List of publications for Adri van Duin

 

2008

 

  1. van Duin, A.C.T., Merinov, B. and Goddard, W.A. (2008) The ReaxFF Reactive Force Field for Solid Oxide Fuel Cell Systems with Application to Oxygen Ion Transport in Yttria-Stabilized Zirconia, Journal of Physical Chemistry A 112, 3133-3140.
  2. van Duin, A.C.T., Merinov, B., Han, S.S., Dorso, C. and Goddard, W.A. (2008) ReaxFF Reactive Force Field Study of Grain and Grain Boundary Proton Diffusion in Y-doped BaZrO3, accepted for publication in Journal of Physical Chemistry.
  3. Sanz-Navarro, C.F., Astrand, P., Chen, D., Ronning M., van Duin A.C.T., Jacob T. and Goddard III, W.A. (2008) Molecular dynamics simulations of the interactions between platinum clusters and carbon platelets, Journal of Physical Chemistry A 122, 1392-1402.
  4. Raymand, D., van Duin A.C.T., Baudin M. and Hermannson K. (2008) A reactive force field (ReaxFF) for Zinc Oxide, Surface Science 602, 1020-1031.
  5. Zhu, R., Janetzko, F., Zhang, Y., van Duin, A.C.T., Goddard, W.A., Salahub, D.R. (2008) Characterization of the active site of yeast RNA polymerase II by DFT and ReaxFF calculations, accepted for publication in Theorectical Chemical Accounts.
  6. Ojwang J.G.O., van Santen R., Kramer G.J., van Duin A.C.T. and Goddard W.A. (2008) Modeling the sorption dynamics of NaH using a reactive force field. J. Chem. Phys 128, 164714.
  7. Nakano, A., Kalia, R.K., Nomura, K. , Sharma, A., Vashista, P., Shimojo, F., van Duin, A.C.T., Goddard, W.A., Biswas, R. Srivastava, D. and Yang, L.H.(2008) De Novo Ultrascale Atomistic Simulations on high-end parallel supercomputers, International Journal for High Performance Computing Applications 22, 113-128.
  8. Bryantsev, V.S., Diallo, M.S., van Duin, A.C.T. and Goddard, W.A. (2008) The hydration of copper(II): new insights from density functional theory and the COSMO solvation model, Journal of Physical Chemistry A., 112, 9104-9112.
  9. Salmon, E., van Duin, A.C.T., Lorant, F., Marquaire, P.M. and Goddard, W.A. (2008) Thermal decomposition process in algaenan race L. Part 2: Molecular dynamics simulations using the ReaxFF reactive force field, accepted for publication in Organic Geochemistry.
  10. Chenoweth, K., van Duin A.C.T., Persson, P., Cheng M.J., Oxgaard, J. and Goddard W.A. (2008) Development and application of a ReaxFF reactive force field for oxidative dehydrogenation on vanadium oxide catalysts, J. Phys. Chem. C, 112, 14645-14654.
  11. Liu, B., Lusk, M., Ely, J.F., van Duin, A.C.T. and Goddard, W.A. (2008) Reactive molecular dynamics force field for the dissociation of light hydrocarbons on Ni(111), Molecular Simulation, in print.
  12. Sanz-Navarro, C.F., Astrand, P.F., Chen, D., Ronning, M., van Duin, A.C.T., Mueller, J.E. and Goddard, W.A. (2008) Molecular dynamics simulations of carbon-supported Ni-clusters using the Reax reactive force field. Journal of Physical Chemistry C 112, 12663-12668.
  13. Ning, N., Calvo, F., van Duin A.C.T., Wales, D.J. and Vach, H. (2008)  Sponaneous self-assembly of silica nanocages into inorganic framework materials, accepted for publication in Journal of Physical Chemistry A.
  14. Ojwang’, J.G.O., van Santen, R., Kramer, G.J., van Duin, A.C.T. and Goddard III, W.A. (2008) Predictions on melting, crystallization and local atomic arrangements of aluminium clusters using a reactive force field, submitted to Journal of Chemistry and Physics.
  15. Davis, S.M., Belonoshko, A.B., Rosengren, A., van Duin, A.C.T. and Johansson, B (2008), Molecular dynamics simulation on zirconia melting: comparison of two models. Submitted to Physical Review B.
  16. Salmon, E., van Duin, A.C.T., Lorant, F., Marquaire, P.M. and Goddard, W.A. (2008) Thermal decomposition process in coal. Part 2: Molecular dynamics simulation using the ReaxFF reactive force field of Morwell Brown Coal. Manuscript in preparation.
  17. Chenoweth, K, van Duin, A.C.T., Dasgupta, S. and Goddard III, W.A. (2008) Initiation mechanisms and kinetics for pyrolysis and combustion of JP-10 hydrocarbon jet fuel. Submitted to Journal of Physical Chemistry.
  18. Raymand, D., Edvinsson, T., Spangberg, D., van Duin, A. and Hermansson, K. (2008) Water adorption beyond monolayer coverage on ZnO surfaces and nanoclusters. Proc. of SPIE volume 7044.
  19. Goddard, W.A., Chenoweth, K., Pudar, S., van Duin A.C.T. and Cheng, M.J. (2008) Structures, mechanisms and kinetics of selective ammoxidation and oxidation of propane over Multi-metal oxide catalysts, Topics in Catalysis 50, 2-18.
  20. Chenoweth, K, van Duin, A.C.T. and Goddard, W.A. (2008), A ReaxFF Reactive Force Field for Molecular Dynamics Simulations of Hydrocarbon Oxidation, J. Phys. Chem. A 112, 1040-1053.

