Highlights

Enhancement of macromolecular ice recrystallization inhibition activity by exploiting depletion forces


Journal of Physics D: Applied Physics

Just accepted

DOI: 10.1088/1361-6463/ab5478

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.

 

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Less may be more: an informed reflection on molecular descriptors for drug design and discovery


Molecular Systems Design and Engineering

Just accepted

DOI: 10.1039/C9ME00109C

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!

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Harnessing machine learning potentials to understand the functional properties of phase-change materials


MRS Bulletin

Published 05-09-19

DOI: 10.1557/mrs.2019.202

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.

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Enhancement of macromolecular ice recrystallization inhibition activity by exploiting depletion forces


ACS Macro Letters

Published 09-08-19

DOI: 10.1021/acsmacrolett.9b00386

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!

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Promoting transparency and reproducibility in enhanced molecular simulations


Nature Methods

Just accepted

DOI: 10.1038/s41592-019-0506-8

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 BonomiGiovanni BussiCarlo CamilloniGareth 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!

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High and low density patches in simulated liquid water


The Journal of Chemical Physics

Just accepted

DOI: 10.1063/1.5053559

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!

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Priming Effects in the Crystallization of the Phase Change Compound GeTe from Atomistic Simulations


Faraday Discussions

Just accepted

10.1039/C8FD00101D

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!

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Unravelling the Origins of Ice Nucleation on Organic Crystals


Chemical Science

Just accepted

DOI:10.1039/C8SC02753F

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!

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Heterogeneous seeded molecular dynamics as a tool to probe the ice nucleating ability of crystalline surfaces


The Journal of Chemical Physics

Just accepted

DOI:10.1063/1.5029336

When it comes to enhanced sampling simulations of rare event, one usually choose something along the lines of either free energy or path sampling techniques. Unfortunately, these are computationally costly. Seeded molecular dynamics is a much less demanding alternative that has been successfully applied already to study the homogeneous freezing of water. However, in the case of heterogeneous ice nucleation, nature’s favourite route to form ice, an array of suitable interfaces between the ice seeds and the substrate of interest has to be built, and this is no trivial task. In this paper, we present a Heterogeneous SEEDing (HSEED) approach which harnesses a random structure search framework to tackle the ice-substrate challenge, thus enabling seeded molecular dynamics simulations of heterogeneous ice nucleation on crystalline surfaces. Here's the online version, but you are welcome to just grab a .pdf as well.

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Understanding the thermal properties of amorphous solids using machine-learning-based interatomic potentials


Molecular Simulation

Just accepted

DOI: 10.1080/08927022.2018.1447107

There is no point in petending otherwise: “Machine Learning” is so much hyped it’s just not true. However, it turns out these clever (?) algorithms can help us with a number of things. For instance, building interatomic potentials for complex systems (for which electronic structure calculations would cost too much) enabling large scale molecular dynamics simulations. To what end? Many. In here, we focus on what can be done with respect to the thermal properties of amorphous systems. If it sounds cumbersome, think about your window glasses basking in the sun – and there’s more, I promise...

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Full Publications List

78 entries « 2 of 2 »

2013

Caravati, Sebastiano; Sosso, Gabriele C; Bernasconi, Marco; Parrinello, Michele

Density functional simulations of hexagonal Ge2Sb2Te5 at high pressure Journal Article

Physical Review B, 87 (9), 2013, ISSN: 1098-0121, 1550-235X.

Links | BibTeX

Sosso, Gabriele C; Miceli, Giacomo; Caravati, Sebastiano; Giberti, Federico; Behler, Jörg; Bernasconi, Marco

Fast Crystallization of the Phase Change Compound GeTe by Large-Scale Molecular Dynamics Simulations Journal Article

The Journal of Physical Chemistry Letters, 4 (24), pp. 4241–4246, 2013, ISSN: 1948-7185.

