Optical properties of an atomic ensemble coupled to a band edge of a photonic crystal waveguide

We study the optical properties of an ensemble of two-level atoms coupled to a 1D photonic crystal waveguide (PCW), which mediates long-range coherent dipole-dipole interactions between the atoms. We show that the long-range interactions can dramatically alter the linear and nonlinear optical behavior, as compared to a typical atomic ensemble. In particular, in the linear regime, we find that the transmission spectrum reveals multiple transmission dips, whose properties we show how to characterize. In the many-photon regime the system response can be highly non-linear, and under certain circumstances the ensemble can behave like a single two-level system, which is only capable of absorbing and emitting a single excitation at a time. Our results are of direct relevance to atom-PCW experiments that should soon be realizable

The Houdayer Algorithm: Overview, Extensions, and Applications

The study of spin systems with disorder and frustration is known to be a computationally hard task. Standard heuristics developed for optimizing and sampling from general Ising Hamiltonians tend to produce correlated solutions due to their locality, resulting in a suboptimal exploration of the search space. To mitigate these effects, cluster Monte-Carlo methods are often employed as they provide ways to perform non-local transformations on the system. In this work, we investigate the Houdayer algorithm, a cluster Monte-Carlo method with small numerical overhead which improves the exploration of configurations by preserving the energy of the system. We propose a generalization capable of reaching exponentially many configurations at the same energy, while offering a high level of adaptability to ensure that no biased choice is made. We discuss its applicability in various contexts, including Markov chain Monte-Carlo sampling and as part of a genetic algorithm. The performance of our generalization in these settings is illustrated by sampling for the Ising model across different graph connectivities and by solving instances of well-known binary optimization problems. We expect our results to be of theoretical and practical relevance in the study of spin glasses but also more broadly in discrete optimization, where a multitude of problems follow the structure of Ising spin systems.Comment: 24 pages, 9 figure

Photon scattering by an atomic ensemble coupled to a one-dimensional nanophotonic waveguide

We theoretically investigate the quantum scattering of a single-photon pulse interacting with an ensemble of $\Lambda$-type three-level atoms coupled to a one-dimensional waveguide. With an effective non-Hermitian Hamiltonian, we study the collective interaction between the atoms mediated by the waveguide mode. In our scheme, the atoms are randomly placed in the lattice along the axis of the one-dimensional waveguide, which closely corresponds to the practical condition that the atomic positions can not be controlled precisely in experiment. Many interesting optical properties occur in our waveguide-atom system, such as electromagnetically induced transparency (EIT) and optical depth. Moreover, we observe that strong photon-photon correlation with quantum beats can be generated in the off-resonant case, which provides an effective candidate for producing non-classical light in experiment. With remarkable progress in waveguide-emitter system, our scheme may be feasible in the near future.Comment: 10 pages,7 figure

Population mixing due to dipole-dipole interactions in a 1D array of multilevel atoms

We examine theoretically how dipole-dipole interactions arising from multiple photon scattering lead to a modified distribution of ground state populations in a driven, ordered 1D array of multilevel atoms. Specifically, we devise a level configuration in which a ground-state population accumulated due solely to dipole-dipole interactions can be up to 20\% in regimes accessible to current experiments with neutral atom arrays. For much larger systems, the steady state can consist of an equal distribution of population across the ground state manifold. Our results illustrate how dipole-dipole interactions can be accentuated through interference, and regulated by the geometry of ordered atom arrays. More generally, control techniques for multilevel atoms that can be degraded by multiple scattering, such as optical pumping, will benefit from an improved understanding and control of dipole-dipole interactions available in ordered arrays.Comment: paper is now identical to published versio

Polarized cell motility induces hydrogen peroxide to inhibit cofilin via cysteine oxidation

