Non-Markovian dynamics of clusters during nucleation (2009)
Most theories of homogeneous nucleation are based on a Fokker-Planck-like description of the behavior of the mass of clusters. Here we will show that these approaches are incomplete for a large class...
Monte Carlo studies of extensions of the Blume-Emery-Griffiths model (2008)
Loois, C. C., Barkema, G. T., Smith, C. Morais
We extend the Blume-Emery-Griffiths (BEG) model to a two-component BEG model in order to study 2D systems with two order parameters, such as magnetic superconductors or two-component Bose-Einstein...
Monte Carlo study of multiply crosslinked semiflexible polymer networks (2008)
Huisman, E. M., Storm, C., Barkema, G. T.
We present a method to generate realistic, three-dimensional networks of crosslinked semiflexible polymers. The free energy of these networks is obtained from the force-extension characteristics of...
Unbiased computation of transition times by pathway recombination (2008)
In many systems, the time scales of the microscopic dynamics and macroscopic dynamics of interest are separated by many orders of magnitude. Examples abound, for instance nucleation, protein folding,...
Abstract Partitioning 3D space for parallel many-particle simulations (2008)
M. A. Stijnman, R. H. Bisseling, G. T. Barkema
In a common approach for parallel processing applied to simulations of manyparticle systems with short-ranged interactions and uniform density, the simulation cell is partitioned into domains of...
Abstract Partitioning 3D space for parallel many-particle simulations (2008)
M. A. Stijnman, R. H. Bisseling, G. T. Barkema
In a common approach for parallel processing applied to simulations of manyparticle systems with short-ranged interactions and uniform density, the simulation cell is partitioned into domains of...
Monte Carlo study of multiply crosslinked semiflexible polymer networks (2008)
Huisman, E.M., Storm, C., Barkema, G.T.
We present a method to generate realistic, three-dimensional networks of crosslinked semiflexible polymers. The free energy of these networks is obtained from the force-extension characteristics of...
Modeling background intensity in DNA microarrays (2008)
Kroll, K.M., Barkema, G.T., Carlon, E.
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...
Unbiased computation of transition times by pathway recombination (2008)
In many systems, the time scales of the microscopic dynamics and macroscopic dynamics of interest are separated by many orders of magnitude. Examples abound, for instance, nucleation, protein...
Modelling background intensity in Affymetrix Genechips (2007)
Kroll, K. M., Barkema, G. T., Carlon, E.
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...
Sampling activated mechanisms in proteins with the activation-relaxation technique. (2007)
Normand Mousseau, G. T. Barkema, R. Malek
The activated dynamics of proteins occurs on time scales of milliseconds and longer. Standard all-atom molecular dynamics simulations are limited to much shorter times, of the order of tens of...
DNA electrophoresis studied with the cage model (2007)
A. Van Heukelum, G. T. Barkema, R. H. Bisseling
The cage model for polymer reptation, proposed by Evans and Edwards, and its recent extension to model DNA electrophoresis, are studied by numerically exact computation of the drift velocities for...
A. Van Heukelum, G. T. Barkema, R. H. Bisseling
band collapse, diffusion coefficient The cage model for polymer reptation, proposed by Evans and Edwards, and its recent extension to model DNA electrophoresis, are studied by numerically exact...
Basic mechanisms of structural relaxation and diffusion in amorphous silicon (2007)
G. T. Barkema, Parthapratim Biswas
The low-temperature dynamics in amorphous silicon occurs through a sequence of discrete, activated events that reorganize the topology of the network. In this review, we present some recent work done...
Universality class of the pair contact process with diffusion (2007)
Smallenburg, F., Barkema, G. T.
The pair contact process with diffusion (PCPD) is studied with a standard Monte Carlo approach and with simulations at fixed densities. A standard analysis of the simulation results, based on the...
An analysis of the fluctuations of the geomagnetic dipole (2007)
Brendel, K., Kuipers, J., Barkema, G. T., Hoyng, P.
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...
Carlon, E., Heim, T., Wolterink, J. Klein, Barkema, G. T.
In a recent paper [Phys. Rev. E 68, 011906 (2003)], Naef and Magnasco suggested that the "bright" mismatches observed in Affymetrix microarray experiments are caused by the fluorescent molecules used...
