Stamatakis Research Group

Journal Articles

A comprehensive list of all the papers published by our group (as well as some older papers by Michail) can be found below. Each “doi” link points to the respective article on the website of the Journal it was published. If you do not have access to these Journals, you can download the article of interest from UCL Discovery (the publications repository of UCL), by following the corresponding link. Note, however, that certain publishers impose an embargo period, so not all of our papers can be obtained from UCL Discovery at the moment.

2021

Methoxy and formaldehyde coupling on gold.

Transition state for the coupling of
methoxy and formaldehyde on gold.

Papanikolaou, K. G. and M. Stamatakis (2021). “The Catalytic Decomposition of Nitrous Oxide and the NO + CO Reaction over Ni/Cu Dilute and Single Atom Alloy Surfaces: First-principles Microkinetic Modelling”. Catalysis Science & Technology Accepted. (doi: 10.1039/D1CY00011J)
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 Accepted. (doi: 10.1039/C9FD00134D) Get manuscript from UCL Discovery.
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)
Darby, M. T. and M. Stamatakis (2021). “Single-Atom Alloys for the Electrochemical Oxygen Reduction Reaction”. ChemPhysChem 22: 499-508. (doi: 10.1002/cphc.202000869) Get manuscript from UCL Discovery.
Apostolopoulou, M., Stamatakis, M., Striolo, A., Dusterhoft, R., Hull, R. and R. Day (2021). “A Novel Modeling Approach to Stochastically Evaluate the Impact of Pore Network Geometry, Chemistry and Topology on Fluid Transport”. Transport in Porous Media 136: 495-520. (doi: 10.1007/s11242-020-01522-w) Get manuscript from UCL Discovery.

2020

Wang, Y., Papanikolaou, K. G., Hannagan, R. T., Patel, D. A., Balema, T. A., Cramer, L. A., Kress, P. L., Stamatakis, M. and E. C. H. Sykes (2020). “Surface facet dependence of competing alloying mechanisms”. The Journal of Chemical Physics 153(24): 244702. (doi: 10.1063/5.0034520) Get manuscript from UCL Discovery.
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) Get manuscript from UCL Discovery.
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) Get manuscript from UCL Discovery.
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) Get manuscript from UCL Discovery.
Papanikolaou, K. G. and M. Stamatakis (2020). “On the behaviour of structure-sensitive reactions on single atom and dilute alloy surfaces”. Catalysis Science & Technology 10: 5815-5828. (doi: 10.1039/D0CY00904K) Get manuscript from UCL Discovery.
Chutia, A., Thetford, A., Stamatakis, M. and C. R. A. Catlow (2020). “A DFT and KMC Based Study on the Mechanism of Water Gas Shift Reaction on Pd(100) Surface”. Physical Chemistry Chemical Physics 22: 3620-3632. (doi: 10.1039/C9CP05476F) Get manuscript from UCL Discovery.
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. (doi: 10.1021/acscatal.9b04029) Get manuscript from UCL Discovery.

2019

Réocreux, R., Uhlman, M., Thuening, T., Kress, P., Hannagan, R., Stamatakis, M. and E. C. H. Sykes (2019). “Efficient and Selective Carbon-Carbon Coupling on Coke-Resistant PdAu Single-Atom Alloys”. Chemical Communications 55: 15085-15088. (doi: 10.1039/C9CC07932G) Get manuscript from UCL Discovery.
Apostolopoulou, M., Simoes Santos, M., Hamza, M., Bui, T., Economou, I. G., Stamatakis, M. and A. Striolo (2019). “Quantifying Pore Width Effects on Diffusivity via a Novel 3D Stochastic Approach with Input from Atomistic Molecular Dynamics Simulations”. Journal of Chemical Theory and Computation 15(12): 6907-6922. (doi: 10.1021/acs.jctc.9b00776) Get manuscript from UCL Discovery.
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(10): 9446-9457. (doi: 10.1021/acs.jpcc.9b01213) Get manuscript from UCL Discovery.
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) Get manuscript from UCL Discovery.
Papanikolaou, K. G., Darby, M. T. and M. Stamatakis (2019). “CO-Induced Aggregation and Segregation of Highly Dilute Alloys: A Density Functional Theory Study”. The Journal of Physical Chemistry C 123(14): 9128-9138. (doi: 10.1021/acs.jpcc.9b00649) Get manuscript from UCL Discovery.
Apostolopoulou, M., Dusterhoft, R., Day, R., Stamatakis, M., Coppens, M.-O. and A. Striolo (2019). “Estimating permeability in shales and other heterogeneous porous media: Deterministic vs. stochastic investigations”. International Journal of Coal Geology 205: 140-154. (doi: 10.1016/j.coal.2019.02.009) Get manuscript from UCL Discovery.