Mesenchymal cell motility is driven by polarized actin polymerization [1]. Signals at the leading edge recruit actin polymerization machinery to promote membrane protrusion, while matrix adhesion generates tractive force to propel forward movement. To work effectively, cell motility is regulated by a complex network of signaling events that affect protein activity and localization. H2O2 has an important role as a diffusible second messenger [2], and mediates its effects through oxidation of cysteine thiols. One cell activity influenced by H2O2 is motility [3]. However, a lack of sensitive and H2O2-specific probes for measurements in live cells has not allowed for direct observation of H2O2 accumulation in migrating cells or protrusions. In addition, the identities of proteins oxidized by H2O2 that contribute to actin dynamics and cell motility have not been characterized. We now show, as determined by fluorescence lifetime imaging microscopy, that motile cells generate H2O2 at membranes and cell protrusions and that H2O2 inhibits cofilin activity through oxidation of cysteines 139 (C139) and 147 (C147). Molecular modeling suggests that C139 oxidation would sterically hinder actin association, while the increased negative charge of oxidized C147 would lead to electrostatic repulsion of the opposite negatively charged surface. Expression of oxidation-resistant cofilin impairs cell spreading, adhesion, and directional migration. These findings indicate that H2O2 production contributes to polarized cell motility through localized cofilin inhibition and that there are additional proteins oxidized during cell migration that might have similar roles

Multi-Objective Optimization and Network Routing with Near-Term Quantum Computers

Multi-objective optimization is a ubiquitous problem that arises naturally in many scientific and industrial areas. Network routing optimization with multi-objective performance demands falls into this problem class, and finding good quality solutions at large scales is generally challenging. In this work, we develop a scheme with which near-term quantum computers can be applied to solve multi-objective combinatorial optimization problems. We study the application of this scheme to the network routing problem in detail, by first mapping it to the multi-objective shortest path problem. Focusing on an implementation based on the quantum approximate optimization algorithm (QAOA) -- the go-to approach for tackling optimization problems on near-term quantum computers -- we examine the Pareto plot that results from the scheme, and qualitatively analyze its ability to produce Pareto-optimal solutions. We further provide theoretical and numerical scaling analyses of the resource requirements and performance of QAOA, and identify key challenges associated with this approach. Finally, through Amazon Braket we execute small-scale implementations of our scheme on the IonQ Harmony 11-qubit quantum computer

Dynamic, adaptive sampling during nanopore sequencing using Bayesian experimental design

Nanopore sequencers can select which DNA molecules to sequence, rejecting a molecule after analysis of a small initial part. Currently, selection is based on predetermined regions of interest that remain constant throughout an experiment. Sequencing efforts, thus, cannot be re-focused on molecules likely contributing most to experimental success. Here we present BOSS-RUNS, an algorithmic framework and software to generate dynamically updated decision strategies. We quantify uncertainty at each genome position with real-time updates from data already observed. For each DNA fragment, we decide whether the expected decrease in uncertainty that it would provide warrants fully sequencing it, thus optimizing information gain. BOSS-RUNS mitigates coverage bias between and within members of a microbial community, leading to improved variant calling; for example, low-coverage sites of a species at 1% abundance were reduced by 87.5%, with 12.5% more single-nucleotide polymorphisms detected. Such data-driven updates to molecule selection are applicable to many sequencing scenarios, such as enriching for regions with increased divergence or low coverage, reducing time-to-answer

eIF4A1-dependent mRNAs employ purine-rich 5’UTR sequences to activate localised eIF4A1-unwinding through eIF4A1-multimerisation to facilitate translation

Altered eIF4A1 activity promotes translation of highly structured, eIF4A1-dependent oncogene mRNAs at root of oncogenic translational programmes. It remains unclear how these mRNAs recruit and activate eIF4A1 unwinding specifically to facilitate their preferential translation. Here, we show that single-stranded RNA sequence motifs specifically activate eIF4A1 unwinding allowing local RNA structural rearrangement and translation of eIF4A1-dependent mRNAs in cells. Our data demonstrate that eIF4A1-dependent mRNAs contain AG-rich motifs within their 5’UTR which specifically activate eIF4A1 unwinding of local RNA structure to facilitate translation. This mode of eIF4A1 regulation is used by mRNAs encoding components of mTORC-signalling and cell cycle progression, and renders these mRNAs particularly sensitive to eIF4A1-inhibition. Mechanistically, we show that binding of eIF4A1 to AG-rich sequences leads to multimerization of eIF4A1 with eIF4A1 subunits performing distinct enzymatic activities. Our structural data suggest that RNA-binding of multimeric eIF4A1 induces conformational changes in the RNA resulting in an optimal positioning of eIF4A1 proximal to the RNA duplex enabling efficient unwinding. Our data proposes a model in which AG-motifs in the 5’UTR of eIF4A1-dependent mRNAs specifically activate eIF4A1, enabling assembly of the helicase-competent multimeric eIF4A1 complex, and positioning these complexes proximal to stable localised RNA structure allowing ribosomal subunit scanning