# gst: evolution of robust cell differentiation mechanisms under epigenetic feedback

<< In multi-cellular organisms, cells differentiate into multiple types as they divide. States of these cell types, as well as their numbers, are known to be robust to external perturbations; as conceptualized by Waddington's epigenetic landscape where cells embed themselves in valleys corresponding with final cell types. >>

<< How is such robustness achieved by developmental dynamics and evolution? To address this question, (AA) consider a model of cells with gene expression dynamics and epigenetic feedback, governed by a gene regulation network. By evolving the network to achieve more cell types, (They) identified three major differentiation mechanisms exhibiting different properties regarding their variance, attractors, stability, and robustness. >>

<< The first of these mechanisms, type A, exhibits chaos and long-lived oscillatory dynamics that slowly transition until reaching a steady state. The second, type B, follows a channeled annealing process where the epigenetic changes in combination with noise shift the stable landscape of the cells towards varying final cell states. Lastly, type C exhibits a quenching process where cell fate is quickly decided by falling into pre-existing fixed points while cell trajectories are separated through periodic attractors or saddle points. >>

AA << find types A and B to correspond well with Waddington's landscape while being robust. Finally, the dynamics of type B demonstrate a novel method through dimensional reduction of gene-expression states during differentiation. >>

Davey Plugers, Kunihiko Kaneko. Evolution of robust cell differentiation mechanisms under epigenetic feedback. arXiv: 2503.20651v1 [physics.bio-ph]. Mar 26, 2025. 

https://arxiv.org/abs/2503.20651

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

Keywords: gst, evolution, noise, epigenetics, epigenetic feedback, differentiation

# gst: noise as endogenous control

<< Systems biology faces the monumental task of synthesizing vast amounts of molecular facts into a cohesive whole. While it is recognized that stochasticity is ubiquitous in the cell, with noise playing a role in gene expression, differentiation, and switching (..), it is still commonly argued that the cell functions in spite of the noisy cellular environment. >>️

<< Stochastic systems have a control-theoretic interpretation in which noise plays the role of endogenous control. In the weak-noise limit, relevant at low temperatures or in large populations, control is optimal and an exact mathematical mapping from noise to control is described, where the maximizing the probability of a state becomes the control objective. >>

<< In Langevin dynamics noise is identified directly with control, while in general Markov jump processes, which include chemical reaction networks and electronic circuits, (AA) use the Doi-Zel'dovich-Grassberger-Goldenfeld-Peliti path integral to identify the `response' or `tilt' field π as control, which is proportional to the noise in the semiclassical limit. This solves the longstanding problem of interpreting π. >>

AA << illustrate the mapping on multistable chemical reaction networks and systems with unstable fixed points. The noise-control mapping builds intuition for otherwise puzzling phenomena of stochastic systems: why the probability is generically a non-smooth function of state out of thermal equilibrium; why biological mechanisms can work better in the presence of noise; and how agentic behavior emerges naturally without recourse to mysticism. >>

Eric De Giuli. Noise equals endogenous control. arXiv: 2503.15670v2 [q-bio.MN]. Mar 24, 2025.

https://arxiv.org/abs/2503.15670

Also: noise, disorder & fluctuations, transition, dance, jazz, in https://www.inkgmr.net/kwrds.html 

Keywords: gst, noise, disorder, transition, ethno, crosstalk, gossip, misinformation, fake news, dance, jazz

# qubit: stability of classical shadows under gate-dependent noise

<< Expectation values of observables are routinely estimated using so-called classical shadows—the outcomes of randomized bases measurements on a repeatedly prepared quantum state. In order to trust the accuracy of shadow estimation in practice, it is crucial to understand the behavior of the estimators under realistic noise. >>

<< In this Letter, (AA) prove that any shadow estimation protocol involving Clifford unitaries is stable under gate-dependent noise for observables with bounded stabilizer norm—originally introduced in the context of simulating Clifford circuits. In contrast, (They) demonstrate with concrete examples that estimation of “magic” observables can lead to highly misleading results in the presence of miscalibration errors and a worst case bias scaling exponentially in the system size. >>