Theory, surface science and catalysis in synergy.

Synergy between theory and experiment
in predicting single-atom alloys
that break linear scaling.

2018

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) Get manuscript from UCL Discovery.
Pineda, M. and M. Stamatakis (2018). “Non-Equilibrium Thermodynamics and Stochastic Dynamics of a Bistable Catalytic Surface Reaction”. Entropy 20(11): 811. (doi: 10.3390/e20110811) Get manuscript from UCL Discovery.
Darby, M. T., Stamatakis, M., Michaelides, A. and E. C. H. Sykes (2018). “Lonely Atoms with Special Gifts: Breaking Linear Scaling Relationships in Heterogeneous Catalysis with Single-Atom Alloys”. The Journal of Physical Chemistry Letters 9: 5636-5646. (doi: 10.1021/acs.jpclett.8b01888) Get manuscript from UCL Discovery.
Pineda, M. and M. Stamatakis (2018). “On the stochastic modelling of surface reactions through reflected chemical Langevin equations”. Computers & Chemical Engineering 117: 145-158. (doi: 10.1016/j.compchemeng.2018.05.003) Get manuscript from UCL Discovery.
Darby, M. T., Réocreux, R., Sykes, E. C. H., Michaelides, A. and M. Stamatakis (2018). “Elucidating the Stability and Reactivity of Surface Intermediates on Single Atom Alloy Catalysts”. ACS Catalysis 8(6): 5038-5050. (doi: 10.1021/acscatal.8b00881) Get manuscript from UCL Discovery.
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) Get manuscript from UCL Discovery.
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) Get manuscript from UCL Discovery.

2017

Apostolopoulou, M., Day, R., Hull, R., Stamatakis, M. and A. Striolo (2017). “A kinetic Monte Carlo approach to study fluid transport in pore networks”. The Journal of Chemical Physics 147(13): 134703. (doi: 10.1063/1.4985885) Get manuscript from UCL Discovery.
Vignola, E., Steinmann, S. N., Vandegehuchte, B. D., Curulla, D., Stamatakis, M. and P. Sautet (2017). “A machine learning approach to graph-theoretical cluster expansions of the energy of adsorbate layers”. The Journal of Chemical Physics 147(5): 054106. (doi: 10.1063/1.4985890) Get manuscript from UCL Discovery.
Liu, G., Robertson, A. W., Li, M. M.-J., Kuo, W. C. H., Darby, M. T., Muhieddine, M. H., Lin, Y.-C., Suenaga, K., Stamatakis, M., Warner, J. H. and S. C. E. Tsang (2017). “MoS₂ monolayer catalyst doped with isolated Co atoms for the hydrodeoxygenation reaction”. Nature Chemistry, 9(8): 810-816. (doi: 10.1038/nchem.2740) Get manuscript from UCL Discovery.
Pineda, M. and M. Stamatakis (2017). “Beyond mean-field approximations for accurate and computationally efficient models of on-lattice chemical kinetics”. The Journal of Chemical Physics, 147(2): 024105. (doi: 10.1063/1.4991690) Get manuscript from UCL Discovery.
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) Get manuscript from UCL Discovery.

Decomposing the factors shaping apparent CO oxidation kinetics on Pd(111).

