Difference between revisions of "Hauptseminar Multiscale Simulations SS 2016"

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(Schedule, speakers and resources)
(Schedule, speakers and resources)
 
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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. <!--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 in February 2015, probably during the first week of the winter break 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.
  
 
== Schedule, speakers and resources ==
 
== Schedule, speakers and resources ==
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| tba
 
| tba
 
| tba
 
| tba
| [[Hauptseminar_Multiscale_Simulations_SS_2016/Transverse_currents_for_DNA_readout| Using transverse current measurements in a nanopore to read-out DNA | tba]]
+
| [[Hauptseminar_Multiscale_Simulations_SS_2016/DFT_simulating_DNA| Density functional theory: simulating DNA| tba]]
| tba || [[Maria Fyta]], [[Bibek Adhikari]]
+
| tba || [[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
 
| tba
 
| tba
| [[Hauptseminar_Multiscale_Simulations_SS_2016/Functionalized_nanopores_and_DNA_translocation| Functionalized nanopores and DNA translocation | tba]]
+
| [[Hauptseminar_Multiscale_Simulations_SS_2016/XCfunctionals_DFT_electronic_properties_DNA| Exchange-correlation functionals in density functional theory: electronic properties of DNA | tba]]
| tba || [[Maria Fyta]], [[Ganesh Sivaraman]]
+
| 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}}-->
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| tba
 
| tba
 
| tba
 
| tba
| [[Hauptseminar_Multiscale_Simulations_SS_2016/2D_materials_for_translocating_and_sensing_DNA| 2D materials for translocating and sensing DNA | tba]]
+
| [[Hauptseminar_Multiscale_Simulations_SS_2016/Quantum_transport_sensing_DNA| Quantum transport simulations: sensing DNA | tba]]
| tba || [[Maria Fyta]], [[Bibek Adhikari]]
+
| tba || [[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
 
| tba
 
| tba
| [[Hauptseminar_Multiscale_Simulations_SS_2016/Graphene_nanopores| DNA translocation through graphene nanopores | tba]]
+
| [[Hauptseminar_Multiscale_Simulations_SS_2016/coupling_MD_DFT_DNA_translocation_pores| Coupling MD and DFT: DNA translocation through pores | tba]]
| tba || [[Maria Fyta]], [[Frank Maier]]
+
| tba || [[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
 
| tba
 
| tba
| [[Hauptseminar_Multiscale_Simulations_SS_2016/Free energy methods for protein and DNA unfolding and folding equilibria| Free energy methods for protein and DNA unfolding and folding equilibria | tba]]
+
| [[Hauptseminar_Multiscale_Simulations_SS_2016/Ab initio molecular dynamics: Proton transport in water | Ab initio molecular dynamics: Proton transport in water | tba]]
| tba || tba
+
| tba || [[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
 
| tba
 
| tba
| [[Hauptseminar_Multiscale_Simulations_SS_2016/Coarse-grained force fields for macromolecules| Coarse-grained force fields for macromolecules | 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 || tba
+
| tba || [[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/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 || tba
+
| tba || [[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}}-->
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| tba
 
| 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]]
 
| [[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 || tba
+
| 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
 +
| tba
 +
| [[Hauptseminar_Multiscale_Simulations_SS_2016/Ion transport through nanopores via atomistic simulations| Ion transport through nanopores via atomistic simulations| tba]]
 +
| tba || [[Florian Weik]]
 +
| Talk<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_presentation_HSAM.pptx|Talk}} -->
 +
| Handout<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_handout_HSAM.pdf|Handout}}-->
 +
 +
 +
|-
 +
| 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]]
 +
| tba || [[Gary Davies]]
 +
| Talk<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_presentation_HSAM.pptx|Talk}} -->
 +
| Handout<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_handout_HSAM.pdf|Handout}}-->
 +
 +
|-
 +
| tba
 +
| 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]]
 +
| Talk<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_presentation_HSAM.pptx|Talk}} -->
 +
| Handout<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_handout_HSAM.pdf|Handout}}-->
 +
 +
 +
|-
 +
| tba
 +
| tba
 +
| [[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]]
 +
| tba || [[Georg Rempfer]]
 +
| Talk<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_presentation_HSAM.pptx|Talk}} -->
 +
| Handout<!--{{DownloadExt|/teaching/2015-ss-hauptseminar/Richard_handout_HSAM.pdf|Handout}}-->
 +
  
  

Latest revision as of 13:46, 20 January 2016

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
4 SWS = 6 CP (ECTS)
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. 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

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



tba tba Coupling MD and DFT: DNA translocation through pores | tba tba Maria Fyta Talk Handout



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


tba tba Classical atomistic force fields for single- and double-stranded DNA | tba tba Ewa Anna Oprzeska-Zingrebe 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 Ion transport through nanopores via atomistic simulations| tba tba Florian Weik Talk Handout


tba tba A coarse grained model for electrokinetic applications of DNA transport through nanopores| tba tba Gary Davies 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 the FEM based COMSOL program| 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 (50%)
    • The quality of the final presentation (25%)
    • The level of participation in the discussion (25%)