Highlights
Combining High-resolution Scanning Tunnelling Microscopy and First-principles Simulations to Identify Halogen Bonding
Nature Communications
This one took about two years! A collaborative work led by the Costantini Group where we used a combination of (very) fancy STM techniques and some density functional theory calculations to elucidate the emergence of halogen bonding in self-assembled monolayers. That's right, for once we took electrons into account - very refreshing to get back to CP2K. Also, obligatory kudos to Ondřej Krejčí & Co., who have implemented a very useful code for simulating STM images via DFT simulations. Have a look at our paper online or grab a .pdf. See it highlighted on the Nature website here!
Insights into the Emerging Networks of Voids in Simulated Supercooled Water
Journal of Physical Chemistry B
Another outcome of our collaboration with the group of Dr. Ali Hassanali (ICTP Trieste, IT)! This time, we have been looking at some subtle details of the structure of supercooled water in relation to the emergence of regions of empty space in the liquid. Far from being just a curiosity, these findings provide an interesting take on the (in)famous low- vs high-density water debate and offer a novel perspective on the structural properties of supercooled liquids as we approach the glass transition temperature. Looking at the dynamical properties of these cavities would be the natural next step… but we’re also working on a piece of code that might be of use to tackle the characterisation of regions of empty space across a variety of different systems. In a nutshell: stay tuned, folks… meanwhile, have a look at the paper online or grab a .pdf.
Enhancement of macromolecular ice recrystallization inhibition activity by exploiting depletion forces
Journal of Physics D: Applied Physics
Yet another exploit for the machine learning-based interatomic potential we have developed in 2012 for the phase change material GeTe. In this paper, we have computed the thermal conductivity of GeTe nanowires (a key component of a rather fancy device architecture for non-volatile memories) by means of large scale molecular dynamics simulations - only possible thanks to the power of neural networks (and a tad bit of physical intuition, I should add). Some interesting trends emerged… have a look at the paper online or grab a .pdf.
Less may be more: an informed reflection on molecular descriptors for drug design and discovery
Molecular Systems Design and Engineering
This is the very first paper from the SossoGroup! Harry, Steven and Trent have all worked on this during their Master's research project, making quite an effort during the last summer to finalise a contribution which will feature in the RSC Molecular Systems Design & Engineering themed collection: MSDE Emerging Investigators 2020. This is preliminary work aimed at probing the potential of specific descriptors to be leveraged in the context of drug design - with a materials science twist, obviously! Have a look at the paper online or grab a .pdf. Of one thing I am quite confident about: there will be more - stay tuned, folks!
Harnessing machine learning potentials to understand the functional properties of phase-change materials
MRS Bulletin
At the very beginning of my PhD (2009, I believe?!) I developed a machine learning potential for the phase change material GeTe. Phase change materials for data storage are quite an essential ingredient of future memory devices - and little did I know at the time that such a potential would be at the heart of so many computational works (more than 15 as we speak) from then on. This paper has been conceived and written by myself and my PhD supervisor - a pivotal figure/influence in my academic career. It is thus with some satisfaction that I would encourage you to have a look at the paper online or grab a .pdf. You will find a hopefully balanced discussion of what machine learning can do for us in the field of phase change materials, with quite a few references to recent advances and a honest take on the limitations we will have to face in the near future.
Enhancement of macromolecular ice recrystallization inhibition activity by exploiting depletion forces
ACS Macro Letters
In case you didn't know, we are lucky enough to have in Warwick a world-leading experimentalist working on ice: Prof. Matt Gibson, who has been looking for a while into the foggy business of ice re-crystallization inhibition, that is the impact of specific chemicals in controlling the growth of ice crystals in the context of e.g. cryopreservation protocols. This paper is about the impact of depletion forces - and as a StatMech person, this was too good an opportunity to jump on board. As such, you'll find a qualitative (pen & paper only!) discussion of said depletion effects providing further support to a very solid set of experimental results, which are very much suggestive of the sheer importance of the aggregation of ice re-crystallization inhibition agents. Have a look at the paper online, or grab a .pdf. This is the very first work featuring a collaboration between the Gibson group and the Sosso Group… stay tuned, I am positive there will be many more to come!
