Alfons G. Hoekstra

The discrete dipole approximation: An overview and recent developments

We present a review of the discrete dipole approximation (DDA), which is a general method to simulate light scattering by arbitrarily shaped particles. We put the method in historical context and discuss recent developments, taking the viewpoint of a general framework based on the integral equations for the electric field. We review both the theory of the DDA and its numerical aspects, the latter being of critical importance for any practical application of the method. Finally, the position of the DDA among other methods of light scattering simulation is shown and possible future developments are discussed.

Optical and non-optical methods for detection and characterization of microparticles and exosomes

Summary.  Microparticles and exosomes are cell‐derived microvesicles present in body fluids that play a role in coagulation, inflammation, cellular homeostasis and survival, intercellular communication, and transport. Despite increasing scientific and clinical interest, no standard procedures are available for the isolation, detection and characterization of microparticles and exosomes, because their size is below the reach of conventional detection methods. Our objective is to give an overview of currently available and potentially applicable methods for optical and non‐optical determination of the size, concentration, morphology, biochemical composition and cellular origin of microparticles and exosomes. The working principle of all methods is briefly discussed, as well as their applications and limitations based on the underlying physical parameters of the technique. For most methods, the expected size distribution for a given microvesicle population is determined. The explanations of the physical background and the outcomes of our calculations provide insights into the capabilities of each method and make a comparison possible between the discussed methods. In conclusion, several (combinations of) methods can detect clinically relevant properties of microparticles and exosomes. These methods should be further explored and validated by comparing measurement results so that accurate, reliable and fast solutions come within reach.

The discrete dipole approximation for simulation of light scattering by particles much larger than the wavelength

In this paper we investigate the capabilities of the discrete dipole approximation (DDA) to simulate scattering from particles that are much larger than the wavelength of the incident light, and describe an optimized publicly available DDA computer program that processes the large number of dipoles required for such simulations. Numerical simulations of light scattering by spheres with size parameters x up to 160 and 40 for refractive index m ¼ 1:05 and 2, respectively, are presented and compared with exact results of the Mie theory. Errors of both integral and angle-resolved scattering quantities generally increase with m and show no systematic dependence on x: Computational times increase steeply with both x and m, reaching values of more than 2 weeks on a cluster of 64 processors. The main distinctive feature of the computer program is the ability to parallelize a single DDA simulation over a cluster of computers, which allows it to simulate light scattering by very large particles, like the ones that are considered in this paper. Current limitations and possible ways for improvement are discussed. r 2007 Elsevier Ltd. All rights reserved.

The distributed ASCI Supercomputer project

The Distributed ASCI Supercomputer (DAS) is a homogeneous wide-area distributed system consisting of four cluster computers at different locations. DAS has been used for research on communication software, parallel languages and programming systems, schedulers, parallel applications, and distributed applications. The paper gives a preview of the most interesting research results obtained so far in the DAS project.

Lattice-Boltzmann hydrodynamics on parallel systems

Realistic lattice-Boltzmann simulations often require large amounts of computational resources and are therefore executed on parallel systems. Generally, parallelization is based on one- and two-dimensional decomposition of the computational grid in equal subvolumes, and load balancing is completely ignored for simplicity. Besides reviewing the existing parallelization strategies we report here a new approach based on the Orthogonal Recursive Bisection (ORB) method. To illustrate the different decomposition methods, two realistic applications were simulated, namely fluid flow in random fibre networks and flow in a centrifugal elutriation chamber. For heterogeneously distributed workloads, the ORB method is found to be 12 to 60% more efficient compared to traditional parallelization strategies. It is shown that high parallel efficiencies can be obtained for both homogeneously and heterogeneously distributed workloads, thus supporting efficient simulations of a variety of realistic systems.

