-
Proceedings
M. A. Prosnikov and V. V. Krzhizhanovskaya.
Обзор основых методов и программ для моделирования наноразмерных систем.
In:
ХLI Неделя науки СПбГПУ.
pp. 128-130.
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Proceedings
V. S. Lebanin and V. V. Krzhizhanovskaya.
Модель кинетики реакции двух нейтральных частиц в газе и плазме.
In:
ХLI Неделя науки СПбГПУ.
pp. 146-149.
-
Proceedings
S. A. Konakov and V. V. Krzhizhanovskaya.
Моделирование механизма образования силаммониевых радикалов в технологии плазмохимического осаждения нитрида кремния азота с малым содержанием.
In:
ХLI Неделя науки СПбГПУ.
pp. 132-135.
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Article
G. Qiu, D. Kandhai, N. F. Johnson, and P. M. A. Sloot.
Understanding complex dynamics in derivatives finance: why do options markets smile?.
Advances in Complex Systems
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Article
J. U. Hammel, M. V. Filatov, J. Herzen, F. Beckmann, J. A. Kaandorp, and M. Nickel.
The non-hierarchical, non-uniformly branching topology of a leuconoid sponge aquiferous system revealed by 3D reconstruction and morphometrics using corrosion casting and X-ray microtomography.
Acta Zoologica
pp. 160-170.
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Article
D. Botman and J. A. Kaandorp.
Spatial gene expression quantification: a tool for analysis of in situ hybridizations in sea anemone Nematostella vectensis.
BMC Research Notes
p. 555.
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Proceedings
A. Mordvintsev, V. Krzhizhanovskaya, M. Lees, and P. Sloot.
Simulation of city evacuation coupled to flood dynamics.
In:
PED 2012: accompanying booklet: abstracts of all presentations and posters: 6th International Conference on Pedestrian and Evacuation Dynamics.
pp. [156-158].
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Proceedings
A. L. Pyayt, I. I. Mokhov, A. P. Kozionov, V. T. Kusherbaeva, V. V. Krzhizhanovskaya, B. J. Broekhuijsen, and R. J. Meijer.
Signal Processing Methods for Flood Early Warning Systems.
In:
Proceedings of 10th International Conference on Hydroinformatics 2012: Hamburg, Germany.
-
Proceedings
R. Cushing, S. Koulouzis, R. Strijkers, A. S. Z. Belloum, and M. Bubak.
Service Level Management for executable papers.
In: Euro-Par 2011: Parallel Processing Workshops.
pp. 116-123.
-
Chapter
A. Adamatzky, M. Lees, and P. M. A. Sloot.
Physarum in the Netherlands: responding to the flood.
In:
Bioevaluation of world transport networks.
pp. 213-234.
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Proceedings
S. Varma, M. C. Villa Uriol, P. Lamata, E. Schileo, B. Ó Nualláin, J. Fenner, N. S. H. Smith, and D. R. Hose.
Patient-Centred Multi-scale Computational Workflows.
In: VPH Conference 2012, London.
-
Proceedings
T. Szepieniec, J. Kocot, T. Schaaf, O. Appleton, M. Heikkurinen, A. S. Z. Belloum, J. Serrat-Fernández, and M. Metzker.
On importance of Service Level Management in Grids.
In: Euro-Par 2011: Parallel Processing Workshops.
pp. 64-75.
-
Article
P. Ramos-Silva, S. Benhamada, N. Le Roy, B. Marie, N. Guichard, I. Zannella-Cléon, L. Plasseraud, M. Corneillat, G. Alcaraz, J. Kaandorp, and F. Marin.
Novel molluskan biomineralization proteins retrieved from proteomics: a case study with Upsalin.
ChemBioChem
pp. 1067-1078.
-
Article
J. Borgdorff, D. Groen, S. Ferlin, I. Saverchenko, J. Suter, A. G. Hoekstra, and P. V. Coveney.
Multiscale Simulations on Distributed European e-Infrastructures.
Inside
pp. 72-77.
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Proceedings
J. A. Kaandorp, D. Botman, C. Tamulonis, and R Dries.
Multi-scale modeling of gene regulation of morphogenesis.
In:
How the World Computes.
pp. 355-362.
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Proceedings
V. V. Krzhizhanovskaya and N. B. Melnikova.
Modeling earthen dikes: sensitivity analysis and calibration of soil properties based on sensor data.
In:
Proceedings of the 12th International Conference on Computational and Mathematical Methods in Science and Engineering: Murcia, Spain, July 2-5, 2012: CMMSE. - Vol. 4.
pp. 1414-1424.
