131 research outputs found
Excitation of superconducting qubits from hot non-equilibrium quasiparticles
Superconducting qubits probe environmental defects such as non-equilibrium
quasiparticles, an important source of decoherence. We show that "hot"
non-equilibrium quasiparticles, with energies above the superconducting gap,
affect qubits differently from quasiparticles at the gap, implying qubits can
probe the dynamic quasiparticle energy distribution. For hot quasiparticles, we
predict a non-neligable increase in the qubit excited state probability P_e. By
injecting hot quasiparticles into a qubit, we experimentally measure an
increase of P_e in semi-quantitative agreement with the model and rule out the
typically assumed thermal distribution.Comment: Main paper: 5 pages, 5 figures. Supplement: 1 page, 1 figure, 1
table. Updated to user-prepared accepted version. Key changes: Supplement
added, Introduction rewritten, Figs.2,3,5 revised, Fig.4 adde
Program Model Checking: A Practitioner's Guide
Program model checking is a verification technology that uses state-space exploration to evaluate large numbers of potential program executions. Program model checking provides improved coverage over testing by systematically evaluating all possible test inputs and all possible interleavings of threads in a multithreaded system. Model-checking algorithms use several classes of optimizations to reduce the time and memory requirements for analysis, as well as heuristics for meaningful analysis of partial areas of the state space Our goal in this guidebook is to assemble, distill, and demonstrate emerging best practices for applying program model checking. We offer it as a starting point and introduction for those who want to apply model checking to software verification and validation. The guidebook will not discuss any specific tool in great detail, but we provide references for specific tools
Computing prime factors with a Josephson phase qubit quantum processor
A quantum processor (QuP) can be used to exploit quantum mechanics to find
the prime factors of composite numbers[1]. Compiled versions of Shor's
algorithm have been demonstrated on ensemble quantum systems[2] and photonic
systems[3-5], however this has yet to be shown using solid state quantum bits
(qubits). Two advantages of superconducting qubit architectures are the use of
conventional microfabrication techniques, which allow straightforward scaling
to large numbers of qubits, and a toolkit of circuit elements that can be used
to engineer a variety of qubit types and interactions[6, 7]. Using a number of
recent qubit control and hardware advances [7-13], here we demonstrate a
nine-quantum-element solid-state QuP and show three experiments to highlight
its capabilities. We begin by characterizing the device with spectroscopy.
Next, we produces coherent interactions between five qubits and verify bi- and
tripartite entanglement via quantum state tomography (QST) [8, 12, 14, 15]. In
the final experiment, we run a three-qubit compiled version of Shor's algorithm
to factor the number 15, and successfully find the prime factors 48% of the
time. Improvements in the superconducting qubit coherence times and more
complex circuits should provide the resources necessary to factor larger
composite numbers and run more intricate quantum algorithms.Comment: 5 pages, 3 figure
Surface loss simulations of superconducting coplanar waveguide resonators
Losses in superconducting planar resonators are presently assumed to
predominantly arise from surface-oxide dissipation, due to experimental losses
varying with choice of materials. We model and simulate the magnitude of the
loss from interface surfaces in the resonator, and investigate the dependence
on power, resonator geometry, and dimensions. Surprisingly, the dominant
surface loss is found to arise from the metal-substrate and substrate-air
interfaces. This result will be useful in guiding device optimization, even
with conventional materials.Comment: Main paper: 4 pages, 4 figures, 1 table. Supplementary material: 4
pages, 2 figures, 1 tabl
Multi-timescale analysis of a metabolic network in synthetic biology: a kinetic model for 3-hydroxypropionic acid production via beta-alanine
A biosustainable production route for 3-hydroxypropionic acid (3HP), an important platform chemical, would allow 3HP to be produced without using fossil fuels. We are interested in investigating a potential biochemical route to 3HP from pyruvate through b -alanine and, in this paper, we develop and solve a mathematical model for the reaction kinetics of the metabolites involved in this pathway. We consider two limiting cases, one where the levels of pyruvate are never replenished, the other where the levels of pyruvate are continuously replenished and thus kept constant. We exploit the natural separation of both the time scales and the metabolite concentrations to make significant asymptotic progress in understanding the system without resorting to computationally expensive parameter sweeps. Using our asymptotic results, we are able to predict the most important reactions to maximize the production of 3HP in this system while reducing the maximum amount of the toxic intermediate compound malonic semialdehyde present at any one time, and thus we are able to recommend which enzymes experimentalists should focus on manipulating
Towards a Processual Microbial Ontology
types: ArticleStandard microbial evolutionary ontology is organized according to a
nested hierarchy of entities at various levels of biological organization. It typically
detects and defines these entities in relation to the most stable aspects of evolutionary