Links | BibTeX

Caravati, Sebastiano; Sosso, Gabriele C; Bernasconi, Marco; Parrinello, Michele

Density functional simulations of hexagonal Ge 2 Sb 2 Te 5 at high pressure Journal Article

Physical Review B, 87 (9), pp. 094117, 2013.

BibTeX

Sosso, Gabriele C; Miceli, Giacomo; Caravati, Sebastiano; Giberti, Federico; Behler, Jörg; Bernasconi, Marco

Fast crystallization of the phase change compound GeTe by large-scale molecular dynamics simulations Journal Article

The journal of physical chemistry letters, 4 (24), pp. 4241–4246, 2013.

BibTeX

Sosso, Gabriele C; Miceli, G; Caravati, Sebastiano; Donadio, Davide; Behler, Jörg; Bernasconi, Marco

Nanosession: Phase Change Materials Incollection

Frontiers in Electronic Materials, pp. 157, Wiley-VCH Verlag GmbH & Co. KGaA, 2013.

BibTeX

2012

Sosso, G C; Behler, J; Bernasconi, M

Breakdown of Stokes-Einstein relation in the supercooled liquid state of phase change materials Journal Article

physica status solidi (b), 249 (10), pp. 1880–1885, 2012, ISSN: 03701972.

Links | BibTeX

Sosso, G C; Behler, J; Bernasconi, M

Breakdown of Stokes-Einstein relation in the supercooled liquid state of phase change materials Journal Article

Physica Status Solidi (b), 249 (10), pp. 1880–1885, 2012, ISSN: 03701972.

Links | BibTeX

Sosso, Gabriele C; Donadio, Davide; Caravati, Sebastiano; Behler, Jörg; Bernasconi, Marco

Thermal transport in phase-change materials from atomistic simulations Journal Article

Physical Review B, 86 (10), 2012, ISSN: 1098-0121, 1550-235X.

Links | BibTeX

Sosso, Gabriele C; Donadio, Davide; Caravati, Sebastiano; Behler, Jörg; Bernasconi, Marco

Thermal transport in phase-change materials from atomistic simulations Journal Article

Physical Review B, 86 (10), 2012, ISSN: 1098-0121, 1550-235X.

Links | BibTeX

Sosso, Gabriele C; Donadio, Davide; Caravati, Sebastiano; Behler, Jörg; Bernasconi, Marco

Thermal transport in phase-change materials from atomistic simulations Journal Article

Physical Review B, 86 (10), 2012, ISSN: 1098-0121, 1550-235X.

Links | BibTeX

Sosso, Gabriele C; Miceli, Giacomo; Caravati, Sebastiano; Behler, Jörg; Bernasconi, Marco

Neural network interatomic potential for the phase change material GeTe Journal Article

Physical Review B, 85 (17), 2012, ISSN: 1098-0121, 1550-235X.

Links | BibTeX

Sosso, Gabriele C; Miceli, Giacomo; Caravati, Sebastiano; Behler, Jörg; Bernasconi, Marco

Neural network interatomic potential for the phase change material GeTe Journal Article

Physical Review B, 85 (17), 2012, ISSN: 1098-0121, 1550-235X.

Links | BibTeX

Sosso, Gabriele C; Miceli, Giacomo; Caravati, Sebastiano; Behler, Jörg; Bernasconi, Marco

Neural network interatomic potential for the phase change material GeTe Journal Article

Physical Review B, 85 (17), 2012, ISSN: 1098-0121, 1550-235X.

Links | BibTeX

Sosso, Gabriele C; Miceli, Giacomo; Caravati, Sebastiano; Behler, Jörg; Bernasconi, Marco

Neural network interatomic potential for the phase change material GeTe Journal Article

Physical Review B, 85 (17), pp. 174103, 2012.

BibTeX

Sosso, Gabriele C; Behler, Joerg; Bernasconi, Marco

Breakdown of Stokes--Einstein relation in the supercooled liquid state of phase change materials Journal Article

physica status solidi (b), 249 (10), pp. 1880–1885, 2012.