Physics-based analysis of Affymetrix microarray data (2006)
Heim, T., Carlon, E., Barkema, G. T.
We analyze publicly available data on Affymetrix microarrays spike-in experiments on the human HGU133 chipset in which sequences are added in solution at known concentrations. The spike-in set...
Effective affinities in microarray data (2006)
Heim, T., Wolterink, J. Klein, Carlon, E., Barkema, G. T.
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...
Spinodal decomposition in polymer mixtures via surface diffusion (2006)
Wolterink, J. Klein, Barkema, G. T., Puri, Sanjay
We present experimental results for spinodal decomposition in polymer mixtures of gelatin and dextran. The domain growth law is found to be consistent with t^1/4-growth over extended time-regimes....
Desorption of polymers: role of the stagnant layer (2006)
Klein Wolterink, J., Cohen Stuart, M.A., Barkema, G.T.
The desorption of polymers is studied theoretically and with Monte Carlo simulations. Two regimes can be distinguished: in one regime the detachment of the polymer from the surface is the slowest...
Vocks, Henk, Chubynsky, M. V., Barkema, G. T., Mousseau, Normand
While the dynamics of many complex systems is dominated by activated events, there are very few simulation methods that take advantage of this fact. Most of these procedures are restricted to...
Phase separation driven by surface diffusion: a Monte Carlo study (2005)
Van Gemmert, S., Barkema, G. T., Puri, Sanjay
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")...
Diffusion and exchange of adsorbed polymers studied by Monte Carlo simulations (2005)
Klein Wolterink, J., Barkema, G.T., Cohen Stuart, M.A.
Monte Carlo simulations are performed of adsorbed polymers with various polymer lengths N and adsorption energies ¿s. Exchange times and the rates of lateral diffusion (along the surface) are...
Binary continuous random networks (2004)
Mousseau, Normand, Barkema, G. T.
Many properties of disordered materials can be understood by looking at idealized structural models, in which the strain is as small as is possible in the absence of long-range order. For covalent...
Accelerated dynamics with the dynamical activation-relaxation technique (2004)
Barkema, G. T., Mousseau, Normand
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...
Mousseau, Normand, Barkema, G. T.
We present an accelerated algorithm that samples correctly the thermodynamic ensemble in complex systems where the dynamics is controlled by activation barriers. The efficiency of the...
Nucleation times in the 2D Ising model (2003)
Brendel, K., Barkema, G. T., Van Beijeren, H.
A theoretical framework is presented for the estimation of nucleation times in systems with Brownian type dynamics. This framework is applied to a prototype system: the two-dimensional Ising model...
Reaching large lengths and long times in polymer dynamics simulations (2003)
Van Heukelum, Alexander, Barkema, G. T.
A lattice model is presented for the simulation of dynamics in polymeric systems. Each polymer is represented as a chain of monomers, residing on a sequence of nearest-neighbor sites of a...
Universality in the pair contact process with diffusion (2003)
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...
Fractionation in a Phase-separated Polydisperse Polymer Mixture (2003)
If a solution of polydisperse A- and B-polymers undergoes phase separation, the molar mass distribution of the A-polymers in the A-rich phase becomes different from that in the B-rich phase. This...
Partitioning 3D Space for Parallel Many-Particle Simulations (2003)
M. A. Stijnman, R. H. Bisseling, G. T. Barkema
In a common approach for parallel processing applied to simulations of manyparticle systems with short-ranged interactions and uniform density, the simulation cell is partitioned into domains of...
Large well-relaxed models of vitreous silica, coordination numbers and entropy (2002)
Vink, R. L. C., Barkema, G. T.
A Monte Carlo method is presented for the simulation of vitreous silica. Well-relaxed networks of vitreous silica are generated containing up to 300,000 atoms. The resulting networks, quenched under...
Magnetization reversal times in the 2D Ising model (2002)
Brendel, Kevin, Barkema, G. T., Van Beijeren, Henk
We present a theoretical framework which is generally applicable to the study of time scales of activated processes in systems with Brownian type dynamics. This framework is applied to a prototype...
Configurational entropy of network-forming materials (2002)
Vink, R. L. C., Barkema, G. T.
We present a computationally efficient method to calculate the configurational entropy of network-forming materials. The method requires only the atomic coordinates and bonds of a single well-relaxed...
