chaotic oscillations in conservative systems. For Hamiltonians with two degrees of freedom, it has been shown how chaos can emerge near a saddle-centre equilibrium possessing a homoclinic orbit. (AA) have seen that higher-dimensional systems having mixed equilibria, i.e., generalisations of a saddle-center where the eigenvalues are only imaginary and reals, also show chaotic behaviour close to those points.  >>️

AA << complement the analysis with some numerical simulations showing the interplay between bifurcations of the origin and transitions to chaos of nearby orbits. A key feature is that the observed chaotic regime emerges at low energies. >>

️

Riccardo Bonetto, Hildeberto Jardón-Kojakhmetov, Christian Kuehn. Networks of Pendula with Diffusive Interactions. arXiv: 2408.02352v1 [math.DS]. Aug 5, 2024.

https://arxiv.org/abs/2408.02352

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

Keywords: gst, pendulum, network, transition, chaos, bifurcation

# gst: emergent chirality in active rotation even with spontaneous chiral symmetry breaking.

<< Collective cell dynamics play a crucial role in many developmental and physiological contexts. While two-dimensional (2D) cell migration has been widely studied, how three-dimensional (3D) geometry and topology interplay with collective cell behavior to determine dynamics and functions remains an open question. >>️

<< Using murine pancreas-derived organoids as a model system, (AA) find that epithelial spheres exhibit persistent rotation, rotational axis drift, and rotation arrest. Using a 3D vertex model, (they) demonstrate how the combined action of traction force and polarity alignment can account for these distinct rotational dynamics near a solid to flow transition. Furthermore, (their) analysis shows that the spherical tissue rotates as an active solid occasionally switching to a flowing state and exhibits spontaneous chiral symmetry breaking. >>️

Tzer Han Tan, Aboutaleb Amiri, et al. Emergent chirality in active solid rotation of pancreas spheres. PRX Life 2, 033006. Aug 8, 2024.

https://journals.aps.org/prxlife/abstract/10.1103/PRXLife.2.033006

AA << say their work shows how symmetry-breaking processes in living active matter can be induced by the interplay of geometry, topology, and collective dynamics. >>️

Charles Day. Emergent Chirality in Active Rotation. Physics 17, s102. Aug 8, 2024. 

https://physics.aps.org/synopsis-for/10.1103/PRXLife.2.033006 

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

Keywords: gst, transition, chiral, chiral symmetry breaking 

# gst: tracking criticality in unknown noise

<< Many real-world systems undergo abrupt changes in dynamics as they move across critical points, often with dramatic and irreversible consequences. >>️

AA << aim to develop noise-robust indicators of the distance to criticality (DTC) for systems affected by dynamical noise in two cases: when the noise amplitude is either fixed or is unknown and variable across recordings. (They) present a highly comparative approach to this problem that compares the ability of over 7000 candidate time-series features to track the DTC in the vicinity of a supercritical Hopf bifurcation. >>️

<< in the variable-noise setting, where these conventional indicators perform poorly, (AA) highlight new types of high-performing time-series features and show that their success is accomplished by capturing the shape of the invariant density (which depends on both the DTC and the noise amplitude) relative to the spread of fast fluctuations (which depends on the noise amplitude). >>

AA << introduce a new high-performing time-series statistic, the rescaled autodensity (RAD), that combines these two algorithmic components. >>️

️

Brendan Harris, Leonardo L. Gollo, Ben D. Fulcher. Tracking the Distance to Criticality in Systems with Unknown Noise. Phys. Rev. X 14, 031021. Aug 8, 2024.

https://journals.aps.org/prx/abstract/10.1103/PhysRevX.14.031021

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

Keywords: gst, noise, brain, mouse visual cortex