Lijst van publicaties

Jaarlijks wordt aan gebruikers gevraagd wat ze aan wetenschappelijke publicaties hebben geproduceerd, waarbij de faciliteiten van het HPC/V een belangrijke rol hebben gespeeld. Zoals u ziet zijn de onderwerpen erg divers, variërend van quantum mechanica, moleculair dynamica, computational fluid dynamics, monto carlo berekeningen, handschriftherkenning, sterrenkunde, genetica, biofysica, farmacie, tot bedrijfskunde.

2013

MJP Simons, W Koch, S Verhulst: "Dietary restriction of rodents decreases aging rate without affecting initial mortality rate‐a meta‐ analysis", Aging Cell 2013

T. Deckers and C. Hanck: "Variable Selection in Cross-Section Regressions: Comparisons and Extensions", OBES 0305-9049 (2013).

Van Heerde, H.J., Gijenberg, M.J., Dekimpe, M.G., & Steenkamp, J-B.E.M.: "Price and Advertising Effectiveness over the Business Cycle", Journal of Marketing Research, 50(2), 177-193 (2013).

T.A. Wassenaar, H.I. Ingólfsson, M. Prieß, S.J. Marrink, and L.V. Schäfer. Mixing MARTINI: "Electrostatic Coupling in Hybrid Atomistic–Coarse-Grained Biomolecular Simulations", J. Phys. Chem. B, 117:3516:3530

C.A. López, Z. Sovova, F.J. van Eerden, A.H. de Vries, S.J. Marrink. Martini force field parameters for glycolipids", JCTC, 9:1694–1708, 2013

C. Arnarez, J.P. Mazat, J. Elezgaray, S.J. Marrink, X. Periole. Evidence for cardiolipin binding sites on the membrane-exposed surface of the cytochrome bc1", JACS, 135:3112–20, 2013

C. Arnarez, S.J. Marrink, X. Periole. Identification of cardiolipin binding sites on cytochrome c oxidase at the entrance of proton channels", Sci. Rep., 3:1263, 2013

M. Hu, D.H. de Jong, S.J. Marrink, M. Deserno. Gaussian curvature elasticity determined from global shape transformations and local stress distributions: A comparative study using the MARTINI model", Farad. Discuss., 161:365-382, 2013

D.H. de Jong, C.A. Lopez, S.J. Marrink. Molecular view on protein sorting into liquid-ordered membrane domains mediated by gangliosides and lipid anchors", Farad. Discuss., 161:347-363, 2013

D.H. de Jong, G. Singh, W.F.D. Bennett, C. Arnarez, T.A. Wassenaar, L.V. Schäfer, X. Periole, D.P. Tieleman, S.J. Marrink. Improved parameters for the Martini coarse-grained protein force field", JCTC, 9:687–697, 2013

2012

R.W.A. Havenith, H.D. de Gier, R. Broer: "Explorative computational study of the singlet fission process", Mol. Phys. 110 (2012), 2445-2454.

R.W.A. Havenith, F. De Proft, L.W. Jenneskens, P.W. Fowler: "Relativistic ring currents in metallabenzenes: An analysis in terms of contributions of localised orbitals", Phys. Chem. Chem. Phys., 14 (2012) 9897- 9905.

Z. Rashid, J.H. van Lenthe, R.W.A. Havenith: "Resonance and aromaticity: An ab initio valence bond approach", J. Phys. Chem. A, 116 (2012) 4778-4788.

J. Robertus, S.F. Reker, T.C. Pijper, A. Deuzeman, W.R. Browne, B.L. Feringa: "Kinetic analysis of the thermal isomerisation pathways in an asymmetric double azobenzene switch", Phys. Chem. Chem. Phys., 14, 4374-4382 (2012)

Arramel, T.C. Pijper, T. Kudernac, N. Katsonis, M. van der Maas, B.L. Feringa, B.J. van Wees: "Electronic properties of individual diarylethene molecules studied using scanning tunneling spectroscopy" J. Appl. Phys. 111, 083716 (2012)

C. Liang and T.L.C. Jansen: "An efficient N3-scaling propagation scheme for simulating two-dimensional infrared and visible spectra" , J. Chem. Theory Comput. 8:1706-1713 (2012)

MJP Simons, M Briga, E Koetsier, R Folkertsma, MD Wubs, C Dijkstra, S Verhulst: "Bill Redness Is Positively Associated with Reproduction and Survival in Male and Female Zebra Finches", PloS one 7 (7), e40721 2012

MJP Simons, AA Cohen, S Verhulst: "What Does Carotenoid-Dependent Coloration Tell? Plasma Carotenoid Level Signals Immunocompetence and Oxidative Stress State in Birds–A Meta-Analysis", PLoS ONE 7 (8), e43088 2012

C. Hanck and C. Bayer: "Combining Non-Contegration Tests", Journal of Time Series analysis.

C. Hank and T. Deckers: "Multiple Testing for Output Convergence", Macro-economic Dynamics.

N. Goga, A.J. Rzepiela, A.H. de Vries, S.J. Marrink, H.J.C. Berendsen: "Efficient algorithms for Langevin and DPD dynamics", JCTC, 8:3637-49, 201

C.A. Lopez, A.H. de Vries, S.J. Marrink: "Amylose folding under the influence of lipids", Carbohydr. Res., 364:1–7, 2012

E. Deplazes, M. Louhivuori, D. Jayatilaka, S.J. Marrink, B. Corry: "Structural investigation of MscL gating using experimental data and coarse grained MD simulations", PLoS Comp. Biol., 8:e1002683, 2012

N. Goga, A. Rzepiela, M. N. Melo, A.H. de Vries, A. Hadar, A.J. Markvoort, S. Nedea, H.J.C. Berendsen: "Methods for multiscale modeling of membranes", Chapter in Advances in Planar Lipid Bilayers and Liposomes, 15:139-170, 2012

H.J. Risselada, G. Marelli, M. Fuhrmans, Y.G. Smirnova, H. Grubmüller, S.J. Marrink, M. Muller: "Line-tension controlled mechanism for influenza fusion", PLoS ONE, 7:e38302, 2012

X. Periole, A.M. Knepp, T.P. Sakmar, S.J. Marrink, T. Huber: "Structural determinants of the supra-molecular organization of G protein-coupled receptors in bilayers", JACS, 134:10959–65, 2012

T.A. Wassenaar, S. de Vries, A.M.J.J. Bonvin, H. Bekker: "SQUEEZE-E: The optimal solution for molecular simulations with periodic boundary conditions", JCTC, 8:3618–27, 2012

D.H. de Jong, X. Periole, S.J. Marrink: "Dimerization of amino acid side chains: lessons from the comparison of different forcefields", JCTC, 8:1003–14, 2012

J. Domanski, S.J. Marrink, L.V. Schaefer: "Transmembrane helices can induce domain formation in crowded model biomembranes", BBA Biomembr., 1818:984-994, 2012

A.M. Knepp, X. Periole, S.J. Marrink, T.P. Sakmar, T. Huber: "Rhodopsin forms a dimer with cytoplasmic helix 8 contacts in native membranes", Biochemistry, 51:1819–21, 2012

M. Fuhrmans, S.J. Marrink: "Molecular view of the role of fusion peptides in promoting positive membrane curvature", JACS, 134:1543–52, 2012

M. Bulacu, X. Periole, S.J. Marrink: "In-silico design of robust bolalipid membranes", Biomacromol., 13:196–205, 2012

2011

R. Baron et al.: "Computing K and D meson masses with N_f = 2+1+1 twisted mass lattice QCD", Comp. Phys. Comm. 182 (2011), pp. 299-316

C. Olbrich, T.L.C. Jansen, J. Liebers, M. Aghtar, J. Strümpfer, K. Schulten, J. Knoester, and U. Kleinekathöfer: "From atomistic modeling to exciton dynamics and two-dimensional spectra of the FMO light-harvesting complex", J. Phys. Chem. B 115:8609-8621 (2011) DOI: 10.1021/jp202619a

I. Ahmad, F. Suits, B. Hoekman, M.A. Swertz, H. Byelas, M. Dijkstra, R. Hooft, D. Katsubo, B. van Breukelen, R. Bischoff, P. Horvatovich: " A high-throughput processing service for retention time alignment of complex proteomics and metabolomics LC-MS data", Bioinformatics 15 (2011) p.1176-1178 »

K.D. de Vries, A.M. van den Berg, O. Scholten, "K. Werner: Coherent Cherenkov Radiation from Cosmic-Ray-Induced Air Showers.", Phys. Rev. Lett. 107(2011)061101

Ćurčić-Blake,B., Swart,M., Ter Horst, G.J., Langers,D.R., Kema,I. and Aleman,A. (2012) Variation of the gene coding for DARPP-32 (PPP1R1B) and brain activation during associative emotional learning. Neuroimage 16;59(2):1540-50

Alonso, D., Bouma, M.J. and Pascual M.: "Epidemic malaria and warmer temperatures in recent decades in an East African highland", Proceedings of the Royal Society B: Biological Sciences, 278 (1712) , pp. 1661-1669 »

C. Hanck and M. Demetrescu: "Unit Root Testing in Heteroskedastic Panels using the Cauchy Estimator". In: Journal of Business & Economic Statistics 30, pp. 256-264

C. Hanck and M. Demetrescu: "A Simple Nonstationary-Volatility Robust Panel Unit Root Test". In: Economics Letters 117, pp. 10-13

Hocuk, S. and Spaans, M.: "Star formation near an obscured AGN. Variations in the initial mass function", AAP 536, dec 2011

Hocuk, S.: "The Origin of Stars: Tales from the Unexpected in Extreme Environments", Phd thesis, nov 2011 »

C. E. Jimenez-Tejero, A. Ramos, L. Tolos and I. Vidana: "Open charm meson in nuclear matter at finit temperature beyond the zero range approximation", Phys. Rev. C 84 (2011) 015208, 1102.4786

E.R.van der Graaf, J. Limburg, R.L. Koomans, M. Thijs: "Monte Carlo based calibration of scintillation detectors for laboratory and in situ gamma ray measurements.", Journal of Environmental Radioactivity 102, 270-282, 2011.

