Lytic and temperate phage naturally coexist in a dynamic population model.

When phage infect their bacterial hosts, they may either lyse the cell and generate a burst of new phage, or lysogenize the bacterium, incorporating the phage genome into it. Phage lysis/lysogeny strategies are assumed to be highly optimized, with the optimal tradeoff depending on environmental conditions. However, in nature, phage of radically different lysis/lysogeny strategies coexist in the same environment, preying on the same bacteria. How can phage preying on the same bacteria coexist if one is more optimal than the other? Here, we address this conundrum within a modeling framework, simulating the population dynamics of communities of phage and their lysogens. We find that coexistence between phage of different lysis/lysogeny strategies is a natural outcome of chaotic population dynamics that arise within sufficiently diverse communities, which ensure no phage is able to absolutely dominate its competitors. Our results further suggest a bet-hedging mechanism at the level of the phage pan-genome, wherein obligate lytic (virulent) strains typically outcompete temperate strains, but also more readily fluctuate to extinction within a local community.

The value of information gathering in phage-bacteria warfare.

Phages-viruses that infect bacteria-have evolved over billions of years to overcome bacterial defenses. Temperate phage, upon infection, can "choose" between two pathways: lysis-in which the phage create multiple new phage particles, which are then liberated by cell lysis, and lysogeny-where the phage's genetic material is added to the bacterial DNA and transmitted to the bacterial progeny. It was recently discovered that some phages can read information from the environment related to the density of bacteria or the number of nearby infection attempts. Such information may help phage make the right choice between the two pathways. Here, we develop a theoretical model that allows an infecting phage to change its strategy (i.e. the ratio of lysis to lysogeny) depending on an outside signal, and we find the optimal strategy that maximizes phage proliferation. While phages that exploit extra information naturally win in competition against phages with a fixed strategy, there may be costs to information, e.g. as the necessary extra genes may affect the growth rate of a lysogen or the burst size of new phage for the lysis pathway. Surprisingly, even when phages pay a large price for information, they can still maintain an advantage over phages that lack this information, indicating the high benefit of intelligence gathering in phage-bacteria warfare.

Erratum: Mechanical Frustration of Phase Separation in the Cell Nucleus by Chromatin [Phys. Rev. Lett. 126, 258102 (2021)].

This corrects the article DOI: 10.1103/PhysRevLett.126.258102.

Identifying an Environment-Induced Localization Transition from Entropy and Conductance.

Environment-induced localization transitions (LT) occur when a small quantum system interacts with a bath of harmonic oscillators. At equilibrium, LTs are accompanied by an entropy change, signaling the loss of coherence. Despite extensive efforts, equilibrium LTs have yet to be observed. Here, we demonstrate that ongoing experiments on double quantum dots that measure entropy using a nearby quantum point contact realize the celebrated spin-boson model and allow to measure the entropy change of its LT. We find a Kosterlitz-Thouless flow diagram, leading to a universal jump in the spin-bath interaction, reflected in a discontinuity in the zero temperature QPC conductance.

Realistic Protocol to Measure Entanglement at Finite Temperatures.

It is desirable to relate entanglement of many-body systems to measurable observables. In systems with a conserved charge, it was recently shown that the number entanglement entropy (NEE)-i.e., the entropy change due to an unselective subsystem charge measurement-is an entanglement monotone. Here we derive finite-temperature equilibrium relations between Rényi moments of the NEE, and multipoint charge correlations. These relations are exemplified in quantum dot systems where the desired charge correlations can be measured via a nearby quantum point contact. In quantum dots recently realizing the multichannel Kondo effect we show that the NEE has a nontrivial universal temperature dependence which is now accessible using the proposed methods.

Entropy Measurement of a Strongly Coupled Quantum Dot.

The spin 1/2 entropy of electrons trapped in a quantum dot has previously been measured with great accuracy, but the protocol used for that measurement is valid only within a restrictive set of conditions. Here, we demonstrate a novel entropy measurement protocol that is universal for arbitrary mesoscopic circuits and apply this new approach to measure the entropy of a quantum dot hybridized with a reservoir. The experimental results match closely to numerical renormalization group (NRG) calculations for small and intermediate coupling. For the largest couplings investigated in this Letter, NRG calculations predict a suppression of spin entropy at the charge transition due to the formation of a Kondo singlet, but that suppression is not observed in the experiment.

Fractional Entropy of Multichannel Kondo Systems from Conductance-Charge Relations.