DNA electrophoresis studied with the cage model (2002)
Van Heukelum And, G. T. Barkema, R. H. Bisseling
This article presents numerically exact computations on the cage model, extended for electrophoresis as in Ref. [19]. As in most models, numerically exact results can only be obtained for relatively...
Device-size atomistic models of amorphous silicon (2001)
Vink, R.L.C., Barkema, G.T., Stijnman, M.A., Bisseling, R.H.
Towards device-size atomistic models of amorphous silicon (2001)
Vink, R. L. C., Barkema, G. T., Stijnman, M. A., Bisseling, R. H.
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...
Partitioning 3D space for parallel many-particle simulations (2001)
Stijnman, M. A., Bisseling, R. H., Barkema, G. T.
In a common approach for parallel processing applied to simulations of many-particle systems with short-ranged interactions and uniform density, the simulation cell is partitioned into domains of...
Diffusion with random distribution of static traps (2001)
Barkema, G. T., Biswas, Parthapratim, Van Beijeren, Henk
The random walk problem is studied in two and three dimensions in the presence of a random distribution of static traps. An efficient Monte Carlo method, based on a mapping onto a polymer model, is...
Simulation of polysilane and polysilyne formation and structure (2001)
Vink, R. L. C., Barkema, G. T., Van Walree, C. A., Jenneskens, L. W.
We present Monte Carlo simulations of the formation and structure of polysilane, hybrid polysilane/polysilyne and polysilyne networks. The simulation technique allows for the investigation of large...
DNA electrophoresis studied with the cage model (2001)
Heukelum, A. Van, Barkema, G.T., Bisseling, R.H.
The cage model for polymer reptation proposed by Evans and Edwards and its recent extension to model DNA electrophoresis are studied by numerically exact computation of the drift velocities for...
DNA electrophoresis studied with the cage model (2001)
Van Heukelum, A., Barkema, G. T., Bisseling, R. H.
The cage model for polymer reptation, proposed by Evans and Edwards, and its recent extension to model DNA electrophoresis, are studied by numerically exact computation of the drift velocities for...
Partitioning 3D space for parallel many-particle stimulations (2001)
Stijnman, M.A., Bisseling, R.H., Barkema, G.T.
In a common approach for parallel processing applied to simulations of manyparticle systems with short-ranged interactions and uniform density, the simulation cell is partitioned into domains of...
Realistic models of paracrystalline silicon (2001)
Nakhmanson, S.M., Voyles, P.M., Mousseau, N., Barkema, G.T., Drabold, D.A.
Efficient tight-binding Monte Carlo structural sampling of complex materials (2000)
Biswas, Parthapratim, Barkema, G. T., Mousseau, Normand, Van Der Weg, W. F.
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...
Equilibrium crystal shapes in the Potts model (2000)
Bikker, R. P., Barkema, G. T., Van Beijeren, H.
The three-dimensional $q$-state Potts model, forced into coexistence by fixing the density of one state, is studied for $q=2$, 3, 4, and 6. As a function of temperature and number of states, we...
Symmetry effects and equivalences in lattice models of hydrophobic interaction (2000)
Schütz, G. M., Ispolatov, I., Barkema, G. T., Widom, B.
We establish the equivalence of a recently introduced discrete model of the hydrophobic interaction, as well as its extension to continuous state variables, with the Ising model in a magnetic field...
Relation between Raman spectra and Structure of Amorphous Silicon (2000)
Vink, R. L. C., Barkema, G. T., Van Der Weg, W. F.
In 1985, Beeman, Tsu and Thorpe established an almost linear relation between the Raman transverse-optic (TO) peak width and the spread in mean bond angle in a-Si. This relation is often used to...
A cluster algorithm for Potts models with fixed spin densities (2000)
A cluster algorithm is presented for the simulation of the q-state Potts models in which the number of spins is conserved in each state. The algorithm constructs Fortuin-Kasteleyn cluster...
Model of Hydrophobic Attraction in Two and Three Dimensions (2000)
An earlier one-dimensional lattice model of hydrophobic attraction is extended to two and three dimensions and studied by Monte Carlo simulation. The solvent-mediated contribution to the potential of...
