Alin M Elena

personal site ⇓

About Me

I was born in 1980 (long time ago) in Dragasani, Valcea, Romania. First years I spent going to nursery school, kindergarden and playing. Then when I was almost 8 and they sent me to school. I did my primary, secondary and High School in my home town. On September 2000 I moved to Bucharest to study Physics at University of Bucharest. On June 2004 I graduated, on August 2004 I moved to Belfast to do my PhD and on February 2009 I moved to Dublin. For more read my CV. I have studied for a PhD at Queen’s University Belfast in the Atomistic Simulation Centre. My supervisors were Prof Tony Paxton and Dr Tchavdar Todorov. My thesis topic was Time Dependent Tight Binding+U: Applications to fluorescent molecules (never submitted). I was employed by Irish Centre for High-End Computing (ICHEC) in the Dublin Offices as Computational Scientist. I got my PhD in School of Physics, at University College Dublin with Professor Giovanni Ciccotti and Dr Simone Meloni. I was employed by Irish Centre for High-End Computing (ICHEC) in the Dublin Offices as Computational Scientist. Currently I am employed by Science and Technology Facilities Council at Daresbury Laboratory as Computational Scientist.

Curriculum vitæ

Work Experience

Science and Technology Facilities Council, Daresbury Laboratory
July 2015 Computational Scientist
Irish Centre for High-End Computing, Dublin Offices
July 2013 – June 2015 Computational Scientist
Irish Centre for High-End Computing, Dublin Offices
February 2009 – August 2010 Computational Scientist

Education

School of Physics, University College Dublin
September 2010 – July 2013, PhD student,
supervisors Professor Giovanni Ciccotti and Dr Simone Meloni
School of Mathematics and Physics, Atomistic Simulation Centre, Queen’s University Belfast
August 2004 – January 2009 PhD student, Time Dependent Tight-Binding+U: Applications to fluorescent molecules (never submitted)
supervisors Professor Tony Paxton and Dr Tchavdar Todorov
Faculty of Physics, University of Bucharest
October 200 - June 2004 , BSc., 9.85/10, Honours, English taught lectures department
Diploma Thesis: Molecular Orbitals Quantum Calculations for Structures Based on Si, C, N – Vibrational Analysis , supervisor Reader Mircea Bercu
High School “Gib Mihaescu” , Dragasani, Informatics class
September 1996 - June 2000 , GPA 9.87/10

Teaching Experience

2014-2015, PH504 Graduate Module, Introduction to Parallel Programming@NUIG
2014, GM training course, Introduction to HPC, Software Installation, Benchmarking, Parallel Programming components
2014 Introduction to Parallel Programming
2013-2014, PH504 Graduate Module, Introduction to Parallel Programming@NUIG
2012 -2013 Tutorials: Computational Biophysics and Nanoscale Simulations @University College Dublin
2011 -2012 Microlabs Introduction to C++ programming @University College Dublin\
2010 -2011 Microlabs Introduction to C++ programming @University College Dublin
2009-2010 Courses Introduction to MPI and OpenMP , Introduction to Modern Fortran @different universities across Ireland
2007-2008 Tutorials Professional Skills Programme (C/C++ Programming) Vector Algebra and Dynamics , Waves and Vector Fields @Queen’s University Belfast
2006-2007 Tutorials Professional Skills Programme (C/C++ Programming) Vector Algebra and Dynamics , Computational Methods in Physics , Computational Modelling in Physics , Waves and Vector Fields @Queen’s University Belfast
2005-2006 Lecture Professional Skills Programme (C/C++ Programming) – second half, Tutorials: Vector Algebra and Dynamics , Computational Methods in Physics , Computational Modelling in Physics , Waves and Vector Fields @Queen’s University Belfast
2004-2005 Tutorials: Vector Algebra and Dynamics , Computational Methods in Physics , Computational Modelling in Physics , Waves and Vector Fields @Queen’s University Belfast