processes, by identifying lineages evolving by a process of vertical inheritance
from an ancestral entity. However, recent advances in microbiology indicate
that such an ontology has important limitations. The various dynamics detected
within microbiological systems reveal that a focus on the most stable entities (or
features of entities) over time inevitably underestimates the extent and nature of
microbial diversity. These dynamics are not the outcome of the process of vertical
descent alone. Other processes, often involving causal interactions between entities
from distinct levels of biological organisation, or operating at different time scales,
are responsible not only for the destabilisation of pre-existing entities, but also for
the emergence and stabilisation of novel entities in the microbial world. In this
article we consider microbial entities as more or less stabilised functional wholes,
and sketch a network-based ontology that can represent a diverse set of processes
including, for example, as well as phylogenetic relations, interactions that stabilise
or destabilise the interacting entities, spatial relations, ecological connections, and
genetic exchanges. We use this pluralistic framework for evaluating (i) the existing
ontological assumptions in evolution (e.g. whether currently recognized entities are
adequate for understanding the causes of change and stabilisation in the microbial
world), and (ii) for identifying hidden ontological kinds, essentially invisible from
within a more limited perspective. We propose to recognize additional classes of
entities that provide new insights into the structure of the microbial world, namely ââprocessually equivalentââ entities, ââprocessually versatileââ entities, and ââstabilizedââ
entities.Economic and Social Research Council, U
Expression profiling of familial breast cancers demonstrates higher expression of FGFR2 in BRCA2-associated tumors
BackgroundBRCA1- and BRCA2-associated tumors appear to have distinct molecular signatures. BRCA1-associated tumors are predominantly basal-like cancers, whereas BRCA2-associated tumors have a predominant luminal-like phenotype. These two molecular signatures reflect in part the two cell types found in the terminal duct lobular unit of the breast. To elucidate novel genes involved in these two spectra of breast tumorigenesis we performed global gene expression analysis on breast tumors from germline BRCA1 and BRCA2 mutation carriers. Methodology Breast tumor RNAs from 7 BRCA1 and 6 BRCA2 mutation carriers were profiled using UHN human 19K cDNA microarrays. Supervised univariate analyses were conducted to identify genes differentially expressed between BRCA1 and BRCA2-associated tumors. Selected discriminatory genes were validated using real time reverse transcription polymerase chain reaction in the tumor RNAs, and/or by immunohistochemistry (IHC) or by in situ hybridization (ISH) on tissue microarrays (TMAs) containing an independent set of 58 BRCA1 and 64 BRCA2-associated tumors. Results Genes more highly expressed in BRCA1-associated tumors included stathmin, osteopontin, TGFÎČ2 and Jagged 1 in addition to genes previously identified as characteristic of basal-like breast cancers. BRCA2-associated cancers were characterized by the higher relative expression of FGF1 and FGFR2. FGFR2 protein was also more highly expressed in BRCA2-associated cancers (P = 0.004). SignificanceBRCA1-associated tumours demonstrated increased expression of component genes of the Notch and TGFÎČ pathways whereas the higher expression of FGFR2 and FGF1 in BRCA2-associated cancers suggests the existence of an autocrine stimulatory loop
Size Doesn't Matter: Towards a More Inclusive Philosophy of Biology
notes: As the primary author, OâMalley drafted the paper, and gathered and analysed data (scientific papers and talks). Conceptual analysis was conducted by both authors.publication-status: Publishedtypes: ArticlePhilosophers of biology, along with everyone else, generally perceive life to fall into two broad categories, the microbes and macrobes, and then pay most of their attention to the latter. âMacrobeâ is the word we propose for larger life forms, and we use it as part of an argument for microbial equality. We suggest that taking more notice of microbes â the dominant life form on the planet, both now and throughout evolutionary history â will transform some of the philosophy of biologyâs standard ideas on ontology, evolution, taxonomy and biodiversity. We set out a number of recent developments in microbiology â including biofilm formation, chemotaxis, quorum sensing and gene transfer â that highlight microbial capacities for cooperation and communication and break down conventional thinking that microbes are solely or primarily single-celled organisms. These insights also bring new perspectives to the levels of selection debate, as well as to discussions of the evolution and nature of multicellularity, and to neo-Darwinian understandings of evolutionary mechanisms. We show how these revisions lead to further complications for microbial classification and the philosophies of systematics and biodiversity. Incorporating microbial insights into the philosophy of biology will challenge many of its assumptions, but also give greater scope and depth to its investigations
Outcomes from elective colorectal cancer surgery during the SARS-CoV-2 pandemic
This study aimed to describe the change in surgical practice and the impact of SARS-CoV-2 on mortality after surgical resection of colorectal cancer during the initial phases of the SARS-CoV-2 pandemic
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