michael muskulus' homepage

Michael Muskulus
(Dipl.-Phys., PhD student)

Mathematical Institute
Leiden University
Niels Bohrweg 1
2333 CA Leiden, The Netherlands
email:
public key fingerprint: A02F E23E 38D7 203A 470D 7572 AB39 64BD 55DD 118D.

Researcher in Dynamical Systems and Natural Computing

Note: These pages are obsolete and will be removed soon.
Please update your links to my new homepage
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in a natural surrounding

"If I ever conceive any original idea, it will be because I have been abnormally prone to confuse ideas...
and have thus found remote analogies and relations which others have not considered!
Others rarely make these confusions, and proceed by precise analysis."
[KJW Craik, 'The Nature of Explanation']

Research statement:

I am interested in Mathematical Biology, Dynamical Systems and Biomedical/Biostatistical Applications.

My research was part of the VIEWS project, funded by NWO under the Computational Life Sciences initiative.
Before starting this PhD, I was working half a year at the Max Planck Institute for Meteorology, Hamburg.

Current interests and projects

• Mathematical analysis and modelling of respiratory function, with special emphasis on obstructive lung diseases.
• Properties of solutions to optimal transportation problems, with special emphasis on applications in time series analysis.
• Modelling and analysis of circadian oscillators (low-dimensional dynamical systems on tori).
• Inverse modelling of neuronal activity by Wasserstein distances.
• Applications of Markov chain theory (in P systems, molecular dynamics and mathematical ecology).
• Statistical analysis of MR images in murine models of Alzheimer's disease.

Curriculum vitae

Note: These pages are obsolete and will be removed soon.
Please update your links to my new homepage
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Publications

Dynamical Systems and Biomedical Applications

• Muskulus, M.; Houweling, S.; Verduyn-Lunel, S.; Daffertshofer, A.: Functional similarities and distance properties.
Journal of Neuroscience Methods, accepted. DOI: 10.1016/j.jneumeth.2009.06.035.

• Boonstra, T.W.; Houweling, S.; Muskulus, M.: Does asynchronous neuronal activity average out on a macroscopic scale?
Journal of Neuroscience 29: 8871-8874 (2009). DOI: 10.1523/JNEUROSCI.2020-09.2009.

• Scheenstra, A.E.H.; Muskulus M.; Staring M.; van den Maagdenberg A.M.J.V.; et al.: The 3D Moore-Rayleigh test for the quantitative groupwise comparison of MR brain images.
IPMI 2009, accepted. (Best Poster Award)

• Muskulus, M.; Scheenstra, A.E.H.; Braakman, N.; Dijkstra, J.; et al.: Prospects for early detection of Alzheimer's disease from serial MR images in transgenic mouse models.
Current Alzheimer Research, accepted.

° Muskulus, M.; Verduyn-Lunel, S.: Reconstruction of functional brain networks by Wasserstein distances in a listening task.
In: Kakigi, R.; Yokosawa, K.; Kuriki, S. (eds): Biomagnetism: Interdisciplinary Research and Exploration. Hokkaido University Press. Sapporo, Japan (2008), pp. 59-61. (Young Investigator Award for Excellent Paper)

• Muskulus, M.; Verduyn-Lunel, S.: The Analysis of Dynamical Diseases by Optimal Transportation Distances.
ERCIM News 73 (2008), 16-17.
Available from http://ercim-news.ercim.org/.

• Muskulus M.; Slats, A.M.; van der Plas D.T.; Verduyn-Lunel, S.J.; Sterk P.J.: Discrimination of asthma and COPD by reconstructing unbiased probability distributions (attractors) from the dynamics of respiratory impedance.
Am J Resp Crit Care Med 177 (2008), A947 (Abstracts Issue).

Natural Computing

• Muskulus, M.: Applications of Page Ranking in P Systems.
In: Corne, D.; et al (Eds.): WMC9 2008, LNCS 5391 (2009), 311-324.

