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Tiemann JKS, Szczuka M, Bouarroudj L, Oussaren M, Garcia S, Howard RJ, Delemotte L, Lindahl E, Baaden M, Lindorff-Larsen K, Chavent M, Poulain P. MDverse, shedding light on the dark matter of molecular dynamics simulations. eLife 2024; 12:RP90061. [PMID: 39212001 PMCID: PMC11364437 DOI: 10.7554/elife.90061] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024] Open
Abstract
The rise of open science and the absence of a global dedicated data repository for molecular dynamics (MD) simulations has led to the accumulation of MD files in generalist data repositories, constituting the dark matter of MD - data that is technically accessible, but neither indexed, curated, or easily searchable. Leveraging an original search strategy, we found and indexed about 250,000 files and 2000 datasets from Zenodo, Figshare and Open Science Framework. With a focus on files produced by the Gromacs MD software, we illustrate the potential offered by the mining of publicly available MD data. We identified systems with specific molecular composition and were able to characterize essential parameters of MD simulation such as temperature and simulation length, and could identify model resolution, such as all-atom and coarse-grain. Based on this analysis, we inferred metadata to propose a search engine prototype to explore the MD data. To continue in this direction, we call on the community to pursue the effort of sharing MD data, and to report and standardize metadata to reuse this valuable matter.
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Affiliation(s)
- Johanna KS Tiemann
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of CopenhagenCopenhagenDenmark
| | - Magdalena Szczuka
- Institut de Pharmacologie et Biologie Structurale, CNRS, Université de ToulouseToulouseFrance
| | - Lisa Bouarroudj
- Université Paris Cité, CNRS, Institut Jacques MonodParisFrance
| | | | | | - Rebecca J Howard
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm UniversityStockholmSweden
| | - Lucie Delemotte
- Department of applied physics, Science for Life Laboratory, KTH Royal Institute of TechnologyStockholmSweden
| | - Erik Lindahl
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm UniversityStockholmSweden
- Department of applied physics, Science for Life Laboratory, KTH Royal Institute of TechnologyStockholmSweden
| | - Marc Baaden
- Laboratoire de Biochimie Théorique, CNRS, Université Paris CitéParisFrance
| | - Kresten Lindorff-Larsen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of CopenhagenCopenhagenDenmark
| | - Matthieu Chavent
- Institut de Pharmacologie et Biologie Structurale, CNRS, Université de ToulouseToulouseFrance
| | - Pierre Poulain
- Université Paris Cité, CNRS, Institut Jacques MonodParisFrance
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Tiemann JKS, Szczuka M, Bouarroudj L, Oussaren M, Garcia S, Howard RJ, Delemotte L, Lindahl E, Baaden M, Lindorff-Larsen K, Chavent M, Poulain P. MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.02.538537. [PMID: 37205542 PMCID: PMC10187166 DOI: 10.1101/2023.05.02.538537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The rise of open science and the absence of a global dedicated data repository for molecular dynamics (MD) simulations has led to the accumulation of MD files in generalist data repositories, constituting the dark matter of MD - data that is technically accessible, but neither indexed, curated, or easily searchable. Leveraging an original search strategy, we found and indexed about 250,000 files and 2,000 datasets from Zenodo, Figshare and Open Science Framework. With a focus on files produced by the Gromacs MD software, we illustrate the potential offered by the mining of publicly available MD data. We identified systems with specific molecular composition and were able to characterize essential parameters of MD simulation such as temperature and simulation length, and could identify model resolution, such as all-atom and coarse-grain. Based on this analysis, we inferred metadata to propose a search engine prototype to explore the MD data. To continue in this direction, we call on the community to pursue the effort of sharing MD data, and to report and standardize metadata to reuse this valuable matter.
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Packman L, Mallo N, Raynor A, Gao M, Babazadeh M, Jin H, Huang DM, Burn PL, Gentle IR, Shaw PE. The impact of film deposition and annealing on the nanostructure and dielectric constant of organic semiconductor thin films. Phys Chem Chem Phys 2023; 25:23867-23878. [PMID: 37642159 DOI: 10.1039/d3cp03038e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
The strategy of using a bulk-heterojunction light-absorbing layer has led to the most efficient organic solar cells. However, optimising the blend morphology to maximise light absorption, charge generation and extraction can be challenging. Homojunction devices containing a single component have the potential to overcome the challenges associated with bulk heterojunction films. A strategy towards this goal is to increase the dielectric constant of the organic semiconductor to ≈10, which in principle would lead to free charge carrier generation upon photoexcitation. However, the factors that affect the thin film dielectric constants are still not well understood. In this work we report an organic semiconductor material that can be solution processed or vacuum evaporated to form good quality thin films to explore the effect of chromophore structure and film morphology on the dielectric constant and other optoelectronic properties. 2,2'-[(4,4,4',4'-Tetrakis{2-[2-methoxyethoxy]ethyl}-4H,4'H-{2,2'-bi[cyclo-penta[2,1-b:3,4-b']dithiophene]}-6,6'-diyl)bis(methaneylylidene)]dimalononitrile [D(CPDT-DCV)] was designed to have high electron-affinity end groups and low ionisation-potential central moieties. It can be processed from solution or be thermally evaporated, with the film morphology changing from face-on to a herringbone arrangement upon solvent or thermal annealing. The glycol solubilising groups led to the static dielectric constant (taken from capacitance measurements) of the films to be between 6 and 7 (independent of processing conditions), while the optical frequency dielectric constant depended on the processing conditions. The less ordered solution processed film was found to have the lowest optical frequency dielectric constant of 3.6 at 2.0 × 1014 Hz, which did not change upon annealing. In contrast, the more ordered evaporated film had an optical frequency dielectric constant 20% higher at 4.2 and thermal annealing further increased it to 4.5, which is amongst the highest reported for an organic semiconductor at that frequency. Finally, the more ordered evaporated films had more balanced charge transport, which did not change upon annealing.
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Affiliation(s)
- Lachlan Packman
- Centre for Organic Photonics & Electronics (COPE), School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Neil Mallo
- Centre for Organic Photonics & Electronics (COPE), School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Aaron Raynor
- Centre for Organic Photonics & Electronics (COPE), School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Mile Gao
- Centre for Organic Photonics & Electronics (COPE), School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Mohammad Babazadeh
- Centre for Organic Photonics & Electronics (COPE), School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Hui Jin
- Centre for Organic Photonics & Electronics (COPE), School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - David M Huang
- Department of Chemistry, School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide South Australia, 5005, Australia
| | - Paul L Burn
- Centre for Organic Photonics & Electronics (COPE), School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Ian R Gentle
- Centre for Organic Photonics & Electronics (COPE), School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Paul E Shaw
- Centre for Organic Photonics & Electronics (COPE), School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia.
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