T.Fievez, F. de Proft, P. Geerlings, B.M. Weckhuysen, R.W.A. Havenith: "Conceptual chemistry approach towards the support effect in supported vanadium oxides: Valence bond calculations on the ionicity of vanadium catalysts", Catal. Today 177, 3-11 2011

L.van het Goor, P.T. van Duijnen, C. Koper, L.W. Jenneskens, R.W.A. Havenith, F. Hartl: "p-dimerization of pleiadiene radical cations at low temperatures revealed by uv–vis spectroelectrochemistry and quantum theory", J.Solid State Electrochem. 15, 2011 pp. 2107-2117.

M. Velinova, D. Sengupta, A.V. Tadjer, S.J. Marrink: "Sphere-to-rod transitions of nonionic surfactant micelles in aqueous solution modeled by molecular dynamic simulations", Langmuir, 27:14071–77, 2011.

M. Fuhrmans, S.J. Marrink: "A tool for the morphological analysis of mixtures of lipids and water in computer simulations", J. Mol. Model, 17:1755-66, 2011

J. Sorensen, X. Periole, K.K. Skeby, S.J. Marrink, B. Schiott: "Protofibrillar assembly towards the formation of amyloid fibrils", J. Phys. Chem. Lett., 2:2385-90, 2011

M. Klacsova, M. Bulacu, N. Kucerka, D. Uhrikova, J. Teixeira, S.J. Marrink, P. Balgavy: "The effect of aliphatic alcohols on fluid bilayers in unilamellar DOPC vesicles - a small-angle neutron scattering and molecular dynamics study", BBA Biomembr., 808:2136-46, 2011

A.J. Rzepiela, M. Louhivuori, C. Peter and S.J. Marrink: "Hybrid Simulations: Combining Atomistic and Coarse-Grained Force Fields using Virtual Sites", PCCP, 13:10437-48, 2011

J. Mika, G. Moiset, A.D. Cirac, L. Feliu, E. Bardaji, M. Planas, D. Sengupta, S.J. Marrink, B. Poolman: "Structural basis for the enhanced activity of cyclic antimicrobial peptides: the case of BPC194", BBA Biomembranes, 1808:2197–2205, 2011

A.D. Cirac, G. Moiset, J.T. Mika, A. Kocer, P. Salvador, B. Poolman, S.J. Marrink, D. Sengupta: "The molecular basis for antimicrobial activity of pore-forming cyclic peptides", Biophys. J., 100:2422-31, 2011

D.H. de Jong, L.V. Schäfer, A.H. de Vries, S.J. Marrink, H.J.C. Berendsen, H. Grubmüller: "Determining Equilibrium Constants for Dimerization Reactions from Molecular Dynamics Simulations", JCC, 32:1919-28, 2011

O.H.S. Ollila, M. Louhivuori, S.J. Marrink, I. Vattulainen: "Protein shape change has a major effect on the gating energy of a mechanosensitive channel", Biophys. J., 100:1651-59, 2011

C.A. López, A.H. de Vries, S.J. Marrink: "Molecular Mechanism of Cyclodextrin Mediated Cholesterol Extraction", PLOS Comp. Biol., 7:e1002020, 2011

Y. Xue, M. O'Mara, P. Surawski, M. Trau, A.E. Mark: "The effect of polyethylene glycol (PEG) spacers on the conformational properties of small peptides: a molecular dynamics study", Langmuir., 27:296-303, 2011

L.V. Schafer, D.H. de Jong, A. Holt, A.J. Rzepiela, A.H. de Vries, B. Poolman, J.A. Killian, S.J. Marrink: "Lipid packing drives the segregation of transmembrane helices into disordered lipid domains in model biomembranes", PNAS 108:1343-48, 2011

2010

Mobach, M.P.: "Virtual Worlds for Organizational Spaces.", Marrewijk, A.H. van, Yanow, D. (eds.) Organizational Spaces. Rematerializing the Workaday World. Cheltenham: Edward Elgar.

L.Nanetti, R. Renken, R. Kortekaas, I. Zijdewind, N. Meulman, A. Kuiper, I. den Daas, P. de Boer, G.J. ter Horst: "fMRImeasurable effects of Benzodiazepine on the cognitive brain: preliminary results on Placebo vs Blank" International Society for Magnetic Resonance in Medicine, Benelux chapter »

L. Nanetti, R. Renken, R. Kortekaas, N. Meulman, I. Zijdewind, A. J. Kuiper, P. de Boer, I. den Daas, J. Wemer, G.J. ter Horst: "Benzodiazepineinduced fMRI measurable effects on the working memory circuit: the 2back task", OHBM »

Ittoo, A., Maruster, L., Wortmann, J.C., Bouma, G. (2010), “Textractor: A Framework for Extracting Relevant Domain Concepts from Irregular Corporate Textual Datasets”. (Book Chapter) In Lecture Notes in Business Information Processing (LNBIP), Volume 47, by Springer.

Ittoo, A., Bouma, G., Maruster, L., Wortmann J.C. (2010): “Extracting Meronymy Relations from Domain-Specific Textual Corporate Databases”. Awarded Reind van de Riet prize for best paper in Natural Language Processing in Information Systems(Book Chapter) In Lecture Notes in Computer Science (LNCS), Volume 6177, Springer.

Ittoo, A., Bouma, G. (2010) : “On learning Subtypes of the Part-Whole Relation: Do Not Mix Your Seeds” Presented at the 48th Annual Meeting of the Association for Computational Linguistics (ACL 2010),Upssala, Sweden.

F. Jin, H. De Raedt, S. Yuan, M.I. Katsnelson, S. Miyashita, and K. Michielsen: "Approach to equilbrium in nano-scale systems at finite temperature".  J. Phys. Soc. Jpn. 79, 124005 (2010)

S. Yuan, H. De Raedt, M.I. Katsnelson: "Electronic Transport in Disordered Bilayer and Trilayer Graphene",  Phys. Rev. B 82, 235409 (2010)

S. Yuan, H. De Raedt, and M.I. Katsnelson: "Modeling electronic structure and transport properties of graphene with resonant scattering centers", Phys. Rev. B 82, 115448 (2010)

F. Jin, S. Yuan, H. De Raedt, and K. Michielsen: "Particle-only model of two-beam interference and double-slit experiments with single photons ", J. Phys. Soc. Jpn. 79, 074401 (2010)

F. Jin, H. De Raedt, and K. Michielsen: "Event-by-event simulation of the Hanbury Brown-Twiss experiment with coherent light", Commun. Comput. Phys. 7, 813-830 (2010)

F. Jin, S. Zhao, S. Yuan, H. De Raedt, and K. Michielsen: "Event-by-event simulation of quantum eraser experiments with single photons", J. Comp. Theor. Nanosci. 7, 1771-1782 (2010)

K. Michielsen, H. De Raedt, and D. Stavenga: "Reflectivity of the gyroid biophotonic crystals in the ventral wing scales of the Green Hairstreak butterfly, Callophrys rubi", J. R. Soc. Lond. Interface 7, 765 (2010)

K. Michielsen, S. Yuan, S. Zhao, F. Jin, H. De Raedt: "Coexistence of full which-path information and interference in Wheelers delayed choice experiment with photons ", Physica E 42, 348 - 353 (2010)

H. De Raedt, S. Zhao, S. Yuan, F. Jin, K. Michielsen, and S. Miyashita: "Event-by-event simulation of quantum phenomena", Physica E 42, 298 - 302 (2010)

K. Michielsen and H. De Raedt: "Quantum interference with macroscopic objects", in Quantum Theory: Reconsiderations of Foundations - 5, edited by A. Khrennikov (AIP Conference Proceedings, Melville and New York, 2010), vol. 1232, p. 27 - 32.

