45 results on '"Koumoutsakos P"'
Search Results
2. Backpropagation algorithms and Reservoir Computing in Recurrent Neural Networks for the forecasting of complex spatiotemporal dynamics
- Author
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Massachusetts Institute of Technology. Department of Mechanical Engineering, Vlachas, P.R., Pathak, J., Hunt, B.R., Sapsis, Themistoklis Panagiotis, Girvan, M., Ott, E., Koumoutsakos, P., Massachusetts Institute of Technology. Department of Mechanical Engineering, Vlachas, P.R., Pathak, J., Hunt, B.R., Sapsis, Themistoklis Panagiotis, Girvan, M., Ott, E., and Koumoutsakos, P.
- Abstract
We examine the efficiency of Recurrent Neural Networks in forecasting the spatiotemporal dynamics of high dimensional and reduced order complex systems using Reservoir Computing (RC) and Backpropagation through time (BPTT) for gated network architectures. We highlight advantages and limitations of each method and discuss their implementation for parallel computing architectures. We quantify the relative prediction accuracy of these algorithms for the long-term forecasting of chaotic systems using as benchmarks the Lorenz-96 and the Kuramoto–Sivashinsky (KS) equations. We find that, when the full state dynamics are available for training, RC outperforms BPTT approaches in terms of predictive performance and in capturing of the long-term statistics, while at the same time requiring much less training time. However, in the case of reduced order data, large scale RC models can be unstable and more likely than the BPTT algorithms to diverge. In contrast, RNNs trained via BPTT show superior forecasting abilities and capture well the dynamics of reduced order systems. Furthermore, the present study quantifies for the first time the Lyapunov Spectrum of the KS equation with BPTT, achieving similar accuracy as RC. This study establishes that RNNs are a potent computational framework for the learning and forecasting of complex spatiotemporal systems., Army Research Office (Grant W911NF-17-1-0306)
- Published
- 2020
3. Learning robust low-rank approximation for crowdsourcing on Riemannian Manifold
- Author
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Koumoutsakos, P, Lees, M, Krzhizhanovskaya, V, Dongarra, J, Sloot, P, Li, Qian, Wang, Zhichao, Li, Gang, Cao, Yanan, Xiong, Gang, Guo, Li, Koumoutsakos, P, Lees, M, Krzhizhanovskaya, V, Dongarra, J, Sloot, P, Li, Qian, Wang, Zhichao, Li, Gang, Cao, Yanan, Xiong, Gang, and Guo, Li
- Abstract
Recently, crowdsourcing has attracted substantial research interest due to its efficiency in collecting labels for machine learning and computer vision tasks. This paper proposes a Rieman-nian manifold optimization algorithm, ROLA (Robust Low-rank Approximation), to aggregate the labels from a novel perspective. Specifically, a novel low-rank approximation model is proposed to capture underlying correlation among annotators meanwhile identify annotator-specific noise. More significantly, ROLA defines the label noise in crowdsourcing as annotator-specific noise, which can be well regularized by l2,1-norm. The proposed ROLA can improve the aggregation performance when compared with state-of-the-art crowdsourcing methods.
- Published
- 2017
4. C-start: optimal start of larval fish
- Author
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Gazzola, M., Van Rees, W. M., Koumoutsakos, P., Gazzola, M., Van Rees, W. M., and Koumoutsakos, P.
- Abstract
We investigate the C-start escape response of larval fish by combining flow simulations using remeshed vortex methods with an evolutionary optimization. We test the hypothesis of the optimality of C-start of larval fish by simulations of larval-shaped, two- and three-dimensional self-propelled swimmers. We optimize for the distance travelled by the swimmer during its initial bout, bounding the shape deformation based on the larval mid-line curvature values observed experimentally. The best motions identified within these bounds are in good agreement with in vivo experiments and show that C-starts do indeed maximize escape distances. Furthermore we found that motions with curvatures beyond the ones experimentally observed for larval fish may result in even larger escape distances. We analyse the flow field and find that the effectiveness of the C-start escape relies on the ability of pronounced C-bent body configurations to trap and accelerate large volumes of fluid, which in turn correlates with large accelerations of the swimmer
- Published
- 2017
5. Learning Robust Low-Rank Approximation for Crowdsourcing on Riemannian Manifold
- Author
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Koumoutsakos, P, Lees, M, Krzhizhanovskaya, V, Dongarra, J, Sloot, P, Li, Q, Wang, Z, Li, G, Cao, Y, Xiong, G, Guo, L, Koumoutsakos, P, Lees, M, Krzhizhanovskaya, V, Dongarra, J, Sloot, P, Li, Q, Wang, Z, Li, G, Cao, Y, Xiong, G, and Guo, L
- Abstract
Recently, crowdsourcing has attracted substantial research interest due to its efficiency in collecting labels for machine learning and computer vision tasks. This paper proposes a Rieman-nian manifold optimization algorithm, ROLA (Robust Low-rank Approximation), to aggregate the labels from a novel perspective. Specifically, a novel low-rank approximation model is proposed to capture underlying correlation among annotators meanwhile identify annotator-specific noise. More significantly, ROLA defines the label noise in crowdsourcing as annotator-specific noise, which can be well regularized by l2,1-norm. The proposed ROLA can improve the aggregation performance when compared with state-of-the-art crowdsourcing methods.
- Published
- 2017
6. Learning Robust Low-Rank Approximation for Crowdsourcing on Riemannian Manifold
- Author
-
Koumoutsakos, P, Lees, M, Krzhizhanovskaya, V, Dongarra, J, Sloot, P, Li, Q, Wang, Z, Li, G, Cao, Y, Xiong, G, Guo, L, Koumoutsakos, P, Lees, M, Krzhizhanovskaya, V, Dongarra, J, Sloot, P, Li, Q, Wang, Z, Li, G, Cao, Y, Xiong, G, and Guo, L
- Abstract
Recently, crowdsourcing has attracted substantial research interest due to its efficiency in collecting labels for machine learning and computer vision tasks. This paper proposes a Rieman-nian manifold optimization algorithm, ROLA (Robust Low-rank Approximation), to aggregate the labels from a novel perspective. Specifically, a novel low-rank approximation model is proposed to capture underlying correlation among annotators meanwhile identify annotator-specific noise. More significantly, ROLA defines the label noise in crowdsourcing as annotator-specific noise, which can be well regularized by l2,1-norm. The proposed ROLA can improve the aggregation performance when compared with state-of-the-art crowdsourcing methods.