Promoting transparency and reproducibility in enhanced molecular simulations
Nature Methods
Alright, hold your horses. My contribution to this ginormous (the words you learn from your kids...) effort is tiny - but it's there! In a nutshell, the amazing people at the very core of the continuous, painstaking, never-ending development and expansion of the PLUMED software, have righteously decided to "outline [their] efforts to promote transparency and reproducibility by disseminating protocols for enhanced-sampling molecular simulations". Via PLUMED, obviously. What's that I hear (very few of you) ask - well, PLUMED is "an open-source library for enhanced-sampling, free-energy calculations and the analysis of molecular dynamics simulations". Check it out here. Now, all this is good - in fact, exceptionally good. First of all, because the unsung heroes at the heart of this PLUMED endeavour are excellent scientists. Massimiliano Bonomi, Giovanni Bussi, Carlo Camilloni, Gareth Tribello - it doesn't get much better than the stuff these guys do, and I mean it. As an example, it is because of Gareth that much of my ice-related research has come to life. You can have some decent ideas, but then you also need some code capable to deal with some rather cumbersome science - PLUMED can do that for you. It interfaces with basically everything under the sun, and can compute almost everything you can think about - if not, ask the community: it really works! Ok, enough with the violins. Have a look at the paper online, or grab a .pdf. Most importantly, get a sense of what can be done with PLUMED by navigating through the plethora of working examples (most of them related to published works) contained in the PLUMED-NEST. Happy enhanced sampling!
High and low density patches in simulated liquid water
The Journal of Chemical Physics
Time ago we looked at density fluctuations in liquid water, particularly the formation of cavities within the molecular network. Why? Because those are related to the cavitation free energy, which in turn is quite important when talking solvation and hydrophobic interactions. Here, we have taken a step further, identifying low- and high- density “patches” of water: yep – it turns out these cavities are not just randomly distributed throughout the liquid… there is more to come, I promise, but for now, have a look at the manuscript online – or just grab a pdf!
Priming Effects in the Crystallization of the Phase Change Compound GeTe from Atomistic Simulations
Faraday Discussions
My first paper about the crystallization of GeTe dates back to 2013. Aside for making me feel a bit old, I guess it is quite intriguing to realize that – some 5 years later – we still haven’t got the whole picture. No shame in that, though – we just have to acknowledge that these phase change materials have really quite a lot to tell/teach us. In this work, we discuss “priming” effects, i.e. what happens to the crystallization kinetics if you treat your parent phase beforehand. Mind you, this is no theoretical excercise… well, it – is – but is also quite key a thing for the actual devices. Have a look at the manuscript online – or just grab a pdf!
Unravelling the Origins of Ice Nucleation on Organic Crystals
Chemical Science
I am really quite proud of this paper. For one thing, it marks my transition from studying ice forming on inorganic materials to exploring the formation of ice in soft and biological matter. Secondly, this work is the result of a combined effort of molecular simulations and state-of-the-art experimental techniques – a contribution for which we have to thank T. Whale, M. Holden and B. Murray, all based at the University of Leeds. Experiments & Simulations together are still fairly rare a sight when it comes to ice – but things are changing, and it feels good to be a part of the tide. While contemplating the exciting possibilities in terms of future work that may be originating from this collaboration, have a look at the manuscript online – or just grab a .pdf!
Full Publications List
2020 |
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Combining high-resolution scanning tunnelling microscopy and first-principles simulations to identify halogen bonding Journal Article Nature Communications, 11 , pp. 2103, 2020. | |
Insights into the Emerging Networks of Voids in Simulated Supercooled Water Journal Article The Journal of Physical Chemistry B, 124 (11), pp. 2180-2190, 2020. | |
Less may be more: an informed reflection on molecular descriptors for drug design and discovery Journal Article Molecular Systems Design and Engineering, 5 , pp. 317-329, 2020. | |
