G. Barkema - Profile on Academia.edu (original) (raw)

Papers by G. Barkema

Symmetries and equivalences in a lattice model for hydrophobic interaction

Workshop on Monte Carlo Approach to Biopolymers and Protein Folding, HLRZ, Forschungszentrum Jülich, Germany, 3-5 December 1997

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).

Physical Review E, 2005

We propose a kinetic Ising model to study phase separation driven by surface diffusion. This mode... more We propose a kinetic Ising model to study phase separation driven by surface diffusion. This model is referred to as Model S, and consists of the usual Kawasaki spin-exchange kinetics (Model B) in conjunction with a kinetic constraint. We use novel multi-spin coding techniques to develop fast algorithms for Monte Carlo simulations of Models B and S. We use these algorithms to study the late stages of pattern dynamics in these systems.

Workshop on Molecular Dynamics on Parallel Computers

The atomic structure of amorphous materials is believed to be well described by the continuous ra... more The atomic structure of amorphous materials is believed to be well described by the continuous random network model. We present an algorithm for the generation of large, high-quality continuous random networks. The algorithm is a variation of the sillium approach introduced by Wooten, Winer, and Weaire. By employing local relaxation techniques, local atomic rearrangements can be tried that scale almost independently of system size. This scaling property of the algorithm paves the way for the generation of realistic device-size atomic networks.

The pair contact process with diffusion is studied by means of multispin Monte Carlo simulations ... more The pair contact process with diffusion is studied by means of multispin Monte Carlo simulations and density matrix renormalization group calculations. Effective critical exponents are found to behave nonmonotonically as functions of time or of system length and extrapolate asymptotically towards values consistent with the directed percolation universality class. We argue that an intermediate regime exists where the effective critical dynamics resembles that of a parity conserving process.

The Journal of Physical Chemistry B, 2006

We analyze publicly available data on Affymetrix microarray spike-in experiments on the human HGU... more 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 2006, 362, 433) that takes into account both probe-target hybridization and target-target partial hybridization in solution. The hybridization free energies are obtained from the nearest-neighbor model with experimentally determined parameters. The molecular-based model suggests a rescaling that should result in a "collapse" of the data at different concentrations into a single universal curve. We indeed find such a collapse, with the same parameters as obtained previously for the older HGU95 chip set. The quality of the collapse varies according to the probe set considered. Artificial sequences, chosen by Affymetrix to be as different as possible from any other human genome sequence, generally show a much better collapse and thus a better agreement with the model than all other sequences. This suggests that the observed deviations from the predicted collapse are related to the choice of probes or have a biological origin rather than being a problem with the proposed model.

Physica A: Statistical Mechanics and its Applications, 1997

We discuss the repton model of agarose gel electrophoresis of DNA. We review previous results, bo... more We discuss the repton model of agarose gel electrophoresis of DNA. We review previous results, both analytic and numerical, as well as presenting a new numerical algorithm for the efficient simulation of the model, and suggesting a new approach to the model's analytic solution.

Journal of Statistical Mechanics: Theory and Experiment, 2011

Europhysics Letters (EPL), 2001

While recent work towards the development of tight-binding and ab initio algorithms has focused o... more While recent work towards the development of tight-binding and ab initio algorithms has focused on molecular dynamics, Monte Carlo methods can often lead to better results with relatively little effort. We present here a multi-step Monte Carlo algorithm that makes use of the possibility of quickly evaluating local energies. For the thermalization of a 1000-atom configuration of a-Si, this algorithm gains about an order of magnitude in speed over standard molecular dynamics. The algorithm can easily be ported to a wide range of materials and can be dynamically optimized for a maximum efficiency.

