GPU Acceleration of Partial Differential Equation Solvers

Differential equations are often directly solvable by analytical means only in their one dimensional version. Partial differential equations are generally not solvable by analytical means in two and three dimensions, with the exception of few special cases. In all other cases, numerical approximation methods need to be utilized. One of the most popular methods is the finite element method. The main areas of focus, here, are the Poisson heat equation and the plate bending equation. The purpose of this paper is to provide a quick walkthrough of the various approaches that the authors followed in pursuit of creating optimal solvers, accelerated with the use of graphical processing units, and comparing them in terms of accuracy and time efficiency with existing or self-made non-accelerated solvers.

A Van der Pol-Mathieu equation for the dynamics of dust grain charge in dusty plasmas

The chaotic profile of dust grain dynamics associated with dust-acoustic oscillations in a dusty plasma is considered. The collective behaviour of the dust plasma component is described via a multi-fluid model, comprising Boltzmann distributed electrons and ions, as well as an equation of continuity possessing a source term for the dust grains, the dust momentum and Poisson's equations. A Van der Pol–Mathieu-type nonlinear ordinary differential equation for the dust grain density dynamics is derived. The dynamical system is cast into an autonomous form by employing an averaging method. Critical stability boundaries for a particular trivial solution of the governing equation with varying parameters are specified. The equation is analysed to determine the resonance region, and finally numerically solved by using a fourth-order Runge–Kutta method. The presence of chaotic limit cycles is pointed out.

Coupled consolidation of a solid, infinite cylinder using a Terzaghi formulation

Axisymmetric consolidation is a classical boundary value problem for geotechnical engineers. Under some circumstances an analysis in which the changes in pore pressure, effective stress and displacement can be uncoupled from each other is sufficient, leading to a Terzaghi formulation of the axisymmetric consolidation equation in terms of the pore pressure. However, representation of the Mandel-Cryer effect usually requires more complex, coupled, Biot formulations. A new coupled formulation for the plane strain, axisymmetric consolidation problem is presented for small, linear elastic deformations. A single, easily evaluated parameter couples changes in pore pressure to changes in effective stress, and the resulting differential equation for pore pressure dissipation is very similar to Terzaghi’s classic formulation. The governing equations are then solved using finite differences and the consolidation of a solid infinite cylinder analysed, calculating the variation with time and with radius of the excess pore pressure and the radial displacement. Comparison with a previously published semi-analytical solution indicates that the formulation successfully embodies the Mandel-Cryer effect.

Analytical description of stochastic field-Line wandering in magnetic turbulence

A nonperturbative nonlinear statistical approach is presented to describe turbulent magnetic systems embedded in a uniform mean magnetic field. A general formula in the form of an ordinary differential equation for magnetic field-line wandering (random walk) is derived. By considering the solution of this equation for different limits several new results are obtained. As an example, it is demonstrated that the stochastic wandering of magnetic field-lines in a two-component turbulence model leads to superdiffusive transport, contrary to an existing diffusive picture. The validity of quasilinear theory for field-line wandering is discussed, with respect to different turbulence geometry models, and previous diffusive results are shown to be deduced in appropriate limits.

Modelling the mechanical response of the Reed-mouthpiece-lip system of a clarinet. Part I. A one-dimensional distributed model

The motion of a clarinet reed that is clamped to a mouthpiece and supported by a lip is simulated in the time-domain using finite difference methods. The reed is modelled as a bar with non-uniform cross section, and is described using a one-dimensional, fourth-order partial differential equation. The interactions with the mouthpiece Jay and the player's lip are taken into account by incorporating conditional contact forces in the bar equation. The model is completed by clamped-free boundary conditions for the reed. An implicit finite difference method is used for discretising the system, and values for the physical parameters are chosen both from laboratory measurements and by accurate tuning of the numerical simulations. The accuracy of the numerical system is assessed through analysis of frequency warping effects and of resonance estimation. Finally, the mechanical properties of the system are studied by analysing its response to external driving forces. In particular, the effects of reed curling are investigated.