- Published
- 2017
7. Self-propulsion of a counter-rotating cylinder pair in a viscous fluid
- Author
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Van Rees, W.M. (author), Novati, G. (author), Koumoutsakos, P. (author), Van Rees, W.M. (author), Novati, G. (author), and Koumoutsakos, P. (author)
- Abstract
We study a self-propelling pair of steadily counter-rotating cylinders in simulations of a two-dimensional viscous fluid. We find two strikingly, opposite directions for the motion of the pair that is characterized by its width and rotational Reynolds number. At low Reynolds numbers and large widths, the cylinder pair moves similarly to an inviscid point vortex pair, while at higher Reynolds numbers and smaller widths, the pair moves in the opposite direction through a jet-like propulsion mechanism. Increasing further the Reynolds number, or decreasing the width, gives rise to non-polarised motion governed by the shedding direction and frequency of the boundary-layer vorticity. We discuss the fundamental physical mechanisms for these two types of motion and the transitions in the corresponding phase diagram. We discuss the fluid dynamics of each regime based on streamline plots, tracer particles, and the vorticity field. The counter rotating cylinder pair serves as a prototype for self-propelled bodies and suggests possible engineering devices composed of simple components and tunable by the rotation and width of the cylinder pair., Mechanical, Maritime and Materials Engineering
- Published
- 2015
8. Continuum Navier-Stokes modelling of water ow past fullerene molecules
- Author
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Walther, J. H., Popadic, A., Koumoutsakos, P., Praprotnik, M., Walther, J. H., Popadic, A., Koumoutsakos, P., and Praprotnik, M.
- Abstract
We present continuum simulations of water flow past fullerene molecules. The governing Navier-Stokes equations are complemented with the Navier slip boundary condition with a slip length that is extracted from related molecular dynamics simulations. We find that several quantities of interest as computed by the present model are in good agreement with results from atomistic and atomistic-continuum simulations at a fraction of the computational cost. We simulate the flow past a single fullerene and an array of fullerenes and demonstrate that such nanoscale flows can be computed efficiently by continuum flow solvers, allowing for investigations into spatiotemporal scales inaccessible to atomistic simulations.
- Published
- 2015
9. Continuum Navier-Stokes modelling of water flow past fullerene molecules
- Author
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Walther, J. H., Popadic, A., Koumoutsakos, P., Praprotnik, M., Walther, J. H., Popadic, A., Koumoutsakos, P., and Praprotnik, M.
- Abstract
We present continuum simulations of water flow past fullerene molecules. The governing Navier-Stokes equations are complemented with the Navier slip boundary condition with a slip length that is extracted from related molecular dynamics simulations. We find that several quantities of interest as computed by the present model are in good agreement with results from atomistic and atomistic-continuum simulations at a fraction of the computational cost. We simulate the flow past a single fullerene and an array of fullerenes and demonstrate that such nanoscale flows can be computed efficiently by continuum flow solvers, allowing for investigations into spatiotemporal scales inaccessible to atomistic simulations.
- Published
- 2015
10. Continuum Simulations of Water Flow in Carbon Nanotube Membranes
- Author
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Walther, Jens Honore, Popadic, A., Koumoutsakos, P., Praprotnik, M., Walther, Jens Honore, Popadic, A., Koumoutsakos, P., and Praprotnik, M.
- Published
- 2014
11. Continuum simulations of water flow in carbon nanotube membranes
- Author
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Popadić, A., Walther, Jens Honore, Koumoutsakos, P, Praprotnik, M., Popadić, A., Walther, Jens Honore, Koumoutsakos, P, and Praprotnik, M.
- Abstract
We propose the use of the Navier–Stokes equations subject to partial-slip boundary conditions to simulate water flows in Carbon NanoTube (CNT) membranes. The finite volume discretizations of the Navier–Stokes equations are combined with slip lengths extracted from molecular dynamics (MD) simulations to predict the pressure losses at the CNT entrance as well as the enhancement of the flow rate in the CNT. The flow quantities calculated from the present hybrid approach are in excellent agreement with pure MD results while they are obtained at a fraction of the computational cost. The method enables simulations of system sizes and times well beyond the present capabilities of MD simulations. Our simulations provide an asymptotic flow rate enhancement and indicate that the pressure losses at the CNT ends can be reduced by reducing their curvature. More importantly, our results suggest that flows at nanoscale channels can be described by continuum solvers with proper boundary conditions that reflect the molecular interactions of the liquid with the walls of the nanochannel.
- Published
- 2014
12. An Iterative Brinkman penalization for particle vortex methods
- Author
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Walther, Jens Honore, Hejlesen, Mads Mølholm, Leonard, A., Koumoutsakos, P., Walther, Jens Honore, Hejlesen, Mads Mølholm, Leonard, A., and Koumoutsakos, P.
- Abstract
We present an iterative Brinkman penalization method for the enforcement of the no-slip boundary condition in vortex particle methods. This is achieved by implementing a penalization of the velocity field using iteration of the penalized vorticity. We show that using the conventional Brinkman penalization method can result in an insufficient enforcement of solid boundaries. The specific problems of the conventional penalization method is discussed and three examples are presented by which the method in its current form has shown to be insufficient to consistently enforce the no-slip boundary condition. These are: the impulsively started flow past a cylinder, the impulsively started flow normal to a flat plate, and the uniformly accelerated flow normal to a flat plate. The iterative penalization algorithm is shown to give significantly improved results compared to the conventional penalization method for each of the presented flow cases
- Published
- 2013
13. Towards a living earth simulator
- Author
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Paolucci, M., Kossman, D., Conte, R., Lukowicz, P., Argyrakis, P., Blandford, A., Bonelli, G., Anderson, S., de Freitas, S., Edmonds, B., Gilbert, N., Gross, M., Kohlhammer, J., Koumoutsakos, P., Krause, A., Linnér, B. -O., Slusallek, P., Sorkine, O., Sumner, R. W., Helbing, D., Paolucci, M., Kossman, D., Conte, R., Lukowicz, P., Argyrakis, P., Blandford, A., Bonelli, G., Anderson, S., de Freitas, S., Edmonds, B., Gilbert, N., Gross, M., Kohlhammer, J., Koumoutsakos, P., Krause, A., Linnér, B. -O., Slusallek, P., Sorkine, O., Sumner, R. W., and Helbing, D.
