Highlights

Levering Genetic Algorithms to Maximise the Predictive Capabilities of the SOAP Descriptor


Molecular Systems Design and Engineering

Just accepted

DOI: 10.1039/d2me00149g

In this collaboration with AstraZeneca, James Darby in Cambridge, and Warwick's Albert Bartók-Partay, we explore the capabilities of genetic algorithms (GAs) when used to optimise the hyperparameters of the popular SOAP descriptor. SOAPs are a commonly used method to encode atomic local environments, with good performance over a wide range of materials. We show that by using our genetic algorithm package (available at https://github.com/gcsosso/SOAP_GAS) the predictive capabilities of SOAPs are improved for a variety of datasets. There were notable improvements when predicting the solubility of molecules in a prototypical molecular database for drug design, and when predicting the polarizability of the QM7b dataset. We also showcase the improvements on both optimisation speed and quality of our GA when compared to the more commonly used random grid search. Have a look at the paper online or grab a pdf here.

 

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Minimalistic ice recrystallisation inhibitors based on phenylalanine


Chemical Communications

Just published

DOI:10.1039/D2CC02531K

The second instalment of our work amino acids, this paper introduces phenylalanine as a minimalistic, yet potent, ice growth inhibitor. We explore the structure-function relationships in a panel of phenylalanine derivatives, revealing the importance of both hydrophobic and hydrophilic regions and a possible role of self-assembly in ice growth inhibition. Have a look at the paper online or grab a pdf here.

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The role of structural order in heterogeneous ice nucleation


Chemical Science

Just published

DOI:10.1039/D1SC06338C

It took some six years for this paper to eventually see the light of day - but it was worth it.
Titled: "The role of structural order in heterogeneous ice nucleation" and published in Chemical Science, this work is a testament to a massive collaborative effort that involved myself (when I was working Angelos Michaelides at UCL, now Cambridge) and a stellar team at the Max Plank in Mainz (Ellen Backus is now in Wien), in addition to our very own Tom Whale (in Leeds at the time).
In a nutshell, with this paper we tried to look at the same thing, cholesterol, in different forms, from crystals to more-or-less disordered monolayers, and get an idea of how well these different forms nucleate ice. This is important for a number of reasons: a fundamental one is that it is usually very hard to isolate the effect of structural disorder on ice nucleation. A more practical one is that cholesterol is part of our own cell membranes - hence it is quite key to investigate what does it do to water and ice. Yet another piece of the puzzle, we think, but this is a long road. Have a look at the paper online or grab a pdf here.

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How do Interfaces Alter the Dynamics of Supercooled Water?


Nanoscale

Just published

DOI: 10.1039/d2nr00387b

It was somewhere in Switzerland (some 10 years ago?), during a conference featuring excellent food, loads of snow, some newly found colleagues who I still call friends and - incidentally - some interesting science as well, when the concept of dynamical heterogeneity (DH) was first pitched to me (by a certain Emanuela del Gado, now at Georgetown University). This paper, to which I only marginally contributed to, represents the very latest chapter of my DH saga (very much still ongoing, fear not!). I am very grateful to Piero (Gasparotto, who led this), Martin (Fitzner), Steve (Cox) and the ICE group at Cambridge for doing all the hard work and for persevering along what was a fairly rocky road. But we did it, and I love this work. It poses interesting questions for the future, and I can only hope to be a part of the team that is going to be answering those in the near future. DH is fun. And it matters. And it also allows for very snazzy figures. Have a look at the paper online or grab a pdf here

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Ice Recrystallization Inhibition by Amino Acids: The Curious Case of Alpha- and Beta-Alanine


The Journal of Physical Chemistry Letters

Just accepted

DOI:10.1021/acs.jcplett.1c04080

In this work, we report the discovery that the amino acid alpha-alanine - a natural building block of proteins - can inhibit ice recrystallisation (growth) at low millimolar concentrations. To understand how this process works at the molecular level, we combined experimental and computational approaches to measure and simulate the growth of ice in the presence of alpha-alanine or beta-alanine. Despite having the same atomic composition as alpha-alanine, beta-alanine does not inhibit ice growth, making for a puzzling case study on this topic. We traced the inhibition activity of alpha-alanine to its ability to resist becoming overgrown by the growing ice front, characterised by its unfavourable fit within the ice lattice. These results represent a key contribution to our growing understanding of ice recrystallisation inhibition and may translate into improved cryopreservation practices. Have a look at the paper online or grab a pdf here.

