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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

Research

to be added

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papers

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workshops

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seminars

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Cups of Coffee/day

Selected Collaborators

Prof Kostya Trachenko

Prof Kostya Trachenko

Collaboration with Kostya’s group on various tools for analysing massive molecular simulations runs, tens of millions of atoms

Prof Y

Prof Y

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Dr Z

Dr Z

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Prof S

Prof S

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Dr T

Dr T

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Random News

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Participating at the electronic structure library workshop in CECAM Lausanne, https://www.cecam.org/workshop-details/85

CCP5 Summer School 2020

CCP5 Summer School 2020

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Registrations are open… https://summer2020.ccp5.ac.uk/

New computer build

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the oil xeon is getting closer to a new life

automation working

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conbee II and xiaomi sensors, plus IKEA lights and switches mixed with wifi sensors based on esp8266-01 and 12e

Latest Posts

The lego mechanical keyboard

motto: know the rules then break them

I have been typing for 31 years or so… Until few years ago I did not really pay too much attention to what I used… Over the years I used quite few keyboards. Commodore 64 and some Romanian clone of ZX Spectrum HC-85, IBM Model F and Model M, some Cherry, plenty of plastic abominations and laptop keyboards…. Around 2015/2016 got an IBM Model M from the way to bin, missing some keycaps and needing some sanitation… Soon was back and working and is still working… Then another Model M, working for a national lab has its own advantages… a lot of old kit going to recycling. This Model M broke soon after and I ended up on https://deskthority.net/ looking for info to fix it. The membrane needed replacement… But being a flaneur of internet… ended up pretty soon on https://deskthority.net/viewtopic.php?f=7&t=6050&start=

Read more
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Contact

Daresbury Laboratory, STFC, Keckwick Lane, Cheshire, WA4 4AD, United Kingdom
Email: alin@elena.re

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