Publications (66)49.18 Total impact
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Dataset: J Theor Biol 2004 Roeland M H Merks
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Chapter: A Framework for Multiscale and Multiscience Modeling and Numerical Simulations
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ABSTRACT: The Complex Automata (CxA) methodology offers a new framework to develop multiscale and multiscience numerical simulations. The CxA approach assumes that a multiscale model can be formulated in terms of several coupled single-scale submodels. With concepts such as the scale separation map, the generic submodel execution loop and the coupling templates, one can define a multiscale modeling language which is a bridge between the application design and the computer implementation.06/2011: pages 2-8; -
Article: The discrete-dipole-approximation code ADDA: Capabilities and known limitations
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ABSTRACT: The open-source code ADDA is described, which implements the discrete dipole approximation (DDA), a method to simulate light scattering by finite 3D objects of arbitrary shape and composition. Besides standard sequential execution, ADDA can run on a multiprocessor distributed-memory system, parallelizing a single DDA calculation. Hence the size parameter of the scatterer is in principle limited only by total available memory and computational speed. ADDA is written in C99 and is highly portable. It provides full control over the scattering geometry (particle morphology and orientation, and incident beam) and allows one to calculate a wide variety of integral and angle-resolved scattering quantities (cross sections, the Mueller matrix, etc.). Moreover, ADDA incorporates a range of state-of-the-art DDA improvements, aimed at increasing the accuracy and computational speed of the method. We discuss both physical and computational aspects of the DDA simulations and provide a practical introduction into performing such simulations with the ADDA code. We also present several simulation results, in particular, for a sphere with size parameter 320 (100-wavelength diameter) and refractive index 1.05.Journal of Quantitative Spectroscopy and Radiative Transfer 03/2011; · 3.19 Impact Factor -
Article: Cellular Automata Simulations on a FPGA cluster.
IJHPCA. 01/2011; 25:193-204. -
Article: Heterogeneous Multiscale Simulations of Suspension Flow.
Multiscale Modeling & Simulation. 01/2011; 9:1301-1326. -
Conference Proceeding: A Principled Approach to Distributed Multiscale Computing, from Formalization to Execution.
IEEE 7th International Conference on E-Science, e-Science 2011, Workshop Proceedings, Stockholm, Sweden, December 5-8, 2011; 01/2011 -
Chapter: Optics of white blood cells: optical models, simulations, and experiments
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ABSTRACT: The role of white blood cells (WBCs), or leukocytes, is to control various disease conditions and eliminate invading microorganisms. Although these cells do most of their work outside the circulatory system, they use the blood for transportation to sites of infection. Five types of white blood cells are normally found in the circulating blood: two mononuclear types (lymphocytes and monocytes) and three types of granulocytes (eosinophils, basophils, and neutrophils). Their presence relative to all leukocytes in normal conditions is in the ranges 18–44%, 2.6–8.5%, 46–73%, 0–4.4%, and 0.2–1.2%, respectively. And their characteristic size is 6–10 µm [1]. Lymphocytes and monocytes are cells with clear, transparent cytoplasm and large round nucleii. The lymphocytes mediate highly specific immunity against microorganisms and other sources of foreign macromolecules. B lymphocytes confer immunity through the production of specific, soluble antibodies, while T lymphocytes direct a large variety of immunity functions, including killing cells that bear foreign molecules on their surface membranes. Granulocytes and monocytes can exit from blood vessels and migrate among the cells of many tissues. These cells play key roles in inflammation and phagocytosis. Contrary to mononuclear cells, the nucleus of granulocytes is separated into definite lobes with a very narrow filament or strand connecting the lobes. Usually, two to three lobes are observed. 4.1.2 Particle Identification and Characterization There exist two levels of scientific description of single particles in a disperse media: identification and characterization. Identification (also known as classification) means attributing the particles to one of several (usually predefined) classes, which Advanced Optical Flow Cytometry: Methods and Disease Diagnoses, First Edition. Edited by Valery V. Tuchin.01/2011: pages 63-93; , ISBN: 9783527409341 -
Article: Application of the discrete dipole approximation to very large refractive indices: Filtered coupled dipoles revived.