F. Jin, H. De Raedt, and K. Michielsen: "Particle-based simulation approach for single-particle interference experiments: Application to double-slit experiments", in Quantum Theory: Reconsiderations of Foundations - 5, edited by A. Khrennikov (AIP Conference Proceedings, Melville and New York, 2010), vol. 1232, p. 93 - 104.

S. Zhao, S. Yuan, H. De Raedt and K. Michielsen: "Event-by-event simulation of Wheelers delayed-choice experiment", in "Computer Simulation Studies in Condensed-Matter Physics XXI", Landau D.P., Lewis S.P., Schuettler H.-B. (Eds.), Physics Procedia 6, 27 (2010)

S.Hocuk and M.Spaans: "The thermodynamics of molecular cloud fragmentation. Star formation under non-Milky Way conditions", Astronomy & Astrophysics 2010, 510, p. A110 »

S.Hocuk and M.Spaans: "The impact of X-rays on molecular cloud fragmentation and the inital mass function", Astronomy and Astrophysics, 522, p. A24 »

R. Baron et al.: "Light hadrons from lattice QCD with light (u,d), strange and charm dynamical quarks", JHEP 1006 (2010), pp. 111

R. Baron et al.: "Kaon and D meson masses with N_f = 2+1+1 twisted mass lattice QCD PoS", (LAT2010) 119

Santanu Roy, Thomas la Cour Jansen, and Jasper Knoester: "Structural classification of the amide I sites of a beta-hairpin with isotope label 2DIR spectroscopy", Phys. Chem. Chem. Phys. 12:9347-9357 (2010)

Arend G. Dijkstra, Thomas la Cour Jansen, and Jasper Knoester: "Two-dimensional spectroscopy of coupled bands of excitations: application to energy transport and relaxation in a polypeptide", J. Phys. Chem. A, 114:7267 (2010) Journal Cover

T. L. C. Jansen, B. M. Auer, Mino Yang, and J. L. Skinner: "Two-dimensional infrared spectroscopy and ultrafast anisotropy decay of water", J. Chem. Phys. 132:224503 (2010)

A. W. Smith, J. Lessing, Z. Ganim, C. S. Peng, A. Tokmakoff, S. Roy, T. L. C. Jansen and J. Knoester: "Melting of a beta-hairpin peptide using isotope-edited 2D IR spectroscopy and simulations", J. Phys. Chem. B, Feature Article, 114:10913-10924 (2010)

Anna Lobanova, Gosse Bouma and Erik Tjong Kim Sang: "Using a Treebank for Finding Opposites", by Proceedings of TLT9, Tartu, Estonia, 2010, pages 139-150. »

J.Rosindell, S.J.Cornell, S.P.Hubbell & R.S.Etienne: "Protracted speciation revitalizes the neutral theory of biodiversity."' Ecology Letters (2010) 13, p. 716–727

David Alonso, Menno J. Bouma and Mercedes Pascual: "Epidemic malaria and warmer temperatures in recent decade in an East African highland", Proc. R. Soc B, published online in advance of the print journal

H.de Waard, A.Amani, J.Kendrick, W.L.J.Hinrichs, H.W.Frijlink, and J.Anwar: "Evaluation and optimization of a force field for crystalline forms of mannitol and sorbitol", J. Phys. Chem. B, 2010, 114(1), p. 429-436.
M.Hinsch and J.Komdeur: "Defence, intrusion and the evolutionary stability of territoriality", Journal of Theoretical Biology 266, p. 606-613.

Erik Bernsen, Henk A. Dijkstra, Jonas Thies, Fred W. Wubs: "The application of Jacobian-free Newton-Krylov methods to reduce the spin-up time of ocean general circulation models", J. Comput. Phys. 229(21) (2010) 8167-8179.

T. Bunnik and A.E.P. Veldman: "Modelling the effect of sloshing on ship motions", Proc. 29th Conf. on Ocean, Offshore and Arctic Eng. OMAE2010, Shanghai, China (2010) paper OMAE-20458.

B. Carpentieri, Y.-F. Jing and T.-Z. Huang: "A novel Lanczos-type procedure for computing eigenelements of Maxwell and Helmholtz problems", Progress In Electromagnetics Research, PIER, 110 (2010) 81-101.

B. Carpentieri, Y.-F. Jing and T.-Z. Huang: "Lanczos biconjugate A-orthonormalization methods for surface integral equations in electromagnetism", PIERS Proceedings, Xian, China, March 22-26 (2010) 678-682.

Joop A. Helder and Roel W.C.P. Verstappen: "On restraining convective subgrid-scale production in Burgers' equation", J.C.F. Pereira and A. Sequeira (eds.) Proc. ECCOMAS CFD 2010, Lisbon (2010) CD-ROM paper 1632.

Yan-Fei Jing, Ting-Zhu Huang, Yong Duan and Bruno Carpentieri: "A comparative study of iterative solutions to linear systems arising in quantum mechanics", J. Comput. Phys. 229(22) (2010) 8511-8520.

Roel Luppes, Arthur E.P. Veldman and Peter R. Wellens: "Absorbing boundary conditions for wave simulations around offshore structures", J.C.F. Pereira and A. Sequeira (eds.) Proc. ECCOMAS CFD 2010, Lisbon (2010) CD-ROM paper 1200.

J. Thies and F.W. Wubs: "A robust parallel ILU solver with grid-independent convergence for the coupled steady incompressible Navier-Stokes equations", J.C.F. Pereira and A. Sequeira (eds.) Proc. ECCOMAS CFD 2010, Lisbon (2010) CD-ROM paper 1421.

F. Xavier Trias, Andrey Gorobets, Roel Verstappen and Assensi Oliva: "Regularization modeling of wall-bounded turbulent flows", J.C.F. Pereira and A. Sequeira (eds.) Proc. ECCOMAS CFD 2010, Lisbon (2010) CD-ROM paper 1670.

F.X. Trias, R.W.C.P. Verstappen, A. Gorobets, M. Soria, A. Oliva: "Parameter-free symmetry-preserving regularization modeling of a turbulent differentially heated cavity", Computers and Fluids 39(10) (2010) 1815-1831.

F.X. Trias, A.Gorobets, A. Oliva and R. Verstappen: "Turbulent flow in a differentially heated cavity: direct numerical simulation and regularization modeling", Proceedings of the 14th International Heat Transfer Conferences IHTC14, ASME, Washington DC, USA, 10 pages, 2010.

Roel W.C.P. Verstappen: "When does eddy viscosity restrict the dynamics to large eddies?", J.C.F. Pereira and A. Sequeira (eds.) Proc. ECCOMAS CFD 2010, Lisbon (2010) CD-ROM paper 1302.

R.W.C.P. Verstappen and F.X. Trias: "Symmetry-preserving regularization models of the Navier-Stokes equations", J.C.F. Pereira and A. Sequeira (eds.) Proc. ECCOMAS CFD 2010, Lisbon (2010) CD-ROM paper 1304.

Roel W.C.P. Verstappen: "Regularizations of turbulent flow", J.C.F. Pereira and A. Sequeira (eds.) Proc. ECCOMAS CFD 2010, Lisbon (2010) CD-ROM paper 1630.

R.W.C.P. Verstappen, S.T. Bose, J. Lee, H. Choi and P. Moin: "A dynamic eddy-viscosity model based on the invariants of the rate-of-strain", Proceedings of the Summer Program 2010, p 183-192, Center for Turbulence Research, Stanford University, 2010.

Roel Verstappen, Sanjeeb Bose, Jungil Lee, Haecheon Choi and Parviz Moin: "A new dynamic eddy viscosity model for LES. Bulletin of the American Physical Society Vol. 55, p. 265 (2010)

2009

Ittoo, A., Bouma, G. (2009), “Semantic Selectional Restrictions for Disambiguating Meronymy Relations”, (Book Chapter) In Computational Linguistics in the Netherlands, pp. 83-98, published by Landelijke Onderzoekschool Taalwetenschap (ISBN 978-94-6093-004-1)

Kostadin Cholakov and Gertjan van Noord: "Combining Finite State and Corpus-based Techniques for Unknown Word Prediction." Recent Advances in Natural Language Processing (RANLP), Borovets, Bulgaria, 2009.

Gertjan van Noord and Gosse Bouma: "Parsed Corpora for Linguistics." Proceedings of EACL Workshop The Interaction between Linguistics and Computational Linguistics: Virtuous, Vicious or Vacuous? Athens, 2009. pp 33-39.

Gertjan van Noord: "Learning Efficient Parsing." EACL 2009. The 12th Conference of the European Chapter of the Association for Computational Linguistics. 30 March - 3 April 2009, Athens, Greece. pp 817-825.

Gertjan van Noord: "Huge Parsed Corpora in LASSY." Frank van Eynde, Anette Frank, Koenraad de Smedt,

Gertjan van Noord (editors), Proceedings of the Seventh International Workshop on Treebanks and Linguistic Theories (TLT 7). January 23-24, 2009, Groningen, The Netherlands. LOT Occasional Series.