- Abstract
The Living Earth Simulator (LES) is one of the core components of the FuturICT architecture. It will work as a federation of methods, tools, techniques and facilities supporting all of the FuturICT simulation-related activities to allow and encourage interactive exploration and understanding of societal issues. Society-relevant problems will be targeted by leaning on approaches based on complex systems theories and data science in tight interaction with the other components of FuturICT. The LES will evaluate and provide answers to real-world questions by taking into account multiple scenarios. It will build on present approaches such as agent-based simulation and modeling, multiscale modelling, statistical inference, and data mining, moving beyond disciplinary borders to achieve a new perspective on complex social systems.
- Published
- 2013
- Full Text
- View/download PDF
14. Towards a living earth simulator
- Author
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Paolucci, M., Kossman, D., Conte, R., Lukowicz, P., Argyrakis, P., Blandford, A., Bonelli, G., Anderson, S., de Freitas, S., Edmonds, B., Gilbert, N., Gross, M., Kohlhammer, J., Koumoutsakos, P, Krause, A., Linnér, Björn-Ola, Slusallek, P, Sorkine, O., Sumner, R. W., Helbing, D., Paolucci, M., Kossman, D., Conte, R., Lukowicz, P., Argyrakis, P., Blandford, A., Bonelli, G., Anderson, S., de Freitas, S., Edmonds, B., Gilbert, N., Gross, M., Kohlhammer, J., Koumoutsakos, P, Krause, A., Linnér, Björn-Ola, Slusallek, P, Sorkine, O., Sumner, R. W., and Helbing, D.
- Abstract
The Living Earth Simulator (LES) is one of the core components of the FuturICT architecture. It will work as a federation of methods, tools, techniques and facilities supporting all of the FuturICT simulation-related activities to allow and encourage interactive exploration and understanding of societal issues. Society-relevant problems will be targeted by leaning on approaches based on complex systems theories and data science in tight interaction with the other components of FuturICT. The LES will evaluate and provide answers to realworld questions by taking into account multiple scenarios. It will build on present approaches such as agent-based simulation and modeling, multiscale modelling, statistical inference, and data mining, moving beyond disciplinary borders to achieve a new perspective on complex social systems.
- Published
- 2012
- Full Text
- View/download PDF
15. Towards a living earth simulator
- Author
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Paolucci, M., Kossman, D., Conte, R., Lukowicz, P., Argyrakis, P., Blandford, A., Bonelli, G., Anderson, S., de Freitas, S., Edmonds, B., Gilbert, N., Gross, M., Kohlhammer, J., Koumoutsakos, P, Krause, A., Linnér, Björn-Ola, Slusallek, P, Sorkine, O., Sumner, R. W., Helbing, D., Paolucci, M., Kossman, D., Conte, R., Lukowicz, P., Argyrakis, P., Blandford, A., Bonelli, G., Anderson, S., de Freitas, S., Edmonds, B., Gilbert, N., Gross, M., Kohlhammer, J., Koumoutsakos, P, Krause, A., Linnér, Björn-Ola, Slusallek, P, Sorkine, O., Sumner, R. W., and Helbing, D.
- Abstract
The Living Earth Simulator (LES) is one of the core components of the FuturICT architecture. It will work as a federation of methods, tools, techniques and facilities supporting all of the FuturICT simulation-related activities to allow and encourage interactive exploration and understanding of societal issues. Society-relevant problems will be targeted by leaning on approaches based on complex systems theories and data science in tight interaction with the other components of FuturICT. The LES will evaluate and provide answers to realworld questions by taking into account multiple scenarios. It will build on present approaches such as agent-based simulation and modeling, multiscale modelling, statistical inference, and data mining, moving beyond disciplinary borders to achieve a new perspective on complex social systems.
- Published
- 2012
- Full Text
- View/download PDF
16. Towards a living earth simulator
- Author
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Paolucci, M., Kossman, D., Conte, R., Lukowicz, P., Argyrakis, P., Blandford, A., Bonelli, G., Anderson, S., de Freitas, S., Edmonds, B., Gilbert, N., Gross, M., Kohlhammer, J., Koumoutsakos, P., Krause, A., Linnér, B-O., Slusallek, P., Sorkine, O., Sumner, R.W., Helbing, D., Paolucci, M., Kossman, D., Conte, R., Lukowicz, P., Argyrakis, P., Blandford, A., Bonelli, G., Anderson, S., de Freitas, S., Edmonds, B., Gilbert, N., Gross, M., Kohlhammer, J., Koumoutsakos, P., Krause, A., Linnér, B-O., Slusallek, P., Sorkine, O., Sumner, R.W., and Helbing, D.
- Abstract
The Living Earth Simulator (LES) is one of the core components of the FuturICT architecture. It will work as a federation of methods, tools, techniques and facilities supporting all of the FuturICT simulation-related activities to allow and encourage interactive exploration and understanding of societal issues. Society-relevant problems will be targeted by leaning on approaches based on complex systems theories and data science in tight interaction with the other components of FuturICT. The LES will evaluate and provide answers to real-world questions by taking into account multiple scenarios. It will build on present approaches such as agent-based simulation and modeling, multiscale modelling, statistical inference, and data mining, moving beyond disciplinary borders to achieve a new perspective on complex social systems.
