Professor Emyr MacDonald

: Welsh speaking

Teams and roles for Emyr MacDonald

Emeritus Professor
Physics & Astronomy

I am an Emeritus Professor, having retired in September 2025.
During my research career I have published over 120 refereed papers in the areas of:

Applications of diffraction techniques to solve timely challenging problems relating to the atomic structure of solids, thin films and surfaces. In particular, we have used grazing incidence x-ray diffraction techniques to develop polymer-based photovoltaic materials and perovskite materials using the European Synchrotron Radiation Source at Grenoble and the Diamond Light Source near Oxford.
Nanoscale electrical measurements on organic semiconductors and on single protein molecules. The latter area involved directed mutagenesis to establish good electrical contacts of single proteins to noble metal surfaces and to graphene and carbon nanotubes as an essential step in developing nanoscale biosensors.
Molecular mechanisms of Free Energy Transduction, in particular in chemiosmotic ATP synthesis and in harnessing the free energy of ATP hydrolysis in ATPases. This is a continuing area of research, outlined under the Research section.

Date
Type

2009

Droge, S. et al., 2009. Grazing Incidence X-ray Diffraction of a Photoaligned Nematic Semiconductor. Journal of Physical Chemistry B 113 (1), pp.49-53. (10.1021/jp803379a)
Simmonds, H. S. et al. 2009. Self-assembled organic nanowires: a structural and electronic study. Journal of Vacuum Science and Technology. B, Nanotechnology and Microelectronics : Materials, Processing, Measurement, and Phenomena 27 (2) 831. (10.1116/1.3054198)
Zeng, X. et al., 2009. 3D ordered gold strings by coating nanoparticles with mesogens. Advanced Materials 21 (17), pp.1746-1750. (10.1002/adma.200803403)

2008

Zeng, X. B. et al., 2008. Small angle X-ray and neutron scattering in the study of polymers and supramolecular systems. Presented at: International Conference on Neutron and X-Ray Scattering Serpong and Bandung, Indonesia 23-31 July 2007. Published in: Ikram, A. ed. Neutron and X-Ray Scattering in Materials Science and Biology. AIP Conference Proceedings Vol. 989. Melville, NY: American Institute of Physics. , pp.68. (10.1063/1.2906097)

2006

Das, A. et al. 2006. Non-Lithographic Fabrication of PEDOT Nanowires Between Fixed Au Electrodes. Organic Electronics 7 (4), pp.181-187. (10.1016/j.orgel.2005.12.006)
Das, A. et al. 2006. EFM Phase Investigation of the Metal-Organic Film Interface. Applied Surface Science 252 (15), pp.5477-5480. (10.1016/j.apsusc.2005.12.091)

2005

Jukes, P. C. et al., 2005. Kinetics of surface crystallization in thin films of poly(ethylene terephthalate). Macromolecules 38 (6), pp.2315-2320. (10.1021/ma0490606)

2004

Lei, C. H. et al., 2004. Au-poly(3-hexylthiophene) Contact Behaviour at High Resolution. Synthetic Materials 145 (2-3), pp.217-220. (10.1016/j.synthmet.2004.05.003)
Lei, C. H. et al., 2004. Quantitative Electrostatic Force Microscopy-Phase Measurements. Nanotechnology 15 (5), pp.627-634. (10.1088/0957-4484/15/5/038)
Bolognesi, A. et al., 2004. Structural features in aligned poly(3-alkylthiophene) films revealed by grazing incidence X-ray diffraction. Polymer 45 (12), pp.4133-4138. (10.1016/j.polymer.2004.03.102)
Macdonald, J. E. et al. 2004. Applications of grazing incidence diffraction to polymer surfaces. Radiation Physics and Chemistry 71 (3-4), pp.811-815. (10.1016/j.radphyschem.2004.04.104)

2003

Lei, C. H. et al., 2003. Conductivity of Macromolecular Networks Measured by Electrostatic Force Microscopy. Applied Physics Letters 83 , pp.482-484. (10.1063/1.1592888)

