162 research outputs found
OQuPy : a Python package to efficiently simulate non-Markovian open quantum systems with process tensors
Funding: G.E.F. acknowledges the support from EPSRC (Grant No. EP/L015110/1) and from ERC under Grant Agreement No. 101053159 (RAVE). J.B. acknowledges the support from the Laidlaw Foundation (Leadership and Research Program scholarship). E.P.B. acknowledges the support from the Irish Research Council (Grant No. GOIPG/2019/1871). D.G. acknowledges the support from the QuantERA II Program that has received funding from the European Union’s Horizon 2020 research and innovation program under Grant Agreement No. 101017733 (“QuSiED”). P.R.E. acknowledges the support from Science Foundation Ireland (Grant No. 21-FFP-10142). E.D.C.L. acknowledges the support from EPSRC (Grant No. EP/T517938/1). R.d.W. acknowledges the support from EPSRC (Grant No. EP/W524505/1). B.W.L. and J.K. acknowledge the support from EPSRC (Grant No. EP/T014032/1).Non-Markovian dynamics arising from the strong coupling of a system to a structured environment is essential in many applications of quantum mechanics and emerging technologies. Deriving an accurate description of general quantum dynamics including memory effects is however a demanding task, prohibitive to standard analytical or direct numerical approaches. We present a major release of our open source software package, OQuPy (Open Quantum System in Python), which provides several recently developed numerical methods that address this challenging task. It utilizes the process tensor approach to open quantum systems in which a single map, the process tensor, captures all possible effects of an environment on the system. The representation of the process tensor in a tensor network form allows an exact yet highly efficient description of non-Markovian open quantum systems (NM-OQS). The OQuPy package provides methods to (1) compute the dynamics and multi-time correlations of quantum systems coupled to single and multiple environments, (2) optimize control protocols for NM-OQS, (3) simulate interacting chains of NM-OQS, and (4) compute the mean-field dynamics of an ensemble of NM-OQS coupled to a common central system. Our aim is to provide an easily accessible and extensible tool for researchers of open quantum systems in fields such as quantum chemistry, quantum sensing, and quantum information.Peer reviewe
Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development.
BACKGROUND: We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development. RESULTS: The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements. CONCLUSIONS: Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution
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A high-resolution map of human evolutionary constraint using 29 mammals.
The comparison of related genomes has emerged as a powerful lens for genome interpretation. Here we report the sequencing and comparative analysis of 29 eutherian genomes. We confirm that at least 5.5% of the human genome has undergone purifying selection, and locate constrained elements covering ∼4.2% of the genome. We use evolutionary signatures and comparisons with experimental data sets to suggest candidate functions for ∼60% of constrained bases. These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. We find 220 candidate RNA structural families, and nearly a million elements overlapping potential promoter, enhancer and insulator regions. We report specific amino acid residues that have undergone positive selection, 280,000 non-coding elements exapted from mobile elements and more than 1,000 primate- and human-accelerated elements. Overlap with disease-associated variants indicates that our findings will be relevant for studies of human biology, health and disease
Clinically Actionable Hypercholesterolemia and Hypertriglyceridemia in Children with Nonalcoholic Fatty Liver Disease
OBJECTIVE:
To determine the percentage of children with nonalcoholic fatty liver disease (NAFLD) in whom intervention for low-density lipoprotein cholesterol or triglycerides was indicated based on National Heart, Lung, and Blood Institute guidelines.
STUDY DESIGN:
This multicenter, longitudinal cohort study included children with NAFLD enrolled in the National Institute of Diabetes and Digestive and Kidney Diseases Nonalcoholic Steatohepatitis Clinical Research Network. Fasting lipid profiles were obtained at diagnosis. Standardized dietary recommendations were provided. After 1 year, lipid profiles were repeated and interpreted according to National Heart, Lung, and Blood Institute Expert Panel on Integrated Guidelines for Cardiovascular Health and Risk Reduction. Main outcomes were meeting criteria for clinically actionable dyslipidemia at baseline, and either achieving lipid goal at follow-up or meeting criteria for ongoing intervention.
