Spectral Analysis of Protein-Protein Interactions in Drosophila melanogaster

Within a case study on the protein-protein interaction network (PIN) of Drosophila melanogaster we investigate the relation between the network's spectral properties and its structural features such as the prevalence of specific subgraphs or duplicate nodes as a result of its evolutionary history. The discrete part of the spectral density shows fingerprints of the PIN's topological features including a preference for loop structures. Duplicate nodes are another prominent feature of PINs and we discuss their representation in the PIN's spectrum as well as their biological implications.Comment: 9 pages RevTeX including 8 figure

Some Exact Results on the Potts Model Partition Function in a Magnetic Field

We consider the Potts model in a magnetic field on an arbitrary graph $G$. Using a formula of F. Y. Wu for the partition function $Z$ of this model as a sum over spanning subgraphs of $G$, we prove some properties of $Z$ concerning factorization, monotonicity, and zeros. A generalization of the Tutte polynomial is presented that corresponds to this partition function. In this context we formulate and discuss two weighted graph-coloring problems. We also give a general structural result for $Z$ for cyclic strip graphs.Comment: 5 pages, late

MERLIN/VLA imaging of the gravitational lens system B0218+357

Gravitational lenses offer the possibility of accurately determining the Hubble parameter (H_0) over cosmological distances, and B0218+357 is one of the most promising systems for an application of this technique. In particular this system has an accurately measured time delay (10.5+/-0.4 d; Biggs et al. 1999) and preliminary mass modelling has given a value for H_0 of 69 +13/-19 km/s/Mpc. The error on this estimate is now dominated by the uncertainty in the mass modelling. As this system contains an Einstein ring it should be possible to constrain the model better by imaging the ring at high resolution. To achieve this we have combined data from MERLIN and the VLA at a frequency of 5 GHz. In particular MERLIN has been used in multi-frequency mode in order to improve substantially the aperture coverage of the combined data set. The resulting map is the best that has been made of the ring and contains many new and interesting features. Efforts are currently underway to exploit the new data for lensing constraints using the LensClean algorithm (Kochanek & Narayan 1992).Comment: Accepted for publication in MNRAS. 6 pages, 4 included PostScript figure

Thermal X-rays from Millisecond Pulsars: Constraining the Fundamental Properties of Neutron Stars

Abridged) We model the X-ray properties of millisecond pulsars (MSPs) by considering hot spot emission from a weakly magnetized rotating neutron star (NS) covered by an optically-thick hydrogen atmosphere. We investigate the limitations of using the thermal X-ray pulse profiles of MSPs to constrain the mass-to-radius ($M/R$) ratio of the underlying NS. The accuracy is strongly dependent on the viewing angle and magnetic inclination. For certain systems, the accuracy is ultimately limited only by photon statistics implying that future X-ray observatories could, in principle, achieve constraints on $M/R$ and hence the NS equation of state to better than $\sim$5%. We demonstrate that valuable information regarding the basic properties of the NS can be extracted even from X-ray data of fairly limited photon statistics through modeling of archival spectroscopic and timing observations of the nearby isolated PSRs J0030+0451 and J2124--3358. The X-ray emission from these pulsars is consistent with the presence of a hydrogen atmosphere and a dipolar magnetic field configuration, in agreement with previous findings for PSR J0437--4715. For both MSPs, the favorable geometry allows us to place interesting limits on the allowed $M/R$ of NSs. Assuming 1.4 M$_{\odot}$, the stellar radius is constrained to be $R > 9.4$ km and $R > 7.8$ km (68% confidence) for PSRs J0030+0451 and J2124--3358, respectively. We explore the prospects of using future observatories such as \textit{Constellation-X} and \textit{XEUS} to conduct blind X-ray timing searches for MSPs not detectable at radio wavelengths due to unfavorable viewing geometry. Using the observational constraints on the pulsar obliquities we are also able to place strong constraints on the magnetic field evolution model proposed by Ruderman.Comment: 9 pages, 7 figures, published in the Astrophysical Journal (Volume 689, Issue 1, pp. 407-415

What is the probability of connecting two points ?

The two-terminal reliability, known as the pair connectedness or connectivity function in percolation theory, may actually be expressed as a product of transfer matrices in which the probability of operation of each link and site is exactly taken into account. When link and site probabilities are $p$ and $\rho$, it obeys an asymptotic power-law behavior, for which the scaling factor is the transfer matrix's eigenvalue of largest modulus. The location of the complex zeros of the two-terminal reliability polynomial exhibits structural transitions as $0 \leq \rho \leq 1$.Comment: a few critical polynomials are at the end of the .tex source fil