2002

Durell, M. et al., 2002. The Role of Surface-Induced Ordering in the Crystallisation of PET Films. Europhysics Letters 58 , pp.844-850. (10.1209/epl/i2002-00451-1)
Kawana, S. et al., 2002. X-ray diffraction study of the structure of thin polyfluorene films. Polymer 43 (6), pp.1907-1913. (10.1016/S0032-3861(01)00753-4)

2001

Lu, J. et al., 2001. Initial stages of molecular-beam epitaxy growth of GaN on 6H-SiC(0001). Applied Physics Letters 78 (8), pp.1080-1083. (10.1063/1.1350430)
Macdonald, J. E. et al. 2001. Surface-induced ordering in polymers [Abstract]. Abstracts of Papers of the American Chemical Society 221 (1), pp.U352.

2000

Haworth, L. et al., 2000. Atomic hydrogen cleaning, nitriding and annealing InSb (100). Applied Surface Science 166 (1-4), pp.253-258. (10.1016/S0169-4332(00)00425-6)
Haworth, L. et al., 2000. Investigation into the influence of buffer and nitrided layers on the initial stages of GaN growth on InSb (100). Applied Surface Science 166 (1-4), pp.418-422. (10.1016/S0169-4332(00)00460-8)

1999

Edwards, K. A. et al., 1999. Observation of a structural transition during the low-temperature growth of the Si(111)7×7?Pb interface. Surface Science 424 (2-3), pp.169-178. (10.1016/S0039-6028(98)00880-2)
Lu, J. et al., 1999. Nitridation of the GaAs(001) surface: Thermal behavior of the (3×3) reconstruction and its evolution. Journal of Vacuum Science & Technology B: Microelectronics and Nanometer Structures 17 (4), pp.1659-1676. (10.1116/1.590806)
Lu, J. et al., 1999. The (3 × 3) reconstruction and its evolution during the nitridation of GaAs(001). Thin Solid Films 343-44 , pp.567-570. (10.1016/S0040-6090(98)01716-7)

1998

Hill, P. et al., 1998. An XPS study of the effect of nitrogen exposure time and temperature on the GaAs(001) surface using atomic nitrogen. Applied Surface Science 123-4 , pp.126-124. (10.1016/S0169-4332(97)00539-4)
Haworth, L. et al., 1998. Formation of an Sb-N compound during nitridation of InSb (001) substrates using atomic nitrogen. Journal of Vacuum Science & Technology B: Microelectronics and Nanometer Structures 16 (4), pp.2254-2261. (10.1116/1.590158)
Howes, P. B. et al., 1998. The atomic structure of the Si(111)-Pb buried interface grown on the reconstruction. Surface Review and Letters 5 (1) 163. (10.1142/S0218625X98000311)

1997

Bennett, M. R. et al., 1997. Photoemission studies of the surfactant-aided growth of Ge on Te-terminated Si(100). Surface Science 380 (2-3), pp.178-189. (10.1016/S0039-6028(96)01149-1)
Hill, P. et al., 1997. Nitridation of the GaAs (001) surface using atomic nitrogen. Journal of Vacuum Science & Technology B: Microelectronics and Nanometer Structures 15 (4), pp.1133-1139. (10.1116/1.589427)
Schmicker, D. et al., 1997. Low-temperature growth of thin Pb layers and the quantum size effect. Journal of Physics: Condensed Matter 9 (5) 969. (10.1088/0953-8984/9/5/004)

1996

Levermann, A. H. et al., 1996. The atomic structure of the Si(111) reconstruction. Applied Surface Science 104-05 , pp.124-129. (10.1016/S0169-4332(96)00132-8)
Levermann, A. H. et al., 1996. An investigation by spot profile analysis low energy electron diffraction of Si grown on GaAs(001). Surface Science 352-54 , pp.812-816. (10.1016/0039-6028(95)01281-8)

1995

Howes, P. B. et al., 1995. A surface X-ray diffraction study of the Si(111)?Pb-buried interface. Surface Science 331-33 (A), pp.646-650. (10.1016/0039-6028(95)00382-7)
Howes, P. B. et al., 1995. Influence of interfacial atomic structure on the Schottky-barrier height of Si(111)-Pb. Physical Review B 51 (24), pp.17740-17743. (10.1103/PhysRevB.51.17740)

