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

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(Getting the credit points)
(Schedule, speakers and resources)
 
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{{Infobox| The Hauptseminar on 05.07.2016 has been shifted to 08.07.2016 at 10am. Note the new time: 13:00 on Tuesdays}}
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== Overview ==
 
== Overview ==
  
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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 13:00 in the ICP meeting room. <!--Wednesday 15.45h; the dates are specified per topic-->
 
;Location
 
;Location
 
:Institut für Computerphysik, room 01.079
 
:Institut für Computerphysik, room 01.079
 
;Credit Points
 
;Credit Points
:4 SWS = 6 CP (ECTS)
+
:6 CP (ECTS) (German MSc Physics Program)
 +
:3 CP (ECTS) (Intern. MSc Physics Program)
 
;Teachers
 
;Teachers
 
:Prof. Dr. [[Christian Holm]] (ICP)
 
:Prof. Dr. [[Christian Holm]] (ICP)
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;Requirements
 
;Requirements
 
:We expect the participants to have fundamental knowledge in classical and statistical mechanics, thermodynamics, electrodynamics, and partial differential equations.
 
: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.  
+
;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.
 
: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.
  
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|-  
 
|-  
| tba
+
| 12.04.2016
| tba
+
| 13:00
 
| [[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 Ribeiro 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
+
| <!--19.04.2016--> tba
| 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]]
 
| [[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--> tba ||  [[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}}-->
 +
  
  
  
 
|-  
 
|-  
| tba
+
| 19.04.2016
| tba
+
| 14:00
| [[Hauptseminar_Multiscale_Simulations_SS_2016/Quantum_transport_sensing_DNA| Quantum transport simulations: sensing DNA | tba]]
+
| [[Hauptseminar_Multiscale_Simulations_SS_2016/Ab initio molecular dynamics: Proton transport in water | Ab initio molecular dynamics: Proton transport in water | tba]]
| tba ||  [[Ganesh Sivaraman]]
+
| Felix Gross ||  [[Frank Uhlig]]
| Talk<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_presentation_HSAM.pptx|Talk}} -->
+
| {{Download|HauptseminarFGross_2016_talk.pdf|Talk}}
| Handout<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_handout_HSAM.pdf|Handout}}-->
+
| {{Download|HauptseminarFGross_2016.pdf|Handout}}
 
 
 
 
  
  
 
|-  
 
|-  
| tba
+
| 10.05.2016
| tba
+
| 14:00
| [[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/Quantum_transport_sensing_DNA| Quantum transport simulations: sensing DNA | tba]]
| tba || [[Maria Fyta]]
+
| Frank Schulz || [[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}}-->
+
| {{Download|Frank_Handout_Hauptseminar_final.pdf|Handout}}
  
  
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|-  
 
|-  
| tba
+
| 31.05.2016
| tba
+
| 14:00
| [[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/Classical atomistic force fields for single- and double-stranded DNA | Classical atomistic force fields for single- and double-stranded DNA | tba]]
| tba || [[Frank Uhlig]]
+
| 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}}-->
+
| {{Download|handout_ilse_HS_SS16.pdf|Handout}}
  
  
  
 
|-  
 
|-  
| tba
+
| 07.06.2016
| tba
+
| 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]]
+
| [[Hauptseminar_Multiscale_Simulations_SS_2016/Ion transport through nanopores via atomistic simulations| Ion transport through nanopores via atomistic simulations| tba]]
| tba || [[Ewa Anna Oprzeska-Zingrebe]]
+
| Carl Bühner || [[Florian Weik]]
 
| 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}}-->
+
| {{Download|handout_buehner_HS_SS16.pdf|Handout}}
 
 
  
  
 
|-  
 
|-  
| tba
+
| 08.07.2016
| tba
+
| 10:00
| [[Hauptseminar_Multiscale_Simulations_SS_2016/Reactive force fields: simulating chemical reactions| Reactive force fields: simulating chemical reactions| tba]]
+
| [[Hauptseminar_Multiscale_Simulations_SS_2016/coupling_MD_DFT_DNA_translocation_pores| Coupling MD and DFT: DNA translocation through pores | tba]]
| tba || [[Narayanan Krishnamoorthy Anand]]
+
| 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
+
| 21.06.2016
| 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]]
+
| [[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 || [[Jens Smiatek]]
+
| 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}}-->
+
| {{Download|handout_boltje_HS_SS16.pdf|Handout}}
 +
<!--| Handout<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_handout_HSAM.pdf|Handout}}-->
  
  
 
|-  
 
|-  
| tba
+
| 28.06.2016
| tba
+
| 14:00
| [[Hauptseminar_Multiscale_Simulations_SS_2016/Ion transport through nanopores via atomistic simulations| Ion transport through nanopores via atomistic simulations| tba]]
+
| [[Hauptseminar_Multiscale_Simulations_SS_2016/Reactive force fields: simulating chemical reactions| Reactive force fields: simulating chemical reactions| tba]]
| tba || [[Florian Weik]]
+
| 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}}-->
+
| {{Download|handout_tischler_HS_SS16.pdf|Handout}}
 +
 
  
  
 
|-  
 
|-  
 
| tba
 
| tba
| tba
+
| 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]]
+
| [[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 || [[Gary Davies]]
+
| tba || [[Jens Smiatek]]
 
| 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}}-->
  
 
|-  
 
|-  
| tba
+
| 08.07.2016
| tba
+
| 10:00
 
| [[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]]
 
| [[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]]
| tba || [[Michael Kuron]]
+
| Raffael Pecoroni || [[Michael Kuron]]
 
| 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}}-->
+
| {{Download|Handout_pecoroni_hs2016ss.pdf|Handout}}
  
  
 
|-  
 
|-  
| tba
+
| 12.07.2016
| tba
+
| 13:00
| [[Hauptseminar_Multiscale_Simulations_SS_2016/Mean-field modelling of EOF and electrophoresis with the FEM based COMSOL program|Mean-field modelling of EOF and electrophoresis with the FEM based COMSOL program| tba]]
+
| [[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]]
| tba || [[Georg Rempfer]]
+
| Tobias Biesner || [[Georg Rempfer]]
 
| 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}}-->
+
| {{Download|Handout_biesner_hs2016ss.pdf|Handout}}
  
  

Latest revision as of 12:06, 12 July 2016

Overview

Type
Seminar (Talks and Discussion)
Date and Time
weekly during the SS 2016; Tuesdays at 13:00 in the ICP meeting room.
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
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%)