-
Article
R. Quax, A. Apolloni, and P. M. A. Sloot.
Information processing reveals how microscopic components affect the macroscopic system-state in complex networks.
Scientific Reports
.
-
Article
P. M. A. Sloot and R. Quax.
Information processing as a paradigm to model and simulate complex systems.
Journal of Computational Science
pp. 247-249.
-
Article
E. Mancini, F. Gastiglione, M. Bernaschi, A. de Luca, and P. M. A. Sloot.
HIV reservoirs and immune surveillance evasion cause the failure of structured treatment interruptions: a computational study.
PLoS ONE
.
-
Article
Y. Kim, R. Sinclair, N. Chindapol, J. A. Kaandorp, and E. De Schutter.
Geometric theory predicts bifurcations in minimal wiring cost trees in biology are flat.
PLoS Computational Biology
p. e1002474.
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Article
X. Wang, H. C. Schröder, K. Wang, J. A. Kaandorp, and W. E. G. Müller.
Genetic, biological and structural hierarchies during sponge spicule formation: From soft sol-gels to solid 3D silica composite structures.
Soft Matter
pp. 9501-9518.
-
Article
B. Pengel, G. S. Shirshov, V. V. Krzhizhanovskaya, N. B. Melnikova, A. Koelewijn, A. L. Pyayt, and I. I. Mokhov.
Flood Early Warning System: Sensors and Internet.
Journal of Flood Risk Management
.
-
MSc Thesis
K. W. Kongsgård.
Expertise Modeling on cQA Sites -- News Feed Optimization.
Supervised by E. Meij.
-
MSc Thesis
P. Firmpas Nisantzis.
Evolving collective and single cell motility in a computational model of tumor invasion.
Supervised by
R. M. H. Merks and J. A. Kaandorp.
-
Article
S. Koulouzis, R. Cushing, K. A. Karasavvas, A. Belloum, and M. Bubak.
Enabling web services to consume and produce large datasets.
IEEE Internet Computing
pp. 52-60.
-
Article
H. Ali, Y. Shi, D. Khazanchi, M. Lees, G. D. van Albada, J. Dongarra, and P. M. A. Sloot.
Empowering Science through Computing, preface for ICCS 2012.
Procedia Computer Science
pp. 1-6.
-
Proceedings
S. Varma, C. Pedronaci, D. Kalra, M. C. Villa Uriol, P. Lamata, E. Schileo, B. Ó Nualláin, N. S. H. Smith, S. Wood, and D. R. Hose.
Embodying a Patient Avatar for Computational Workflows.
In: VPH Conference 2012, London.
-
Proceedings
S. J. Zasada, M. Mamonski, D. Groen, J. Borgdorff, I. Saverchenko, T. Piontek, K. Kurowski, and P. V. Coveney.
Distributed infrastructure for multiscale computing.
In: 2012 IEEE/ACM 16th International Symposium on Distributed Simulation and Real Time Applications: DS-RET 2012: Proceedings.
pp. 65-74.
-
Proceedings
A. L. Pyayt, I. I. Mokhov, A. P. Kozionov, V. T. Kusherbaeva, B. Lang, V. V. Krzhizhanovskaya, and R. J. Meijer.
Data-driven modelling for flood defence structure analysis.
In:
Comprehensive flood risk management: research for policy and practice.
pp. 301-306.
-
Proceedings
A. L. Pyayt, I. I. Mokhov, A. Kozionov, and V. Kusherbaeva.
Data-driven methods in UrbanFlood project for flood defence structure measurements analysis.
-
Proceedings
C. D. Erdbrink, V. V. Krzhizhanovskaya, and P. M. A. Sloot.
Controlling flow-induced vibrations of flood barrier gates with data-driven and finite-element modelling.
In:
Comprehensive flood risk management: research for policy and practice.
pp. 425-434.
-
Proceedings
V. V. Krzhizhanovskaya, N. B. Melnikova, G. S. Shirshov, F. I. Rusadi, R. G. Belleman, J. Lhomme, B. P. Gouldby, A. Topple, and J. Simm.
Computational models in flood early warning systems.
In:
Comprehensive flood risk management: research for policy and practice.
p. 1533.
-
Article
N. Zarrabi, M. Prosperi, R. G. Belleman, M. Colafigli, A. De Luca, and P. M. A. Sloot.
Combining epidemiological and genetic networks signifies the importance of early treatment in HIV-1 transmission.
PLoS ONE
p. e46156.