Advances in Grid Computing - EGC 2005

Telemedical Applications and Grid Technology.- Statistical Modeling and Segmentation in Cardiac MRI Using a Grid Computing Approach.- A Grid Molecular Simulator for E-Science.- Application Driven Grid Developments in the OpenMolGRID Project.- ATLAS Data Challenge 2: A Massive Monte Carlo Production on the Grid.- High Throughput Computing for Spatial Information Processing (HIT-SIP) System on Grid Platform.- The University of Virginia Campus Grid: Integrating Grid Technologies with the Campus Information Infrastructure.- M-Grid: Using Ubiquitous Web Technologies to Create a Computational Grid.- GLIDE: A Grid-Based Light-Weight Infrastructure for Data-Intensive Environments.- HotGrid: Graduated Access to Grid-Based Science Gateways.- Principles of Transactional Grid Deployment.- Experience with the International Testbed in the CrossGrid Project.- eNANOS Grid Resource Broker.- GridARM: Askalons Grid Resource Management System.- A Super-Peer Model for Building Resource Discovery Services in Grids: Design and Simulation Analysis.- Ontology-Based Grid Index Service for Advanced Resource Discovery and Monitoring.- Grid Service Based Collaboration for VL-e: Requirements, Analysis and Design.- A Fully Decentralized Approach to Grid Service Discovery Using Self-organized Overlay Networks.- Dynamic Parallelization of Grid-Enabled Web Services.- Automatic Composition and Selection of Semantic Web Services.- Grid Application Monitoring and Debugging Using the Mercury Monitoring System.- Interactive Visualization of Grid Monitoring Data on Multiple Client Platforms.- GridBench: A Workbench for Grid Benchmarking.- A Method for Estimating the Execution Time of a Parallel Task on a Grid Node.- Performance of a Parallel Astrophysical N-Body Solver on Pan-European Computational Grids.- Introducing Grid Speedup ? : A Scalability Metric for Parallel Applications on the Grid.- A Dynamic Key Infrastructure for Grid.- Experiences of Applying Advanced Grid Authorisation Infrastructures.- Towards a Grid-wide Intrusion Detection System.- International Grid CA Interworking, Peer Review and Policy Management Through the European DataGrid Certification Authority Coordination Group.- Grid Enabled Optimization.- Towards a Coordination Model for Parallel Cooperative P2P Multi-objective Optimization.- A Grid-Oriented Genetic Algorithm.- A Probabilistic Approach for Task and Result Certification of Large-Scale Distributed Applications in Hostile Environments.- A Service Oriented Architecture for Decision Making in Engineering Design.- A Grid Architecture for Comfortable Robot Control.- The Grid-Ireland Deployment Architecture.- UNICORE as Uniform Grid Environment for Life Sciences.- MyGridFTP: A Zero-Deployment GridFTP Client Using the .NET Framework.- On Using Jini and JXTA in Lightweight Grids.- Ticket-Based Grid Services Architecture for Dynamic Virtual Organizations.- Heterogeneity of Computing Nodes for Grid Computing.- Effective Job Management in the Virtual Laboratory.- Workflow Management in the CrossGrid Project.- Workflow-Oriented Collaborative Grid Portals.- Contextualised Workflow Execution in MyGrid.- Real World Workflow Applications in the Askalon Grid Environment.- OpenMolGRID: Using Automated Workflows in GRID Computing Environment.- Implementation of Replication Methods in the Grid Environment.- A Secure Wrapper for OGSA-DAI.- XDTM: The XML Data Type and Mapping for Specifying Datasets.- iGrid, a Novel Grid Information Service.- A Grid-Enabled Digital Library System for Natural Disaster Metadata.- Optimising Parallel Applications on the Grid Using Irregular Array Distributions.- Dynamic Adaptation for Grid Computing.- Improving Multilevel Approach for Optimizing Collective Communications in Computational Grids.- Rough Set Based Computation Times Estimation on Knowledge Grid.- A Behavior Characteristics-Based Reputation Evaluation Method for Grid Entities.- Dynamic Policy Management Framework for Partial Policy Information.