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Lipid Bilayers as Potential Ice Nucleating Agents


Physical Chemistry Chemical Physics

Just accepted

DOI:10.1039/d1cp05465a

This paper is about whether cellular membranes could be responsible for facilitating the ice nucleation process, and what characteristics would make them good or bad ice nucleating agents. We simulated several phospholipids and lipopolysaccharide bilayers at the interface with supercooled liquid water. A bilayer's ability to act as an ice nucleating agent is complex, with both chemical and structural factors of relevance. Such bilayers appear to act as ice nucleating agents, although other impurities likely also play a role in initiating extracellular ice nucleation. These findings represent a first attempt to pinpoint the origin of extracellular ice nucleation, with important implications for the cryopreservation process. Have a look at the paper online or grab a pdf here.

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Recovering Local Structure Information from High-Pressure Total Scattering Experiments


Journal of Applied Crystallography

Just published

DOI:10.1107/S1600576721009420

This work is all about disordered phases at very high pressures. Specifically, a dream team of experimentalists (including our very own Mark Senn from Warwick Chemistry) came up with a clever way to subtract the pair correlation functions of the pressure-transmitting medium (that is, the liquid that is used in experiments to transmit the applied pressure to the actual sample) from those of the material of interest. We only played a little role in this, by providing the pair correlation functions of methanol/ethanol mixtures via molecular dynamics simulations at various pressures. It was great to see our numbers put into the experimental context! Have a look at the paper online or grab a pdf here.

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The Seven Deadly Sins: When Computing Crystal Nucleation Rates, the Devil is in the Details


Journal of Chemical Physics

Just published

DOI: 10.1063/5.0055248

In this paper (chosen as an "Editor's Pick"), we discuss the many different pitfalls that computation of crystal nucleation rates can fall into. Perhaps unsurprisingly, there are rather a lot! Hopefully these are lessons that we all (ourselves included) can learn from. Have a look at the paper online or grab a .pdf.

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A Minimalistic Cyclic Ice-binding Peptide from Phage Display


Nature Communications

Just published

DOI: 10.1038/s41467-021-22883-w

In this collaboration with EPFL, Switzerland and the Gibson group here at Warwick, billions of potential ice-binding peptides were screened using phage display - using a virus to generate loads of peptides and isolating those which display ice-binding activity.

We then used molecular dynamics to investigate exactly how discovered peptides bind to ice, allowing us to probe how structural differences affect ice-binding activity. Screening billions of peptides, and investigating binding activity - exciting stuff! Have a look at the paper online or grab a .pdf. The University of Warwick press release can be found here.

 

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Microscopic Kinetics Pathway of Salt Crystallization in Graphene Nanocapillaries


Physical Review Letters

Just published

DOI: 10.1103/PhysRevLett.126.136001

The humble NaCl crystals strike again! Some impressive microscopy (and some simulations as well - of course!) in this Physical Review Letter we were lucky enough to be involved with. Have a look at our paper online or grab a .pdf.

 

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Full Publications List

93 entries « 1 of 2 »

2022

Warren, MT; Galpin, I; Hasan, M; Hindmarsh, SA; Padrnos, JD; Edwards-Gayle, C; Mathers, RT; Adams, DJ; Sosso, GC; Gibson, MI

Minimalistic ice recrystallisation inhibitors based on phenylalanine Journal Article

In: Chemical Communications, 2022.

Links | BibTeX

Sosso, GC; P, Sudera; Backes, AT; Whale, TF; Fröhlich-Nowoisky, J; Bonn, M; Michaelides, A; Backus, EHG

The role of structural order in heterogeneous ice nucleation Journal Article

In: Chemical Science, vol. 13, iss. 17, pp. 5014-5026, 2022.

