Entrainment of randomly coupled oscillator networks by a pacemaker

Entrainment by a pacemaker, representing an element with a higher frequency, is numerically investigated for several classes of random networks which consist of identical phase oscillators. We find that the entrainment frequency window of a network decreases exponentially with its depth, defined as the mean forward distance of the elements from the pacemaker. Effectively, only shallow networks can thus exhibit frequency-locking to the pacemaker. The exponential dependence is also derived analytically as an approximation for large random asymmetric networks.Comment: 4 pages, 3 figures, revtex 4, submitted to Phys. Rev. Let

Generation of finite wave trains in excitable media

Spatiotemporal control of excitable media is of paramount importance in the development of new applications, ranging from biology to physics. To this end we identify and describe a qualitative property of excitable media that enables us to generate a sequence of traveling pulses of any desired length, using a one-time initial stimulus. The wave trains are produced by a transient pacemaker generated by a one-time suitably tailored spatially localized finite amplitude stimulus, and belong to a family of fast pulse trains. A second family, of slow pulse trains, is also present. The latter are created through a clumping instability of a traveling wave state (in an excitable regime) and are inaccessible to single localized stimuli of the type we use. The results indicate that the presence of a large multiplicity of stable, accessible, multi-pulse states is a general property of simple models of excitable media.Comment: 6 pages, 6 figure

Thermodynamic Behavior of a Model Covalent Material Described by the Environment-Dependent Interatomic Potential

Using molecular dynamics simulations we study the thermodynamic behavior of a single-component covalent material described by the recently proposed Environment-Dependent Interatomic Potential (EDIP). The parameterization of EDIP for silicon exhibits a range of unusual properties typically found in more complex materials, such as the existence of two structurally distinct disordered phases, a density decrease upon melting of the low-temperature amorphous phase, and negative thermal expansion coefficients for both the crystal (at high temperatures) and the amorphous phase (at all temperatures). Structural differences between the two disordered phases also lead to a first-order transition between them, which suggests the existence of a second critical point, as is believed to exist for amorphous forms of frozen water. For EDIP-Si, however, the unusual behavior is associated not only with the open nature of tetrahedral bonding but also with a competition between four-fold (covalent) and five-fold (metallic) coordination. The unusual behavior of the model and its unique ability to simulation the liquid/amorphous transition on molecular-dynamics time scales make it a suitable prototype for fundamental studies of anomalous thermodynamics in disordeered systems.Comment: 48 pages (double-spaced), 13 figure

Large Scale Electronic Structure Calculations with Multigrid Acceleration

We have developed a set of techniques for performing large scale ab initio calculations using multigrid accelerations and a real-space grid as a basis. The multigrid methods permit efficient calculations on ill-conditioned systems with long length scales or high energy cutoffs. The technique has been applied to systems containing up to 100 atoms, including a highly elongated diamond cell, an isolated C$_{60}$ molecule, and a 32-atom cell of GaN with the Ga d-states in valence. The method is well suited for implementation on both vector and massively parallel architectures.Comment: 4 pages, 1 postscript figur

FAD binding, cobinamide binding and active site communication in the corrin reductase (CobR)

Adenosylcobalamin, the coenzyme form of vitamin B12, is one Nature's most complex coenzyme whose de novo biogenesis proceeds along either an anaerobic or aerobic metabolic pathway. The aerobic synthesis involves reduction of the centrally chelated cobalt metal ion of the corrin ring from Co(II) to Co(I) before adenosylation can take place. A corrin reductase (CobR) enzyme has been identified as the likely agent to catalyse this reduction of the metal ion. Herein, we reveal how Brucella melitensis CobR binds its coenzyme FAD (flavin dinucleotide) and we also show that the enzyme can bind a corrin substrate consistent with its role in reduction of the cobalt of the corrin ring. Stopped-flow kinetics and EPR reveal a mechanistic asymmetry in CobR dimer that provides a potential link between the two electron reduction by NADH to the single electron reduction of Co(II) to Co(I)

Seedling development traits in Brassica napus examined by gene expression analysis and association mapping