- Security Architecture for Open Collaborative Environment.- An Experimental Information Grid Environment for Cultural Heritage Knowledge Sharing.- Implementation of Federated Databases Through Updatable Views.- Data Mining Tools: From Web to Grid Architectures.- Fault-Tolerant Scheduling for Bag-of-Tasks Grid Applications.- The Design and Implementation of the KOALA Co-allocating Grid Scheduler.- A Multi-agent Infrastructure and a Service Level Agreement Negotiation Protocol for Robust Scheduling in Grid Computing.- Towards Quality of Service Support for Grid Workflows.- Transparent Fault Tolerance for Grid Applications.- Learning Automata Based Algorithms for Mapping of a Class of Independent Tasks over Highly Heterogeneous Grids.- Grid Resource Broker Using Application Benchmarking.- The Grid Block Device: Performance in LAN and WAN Environments.- WS-Based Discovery Service for Grid Computing Elements.- Rapid Distribution of Tasks on a Commodity Grid.- Modeling Execution Time of Selected Computation and Communication Kernels on Grids.- Parallel Checkpointing on a Grid-Enabled Java Platform.- Fault Tolerance in the R-GMA Information and Monitoring System.- Deployment of Grid Gateways Using Virtual Machines.- Development of Cactus Driver for CFD Analyses in the Grid Computing Environment.- Striped Replication from Multiple Sites in the Grid Environment.- The Gridkit Distributed Resource Management Framework.- Stochastic Approach for Secondary Storage Data Access Cost Estimation.- A Cluster-Based Dynamic Load Balancing Middleware Protocol for Grids.- Reconfigurable Scientific Applications on GRID Services.- Geographic Information Systems Grid.- Tools for Distributed Development and Deployment on the Grid.- DNS-Based Discovery System in Service Oriented Programming.- Experiences with Deploying Legacy Code Applications as Grid Services Using GEMLCA,.- A Framework for Job Management in the NorduGrid ARC Middleware.- Data Management in Flood Prediction.- Adaptive Task Scheduling in Computational GRID Environments.- Large-Scale Computational Finance Applications on the Open Grid Service Environment.- Localized Communications of Data Parallel Programs on Multi-cluster Grid Systems.- VIRGO: Virtual Hierarchical Overlay Network for Scalable Grid Computing.- A Monitoring Architecture for Control Grids.- Mobile-to-Grid Middleware: Bridging the Gap Between Mobile and Grid Environments.- Role of N1 Technology in the Next Generation Grids Middleware.- Optimizing Grid Application Setup Using Operating System Mobility.- GriddLeS Enhancements and Building Virtual Applications for the GRID with Legacy Components.- Application Oriented Brokering in Medical Imaging: Algorithms and Software Architecture.- A Performance Contract System in a Grid Enabling, Component Based Programming Environment.- A WSRF Based Shopping Cart System.- Grid Access Middleware for Handheld Devices.- An Extendable GRID Application Portal.- A Task Replication and Fair Resource Management Scheme for Fault Tolerant Grids.- CrossGrid Integrated Workflow Management System.- Load Balancing by Changing the Graph Connectivity on Heterogeneous Clusters.- Threat Model for Grid Security Services.- A Loosely Coupled Application Model for Grids.- A Locking Protocol for a Distributed Computing Environment.- Grid-Based SLA Management.- A Heuristic Algorithm for Mapping Parallel Applications on Computational Grids.- A Bypass of Cohens Impossibility Result.- Mapping Workflows onto Grid Resources Within an SLA Context.- iShare - Open Internet Sharing Built on Peer-to-Peer and Web.- A Service-Based Architecture for Integrating Globus 2 and Globus 3.- The CampusGrid Test Bed at Forschungszentrum Karlsruhe.- A Model for Flexible Service Use and Secure Resource Management.- Online Performance Monitoring and Analysis of Grid Scientific Workflows.- WebGrid: A New Paradigm for Web System.- Dynamic Failure Management for Parallel Applications on Grids.- A Novel Intrusion Detection Method for Mobile Ad Hoc Networks.