Algorithms for Molecular Biology, 2009

Background: One important preprocessing step in the analysis of microarray data is background sub... more Background: One important preprocessing step in the analysis of microarray data is background subtraction. In high-density oligonucleotide arrays this is recognized as a crucial step for the global performance of the data analysis from raw intensities to expression values. Results: We propose here an algorithm for background estimation based on a model in which the cost function is quadratic in a set of fitting parameters such that minimization can be performed through linear algebra. The model incorporates two effects: 1) Correlated intensities between neighboring features in the chip and 2) sequence-dependent affinities for non-specific hybridization fitted by an extended nearest-neighbor model. Conclusion: The algorithm has been tested on 360 GeneChips from publicly available data of recent expression experiments. The algorithm is fast and accurate. Strong correlations between the fitted values for different experiments as well as between the free-energy parameters and their counterparts in aqueous solution indicate that the model captures a significant part of the underlying physical chemistry.

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...

BMC Bioinformatics, 2009

Background: An algorithm for the analysis of Affymetrix Genechips is presented. This algorithm, r... more 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 balance between these two competing reactions allows for the translation of backgroundsubtracted intensities into transcript concentrations. Results: To validate the ILM, it is applied to publicly available microarray data from a multi-lab comparison study. Here, microarray experiments are performed on samples which deviate only in few genes. The log 2 fold change between these two samples, as obtained from RT-PCR experiments, agrees well with the log 2 fold change as obtained with the ILM, indicating that the ILM determines changes in the expression level accurately. We also show that the ILM allows for the identification of outlying probes, as it yields independent concentration estimates per probe. Conclusion: The ILM is robust and offers an interesting alternative to purely statistical algorithms for microarray data analysis.

Partitioning 3D space for parallel many-particle simulations

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.

We revisit the anchored Toom interface and use KPZ scaling theory to argue that the interface flu... more We revisit the anchored Toom interface and use KPZ scaling theory to argue that the interface fluctuations are governed by the Airy 1 process with the role of space and time interchanged. The predictions, which contain no free parameter, are numerically well confirmed for space-time statistics in the stationary state. In particular the spatial fluctuations of the interface computed numerically agree well with those given by the GOE edge distribution of Tracy and Widom.

The time evolution of the strength of the Earth's virtual axial dipole moment (VADM) is analyzed ... more The time evolution of the strength of the Earth's virtual axial dipole moment (VADM) is analyzed by relating it to the Fokker-Planck equation, which describes a random walk with VADM-dependent drift and diffusion coefficients. We demonstrate first that our method is able to retrieve the correct shape of the drift and diffusion coefficients from a time series generated by a test model. Analysis of the Sint-2000 data shows that the geomagnetic dipole mode has a linear growth time of 20 +13 −7 kyr, and that the nonlinear quenching of the growth rate follows a quadratic function of the type [1−(x/x 0) 2 ]. On theoretical grounds, the diffusive motion of the VADM is expected to be driven by multiplicative noise, and the corresponding diffusion coefficient to scale quadratically with dipole strength. However, analysis of the Sint-2000 VADM data reveals a diffusion which depends only very weakly on the dipole strength. This may indicate that the magnetic field quenches the amplitude of the turbulent velocity in the Earth's outer core.

Journal of Physics A: Mathematical and General, 1996

The cage model for polymer reptation, proposed by E v ans and Edwards, and its recent extension t... more The cage model for polymer reptation, proposed by E v ans and Edwards, 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. In agreement with De Gennes' reptation arguments, we nd that asymptotically for large polymers the di usion coe cient D decreases quadratically with polymer length for the cage model, the proportionality coe cient i s DL 2 = 0 :175(2). Additionally we nd that the leading correction term for nite polymer lengths scales as N ;1=2 , w h e r e N = L ; 1 is the number of bonds. If an electric eld is applied with strength E, the polymer drift velocity v scales initially as v E= L , and then changes into a regime where v E 2 , a s i n t h e Duke-Rubinstein model. We nd con rmation for the existence of a third regime, still in the physically relevant range of eld strengths, where the drift velocity decreases exponentially.