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

Overview

Type

Seminar (Talks and Discussion)

Date and Time

weekly during the SS 2016; Day and time tba ; the dates are specified per topic

Location

Institut für Computerphysik, room 01.079

Credit Points

6 CP (ECTS) (German MSc Physics Program)

3 CP (ECTS) (Intern. MSc Physics Program)

Teachers

Prof. Dr. Christian Holm (ICP)

Dr. Jens Smiatek (ICP)

JP. Dr. Maria Fyta (ICP)

Course Number

tba

Modules

tba

Language

English

Requirements

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
tba	tba	Density functional theory: simulating DNA| tba	tba	Frank Maier	Talk	Handout
tba	tba	Exchange-correlation functionals in density functional theory: electronic properties of DNA | tba	tba	Bibek Adhikari	Talk	Handout
tba	tba	Ab initio molecular dynamics: Proton transport in water | tba	tba	Frank Uhlig	Talk	Handout
tba	tba	Quantum transport simulations: sensing DNA | tba	tba	Ganesh Sivaraman	Talk	Handout
tba	tba	Classical atomistic force fields for single- and double-stranded DNA | tba	tba	Ewa Anna Oprzeska-Zingrebe	Talk	Handout
tba	tba	Ion transport through nanopores via atomistic simulations| tba	tba	Florian Weik	Talk	Handout
tba	tba	Coupling MD and DFT: DNA translocation through pores | tba	tba	Maria Fyta	Talk	Handout
tba	tba	A coarse grained model for electrokinetic applications of DNA transport through nanopores| tba	tba	Gary Davies	Talk	Handout
tba	tba	Reactive force fields: simulating chemical reactions| tba	tba	Narayanan Krishnamoorthy Anand	Talk	Handout
tba	tba	A Forward Flux Sampling approach: Polymer translocation through nanopores| tba	tba	Jens Smiatek	Talk	Handout
tba	tba	An electrokinetic LB based model for ion transport and macromolecular electrophoresis| tba	tba	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%)