Highlights

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.

 

Read More

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.

 

Read More

Solving the Puzzle of Polymers Binding to Ice for Cryopreservation


Nature Communications

Just accepted

DOI: 10.1038/s41467-020-15898-2

Up to now, the ice community has been working under the assumption that short polymers do not bind strongly enough to the ice crystals, but in this work we demonstrate that it is the subtle balance between these binding interactions and the effective volume occupied by the polymers at the interface with ice that determine their effectiveness in hindering ice re-crystallization.

This work brings together experimental measurements of ice recrystallization inhibition and computer simulations. The latter are invaluable tools to gain microscopic insight into processes such as the formation of ice, as they are able to see what is happening in very fast or very small processes which are hard to see via even the most advanced experimental techniques. Have a look at the paper online or grab a .pdf. The University of Warwick press release can be found here.

 

Read More

Modelling the Interactions of NO in a-SiO2


Modelling and Simulations in Materials Science and Engineering

Just accepted

DOI: 10.1088/1361-651X/abdc69

This work has been led by the group of Alex Shluger at UCL Physics. We have helped by quantifying the extent of the regions of empty space (we call them "voids") within the the system (amorphous SiO_2), which is important to understand the diffusion of small molecules such as NO through the amorphous phase. Have a look
at the paper online or grab a .pdf.

Our voids framework, which we have been using quite a lot in the context of liquid water appears to have found yet another playground... stay tuned for some more updates re: the code itself. Soon enough you might find it on GitHub!

Read More

Combining High-resolution Scanning Tunnelling Microscopy and First-principles Simulations to Identify Halogen Bonding


Nature Communications

Just accepted

DOI: 10.1038/s41467-020-15898-2

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!

Read More

Insights into the Emerging Networks of Voids in Simulated Supercooled Water


Journal of Physical Chemistry B

Just accepted

DOI: 10.1021/acs.jpcb.9b10144

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.

Read More

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.

 

Read More

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!

Read More

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.

Read More

Full Publications List

85 entries « 1 of 2 »

2021

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, 155 (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, 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, 126 (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, 29 (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, 12 (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, 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, 124 (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, 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, 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, 44 (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, 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, 16 (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, 149 (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, 149 (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, 16 (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, 8 (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, 13 (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, 121 (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, 147 (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, 8 (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, 121 (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, 13 (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, 8 (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, 16 (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, 147 (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, 121 (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, 8 (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, 145 (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, 213 (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, 116 (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, 7 (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), 213 (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, 116 (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, 7 (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, 145 (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, 121 (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, 137 (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, 119 (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, 27 (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, 117 (1), pp. 015304, 2015, ISSN: 0021-8979, 1089-7550.

Links | BibTeX

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

Functional Properties of Phase Change Materials from Atomistic Simulations Incollection

In: 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.

Links | BibTeX

Gabardi, S; Caravati, S; Sosso, G C; Behler, J; Bernasconi, M

Microscopic origin of resistance drift in the amorphous state of the phase-change compound GeTe Journal Article

In: Physical Review B, 92 (5), 2015, ISSN: 1098-0121, 1550-235X.

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, 117 (1), pp. 015304, 2015.

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, 119 (11), pp. 6428–6434, 2015.

BibTeX

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

Functional Properties of Phase Change Materials from Atomistic Simulations Incollection

In: Molecular Dynamics Simulations of Disordered Materials, pp. 415–440, Springer, 2015.

BibTeX

Campi, D; Baldi, E; Graceffa, G; Sosso, GC; 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, 27 (17), pp. 175009, 2015.

BibTeX

85 entries « 1 of 2 »