-
Chapter
A. Adamatzky, S. Akl, R. Alonso-Sanz, W. van Dessel, Z. Ibrahim, A. Ilachinski, J. Jones, A. V. D. M. Kayem, G. J. Martínez, P. de Oliveira, M. Prokopenko, T. Schubert, P. Sloot, E. Strano, and X.-S. Yang.
Biorationality of motorways.
In:
Bioevaluation of world transport networks.
pp. 309-325.
-
Article
Q. C. Bui and P. M. A. Sloot.
A robust approach to extract biomedical events from literature.
Bioinformatics
pp. 2654-2661.
-
Article
J. Borgdorff, C. Bona-Casas, M. Mamonski, K. Kurowski, T. Piontek, B. Bosak, K. Rycerz, E. Ciepiela, T. Gubala, D. Harezlak, M. Bubak, E. Lorenz, and A. G. Hoekstra.
A distributed multiscale computation of a tightly coupled model using the Multiscale Modeling Language.
Procedia Computer Science
pp. 596-605.
-
MSc Thesis
R. Dries.
3D mass-spring model for studying early development of the starlet sea anemone nematostella vectensis.
Supervised by
C. Tamulonis and J. A. Kaandorp.
-
Proceedings
S. A. Konakov and V. V. Krzhizhanovskaya.
Сравнение двух моделей плазмохимических процессов при осаждении нитрида Кемния.
In:
ХL Неделя науки СПбГПУ.
pp. 132-134.
-
Proceedings
A. S. Afanasieva, S. A. Ponyaev, and V. V. Krzhizhanovskaya.
Подготовка задачи численного моделирования синтеза фуллеренов в углеродсодержащей плазме дугового разряда.
In:
ХL Неделя науки СПбГПУ.
pp. 129-131.
-
Proceedings
V. S. Lebanin and V. V. Krzhizhanovskaya.
Обзор плазмохимических методов получения нитрида Кремния.
In:
ХL Неделя науки СПбГПУ.
pp. 131-132.
-
Proceedings
I. S. Kiseleva and V. V. Krzhizhanovskaya.
Моделирование аргоновой плазмы в установке плазмохимического осаждения с помощью пакета ESI CFD-ACE+.
In:
ХL Неделя науки СПбГПУ.
pp. 126-128.
-
Proceedings
S. A. Konakov and V. V. Krzhizhanovskaya.
Компьютерное моделирование процесса осаждения многослойных структур на основе нитрида кремния методом РЕСVD.
In:
Наука и инновации в технических университетах : Материалы пятого всероссийского форума студентов, аспирантов и молодых ученых.
pp. 12-13.
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Article
N. B. Melnikova, G. S. Shirshov, and V. V. Krzhizhanovskaya.
Virtual Dike: multiscale simulation of dike stability.
Procedia Computer Science
pp. 791-800.
-
Proceedings
N. B. Melnikova, G. S. Shirshov, V. V. Krzhizhanovskaya, and N. N. Shabrov.
Virtual Dike and Flood Simulator: Parallel distributed computing for flood early warning systems.
In:
Параллельные вычислительные технологии (ПаВТ’2011).
pp. 365-373.
-
Proceedings
J. Bernsdorf, G. Berti, B. Chopard, J. Hegewald, M. Krafczyk, D. Wang, E. Lorenz, and A. Hoekstra.
Towards distributed multiscale simulation of biological processes.
In:
The Seventh IEEE International Conference on e-Science. Workshops: eScienceW 2011: proceedings: Stockholm, Sweden, 5-8 December 2011.
pp. 89-96.
-
MSc Thesis
I. Niculescu.
Towards a cell-based model of Neointimal Hyperplasia with Cellular Potts Model.
Supervised by
A. G. Hoekstra and R. M. H. Merks.
-
Article
R. Strijkers, R. Cushing, D. Vasyunin, C. de Laat, A. S. Z. Belloum, and R. Meijer.
Toward executable scientific publications.
Procedia Computer Science
pp. 707-715.
-
Proceedings
B. Pengel, L. Wentholt, V. V. Krzhizhanovskaya, G. Shirshov, N. Melnikova, B. Gouldby, A. Koelewijn, A. Pyayt, I. Mokhov, N. Pals, R. Meijer, and J. Broekhuijsen.
The urbanflood early warning system: sensors and coastal flood safety.
In:
Proceedings of the CoastGIS 2011 Conference.
pp. 20-27.
-
Article
M. A. Yurkin and A. G. Hoekstra.
The discrete-dipole-approximation code ADDA: capabilities and known limitations.
