Below you can find lists of publications pertinent to the development and use of Zacros.

Method Development

Savva, G. D., Benson, R. L., Christidi, I.-A. and M. Stamatakis (2023). “Exact distributed kinetic Monte Carlo simulations for on-lattice chemical kinetics: lessons learnt from medium- and large-scale benchmarks”. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 381(2250): 20220235 [Invited paper]. (doi: 10.1098/rsta.2022.0235)

Savva, G. D., Benson, R. L., Christidi, I.-A. and M. Stamatakis (2023). “Large-scale benchmarks of the Time-Warp/Graph-Theoretical Kinetic Monte Carlo approach for distributed on-lattice simulations of catalytic kinetics”. Physical Chemistry Chemical Physics, 25: 5468-5478 [Invited paper]. (doi: 10.1039/D2CP04424B)

Ravipati, S., Savva, G. D., Christidi, I. A., Guichard, R., Nielsen, J., Réocreux, R. and M. Stamatakis (2022). “Coupling the Time-Warp algorithm with the Graph-Theoretical Kinetic Monte Carlo framework for distributed simulations of heterogeneous catalysts”. Computer Physics Communications, 270: 108148. (doi: 10.1016/j.cpc.2021.108148)

Savva, G. D. and M. Stamatakis (2020). “Comparison of queueing data-structures for kinetic Monte Carlo simulations of heterogeneous catalysts”. The Journal of Physical Chemistry A, 124(38): 7843-7856. (doi: 10.1021/acs.jpca.0c06871)

Ravipati, S., Nielsen, J., d’Avezac, M., Hetherington, J. and M. Stamatakis (2020). “A caching scheme to accelerate kinetic Monte Carlo simulations of catalytic reactions”. The Journal of Physical Chemistry A, 124(35): 7140-7154. (doi: 10.1021/acs.jpca.0c03571)

Nielsen, J., d’Avezac, M., Hetherington, J. and M. Stamatakis (2013). “Parallel kinetic Monte Carlo simulation framework incorporating accurate models of adsorbate lateral interactions”. The Journal of Chemical Physics, 139(22): 224706. (doi: 10.1063/1.4840395)

Stamatakis, M. and D. G. Vlachos (2011). “A Graph-Theoretical Kinetic Monte Carlo framework for on-lattice chemical kinetics”. The Journal of Chemical Physics, 134(21): 214115. (doi: 10.1063/1.3596751)

Applications

Cover art for the 11 May 2023 issue of The Journal of Physical Chemistry C.Yadavalli, S. S., Jones, G., Benson, R. L. and M. Stamatakis (2023). “Assessing the Impact of Adlayer Description Fidelity on Theoretical Predictions of Coking on Ni(111) at Steam Reforming Conditions”. The Journal of Physical Chemistry C, 127(18): 8591–8606  [Featured on the cover of the issue]. (doi: 10.1021/acs.jpcc.3c02323)

Peña-Torres, A., Ali, A., Stamatakis, M., and H. Jónsson (2022). “Indirect Mechanism of Au adatom Diffusion on the Si(100) Surface”. Physical Review B, 105: 205411. (doi: 10.1103/PhysRevB.105.205411)

Han, E., Fang, W., Stamatakis, M., Richardson, J. O., and J. Chen (2022). “Quantum Tunnelling Driven H2 Formation on Graphene”. The Journal of Physical Chemistry Letters, 13: 3173-3181. (doi: 10.1021/acs.jpclett.2c00520)

 

Schumann, J., Bao, Y., Hannagan, R. T., Sykes, E. C. H., Stamatakis, M. and A. Michaelides (2021). “Periodic trends in adsorption energies around single-atom alloy active sites”. The Journal of Physical Chemistry Letters, 12(41): 10060-10067. (doi: 10.1021/acs.jpclett.1c02497)

Réocreux, R., Fampiou, I. and M. Stamatakis (2021). “The role of oxygenated species in the catalytic self-coupling of MeOH on O pre-covered Au(111)”. Faraday Discussions, 229: 251-266. (doi: 10.1039/C9FD00134D)

