A Random Walk of Remarkable Results

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Caveat:
None of my work is done in ‘splendid isolation’ I am thankful for lots of highly qualified and inspiring collaborators (too many to list here), the author list of co-authored papers do justice to that. Some of the results presented were really a team effort, some I was in the front, and some I was in the ‘back’. I list only the ‘keypapers’: for a complete overview of the publications please check this. The ‘discoveries’ are listed in reverse chronological order. The list is not complete, I picked a few that I think are of general interest. This work is mainly done at the University of Amsterdam (Netherlands), at ITMO university in St. Petersburg (Russia) and at the Complexity Institute at NTU (Singapore).

Unraveling and disrupting Criminal Value Chains
The result of some wild out-of-the-box thinking during a nice dinner party with criminologist Paul Duijn: Mapping relations of criminals to scale free complex networks and then studying the resilience and robustness of interventions. We discovered complete new ways of dismantling criminal value chain networks!

P.A.C. Duijn; V. Kashirin and P.M.A. Sloot: The Relative Ineffectiveness of Criminal Network Disruption, Sci. Rep., vol. 4, pp. 4238+15. Nature Publishing Group/Macmillan, 2014. ISSN 2045-2322. (DOI: 10.1038/srep04238)

See also this Documentary.

Stochastic Resonance in Complex Networks
Nature seems to be fond of complex networks to organize itself, or at least that is the way we interpret that self organization. One of the reasons these networks seem to emerge everywhere is their resilience to disruption and noise. We discovered the effect of this noise in the form of Stochastic Resonance. Lots of fun to see how a bit of noise actually makes the information transfer through those networks even better. 

A. Czaplicka.; J.A. Hołyst and P.M.A. Sloot: Noise enhances information transfer in hierarchical networks, Scientific Reports, vol. 3, 2013. Nature Publishing Group/Macmillan. (DOI: 10.1038/srep01223)

Plasmodial slime mould Computation
Andrew I. Adamatzky is a fun guy to work with, wild ideas and absolutely original! We injected slime mold () on a petri dish where we made an image of the Netherlands and had corn flakes represented the main cities. Then we stepped back and watched little miracle happen... The slime mold seems to efficiently predict the network of the Dutch motorways!

A. Adamatzky; M.H. Lees and P.M.A. Sloot: Bio-development of motorway networks in the Netherlands: A slime mould approach, Advances in Complex Systems, vol. 15, nr 4 pp. 1250034+28. 2012. ISSN: 0219-5259, 1793-6802. (DOI: 10.1142/S0219525912500348)

A. Adamatzky; M.H. Lees and P.M.A. Sloot: Physarum in the Netherlands: Responding to the Flood, in A. Adamatzky, editor, Bioevaluation of World Transport Networks, in series Non Linear Science, pp. 1-380. World Scientific, 2012. ISBN: 978-981-4407-03-8.

Tumor Growth: Lab work and Simulation
Not always one has the opportunity to work with excellent experimentalists, but this time we managed. With a group from the Amsterdam Medical Center we worked on a better understanding of tumour growth and the influence of the notorious Cancer Stem Cells. I am very pleased with the results that were accepted for publication in the famous ‘Cancer Research’ Journal:

A. Sottoriva; J.J.C. Verhoeff; T. Borovski; S.K. McWeeney; L.A. Naumov; J.P. Medema; P.M.A. Sloot and L. Vermeulen: Cancer Stem Cell Tumor Model Reveals Invasive Morphology and Increased Phenotypical Heterogeneity, Cancer Research, vol. 70, nr 1 pp. 46-56. American Association for Cancer Research, 2010. Print ISSN: 0008-5472; Online ISSN: 1538-7445. (DOI: 10.1158/0008-5472.CAN-09-3663)

A. Sottoriva; P.M.A. Sloot; J.P. Medema and L. Vermeulen: Exploring Cancer Stem Cell Niche Directed Tumor Growth, Cell Cycle, vol. 9, nr 8 pp. 1472-1479. Landes Bioscience, 2010. (DOI: 10.4161/cc.9.8.11198) 

Multi-scale modeling of HIV infections
P.M.A. Sloot; P.V. Coveney; G. Ertaylan; V. Müller; C.A.B. Boucher and M.T. Bubak: HIV Decision Support: From Molecule to Man, Phil Trans. R. Soc. A, vol. 367, nr 1898 pp. 2691-2703. 2009.

