# gst: acceleration of enzymatic reactions due to nearby inactive binding sites.

<< Many biological molecular motors and machines are driven by chemical reactions that occur in specific catalytic sites. (AA) study whether the arrival of molecules to such an active site can be accelerated by the presence of a nearby inactive site.  >>️

AA << identify two parameter regimes in which the reaction is accelerated. >>️

<< In the first regime, the inactive site stores a molecule in order to release it following a reaction, when the neighboring catalytic site is empty. >>

<< In the second regime, the inactive site releases a molecule when the catalytic site is full, in order to impede the molecules from leaving the active site before they react. For the storage mechanism, which is more likely to be biologically relevant, the acceleration can reach up to 15%, depending on parameters. >>️

Hila Katznelson, Saar Rahav. Acceleration of enzymatic reactions due to nearby inactive binding sites. arXiv: 2501.01662v1 [cond-mat.stat-mech]. Jan 3, 2025.

https://arxiv.org/abs/2501.01662  

Phys. Rev. Research 6, 043330. Dec 30, 2024. 

https://journals.aps.org/prresearch/abstract/10.1103/PhysRevResearch.6.043330

Keywords: gst, enzymes, enzymatic catalysis, catalytic sites, inactivity, inactive binding sites

# gst: dynamics of swarmalators in the presence of a contrarian.

<< Swarmalators are entities that combine the swarming behavior of particles with the oscillatory dynamics of coupled phase oscillators and represent a novel and rich area of study within the field of complex systems. >>

<< Unlike traditional models that treat spatial movement and phase synchronization separately, swarmalators exhibit a unique coupling between their positions and internal phases, leading to emergent behaviors that include clustering, pattern formation, and the coexistence of synchronized and desynchronized states, etc. >>

This AA paper << presents a comprehensive analysis of a two-dimensional swarmalator model in the presence of a predatorlike agent that (They) call a contrarian. The positions and the phases of the swarmalators are influenced by the contrarian and (They)  observe the emergence of intriguing collective states. >>

AA find << that swarmalator phases are synchronized even with negative coupling strength when their interaction with the contrarian is comparatively strong. Through a combination of analytical methods and simulations, (They) demonstrate how varying these parameters can lead to transitions between different collective states. >>

Gourab Kumar Sar, Sheida Ansarinasab, et al. Dynamics of swarmalators in the presence of a contrarian. Phys. Rev. E 111, 014209. Jan 7, 2025.

https://journals.aps.org/pre/abstract/10.1103/PhysRevE.111.014209 

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

Keywords: gst, swarm, swarmalators, transitions, behavior, behaviour

# gst: trade-off between coherence and dissipation for excitable phase oscillators.

<< Thermodynamic uncertainty relation (TUR) bounds coherence in stochastic oscillatory systems. In this paper, (AA) show that both dynamical and thermodynamic bounds play important roles for the excitable oscillators, e.g. neurons. >>

<< Excitable systems such as neurons have distinctive coherence features compared with other oscillators having no excitability. >>️

AA << combined the well-established results, i.e. the fluctuation of the ISI (inter-spike-interval) limited by 1/3 and the coherence resonance phenomenon, together with the TUR developed in recent years to investigate the coherence in the excitable phase oscillators. (AA) find quite different trade-off relation in the subthreshold (excitable) region and superthreshold (oscillatory) region, separated by the SNIC (saddle-node on an invariant circle) bound but meanwhile lower bounded by the TUR. Furthermore, (They) found that there is an optimal entropy production corresponding to the maximum coherence, which could serve as an alternative interpretation of the coherence resonance. It implies that more entropy production does not necessarily result in higher accuracy of currents. >>️

Chunming Zheng. Trade-off between coherence and dissipation for excitable phase oscillators. arXiv: 2412.16603v1 [cond-mat.stat-mech]. Dec 21, 2024.

https://arxiv.org/abs/2412.16603

Also: brain, entropy, dissipation, uncertainty, in https://www.inkgmr.net/kwrds.html 

Keywords: gst, brain, neurons, entropy, oscillators, excitable phase oscillators, coherence, dissipation, uncertainty