Thomas l. C. Jansen, Dan Cringus, and Maxim S. Pshenichnikov: "Dissimilar Dynamics of Coupled Water Vibrations"
, J. Phys. Chem. A113:6260 (2009)

Thomas l. C. Jansen, Dan Cringus, and Maxim S. Pshenichnikov: "Hydrophobic Solvation: A 2D IR Spectroscopic Inquest", J. Phys. Chem. A 113:6260 (2009)

Artem Bakulin, Chungwen Liang, Thomas l. C. Jansen, Douwe A. Wiersma, Huib Bakker, and Maxim S. Pshenichnikov, Accounts of Chemical Research, 42:1229 (2009)

Perry, G.L.W., N.J. Enright, B.P. Miller, B.B. Lamont, & R.S. Etienne: Dispersal, edaphic fidelity, and speciation in species-rich Western Australian shrublands: evaluating a neutral model of biodiversity." Oikos 118:1349-1362. »

Etienne, R.S.: "Maximum likelihood estimation of neutral model parameters for multiple samples with different degrees of dispersal limitation." Journal of Theoretical Biology, 257: 510-514. »

Etienne, R.S.: "Improved estimation of neutral model parameters for multiple samples with different degrees of dispersal limitation."  Ecology 90: 847-852 »

Daniël de Kok, Jianqiang Ma, and Gertjan van Noord:  "A generalized method for iterative error mining in parsing results" in Proceedings of the 2009 Workshop on Grammar Engineering Across Frameworks, Association for Computational Linguistics

Alies Hoitsma: "Mag het licht uit?", Master thesis Research Master Human Behaviour in Social Contexts. »

Mobach, M.P.: "Een organisatie van vlees en steen". Assen: Van Gorcum. ISBN: 9789023245315. 436 pages. »

Mobach, M.P. "Counter Design Influences the Privacy of Patients in Health Care", Social Science & Medicine. 68(6): 1000-5.

Christine Boomsma: "Resolving the conflict of reduced street lighting: Two ways to increase the acceptability of reduced street lighting", Master thesis Research Master Human Behaviour in Social Contexts. »

Barbara Plank: "A Comparison of Structural Correspondence Learning and Self-training for Discriminative Parse Selection, Proceedings of the NAACL HLT Workshop on Semi-supervised Learning for Natural Language Processing.

M.J. Hinner, S.J. Marrink, A.H. de Vries. Location, tilt, and binding: "a molecular dynamics study of voltage sensitve dyes" in biomembranes. J. Phys. Chem. B, 113:15807-15819, 2009.

C.A. Lopez, A. Rzepiela, A.H. de Vries, L. Dijkhuizen, P.H. Huenenberger, S.J. Marrink: "The Martini coarse grained force field: extension to carbohydrates." J. Chem. Th. Comp., 5:3195-3210, 2009.

D. Sengupta, A. Rampioni, S.J. Marrink: "Simulations of the C-subunit of ATP-synthase reveal helix rearrangements." Mol. Membr. Biol., 26:422-434, 2009.

H.J. Risselada, S.J. Marrink: "The freezing process of small lipid vesicles at molecular resolution." Soft Matter, 5:4531-4541, 2009.

H. Lee, A.H. de Vries, S.J. Marrink, R.W. Pastor: "A coarse-grained model for polyethylene oxide: conformation and hydrodynamics." J. Phys. Chem. B, 113:13186-13194, 2009.

X. Periole, M. Cavalli, S.J. Marrink, M. Ceruso: "Combining an elastic network with a coarse-grained molecular force field: structure, dynamics and intermolecular recognition." J. Chem. Th. Comp., 5:2531-2543, 2009.

W.F.D. Bennett, J.L. MacCallum, M.J. Hinner, S.J. Marrink, D.P. Tieleman: "A molecular view of cholesterol flip-flop and chemical potential in different membrane environments." JACS, 131:12714-12720, 2009.

N. Kucerka, J. Gallova, D. Uhrikova, P. Balgavy, M. Bulacu, S.J. Marrink, J. Katsaras: "Areas of monounsaturated diacylphosphatidylcholines." Biophys. J., 97:1926-1932, 2009.

M. Fuhrmans, V. Knecht, S.J. Marrink: "A single bicontinuous cubic phase induced by fusion peptides." JACS, 131:9166-9167, 2009.

R.P.A. Berntsson, M.K. Doeven, F. Fusetti, R.H. Duurkens, D. Sengupta, S.J. Marrink, A.M.W.H. Thunnissen, B. Poolman, D.J. Slotboom: "The structural basis for peptide selection by the transport receptor OppA." EMBO J., 28:1332-1340, 2009.

H.J. Risselada, S.J. Marrink: "Curvature effects on lipid packing and dynamics in liposomes revealed by coarse grained molecular dynamics simulations." Phys. Chem. Chem. Phys., 11:2056-2067, 2009.

O.H.S. Ollila, H.J. Risselada, M. Louhivuori, E. Lindahl, I. Vattulainen, S.J. Marrink: "3D Pressure distribution in lipid membranes and membrane-protein complexes." Phys. Rev. Lett., 102:078101, 2009.

M.E. Siwko, A.H. de Vries, A.E. Mark, A. Kozubek, S.J. Marrink: "Disturb or stabilise? A molecular dynamics study of the effects of resorcinolic lipids on phospholipid bilayers" Biophys. J. 96 (2009) (8) 3140-3153

Xavier Periole, Aldo Rampioni, Michele Vendruscolo, and Alan E. Mark: "Factors That Affect the Degree of Twist in b-Sheet Structures: A Molecular Dynamics Simulation Study of a Cross-b Filament of the GNNQQNY Peptide." J. Phys. Chem. B. 113 (6) (2009) 1728-1737

S. Yesylevskyy  , S.J. Marrink, A.E. Mark: "Alternative mechanisms for the interaction of the cell-penetrating peptides Penetratin and the TAT peptide with lipid bilayers" Biophys. J. 97 (2009) 40-49

M.F. Masman, U.L.M. Eisel, I.G. Csizmadia, B. Penke, R.D. Enriz, S.J. Marrink, P.G.M. Luiten: "In silico study of full length amyloid beta 1-42 tri- and penta-oligomers in solution." J. Phys. Chem. B 113 (2009) 11710-11719

2008

Mark P. Mobach: "Do Virtual Worlds Create Better Real Worlds?", Virtual Reality, Springer

E. Bernsen, H.A. Dijkstra and F.W. Wubs, "A method to reduce the spin-up time of ocean models. "Ocean Modelling 20 (2008) 380-392.

Joop Helder and Roel Verstappen, "On restraining convective subgrid-scale production in Burgers' equation." Int. J. Numer. Meth. Fluids 56 (2008) 1289-1295.

G. Rozema, N.M. Maurits and A.E.P. Veldman, "Linking an artery to the circulation: introducing a quasi-simultaneous coupling approach for partitioned systems in hemodynamics." In: J. Vander Sloten, et al. (eds.):  ECIFMBE 2008, IFMBE Proceedings 22, Antwerpen (2008) 1930-1934.

F.X. Trias, R.W.C.P. Verstappen, M. Soria, A. Gorobets and A. Oliva, Regularization modelling of a turbulent differentailly heated cavity at Ra =10^11. In: G.G.M. Stoffels et al. (eds.) Proc. 5th European Thermal-Sciences Conference, Eurotherm 2008, Eindhoven (2008).

F.X. Trias, R. Verstappen, M. Soria and A. Oliva,  "Symmetry-preserving regularization modelling of a turbulent differentially heated cavity." In: Proc. Conf. LES in Science and Technology, Poznan, 21-22 April 2008.

R. Verstappen, On restraining the production of small scales of motion in a turbulent channel flow. Comp. Fluids 37 (2008) 887-897.

R. Wemmenhove, R. Luppes and A.E.P. Veldman, "Application of a VOF method to model compressible two-phase flow in sloshing tanks." In: Proc. 27th Conf. Offshore Mech. Arctic Eng.,  Estoril (2008)  paper OMAE2008-57254.

Etzel, J. A., Gazzola, V., Keysers, C. (2009) “An Introduction to Anatomical ROI-based fMRI Classification Analysis.” Brain Research, 1282: 114-125.

Etzel, J. A., Gazzola, V., Keysers, C. (2008). "Testing Simulation Theory with Cross-Modal Multivariate Classification of fMRI Data." PLoS One 3(11): e3690.