- Published
- 2012
17. Towards a living earth simulator
- Author
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Paolucci, M, Conte, R, Bonelli, G, Kossman, D, Gross, M, Koumoutsakos, P, Krause, A, Sorkine, O, Helbing, D, Lukowicz, P, Slusallek, P, Argyrakis, P, Blandford, A, Anderson, S, de Freitas, S, Edmonds, B, Gilbert, N, Kohlhammer, J, Linnér, B-O, Sumner, RW, Paolucci, M, Conte, R, Bonelli, G, Kossman, D, Gross, M, Koumoutsakos, P, Krause, A, Sorkine, O, Helbing, D, Lukowicz, P, Slusallek, P, Argyrakis, P, Blandford, A, Anderson, S, de Freitas, S, Edmonds, B, Gilbert, N, Kohlhammer, J, Linnér, B-O, and Sumner, RW
- Abstract
The Living Earth Simulator (LES) is one of the core components of the FuturICT architecture. It will work as a federation of methods, tools, techniques and facilities supporting all of the FuturICT simulation-related activities to allow and encourage interactive exploration and understanding of societal issues. Society-relevant problems will be targeted by leaning on approaches based on complex systems theories and data science in tight interaction with the other components of FuturICT. The LES will evaluate and provide answers to realworld questions by taking into account multiple scenarios. It will build on present approaches such as agent-based simulation and modeling, multiscale modelling, statistical inference, and data mining, moving beyond disciplinary borders to achieve a new perspective on complex social systems. © The Author(s) 2012.
- Published
- 2012
18. Towards a living earth simulator
- Author
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Paolucci, M, Kossman, D, Conte, R, Lukowicz, P, Argyrakis, P, Blandford, A, Bonelli, G, Anderson, S, de Freitas, S, Edmonds, B, Gilbert, N, Gross, M, Kohlhammer, J, Koumoutsakos, P, Krause, A, Linnér, BO, Slusallek, P, Sorkine, O, Sumner, RW, Helbing, D, Paolucci, M, Kossman, D, Conte, R, Lukowicz, P, Argyrakis, P, Blandford, A, Bonelli, G, Anderson, S, de Freitas, S, Edmonds, B, Gilbert, N, Gross, M, Kohlhammer, J, Koumoutsakos, P, Krause, A, Linnér, BO, Slusallek, P, Sorkine, O, Sumner, RW, and Helbing, D
- Abstract
The Living Earth Simulator (LES) is one of the core components of the FuturICT architecture. It will work as a federation of methods, tools, techniques and facilities supporting all of the FuturICT simulation-related activities to allow and encourage interactive exploration and understanding of societal issues. Society-relevant problems will be targeted by leaning on approaches based on complex systems theories and data science in tight interaction with the other components of FuturICT. The LES will evaluate and provide answers to realworld questions by taking into account multiple scenarios. It will build on present approaches such as agent-based simulation and modeling, multiscale modelling, statistical inference, and data mining, moving beyond disciplinary borders to achieve a new perspective on complex social systems. © The Author(s) 2012.
- Published
- 2012
19. Towards a living earth simulator
- Author
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Paolucci, M., Kossman, D., Conte, R., Lukowicz, P., Argyrakis, P., Blandford, A., Bonelli, G., Anderson, S., de Freitas, S., Edmonds, B., Gilbert, N., Gross, M., Kohlhammer, J., Koumoutsakos, P., Krause, A., Linnér, B-O., Slusallek, P., Sorkine, O., Sumner, R.W., Helbing, D., Paolucci, M., Kossman, D., Conte, R., Lukowicz, P., Argyrakis, P., Blandford, A., Bonelli, G., Anderson, S., de Freitas, S., Edmonds, B., Gilbert, N., Gross, M., Kohlhammer, J., Koumoutsakos, P., Krause, A., Linnér, B-O., Slusallek, P., Sorkine, O., Sumner, R.W., and Helbing, D.
- Abstract
The Living Earth Simulator (LES) is one of the core components of the FuturICT architecture. It will work as a federation of methods, tools, techniques and facilities supporting all of the FuturICT simulation-related activities to allow and encourage interactive exploration and understanding of societal issues. Society-relevant problems will be targeted by leaning on approaches based on complex systems theories and data science in tight interaction with the other components of FuturICT. The LES will evaluate and provide answers to real-world questions by taking into account multiple scenarios. It will build on present approaches such as agent-based simulation and modeling, multiscale modelling, statistical inference, and data mining, moving beyond disciplinary borders to achieve a new perspective on complex social systems.
- Published
- 2012
20. Towards a living earth simulator
- Author
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Paolucci, M., Kossman, D., Conte, R., Lukowicz, P., Argyrakis, P., Blandford, A., Bonelli, G., Anderson, S., de Freitas, S., Edmonds, B., Gilbert, N., Gross, M., Kohlhammer, J., Koumoutsakos, P, Krause, A., Linnér, Björn-Ola, Slusallek, P, Sorkine, O., Sumner, R. W., Helbing, D., Paolucci, M., Kossman, D., Conte, R., Lukowicz, P., Argyrakis, P., Blandford, A., Bonelli, G., Anderson, S., de Freitas, S., Edmonds, B., Gilbert, N., Gross, M., Kohlhammer, J., Koumoutsakos, P, Krause, A., Linnér, Björn-Ola, Slusallek, P, Sorkine, O., Sumner, R. W., and Helbing, D.
- Abstract
The Living Earth Simulator (LES) is one of the core components of the FuturICT architecture. It will work as a federation of methods, tools, techniques and facilities supporting all of the FuturICT simulation-related activities to allow and encourage interactive exploration and understanding of societal issues. Society-relevant problems will be targeted by leaning on approaches based on complex systems theories and data science in tight interaction with the other components of FuturICT. The LES will evaluate and provide answers to realworld questions by taking into account multiple scenarios. It will build on present approaches such as agent-based simulation and modeling, multiscale modelling, statistical inference, and data mining, moving beyond disciplinary borders to achieve a new perspective on complex social systems.
- Published
- 2012
- Full Text
- View/download PDF
21. Towards a living earth simulator
- Author
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Paolucci, M, Kossman, D, Conte, R, Lukowicz, P, Argyrakis, P, Blandford, A, Bonelli, G, Anderson, S, de Freitas, S, Edmonds, B, Gilbert, N, Gross, M, Kohlhammer, J, Koumoutsakos, P, Krause, A, Linnér, BO, Slusallek, P, Sorkine, O, Sumner, RW, Helbing, D, Paolucci, M, Kossman, D, Conte, R, Lukowicz, P, Argyrakis, P, Blandford, A, Bonelli, G, Anderson, S, de Freitas, S, Edmonds, B, Gilbert, N, Gross, M, Kohlhammer, J, Koumoutsakos, P, Krause, A, Linnér, BO, Slusallek, P, Sorkine, O, Sumner, RW, and Helbing, D
- Abstract
The Living Earth Simulator (LES) is one of the core components of the FuturICT architecture. It will work as a federation of methods, tools, techniques and facilities supporting all of the FuturICT simulation-related activities to allow and encourage interactive exploration and understanding of societal issues. Society-relevant problems will be targeted by leaning on approaches based on complex systems theories and data science in tight interaction with the other components of FuturICT. The LES will evaluate and provide answers to realworld questions by taking into account multiple scenarios. It will build on present approaches such as agent-based simulation and modeling, multiscale modelling, statistical inference, and data mining, moving beyond disciplinary borders to achieve a new perspective on complex social systems. © The Author(s) 2012.
