I try to understand how nature processes information. I study this 'natural information processing' in complex systems by computational modeling and simulation as well as through formal methods. My work is applied to a large variety of applications with a focus on -but not limited to- Biomedicine. Recent work is on modeling the virology and epidemiology of infectious diseases, notably HIV, through Complex Networks and Cellular Automata. Currently I lead two EU projects: ViroLab and DynaNets and supervise research from various NIH, NSF and NWO projects, see my Research Group.
My YouTube Channel: Here you can find some movies related to my work and interest. See: http://www.youtube.com/watch?v=Pfbzqn9ciTA&lr=1&user=PeterSloot1
Proceedings of the Institution of Civil Engineers - Geotechnical Engineering, 2015
The paper analyses the experimental slope failure of a full-scale earthen dyke (levee) in Boonesc... more The paper analyses the experimental slope failure of a full-scale earthen dyke (levee) in Booneschans (Groningen, the Netherlands). The goals of the experiment were to develop efficient dyke-monitoring systems predicting various modes of failure well in advance of onset and to test the ability of numerical geotechnical models to predict the mode of failure and the time of collapse. Prior to the experiments, a special competition for the best prediction for all three planned tests had been announced. Several commercial corporations and scientific research organisations modelling dykes participated in the competition; the authors of this paper provided the best prediction for the macro-instability experiment, according to the decision of jury. The IJkDijk macro-instability test prediction has become the ultimate validation of the Virtual Dike simulation module, which is a functional part of the UrbanFlood early warning system for flood protection. Regarding sensor recordings, tilt mea...
Journal of Statistical Mechanics: Theory and Experiment, 2014
ABSTRACT Many diffusive processes occur on structured networks with weighted links, such as disea... more ABSTRACT Many diffusive processes occur on structured networks with weighted links, such as disease spread by airplane transport or information diffusion in social networks or blogs. Understanding the impact of weight-connectivity correlations on epidemic spreading in weighted networks is crucial to support decision-making on disease control and other diffusive processes. However, a real understanding of epidemic spreading velocity in weighted networks is still lacking. Here we conduct a numerical study of the velocity of a Reed–Frost epidemic spreading process in various weighted network topologies as a function of the correlations between edge weights and node degrees. We find that a positive weight-connectivity correlation leads to a faster epidemic spreading compared to an unweighted network. In contrast, we find that both uncorrelated and negatively correlated weight distributions lead to slower spreading processes. In the case of positive weight-connectivity correlations, the acceleration of spreading velocity is weak when the heterogeneity of weight distribution increases.
Recent Advances in Parallel Virtual Machine and Message Passing Interface, 2002
Traditionally, PVM and MPI programs live on message passing systems, from clusters of non-dedicat... more Traditionally, PVM and MPI programs live on message passing systems, from clusters of non-dedicated workstations to MPP machines. The performance of a parallel program in such an environment is usually determined by the single least performing task in that program. In a homogeneous, stable environment, such as an MPP machine, this can only be repaired by improving the workload balance between the individual tasks. In a cluster of workstations, differences in the performance of individual nodes and network components can be an ...
... Liddell Hai-Xiang Lin Markus Lindermeier Peter Lockey Thomas Ludwig Peter Luksch Bob Madahar ... more ... Liddell Hai-Xiang Lin Markus Lindermeier Peter Lockey Thomas Ludwig Peter Luksch Bob Madahar Ursula Maier Dmitry Malashonok J ... 1215 M. Migliardi, V. Sunderam Coordination Models and Facilities Could Be Parallel Software Accelerators 1219 AE Doroshenko, L.-E ...
Solutions to Parallel and Distributed Computing Problems, …
Manyfundamentalproblemsfromnaturalsciencesdealwith complexsystems. We dene a complex system as a ... more Manyfundamentalproblemsfromnaturalsciencesdealwith complexsystems. We dene a complex system as a population of unique elements with well de- ned microscopic attributes and interactions, showing emerging macroscopic behavior. This ...
A variety of slowly driven diffusive systems have been shown to self organize into a critical sta... more A variety of slowly driven diffusive systems have been shown to self organize into a critical state. In this paper we study the dynamic runtime behavior of the optimistic parallel Time Warp simulation method. The method is based on an asynchronous execution of timed events. The basic problem is the out of order execution of events. A causality error results in so-called rollback of processed events until the causality error is resolved. By using the Ising spin model we show experimentally that the distribution of number of rolled back events behaves as a power-law distribution over a large range of sub-critical Ising temperatures and decays exponentially above for super-critical Ising temperatures. For critical Ising temperatures, the computational complexity of Time Warp and physical complexity of the Ising spin model are entangled and contribute both to the runtime behavior in a non-linear way.