Links | BibTeX

Warren, MT; Galpin, I; Bachtiger, F; Gibson, MI; Sosso, GC

Ice recrystallization inhibition by amino acids: the curious case of alpha- and beta-alanine Journal Article

In: The Journal of Physical Chemistry Letters, vol. 13, no. 9, pp. 2237-2244, 2022.

Links | BibTeX

Miles, CM; Hsu, P-C; Dixon, AM; Khalid, S; Sosso, GC

Lipid bilayers as potential ice nucleating agents Journal Article

In: Physical Chemistry Chemical Physics, vol. 24, iss. 11, pp. 6476-6491, 2022.

Links | BibTeX

Gasparotto, P; Fitzner, M; Cox, SJ; Sosso, GC; Michaelides, A

How do interfaces alter the dynamics of supercooled water? Journal Article

In: Nanoscale, vol. 14, iss. 11, pp. 4254-4262, 2022.

Links | BibTeX

2021

Herlihy, A; Geddes, HS; Sosso, GC; Bull, CL; Ridley, CK; Goodwin, AL; Senn, MS; Funnell, NP

Recovering local structure information from high-pressure total scattering experiments Journal Article

In: Journal of Applied Crystallography, vol. 54, no. 6, pp. 1546-1554, 2021.

Links | BibTeX

Blow, KE; Quigley, D; Sosso, GC

The seven deadly sins: When computing crystal nucleation rates, the devil is in the details Journal Article

In: The Journal of Chemical Physics, vol. 155, no. 4, pp. 040901, 2021.

Links | BibTeX

Stevens, CA; Bachtiger, F; Kong, X-D; Abriata, LA; Sosso, GC; Gibson, MI; Klok, H-A

A minimalistic cyclic ice-binding peptide from phage display Journal Article

In: Nature Communications, vol. 12, pp. 2675, 2021.

Links | BibTeX

Wang, L; Chen, J; Cox, SJ; Liu, L; Sosso, GC; Li, N; Gao, P; Michaelides, A; Wang, E; Bai, X

Microscopic Kinetics Pathway of Salt Crystallization in Graphene Nanocapillaries Journal Article

In: Physical Review Letters, vol. 126, no. 13, pp. 136001, 2021.

Links | BibTeX

Mistry, MV; Cottom, J; Patel, K; Shluger, AL; Sosso, GC; Pobegen, G

Modelling the interactions and diffusion of NO in amorphous SiO2 Journal Article

In: Modelling and Simulation in Materials Science and Engineering, vol. 29, no. 3, pp. 035008, 2021.

Links | BibTeX

Bachtiger, F; Congdon, TR; Stubbs, C; Gibson, MI; Sosso, GC

The atomistic details of the ice recrystallisation inhibition activity of PVA. Journal Article

In: Nature Communications, vol. 12, no. 1323, 2021.

Links | BibTeX

2020

Lawrence, J; Sosso, GC; Đorđević, L; Pinfold, H; Bonifazi, D; Constantini, G

Combining high-resolution scanning tunnelling microscopy and first-principles simulations to identify halogen bonding Journal Article

In: Nature Communications, vol. 11, pp. 2103, 2020.

Links | BibTeX

Ansari, N; Onat, B; Sosso, GC; Hassanali, A

Insights into the Emerging Networks of Voids in Simulated Supercooled Water Journal Article

In: The Journal of Physical Chemistry B, vol. 124, no. 11, pp. 2180-2190, 2020.

Links | BibTeX

Barnard, T; Hagan, H; Tseng, S; Sosso, GC

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

In: Molecular Systems Design and Engineering, vol. 5, pp. 317-329, 2020.

Links | BibTeX

Bosoni, E; Campi, D; Donadio, D; Sosso, G C; Behler, J; Bernasconi, M

Atomistic simulations of thermal conductivity in GeTe nanowires Journal Article

In: Journal of Physics D: Applied Physics, vol. 53, pp. 054001, 2020.

Links | BibTeX

2019

Sosso, GC; Bernasconi, M

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

In: MRS Bulletin, vol. 44, no. 9, pp. 705-709, 2019.