2016

Teixeira, I. F., Lo, B. T. W., Kostetskyy, P., Stamatakis, M., Ye, L., Tang, C. C., Mpourmpakis, G., and S. C. E. Tsang (2016). “A New Facilitated Process of Biomass-Derived Furans to p-Xylene with Ethanol over Zeolite”. Angewandte Chemie International Edition, 55(42): 13061-13066. (doi: 10.1002/anie.201604108) Get manuscript from UCL Discovery.
Campbell, C., Bowker, M., Stamatakis, M., Hutchings, G., Davies, P., Earley, J., Howard, M., Garrett, B., Oloye, F., Gross, E., et al. (2016). “Bridging model and real catalysts: general discussion”. Faraday Discussions, 188: 565-589. (doi: 10.1039/C6FD90017H)
Campbell, C., van Santen, R., Stamatakis, M., Collis, N., Freund, H.-J., Plaisance, C., Sauer, J., Garrett, B., Gross, E., et al. (2016). “Catalyst design from theory to practice: general discussion”. Faraday Discussions, 188: 279-307. (doi: 10.1039/C6FD90016J)
Wang, Z.-T., Darby, M. T., Therrien, A. J., El-Soda, M., Michaelides, A., Stamatakis, M., and E. C. H. Sykes (2016). “Preparation, Structure, and Surface Chemistry of Ni-Au Single Atom Alloys”. The Journal of Physical Chemistry C, 120: 13574-13580. (doi: 10.1021/acs.jpcc.6b03473) Get manuscript from UCL Discovery.
Stamatakis, M. and S. Piccinin (2016). “Rationalising the relation between adlayer structure and observed kinetics in catalysis”. ACS Catalysis, 6: 2105-2111. (doi: 10.1021/acscatal.5b02876) Get manuscript from UCL Discovery.
Lucci, F. R., Darby, M. T., Mattera, M. F. G., Ivimey, C. J., Therrien, A. J., Michaelides, A., Stamatakis, M. and E. C. H. Sykes (2016). “Controlling Hydrogen Activation, Spillover, and Desorption with Pd-Au Single Atom Alloys”. The Journal of Physical Chemistry Letters, 7: 480-485. (doi: 10.1021/acs.jpclett.5b02400) Get manuscript from UCL Discovery.

2015

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. (doi: 10.1039/C4CY01295J) Get manuscript from UCL Discovery.
M. Stamatakis (2015). “Kinetic modelling of heterogeneous catalytic systems”. Journal of Physics: Condensed Matter, 27: 013001. (doi: 10.1088/0953-8984/27/1/013001) Get manuscript from UCL Discovery.

2014

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) Get manuscript from UCL Discovery.
Herrmann, S., Stamatakis, M., Andriotis, A. N. and G. Mpourmpakis (2014). “Adsorption Behavior of Noble Metal Clusters and Their Alloys”. Journal of Computational and Theoretical Nanoscience, 11(2): 511-520. (doi: 10.1166/jctn.2014.3387) Get manuscript from UCL Discovery.

2013

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) Get manuscript from UCL Discovery.
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) Get manuscript from UCL Discovery.
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) Get manuscript from UCL Discovery.
M. Stamatakis (2013). “Cell Population Balance and Hybrid Modeling of Population Dynamics for a Single Gene with Feedback”. Computers & Chemical Engineering, 53: 25-34. (doi: 10.1016/j.compchemeng.2013.02.006) Get manuscript from UCL Discovery.

Potential energy surface for a reaction event.

An elementary reaction viewed as barrier-crossing on a potential energy surface.

2012

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) Get manuscript from UCL Discovery.
Stamatakis, M., Christiansen, M., D. G. Vlachos 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) Get manuscript from UCL Discovery.

