# gst: randomness with constraints: constructing minimal models for high-dimensional biology.

<< ️Biologists and physicists have a rich tradition of modeling living systems with simple models composed of a few interacting components. Despite the remarkable success of this approach, it remains unclear how to use such finely tuned models to study complex biological systems composed of numerous heterogeneous, interacting components. >>

<< ️One possible strategy for taming this biological complexity is to embrace the idea that many biological behaviors we observe are ``typical'' and can be modeled using random systems that respect biologically-motivated constraints. Here, (AA) review recent works showing how this approach can be used to make close connection with experiments in biological systems ranging from neuroscience to ecology and evolution and beyond. Collectively, these works suggest that the ``random-with-constraints'' paradigm represents a promising new modeling strategy for capturing experimentally observed dynamical and statistical features in high-dimensional biological data and provides a powerful minimal modeling philosophy for biology. >>

Ilya Nemenman, Pankaj Mehta. Randomness with constraints: constructing minimal models for high-dimensional biology. arXiv: 2509.03765v1 [physics.bio-ph]. Sep 3, 2025.

https://arxiv.org/abs/2509.03765

Also: random, transition, disorder & fluctuations, fly at random, quasi-stochastic poetry, in https://www.inkgmr.net/kwrds.html 

Keywords: gst, randomness, transitions, disorder & fluctuations, random-with-constraints, fly at random, quasi-stochastic poetry.

# brain: to trace transitions from consciousness to unconscious subliminal perception

AA << study the transition in the functional networks that characterize the human brains’ conscious-state to an unconscious subliminal state of perception >>

<< the most inner core (i.e., the most connected kernel) of the conscious-state functional network corresponds to areas which remain functionally active when the brain transitions from the conscious-state to the subliminal-state. That is, the inner core of the conscious network coincides with the subliminal-state. >>

<< This finding imposes constraints to theoretical models of consciousness, in that the location of the core of the functional brain network is in the unconscious part of the brain rather than in the conscious state as previously thought. >>

Francesca Arese Lucini, Gino Del Ferraro, et al. How the Brain Transitions from Conscious to Subliminal Perception. Neuroscience. Volume 411, Jul 15, 2019, Pages 280-290.

https://www.sciencedirect.com/science/article/abs/pii/S0306452219302052

<< The k-core of the conscious state is reduced to three active regions of the brain, the fusiform gyrus (left and right) and the precentral gyrus. These regions are the only active in the subliminal state. >>

Physicists use mathematics to trace neuro transitions. City College of New York. Jul 18, 2019.

https://m.medicalxpress.com/news/2019-07-physicists-mathematics-neuro-transitions.html  

# gene: point code cracking machines (without detectable byproducts)

DNA cracking machine

<< The spontaneous deamination of cytosine is a major source of C•G to T•A transitions, which account for half of known human pathogenic point mutations. The ability to efficiently convert target A•T base pairs to G•C could therefore advance the study and treatment of genetic diseases >>

AA << report adenine base editors (ABEs) that mediate conversion of A•T to G•C in genomic DNA >>

<< ABEs advance genome editing by enabling the direct, programmable introduction of all four transition mutations without double-stranded DNA cleavage >>

Nicole M. Gaudelli, Alexis C. Komor, et al. Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature 2017 doi: 10.1038/nature24644 Oct 25, 2017
   
https://www.nature.com/nature/journal/vaap/ncurrent/full/nature24644.html

<< there are virtually no detectable byproducts such as random insertions, deletions, translocations, or other base-to-base conversions >>

Researchers extend power of gene editing by developing a new class of DNA base editors. Oct 25, 2017

https://m.phys.org/news/2017-10-enzyme-rewrites-genome.html

RNA cracking machine

<< RNA Editing for Programmable A to I Replacement (REPAIR), which has no strict sequence constraints, can be used to edit full-length transcripts containing pathogenic mutations >>

