Multifractality in spin glasses.

We unveil the multifractal behavior of Ising spin glasses in their low-temperature phase. Using the Janus II custom-built supercomputer, the spin-glass correlation function is studied locally. Dramatic fluctuations are found when pairs of sites at the same distance are compared. The scaling of these fluctuations, as the spin-glass coherence length grows with time, is characterized through the computation of the singularity spectrum and its corresponding Legendre transform. A comparatively small number of site pairs controls the average correlation that governs the response to a magnetic field. We explain how this scenario of dramatic fluctuations (at length scales smaller than the coherence length) can be reconciled with the smooth, self-averaging behavior that has long been considered to describe spin-glass dynamics.

Configurational entropy is an intrinsic driver of tissue structural heterogeneity.

Tissues comprise ordered arrangements of cells that can be surprisingly disordered in their details. How the properties of single cells and their microenvironment contribute to the balance between order and disorder at the tissue-scale remains poorly understood. Here, we address this question using the self-organization of human mammary organoids as a model. We find that organoids behave like a dynamic structural ensemble at the steady state. We apply a maximum entropy formalism to derive the ensemble distribution from three measurable parameters - the degeneracy of structural states, interfacial energy, and tissue activity (the energy associated with positional fluctuations). We link these parameters with the molecular and microenvironmental factors that control them to precisely engineer the ensemble across multiple conditions. Our analysis reveals that the entropy associated with structural degeneracy sets a theoretical limit to tissue order and provides new insight for tissue engineering, development, and our understanding of disease progression.

A high-resolution flux-matrix model describes the spread of diseases in a spatial network and the effect of mitigation strategies.

Propagation of an epidemic across a spatial network of communities is described by a variant of the SIR model accompanied by an intercommunity infectivity matrix. This matrix is estimated from fluxes between communities, obtained from cell-phone tracking data recorded in the USA between March 2020 and February 2021. We apply this model to the SARS-CoV-2 pandemic by fitting just one global parameter representing the frequency of interaction between individuals. We find that the predicted infections agree reasonably well with the reported cases. We clearly see the effect of "shelter-in-place" policies introduced at the onset of the pandemic. Interestingly, a model with uniform transmission rates produces similar results, suggesting that the epidemic transmission was deeply influenced by air travel. We then study the effect of alternative mitigation policies, in particular restricting long-range travel. We find that this policy is successful in decreasing the epidemic size and slowing down the spread, but less effective than the shelter-in-place policy. This policy can result in a pulled wave of infections. We express its velocity and characterize the shape of the traveling front as a function of the epidemiological parameters. Finally, we discuss a policy of selectively constraining travel based on an edge-betweenness criterion.

A random-walk-based epidemiological model.

Random walkers on a two-dimensional square lattice are used to explore the spatio-temporal growth of an epidemic. We have found that a simple random-walk system generates non-trivial dynamics compared with traditional well-mixed models. Phase diagrams characterizing the long-term behaviors of the epidemics are calculated numerically. The functional dependence of the basic reproductive number [Formula: see text] on the model's defining parameters reveals the role of spatial fluctuations and leads to a novel expression for [Formula: see text]. Special attention is given to simulations of inter-regional transmission of the contagion. The scaling of the epidemic with respect to space and time scales is studied in detail in the critical region, which is shown to be compatible with the directed-percolation universality class.

Polymorphism of genetic ambigrams.

Double synonyms in the genetic code can be used as a tool to test competing hypotheses regarding ambigrammatic narnavirus genomes. Applying the analysis to recent observations of Culex narnavirus 1 and Zhejiang mosquito virus 3 ambigrammatic viruses indicates that the open reading frame on the complementary strand of the segment coding for RNA-dependent RNA polymerase does not code for a functional protein. Culex narnavirus 1 has been shown to possess a second segment, also ambigrammatic, termed 'Robin'. We find a comparable segment for Zhejiang mosquito virus 3, a moderately diverged relative of Culex narnavirus 1. Our analysis of Robin polymorphisms suggests that its reverse open reading frame also does not code for a functional protein. We make a hypothesis about its role.

