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Papers by G. Barkema

Modelling protein folding by Monte Carlo dynamics - Chevron plots, Chevron rollover and non-arrhe... more Modelling protein folding by Monte Carlo dynamics - Chevron plots, Chevron rollover and non-arrhenius kinetics a second course in dynamical Monte Carlo the Monte Carlo growth method dynamical parameter algorithms for protein folding protein folding in contact map space phase diagram of semi-stiff homopolymers testing a new Monte Carlo strategy for folding model proteins heteropolymer folding in the two-dimensional HAP model PERM - a Monte Carlo strategy for simulating polymers and other things exploring energy landscapes with the activation-relaxation technique. (Part contents).

The Journal of Physical Chemistry B, 2006

Physica A: Statistical Mechanics and its Applications, 1997

Journal of Statistical Mechanics: Theory and Experiment, 2011

Europhysics Letters (EPL), 2001

Algorithms for Molecular Biology, 2009

We have carried out extensive computer simulations of one-dimensional models related to the low n... more We have carried out extensive computer simulations of one-dimensional models related to the low noise (solid-on-solid) non-equilibrium interface of a two dimensional anchored Toom model with unbiased and biased noise. For the unbiased case the computed fluctuations of the interface in this limit provide new numerical evidence for the logarithmic correction to the subnormal L 1 2 variance which was predicted by the dynamic renormalization group calculations on the modified Edwards-Wilkinson equation. In the biased case the simulations are in close quantitative agreement with the predictions of the Collective Variable Approximation (CVA), which gives the same L 2 3 behavior of the variance as the KPZ equation. 3 Also Department of Physics, Rutgers University. I. INTRODUCTION The nature of the interface separating two equilibrium phases, or more generally any two distinct bulk states of matter, is a problem of continuing interest. While there is in most cases some fuzziness in the t...

arXiv: Materials Science, 2004

The dynamics of many atomic systems is controlled by activated events taking place on a time scal... more The dynamics of many atomic systems is controlled by activated events taking place on a time scale which is long compared to that associated with thermal vibrations. This often places problems of interest outside the range of standard simulation methods such as molecular dynamics. We present here an algorithm, the dynamical activation-relaxation technique (DART), which slows down thermal vibrations, while leaving untouched the activated processes which constitute the long-time dynamics. As an example, we show that it is possible to accelerate considerably the dynamics of self-defects in a 1000-atom cell of c-Si over a wide range of temperatures.

Journal of Physics A: Mathematical and General, 1996

Modelling protein folding by Monte Carlo dynamics - Chevron plots, Chevron rollover and non-arrhe... more Modelling protein folding by Monte Carlo dynamics - Chevron plots, Chevron rollover and non-arrhenius kinetics a second course in dynamical Monte Carlo the Monte Carlo growth method dynamical parameter algorithms for protein folding protein folding in contact map space phase diagram of semi-stiff homopolymers testing a new Monte Carlo strategy for folding model proteins heteropolymer folding in the two-dimensional HAP model PERM - a Monte Carlo strategy for simulating polymers and other things exploring energy landscapes with the activation-relaxation technique. (Part contents).

The Journal of Physical Chemistry B, 2006

Physica A: Statistical Mechanics and its Applications, 1997

Journal of Statistical Mechanics: Theory and Experiment, 2011

Europhysics Letters (EPL), 2001

Algorithms for Molecular Biology, 2009

We have carried out extensive computer simulations of one-dimensional models related to the low n... more We have carried out extensive computer simulations of one-dimensional models related to the low noise (solid-on-solid) non-equilibrium interface of a two dimensional anchored Toom model with unbiased and biased noise. For the unbiased case the computed fluctuations of the interface in this limit provide new numerical evidence for the logarithmic correction to the subnormal L 1 2 variance which was predicted by the dynamic renormalization group calculations on the modified Edwards-Wilkinson equation. In the biased case the simulations are in close quantitative agreement with the predictions of the Collective Variable Approximation (CVA), which gives the same L 2 3 behavior of the variance as the KPZ equation. 3 Also Department of Physics, Rutgers University. I. INTRODUCTION The nature of the interface separating two equilibrium phases, or more generally any two distinct bulk states of matter, is a problem of continuing interest. While there is in most cases some fuzziness in the t...

arXiv: Materials Science, 2004

The dynamics of many atomic systems is controlled by activated events taking place on a time scal... more The dynamics of many atomic systems is controlled by activated events taking place on a time scale which is long compared to that associated with thermal vibrations. This often places problems of interest outside the range of standard simulation methods such as molecular dynamics. We present here an algorithm, the dynamical activation-relaxation technique (DART), which slows down thermal vibrations, while leaving untouched the activated processes which constitute the long-time dynamics. As an example, we show that it is possible to accelerate considerably the dynamics of self-defects in a 1000-atom cell of c-Si over a wide range of temperatures.

Journal of Physics A: Mathematical and General, 1996

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