Publications
2025
Scholarly publications
2024
Scholarly publications
2023
Scholarly publications
Liu, Z., Vatansever, E., Barkema, G. T., & Fytas, N. G. (2023). Critical dynamical behavior of the Ising model. Physical Review E, 108(3), 1-5. [DOI] [Repository]
Liu, Z., Panja, D., & Barkema, G. (2023). Domain growth in polycrystalline graphene. Nanomaterials, 13(24), 1-13. Article 3127. [DOI] [Repository]
2022
Scholarly publications
D'Ambrosio, F., Bodlaender, H. L., & Barkema, G. T. (2022). Dynamic sampling from a discrete probability distribution with a known distribution of rates. Computational Statistics, 37(3), 1203-1228. [DOI] [Repository]
Kole, A. H., Barkema, G. T., & Fritz, L. (2022). Comparison of cluster algorithms for the bond-diluted Ising model. Physical Review E, 105(1), 1-5. Article 015313. [DOI] [Repository]
Liu, Z., Panja, D., & Barkema, G. (2022). Structural dynamics of polycrystalline graphene. Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, 105(4), 1-7. Article 044116. [DOI] [Repository]
2021
Scholarly publications
Kole, A. H., Barkema, G. T., & Fritz, L. (2021). A comparison of cluster algorithms for the bond-diluted Ising model. (pp. 1-7). arXiv. [DOI] [Repository]
D'Ambrosio, F., Barkema, G., & Barkema, J. (2021). Efficient Structural Relaxation of Polycrystalline Graphene Models. Nanomaterials, 11(5), 1-11. Article 1242. [DOI] [Repository]
2020
Scholarly publications
Zhong, W., Barkema, G. T., & Panja, D. (2020). Super slowing down in the bond-diluted Ising model. Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, 102(2), Article 022132. [DOI] [Repository]
2019
Scholarly publications
D'Ambrosio, F., Barkema, G. T., & Juričić, V. (2019). Discontinuous evolution of the structure of stretching polycrystalline graphene. Physical Review B, 100(16), Article 161402. [DOI] [Repository]
Zhong, W., Panja, D., & Barkema, G. T. (2019). Approximate dynamical eigenmodes of the Ising model with local spin-exchange moves. Physical Review. E, Statistical, nonlinear, and soft matter physics, 100(1), Article 012132. [DOI] [Repository]
2018
Scholarly publications
Panja, D., Barkema, G. T., Zhong, W., & Ball, R. C. (2018). Critical dynamical exponent of the two-dimensional scalar ϕ4 model with local moves. Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, 98(6), Article 062128. [DOI] [Repository]
Schram, R. D., & Barkema, G. T. (2018). Simulation of ring polymer melts with GPU acceleration. Journal of Computational Physics, 363, 128-139. [DOI] [Repository]
Panja, D., Barkema, G. T., Zhong, W., & Ball, R. (2018). Generalized Langevin equation formulation for anomalous diffusion in the Ising model at the critical temperature. Physical Review. E, Statistical, nonlinear, and soft matter physics, 98(1), Article 012124. [DOI] [Repository]
2017
Scholarly publications
Schram, R. D., Barkema, G. T., Bisseling, R. H., & Clisby, N. (2017). Exact enumeration of self-avoiding walks on BCC and FCC lattices. Journal of Statistical Mechanics: Theory and Experiment, 2017(8), Article 083208. [DOI] [Repository]
Tompitak, M., Barkema, G. T., & Schiessel, H. (2017). Benchmarking and refining probability-based models for nucleosome-DNA interaction. BMC Bioinformatics, 18(1), Article 157. [DOI] [Repository]
Pool, A. J., Jain, S. K., & Barkema, G. T. (2017). Structural characterization of carbon nanotubes via the vibrational density of states. Carbon, 118, 261-267. [DOI] [Repository]
Barkema, G. T., & Van Leeuwen, J. M. J. (2017). Efficient simulation of semiflexible polymers with stiff bonds. Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, 95(1), Article 012502. [DOI] [Repository]
Jain, S. K., Juricic, V., & Barkema, G. T. (2017). Probing the shape of a graphene nanobubble. Physical Chemistry Chemical Physics, 19(11), 7465-7470. [DOI] [Repository]
2016
Scholarly publications
Tompitak, M., Schiessel, H., & Barkema, G. T. (2016). Force responses of strongly intrinsically curved DNA helices deviate from worm-like chain predictions. Europhysics Letters, 116(6), Article 68005. [DOI] [Repository]