Polysomally protected viruses.

It is conceivable that an RNA virus could use a polysome, that is, a string of ribosomes covering the RNA strand, to protect the genetic material from degradation inside a host cell. This paper discusses how such a virus might operate, and how its presence might be detected by ribosome profiling. There are two possible forms for such apolysomally protected virus, depending upon whether just the forward strand or both the forward and complementary strands can be encased by ribosomes (these will be termed type 1 and type 2, respectively). It is argued that in the type 2 case the viral RNA would evolve anambigrammaticproperty, whereby the viral genes are free of stop codons in a reverse reading frame (with forward and reverse codons aligned). Recent observations of ribosome profiles of ambigrammatic narnavirus sequences are consistent with our predictions for the type 2 case.

A minimal model for household effects in epidemics.

Shelter-in-place and other confinement strategies implemented in the current COVID-19 pandemic have created stratified patterns of contacts between people: close contacts within households and more distant contacts between the households. The epidemic transmission dynamics is significantly modified as a consequence. We introduce a minimal model that incorporates these household effects in the framework of mean-field theory and numerical simulations. We show that the reproduction number R 0 depends on the household size in a surprising way: linearly for relatively small households, and as a square root of size for larger households. We discuss the implications of the findings for the lockdown, test, tracing, and isolation policies.

An exploration of ambigrammatic sequences in narnaviruses.

Narnaviruses have been described as positive-sense RNA viruses with a remarkably simple genome of ~3 kb, encoding only a highly conserved RNA-dependent RNA polymerase (RdRp). Many narnaviruses, however, are 'ambigrammatic' and harbour an additional uninterrupted open reading frame (ORF) covering almost the entire length of the reverse complement strand. No function has been described for this ORF, yet the absence of stops is conserved across diverse narnaviruses, and in every case the codons in the reverse ORF and the RdRp are aligned. The >3 kb ORF overlap on opposite strands, unprecedented among RNA viruses, motivates an exploration of the constraints imposed or alleviated by the codon alignment. Here, we show that only when the codon frames are aligned can all stop codons be eliminated from the reverse strand by synonymous single-nucleotide substitutions in the RdRp gene, suggesting a mechanism for de novo gene creation within a strongly conserved amino-acid sequence. It will be fascinating to explore what implications this coding strategy has for other aspects of narnavirus biology. Beyond narnaviruses, our rapidly expanding catalogue of viral diversity may yet reveal additional examples of this broadly-extensible principle for ambigrammatic-sequence development.

Self-Driven Phase Transitions Drive Myxococcus xanthus Fruiting Body Formation.

Combining high-resolution single cell tracking experiments with numerical simulations, we show that starvation-induced fruiting body formation in Myxococcus xanthus is a phase separation driven by cells that tune their motility over time. The phase separation can be understood in terms of cell density and a dimensionless Péclet number that captures cell motility through speed and reversal frequency. Our work suggests that M. xanthus takes advantage of a self-driven nonequilibrium phase transition that can be controlled at the single cell level.

The Mpemba effect in spin glasses is a persistent memory effect.

The Mpemba effect occurs when a hot system cools faster than an initially colder one, when both are refrigerated in the same thermal reservoir. Using the custom-built supercomputer Janus II, we study the Mpemba effect in spin glasses and show that it is a nonequilibrium process, governed by the coherence length ξ of the system. The effect occurs when the bath temperature lies in the glassy phase, but it is not necessary for the thermal protocol to cross the critical temperature. In fact, the Mpemba effect follows from a strong relationship between the internal energy and ξ that turns out to be a sure-tell sign of being in the glassy phase. Thus, the Mpemba effect presents itself as an intriguing avenue for the experimental study of the coherence length in supercooled liquids and other glass formers.

Curvature-dependent tension and tangential flows at the interface of motility-induced phases.

