Optimal branching asymmetry of hydrodynamic pulsatile trees

Most of the studies on optimal transport are done for steady state regime conditions. Yet, there exists numerous examples in living systems where supply tree networks have to deliver products in a limited time due to the pulsatile character of the flow. This is the case for mammals respiration for which air has to reach the gas exchange units before the start of expiration. We report here that introducing a systematic branching asymmetry allows to reduce the average delivery time of the products. It simultaneously increases its robustness against the unevitable variability of sizes related to morphogenesis. We then apply this approach to the human tracheobronchial tree. We show that in this case all extremities are supplied with fresh air, provided that the asymmetry is smaller than a critical threshold which happens to fit with the asymmetry measured in the human lung. This could indicate that the structure is adjusted at the maximum asymmetry level that allows to feed all terminal units with fresh air.Comment: 4 pages, 4 figure

Efficient Recursion Method for Inverting Overlap Matrix

A new O(N) algorithm based on a recursion method, in which the computational effort is proportional to the number of atoms N, is presented for calculating the inverse of an overlap matrix which is needed in electronic structure calculations with the the non-orthogonal localized basis set. This efficient inverting method can be incorporated in several O(N) methods for diagonalization of a generalized secular equation. By studying convergence properties of the 1-norm of an error matrix for diamond and fcc Al, this method is compared to three other O(N) methods (the divide method, Taylor expansion method, and Hotelling's method) with regard to computational accuracy and efficiency within the density functional theory. The test calculations show that the new method is about one-hundred times faster than the divide method in computational time to achieve the same convergence for both diamond and fcc Al, while the Taylor expansion method and Hotelling's method suffer from numerical instabilities in most cases.Comment: 17 pages and 4 figure

A comprehensive computational model of sound transmission through the porcine lung

A comprehensive computational simulation model of sound transmission through the porcine lung is introduced and experimentally evaluated. This subject-specific model utilizes parenchymal and major airway geometry derived from x-ray CT images. The lung parenchyma is modeled as a poroviscoelastic material using Biot theory. A finite element (FE) mesh of the lung that includes airway detail is created and used in COMSOL FE software to simulate the vibroacoustic response of the lung to sound input at the trachea. The FE simulation model is validated by comparing simulation results to experimental measurements using scanning laser Doppler vibrometry on the surface of an excised, preserved lung. The FE model can also be used to calculate and visualize vibroacoustic pressure and motion inside the lung and its airways caused by the acoustic input. The effect of diffuse lung fibrosis and of a local tumor on the lung acoustic response is simulated and visualized using the FE model. In the future, this type of visualization can be compared and matched with experimentally obtained elastographic images to better quantify regional lung material properties to noninvasively diagnose and stage disease and response to treatment

Characterization of spotted hyena, Crocuta crocuta microsatellite loci

We have isolated 10 polymorphic microsatellite loci in the spotted hyena,Crocuta crocuta.The loci displayed between eight and 14 alleles in a minimum of 12 individuals tested. These loci will be used to investigate relatedness within social groups, the genetic structure of populations, sexual selection, and mate choice in spotted hyenas

Could humans recognize odor by phonon assisted tunneling?

Our sense of smell relies on sensitive, selective atomic-scale processes that are initiated when a scent molecule meets specific receptors in the nose. However, the physical mechanisms of detection are not clear. While odorant shape and size are important, experiment indicates these are insufficient. One novel proposal suggests inelastic electron tunneling from a donor to an acceptor mediated by the odorant actuates a receptor, and provides critical discrimination. We test the physical viability of this mechanism using a simple but general model. Using values of key parameters in line with those for other biomolecular systems, we find the proposed mechanism is consistent both with the underlying physics and with observed features of smell, provided the receptor has certain general properties. This mechanism suggests a distinct paradigm for selective molecular interactions at receptors (the swipe card model): recognition and actuation involve size and shape, but also exploit other processes.Comment: 10 pages, 1 figur

Avalanches in the lung: A statistical mechanical model

We study a statistical mechanical model for the dynamics of lung inflation which incorporates recent experimental observations on the opening of individual airways by a cascade or avalanche mechanism. Using an exact mapping of the avalanche problem onto percolation on a Cayley tree, we analytically derive the exponents describing the size distribution of the first avalanches and test the analytical solution by numerical simulations. We find that the tree-like structure of the airways together with the simplest assumptions concerning opening threshold pressures of each airway, is sufficient to explain the existence of power-law distributions observed experimentally.Comment: 4 pages, Figures avaliable by mail from [email protected], REVTE

