Highlights
Understanding the Emergence of the Boson Peak in Molecular Glasses
Nature Communications
The boson peak is a fundamental, very unique feature of glassy materials. As such, people have been arguing about the actual origin of the boson peak for many years indeed. In this work, spearheaded by Klaas Wynne (Glasgow University) and featuring molecular simulations by our very own Trent Barnard (amongst a real arsenal of other techniques), we pinpoint the emergence of specific structural features as the motivation behind the occurrence of the boson peak – at least in this class of molecular glasses! Understanding the boson peak in general terms is still very much an ongoing quest, but with this work, now published in Nature Communications (https://www.nature.com/articles/s41467-023-35878-6) we have provided an important piece of the puzzle. Check it out here.
Levering Genetic Algorithms to Maximise the Predictive Capabilities of the SOAP Descriptor
Molecular Systems Design and Engineering
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.
Minimalistic ice recrystallisation inhibitors based on phenylalanine
Chemical Communications
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.
The role of structural order in heterogeneous ice nucleation
Chemical Science
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.
How do Interfaces Alter the Dynamics of Supercooled Water?
Nanoscale
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
Ice Recrystallization Inhibition by Amino Acids: The Curious Case of Alpha- and Beta-Alanine
The Journal of Physical Chemistry Letters
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.
Lipid Bilayers as Potential Ice Nucleating Agents
Physical Chemistry Chemical Physics
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.
Recovering Local Structure Information from High-Pressure Total Scattering Experiments
Journal of Applied Crystallography
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.
The Seven Deadly Sins: When Computing Crystal Nucleation Rates, the Devil is in the Details
Journal of Chemical Physics
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.
A Minimalistic Cyclic Ice-binding Peptide from Phage Display
Nature Communications
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.
Full Publications List
2023
Understanding the emergence of the boson peak in molecular glasses Journal Article
In: Nature Communications, vol. 14, no. 1, pp. 1–11, 2023.
2022
Leveraging genetic algorithms to maximise the predictive capabilities of the SOAP descriptor Journal Article
In: Molecular Systems Design & Engineering, 2022.
Minimalistic ice recrystallisation inhibitors based on phenylalanine Journal Article
In: Chemical Communications, vol. 58, no. 55, pp. 7658–7661, 2022.
The role of structural order in heterogeneous ice nucleation Journal Article
In: Chemical Science, vol. 13, iss. 17, pp. 5014-5026, 2022.
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.
Lipid bilayers as potential ice nucleating agents Journal Article
In: Physical Chemistry Chemical Physics, vol. 24, iss. 11, pp. 6476-6491, 2022.
How do interfaces alter the dynamics of supercooled water? Journal Article
In: Nanoscale, vol. 14, iss. 11, pp. 4254-4262, 2022.
2021
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.
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.
A minimalistic cyclic ice-binding peptide from phage display Journal Article
In: Nature Communications, vol. 12, pp. 2675, 2021.
Microscopic Kinetics Pathway of Salt Crystallization in Graphene Nanocapillaries Journal Article
In: Physical Review Letters, vol. 126, no. 13, pp. 136001, 2021.
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.
The atomistic details of the ice recrystallisation inhibition activity of PVA. Journal Article
In: Nature Communications, vol. 12, no. 1323, 2021.
2020
Combining high-resolution scanning tunnelling microscopy and first-principles simulations to identify halogen bonding Journal Article
In: Nature Communications, vol. 11, pp. 2103, 2020.
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.
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.
Atomistic simulations of thermal conductivity in GeTe nanowires Journal Article
In: Journal of Physics D: Applied Physics, vol. 53, pp. 054001, 2020.
2019
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.
Enhancement of Macromolecular Ice Recrystallization Inhibition Activity by Exploiting Depletion Forces Journal Article
In: ACS Macro Letters, vol. 8, pp. 1063-1067, 2019.
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.
Promoting transparency and reproducibility in enhanced molecular simulations Journal Article
In: Nature Methods, vol. 16, no. 8, pp. 670–673, 2019, ISSN: 1548-7105.
2018
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.
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.
Unravelling the origins of ice nucleation on organic crystals Journal Article
In: Chemical Science, 2018, ISSN: 2041-6520, 2041-6539.
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.
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.
2017
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.
Pre-critical fluctuations and what they disclose about heterogeneous crystal nucleation Journal Article
In: Nature Communications, vol. 8, no. 1, 2017, ISSN: 2041-1723.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Pre-critical fluctuations and what they disclose about heterogeneous crystal nucleation Journal Article
In: Nature Communications, vol. 8, no. 1, pp. 2257, 2017.
2016
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.
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.
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.
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.
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.
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.
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.
Ice formation on kaolinite: Insights from molecular dynamics simulations Journal Article
In: The Journal of Chemical Physics, vol. 145, no. 21, pp. 211927, 2016.
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.
2015
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.
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.
DImEnsION @ Warwick focuses onMolecular Simulations of Disordered Systems and Phase Transitions.
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