High-quality continuous random networks (1999)
The continuous random network (CRN) model is an idealized model for perfectly coordinated amorphous semiconductors. The quality of a CRN can be assessed in terms of topological and configurational...
Susceptibility amplitude ratios in the two-dimensional Potts model and percolation (1999)
Delfino, G., Barkema, G. T., Cardy, John
The high-temperature susceptibility of the $q$-state Potts model behaves as $\Gamma|T-T_c|^{-\gamma}$ as $T\to T_c+$, while for $T\to T_c-$ one may define both longitudinal and transverse...
Activated mechanisms in amorphous silicon: an activation-relaxation-technique study (1999)
Mousseau, Normand, Barkema, G. T.
At low temperatures, dynamics in amorphous silicon occurs through a sequence of discrete activated events that locally reorganize the topological network. Using the activation-relaxation technique, a...
Elementary mechanisms governing the dynamics of silica (1999)
Mousseau, Normand, Barkema, G. T., De Leeuw, Simon W.
A full understanding of glasses requires an accurate atomistic picture of the complex activated processes that constitute the low-temperature dynamics of these materials. To this end, we generate...
Reptation of star polymers in a network: Monte Carlo results of diffusion coefficients (1998)
Barkema, G. T., Baumgaertner, A.
We report on Monte Carlo results of diffusion coefficients of lattice star polymers trapped inside a fixed network (de Gennes model). It is found that our data are in agreement with the...
Barkema, G. T., Mousseau, Normand
Structural mechanisms in disordered materials like amorphous semi-conductors and glasses can be explored with the activation-relaxation technique (ART). The application of a sequence of such...
Long-time dynamics of de Gennes' model for reptation (1998)
Barkema, G. T., Krenzlin, H. M.
Diffusion of a polymer in a gel is studied within the framework of de Gennes' model for reptation. Our results for the scaling of the diffusion coefficient D and the longest relaxation time tau are...
Identification of relaxation and diffusion mechanisms in amorphous silicon (1998)
Barkema, G. T., Mousseau, Normand
The dynamics of amorphous silicon at low temperatures can be characterized by a sequence of discrete activated events, through which the topological network is locally reorganized. Using the...
Mousseau, Normand, Barkema, G. T.
A detailed description of the activation-relaxation technique (ART) is presented. This method defines events in the configurational energy landscape of disordered materials, such as a-Si, glasses and...
Two-dimensional oriented self-avoiding walks with parallel contacts (1997)
Barkema, G. T., Bastolla, U., Grassberger, P.
Two closely related models of oriented self-avoiding walks (OSAWs) on a square lattice are studied. We use the pruned-enriched Rosenbluth method to determine numerically the phase diagram. Both...
Monte Carlo simulation of ice models (1997)
Barkema, G. T., Newman, M. E. J.
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...
New Monte Carlo algorithms for classical spin systems (1997)
Barkema, G. T., Newman, M. E. J.
We describe a number of recently developed cluster-flipping algorithms for the efficient simulation of classical spin models near their critical temperature. These include the algorithms of Wolff,...
Diffusion constant for the repton model of gel electrophoresis (1997)
Newman, M. E. J., Barkema, G. T.
The repton model is a simple model of the "reptation" motion by which DNA diffuses through a gel during electrophoresis. In this paper we show that the model can be mapped onto a system consisting of...
Di#usion constant for the repton model of gel electrophoresis, Phys (1997)
The repton model is a simple model of the "reptation " motion by which DNA diffuses through a gel during electrophoresis. In this paper we show that the model can be mapped onto a...
The Repton Model of Gel Electrophoresis (1997)
this article we will consider the physics of the agarose gel process, which is commonly applied to DNA, although it can in principle be applied to other polymers, such as RNA for example. (The other...
The repton model of gel electrophoresis (1996)
Barkema, G. T., Newman, M. E. J.
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...
Numerical study of a non-equilibrium interface model (1996)
Subramanian, B., Barkema, G. T., Lebowitz, J. L., Speer, E. R.
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...
Event-based relaxation of continuous disordered systems (1996)
Barkema, G. T., Mousseau, Normand
A computational approach is presented to obtain energy-minimized structures in glassy materials. This approach, the activation-relaxation technique (ART), achieves its efficiency by focusing on...