Jain, S. K., Juricic, V., & Barkema, G. T. (2016). Structure of twisted and buckled bilayer graphene. 2D Materials, 4(1). [DOI]
Tompitak, M., Mossalam, B. E., Barkema, G. T., & Schiessel, H. (2016). Can Markov Chain Models Predict Nucleosome Positioning. Biophysical Journal, 110(3), 404a. [DOI]
Panja, D., Barkema, G. T., & Van Leeuwen, J. M. J. (2016). Dynamics of a double-stranded DNA segment in a shear flow. Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, 93(4), 1-10. Article 042501. [DOI] [Repository]
Keesman, R., Lamers, J., Duine, R. A., & Barkema, G. T. (2016). Finite-size scaling at infinite-order phase transitions. Journal of Statistical Mechanics: Theory and Experiment, 2016(9), Article 093201. [DOI]
Keesman, R., Raaijmakers, M., Baerends, A. E., Barkema, G. T., & Duine, R. A. (2016). Skyrmions in square-lattice antiferromagnets. Physical Review B - Condensed Matter and Materials Physics, 94(5), Article 054402. [DOI] [Repository]
Jain, S. K., Juricic, V., & Barkema, G. T. (2016). Boundaries determine the formation energies of lattice defects in two-dimensional buckled materials. Physical Review B-Condensed Matter, 94(2). [DOI] [Repository]
2015
Scholarly publications
Jain, S. K., Juricic, V., & Barkema, G. T. (2015). Probing Crystallinity of Graphene Samples via the Vibrational Density of States. Journal of Physical Chemistry Letters, 6(19), 3897-3902. [DOI] [Repository]
Pham, H. H., Barkema, G. T., & Wang, L.-W. (2015). DFT plus U studies of Cu doping and p-type compensation in crystalline and amorphous ZnS. Physical Chemistry Chemical Physics, 17(39), 26270-26276. [DOI] [Repository]
Walter, J. .-C., & Barkema, G. T. (2015). An introduction to Monte Carlo methods. Physica. A, theoretical and statistical physics, 418, 78-87. [DOI] [Repository]
Schram, R. D., & Barkema, G. T. (2015). Monte Carlo methods beyond detailed balance. Physica. A, theoretical and statistical physics, 418, 88-93. [DOI] [Repository]
Panja, D., Barkema, G. T., & Ball, R. C. (2015). Complex Interactions with the Surroundings Dictate a Tagged Chain's Dynamics in Unentangled Polymer Melts. Macromolecules, 48(5), 1442-1453. [DOI] [Repository]
Jain, S. K., Barkema, G. T., Mousseau, N., Fang, C.-M., & van Huis, M. A. (2015). Strong Long-Range Relaxations of Structural Defects in Graphene Simulated Using a New Semiempirical Potential. Journal of Physical Chemistry C, 119(17), 9646-9655. [DOI] [Repository]
Panja, D., Barkema, G. T., & van Leeuwen, J. M. J. (2015). Efficient simulation of semiflexible polymers. Physical Review. E, Statistical, nonlinear, and soft matter physics, 92(3), Article 032603. [DOI] [Repository]
Keesman, R., Leonov, A. O., van Dieten, P., Buhrandt, S., Barkema, G. T., Fritz, L., & Duine, R. A. (2015). Degeneracies and fluctuations of Neel skyrmions in confined geometries. Physical review. B, Condensed matter and materials physics, 92(13), Article 134405. [DOI] [Repository]
2014
Scholarly publications
Kandemir, E. B., Gonul, B., Barkema, G. T., Yu, K. M., Walukiewicz, W., & Wang, L. W. (2014). Modeling of the atomic structure and electronic properties of amorphous GaN1-xAsx. Computational Materials Science, 82, 100-106. [DOI]
Barkema, G. T., Ferrari, P. L., Lebowitz, J. L., & Spohn, H. (2014). Kardar-Parisi-Zhang universality class and the anchored Toom interface. Physical Review. E, Statistical, nonlinear, and soft matter physics, 90(4), Article 042116. [DOI] [Repository]
2013
Scholarly publications
Walter, J. .-C., Baiesi, M., Barkema, G. T., & Carlon, E. (2013). Unwinding Relaxation Dynamics of Polymers. Physical Review Letters, 110(6), Article 068301. [DOI]
Schram, R. D., & Barkema, G. T. (2013). Universality of the triplet contact process with diffusion. Journal of Statistical Mechanics: Theory and Experiment, Article 04020. [DOI]
Schram, R. D., Barkema, G. T., & Schiessel, H. (2013). On the stability of fractal globules. Journal of Chemical Physics, 138(22), Article 224901. [DOI]
Keesman, R., Barkema, G. T., & Panja, D. (2013). Dynamical eigenmodes of star and tadpole polymers. Journal of Statistical Mechanics: Theory and Experiment, 2013, P02021/1-P02021/21. Article P02021. [DOI] [Repository]
