-
Proceedings
M. A. Prosnikov and V. V. Krzhizhanovskaya.
Обзор основых методов и программ для моделирования наноразмерных систем.
In:
ХLI Неделя науки СПбГПУ .
6, pp. 128-130.
-
Proceedings
V. S. Lebanin and V. V. Krzhizhanovskaya.
Модель кинетики реакции двух нейтральных частиц в газе и плазме.
In:
ХLI Неделя науки СПбГПУ .
6, 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 .
6, pp. 132-135.
-
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
15(5), 1250050.
-
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
93(2), pp. 160-170.
-
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
5, p. 555.
-
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].
-
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.
ISBN
9783941492455.
-
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.
ISBN 9783642297403.
2, pp. 116-123.
-
PhD Thesis
Q. C. Bui.
Relation extraction methods for biomedical literature.
ISBN
9789064645785.
Supervised by
P. M. A. Sloot.
-
Book
H. Ali, Y. Shi, D. Khazanchi, M. Lees, G. D. van Albada, J. Dongarra, and P. M. A. Sloot.
Proceedings of the International Conference on Computational Science, ICCS 2012.
-
Chapter
A. Adamatzky, M. Lees, and P. M. A. Sloot.
Physarum in the Netherlands: responding to the flood.
In:
Bioevaluation of world transport networks.
ISBN
9789814407038.
pp. 213-234.
-
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.
ISBN 9783642297403.
2, 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
13(7), 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
10(1), pp. 72-77.
-
Proceedings
J. A. Kaandorp, D. Botman, C. Tamulonis, and R Dries.
Multi-scale modeling of gene regulation of morphogenesis.
In:
How the World Computes.
ISBN
9783642308703.
pp. 355-362.
-
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.
ISBN
9788461553921.
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
3(5), 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
7(4), e36108.
-
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
8(4), p. e1002474.
-
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
8(37), 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
16(1), 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
9, 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.
ISBN
9781467329545.
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.
ISBN
9780415621441.
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.
ISBN
9780415621441.
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.
ISBN
9780415621441.
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
7(9), 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.
ISBN
9789814407038.
pp. 309-325.
-
Article
Q. C. Bui and P. M. A. Sloot.
A robust approach to extract biomedical events from literature.
Bioinformatics
28(20), 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
9, 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.
6, 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.
6, pp. 129-131.
-
Proceedings
V. S. Lebanin and V. V. Krzhizhanovskaya.
Обзор плазмохимических методов получения нитрида Кремния.
In:
ХL Неделя науки СПбГПУ.
6, 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.
6, 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.
-
Article
N. B. Melnikova, G. S. Shirshov, and V. V. Krzhizhanovskaya.
Virtual Dike: multiscale simulation of dike stability.
Procedia Computer Science
4, 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).
ISBN
9785696040905.
pp. 365-373.
-
PhD Thesis
G. Qiu.
Understanding the complex dynamics of financial markets through microsimulation.
ISBN
9789491211010.
Supervised by
P. M. A. Sloot and D. Kandhai.
-
PhD Thesis
J. T. Mościcki.
Understanding and mastering dynamics in computing grids: processing moldable tasks with user-level overlay.
Supervised by
M. T. Bubak and P. M. A. Sloot.
-
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.
ISBN
9781467300261.
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
4, 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.
ISBN
9788889405246.
4, 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
112(13), 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.
ISBN
9789400701137.
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
9(2), 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
27(6), pp. 725-736.
-
Book
M. Sato, S. Matsuoka, P. M. A. Sloot, G. D. van Albada, and J. Dongarra.
Proceedings of the International Conference on Computational Science, ICCS 2011.
-
Article
M. Sato, S. Matsuoka, G. D. van Albada, J. Dongarra, and P. M. A. Sloot.
Preface.
Procedia Computer Science
4, 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.
ISBN 9781450310680.
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.
ISBN
9783527409341.
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
1(3), pp. 365-373.
-
PhD Thesis
L. A. Naumov.
Modelling with cellular automata: problem solving environments and multidimensional applications.
ISBN
9789057762253.
Supervised by
P. M. A. Sloot and A. G. Hoekstra.
-
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
6(7).
-
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
78, 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
11(118).
-
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.
ISBN 9780769545721, 9780769545726.
pp. 224-225.
-
Article
E. Lorenz and A. G. Hoekstra.
Heterogeneous multiscale simulations of suspension flow.
Multiscale Modeling & Simulation
9(4), 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
33(8), 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
4, 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.
ISBN
9788890580505.
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.
ISBN
9781937284091.
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.
ISBN 9780769545974.
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).