Decision Support Patent and Trademark
As part of our EU project Virolab we obtained a Patent and trademark of a piece of software on decision support in infectious diseases.
Retrogram: A decision support system for HIV drugs ranking, Trademark world coverage: 713908: US Software Patent 10/058622, 2006.

HIV Dynamics Modeled with Simple Cellular Automata
A few years ago I started to study with Charles Boucher and Fan Chen some simple models that could explain the long term dynamics of HIV infection as given by this prototypical graph:

HIV DYNAMICS
We modeled infection in the lymphnodes and some relative simple cell motility. The 3 components of infection (Entry-Transcription-Integration) were abstracted into probability functions. Some promising results are shown below:

HIV DYNAMICS CA SIMULATIONS
P.M.A. Sloot; F. Chen and C.A. Boucher: Cellular Automata Model of Drug Therapy for HIV Infection, in S. Bandini; B. Chopard and M. Tomassini, editors, 5th International Conference on Cellular Automata for Research and Industry, ACRI 2002, Geneva, Switzerland, October 9-11, 2002. Proceedings, in series Lecture Notes in Computer Science, vol. 2493, pp. 282-293. October 2002. [PDF]

P.M.A. Sloot; A.V. Boukhanovsky; W. Keulen; A. Tirado Ramos and C.A. Boucher: A Grid-based HIV Expert System, Journal of Clinical Monitoring and Computing, vol. 19, nr 4-5 . October 2005. ISSN: 11387-1307. [PDF]

Within the ViroLab project we are now working on much more elaborate (particle and agent based) models.

P.M.A. Sloot; A. Tirado Ramos; I. Altintas; M.T. Bubak and C.A. Boucher: From Molecule to Man: Decision Support in Individualized E-Health, IEEE Computer, (Cover feature) vol. 39, nr 11 pp. 40-46. November 2006. [PDF]

A By-Pass in virtual reality
After our first experiments with virtual reality as a methodology to understand representation and interaction with high dimensional and complex data resulted in a nice PhD thesis by Rob Belleman [Thesis], we took the thing one step further and developed –after some initial suggestions by Charley Taylor and Chris Zarins (Stanford, USA) – a grid-based system to plan a abdominal by-pass surgery in virtual reality. We spend some 6 year with medical doctors to come up with a working prototype.

A DISTRIBUTED VIRTUAL THEATRE
We learned a tremendous amount of new things from this, not only technical but also fundamental aspects on visualization, interaction and representation in a distributed world.

For a popular account of this see: P.M.A. Sloot and A.G. Hoekstra: Virtual Vascular Surgery on the Grid, ERCIM news, October 2004 [PDF]. This work resulted in 3 PhD theses (Belleman, Zhao, Tirado-Ramos [Links]) and lots of new insights published in the peer reviewed literature [link].

One of the problems we had to tackle was the efficient (High Performance) simulation of blood flow… now that proved to be something…

Cellular Automata and BloodFlow  
This is maybe not the place to reflect on the endless discussion of how and why Cellular Automata based models like Lattice Boltzmann (LBE), sometimes can outperform the more conventional models… After the initial work our PhD student Drona Kandhai on modeling (among others) a chemical reactor [Thesis], we started to work on casting bloodflow into LBE described in the thesis by our PhD Student Artoli [Thesis].

LBE BLOODFLOW [MOVIE]

A.M.M. Artoli; B.D. Kandhai; H.C.J. Hoefsloot; A.G. Hoekstra and P.M.A. Sloot: Lattice BGK of flow in a symmetric bifurcation, Future Generation Computer Systems, vol. 20, nr 6 pp. 909-916. 2004. [PDF]

A.M.M. Artoli; A.G. Hoekstra and P.M.A. Sloot: Mesoscopic simulations of systolic flow in the Human abdominal aorta, Journal of Biomechanics, vol. 39, nr 5 pp. 873-884. 2006. [PDF]

Cellular Automata and Coral Growth
With the creative idea’s of Jaap Kaandorp, Roeland Merks and many others we managed to develop a computer simulation of Stony Coral growth that includes nutrient flow and diffusion, photosynthesis, differential growth etc.

