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Postdoctoral simulator {[SIAM-DY] Postdoctoral position}

Postdoctoral fellowship is available as part of an ongoing project to add Reaction-Diffusion simulation to the widely-used NEURON neural simulator (www.neuron.yale.edu).  Although this postdoctoral experience will be highly technical, the context is biology and we ensure that all of our advances are published and accessible for dissemination to a biological audience -- ie there is ample opportunity for authorship. 

Candidates should have a strong background in computer programming, with demonstrated fluency in C/C++ or Python or some other major programming language, ideally with a substantial software project to show for it. Familiarity with cell biology, neurobiology or chemistry simulation is a plus.  Familiarity with Unix is important. Numerical integration, MPI/HPC, version control (we use hg) nice too. 

This position offers an opportunity to link develop novel software tools that will be widely used by the research community.  The postdoc will receive training in a wide range of interdisciplinary skills from computer science, applied math, biophysics, cell biology, electrophysiology, etc.  The work is being performed in close collaboration with experimental laboratories, giving the opportunity to immediately determine how closely a modeling technique can match the experimental reality (or in rare cases, how adequately experimental artifact can be reduced so as to match models).  The work is being done under the auspices of the National Institute of Mental Health and has substantial  clinical translational potential for making linkages between genomics, proteomics, pharmacotherapy and neuronal/network outcomes for psychiatric and neurological disorders.  The NIH and other agencies (FDA,NASA,NSF,DARPA,others) have a strong interest in this multiscale modeling approach, sponsoring an annual meeting for which the laboratory has taken major initiatives.

Further details: This project offers a number of interfacing and development challenges.  1. Ion concentrations at the surface determine driving forces for channels, calculated as a Nernst potential or via Goldman-Hodgkin-Katz equations.  These surface-layer concentrations must be in placed into equilibrium with diffusing ion concentrations within cytoplasm.  2. Potential gradients also arise across internal membranes.  It has been hypothesized that the endoplasmic reticulum (ER) exists as a "neuron within the neuron" that signals both via electrical and calcium signaling.  3. One cannot simply handle the whole neuron as 1 big diffusion problem: neurons are too big and have different cytoplasmic domains that require different types of simulation: stochastic 3D for spines, deterministc 1D for major dendrites, deterministic 3D for soma.  This requires developing a number of simulators within the simulator and interfacing all of them properly.  4. Standard neural tracings, which are quite adequate for electrical simulation, lack the detail required to produce watertight volumes for reaction-diffusion modeling -- we are developing algorithms to map the approximate full surface and instrument both surfaces and the enclosed volumes. 5. Reaction schemes can be extremely complex, yet often lacking in the kinetic parameters that would be needed to produce an accurate ODE representation.  Therefore instead of using full kinetic descriptions we may need to use highly simplified Boolean networks (BNs) or other rule-based representations.  These representations must then be interfaced with kinetic representations and with diffusion mechanisms.

Applicants should contact Bill Lytton by email (billl [at] neurosim [dot] downstate [dot] edu; no snail please) with a CV and cover letter. SUNY is an equal opportunity employer.


Postdoc position in Lyon (ENS or University, or both)

Announcement of 2 post-doc positions available in mathematics and/or computer science in Lyon, starting in October 2013. The welcoming departments can be the Mathematics Department at the École  Normale Supérieure de Lyon or at the University Lyon 1, the Computer Science Department at the École  Normale Supérieure de Lyon, or even a combination of them over the 2 years, since the goal of the funding institution (labex MILYON) is to develop cooperation between them.

For more information, please visit the link: 



The Instituto de Ciencias Matemáticas (ICMAT-Institute of Mathematical Sciences) offers five postdoctoral appointments for researchers in Mathematics with an excellent curriculum who wish to pursue their research career at the ICMAT. The contracts will be for two years and with competitive financial conditions, similar to those offered in equivalent European Programmes.

The five contracts are linked to the ICMAT Laboratories (one contract per lab):

•           Charles L. Fefferman Laboratory

•           Viktor Ginzburg Laboratory

•           Marius Junge Laboratory

•           Stephen Wiggins Laboratory

•           Nigel Hitchin Laboratory

How to apply. Send the following documents:

•           Letter of motivation applying for an ICMAT-Postdoc appointment, indicating the Laboratory of interest andany other information that may be relevant

•           Curriculum vitae

•           Two letters of recommendation

Please send to: postdoc [at] icmat [dot] es (postdoc [at] icmat [dot] es) indicating in the subject the requested Laboratory. The deadline for submission is January 20, 2013.

Each applicant will receive a personal reply and preselected applicants will be interviewed individually in due course.

For further information, visit our website: http://www.icmat.es and http://www.icmat.es/laboratories

Postdoctoral, Ph.D. and internships positions in mathematical and computational neuroscience are available at Inria

Postdoctoral, Ph.D. and internships positions are available at Inria (France) in the mathematical and computational neuroscience team Neuromathcomp headed by Olivier Faugeras. The research effort
involves several projects on modelling and analysing neural activity at different scales with applications to the understanding of the visual system.

Your profile: You have a background in Computational Neuroscience, Applied Mathematics, Physics or Engineering Science and you are highly motivated to have an interdisciplinary experience between
Neuroscience, Mathematics and Computer Science? We offer an exciting environment strongly conductive to academic research with excellent working conditions.

Please visit our website to check our current offers: http://www-sop.inria.fr/neuromathcomp/public/jobs.shtml

Postdoctoral Position in Computational Biology

Department of Physiology, McGill University, Montreal QC Canada

Applications are invited for an NIH-funded postdoctoral position in modeling different aspects of autoimmune type 1 diabetes (T1D). More specifically, this project will focus on understanding the role of islet-specific autoantibodies in T1D, and designing algorithms to predict disease onset. Candidates are expected to have (or in the process of receiving) a Ph.D. degree in Mathematical and Computational Biology (or related field); have a high degree of academic excellence as demonstrated by a good record of publications; and possess expertise in nonlinear dynamics, MATLAB programming and the use of numerous numerical techniques for solving integro-differential equations. Having some background in immunology will be considered an asset. This work will be conducted in close collaboration with experimental laboratory at the University of Michigan. The initial appointment will be for one year with an option for further extension.

Department of Physiology at McGill University, located in the beautiful city of Montreal, has a large and productive theoretical group. It has an outstanding reputation for fostering experimental collaborations and conducting interdisciplinary research in both experimental and theoretical physiology/biology. Interested candidates with the required qualifications are encouraged to apply. To be considered for the position, please send your CV, your list of publications and two reference letters to anmar [dot] khadra [at] mcgill [dot] ca" title="email Anmar Khadra ">Anmar Khadra (Email: anmar [dot] khadra [at] mcgill [dot] ca) by November 7. (Master and Ph.D. positions are also available for interested students.)