AA << further find that so-called robust shadows, aiming at mitigating noise, can introduce a large bias in the presence of gate-dependent noise compared to unmitigated classical shadows. Nevertheless, (AA) guarantee the functioning of robust shadows for a more general noise setting than in previous works. On a technical level, (They) identify average noise channels that affect shadow estimators and allow for a more fine-grained control of noise-induced biases. >>️

Raphael Brieger, Markus Heinrich, et al. Stability of Classical Shadows under Gate-Dependent Noise. Phys. Rev. Lett. 134, 090801. Mar 4, 2025. 

https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.134.090801  arXiv: 2310.19947v3 [quant-ph]. Feb 19, 2025.   https://arxiv.org/abs/2310.19947

Also: qubit, in FonT  https://flashontrack.blogspot.com/search?q=qubit  noise, ai (artificial intell) (bot), in https://www.inkgmr.net/kwrds.html   

Keywords: qubit, noise, realistic noise, shadows, robust shadows

# qubit: communication power of a noisy qubit.

<< A fundamental limitation of quantum communication is that a single qubit can carry at most one bit of classical information. For an important class of quantum communication channels, known as entanglement breaking, this limitation holds even if the sender and receiver share entangled particles. But does this mean that, for the purpose of communicating classical messages, a noisy entanglement-breaking qubit channel can be replaced by a noisy bit channel? >>

Here AA << answer the question in the negative. (They) introduce a game, similar to the Monty Hall problem in classical statistics, where a sender assists a receiver in finding a valuable item (the “prize”) hidden in one of four possible boxes, while avoiding a hazardous item (the “bomb”) hidden in one of the remaining three boxes. (AA) show that no classical strategy using a noisy bit channel can ensure that the bomb is avoided, even if the sender and receiver share arbitrary amounts of randomness. >>

<< In contrast, communication of a qubit through a class of noisy entanglement-breaking channels, which (They) call quantum not channels, allows the players to deterministically avoid the bomb and to find the prize with a guaranteed nonzero probability. >>

AA << findings show that the communication of classical messages through a noisy entanglement-breaking qubit channel assisted by quantum entanglement cannot, in general, be simulated by communication through a noisy bit channel assisted by classical correlations. >>️

Giulio Chiribella, Saptarshi Roy, et al. Communication Power of a Noisy Qubit. Phys. Rev. Lett. 134, 080803. Feb 28, 2025. 

https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.134.080803     arXiv: 2405.17946v2 [quant-ph]. https://arxiv.org/abs/2405.17946  

Also: qubit, in https://flashontrack.blogspot.com/search?q=qubit  game, in  https://flashontrack.blogspot.com/search?q=game  noise, in  https://flashontrack.blogspot.com/search?q=noise 

Keywords: qubit, games, noise

# gst: apropos of the impact of noise, stochastic Kuramoto oscillators with inertia and higher-order interactions.

<< The impact of noise in coupled oscillators with pairwise interactions has been extensively explored. Here, (AA) study stochastic second-order coupled Kuramoto oscillators with higher-order interactions and show that as noise strength increases, the critical points associated with synchronization transitions shift toward higher coupling values. By employing the perturbation analysis, (They) obtain an expression for the forward critical point as a function of inertia and noise strength. Further, for overdamped systems, (AA) show that as noise strength increases, the first-order transition switches to second-order even for higher-order couplings. >>

️

Priyanka Rajwani, Sarika Jalan. Stochastic Kuramoto oscillators with inertia and higher-order interactions. Phys. Rev. E 111, L012202. Jan 13, 2025.

https://journals.aps.org/pre/abstract/10.1103/PhysRevE.111.L012202   arXiv: 2407.14874v1 [nlin.AO]. Jul 20, 2024. https://arxiv.org/abs/2407.14874 

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

Keywords: gst, noise, transition, coupled oscillators, synchronization transition

# gst: alignment-induced self-organization of autonomously steering microswimmers: turbulence, clusters, vortices, and jets.

