Eric Lorenz | University of Amsterdam (original) (raw)
Papers by Eric Lorenz
2011 IEEE Seventh International Conference on e-Science Workshops, 2011
The understanding of biological processes, e.g. related to cardio-vascular disease and treatment,... more The understanding of biological processes, e.g. related to cardio-vascular disease and treatment, can significantly be improved by numerical simulation. In this paper, we present an approach for a multiscale simulation environment, applied for the prediction of in-stent re-stenos is. Our focus is on the coupling of distributed, heterogeneous hardware to take into account the different requirements of the coupled sub-systems concerning computing power. For such a concept, which is an extension of the standard multiscale computing approach, we want to apply the term Distributed Multiscale Computing.
International Journal of Modern Physics C, 2014
Lecture Notes in Computer Science, 2007
Proceedings - 7th IEEE International Conference on e-Science Workshops, eScienceW 2011, 2011
In several disciplines, a multiscale approach is being used to model complex natural processes ye... more In several disciplines, a multiscale approach is being used to model complex natural processes yet a principled background to multiscale modeling is not clear. Additionally, some multiscale models requiring distributed resources to be computed in an acceptable timeframe, while no standard framework for distributed multiscale computing is place. In this paper a principled approach to distributed multiscale computing is taken,
Understanding Complex Systems, 2010
Cellular Automata (CA) are generally acknowledged to be a powerful way to describe and model natu... more 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, eg [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?
Lecture Notes in Computer Science, 2009
Interface focus, Jan 6, 2011
Neointimal hyperplasia, a process of smooth muscle cell re-growth, is the result of a natural wou... more Neointimal hyperplasia, a process of smooth muscle cell re-growth, is the result of a natural wound healing response of the injured artery after stent deployment. Excessive neointimal hyperplasia following coronary artery stenting results in in-stent restenosis (ISR). Regardless of recent developments in the field of coronary stent design, ISR remains a significant complication of this interventional therapy. The influence of stent design parameters such as strut thickness, shape and the depth of strut deployment within the vessel wall on the severity of restenosis has already been highlighted but the detail of this influence is unclear. These factors impact on local haemodynamics and vessel structure and affect the rate of neointima formation. This paper presents the first results of a multi-scale model of ISR. The development of the simulated restenosis as a function of stent deployment depth is compared with an in vivo porcine dataset. Moreover, the influence of strut size and sh...
Multiscale Modeling & Simulation, 2011
Procedia Computer Science, 2013
Journal of Parallel and Distributed Computing, 2013
ABSTRACT Inherently complex problems from many scientific disciplines require a multiscale modeli... more ABSTRACT Inherently complex problems from many scientific disciplines require a multiscale modeling approach. Yet its practical contents remain unclear and inconsistent. Moreover, multiscale models can be very computationally expensive, and may have potential to be executed on distributed infrastructure. In this paper we propose firm foundations for multiscale modeling and distributed multiscale computing. Useful interaction patterns of multiscale models are made predictable with a submodel execution loop (SEL), four coupling templates, and coupling topology properties. We enhance a high-level and well-defined Multiscale Modeling Language (MML) that describes and specifies multiscale models and their computational architecture in a modular way. The architecture is analyzed using directed acyclic task graphs, facilitating validity checking, scheduling distributed computing resources, estimating computational costs, and predicting deadlocks. Distributed execution using the multiscale coupling library and environment (MUSCLE) is outlined. The methodology is applied to two selected applications in nanotechnology and biophysics, showing its capabilities.
Journal of Computational Science, 2011
International Journal for Multiscale Computational Engineering, 2007
Complex Automata were recently proposed as a paradigm to model multiscale complex systems. The co... more Complex Automata were recently proposed as a paradigm to model multiscale complex systems. The concept is formalized and the scale separation map is further investigated in relation with its capability to specify the components of Complex Automata. Five classes of scale ...
COAST (Complex Automata Simulation Technique) is a European Union FP6 funded project which has de... more COAST (Complex Automata Simulation Technique) is a European Union FP6 funded project which has developed a methodology for multi-science, multi-scale simulation of complex systems. The resulting framework (MUSCLE: Multiscale Simulation Coupling Library and Environment is now publically available. As an exemplar, MUSCLE has been applied to the model of a complex biomedical pathology, that of in-stent restenosis, resulting in a hierarchical aggregation of coupled cellular automata and agent based models coined "complex automaton". Currently, three simple, single scale models have been coupled to simulate the pathological response of the arterial wall to stent-deployment: an agent based model of smooth muscle cell dynamics (modeling cell cycle and cell-cell interaction), a lattice Boltzmann model of blood flow (defining wall shear stress and oscillatory shear index at the vessel surface) and a finite difference drug diffusion model (defining stent-eluted drug concentrations across the vessel wall). These sub-models operate on distinct temporal scales and can be plotted on a scale separation map. This conceptual tool defines the temporal separation of the processes and the coupling template required for interaction between them [3]. Coupling is implemented using smart conduits and in some situations, mapper agents, which transfer information between models with lattice based domains (blood flow, drug diffusion) to those with continuous domains (smooth muscle behaviour). Here we present preliminary output of a simple 2D model of in-stent restenosis. The present model captures the relationship between degree of stent induced injury and the smooth muscle cell hyperplastic response. The generation of realistic output correlates well with experimental data and paves the way for computer-aided design of stent-based therapies.
