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

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Seminar (Talks and Discussion)
Date and Time
weekly during the SS 2016; Tuesdays at 13:00 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 13:00 Density functional theory: simulating DNA| tba Evangelos Ribeiro Tzaras Frank Maier Talk Handout

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

19.04.2016 14:00 Ab initio molecular dynamics: Proton transport in water | tba Felix Gross Frank Uhlig application_pdf.pngTalk (1.5 MB)Info circle.png application_pdf.pngHandout (1.01 MB)Info circle.png

10.05.2016 14:00 Quantum transport simulations: sensing DNA | tba Frank Schulz Ganesh Sivaraman Talk application_pdf.pngHandout (2.15 MB)Info circle.png

31.05.2016 14:00 Classical atomistic force fields for single- and double-stranded DNA | tba Sven Erik Ilse Ewa Anna Oprzeska-Zingrebe Talk application_pdf.pngHandout (3.53 MB)Info circle.png

07.06.2016 14:00 Ion transport through nanopores via atomistic simulations| tba Carl Bühner Florian Weik Talk application_pdf.pngHandout (2.47 MB)Info circle.png

08.07.2016 10:00 Coupling MD and DFT: DNA translocation through pores | tba Felix Huber Maria Fyta Talk Handout

21.06.2016 14:00 A coarse grained model for electrokinetic applications of DNA transport through nanopores| tba Daan Boltje Gary Davies Talk application_pdf.pngHandout (1.44 MB)Info circle.png

28.06.2016 14:00 Reactive force fields: simulating chemical reactions| tba Ingo Tischler Narayanan Krishnamoorthy Anand Talk application_pdf.pngHandout (564 KB)Info circle.png

tba 14:00 A Forward Flux Sampling approach: Polymer translocation through nanopores| tba tba Jens Smiatek Talk Handout
08.07.2016 10:00 An electrokinetic LB based model for ion transport and macromolecular electrophoresis| tba Raffael Pecoroni Michael Kuron Talk application_pdf.pngHandout (1.07 MB)Info circle.png

12.07.2016 13:00 Mean-field modelling of EOF and electrophoresis with an FEM based approach| tba Tobias Biesner Georg Rempfer Talk application_pdf.pngHandout (1.2 MB)Info circle.png

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%)