2011

Stamatakis, M., Adams, R. M. and G. Balázsi (2011). “A Common Repressor Pool Results in Indeterminacy of Extrinsic Noise”. Chaos, 21: 047523. Focus Issue: “Nonlinear and Stochastic Physics in Biology” dedicated to the memory of Frank Moss. (doi: 10.1063/1.3658618) Get manuscript from UCL Discovery.
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) Get manuscript from UCL Discovery.
Mpourmpakis, G., Stamatakis, M., Herrmann, S., Vlachos, D. G. and A. N. Andriotis (2011). “Predicting the Adsorption Behavior in Bulk from Metal Clusters”. Chemical Physics Letters, 518: 99-103. (doi: 10.1016/j.cplett.2011.11.004) Get manuscript from UCL Discovery.
Stamatakis, M. and D. G. Vlachos (2011). “Equivalence of on-Lattice Stochastic Chemical Kinetics with the Well-Mixed Chemical Master Equation in the Limit of Fast Diffusion”. Computers & Chemical Engineering, 35(12): 2602-2610. (doi: 10.1016/j.compchemeng.2011.05.008) Get manuscript from UCL Discovery.
Salciccioli, M., Stamatakis, M., Caratzoulas, S. and D. G. Vlachos (2011). “A Review of Multiscale Modeling of Metal-Catalyzed Reactions: Mechanism Development for Complexity and Emergent Behavior”. Chemical Engineering Science, 66(19): 4319-4355. (doi: 10.1016/j.ces.2011.05.050) Get manuscript from UCL Discovery.
Stamatakis, M. and K. Zygourakis (2011). “Deterministic and Stochastic Population-Level Simulations of an Artificial lac Operon Genetic Network”. BMC Bioinformatics, 12: 301. (doi: 10.1186/1471-2105-12-301) Get manuscript from UCL Discovery.
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) Get manuscript from UCL Discovery.

2010

Wang, H., Stamatakis, M., Hansgen, D., Caratzoulas, S., and D. Vlachos (2010). “Understanding Mixing of Ni and Pt in the Ni/Pt(111) Bimetallic Catalyst via Molecular Simulation and Experiments”. The Journal of Chemical Physics, 133(22): 224503. (doi: 10.1063/1.3512644) Get manuscript from UCL Discovery.
Stamatakis, M. and N. V. Mantzaris (2010). “Intrinsic Noise and Division Cycle Effects on an Abstract Biological Oscillator”. Chaos, 20: 033118. (doi: 10.1063/1.3484868) Get manuscript from UCL Discovery.
Stamatakis, M. and K. Zygourakis (2010). “A Mathematical and Computational Approach for Integrating the Major Sources of Cell Population Heterogeneity.” Journal of Theoretical Biology, 266(1): 41-61. (doi: 10.1016/j.jtbi.2010.06.002) Get manuscript from UCL Discovery.
Collins, S., Stamatakis, M. and D. G. Vlachos (2010) “Adaptive Coarse-Grained Monte Carlo Simulation of Reaction and Diffusion Dynamics in Heterogeneous Plasma Membranes.” BMC Bioinformatics, 11: 218. (doi: 10.1186/1471-2105-11-218) Get manuscript from UCL Discovery.
M. Stamatakis (2010). “Cell Population Balance, Ensemble and Continuum Modeling Frameworks: Conditional Equivalence and Hybrid Approaches.” Chemical Engineering Science, 65(2): 1008-1015. (doi: 10.1016/j.ces.2009.09.054) Get manuscript from UCL Discovery.

Surface plot of LacY permease stationary potential.

Comparison of bistable regimes for deterministic and stochastic lac operon models.

2006-2009

Stamatakis, M. and N. V. Mantzaris (2009). “Comparison of Deterministic and Stochastic Models of the lac Operon Genetic Network.” Biophysical Journal, 96(3): 887-906. (doi: 10.1016/j.bpj.2008.10.028) Get manuscript from UCL Discovery.
Stamatakis, M. and N. V. Mantzaris (2007). “Astrocyte Signaling in the Presence of Spatial Inhomogeneities.” Chaos, 17: 033123. (doi: 10.1063/1.2767409) Get manuscript from UCL Discovery.
Stamatakis, M. and N. V. Mantzaris (2006). “Modeling of ATP-Mediated Signal Transduction and Wave Propagation in Astrocytic Cellular Networks.” Journal of Theoretical Biology, 241(3): 649-668. (doi: 10.1016/j.jtbi.2006.01.002) Get manuscript from UCL Discovery.

Book Chapters

2020

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).

2016

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).

Selected Conference Papers

2019

Inyang, U., Cortez-Montalvo, J., Dusterhoft, R., Apostolopoulou, M., Striolo, A. and M. Stamatakis (2019). “A Kinetic Monte Carlo Study to Investigate the Effective Permeability and Conductivity of Microfractures within Unconventional Reservoirs”. SPE Oklahoma City Oil and Gas Symposium, 9-10 April, Oklahoma City, Oklahoma, USA. Doc. ID: SPE-195220-MS (doi: 10.2118/195220-MS)