Publications

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

Method Development

Prats, H., Li, W. and M. Stamatakis (2025). “A General Stiffness-Scaling Framework for Accelerating Graph-Theoretical Kinetic Monte Carlo Simulations”. Journal of Chemical Theory and Computation, In Press. (doi: 10.1021/acs.jctc.5c01394)

Benson, R. L., Yadavalli, S. S. and M. Stamatakis (2023). “Speeding up the Detection of Adsorbate Lateral Interactions in Graph-Theoretical Kinetic Monte Carlo Simulations”. The Journal of Physical Chemistry A, 127: 10307-10319. (doi: 10.1021/acs.jpca.3c05581)

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

Yadavalli, S. S., Jones, G., Fonte, C. and M. Stamatakis (2025). “Elucidating the Role of Potassium in Methane Steam Reforming using First-Principles-Based Kinetic Monte Carlo Simulations”. Journal of Catalysis, 448: 116203. (doi: 10.1016/j.jcat.2025.116203)

Prats, H. and M. Stamatakis (2025). “First-Principles Kinetic Monte Carlo Simulations for Single-Cluster Catalysis: Study of CO₂ and CH₄ Conversion on Pt/HfC”. ACS Catalysis, 15: 2904–2915. (doi: 10.1021/acscatal.4c07877)

Colombi Manzi, E., Stamatakis, M., Di Liberto, G. and G. Pacchioni (2025). “Hydrogen complexes on single-atom alloys: A combined DFT — Kinetic Monte Carlo study”. Surface Science, 754: 122688. (doi: 10.1016/j.susc.2024.122688)

Berger, F., Schumann, J., Réocreux, R., Stamatakis, M. and A. Michaelides (2024). “Bringing Molecules Together: Synergistic Coadsorption at Dopant Sites of Single Atom Alloys”. Journal of the American Chemical Society, 146(41): 28119-28130. (doi: 10.1021/jacs.4c07621)

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)

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)

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

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

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)