1994

Finney, M. S. et al., 1994. The growth and atomic structure of the Si(1 1 1)-indium interface studied by surface X-ray diffraction. Physica B: Condensed matter 198 (1-3), pp.246-248. (10.1016/0921-4526(94)90171-6)
Tabata, A. et al., 1994. Strain relaxation studied by photoluminescence and by double crystal X-ray diffraction measurements in strained InGaAs. Materials Science and Engineering: B 22 (2-3), pp.222-226. (10.1016/0921-5107(94)90248-8)

1993

MacDonald, J. E. et al. 1993. Strain distribution during growth of GE/SI(001) and the effect of surfactant layers. Journal of Scanning Microscopy 7 (2), pp.497-502.
Tabata, A. et al., 1993. Photoluminescence study of the 2D electron gas formed at the interface of strained InGaAs/InP single heterostructures. Applied Surface Science 65-66 , pp.814-820. (10.1016/0169-4332(93)90761-Y)

1992

Clark, S. A. et al., 1992. Relaxation in InxGa1-xAs/InP for compressive and tensile strain. Journal of Crystal Growth 121 (4), pp.743-750. (10.1016/0022-0248(92)90582-4)
Edge, S. et al., 1992. Extended X-ray absorption fine structure (EXAFS) spectroscopy studies on polypyrrole bromide. Synthetic Metals 52 (3), pp.383-386. (10.1016/0379-6779(92)90037-J)
Griffiths, C. L. , MacDonald, J. E. and Williams, R. H. 1992. The growth and characterisation of epitaxial insulating HoF3 layers on silicon. Applied Surface Science 56-58 (2), pp.782-788. (10.1016/0169-4332(92)90338-X)
Lohmeier, M. et al., 1992. Asymmetrical dimers on the Ge(001)-2 × 1-Sb surface observed using X-ray diffraction. Surface Science 275 (3), pp.190-200. (10.1016/0039-6028(92)90793-6)
Thornton, J. M. C. et al., 1992. Strain relaxation during the surfactant modified epitaxial growth of Ge/Si(001). Surface Science 273 (1-2), pp.1-8. (10.1016/0039-6028(92)90270-G)

1991

Griffiths, C. L. , MacDonald, J. E. and Williams, R. H. 1991. Growth of pseudomorphic insulating HoF3 layers on Si(111). Journal of Applied Physics 70 (3), pp.1858-1861. (10.1063/1.349506)
Johnson, A. et al., 1991. Combined (1×2)?(1×1) transition and atomic roughening of Ge(001) studied with surface x-ray diffraction. Physical Review B 44 (3), pp.1134-1138. (10.1103/PhysRevB.44.1134)
MacDonald, J. E. et al. 1991. Grazing-incidence x-ray-diffraction studies of strain relaxation in monolayer-thick films. Presented at: 7th Conference on Microscopy of Semiconducting Materials Oxford, UK 25-28 March 1991. Published in: Cullis, A. G. and Long, N. J. eds. Microscopy of semiconducting materials 1991: Conference Papers. Vol. 117.Institute of Physics Conference Series London: Institute of Physics. , pp.645-650.
Petrich, G. S. et al., 1991. The effect of submonolayer Sn δ-doping layers on the growth of InGaAs and GaAs. Journal of Vacuum Science & Technology B: Microelectronics and Nanometer Structures 9 (4), pp.2150-2154. (10.1116/1.585755)
Thornton, J. M. C. et al., 1991. The influence of Sb as a surfactant on the strain relaxation of Ge/Si(001). Journal of Vacuum Science & Technology B: Microelectronics and Nanometer Structures 9 (4), pp.2146-2150. (10.1116/1.585754)
Williams, A. et al. 1991. Strain relaxation during the initial stages of growth in Ge/Si(001). Physical Review B 43 (6), pp.5001-5011. (10.1103/PhysRevB.43.5001)

