UK R-matrix Atomic and Molecular Physics HPC Code Development Project (UK-RAMP)

Lead Research Organisation: Open University
Department Name: Physical Sciences

Abstract

New areas of Science are emerging for which multi-electron dynamics in atoms and molecules are crucial. One important example is the field of Atto-second Science where laser light and the electrons of matter interact on the atto-second time-scale making possible, for example, the shortest-ever pulses of VUV light. One atto-second is only one millionth-millionth-millionth of a second but electrons driven by strong laser light collide violently with others and move distances large compared to the size of an atom on the atto-second time-scale of several hundred atto-seconds. Another important example is the recent appreciation that ionizing radiation damages living animals and plants by bringing about strand breaks in the DNA molecule through a multi-electron interaction.Such newly emerging areas of Science involve large experimental teams in the UK and around the world who publish their research findings in top journals such as Nature and Science. Despite this, there does not yet exist anywhere in the world a set of computer codes capable of calculations of sufficient sophistication to be useful in conjunction with the laboratory experiment effort, in driving the Science forward. Such calculations demand the full power of present (and prospective) High Performance Computing - available through machines which presently can cost 100M and upwards.The purpose of the proposed research is to develop a suite of high-quality computer codes that will be widely used; will harness such high performance computing machines most effectively over many years; and will relate directly to areas of Science (brief descriptions of two such areas given above) where a detailed account of multi-electron dynamics in electrons and molecules is essential to driving the Science forward.

Publications

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Bingham P (2019) reskit: A toolkit to determine the poles of an S-matrix in Computer Physics Communications

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Brambila D (2015) The role of multichannel effects in the photoionization of the NO 2 molecule: an ab initio R -matrix study in Journal of Physics B: Atomic, Molecular and Optical Physics

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Carr J (2012) UKRmol: a low-energy electron- and positron-molecule scattering suite in The European Physical Journal D

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Fabrikant II (2012) Electron attachment to molecules in a cluster environment. in The Journal of chemical physics

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Gorfinkiel J (2017) Electron scattering from molecules and molecular aggregates of biological relevance in Journal of Physics B: Atomic, Molecular and Optical Physics

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Loupas A (2018) Cross sections for electron scattering from thiophene for a broad energy range. in The Journal of chemical physics

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Loupas A (2017) Resonances in low-energy electron scattering from para-benzoquinone. in Physical chemistry chemical physics : PCCP

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Loupas A (2019) Shape and core-excited resonances in electron scattering from alanine. in The Journal of chemical physics

 
Description We have discovered that substituted benzene molecules have a complex resonance spectrum. Comparison of our calculations with electron energy loss spectra have confirmed that these resonances have an effect on the physics of these systems.
We have also discovered that microhydration has a specific effect on the resonances of nucleobases.
Exploitation Route The findings can be used to understand how low energy electrons interact with cell constituents and break DNA. This has applications in the modeling of biological radiation damage and the use of radiation both for imaging and treatment.
Sectors Pharmaceuticals and Medical Biotechnology

 
Description Some of the software we develop is being commercialized by Quantemol Ltd.
Sector Digital/Communication/Information Technologies (including Software)
Impact Types Economic

 
Description Embedded CSE (eCSE) support (ARCHER)
Amount £73,000 (GBP)
Organisation University of Edinburgh 
Department Edinburgh Parallel Computing Centre (EPCC)
Sector Academic/University
Country United Kingdom
Start 06/2014 
End 06/2015
 
Description H2020-TWINN-2015
Amount € 250,000 (EUR)
Organisation European Commission 
Sector Public
Country European Union (EU)
Start 01/2016 
End 12/2018
 
Description HECToR Distributed CSE Support
Amount £44,000 (GBP)
Organisation Numerical Algorithms Group Ltd 
Sector Private
Country United Kingdom
Start 03/2011 
End 09/2012
 
Description High End Computing Consortia Call 2017
Amount £368,071 (GBP)
Funding ID EP/R029342/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Academic/University
Country United Kingdom
Start 07/2018 
End 09/2022
 
Description Software Infrastructure
Amount £433,575 (GBP)
Funding ID EP/P022146/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Academic/University
Country United Kingdom
Start 09/2017 
End 08/2019
 
Description Accurate cross sections for electron-molecule scattering 
Organisation Flinders University
Country Australia 
Sector Academic/University 
PI Contribution Provision of accurate calculated inelastic cross sections
Collaborator Contribution Determination of experimental inelastic cross sections
Impact Four papers
Start Year 2012
 