Keesman, R., Barkema, G. T., & Panja, D. (2013). Dynamical eigenmodes of a polymerized membrane. Journal of Statistical Mechanics: Theory and Experiment, 2013, P04009/1-P04009/17. Article P04009. [DOI] [Repository]
Schram, R. D., Barkema, G. T., & Bisseling, R. H. (2013). SAWdoubler: A program for counting self-avoiding walks. Computer Physics Communications, 184(3), 891-898. [DOI] [Repository]
Panja, D., Barkema, G. T., & Kolomeisky, A. B. (2013). Through the eye of the needle: recent advances in understanding biopolymer translocation. Journal of physics. Condensed matter, 25(41), 413101 /1-413101 /15. Article 413101. [DOI]
2012
Scholarly publications
Schram, R. D., & Barkema, G. T. (2012). Critical exponents of the pair contact process with diffusion. Journal of Statistical Mechanics: Theory and Experiment, 2012(3), Article P03009. [DOI]
Barkema, G. T., & van Leeuwen, J. M. J. (2012). A model for the dynamics of extensible semiflexible polymers. Journal of Statistical Mechanics: Theory and Experiment, 2012(12), Article P12019. [DOI] [Repository]
2011
Scholarly publications
Walter, J.-C., Barkema, G. T., & Carlon, E. (2011). The equilibrium winding angle of a polymer around a bar. Journal of Statistical Mechanics: Theory and Experiment, Article 10020. [DOI]
Safaverdi, S., Barkema, G. T., Kunnen, E., Urbanowicz, A. M., & Maes, C. (2011). Saturation of front propagation in a reaction diffusion process describing plasma damage in porous low-k materials. Physical review. B, Condensed matter and materials physics, 83(24), Article 245320. [DOI]
Kunnen, E., Barkema, G. T., Maes, C., Shamiryan, D., Urbanowicz, A., Struyf, H., & Baklanov, M. R. (2011). Integrated diffusion-recombination model for describing the logarithmic time dependence of plasma damage in porous low-k materials. Microelectronic Engineering, 88(5), 631-634. [DOI]
Singh, A., Mukherjee, A., Vermeulen, H. M., Barkema, G. T., & Puri, S. (2011). Control of structure formation in phase-separating systems. Journal of Chemical Physics, 134(044910). [DOI] [Repository]
Schram, R. D., Barkema, G. T., & Bisseling, R. H. (2011). Exact enumeration of self-avoiding walks. Journal of Statistical Mechanics: Theory and Experiment, 2011, Article 06019. [DOI] [Repository]
2010
Scholarly publications
Huisman, E. M., Heussinger, C., Storm, C., & Barkema, G. T. (2010). Semiflexible filamentous composites. Physical Review Letters, 105(11), 118101/1-118101/4. Article 118101. [DOI] [Repository]
Huisman, E. M., Storm, C., & Barkema, G. T. (2010). Frequency-dependent stiffening of semiflexible networks: a dynamical nonaffine to affine transition. Physical Review. E, Statistical, nonlinear, and soft matter physics, 82(6), 061902/1-061902/7. [DOI] [Repository]
Stuiver, A., & Barkema, G. T. (2010). Simulations of color development in tinted paints. Journal of Colloid and Interface Science, 344(2), 256-260. [DOI]
Panja, D., & Barkema, G. T. (2010). Simulations of two-dimensional unbiased polymer translocation using the bond fluctuation model. Journal of Chemical Physics, 132(1), 014902/1-014902/10. [DOI] [Repository]
Baiesi, M., Barkema, G. T., Carlon, E., & Panja, D. (2010). Unwinding dynamics of double-stranded polymers. Journal of Chemical Physics, 133(15), 154907/1-154907/4. [DOI] [Repository]
Kuipers, J., & Barkema, G. T. (2010). Limitations of a Fokker-Planck description of nucleation. Physical Review. E, Statistical, nonlinear, and soft matter physics, 82(1), 011128/1-011128/5. [DOI] [Repository]
Baiesi, M., Barkema, G. T., & Carlon, E. (2010). Elastic lattice polymers. Physical Review. E, Statistical, nonlinear, and soft matter physics, 81(6), 061801/1-061801/9. [DOI] [Repository]
Kuipers, J., & Barkema, G. T. (2010). Simulations of a non-Markovian description of nucleation. Journal of Chemical Physics, 132(18), 184109/1-184109/5. [DOI] [Repository]
2009
Scholarly publications
Panja, D., Barkema, G. T., & Kolomeisky, A. B. (2009). Non-equilibrium dynamics of single polymer adsorption to solid surfaces. Journal of Physics: Condensed Matter, 21(24), 242101/1-242101/6.