1990

MacDonald, J. E. 1990. X-Ray scattering from semiconductor interfaces. Faraday Discussions of the Chemical Society 89 , pp.191-200. (10.1039/dc9908900191)
Prince, K. C. et al., 1990. Structure of surfaces and interfaces as studied using synchrotron radiation - general discussion. Faraday Discussions of the Chemical Society 89 , pp.329-340. (10.1039/dc9908900329)
Robinson, I. K. et al., 1990. Structure of surfaces and interfaces as studied using synchrotron radiation - discussion. Faraday Discussions of the Chemical Society 89 , pp.201-210. (10.1039/dc9908900201)
Slijkerman, W. F. J. et al., 1990. X-ray reflectivity of an Sb delta-doping layer in silicon. Journal of Applied Physics 68 (10), pp.5105-5109. (10.1063/1.347047)
van Silfhout, R. G. et al., 1990. Structure of the Ge(111)-c(2 ? 8) surface as determined from scattered X-ray intensities along crystal truncation rods. Faraday Discussions of the Chemical Society 89 , pp.169-180. (10.1039/dc9908900169)

1989

Barnett, S. J. et al., 1989. Double crystal x-ray-diffraction characterization of InSb/CdTe superlattice structures. Institute of Physics: Conference Series 100 , pp.485 -490.
Clausen, K. N. et al., 1989. Coherent diffuse neutron scattering from UO2 and ThO2 at temperatures above 2000 K. Physica B: Condensed matter 156-57 , pp.103-565. (10.1016/0921-4526(89)90600-5)
Conway, K. M. et al., 1989. The structure of the surface determined using X-ray diffraction. Surface Science 215 (3), pp.555-565. (10.1016/0039-6028(89)90275-6)
Gay, J. M. et al., 1989. X-ray reflectivity study of surface melting on Pb (110). Journal de Physique Colloques 50 (C7), pp.289-293. (10.1051/jphyscol:1989730)
Johnson, A. D. et al., 1989. X-ray scattering from a vicinal Ge(001) surface. Journal of Physics: Condensed Matter 1 (Supp B), pp.SB275-SB277. (10.1088/0953-8984/1/SB/074)
Pluis, B. et al., 1989. X-ray reflectivity study of surface-initiated melting: Density profile at the pb(110) surface. Surface Science 222 (2-3), pp.L845-L852. (10.1016/0039-6028(89)90354-3)
van Silfhout, R. G. et al., 1989. In situ x-ray scattering studies of the deposition of Ge atoms on Ge (111). Journal de Physique Colloques 50 (C7), pp.295-300. (10.1051/jphyscol:1989731)
van Silfhoutl, R. G. et al., 1989. X-ray intensity oscillations occurring during growth of Ge on Ge(111)-a comparison with RHEED. Journal of Physics: Condensed Matter 1 (Supp B), pp.SB213-SB214. (10.1088/0953-8984/1/SB/047)
Vlieg, E. et al., 1989. The structure of Si(111)-()R30°-Ag determined by surface X-ray diffraction. Surface Science 209 (1-2), pp.100-114. (10.1016/0039-6028(89)90061-7)
Vlieg, E. et al., 1989. X-ray diffraction from rough, relaxed and reconstructed surfaces. Surface Science 210 (3), pp.301-321. (10.1016/0039-6028(89)90598-0)
Williams, A. A. et al., 1989. The initial stages of growth of Ge on Si(001) studied by X-ray diffraction. Journal of Physics: Condensed Matter 1 (Supp B), pp.SB273-SB274. (10.1088/0953-8984/1/SB/073)

1988

MacDonald, J. E. et al. 1988. Epitaxial growth studied by surface X-Ray diffraction. Presented at: 2nd International Conference on the Structure of Surfaces (ICSOS II) Amsterdam, The Netherlands 22–25 June 1987. Published in: van der Veen, J. F. and Van Hove, M. A. eds. Epitaxial Growth Studied by Surface X-Ray Diffraction:The Structure of Surfaces II. Springer Series in Surface Sciences Vol. 11. Berlin, Germany: Springer Berlin Heidelberg. , pp.438-442. (10.1007/978-3-642-73343-7_72)
MacDonald, J. E. , Saunders, G. A. and Clausen, K. N. 1988. The transition from zero- to first-sound phonon propagation in lead at high temperatures. Journal of Physics C: Solid State Physics 21 (1) L1. (10.1088/0022-3719/21/1/001)
Vlieg, E. et al., 1988. Surface X-Ray scattering during crystal growth: Ge on Ge(111). Physical Review Letters 61 (19), pp.2241-2244. (10.1103/PhysRevLett.61.2241)