 

2007

 

  1. Nakano, A., Kalia, R.K., Nomura, K., Sharma, A., Vashista, P., Shimojo, F.,van Duin, A.C.T., Goddard, W.A., Biswas, R. and Srivastava, D. (2007) A divide-and-conquer/cellular-decomposition framework for million-to-billion atom simulations of chemical reactions, Computational Materials Science 38 642-652.
  2. Su, H, Nielsen, R.J., van Duin, A.C.T. and Goddard, W.A. (2007) Simulations on the effects of confinement and Ni-catalysis on the formation of tubular fullerene structures from peapod structures, Phys. Rev. B. 75,134107.
  3. Cheng, M-J., Chenoweth, K., Oxgaard, J., van Duin, A.C.T.  and Goddard, W.A. (2007) The Single-Site Vanadyl Activation, Functionalization, and Re-oxidation Reaction Mechanism for Propane Oxidative Dehydrogenation on the Cubic V4O10 Cluster, J. Phys. Chem. C. 111, 5115-5127.
  4. Buehler, M.J., Dodson, J., Meulbroek, P., van Duin, A.C.T. and Goddard, W.A. (2006) "The Computational Materials Design Facility (CMDF): A powerful framework for multiparadigm multi-scale simulations." Mat. Res. Soc. Proceedings, Vol. 894, LL3.8.
  5. Pudar, S., Oxgaard, J., Chenoweth, K., van Duin, A.C.T. and Goddard, W.A. (2007) The Mechanism of Selective Oxidation of Propene to Acrolein on Bismuth Molybdates from Quantum Mechanical Calculations, Journal of Physical Chemistry C 111, 16405.
  6. Buehler, M.J., Tang, H., van Duin, A.C.T. and Goddard, W.A. (2007) Threshold crack speed controls dynamical fracture of silicon single crystals, Physical Review Letters 90, 165502.
  7. Nomora, K., Kalia, R.K., Nakano, A., Vashista, P., van Duin, A.C.T. and Goddard, W.A. (2007) Dynamic transition in the shock structure of an energetic crystal, Physical Review Letters. 99, 148303.

 

2006

 

  1. Ludwig, J., Vlachos, D.G., van Duin A.C.T. and Goddard, W.A. (2006) Dynamics of the dissociation of hydrogen on stepped platinum surfaces using the ReaxFF reactive force field, Journal of Physical Chemistry B 110, 4274-4282.
  2. Buehler, M.J., van Duin A.C.T. and Goddard, W.A. (2006) Multi-paradigm modelling of dynamical crack propagation in silicon using the ReaxFF reactive force field, Physical Review Letters 96, 095505.
  3. Hudson, T.S., Nguyen-Manh, D., van Duin, A.C.T. and Sutton, A.P. (2006) Grand canonical Monte Carlo simulations of intergranular glassy films in b-silicon nitride, Materials Science and Engineering A 422, 123-135..
  4. Goddard, W.A., van Duin, A.C.T., Chenoweth, K., Cheng, M., Pudar, S., Oxgaard, J., Merinov, B., Jang, Y.H., and Persson, P. (2006) Development of the ReaxFF Reactive Force Field for Mechanistic Studies of Catalytic Selective Oxidation processes on BiMoOx , Topics in Catalysis 38 (1-3) 93-103.
  5. Goddard, W., Merinov B., van Duin A., Jacob T., Blanco M., Molinero, V., Jang S.S. and Jang, Y.H. (2006) Multi-paradigm multi-scale simulations for fuel cell catalysts and membranes. Molecular Simulation 32, 251-268.