RESULTS:
There were 585 participants, with a mean age of 12.8 years. The prevalence of children warranting intervention for low-density lipoprotein cholesterol at baseline was 14%. After 1 year of recommended dietary changes, 51% achieved goal low-density lipoprotein cholesterol, 27% qualified for enhanced dietary and lifestyle modifications, and 22% met criteria for pharmacologic intervention. Elevated triglycerides were more prevalent, with 51% meeting criteria for intervention. At 1 year, 25% achieved goal triglycerides with diet and lifestyle changes, 38% met criteria for advanced dietary modifications, and 37% qualified for antihyperlipidemic medications.
CONCLUSIONS:
More than one-half of children with NAFLD met intervention thresholds for dyslipidemia. Based on the burden of clinically relevant dyslipidemia, lipid screening in children with NAFLD is warranted. Clinicians caring for children with NAFLD should be familiar with lipid management
OQuPy : A Python package to efficiently simulate non-Markovian open quantum systems with process tensors
Non-Markovian dynamics arising from the strong coupling of a system to a structured environment is essential in many applications of quantum mechanics and emerging technologies. Deriving an accurate description of general quantum dynamics including memory effects is, however, a demanding task, prohibitive to standard analytical or direct numerical approaches. We present a major release of our open source software package, OQuPy (Open Quantum System in Python), which provides several recently developed numerical methods that address this challenging task. It utilizes the process tensor approach to open quantum systems (OQS) in which a single map, the process tensor, captures all possible effects of an environment on the system. The representation of the process tensor in a tensor network form allows for an exact yet highly efficient description of non-Markovian OQS (NM-OQS). The OQuPy package provides methods to (1) compute the dynamics and multi-time correlations of quantum systems coupled to single and multiple environments, (2) optimize control protocols for NM-OQS, (3) simulate interacting chains of NM-OQS, and (4) compute the mean-field dynamics of an ensemble of NM-OQS coupled to a common central system. Our aim is to provide an easily accessible and extensible tool for researchers of OQS in fields such as quantum chemistry, quantum sensing, and quantum information
OQuPy : a Python package to efficiently simulate non-Markovian open quantum systems with process tensors
Non-Markovian dynamics arising from the strong coupling of a system to a structured environment is essential in many applications of quantum mechanics and emerging technologies. Deriving an accurate description of general quantum dynamics including memory effects is however a demanding task, prohibitive to standard analytical or direct numerical approaches. We present a major release of our open source software package, OQuPy (Open Quantum System in Python), which provides several recently developed numerical methods that address this challenging task. It utilizes the process tensor approach to open quantum systems in which a single map, the process tensor, captures all possible effects of an environment on the system. The representation of the process tensor in a tensor network form allows an exact yet highly efficient description of non-Markovian open quantum systems (NM-OQS). The OQuPy package provides methods to (1) compute the dynamics and multi-time correlations of quantum systems coupled to single and multiple environments, (2) optimize control protocols for NM-OQS, (3) simulate interacting chains of NM-OQS, and (4) compute the mean-field dynamics of an ensemble of NM-OQS coupled to a common central system. Our aim is to provide an easily accessible and extensible tool for researchers of open quantum systems in fields such as quantum chemistry, quantum sensing, and quantum information
The common marmoset genome provides insight into primate biology and evolution
We report the whole-genome sequence of the common marmoset (Callithrix jacchus). The 2.26-Gb genome of a female marmoset was assembled using Sanger read data (6×) and a whole-genome shotgun strategy. A first analysis has permitted comparison with the genomes of apes and Old World monkeys and the identification of specific features that might contribute to the unique biology of this diminutive primate, including genetic changes that may influence body size, frequent twinning and chimerism. We observed positive selection in growth hormone/insulin-like growth factor genes (growth pathways), respiratory complex I genes (metabolic pathways), and genes encoding immunobiological factors and proteases (reproductive and immunity pathways). In addition, both protein-coding and microRNA genes related to reproduction exhibited evidence of rapid sequence evolution. This genome sequence for a New World monkey enables increased power for comparative analyses among available primate genomes and facilitates biomedical research application. © 2014 Nature America, Inc