1987

Clausen, K. et al., 1987. Inelastic neutron scattering investigation of the lattice dynamics of ThO2 and CeO2. Journal of the Chemical Society, Faraday Transactions 2 83 (7), pp.1109-1112. (10.1039/f29878301109)
Comins, J. D. et al., 1987. A search for relaxation in a bulk Pd40Ni40P20metallic glass. Journal of Physics F: Metal Physics 17 (1), pp.19-28. (10.1088/0305-4608/17/1/008)
Comins, J. D. et al., 1987. The elastic bahaviour and vibrational anharmonicity of molybdenum phosphate glasses. Journal of Materials Science 22 (6), pp.2113-2118. (10.1007/BF01132947)
Vlieg, E. et al., 1987. Angle calculations for a five-circle diffractometer used for surface X-ray diffraction. Journal of Applied Crystallography 20 (5), pp.330-337. (10.1107/S0021889887086527)

1986

Andersen, N. H. et al., 1986. The defect structure of yttria-stabilized zirconia, studied by quasielastic diffuse neutron scattering. Physica B+C 136 (1-3), pp.315-317. (10.1016/S0378-4363(86)80081-X)
Hackett, M. A. et al., 1986. Coherent diffuse neutron scattering study of vacancy correlations in yttria-stabilised zirconia. In: Chadwick, A. V. and Terenzi, M. eds. Defects in Solids: Modern Techniques (Nato Science Series B:). NATO ASI Series:B: Physics US: Springer. , pp.435.
Lambson, E. et al., 1986. Elastic behavior and vibrational anharmonicity of a bulk Pd40Ni40}P20 metallic glass. Physical Review B 33 (4), pp.2380-2385. (10.1103/PhysRevB.33.2380)
Osborn, R. et al., 1986. Neutron scattering investigation of the defect structure of Y2O3 - stabilised ZrO2 and its dynamical behaviour at high temperatures. Presented at: Kinetics and Mass Transport in Silicate and Oxide Systems London, UK September 1984. Published in: Freer, R. and Dennis, P. F. eds. Kinetics and Mass Transport in Silicate and Oxide Systems: Proceedings of an International Symposium, London, 1984 (Materials Science Forum). Material science forum Vol. 7. London, UK: Trans Tech Publications. , pp.55-62.
Salleh, M. D. et al., 1986. Hydrostatic pressure dependences of elastic constants and vibrational anharmonicity of uranium nitride. Journal of Materials Science 21 (7), pp.2577-2580. (10.1007/BF01114310)
Saunders, G. et al., 1986. Thermodynamics of a ferroelastic phase transition. Physical Review B 34 (3), pp.2064-2066. (10.1103/PhysRevB.34.2064)
Saunders, G. A. et al., 1986. The elastic behaviour of orthorhombic sulphur under pressure. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 407 (1833), pp.325-342. (10.1098/rspa.1986.0100)