Fractional entropy is a signature of nonlocal degrees of freedom, such as Majorana zero modes or more exotic non-Abelian anyons. Although direct experimental measurements remain challenging, Maxwell relations provide an indirect route to the entropy through charge measurements. Here we consider multichannel charge-Kondo systems, which are predicted to host exotic quasiparticles due to a frustration of Kondo screening at low temperatures. In the absence of experimental data for the charge occupation, we derive relations connecting the latter to the conductance, for which experimental results have recently been obtained. Our analysis indicates that Majorana and Fibonacci anyon quasiparticles are well developed in existing two- and three-channel charge-Kondo devices, and that their characteristic k_{B}logsqrt[2] and k_{B}log[(1+sqrt[5])/2] entropies are experimentally measurable.

piRNAs of Caenorhabditis elegans broadly silence nonself sequences through functionally random targeting.

Small noncoding RNAs such as piRNAs are guides for Argonaute proteins, enabling sequence-specific, post-transcriptional regulation of gene expression. The piRNAs of Caenorhabditis elegans have been observed to bind targets with high mismatch tolerance and appear to lack specific transposon targets, unlike piRNAs in Drosophila melanogaster and other organisms. These observations support a model in which C. elegans piRNAs provide a broad, indiscriminate net of silencing, competing with siRNAs associated with the CSR-1 Argonaute that specifically protect self-genes from silencing. However, the breadth of piRNA targeting has not been subject to in-depth quantitative analysis, nor has it been explained how piRNAs are distributed across sequence space to achieve complete coverage. Through a bioinformatic analysis of piRNA sequences, incorporating an original data-based metric of piRNA-target distance, we demonstrate that C. elegans piRNAs are functionally random, in that their coverage of sequence space is comparable to that of random sequences. By possessing a sufficient number of distinct, essentially random piRNAs, C. elegans is able to target arbitrary nonself sequences with high probability. We extend this approach to a selection of other nematodes, finding results which elucidate the mechanism by which nonself mRNAs are silenced, and have implications for piRNA evolution and biogenesis.

Motif-pattern dependence of biomolecular phase separation driven by specific interactions.

Eukaryotic cells partition a wide variety of important materials and processes into biomolecular condensates-phase-separated droplets that lack a membrane. In addition to nonspecific electrostatic or hydrophobic interactions, phase separation also depends on specific binding motifs that link together constituent molecules. Nevertheless, few rules have been established for how these ubiquitous specific, saturating, motif-motif interactions drive phase separation. By integrating Monte Carlo simulations of lattice-polymers with mean-field theory, we show that the sequence of heterotypic binding motifs strongly affects a polymer's ability to phase separate, influencing both phase boundaries and condensate properties (e.g. viscosity and polymer diffusion). We find that sequences with large blocks of single motifs typically form more inter-polymer bonds, which promotes phase separation. Notably, the sequence of binding motifs influences phase separation primarily by determining the conformational entropy of self-bonding by single polymers. This contrasts with systems where the molecular architecture primarily affects the energy of the dense phase, providing a new entropy-based mechanism for the biological control of phase separation.

Enzyme regulation and mutation in a model serial-dilution ecosystem.

Microbial communities are ubiquitous in nature and come in a multitude of forms, ranging from communities dominated by a handful of species to communities containing a wide variety of metabolically distinct organisms. This huge range in diversity is not a curiosity-microbial diversity has been linked to outcomes of substantial ecological and medical importance. However, the mechanisms underlying microbial diversity are still under debate, as simple mathematical models only permit as many species to coexist as there are resources. A plethora of mechanisms have been proposed to explain the origins of microbial diversity, but many of these analyses omit a key property of real microbial ecosystems: the propensity of the microbes themselves to change their growth properties within and across generations. In order to explore the impact of this key property on microbial diversity, we expand upon a recently developed model of microbial diversity in fluctuating environments. We implement changes in growth strategy in two distinct ways. First, we consider the regulation of a cell's enzyme levels within short, ecological times, and second we consider evolutionary changes driven by mutations across generations. Interestingly, we find that these two types of microbial responses to the environment can have drastically different outcomes. Enzyme regulation may collapse diversity over long enough times while, conversely, strategy-randomizing mutations can produce a "rich-get-poorer" effect that promotes diversity. This paper makes explicit, using a simple serial-dilutions framework, the conflicting ways that microbial adaptation and evolution can affect community diversity.

Kondo effect and spin-orbit coupling in graphene quantum dots.

The Kondo effect is a cornerstone in the study of strongly correlated fermions. The coherent exchange coupling of conduction electrons to local magnetic moments gives rise to a Kondo cloud that screens the impurity spin. Here we report on the interplay between spin-orbit interaction and the Kondo effect, that can lead to a underscreened Kondo effects in quantum dots in bilayer graphene. More generally, we introduce a different experimental platform for studying Kondo physics. In contrast to carbon nanotubes, where nanotube chirality determines spin-orbit coupling breaking the SU(4) symmetry of the electronic states relevant for the Kondo effect, we study a planar carbon material where a small spin-orbit coupling of nominally flat graphene is enhanced by zero-point out-of-plane phonons. The resulting two-electron triplet ground state in bilayer graphene dots provides a route to exploring the Kondo effect with a small spin-orbit interaction.

