1,028 research outputs found
Coherently controlled entanglement generation in a binary Bose-Einstein condensate
Considering a two-component Bose-Einstein condensate in a double-well
potential, a method to generate a Bell state consisting of two spatially
separated condensates is suggested. For repulsive interactions, the required
tunnelling control is achieved numerically by varying the amplitude of a
sinusoidal potential difference between the wells. Both numerical and
analytical calculations reveal the emergence of a highly entangled mesoscopic
state.Comment: 6 pages, 6 figures, epl2.cl
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Protein domain organisation: adding order.
BACKGROUND: Domains are the building blocks of proteins. During evolution, they have been duplicated, fused and recombined, to produce proteins with novel structures and functions. Structural and genome-scale studies have shown that pairs or groups of domains observed together in a protein are almost always found in only one N to C terminal order and are the result of a single recombination event that has been propagated by duplication of the multi-domain unit. Previous studies of domain organisation have used graph theory to represent the co-occurrence of domains within proteins. We build on this approach by adding directionality to the graphs and connecting nodes based on their relative order in the protein. Most of the time, the linear order of domains is conserved. However, using the directed graph representation we have identified non-linear features of domain organization that are over-represented in genomes. Recognising these patterns and unravelling how they have arisen may allow us to understand the functional relationships between domains and understand how the protein repertoire has evolved. RESULTS: We identify groups of domains that are not linearly conserved, but instead have been shuffled during evolution so that they occur in multiple different orders. We consider 192 genomes across all three kingdoms of life and use domain and protein annotation to understand their functional significance. To identify these features and assess their statistical significance, we represent the linear order of domains in proteins as a directed graph and apply graph theoretical methods. We describe two higher-order patterns of domain organisation: clusters and bi-directionally associated domain pairs and explore their functional importance and phylogenetic conservation. CONCLUSION: Taking into account the order of domains, we have derived a novel picture of global protein organization. We found that all genomes have a higher than expected degree of clustering and more domain pairs in forward and reverse orientation in different proteins relative to random graphs with identical degree distributions. While these features were statistically over-represented, they are still fairly rare. Looking in detail at the proteins involved, we found strong functional relationships within each cluster. In addition, the domains tended to be involved in protein-protein interaction and are able to function as independent structural units. A particularly striking example was the human Jak-STAT signalling pathway which makes use of a set of domains in a range of orders and orientations to provide nuanced signaling functionality. This illustrated the importance of functional and structural constraints (or lack thereof) on domain organisation.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are
Collective Oscillations of an Imbalanced Fermi Gas: Axial Compression Modes and Polaron Effective Mass
We investigate the low-lying compression modes of a unitary Fermi gas with
imbalanced spin populations. For low polarization, the strong coupling between
the two spin components leads to a hydrodynamic behavior of the cloud. For
large population imbalance we observe a decoupling of the oscillations of the
two spin components, giving access to the effective mass of the Fermi polaron,
a quasi-particle composed of an impurity dressed by particle-hole pair
excitations in a surrounding Fermi sea. We find , in agreement
with the most recent theoretical predictions.Comment: 4 pages, 4 figures, submitted to PR
Expansion of a lithium gas in the BEC-BCS crossover
We report on experiments in Li Fermi gases near Feshbach resonances. A
broad s-wave resonance is used to form a Bose-Einstein condensate of weakly
bound Li molecules in a crossed optical trap. The measured
molecule-molecule scattering length of nm at 770 G is found
in good agreement with theory. The expansion energy of the cloud in the BEC-BCS
crossover region is measured. Finally we discuss the properties of p-wave
Feshbach resonances observed near 200 Gauss and new s-wave resonances in the
heteronuclear Li- Li mixture.Comment: 10 pages, 3 figures, Proceedings of ICAP 200
Unsteady Aerodynamic Analysis of a Bird-Damaged Turbofan
Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/106438/1/AIAA2013-1773.pd
Bose-Einstein condensates in a double well: mean-field chaos and multi-particle entanglement
A recent publication [Phys. Rev. Lett. 100, 140408 (2008)] shows that there
is a relation between mean-field chaos and multi-particle entanglement for BECs
in a periodically shaken double well. 'Schrodinger-cat' like mesoscopic
superpositions in phase-space occur for conditions for which the system
displays mean-field chaos. In the present manuscript, more general
highly-entangled states are investigated. Mean-field chaos accelerates the
emergence of multi-particle entanglement; the boundaries of stable regions are
particularly suited for entanglement generation.Comment: 5 Pages, 5 jpg-figures, to be published in the proceedings of the
LPHYS0
DBD: a transcription factor prediction database.