- Published
- 2012
22. Towards a living earth simulator
- Author
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Paolucci, M., Kossman, D., Conte, R., Lukowicz, P., Argyrakis, P., Blandford, A., Bonelli, G., Anderson, S., de Freitas, S., Edmonds, B., Gilbert, N., Gross, M., Kohlhammer, J., Koumoutsakos, P, Krause, A., Linnér, Björn-Ola, Slusallek, P, Sorkine, O., Sumner, R. W., Helbing, D., Paolucci, M., Kossman, D., Conte, R., Lukowicz, P., Argyrakis, P., Blandford, A., Bonelli, G., Anderson, S., de Freitas, S., Edmonds, B., Gilbert, N., Gross, M., Kohlhammer, J., Koumoutsakos, P, Krause, A., Linnér, Björn-Ola, Slusallek, P, Sorkine, O., Sumner, R. W., and Helbing, D.
- Abstract
The Living Earth Simulator (LES) is one of the core components of the FuturICT architecture. It will work as a federation of methods, tools, techniques and facilities supporting all of the FuturICT simulation-related activities to allow and encourage interactive exploration and understanding of societal issues. Society-relevant problems will be targeted by leaning on approaches based on complex systems theories and data science in tight interaction with the other components of FuturICT. The LES will evaluate and provide answers to realworld questions by taking into account multiple scenarios. It will build on present approaches such as agent-based simulation and modeling, multiscale modelling, statistical inference, and data mining, moving beyond disciplinary borders to achieve a new perspective on complex social systems.
- Published
- 2012
- Full Text
- View/download PDF
23. Towards a living earth simulator
- Author
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Paolucci, M., Kossman, D., Conte, R., Lukowicz, P., Argyrakis, P., Blandford, A., Bonelli, G., Anderson, S., de Freitas, S., Edmonds, B., Gilbert, N., Gross, M., Kohlhammer, J., Koumoutsakos, P, Krause, A., Linnér, Björn-Ola, Slusallek, P, Sorkine, O., Sumner, R. W., Helbing, D., Paolucci, M., Kossman, D., Conte, R., Lukowicz, P., Argyrakis, P., Blandford, A., Bonelli, G., Anderson, S., de Freitas, S., Edmonds, B., Gilbert, N., Gross, M., Kohlhammer, J., Koumoutsakos, P, Krause, A., Linnér, Björn-Ola, Slusallek, P, Sorkine, O., Sumner, R. W., and Helbing, D.
- Abstract
The Living Earth Simulator (LES) is one of the core components of the FuturICT architecture. It will work as a federation of methods, tools, techniques and facilities supporting all of the FuturICT simulation-related activities to allow and encourage interactive exploration and understanding of societal issues. Society-relevant problems will be targeted by leaning on approaches based on complex systems theories and data science in tight interaction with the other components of FuturICT. The LES will evaluate and provide answers to realworld questions by taking into account multiple scenarios. It will build on present approaches such as agent-based simulation and modeling, multiscale modelling, statistical inference, and data mining, moving beyond disciplinary borders to achieve a new perspective on complex social systems.
- Published
- 2012
- Full Text
- View/download PDF
24. Towards a living earth simulator
- Author
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Paolucci, M., Kossman, D., Conte, R., Lukowicz, P., Argyrakis, P., Blandford, A., Bonelli, G., Anderson, S., de Freitas, Sara, Edmonds, B., Gilbert, N., Gross, M., Kohlhammer, J., Koumoutsakos, P., Krause, A., Linner, B., Slusallek, P., Sorkine, O., Summer, R., Helbing, D., Paolucci, M., Kossman, D., Conte, R., Lukowicz, P., Argyrakis, P., Blandford, A., Bonelli, G., Anderson, S., de Freitas, Sara, Edmonds, B., Gilbert, N., Gross, M., Kohlhammer, J., Koumoutsakos, P., Krause, A., Linner, B., Slusallek, P., Sorkine, O., Summer, R., and Helbing, D.
- Abstract
The Living Earth Simulator (LES) is one of the core components of the FuturICT architecture. It will work as a federation of methods, tools, techniques and facilities supporting all of the FuturICT simulation-related activities to allow and encourage interactive exploration and understanding of societal issues. Society-relevant problems will be targeted by leaning on approaches based on complex systems theories and data science in tight interaction with the other components of FuturICT. The LES will evaluate and provide answers to real-world questions by taking into account multiple scenarios. It will build on present approaches such as agent-based simulation and modeling, multiscale modelling, statistical inference, and data mining, moving beyond disciplinary borders to achieve a new perspective on complex social systems.
- Published
- 2012
25. Particle simulations of morphogenesis
- Author
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Koumoutsakos, P, Bayati, B, Milde, F, Tauriello, G, Koumoutsakos, P, Bayati, B, Milde, F, and Tauriello, G
- Abstract
The simulation of the creation and evolution of biological forms requires the development of computational methods that are capable of resolving their hierarchical, spatial and temporal complexity. Computations based on interacting particles, provide a unique computational tool for discrete and continuous descriptions of morphogenesis of systems ranging from the molecular to the organismal level. The capabilities of particle methods hinge on the simplicity of their formulation which enables the formulation of a unifying computational framework encompassing deterministic and stochastic models. In this paper, we discuss recent advances in particle methods for the simulation of biological systems at the mesoscopic and the macroscale level. We present results from applications of particle methods including reaction diffusion on deforming surfaces, deterministic and stochastic descriptions of tumor growth and angiogenesis and discuss successes and challenges of this approach.