Kroll, K. M., Barkema, G. T., & Carlon, E. (2009). Linear model for fast background subtraction in oligonucleotide microarrays. Algorithms for Molecular Biology, 4:15, 1-15. [Repository]
Mulders, G. C. W. M., Barkema, G. T., & Carlon, E. (2009). Inverse Langmuir method for oligonucleotide microarray analysis. BMC Bioinformatics, 10:64, 1-8. [Repository]
Panja, D., & Barkema, G. T. (2009). Rouse modes of self-avoiding flexible polymers. Journal of Chemical Physics, 131(15), 154903/1-154903/7. [Repository]
Kuipers, J., Hoyng, P., Wicht, J., & Barkema, G. T. (2009). Analysis of the variability of the axial dipole moment of a numerical geodynamo model. Physics of the Earth and Planetary Interiors, 173(3-4), 228-232.
Vocks, H., Panja, D., & Barkema, G. T. (2009). Amplitude and frequency spectra of thermal fluctuations of a translocating RNA molecule. Journal of Physics: Condensed Matter, 21(37), 375105/-375105/7.
Panja, D., Barkema, G. T., & Ball, R. C. (2009). Reply to the comment on ‘Anomalous dynamics of unbiased polymer translocation through a narrow pore’ and other recent papers by D Panja, G Barkema and R Ball. Journal of Physics: Condensed Matter, 21, 098002/1-098002/3.
Kuipers, J., & Barkema, G. T. (2009). Non-Markovian dynamics of clusters during nucleation. Physical Review. E, Statistical, nonlinear, and soft matter physics, 79(6), 062101/1-062101/4. [Repository]
2008
Scholarly publications
Loois, C. C., Barkema, G. T., & de Morais Smith, C. (2008). Monte Carlo studies of extensions of the Blume-Emery-Griffiths model. Physical review. B, Condensed matter and materials physics, 78, Article 184519. [DOI]
Kuipers, J., & Barkema, G. T. (2008). Unbiased computation of transition times by pathway recombination. Journal of Chemical Physics, 128(174108), 1-5. [Repository]
Panja, D., Barkema, G. T., & Ball, R. C. (2008). Polymer translocation out of planar confinements. Journal of physics. Condensed matter, 20, 075101.
Panja, D., & Barkema, G. T. (2008). Passage Times for Polymer Translocation Pulled through a Narrow Pore. Biophysical Journal, 94(5), 1630-1637. [DOI]
Smallenburg, F., & Barkema, G. T. (2008). Universality class of the pair contact process with diffusion. Physical Review. E, Statistical, nonlinear, and soft matter physics, 78, 031129.
Barkema, G. T. (2008). Monte Carlo simulations of domain growth. In S. Puri, & V. Wadhawan (Eds.), Kinetics of phase transitions Academic Press.
Vocks, H., Panja, D., Barkema, G. T., & Ball, R. C. (2008). Pore-blockade times for field-driven polymer translocation. Journal of physics. Condensed matter, 20, 095224.
Huisman, E. M., Storm, C., & Barkema, G. T. (2008). Monte Carlo study of multiply crosslinked semiflexible polymer networks. Physical Review. E, Statistical, nonlinear, and soft matter physics, 78(051801), 1-11. [Repository]
Kroll, K. M., Barkema, G. T., & Carlon, E. (2008). Modeling background intensity in DNA microarrays. Physical Review. E, Statistical, nonlinear, and soft matter physics, 77(061915), 1-8. [Repository]
2007
Scholarly publications
Brendel, K., Kuipers, J., Barkema, G. T., & Hoyng, P. (2007). An analysis of the fluctuations of the geomagnetic dipole. Physics of the Earth and Planetary Interiors, 162(3-4), 249-255. [DOI]
Panja, D., Barkema, G. T., & Ball, R. C. (2007). Anomalous dynamics of unbiased polymer translocation through a narrow pore. Journal of physics. Condensed matter, 19(43), Article 432202. [DOI]
2006
Scholarly publications
Wolterink, J. K., Barkema, G. T., & Puri, S. (2006). Spinodal decomposition via surface diffusion in polymer mixtures. Physical Review. E, Statistical, nonlinear, and soft matter physics, 74(1), Article 011804. [DOI]
Wolterink, JK., Stuart, MAC., & Barkema, GT. (2006). Desorption of polymers: role of the stagnant layer. Molecular Physics, 104(4), 639-645. [DOI]
Heim, T., Wolterink, JK., Carlon, E., & Barkema, GT. (2006). Effective affinities in microarray data. Journal of physics. Condensed matter, 18(18), S525-S536. [DOI]
Carlon, E., Heim, T., Wolterink, J. K., & Barkema, G. T. (2006). Comment on "Solving the riddle of the bright mismatches: Labeling and effective binding in oligonucleotide arrays". Physical Review. E, Statistical, nonlinear, and soft matter physics, 73(6), Article 063901. [DOI]
Wolterink, JK., Barkema, GT., & Panja, D. (2006). Passage times for unbiased polymer translocation through a narrow pore. Physical Review Letters, 96(20), Article 208301. [DOI]
Chubynsky, M. V., Vocks, H., Barkema, G. T., & Mousseau, N. (2006). Exploiting memory in event-based simulations. Journal of Non-Crystalline Solids, 352(42-49), 4424-4429. [DOI]
Heim, T., Tranchevent, L. .-C., Carlon, E., & Barkema, G. T. (2006). Physical-chemistry-based analysis of Affymetrix microarray data. Journal of Physical Chemistry. B, 110(45), 22786-22795. [DOI]
Other output
Mousseau, N., Barkema, G. T., Chubynsky, M. V., Derreumaux, P., El-Mellouhi, F., & Vocks, H. (2006). PHYS 4-Applications of activated methods to proteins and materials science. Abstracts of Papers of the American Chemical Society, 232.