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ABSTRACT: We compared three formulations of the discrete dipole approximation (DDA) for simulation of light scattering by particles with refractive indices m=10+10i , 0.1+i , and 1.6+0.01i . These formulations include the filtered coupled dipoles (FCD), the lattice dispersion relation (LDR) and the radiative reaction correction. We compared the number of iterations required for the convergence of the iterative solver (proportional to simulation time) and the accuracy of final results. We showed that the LDR performance for m=10+10i is especially bad, while the FCD is a good option for all cases studied. Moreover, we analyzed the detailed structure of DDA errors and the spectrum of the DDA interaction matrix to understand the performance of the FCD. In particular, this spectrum, obtained with the FCD for particles smaller than the wavelength, falls into the bounds, physically implied for the spectrum of the infinite-dimensional integral scattering operator, contrary to two other DDA formulations. Finally, such extreme refractive indices can now be routinely simulated using modern desktop computers using the publicly available ADDA code, which includes an efficient implementation of the FCD.Physical Review E 09/2010; 82(3 Pt 2):036703. · 2.26 Impact Factor -
Chapter: Complex Automata: Multi-scale Modeling with Coupled Cellular Automata
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ABSTRACT: Cellular Automata (CA) are generally acknowledged to be a powerful way to describe and model natural phenomena [1–3]. There are even tempting claims that nature itself is one big (quantum) information processing system, e.g. [4], and that CA may actually be nature’s way to do this processing [5–7]. We will not embark on this philosophical road, but ask ourselves a more mundane question. Can we use CA to model the inherently multi-scale processes in nature and use these models for efficient simulations on digital computers?06/2010: pages 29-57; -
Chapter: Introduction to Modeling of Complex Systems Using Cellular Automata
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ABSTRACT: Since the sixteenth century there have been two main paradigms in the methodology of doing science. The first one is referred to as “the experimental” paradigm. During an experiment we observe, measure, and quantify natural phenomena in order to solve a specific problem, answer a question, or to decide whether a hypothesis is true or false. The second paradigm is known as “the theoretical” paradigm. A theory is generally understood as a fundamental, for instance logical and/or mathematical explanation of an observed natural phenomenon. Theory can be supported or falsified through experimentation.03/2010: pages 1-16; -
Article: Accuracy of the discrete dipole approximation for simulation of optical properties of gold nanoparticles
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ABSTRACT: We studied the accuracy of the discrete dipole approximation (DDA) for simulations of absorption and scattering spectra by gold nanoparticles (spheres, cubes, and rods ranging in size from 10 to 100 nm). We varied the dipole resolution and applied two DDA formulations, employing the standard lattice dispersion relation (LDR) and the relatively new filtered coupled dipoles (FCD) approach. The DDA with moderate dipole resolutions is sufficiently accurate for scattering efficiencies or positions of spectral peaks, but very inaccurate for e.g. values of absorption efficiencies in the near-IR. To keep relative errors of the latter within 10% about 10^7 dipoles per sphere are required. Surprisingly, errors for cubes are about 10 times smaller than that for spheres or rods, which we explain in terms of shape errors. The FCD is generally more accurate and leads to up to 2 times faster computations than the LDR. Therefore, we recommend FCD as the DDA formulation of choice for gold and other metallic nanoparticles.Journal of Nanophotonics 02/2010; 4(1):041585. · 1.57 Impact Factor -
Article: The influence of mitoses rate on growth dynamics of a cellular automata model of tumour growth.
Procedia CS. 01/2010; 1:971-978. -
Article: Multi-scale modelling in computational biomedicine.
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ABSTRACT: The inherent complexity of biomedical systems is well recognized; they are multi-scale, multi-science systems, bridging a wide range of temporal and spatial scales. This article reviews the currently emerging field of multi-scale modelling in computational biomedicine. Many exciting multi-scale models exist or are under development. However, an underpinning multi-scale modelling methodology seems to be missing. We propose a direction that complements the classic dynamical systems approach and introduce two distinct case studies, transmission of resistance in human immunodeficiency virus spreading and in-stent restenosis in coronary artery disease.Briefings in Bioinformatics 12/2009; 11(1):142-52. · 5.20 Impact Factor -
Article: Corrected momentum exchange method for lattice Boltzmann simulations of suspension flow.
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ABSTRACT: Standard methods for lattice Boltzmann simulations of suspended particles, based on the momentum exchange algorithm, might lack accuracy or violate Galilean invariance in some particular situations. Aiming at simulations of dense suspensions in high-shear flows, we motivate and investigate necessary correction terms. We propose an approach which, combining accurate treatments of fluid-structure interaction and moving boundaries, is able to preserve Galilean invariance in relevant orders and to improve the physical behavior of the system. We validate the approach in a comparison with standard methods in simple test problems.Physical Review E 04/2009; 79(3 Pt 2):036705. · 2.26 Impact Factor -
Article: Lees-Edwards boundary conditions for lattice Boltzmann suspension simulations.