David B. T. Cox, Jonathan S. Gootenberg, et al. RNA editing with CRISPR-Cas13. Science. Oct 25, 2017:eaaq0180 doi: 10.1126/science.aaq0180

http://science.sciencemag.org/content/early/2017/10/24/science.aaq0180

Researchers engineer CRISPR to edit single RNA letters in human cells. Oct 25, 2017

https://m.phys.org/news/2017-10-crispr-rna-letters-human-cells.html

Lauran Neergaard. Scientists working toward reversible kind of gene editing. Oct. 25, 2017

https://m.phys.org/news/2017-10-scientists-reversible-kind-gene.html

also:

http://flashontrack.blogspot.it/search?q=crispr

# gst: modeling complex nanofibril-based (cell) walls to meet diverse (bio-physical) constraints.

<< A plant cell wall's unique ability to expand without weakening or breaking -- a quality required for plant growth -- is due to the movement of its cellulose skeleton >>️

<< The new model, (..) reveals that chains of cellulose bundle together within the cell wall, providing strength, and slide against each other when the cell is stretched, providing extensibility. >>

<< The new study, (..) presents a new concept of the plant cell wall, gives insights into plant cell growth, and could provide inspiration for the design of polymeric materials with new properties. >>

<< For a long time, the prevailing concept of a plant cell wall has been that of a gel that is reinforced by cellulose fibers, with the stiff cellulose rods acting like steel rebar in cement, (..) However, we determined that cellulose chains instead stick to each other to form a network of cellulose bundles, which provides a lot more mechanical strength than disconnected rods floating in a gel. And it's the cellulose chains, rather than other components, that limit cell wall expansion, sliding alongside each other like an extension ladder when the cell is stretched. >> Daniel Cosgrove. ️

️

What makes plant cell walls both strong and extensible? Penn State. May 13, 2021. 

https://www.sciencedaily.com/releases/2021/05/210513142432.htm

Yao Zhang, Jingyi Yu, et al. Molecular insights into the complex mechanics of plant epidermal cell walls. Science. 

Vol. 372, Issue 6543, pp. 706-711

doi: 10.1126/ science.abf2824. May 14,  2021. 

https://science.sciencemag.org/content/372/6543/706

# astro: could we observe an exploding black hole in the near future?

<< ️Observation of gamma rays from an exploding black hole would provide strong evidence for primordial black holes, the first direct evidence of Hawking radiation, and definitive information on the particles present in nature. However, indirect constraints suggest that direct observation of an exploding Schwarzschild black hole at current or upcoming gamma ray observatories is implausible. >>

<< ️(AA) introduce a dark-QED (Quantum Electrodynamics) toy model consisting of a dark photon and a heavy dark electron. In this scenario a population of light primordial black holes charged under the dark 𝑢⁡(1) symmetry can become quasiextremal, so they survive much longer than if they were uncharged, before discharging and exhibiting a Schwarzschild-like final explosion. (They) show that the answer is “yes,” in this scenario the probability of observing an exploding black hole over the next 10 years could potentially be over 90%. >>

Michael J. Baker, Joaquim Iguaz Juan, et al. Could We Observe an Exploding Black Hole in the Near Future? Phys. Rev. Lett. 135, 111002. Sep 10, 2025. 

https://journals.aps.org/prl/abstract/10.1103/nwgd-g3zl

Marric Stephens. Dark Charge Could Make Exploding Black Holes More Common. (Synopsis). Physics 18, s112. Sep 10, 2025. 

https://link.aps.org/doi/10.1103/Physics.18.s112

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

Keywords: black holes, evaporating black holes, astrophysics.

# 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 shape transitions, midveins regulate the shape formation of drying leaves.

