Difference between revisions of "Hauptseminar Modern Simulation Methods for Structure and Properties of Charged Complex Molecules"

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:Seminar (Talks and Discussion)
 
:Seminar (Talks and Discussion)
 
;Date and Time
 
;Date and Time
:weekly during the SS 2016; Day and time tba <!--Wednesday 15.45h-->; the dates are specified per topic
+
:weekly during the SS 2016; Tuesdays at 14:00. <!--Wednesday 15.45h-->; the dates are specified per topic
 
;Location
 
;Location
 
:Institut für Computerphysik, room 01.079
 
:Institut für Computerphysik, room 01.079
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| tba
 
| tba
 
| [[Hauptseminar_Multiscale_Simulations_SS_2016/DFT_simulating_DNA| Density functional theory: simulating DNA| tba]]
 
| [[Hauptseminar_Multiscale_Simulations_SS_2016/DFT_simulating_DNA| Density functional theory: simulating DNA| tba]]
| tba ||  [[Frank Maier]]
+
| [[Evangelos Tzaras]] ||  [[Frank Maier]]
 
| Talk<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_presentation_HSAM.pptx|Talk}} -->
 
| Talk<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_presentation_HSAM.pptx|Talk}} -->
 
| Handout<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_handout_HSAM.pdf|Handout}}-->
 
| Handout<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_handout_HSAM.pdf|Handout}}-->
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| tba
 
| tba
 
| [[Hauptseminar_Multiscale_Simulations_SS_2016/XCfunctionals_DFT_electronic_properties_DNA| Exchange-correlation functionals in density functional theory: electronic properties of DNA  | tba]]
 
| [[Hauptseminar_Multiscale_Simulations_SS_2016/XCfunctionals_DFT_electronic_properties_DNA| Exchange-correlation functionals in density functional theory: electronic properties of DNA  | tba]]
| tba ||  [[Bibek Adhikari]]
+
| Ediz Herkert ||  [[Bibek Adhikari]]
 
| Talk<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_presentation_HSAM.pptx|Talk}} -->
 
| Talk<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_presentation_HSAM.pptx|Talk}} -->
 
| Handout<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_handout_HSAM.pdf|Handout}}-->
 
| Handout<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_handout_HSAM.pdf|Handout}}-->
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| tba
 
| tba
 
| [[Hauptseminar_Multiscale_Simulations_SS_2016/Ab initio molecular dynamics: Proton transport in water | Ab initio molecular dynamics: Proton transport in water | tba]]
 
| [[Hauptseminar_Multiscale_Simulations_SS_2016/Ab initio molecular dynamics: Proton transport in water | Ab initio molecular dynamics: Proton transport in water | tba]]
| tba ||  [[Frank Uhlig]]
+
| Felix Gross ||  [[Frank Uhlig]]
 
| Talk<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_presentation_HSAM.pptx|Talk}} -->
 
| Talk<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_presentation_HSAM.pptx|Talk}} -->
 
| Handout<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_handout_HSAM.pdf|Handout}}-->
 
| Handout<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_handout_HSAM.pdf|Handout}}-->
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| tba
 
| tba
 
| [[Hauptseminar_Multiscale_Simulations_SS_2016/Quantum_transport_sensing_DNA| Quantum transport simulations: sensing DNA | tba]]
 
| [[Hauptseminar_Multiscale_Simulations_SS_2016/Quantum_transport_sensing_DNA| Quantum transport simulations: sensing DNA | tba]]
| tba ||  [[Ganesh Sivaraman]]
+
| Frank Schultz ||  [[Ganesh Sivaraman]]
 
| Talk<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_presentation_HSAM.pptx|Talk}} -->
 
| Talk<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_presentation_HSAM.pptx|Talk}} -->
 
| Handout<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_handout_HSAM.pdf|Handout}}-->
 
| Handout<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_handout_HSAM.pdf|Handout}}-->
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| tba
 
| tba
 
| [[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]]
 
| [[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]]
| tba || [[Ewa Anna Oprzeska-Zingrebe]]
+
| Sven Erik Ilse || [[Ewa Anna Oprzeska-Zingrebe]]
 
| Talk<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_presentation_HSAM.pptx|Talk}} -->
 
| Talk<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_presentation_HSAM.pptx|Talk}} -->
 
| Handout<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_handout_HSAM.pdf|Handout}}-->
 
| Handout<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_handout_HSAM.pdf|Handout}}-->
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| tba
 
| tba
 
| [[Hauptseminar_Multiscale_Simulations_SS_2016/coupling_MD_DFT_DNA_translocation_pores| Coupling MD and DFT: DNA translocation through pores | tba]]
 
| [[Hauptseminar_Multiscale_Simulations_SS_2016/coupling_MD_DFT_DNA_translocation_pores| Coupling MD and DFT: DNA translocation through pores | tba]]
| tba || [[Maria Fyta]]
+
| Felix Huber || [[Maria Fyta]]
 
| Talk<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_presentation_HSAM.pptx|Talk}} -->
 
| Talk<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_presentation_HSAM.pptx|Talk}} -->
 
| Handout<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_handout_HSAM.pdf|Handout}}-->
 
| Handout<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_handout_HSAM.pdf|Handout}}-->
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| tba
 
| tba
 
| [[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]]
 
| [[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]]
| tba || [[Gary Davies]]
+
| Daan Boltje || [[Gary Davies]]
 
| Talk<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_presentation_HSAM.pptx|Talk}} -->
 
| Talk<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_presentation_HSAM.pptx|Talk}} -->
 
| Handout<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_handout_HSAM.pdf|Handout}}-->
 
| Handout<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_handout_HSAM.pdf|Handout}}-->
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| tba
 
| tba
 
| [[Hauptseminar_Multiscale_Simulations_SS_2016/Reactive force fields: simulating chemical reactions| Reactive force fields: simulating chemical reactions| tba]]
 
| [[Hauptseminar_Multiscale_Simulations_SS_2016/Reactive force fields: simulating chemical reactions| Reactive force fields: simulating chemical reactions| tba]]
| tba || [[Narayanan Krishnamoorthy Anand]]
+
| Ingo Tischler || [[Narayanan Krishnamoorthy Anand]]
 
| Talk<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_presentation_HSAM.pptx|Talk}} -->
 
| Talk<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_presentation_HSAM.pptx|Talk}} -->
 
| Handout<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_handout_HSAM.pdf|Handout}}-->
 
| Handout<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_handout_HSAM.pdf|Handout}}-->

Revision as of 09:00, 5 February 2016

Overview

Type
Seminar (Talks and Discussion)
Date and Time
weekly during the SS 2016; Tuesdays at 14:00. ; 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 Evangelos Tzaras Frank Maier Talk Handout


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



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


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



tba tba Classical atomistic force fields for single- and double-stranded DNA | tba Sven Erik Ilse 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 Felix Huber Maria Fyta Talk Handout



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


tba tba Reactive force fields: simulating chemical reactions| tba Ingo Tischler 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%)