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ABSTRACT: When sheared suspensions are simulated, Lees-Edwards boundary conditions allow more realistic computational setups as they remove the need of a domain bounded by shearing walls (as in Couette-type flow) which bias typical flow structures. Lees-Edwards boundary conditions therefore allow investigation of pure bulk properties in a quasi-infinite system. In addition, they improve the computational efficiency of the simulations as the whole domain can be used to calculate averages. We propose an implementation of Lees-Edwards boundary conditions for lattice Boltzmann simulations of particulate suspensions, combined with an accurate treatment of fluid-particle interactions. The algorithm is validated using a simple single-particle benchmark and further applied to a fully resolved suspension flow. Shear-thickening behavior, which is prolonged to higher shear rates as compared to Couette flow results, could be observed.Physical Review E 04/2009; 79(3 Pt 2):036706. · 2.26 Impact Factor -
Article: Compute Bound and I/O Bound Cellular Automata Simulations on FPGA Logic.
TRETS. 01/2009; 1. -
Article: Is there a difference between T-and B-lymphocyte morphology?
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ABSTRACT: We characterize T-and B-lymphocytes from several donors, determining cell diameter, ratio of nucleus to cell diameter, and re-fractive index of the nucleus and cytoplasm for each individual cell. We measure light-scattering profiles with a scanning flow cytometer and invert the signals using a coated sphere as an optical model of the cell and by relying on a global optimization technique. The main difference in morphology of T-and B-lymphocytes is found to be the larger mean diameters of the latter. However, the difference is smaller than the natural biological variability of a single cell. We propose nuclear inhomogeneity as a possible reason for the deviation of mea-sured light-scattering profiles from real lymphocytes from those ob-tained from the coated sphere model.Journal of Biomedical Optics 01/2009; 14:064036. · 3.16 Impact Factor -
Article: Asymptotic analysis of Complex Automata models for reaction-diffusion systems
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ABSTRACT: Complex Automata (CxA) have been recently introduced as a paradigm to simulate multiscale multiscience systems as a collection of generalized Cellular Automata on different scales. The approach yields numerical and computational challenges and can become a powerful tool for the simulation of particular complex systems. We present a mathematical framework for CxA modeling to investigate the behavior of the model depending on scale separation and modeling choices. For a simple CxA model for a reaction–diffusion process, we define a Complex Automata model, deriving theoretical error estimates, which are numerically validated.Applied Numerical Mathematics. 01/2009; 59:2023-2034. -
Article: Erythrocyte lysis in isotonic solution of ammonium chloride: theoretical modeling and experimental verification.
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ABSTRACT: A mathematical model of erythrocyte lysis in isotonic solution of ammonium chloride is presented in frames of a statistical approach. The model is used to evaluate several parameters of mature erythrocytes (volume, surface area, hemoglobin concentration, number of anionic exchangers on membrane, elasticity and critical tension of membrane) through their sphering and lysis measured by a scanning flow cytometer (SFC). SFC allows measuring the light-scattering pattern (indicatrix) of an individual cell over the angular range from 10 degrees to 60 degrees . Comparison of the experimentally measured and theoretically calculated light scattering patterns allows discrimination of spherical from non-spherical erythrocytes and evaluation of volume and hemoglobin concentration for individual spherical cells. Three different processes were applied for erythrocytes sphering: (1) colloid osmotic lysis in isotonic solution of ammonium chloride, (2) isovolumetric sphering in the presence of sodium dodecyl sulphate and albumin in neutrally buffered isotonic saline, and (3) osmotic fragility test in hypotonic media. For the hemolysis in ammonium chloride, the evolution of distributions of sphered erythrocytes on volume and hemoglobin content was monitored in real-time experiments. The analysis of experimental data was performed in the context of a statistical approach, taking into account that parameters of erythrocytes vary from cell to cell.Journal of Theoretical Biology 04/2008; 251(1):93-107. · 2.21 Impact Factor -
Conference Proceeding: Scale-Splitting Error in Complex Automata Models for Reaction-Diffusion Systems.
Computational Science - ICCS 2008, 8th International Conference, Kraków, Poland, June 23-25, 2008, Proceedings, Part II; 01/2008
Top co-authors
Top Journals
Institutions
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1994–2013
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Universiteit van Amsterdam
- • Department of Computational Science
- • Faculty of Science
- • Department of Computer Systems
Amsterdam, North Holland, Netherlands
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2004–2005
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Sobolev Institute of Mathematics of the Siberian Branch of the Russian Academy of Sciences
Novosibirsk, Novosibirskaya Oblast', Russia
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