1985

Andersen, N. A. et al., 1985. Coherent neutron scattering investigation of the defect structure of yttria-stabilised zirconia. Presented at: Transport-structure relations in fast ion and mixed conductors : 6th Risø International Symposium on Metallurgy and Materials Science Risø, Denmark 9-13 September 1985. Transport-structure relations in fast ion and mixed conductors : proceedings of the 6th Risø International Symposium on Metallurgy and Materials Science, 9-13 September 1985. Roskilde, Denmark: Risø National Laboratory. , pp.279-284.
Clausen, K. et al., 1985. Lattice-dynamics and elastic-constants of uranium-dioxide at high-temperatures investigated by neutron-scattering. High Temperature Science 19 (2), pp.189-196.
Hutchings, M. T. et al., 1985. Oxygen Frenkel Disorder in UO2 and THO2 observed above 2000-k using neutron-scattering techniques. High Temperature Science 20 (1), pp.97-108.
MacDonald, J. E. et al. 1985. Thermally induced frenkel disorder in UO//2 and ThO//2. High Temperatures - High Pressures 17 (1), pp.27-29.
Macdonald, J. E. et al. 1985. Comparison of the elastic behaviour of CuGe4P3 with that of CuGe2P3. physica status solidi (a) 89 (2), pp.K137-K141. (10.1002/pssa.2210890241)
MacDonald, J. E. et al. 1985. Elastic behaviour under pressure of the cluster compound (Ag6Ge4P12)Ge6. Journal of Physics and Chemistry of Solids 46 (8), pp.951-956. (10.1016/0022-3697(85)90098-8)

1984

Clausen, K. et al., 1984. Investigation of oxygen disorder, thermal parameters, lattice vibrations and elastic constants of UO2 and ThO2 at temperatures up to 2 930 K. Revue de Physique Appliquée 19 (9), pp.719-722. (10.1051/rphysap:01984001909071900)
Clausen, K. et al., 1984. Observation of oxygen Frenkel disorder in uranium dioxide above 2000 K by use of neutron-scattering techniques. Physical Review Letters 52 (14), pp.1238-1241. (10.1103/PhysRevLett.52.1238)

1983

Clausen, K. et al., 1983. Neutron scattering investigation of disorder in UO 2 and ThO 2 at high temperatures. High Temperatures. High Pressures 15 (4), pp.383-390.

My current research interest is the molecular mechanism of free energy transduction in ATPases in life.

Virtually all processes in life are energised by hydrolysis of adenosine triphosphate (ATP), the most common of enzymatic reactions. ATP is largely generated by the ATP synthase, a reversible, bidirectional motor which either synthesises ATP or hydrolyses ATP depending on the direction of rotation. Together with Paul Ashby (a chemist at the Molecular Foundry, Lawrence Berkeley National Laboratory), we reviewed the detailed molecular mechanism of ATP synthase, elucidated through structural studies, single molecule experiments and molecular modelling [1].

It is now clear for ATP synthase that the free energy of ATP hydrolysis is not harnessed primarily at the catalytic hydrolysis step but rather during the binding of ATP to the catalytic site through progressive formation of hydrogen bonds. Subsequent scission of the terminal phosphate of ATP involves minimal change in free energy, its main role being to reset the motor for its next cycle. Simple physical reasoning suggests that all ATPases, and possibly kinases, should share these characteristics. This is being explored by enhanced sampling molecular dynamics approaches. Please email me at [email protected] if you wish to explore this area further.

[1] J E Macdonald and P Ashby, Biophysical Journal 124 (2025) 2103-2119 DOI: 10.1016/j.bpj.2025.05.017

Modules I have taught over recent years include:
PX2231 Thermal and Statistical Physics (double module)
PX4119 Large Molecules and Life
PX2223 Physics of Solids and Soft Matter
PX3109 Solid State Physics
PX2221 Physics Applied

Education and Qualifications

1984: DPhil (Physics), University of Oxford
1980: B.Sc. Physics, Cardiff University (then University College Cardiff)

Career Overview

2025 - : Emeritus Professor at Cardiff University
2015 - 2025: Professor at Cardiff University
2004 - 2015: Reader at Cardiff University
1988 - 2004: Lecturer and Senior Lecturer at Cardiff University
1986 - 1988: Postdoctoral Research Fellow at University of Wales Cardiff
1984 - 1986: Postdoctoral Research Fellow at the University of Bath

Professional memberships

Member of the Institute of Physics

Contact Details

[email protected]

Queen's Buildings - West Building Extension, Room WX/3.08, 5 The Parade, Newport Road, Cardiff, CF24 3AA

External profiles

ORCID

Professor Emyr MacDonald

Teams and roles for Emyr MacDonald

Emeritus Professor

Overview

Publication

2025

2024

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