Universality of dissipative self-assembly from quantum dots to human cells

Makey, Ghaith; Galioglu, Sezin; Ghaffari, Roujin; Engin, Evren Doruk; Yildirim, Gökhan; Yavuz, Özgün; Bektaş, Onurcan; Nizam, Ü. Seleme; Akbulut, Özge; Şahin, Özgür; Gungor, Kivanc; Dede, Didem; Demir, Hilmi Volkan; İlday, F. Ömer; İlday, Serim

doi:10.1038/s41567-020-0879-8

Cited by 50 publications

(40 citation statements)

References 67 publications

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“…4(f)]. TW distributions were recently reported for growing fluctuating fronts [52], dynamics of self-assembly [53], active particle dynamics [54,55], and phase transitions between strongly and weakly coupling regimes [56]. We also find TW motif size distributions in the ABP and fly wing data when subsampling from the liquid like phase [23], suggesting that TW distributions play a central role in the topostatistics of amorphous and nonequilbrium systems.…”

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confidence: 72%

Topological Metric Detects Hidden Order in Disordered Media

et al. 2021

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Recent advances in microscopy techniques make it possible to study the growth, dynamics, and response of complex biophysical systems at single-cell resolution, from bacterial communities to tissues and organoids. In contrast to ordered crystals, it is less obvious how one can reliably distinguish two amorphous yet structurally different cellular materials. Here, we introduce a topological earth mover's (TEM) distance between disordered structures that compares local graph neighborhoods of the microscopic cell-centroid networks. Leveraging structural information contained in the neighborhood motif distributions, the TEM metric allows an interpretable reconstruction of equilibrium and nonequilibrium phase spaces and embedded pathways from static system snapshots alone. Applied to cell-resolution imaging data, the framework recovers time ordering without prior knowledge about the underlying dynamics, revealing that fly wing development solves a topological optimal transport problem. Extending our topological analysis to bacterial swarms, we find a universal neighborhood size distribution consistent with a Tracy-Widom law.

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confidence: 72%

Topological Metric Detects Hidden Order in Disordered Media

et al. 2021

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“…The longest increasing subsequence for uniformly random permutations is an example of a model from the Kardar-Parisi-Zhang universality class [5]. Its study has provided a rich research program for mathematicians and physicists for the last fifty years and produced profound results in mathematics and physics, see [5,10] and references therein. Three Tracy-Widom distributions (GUE, GOE, GSE) from random matrix ensembles also appear as the limiting distributions for various subsequence problems for permutations [4,8].…”

Section: Discussionmentioning

confidence: 99%

Variations on Hammersley’s interacting particle process

2021

Discrete Math. Lett.

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The longest increasing subsequence problem for permutations has been studied extensively in the last fifty years. The interpretation of the longest increasing subsequence as the longest 21-avoiding subsequence in the context of permutation patterns leads to many interesting research directions. We introduce and study the statistical properties of Hammersleytype interacting particle processes related to these generalizations and explore the finer structures of their distributions. We also propose three different interacting particle systems in the plane analogous to the Hammersley process in one dimension and obtain estimates for the asymptotic orders of the mean and variance of the number of particles in the systems.

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“…From Eqs. ( 6), (12), and the definition ξðtÞ j i U a; 1 a j i, we have that Using H I from Eq. ( 9), we have that b; 1 a h jH I b; 1 a j i¼ 0 and ξðtÞ h jH I ξðtÞ j i¼2ð_g a Im½ψ Ã ðtÞϕ a ðÀct; 0Þ þ _g b Im½ψ Ã ðtÞϕ b ðÀct; 0ÞÞ.…”

Section: Methodsmentioning

confidence: 99%

Quantum dissipative adaptation

2021

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Dissipative adaptation is a general thermodynamic mechanism that explains self-organization in a broad class of driven classical many-body systems. It establishes how the most likely (adapted) states of a system subjected to a given drive tend to be those following trajectories of highest work absorption, followed by dissipated heat to the reservoir. Here, we extend the dissipative adaptation phenomenon to the quantum realm. We employ a fully-quantized exactly solvable model, where the source of work on a three-level system is a single-photon pulse added to a zero-temperature infinite environment, a scenario that cannot be treated by the classical framework. We find a set of equalities relating adaptation likelihood, absorbed work, heat dissipation and variation of the informational entropy of the environment. Our proof of principle provides the starting point towards a quantum thermodynamics of driven self-organization.

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Universality of dissipative self-assembly from quantum dots to human cells

Cited by 50 publications

References 67 publications

Topological Metric Detects Hidden Order in Disordered Media

Topological Metric Detects Hidden Order in Disordered Media

Variations on Hammersley’s interacting particle process

Quantum dissipative adaptation

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