In this paper we study hierarchical job scheduling strategies for clusters of workstations. Our a... more In this paper we study hierarchical job scheduling strategies for clusters of workstations. Our approach uses two-level scheduling: global scheduling and local scheduling. The local scheduler refines the scheduling decisions made by the global scheduler, taking into account the most recent information. In this paper, we explore the First Come First Served (FCFS), the Shortest Job First (SJF), and the First Fit (FF) policies at the global level and the local level. In addition, we use separate queues at the global level for arriving jobs, where ...
Proceedings 15th Workshop on Parallel and Distributed Simulation
Abstract In this paper we study the influence of spatio-temporal correlations on the dynamic runt... more Abstract In this paper we study the influence of spatio-temporal correlations on the dynamic runtime behavior of the optimistic parallel Time Warp simulation method. By using the Ising spin model, we show experimentally that the distribution of the number of rolled back events behaves as a power-law distribution over a large range of sub-critical Ising temperatures and decays exponentially for super-critical Ising temperatures. For critical Ising temperatures, where long-range correlations occur, the computational complexity of Time ...
This paper presents the design of a system that supports execution of a HLA distributed interacti... more This paper presents the design of a system that supports execution of a HLA distributed interactive simulations in an unreliable Grid environment. The design of the architecture is based on the OGSA concept that allows for modularity and compatibility with Grid Services already being developed. First of all, we focus on the part of the system that is responsible for migration of a HLA-connected component or components of the distributed application in the Grid environment. We present a runtime support library for easily plugging HLA ...
Hybrid Architectures consist of Special Purpose Devices (SPD) used in conjunction with parallel c... more Hybrid Architectures consist of Special Purpose Devices (SPD) used in conjunction with parallel computers. They have the potential of being a major computing tool for various applications of Computational Science. Mapping the application tasks to the hybrid machine is not trivial, and bottlenecks can arise quite easily. Performance Modeling is a suitable method to tackle this problem. The performance model
The origin of the volatility smile phenomenon observed in options markets has eluded the financia... more The origin of the volatility smile phenomenon observed in options markets has eluded the financial world for more than two decades. We provide a new explanation of this phenomenon using a microscopic multi-agent description of markets. In our model individual trading behavior is explicitly included and the prices of the options are determined by demand and supply. Our results reproduce the empirical observations in respect to the shape and dynamic properties of the volatility smile, suggesting that this phenomenon is a natural consequence of traders' heterogeneous behavior and expectations about the future.
Disclaimer/Klachtenregeling Meent u dat de digitale beschikbaarstelling van bepaald materiaal inb... more Disclaimer/Klachtenregeling Meent u dat de digitale beschikbaarstelling van bepaald materiaal inbreuk maakt op enig recht dat u toekomt of uw (privacy)belangen schaadt, dan kunt u dit onderbouwd aan de Universiteitsbibliotheek laten weten. Bij een gegronde klacht zal de Universiteitsbibliotheek het materiaal ontoegankelijk maken en/of van de website verwijderen, dan wel samen met u bekijken hoe op een andere manier aan uw klacht tegemoet kan worden gekomen. Stuurt u hiervoor een e-mail naar: dare@uva.nl, of een brief naar: Bibliotheek van de Universiteit ...
EU workshop on simulation, Visualisation, Interaction and Mixed Reality, 2005
Physics, chemistry, biology, medicine, engineering, economics, psychology; simulation models are ... more Physics, chemistry, biology, medicine, engineering, economics, psychology; simulation models are used in just about any imaginable scientific field. Simulations have become invaluable for the testing of new scientific theories, the design and development of new products, and for the education and training of young professionals. Recent advances in Information and Communication Technology (ICT) have allowed researchers to perform simulations of increasing size, resolution and complexity. One of the major challenges is ...
Disclaimer/Klachtenregeling Meent u dat de digitale beschikbaarstelling van bepaald materiaal inb... more Disclaimer/Klachtenregeling Meent u dat de digitale beschikbaarstelling van bepaald materiaal inbreuk maakt op enig recht dat u toekomt of uw (privacy)belangen schaadt, dan kunt u dit onderbouwd aan de Universiteitsbibliotheek laten weten. Bij een gegronde klacht zal de Universiteitsbibliotheek het materiaal ontoegankelijk maken en/of van de website verwijderen, dan wel samen met u bekijken hoe op een andere manier aan uw klacht tegemoet kan worden gekomen. Stuurt u hiervoor een e-mail naar: dare@uva.nl, of een brief naar: Bibliotheek van de Universiteit ...