Mechanical Frustration of Phase Separation in the Cell Nucleus by Chromatin.

Liquid-liquid phase separation is a fundamental mechanism underlying subcellular organization. Motivated by the striking observation that optogenetically generated droplets in the nucleus display suppressed coarsening dynamics, we study the impact of chromatin mechanics on droplet phase separation. We combine theory and simulation to show that cross-linked chromatin can mechanically suppress droplets' coalescence and ripening, as well as quantitatively control their number, size, and placement. Our results highlight the role of the subcellular mechanical environment on condensate regulation.

Decoding the physical principles of two-component biomolecular phase separation.

Cells possess a multiplicity of non-membrane-bound compartments, which form via liquid-liquid phase separation. These condensates assemble and dissolve as needed to enable central cellular functions. One important class of condensates is those composed of two associating polymer species that form one-to-one specific bonds. What are the physical principles that underlie phase separation in such systems? To address this question, we employed coarse-grained molecular dynamics simulations to examine how the phase boundaries depend on polymer valence, stoichiometry, and binding strength. We discovered a striking phenomenon - for sufficiently strong binding, phase separation is suppressed at rational polymer stoichiometries, which we termed the magic-ratio effect. We further developed an analytical dimer-gel theory that confirmed the magic-ratio effect and disentangled the individual roles of polymer properties in shaping the phase diagram. Our work provides new insights into the factors controlling the phase diagrams of biomolecular condensates, with implications for natural and synthetic systems.

Nutrient levels and trade-offs control diversity in a serial dilution ecosystem.

Microbial communities feature an immense diversity of species and this diversity is linked to outcomes ranging from ecosystem stability to medical prognoses. Yet the mechanisms underlying microbial diversity are under debate. While simple resource-competition models don't allow for coexistence of a large number of species, it was recently shown that metabolic trade-offs can allow unlimited diversity. Does this diversity persist with more realistic, intermittent nutrient supply? Here, we demonstrate theoretically that in serial dilution culture, metabolic trade-offs allow for high diversity. When a small amount of nutrient is supplied to each batch, the serial dilution dynamics mimic a chemostat-like steady state. If more nutrient is supplied, community diversity shifts due to an 'early-bird' effect. The interplay of this effect with different environmental factors and diversity-supporting mechanisms leads to a variety of relationships between nutrient supply and diversity, suggesting that real ecosystems may not obey a universal nutrient-diversity relationship.

In most environments, organisms compete for limited resources. The number and relative abundance of species that an ecosystem can host is referred to as 'species diversity'. The competitive-exclusion principle is a hypothesis which proposes that, in an ecosystem, competition for resources results in decreased diversity: only species best equipped to consume the available resources thrive, while their less successful competitors die off. However, many natural ecosystems foster a wide array of species despite offering relatively few resources. Researchers have proposed many competing theories to explain how this paradox can emerge, but they have mainly focused on ecosystems where nutrients are steadily supplied. By contrast, less is known about the way species diversity is maintained when nutrients are only intermittently available, for example in ecosystems that have seasons. To address this question, Erez, Lopez et al. modeled communities of bacteria in which nutrients were repeatedly added and then used up. Depending on conditions, a variety of relationships between the amount of nutrient supplied and community diversity could emerge, suggesting that ecosystems do not follow a simple, universal rule that dictates species diversity. In particular, the resulting communities displayed a higher diversity of microbes than the limit imposed by the competitive-exclusion principle. Further observations allowed Erez, Lopez et al. to suggest guiding principles for when diversity in ecosystems will be maintained or lost. In this framework, 'early-bird' species, which rapidly use a subset of the available nutrients, grow to dominate the ecosystem. Even though 'late-bird' species are more effective at consuming the remaining resources, they cannot compete with the increased sheer numbers of the 'early-birds', leading to a 'rich-get-richer' phenomenon. Oceanic plankton, arctic permafrost and many other threatened, resource-poor ecosystems across the world can dramatically influence our daily lives. Closer to home, shifts in the microbe communities that live on the surface of the human body and in the digestive system are linked to poor health. Understanding how species diversity emerges and changes will help to protect our external and internal environments.

An experimental test of the geodesic rule proposition for the noncyclic geometric phase.

The geometric phase due to the evolution of the Hamiltonian is a central concept in quantum physics and may become advantageous for quantum technology. In noncyclic evolutions, a proposition relates the geometric phase to the area bounded by the phase-space trajectory and the shortest geodesic connecting its end points. The experimental demonstration of this geodesic rule proposition in different systems is of great interest, especially due to the potential use in quantum technology. Here, we report a previously unshown experimental confirmation of the geodesic rule for a noncyclic geometric phase by means of a spatial SU(2) matter-wave interferometer, demonstrating, with high precision, the predicted phase sign change and π jumps. We show the connection between our results and the Pancharatnam phase. Last, we point out that the geodesic rule may be applied to obtain the red shift in general relativity, enabling a new quantum tool to measure gravity.

