Optomechanical state reconstruction and nonclassicality verification beyond the resolved-sideband regime

Quantum optomechanics uses optical means to generate and manipulate quantum states of motion of mechanical resonators. This provides an intriguing platform for the study of fundamental physics and the development of novel quantum devices. Yet, the challenge of reconstructing and verifying the quantum state of mechanical systems has remained a major roadblock in the field. Here, we present a novel approach that allows for tomographic reconstruction of the quantum state of a mechanical system without the need for extremely high quality optical cavities. We show that, without relying on the usual state transfer presumption between light an mechanics, the full optomechanical Hamiltonian can be exploited to imprint mechanical tomograms on a strong optical coherent pulse, which can then be read out using well-established techniques. Furthermore, with only a small number of measurements, our method can be used to witness nonclassical features of mechanical systems without requiring full tomography. By relaxing the experimental requirements, our technique thus opens a feasible route towards verifying the quantum state of mechanical resonators and their nonclassical behaviour in a wide range of optomechanical systems.Comment: 12 pages + 9 pages of appendices, 4 figure

Probing the Non-Classicality of Temporal Correlations

Correlations between spacelike separated measurements on entangled quantum systems are stronger than any classical correlations and are at the heart of numerous quantum technologies. In practice, however, spacelike separation is often not guaranteed and we typically face situations where measurements have an underlying time order. Here we aim to provide a fair comparison of classical and quantum models of temporal correlations on a single particle, as well as timelike-separated correlations on multiple particles. We use a causal modeling approach to show, in theory and experiment, that quantum correlations outperform their classical counterpart when allowed equal, but limited communication resources. This provides a clearer picture of the role of quantum correlations in timelike separated scenarios, which play an important role in foundational and practical aspects of quantum information processing.Comment: 8 pages, 6 figures, 2 pages appendix, Accepted versio

IST Austria Thesis

This thesis is concerned with the inference of current population structure based on geo-referenced genetic data. The underlying idea is that population structure affects its spatial genetic structure. Therefore, genotype information can be utilized to estimate important demographic parameters such as migration rates. These indirect estimates of population structure have become very attractive, as genotype data is now widely available. However, there also has been much concern about these approaches. Importantly, genetic structure can be influenced by many complex patterns, which often cannot be disentangled. Moreover, many methods merely fit heuristic patterns of genetic structure, and do not build upon population genetics theory. Here, I describe two novel inference methods that address these shortcomings. In Chapter 2, I introduce an inference scheme based on a new type of signal, identity by descent (IBD) blocks. Recently, it has become feasible to detect such long blocks of genome shared between pairs of samples. These blocks are direct traces of recent coalescence events. As such, they contain ample signal for inferring recent demography. I examine sharing of IBD blocks in two-dimensional populations with local migration. Using a diffusion approximation, I derive formulas for an isolation by distance pattern of long IBD blocks and show that sharing of long IBD blocks approaches rapid exponential decay for growing sample distance. I describe an inference scheme based on these results. It can robustly estimate the dispersal rate and population density, which is demonstrated on simulated data. I also show an application to estimate mean migration and the rate of recent population growth within Eastern Europe. Chapter 3 is about a novel method to estimate barriers to gene flow in a two dimensional population. This inference scheme utilizes geographically localized allele frequency fluctuations - a classical isolation by distance signal. The strength of these local fluctuations increases on average next to a barrier, and there is less correlation across it. I again use a framework of diffusion of ancestral lineages to model this effect, and provide an efficient numerical implementation to fit the results to geo-referenced biallelic SNP data. This inference scheme is able to robustly estimate strong barriers to gene flow, as tests on simulated data confirm

hapCon: Estimating contamination of ancient genomes by copying from reference haplotypes