Proceedings of the Institution of Civil Engineers - Geotechnical Engineering, 2015
The paper analyses the experimental slope failure of a full-scale earthen dyke (levee) in Boonesc... more The paper analyses the experimental slope failure of a full-scale earthen dyke (levee) in Booneschans (Groningen, the Netherlands). The goals of the experiment were to develop efficient dyke-monitoring systems predicting various modes of failure well in advance of onset and to test the ability of numerical geotechnical models to predict the mode of failure and the time of collapse. Prior to the experiments, a special competition for the best prediction for all three planned tests had been announced. Several commercial corporations and scientific research organisations modelling dykes participated in the competition; the authors of this paper provided the best prediction for the macro-instability experiment, according to the decision of jury. The IJkDijk macro-instability test prediction has become the ultimate validation of the Virtual Dike simulation module, which is a functional part of the UrbanFlood early warning system for flood protection. Regarding sensor recordings, tilt mea...
Journal of Statistical Mechanics: Theory and Experiment, 2014
ABSTRACT Many diffusive processes occur on structured networks with weighted links, such as disea... more ABSTRACT Many diffusive processes occur on structured networks with weighted links, such as disease spread by airplane transport or information diffusion in social networks or blogs. Understanding the impact of weight-connectivity correlations on epidemic spreading in weighted networks is crucial to support decision-making on disease control and other diffusive processes. However, a real understanding of epidemic spreading velocity in weighted networks is still lacking. Here we conduct a numerical study of the velocity of a Reed–Frost epidemic spreading process in various weighted network topologies as a function of the correlations between edge weights and node degrees. We find that a positive weight-connectivity correlation leads to a faster epidemic spreading compared to an unweighted network. In contrast, we find that both uncorrelated and negatively correlated weight distributions lead to slower spreading processes. In the case of positive weight-connectivity correlations, the acceleration of spreading velocity is weak when the heterogeneity of weight distribution increases.
Recent Advances in Parallel Virtual Machine and Message Passing Interface, 2002
Traditionally, PVM and MPI programs live on message passing systems, from clusters of non-dedicat... more Traditionally, PVM and MPI programs live on message passing systems, from clusters of non-dedicated workstations to MPP machines. The performance of a parallel program in such an environment is usually determined by the single least performing task in that program. In a homogeneous, stable environment, such as an MPP machine, this can only be repaired by improving the workload balance between the individual tasks. In a cluster of workstations, differences in the performance of individual nodes and network components can be an ...
... Liddell Hai-Xiang Lin Markus Lindermeier Peter Lockey Thomas Ludwig Peter Luksch Bob Madahar ... more ... Liddell Hai-Xiang Lin Markus Lindermeier Peter Lockey Thomas Ludwig Peter Luksch Bob Madahar Ursula Maier Dmitry Malashonok J ... 1215 M. Migliardi, V. Sunderam Coordination Models and Facilities Could Be Parallel Software Accelerators 1219 AE Doroshenko, L.-E ...
Solutions to Parallel and Distributed Computing Problems, …
Manyfundamentalproblemsfromnaturalsciencesdealwith complexsystems. We dene a complex system as a ... more Manyfundamentalproblemsfromnaturalsciencesdealwith complexsystems. We dene a complex system as a population of unique elements with well de- ned microscopic attributes and interactions, showing emerging macroscopic behavior. This ...
A variety of slowly driven diffusive systems have been shown to self organize into a critical sta... more A variety of slowly driven diffusive systems have been shown to self organize into a critical state. In this paper we study the dynamic runtime behavior of the optimistic parallel Time Warp simulation method. The method is based on an asynchronous execution of timed events. The basic problem is the out of order execution of events. A causality error results in so-called rollback of processed events until the causality error is resolved. By using the Ising spin model we show experimentally that the distribution of number of rolled back events behaves as a power-law distribution over a large range of sub-critical Ising temperatures and decays exponentially above for super-critical Ising temperatures. For critical Ising temperatures, the computational complexity of Time Warp and physical complexity of the Ising spin model are entangled and contribute both to the runtime behavior in a non-linear way.
In this paper we study hierarchical job scheduling strategies for clusters of workstations. Our a... more In this paper we study hierarchical job scheduling strategies for clusters of workstations. Our approach uses two-level scheduling: global scheduling and local scheduling. The local scheduler refines the scheduling decisions made by the global scheduler, taking into account the most recent information. In this paper, we explore the First Come First Served (FCFS), the Shortest Job First (SJF), and the First Fit (FF) policies at the global level and the local level. In addition, we use separate queues at the global level for arriving jobs, where ...