2005
Scholarly publications
Klein Wolterink, J., & Barkema, G. T. (2005). Polymer diffusion in a lattice polymer model with an intrinsic reptation mechanism. Molecular Physics, 103, 3083-3089.
van Gemmert, S., Barkema, G. T., & Puri, S. (2005). Phase Separation driven by surface diffusion:a Monte Carlo study. Physical Review. E, Statistical, nonlinear, and soft matter physics, 72(046131). [Repository]
Brendel, K., Barkema, G. T., & van Beijeren, H. (2005). Nucleation times in the 2D Ising model. Physical Review. E, Statistical, nonlinear, and soft matter physics, 71(031601). [Repository]
Vocks, H., Barkema, G. T., Chubynsky, M. V., & Mousseau, N. (2005). Activated sampling in complex materials at finite temperature: The properly obeying probability activation-relaxation technique. Journal of Chemical Physics, 123(244707).
Klein Wolterink, J., Barkema, G. T., & Cohen Stuart, M. A. (2005). Diffusion and exchange of adsorbed polymers studied by Monte Carlo simulations. Macromolecules, 38, 2009-2014.
Brendel, K., Barkema, G. T., & van Beijeren, H. (2005). Nucleation time distribution in the two-dimensional Ising model with Spin-flip dynamics. In Unsloved problems of Noise
Professional publications
Barkema, G. T., & Arts, T. (2005). Graduate Research Examination als toelatingscriterium masters. Nederlands Tijdschrift voor Natuurkunde, 71(312).
2004
Scholarly publications
Mousseau, N., & Barkema, G. T. (2004). Binary continuous random networks. Journal of physics. Condensed matter, 16, S5183-S5190.
2003
Scholarly publications
Barkema, G. T., & Carlon, E. (2003). Universality in the pair contact process with diffusion. Physical Review. E, Statistical, nonlinear, and soft matter physics, E68(036113). [Repository]
Brendel, K., Barkema, G. T., & van Beijeren, H. (2003). Magnetisation reversal time in the 2D Ising model. Physical Review. E, Statistical, nonlinear, and soft matter physics, 67(026119). [Repository]
van Heukelum, A., & Barkema, G. T. (2003). Reaching large lengths and long times in polymer dynamics simulations. Journal of Chemical Physics, 119(15), 8197-8202.
Stijnman, M. A., Bisseling, R. H., & Barkema, G. T. (2003). Partitioning 3D space for parallel many-particle simulations. Computer Physics Communications, 149(3), 121-134. [DOI] [Repository]
van Heukelum, A., Barkema, G. T., Edelman, M. W., van der Linden, E., & de Hoog, E. H. A. (2003). Fractionation in aphase-separated polydisperse polymer mixture. Macromolecules, 36(17), 66662-6667.
Vink, R. L. C., & Barkema, G. T. (2003). Large well-relaxed models of vitreous silica, coordination numbers and entropy. Physical review. B, Condensed matter and materials physics, B67(245201). [Repository]
2002
Scholarly publications
Vink, R. L. C., & Barkema, G. T. (2002). Configutational entropy of network-forming materials. Physical Review Letters, 89(7), 1-4. Article 076405. [Repository]
Mousseau, N., Barkema, G. T., & Nakhmanson, S. M. (2002). Recent developments in the study of continuous random networks. Philosophical magazine B, 82, 171-183.
