Random walk simulations of fossil proxy data

A wealth of palaeoecological studies (e.g. pollen, diatoms, chironomids and macrofossils from deposits such as lakes or bogs) have revealed major as well as more subtle ecosystem changes over decadal to multimillennial timescales. Such ecosystem changes are usually assumed to have been forced by specific environmental changes. Here, we test if the observed changes in palaeoecological records may be reproduced by random simulations, and we find that simple procedures generate abrupt events, long-term trends, quasi-cyclic behaviour, extinctions and immigrations. Our results highlight the importance of replicated and multiproxy data for reliable reconstructions of past climate and environmental changes.

Evidence That Interspecies Polymorphism in the Human and Rat Cholecystokinin Receptor-2 Affects Structure of the Binding Site for the Endogenous Agonist Cholecystokinin

The cholecystokinin (CCK) receptor-2 exerts very important central and peripheral functions by binding the neuropeptides cholecystokinin or gastrin. Because this receptor is a potential therapeutic target, great interest has been devoted to the identification of efficient antagonists. However, interspecies genetic polymorphism that does not alter cholecystokinin-induced signaling was shown to markedly affect activity of synthetic ligands. In this context, precise structural study of the agonist binding site on the human cholecystokinin receptor-2 is a prerequisite to elucidating the molecular basis for its activation and to optimizing properties of synthetic ligands. In this study, using site-directed mutagenesis and molecular modeling, we delineated the binding site for CCK on the human cholecystokinin receptor-2 by mutating amino acids corresponding to that of the rat homolog. By doing so, we demonstrated that, although resembling that of rat homolog, the human cholecystokinin receptor-2 binding site also displays important distinct structural features that were demonstrated by susceptibility to several point mutations (F120A, Y189A, H207A). Furthermore, docking of CCK in the human and rat cholecystokinin receptor-2, followed by dynamic simulations, allowed us to propose a plausible structural explanation of the experimentally observed difference between rat and human cholecystokinin-2 receptors.

A Geostatistical Investigation into Changing Permeability of Sandstones During Weathering Simulations

The ability to predict the behavior of masonry materials is crucial to conserve building stone. Natural stone, such as sandstone, is not immune from the processes of weathering in the built environment and suffers from decay by granular disintegration, contour scaling, and multiple flaking. Spatial variation of rock properties is a major contributing factor to inconsistent responses to weathering. This has implications for moisture movement and salt input and output and storage, and results in unpredictability in the decay dynamics of masonry materials. This article explores the use of variography and kriging to investigate the spatial interactions between the trigger factors of stone decay, in particular, permeability and its effect on salt penetration. Sandstone blocks were used to represent fresh building stones from a weathering perspective and gave baseline characteristics for the interpretation of subsequent deterioration and decay pathways. Simulated weathering trials involved preloading a sandstone block with salt and subjecting a separate block to 20 cycles of a weathering trial designed to simulate a temperate weathering regime. Geostatistical analysis indicated differences in the spatial variation of permeability of the fresh rock and that subjected to the weathering regimes. Spatial prediction and visualization showed differences in the spatial continuity of permeability in a horizontal and vertical direction through the preloaded block after salt weathering. Continual wetting with salt and alternate heating increased permeability in a vertical direction, enabling the ingress and movement of salt and moisture more effectively through the stone.

Numerical simulations of fluid-structure interactions in single-reed mouthpieces

Most single-reed woodwind instrument models rely on a quasistationary approximation to describe the relationship between the volume flow and. the pressure difference across the reed channel. Semiempirical models based on the quasistationary approximation are very useful in explaining the fundamental characteristics of this family of instruments such as self-sustained oscillations and threshold of blowing pressure. However, they fail at explaining more complex phenomena associated with the fluid-structure interaction during dynamic flow regimes, such as the transient and steady-state behavior of the system as a function. of the mouthpiece geometry. Previous studies have discussed the accuracy of the quasistationary approximation but the amount of literature on the subject is sparse, mainly due to the difficulties involved in the measurement of dynamic flows in channels with an oscillating reed. In this paper, a numerical technique based on the lattice Boltzmann method and a finite difference scheme is proposed in order to investigate the characteristics of fully coupled fluid-structure interaction in single-reed mouthpieces with different channel configurations. Results obtained for a stationary simulation with a static reed agree very well with those predicted by the literature based on the quasistationary approximation. However, simulations carried out for a dynamic regime with dn oscillating reed show that the phenomenon associated with flow detachment and reattachment diverges considerably frorn the theoretical assumptions. Furthermore, in the case of long reed channels, the results obtained for the vena contracta factor are in significant disagreement with those predicted by theory. For short channels, the assumption of constant vena contracta was found to be valid for only 40% of the duty cycle. (c) 2007 Acoustical Society of America.