Two-dimensional oriented self-avoiding walks with parallel contacts (1996)
Oriented self-avoiding walks (OSAWs) on a square lattice are studied, with binding energies between steps that are oriented parallel across a face of the lattice. By means of exact enumeration and...
Magnetophoresis of Tagged Polymers (1996)
We present quantitative results for the drift velocity of a polymer in a gel if a force (e.g. through an electric or magnetic field) acts on a tag, attached to one of its ends. This is done by...
Shear Flows and Segregation in the Reaction $A+B\to\emptyset$ (1996)
We study theoretically and numerically the effects of the linear velocity field ${\bf v}=v_0y{\bf\hat x}$ on the irreversible reaction $A+B\rightarrow\emptyset$. Assuming homogeneous initial...
The Reaction-Diffusion Front for $A+B \to\emptyset$ in One Dimension (1996)
Barkema, G. T., Howard, M. J., Cardy, J. L.
We study theoretically and numerically the steady state diffusion controlled reaction $A+B\rightarrow\emptyset$, where currents $J$ of $A$ and $B$ particles are applied at opposite boundaries. For a...
Numerical Study of a Non-Equilibrium Interface Model (1996)
Balakrishna Subramanian, G.T. Barkema, J. L. Lebowitz, E. R. Speer
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...
Monte Carlo study of the random-field Ising model (1995)
Newman, M. E. J., Barkema, G. T.
Using a cluster-flipping Monte Carlo algorithm combined with a generalization of the histogram reweighting scheme of Ferrenberg and Swendsen, we have studied the equilibrium properties of the thermal...
Monte Carlo Study of the Random-field Ising Model (1995)
Using a cluster-flipping Monte Carlo algorithm combined with a generalization of the histogram reweighting scheme of Ferrenberg and Swendsen, we have studied the equilibrium properties of the thermal...
Monte Carlo Study of the Random-field Ising Model (1995)
Using a cluster-flipping Monte Carlo algorithm combined with a generalization of the histogram reweighting scheme of Ferrenberg and Swendsen, we have studied the equilibrium properties of the thermal...
Rate Equations for the Growth of Cu Islands on Cu(001) (1994)
Biham, Ofer, Barkema, G.T., Breeman, M.
The kinetics of island nucleation and growth during deposition of Cu atoms on Cu(001) is studied using rate equations. The equations are derived using microscopic calculations of the energy landscape...
Rate Equations for the Growth of Cu Islands on Cu(001) (1994)
Biham, Ofer, Barkema, G.T., Breeman, M.
The kinetics of island nucleation and growth during deposition of Cu atoms on Cu(001) is studied using rate equations. The equations are derived using microscopic calculations of the energy landscape...
A model for the shapes of islands and pits on (111) surfaces of fcc metals (1994)
Barkema, G. T., Newman, M. E. J., Breeman, M.
It is experimentally observed that adsorbate atoms and vacancies on (111) surfaces of fcc metals cluster into islands which are approximately hexagonal, but which on closer inspection turn out to...
Parallel Simulation of the Ising Model (1994)
MacFarland, T., Barkema, G. T.
(The following contains mathematical formula and symbols that may become distorted in ASCII text.) New methods for parallelizing Ising model simulations are presented. A parallel single-spin...
Parallel Simulation of the Ising Model (1994)
MacFarland, T., Barkema, G. T.
(The following contains mathematical formula and symbols that may become distorted in ASCII text.) New methods for parallelizing Ising model simulations are presented. A parallel single-spin...
Real-space renormalization group for the random-field Ising model (1993)
Newman, M. E. J., Roberts, B. W., Barkema, G. T., Sethna, J. P.
We present real--space renormalization group (RG) calculations of the critical properties of the random--field Ising model on a cubic lattice in three dimensions. We calculate the RG flows in a...
Monte Carlo Simulation of Ice Models
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 color model, appears to have a...
New Monte Carlo Algorithms for Classical Spin Systems
We describe a number of recently developed cluster-flipping algorithms for the efficient stimulation of classical spin models near their critical temperature. These include the algorithms of Wolff,...
Diffusion Constant for the Repton Model of Gel Electrophoresis
The repton model is a simple model of the ``reptation'' motion by which DNA diffuses through a gel during electrophoresis. In this paper we show that the model can be mapped onto a system consisting...