Rigidity enhances a magic-number effect in polymer phase separation.

Cells possess non-membrane-bound bodies, many of which are now understood as phase-separated condensates. One class of such condensates is composed of two polymer species, where each consists of repeated binding sites that interact in a one-to-one fashion with the binding sites of the other polymer. Biologically-motivated modeling revealed that phase separation is suppressed by a "magic-number effect" which occurs if the two polymers can form fully-bonded small oligomers by virtue of the number of binding sites in one polymer being an integer multiple of the number of binding sites of the other. Here we use lattice-model simulations and analytical calculations to show that this magic-number effect can be greatly enhanced if one of the polymer species has a rigid shape that allows for multiple distinct bonding conformations. Moreover, if one species is rigid, the effect is robust over a much greater range of relative concentrations of the two species.

How to measure the entropy of a mesoscopic system via thermoelectric transport.

Entropy is a fundamental thermodynamic quantity indicative of the accessible degrees of freedom in a system. While it has been suggested that the entropy of a mesoscopic system can yield nontrivial information on emergence of exotic states, its measurement in such small electron-number system is a daunting task. Here we propose a method to extract the entropy of a Coulomb-blockaded mesoscopic system from transport measurements. We prove analytically and demonstrate numerically the applicability of the method to such a mesoscopic system of arbitrary spectrum and degeneracies. We then apply our procedure to measurements of thermoelectric response of a single quantum dot, and demonstrate how it can be used to deduce the entropy change across Coulomb-blockade valleys, resolving, along the way, a long-standing puzzle of the experimentally observed finite thermoelectric response at the apparent particle-hole symmetric point.

Auger-spectroscopy in quantum Hall edge channels and the missing energy problem.

Quantum Hall edge channels offer an efficient and controllable platform to study quantum transport in one dimension. Such channels are a prospective tool for the efficient transfer of quantum information at the nanoscale, and play a vital role in exposing intriguing physics. Electric current along the edge carries energy and heat leading to inelastic scattering, which may impede coherent transport. Several experiments attempting to probe the concomitant energy redistribution along the edge reported energy loss via unknown mechanisms of inelastic scattering. Here we employ quantum dots to inject and extract electrons at specific energies, to spectrally analyse inelastic scattering inside quantum Hall edge channels. We show that the missing energy puzzle could be untangled by incorporating non-local Auger-like processes, in which energy is redistributed between spatially separate parts of the sample. Our theoretical analysis, accounting for the experimental results, challenges common-wisdom analyses which ignore such non-local decay channels.

Concerted 2-5A-Mediated mRNA Decay and Transcription Reprogram Protein Synthesis in the dsRNA Response.

Viral and endogenous double-stranded RNA (dsRNA) is a potent trigger for programmed RNA degradation by the 2-5A/RNase L complex in cells of all mammals. This 2-5A-mediated decay (2-5AMD) is a conserved stress response switching global protein synthesis from homeostasis to production of interferons (IFNs). To understand this mechanism, we examined 2-5AMD in human cells and found that it triggers polysome collapse characteristic of inhibited translation initiation. We determined that translation initiation complexes and ribosomes purified from translation-arrested cells remain functional. However, spike-in RNA sequencing (RNA-seq) revealed cell-wide decay of basal mRNAs accompanied by rapid accumulation of mRNAs encoding innate immune proteins. Our data attribute this 2-5AMD evasion to better stability of defense mRNAs and positive feedback in the IFN response amplified by RNase L-resistant molecules. We conclude that 2-5AMD and transcription act in concert to refill mammalian cells with defense mRNAs, thereby "prioritizing" the synthesis of innate immune proteins.

Quantum phase transition in a realistic double-quantum-dot system.

Observing quantum phase transitions in mesoscopic systems is a daunting task, thwarted by the difficulty of experimentally varying the magnetic interactions, the typical driving force behind these phase transitions. Here we demonstrate that in realistic coupled double-dot systems, the level energy difference between the two dots, which can be easily tuned experimentally, can drive the system through a phase transition, when its value crosses the difference between the intra- and inter-dot Coulomb repulsion. Using the numerical renormalization group and the semi-analytic slave-boson mean-field theory, we study the nature of this phase transition, and demonstrate, by mapping the Hamiltonian into an even-odd basis, that indeed the competition between the dot level energy difference and the difference in repulsion energies governs the sign and magnitude of the effective magnetic interaction. The observational consequences of this transition are discussed.