Vink, R. L. C., Barkema, G. T., van Walree, C. A., & Jenneskens, L. W. (2002). Simulation of polysilane and polysilyne formation and structure. Journal of Chemical Physics, 116, 854-859.
Barkema, G. T., & Biswas, P. (2002). Tight-binding calculations on large amorphous silicon samples. In M. Popescu (Ed.), Physics and applications of disordered materials (pp. 53-64). INOE.
van Heukelum, A., Barkema, G. T., & Bisseling, R. H. (2002). DNA electrophoresis studied with the cage model. Journal of Computational Physics, 180(1), 313-326. [DOI] [Repository]
van Heukelum, A., & Barkema, G. T. (2002). Lattice models of DNA electrophoresis. Electrophoresis, 23, 2562-2568.
2001
Scholarly publications
Vink, R. L. C., Barkema, G. T., Stijnman, M. A., & Bisseling, R. H. (2001). Device-size atomistic models of amorphous silicon. Physical review. B, Condensed matter and materials physics, 64, Article 245214. [DOI] [Repository]
Vink, R. L. C., Barkema, G. T., van der Weg, W., & Mousseau, N. (2001). Fitting the stillinger-weber potential to amorphous silicon. Journal of Non-Crystalline Solids, 282, 248-255.
Mousseau, N., & Barkema, G. T. (2001). Fast bond-transposition algorithms for generating covalent amorphous structures. Current opinion in solid state & materials science, 5, 497-502.
Vink, R. L. C., Barkema, G. T., & van der Weg, W. (2001). Raman spectra and structure of amorphous silicon. Physical review. B, Condensed matter and materials physics, 63, 115210. [Repository]
Mousseau, N., Derreumaux, P., Barkema, G. T., & Malek, R. (2001). Sampling activated mechanisms in proteins with the activation-relaxation technique. Journal of Molecular Graphics and Modelling, 19, 78-86.
Barkema, G. T., & Mousseau, N. (2001). The activation-relaxation technique: an efficient algorithm for sampling energy landscapes. Computational Materials Science, 20, 285-292.
Biswas, P., Barkema, G. T., Mousseau, N., & van der Weg, W. (2001). Efficient Monte Carlo structural sampling of complex materials with tight-binding interactions. Europhysics Letters, 56, 427-433.
Bikker, R. P., Barkema, G. T., & van Beijeren, H. (2001). Equilibrium crystal shapes in the Potts model. Physical Review. E, Statistical, nonlinear, and soft matter physics, 64, 16125. [Repository]
Barkema, G. T., Biswas, P., & van Beijeren, H. (2001). Diffusion with random distribution of static traps. Physical Review Letters, 87(17), 1-4. Article 170601. [Repository]
Barkema, G. T., Mousseau, N., Vink, R. L. C., & Biswas, P. (2001). Basic mechanisms of structural relaxation and diffusion in amorphous silicon. Materials Research Society symposia proceedings, 664, A28.1.1.
Malek, R., Mousseau, N., & Barkema, G. T. (2001). Characterization of the activation-relaxation technique: recent results on models of amorphous silicon. Materials Research Society symposia proceedings, 677.
Nakhmanson, S. M., Voyles, P. M., Mousseau, N., Barkema, G. T., & Drabold, D. A. (2001). Realistic models of paracrystalline silicon. Physical review. B, Condensed matter and materials physics, 63, 235207. [Repository]
Nakhmanson, S. M., Mousseau, N., Barkema, G. T., Voyles, P. M., & Drabold, D. A. (2001). Models of paracrystalline silicon with a defect-free bandgap. International journal of modern physics B., 15, 3253-3257.
Schütz, G. M., Ispolatov, I., Barkema, G. T., & Widom, B. (2001). Symmetry effects and equivalences in lattice models of hydrophobic interaction. Physica. A, theoretical and statistical physics, 291, 24-38.
2000
Scholarly publications
Mousseau, N., & Barkema, G. T. (2000). Activated mechanisms in amorphous silicon: an activation-relaxation-technique study. Physical review. B, Condensed matter and materials physics. [Repository]
Barkema, G. T., & Mousseau, N. (2000). High-quality continuous random networks. Physical review. B, Condensed matter and materials physics. [Repository]
Mousseau, N., Barkema, G. T., & de Leeuw, S. W. (2000). Elementary mechanisms governing the dynamics of silica. Journal of Chemical Physics.
Barkema, G. T., & Widom, B. (2000). Model of hydrophobic attraction in two and three dimensions. Journal of Chemical Physics.
Delfino, G., Barkema, G. T., & Cardy, J. (2000). Susceptibility amplitude ratios in the two-dimensional Potts model and percolation. Nuclear physics. Series B.