<< Microorganisms can sense their environment and adapt their movement accordingly, which gives rise to a multitude of collective phenomena, including active turbulence and bioconvection. In fluid environments, collective self-organization is governed by hydrodynamic interactions. >>

<< By large-scale mesoscale hydrodynamics simulations, (AA) study the collective motion of polar microswimmers, which align their propulsion direction by hydrodynamic steering with that of their neighbors. The simulations of the employed squirmer model reveal a distinct dependence on the type of microswimmer—puller or pusher—flow field. No global polar alignment emerges in both cases. Instead, the collective motion of pushers is characterized by active turbulence, with nearly homogeneous density and a Gaussian velocity distribution; strong self-steering enhances the local coherent movement of microswimmers and leads to local fluid-flow speeds much larger than the individual swim speed. >>

<< Pullers exhibit a strong tendency for clustering and display velocity and vorticity distributions with fat exponential tails; their dynamics is chaotic, with a temporal appearance of vortex rings and fluid jets. >>

AA << results show that the collective behavior of autonomously steering microswimmers displays a rich variety of dynamic self-organized structures. >>

Segun Goh, Elmar Westphal, et al. Alignment-induced self-organization of autonomously steering microswimmers: Turbulence, clusters, vortices, and jets. Phys. Rev. Research 7, 013142. Feb 7, 2025. 

https://journals.aps.org/prresearch/abstract/10.1103/PhysRevResearch.7.013142 

Also: swim, microswimmer, particle, turbulence, chaos, noise, in https://www.inkgmr.net/kwrds.html 

Keywords: gst, swim, swimmer, microswimmers, particle, turbulence, chaos, noise

# gst: stochastic adaptation, stochastic resonance.

<< Stochastic resonance is a phenomenon possessed by some nonlinear oscillators, in which a weak signal is boosted by noise. Both the monostable and bistable Duffing oscillators can exhibit this property. However, stochastic resonance has a strong frequency-dependence, as only a band of frequencies may be boosted by noise. >>️

<< Adaptive oscillators are a subset of nonlinear oscillators that can learn the features of an external force. (In this AA work), an adaptive state is added to a Duffing oscillator. This adaptive state enables the Duffing adaptive oscillator to outperform stochastic resonance over a wide range of frequencies by learning a resonance condition. >>️

Edmon Perkins. Comparison of stochastic adaptation and stochastic resonance. Phys. Rev. E 110, 064225. Dec 27, 2024.

https://journals.aps.org/pre/abstract/10.1103/PhysRevE.110.064225 

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

Keywords: gst, fluctuations, noise, transition, stochasticity, stochastic adaptation, stochastic resonance

# gst: apropos of noise-assisted phenomena, self-organized transport in noisy dynamic networks.

AA << present a numerical study of multicommodity transport in a noisy, nonlinear network. The nonlinearity determines the dynamics of the edge capacities, which can be amplified or suppressed depending on the local current flowing across an edge. (AA) consider network self-organization for three different nonlinear functions: For all three (They) identify parameter regimes where noise leads to self-organization into more robust topologies, that are not found by the sole noiseless dynamics. Moreover, the interplay between noise and specific functional behavior of the nonlinearity gives rise to different features, such as (i) continuous or discontinuous responses to the demand strength and (ii) either single or multistable solutions. (AA) study shows the crucial role of the activation function on noise-assisted phenomena. >>️

Frederic Folz, Kurt Mehlhorn, Giovanna Morigi. Self-organized transport in noisy dynamic networks. Phys. Rev. E 110, 044310. Oct 21, 2024. 

https://journals.aps.org/pre/abstract/10.1103/PhysRevE.110.044310

Also: network, noise, behavior, self-assembly, instability, in https://www.inkgmr.net/kwrds.html 

Keywords: gst, network, noise, behavior, self-assembly, stability 

# gst: apropos of fluctuations, an unconventional approach to (fuzzy) morphogenesis

AA << propose an unconventional mechanism where stochastic fluctuations drive the emergence of morphological patterns. >>️

In this approach << the inherent fluctuations determine the nature of the dynamics and are not incidental noise in the background of the otherwise deterministic dynamics. Instead, they play an important role as a driving force that defines the attributes of the pattern formation dynamics and the nature of the transition itself.  >>️