° Muskulus, M.: Identification of P system models assisted by biochemical databases.
In: Ibarra, O. H.; Sosik, P. (Eds.) Prague International Workshop on Membrane Computing. Preliminary proceedings, Sileasian University in Opava, Faculty of Philosophy and Science (2008), pp. 46-49.

• Brijder, R.; Hoogeboom, H.J.; Muskulus, M.: Strategies of Loop Recombination in Ciliates.
Discrete Applied Mathematics 156 (2008), 1736-1753, doi: 10.1016/j.dam.2007.08.032.
arXiv preprint cs.LO/0601135.

• Muskulus, M.; Besozzi, D.; Brijder, R.; Cazzaniga, P.; Houweling, S.; Pescini, D., Rozenberg, G.: Cycles and Communicating Classes in Membrane Systems and Molecular Dynamics.
Theoretical Computer Science 372 (2007), no. 2-3, 242-266, doi: 10.1016/j.tcs.2006.11.027.
Postprint version (PDF).

• Muskulus, M.; Brijder, R.: Complexity of Biocomputation: Symbolic Dynamics in Membrane Systems.
Int. J. Found. Comp. Sci. 17 (2006), no. 1, 147-165, doi: 10.1142/S0129054106003747
Postprint version (postscript).

° Muskulus, M.; Houweling, S.; Rozenberg, G.; Besozzi, D.; Cazzaniga, P.; Pescini, D.; Brijder, R.: Reaction Cycles in Membrane Systems and Molecular Dynamics.
in: Vol. 2 of Fourth Brainstorming Week on Membrane Computing, eds. C. Graciani, Gh. Paun, A. Romero-Jimenez, D. Sancho-Caparrini; pp. 185-208.
Fenix Editora, Sevilla (2006).

° Brijder, R.; Hoogeboom, H. J.; Muskulus, M.: Applicability of Loop Recombination in Ciliates Using the Breakpoint Graph.
in: Computational Life Sciences II (CompLife 2006), eds. M.R. Berthold, R. Glen, I. Fischer; Lecture Notes in Computer Science 4216 (2006), 97-106, doi: 10.1007/11875741_10

° Muskulus, M.; Brijder, R.: First Steps towards a Geometry of Computation.
in: Third Brainstorming Week on Membrane Computing, eds. M.A. Gutierrez-Naranjo, A. Riscos-Nunez, F. J. Romero-Campero, D. Sburlan.
Fenix Editora, Sevilla (2005).
Available from: http://www.gcu.us.es/3BWMC

° Muskulus, M.: An Observation on the Sevilla Complexity.
in: Cellular Computing (Complexity Aspects), Fenix Editora, Sevilla (2005).
Available from: http://www.gcu.us.es/ESF

Applied Mathematics

° ten Cate, A.; Geurts, B. J.; Muskulus, M.; et al.: Modeling and simulation of phase-transitions in multi-alloy aluminium casting.
in: Proceedings of the sixty-third European Study Group Mathematics with Industry, Enschede, The Netherlands (2008). Eds.: O. Bokhove, J. Hurink, G. Meinsma, et al., 117-139.

° Muskulus, M.: Three approaches to extend the Heston model.
in: Mathematics in Industry. European Study Group with Industry 2007 (SWI2007), Utrecht, The Netherlands (2008). Eds: M. Vellekoop, W. van der Weij, K. Oosterlee, et al., 93-100.
Available from: http://www.math.uu.nl/swi2007/ (pdf version).

Meteorology

• Jacob, D.; Goettel, H.; Jungclaus, J.; Muskulus, M.; Podzun, R.; Marotzke, J.: Slowdown of the Thermohaline Circulation Causes Enhanced Maritime Climate Influence and Snow Cover over Europe.
Geophysical Research Letters 32 (2005), L21711, doi:10.1029/2005GL023286
Available from: http://www.agu.org/pubs/crossref/2005/2005GL023286.shtml

• Muskulus, M.; Jacob, D.: Tracking cyclones in regional model data: the future of Mediterranean storms.
Advances in Geosciences 2 (2005), 13-19.
Available from: http://direct.sref.org/1680-7359/adgeo/2005-2-13

