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Latest articles for Reports on Progress in Physics
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Fluctuations and the limit of predictability in protein evolution
Protein evolution involves mutations occurring across a wide range of time scales. In analogy with disordered systems in statistical physics, this dynamical heterogeneity suggests strong correlations between mutations happening at distinct sites and times. To quantify these correlations, we examine the role of various fluctuation sources in protein evolution, simulated using a data-driven energy landscape as a proxy for protein fitness. By applying spatio-temporal correlation functions developed in the context of disordered physical systems, we disentangle fluctuations originating from the initial condition, i.e. the ancestral sequence from which the evolutionary process originated, from those driven by stochastic mutations along independent evolutionary paths. Our analysis shows that, in diverse protein families, fluctuations from the ancestral sequence predominate at shorter time scales. This allows us to identify a time scale over which ancestral sequence information persists, enabling its reconstruction. We link this persistence to the strength of epistatic interactions: ancestral sequences with stronger epistatic signatures impact evolutionary trajectories over extended periods. At longer time scales, however, ancestral influence fades as epistatically constrained sites evolve collectively. To confirm this idea, we apply a standard ancestral sequence reconstruction (ASR) algorithm and verify that the time-dependent recovery error is influenced by the properties of the ancestor itself. Overall, our results reveal that the properties of ancestral sequences—particularly their epistatic constraints—influence the initial evolutionary dynamics and the performance of standard ASR algorithms.
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Quantum Fisher information and its dynamical nature
The importance of the Fisher information metrics and its quantum generalisations is testified by the number of applications that this has in very different fields, ranging from hypothesis testing to metrology, passing through thermodynamics. Still, from the rich range of possible quantum Fisher informations, only a handful are typically used and studied. This review aims at collecting a number of results scattered in the literature and provide a cohesive treatment to people who begin the study of Fisher information and to those who are already working on it to have a more organic understanding of the topic. Moreover, we complement the review with new results about the relation between Fisher information and physical evolutions. Extending previous works, we show that dynamical properties such as (complete) positivity, Markovianity, detailed balance, retrodictive power of evolution maps can be characterised in terms of their relation with respect to the Fisher information metrics. These results show a fact that was partially overseen in the literature, namely the inherently dynamical nature of Fisher information.
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A review of the fraction of four-coordinated boron in binary borate glasses and melts
In borate materials, boron is found predominantly in either trigonal planar, or tetrahedral coordination states with oxygen, which are the two most ubiquitous building blocks of borate glasses. The fraction of tetrahedral boron, N4, is found to vary considerably with both glass composition and applied pressure, as well as with fictive temperature – a result of its underlying dependence on temperature in the molten and supercooled liquid states. As such, the parameter N4 is of fundamental structural importance, along with the mechanisms driving its evolution and its strong influence on thermophysical material properties. N4 in glasses has been experimentally determined using a variety of means including nuclear magnetic resonance (NMR) spectroscopy, vibrational spectroscopy, and x-ray and neutron diffraction. In this review, we discuss how the techniques for the measurement of N4 have evolved and improved since the pioneering x-ray diffraction measurements of the 1930s, up to the present day. A database is compiled of the available high-quality numerical experimental data for N4, with a non-exclusive focus on binary borate glasses of the form RM2Oz–B2O3 where R is the molar ratio of modifier to boron oxide and M is a metal cation of formal charge z+, other than boron. In addition, we report new N4 values for a series of strontium borate glasses, measured by 11B magic angle spinning NMR, where a disparity in the literature is found. Based on the findings of the review, we are able to point to the gaps in our knowledge where future resources could best be focused, as well as summarizing overarching trends, the present state-of-the-art, and making recommendations for best practices.
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Revealing quantum geometry in nonlinear quantum materials
Berry curvature-related topological phenomena have been a central topic in condensed matter physics. Yet, until recently other quantum geometric quantities such as the metric and connection received only little attention due to the relatively few effects which have been documented for them. This review gives a modern perspective how quantum geometric quantities naturally enter the nonlinear responses of quantum materials and demonstrate their deep connection with excitation energy, lifetimes, symmetry, and corresponding physical processes. The multitude of nonlinear responses can be subdivided into nonlinear optical effects, subgap responses, and nonlinear transport phenomena. Such a distinction by energy scales facilitates an intuitive understanding of the underlying electronic transitions, giving rise to a unified picture of the electron motion beyond linear order. The well-known injection and shift currents constitute the main resonances in the optical regime. Exploiting their respective lifetime and symmetry dependencies, this review elucidates how these resonances can be distinguished by a corresponding quantum geometric quantity that shares the same symmetry. This is followed by a brief exposition of the role of quasiparticle lifetimes for nonlinear subgap responses, which presents a window into the microscopic short-term dynamics as well as the ground state correlation and localization. We conclude with an account of the anomalous motion due to the Berry curvature dipole and quantum metric dipole in nonlinear transport, clarifying the correspondence between physical observables and the underlying mechanisms. This review highlights the close relationship between quantum geometry and nonlinear response, showing the way towards promising probes of quantum geometry and enabling novel avenues to characterize complex materials.
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Designed self-assembly of programmable colloidal atom-electron equivalents
To unlock the potential for assembling complex colloidal ‘molecules’, we investigate a minimal binary system of programmable colloidal atom-electron equivalents (PAE-EE), where electron equivalents (EEs) are multivalent linkers with two distinct types of single-stranded DNA (ssDNA) ends complementary to those ssDNAs on binary programmable atom equivalents (PAEs). We derive a statistical mechanical framework for calculating the effective interaction between PAEs mediated by EEs with arbitrary valency, which quantitatively agrees with simulations using explicit EEs. Our analysis reveals an anomalous dependence of PAE-PAE interactions on the EE valency, showing that EE-mediated interactions converge at the large valency limit. Moreover, we identify an optimal EE valency that maximizes the interaction difference between targeted and non-targeted binding pairs of PAEs. These findings offer design principles for targeted self-assembly in PAE-EE systems.