Purely repulsive active particles spontaneously undergo motility-induced phase separation (MIPS) into condensed and dilute phases. Remarkably, the mechanical tension measured along the interface between these phases is negative. In equilibrium this would imply an unstable interface that wants to expand, but these out-of-equilibrium systems display long-time stability and have intrinsically stiff boundaries. Here, we study this phenomenon in detail using active Brownian particle simulations and a novel frame of reference. By shifting from the global (or laboratory) frame to a local frame that follows the dynamics of the phase boundary, we observe correlations between the local curvature of the interface and the measured value of the tension. Importantly, our analysis reveals that curvature drives sustained local tangential motion of particles within a surface layer in both the gas and the dense regions. The combined tangential current in the gas and local "self-shearing" of the surface of the dense phase suggest a stiffening interface that redirects particles along itself to heal local fluctuations. These currents restore the otherwise wildly fluctuating interface through an out-of-equilibrium Marangoni effect. We discuss the implications of our observations on phenomenological models of interfacial dynamics.

Thermal crumpling of perforated two-dimensional sheets.

Thermalized elastic membranes without distant self-avoidance are believed to undergo a crumpling transition when the microscopic bending stiffness is comparable to kT, the scale of thermal fluctuations. Most potential physical realizations of such membranes have a bending stiffness well in excess of experimentally achievable temperatures and are therefore unlikely ever to access the crumpling regime. We propose a mechanism to tune the onset of the crumpling transition by altering the geometry and topology of the sheet itself. We carry out extensive molecular dynamics simulations of perforated sheets with a dense periodic array of holes and observe that the critical temperature is controlled by the total fraction of removed area, independent of the precise arrangement and size of the individual holes. The critical exponents for the perforated membrane are compatible with those of the standard crumpling transition.

Kinetics of motility-induced phase separation and swim pressure.

Active Brownian particles (ABPs) represent a minimal model of active matter consisting of self-propelled spheres with purely repulsive interactions and rotational noise. Here we examine the pressure of ABPs in two dimensions in both closed boxes and systems with periodic boundary conditions and show that its nonmonotonic behavior with density is a general property of ABPs and is not the result of finite-size effects. We correlate the time evolution of the mean pressure towards its steady-state value with the kinetics of motility-induced phase separation. For parameter values corresponding to phase-separated steady states, we identify two dynamical regimes. The pressure grows monotonically in time during the initial regime of rapid cluster formation, overshooting its steady-state value and then quickly relaxing to it, and remains constant during the subsequent slower period of cluster coalescence and coarsening. The overshoot is a distinctive feature of active systems.

A statics-dynamics equivalence through the fluctuation-dissipation ratio provides a window into the spin-glass phase from nonequilibrium measurements.

We have performed a very accurate computation of the nonequilibrium fluctuation-dissipation ratio for the 3D Edwards-Anderson Ising spin glass, by means of large-scale simulations on the special-purpose computers Janus and Janus II. This ratio (computed for finite times on very large, effectively infinite, systems) is compared with the equilibrium probability distribution of the spin overlap for finite sizes. Our main result is a quantitative statics-dynamics dictionary, which could allow the experimental exploration of important features of the spin-glass phase without requiring uncontrollable extrapolations to infinite times or system sizes.

Thermodynamic glass transition in a spin glass without time-reversal symmetry.

Spin glasses are a longstanding model for the sluggish dynamics that appear at the glass transition. However, spin glasses differ from structural glasses in a crucial feature: they enjoy a time reversal symmetry. This symmetry can be broken by applying an external magnetic field, but embarrassingly little is known about the critical behavior of a spin glass in a field. In this context, the space dimension is crucial. Simulations are easier to interpret in a large number of dimensions, but one must work below the upper critical dimension (i.e., in d < 6) in order for results to have relevance for experiments. Here we show conclusive evidence for the presence of a phase transition in a four-dimensional spin glass in a field. Two ingredients were crucial for this achievement: massive numerical simulations were carried out on the Janus special-purpose computer, and a new and powerful finite-size scaling method.