Training

21-25 June 2010 , Basic techniques and tools for development and maintenance of atomic-scale software , CECAM, Zaragoza, Spain
14-16 April 2009 , Intel Cluster Software Development Tools , SGI, Reading, UK
January 2007 , Programming SMP Computers , HPCx, Belfast, UK
December 2006 , Winter School, Electronic excitations and spectroscopies : Theory and Codes , CECAM, Lyon, France
July 2006 , Summer School, UK Grad Programme , University of Exeter, UK
January 2006 , Winter School, Programming Parallel Computers , , CECAM, Julich, Germany
October-November 2005 , Autumn School, Understanding Molecular Simulations , , CECAM, Amsterdam, Holland
August-September 2004 , Summer School, Time Dependent Density Functional Theory: Applications and Prospects , Benasque, Spain
August-September 2003 , Research Stage, High resolution fluorescent laser spectroscopy , at Joint Institute for Nuclear Research, Dubna, Moscow Region, Russia
June 2003 , Intensive Lectures, Simulation and characterization spectrometric methods of physical processes for micro and nanotechnologies , at INCDM Bucharest, MINAMAT-NET
August-September 2002 , Research Stage, High resolution fluorescent laser spectroscopy , at Joint Institute for Nuclear Research, Dubna, Moscow Region, Russia

Prizes

2005 – Musgrave Demonstrators' Prize
2004 – Best Academic Results by Bucovineni Sarghie Brothers' Foundation and University of Bucharest
2004 – Honourous Mention, CyberEducation Contest , organised by University of Bucharest , Project Didactical Molecular Dynamics

Skills

Programming: Fortran 90&95, C/C++, on different platforms, parallel (MPI and OpenMP)
libraries and serial versions; scientific programming for atomic and molecular physics
Project Building: cross-OS experience with CMake – since 2006 I have used
CMake to build and port different scientific applications on Linux/MacOSX/Windows platforms
( TDTB+UJ , ATEN )
Web: HTML, CSS, php+Mysql – September 2004 – September 2007 webmaster of the Atomistic Simulation Centre http://titus.phy.qub.ac.uk
Hardware troubleshooting solving skills
Installation and maintenance of different operating systems from Microsoft, Unix/Linux like

Languages


English	spoken good/fluent written good
French	above beginner
Spanish	beginner
Romanian	mother tongue

Membership

Institute of Physics
OpenSUSE
Collège de ‘Pataphysique

Hobbies

philosophy, music, urban culture and architecture, contemporary and absurd literature

