Biomedical subjects

P V Coveney

Publications and source records attributed to P V Coveney.

11 recordsLinked to original sources

PubMed2006

Multiscale modeling of liquids with molecular specificity.

The separation between molecular and mesoscopic length and time scales poses a severe limit to molecular simulations of mesoscale phenomena. We describe a hybrid multiscale computational technique which addresses this problem by keeping the full molecular nature of the system where it is of interest and coarse graining it elsewhere. This is made possible by coupling molecular dynamics with a mesoscopic description of realistic liquids based on Landau's fluctuating hydrodynamics. We show that our scheme correctly couples hydrodynamics and that fluctuations, at both the molecular and continuum levels, are thermodynamically consistent. Hybrid simulations of sound waves in bulk water and reflected by a lipid monolayer are presented as illustrations of the scheme.

Journal Article↗

PubMed2005

Towards performance control on the Grid.

Advances in computational Grid technologies are enabling the development of simulations of complex biological and physical systems. Such simulations can be assembled from separate components--separately deployable computation units of well-defined functionality. Such an assemblage can represent an application composed of interacting simulations or might comprise multiple instances of a simulation executing together, each running with different simulation parameters. However, such assemblages need the ability to cope with heterogeneous and dynamically changing execution environments, particularly where such changes can affect performance. This paper describes the design and implementation of a prototype performance control system (PerCo), which is capable of monitoring the progress of simulations and redeploying them so as to optimize performance. The ability to control performance by redeployment is demonstrated using an assemblage of lattice Boltzmann simulations running with and without control policies. The cost of using PerCo is evaluated and it is shown that PerCo is able to reduce overall execution time.

Benchmarking↗

PubMed2005

Improving scientists' interaction with complex computational-visualization environments based on a distributed grid infrastructure.

The grid has the potential to transform collaborative scientific investigations through the use of closely coupled computational and visualization resources, which may be geographically distributed, in order to harness greater power than is available at a single site. Scientific applications to benefit from the grid include visualization, computational science, environmental modelling and medical imaging. Unfortunately, the diversity, scale and location of the required resources can present a dilemma for the scientific worker because of the complexity of the underlying technology. As the scale of the scientific problem under investigation increases so does the nature of the scientist's interaction with the supporting infrastructure. The increased distribution of people and resources within a grid-based environment can make resource sharing and collaborative interaction a critical factor to their success. Unless the technological barriers affecting user accessibility are reduced, there is a danger that the only scientists to benefit will be those with reasonably high levels of computer literacy. This paper examines a number of important human factors of user interaction with the grid and expresses this in the context of the science undertaken by RealityGrid, a project funded by the UK e-Science programme. Critical user interaction issues will also be highlighted by comparing grid computational steering with supervisory control systems for local and remote access to the scientific environment. Finally, implications for future grid developers will be discussed with a particular emphasis on how to improve the scientists' access to what will be an increasingly important resource.

Computer Graphics↗

PubMed2005

A grid-enabled lightweight computational steering client: a .NET PDA implementation.

The grid has been developed to support large-scale computer simulations in a diverse range of scientific and engineering fields. Consequently, the increasing availability of powerful distributed computing resources is changing how scientists undertake large-scale modelling/simulation. Instead of being limited to local computing resources, scientists are now able to make use of supercomputing facilities around the world. These grid resources comprise specialized distributed three-dimensional visualization environments through to massive computational systems. The scientist usually accesses these resources from reasonably high-end desktop computers. Even though most modern desktop computers are provided with reasonably powerful three-dimensional graphical hardware, not all scientific applications require high-end three-dimensional visualization because the data of interest is essentially numerical or two-dimensional graphical data. For these applications, a much simpler two-dimensional graphical displays can be used. Since large jobs can take many hours to complete the scientist needs access to a technology that will allow them to still monitor and control their job while away from their desks. This paper describes an effective method of monitoring and controlling a set of chained computer simulations by means of a lightweight steering client based on a small personal digital assistant (PDA). The concept of using a PDA to steer a series of computational jobs across a supercomputing resource may seem strange at first but when scientists realize they can use these devices to connect to their computation wherever there is a wireless network (or cellular phone network) the concept becomes very compelling. Apart from providing a much needed easy-to-use interface, the PDA-based steering client has the benefit of freeing the scientist from the desktop. It is during this monitoring stage that the hand-held PDA client is of particular value as it gives the application scientist greater freedom to leave his or her desk but still communicate with their simulation, with the proviso that they remain within the range of a wireless network.

Computer Graphics↗

PubMed2005

Determination of the chemical potential using energy-biased sampling.

An energy-biased method to evaluate ensemble averages requiring test-particle insertion is presented. The method is based on biasing the sampling within the subdomains of the test-particle configurational space with energies smaller than a given value freely assigned. These energy wells are located via unbiased random insertion over the whole configurational space and are sampled using the so-called Hit-and-Run algorithm, which uniformly samples compact regions of any shape immersed in a space of arbitrary dimensions. Because the bias is defined in terms of the energy landscape it can be exactly corrected to obtain the unbiased distribution. The test-particle energy distribution is then combined with the Bennett relation for the evaluation of the chemical potential. We apply this protocol to a system with relatively small probability of low-energy test-particle insertion, liquid argon at high density and low temperature, and show that the energy-biased Bennett method is around five times more efficient than the standard Bennett method. A similar performance gain is observed in the reconstruction of the energy distribution.

Journal Article↗

PubMed2003

Continuum-particle hybrid coupling for mass, momentum, and energy transfers in unsteady fluid flow.