Procedia Computer Science, 2012
2011 IEEE Seventh International Conference on e-Science Workshops, 2011
The understanding of biological processes, e.g. related to cardio-vascular disease and treatment,... more The understanding of biological processes, e.g. related to cardio-vascular disease and treatment, can significantly be improved by numerical simulation. In this paper, we present an approach for a multiscale simulation environment, applied for the prediction of in-stent re-stenos is. Our focus is on the coupling of distributed, heterogeneous hardware to take into account the different requirements of the coupled sub-systems concerning computing power. For such a concept, which is an extension of the standard multiscale computing approach, we want to apply the term Distributed Multiscale Computing.
International Journal of Modern Physics C, 2014
Lecture Notes in Computer Science, 2007
Proceedings - 7th IEEE International Conference on e-Science Workshops, eScienceW 2011, 2011
In several disciplines, a multiscale approach is being used to model complex natural processes ye... more In several disciplines, a multiscale approach is being used to model complex natural processes yet a principled background to multiscale modeling is not clear. Additionally, some multiscale models requiring distributed resources to be computed in an acceptable timeframe, while no standard framework for distributed multiscale computing is place. In this paper a principled approach to distributed multiscale computing is taken,
Understanding Complex Systems, 2010
Cellular Automata (CA) are generally acknowledged to be a powerful way to describe and model natu... more 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, eg [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?
Lecture Notes in Computer Science, 2009
Interface focus, Jan 6, 2011
Neointimal hyperplasia, a process of smooth muscle cell re-growth, is the result of a natural wou... more Neointimal hyperplasia, a process of smooth muscle cell re-growth, is the result of a natural wound healing response of the injured artery after stent deployment. Excessive neointimal hyperplasia following coronary artery stenting results in in-stent restenosis (ISR). Regardless of recent developments in the field of coronary stent design, ISR remains a significant complication of this interventional therapy. The influence of stent design parameters such as strut thickness, shape and the depth of strut deployment within the vessel wall on the severity of restenosis has already been highlighted but the detail of this influence is unclear. These factors impact on local haemodynamics and vessel structure and affect the rate of neointima formation. This paper presents the first results of a multi-scale model of ISR. The development of the simulated restenosis as a function of stent deployment depth is compared with an in vivo porcine dataset. Moreover, the influence of strut size and sh...
Multiscale Modeling & Simulation, 2011
Procedia Computer Science, 2013
Journal of Parallel and Distributed Computing, 2013
ABSTRACT Inherently complex problems from many scientific disciplines require a multiscale modeli... more ABSTRACT Inherently complex problems from many scientific disciplines require a multiscale modeling approach. Yet its practical contents remain unclear and inconsistent. Moreover, multiscale models can be very computationally expensive, and may have potential to be executed on distributed infrastructure. In this paper we propose firm foundations for multiscale modeling and distributed multiscale computing. Useful interaction patterns of multiscale models are made predictable with a submodel execution loop (SEL), four coupling templates, and coupling topology properties. We enhance a high-level and well-defined Multiscale Modeling Language (MML) that describes and specifies multiscale models and their computational architecture in a modular way. The architecture is analyzed using directed acyclic task graphs, facilitating validity checking, scheduling distributed computing resources, estimating computational costs, and predicting deadlocks. Distributed execution using the multiscale coupling library and environment (MUSCLE) is outlined. The methodology is applied to two selected applications in nanotechnology and biophysics, showing its capabilities.
Journal of Computational Science, 2011
International Journal for Multiscale Computational Engineering, 2007
Complex Automata were recently proposed as a paradigm to model multiscale complex systems. The co... more Complex Automata were recently proposed as a paradigm to model multiscale complex systems. The concept is formalized and the scale separation map is further investigated in relation with its capability to specify the components of Complex Automata. Five classes of scale ...
COAST (Complex Automata Simulation Technique) is a European Union FP6 funded project which has de... more COAST (Complex Automata Simulation Technique) is a European Union FP6 funded project which has developed a methodology for multi-science, multi-scale simulation of complex systems. The resulting framework (MUSCLE: Multiscale Simulation Coupling Library and Environment is now publically available. As an exemplar, MUSCLE has been applied to the model of a complex biomedical pathology, that of in-stent restenosis, resulting in a hierarchical aggregation of coupled cellular automata and agent based models coined "complex automaton". Currently, three simple, single scale models have been coupled to simulate the pathological response of the arterial wall to stent-deployment: an agent based model of smooth muscle cell dynamics (modeling cell cycle and cell-cell interaction), a lattice Boltzmann model of blood flow (defining wall shear stress and oscillatory shear index at the vessel surface) and a finite difference drug diffusion model (defining stent-eluted drug concentrations across the vessel wall). These sub-models operate on distinct temporal scales and can be plotted on a scale separation map. This conceptual tool defines the temporal separation of the processes and the coupling template required for interaction between them [3]. Coupling is implemented using smart conduits and in some situations, mapper agents, which transfer information between models with lattice based domains (blood flow, drug diffusion) to those with continuous domains (smooth muscle behaviour). Here we present preliminary output of a simple 2D model of in-stent restenosis. The present model captures the relationship between degree of stent induced injury and the smooth muscle cell hyperplastic response. The generation of realistic output correlates well with experimental data and paves the way for computer-aided design of stent-based therapies.
Procedia Computer Science, 2012