Description Accurate determination of core-excited resonances for biologically relevant molecules 
Organisation University of Fribourg
Country Switzerland 
Sector Academic/University 
PI Contribution We provided theoretical confirmation of the presence and characteristics of core-excited resonances in biological molecules (pyrimidin, thiophene) observed using electron energy loss spectroscopy.
Collaborator Contribution They performed the experiments.
Impact Four papers: Shape and core-excited resonances in thiophene A. Loupas, K. Regeta, M. Allan and J. D. Gorfinkiel, J. Phys. Chem. A, 122, 1146 (2018) Absolute cross sections for electronic excitation of pyrimidine by electron impact K. Regeta, M. Allan, Z. Masin and J. D. Gorfinkiel, J. Chem. Phys., 144, 024302 (2016) Resonance effects in elastic cross sections for electron scattering from pyrimidine: experiment and theory K. Regeta, M. Allan, C. Winstead, V.McKoy, Z. Masin and J. D. Gorfinkiel, J. Chem. Phys., 144, 024301 (2016)Recent research directions in Fribourg: nuclear dynamics in resonances revealed by 2-dimensional EEL spectra, electron collisions with ionic liquids and electronic excitation of pyrimidine M. Allan, K. Regeta, J. D. Gorfinkiel, Z. Masin, Stefan Grimme and Christoph Bannwarth, EPJD, 70, 123 (2016)
Start Year 2015
 
Description Positrons in biosystems 
Organisation Australian National University (ANU)
Department College of Medicine, Biology & Environment (CMBE)
Country Australia 
Sector Academic/University 
PI Contribution Provide theoretical back-up for experiments and modelling
Collaborator Contribution Perform a variety of experiments and develop modeling methodology
Impact None yet
Start Year 2019
 
Title ukrmol-in suite 
Description Release of the inner region UKRmol suite of codes 
Type Of Technology Software 
Year Produced 2010 
Open Source License? Yes  
Impact So0me of the sogftware is used bu Quantemol LTD., who sell it commercially 
URL http://ccpforge.cse.rl.ac.uk/gf/project/ukrmol-in/
 
Title ukrmol-in suite, release 1.0 
Description Software to describe the discretized continuum of a molecule, particularly designed for applications using the R-matrix method 
Type Of Technology Software 
Year Produced 2015 
Impact More groups worldwide using the software 
URL http://ccpforge.cse.rl.ac.uk/gf/project/ukrmol-in
 
Description Core-excited resonances in biological molecules 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Disemination of current research to an international audience
Year(s) Of Engagement Activity 2017
 
Description International Meeting on Atomic and Molecular Physics and Chemistry 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Increased interest by experimental groups in Europe in my research
Year(s) Of Engagement Activity 2016
 
Description Joint IAEA-ITAMP Technical Meeting on Uncertainty Assessment for Theoretical Atomic and Molecular Scattering Data 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact The primary goal was to come up with reasonable uncertainty estimates for calculations using the various methods of collision physics. A report was produced by the IAEA

A sumary report was produced by the INDC International Nuclear Data Committee
Year(s) Of Engagement Activity 2014
URL https://www-amdis.iaea.org/meetings/ITAMP/
 
Description Symposium on Applications of Plasma Processes 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Dissemination of my work to researchers in the area of Plasma applications
Year(s) Of Engagement Activity 2017
 
Description Temporary Anion States of Biologically Relevant Molecules 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Presentation and discussion with colleagues mainly from Chemistry about the applicability of the software I develop for the study of photon induced molecular processes.
Year(s) Of Engagement Activity 2017
 
Description Towards an R-matrix suite for attosecond multielectron dynamics in molecules 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Exchange of know-how and expertise in the development of high-performance software for the study of multielectron dynamics of molecules
Year(s) Of Engagement Activity 2017
 
Description UKRmol-in 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact Website for the re-engineering of the inner region programs in the UK molecular R-matrix

suites in order to improve efficiency and increase the variety of targets and processes that can be studied.

Website allows researchers world-wide to access and download software, report bugs and feature request and keep up to date with improvements to the software
Year(s) Of Engagement Activity 2009
 
Description UKRmol-out 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact Website for the re-engineering of the outer region programs in the UK molecular R-matrix

suites in order to improve efficiency and increase the variety of targets and processes that can be studied.

Website allows researchers world-wide to access and download software, report bugs and feature request and keep up to date with improvements to the software
Year(s) Of Engagement Activity 2009