# gst: stochastic Scovil-Schulz-DuBois (SSDB) machine and its three types of cycles

<< Three types of cycles are identified in the quantum jump trajectories of the Scovil–Schulz-DuBois (SSDB) machine. An R cycle as refrigeration, an H cycle as a heat engine, and an N cycle in which the machine is neutral. >>

AA << find that in the large time limit, whether the machine operates as a heat engine or refrigerator depends on the ratio between the numbers of R cycles and H cycles per unit time. Further increasing the hot bath temperature above a certain threshold does not increase the machine's power output. The cause is that, in this situation, the N cycle has a greater probability than the H cycle and R cycle. >>

<< Although the SSDB machine operates by randomly switching between these three cycles, at the level of a single quantum jump trajectory, its heat engine efficiency and the refrigerator's coefficient of performance remain constant. >>

Fei Liu, Jiayin Gu. Stochastic Scovil–Schulz-DuBois machine and its three types of cycles. Phys. Rev. E 111, 014108. Jan 3, 2025. 

https://journals.aps.org/pre/abstract/10.1103/PhysRevE.111.014108 

arXiv: 2409.04124v2 [cond-mat.stat-mech]. Jan 5, 2025. 

https://arxiv.org/abs/2409.04124

Keywords: gst, stochasticity, quantum heat engines & refrigerators, stochastic Scovil–Schulz-DuBois (SSDB) machine 

# 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

# gst: black swan ... or black rabbit?

<<

In his book The Black Swan: The Impact of the Highly Improbable, Nassim Nicholas Taleb explores the profound and unpredictable events that shape our world, which he calls “Black Swans.” These events are characterized by three main features: they are rare and unpredictable, they have an extreme impact, and in hindsight, they often seem explainable or inevitable. Taleb argues that our world is increasingly shaped by these Black Swans, from financial crises to technological breakthroughs, and yet humans are inherently ill equipped to anticipate them due to cognitive biases and reliance on standard predictive models. By analogy with this term, (AA) have named Black Rabbits events that exhibit all the external characteristics of a Black Swan but are entirely determined by the state of the system itself. These phenomena are not artificial examples or mere curiosities; they exist wherever hyperbolic meadows are found. When we witness a social catastrophe or a financial crisis, could it be not a stray Black Swan but a local Black Rabbit? How can one determine in advance that a system is pregnant with a crisis? What indicators can be used? Is it possible to control the system to prevent it from becoming unstable? These are intriguing questions, perhaps too complex, especially when dealing not with simple mathematical models but with real-world systems. Yet, we must still strive to find answers to them.

>>

Alexey Solyanik. The Black Rabbits of Fibonacci. arXiv: 2412.20222v1 [math.DS]. Dec 28, 2024.

https://arxiv.org/abs/2412.20222

Also: gst - general system theory, analogy, in https://www.inkgmr.net/kwrds.html 

Keywords: gst, analogy

# life: a bizarre 'aleatorio torneamento' revisited; Mickey Mouse (et al.) collapsed, by Ann

<< nelle gronde d' estremo tono dal ristagno d' eterno memento ... //

(..)

tr'astratti lamenti dallo sciamante stenotermo sognante tremore // >>

Aleatorio torneamento. Notes. (quasi-stochastic poetry). Feb 09, 2006.

https://inkpi.blogspot.com/2006/02/1955-aleatorio-torneamento.html 

<< Ann Telnaes, a long-time Washington Post cartoonist, created a cartoon of Mr Bezos and other tycoons kneeling before a statue of President-elect Donald Trump. >>

<< In the cartoon, Mr Bezos, Meta founder Mark Zuckerberg and OpenAI's Sam Altman are depicted on their knees giving bags of cash to a statue of Trump.

Mickey Mouse is also depicted prostrate in the cartoon. ABC News – which is owned by Disney – last month agreed to pay $15m to settle a defamation lawsuit filed by Trump. >>

Ana Faguy. Washington Post cartoonist quits after Bezos satire is rejected. Jan 4, 2025. https://www.bbc.com/news/articles/cn4xk4y2emro  

Ann Telnaes. Why I'm quitting the Washington Post. Jan 4, 2025. 

https://anntelnaes.substack.com/p/why-im-quitting-the-washington-post     https://anntelnaes.com     https://x.com/AnnTelnaes     https://en.m.wikipedia.org/wiki/Ann_Telnaes

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

Keywords: life, Donald, Potus, Potus race