Zhu J., Fan H., Periole X., Honig B., Mark A.E., Refining homology models by combining replica-exchange molecular dynamics and statistical potentials."in Proteins-structure function and bioinformatics, 72, 1171-1188, Sept 2008

S. Zhao, S. Yuan, H. De Raedt and K. Michielsen, "Computer simulation of Wheeler's delayed choice experiment with photons", Europhys. Lett. 82, 40004 (2008)

H. De Raedt, "Event-by-event simulation of quantum phenomena", Brazilian Journal of Physics 38, 26 - 36 (2008)

S. Zhao and H. De Raedt, Event-by-event simulation of quantum cryptography protocols, J. Comp. Theor. Nanosci. 5, 490504 (2008)

S. Zhao, H. De Raedt, and  K. Michielsen, "Event-by-event simulation model of Einstein-Podolsky-Rosen-Bohm experiments", Found. Phys. 38, 322-347 (2008)

S. Yuan, M.I. Katsnelson, and H. De Raedt, "Decoherence by a spin thermal bath: Role of spin-spin interactions and initial state of the bath", Phys.Rev. B 77, 184301 (2008)

Yuan, Shengjun, "Relaxation and decoherence in quantum spin system" Phd Thesis (2008)

Alan R. Duffy, Joop Schaye, Scott T. Kay, Claudio Dalla Vecchia. "Dark matter halo concentrations in the Wilkinson Microwave Anisotropy Probe year 5 cosmology." 2008, MNRAS, 390, L64

Andreas H. Pawlik, Joop Schaye. "TRAPHIC - Radiative transfer for smoothed particle hydrodynamics simulations." 2008, MNRAS, 389, 651

Claudio Dalla Vecchia, Joop Schaye. "Simulating galactic outflows with kinetic supernova feedback." 2008, MNRAS, 387, 1431

Joop Schaye, Claudio Dalla Vecchia. "On the relation between the Schmidt and Kennicutt-Schmidt star formation laws and its implications for numerical simulations." 2008, MNRAS, 383, 1210

van der Zant, T., Schomaker, L.R.B., Valentijn, E. "Large-scale parallel document-image processing." In: B.A. Yanikoglu and K. Berkner (Eds.), Proceedings of Document Recognition and Retrieval XV, IS&T/SPIE International Symposium on Electronic Imaging, pp. 6815-28, 2008

Schomaker, L.R.B. "Word mining in a sparsely-labeled handwritten collection." In: B.A. Yanikoglu and K. Berkner (Eds.), Proceedings of Document Recognition and Retrieval XV, IS&T/SPIE International Symposium on Electronic Imaging, pp. 6815-23, 2008

S.J. Marrink, M. Fuhrmans, H.J. Risselada, X. Periole. "The MARTINI force field." In: Coarse graining of condensed phase and biomolecular systems, G. Voth ed., CRC press, Chapter 2, 2008. 

H.J. Risselada, S.J. Marrink. "The molecular face of lipid rafts in model membranes." PNAS, 105:17367-17372, 2008.

D. Sengupta, H. Leontiadou, A.E. Mark, S.J. Marrink. "Toroidal pores formed by antimicrobial peptides show significant disorder." BBA Biomembr., 1778:2308-2317, 2008.

S. Baoukina, L. Monticelli, H.J. Risselada, S.J. Marrink, D.P. Tieleman. "The molecular mechanism of lipid monolayer collapse." PNAS, 105:10803-10808, 2008.

H.J. Risselada, A.E. Mark, S.J. Marrink. "The application of mean field boundary potentials in simulations of lipid vesicles." J. Phys. Chem. B, 112:7438-7447, 2008.

L. Monticelli, S.K. Kandasamy, X. Periole, R.G. Larson, D.P. Tieleman, S.J. Marrink. "The MARTINI coarse-grained force field: extension to proteins." J. Chem. Th. Comp., 4:819-834, 2008.

S.J. Marrink, A.H. de Vries, T.A. Harroun, J. Katsaras, S.R. Wassall. "Cholesterol shows preference for the interior of polyunsaturated lipid membranes." JACS, 130:10-11, 2008.

S. Yefimov, P.R. Onck, E. van der Giessen, S.J. Marrink. "Mechanosensitive membrane channels in action." Biophys. J., 94:2994-3002, 2008.

V. Knecht, H.J. Risselada, A.E. Mark, S.J. Marrink. "Electrophoretic mobility does not always reflect the charge on an oil droplet" J. Colloid. Int. Sci., 318:477-486, 2008.

2007

Marius Bulacu, Lambert Schomaker: "Text-independent writer identification and verification using textural and allographic features", IEEE Trans. on Pattern Analysis and Machine Intelligence (PAMI), Special Issue - Biometrics: Progress and Directions, IEEE Computer Society, vol. 29, no. 4, 701-717, April 2007.

Fu J, Swertz MA, Keurentjes JJB, Jansen RC:  "MetaNetwork: a computational protocol for the genetic study of metabolic networks." Nature Protocols 2:685-694 2007

Keurentjes JJB, Fu J, Terpstra IR, Garcia JM, Van Den Ackerveken G, Snoek LB, Peeters AJM, Vreugdenhil D, Koornneef M, Jansen RC: "Regulatory Network Construction in Arabidopsis using genome-wide gene expression QTLs".  PNAS 104:1708-1713 2007

Gosse Bouma, Geert Kloosterman, Jori Mur, Gertjan van Noord, Lonneke van der Plas, and Jörg Tiedemann: "Question Answering with Joost" at CLEF 2007, CLEF 2007 Working Notes.

Gertjan van Noord: "Using Self-Trained Bilexical Preferences to Improve Disambiguation Accuracy." In: Proceedings of the Tenth International Conference on Parsing Technologies. IWPT 2007, Prague. Pages 1--10.

Gosse Bouma, Ismail Fahmi, Jori Mur, Gertjan van Noord, Lonneke van der Plas, Jörg Tiedemann: "Using Syntactic Knowledge for QA." In: Evaluation of Multilingual and Multi-modal Information Retrieval. Lecture Notes in Computer Science 4730/2007. Springer. pp 318--327.

Martijn Wieling, Mark-Jan Nederhof, Gertjan van Noord: " Parsing Partially Bracketed Input." In: CLIN 2005. Proceedings of the 16th Meeting of Computational Linguistics in the Netherlands. Pages 1--16.

Gosse Bouma, Ismail Fahmi, Jori Mur, Gertjan van Noord, Lonneke van der Plas, Jörg Tiedemann: "Linguistic Knowledge and Question Answering." In: Traitement Automatique des Languages 46 (3)/2005. Pages 15--39. Appeared in 2007.

Gosse Bouma and Geert Kloosterman: "Mining Syntactically Annotated Corpora using XQuery." Proceedings of the Linguistic Annotation Workshop (ACL 07). Prague 2007.

Marc Droege: " Cartesian grid methods for turbulent flow simulation in complex geometries." PhD thesis, University of Groningen (2007).

J. Helder and R. Verstappen: "On restraining the convective subgrid-scale production in Burgers' equation."  In: Advances in Turbulence XI, Springer Proceedings in Physics, Vol 117 (2007) 737.

J. Helder and R. Verstappen: "On restraining convective subgrid-scale production in Burgers' equation." In: Proc. 9th ICFD Conf. Numer. Methods Fluid Dyn.,  Reading  (2007) paper 40.

A.J.A. Kort, R.W.C.P. Verstappen, F.W. Wubs and A.E.P. Veldman: "Symmetry-preserving discretizations for local grid refinement." In:  Progress in Turbulence 2, Springer Proceedings in Physics, Vol 109 (2007) 4 pags.

N.M. Maurits, E. Loots and A.E.P. Veldman: "The influence of vessel wall elasticity and peripheral resistance on the flow wave form in the carotidartery: a CFD model compared to in-vivo ultrasound measurements." J. Biomech. 40 (2007) 427-436.

Arie de Niet: "Solving large linear systems in an implicit thermohaline ocean model." PhD thesis, University of Groningen (2007).

A.C. de Niet and F.W. Wubs: "Two preconditioners for saddle point problems in fluid flows." Int. J. Numer. Meth. Fluids 54 (2007) 355-377.

A.C. de Niet, F.W. Wubs, H.A. Dijkstra, and A. Terwisscha van Scheltinga: "A tailored solver for bifurcations analysis of ocean-climate models." J. Comput. Phys. 227 (2007) 654-679.

A.E.P. Veldman, J. Gerrits, R. Luppes, J.A. Helder and J.P.B Vreeburg: "The numerical simulation of liquid sloshing on board spacecraft." J. Comput. Phys. 224 (2007) 82-99.

Roel Verstappen: "Symmetry-preserving regularization modeling of turbulent channel flow." In: Progress in Turbulence 2, Springer Proceedings in Physics, Vol 109 (2007).

R. Verstappen: "On the inertial range of symmetry-preserving regularization models for turbulent flow." In: Proc. 6th Int. Cong. Indust. Appl. Math. ICIAM07, ETH Zurich (2007) paper 692.

R. Verstappen: "On restraining the production of small scales of motion in a turbulent channel flow.", Computers and Fluids, available online DOI:10.19016 / j.compfluid.2007.01.013.