- Published
- 2011
26. A Fourier-based elliptic solver for vortical flows with periodic and unbounded directions
- Author
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UCL - EPL/EPL - Ecole Polytechnique de Louvain, UCL - SST/IMMC/TFL - Thermodynamics and fluid mechanics, Chatelain, Philippe, Koumoutsakos, P., UCL - EPL/EPL - Ecole Polytechnique de Louvain, UCL - SST/IMMC/TFL - Thermodynamics and fluid mechanics, Chatelain, Philippe, and Koumoutsakos, P.
- Abstract
We present a computationally efficient, adaptive solver for the solution of the Poisson and Helmholtz equation used in flow simulations in domains with combinations of unbounded and periodic directions. The method relies on using FFTs on an extended domain and it is based on the method proposed by Hockney and Eastwood for plasma simulations. The method is well-suited to problems with dynamically growing domains and in particular flow simulations using vortex particle methods. The efficiency of the method is demonstrated in simulations of trailing vortices.
- Published
- 2010
27. Control algorithm for multiscale flow simulations of water
- Author
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Kotsalis, E. M., Walther, Jens Honore, Kaxiras, E., Koumoutsakos, P., Kotsalis, E. M., Walther, Jens Honore, Kaxiras, E., and Koumoutsakos, P.
- Abstract
We present a multiscale algorithm to couple atomistic water models with continuum incompressible flow simulations via a Schwarz domain decomposition approach. The coupling introduces an inhomogeneity in the description of the atomistic domain and prevents the use of periodic boundary conditions. The use of a mass conserving specular wall results in turn to spurious oscillations in the density profile of the atomistic description of water. These oscillations can be eliminated by using an external boundary force that effectively accounts for the virial component of the pressure. In this Rapid Communication, we extend a control algorithm, previously introduced for monatomic molecules, to the case of atomistic water and demonstrate the effectiveness of this approach. The proposed computational method is validated for the cases of equilibrium and Couette flow of water.
- Published
- 2009
28. A stochastic model for microtubule motors describes the in vivo cytoplasmic transport of human adenovirus
- Author
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Gazzola, M, Burckhardt, C J, Bayati, B, Engelke, M, Greber, U F, Koumoutsakos, P, Gazzola, M, Burckhardt, C J, Bayati, B, Engelke, M, Greber, U F, and Koumoutsakos, P
- Abstract
Cytoplasmic transport of organelles, nucleic acids and proteins on microtubules is usually bidirectional with dynein and kinesin motors mediating the delivery of cargoes in the cytoplasm. Here we combine live cell microscopy, single virus tracking and trajectory segmentation to systematically identify the parameters of a stochastic computational model of cargo transport by molecular motors on microtubules. The model parameters are identified using an evolutionary optimization algorithm to minimize the Kullback-Leibler divergence between the in silico and the in vivo run length and velocity distributions of the viruses on microtubules. The present stochastic model suggests that bidirectional transport of human adenoviruses can be explained without explicit motor coordination. The model enables the prediction of the number of motors active on the viral cargo during microtubule-dependent motions as well as the number of motor binding sites, with the protein hexon as the binding site for the motors.
- Published
- 2009
29. Edge detection in microscopy images using curvelets.
- Author
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Gebäck, T, Koumoutsakos, P, Gebäck, T, and Koumoutsakos, P
- Abstract
BACKGROUND: Despite significant progress in imaging technologies, the efficient detection of edges and elongated features in images of intracellular and multicellular structures acquired using light or electron microscopy is a challenging and time consuming task in many laboratories. RESULTS: We present a novel method, based on the discrete curvelet transform, to extract a directional field from the image that indicates the location and direction of the edges. This directional field is then processed using the non-maximal suppression and thresholding steps of the Canny algorithm to trace along the edges and mark them. Optionally, the edges may then be extended along the directions given by the curvelets to provide a more connected edge map. We compare our scheme to the Canny edge detector and an edge detector based on Gabor filters, and show that our scheme performs better in detecting larger, elongated structures possibly composed of several step or ridge edges. CONCLUSION: The proposed curvelet based edge detection is a novel and competitive approach for imaging problems. We expect that the methodology and the accompanying software will facilitate and improve edge detection in images available using light or electron microscopy.
- Published
- 2009
30. An exact accelerated stochastic simulation algorithm.
- Author
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Mjolsness, E, Orendorff, D, Chatelain, P, Koumoutsakos, P, Mjolsness, E, Orendorff, D, Chatelain, P, and Koumoutsakos, P
- Abstract
An exact method for stochastic simulation of chemical reaction networks, which accelerates the stochastic simulation algorithm (SSA), is proposed. The present "ER-leap" algorithm is derived from analytic upper and lower bounds on the multireaction probabilities sampled by SSA, together with rejection sampling and an adaptive multiplicity for reactions. The algorithm is tested on a number of well-quantified reaction networks and is found experimentally to be very accurate on test problems including a chaotic reaction network. At the same time ER-leap offers a substantial speedup over SSA with a simulation time proportional to the 23 power of the number of reaction events in a Galton-Watson process.
- Published
- 2009
31. Contrasting actions of selective inhibitors of angiopoietin-1 and angiopoietin-2 on the normalization of tumor blood vessels.
- Author
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Falcón, B L, Hashizume, H, Koumoutsakos, P, Chou, J, Bready, J V, Coxon, A, Oliner, J D, McDonald, D M, Falcón, B L, Hashizume, H, Koumoutsakos, P, Chou, J, Bready, J V, Coxon, A, Oliner, J D, and McDonald, D M
- Abstract
Angiopoietin-1 (Ang1) and angiopoietin-2 (Ang2) have complex actions in angiogenesis and vascular remodeling due to their effects on Tie2 receptor signaling. Ang2 blocks Ang1-mediated activation of Tie2 in endothelial cells under certain conditions but is a Tie2 receptor agonist in others. We examined the effects of selective inhibitors of Ang1 (mL4-3) or Ang2 (L1-7[N]), alone or in combination, on the vasculature of human Colo205 tumors in mice. The Ang2 inhibitor decreased the overall abundance of tumor blood vessels by reducing tumor growth and keeping vascular density constant. After inhibition of Ang2, tumor vessels had many features of normal blood vessels (normalization), as evidenced by junctional accumulation of vascular endothelial-cadherin, junctional adhesion molecule-A, and platelet/endothelial cell adhesion molecule-1 in endothelial cells, increased pericyte coverage, reduced endothelial sprouting, and remodeling into smaller, more uniform vessels. The Ang1 inhibitor by itself had little noticeable effect on the tumor vasculature. However, when administered with the Ang2 inhibitor, the Ang1 inhibitor prevented tumor vessel normalization, but not the reduction in tumor vascularity produced by the Ang2 inhibitor. These findings are consistent with a model whereby inhibition of Ang2 leads to normalization of tumor blood vessels by permitting the unopposed action of Ang1, but decreases tumor vascularity primarily by blocking Ang2 actions.