Links | BibTeX

Ishibe, T; Congdon, T; Stubbs, C; Hasan, M; Sosso, GC; Gibson, MI

Enhancement of Macromolecular Ice Recrystallization Inhibition Activity by Exploiting Depletion Forces Journal Article

In: ACS Macro Letters, vol. 8, pp. 1063-1067, 2019.

Links | BibTeX

Fitzner, Martin; Sosso, Gabriele C; Cox, Stephen J; Michaelides, Angelos

Ice is born in low-mobility regions of supercooled liquid water Journal Article

In: Proceedings of the National Academy of Sciences, pp. 201817135, 2019, ISSN: 0027-8424, 1091-6490.

Links | BibTeX

Bonomi, Massimiliano; Bussi, Giovanni; Camilloni, Carlo; Tribello, Gareth A; Consortium, The PLUMED

Promoting transparency and reproducibility in enhanced molecular simulations Journal Article

In: Nature Methods, vol. 16, no. 8, pp. 670–673, 2019, ISSN: 1548-7105.

Abstract | Links | BibTeX

2018

Pedevilla, Philipp; Fitzner, Martin; Sosso, Gabriele C; Michaelides, Angelos

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

In: The Journal of Chemical Physics, vol. 149, no. 7, pp. 072327, 2018, ISSN: 0021-9606.

Links | BibTeX

Sosso, Gabriele C; Deringer, Volker L; Elliott, Stephen R; Csányi, Gábor

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

In: Molecular Simulation, pp. 1–15, 2018, ISSN: 0892-7022, 1029-0435.

Links | BibTeX

Sosso, Gabriele C; Whale, Thomas F; Holden, Mark A; Pedevilla, Philipp; Murray, Benjamin J; Michaelides, Angelos

Unravelling the origins of ice nucleation on organic crystals Journal Article

In: Chemical Science, 2018, ISSN: 2041-6520, 2041-6539.

Links | BibTeX

Gabardi, Silvia; Sosso, Gabriele G; Behler, Joerg; Bernasconi, Marco

Priming effects in the crystallization of the phase change compound GeTe from atomistic simulations Journal Article

In: Faraday Discussions, 2018, ISSN: 1359-6640, 1364-5498.

Links | BibTeX

Ansari, N; Dandekar, R; Caravati, S; Sosso, G C; Hassanali, A

High and low density patches in simulated liquid water Journal Article

In: The Journal of Chemical Physics, vol. 149, no. 20, pp. 204507, 2018, ISSN: 0021-9606, 1089-7690.

Links | BibTeX

2017

Bosoni, Emanuele; Sosso, Gabriele Cesare; Bernasconi, Marco

Grüneisen parameters and thermal conductivity in the phase change compound GeTe Journal Article

In: Journal of Computational Electronics, vol. 16, no. 4, pp. 997–1002, 2017, ISSN: 1569-8025, 1572-8137.

Links | BibTeX

Fitzner, Martin; Sosso, Gabriele C; Pietrucci, Fabio; Pipolo, Silvio; Michaelides, Angelos

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

In: Nature Communications, vol. 8, no. 1, 2017, ISSN: 2041-1723.

Links | BibTeX

Tribello, Gareth A; Giberti, Federico; Sosso, Gabriele C; Salvalaglio, Matteo; Parrinello, Michele

Analyzing and Driving Cluster Formation in Atomistic Simulations Journal Article

In: Journal of Chemical Theory and Computation, vol. 13, no. 3, pp. 1317–1327, 2017, ISSN: 1549-9618, 1549-9626.

Links | BibTeX

Gabardi, S; Baldi, E; Bosoni, E; Campi, D; Caravati, S; Sosso, G C; Behler, J; Bernasconi, M

Atomistic Simulations of the Crystallization and Aging of GeTe Nanowires Journal Article

In: The Journal of Physical Chemistry C, vol. 121, no. 42, pp. 23827–23838, 2017, ISSN: 1932-7447, 1932-7455.