R. Wemmenhove, R. Luppes, T. Bunnik and A.E.P. Veldman: "Numerical simulation and model experiments of sloshing in LNG tanks." Comp. Meth. in Marine Eng.: MARINE 2007, Barcelona (2007).

R. Wemmenhove, R. Luppes, A.E.P. Veldman and T. Bunnik: "Numerical simulation of sloshing in LNG tanks with a compressible two-phase model." In: Proc. OMAE 2007, San Diego (2007) Paper 29294.

F. Wubs, A. de Niet and J. Thies: "Preconditioning of ocean model equations."  In: Proc.2007 Int. Conf. on Preconditioning Techniques for Large Sparse Matrix Problems in Scientific and Industrial Applications, Toulouse (2007) 91-93.

Siwko, M.E., Marrink, S.J., Vries, A.H. de, Kozubek, A., Schoot Uiterkamp, A.J.M., Mark, A.E.: "Does isoprene protect plant membranes from thermal shock? A molecular dynamics study",
Biochimica et Biofysica Acta 1768 (2007) 198-206.

Periole, X. and Mark, A.E.: "Convergence and sampling efficiency in replica exchange simulations of peptide folding in explicit solvent", J. Chem. Phys. 126 (2007) 014903.
     
Leontiadou, H., Mark, A.E., Marrink, S.J.: "Ion transport across transmembrane pores", Biophys. J., 92 (2007) 4209 - 4215.
       
Knecht, V., and Marrink, S.J.: "Molecular dynamics simulations of lipid vesicle fusion in atomic detail", Biophys. J., 92 (2007) 4254 - 4261 .     

Baron, R., Trzesniak, D. Vries, A.H. de, Elsener, A., Marrink, S.J. and Gunsteren, W.F. van.: "Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models", Chem. Phys. Chem. B. (2007) 452-461.

Bogaart, G. van den, Hermans, N., Krasnikov, V., Vries, A.H. de, Poolman, B.: "On the decrease in lateral mobility of phospholipids by sugars", Biophysical Journal 92 (2007) 1598-1605.

Piñeiro, Á., Banquy,X., Pérez-Casas,S., Tovar, E., García,A., Villa, A., Amigo, A., Mark, A.E. and Costas, M.: "On the characterization of host-guest complexes. Surface tension, calorimetry and molecular dynamics of cyclodextrins with a non-ionic surfactant", J. Phys. Chem. B. 111 (2007) 4383-4392.

Villa, A., Fan, H., Wassenaar, T.A., Mark, A.E.: "How sensitive are nanosecond molecular dynamics simulations of proteins to changes in the force field?", J. Phys. Chem. B. 111 (2007) 6015-6025.

Periole, X., Huber, T., Marrink, S.J., Sakmar, T.P.: "G protein-coupled receptors self-assemble in dynamics simulations of model bilayers", J. Am. Chem. Soc. 129 (2007) 10126-10132.

S.J. Marrink, H.J. Risselada, S. Yefimov, D.P. Tieleman, A.H. de Vries: "The MARTINI forcefield: coarse grained model for biomolecular simulations", J. Phys. Chem. B 111 (2007) 7812-7824.

Periole, X., Vendruscolo, M., Mark, A.E.: "Molecular dynamics simulations from putative transition states of -spectrin SH3 domain", Proteins 69 (2007) 536-550.

S. Yuan, H. De Raedt, and S. Miyashita: "Domain-wall dynamics near a quantum critical point", Phys. Rev. B 75, 184305 (2007)

S. Yuan, M.I. Katsnelson, and H. De Raedt: "Evolution of a quantum spin system to its ground state: Role of entanglement and interaction symmetry", Phys. Rev. A 75, 052109 (2007)

K. De Raedt, K. Michielsen, H. De Raedt, B. Trieu, G. Arnold, M. Richter, Th. Lippert, H. Watanabe, N. Ito, "Massive Parallel Quantum Computer Simulator", Comp. Phys. Comm. 176, 121 - 136 (2007)

K. De Raedt, H. De Raedt, and K. Michielsen "A computer program to simulate the Einstein-Podolsky-Rosen-Bohm experiment with photons", Comp. Phys. Comm. 176, 642 - 651 (2007)

H. De Raedt, K. Michielsen, S. Miyashita, and K. Keimpema: "Reply to Comment on 'A local realist model for correlations of the singlet state' ", Euro. Phys. J. B 58, 55 - 59 (2007)

H. De Raedt and K. Michielsen: "Unconditionally Stable Perfectly Matched Layer Boundary Conditions", Phys. Stat. Sol. B 244, 3497 - 3505, (2007)

H. De Raedt, K. De Raedt, K. Michielsen, K. Keimpema, and S. Miyashita: "Event-by-event simulation of quantum phenomena: Application to Einstein-Podolsky-Rosen-Bohm experiments", J. Comp. Theor. Nanosci. 4, 957 - 991 (2007)

H. De Raedt, K. De Raedt, K. Michielsen, K. Keimpema, and S. Miyashita: "Event-based computer simulation model of Aspect-type experiments strictly satisfying Einstein's locality conditions", J. Phys. Soc. Jpn. 76, 104005 (2007)

2006

John W. Romein, P. Chris Broekema, Ellen van Meijeren, Kjeld van der Schaaf and Walther H. Zwart: "Astronomical Real-Time Streaing Signal Processing on a Blue Gene/L Supercomputer", ACM Symposium on Parallel Algorithms and Architectures (SPAA'06), 59-66, Cambridge, MA, July 2006.

D. R. Poelman & M. Spaans: "Line profiles of water for the photon dominated region and embedded sources in the S140 region", Astronomy & Astrophysics, volume 453, 615-620

W.A. Mulder, L. Nicoletis, and T.A. Alkhalifah: "The EAGE 3D Anisotropic Elastic Modelling Project", Extended Abstract H048, EAGE 68th Conference & Exhibition, Vienna, 12–15 June, 2006. »

S. Yuan, M.I. Katsnelson, and H. De Raedt: "Giant enhancement of quantum decoherence by frustrated environments", JETP Lett. 84, 105 - 109 (2006) ( » ), JETP Letters, 84, 99–103, 2006 »

S. Yuan, H. De Raedt, and S. Miyashita: "Quantum Dynamics of Spin Wave Propagation Through Domain Walls", J. Phys. Soc. Jpn. 75, 084703-1 - 084703-4 (2006) »

C. Shen, K. Michielsen, and H. De Raedt: "Spontaneous-emission rate in microcavities: Application to two-dimensional photonic crystals", Phys. Rev. Lett. 96, 120401 (2006) »

C. Shen, K. Michielsen, and H. De Raedt: "Image transfer by cascaded stack of photonic crystal and air layers", Opt. Express, 14, 879 - 886 (2006) »

H. De Raedt, K. De Raedt, K. Michielsen, and S. Miyashita: "Efficient data processing and quantum phenomena: Single-particle systems", Comp. Phys. Comm. 174, 803 - 817 (2006), see also Deterministic Learning Machines   »

H. De Raedt, K. De Raedt, and K. Michielsen: "Event-by-event simulation of quantum phenomena", in "Computer Simulation Studies in Condensed-Matter Physics XVIII", Landau D.P., Lewis S.P., Schüttler H.-B. (Eds.), Springer Proceedings in Physics , Vol. 105, 27 - 31 (2006) »

K.Michielsen, H. De Raedt, and K. De Raedt: "Deterministic event-based simulation of universal quantum computation", in "Computer Simulation Studies in Condensed-Matter Physics XVIII", Landau D.P., Lewis S.P., Schüttler H.-B. (Eds.), Springer Proceedings in Physics , Vol. 105, 32 - 36 (2006) »

H. De Raedt and K. Michielsen: "Computational Methods for Simulating Quantum Computers", Handbook of Theoretical and Computational Nanotechnology, Vol. 3: Quantum and molecular computing, quantum simulations, Chapter 1, pp. 2 – 48, M. Rieth and W. Schommers eds.,American Scientific Publisher, Los Angeles (2006)  »

DeVane R, Space B, Jansen TLC, Keyes T.:  "Time correlation function and finite field approaches to the calculation of the fifth order Raman response in liquid xenon" JOURNAL OF CHEMICAL PHYSICS 125 (23): Art. No. 234501 (2006)

Milne CJ, Li YL, Jansen TLC, Huang L, Miller RJD: Fifth-order Raman spectroscopy of liquid benzene: Experiment and theory", Journal of Physical Chemistry B 110 (40): 19867-19876 (2006)

Gosse Bouma, Ismail Fahmi, Jori Mur, Gertjan van Noord, Lonneke van der Plas, Jörg Tiedemann: "The University of Groningen at QA@CLEF2006. Using Syntactic Knowledge for QA". CLEF2006 Working Notes.

Gosse Bouma, Jori Mur, Gertjan van Noord, Lonneke van der Plas, and Jörg Tiedemann: "Question Answering for Dutch using Dependency Relations", Proceedings of the CLEF2005 workshop. Lecture Notes in Computer Science. Springer, 2006.