BACKGROUND: An optimal seedling development of Brassica napus plants leads to a higher yield stability even under suboptimal growing conditions and has therefore a high importance for plant breeders. The objectives of our study were to (i) examine the expression levels of candidate genes in seedling leaves of B. napus and correlate these with seedling development as well as (ii) detect genome regions associated with gene expression levels and seedling development traits in B. napus by genome-wide association mapping. RESULTS: The expression levels of the 15 candidate genes examined in the 509 B. napus inbreds showed an averaged standard deviation of 5.6 across all inbreds and ranged from 3.2 to 8.8. The gene expression differences between the 509 B. napus inbreds were more than adequate for the correlation with phenotypic variation of seedling development. The average of the absolute value correlations of the correlation coefficients of 0.11 were observed with a range from 0.00 to 0.39. The candidate genes GER1, AILP1, PECT, and FBP were strongly correlated with the seedling development traits. In a genome-wide association study, we detected a total of 63 associations between single nucleotide polymorphisms (SNPs) and the seedling development traits and 31 SNP-gene associations for the candidate genes with a P-value < 0.0001. For the projected leaf area traits we identified five different association hot spots on the chromosomes A2, A7, C3, C6, and C7. CONCLUSION: A total of 99.4% of the adjacent SNPs on the A genome and 93.0% of the adjacent SNPs on the C genome had a distance smaller than the average range of linkage disequilibrium. Therefore, this genome-wide association study is expected to result on average in 14.7% of the possible power. Compared to previous studies in B. napus, the SNP marker density of our study is expected to provide a higher power to detect SNP-trait/-gene associations in the B. napus diversity set. The large number of associations detected for the examined 14 seedling development traits indicated that these are genetically complex inherited. The results of our analyses suggested that the studied genes ribulose 1,5-bisphosphate carboxylase/oxygenase small subunit (RBC) on the chromosomes A4 and C4 and fructose-1,6-bisphosphatase precursor (FBP) on the chromosomes A9 and C8 are cis-regulated. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12870-015-0496-3) contains supplementary material, which is available to authorized users

Reply to Comment on “The earthquakes of 29 July 2003, 12 February 2007, and 17 December 2009 in the region of Cape Saint Vincent (SW Iberia) and their relation with the 1755 Lisbon earthquake

Indeed, the Lisbon earthquake is a very unusual seismic event and an exception to the rule because most great tsunami-generating earth- quakes are related to well-defined subduction zones. The epicentral region, focal mechanism and the structures involved at the origin of this earthquake are still a matter of debate, with several models having been proposed (e.g. Baptista et al., 2003; Grandin et al., 2007a,b; Gutscher et al., 2006; Ribeiro et al., 2006; Vilanova et al., 2003; Zitellini et al., 2001)

Water Chemisorption and Reconstruction of the MgO Surface

The observed reactivity of MgO with water is in apparent conflict with theoretical calculations which show that molecular dissociation does not occur on a perfect (001) surface. We have performed ab-initio total energy calculations which show that a chemisorption reaction involving a reconstruction to form a (111) hydroxyl surface is strongly preferred with Delta E = -90.2kJ/mol. We conclude that protonation stabilizes the otherwise unstable (111) surface and that this, not the bare (001), is the most stable surface of MgO under ambient conditions.Comment: RevTeX, 4 pages, 1 Encapsulated Postscript Figur

The Relationship Between Belief and Credence

Sometimes epistemologists theorize about belief, a tripartite attitude on which one can believe, withhold belief, or disbelieve a proposition. In other cases, epistemologists theorize about credence, a fine-grained attitude that represents one’s subjective probability or confidence level toward a proposition. How do these two attitudes relate to each other? This article explores the relationship between belief and credence in two categories: descriptive and normative. It then explains the broader significance of the belief-credence connection and concludes with general lessons from the debate thus far

Biofilm-inhibiting effect and anti-infective activity of N,C-linked aryl isoquinolines and the use thereof

Anti-infective and biofilm-inhibiting activities of aryl isoquinoline-derivatives of the general formulae 1 to 3 Figure US08173673-20120508-C00001 are described