 

2005

 

  1. Strachan, E. Kober, A.C.T. van Duin,  J. Oxgaard and W.A. Goddard III (2005) Thermal decomposition of RDX from reactive molecular dynamics, J. Chem. Phys. 122, 054502.
  2. Nielson, K.D., van Duin, A.C.T., Oxgaard, J.., Deng, W. and Goddard III, W.A. (2005) Development of the ReaxFF reactive force field for describing transition metal catalyzed reactions, with application to the initial stages of the catalytic formation of carbon nanotubes. J. Phys. Chem. A. 109, 493.
  3. Cheung, S, Deng, W., van Duin, A.C.T. and Goddard III, W.A. (2005) ReaxFFMgH Reactive Force Field for Magnesium Hydride Systems, J. Phys. Chem. A. 109, 851.
  4. Chen, N., Lusk, M.T., van Duin, A.C.T. and Goddard, W.A. (2005) Mechanical properties of connected carbon nanorings from molecular dynamics, Physical Review B. 72, 085416.
  5. Han, S.S., van Duin, A.C.T., Goddard W.A. and Lee, H.M. (2005) Optimization and application of Lithium parameters for the reactive force field ReaxFF, Journal of Physical Chemistry A. 109, 4575-4582.
  6. Han, S.S., Kang, J.K., van Duin, A.C.T., Goddard, W.A. and Lee, H.M. (2005) Liquefaction of hydrogen molecules upon carbon nanotube bundle surface, Applied Physics Letters 86, 203108.
  7. Chenoweth, K., Cheung, S., van Duin, A.C.T., Goddard, W.A. and Kober, E.M. (2005) Simulations on the thermal decompositions of a poly(dimethylsiloxane) polymer using the ReaxFF reactive force field, Journal of the American Chemical Society, 127, 7192-7202.
  8. van Duin, A.C.T., Zeiri, Y., Dubnilova, F., Kosloff, R. and Goddard, W.A (2005) Atomistic scale simulations of the initial chemical events in the thermal initiation of triacetonetriperoxide, Journal of the American Chemical Society 127, 11053-11062.
  9. Han, S.S., Kang, J.K., Lee, H.M., van Duin, A.C.T. and Goddard, W.A. (2005) The theoretical study on interaction of hydrogen with single-walled boron nitride nanotubes. I. The reactive force field ReaxFFHBN development. Journal of Chemical Physics 123, 114703.
  10. Han, S.S., Kang, J.K., Lee, H.M., van Duin, A.C.T. and Goddard, W.A. (2005) Theoretical study on interaction of hydrogen with single-walled boron nitride nanotubes. II. Collision, storage and adsorption. Journal of Chemical Physics 123, 114704.

 

2004

 

  1. Q. Zhang, T. Cagin, A.C.T. van Duin, W.A. Goddard, Y. Qi and L.G. Hector (2004) Adhesion and nonwetting-wetting transition in the Al/a-Al2O3 interface. Phys. Rev. B 69, 045423.
  2. M.A.Sugden, A.C.T. van Duin and G.D. Abbott (2004) Degradation of 5a-cholestane into dimethylperhydrophenanthrenes: an experimental and theoretical study. Org. Geochem.  In press.

