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Thomas Garel

Publications and source records attributed to Thomas Garel.

58 records · Page 4Linked to original sources

Spin-glass chain in a magnetic field : influence of the disorder distribution on ground state properties and low-energy excitations

For the spin-glass chain in an external field $h$, a non-zero weight at the origin of the bond distribution $ρ(J)$ is known to induce a non-analytical magnetization at zero temperature : for $ρ(J) \sim A | J |^{μ-1}$ near $J \to 0$, the magnetization follows the Chen-Ma scaling $M \sim h^{μ/(2+μ)}$. In this paper, we numerically revisit this model to obtain detailed statistical information on the ground state configuration and on the low-energy two-level excitations that govern the low temperature properties. The ground state consists of long unfrustrated intervals separated by weak frustrated bonds: We accordingly compute the strength distribution of these frustrated bonds, as well as the length- and magnetization- distributions of the unfrustrated intervals. We find that the low-energy excitations are of two types (i) one frustrated bond of the ground state may have two positions that are nearly degenerate in energy (ii) two neighboring frustrated bonds of the ground state may be annihilated or created with nearly zero energy cost. For each excitation type, we compute its probability density as a function of its length. We moreover show that the contributions of these excitations to various observables (specific heat, Edwards-Anderson order parameter, susceptibility) are in full agreement with direct transfer matrix evaluations at low temperature. Finally, following the special bimodal case $\pm J$, where a Ma-Dasgupta RG procedure has been previously used to compute explicitly the above observables, we discuss the possibility of an extended RG procedure : we find that the ground state can be seen as the result of a hierarchical `fragmentation' procedure that we describe.

cond-mat.dis-nn↗

Generalized Poland-Scheraga model for DNA hybridization

The Poland-Scheraga (PS) model for the helix-coil transition of DNA considers the statistical mechanics of the binding (or hybridization) of two complementary strands of DNA of equal length, with the restriction that only bases with the same index along the strands are allowed to bind. In this paper, we extend this model by relaxing these constraints: We propose a generalization of the PS model which allows for the binding of two strands of unequal lengths $N_{1}$ and $N_{2}$ with unrelated sequences. We study in particular (i) the effect of mismatches on the hybridization of complementary strands (ii) the hybridization of non complementary strands (as resulting from point mutations) of unequal lengths $N_{1}$ and $N_{2}$. The use of a Fixman-Freire scheme scales down the computational complexity of our algorithm from $O(N_{1}^{2}N_{2}^{2})$ to $O(N_{1}N_{2})$.The simulation of complementary strands of a few kbps yields results almost identical to the PS model. For short strands of equal or unequal lengths, the binding displays a strong sensitivity to mutations. This model may be relevant to the experimental protocol in DNA microarrays, and more generally to the molecular recognition of DNA fragments. It also provides a physical implementation of sequence alignments.

q-bio.BM↗

Generalized Poland-Scheraga model for supercoiled DNA

The Poland-Scheraga (PS) model for the helix-coil transition of DNA considers the statistical mechanics of the thermally induced binding of two complementary strands of DNA. In this paper, we show how to modify the PS model when a torque is applied to the extremities of DNA: We propose a simple model for the energy of twisted DNA and compute the entropy of a loop, subject to angular constraints (supercoiling). The denaturation curves are shifted towards lower or higher temperatures depending on the sign of the torque, and the UV absorption peaks are softened. The properties of supercoiled DNA can be deduced through the use of a numerical Legendre transform. In the homogeneous case, we find that for weak supercoiling, the phenomenological quadratic law relating the torsional energy to the number of unpaired bases is recovered.

q-bio.BM↗

Directed polymers and interfaces in random media : free-energy optimization via confinement in a wandering tube

We analyze, via Imry-Ma scaling arguments, the strong disorder phases that exist in low dimensions at all temperatures for directed polymers and interfaces in random media. For the uncorrelated Gaussian disorder, we obtain that the optimal strategy for the polymer in dimension $1+d$ with $0 1/2$ for the wandering of the best favorable tube available. The corresponding free-energy then scales as $F \sim L^ω$ with $ω=2 ν-1$ and the left tail of the probability distribution involves a stretched exponential of exponent $η= (4-d)/2$. These results generalize the well known exact exponents $ν=2/3$, $ω=1/3$ and $η=3/2$ in $d=1$, where the subleading transverse length $R_S \sim L^{1/3}$ is known as the typical distance between two replicas in the Bethe Ansatz wave function. We then extend our approach to correlated disorder in transverse directions with exponent $α$ and/or to manifolds in dimension $D+d=d_{t}$ with $0 0$). In particular, for an interface of dimension $(d_t-1)$ in a space of total dimension $5/3<d_t<3$ with random-bond disorder, our approach yields the confinement exponent $ν_S = (d_t-1)(3-d_t)/(5d_t-7)$. Finally, we study the exponents in the presence of an algebraic tail $1/V^{1+μ}$ in the disorder distribution, and obtain various regimes in the $(μ,d)$ plane.

cond-mat.dis-nn↗