Modeling Frequency-Dependent Boundaries as Digital Impedance Filters in FDTD and K-DWM Room Acoustics Simulations

A new method for modeling-frequency-dependent boundaries in finite-difference time-domain (FDTD) and Kirchhoff variable digital waveguide mesh (K-DWM) room acoustics simulations is presented. The proposed approach allows the direct incorporation of a digital impedance filter (DIF) in the Multidimensional (2D or 3D) FDTD boundary model of a locally reacting surface. An explicit boundary update equation is obtained by carefully constructing a Suitable recursive formulation. The method is analyzed in terms of pressure wave reflectance for different wall impedance filters and angles of incidence. Results obtained from numerical experiments confirm the high accuracy of the proposed digital impedance filter boundary model, the reflectance of which matches locally reacting surface (LRS) theory closely. Furthermore a numerical boundary analysis (NBA) formula is provided as a technique for an analytic evaluation of the numerical reflectance of the proposed digital impedance filter boundary formulation.

A Phase Grating Approach to Modeling Surface Diffusion in FDTD Room Acoustics Simulations

In this paper, a method for modeling diffusive boundaries in finite difference time domain (FDTD) room acoustics simulations with the use of impedance filters is presented. The proposed technique is based on the concept of phase grating diffusers, and realized by designing boundary impedance filters from normal-incidence reflection filters with added delay. These added delays, that correspond to the diffuser well depths, are varied across the boundary surface, and implemented using Thiran allpass filters. The proposed method for simulating sound scattering is suitable for modeling high frequency diffusion caused by small variations in surface roughness and, more generally, diffusers characterized by narrow wells with infinitely thin separators. This concept is also applicable to other wave-based modeling techniques. The approach is validated by comparing numerical results for Schroeder diffusers to measured data. In addition, it is proposed that irregular surfaces are modeled by shaping them with Brownian noise, giving good control over the sound scattering properties of the simulated boundary through two parameters, namely the spectral density exponent and the maximum well depth.

Computer simulations of seasonal outbreak and diurnal vertical migration of cyanobacteria

Algal blooms caused by cyanobacteria are characterized by two features with different time scales: one is seasonal outbreak and collapse of a bloom and the other is diurnal vertical migration. Our two-component mathematical model can simulate both phenomena, in which the state variables are nutrients and cyanobacteria. The model is a set of one-dimensional reaction-advection-diffusion equations, and temporal changes of these two variables are regulated by the following five factors: (1) annual variation of light intensity, (2) diurnal variation of light intensity, (3) annual variation of water temperature, (4) thermal stratification within a water column and (5) the buoyancy regulation mechanism. The seasonal change of cyanobacteria biomass is mainly controlled by factors, (1), (3) and (4), among which annual variations of light intensity and water temperature directly affect the maximum growth rate of cyanobacteria. The latter also contributes to formation of the thermocline during the summer season. Thermal stratification causes a reduction in vertical diffusion and largely prevents mixing of both nutrients and cyanobacteria between the epilimnion and the hypolimnion. Meanwhile, the other two factors, (2) and (5), play a significant role in diurnal vertical migration of cyanobacteria. A key mechanism of vertical migration is buoyancy regulation due to gas-vesicle synthesis and ballast formation, by which a quick reversal between floating and sinking becomes possible within a water column. The mechanism of bloom formation controlled by these five factors is integrated into the one-dimensional model consisting of two reaction-advection-diffusion equations.

Molecular Modeling on Inhibitor Complexes and Active-Site Dynamics of Cytochrome P450 C17, a Target for Prostate Cancer Therapy

A molecular model for the P450 enzyme cytochrome P450 C17 (CYP17) is presented based on sequence alignments of multiple template structures and homology modeling. This enzyme plays a central role in the biosynthesis of testosterone and is emerging as a major target in prostate cancer, with the recently developed inhibitor abiraterone currently in advanced clinical trials. The model is described in detail, together with its validation, by providing structural explanations to available site-directed mutagenesis data. The CYP17 molecule in this model is in the form of a triangular prism, with an edge of similar to 55 angstrom and a thickness of similar to 37 angstrom. It is predominantly helical, comprising 13 alpha helices interspersed by six 3(10) helices and 11 beta-sheets. Multinanosecond molecular dynamics simulations in explicit solvent have been carried out, and principal components analysis has been used to reveal the details of dynamics around the active site. Coarse-grained methods have also been used to verify low-frequency motions, which have been correlated with active-site gating. The work also describes the results of docking synthetic inhibitors, including the drug abiraterone and the natural substrate pregnenolone, in the CYP17 active site together with molecular dynamics simulations on the complexes. (C) 2010 Elsevier Ltd. All rights reserved.