Atomistic simulations of thermal conductivity in GeTe nanowires Journal Article Journal of Physics D: Applied Physics, 53 , pp. 054001, 2020. | |
2019 |
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Harnessing machine learning potentials to understand the functional properties of phase-change materials Journal Article MRS Bulletin, 44 (9), pp. 705-709, 2019. | |
Enhancement of Macromolecular Ice Recrystallization Inhibition Activity by Exploiting Depletion Forces Journal Article ACS Macro Letters, 8 , pp. 1063-1067, 2019. | |
Ice is born in low-mobility regions of supercooled liquid water Journal Article Proceedings of the National Academy of Sciences, pp. 201817135, 2019, ISSN: 0027-8424, 1091-6490. | |
Promoting transparency and reproducibility in enhanced molecular simulations Journal Article Nature Methods, 16 (8), pp. 670–673, 2019, ISSN: 1548-7105. | |
2018 |
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Heterogeneous seeded molecular dynamics as a tool to probe the ice nucleating ability of crystalline surfaces Journal Article The Journal of Chemical Physics, 149 (7), pp. 072327, 2018, ISSN: 0021-9606. | |
Understanding the thermal properties of amorphous solids using machine-learning-based interatomic potentials Journal Article Molecular Simulation, pp. 1–15, 2018, ISSN: 0892-7022, 1029-0435. | |
Unravelling the origins of ice nucleation on organic crystals Journal Article Chemical Science, 2018, ISSN: 2041-6520, 2041-6539. | |
Priming effects in the crystallization of the phase change compound GeTe from atomistic simulations Journal Article Faraday Discussions, 2018, ISSN: 1359-6640, 1364-5498. | |
High and low density patches in simulated liquid water Journal Article The Journal of Chemical Physics, 149 (20), pp. 204507, 2018, ISSN: 0021-9606, 1089-7690. | |
2017 |
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Grüneisen parameters and thermal conductivity in the phase change compound GeTe Journal Article Journal of Computational Electronics, 16 (4), pp. 997–1002, 2017, ISSN: 1569-8025, 1572-8137. | |
Pre-critical fluctuations and what they disclose about heterogeneous crystal nucleation Journal Article Nature Communications, 8 (1), 2017, ISSN: 2041-1723. | |
Analyzing and Driving Cluster Formation in Atomistic Simulations Journal Article Journal of Chemical Theory and Computation, 13 (3), pp. 1317–1327, 2017, ISSN: 1549-9618, 1549-9626. | |
Atomistic Simulations of the Crystallization and Aging of GeTe Nanowires Journal Article The Journal of Physical Chemistry C, 121 (42), pp. 23827–23838, 2017, ISSN: 1932-7447, 1932-7455. | |
Communication: Truncated non-bonded potentials can yield unphysical behavior in molecular dynamics simulations of interfaces Journal Article The Journal of Chemical Physics, 147 (12), pp. 121102, 2017, ISSN: 0021-9606, 1089-7690. | |
Is High-Density Amorphous Ice Simply a “Derailed” State along the Ice I to Ice IV Pathway? Journal Article The Journal of Physical Chemistry Letters, 8 (7), pp. 1645–1650, 2017, ISSN: 1948-7185. | |
On the Role of Nonspherical Cavities in Short Length-Scale Density Fluctuations in Water Journal Article The Journal of Physical Chemistry A, 121 (1), pp. 370–380, 2017, ISSN: 1089-5639, 1520-5215. | |
Analyzing and Driving Cluster Formation in Atomistic Simulations Journal Article Journal of chemical theory and computation, 13 (3), pp. 1317–1327, 2017. | |
Is High-Density Amorphous Ice Simply a “Derailed” State along the Ice I to Ice IV Pathway? Journal Article The Journal of Physical Chemistry Letters, 8 (7), pp. 1645–1650, 2017. | |
Grüneisen parameters and thermal conductivity in the phase change compound GeTe Journal Article Journal of Computational Electronics, 16 (4), pp. 997–1002, 2017. | |
Communication: Truncated non-bonded potentials can yield unphysical behavior in molecular dynamics simulations of interfaces Journal Article The Journal of Chemical Physics, 147 (12), pp. 121102, 2017. | |
Atomistic Simulations of the Crystallization and Aging of GeTe Nanowires Journal Article The Journal of Physical Chemistry C, 121 (42), pp. 23827–23838, 2017. | |
Pre-critical fluctuations and what they disclose about heterogeneous crystal nucleation Journal Article Nature Communications, 8 (1), pp. 2257, 2017. | |
2016 |
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Ice formation on kaolinite: Insights from molecular dynamics simulations Journal Article The Journal of Chemical Physics, 145 (21), pp. 211927, 2016, ISSN: 0021-9606, 1089-7690. | |