Positive regulation of c-Myc by cohesin is direct, and evolutionarily conserved

AbstractContact between sister chromatids from S phase to anaphase depends on cohesin, a large multi-subunit protein complex. Mutations in sister chromatid cohesion proteins underlie the human developmental condition, Cornelia de Lange syndrome. Roles for cohesin in regulating gene expression, sometimes in combination with CCCTC-binding factor (CTCF), have emerged. We analyzed zebrafish embryos null for cohesin subunit rad21 using microarrays to determine global effects of cohesin on gene expression during embryogenesis. This identified Rad21-associated gene networks that included myca (zebrafish c-myc), p53 and mdm2. In zebrafish, cohesin binds to the transcription start sites of p53 and mdm2, and depletion of either Rad21 or CTCF increased their transcription. In contrast, myca expression was strongly downregulated upon loss of Rad21 while depletion of CTCF had little effect. Depletion of Rad21 or the cohesin-loading factor Nipped-B in Drosophila cells also reduced expression of myc and Myc target genes. Cohesin bound the transcription start site plus an upstream predicted CTCF binding site at zebrafish myca. Binding and positive regulation of the c-Myc gene by cohesin is conserved through evolution, indicating that this regulation is likely to be direct. The exact mechanism of regulation is unknown, but local changes in histone modification associated with transcription repression at the myca gene were observed in rad21 mutants

O(N) methods in electronic structure calculations

Linear scaling methods, or O(N) methods, have computational and memory requirements which scale linearly with the number of atoms in the system, N, in contrast to standard approaches which scale with the cube of the number of atoms. These methods, which rely on the short-ranged nature of electronic structure, will allow accurate, ab initio simulations of systems of unprecedented size. The theory behind the locality of electronic structure is described and related to physical properties of systems to be modelled, along with a survey of recent developments in real-space methods which are important for efficient use of high performance computers. The linear scaling methods proposed to date can be divided into seven different areas, and the applicability, efficiency and advantages of the methods proposed in these areas is then discussed. The applications of linear scaling methods, as well as the implementations available as computer programs, are considered. Finally, the prospects for and the challenges facing linear scaling methods are discussed.Comment: 85 pages, 15 figures, 488 references. Resubmitted to Rep. Prog. Phys (small changes

Characterization of white matter damage in ischemic leukoaraiosis with diffusion tensor MRI

BACKGROUND AND PURPOSE: Information on the neuropathological changes underlying ischemic leukoaraiosis is only available postmortem, and there are limited data on histological appearances early in the disease. Diffusion tensor imaging allows determination of the directionality of diffusion, which is greater in the direction of white matter bundles. Therefore, the technique might be expected to show loss of anisotropy (directional diffusion) in leukoaraiosis. METHODS: Nine patients with ischemic leukoaraiosis (radiological leukoaraiosis and clinical lacunar stroke) and 10 age-matched controls were studied. Diffusion tensor imaging was performed, and maps of diffusion trace and fractional anisotropy were constructed. Mean values of trace and fractional anisotropy were determined in standard regions of the anterior and posterior white matter in both hemispheres. RESULTS: In all patients with ischemic leukoaraiosis, a characteristic abnormal pattern was found, with loss of anisotropy and increased trace in the white matter. For example, in the right anterior white matter mean (SD) trace/3 was 1.12 (0.33) x10(-3) mm2 s-1 in patients and 0.75 (0.11) in controls (P=0.001). In the same region, fractional anisotropy was 0.53 (0.11) in patients and 0.78 (0.09) in controls (P<0.001). Within the white matter regions, there was a strong negative correlation between mean diffusivity and anisotropy (r=-0.92, P<0.0001). CONCLUSIONS: The characteristic pattern found on diffusion tensor imaging in this patient group is consistent with axonal loss and gliosis leading to impairment to and loss of directional diffusion. The "in vivo histological" information obtained may be useful in monitoring disease progression and in investigating the pathogenesis of the cognitive impairment that may be present

Proportional Relations Between Systolic, Diastolic and Mean Pulmonary Artery Pressure are Explained by Vascular Properties

Recently, it was shown that proportional relationships exist between systolic, diastolic and mean pulmonary artery pressure (Psys, Pdia and Pmean) and that they are maintained under various conditions in both health and disease. An arterial-ventricular interaction model was used to study the contribution of model parameters to the ratios Psys/Pmean, and Pdia/Pmean. The heart was modeled by a time-varying elastance function, and the arterial system by a three-element windkessel model consisting of peripheral resistance, Rp, arterial compliance Ca, and pulmonary artery characteristic impedance Z0. Baseline model parameters were estimated in control subjects and compared to values estimated in patients with pulmonary hypertension. Results indicate that experimentally derived ratios Psys/Pmean and Pdia/Pmean could be accurately reproduced using our model (1.59 and 0.61 vs. 1.55 and 0.64, respectively). Sensitivity analysis showed that the (empirical) constancy of Psys/Pmean and Pdia/Pmean was primarily based on the inverse hyperbolic relation between total vascular resistance (RT; calculated as Rp + Z0) and Ca, (i.e. constant RTCa product). Of the cardiac parameters, only heart rate affected the pressure ratios, but the contribution was small. Therefore, we conclude that proportional relations between systolic, diastolic and mean pulmonary artery pressure result from the constancy of RTCa thus from pulmonary arterial properties, with only little influence of heart rate