Regulation of gene expression influences almost all biological processes in an organism; sequence-specific DNA-binding transcription factors are critical to this control. For most genomes, the repertoire of transcription factors is only partially known. Hitherto transcription factor identification has been largely based on genome annotation pipelines that use pairwise sequence comparisons, which detect only those factors similar to known genes, or on functional classification schemes that amalgamate many types of proteins into the category of 'transcription factor'. Using a novel transcription factor identification method, the DBD transcription factor database fills this void, providing genome-wide transcription factor predictions for organisms from across the tree of life. The prediction method behind DBD identifies sequence-specific DNA-binding transcription factors through homology using profile hidden Markov models (HMMs) of domains. Thus, it is limited to factors that are homologus to those HMMs. The collection of HMMs is taken from two existing databases (Pfam and SUPERFAMILY), and is limited to models that exclusively detect transcription factors that specifically recognize DNA sequences. It does not include basal transcription factors or chromatin-associated proteins, for instance. Based on comparison with experimentally verified annotation, the prediction procedure is between 95% and 99% accurate. Between one quarter and one-half of our genome-wide predicted transcription factors represent previously uncharacterized proteins. The DBD (www.transcriptionfactor.org) consists of predicted transcription factor repertoires for 150 completely sequenced genomes, their domain assignments and the hand curated list of DNA-binding domain HMMs. Users can browse, search or download the predictions by genome, domain family or sequence identifier, view families of transcription factors based on domain architecture and receive predictions for a protein sequence
Case study for the assessment of the biogeophysical effects of a potential afforestation in Europe
BACKGROUND: A regional-scale sensitivity study has been carried out to investigate the climatic effects of forest cover change in Europe. Applying REMO (regional climate model of the Max Planck Institute for Meteorology), the projected temperature and precipitation tendencies have been analysed for summer, based on the results of the A2 IPCC-SRES emission scenario simulation. For the end of the 21st century it has been studied, whether the assumed forest cover increase could reduce the effects of the greenhouse gas concentration change.
RESULTS: Based on the simulation results, biogeophysical effects of the hypothetic potential afforestation may lead to cooler and moister conditions during summer in most parts of the temperate zone. The largest relative effects of forest cover increase can be expected in northern Germany, Poland and Ukraine, which is 15-20% of the climate change signal for temperature and more than 50% for precipitation. In northern Germany and France, potential afforestation may enhance the effects of emission change, resulting in more severe heavy precipitation events. The probability of dry days and warm temperature extremes would decrease.
CONCLUSIONS: Large contiguous forest blocks can have distinctive biogeophysical effect on the climate on regional and local scale. In certain regions of the temperate zone, climate change signal due to greenhouse gas emission can be reduced by afforestation due to the dominant evaporative cooling effect during summer. Results of this case study with a hypothetical land cover change can contribute to the assessment of the role of forests in adapting to climate change. Thus they can build an important basis of the future forest policy
Axonopathy in the central nervous system is the hallmark of mice with a novel intragenic null mutation of dystonin.
Dystonia musculorum is a neurodegenerative disorder caused by a mutation in the dystonin gene. It has been described in mice and humans where it is called hereditary sensory autonomic neuropathy. Mutated mice show severe movement disorders and die at the age of 3-4 weeks. This study describes the discovery and molecular, clinical, as well as pathological characterization of a new spontaneously occurring mutation in the dystonin gene in C57BL/6N mice. The mutation represents a 40-kb intragenic deletion allele of the dystonin gene on chromosome 1 with exactly defined deletion borders. It was demonstrated by Western blot, mass spectrometry, and immunohistology that mice with a homozygous mutation were entirely devoid of the dystonin protein. Pathomorphological lesions were restricted to the brain stem and spinal cord and consisted of swollen, argyrophilic axons and dilated myelin sheaths in the white matter and, less frequently, total chromatolysis of neurons in the gray matter. Axonal damage was detected by amyloid precursor protein and nonphosphorylated neurofilament immunohistology. Axonopathy in the central nervous system (CNS) represents the hallmark of this disease. Mice with the dystonin mutation also showed suppurative inflammation in the respiratory tract, presumably due to brain stem lesion-associated food aspiration, whereas skeletal muscles showed no pathomorphological changes. This study describes a novel mutation in the dystonin gene in mice leading to axonopathy in the CNS. In further studies, this model may provide new insights into the pathogenesis of neurodegenerative diseases and may elucidate the complex interactions of dystonin with various other cellular proteins especially in the CNS
Visualizing the emergence of the pseudogap state and the evolution to superconductivity in a lightly hole-doped Mott insulator
Superconductivity emerges from the cuprate antiferromagnetic Mott state with
hole doping. The resulting electronic structure is not understood, although
changes in the state of oxygen atoms appear paramount. Hole doping first
destroys the Mott state yielding a weak insulator where electrons localize only
at low temperatures without a full energy gap. At higher doping, the
'pseudogap', a weakly conducting state with an anisotropic energy gap and
intra-unit-cell breaking of 90\degree-rotational (C4v) symmetry appears.
However, a direct visualization of the emergence of these phenomena with
increasing hole density has never been achieved. Here we report atomic-scale
imaging of electronic structure evolution from the weak-insulator through the
emergence of the pseudogap to the superconducting state in Ca2-xNaxCuO2Cl2. The
spectral signature of the pseudogap emerges at lowest doping from a weakly
insulating but C4v-symmetric matrix exhibiting a distinct spectral shape. At
slightly higher hole-density, nanoscale regions exhibiting pseudogap spectra
and 180\degree-rotational (C2v) symmetry form unidirectional clusters within
the C4v-symmetric matrix. Thus, hole-doping proceeds by the appearance of
nanoscale clusters of localized holes within which the broken-symmetry
pseudogap state is stabilized. A fundamentally two-component electronic
structure11 then exists in Ca2-xNaxCuO2Cl2 until the C2v-symmetric clusters
touch at higher doping, and the long-range superconductivity appears.Comment: See the Nature Physics website for the published version available at
http://dx.doi.org/10.1038/Nphys232
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