Human ancient DNA (aDNA) studies have surged in recent years, revolutionizing the study of the human past. Typically, aDNA is preserved poorly, making such data prone to contamination from other human DNA. Therefore, it is important to rule out substantial contamination before proceeding to downstream analysis. As most aDNA samples can only be sequenced to low coverages (<1× average depth), computational methods that can robustly estimate contamination in the low coverage regime are needed. However, the ultra low-coverage regime (0.1× and below) remains a challenging task for existing approaches.We present a new method to estimate contamination in aDNA for male modern humans. It utilizes a Li&Stephens haplotype copying model for haploid X chromosomes, with mismatches modeled as errors or contamination. We assessed this new approach, hapCon, on simulated and down-sampled empirical aDNA data. Our experiments demonstrate that hapCon outperforms a commonly used tool for estimating male X contamination (ANGSD), with substantially lower variance and narrower confidence intervals, especially in the low coverage regime. We found that hapCon provides useful contamination estimates for coverages as low as 0.1× for SNP capture data (1240k) and 0.02× for whole genome sequencing data, substantially extending the coverage limit of previous male X chromosome-based contamination estimation methods. Our experiments demonstrate that hapCon has little bias for contamination up to 25–30\% as long as the contaminating source is specified within continental genetic variation, and that its application range extends to human aDNA as old as ∼45 000 and various global ancestries.We make hapCon available as part of a python package (hapROH), which is available at the Python Package Index (https://pypi.org/project/hapROH) and can be installed via pip. The documentation provides example use cases as blueprints for custom applications (https://haproh.readthedocs.io/en/latest/hapCon.html). The program can analyze either BAM files or pileup files produced with samtools. An implementation of our software (hapCon) using Python and C is deposited at https://github.com/hyl317/hapROH.Supplementary data are available at Bioinformatics online

Characterizing quantum dynamics with initial system-environment correlations

We fully characterize the reduced dynamics of an open quantum system initially correlated with its environment. Using a photonic qubit coupled to a simulated environment we tomographically reconstruct a superchannel---a generalised channel that treats preparation procedures as inputs---from measurement of the system alone, despite its coupling to the environment. We introduce novel quantitative measures for determining the strength of initial correlations, and to allow an experiment to be optimised in regards to its environment.Comment: 10 pages, 15 figure

Generation of mechanical interference fringes by multi-photon counting

Exploring the quantum behaviour of macroscopic objects provides an intriguing avenue to study the foundations of physics and to develop a suite of quantum-enhanced technologies. One prominent path of study is provided by quantum optomechanics which utilizes the tools of quantum optics to control the motion of macroscopic mechanical resonators. Despite excellent recent progress, the preparation of mechanical quantum superposition states remains outstanding due to weak coupling and thermal decoherence. Here we present a novel optomechanical scheme that significantly relaxes these requirements allowing the preparation of quantum superposition states of motion of a mechanical resonator by exploiting the nonlinearity of multi-photon quantum measurements. Our method is capable of generating non-classical mechanical states without the need for strong single photon coupling, is resilient against optical loss, and offers more favourable scaling against initial mechanical thermal occupation than existing schemes. Moreover, our approach allows the generation of larger superposition states by projecting the optical field onto NOON states. We experimentally demonstrate this multi-photon-counting technique on a mechanical thermal state in the classical limit and observe interference fringes in the mechanical position distribution that show phase superresolution. This opens a feasible route to explore and exploit quantum phenomena at a macroscopic scale.Comment: 16 pages, 4 figures. v1: submitted for review on 28 Jan 2016. v2: significantly revised manuscript. v3: some further revisions and some extra results included. v3: new results added, extra author added, close to published version, supplementary material available with published versio

Parental relatedness through time revealed by runs of homozygosity in ancient DNA