Journal of Quantitative Spectroscopy & Radiative Transfer
pp. 2234-2247.
-
Chapter
J. A. Kaandorp, M. Filatov, and N. Chindapol.
Simulating and quantifying the environmental influence on coral colony growth and form.
In:
Coral reefs: An ecosystem in transition.
pp. 177-185.
-
Proceedings
R. S. Cushing, S. Koulouzis, A. S. Z. Belloum, R. J. Strijkers, and M. T. Bubak.
Service Level Management for Executable Papers.
In: 7th International European Conference on Parallel and Distributed Computing (Euro-Par 2011), workshop MDGS2011.
-
Article
R. Quax, D. A. Bader, and P. M. A. Sloot.
SEECN: simulating complex systems using dynamic complex networks.
International Journal for Multiscale Computational Engineering
pp. 201-214.
-
Article
J. T. Mościcki, M. Lamanna, M. Bubak, and P. M. A. Sloot.
Processing moldable tasks on the grid: late job binding with lightweight user-level overlay.
Future Generation Computer Systems
pp. 725-736.
-
Article
M. Sato, S. Matsuoka, G. D. van Albada, J. Dongarra, and P. M. A. Sloot.
Preface.
Procedia Computer Science
pp. 1-6.
-
Proceedings
R. Cushing, S. Koulouzis, A. S. Z. Belloum, and M. Bubak.
Prediction-based auto-scaling of scientific workflows.
In: Proceedings of the 9th International Workshop on Middleware for Grids, Clouds and e-Science: MGC 2011, co-located with ACM/IFIP/USENIX 12th International Middleware Conference, December 12-16, 2011, Lisbon, Portugal.
p. 1.
-
MSc Thesis
F. Speelman.
Position-Based Quantum Cryptography and the Garden-Hose Game.
Supervised by H. Buhrman and C. Schaffner.
-
MSc Thesis
J. Teunissen.
Particle based 3D modeling of positive streamer inception.
Supervised by U. Ebert.
-
Article
V. V. Krzhizhanovskaya.
Overstromingsrisico's in Kaart Brenger met de HPC Cloud.
"High Performance Computing E-Science Support", SARA Jaarverslag 2010
pp. 38-38.
-
Chapter
V. P. Maltsev, A. G. Hoekstra, and M. A. Yurkin.
Optics of white blood cells: optical models, simulations, and experiments.
In:
Advanced optical flow cytometry: methods and disease diagnoses.
pp. 63-93.
-
Article
H. Tahir, A. G. Hoekstra, E. Lorenz, P. V. Lawford, D. R. Hose, J. Gunn, and D. J. W. Evans.
Multi-scale simulations of the dynamics of in-stent restenosis: impact of stent deployment and design.
Interface Focus
pp. 365-373.
-
Article
C. Tamulonis, M. Postma, and J. Kaandorp.
Modeling filamentous cyanobacteria reveals the advantages of long and fast trichomes for optimizing light exposure.
PLoS ONE
.
-
Article
A. L. Pyayt, I. I. Mokhov, B. Lang, V. V. Krzhizhanovskaya, and R. J. Meijer.
Machine learning methods for environmental monitoring and flood protection.
World Academy of Science, Engineering and Technology. Proceedings
pp. 118-123.
-
Proceedings
A. L. Pyayt, I. I. Mokhov, B. Lang, V. V. Krzhizhanovskaya, and R. J. Meijer.
Machine Learning Methods for Environmental Monitoring and Flood Protection.
World Academy of Science, Engineering and Technology
78, pp. 118-123.
-
Article
A. Mei Shan, R. Quax, D. van de Vijver, Y. Zhu, and P. M. A. Sloot.
Increasing risk behaviour can outweigh the benefits of antiretroviral drug treatment on the HIV incidence among men-having-sex-with-men in Amsterdam.
BMC Infectious Diseases
.
-
Proceedings
M. Gerhards, V. Sander, A. Belloum, D. Vasunin, and A. Benabdelkader.
HisT/PLIER: A two-fold Provenance Approach for Grid-enabled Scientific Workflows using WS-VLAM.
In: 2011 12th IEEE/ACM International Conference on Grid Computing : Grid 2011.
pp. 224-225.
-
Article
E. Lorenz and A. G. Hoekstra.
Heterogeneous multiscale simulations of suspension flow.
Multiscale Modeling & Simulation
pp. 1301-1326.
-
Article
C. A. D. Leguy, E. M. H. Bosboom, A. S. Z. Belloum, A. P. G. Hoeks, and F. N. van de Vosse.
Global sensitivity analysis of a wave propagation model for arm arteries.