BibTeX

Sosso, Gabriele C; Donadio, Davide; Caravati, Sebastiano; Behler, Jörg; Bernasconi, Marco

Thermal transport in phase-change materials from atomistic simulations Journal Article

Physical Review B, 86 (10), pp. 104301, 2012.

BibTeX

2011

Sosso, Gabriele C; Caravati, Sebastiano; Mazzarello, Riccardo; Bernasconi, Marco

Raman spectra of cubic and amorphous Ge2Sb2Te5 from first principles Journal Article

Physical Review B, 83 (13), 2011, ISSN: 1098-0121, 1550-235X.

Links | BibTeX

Sosso, Gabriele C; Caravati, Sebastiano; Mazzarello, Riccardo; Bernasconi, Marco

Raman spectra of cubic and amorphous Ge2Sb2Te5 from first principles Journal Article

Physical Review B, 83 (13), 2011, ISSN: 1098-0121, 1550-235X.

Links | BibTeX

Sosso, Gabriele C; Caravati, Sebastiano; Mazzarello, Riccardo; Bernasconi, Marco

Raman spectra of cubic and amorphous Ge2Sb2Te5 from first principles Journal Article

Physical Review B, 83 (13), 2011, ISSN: 1098-0121, 1550-235X.

Links | BibTeX

Sosso, Gabriele C; Caravati, Sebastiano; Mazzarello, Riccardo; Bernasconi, Marco

Raman spectra of cubic and amorphous Ge 2 Sb 2 Te 5 from first principles Journal Article

Physical Review B, 83 (13), pp. 134201, 2011.

BibTeX

2009

Sosso, G C; Caravati, S; Gatti, C; Assoni, S; Bernasconi, M

Vibrational properties of hexagonal Ge2Sb2Te5 from first principles Journal Article

Journal of Physics: Condensed Matter, 21 (24), pp. 245401, 2009, ISSN: 0953-8984, 1361-648X.

Links | BibTeX

Sosso, G C; Caravati, S; Gatti, C; Assoni, S; Bernasconi, M

Vibrational properties of hexagonal Ge2Sb2Te5 from first principles Journal Article

Journal of Physics: Condensed Matter, 21 (24), pp. 245401, 2009, ISSN: 0953-8984, 1361-648X.

Links | BibTeX

Sosso, G C; Caravati, S; Gatti, C; Assoni, S; Bernasconi, M

Vibrational properties of hexagonal Ge2Sb2Te5 from first principles Journal Article

Journal of Physics: Condensed Matter, 21 (24), pp. 245401, 2009, ISSN: 0953-8984, 1361-648X.

Links | BibTeX

Sosso, G C; Caravati, S; Bernasconi, M

Vibrational properties of crystalline Sb2Te3 from first principles Journal Article

Journal of Physics: Condensed Matter, 21 (9), pp. 095410, 2009, ISSN: 0953-8984, 1361-648X.

Links | BibTeX

Sosso, G C; Caravati, S; Bernasconi, M

Vibrational properties of crystalline Sb2Te3 from first principles Journal Article

Journal of Physics: Condensed Matter, 21 (9), pp. 095410, 2009, ISSN: 0953-8984, 1361-648X.

Links | BibTeX

Sosso, G C; Caravati, S; Bernasconi, M

Vibrational properties of crystalline Sb2Te3 from first principles Journal Article

Journal of Physics: Condensed Matter, 21 (9), pp. 095410, 2009, ISSN: 0953-8984, 1361-648X.

Links | BibTeX

Sosso, GC; Caravati, S; Bernasconi, M

Vibrational properties of crystalline Sb2Te3 from first principles Journal Article

Journal of Physics: Condensed Matter, 21 (9), pp. 095410, 2009.

BibTeX

Sosso, GC; Caravati, S; Gatti, C; Assoni, S; Bernasconi, M

Vibrational properties of hexagonal Ge2Sb2Te5 from first principles Journal Article

Journal of Physics: Condensed Matter, 21 (24), pp. 245401, 2009.

BibTeX

78 entries « 2 of 2 »