Parental relatedness of present-day humans varies substantially across the globe, but little is known about the past. Here we analyze ancient DNA, leveraging that parental relatedness leaves genomic traces in the form of runs of homozygosity. We present an approach to identify such runs in low-coverage ancient DNA data aided by haplotype information from a modern phased reference panel. Simulation and experiments show that this method robustly detects runs of homozygosity longer than 4 centimorgan for ancient individuals with at least 0.3 × coverage. Analyzing genomic data from 1,785 ancient humans who lived in the last 45,000 years, we detect low rates of first cousin or closer unions across most ancient populations. Moreover, we find a marked decay in background parental relatedness co-occurring with or shortly after the advent of sedentary agriculture. We observe this signal, likely linked to increasing local population sizes, across several geographic transects worldwide

An extended admixture pulse model reveals the limitations to human-Neandertal introgression dating

Neandertal DNA makes up 2–3% of the genomes of all non-African individuals. The patterns of Neandertal ancestry in modern humans have been used to estimate that this is the result of gene flow that occurred during the expansion of modern humans into Eurasia, but the precise dates of this event remain largely unknown. Here, we introduce an extended admixture pulse model that allows joint estimation of the timing and duration of gene flow. This model leads to simple expressions for both the admixture segment distribution and the decay curve of ancestry linkage disequilibrium, and we show that these two statistics are closely related. In simulations, we find that estimates of the mean time of admixture are largely robust to details in gene flow models, but that the duration of the gene flow can only be recovered if gene flow is very recent and the exact recombination map is known. These results imply that gene flow from Neandertals into modern humans could have happened over hundreds of generations. Ancient genomes from the time around the admixture event are thus likely required to resolve the question when, where, and for how long humans and Neandertals interacted

Enhanced Multi-Qubit Phase Estimation in Noisy Environments by Local Encoding

The first generation of multi-qubit quantum technologies will consist of noisy, intermediate-scale devices for which active error correction remains out of reach. To exploit such devices, it is thus imperative to use passive error protection that meets a careful trade-off between noise protection and resource overhead. Here, we experimentally demonstrate that single-qubit encoding can significantly enhance the robustness of entanglement and coherence of four-qubit graph states against local noise with a preferred direction. In particular, we explicitly show that local encoding provides a significant practical advantage for phase estimation in noisy environments. This demonstrates the efficacy of local unitary encoding under realistic conditions, with potential applications in multi-qubit quantum technologies for metrology, multi-partite secrecy and error correction.Comment: 7 figure

Rapid automated characterization of transposon insertion mutants in Desulfovibrio vulgaris Hildenborough by srnPCR [abstract]

Abstract only availableTn5 transposon mutagenesis occurs by a mechanism in which a segment of DNA (transposon) encoded in a plasmid is inserted into genomic DNA (the target) by a conservative (cut-and-paste) mechanism (Fig. 2). When the insertion position is in a coding sequence or regulatory region of DNA, the insertion results in a mutation. The plasmid pRL27 (a generous gift from Bill Metcalf) encodes a mini-Tn5 transposon, Tn5 transposase, and kanamycin resistance (neo), and was used to transform Desulfovibrio vulgaris Hildenborough by electroporation. Transposon insertion mutants were identified by their ability to grow in the presence of kanamycin. To locate the insertion site of the transposon, in theory, one should be able to directly sequence from the transposon into chromosomal DNA (Fig. 3.1) and identify the mutation site by comparison with the known genome BLAST. Unlike sequencing of plasmid DNA or PCR products, direct genomic sequencing has a limited success rate. Therefore, a method of enriching the transposon-flanking sequence is needed. Nested semi-random PCR (Fig. 3.2) is an efficient and cost effective enrichment method. Sequencing these enriched products allows us to identify the transposon insertion site. The factors that influence characterization success rate are: frequency and location of priming sites, reaction volume, and reaction conditions (annealing temperature, extension time, etc.). By varying these factors, we have developed an efficient and reliable method for characterizing transposon insertion mutants. Utilizing high-throughput robotics and nested semi-random PCR, we have generated single gene mutants that may provide valuable biological data.U.S. Department of Energy Genomes to Life gran