Proceedings 15th Workshop on Parallel and Distributed Simulation
Abstract In this paper we study the influence of spatio-temporal correlations on the dynamic runt... more Abstract In this paper we study the influence of spatio-temporal correlations on the dynamic runtime behavior of the optimistic parallel Time Warp simulation method. By using the Ising spin model, we show experimentally that the distribution of the number of rolled back events behaves as a power-law distribution over a large range of sub-critical Ising temperatures and decays exponentially for super-critical Ising temperatures. For critical Ising temperatures, where long-range correlations occur, the computational complexity of Time ...
This paper presents the design of a system that supports execution of a HLA distributed interacti... more This paper presents the design of a system that supports execution of a HLA distributed interactive simulations in an unreliable Grid environment. The design of the architecture is based on the OGSA concept that allows for modularity and compatibility with Grid Services already being developed. First of all, we focus on the part of the system that is responsible for migration of a HLA-connected component or components of the distributed application in the Grid environment. We present a runtime support library for easily plugging HLA ...
Hybrid Architectures consist of Special Purpose Devices (SPD) used in conjunction with parallel c... more Hybrid Architectures consist of Special Purpose Devices (SPD) used in conjunction with parallel computers. They have the potential of being a major computing tool for various applications of Computational Science. Mapping the application tasks to the hybrid machine is not trivial, and bottlenecks can arise quite easily. Performance Modeling is a suitable method to tackle this problem. The performance model
The origin of the volatility smile phenomenon observed in options markets has eluded the financia... more The origin of the volatility smile phenomenon observed in options markets has eluded the financial world for more than two decades. We provide a new explanation of this phenomenon using a microscopic multi-agent description of markets. In our model individual trading behavior is explicitly included and the prices of the options are determined by demand and supply. Our results reproduce the empirical observations in respect to the shape and dynamic properties of the volatility smile, suggesting that this phenomenon is a natural consequence of traders' heterogeneous behavior and expectations about the future.
Disclaimer/Klachtenregeling Meent u dat de digitale beschikbaarstelling van bepaald materiaal inb... more Disclaimer/Klachtenregeling Meent u dat de digitale beschikbaarstelling van bepaald materiaal inbreuk maakt op enig recht dat u toekomt of uw (privacy)belangen schaadt, dan kunt u dit onderbouwd aan de Universiteitsbibliotheek laten weten. Bij een gegronde klacht zal de Universiteitsbibliotheek het materiaal ontoegankelijk maken en/of van de website verwijderen, dan wel samen met u bekijken hoe op een andere manier aan uw klacht tegemoet kan worden gekomen. Stuurt u hiervoor een e-mail naar: dare@uva.nl, of een brief naar: Bibliotheek van de Universiteit ...
EU workshop on simulation, Visualisation, Interaction and Mixed Reality, 2005
Physics, chemistry, biology, medicine, engineering, economics, psychology; simulation models are ... more Physics, chemistry, biology, medicine, engineering, economics, psychology; simulation models are used in just about any imaginable scientific field. Simulations have become invaluable for the testing of new scientific theories, the design and development of new products, and for the education and training of young professionals. Recent advances in Information and Communication Technology (ICT) have allowed researchers to perform simulations of increasing size, resolution and complexity. One of the major challenges is ...
Disclaimer/Klachtenregeling Meent u dat de digitale beschikbaarstelling van bepaald materiaal inb... more Disclaimer/Klachtenregeling Meent u dat de digitale beschikbaarstelling van bepaald materiaal inbreuk maakt op enig recht dat u toekomt of uw (privacy)belangen schaadt, dan kunt u dit onderbouwd aan de Universiteitsbibliotheek laten weten. Bij een gegronde klacht zal de Universiteitsbibliotheek het materiaal ontoegankelijk maken en/of van de website verwijderen, dan wel samen met u bekijken hoe op een andere manier aan uw klacht tegemoet kan worden gekomen. Stuurt u hiervoor een e-mail naar: dare@uva.nl, of een brief naar: Bibliotheek van de Universiteit ...
The Fisher–Rao metric from information geometry is related to phase transition phenomena in class... more The Fisher–Rao metric from information geometry is related to phase transition phenomena in classical statistical mechanics. Several studies propose to extend the use of information geometry to study more general phase transitions in complex systems. However, it is unclear whether the Fisher–Rao metric does indeed detect these more general transitions, especially in the absence of a statistical model. In this paper we study the transitions between patterns in the Gray-Scott reaction–diffusion model using Fisher information. We describe the system by a probability density function that represents the size distribution of blobs in the patterns and compute its Fisher information with respect to changing the two rate parameters of the underlying model. We estimate the distribution non-parametrically so that we do not assume any statistical model. The resulting Fisher map can be interpreted as a phase-map of the different patterns. Lines with high Fisher information can be considered as boundaries between regions of parameter space where patterns with similar characteristics appear. These lines of high Fisher information can be interpreted as phase transitions between complex patterns.
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Papers by Peter M A Sloot