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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)

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

- Geert C. W. M. Mulders, Gerard T. Barkema, Enrico Carlon
- BMC Bioinformatics
- 2009

BACKGROUND
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… (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)

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)

- A. van Heukelum, G. T. Barkema, R. H. Bisseling
- 2001

The cage model for polymer reptation, proposed by Evans and Ed-wards, and its recent extension to model DNA electrophoresis, are studied by numerically exact computation of the drift velocities for polymers with a length L of up to 15 monomers. The computations show the Nernst-Einstein regime (v ∼ E) followed by a regime where the velocity decreases… (More)

- Henk Vocks, Debabrata Panja, Gerard T Barkema
- Journal of physics. Condensed matter : an…
- 2009

Using a combination of theory and computer simulations, we study the translocation of an RNA molecule, pulled through a solid-state nanopore by an optical tweezer, as a method for determining its secondary structure. The resolution with which the elements of the secondary structure can be determined is limited by thermal fluctuations. We present a detailed… (More)