Theoretical Approaches for the Genome TAG'08

School : 20-22 October 2008 + Workshop : 23-24 October 2008


PRELIMINARY PROGRAM

 

SCHOOL

Registration : Monday 9:00 - 9:30

 
  Monday Tuesday Wednesday
9:30 - 10:30

A. ARNEODO - 1

J. BERG - 2 J. BERG - 4
10:30 - 11:00 Coffee break / Discussion Coffee break / Discussion Coffee break / Discussion
11:00 - 12:00 A. ARNEODO - 2 J. BERG - 3 J. BERG - 5
12:00 - 14:00 Lunch Lunch Lunch
14:00 - 15:00 S. HOLMES - 1 A. ARNEODO - 3 S. HOLMES - 4
15:00 - 15:15 Break / Discussion Break / Discussion Break / Discussion
15:15 - 16:15 S. HOLMES - 2 A. ARNEODO - 4 S. HOLMES - 5
16:15 - 16:45 Coffee break / Discussion Coffee break / Discussion Coffee break / Discussion
16:45 - 17:45 J. BERG - 1 S. HOLMES - 3 A. ARNEODO - 5
 
 

WORKSHOP

Registration : Thursday 9:00 - 9:30

  Thursday Friday
9:30 - 10:30 C. THERMES R. TWAROCK
10:30 - 11:00 Coffee break / Discussion Coffee break / Discussion
11:00 - 12:00 M. CASELLE J. LOBRY
12:00 - 14:00 Lunch Lunch
14:00 - 15:00 M. NICODEMI E. REMY
15:00 - 15:15 Break / Discussion Break / Discussion
15:15 - 16:15 C. LESIEUR H. ORLAND
16:15 - 16:45 Coffee break / Discussion M. PEYRARD
16:45 - 17:15 G. FEVERATI
17:15 - 17:45 J. CURUKSU  
17:45 - 18:15 B. DRAGOVICH

A poster session will be organised during the workshop

 


Titles of Lectures (School)



Titles of Talks (Workshop)


DNA bending stress in molecular dynamics simulations.

Many biological functions directed by DNA bending flexibility reflect dynamical hinge properties between specific base pair components. Recent experiments on minicircles [1] suggest that this DNA propensity is much higher than expected from the canonical persistence length of 50 nm. Subsequent molecular dynamics simulation of these minicircles [2] found base-pair kink motifs referred to as type I (adjacent base pair unstacking without base pair disruption) and type II (strong unstacking associated with base pair disruption) provide ways to relax DNA elastic energy. We impose a controlled bending deformation of short DNA oligonucleotides during molecular dynamics [3] to estimate free energy costs and dynamical bending response of DNA as a function of sequence. We summarize the results in terms of base pair kink motifs and global DNA bending. Local DNA stiffness constants depend significantly on the nature of such motifs, and can reduce canonical DNA values by as much as an order of magnitude in the case of type II kink formation.
1.T.E. Cloutier, J. Widom (2004) Mol. Cell., 14: 355-62. 2.F. Lankas, R. Lavery, J.D. Maddocks (2006) Structure, 14: 1527-34. 3.J. Curuksu, K. Zakrzewska, M. Zacharias (2008) Nucleic Acids Res., 36: 2268-83.

p-Adic Approach to the Genetic Code and the Genome

Abstract of talk: We present the foundations of p-adic approach to genomics. Nucleotides, codons, DNA and RNA sequences, amino acids and proteins are considered as p-adic information systems. Each of these systems has its characteristic prime number which generate the related information space. It is shown that degeneration of the genetic code is a p-adic phenomenon. We also propose evolution of the genetic code assuming that primitive code started by single nucleotides and the first four amino acids (Gly, Ala, Asp and Val).
References: arXiv: q-bio.GN/0607018, arXiv:07070764[q-bio.GN], arXiv:0707.3043[q-bio.OT] .