Performance Analysis


° Li, H.; Muskulus, M.; Wolters, L.: Modeling correlated workloads by combining model based clustering and a localized sampling algorithm.
In: International Conference on Supercomputing 2007, 64-72, doi: 10.1145/1274971.1274983

• Li, H.; Muskulus, M.: Analysis and modeling of job arrivals in a production grid.
ACM SIGMETRICS Performance Evaluation Review 34 (2007), 59-70, doi: 10.1145/1243401.1243402
Preprint available from Hui Li's publication list.

° Li, H.; Heusdens, R.; Muskulus, M.; Wolters, L.: Analysis and Synthesis of Pseudo-Periodic Job Arrivals in Grids: A Matching Pursuit Approach.
In: Cluster Computing and the Grid. CCGRID 2007, 183-196, doi: 10.1109/CCGRID.2007.23

° Li, H.; Muskulus, M.; Wolters, L.: Modeling Job Arrivals in a Data-Intensive Grid.
In: JSSPP 2006, LNCS 4376 (2007), 210-231, doi: 10.1007/978-3-540-71035-6_11

Other Topics

° Muskulus, M.; de Waal H.: Over luie studenten, groepsdynamica en pokeren.
Nieuw Archief voor Wiskunde 5/9 (2008), 287-290.

° Muskulus, M.: Speltheorie voor beginners.
Eureka! 20 (2008), 8-10.
Available from www.physics.leidenuniv.nl/eureka. Original version.

Note: These pages are obsolete and will be removed soon.
Please update your links to my new homepage
folk.ntnu.no/muskulus

Conferences/Workshops

• Oral Presentation: Circadian clocks - current models & questions. Analysis Seminar, Leiden, October 2, 2008.
• Poster Presentation: Reconstruction of functional brain networks by Wasserstein distances in a listening task, BIOMAG International Conference on Biomagnetism: Sapporo, Japan. August 24-29, 2008.
• Oral Presentation: Identification of P system models assisted by biochemical databases, Prague International Workshop on Membrane Computing, Prague, Czech Republic. June 2, 2008.
• Poster Presentation: Discrimination of asthma and COPD by reconstructing unbiased probability distributions (attractors) from the dynamics of respiratory impedance, American Thoracic Society (ATS) International Conference, Toronto, Canada. May 17-21, 2008.
• Oral Presentation: Solidification in alloys. Analysis Seminar, Leiden, March 6, 2008.
• Oral Presentation: Game theory for beginners: On lazy students, poker and group dynamics, Invited talk in front of student society "De Leidse Flesch", Leiden (The Netherlands), November 14, 2007. Dutch version: Speltheorie voor eerstejaars: Over luie studenten, pokeren en groepsdynamica.
• Oral Presentation: Classification of lung diseases and residual transportation cost. Analysis Seminar, Leiden, September 20, 2007.
• Oral Presentation: Estimating differences between probability densities and time series. Analysis Seminar, Leiden, December 14, 2006.
• Oral Presentation: Modeling Job Arrivals in a Data-Intensive Grid, 12th Workshop on Job Scheduling Strategies for Parallel Processing (JSSPP), Saint-Malo (France), June 26, 2006.
• Oral Presentation: Markov Chains. An Introduction for Pedestrians. LIACS PhD Talk, Leiden, January 26, 2006.
• Oral Presentation: Metabolism-Repair Systems, Artificial Chemistry and Complex Networks. An Introduction to Theories of (Self-) Organization. LIACS PhD Talk, Leiden, May 12, 2005.
• Invited Poster Presentation: Views on Membranes and Ciliates: Interdisciplinary Research in Natural Computing. NWO Computational Life Sciences Meeting, Utrecht, February 25, 2005. The original poster is available from the VIEWS project website.
• Oral Presentation: Dynamics of P Systems. LIACS PhD Talk, Leiden, November 3, 2004.
• Oral Presentation: Tracking cyclones in regional model data: The future of Mediterranean storms, 6th Plinius Conference on Mediterranean Storms (PLC6), Mediterranean Sea (Genoa-Naples-Palermo-Tunis-Palma de Mallorca-Barcelona-Marseille-Genoa), October 17-24, 2004.
• Oral Presentation: Tracking cyclones in regional model data: The future of Vb cyclones, 4th Annual Meeting of the European Meteorological Society (EMS4), Nice (France), September 26-30, 2004.