Comparative and demographic analysis of orang-utan genomes
Orang-utan- is derived from a Malay term meaning man of the forest- and aptly describes the southeast Asian great apes native to Sumatra and Borneo. The orang-utan species, Pongo abelii (Sumatran) and Pongo pygmaeus (Bornean), are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution. Here we present a Sumatran orang-utan draft genome assembly and short read sequence data from five Sumatran and five Bornean orang-utan genomes. Our analyses reveal that, compared to other primates, the orang-utan genome has many unique features. Structural evolution of the orang-utan genome has proceeded much more slowly than other great apes, evidenced by fewer rearrangements, less segmental duplication, a lower rate of gene family turnover and surprisingly quiescent Alu repeats, which have played a major role in restructuring other primate genomes. We also describe a primate polymorphic neocentromere, found in both Pongo species, emphasizing the gradual evolution of orang-utan genome structure. Orang-utans have extremely low energy usage for a eutherian mammal, far lower than their hominid relatives. Adding their genome to the repertoire of sequenced primates illuminates new signals of positive selection in several pathways including glycolipid metabolism. From the population perspective, both Pongo species are deeply diverse; however, Sumatran individuals possess greater diversity than their Bornean counterparts, and more species-specific variation. Our estimate of Bornean/Sumatran speciation time, 400,000years ago, is more recent than most previous studies and underscores the complexity of the orang-utan speciation process. Despite a smaller modern census population size, the Sumatran effective population size (N e) expanded exponentially relative to the ancestral N e after the split, while Bornean N e declined over the same period. Overall, the resources and analyses presented here offer new opportunities in evolutionary genomics, insights into hominid biology, and an extensive database of variation for conservation efforts. © 2011 Macmillan Publishers Limited. All rights reserved
The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe
The preponderance of matter over antimatter in the early Universe, the
dynamics of the supernova bursts that produced the heavy elements necessary for
life and whether protons eventually decay --- these mysteries at the forefront
of particle physics and astrophysics are key to understanding the early
evolution of our Universe, its current state and its eventual fate. The
Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed
plan for a world-class experiment dedicated to addressing these questions. LBNE
is conceived around three central components: (1) a new, high-intensity
neutrino source generated from a megawatt-class proton accelerator at Fermi
National Accelerator Laboratory, (2) a near neutrino detector just downstream
of the source, and (3) a massive liquid argon time-projection chamber deployed
as a far detector deep underground at the Sanford Underground Research
Facility. This facility, located at the site of the former Homestake Mine in
Lead, South Dakota, is approximately 1,300 km from the neutrino source at
Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino
charge-parity symmetry violation and mass ordering effects. This ambitious yet
cost-effective design incorporates scalability and flexibility and can
accommodate a variety of upgrades and contributions. With its exceptional
combination of experimental configuration, technical capabilities, and
potential for transformative discoveries, LBNE promises to be a vital facility
for the field of particle physics worldwide, providing physicists from around
the globe with opportunities to collaborate in a twenty to thirty year program
of exciting science. In this document we provide a comprehensive overview of
LBNE's scientific objectives, its place in the landscape of neutrino physics
worldwide, the technologies it will incorporate and the capabilities it will
possess.Comment: Major update of previous version. This is the reference document for
LBNE science program and current status. Chapters 1, 3, and 9 provide a
comprehensive overview of LBNE's scientific objectives, its place in the
landscape of neutrino physics worldwide, the technologies it will incorporate
and the capabilities it will possess. 288 pages, 116 figure
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