 

2003

 

  1. A.C.T. van Duin and J.S. Sinninghe Damsté (2003) Computational chemical investigation into isorenieratene cyclisation. Org. Geochem 34, 515-526
  2. A.C.T. van Duin, A. Strachan, S. Stewman, Q. Zhang and W.A. Goddard III (2003) ReaxFFSiO reactive force field for silicon and silicon oxide systems, J. Phys. Chem. A 107, 3803-3811.
  3. A. Strachan, A.C.T. van Duin, D. Chakraborty, S. Dasgupta and W.A. Goddard III (2003) Shock waves in high-energy materials: the initial chemical events in nitramine RDX. Phys. Rev. Letters 91, 098301.
  4. D. Nguyen-Manh, D.J.H. Cockayne, M. Doeblinger, C. Marsh, A.P. Sutton and A.C.T. van Duin (2003) Structural modelling of nano-amorphous Si-O-N films in silicon nitride ceramics. Inst. Phys. Conf. Ser. No 179; Section 2, 139.

 

2002

 

  1. T.B.P. Oldenburg, H. Wilkes, B. Horsfield, A.C.T. van Duin, D. Stoddart, and A. Wilhelms (2002) Xanthones-novel aromatic oxygen-containing compounds in crude oils, Org. Geochem. 33, 595-609.
  2. C.M. Aitken, A.C.T. van Duin and M.J. Collins (2002) Understanding bioavailability of polycyclic aromatic hydrocarbons: Mechanisms and prediction, in Bioremediation: a critical review (eds. I. Singleton, I.M. Head and  M.G. Milner), Horizon Press, Norfolk, England.
  3. J.S. Watson, D.M. Jones, R.P.J. Swannell and A.C.T. van Duin (2002) Formation of carboxylic acids during biodegradation of crude oil and evidence of microbial oxidation of hopanes, accepted for publication in Org. Geochem.
  4. J. S. Sinninghe Damsté, M. Strous, W. I. C. Rijpstra, E. C. Hopmans, J. A.J. Geenevasen, A. C.T. van Duin, L.A. van Niftrik and M.S.M. Jetten (2002) Linearly concatenated cyclobutane lipids form a dense bacterial membrane, Nature, 419, 708-712.
  5. J.S. Sinninghe Damsté, S. Schouten, E.C. Hopmans, A.C.T. van Duin and J.A.J. Geenevasen (2002) Crenarchaeol: the characteristic core glycerol dibiphytanyl glycerol tetraether membrane lipid of cosmopolitan pelagic crenarchaeota, J. Lipid Res. 43, 1641-1651

 

2001

 

  1. A.C.T. van Duin and S.R. Larter (2001) Molecular dynamics investigation into the adsorption of organic compounds on kaolinite surfaces, Org. Geochem. 32, 143-150..
  2. J.S. Sinninghe Damsté, S. Schouten and A.C.T. van Duin (2001) Isorenieratene derivatives in sediments: Possible controls on their distribution, Geochim. Cosmochim. Acta 65, 1557-1571.
  3. A.C.T. van Duin, S. Dasgupta, F. Lorant and W.A. Goddard (2001) ReaxFF: a reactive force field for hydrocarbons,  J. Phys. Chem. A 105, 9396-9409.
  4. A.C.T. van Duin and S.R. Larter (2001) A computational chemical study of penetration and displacement of water films near mineral surfaces, Geochem. Trans. 6.

 

2000

 

  1. S.T. Belt, W.G. Allard, J. Rintatalo, L.A.Johns, A.C.T. van Duin and S.J. Rowland (2000) Clay and acid catalysed isomerisation and cyclisation reactions of highly branched isoprenoids (HBI) alkenes: implications for sedimentary reactions and distributions, Geochim. Cosmochim. Acta 64, 3337-3345.
  2. C. Jiang, M. Li and A.C.T. van Duin (2000) Inadequate separation of saturate and monoaromatic hydrocarbons in crude oils and rock extracts by alumina column chromatography, Org. Geochem. 31, 751-756.

 

1999

 

  1. J.S. Sinninghe Damsté, S. Schouten, J.W. de Leeuw, A.C.T. van Duin and J.A.J. Geenevasen (1999) Identification of novel sulfur-containing steroids in sediments and petroleum. Evidence for the incorporation of sulfur into D5,7-sterols during early diagenesis, Geochim. Cosmochim. Acta. 63, 31-38.
  2. E.R. Waite, M.J. Collins and A.C.T. van Duin (1999) Hydroxyproline interference during the gas chromatographic analysis of D/L aspartic acid in dentine, Int. Journal of Legal Medicine, 112, 124-131.
  3. M.J. Collins, E.R. Waite and A.C.T. van Duin (1999) Predicting protein decomposition, the case of aspartic acid racemization kinetics, Phil. Trans. Roy. Soc. Ser. B. 354, 51-64.