<< ️Dried leaves in nature often exhibit curled and crumpled morphologies, typically attributed to internal strain gradients that produce dome-like shapes. However, the origin of these strain gradients remains poorly understood. Although leaf veins--particularly the midvein--have been suggested to influence shape formation, their mechanical role has not been systematically investigated. >>

<< ️Here, (AA) demonstrate that mechanical constraints imposed by the midvein play a crucial role in generating the diverse morphologies that emerge during leaf drying. Combining numerical simulations and theoretical analysis, (They) show that a uniformly shrinking leaf lamina constrained by a non-shrinking midvein gives rise to two distinct types of configurations: curling-dominated and folding-dominated morphologies. In the curling-dominated regime, both S-curled and C-curled shapes emerge, with C-curled configurations more commonly observed due to their lower elastic energy. In contrast, the folding-dominated regime features folding accompanied by edge waviness. Theoretical modeling reveals a linear relationship between midvein curvature and mismatch strain, consistent with simulation results. >>

<< ️Moreover, (AA) find that the morphological outcome is governed by the ratio of bending stiffnesses between the lamina and the midvein. (They) construct a comprehensive phase diagram for the transitions between different configurations. These findings provide a mechanical framework for understanding shape formation in drying leaves, offering new insights into natural morphing processes and informing the design of bio-inspired morphable structures. >>

Kexin Guo, Yafei Zhang, et al. Midveins regulate the shape formation of drying leaves. arXiv: 2507.01813v1 [cond-mat.soft]. Jul 2, 2025.

https://arxiv.org/abs/2507.01813

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

Keywords: gst, waves, transition, leaf drying, curled and crumpled morphologies, internal strain gradients, dome-like shapes, curling-dominated and folding-dominated morphologies, edge waviness, midvein curvature and mismatch strain, life.

# phys: nature does not always respect symmetry, the hypothesis

<< Physicists have been looking for laws that explain both the microscopic world of elementary particles and the macroscopic world of the universe and the Big Bang at its beginning, expecting that such fundamental laws should have symmetry in all circumstances. However, last year, two physicists found a theoretical proof that, at the most fundamental level, nature does not respect symmetry. >>

<< To try to understand gravity on the quantum level, Hirosi Ooguri, (..) and Daniel Harlow, (..) started with the holographic principle. This principle explains three-dimensional phenomena influenced by gravity on a two-dimensional flat space that is not influenced by gravity.  >>

<< The researchers showed that symmetry only affects the shaded regions in the diagram, not around the spot in the middle, thus there cannot be global symmetry.  >>

Motoko Kakubayashi. Gravity: We might have been getting it wrong this whole time. Kavli Institute for the Physics and Mathematics of the Universe. Jan 24, 2020.

https://m.phys.org/news/2020-01-gravity-wrong.html

Daniel Harlow, Hirosi Ooguri. Constraints on Symmetries from Holography. Phys. Rev. Lett. 122, 191601. doi: 10.1103/ PhysRevLett.122.191601. May 17, 2019.

https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.122.191601

Daniel Harlow, Hirosi Ooguri. Symmetries in quantum field theory and quantum gravity. arXiv: 1810.05338v2 [hep-th]. Jun 6, 2019.

https://arxiv.org/abs/1810.05338

# 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

# s-acad: more 'soft' sci res, more stat positive (true H1 alternative hypothesis) results

<< This study analysed 2434 papers published in all disciplines and that declared to have tested a hypothesis. It was determined how many papers reported a “positive” (full or partial) or “negative” support for the tested hypothesis. If the hierarchy hypothesis is correct, then researchers in “softer” sciences should have fewer constraints to their conscious and unconscious biases, and therefore report more positive outcomes. Results confirmed the predictions at all levels considered: discipline, domain and methodology broadly defined >>

Daniele Fanelli. “Positive” Results Increase Down the Hierarchy of the Sciences.  PLoS ONE 2016; 5(4): e10068. doi:10.1371/journal.pone.0010068

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0010068

# gst: pseudo epileptic seizures in self-organized bistability

<< Self-organized bistability (SOB) stands as a critical behavior for the systems delicately adjusting themselves to the brink of bistability, characterized by a first-order transition. >>️