Medical Engineering & Physics
pp. 1008-1016.
-
Proceedings
B. Pengel, G. S. Shirshov, V. V. Krzhizhanovskaya, A. R. Koelewijn, I. I. Mokhov, A. L. Pyayt, and N. B. Melnikova.
Flood early warning system: sensors and internet.
In:
Abstract proceedings: 5th International CConference on Flood Management (ICFM5): Floods: from Risk to Opportunity: 27 to 29 September 2011, Tokyo-Japan.
pp. 212-221.
-
Article
V. V. Krzhizhanovskaya, G. S. Shirshov, N. B. Melnikova, R. G. Belleman, F. I. Rusadi, B. J. Broekhuijsen, B. P. Gouldby, J. Lhomme, B. Balis, M. Bubak, A. L. Pyayt, I. I. Mokhov, A. V. Ozhigin, B. Lang, and R. J. Meijer.
Flood early warning system: design, implementation and computational modules.
Procedia Computer Science
pp. 106-115.
-
Proceedings
P. Ramos-Silva, C. Combet, F. Marin, and J. A. Kaandorp.
Finding patterns and differences on biomineralization-related proteins from Metazoans.
In:
Molecular iomineralization in marine organisms: Nanobiotechnology and biomedical application.
p. 21.
-
Proceedings
Q. C. Bui and P. M. A. Sloot.
Extracting biological events from text using simple syntactic patterns.
In:
Proceedings of BioNLP Shared Task 2011 Workshop: Portland, Oregon, USA, 24 June, 2011.
pp. 143-146.
-
MSc Thesis
J. Jänes.
Efficient integration of multiscale N-body systems.
Supervised by F. I. Pelupessy and S. F. Portegies Zwart.
-
Proceedings
R. Cushing, S. Koulouzis, A. Belloum, and M. Bubak.
Dynamic handling for cooperating scientific web services.
In: Proceedings 2011 IEEE Seventh International Conference on eScience: 5-8 December 2011, Stockholm, Sweden.
pp. 232-239.
-
Other: misc
M. C. F. Prosperi, M. Rosen-Zvi, A. Altmann, M. Zazzi, S. Di Giambenedetto, R. Kaiser, E. Schülter, D. Struck, P. M. A. Sloot, D. A. M. C. van de Vijver, A.-M. Vandamme, and A. Sönnerborg.
Correction: Antiretroviral Therapy Optimisation without Genotype Resistance Testing: A Perspective on Treatment History Based Models.
PLoS ONE
6(4).
-
MSc Thesis
H. Þorsdottir.
Conservation Properties of the Hamiltonian Particle-Mesh method for the Quasi-Geostrophic Equations on a sphere.
Supervised by J. Frank.
-
Article
A. Belloum, M. A. Inda, D. Vasunin, V. Korkhov, Z. Zhao, H. Rauwerda, T. M. Breit, M. Bubak, and L. O. Hertzberger.
Collaborative e-Science Experiments and Scientific Workflows.
IEEE Internet Computing
pp. 39-47.
-
Article
S. Murtaza, A. G. Hoekstra, and P. M. A. Sloot.
Cellular automata simulations on a FPGA cluster.
International Journal of High Performance Computing Applications
pp. 193-204.
-
Article
L. Naumov, A. Hoekstra, and P. Sloot.
Cellular automata models of tumour natural shrinkage.
Physica A : Statistical Mechanics and its Applications
pp. 2283-2290.
-
Article
V. V. Krzhizhanovskaya.
Better Flood Protection thanks to SARA's HPC Cloud.
"High Performance Computing E-Science Support", SARA Annual Report 2010
pp. 39-39.
-
Proceedings
A. L. Pyayt, I. I. Mokhov, A. Kozionov, V. Kusherbaeva, N. B. Melnikova, V. V. Krzhizhanovskaya, and R. J. Meijer.
Artificial intelligence and finite element modelling for monitoring flood defence structures.
In:
EESMS 2011 proceedings.
-
Proceedings
A. L. Pyayt, I. I. Mokhov, A. Kozionov, V. Kusherbaeva, N. B. Melnikova, V. V. Krzhizhanovskaya, and R. J. Meijer.
Artificial Intelligence and Finite Element Modelling for Monitoring Flood Defence Structures.
-
Proceedings
D. Botman and J. A. Kaandorp.
An integrated approach to infer the gene network in early development of the cnidarian Nematostella vectensis..
Publications of the CSL group