Hauptseminar Modern Simulation Methods for Structure and Properties of Charged Complex Molecules

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Revision as of 12:37, 15 February 2016 by Etzaras (talk | contribs) (Schedule, speakers and resources)
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Seminar (Talks and Discussion)
Date and Time
weekly during the SS 2016; Tuesdays at 14:00 in the ICP meeting room.
Institut für Computerphysik, room 01.079
Credit Points
6 CP (ECTS) (German MSc Physics Program)
3 CP (ECTS) (Intern. MSc Physics Program)
Prof. Dr. Christian Holm (ICP)
Dr. Jens Smiatek (ICP)
JP. Dr. Maria Fyta (ICP)
Course Number
We expect the participants to have fundamental knowledge in classical and statistical mechanics, thermodynamics, electrodynamics, and partial differential equations.
Registration for the Seminar
Please write an email to Maria Fyta until February 1st at 24:00. A date for a first meeting will be announced soon to gauge the interest of the students, discuss the topics, and handle the topic assignment.
There will be organizational meeting that will be mandatory to all participants on February 4, 2016 at 13:00 to discuss topics and style and other requirements.

Schedule, speakers and resources

Date Time Topic Speaker Tutor
12.04.2016 14:00 Density functional theory: simulating DNA| tba Evangelos Ribeiro Tzaras Frank Maier Talk Handout

19.04.2016 14:00 Exchange-correlation functionals in density functional theory: electronic properties of DNA | tba Ediz Herkert Bibek Adhikari Talk Handout

10.05.2016 14:00 Ab initio molecular dynamics: Proton transport in water | tba Felix Gross Frank Uhlig Talk Handout

14:00 Quantum transport simulations: sensing DNA | tba Frank Schultz Ganesh Sivaraman Talk Handout

14:00 Classical atomistic force fields for single- and double-stranded DNA | tba Sven Erik Ilse Ewa Anna Oprzeska-Zingrebe Talk Handout

14:00 Ion transport through nanopores via atomistic simulations| tba Carl Bühner Florian Weik Talk Handout

14:00 Coupling MD and DFT: DNA translocation through pores | tba Felix Huber Maria Fyta Talk Handout

14:00 A coarse grained model for electrokinetic applications of DNA transport through nanopores| tba Daan Boltje Gary Davies Talk Handout

14:00 Reactive force fields: simulating chemical reactions| tba Ingo Tischler Narayanan Krishnamoorthy Anand Talk Handout

tba 14:00 A Forward Flux Sampling approach: Polymer translocation through nanopores| tba tba Jens Smiatek Talk Handout
tba 14:00 An electrokinetic LB based model for ion transport and macromolecular electrophoresis| tba Raffael Pecoroni Michael Kuron Talk Handout

tba tba Mean-field modelling of EOF and electrophoresis with an FEM based approach| tba tba Georg Rempfer Talk Handout

Getting the credit points

To get the credit points for the seminar, the following criteria should be met:

  • All participants must:
    • Make the first appointment with their supervisor 2 months (a minimum of 8 weeks) before giving their talk
    • Have read the literature provided on the website/by the supervisor before this first meeting
    • Hand in a draft of their presentation 1 month (a minimum of 4 weeks) before giving their talk
    • Give a trial talk 2 weeks in advance of their public talk and hand in their final draft of the handout
    • Hand in the final version of their handout 1 week in advance
    • Give their talk at the arranged time
    • Be present at all talks
    • Take part in the discussions following the talks
  • The handout:
    • Consists of 8 to 10 A4 pages (incl. pictures; 10 pt font, single space text)
    • Describes the contents of the talk, written out in full
    • Is written for the other participants
    • Is written in English
  • The talk:
    • Consists of material pertaining to the topic
    • Has a length of 45 minutes
    • Is prepared in electronic form
    • Is held in English
  • Participants are graded according to:
    • The quality of the trial talk and final draft of the hand out (as well as self-dependent preparation of both) (50%)
    • The quality of the final presentation (25%)
    • The level of participation in the discussion (25%)