- Published
- 2009
32. A hybrid model for three-dimensional simulations of sprouting angiogenesis.
- Author
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Milde, F, Bergdorf, M, Koumoutsakos, P, Milde, F, Bergdorf, M, and Koumoutsakos, P
- Abstract
Recent advances in cancer research have identified critical angiogenic signaling pathways and the influence of the extracellular matrix on endothelial cell migration. These findings provide us with insight into the process of angiogenesis that can facilitate the development of effective computational models of sprouting angiogenesis. In this work, we present the first three-dimensional model of sprouting angiogenesis that considers explicitly the effect of the extracellular matrix and of the soluble as well as matrix-bound growth factors on capillary growth. The computational model relies on a hybrid particle-mesh representation of the blood vessels and it introduces an implicit representation of the vasculature that can accommodate detailed descriptions of nutrient transport. Extensive parametric studies reveal the role of the extracellular matrix structure and the distribution of the different vascular endothelial growth factors isoforms on the dynamics and the morphology of the generated vascular networks.
- Published
- 2008
33. Multiresolution stochastic simulations of reaction-diffusion processes.
- Author
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Bayati, B, Chatelain, P, Koumoutsakos, P, Bayati, B, Chatelain, P, and Koumoutsakos, P
- Abstract
Stochastic simulations of reaction-diffusion processes are used extensively for the modeling of complex systems in areas ranging from biology and social sciences to ecosystems and materials processing. These processes often exhibit disparate scales that render their simulation prohibitive even for massive computational resources. The problem is resolved by introducing a novel stochastic multiresolution method that enables the efficient simulation of reaction-diffusion processes as modeled by many-particle systems. The proposed method quantifies and efficiently handles the associated stiffness in simulating the system dynamics and its computational efficiency and accuracy are demonstrated in simulations of a model problem described by the Fisher-Kolmogorov equation. The method is general and can be applied to other many-particle models of physical processes.
- Published
- 2008
34. Control of density fluctuations in atomistic-continuum simulations of dense liquids
- Author
-
Kotsalis, E.M., Walther, Jens Honore, Koumoutsakos, P., Kotsalis, E.M., Walther, Jens Honore, and Koumoutsakos, P.
- Abstract
We present a control algorithm to eliminate spurious density fluctuations associated with the coupling of atomistic and continuum descriptions for dense liquids. A Schwartz domain decomposition algorithm is employed to couple molecular dynamics for the simulation of the atomistic system with a continuum solver for the simulation of the Navier-Stokes equations. The lack of periodic boundary conditions in the molecular dynamics simulations hinders the proper accounting for the virial pressure leading to spurious density fluctuations at the continuum-atomistic interface. An ad hoc boundary force is usually employed to remedy this situation.We propose the calculation of this boundary force using a control algorithm that explicitly cancels the density fluctuations. The results demonstrate that the present approach outperforms state-of-the-art algorithms. The conceptual and algorithmic simplicity of the method makes it suitable for any type of coupling between atomistic and continuum descriptions of dense fluids. D
- Published
- 2007
35. Control of density fluctuations in atomistic-continuum simulations of dense liquids
- Author
-
Kotsalis, E.M., Walther, Jens Honore, Koumoutsakos, P., Kotsalis, E.M., Walther, Jens Honore, and Koumoutsakos, P.
- Abstract
We present a control algorithm to eliminate spurious density fluctuations associated with the coupling of atomistic and continuum descriptions for dense liquids. A Schwartz domain decomposition algorithm is employed to couple molecular dynamics for the simulation of the atomistic system with a continuum solver for the simulation of the Navier-Stokes equations. The lack of periodic boundary conditions in the molecular dynamics simulations hinders the proper accounting for the virial pressure leading to spurious density fluctuations at the continuum-atomistic interface. An ad hoc boundary force is usually employed to remedy this situation.We propose the calculation of this boundary force using a control algorithm that explicitly cancels the density fluctuations. The results demonstrate that the present approach outperforms state-of-the-art algorithms. The conceptual and algorithmic simplicity of the method makes it suitable for any type of coupling between atomistic and continuum descriptions of dense fluids. D
- Published
- 2007
36. Control of density fluctuations in atomistic-continuum simulations of dense liquids
- Author
-
Kotsalis, E.M., Walther, Jens Honore, Koumoutsakos, P., Kotsalis, E.M., Walther, Jens Honore, and Koumoutsakos, P.
- Abstract
We present a control algorithm to eliminate spurious density fluctuations associated with the coupling of atomistic and continuum descriptions for dense liquids. A Schwartz domain decomposition algorithm is employed to couple molecular dynamics for the simulation of the atomistic system with a continuum solver for the simulation of the Navier-Stokes equations. The lack of periodic boundary conditions in the molecular dynamics simulations hinders the proper accounting for the virial pressure leading to spurious density fluctuations at the continuum-atomistic interface. An ad hoc boundary force is usually employed to remedy this situation.We propose the calculation of this boundary force using a control algorithm that explicitly cancels the density fluctuations. The results demonstrate that the present approach outperforms state-of-the-art algorithms. The conceptual and algorithmic simplicity of the method makes it suitable for any type of coupling between atomistic and continuum descriptions of dense fluids. D
- Published
- 2007
37. Multiscale modelling and simulation
- Author
-
Attinger, Sabine, Koumoutsakos, P., Attinger, Sabine, and Koumoutsakos, P.
- Published
- 2004
38. Multiscale modelling and simulation
- Author
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Attinger, Sabine, Koumoutsakos, P., Attinger, Sabine, and Koumoutsakos, P.
