Constriction flows of monodisperse linear entangled polymers: Multiscale modeling and flow visualization

We explore both the rheology and complex flow behavior of monodisperse polymer melts. Adequate quantities of monodisperse polymer were synthesized in order that both the materials rheology and microprocessing behavior could be established. In parallel, we employ a molecular theory for the polymer rheology that is suitable for comparison with experimental rheometric data and numerical simulation for microprocessing flows. The model is capable of matching both shear and extensional data with minimal parameter fitting. Experimental data for the processing behavior of monodisperse polymers are presented for the first time as flow birefringence and pressure difference data obtained using a Multipass Rheometer with an 11:1 constriction entry and exit flow. Matching of experimental processing data was obtained using the constitutive equation with the Lagrangian numerical solver, FLOWSOLVE. The results show the direct coupling between molecular constitutive response and macroscopic processing behavior, and differentiate flow effects that arise separately from orientation and stretch. (c) 2005 The Society of Rheology.

Modeling hybridoma cell metabolism using a generic genome-scale metabolic model of Mus musculus

The reconstructed cellular metabolic network of Mus musculus, based on annotated genomic data, pathway databases, and currently available biochemical and physiological information, is presented. Although incomplete, it represents the first attempt to collect and characterize the metabolic network of a mammalian cell on the basis of genomic data. The reaction network is generic in nature and attempts to capture the carbon, energy, and nitrogen metabolism of the cell. The metabolic reactions were compartmentalized between the cytosol and the mitochondria, including transport reactions between the compartments and the extracellular medium. The reaction list consists of 872 internal metabolites involved in a total of 1220 reactions, whereof 473 relate to known open reading frames. Initial in silico analysis of the reconstructed model is presented.

Reply to comment by A. G. J. Hilberts and P. A. Troch on "Influence of capillarity on a simple harmonic oscillating water table: Sand column experiments and modeling"

We thank Hilberts and Troch [2006] for their comment on our paper [Cartwright et al, 2005]. Before proceeding with our specific replies to the comments we would first like to clarify the definitions and meanings of equations (1)-(3) as presented by Hilberts and Troch [2006]. First, equation (1) is the fundamental definition of the (complex) effective porosity as derived by Nielsen and Perrochet [2000]. Equations (2) and (3), however, represent the linear frequency response function of the water table in the sand column responding to simple harmonic forcing. This function, which was validated by Nielsen and Perrochet [2000], provides an alternative method for estimating the complex effective porosity from the experimental sand column data in the absence of direct measurements of h_(tot) (which are required if equation (1) is to be used).

Biomechanics of the rostrum in crocodilians: A comparative analysis using finite-element modeling

This article reports the use of simple beam and finite-element models to investigate the relationship between rostral shape and biomechanical performance in living crocodilians under a range of loading conditions. Load cases corresponded to simple biting, lateral head shaking, and twist feeding behaviors. The six specimens were chosen to reflect, as far as possible, the full range of rostral shape in living crocodilians: a juvenile Caiman crocodilus, subadult Alligator mississippiensis and Crocodylus johnstoni, and adult Caiman crocodilus, Melanosuchus niger, and Paleosuchus palpebrosus. The simple beam models were generated using morphometric landmarks from each specimen. Three of the finite-element models, the A. mississippiensis, juvenile Caiman crocodilus, and the Crocodylus johnstoni, were based on CT scan data from respective specimens, but these data were not available for the other models and so these-the adult Caiman crocodilus, M. niger, and P. palpebrosus-were generated by morphing the juvenile Caiman crocodilus mesh with reference to three-dimensional linear distance measured from specimens. Comparison of the mechanical performance of the six finite-element models essentially matched results of the simple beam models: relatively tall skulls performed best under vertical loading and tall and wide skulls performed best under torsional loading. The widely held assumption that the platyrostral (dorsoventrally flattened) crocodilian skull is optimized for torsional loading was not supported by either simple beam theory models or finite-element modeling. Rather than being purely optimized against loads encountered while subduing and processing food, the shape of the crocodilian rostrum may be significantly affected by the hydrodynamic constraints of catching agile aquatic prey. This observation has important implications for our understanding of biomechanics in crocodilians and other aquatic reptiles.