Kress, P., Romain Réocreux, Hannagan, R., Thuening, T., Boscoboinik, J. A., Stamatakis, M. and E. C. H. Sykes (2021). “Mechanistic insights into carbon–carbon coupling on NiAu and PdAu single-atom alloys”. The Journal of Chemical Physics, 154(20): 204701. (doi: 10.1063/5.0048977)

Ouyang, M., Papanikolaou, K. G., Boubnov, A., Hoffman, A. S., Giannakakis, G., Bare, S. R., Stamatakis, M., Flytzani-Stephanopoulos, M. and E. Charles H. Sykes (2021). “Directing reaction pathways via in situ control of active site geometries in PdAu single-atom alloy catalysts”. Nature Communications, 12: 1549. (doi: 10.1038/s41467-021-21555-z)

Réocreux, R., Kress, P. L., Hannagan, R. T., Çinar, V., Stamatakis, M. and E. C. H. Sykes (2020). “Controlling Hydrocarbon (De)Hydrogenation Pathways with Bifunctional PtCu Single-Atom Alloys”. The Journal of Physical Chemistry Letters, 11(20): 8751-8757. (doi: 10.1021/acs.jpclett.0c02455)

Cover art of 17 January 2020 issue of ACS Catalysis

Papanikolaou, K. G., Darby, M. T. and M. Stamatakis (2020). “Engineering the surface architecture of highly dilute alloys: an ab initio Monte-Carlo approach”. ACS Catalysis, 10: 1224-1236 [Featured on the cover of the issue]. (doi: 10.1021/acscatal.9b04029)

Réocreux, R., Uhlman, M., Thuening, T., Kress, P., Hannagan, R., Stamatakis, M. and C. Sykes (2019). “Efficient and Selective Carbon-Carbon Coupling on Coke-Resistant PdAu Single-Atom Alloys”. Chemical Communications, 55: 15085-15088. (doi: 10.1039/C9CC07932G)

Chen, B. W. J., Stamatakis, M. and M. Mavrikakis (2019). “Kinetic Isolation between Turnovers on Au18 Nanoclusters: Formic Acid Decomposition One Molecule at a Time”. ACS Catalysis, 9: 9446-9457. (doi: 10.1021/acscatal.9b02167)

Darby, M. T., Lucci, F. R., Marcinkowski, M. D., Therrien, A., Michaelides, A., Stamatakis, M. and E. C. H. Sykes (2019). “Carbon Monoxide Mediated Hydrogen Release from PtCu Single-Atom Alloys: The Punctured Molecular Cork Effect”. The Journal of Physical Chemistry C, 123(16): 10419-10428. (doi: 10.1021/acs.jpcc.9b01213)

Papanikolaou, K. G., Darby, M. T. and M. Stamatakis (2018). “Adlayer structure and lattice size effects on catalytic rates predicted from KMC simulations: NO oxidation on Pt(111)”. The Journal of Chemical Physics, 149(18): 184701. (doi: 10.1063/1.5048787)

Darby, M. T., Sykes, E. C. H., Michaelides, A. and M. Stamatakis (2018). “Carbon Monoxide Poisoning Resistance and Structural Stability of Single Atom Alloys”. Topics in Catalysis, 61(5–6): 428-438. (doi: 10.1007/s11244-017-0882-1)

 

Marcinkowski, M. D., Darby, M. T., Liu, J., Wimble, J. M., Lucci, F. R., Lee, S., Michaelides, A., Flytzani-Stephanopoulos, M., Stamatakis, M. and E. C. H. Sykes (2018). “Pt/Cu single-atom alloys as coke-resistant catalysts for efficient C–H activation”. Nature Chemistry, 10: 325-332. (doi: 10.1038/nchem.2915)

