Concept

Nucleic acid double helix

Publications associées (165)

Thermodynamics of Writhe in DNA Minicircles from Molecular Dynamics Simulations

DNA supercoiling plays a role in genetic control by imposing torsional stress. This can induce writhe, which changes the global shape of the DNA. We have used atomistic molecular dynamics simulations to partition the free energy changes driving the writhin ...

Amer Physical Soc2013

A sequence-dependent rigid-base model of DNA

John Maddocks, Daiva Petkeviciute

A novel hierarchy of coarse-grain, sequence-dependent, rigid-base models of B-form DNA in solution is introduced. The hierarchy depends on both the assumed range of energetic couplings, and the extent of sequence dependence of the model parameters. A signi ...

Amer Inst Physics2013

Bifurcated Helical Core Equilibrium States in Tokamaks

Olivier Sauter, Basil Duval, Stefano Coda, Jonathan Graves, Wilfred Anthony Cooper, Holger Reimerdes, Benoît Labit, Antoine Pochelon, Trach-Minh Tran, David Pfefferlé, Federico David Halpern, Daniele Brunetti

Tokamaks with weak to moderate reversed central shear in which the minimum inverse rotational transform (safety factor) qmin is in the neighbourhood of unity can trigger bifurcated magnetohydrodynamic equilibrium states, one of which is similar to a satura ...

IOP Publishing2013

Computational analysis of the interplay between tRNA competitive behavior and decoding type on the modulation of translation elongation rate

Vassily Hatzimanikatis, Julien Racle, Joana Raquel Pinto Vieira

There has been much discussion in the literature regarding the determinants of ribosomal decoding speed during the mRNA translation process. Computational results based on mechanistic models for ribosomal kinetics have predicted a major role for near-cogna ...

2013

Mechanism to Trigger Unfolding in O6--Alkylguanine-DNA Alkyltransferase

Ursula Röthlisberger, Elizabeth Claire Brunk, Birgit Mollwitz

O6-alkylguanine-DNA alkyltransferase (AGT) adopts a non-enzymatic suicide mechanism for the repair of methylated guanine bases by transferring the methyl adduct to itself, thereby initiating unfolding and fast degradation. Classical molecular dynamics simu ...

Wiley-Blackwell2013

Comment une situation d’investigation policière fait évoluer les conceptions d’élèves de troisième sur l’ADN

The work presented focuses on the analysis of a police investigation implemented in the computing environment SCY-Lab. The prime objective is to check if the implementation of the situation helps pupils change their conceptions concerning the DNA molecule ...

2013

Analysis of the dynamics and competition for resources in the system of protein translation using stochastic simulations

Vassily Hatzimanikatis, Julien Racle, Joana Raquel Pinto Vieira

Protein synthesis plays an important role in biological systems since its products, proteins and enzymes, constitute most of the molecular machinery required for cell regulation, growth and function in the tissue. Understanding the mechanisms of decoding a ...

2013

Twist and Stretch of Helices Explained via the Kirchhoff-Love Rod Model of Elastic Filaments

John Maddocks

In various single-molecule experiments, a chiral polymer, such as DNA, is simultaneously pulled and twisted. We address an elementary but fundamental question raised by various authors: does the molecule overwind or unwind under tension? We show that withi ...

Amer Physical Soc2013

A weakly nonlinear mechanism for mode selection in swirling jets

François Gallaire, Philippe Meliga

Global linear and nonlinear bifurcation analysis is used to revisit the spiral vortex breakdown of nominally axisymmetric swirling jets. For the parameters considered herein, stability analyses single out two unstable linear modes of azimuthal wavenumber m ...

Cambridge University Press2012

Quantifying supercoiling-induced denaturation bubbles in DNA

Giovanni Dietler

In both eukaryotic and prokaryotic DNA sequences of 30-100 base-pairs rich in AT base-pairs have been identified at which the double helix preferentially unwinds. Such DNA unwinding elements are commonly associated with origins for DNA replication and tran ...

Royal Society of Chemistry2012

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