Atom-by-atom construction of attractors in a tunable finite size spin array

Kolmus, Alex; Katsnelson, M. I.; Khajetoorians, Alexander A.; Kappen, Hilbert J.

doi:10.1088/1367-2630/ab6f91

Cited by 9 publications

(13 citation statements)

References 38 publications

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“…However, the energy landscape of spin glasses contains too many minima that are too shallow to account for long-term memory that is central to biology (12,41). Thus, some generalization of the spin glass concept is likely to be required for productive application in evolutionary biology (95).…”

Section: Discussionmentioning

confidence: 99%

Toward a theory of evolution as multilevel learning

Vanchurin

Wolf

Katsnelson

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

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We apply the theory of learning to physically renormalizable systems in an attempt to outline a theory of biological evolution, including the origin of life, as multilevel learning. We formulate seven fundamental principles of evolution that appear to be necessary and sufficient to render a universe observable and show that they entail the major features of biological evolution, including replication and natural selection. It is shown that these cornerstone phenomena of biology emerge from the fundamental features of learning dynamics such as the existence of a loss function, which is minimized during learning. We then sketch the theory of evolution using the mathematical framework of neural networks, which provides for detailed analysis of evolutionary phenomena. To demonstrate the potential of the proposed theoretical framework, we derive a generalized version of the Central Dogma of molecular biology by analyzing the flow of information during learning (back propagation) and predicting (forward propagation) the environment by evolving organisms. The more complex evolutionary phenomena, such as major transitions in evolution (in particular, the origin of life), have to be analyzed in the thermodynamic limit, which is described in detail in the paper by Vanchurin et al. [V. Vanchurin, Y. I. Wolf, E. V. Koonin, M. I. Katsnelson, Proc. Natl. Acad. Sci. U.S.A. 119, 10.1073/pnas.2120042119 (2022)].

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Section: Discussionmentioning

confidence: 99%

Toward a theory of evolution as multilevel learning

Vanchurin

Wolf

Katsnelson

et al. 2022

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

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“…Such systems would spontaneously “glue” to selected configurations from some “library” to form a complex but not completely disordered pattern. Recently, such behavior has been demonstrated in a very simple system, namely, the Ising model with oscillating long-range interactions (“multiwell state”) ( 74 ). Such patterned glass-like (multiwall) systems are likely to yield better models for biological phenomena than classical glass.…”

Section: Glasses Patterns Frustrated States and Socmentioning

confidence: 99%

“…Such patterned glass-like (multiwall) systems are likely to yield better models for biological phenomena than classical glass. Here, we assume that there are many distinct “attractors” and that the energy landscape of the system consists of glass-like parts separated by gaps ( 74 ). This model immediately invokes an analogy with pattern recognition in learning theory that has been successfully studied within the framework of the spin-glass formalism ( 7 , 66 ).…”

Section: Glasses Patterns Frustrated States and Socmentioning

confidence: 99%

Physical foundations of biological complexity

Wolf

Katsnelson

Koonin

2018

Proc. Natl. Acad. Sci. U.S.A.

109

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SignificanceLiving organisms are characterized by a degree of hierarchical complexity that appears to be inaccessible to even the most complex inanimate objects. Routes and patterns of the evolution of complexity are poorly understood. We propose a general conceptual framework for emergence of complexity through competing interactions and frustrated states similar to those that yield patterns in striped glasses and cause self-organized criticality. We show that biological evolution is replete with competing interactions and frustration that, in particular, drive major transitions in evolution. The key distinction between biological and nonbiological systems seems to be the existence of long-term digital memory and phenotype-to-genotype feedback in living matter.

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“…Discussion and Outlooks-Recently, self-induced spin glassiness has been proposed to describe the unconventional spin glass state arising in crystalline neodymium [43] and predicted to occur in two-and three-dimensional arrays of Ising spins with long-range interactions [44,45]. Remarkably, the investigation of self-induced glassy phases in confocal CQED presents two major advantages over traditional solid state systems: (i) in CQED the experimental setup is highly controllable: the interaction can be tuned by manipulating the atoms positions (e.g.…”

Section: Exponential Number Of Metastable States At T = 0-mentioning

confidence: 99%