bye, my academic dream

[ FILED UNDER: General, ON 2010/09/06 ]

I quite to pursue my academic dream, because I failed to obtain a permanent academic job in 7 years after my Ph.D.

I found an engineering job, in a small company which develops power electronic related products. I need to recall my knowledge of undergraduate to fit the work.

Bye, with a little bit regrets, my academic dream.

Good luck to those post-doc who are still fighting for a permanent job.

Our paper was cited

[ FILED UNDER: General, ON 2010/04/07 ]

Our paper on biological clock was cited, more precisely mentioned, by a Nature article: A synchronized quorum of genetic clocks. It appeared in the modeling part of Supplementary information:

There has been much work on modeling asynchronous, oscillating cells coming into synchrony in the context of synthetic biology (McMillen et al. (2002); Garcia-Ojalvo et al. (2004)), though less attention has been focused on gene networks that do not oscillate in individual cells but oscillate collectively (Ma and Yoshikawa (2009)).

Our latest paper about spatial periodic pattern formation

[ FILED UNDER: General, ON 2009/08/24 ]

Spatiotemporal pattern in somitogenesis: A non-Turing scenario with wave propagation

Phys. Rev. E 80, 021906 (2009) [7 pages]

Hiroki Nagahara, Yue Ma, Yoshiko Takenaka, Ryoichiro Kageyama, and Kenichi Yoshikawa


Living organisms maintain their lives under far-from-equilibrium conditions by creating a rich variety of spatiotemporal structures in a self-organized manner, such as temporal rhythms, switching phenomena, and development of the body. In this paper, we focus on the dynamical process of morphogens in somitogenesis in mice where propagation of the gene expression level plays an essential role in creating the spatially periodic patterns of the vertebral columns. We present a simple discrete reaction-diffusion model which includes neighboring interaction through an activator, but not diffusion of an inhibitor. We can produce stationary periodic patterns by introducing the effect of spatial discreteness to the field. Based on the present model, we discuss the underlying physical principles that are independent of the details of biomolecular reactions. We also discuss the framework of spatial discreteness based on the reaction-diffusion model in relation to a cellular array, by comparison with an actual experimental observation.

Get the PDF file

Paper published

[ FILED UNDER: General, ON 2009/04/23 ]

Finally, my first paper at Kyoto got published, online. I made a related site for supplying animations.

Phys. Rev. E 79, 046217 (2009) [11 pages]

Self-sustained collective oscillation generated in an array of nonoscillatory cells

Yue Ma and Kenichi Yoshikawa

Spatio-Temporal Order Project, ICORP, Japan Science and Technology Agency (JST), Tokyo 102–0075, Japan
and Department of Physics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan

Oscillations are ubiquitous phenomena in biological systems. Conventional models of biological periodic oscillations usually invoke interconnecting transcriptional feedback loops. Some specific proteins function as transcription factors, which in turn negatively regulate the expression of the genes that encode these “clock proteins.” These loops may lead to rhythmic changes in gene expression in a cell. In the case of multicellular tissue, collective oscillation is often due to the synchronization of these cells, which manifest themselves as autonomous oscillators. In contrast, we propose here a different scenario for the occurrence of collective oscillation in a group of nonoscillatory cells. Neither periodic external stimulation nor pacemaker cells with intrinsically oscillator are included in the present system. By adopting a spatially inhomogeneous active factor, we observe and analyze a coupling-induced oscillation, inherent to the phenomenon of wave propagation due to intracellular communication.

Coming Conferences

[ FILED UNDER: Conferences, ON 2009/03/26 ]
  • Joint Conference of the Society for Mathematical Biology and the Chinese Society for Mathematical Biology
    June 14-17, 2009 , Hangzhou , P.R. China
  • 2009 International Symposium on Nonlinear Theory and its Applications
    October 18-21, 2009, Hokkaido, Japan
  • Novel Computing Substrates: Workshop at the Unconventional Computation 2009 Conference
    September 7-11, 2009, Ponta Delgada (Azores), Portugal

Some related conferences in 2009

[ FILED UNDER: Conferences, ON 2008/10/15 ]

more is coming.

Matlab R2008b released

[ FILED UNDER: Tools, ON 2008/10/15 ]

Mathworks News

Released October 9, 2008

What’s New in Release 2008b

Release 2008b includes new features in MATLAB and Simulink, two new products, and updates and bug fixes to 91 other products, including PolySpace code verification products. Subscribers to MathWorks Software Maintenance Service can download product updates.

