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researcher

Donal MacKernan

Director, Cecam Ireland

School of Physics

Tel: 7162612
Email: donal.mackernan@ucd.ie

Biography

I am a physicist (PhD Brussels) with several years research experience in European and Irish funded projects lying in the broad areas of ICT, energy, novel materials, and most recently in the design of fluorescent probe-linker systems.

  • The tools/methods we use in these quite disparate areas are statistical mechanics, and computer based simulation at a molecular level combined with advanced biased sampling developed to overcome the time scales relevant to the phenomena of interest and the generally much shorter timescales of standard molecular based simulation.The difference in time scales can be many orders of magnitude.
  • Additional theoretical projects  are focused on theory and algorithm development where the goal is in developing general methods, rather than specific applications. The areas include statistical approaches to low dimensional dynamical chaos, non-adiabatic quantum dynamics (relevant for instance to quantum computation), and rare-events. 
  • I have lectured to third and fourth year undergraduates in physics and chemistry on advanced programming methods, and advanced quantum mechanics, and co-supervise PhD students in computer based simulation.
  • I am also a consultant to an international (but UK based) Patent and Intellectual Property firm (Origin Ltd), providing advise to date mostly on ICT issues stemming from patent applications to the UK, US, and European Patent offices.
  • My PhD thesis entitled ¿Generalized Markov Coarse Graining and the Observables of Chaos¿ was focused on the statistical and spectral properties of dynamical chaos. 
  • I also have worked as a scientific co-coordinator of a European Science Foundation (ESF) programme involving over 120 laboratories across Europe, and on Irish based initiatives, and in that role also been editor and chief of it's newsletter/journal (http://simu.ulb.ac.be).

Publications

 

Book Chapters

Donal MacKernan (2015) 'Coarse Graining Approach to Chaos' In: Gregoire Nicolis1 Vasileios Basios (eds). Chaos, Information Processing and Paradoxical Games. Singapore: World Scientific. [DOI] [Details]
Bonella, S., Coker, D.F., Mackernan, D., Kapral, R. and Ciccotti, G.; (2009) 'Trajectory based simulations of quantum-classical systems' In: Burghardt, I., May, V., Micha, D.A. and Bittner, E.R (eds). Energy Transfer Dynamics in Biomaterial Systems, Springer Series in Chemical Physics, Vol. 93. Berlin: Springer Verlag. [Details]
 

Peer Reviewed Journals

Shourjya Sanyal1, Donal MacKernan and David F Coker (2015) 'Multiscale Modelling of UniMolecular FRET Probes Using Monte Carlo Simulations'. Institute of Physics Conference Series, 640 (1). [Details]
Y. Wang, D. MacKernan, D. Cubero, D. F. Coker, and N. Quirke (2014) 'Single electron states in polyethylene'. Chemical Physics, 140 . [DOI] [Details]
Lucid, J,Meloni, S,MacKernan, D,Spohr, E,Ciccotti, G (2013) 'Probing the Structures of Hydrated Nafion in Different Morphologies Using Temperature-Accelerated Molecular Dynamics Simulations'. Journal of Physical Chemistry C, 117 :774-782. [DOI] [Details]
Basios, V,Mac Kernan, D (2011) 'SYMBOLIC DYNAMICS, COARSE GRAINING AND THE MONITORING OF COMPLEX SYSTEMS'. International Journal of Bifurcation and Chaos, 21 :3465-3475. [DOI] [Details]
Vasileios Basios and Donal MacKernan; (2011) 'Symbolic dynamics, coarse graining and the monitoring of complex systems'. International Journal of Bifurcation and Chaos, 21 (12(2011)):3465-3475. [DOI] [Details]
Éimhín M. Ní Mhuircheartaigh, Silvia Giordani, Donal MacKernan, Sharon M. King, David Rickard, Lisa M. Val Verde, Mathias O. Senge, and Werner J. Blau; (2011) 'Molecular Engineering of Nonplanar Porphyrin and Carbon Nanotube Assemblies: A Linear and Nonlinear Spectroscopic and Modeling Study'. Nanotechnology, 2011 . Available Online [DOI] [Details]
Donal MacKernan and Vasilis Basios; (2009) 'Local and global statistical dynamical properties of chaotic Markov analytic maps and repellers: A coarse grained and spectral perspective'. Chaos Solitons &Amp; Fractals, 42 (1):291-302. [DOI] [Details]
Mac Kernan, D,Blau, WJ; (2008) 'Exploring the mechanisms of carbon-nanotube dispersion aggregation in a highly polar solvent'. Europhysics Letters, 83 . [DOI] [Details]
Mac Kernan, D,Ciccotti, G,Kapral, R; (2008) 'Trotter-based simulation of quantum-classical dynamics'. Journal of Physical Chemistry, 112 :424-432. [DOI] [Details]

Other Journals

Mac Kernan, D. and Ni Mhuircheartaigh, E. and Blau, W.J.; (2007) 'Porphyrin and carbon nanotube assemblies in polar solvents' Spie Newsroom . Available Online [Details]

Conference Publications

Yang Wang, Kai Wu, D. Cubero, D. Mackernan, D. Coker, N. Quirke (2013) Electron trapping in polyethylene 2013 IEEE International Conference on Solid Dielectrics, Bologna, Italy, June 30 ¿ July 4, 2013 [DOI] [Details]
                                                                                         

Research

Research Interests

My current research  projects listed below involve the use of advanced statistical methods, algorithm development for computer based simulation, and in many cases used supercomputer facilities provided by the Irish centre for high end computing.

  • Non-adiabatic quantum classical dynamics ¿ Theory & Algorithm Development including several academic publications cited in aggregate some 250 times to date (in all but one case as senior/lead author.) My focus has been on the derivation of algorithms implementing Dyson integral equations, and the Trotter approximation for exponentiation of non-commuting operators (frequently used in quantum path integrals) using recursive methods. This body of work has been highly cited (notwithstanding its highly specialised nature) in part because the algorithmic approach developed has been exploited in other integration schemes.

  • Rare-event based simulation methods applied to problems in advanced materials (carbon nanotube dispersion studies in specialised solvents, hydrogen fuel cells, and electron trapping in polyethylene (relevant to high tension power transmission), with some 40 citations to date.

  • Rare-event based statistical simulation methods applied to problems in biology ¿ currently the study of the GPCR protein receptor known as GLP-1R in collaboration with the UCD School of Health; Coarse grained models applied to development of FRET based unimolecular biosensors. The latter has led both to a scientific manuscript currently under review and two provisional patent applications submitted to the UK patent office in 2015.

  • Statistical approaches to Chaos leading to several publications cited in aggregate 200 times to date (in most cases as senior/lead author.) While on the face of it classical chaos has nothing to do quantum dynamics, it turns out at an algorithmic level the methods used to manipulate transfer operators and quantum classical Liouville like operators are very similar.

All of the listed projects use advanced statistical methods, algorithm development for computer based simulation, and in many cases supercomputer facilities provided by the Irish Centre for High End Computing, combining advanced mathematical methods, statistical mechanics, quantum dynamics, and some cases chaos theory with symbolic packages (e.g., Mathematica and Maple) and modifications of LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) from Sandia National Labs, to produce algorithms which are then implemented in C or C++.   

     

Collaborators

Internal Collaborators

David Coker
Giovanni Ciccotti
Shourjya Sanyal

External Collaborators

Nick Quirke (Imperial)

Raymond Kapral (Toronto)

Gregoire Nicolis (Brussels)

Vasileios Basios (Brussels)

Werner J. Blau (Trinity College Dublin)

Eckhard Spohr (Essen)