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Arnaud Buhot

Publications and source records attributed to Arnaud Buhot.

4 recordsLinked to original sources
PubMed2005

Cluster algorithm for nonadditive hard-core mixtures.

In this paper, we present a cluster algorithm for the numerical simulations of nonadditive hard-core mixtures. This algorithm allows one to simulate and equilibrate systems with a number of particles two orders of magnitude larger than previous simulations. The phase separation for symmetric binary mixtures is studied for different nonadditivities as well as for the Widom-Rowlinson model [B. Widom and J. S. Rowlinson, J. Chem. Phys. 52, 1670 (1970)] in two and three dimensions. The critical densities are determined from finite size scaling. The critical exponents for all the nonadditivities are consistent with the Ising universality class.

Journal Article↗
PubMed2004

Hybridization isotherms of DNA microarrays and the quantification of mutation studies.

BACKGROUND: Diagnostic DNA arrays for detection of point mutations as markers for cancer usually function in the presence of a large excess of wild-type DNA. This excess can give rise to false positives as a result of competitive hybridization of the wild-type target at the mutation spot. Analysis of the DNA array data is typically qualitative, aimed at establishing the presence or absence of a particular point mutation. Our theoretical approach yields methods for quantifying the analysis to obtain the ratio of concentrations of mutated and wild-type DNA. METHOD: The theory is formulated in terms of the hybridization isotherms relating the hybridization fraction at the spot to the composition of the sample solutions at thermodynamic equilibrium. It focuses on samples containing an excess of single-stranded DNA and on DNA arrays with a low surface density of probes. The hybridization equilibrium constants can be obtained by the nearest-neighbor method. RESULTS: Two approaches allow acquisition of quantitative results from the DNA array data. In one, the signal of the mutation spot is compared with that of the wild-type spot. The implementation requires knowledge of the saturation intensity of the two spots. The second approach requires comparison of the intensity of the mutation spot at two different temperatures. In this case, knowledge of the saturation signal is not always necessary. CONCLUSIONS: DNA arrays can be used to obtain quantitative results on the concentration ratio of mutated DNA to wild-type DNA in studies of somatic point mutations.

Algorithms↗
PubMed2002

Fluctuation-dissipation relations in the activated regime of simple strong-glass models.

We study the out-of-equilibrium fluctuation-dissipation (FD) relations in the low-temperature, finite-time, physical-aging regime of two simple models with strong glass behavior, the Fredrickson-Andersen model and the square-plaquette interaction model. We explicitly show the existence of unique, waiting-time independent dynamical FD relations. While in the Fredrickson-Andersen model the FD theorem is obeyed at all times, the plaquette model displays piecewise-linear FD relations, similar to what is found in disordered mean-field models and in simulations of supercooled liquids, and despite the fact that its static properties are trivial. We discuss the wider implications of these results.

Journal Article↗