Since R2008a, the MATLAB and Simulink product families require activation. R2008b includes enhancements to the License Center, the online tool for managing your license and user information.
New capabilities for the MATLAB product family include:

  1. Function Browser for finding functions, and automatic help for function arguments, in MATLAB
  2. New algorithms for random number generation in MATLAB, including ability to create multiple independent streams
  3. Support for netCDF and JPEG 2000 file formats in MATLAB
  4. Ability to deploy Parallel Computing Toolbox applications using MATLAB Compiler that run with MATLAB Distributed Computing Server
  5. New notebook interface in Symbolic Math Toolbox for managing and documenting symbolic computations, plus access to MuPAD symbolic engine and language directly from MATLAB
  6. Nonlinear mixed-effects (NLME) models in Statistics Toolbox
  7. Econometrics Toolbox, a new product for economic forecasting and risk management that incorporates the functionality of GARCH Toolbox

New capabilities for the Simulink product family include:

  1. MATLAB based language in Simscape for authoring of physical modeling components
  2. Fixed-point data types up to 128 bits for accelerated simulation, automatic code generation, Embedded MATLAB code, and Simulink Fixed Point
  3. Support for embedding Simulink function-call subsystems in Stateflow charts
  4. Target-specific code generation for Embedded MATLAB code, and generation of encapsulated C++ class interfaces, in Real-Time Workshop Embedded Coder
  5. CD and network boot options and real-time Ethernet I/O support in xPC Target
  6. SimElectronics, a new product for modeling and simulating electronic and electromechanical systems

Some nonlinear challenges in biology

[ FILED UNDER: General, ON 2008/08/21 ]

Nonlinearity 21 (2008) T131–T147

OPEN PROBLEM : Some nonlinear challenges in biology

Francesco Mosconi, Thomas Julou, Nicolas Desprat, Deepak Kumar
Sinha, Jean-Franc¸ ois Allemand, Vincent Croquette and David Bensimon


Driven by a deluge of data, biology is undergoing a transition to a more quantitative science. Making sense of the data, building new models, asking the right questions and designing smart experiments to answer them are becoming ever more relevant. In this endeavour, nonlinear approaches can play a fundamental role. The biochemical reactions that underlie life are very often nonlinear. The functional features exhibited by biological systems at all levels (from the activity of an enzyme to the organization of a colony of ants, via the development of an organism or a functional module like the one responsible for chemotaxis in bacteria) are dynamically robust. They are often unaffected by
order of magnitude variations in the dynamical parameters, in the number or concentrations of actors (molecules, cells, organisms) or external inputs (food, temperature, pH, etc). This type of structural robustness is also a common feature of nonlinear systems, exemplified by the fundamental role played by dynamical fixed points and attractors and by the use of generic equations (logistic map, Fisher–Kolmogorov equation, the Stefan problem, etc.) in the study of a plethora of nonlinear phenomena. However, biological systems differ from these examples in two important ways: the intrinsic stochasticity arising from the often very small number of actors and the role played by evolution. On an evolutionary time scale, nothing in biology is frozen. The systems observed today have evolved from solutions adopted in the past and they will have to adapt in response to future conditions. The evolvability of biological system uniquely characterizes them and is central to biology. As the great biologist T Dobzhansky once wrote: ‘nothing in biology makes sense except in the light of evolution’.

Why Are Computational Neuroscience and Systems Biology So Separate?

[ FILED UNDER: References, ON 2008/06/03 ]

PLoS Computational Biology published a review article entitled by “Why Are Computational Neuroscience and Systems Biology So Separate?“. Very good. Following is its abstract.

Despite similar computational approaches, there is surprisingly little interaction between the computational neuroscience and the systems biology research communities. In this review I reconstruct the history of the two disciplines and show that this may explain why they grew up apart. The separation is a pity, as both fields can learn quite a bit from each other. Several examples are given, covering sociological, software technical, and methodological aspects. Systems biology is a better organized community which is very effective at sharing resources, while computational neuroscience has more experience in multiscale modeling and the analysis of information processing by biological systems. Finally, I speculate about how the relationship between the two fields may evolve in the near future.

Several related conferences this year

[ FILED UNDER: Conferences, ON 2008/05/26 ]
  1. iCBBE – The 2nd International Conference on Bioinformatics and Biomedical Engineering, May 16-18, ShangHai, China.
  2. Systems Biology: The Challenge of Complixity, June 30 – July 2, Tokyo, Japan.
  3. The Second China-Japan Colloquium of Mathematical Biology, August 4-7, Okayama, Japan.
  4. NOLTA 2008 – 2008 International Symposium on Nonlinear Theory and its Applications, September 7-10, Budapest, Republic of Hungary.
  5. DDAP5 – Dynamics Days Asia Pacific, September 9-12, Nara, Japan.
  6. 2008 International Workshop on Chaos-Fractals Theories and Applications, November 18-21, Zhang Jia-jie, China.
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