Links | BibTeX

Fitzner, Martin; Joly, Laurent; Ma, Ming; Sosso, Gabriele C; Zen, Andrea; Michaelides, Angelos

Communication: Truncated non-bonded potentials can yield unphysical behavior in molecular dynamics simulations of interfaces Journal Article

In: The Journal of Chemical Physics, vol. 147, no. 12, pp. 121102, 2017, ISSN: 0021-9606, 1089-7690.

Links | BibTeX

Shephard, Jacob J; Ling, Sanliang; Sosso, Gabriele C; Michaelides, Angelos; Slater, Ben; Salzmann, Christoph G

Is High-Density Amorphous Ice Simply a “Derailed” State along the Ice I to Ice IV Pathway? Journal Article

In: The Journal of Physical Chemistry Letters, vol. 8, no. 7, pp. 1645–1650, 2017, ISSN: 1948-7185.

Links | BibTeX

Sosso, Gabriele Cesare; Caravati, Sebastiano; Rotskoff, Grant; Vaikuntanathan, Suriyanarayan; Hassanali, Ali

On the Role of Nonspherical Cavities in Short Length-Scale Density Fluctuations in Water Journal Article

In: The Journal of Physical Chemistry A, vol. 121, no. 1, pp. 370–380, 2017, ISSN: 1089-5639, 1520-5215.

Links | BibTeX

Tribello, Gareth A; Giberti, Federico; Sosso, Gabriele C; Salvalaglio, Matteo; Parrinello, Michele

Analyzing and Driving Cluster Formation in Atomistic Simulations Journal Article

In: Journal of chemical theory and computation, vol. 13, no. 3, pp. 1317–1327, 2017.

BibTeX

Shephard, Jacob J; Ling, Sanliang; Sosso, Gabriele C; Michaelides, Angelos; Slater, Ben; Salzmann, Christoph G

Is High-Density Amorphous Ice Simply a “Derailed” State along the Ice I to Ice IV Pathway? Journal Article

In: The Journal of Physical Chemistry Letters, vol. 8, no. 7, pp. 1645–1650, 2017.

BibTeX

Bosoni, Emanuele; Sosso, Gabriele Cesare; Bernasconi, Marco

Grüneisen parameters and thermal conductivity in the phase change compound GeTe Journal Article

In: Journal of Computational Electronics, vol. 16, no. 4, pp. 997–1002, 2017.

BibTeX

Fitzner, Martin; Joly, Laurent; Ma, Ming; Sosso, Gabriele C; Zen, Andrea; Michaelides, Angelos

Communication: Truncated non-bonded potentials can yield unphysical behavior in molecular dynamics simulations of interfaces Journal Article

In: The Journal of Chemical Physics, vol. 147, no. 12, pp. 121102, 2017.

BibTeX

Gabardi, S; Baldi, E; Bosoni, E; Campi, D; Caravati, S; Sosso, GC; Behler, J; Bernasconi, M

Atomistic Simulations of the Crystallization and Aging of GeTe Nanowires Journal Article

In: The Journal of Physical Chemistry C, vol. 121, no. 42, pp. 23827–23838, 2017.

BibTeX

Fitzner, Martin; Sosso, Gabriele C; Pietrucci, Fabio; Pipolo, Silvio; Michaelides, Angelos

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

In: Nature Communications, vol. 8, no. 1, pp. 2257, 2017.

BibTeX

2016

Sosso, Gabriele C; Tribello, Gareth A; Zen, Andrea; Pedevilla, Philipp; Michaelides, Angelos

Ice formation on kaolinite: Insights from molecular dynamics simulations Journal Article

In: The Journal of Chemical Physics, vol. 145, no. 21, pp. 211927, 2016, ISSN: 0021-9606, 1089-7690.

Links | BibTeX

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

Atomic mobility in the overheated amorphous GeTe compound for phase change memories: Atomic mobility in overheated amorphous GeTe Journal Article

In: Physica Status Solidi A, vol. 213, no. 2, pp. 329–334, 2016, ISSN: 18626300.

Links | BibTeX

Sosso, Gabriele C; Chen, Ji; Cox, Stephen J; Fitzner, Martin; Pedevilla, Philipp; Zen, Andrea; Michaelides, Angelos

Crystal Nucleation in Liquids: Open Questions and Future Challenges in Molecular Dynamics Simulations Journal Article

In: Chemical Reviews, vol. 116, no. 12, pp. 7078–7116, 2016, ISSN: 0009-2665, 1520-6890.