Oded Agam and Erez Braun. Fluctuation-driven morphological patterning: An unconventional approach to morphogenesis. Phys. Rev. Research 6, 043027. Oct 10, 2024.

https://journals.aps.org/prresearch/abstract/10.1103/PhysRevResearch.6.043027

Also: disorder & fluctuations, self-assembly, metamorphosis, transition, noise, in https://www.inkgmr.net/kwrds.html 

Keywords: gst, disorder, fluctuations,  self-assembly, metamorphosis, transition, noise

# gst: simultaneous presence of attraction and repulsion in quantum self-sustained oscillators

AA << study the emergent dynamics of quantum self-sustained oscillators induced by the simultaneous presence of attraction and repulsion in the coupling path. >>

They << discover an interesting symmetry-breaking transition from quantum limit cycle oscillation to a quantum inhomogeneous steady state. This transition is contrary to the previously known symmetry-breaking transition from a quantum homogeneous state to an inhomogeneous steady state. >>

<< Remarkably, (they) find the generation of entanglement associated with the symmetry-breaking transition that has no analog in the classical domain. >>

Bulti Paul, Biswabibek Bandyopadhyay, Tanmoy Banerjee. Attractive-repulsive interaction in coupled quantum oscillators. Phys. Rev. E 110, 034210. Sept 19, 2024. 

https://journals.aps.org/pre/abstract/10.1103/PhysRevE.110.034210

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

Keywords: gst, transition, symmetry-breaking transition, noise, attractive-repulsive interaction, coupled qu-oscillator

# gst: critical crack length during fracture.

AA << established an inverse correlation between the strength of the material and the cracks which grow inside it—both the maximum crack and the one that sets in instability within the system, defined to be the critical crack. >>

AA << found that the maximum and the critical crack often differ from each other unless the disorder strength is extremely low. A phase diagram on the plane of disorder vs system size demarcates between the regions where the largest crack is the most vulnerable one and where they differ from each other but still show moderate correlation. >>️

Viswakannan R.K., Subhadeep Roy. Critical crack length during fracture. Phys. Rev. E 110, 024134. Aug 26, 2024.

https://journals.aps.org/pre/abstract/10.1103/PhysRevE.110.024134

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

Keywords: gst, crack, instability, fluctuations, noise, criticality

# gst: attractive-repulsive interaction in coupled qu-oscillators, when a symmetry-breaking state could be a prominent state.

AA << have explored the role of attractive repulsive coupling in shaping the collective behavior of coupled oscillators in the quantum domain. >>

<< A direct simulation (..) showed a symmetry breaking transition from quantum limit cycle to quantum oscillation death state with increasing coupling strength. >>️

<< This is in contrast to the quantum symmetry-breaking transitions reported earlier where inhomogeneity emerges from the homogeneous steady state. >>️

<< The phenomenon is general as it occurs at both weak and deep quantum regime. Specially, in the deep quantum regime where quantum noise is strong, yet it can not wash out the inhomogeneous state indicating that the symmetry-breaking state is indeed a prominent state. >>️️

Bulti Paul, Biswabibek Bandyopadhyay, Tanmoy Banerjee. Attractive-repulsive interaction in coupled quantum oscillators. arXiv: 2408.12972v1 [quant-ph]. Aug 23, 2024.

https://arxiv.org/abs/2408.12972

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

Keywords: gst, transition, symmetry-breaking transition, noise, attractive-repulsive interaction, coupled qu-oscillator

# 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: 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

# 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

# music: masters of noise, Frank Zappa plays bicycles

Frank Zappa teaches Steve Allen to play The Bicycle (aired March 3, 1963).

https://youtu.be/QF0PYQ8IOL4

<< This televisual gem inspired me follow along which got me into endless trouble at family picnics and barbecues for playing my own symphonic masterpieces which, for some strange reason, nobody else seemed to enjoy. I extended Frank's genius to my exploration of the vacuum cleaner, ping pong balls and paddles, (..)  The next time you're out in a forest I challenge you to explore the musical nature of nature for yourself. Trees make great drums and often ring with higher tones - not to mention the musical benefits of rocks and stones. >>️️

