Network growth models and genetic regulatory networks

We study a class of growth algorithms for directed graphs that are candidate models for the evolution of genetic regulatory networks. The algorithms involve partial duplication of nodes and their links, together with innovation of new links, allowing for the possibility that input and output links from a newly created node may have different probabilities of survival. We find some counterintuitive trends as parameters are varied, including the broadening of indegree distribution when the probability for retaining input links is decreased. We also find that both the scaling of transcription factors with genome size and the measured degree distributions for genes in yeast can be reproduced by the growth algorithm if and only if a special seed is used to initiate the process.Comment: 8 pages with 7 eps figures; uses revtex4. Added references, cleaner figure

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

Scaling property of the critical hopping parameters for the Bose-Hubbard model

Recently precise results for the boundary between the Mott insulator phase and the superfluid phase of the homogeneous Bose-Hubbard model have become available for arbitrary integer filling factor g and any lattice dimension d > 1. We use these data for demonstrating that the critical hopping parameters obey a scaling relationship which allows one to map results for different g onto each other. Unexpectedly, the mean-field result captures the dependence of the exact critical parameters on the filling factor almost fully. We also present an approximation formula which describes the critical parameters for d > 1 and any g with high accuracy.Comment: 5 pages, 5 figures. to appear in EPJ

Strong coupling expansion for the Bose-Hubbard and the Jaynes-Cummings lattice model

A strong coupling expansion, based on the Kato-Bloch perturbation theory, which has recently been proposed by Eckardt et al. [Phys. Rev. B 79, 195131] and Teichmann et al. [Phys. Rev. B 79, 224515] is implemented in order to study various aspects of the Bose-Hubbard and the Jaynes-Cummings lattice model. The approach, which allows to generate numerically all diagrams up to a desired order in the interaction strength is generalized for disordered systems and for the Jaynes-Cummings lattice model. Results for the Bose-Hubbard and the Jaynes-Cummings lattice model will be presented and compared with results from VCA and DMRG. Our focus will be on the Mott insulator to superfluid transition.Comment: 29 pages, 21 figure

Experimental Study of the BEC-BCS Crossover Region in Lithium 6

We report Bose-Einstein condensation of weakly bound $^6$Li$_2$molecules in a crossed optical trap near a Feshbach resonance. We measure a molecule-molecule scattering length of$170^{+100}_{-60}$ nm at 770 G, in good agreement with theory.We study the expansion of the cloud in the BEC-BCS crossoverregion.Comment: 4 pages, 3 figures, submitted to PR

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

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

A multi-model climate response over tropical Africa at +2 °C

The impact of a +2 °C global warming on temperature and precipitation over tropical Africa is examined, based on an ensemble of 12 regional climate model scenario simulations. These 12 scenarios are re-phased so that they all correspond to the same global warming of 2 °C with respect to pre-industrial conditions. The continental temperature increase is above the global average. If heat waves are defined with the same temperature threshold in the reference climate and in the scenario, their frequency increases by a factor of 10. When the temperature threshold is adapted to future conditions, there is still a slight increase in frequency. The average precipitation does not show a significant response, due to model-to-model spread. However two compensating phenomena occur, which are robust among the models: (a) the number of rain days decreases whereas the precipitation intensity increases, and (b) the rain season occurs later during the year with less precipitation in early summer and more precipitation in late summer. Simulated daily temperature and precipitation data are combined in two impact models, one for the hydrology of the Nile and Niger basins, one for the food security of the different countries. They show that the main feature of the climate change is not a continuous trend signal, but an alternation of dry and wet decadal to multidecadal episodes

The hRPC62 subunit of human RNA polymerase III displays helicase activity.

In Eukaryotes, tRNAs, 5S RNA and U6 RNA are transcribed by RNA polymerase (Pol) III. Human Pol III is composed of 17 subunits. Three specific Pol III subunits form a stable ternary subcomplex (RPC62-RPC39-RPC32α/β) being involved in pre-initiation complex formation. No paralogues for subunits of this subcomplex subunits have been found in Pols I or II, but hRPC62 was shown to be structurally related to the general Pol II transcription factor hTFIIEα. Here we show that these structural homologies extend to functional similarities. hRPC62 as well as hTFIIEα possess intrinsic ATP-dependent 3'-5' DNA unwinding activity. The ATPase activities of both proteins are stimulated by single-stranded DNA. Moreover, the eWH domain of hTFIIEα can replace the first eWH (eWH1) domain of hRPC62 in ATPase and DNA unwinding assays. Our results identify intrinsic enzymatic activities in hRPC62 and hTFIIEα

Inhibitory Control Over Ca2+ Sparks via Mechanosensitive Channels Is Disrupted in Dystrophin Deficient Muscle but Restored by Mini-Dystrophin Expression

Background: In dystrophic skeletal muscle, osmotic stimuli somehow relieve inhibitory control of dihydropyridine receptors (DHPR) on spontaneous sarcoplasmic reticulum elementary Ca release events (ECRE) in high Ca external environments. Such 'uncontrolled' Ca sparks were suggested to act as dystrophic signals. They may be related to mechanosensitive pathways but the mechanisms are elusive. Also, it is not known whether truncated dystrophins can correct the dystrophic disinhibition. Methodology/Principal Findings: We recorded ECRE activity in single intact fibers from adult wt, mdx and mini-dystrophin expressing mice (MinD) under resting isotonic conditions and following hyper-/ hypo-osmolar external shock using confocal microscopy and imaging techniques. Isotonic ECRE frequencies were small in wt and MinD fibers, but were markedly increased in mdx fibers. Osmotic challenge dramatically increased ECRE activity in mdx fibers. Sustained osmotic challenge induced marked exponential ECRE activity adaptation that was three times faster in mdx compared to wt and MinD fibers. Rising external Ca concentrations amplified osmotic ECRE responses. The eliminated ECRE suppression in intact osmotically stressed mdx fibers was completely and reversibly resuscitated by streptomycine (200 μM), spider peptide GsMTx-4 (5 μM) and Gd (20 μM) that block unspecific, specific cationic and Ca selective mechanosensitive channels (MsC), respectively. ECRE morphology was not substantially altered by membrane stress. During hyperosmotic challenge, membrane potentials were polarised and a putative depolarisation through aberrant MsC negligible excluding direct activation of ECRE through tubular depolarisation. Conclusions/Significance: Dystrophin suppresses spontaneous ECRE activity by control of mechanosensitive pathways which are suggested to interact with the inhibitory DHPR loop to the ryanodine receptor. MsC-related disinhibition prevails in dystrophic muscle and can be resuscitated by transgenic mini-dystrophin expression. Our results have important implications for the pathophysiology of DMD where abnormal MsC in dystrophic muscle confer disruption of microdomain Ca homeostasis. MsC blockers should have considerable therapeutic potential if more muscle specific compounds can be found