(AA) << embark on a theoretical exploration that extends the boundaries of the SOB concept on a higher-order network (implicitly embedded microscopically within a simplicial complex) while considering the limitations imposed by coupling constraints. >>️

AA << use continuous synchronization diagrams and statistical data from spontaneous synchronized events to demonstrate the crucial role SOB plays in initiating and terminating temporary synchronized events. (They) show that under weak coupling consumption, these spontaneous occurrences closely resemble the statistical traits of the epileptic brain functioning. >>

️

Md Sayeed Anwar, Nikita Frolov, Alexander E. Hramov, Dibakar Ghosh. Self-organized bistability on globally coupled higher-order networks. arXiv: 2401.02825v1 [nlin.AO]. Jan 5, 2024.

https://arxiv.org/abs/2401.02825

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

Keywords: gst, transition, self-assembly, bistability, self-organized bistability, brain, epileptic seizure

# gst: approaching uncertainty among many-body real-time dynamics

<< Analog quantum simulation is emerging as a powerful tool for uncovering classically unreachable physics such as many-body real-time dynamics. >>️

AA << examines the interplay of errors arising from simulation of approximate time evolution with those due to practical, real-world device constraints. >>️

Nikita A. Zemlevskiy, Henry F. Froland, Stephan Caspar. Optimization of algorithmic errors in analog quantum simulations. Phys. Rev. A 109, 052425. May 15, 2024. 

https://journals.aps.org/pra/abstract/10.1103/PhysRevA.109.052425

<< The new technique focuses on two sources of error that arise from the approximations used to map the quantum system of interest to the analog quantum simulator. In a real-world simulator, these error sources are linked in a complex way, and individually minimizing each error can increase the overall uncertainty of a simulation. (AA) tackled this problem by first isolating the two error sources and then carefully studying their interplay. This analysis enabled the researchers to finely tune a simulation’s parameters to minimize its overall uncertainty and to maximize its precision. >>️

Ryan Wilkinson. Quantifying Uncertainties in Quantum Simulations. 

Physics 17, s51. May 15, 2024. 

https://physics.aps.org/articles/v17/s51

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

Keywords: gst, uncertainty, error, noise

# ai.bot: "Machine Behaviour", the multi-disciplinary, ethological approach to "Intelligent Machines", by MIT

<< Rather than simply being scared of "intelligent machines," (..) society needs to study algorithms with a multi-disciplinary approach akin to the field of ethology. >>

Tiernan Ray. MIT finally gives a name to the sum of all AI fears. Apr 25, 2019.

https://www.zdnet.com/article/mit-finally-gives-a-name-to-the-sum-of-all-ai-fears/

<< Machines powered by artificial intelligence increasingly mediate our social, cultural, economic and political interactions. >>

AA << first outline a set of questions that are fundamental to this emerging field and then explore the technical, legal and institutional constraints on the study of machine behaviour. >>

Iyad Rahwan, Manuel Cebrian, et al. Machine behaviour. Nature volume 568, pages477–486 Apr 24, 2019.

https://www.nature.com/articles/s41586-019-1138-y

Also

anomalous formation of molecules after vapor deposition. Dec 31, 2015

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

# brain: changing like a skilled jazz player

<< The new findings are just the latest evidence that our brains are capable of changing in response to experiential learning from a very early age, (..) but that there are underlying constraints hardwired into the brain that shape and guide how those changes unfold. Like a skilled jazz player who spontaneously invents fresh melodies while still respecting the grammar of music, the brain is a master improviser that can create new activations (..), but it must still follow certain rules-like those regarding objects preferentially viewed with our central gaze-about where these category-preferring activations can take place. >> Kalanit Grill-Spector.