Gertjan van Noord, Ineke Schuurman, Vincent Vandeghinste: "Syntactic Annotation of Large Corpora in STEVIN", Proceedings of LREC 2006. Genoa, Italy. page 1811-1814.

Gertjan van Noord: "At Last Parsing Is Now Operational", Piet Mertens, Cedrick Fairon, Anne Dister, Patrick Watrin (editors): TALN06. Verbum Ex Machina. Actes de la 13e conference sur le traitement automatique des langues naturelles. Page 20-42.

Wassenaar, T.A. and Mark, A.E. : "The effect of box shape on the dynamic properties of proteins simulated under periodic boundary conditions", J. Comp. Chem. 27: 316-325.

Villa, A., Mark, A.E., Saracino, G.A.A., Cosentino, U., Pitea, D., Moro, G. and Salmona, M.: "Conformational polymorphism of the PrP106-126 peptide in different environments: A molecular dynamics study", J. Phys. Chem B 110: 1423-1428.

Knecht, V., Mark, A.E. and Marrink, S.J.: "Phase behavior of fatty acids/lipid/water mixture studied in atomic detail" J. Am. Chem. Soc. 128: 2030-2034.

Fan, H. and Mark, A.E.: "Mimicking the action of GroEL in molecular dynamics simulations: Application to the refinement of protein structures", Protein Science 15: 441- 448.

Fan, H., Wang, X., Zhu, J., Robillard, G.T. and Mark, A.E.: "Molecular dynamics simulations of the hydrophobin SC3 at a hydrophobic/hydrophilic interface" Proteins 64: 863-873.

Leontiadou, H., Mark, A.E. and Marrink, S.J.: "Antimicrobial peptides in action", J. Am. Chem. Soc. 128: 12156-12161.

Fan, H. : "Refining protein structures: a dynamic approach", Thesis, University ofGroningen, 31 March 2006

Wassenaar, T.A.: "Molecular dynamics of sense and sensibility in processing and analysis of data", Thesis, University of Groningen, 11 September 2006.

Bolt. A.: "De apotheek in 3D.", Optima Farma, 3 (3): 12-13

Mobach MP.: "Virtual Organizational Space.", Research in interactive design -Vol. 2, Fischer X, Coutellier D (eds). Springer: Paris. ISBN 2-287-48363-2

Mobach MP.: "An Organization of Flesh and Stone.", Asia-Pacific Researchers in Organisation Studies, Muetzelfeldt, M (ed.). Melbourne: RMIT Publishing, 34-43. EISBN: 192116638X

arXiv:hep-lat/0612026
Title: Hyperon-Nucleon Scattering from Fully-Dynamical
Lattice QCD

Silas R. Beane, Paulo F. Bedaque, Thomas C. Luu, Kostas Orginos, Elisabetta Pallante, Assumpta Parreno, Martin J. Savage: "Hyperon-Nucleon Scattering from Fully-Dynamical Lattice QCD", arXiv:hep-lat/0612026

2005

Marius Bulacu, Lambert Schomaker: "A comparison of clustering methods for writer identification and verification", Proc. of 8th Int. Conf. on Document Analysis and Recognition (ICDAR 2005), IEEE Computer Society, pp. 1275-1279, vol. II.

Dunner, Rolando; Araya, Pablo A.; Meza, Andres; Reisenegger, Andreas: "The limits of bound structures in the accelerating Universe", (2006), MNRAS, 366, 803D.

D. R. Poelman & M. Spaans: “The excitation of water in the S140 photon dominated region”; Astronomy & Astrophysics 440, (2005)559-567.

Donnini, S., Mark, A.E., Juffer, A.H. and Villa, A.: “Incorporating the effect of ionic strength in free energy calculations using explicit ions“, J. Comp. Chem. 26, Issue (2005) 115-122.

Soto, P., Cladera, J., Mark, A.E. and Daura, X.: “Stability of SIV gp32 Fusion Peptide Single Layer Protofibrils as Monitored by Molecular Dynamics Simulations”, Angewandte Chemie 17, Issue 7 (2005) 1089-1091

Knecht, V., Mueller, M., Bonn , M., Marrink, S.J. and Mark, A.E.: “Simulation studies of pore and domain formation in a phospholipids monolayer”, J. Chem. Phys. 122 (2005) 24704-24713

Zangi, R. and Engberts, J.B.: “Physisorption of hydroxide ions from aqueous solution to a hydrophobic surface”, J. Am Chem Soc. 127, issue 7 (2005) 2272-2276

Marrink, S.J., Risselada, H.J. and Mark, A.E.: “Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model”, Chem. Phys. Lip. 135 (2005) 223-244

Piñeiro, Á., Villa, A., Vagt, T., Koksch, B. and Mark, A.E.: “A molecular dynamics study of the formation, stability, and oligomerization state of two designed coiled coils: Possibilities and limitations”, Biophysical Journal 89, (2005) 3701-3713

A.H. de Vries, S. Yefimov, A.E. Mark, S.J. Marrink: “Molecular structure of the lecithin ripple phase”,PNAS 102, 5392-5396 (2005)

Fan H, Mark AE, Zhu J, Honig B, “Comparative study of generalized Born models: Protein dynamics”, PNAS, 102 (19): 6760-6764 (2005)

Hao Fan, Xiaoqin Wang, Jiang Zhu, George T. Robillard, Alan E. Mark: “Molecular dynamics simulations of the hydrophobin SC3 at a hydrophobic/hydrophilic interface”, Proteins: Structure, Function, and Bioinformatics, submitted 2005, in press 2006.

M.T. Droge and R.W.C.P. Verstappen: “A new symmetry-preserving Cartesian-grid method for computing flow past arbitrarily-shaped objects”, Int. J. Numer. Meth. Fluids 47(8-9) (2005) 979-985.

M.T. Droge and R.W.C.P. Verstappen: “A symmetry-preserving Cartesian grid method for computing the flow past a circular cylinder at Re=3900”, N.A. Adams and M. Manhart (eds.) Proc. Large-eddy simulations of complex flows, Dresden (2005) 73-74.

Theresa.Kleefsman: “Water impact loading on offshore structures - a numerical study”, PhD thesis, University of Groningen , November 2005.

K.M.T. Kleefsman, G. Fekken, A.E.P. Veldman, B. Iwanowski and B. Buchner: “A Volume-of-Fluid based simulation method for wave impact problems”, J. Comp. Phys. 206 (2005) 363-393.

K.M.T. Kleefsman, G.E. Loots, A.E.P. Veldman, B. Buchner, T. Bunnik and E. Falkenberg: “The numerical solution of green water loading including vessel motions and the incoming wave field”, Proc. 24th Int. Conf. Offshore Mech. Arctic Eng., (2005) paper OMAE2005-67448.

A.J.A. Kort, R.W.C.P. Verstappen, F.W. Wubs and A.E.P. Veldman: “Symmetry-preservation in discretizations for local grid refinement”, IASME Transactions 6(2) (2005) 843-853.

A.J.A Kort, R.W.C.P. Verstappen, F.W. Wubs and A.E.P. Veldman: “Fully conservative discretizations for local grid refinement”, I. Hassan et al (eds.) Proceedings 3^rd IASME/WSEAS International Conference on Fluid Mechanics and Aerodynamics. ISBN: 960-8457-33-5, 261-266, 2005.

A.J.A. Kort, R.W.C.P. Verstappen, F.W. Wubs and A.E.P. Veldman: “Symmetry-preserving discretizations for local grid refinement”, J. Peinke, et al (eds.) Proc. ITI Conf. on Turbulence, Springer Proceedings in Physics  (2006) 4 pags.

S. van Mourik, A.E.P. Veldman and M. Dreyer: “Simulation of capillary flow with a dynamic contact angle”, Microgravity Science and Technology 17(3) (2005) 91-98.

A.E.P. Veldman, K.M.T. Kleefsman and G. Fekken: “Numerical simulation of wave impact”, P. Bergan et al. (eds.) Computational Methods in Marine Engineering, CIMNE, (2005) 323-332.

Roel Verstappen: “A projective similarity/eddy-viscosity model for large-eddy simulation”, J. Peinke, A. Kittel, S. Barth, M. Oberlack (eds.) Progress in Turbulence. Springer Proceeding in Physics, Vol. 101, ISBN 3-540-23216-8 (2005) 219--222.

Roel Verstappen: “Conservative smoothers for turbulent convection: an alternative
simulation shortcut”, J.A.C. Humphrey, T.B. Gatski, J.K. Eaton, R. Friedrich, N. Kasagi and M.A. Leschziner (eds.),  Turbulence and Shear Flow Phenomena 4 (2005) 859--864.

R. Verstappen and M. Droge: “A symmetry-preserving Cartesian grid method forcomputing viscous flow past a circular cylinder”, Comptes Rendus Mecanique 333(1) (2005) 51-57.