Awards

• Best Poster Award.
Scheenstra, A.E.H.; Muskulus M.; Staring M.; van den Maagdenberg A.M.J.V.; et al.: The 3D Moore-Rayleigh test for the quantitative groupwise comparison of MR brain images.
Information Processing in Medical Imaging 2009 (IPMI'09): Williamsburg, USA. July 5-10, 2009.

• Young Investigator Award for Excellent Paper.
Reconstruction of functional brain networks by Wasserstein distances in a listening task, BIOMAG International Conference on Biomagnetism: Sapporo, Japan. August 24-29, 2008.

Conferences/Workshops (Attendance)

• BrainModes 2008, Amsterdam, December 12-13, 2008.
• Oberwolfach Seminar on Applied Time Series Analysis in Scientific Computing, Oberwolfach (Germany), November 23-29, 2008 (invited).
• 5th European Congress of Mathematics, Amsterdam (The Netherlands), July 14-18, 2008.
• 63rd Study Group Mathematics with Industry (SWI2008), University of Twente (The Netherlands), January 28-February 1, 2008.
• 58th Study Group Mathematics with Industry (SWI2007), Utrecht University (The Netherlands), January 29-February 2, 2007.
• Space, Time and the Organization of Life, Summer school for computational life sciences, Conferentiecentrum Kapellerput (The Netherlands), June 19-22, 2006.
• Fourth Brainstorming Week on Membrane Computing (BWMC 2006), Sevilla (Spain), January 30 - February 3, 2005.
• Biology for Physicists Workshop, Lorentz Center, Leiden (Netherlands), October 24-28, 2005.
• Mathematics of Life Sciences: Kick Off Workshop NWO-Cluster Nonlinear Dynamics of Natural Systems, Groningen (Netherlands), October 10-13, 2005.
• Control Theory with Modeling Applications to Physiology and Medicine, Summer School, Graz (Austria), July 24 - August 5, 2005.
• 6th International Workshop on Membrance Computing WMC6, Wien (Austria), July 18-21, 2005.
• Oscillations and instability: Workshop on control near and far from equilibrium in biology, Lorentz Center, Leiden (Netherlands), May 23-25, 2005.
• NWO/Science's Next Wave Talentendag, Slot Zeist (Netherlands), April 5, 2005.
• Third Brainstorming Week on Membrane Computing (BWMC 2005), Sevilla (Spain), January 31 - February 4, 2005.
• ESF Exploratory Workshop (PESC): Cellular Computing (Complexity Aspects), Sevilla (Spain), January 31 - February 2, 2005.
• Don't Panic! A functional response to Hans Metz, Symposium, Leiden, December 9-10, 2004.
• Molecular Computing Workshop, Lorentz Center, Leiden (Netherlands), November 22-26, 2004.
• Fifth Workshop on Membrane Computing (WMC5), Milan (Italy), June 14-16, 2004.

Note: These pages are obsolete and will be removed soon.
Please update your links to my new homepage
folk.ntnu.no/muskulus

Software

All software listed in this section is free software, unless otherwise stated, licensed under the GPL which gives you the rights to freely use, copy and modify the software under certain conditions. Licenses for commercial or other use can be otained separately.
Read GPL license text.

Academic users, although you are not required by the license to do so, please give credit and cite the given paper or technical report if you use the software in your own research. It would also be appreciated very much, if you send me a preprint/reprint (preferred electronically) of publications using or making reference to the software.

