An agent-based approach to immune modelling

This study focuses on trying to understand why the range of experience with respect to HIV infection is so diverse, especially as regards to the latency period. The challenge is to determine what assumptions can be made about the nature of the experience of antigenic invasion and diversity that can be modelled, tested and argued plausibly. To investigate this, an agent-based approach is used to extract high-level behaviour which cannot be described analytically from the set of interaction rules at the cellular level. A prototype model encompasses local variation in baseline properties contributing to the individual disease experience and is included in a network which mimics the chain of lymphatic nodes. Dealing with massively multi-agent systems requires major computational efforts. However, parallelisation methods are a natural consequence and advantage of the multi-agent approach. These are implemented using the MPI library

Design and evaluation of Nemesis, a scalable, low-latency, message-passing communication subsystem

This paper presents a new low-level communication subsystem called Nemesis. Nemesis has been designed and implemented to be scalable and efficient both in the intranode communication context using shared-memory and in the internode communication case using high-performance networks and is natively multimethod-enabled. Nemesis has been integrated in MPICH2 as a CH3 channel and delivers better performance than other dedicated communication channels in MPICH2. Furthermore, the resulting MPICH2 architecture outperforms other MPI implementations in point-to-point benchmarks

Breakup of the aligned H2_2 molecule by xuv laser pulses: A time-dependent treatment in prolate spheroidal coordinates

We have carried out calculations of the triple-differential cross section for one-photon double ionization of molecular hydrogen for a central photon energy of $75$~eV, using a fully {\it ab initio}, nonperturbative approach to solve the time-dependent \Schro equation in prolate spheroidal coordinates. The spatial coordinates $\xi$ and $\eta$ are discretized in a finite-element discrete-variable representation. The wave packet of the laser-driven two-electron system is propagated in time through an effective short iterative Lanczos method to simulate the double ionization of the hydrogen molecule. For both symmetric and asymmetric energy sharing, the present results agree to a satisfactory level with most earlier predictions for the absolute magnitude and the shape of the angular distributions. A notable exception, however, concerns the predictions of the recent time-independent calculations based on the exterior complex scaling method in prolate spheroidal coordinates [Phys.~Rev.~A~{\bf 82}, 023423 (2010)]. Extensive tests of the numerical implementation were performed, including the effect of truncating the Neumann expansion for the dielectronic interaction on the description of the initial bound state and the predicted cross sections. We observe that the dominant escape mode of the two photoelectrons dramatically depends upon the energy sharing. In the parallel geometry, when the ejected electrons are collected along the direction of the laser polarization axis, back-to-back escape is the dominant channel for strongly asymmetric energy sharing, while it is completely forbidden if the two electrons share the excess energy equally.Comment: 17 pages, 9 figure

Finding apparent horizons and other two-surfaces of constant expansion

Apparent horizons are structures of spacelike hypersurfaces that can be determined locally in time. Closed surfaces of constant expansion (CE surfaces) are a generalisation of apparent horizons. I present an efficient method for locating CE surfaces. This method uses an explicit representation of the surface, allowing for arbitrary resolutions and, in principle, shapes. The CE surface equation is then solved as a nonlinear elliptic equation. It is reasonable to assume that CE surfaces foliate a spacelike hypersurface outside of some interior region, thus defining an invariant (but still slicing-dependent) radial coordinate. This can be used to determine gauge modes and to compare time evolutions with different gauge conditions. CE surfaces also provide an efficient way to find new apparent horizons as they appear e.g. in binary black hole simulations.Comment: 21 pages, 8 figures; two references adde

A framework for large-scale relativistic simulations in the characteristic approach

We present a new computational framework (LEO), that enables us to carry out the very first large-scale, high-resolution computations in the context of the characteristic approach in numerical relativity. At the analytic level, our approach is based on a new implementation of the ``eth'' formalism, using a non-standard representation of the spin-raising and lowering angular operators in terms of non-conformal coordinates on the sphere; we couple this formalism to a partially first-order reduction (in the angular variables) of the Einstein equations. The numerical implementation of our approach supplies the basic building blocks for a highly parallel, easily extensible numerical code. We demonstrate the adaptability and excellent scaling of our numerical code by solving, within our numerical framework, for a scalar field minimally coupled to gravity (the Einstein-Klein-Gordon problem) in 3-dimensions. The nonlinear code is globally second-order convergent, and has been extensively tested using as reference a calibrated code with the same boundary-initial data and radial marching algorithm. In this context, we show how accurately we can follow quasi-normal mode ringing. In the linear regime, we show energy conservation for a number of initial data sets with varying angular structure. A striking result that arises in this context is the saturation of the flow of energy through the Schwarzschild radius. As a final calibration check we perform a large simulation with resolution never achieved before.Comment: RevTeX4, 22 pages, 21 figures, to appear in Phys. Rev.

Improving the Performance of Tensor Matrix Vector Multiplication in Quantum Chemistry Codes.

Cumulative reaction probability (CRP) calculations provide a viable computational approach to estimate reaction rate coefficients. However, in order to give meaningful results these calculations should be done in many dimensions (ten to fifteen). This makes CRP codes memory intensive. For this reason, these codes use iterative methods to solve the linear systems, where a good fraction of the execution time is spent on matrix-vector multiplication. In this paper, we discuss the tensor product form of applying the system operator on a vector. This approach shows much better performance and provides huge savings in memory as compared to the explicit sparse representation of the system matrix

R.A.Fisher, design theory, and the Indian connection

Design Theory, a branch of mathematics, was born out of the experimental statistics research of the population geneticist R. A. Fisher and of Indian mathematical statisticians in the 1930s. The field combines elements of combinatorics, finite projective geometries, Latin squares, and a variety of further mathematical structures, brought together in surprising ways. This essay will present these structures and ideas as well as how the field came together, in itself an interesting story.Comment: 11 pages, 3 figure