Planning

Monday, May 20, 2013

Time Event  
14:00 - 18:45 Arrival - Arrival  
19:30 - 21:00 Dinner  

Tuesday, May 21, 2013

Time Event  
07:45 - 08:30 Breakfast  
08:30 - 08:45 Introduction  
08:45 - 10:15 Lavery 1 - DNA fine structure and conformation flexibility  
10:15 - 10:45 Coffee break  
10:45 - 12:15 Schiessel 1 - DNA as a wormlike chain (Euler elastica, Kirchhoff analogy, stretching DNA under an external force)  
12:15 - 14:00 Lunch  
17:15 - 18:45 Lavery 2 - All-atom molecular simulation techniques for nucleic acids  
19:30 - 21:00 Dinner  

Wednesday, May 22, 2013

Time Event  
07:45 - 08:45 Breakfast  
08:45 - 10:15 Schiessel 2 - Nucleosome as a DNA spool (nucleosome breathing and force-induced unwrapping)  
10:15 - 10:45 Coffee break  
10:45 - 12:15 Lavery 3 - Modeling DNA structure and dynamics  
12:15 - 14:00 Lunch  
14:00 - 16:00 Practical work  
17:15 - 18:45 de Pablo 1 - Coarse grain models of DNA, and the role of hydrodynamic interactions in dynamics  
19:30 - 21:00 Dinner  

Thursday, May 23, 2013

Time Event  
07:45 - 08:45 Breakfast  
08:45 - 10:15 Lavery 4 - Modeling DNA-ligand and DNA-protein interactions  
10:15 - 10:45 Coffee break  
10:45 - 12:15 de Pablo 2 - Atomistic and mesoscale models of DNA, their advantages and limitations  
12:15 - 14:00 Lunch  
14:00 - 16:00 Practical work  
17:15 - 18:45 Schiessel 3 - Chromatin fiber as a problem in geometry (two-angle model, multi-ribbon model)  
19:30 - 21:00 Dinner  

Friday, May 24, 2013

Time Event  
07:45 - 08:45 Breakfast  
08:45 - 10:15 de Pablo 3 - Coarse-grained models of DNA-histone interactions, and relevance for the study of chromatin  
10:15 - 10:45 Coffee break  
10:45 - 12:15 Weigt 1 - Regulatory DNA motifs I: From the biophysics of protein-DNA interaction to the bioinformatics of transcription factor binding sites  
12:15 - 14:00 Lunch  
14:00 - 16:00 Practical work  
17:15 - 18:45 Seminar: Everaers - Universal Aspects of Chromosome Folding  
19:30 - 21:00 Dinner  

Saturday, May 25, 2013

Time Event  
07:45 - 08:45 Breakfast  
08:45 - 10:15 Weigt 2 - How similar are two biological sequences: Algorithms for sequence alignment  
10:15 - 10:45 Coffee break  
10:45 - 12:15 Arneodo 1 - Long-range correlations in eukaryotic DNA: a footprint of nucleosome packaging  
12:15 - 14:00 Lunch  
19:30 - 21:00 Dinner  

Sunday, May 26, 2013

Time Event  
07:45 - 08:45 Breakfast  
12:15 - 14:00 Lunch  
19:30 - 21:00 Dinner  

Monday, May 27, 2013

Time Event  
07:45 - 08:45 Breakfast  
08:45 - 10:15 Schiessel 4 - Chromosome as a fractal globule (internal distances, contact probabilities, molten vs. fractal globule)  
10:15 - 10:45 Coffee break  
10:45 - 12:15 Weigt 3 - Regulatory DNA motifs II: Using phylogeny for motif inference  
12:15 - 14:00 Lunch  
14:00 - 16:00 Practical work  
17:15 - 18:45 ten Wolde 1 - Overview of noise in biochemical networks  
19:30 - 21:00 Dinner  

Tuesday, May 28, 2013

Time Event  
07:45 - 08:45 Breakfast  
08:45 - 10:15 ten Wolde 2 - Modeling biochemical networks  
10:15 - 10:45 Coffee break  
10:45 - 12:15 Arneodo 2 - DNA sequence effect on the nucleosomal organization of the eukaryotic chromatin fiber  
12:15 - 14:00 Lunch  
17:15 - 18:45 Weigt 4 - Co-evolution in proteins: From maximum-entropy modeling of protein families to 3D protein structure prediction  
19:30 - 21:00 Dinner  

Wednesday, May 29, 2013

Time Event  
07:45 - 08:45 Breakfast  
08:45 - 10:15 Arneodo 3 - Large-scale analysis of genomic sequences: from the detection of replication origins to the modeling of replication in higher eukaryotes  
10:15 - 10:45 Coffee break  
10:45 - 12:15 ten Wolde 3 - Simulating biochemical networks  
12:15 - 14:00 Lunch  
14:00 - 16:00 Practical work  
17:15 - 18:45 Seminar: Rivoire -  
19:30 - 21:00 Dinner  

Thursday, May 30, 2013

Time Event  
07:45 - 08:45 Breakfast  
08:45 - 10:15 ten Wolde 4 - Quantifying information transmission in biochemical networks using measures from information theory  
10:15 - 10:45 Coffee break  
10:45 - 12:15 Arneodo 4 - Spatio-temporal organization of replication: On genome evolution and large-scale chromatin folding  
12:15 - 14:00 Lunch  
14:00 - 16:00 Practical work  
17:15 - 18:45 Presentations by participants  
19:30 - 21:00 Dinner  

Friday, May 31, 2013

Time Event  
07:45 - 08:45 Breakfast  
08:45 - 10:15 Presentations by participants  
10:15 - 10:45 Break  
10:45 - 12:15 Presentations by participants  
12:15 - 14:00 Lunch  
14:00 - 18:45 Departure - Departure  
  
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