last updated 2015

to be updated 01/03/2020

Publications

Papers

A Diver, O Dicks, IT Todorov, AM Elena, K Trachenko, Radiation damage effects in amorphous zirconolite, Journal of Nuclear Materials 2021, 544, 152654, DOI: https://doi.org/10.1016/j.jnucmat.2020.152654
Micael JT Oliveira, Nick Papior, Yann Pouillon, Volker Blum, Emilio Artacho, Damien Caliste, Fabiano Corsetti, Stefano De Gironcoli, Alin M Elena, Alberto García, Víctor M García-Suárez, Luigi Genovese, William P Huhn, Georg Huhs, Sebastian Kokott, Emine Küçükbenli, Ask H Larsen, Alfio Lazzaro, Irina V Lebedeva, Yingzhou Li, David López-Durán, Pablo López-Tarifa, Martin Lüders, Miguel AL Marques, Jan Minar, Stephan Mohr, Arash A Mostofi, Alan O’Cais, Mike C Payne, Thomas Ruh, Daniel GA Smith, José M Soler, David A Strubbe, Nicolas Tancogne-Dejean, Dominic Tildesley, Marc Torrent, Victor Wen-zhe Yu, The CECAM electronic structure library and the modular software development paradigm, The Journal of Chemical Physics 2020, 153 (2), 024117, DOI: https://doi.org/10.1063/5.0012901
A Diver, O Dicks, AM Elena, IT Todorov, K Trachenko, 2020, Evolution of amorphous structure under irradiation: zircon case study Journal of Physics: Condensed Matter 32 (41), 415703, DOI: https://doi.org/10.1088/1361-648X/ab9f51
I Scivetti, K Sen, AM Elena, I Todorov, Reactive Molecular Dynamics at Constant Pressure via Nonreactive Force Fields: Extending the Empirical Valence Bond Method to the Isothermal-Isobaric Ensemble The Journal of Physical Chemistry A 2020, 124 (37), 7585-7597, DOI: https://doi.org/10.1021/acs.jpca.0c05461
Janou A Koskamp, Sergio E Ruiz-Hernandez, Devis Di Tommaso, Alin Marin Elena, Nora H De Leeuw, Mariette Wolthers, Reconsidering Calcium Dehydration as the Rate-Determining Step in Calcium Mineral Growth
The Journal of Physical Chemistry C, 2019 123 (44), 26895-26903, DOI: https://doi.org/10.1021/acs.jpcc.9b06403
Martyn F. Guest, Aidan B. G. Chalk and Alin M. Elena DL_POLY - A performance overview analysing, understanding and exploiting available HPC technology Molecular Simulation, 2019
DOI: https://doi.org/10.1080/08927022.2019.1603380
Aidan B. G. Chalk and Alin M. Elena Task-Based Parallelism with OpenMP: a case study with DL_POLY_4 Molecular Simulations, 2019
DOI: https://doi.org/10.1080/08927022.2019.1606424
Aidan B.G. Chalk, Alin M. Elena, Task Based Parallelism with OpenMP: A Case Study with DL_POLY_4 chapter in Volume 32: Parallel Computing is Everywhere
pages: 497 - 506, DOI: 10.3233/978-1-61499-843-3-497
Christian Trott, Tzu-Ray Shan, Stan Moore, Aidan Thompson, Steve Plimpton, Markus Höhnerbach, Ahmed Ismail, Paolo Bientinesi, Alin Marin Elena, Christian Lalanne, Victor Gamayunov, Gilles Civario, Michael Lysaght, Ilian Todorov, Iain Bethune, Antonia Collis, Gianpaolo Gobbo, Benedict Leimkuhler, Sapna Sarupria, Walter Hanger, Ryan DeFever, Linh Ngo, Amy Apon, Jesús Izaguirre, Douglas Thain, Eric Darve, Roberto Di Remigio, Daniel Crawford, Luca Frediani, Erik Lindahl, James Phillips, Ross Walker
Proceedings of the SC15 Workshop on Producing High Performance and Sustainable Software for Molecular Simulation, 2016
Alin Marin Elena and Ivan Rungger. Enabling Smeagol on Xeon Phi: Lessons Learned. PRACE White Paper, 2014
www.prace-ri.eu/IMG/pdf/wp134.pdf
Alin Marin Elena, Simone Meloni and Giovanni Ciccotti Equilibrium and Rate Constants, and Reaction Mechanism of the HF Dissociation in the HF(H2O)7 Cluster by ab Initio Rare Event Simulations J. Phys. Chem. A 2013 117, 49, 13039-13050
DOI: https://doi.org/10.1021/jp406982h
A.T. Paxton, T.N. Todorov and A.M. Elena Ring currents in azulene Chemical Physics Letters 483(1–3), 2009, Pages 154-158
DOI: https://doi.org/10.1016/j.cplett.2009.10.041
Alin M. Elena and Matthias Meister Automatic generation of matrix element derivatives for tight binding models Phys. Rev. B 72, 165107, 2005
DOI: https://doi.org/10.1103/PhysRevB.72.165107

Presentations

talk, A M Elena, IPCC Users' Group meeting, Dublin, February 25, 2015
talk, A M Elena, CECAM: Exploiting heterogeneous multi-core and many-core platforms for atomic and molecular simulations, STFC Hartree Centre, Daresbury, UK, September 11, 2014
poster, A M Elena, S Meloni, G Ciccotti, EU-US HPC Summer School, Dublin.Deprotonation mechanism of (H2O)7HF, June 26, 2012
poster, A M Elena, S Meloni, G Ciccotti, CECAM: Free-Energy Calculations, École des Ponts et Chaussées, Paris. Deprotonation mechanism of (H2O)7HF, June 6, 2012
talk, A M Elena, S Meloni, G Ciccotti, Nanoscale Simulators Ireland Meeting, Trinity College Dublin.Deprotonation mechanism of hydrofluoric acid(H2O)7HF cluster by ab-initio rare event simulations, January 13, 2012
poster, A M Elena, M Meister, CECAM: Programming Parallel Computers, Jülich, Germany. Automatic Generation of Matrix Element Derivatives for Tight Binding Models, January 2006
talk, M. Elena, M. Bercu, Electron Transfer in Disordered One-dimensional Systems , Annual Scientific Conference, Faculty of Physics, University of Bucharest, May 30, 2003
talk, M. A. Elena, Mircea Bercu, Simulation of H-H Collision Based on Molecular Dynamics , Annual Scientific Conference, Faculty of Physics, University of Bucharest, May 31, 2002
talk, V. Barna, A. Elena, D. Nedelcu, Effect of Specimen Thickness on Crystallisation Rate , Annual Scientific Conference, Faculty of Physics, University of Bucharest, May 31, 2002