Bikker, R. P., & Barkema, G. T. (2000). Cluster algorithm for Potts models with fixed spin densities. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, 62(4), 5830-5834. [DOI] [Repository]
1999
Scholarly publications
Zotov, N., Marinov, M., Mousseau, N., & Barkema, G. T. (1999). Dependence of the vibrational spectra of amorphous silicon on the defect concentration and ring distribution. Journal of physics. Condensed matter, 11, 9647-9658.
Mousseau, N., & Barkema, G. T. (1999). Exploring high-dimensional energy landscapes. Computing in science & engineering, 1, 74-80.
Newman, M. E. J., & Barkema, G. T. (1999). Monte Carlo methods in statistical physics. Oxford University Press.
1998
Scholarly publications
Mousseau, N., & Barkema, G. T. (1998). Traveling through potential energy surfaces of disordered materials: the activation-relaxation technique. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, 57(2), 2419-2424. [DOI] [Repository]
Barkema, G. T., & Mousseau, N. (1998). Exploring structural mechanisms in disordered materials using the activation-relaxation technique. Computer Physics Communications, 121/122, 206-209.
Barkema, G. T., Bastolla, U., & Grassberger, P. (1998). Two-dimensional oriented self-avoiding walks with parallel contacts. Journal of Statistical Physics, 90, 1311-1324.
Barkema, G. T., & Newman, M. E. J. (1998). Monte Carlo simulation of ice models. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, 57(1), 1155-1166. [DOI] [Repository]
Barkema, G. T., & Krenzlin, H. M. (1998). Long-time dynamics of de Gennis' model for reptation. Journal of Chemical Physics, 109, 6486-6489.
Barkema, G. T., & Baumgärtner, A. (1998). Reptation of star polymers in a network: Monte Carlo results of diffusion coefficients. Macromolecules, 32, 911-914.
Barkema, G. T., & Mousseau, N. (1998). Identification of relaxation and diffusion mechanisms in amorphous silicon. Physical Review Letters, 81(9), 1865-1868. [Repository]
Barkema, G. T., & Newman, M. E. J. (1998). New Monte Carlo algorithms for classical spin systems. In D. Ferguson, J. I. Siepmann, & D. G. Truhlar (Eds.), Monte Carlo Methods in Chemical Physics (pp. 483-517). Wiley.
Barkema, G. T., & Mousseau, N. (1998). The activation-relaxation technique: an efficient algorithm for sampling energy landscapes. In Proc. VIIIth workshop on computational materials science
1997
Scholarly publications
Newman, M. E. J., & Barkema, G. T. (1997). Diffusion constant for the repton model of electrophoresis. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, 56(3), 3468-3473. [DOI] [Repository]
Barkema, G. T., & Newman, M. E. J. (1997). The repton model for gel electrophoresis. Physica. A, theoretical and statistical physics, 244, 25.
Schmicker, D., Hibma, T., Edwards, K. A., Howes, P. B., MacDonald, J. E., James, M. A., Breeman, M., & Barkema, G. T. (1997). Low-temperature growth of thin Pb layers and the quantum size effect. Journal of Physics A-Mathematical and General, 9, 969.
1996
Scholarly publications
MacFarland, T., Barkema, G. T., & Marko, J. F. (1996). Equilibrium Phase Transitions in a Porous Medium. Physical review. B, condensed matter, 53, 1-11. Article 148. [DOI] [Repository]
Barkema, G. T., & Schütz, G. M. (1996). Magnetophoresis of Tagged Polymers. Europhysics Letters, 35, 139.
Barkema, G. T., & Mousseau, N. (1996). Event-based relaxation of continuous disordered systems. Physical Review Letters, 77(21), 4358-4361. [Repository]
Barkema, G. T., & Flesia, S. (1996). Two-dimensional Oriented Self-avoiding Walks with Parallel Contacts. Journal of Statistical Physics, 85, 363.
Breeman, M., Barkema, G. T., Langelaar, M. H., & Boerma, D. O. (1996). Computer simulation of metal-on-metal epitaxy. Thin Solid Films, 272, 195.
Barkema, G. T., Caron, C., & Marko, J. F. (1996). Scaling Properties of DC Gel Electrophoresis of DNA. Biopolymers, 38, 665.
Newman, M. E. J., & Barkema, G. T. (1996). Monte Carlo Study of the Random-Field Ising Model. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, 53(1), 393-404. [DOI] [Repository]
Barkema, G. T., Howard, M. J., & Cardy, J. (1996). Reaction-diffusion front for A+B→∅ in one dimension. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, 53(3), 2017-2020. [DOI] [Repository]
Barkema, G. T., Speer, E., & Lebowitz, J. L. (1996). Numerical study of a one-dimensional interface model. Journal of Physics A-Mathematical and General, 29, 7475.
