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We propose a number of Monte Carlo algorithms for the simulation of ice models and compare their efficiency. One of them, a cluster algorithm for the equivalent three colour model, appears to have a dynamic exponent close to zero, making it particularly useful for simulations of critical ice models. We have performed extensive simulations using our… (More)

A prototypical problem on which techniques for exact enumeration are tested and compared is the enumeration of self-avoiding walks. Here, we show an advance in the methodology of enumeration, making the process thousands or millions of times faster. This allowed us to enumerate self-avoiding walks on the simple cubic lattice up to a length of 36 steps.

- G T Barkema, M J Howard, J L Cardy
- 1996

We study theoretically and numerically the steady state diffusion controlled reaction A + B → ∅, where currents J of A and B particles are applied at opposite boundaries. For a reaction rate λ, and equal diffusion constants D, we find that when λJ −1/2 D −1/2 ≪ 1 the reaction front is well described by mean field theory. However, for λJ −1/2 D −1/2 ≫ 1, the… (More)

- Raoul D Schram, Gerard T Barkema, Helmut Schiessel
- The Journal of chemical physics
- 2013

The fractal globule, a self-similar compact polymer conformation where the chain is spatially segregated on all length scales, has been proposed to result from a sudden polymer collapse. This state has gained renewed interest as one of the prime candidates for the non-entangled states of DNA molecules inside cell nuclei. Here, we present Monte Carlo… (More)

- K M Kroll, G T Barkema, E Carlon
- Physical review. E, Statistical, nonlinear, and…
- 2008

DNA microarrays are devices that are able, in principle, to detect and quantify the presence of specific nucleic acid sequences in complex biological mixtures. The measurement consists in detecting fluorescence signals from several spots on the microarray surface onto which different probe sequences are grafted. One of the problems of the data analysis is… (More)

- T Heim, L-C Tranchevent, E Carlon, G T Barkema
- The journal of physical chemistry. B
- 2006

We analyze publicly available data on Affymetrix microarray spike-in experiments on the human HGU133 chipset in which sequences are added in solution at known concentrations. The spike-in set contains sequences of bacterial, human, and artificial origin. Our analysis is based on a recently introduced molecular-based model (Carlon, E.; Heim, T. Physica A… (More)

- Geert C. W. M. Mulders, Gerard T. Barkema, Enrico Carlon
- BMC Bioinformatics
- 2008

An algorithm for the analysis of Affymetrix Genechips is presented. This algorithm, referred to as the Inverse Langmuir Method (ILM), estimates the binding of transcripts to complementary probes using DNA/RNA hybridization free energies, and the hybridization between partially complementary transcripts in solution using RNA/RNA free energies. The balance… (More)

In the past couple of years several studies have shown that hybridization in Affymetrix DNA microarrays can be rather well understood on the basis of simple models of physical chemistry. In the majority of the cases a Langmuir isotherm was used to fit experimental data. Although there is a general consensus about this approach, some discrepancies between… (More)

- Normand Mousseau, Gerard T. Barkema
- Computing in Science and Engineering
- 1999

We consider a polymer of length $N$ translocating through a narrow pore in the absence of external fields. Characterization of its purportedly anomalous dynamics has so far remained incomplete. We show that the polymer dynamics is anomalous until the Rouse time $\tau_{R}\sim N^{1+2\nu}$, with a mean square displacement through the pore consistent with… (More)