On-lattice agent-based simulation of populations of cells within the open-source chaste framework

Over the years, agent-based models have been developed that combine cell division and reinforced random walks of cells on a regular lattice, reaction-diffusion equations for nutrients and growth factors and ordinary differential equations (ODEs) for the subcellular networks regulating the cell cycle. When linked to a vascular layer, this multiple scale model framework has been applied to tumour growth and therapy. Here we report on the creation of an agent-based multiscale environment amalgamating the characteristics of these models within a Virtual Pysiological Human (VPH) Exemplar Project. This project enables re-use, integration, expansion and sharing of the model and relevant data. The agent-based and reactiondiffusion parts of the multiscale model have been implemented and are available for download as part of the latest public release of Chaste (“Cancer, Heart and Soft Tissue Environment”), (http://www.cs.ox.ac.uk/chaste/) version 3.1, part of the VPH Toolkit (http://toolkit.vph-noe.eu/). The environment functionalities are verified against the original models, in addition to extra validation of all aspects of the code. In this work, we present the details of the implementation of the agent-based environment, including the system description, the conceptual model, the development of the simulation model and the processes of verification and validation of the simulation results. We explore the potential use of the environment by presenting exemplar applications of the “what if” scenarios that can easily be studied in the environment. These examples relate to tumour growth, cellular competition for resources and tumour responses to hypoxia. We conclude our work by summarising the future steps for the expansion of the current system

Structured Deformations of Continua: Theory and Applications

The scope of this contribution is to present an overview of the theory of structured deformations of continua, together with some applications. Structured deformations aim at being a unified theory in which elastic and plastic behaviours, as well as fractures and defects can be described in a single setting. Since its introduction in the scientific community of rational mechanicists (Del Piero-Owen, ARMA 1993), the theory has been put in the framework of variational calculus (Choksi-Fonseca, ARMA 1997), thus allowing for solution of problems via energy minimization. Some background, three problems and a discussion on future directions are presented.Comment: 11 pages, 1 figure, 1 diagram. Submitted to the Proceedings volume of the conference CoMFoS1

High-frequency high-voltage high-power DC-to-DC converters

The current and voltage waveshapes associated with the power transitor and the power diode in an example current-or-voltage step-up (buck-boost) converter were analyzed to highlight the problems and possible tradeoffs involved in the design of high voltage high power converters operating at switching frequencies in the range of 100 Khz. Although the fast switching speeds of currently available power diodes and transistors permit converter operation at high switching frequencies, the resulting time rates of changes of current coupled with parasitic inductances in series with the semiconductor switches, produce large repetitive voltage transients across the semiconductor switches, potentially far in excess of the device voltage ratings. The need is established for semiconductor switch protection circuitry to control the peak voltages appearing across the semiconductor switches, as well as to provide the waveshaping action require for a given semiconductor device. The possible tradeoffs, as well as the factors affecting the tradeoffs that must be considered in order to maximize the efficiency of the converters are enumerated

Analysis of transistor and snubber turn-off dynamics in high-frequency high-voltage high-power converters

Dc to dc converters which operate reliably and efficiently at switching frequencies high enough to effect substantial reductions in the size and weight of converter energy storage elements are studied. A two winding current or voltage stepup (buck boost) dc-to-dc converter power stage submodule designed to operate in the 2.5-kW range, with an input voltage range of 110 to 180 V dc, and an output voltage of 250 V dc is emphasized. In order to assess the limitations of present day component and circuit technologies, a design goal switching frequency of 10 kHz was maintained. The converter design requirements represent a unique combination of high frequency, high voltage, and high power operation. The turn off dynamics of the primary circuit power switching transistor and its associated turn off snubber circuitry are investigated

Deep-space navigation applications of improved ground-based optical astrometry

Improvements in ground-based optical astrometry will eventually be required for navigation of interplanetary spacecraft when these spacecraft communicate at optical wavelengths. Although such spacecraft may be some years off, preliminary versions of the astrometric technology can also be used to obtain navigational improvements for the Galileo and Cassini missions. This article describes a technology-development and observational program to accomplish this, including a cooperative effort with U.S. Naval Observatory Flagstaff Station. For Galileo, Earth-based astrometry of Jupiter's Galilean satellites may improve their ephemeris accuracy by a factor of 3 to 6. This would reduce the requirements for onboard optical navigation pictures, so that more of the data transmission capability (currently limited by high-gain antenna deployment problems) can be used for science data. Also, observations of European Space Agency (ESA) Hipparcos stars with asteroid 243 Ida may provide significantly improved navigation accuracy for a planned August 1993 Galileo spacecraft encounter

Systems analysis for ground-based optical navigation

Deep-space telecommunications systems will eventually operate at visible or near-infrared regions to provide increased information return from interplanetary spacecraft. This would require an onboard laser transponder in place of (or in addition to) the usual microwave transponder, as well as a network of ground-based and/or space-based optical observing stations. This article examines the expected navigation systems to meet these requirements. Special emphasis is given to optical astrometric (angular) measurements of stars, solar system target bodies, and (when available) laser-bearing spacecraft, since these observations can potentially provide the locations of both spacecraft and target bodies. The role of astrometry in the navigation system and the development options for astrometric observing systems are also discussed

Carbon and nitrogen dynamics: Greenhouse gases in groundwater beneath a constructed wetland treating municipal wastewater

Conference oral presentationConstructed wetlands (CW) act as nitrogen (N) sinks and reactors facilitating a number of physical, chemical and biological processes. The N removal efficiency of through-flowing water in such systems when used to treat municipal wastewater is variable. Their overall removal efficiencies do not specifically explain which N species have been removed by physical attenuation, and by biological assimilation or transformation to other forms. A wider understanding of how N removal occurs would help elucidate how losses of N and associated gases from CW impact on water and air quality. The objective of this study is to investigate the C and N cycling processes in the porewater of soils immediately adjacent, up-gradient and down- gradient to helophyte —vegetated CW cells

A Deep Radio Survey of Abell 2125 III: The Cluster Core - Merging and Stripping

We use radio, near-IR, optical, and X-ray observations to examine dynamic processes in the central region of Abell 2125. In addition to the central triple, including members of both major dynamical subsystems identified from a redshift survey, this region features a galaxy showing strong evidence for ongoing gas stripping during a high-velocity passage through the gas in the cluster core. The disk galaxy C153 exhibits a plume stretching toward the cluster center seen in soft X-rays by Chandra, parts of which are also seen in [O II] emission and near-UV continuum light. HST imaging shows a distorted disk, with star-forming knots asymmetrically distributed and remnant spiral structure possibly defined by dust lanes. The stars and ionized gas in its disk are kinematically decoupled, demonstrating that pressure stripping must be important, and that tidal disruption is not the only mechanism at work. Comparison of the gas properties seen in the X-ray and optical data on the plume highlight significant features of the history of stripped gas in the intracluster medium. The nucleus of C153 also hosts an AGN, shown by the weak and distorted extended radio emission and a radio compact core. The unusual strength of the stripping signatures in this instance is likely related to the high relative velocity of the galaxy with respect to the intracluster medium, during a cluster/cluster merger, and its passage very near the core of the cluster. Another sign of recent dynamical events is diffuse starlight asymmetrically placed about the central triple in a cD envelope. Transient and extreme dynamical events as seen in Abell 2125 may be important drivers of galaxy evolution in the cores of rich clusters.Comment: 36 pages, 16 figures, accepted AJ, paper with full resolution figures is available at http:www.aoc.nrao.edu/~fowen/papers/a2125/a2125paper3.ps.g