Fu J, ,Keurentjes JJB, de Vos CHR, Lommen A, Hall RD, Bino RJ, van der Plas LHW, Jansen RC, Vreugdenhil D, Koornneef M: “The genetics of plant metabolism”, Nature Genetics 38 (2006): 842-849.

Fu J and Jansen RC: “Optimal Design and Analysis of Genetic Studies on Gene Expression”, Genetics 172 (2006): 1993-1999.

Fu J, Alberts R, Swertz , MA , Lubber LA, Albers CJ and Jansen RC: “Combining microarrays and genetic analysis”, Briefings in Bioinformatics 6(2) (2005) 135-45.

J. Lages, V.V. Dobrovitski, M.I. Katsnelson, H.A. De Raedt, B.N. Harmon : "Decoherence by a chaotic many-spin bath", Phys. Rev. E 72, 026225 (2005).

M.T. Figge: "Stochastic discrete event simulation of germinal center reactions", Phys. Rev. E 71, 051907 (2005).

H. De Raedt, K. De Raedt, and K. Michielsen, "Event-based simulation of single-photon beam splitters and Mach-Zehnder interferometers", Europhys. Lett. 69, 861 - 867 (2005).

K. Michielsen, K. De Raedt, and H. De Raedt: "Simulation of Quantum Computation: A deterministic event-based approach", J. Comp. Theor. Nanoscience 2, 227 - 239 (2005).

H. De Raedt, K. De Raedt, and K. Michielsen: "New method to simulate quantum interference using deterministic processes and application to event-based simulation of quantum computation", J. Phys. Soc. Jpn. Suppl. 74, 16 - 25 (2005).

K. De Raedt, H. De Raedt, and K. Michielsen: "Deterministic event-based simulation of quantum interference", Comp. Phys. Comm. 171, 19-39 (2005).

G. Palasantzas , J.Th.M. De Hosson, K.F.L. Michielsen, D.G. Stavenga: "Optical Properties and Wettability of Nanostructured Biomaterials: Moth eyes, Lotus Leaves, and Insect Wings", Handbook of Nanostructured Biomaterials and Their Applications, edited by H.S. Nalwa, Chap.7, 274 - 301 (American Scientific Publishers 2005).

H. De Raedt, J.S. Kole, K.F.L. Michielsen, and M.T. Figge: "New numerical methods for solving the Time-Dependent Maxwell equations", Computational Accelerator Physics 2002, 175, 63-72 (2005).

H. De Raedt: "Advances in Unconditionally Stable Techniques", Computational Electrodynamics: The Finite-Difference Time-Domain Method, 3rd edition, chapter 18, A. Taflove and S.C. Hagness, (Artech House, MA USA, 2005).

M.P. Mobach: “Improvements in the design process of organization and
building with virtual reality”, Research in interactive design,
Fischer X, Coutellier D (eds). Springer: Paris . ISBN 2-287-28772-8 (2005)

M.P. Mobach: “An organization of flesh and stone”, Asia-Pacific
Researchers in Organization Studies (APROS), 11th International
Colloquium, 4-7 December 2005, Melbourne , Australia .

M.P. Mobach: “The virtual pharmacy, 3D becomes reality?”, Pharmacy World & Science
2005; 27(4): 271-272.

J. Klein Haneveld: “Architectuur verbetert patiëntenzorg”, Pharmaceutisch Weekblad
2005; 140 (15): 496-499.

2004

Refinement of homology-based protein structures by molecular dynamics simulation techniques Fan H, Mark AE PROTEIN SCIENCE 13 (1): 211-220 JAN 2004

H. De Raedt, S. Miyashita, K. Michielsen, and  M. Machida, "Dzyaloshinskii-Moriya interactions and adiabatic magnetization dynamics in molecular magnets", Phys. Rev.B 70, 064401 (2004),

A. Melikidze, V. V. Dobrovitski, H. A. De Raedt, M. I. Katsnelson, B. N. Harmon, "Parity Effects in Spin Decoherence", Phys. Rev. B 70, 014435 (2004),

H. De Raedt and V. V. Dobrovitski, "Decoherence in quantum spin systems", in "Computer Simulation Studies in Condensed-Matter Physics XVI", Landau D.P., Lewis S.P., Schüttler H.-B. (Eds.), Vol. 95,  ISBN 3-540-20021-5

K.Michielsen, M.T.Figge, H. De Raedt, and J.Th.M. De Hosson, "Molecular dynamics simulation of nanoindentation", in "Computer Simulation Studies in Condensed-Matter Physics XVI", Landau D.P., Lewis S.P., Schüttler H.-B. (Eds.), Vol. 95,  ISBN 3-540-20021-5

H. De Raedt, S. Miyashita, and K. Michielsen, "Energy-level diagrams of high-spin and low-spin molecules", Phys. Stat. Sol. 241, 1180 –1185 (2004)
download .pdf file (104Kb)

V. V. Dobrovitski, H. A. De Raedt, M. I. Katsnelson, and B. N. Harmon, "Numerical simulations of decoherence suppression in open quantum systems", HAIT J. Sci. Eng. 1, 586 - 597 (2004)

K.M. Theresa Kleefsman, Geert Fekken, Arthur E.P. Veldman and Bogdan Iwanowski: An improved Volume-Of-Fluid method for wave impact type problems. In: J.S. Chung, K. Izumiyama, M. Sayed and S.W. Hong (eds.) Proc. 14th Int. Offshore and Polar Engineering Conference ISOPE2004, Vol. I, pp. 334-341 (2004).

K.M. Theresa Kleefsman and Arthur E.P. Veldman: An improved Volume-Of-Fluid method for wave impact. In: P. Neittaanmaki et al. (eds.) Proceedings ECCOMAS2004, Jyvaskyla (2004).

K.M. Theresa Kleefsman, Arthur E.P. Veldman and T. Bunnik: An improved Volume-Of-Fluid (IVOF) method for wave impact type problems. In: Proc. OMAE Speciality Symposium on FPSO Integrity, Houston , paper OMAE-FPSO04-0066 (2004).

A.C. de Niet and F.W. Wubs: Two preconditioners for the saddle point equation. In: P. Neittaanmaki et al. (eds.) Proceedings ECCOMAS2004, Jyvaskyla (2004).

R.W.C.P. Verstappen: A synthesis of similarity and eddy-viscosity models. In: R. Friedrich. B.J. Geurts and O. Metais (eds.) Direct and Large-Eddy Simulation V. Kluwer, Dordrecht (2004) 89-96.

R.W.C.P. Verstappen, M.T. Drö ge and A.E.P. Veldman Symmetry-preserving discretization for DNS. In: R. Friedrich. B.J. Geurts and O. Metais (eds.) Direct and Large-Eddy Simulation V. Kluwer, Dordrecht (2004) 135-146.

Maučec, M., Rigollet, C. Monte Carlo simulations to advance characterisation of landmines by pulsed fast/thermal neutron analysis. Appl. Radiat. Isotopes. 61, 35(2004).

Maučec, M., de Meijer, R.J., Rigollet, C., Hendriks, P.H.G.M., Jonel, D.G. Detection of radioactive particles offshore by gamma-ray spectrometry, Part I: Monte Carlo assessment of detection limits. Nucl. Instrum. Methods A 525, 539 (2004).

Maučec, M., de Meijer, R.J., van der Klis, M.M.I.P., Hendriks, P.H.G.M., Jones, D.G. Detection of radioactive particles offshore by gamma-ray spectrometry Part II: Monte Carlo assessment of acquisition times. Nucl. Instrum. Methods A525, 610 (2004).

Maučec, M., Application of nuclear methods to earth sciences and environmental monitoring. 5th International Conference of Yugoslav Nuclear Society, YUNSC-2004, September 27th 30th, 2004, Belgrade. YUNSC-2004. Beograd: Yugoslav Nuclear Society, 2004.

Maučec, M., Wörtche, H.J., de Meijer, R.J. Monte Carlo simulations of neutron and positron distribution from inverse neutron beta decay. Annual Meeting of the Dutch Physical Society, Nuclear Physics and High-Energy Physics, Lunteren, 29. October 2004. Abstracts. Lunteren: Dutch Physical Society, 2004, pp. 8.

Maučec, M., Rigolett, C. Determination of broadening functions of core logger PHAROS by Monte Carlo simulations. International Conference on Radiation Shielding/13th ANS Radiation Protection and Shielding Division Topical Meeting, Funchal, May 9-14, 2004. Programme and book of abstracts. Funchal: Instituto Technologico e Nuclear, 2004, pp. 196.

Maučec, M., Kodeli, I.A. Variance-reduction techniques for Monte Carlo nuclear logging calculations with neutron sources. International Conference on Radiation Shielding/13th ANS Radiation Protection and Shielding Division Topical Meeting, Funchal, May 9-14, 2004. Programme and book of abstracts. Funchal: Instituto Technologico e Nuclear, 2004, pp. 425.