The aim of hybrid methods in simulations is to communicate regions with disparate time and length scales. Here, a fluid described at the atomistic level within an inner region P is coupled to an outer region C described by continuum fluid dynamics. The matching of both descriptions of matter is made across an overlapping region and, in general, consists of a two-way coupling scheme (C-->P and P-->C) that conveys mass, momentum, and energy fluxes. The contribution of the hybrid scheme hereby presented is twofold. First, it treats unsteady flows and, more importantly, it handles energy exchange between both C and P regions. The implementation of the C-->P coupling is tested here using steady and unsteady flows with different rates of mass, momentum and energy exchange. In particular, relaxing flows described by linear hydrodynamics (transversal and longitudinal waves) are most enlightening as they comprise the whole set of hydrodynamic modes. Applying the hybrid coupling scheme after the onset of an initial perturbation, the cell-averaged Fourier components of the flow variables in the P region (velocity, density, internal energy, temperature, and pressure) evolve in excellent agreement with the hydrodynamic trends. It is also shown that the scheme preserves the correct rate of entropy production. We discuss some general requirements on the coarse-grained length and time scales arising from both the characteristic microscopic and hydrodynamic scales.

Journal Article↗

PubMed2001

Lattice-Boltzmann simulations of self-assembly of a binary water-surfactant system into ordered bicontinuous cubic and lamellar phases.

We used our recently developed mesoscale amphiphilic lattice-Boltzmann method (Nekovee, M.; Coveney, P. V.; Chen, H.; Boghosian, B. M. Phys. Rev. E 2000, 62, 8282-8894) to investigate the dynamics of self-assembly of the bicontinuous cubic phase in a binary water-surfactant system, and the transition from the lamellar structure to a bicontinuous cubic phase. Our study provides insight into how such structures emerge as a result of competing molecular interactions between water and amphiphiles and among amphiphilic molecules themselves, and represents the first application of any lattice-Boltzmann model to amphiphilic systems in three dimensions.

Journal Article↗

PubMed2001

Plane-wave density functional theoretic study of formation of clay-polymer nanocomposite materials by self-catalyzed in situ intercalative polymerization.

It has recently been shown that the intercalation and subsequent in situ polymerization of organic monomers within the interlayer of clay minerals yields nanocomposites with novel material properties. We present results of plane-wave density functional theory (DFT) based investigations into the initial stages of the polymerization of methanal and ethylenediamine within the interlayer of sodium montmorillonite. Nucleophilic attack of the amine on the aldehyde is only observed when the aldehyde is protonated or coordinated to a metal ion. No evidence is found for the dissociation of water in the hydration sphere of the sodium counterions. The Brønsted acidity of the hydroxyl groups present in the silicate layers is significantly affected by their proximity to sites of isomorphic substitution. However, the most obvious Brønsted acid sources are shown to be unlikely to catalyze the reaction. Instead catalysis is shown to occur at the clay mineral lattice-edge where hydroxyl groups and exposed aluminum ions act as strong Brønsted and Lewis acid sites, respectively.

Journal Article↗

PubMed2001

Three-dimensional hydrodynamic lattice-gas simulations of binary immiscible and ternary amphiphilic flow through porous media.

We report the results of a study of multiphase flow in porous media. A Darcy's law for steady multiphase flow was investigated for both binary and ternary amphiphilic flow. Linear flux-forcing relationships satisfying Onsager reciprocity were shown to be a good approximation of the simulation data. The dependence of the relative permeability coefficients on water saturation was investigated and showed good qualitative agreement with experimental data. Nonsteady-state invasion flows were investigated, with particular interest in the asymptotic residual oil saturation. The addition of surfactant to the invasive fluid was shown to significantly reduce the residual oil saturation.

Journal Article↗

PubMed2001

Three-dimensional hydrodynamic lattice-gas simulations of domain growth and self-assembly in binary immiscible and ternary amphiphilic fluids.

We simulate the dynamics of phase assembly in binary immiscible fluids and ternary microemulsions using a three-dimensional hydrodynamic lattice-gas approach. For critical spinodal decomposition we perform the scaling analysis in reduced variables introduced by Jury et al. [Phys. Rev. E 59, R2535 (1999)] and by Bladon et al. [Phys. Rev. Lett. 83, 579 (1999)]. We find a late-stage scaling exponent consistent with the R approximately t(2/3) inertial regime. However, as observed with the previous lattice-gas model of Appert et al. [J. Stat. Phys. 81, 181 (1995)] our data do not fall in the same range of reduced length and time as those of Jury et al. and Bladon et al. For off-critical binary spinodal decomposition we observe a reduction of the effective exponent with decreasing volume fraction of the minority phase. However, the n=1 / 3 Lifshitz-Slyzov-Wagner droplet coalescence exponent is not observed. Adding a sufficient number of surfactant particles to a critical quench of binary immiscible fluids produces a ternary bicontinuous microemulsion. We observe a change in scaling behavior from algebraic to logarithmic growth for amphiphilic fluids in which the domain growth is not arrested. For formation of a microemulsion where the domain growth is halted we find that a stretched exponential growth law provides the best fit to the data.

Journal Article↗

PubMedDate not supplied

An integrated instrument control and informatics system for combinatorial materials research.

The use of high-throughput synthesis and characterization techniques is increasingly prevalent in materials science research. We describe the London University Search Instrument, a research apparatus designed for the high-throughput synthesis and characterization of thick-film sample libraries of ceramic compounds. The instrument is constructed largely from commodity components, which pose particular engineering challenges for achieving the automated operation required for efficient high-throughput experimentation. This paper describes the architecture and implementation of the software system that provides integrated instrument control and data management functions.

Journal Article↗