- Published
- 2004
39. Homogenization method for transport of DNA particles in heterogeneous arrays
- Author
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Attinger, S., Koumoutsakos, P., Abdulle, A., Attinger, Sabine, Attinger, S., Koumoutsakos, P., Abdulle, A., and Attinger, Sabine
- Abstract
In this paper we study the large scale transport of the DNA particles through a heterogeneous micro array in the framework of homogenization theory. We derive the macro scale particle transport equation and show that for transport of particles in a divergence free electric field as proposed by Duke and Austin [Du98] and Ertas [Er98] separation according to particle mass or size cannot been achieved. Our results explain the experimental findings of Duke and Austin [Du98] and Ertas [Er98] and thus close the gap between theory and experiment.
- Published
- 2004
40. Knots and braids on the Sun
- Author
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Gyr, A, Koumoutsakos, P, Burr, U, Ricca, R, RICCA, RENZO, Gyr, A, Koumoutsakos, P, Burr, U, Ricca, R, and RICCA, RENZO
- Abstract
In this paper we show how new techniques of topological fluid mechanics and physical knot theory can be applied to estimate magnetic energy levels in solar physics. In particular, we show that magnetic energy stored in complex configurations of plasma loops present on the Sun can be quantified by geometric and topological information. These studies find important applications in the energetics of solar and stellar physics and in laboratory plasmas.
- Published
- 2000
41. Knots and braids on the Sun
- Author
-
Gyr, A, Koumoutsakos, P, Burr, U, Ricca, R, RICCA, RENZO, Gyr, A, Koumoutsakos, P, Burr, U, Ricca, R, and RICCA, RENZO
- Abstract
In this paper we show how new techniques of topological fluid mechanics and physical knot theory can be applied to estimate magnetic energy levels in solar physics. In particular, we show that magnetic energy stored in complex configurations of plasma loops present on the Sun can be quantified by geometric and topological information. These studies find important applications in the energetics of solar and stellar physics and in laboratory plasmas.
- Published
- 2000
42. Miniature Biomimetic Acoustic Sensors
- Author
-
TORONTO UNIV (ONTARIO) DEPT OF ELECTRICAL AND COMPUTER ENGINEERING, Noca, F., Hoenk, M. E., Hunt, B., Tang, W., Xu, J., Koumoutsakos, P., TORONTO UNIV (ONTARIO) DEPT OF ELECTRICAL AND COMPUTER ENGINEERING, Noca, F., Hoenk, M. E., Hunt, B., Tang, W., Xu, J., and Koumoutsakos, P.
- Abstract
Stereocilia, Nature's fundamental acoustic sensors are found in all hearing living systems. They are located on hair cells in the cochlea. Deflection of stereocilia, induced by shear in the endolymphatic fluid, generates neural impulses. Stereocilia are also found in the lateral line of fish for water flow detection. Even in non-hearing organisms (hydra, jellyfish, sea anemones), stereocilia may be present as mechanoreceptors for swimming prey detection (plankton). Highly ordered arrays of parallel carbon nanotubes were grown by pyrolysis of acetylene on cobalt within a hexagonal close-packed nanochannel alumina template at 650 degrees Celsius. The nanotubes are characterized by a narrow size distribution, large scale periodicity and high densities. Using this method ordered nanotubes with diameters from 10 nanometers to several hundred nanometers and lengths up to 100 micrometers can be produced. Stereocilia as sensors: 1. Miniature microphones/hydrophones 2. Miniature acoustic imaging arrays 3. Micro-flow detectors 4. Shear stress micro-sensors 5. Microscale bio-sound detectors. Stereocilia as actuators: 1. Similar to crustacean/insect stridulatory pegs 2. Micro-Sonar/Sodar emitting arrays, Handheld Sonars, Air-Coupled Acoustic Sensors., Presented at the Defense Advanced Research Projects Agency (DARPA) Air-Coupled Acoustic Microsensors Workshop held in Crystal City, Virginia on 24-25 August 1999. The original document contains color images. Document contains briefing charts.
- Published
- 1999
43. Numerical simulation of chemically-reacting shear layers via three-dimensional fast particle methods
- Author
-
UCL - FSA/MECA - Département de mécanique, Chua, K., Boschitsch, A.H., Koumoutsakos, P., Winckelmans, Grégoire, Leonard, A., AIAA 32nd Aerospace Sciences Meeting & Exhibit, UCL - FSA/MECA - Département de mécanique, Chua, K., Boschitsch, A.H., Koumoutsakos, P., Winckelmans, Grégoire, Leonard, A., and AIAA 32nd Aerospace Sciences Meeting & Exhibit
- Published
- 1994
44. Identification of failing banks using clustering with self-organising neural networks
- Author
-
Koumoutsakos, P, Lees, M, Krzhizhanovskaya, V, Dongarra, J, Sloot, P, Negnevitsky, M, Koumoutsakos, P, Lees, M, Krzhizhanovskaya, V, Dongarra, J, Sloot, P, and Negnevitsky, M
- Abstract
This paper presents experimental results of cluster analysis using self organising neural networks for identifying failing banks. The paper first describes major reasons and likelihoods of bank failures. Then it demonstrates an application of a self-organising neural network and presents results of the study. Findings of the paper demonstrate that a self-organising neural network is a powerful tool for identifying potentially failing banks. Finally, the paper discusses some of the limitations of cluster analysis related to understanding of the exact meaning of each cluster.
45. C-start: optimal start of larval fish
- Author
-
Gazzola, M., Van Rees, W. M., Koumoutsakos, P., Gazzola, M., Van Rees, W. M., and Koumoutsakos, P.
- Abstract
We investigate the C-start escape response of larval fish by combining flow simulations using remeshed vortex methods with an evolutionary optimization. We test the hypothesis of the optimality of C-start of larval fish by simulations of larval-shaped, two- and three-dimensional self-propelled swimmers. We optimize for the distance travelled by the swimmer during its initial bout, bounding the shape deformation based on the larval mid-line curvature values observed experimentally. The best motions identified within these bounds are in good agreement with in vivo experiments and show that C-starts do indeed maximize escape distances. Furthermore we found that motions with curvatures beyond the ones experimentally observed for larval fish may result in even larger escape distances. We analyse the flow field and find that the effectiveness of the C-start escape relies on the ability of pronounced C-bent body configurations to trap and accelerate large volumes of fluid, which in turn correlates with large accelerations of the swimmer
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