Howard, M. J., & Barkema, G. T. (1996). Shear flows and segregation in the reaction A+B→∅. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, 53(6), 5949-5956. [DOI] [Repository]
Barkema, G. T., & McCabe, J. (1996). Monte Carlo Simulations of Conformal Theory Predictions for the 3-state Potts Model. Journal of Statistical Physics, 84, 1067.
1994
Scholarly publications
MACFARLAND, T., & Barkema, G. T. (1994). PARALLEL SIMULATION OF THE ISING-MODEL. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, 50(2), 1623-1628.
MARKO, JF., WIDOM, B., & Barkema, G. T. (1994). ELECTROPHORESIS OF CHARGED POLYMERS - SIMULATION AND SCALING IN A LATTICE MODEL OF REPTATION. Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics, 49(6), 5303-5309.
BREEMAN, M., BOERMA, DO., & Barkema, G. T. (1994). ATOMISTIC CALCULATIONS ON LOW-TEMPERATURE LAYER-BY-LAYER GROWTH. Surface Science, 307, 526-530.
LEE, C., BREEMAN, M., PASQUARELLO, A., CAR, R., & Barkema, G. T. (1994). DIFFUSION MECHANISM OF CU ADATOMS ON A CU(001) SURFACE. Surface Science, 306(3), L575-L578.
BIHAM, O., BREEMAN, M., BOERMA, DO., VIDALI, G., & Barkema, G. T. (1994). CHARACTERIZATION OF SUBMONOLAYER GROWTH OF CU ISLANDS ON CU(001). Surface Science, 306(3), L569-L574.
BREEMAN, M., BOERMA, DO., & Barkema, G. T. (1994). ONE-DIMENSIONAL ORDERING OF IN ATOMS IN A CU(100) SURFACE. Physical review. B, condensed matter, 49(7), 4871-4880.
BREEMAN, M., BOERMA, DO., & Barkema, G. T. (1994). ANNEALING OF CU-ADATOM CONFIGURATIONS ON CU(100). Surface Science, 303(1-2), 25-35.
BREEMAN, M., BOERMA, DO., & Barkema, G. T. (1994). ATOMISTIC CALCULATIONS ON THE SURFACTANT ROLE OF INDIUM IN THE HOMOEPITAXIAL GROWTH OF CU ON CU(100). In SM. Yalisove, CV. Thompson, & DJ. Eaglesham (Eds.), MECHANISMS OF THIN FILM EVOLUTION (pp. 329-334). (MATERIALS RESEARCH SOCIETY SYMPOSIUM PROCEEDINGS; Vol. 317). MATERIALS RESEARCH SOC.
MARKO, JF., DEBOER, J., & Barkema, G. T. (1994). TRANSIENT AND ASYMPTOTIC DOMAIN GROWTH IN THE 3D ISING-MODEL WITH CONSERVED SPIN. Europhysics Letters, 26(9), 653-658.
1993
Scholarly publications
NEWMAN, MEJ., ROBERTS, BW., SETHNA, JP., & Barkema, G. T. (1993). REAL-SPACE RENORMALIZATION-GROUP FOR THE RANDOM-FIELD ISING-MODEL. Physical review. B, condensed matter, 48(22), 16533-16538.
MARKO, JF., & Barkema, G. T. (1993). ACCELERATING DIFFUSIVE NONEQUILIBRIUM PROCESSES IN DISCRETE SPIN SYSTEMS. Physical Review Letters, 71(13), 2070-2073.
ANDREE, HMA., TAAL, A., & Barkema, G. T. (1993). THE PATCH ALGORITHM - FAST DESIGN OF BINARY FEEDFORWARD NEURAL NETWORKS. Network-Computation in Neural Systems, 4(3), 393-407.
DEBOER, J., & Barkema, G. T. (1993). PROPERTIES OF A STATISTICAL-MODEL OF ICE AT LOW-TEMPERATURES. Journal of Chemical Physics, 99(3), 2059-2067.
ANDREE, HMA., BARKEMA, GT., LOURENS, W., TAAL, A., VERMEULEN, JC., & Barkema, G. T. (1993). A COMPARISON STUDY OF BINARY FEEDFORWARD NEURAL NETWORKS AND DIGITAL CIRCUITS. Neural Networks, 6(6), 785-790.
1992
Scholarly publications
KEIBEK, SAJ., ANDREE, HMA., SAVENIJE, MHF., TAAL, A., & Barkema, G. T. (1992). A FAST PARTITIONING ALGORITHM AND A COMPARISON OF BINARY FEEDFORWARD NEURAL NETWORKS. Europhysics Letters, 18(6), 555-559.