The application of multiscale modelling to the process of development and prevention of stenosis in a stented coronary artery

The inherent complexity of biomedical systems is well recognized; they are multiscale, multiscience systems, bridging a wide range of temporal and spatial scales. While the importance of multiscale modelling in this context is increasingly recognized, there is little underpinning literature on the methodology and generic description of the process. The COAST (complex autonoma simulation technique) project aims to address this by developing a multiscale, multiscience framework, coined complex autonoma (CxA), based on a hierarchical aggregation of coupled cellular automata (CA) and agent-based models (ABMs). The key tenet of COAST is that a multiscale system can be decomposed into N single-scale CA or ABMs that mutually interact across the scales. Decomposition is facilitated by building a scale separation map on which each single-scale system is represented according to its spatial and temporal characteristics. Processes having well-separated scales are thus easily identified as the components of the multiscale model. This paper focuses on methodology, introduces the concept of the CxA and demonstrates its use in the generation of a multiscale model of the physical and biological processes implicated in a challenging and clinically relevant problem, namely coronary artery in-stent restenosis.

Light scattering by red blood cells in ektacytometry: Fraunhofer versus anomalous diffraction

In the present literature on ektacytometry, small angle light scattering by ellipsoidal red blood cells is commonly approximated by Fraunhofer diffraction. Calculations on a sphere with the size and relative refractive index of a red cell, however, show that Fraunhofer diffraction deviates significantly from exact Mie theory. Anomalous diffraction is found to be a much better approximation. The anomalous diffraction theory is used to calculate the intensity distribution of the light scattered by an ellipsoidally deformed red blood cell. The derived expression shows that the ellipticity of isointensity curves in forward scattered light are equal to the ellipticity of the red blood cell. The theoretical expression is fitted to the intensity patterns measured with an ektacytometer. For the small observation angles used in ektacytometry, the experimental results confirm the validity of the anomalous diffraction approach.

Experimental and theoretical study of light scattering by individual mature red blood cells by use of scanning flow cytometry and a discrete dipole approximation

Elastic light scattering by mature red blood cells (RBCs) was theoretically and experimentally analyzed by use of the discrete dipole approximation (DDA) and scanning flow cytometry (SFC), respectively. SFC permits measurement of the angular dependence of the light-scattering intensity (indicatrix) of single particles. A mature RBC is modeled as a biconcave disk in DDA simulations of light scattering. We have studied the effect of RBC orientation related to the direction of the light incident upon the indicatrix. Numerical calculations of indicatrices for several axis ratios and volumes of RBC have been carried out. Comparison of the simulated indicatrices and indicatrices measured by SFC showed good agreement, validating the biconcave disk model for a mature RBC. We simulated the light-scattering output signals from the SFC with the DDA for RBCs modeled as a disk-sphere and as an oblate spheroid. The biconcave disk, the disk-sphere, and the oblate spheroid models have been compared for two orientations, i.e., face-on and rim-on incidence, relative to the direction of the incident beam. Only the oblate spheroid model for rim-on incidence gives results similar to those of the rigorous biconcave disk model.

Simulating Complex Systems by Cellular Automata

Deeply rooted in fundamental research in Mathematics and Computer Science, Cellular Automata (CA) are recognized as an intuitive modeling paradigm for Complex Systems. Already very basic CA, with extremely simple micro dynamics such as the Game of Life, show an almost endless display of complex emergent behavior. Conversely, CA can also be designed to produce a desired emergent behavior, using either theoretical methodologies or evolutionary techniques. Meanwhile, beyond the original realm of applications - Physics, Computer Science, and Mathematics CA have also become work horses in very different disciplines such as epidemiology, immunology, sociology, and finance. In this context of fast and impressive progress, spurred further by the enormous attraction these topics have on students, this book emerges as a welcome overview of the field for its practitioners, as well as a good starting point for detailed study on the graduate and post-graduate level. The book contains three parts, two major parts on theory and applications, and a smaller part on software. The theory part contains fundamental chapters on how to design and/or apply CA for many different areas. In the applications part a number of representative examples of really using CA in a broad range of disciplines is provided - this part will give the reader a good idea of the real strength of this kind of modeling as well as the incentive to apply CA in their own field of study. Finally, we included a smaller section on software, to highlight the important work that has been done to create high quality problem solving environments that allow to quickly and relatively easily implement a CA model and run simulations, both on the desktop and if needed, on High Performance Computing infrastructures.