Atomic mobility in the overheated amorphous GeTe compound for phase change memories: Atomic mobility in overheated amorphous GeTe Journal Article Physica Status Solidi A, 213 (2), pp. 329–334, 2016, ISSN: 18626300. | |
Crystal Nucleation in Liquids: Open Questions and Future Challenges in Molecular Dynamics Simulations Journal Article Chemical Reviews, 116 (12), pp. 7078–7116, 2016, ISSN: 0009-2665, 1520-6890. | |
Microscopic Mechanism and Kinetics of Ice Formation at Complex Interfaces: Zooming in on Kaolinite Journal Article The Journal of Physical Chemistry Letters, 7 (13), pp. 2350–2355, 2016, ISSN: 1948-7185. | |
Atomic mobility in the overheated amorphous GeTe compound for phase change memories Journal Article physica status solidi (a), 213 (2), pp. 329–334, 2016. | |
Crystal nucleation in liquids: Open questions and future challenges in molecular dynamics simulations Journal Article Chemical reviews, 116 (12), pp. 7078–7116, 2016. | |
Microscopic mechanism and kinetics of ice formation at complex interfaces: Zooming in on kaolinite Journal Article The journal of physical chemistry letters, 7 (13), pp. 2350–2355, 2016. | |
Ice formation on kaolinite: Insights from molecular dynamics simulations Journal Article The Journal of Chemical Physics, 145 (21), pp. 211927, 2016. | |
On the Role of Nonspherical Cavities in Short Length-Scale Density Fluctuations in Water Journal Article The Journal of Physical Chemistry A, 121 (1), pp. 370–380, 2016. | |
2015 |
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The Many Faces of Heterogeneous Ice Nucleation: Interplay Between Surface Morphology and Hydrophobicity Journal Article Journal of the American Chemical Society, 137 (42), pp. 13658–13669, 2015, ISSN: 0002-7863, 1520-5126. | |
Heterogeneous Crystallization of the Phase Change Material GeTe via Atomistic Simulations Journal Article The Journal of Physical Chemistry C, 119 (11), pp. 6428–6434, 2015, ISSN: 1932-7447, 1932-7455. | |
Electron–phonon interaction and thermal boundary resistance at the interfaces of Ge2Sb2Te5 with metals and dielectrics Journal Article Journal of Physics: Condensed Matter, 27 (17), pp. 175009, 2015, ISSN: 0953-8984, 1361-648X. | |
Electron-phonon interaction and thermal boundary resistance at the crystal-amorphous interface of the phase change compound GeTe Journal Article Journal of Applied Physics, 117 (1), pp. 015304, 2015, ISSN: 0021-8979, 1089-7550. | |
Functional Properties of Phase Change Materials from Atomistic Simulations Incollection Massobrio, Carlo; Du, Jincheng; Bernasconi, Marco; Salmon, Philip S (Ed.): Molecular Dynamics Simulations of Disordered Materials, 215 , pp. 415–440, Springer International Publishing, Cham, 2015, ISBN: 978-3-319-15674-3 978-3-319-15675-0. | |
Microscopic origin of resistance drift in the amorphous state of the phase-change compound GeTe Journal Article Physical Review B, 92 (5), 2015, ISSN: 1098-0121, 1550-235X. | |
Electron-phonon interaction and thermal boundary resistance at the crystal-amorphous interface of the phase change compound GeTe Journal Article Journal of Applied Physics, 117 (1), pp. 015304, 2015. | |
Heterogeneous crystallization of the phase change material GeTe via atomistic simulations Journal Article The Journal of Physical Chemistry C, 119 (11), pp. 6428–6434, 2015. | |
Functional Properties of Phase Change Materials from Atomistic Simulations Incollection Molecular Dynamics Simulations of Disordered Materials, pp. 415–440, Springer, 2015. | |
Electron--phonon interaction and thermal boundary resistance at the interfaces of Ge2Sb2Te5 with metals and dielectrics Journal Article Journal of Physics: Condensed Matter, 27 (17), pp. 175009, 2015. | |
Microscopic origin of resistance drift in the amorphous state of the phase-change compound GeTe Journal Article Physical Review B, 92 (5), pp. 054201, 2015. | |
The many faces of heterogeneous ice nucleation: Interplay between surface morphology and hydrophobicity Journal Article Journal of the American Chemical Society, 137 (42), pp. 13658–13669, 2015. | |
2014 |
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The role of the umbrella inversion mode in proton diffusion Journal Article Chemical Physics Letters, 599 , pp. 133–138, 2014, ISSN: 00092614. | |
Dynamical Heterogeneity in the Supercooled Liquid State of the Phase Change Material GeTe Journal Article The Journal of Physical Chemistry B, 118 (47), pp. 13621–13628, 2014, ISSN: 1520-6106, 1520-5207. | |
The role of the umbrella inversion mode in proton diffusion Journal Article Chemical Physics Letters, 599 , pp. 133–138, 2014. | |