Harnessing the complexity of gene expression data from cancer: from single gene to structural pathway methods

High-dimensional gene expression data provide a rich source of information because they capture the expression level of genes in dynamic states that reflect the biological functioning of a cell. For this reason, such data are suitable to reveal systems related properties inside a cell, e.g., in order to elucidate molecular mechanisms of complex diseases like breast or prostate cancer. However, this is not only strongly dependent on the sample size and the correlation structure of a data set, but also on the statistical hypotheses tested. Many different approaches have been developed over the years to analyze gene expression data to (I) identify changes in single genes, (II) identify changes in gene sets or pathways, and (III) identify changes in the correlation structure in pathways. In this paper, we review statistical methods for all three types of approaches, including subtypes, in the context of cancer data and provide links to software implementations and tools and address also the general problem of multiple hypotheses testing. Further, we provide recommendations for the selection of such analysis methods.

Combined R-matrix eigenstate basis set and finite-difference propagation method for the time-dependent Schrodinger equation: The one-electron case

In this work we present the theoretical framework for the solution of the time-dependent Schrödinger equation (TDSE) of atomic and molecular systems under strong electromagnetic fields with the configuration space of the electron’s coordinates separated over two regions; that is, regions I and II. In region I the solution of the TDSE is obtained by an R-matrix basis set representation of the time-dependent wave function. In region II a grid representation of the wave function is considered and propagation in space and time is obtained through the finite-difference method. With this, a combination of basis set and grid methods is put forward for tackling multiregion time-dependent problems. In both regions, a high-order explicit scheme is employed for the time propagation. While, in a purely hydrogenic system no approximation is involved due to this separation, in multielectron systems the validity and the usefulness of the present method relies on the basic assumption of R-matrix theory, namely, that beyond a certain distance (encompassing region I) a single ejected electron is distinguishable from the other electrons of the multielectron system and evolves there (region II) effectively as a one-electron system. The method is developed in detail for single active electron systems and applied to the exemplar case of the hydrogen atom in an intense laser field.

High speed DSC (hyper-DSC) as a tool to measure the solubility of a drug within a solid or semi-solid matrix

Conventional differential scanning calorimetry (DSC) techniques are commonly used to quantify the solubility of drugs within polymeric-controlled delivery systems. However, the nature of the DSC experiment, and in particular the relatively slow heating rates employed, limit its use to the measurement of drug solubility at the drug's melting temperature. Here, we describe the application of hyper-DSC (HDSC), a variant of DSC involving extremely rapid heating rates, to the calculation of the solubility of a model drug, metronidazole, in silicone elastomer, and demonstrate that the faster heating rates permit the solubility to be calculated under non-equilibrium conditions such that the solubility better approximates that at the temperature of use. At a heating rate of 400 degrees C/min (HDSC), metronidazole solubility was calculated to be 2.16 mg/g compared with 6.16 mg/g at 20 degrees C/min. (C) 2005 Elsevier B.V. All rights reserved.

On solvability of linear differential equations in ${\Bbb R}^{\Bbb N}$

We construct $x^0$ in ${\Bbb R}^{\Bbb N}$ and a row-finite matrix $T=\{T_{i,j}(t)\}_{i,j\in\N}$ of polynomials of one real variable $t$ such that the Cauchy problem $\dot x(t)=T_tx(t)$, $x(0)=x^0$ in the Fr\'echet space $\R^\N$ has no solutions. We also construct a row-finite matrix $A=\{A_{i,j}(t)\}_{i,j\in\N}$ of $C^\infty(\R)$ functions such that the Cauchy problem $\dot x(t)=A_tx(t)$, $x(0)=x^0$ in ${\Bbb R}^{\Bbb N}$ has no solutions for any $x^0\in{\Bbb R}^{\Bbb N}\setminus\{0\}$. We provide some sufficient condition of solvability and of unique solvability for linear ordinary differential equations $\dot x(t)=T_tx(t)$ with matrix elements $T_{i,j}(t)$ analytically dependent on $t$.