Ker Than. Researchers identify brain region activated by Pokemon characters. Stanford University. May 6, 2019.

https://m.medicalxpress.com/news/2019-05-brain-region-pokemon-characters.html

Jesse Gomez, Michael Barnett, Kalanit Grill-Spector. Extensive childhood experience with Pokémon suggests eccentricity drives organization of visual cortex. Nature Human Behaviour. doi: 10.1038/s41562-019-0592-8. May 6, 2019

https://www.nature.com/articles/s41562-019-0592-8

Also

"jazz"

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

# gst: like grains of sand in a sandcastle

<< Cells comprising a tissue can pack into disorderly geometries much as do grains of sand in a sandcastle. In doing so they can freeze into a fixed shape—as in a sandcastle—or flow like sand poured from a beach bucket >>

<< This finding makes a deep connection between the physics of inert granular matter such as sand and the geometry of multicellular living systems >> Lior Atia.

Harvard T.H. Chan School of Public Health. Sandcastles and surprising origins of basic cellular functions. Apr 2, 2018

https://m.phys.org/news/2018-04-sandcastles-basic-cellular-functions.html

Lior Atia, Dapeng Bi, et al. Geometric constraints during epithelial jamming. Nature Physics. doi: 10.1038/s41567-018-0089-9. Apr 2, 2018.

https://www.nature.com/articles/s41567-018-0089-9

# gst: attraction-enhanced emergence of friction (in colloidal matter)

<< How frictional effects emerge at the microscopic level in particulate materials remains a challenging question, particularly in systems subject to thermal fluctuations due to the transient nature of interparticle contacts. >>

Here, AA << directly relate particle-level frictional arrest to local coordination in an attractive colloidal model system. (They) reveal that the orientational dynamics of particles slows down exponentially with increasing coordination number due to the emergence of frictional interactions, the strength of which can be tuned simply by varying the attraction strength. Using a simple computer simulation model, (they) uncover how the interparticle interactions govern the formation of frictional contacts between particles. >>

AA << results establish quantitative relations between friction, coordination, and interparticle interactions. This is a key step toward using interparticle friction to tune the mechanical properties of particulate materials. >>️

<< Importantly, almost all theoretical and simulation studies on such systems do not account for interparticle friction. Incorporating frictional constraints to rolling and sliding between particles will likely have a pronounced effect on a variety of phenomena studied in attractive colloidal matter such as gel formation, coarsening and failure. >>

️

Berend van der Meer, Taiki Yanagishima, Roel P. A. Dullens. Attraction-Enhanced Emergence of Friction in Colloidal Matter. Phys. Rev. Lett. 134, 078202. Feb 21, 2025. 

https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.134.078202

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

Keywords: gst, particles, colloids, friction, coordination,  interparticle friction, interparticle interactions

# 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: equilibrium and breakup regimes of stretched soap bubbles

AA << combine experiments and theoretical derivations to study the evolution of a stretched soap bubble and compare it with an open film to highlight the effect of volume conservation. (They) identify a critical length for both surfaces, beyond which a bottleneck develops in the middle and begins to shrink irreversibly, ultimately pinching off into multiple compartments. >>

<< Before leaving the equilibrium regime, surface energy minimization governs the shape, which can be addressed theoretically via the variational method. In contrast to open films, soap bubble volume conservation introduces a Lagrange multiplier, analogous to a pressure difference, mediating long-range shape evolution. >>

<< By examining how boundary constraints influence deformation, (AA) contrast the bubble's convex-to-concave transition with the behavior of soap films under similar conditions. (Their) analysis of equilibrium and breakup regimes reveals critical differences between bubble and film stability profiles, shedding light on universal behaviors in non-equilibrium fluid mechanics, with implications for biological and material sciences.

>>️

Wei-Chih Li, Chih-Yao Shih, et al. How soap bubbles change shape while maintaining a fixed volume of air? arXiv: 2412.17870v1 [physics.flu-dyn]. Dec 21, 2024. 

https://arxiv.org/abs/2412.17870

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

Keywords: gst, bubble, drop, droplet, droploid, transition