Properties of dense partially random graphs

We study the properties of random graphs where for each vertex a {\it neighbourhood} has been previously defined. The probability of an edge joining two vertices depends on whether the vertices are neighbours or not, as happens in Small World Graphs (SWGs). But we consider the case where the average degree of each node is of order of the size of the graph (unlike SWGs, which are sparse). This allows us to calculate the mean distance and clustering, that are qualitatively similar (although not in such a dramatic scale range) to the case of SWGs. We also obtain analytically the distribution of eigenvalues of the corresponding adjacency matrices. This distribution is discrete for large eigenvalues and continuous for small eigenvalues. The continuous part of the distribution follows a semicircle law, whose width is proportional to the "disorder" of the graph, whereas the discrete part is simply a rescaling of the spectrum of the substrate. We apply our results to the calculation of the mixing rate and the synchronizability threshold.Comment: 14 pages. To be published in Physical Review

Identification of climatological sub-regions within the Tully mill area

Identifying optimal nitrogen application rates that reduce nitrogen loss without adversely reducing yields would benefit growers and the environment. In order to identify optimal nitrogen application rates throughout the Tully mill area, it is important to identify sub-regions that share similar topographical, soil, farm management, productivity or climatological attributes. While current SIX EASY STEPS nitrogen guidelines enable a hierarchy of district, soil, block and crop nitrogen requirements for sugarcane, it would be beneficial for management zones to also take spatial climate variability information into account. Unfortunately, spatial climate variability within a region, is generally not considered when developing nitrogen management practices. The objective of this paper was to identify sub-regions within the Tully mill area based on climatological attributes as a first step towards better informing nitrogen management decisions. Rainfall, radiation and temperature data were obtained on a 0.05 by 0.05˚ grid (approximately 5 km by 5 km) for sugarcane-growing areas within the Tully Mill region. A K-means clustering algorithm was then used to cluster these grid cells into distinct sub-regions based on seasonal or annual climate data. Two distinct sub-regions were identified based on total annual rainfall and annual average daily radiation data. These sub-regions were identified as a northern and southern sub-region, divided roughly along the Tully River. The northern sub-region was characterised by lower radiation, lower temperatures and higher rainfall than the southern sub-region. Crop simulation models will now be able to use this knowledge to assess if nitrogen management plans should vary between the two sub-regions in Tully

XMM-Newton Observations of Radio Pulsars B0834+06 and B0826-34 and Implications for Pulsar Inner Accelerator

We report the X-ray observations of two radio pulsars with drifting subpulses: B0834 + 06 and B0826 - 34 using \xmm\. PSR B0834 + 06 was detected with a total of 70 counts from the three EPIC instruments over 50 ks exposure time. Its spectrum was best described as that of a blackbody (BB) with temperature $T_s=(2.0^{+2.0}_{-0.9}) \times 10^6$ K and bolometric luminosity of $L_b=(8.6^{+14.2}_{-4.4}) \times 10^{28}$ erg s$^{-1}$. As it is typical in pulsars with BB thermal components in their X-ray spectra, the hot spot surface area is much smaller than that of the canonical polar cap, implying a non-dipolar surface magnetic field much stronger than the dipolar component derived from the pulsar spin-down (in this case about 50 times smaller and stronger, respectively). The second pulsar PSR B0826 - 34 was not detected over 50 ks exposure time, giving an upper limit for the bolometric luminosity $L_b \leq 1.4 \times 10^{29}$ erg s$^{-1}$. We use these data as well as the radio emission data concerned with drifting subpulses to test the Partially Screened Gap (PSG) model of the inner accelerator in pulsars.Comment: Accepted for publication by The Astrophysical Journa

Ground State Entropy of Potts Antiferromagnets: Bounds, Series, and Monte Carlo Measurements

We report several results concerning $W(\Lambda,q)=\exp(S_0/k_B)$, the exponent of the ground state entropy of the Potts antiferromagnet on a lattice $\Lambda$. First, we improve our previous rigorous lower bound on $W(hc,q)$ for the honeycomb (hc) lattice and find that it is extremely accurate; it agrees to the first eleven terms with the large-$q$ series for $W(hc,q)$. Second, we investigate the heteropolygonal Archimedean $4 \cdot 8^2$ lattice, derive a rigorous lower bound, on $W(4 \cdot 8^2,q)$, and calculate the large-$q$ series for this function to $O(y^{12})$ where $y=1/(q-1)$. Remarkably, these agree exactly to all thirteen terms calculated. We also report Monte Carlo measurements, and find that these are very close to our lower bound and series. Third, we study the effect of non-nearest-neighbor couplings, focusing on the square lattice with next-nearest-neighbor bonds.Comment: 13 pages, Latex, to appear in Phys. Rev.

Geometric approach to Fletcher's ideal penalty function

Original article can be found at: www.springerlink.com Copyright Springer. [Originally produced as UH Technical Report 280, 1993]In this note, we derive a geometric formulation of an ideal penalty function for equality constrained problems. This differentiable penalty function requires no parameter estimation or adjustment, has numerical conditioning similar to that of the target function from which it is constructed, and also has the desirable property that the strict second-order constrained minima of the target function are precisely those strict second-order unconstrained minima of the penalty function which satisfy the constraints. Such a penalty function can be used to establish termination properties for algorithms which avoid ill-conditioned steps. Numerical values for the penalty function and its derivatives can be calculated efficiently using automatic differentiation techniques.Peer reviewe