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

{{Infobox| The Hauptseminar on 05.07.2016 has been shifted to 08.07.2016 at 10am. Note the new time: 13:00 on Tuesdays}}

== Overview ==

;Type
:Seminar (Talks and Discussion)
;Date and Time
:weekly during the SS 2016; Tuesdays at 13:00 in the ICP meeting room. <!--Wednesday 15.45h; 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. <!--On December 10th at 13.15h at the ICP (seminar room 1.095) there will be--> 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. <!--Topics must be chosen before February 15. -->
: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 ==

{| class="wikitable"

|-
! Date !! Time !! Topic !! Speaker !! Tutor

|- 
| 12.04.2016
| 14:00
| [[Hauptseminar_Multiscale_Simulations_SS_2016/DFT_simulating_DNA| Density functional theory: simulating DNA| tba]]
| [[Evangelos Ribeiro Tzaras]] ||  [[Frank Maier]]
| Talk<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_presentation_HSAM.pptx|Talk}} -->
| Handout<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_handout_HSAM.pdf|Handout}}-->


|- 
| <!--19.04.2016--> tba
| 14:00
| [[Hauptseminar_Multiscale_Simulations_SS_2016/XCfunctionals_DFT_electronic_properties_DNA| Exchange-correlation functionals in density functional theory: electronic properties of DNA  | tba]]
| <!--Ediz Herkert--> tba ||  [[Bibek Adhikari]]
| Talk<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_presentation_HSAM.pptx|Talk}} -->
| Handout<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_handout_HSAM.pdf|Handout}}-->




|- 
| 19.04.2016
| 14:00
| [[Hauptseminar_Multiscale_Simulations_SS_2016/Ab initio molecular dynamics: Proton transport in water | Ab initio molecular dynamics: Proton transport in water | tba]]
| Felix Gross ||  [[Frank Uhlig]]
| {{Download|HauptseminarFGross_2016_talk.pdf|Talk}}
| {{Download|HauptseminarFGross_2016.pdf|Handout}}


|- 
| 10.05.2016
| 14:00
| [[Hauptseminar_Multiscale_Simulations_SS_2016/Quantum_transport_sensing_DNA| Quantum transport simulations: sensing DNA | tba]]
| Frank Schulz ||  [[Ganesh Sivaraman]]
| Talk<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_presentation_HSAM.pptx|Talk}} -->
| {{Download|Frank_Handout_Hauptseminar_final.pdf|Handout}}




|- 
| 31.05.2016
| 14:00
| [[Hauptseminar_Multiscale_Simulations_SS_2016/Classical atomistic force fields for single- and double-stranded DNA | Classical atomistic force fields for single- and double-stranded DNA | tba]]
| Sven Erik Ilse || [[Ewa Anna Oprzeska-Zingrebe]]
| Talk<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_presentation_HSAM.pptx|Talk}} -->
| {{Download|handout_ilse_HS_SS16.pdf|Handout}}



|- 
| 07.06.2016
| 14:00
| [[Hauptseminar_Multiscale_Simulations_SS_2016/Ion transport through nanopores via atomistic simulations| Ion transport through nanopores via atomistic simulations| tba]]
| Carl Bühner || [[Florian Weik]]
| Talk<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_presentation_HSAM.pptx|Talk}} -->
| {{Download|handout_buehner_HS_SS16.pdf|Handout}}


|- 
| 14.06.2016
| 14:00
| [[Hauptseminar_Multiscale_Simulations_SS_2016/coupling_MD_DFT_DNA_translocation_pores| Coupling MD and DFT: DNA translocation through pores | tba]]
| Felix Huber || [[Maria Fyta]]
| Talk<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_presentation_HSAM.pptx|Talk}} -->
| Handout<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_handout_HSAM.pdf|Handout}}-->



|- 
| 21.06.2016
| 14:00
| [[Hauptseminar_Multiscale_Simulations_SS_2016/A coarse grained model for electrokinetic applications of DNA transport through nanopores|A coarse grained model for electrokinetic applications of DNA transport through nanopores| tba]]
| Daan Boltje || [[Gary Davies]]
| Talk<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_presentation_HSAM.pptx|Talk}} -->
| {{Download|handout_boltje_HS_SS16.pdf|Handout}}
<!--| Handout<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_handout_HSAM.pdf|Handout}}-->


|- 
| 28.06.2016 
| 14:00
| [[Hauptseminar_Multiscale_Simulations_SS_2016/Reactive force fields: simulating chemical reactions| Reactive force fields: simulating chemical reactions| tba]]
| Ingo Tischler || [[Narayanan Krishnamoorthy Anand]]
| Talk<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_presentation_HSAM.pptx|Talk}} -->
| Handout<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_handout_HSAM.pdf|Handout}}-->



|- 
| tba
| 14:00
| [[Hauptseminar_Multiscale_Simulations_SS_2016/A Forward Flux Sampling approach: Polymer translocation through nanopores| A Forward Flux Sampling approach: Polymer translocation through nanopores| tba]]
| tba || [[Jens Smiatek]]
| Talk<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_presentation_HSAM.pptx|Talk}} -->
| Handout<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_handout_HSAM.pdf|Handout}}-->

|- 
| 05.07.2016
| 14:00
| [[Hauptseminar_Multiscale_Simulations_SS_2016/An electrokinetic LB based model for ion transport and macromolecular electrophoresis|An electrokinetic LB based model for ion transport and macromolecular electrophoresis| tba]]
| Raffael Pecoroni || [[Michael Kuron]]
| Talk<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_presentation_HSAM.pptx|Talk}} -->
| Handout<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_handout_HSAM.pdf|Handout}}-->


|- 
| 12.07.2016
| 14:00
| [[Hauptseminar_Multiscale_Simulations_SS_2016/Mean-field modelling of EOF and electrophoresis with an FEM based approach|Mean-field modelling of EOF and electrophoresis with an FEM based approach| tba]]
| Tobias Biesner || [[Georg Rempfer]]
| Talk<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_presentation_HSAM.pptx|Talk}} -->
| Handout<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_handout_HSAM.pdf|Handout}}-->




|}

<!--The (T) or (E) after the talk title indicate if this topic would count towards an experimental or theoretical Seminar certificate:

(T): Theoretical Seminar Talk
(E): Experimental Seminar Talk
-->

== 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%)