• ccprecycles & ccdefect    (DELAYED)
A C++ class and example programs which calculate minimal precycles for stoichiometric matrices and defects for application vectors. Optionally the defect tree is output in DOT format.
Download cc.tar.gz
Read communication classes paper. Show BibTeX.

• dtsr   (beta-release 2008/01/22 version 0.9.1)
A R package for dissimilarity analysis of (multi-dimensional) time series by residual Wasserstein distances.
Creative Commons License
Important: Part of this code is based on an implementation of Bertsekas Auction algorithm (available here), which has been released by the author under the condition that no commercial use is made of it. To comply with this, this software package is licensed under a Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported License.
Download dtsr_0.9.1.tar.gz
Read technical report. Show BibTeX citation.

• MooreRayleigh   (beta-release 2009/01/20 version 1.0-2) changelog
A R-package for the generalized Moore-Rayleigh test in 1 or 3 dimensions.
Download MooreRayleigh_1.0-2.tar.gz

Administrative Work

Member of Organizing Committee:
Seventh Workshop on Membrane Computing WMC7, Leiden, July 17-21, 2006. Call for participation.

Refereed Papers for:

Advances in Geosciences
Theoretical Computer Science
Proceedings of the Royal Society A
Journal of Zhejiang University SCIENCE A
Soft Computing

Teaching Activities

2005: Course assistant: Basic mathematics for biologists (1st trimester, spring).
2005: Course assistant: Analysis III (2nd year, autumn).
2006: Course assistant: Mathematics of Developments (6th semester LST, spring).
2006: Course assistant: Analysis III (2nd year, autumn).
2007: Lecturer: Mathematics of Development (2nd year LST, spring).
2007: Lecturer: Mathematics 1A (1st year MST, autumn).
2008: Lecturer: Workshop on Synergetics (PhD students, spring).
2008: Lecturer: Mathematics of Development (2nd year LST, spring).
2008: Course assistant: Linear Algebra 2 (2nd year Physics, autumn).
2009: Lecturer: Mathematics of Development (2nd year LST, spring).

Useful stuff

The following technical tips are solutions to problems encountered during my daily computer work. The solutions are not so obvious and cost me quite some time to realize. I hope they will spare others the same work.

• Compiling ChemApp light (available here) with gfortran (gcc) 4.1.1 and glibc6.
Problem: When linking to the static ChemApp libraries, one symbol is broken, resulting in an undefined reference to G77_date_and_time_0. This is actually a call to libgfortran and the correct symbol name will be gfortran_date_and_time, as you can check with nm libgfortran.a 2> /dev/null | grep date.
Solution: Download the following wrapper.c code, compile with gcc -c wrapper.c and tell the linker about the wrapping. The latter is done by adding wrapper.o to LIBS, and adding -Wl,--wrap,G77_date_and_time_0 to FFLAGS in your Makefile. Everything should compile, and the example cademo1 should run without problems. This works for both Fortran and C code, but in the latter case you need to add a int MAIN__(void) { main(); } to cademo1.c and link with gfortran, as is standard when using the f2c library.
Note: Unfortunately, if you want to link to the dynamic libraries, your program will be broken and crash (due to dynamically missing symbol).

Further Information


• General Reading
The books in my personal research library.
If you are interested in borrowing one of these, please contact me.

• Pictures
Mostly from holidays and (hopefully, in the future!) some art projects

• Literary Recommendations
Mercier, Pascal: Perlmanns Schweigen.
Franzen, Jonathan: The Corrections.
Frisch, Max: Stiller.
Banks, Iain: The Business.
Danielewski, Mark Z.: House of Leaves.
Foster Wallace, David: Infinite Jest.
Winterson, Jeanette: The Stone Gods.
Arion, Frank M.: Dubbelspel.
• EGF rating: 1794 (3k)
• ING Marathon Amsterdam: 4h 10min  (Startnumber 2060, 2005)

Note: These pages are obsolete and will be removed soon.
Please update your links to my new homepage
folk.ntnu.no/muskulus

Additional links

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Michael Muskulus

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Last modified: Wed Aug 6 20:35:02 CEST 2008