ReaDDy - A particle-based
reaction-diffusion simulator

Summer workshop 2018

The workshop adresses young scientists at M.Sc. or Ph.D. student level with a background in physics, chemistry, bioinformatics or computer science. FU-students can receive the equivalent of a 2 SWS module (5 ECTS points) for a successful completion. The workshop is from Monday 23.07.2018 until Friday 27.07.2018, each day from 9h to 15h. It will be located in the basement of the computer-science building

Takustr. 9
14195 Berlin
Room K46

Main topics will be:

  • Macromolecular diffusion and crowding
  • Simulation of signal transduction in cells
  • Particle-based reaction-diffusion simulation
  • The Python/C++ based ReaDDy simulation package

Program

We will have one talk each morning and hands-on practical sessions afterwards. Friday will be all-day session.

PS=Practical session

  Monday Tuesday Wednesday Thursday Friday
9 - ~10 Introduction Reaction diffusion methods MD and coarse graining ReaDDy Software PS
coffee break          
~10 - 12 PS - ReaDDy PS - Predator prey PS - Topologies PS - C++ potential PS
lunch          
13 - 15 PS - Observables PS - Diffusion-influenced PS - Topology reactions PS - Nuclear waffles PS

Prerequisites

There will be Linux PCs available. You are free to bring your own laptop, but note that we currently support Linux and Mac only. If you bring your own laptop, make sure you have a working installation of VMD. You should be able to run vmd from the commandline.

The practical sessions are done in ipython notebooks. A bit of python coding might come in handy, but is not required. You will learn the necessary.

Information for non-resident applicants

PhD students and PostDocs interested in ReaDDy are welcome to participate. To register, send an email to christoph.froehner(at)fu-berlin.de stating your affiliation and research focus.

FindUs

The workshop takes place at Freie Universität, Department of Mathematics and Informatics. The nearest bus stop is “Arnimallee” on the Bus X83 route (connecting U Dahlem with S + U Rathaus Steglitz). For an area map and directions see here.

Accomodation

Freie Universität does not operate on-campus guest houses or student dormitories. Therefore, participants from outside of Berlin must arrange their own accommodation. The best way to find accommodation and benefit from special deals is booking.com. Districts well connected to campus are Steglitz-Zehlendorf, Tempelhof-Schöneberg, Charlottenburg-Wilmersdorf as well as anything within the so called ‘Ringbahn’ loop.

Getting around

Berlin has an extensive public transit network (undergound, urban rail, buses, trams) with 3 tariff zones. Ticket AB (2.80€) will get you anywhere in Berlin including Tegel Airport (TXL). For Schönefeld Airport (SFX) you will need Ticket ABC (3.40€). See here for reference.

Provisions

The workshop takes place during term break and the nearby student cafeteria will be closed. For lunch please bring your own provisions or use one of the following options:

Contact

scientific coordinator, registration inquiries:

Christoph Fröhner christoph.froehner(at)fu-berlin.de

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