Regulation and consequences of differential gene expression in diabetic kidney disease

DIN (diabetic nephropathy) is the leading cause of end-stage renal disease worldwide and develops in 25-40% of patients with Type 1 or Type 2 diabetes mellitus. Elevated blood glucose over long periods together with glomerular hypertension leads to progressive glomerulosclerosis and tubulointerstitial fibrosis in susceptible individuals. Central to the pathology of DIN are cytokines and growth factors such as TGF-beta (transforming growth factor beta) superfamily members, including BMPs (bone morphogenetic protein) and TGF-beta 1, which play key roles in fibrogenic responses of the kidney, including podocyte loss, mesangial cell hypertrophy, matrix accumulation and tubulointerstitial fibrosis. Many of these responses can be mimicked in in vitro models of cells cultured in high glucose. We have applied differential gene expression technologies to identify novel genes expressed in in vitro and in vivo models of DN and, importantly, in human renal tissue. By mining these datasets and probing the regulation of expression and actions of specific molecules, we have identified novel roles for molecules such as Gremlin, IHG-1 (induced in high glucose-1) and CTGF (connective tissue growth factor) in DIN and potential regulators of their bioactions.

Potential roles for differential body size and microhabitat complexity in mediating biotic interactions within invasive freshwater amphipod assemblages

Cannibalism and intraguild predation (IGP) are common amongst freshwater amphipod crustacean aswsemblages, particularly between individuals of different body size, with IGP of smaller by larger species. The decline of Gammarus tigrinus Populations in mainland Europe has been accompanied by the arrival of the Ponto-Caspian invader Dikerogammarus villosus and previous studies have implicated IGP of G. tigrinus by the larger D. villosus as the principal driving force in this replacement. We examined how factors such as microhabitat and body size may mediate both cannibalism within G. tigrinus populations and IGP by D. villosus and thus contribute to field patterns of coexistence and exclusion. A field Survey of an invaded Dutch fake indicated that G. tigrinus and D. villosus differed in distribution. with D. villosus being the numerically dominant amphipod (80-96 %) on the rocky boulder Substrate of the shoreline and G. tigrinus being the dominant amphipod (100 %) in the crushed shell/sand matrix immediately adjacent to this. Laboratory microcosm experiments indicated that G. tigrinus cannibalism, particularly of smaller by larger size classes, may be common. In addition, although D. villosus predation of all G. tigrinus size classes was extreme, the smallest size classes Suffered the highest predation. Indeed, when exposed to D. villosus, predation of larger G. tigrinus was lowest when smaller G. tigrinus were also present. Increasing microhabitat complexity from a simple bare substrate littered with Dreissena polymorpha zebra mussels to a Crushed shell/sand matrix significantly reduced both cannibalism and IGP. Our Study emphasizes the need to consider both life history stages and habitat template, when considering the impacts of biotic interactions and it also emphasizes that complex, interacting factors may be mediating the range expansion of D. villosus.

SOLVING THE INHOMOGENEOUS SCHRODINGER-EQUATION ON A BIDIRECTIONAL PIPELINE OF TRANSPUTERS

In this paper we describe the design of a parallel solution of the inhomogeneous Schrodinger equation, which arises in the construction of continuum orbitals in the R-matrix theory of atomic continuum processes. A prototype system is described which has been programmed in occam2 and implemented on a bi-directional pipeline of transputers. Some timing results for the prototype system are presented, and the development of a full production system is discussed.

Solutions of fourth-order parabolic equation modeling thin film growth

In this paper we study the well-posedness for a fourth-order parabolic equation modeling epitaxial thin film growth. Using Kato's Method [1], [2] and [3] we establish existence, uniqueness and regularity of the solution to the model, in suitable spaces, namelyC⁰([0,T];L^p(Ω)) where  with 1<α<2, n∈N and n≥2. We also show the global existence solution to the nonlinear parabolic equations for small initial data. Our main tools are L_p–L_q-estimates, regularization property of the linear part of e^−tΔ2 and successive approximations. Furthermore, we illustrate the qualitative behavior of the approximate solution through some numerical simulations. The approximate solutions exhibit some favorable absorption properties of the model, which highlight the stabilizing effect of our specific formulation of the source term associated with the upward hopping of atoms. Consequently, the solutions describe well some experimentally observed phenomena, which characterize the growth of thin film such as grain coarsening, island formation and thickness growth.