Piccinin, S. and M. Stamatakis (2017). “Steady-State CO Oxidation on Pd(111): First-Principles Kinetic Monte Carlo Simulations and Microkinetic Analysis”. Topics in Catalysis, 60(1): 141-151. (doi: 10.1007/s11244-016-0725-5)

Stamatakis, M. and S. Piccinin (2016). “Rationalising the relation between adlayer structure and observed kinetics in catalysis”. ACS Catalysis, 6(3): 2105-2111. (doi: 10.1021/acscatal.5b02876)

Cover art of January 2015 issue of Catalysis Science and Technology

 

Nikbin, N., Austin, N., Vlachos, D., Stamatakis, M. and G. Mpourmpakis (2015). “Catalysis at the Sub-Nanoscale: Complex CO Oxidation Chemistry on a Few Au Atoms”. Catalysis Science & Technology, 5(1): 134-141 [Featured on the cover of the issue]. (doi: 10.1039/C4CY01295J)

Piccinin, S. and M. Stamatakis (2014). “CO Oxidation on Pd(111): A First-Principles Based Kinetic Monte Carlo Study”. ACS Catalysis, 4: 2143-2152. (doi: 10.1021/cs500377j)

Guo, W., Stamatakis, M. and D. G. Vlachos (2013). “Design Principles of Heteroepitaxial Bimetallic Catalysts”. ACS Catalysis, 3(10): 2248-2255. (doi: 10.1021/cs4005166)

Marcinkowski, M. D., Jewell, A. D., Stamatakis, M., Boucher, M. B., Lewis, E. A., Murphy, C. J., Kyriakou, G. and E. C. H. Sykes (2013). “Controlling a Spillover Pathway with the Molecular Cork Effect”. Nature Materials, 12(6): 523-528. (doi: 10.1038/nmat3620)

Stamatakis, M., Christiansen, M.,Vlachos, D. G. and G. Mpourmpakis (2012). “Multiscale Modeling Reveals Poisoning Mechanisms on MgO-supported Au Catalysts in CO Oxidation”. Nano Letters, 2(7): 3621-3626. (doi: 10.1021/nl301318b)

Stamatakis, M., Chen, Y. and D. G. Vlachos (2011). “First Principles-Based Kinetic Monte Carlo Simulation of the Structure-Sensitivity of the Water-Gas Shift Reaction on Platinum Surfaces”. Journal of Physical Chemistry C, 115(50): 24750-24762. (doi: 10.1021/jp2071869)

Reviews

Cover art of the 28 March 2022 issue of The Journal of Chemical Physics

 

Pineda, M., and M. Stamatakis (2022). “Kinetic Monte Carlo simulations for heterogeneous catalysis: Fundamentals, current status and challenges”. The Journal of Chemical Physics, 156(12): 120902. (doi: 10.1063/5.0083251)

M. Stamatakis (2015). “Kinetic modelling of heterogeneous catalytic systems”. Journal of Physics: Condensed Matter 27: 013001. (doi: 10.1088/0953-8984/27/1/013001)

Stamatakis, M. and D. G. Vlachos (2012). “Unraveling the Complexity of Catalytic Reactions via Kinetic Monte Carlo Simulation: Current Status and Frontiers”. ACS Catalysis 2(12): 2648-2663. (doi: 10.1021/cs3005709)

Book Chapters

Papanikolaou, K. G. and M. Stamatakis (2020). “Chapter 7: Toward the accurate modeling of the kinetics of surface reactions using the kinetic Monte Carlo method” in Grammatikopoulos, P. (Ed.), Computational Modelling of Nanomaterials, Amsterdam, Netherlands: Elsevier. (doi: 10.1016/B978-0-12-821495-4.00007-5)

Darby, M. T., Piccinin, S. and M. Stamatakis (2016). “Chapter 4: First principles-based kinetic Monte Carlo simulation in catalysis” in Kasai, H. and M. C. S. E. Escaño (Eds.), Physics of Surface, Interface and Cluster Catalysis, Bristol, UK: IOP Publishing. (doi: 10.1088/978-0-7503-1164-9ch4)