 

1998

 

  1. A.C.T. van Duin and S.R. Larter (1998) Application of molecular dynamics calculations in the prediction of dynamical molecular properties, Org. Geochem. 29, 1043-1050.
  2. A.C.T. van Duin and M. Collins (1998) The effects of conformational constraints on aspartic acid racemization, Org. Geochem. 29, 1227-1232.
  3. M.J. Collins, A.M. Child, A.C.T. van Duin and C. Vermeer (1998) Is osteocalcin stabilised in ancient bones by adsorption to bioapatite? Ancient Biomolecules. 2, 223-233.

 

1997

 

  1. A.C.T. van Duin, J.S. Sinninghe Damsté, M.P. Koopmans, B. van de Graaf and J.W. de Leeuw (1997) A kinetic calculation method of homohopanoid maturation: Applications in the reconstruction of burial histories of sedimentary basins. Geochim. Cosmochim. Acta 61, 2409-2429.
  2. A.C.T. van Duin, J.M.A. Baas, B. van de Graaf, J.W. de Leeuw, T.M. Bastow and R. Alexander (1997) Comparison of calculated equilibrium mixtures of alkylnaphthalenes and alkylphenanthrenes with experimental and sedimentary data; The importance of entropy calculations, Org. Geochem.26, 275-280.
  3. A.C.T. van Duin and S.R. Larter (1997) Unravelling Mango's mysteries: a kinetic scheme  describing the diagenetic fate of  C7-alkanes in petroleum systems. Org. Geochem.27, 597-599.

 

1996

 

  1. A.C.T. van Duin, J.M.A. Baas and B. van de Graaf (1996) Molecular mechanics force field for tertiary carbocations, J. Chem. Soc. Faraday Trans., 92, 353-362.
  2. A.C.T. van Duin, T.M. Peakman, B. van de Graaf and J.W. de Leeuw (1996) Novel aspects of the diagenesis of D7-5a-sterenes as revealed by a combined molecular mechanics calculations and laboratory simulations approach, Org. Geochem., 24, 473-493.
  3. A.C.T. van Duin, B. Hollanders, R.J.A. Smits, M.P. Koopmans, J.M.A. Baas, B. van de Graaf and J.W. de Leeuw (1996) Molecular mechanics calculation of the rotational barriers of 2,2',6'-trialkylbiphenyls to explain their GC-elution behaviour, Org. Geochem., 24, 587-591.
  4. Wei-Chuan Lai, Chunsan Song, A.C.T. van Duin and J.W. de Leeuw (1996) Ring-shift isomerization of [sym]-octahydrophenanthrene into [sym]-octahydrophenanthrene. Effects of zeolite catalysis and equilibrium compositions. Catal. Today  31 (1-2), 145-161.
  5. E.J. Creyghton, A.C.T. van Duin, J.C. Jansen, H. v. Bekkum, P.J. Kooyman and H.W. Zandbergen (1996) Synthesis of Pt-clusters in zeolite BEA: Effect of reduction rate on cluster size and location, J. Chem. Soc. Faraday Trans., 92, 4637-4642.

 

1993-1995

 

  1. J.S. Sinninghe Damsté, A.C.T. van Duin, D. Hollander, M.E.L. Kohnen and J.W. de Leeuw (1995) Early diagenesis of bacteriohopanepolyol derivatives:Formation of fossil homohopanoids, Geochim. Cosmochim. Acta 59, 5141-5157.
  2. A.C.T. van Duin, J.M.A. Baas and B. van de Graaf (1994) Delft molecular mechanics:A new approach to hydrocarbon force fields, J. Chem. Soc. Faraday Trans.90, 2881-2895.
  3. A.D. van Langeveld, A.C.T. van Duin, J.W. Bijsterbosch, F. Kapteijn and J.A. Moulijn (1993) Correlation of bulk and surface thermodynamics of some transition-metal oxides - applications to exhaust-gas catalysts, Stud. Surf. Sci. and Catal. 75, 2693-2696.