Measuring and predicting the dynamics of linear monodisperse entangled polymers in rapid flow through an abrupt contraction. A small angle neutron scattering study

Small-angle neutron scattering measurements on a series of monodisperse linear entangled polystyrene melts in nonlinear flow through an abrupt 4:1 contraction have been made. Clear signatures of melt deformation and subsequent relaxation can be observed in the scattering patterns, which were taken along the centerline. These data are compared with the predictions of a recently derived molecular theory. Two levels of molecular theory are used: a detailed equation describing the evolution of molecular structure over all length scales relevant to the scattering data and a simplified version of the model, which is suitable for finite element computations. The velocity field for the complex melt flow is computed using the simplified model and scattering predictions are made by feeding these flow histories into the detailed model. The modeling quantitatively captures the full scattering intensity patterns over a broad range of data with independent variation of position within the contraction geometry, bulk flow rate and melt molecular weight. The study provides a strong, quantitative validation of current theoretical ideas concerning the microscopic dynamics of entangled polymers which builds upon existing comparisons with nonlinear mechanical stress data. Furthermore, we are able to confirm the appreciable length scale dependence of relaxation in polymer melts and highlight some wider implications of this phenomenon.

Modeling and exploiting behavior patterns in dynamic environments

This paper presents a new approach to improving the effectiveness of autonomous systems that deal with dynamic environments. The basis of the approach is to find repeating patterns of behavior in the dynamic elements of the system, and then to use predictions of the repeating elements to better plan goal directed behavior. It is a layered approach involving classifying, modeling, predicting and exploiting. Classifying involves using observations to place the moving elements into previously defined classes. Modeling involves recording features of the behavior on a coarse grained grid. Exploitation is achieved by integrating predictions from the model into the behavior selection module to improve the utility of the robot's actions. This is in contrast to typical approaches that use the model to select between different strategies or plays. Three methods of adaptation to the dynamic features of the environment are explored. The effectiveness of each method is determined using statistical tests over a number of repeated experiments. The work is presented in the context of predicting opponent behavior in the highly dynamic and multi-agent robot soccer domain (RoboCup)

Towards a Modeling Environment for Earth Systems Simulations

The developments of models in Earth Sciences, e.g. for earthquake prediction and for the simulation of mantel convection, are fare from being finalized. Therefore there is a need for a modelling environment that allows scientist to implement and test new models in an easy but flexible way. After been verified, the models should be easy to apply within its scope, typically by setting input parameters through a GUI or web services. It should be possible to link certain parameters to external data sources, such as databases and other simulation codes. Moreover, as typically large-scale meshes have to be used to achieve appropriate resolutions, the computational efficiency of the underlying numerical methods is important. Conceptional this leads to a software system with three major layers: the application layer, the mathematical layer, and the numerical algorithm layer. The latter is implemented as a C/C++ library to solve a basic, computational intensive linear problem, such as a linear partial differential equation. The mathematical layer allows the model developer to define his model and to implement high level solution algorithms (e.g. Newton-Raphson scheme, Crank-Nicholson scheme) or choose these algorithms form an algorithm library. The kernels of the model are generic, typically linear, solvers provided through the numerical algorithm layer. Finally, to provide an easy-to-use application environment, a web interface is (semi-automatically) built to edit the XML input file for the modelling code. In the talk, we will discuss the advantages and disadvantages of this concept in more details. We will also present the modelling environment escript which is a prototype implementation toward such a software system in Python (see www.python.org). Key components of escript are the Data class and the PDE class. Objects of the Data class allow generating, holding, accessing, and manipulating data, in such a way that the actual, in the particular context best, representation is transparent to the user. They are also the key to establish connections with external data sources. PDE class objects are describing (linear) partial differential equation objects to be solved by a numerical library. The current implementation of escript has been linked to the finite element code Finley to solve general linear partial differential equations. We will give a few simple examples which will illustrate the usage escript. Moreover, we show the usage of escript together with Finley for the modelling of interacting fault systems and for the simulation of mantel convection.