Links | BibTeX

Sosso, Gabriele C; Li, Tianshu; Donadio, Davide; Tribello, Gareth A; Michaelides, Angelos

Microscopic Mechanism and Kinetics of Ice Formation at Complex Interfaces: Zooming in on Kaolinite Journal Article

In: The Journal of Physical Chemistry Letters, vol. 7, no. 13, pp. 2350–2355, 2016, ISSN: 1948-7185.

Links | BibTeX

Sosso, GC; Behler, J; Bernasconi, M

Atomic mobility in the overheated amorphous GeTe compound for phase change memories Journal Article

In: physica status solidi (a), vol. 213, no. 2, pp. 329–334, 2016.

BibTeX

Sosso, Gabriele C; Chen, Ji; Cox, Stephen J; Fitzner, Martin; Pedevilla, Philipp; Zen, Andrea; Michaelides, Angelos

Crystal nucleation in liquids: Open questions and future challenges in molecular dynamics simulations Journal Article

In: Chemical reviews, vol. 116, no. 12, pp. 7078–7116, 2016.

BibTeX

Sosso, Gabriele C; Li, Tianshu; Donadio, Davide; Tribello, Gareth A; Michaelides, Angelos

Microscopic mechanism and kinetics of ice formation at complex interfaces: Zooming in on kaolinite Journal Article

In: The journal of physical chemistry letters, vol. 7, no. 13, pp. 2350–2355, 2016.

BibTeX

Sosso, Gabriele C; Tribello, Gareth A; Zen, Andrea; Pedevilla, Philipp; Michaelides, Angelos

Ice formation on kaolinite: Insights from molecular dynamics simulations Journal Article

In: The Journal of Chemical Physics, vol. 145, no. 21, pp. 211927, 2016.

BibTeX

Sosso, Gabriele Cesare; Caravati, Sebastiano; Rotskoff, Grant; Vaikuntanathan, Suriyanarayan; Hassanali, Ali

On the Role of Nonspherical Cavities in Short Length-Scale Density Fluctuations in Water Journal Article

In: The Journal of Physical Chemistry A, vol. 121, no. 1, pp. 370–380, 2016.

BibTeX

2015

Fitzner, Martin; Sosso, Gabriele C; Cox, Stephen J; Michaelides, Angelos

The Many Faces of Heterogeneous Ice Nucleation: Interplay Between Surface Morphology and Hydrophobicity Journal Article

In: Journal of the American Chemical Society, vol. 137, no. 42, pp. 13658–13669, 2015, ISSN: 0002-7863, 1520-5126.

Links | BibTeX

Sosso, Gabriele C; Salvalaglio, Matteo; Behler, Jörg; Bernasconi, Marco; Parrinello, Michele

Heterogeneous Crystallization of the Phase Change Material GeTe via Atomistic Simulations Journal Article

In: The Journal of Physical Chemistry C, vol. 119, no. 11, pp. 6428–6434, 2015, ISSN: 1932-7447, 1932-7455.

Links | BibTeX

Campi, D; Baldi, E; Graceffa, G; Sosso, G C; Bernasconi, M

Electron–phonon interaction and thermal boundary resistance at the interfaces of Ge2Sb2Te5 with metals and dielectrics Journal Article

In: Journal of Physics: Condensed Matter, vol. 27, no. 17, pp. 175009, 2015, ISSN: 0953-8984, 1361-648X.

Links | BibTeX

Campi, Davide; Donadio, Davide; Sosso, Gabriele C; Behler, Jörg; Bernasconi, Marco

Electron-phonon interaction and thermal boundary resistance at the crystal-amorphous interface of the phase change compound GeTe Journal Article

In: Journal of Applied Physics, vol. 117, no. 1, pp. 015304, 2015, ISSN: 0021-8979, 1089-7550.

Links | BibTeX

93 entries « 1 of 2 »

DImEnsION @ Warwick focuses onMolecular Simulations of Disordered Systems and Phase Transitions.


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