Highlights

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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Pre-critical fluctuations and what they disclose about heterogeneous crystal nucleation


Nature Communications

8 (1), 2017,  2041-1723

DOI: 10.1038/s41467-017-02300-x

One of the central quantities in the context of crystal nucleation is the critical nucleus: a bunch of atoms/molecules/particles large just enough for the system to proceed to the growth of the newborn crystalline phase. However, we argue in this work that pre-critical nuclei can provide some unexpectedly important insight as well. And, in the process of figuring this out, we actually came up with a modification of classical nucleation theory (the tool of the trade when talking nucleation…) which is necessary when the crystalline polymorph nucleating heterogeneously differs from what you get from homogeneous nucleation...

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Truncated non-bonded potentials can yield unphysical behavior in molecular dynamics simulations of interfaces


The Journal of Chemical Physics

147, 121102 (2017)

DOI: 10.1063/1.4997698

This work is about the dreadful things that happen to those (well, basically everyone…) who dare truncating non-bonded terms when performing molecular dynamics simulations of interfaces. It has recently been accepted in The Journal of Physical Chemistry, and involves quite a number of people across several institutions: (chiefly) the University College London [UK], the University of Lyon [France] and Tsinghua University [China]...

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Full Publications List

74 entries « 2 of 2 »

2013

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

74 entries « 2 of 2 »