That Hairy Canadian. Jun 21, 2014. 

https://m.youtube.com/@ThatHairyCanadian

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

Keywords: music, jazz, noise, error

# gst: a case of noise-induced excitation wave (in coupled FH-N eq.)

<< There are various research topics such as stochastic resonance, coherent resonance, and neuroavalanche in excitable systems under external noises. >>️

AA << have studied the propagation of excitation waves in the coupled noisy FitzHugh-Nagumo equations with a one-dimensional pacemaker region and found that there is a phase-transition-like phenomenon from the short-range propagation to the whole-system propagation by changing the noise strength T.  >>️

Hidetsugu Sakaguchi. Noise-induced excitation wave and its size distribution in coupled FitzHugh-Nagumo equations on a square lattice. Phys. Rev. E 109, 044211. Apr 19, 2024.

https://journals.aps.org/pre/abstract/10.1103/PhysRevE.109.044211

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

Keywords: gst, waves, noise, transition

# gst: sudden noise-induced expansions beyond the onset of a steady symmetry-breaking bifurcation.

AA << consider fluid flows (..) subject to a steady symmetry-breaking bifurcation and forced by a weak noise acting on a slow timescale. >>

The validity of their proposed model << is tested on the flow past a sudden expansion for a given Reynolds number and different noise amplitudes. At a very low numerical cost, the statistics obtained from the amplitude equation accurately reproduce those of long-time direct numerical simulations. >>

Yves-Marie Ducimetière, Edouard Boujo, François Gallaire. Noise-induced transitions past the onset of a steady symmetry-breaking bifurcation: The case of the sudden expansion. Phys. Rev. Fluids 9, 053905. May 3, 2024. 

https://journals.aps.org/prfluids/abstract/10.1103/PhysRevFluids.9.053905

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

Keywords: gst, transition, noise

# gst: apropos of uncertainty, notes on uncertainty, information, and classical dynamics.

<< Survival in this world is an adventure because we are so ignorant and everything around us seems so uncertain. In fact, it is hard to think of any realistic phenomenon that is completely free from one of the three kinds of uncertainty—deterministic (chaotic), stochastic, and quantum; more often than not, all of the three are present in various degrees. Thus, in order to gain any knowledge about any realistic system, one must understand how to characterize, quantify, and interpret these uncertainties. >>️

Sagar Chakraborty. Eclectic Notes on Uncertainty, Information, and Classical Dynamics. arXiv: 2404.13511v1 [physics.class-ph]. Apr 21, 2024.

https://arxiv.org/abs/2404.13511

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

Keywords: gst, information, uncertainty, ambiguity, noise, error 

# gst: Lévy flights and Lévy walks under stochastic resetting.

<< Stochastic resetting is a protocol of starting anew, which can be used to facilitate the escape kinetics. (AA)  demonstrate that restarting can accelerate the escape kinetics from a finite interval restricted by two absorbing boundaries also in the presence of heavy-tailed, Lévy-type, α

-stable noise. However, the width of the domain where resetting is beneficial depends on the value of the stability index α determining the power-law decay of the jump length distribution. For heavier (smaller α) distributions, the domain becomes narrower in comparison to lighter tails. >>

<< Additionally, (AA) explore connections between Lévy flights (LFs) and Lévy walks (LWs) in the presence of stochastic resetting. First of all, (They) show that for Lévy walks, the stochastic resetting can also be beneficial in the domain where the coefficient of variation is smaller than 1. Moreover, (They) demonstrate that in the domain where LWs are characterized by a finite mean jump duration (length), with the increasing width of the interval, the LWs start to share similarities with LFs under stochastic resetting. >>️

Bartosz Żbik, Bartłomiej Dybiec. Lévy flights and Lévy walks under stochastic resetting. Phys. Rev. E 109, 044147. April 22, 2024.

https://journals.aps.org/pre/abstract/10.1103/PhysRevE.109.044147

Also: keyword Lévy in FonT

https://flashontrack.blogspot.com/search?q=Lévy&m=1

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

Keywords: gst, escape, noise, stochastic resetting, Lévy