Some nice visualization is shown below where the white tips indicate the most recent growth-sites. The growth is dominated by diffusion.


J.A. Kaandorp; C.P. Lowe; D. Frenkel and P.M.A. Sloot: The effect of nutrient diffusion and flow on coral morphology, Physical Review Letters, vol. 77, nr 11 pp. 2328-2331. March 1996

Self-organized Critical in Discrete Event Simulation of Cellular Automata
Self-organization and Selforganized Criticality is a truly remarkable emerging property of complex systems. We were quite amazed to find it in our generic Distributed Event Simulation system. Below a drawing of the roll-back length of a time-warped discrete event simulation (TBD).

SOC IN TIME-WARP
P.M.A. Sloot; B.J. Overeinder and A. Schoneveld: Self-organized criticality in simulated correlated systems, Computer Physics Communications, vol. 142, nr 1-3 pp. 76-81. December 2001. [PDF].

Dancing on a sphere
Years ago at the Netherlands Cancer Institute, Willy Bont got me interested in human vesicles (spherical phospholipids bi-layers). According to him their sizes are quantified, meaning that only particular sizes exist in nature. This is hard to believe if you consider the biological spread in things. With the strong push of Rene van Dantzig and the help of one of my PhD students (Jeroen Voogd) we set out to model the size distributions of such vesicles.

It proved to be tremendous harder than we ever thought… in all respects, the models, the computations, the experiments, the analyses.

We discovered that sharp jumps for tiny changes in R (Radius of the vesicle) between trajectories with major differences in topological structure correspond to avalanche-like J.M. Voogd; P.M.A. Sloot and R. van Dantzig: Equilibrium spherically curved two-dimensional Lennard-Jones systems , J. Chem. Phys., vol. 123, nr 084105 pp. 1-5. 2005. (DOI: 10.1063/1.2007707) [PDF]
LENNARD-JONES VESICLE [MOVIE]

J.M. Voogd: Crystallisation on a Sphere - Computational Studies of two-dimensional Lennard-Jones Systems, PhD thesis, University of Amsterdam, Amsterdam, The Netherlands, (Promotor: Prof. Dr. P.M.A. Sloot, co-promotor: Dr. R. van Dantzig) 1998. [PDF]

Swelling of Lymphocyte Nucleus revealed through Elastic Light Scattering.
Through novel flowcytometry methods and numerical models of the interaction of light with nucleated bloodcells we discovered the unexpected link between the swelling of the cytoplasm and nucleus under hypertonic shocks.
OSMO SHOCK SIM

P.M.A. Sloot and C.G. Figdor: Elastic light scattering from nucleated bloodcells: Rapid numerical analysis, Applied Optics, vol. 25, pp. 3559 -. 1986. [PDF]

P.M.A. Sloot; A.G. Hoekstra and C.G. Figdor: Osmotic response of lymphocytes measured by means of forward lightscattering: Theoretical considerations, Cytometry, vol. 9, pp. 636-641. 1988. [PDF]

P.M.A. Sloot; A.G. Hoekstra; H. van de Liet and C.G. Figdor: Scatter matrix elements of biological particles measured in a flow-through system: Theory and practice, Applied Optics, vol. 28, pp. 1752-1762. 1989 [PDF]

A.G. Hoekstra; J. Aten and P.M.A. Sloot: The effect of aniosmotic media on the volume of the T-lymphocyte nucleus, Biophysical Journal, vol. 59, pp. 765-774. 1991 [PDF].

Patent: CACE: Computer Assisted Centrifugal Elutriation of White Blood-cells: USA patent:4.939.081. (1990)

New flowcytometer for nucleated cell detection through light scattering
In this work we developed a detection system and data acquisition technique that allowed us for the first time to automatically identify peripheral nucleated bloodcells with high accuracy without staining techniques

P.M.A. Sloot; M.J. Carels; P. Tensen and C.G. Figdor: Computer Assisted Centrifugal Elutriation I: Detection system and data acquisition equipment, Computer Methods and Programs in Biomedicine, vol. 8, pp. 179. 1987. [PDF]

P.M.A. Sloot; E.H.M. van der Donk and C.G. Figdor: Computer Assisted Centrifugal Elutriation II: Multiparametric statistical analysis, Computer Methods and Programs in Biomedicine, vol. 27, pp. 37-46. 1988. [PDF]