David J. Bray

Dr. David J. Bray

The Hartree Centre, Science and Technology Facilites Council, Warrington WA4 4AD, UK

Research Focus & Metrics

Academic Career Length

20Years (2007-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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23 March 2018 in Journal of Chemical Theory and Computation
Verified
Journal Article
Closed access
Richard L. AndersonRichard L. Anderson
Richard L. Anderson
David J. BrayDavid J. Bray
David J. Bray
ARAnnalaura Del Regno
Annalaura Del Regno
MSMichael A. Seaton
Michael A. Seaton
AFAndrea S. Ferrante
Andrea S. Ferrante
PWPatrick B. Warren
Patrick B. Warren

1 December 2013 in Polymer
Verified
Journal Article
Open access
David J. BrayDavid J. Bray
David J. Bray
PDP. Dittanet
P. Dittanet
FGF.J. Guild
F.J. Guild
AKAnthony Kinloch
Anthony Kinloch
KMK. Masania
K. Masania
ATAmbrose Taylor
Ambrose Taylor
Silica nanoparticles possessing three different diameters (23, 74 and 170 nm) were used to modify a piperidine-cured epoxy polymer. Fracture tests were performed and values of the toughness increased steadily as the concentration of silica nanoparticles was increased. However, no significant effects of particle size were found on the measured value of toughness. The toughening mechanisms were identified as (i) the formation of localised shear-band yielding in the epoxy matrix polymer which is initiated by the silica nanoparticles, and (ii) debonding of the silica nanoparticles followed by plastic void growth of the epoxy matrix polymer. These mechanisms, and hence the toughness of the epoxy polymers containing the silica nanoparticles, were modelled using the Hsieh et al. approach (Polymer 51, 2010, 6284–6294). However, it is noteworthy that previous modelling work has required the volume fraction of debonded silica particles to be measured from the fracture surfaces but in the present paper a new and more fundamental approach has been proposed. Here finite-element modelling has demonstrated that once one silica nanoparticle debonds then its nearest neighbours are shielded from the applied stress field, and hence may not debond. Statistical analysis showed that, for a good, i.e. random, dispersion of nanoparticles, each nanoparticle has six nearest neighbours, so only one in seven particles would be predicted to debond. This approach therefore predicts that only 14.3% of the nanoparticles present will debond, and this value is in excellent agreement with the value of 10–15% of those nanoparticles present debonding which was recorded via direct observations of the fracture surfaces. Further, this value of about 15% of silica nanoparticles particles present debonding has also been noted in other published studies, but has never been previously explained. The predictions from the modelling studies of the toughness of the various epoxy polymers containing the silica nanoparticles were compared with the measured fracture energies and the agreement was found to be good

6 September 2017 in The Journal of Chemical Physics
Verified
Journal Article
Closed access
Richard L. AndersonRichard L. Anderson
Richard L. Anderson
David J. BrayDavid J. Bray
David J. Bray
AFAndrea S. Ferrante
Andrea S. Ferrante
MNMassimo G. Noro
Massimo G. Noro
ISIan P. Stott
Ian P. Stott
PWPatrick Warren
Patrick Warren
We present a systematic, top-down, thermodynamic parametrization scheme for dissipative particle dynamics (DPD) using water-octanol partition coefficients, supplemented by water-octanol phase equilibria and pure liquid phase density data. We demonstrate the feasibility of computing the required partition coefficients in DPD using brute-force simulation, within an adaptive semi-automatic staged optimization scheme. We test the methodology by fitting to experimental partition coefficient data for twenty one small molecules in five classes comprising alcohols and poly-alcohols, amines, ethers and simple aromatics, and alkanes (i.e., hexane). Finally, we illustrate the transferability of a subset of the determined parameters by calculating the critical micelle concentrations and mean aggregation numbers of selected alkyl ethoxylate surfactants, in good agreement with reported experimental values.

4 January 2024 in Proceedings of the National Academy of Sciences
Verified
Journal Article
Open access
GTGiulio Tesei
Giulio Tesei
YHYa-Wen Hsiao
Ya-Wen Hsiao
ADAleksandra Dabkowska
Aleksandra Dabkowska
GGGunnar Grönberg
Gunnar Grönberg
MAMarianna Yanez Arteta
Marianna Yanez Arteta
LLLennart Lindfors
Lennart Lindfors
The ionizable-lipid component of RNA-containing nanoparticles controls the pH-dependent behavior necessary for an efficient delivery of the cargo—the so-called endosomal escape. However, it is still an empirical exercise to identify optimally performing lipids. Here, we study two well-known ionizable lipids, DLin-MC3-DMA and DLin-DMA using a combination of experiments, multiscale computer simulations, and electrostatic theory. All-atom molecular dynamics simulations, and experimentally measured polar headgroup p K a values, are used to develop a coarse-grained representation of the lipids, which enables the investigation of the pH-dependent behavior of lipid nanoparticles (LNPs) through Monte Carlo simulations, in the absence and presence of RNA molecules. Our results show that the charge state of the lipids is determined by the interplay between lipid shape and headgroup chemistry, providing an explanation for the similar pH-dependent ionization state observed for lipids with headgroup p K a values about one-pH-unit apart. The pH dependence of lipid ionization is significantly influenced by the presence of RNA, whereby charge neutrality is achieved by imparting a finite and constant charge per lipid at intermediate pH values. The simulation results are experimentally supported by measurements of α-carbon 13 C-NMR chemical shifts for eGFP mRNA LNPs of both DLin-MC3-DMA and DLin-DMA at various pH conditions. Further, we evaluate the applicability of a mean-field Poisson–Boltzmann theory to capture these phenomena.

9 May 2016 in The Journal of Physical Chemistry B
Verified
Journal Article
Closed access
MJMichael A. Johnston
Michael A. Johnston
WSWilliam C. Swope
William C. Swope
KJKirk E. Jordan
Kirk E. Jordan
PWPatrick B. Warren
Patrick B. Warren
MNMassimo G. Noro
Massimo G. Noro
Richard L. AndersonRichard L. Anderson
Richard L. Anderson

24 September 2019 in Journal of Chemical Information and Modeling
Verified
Journal Article
Closed access
JMJames L. McDonagh
James L. McDonagh
ASArdita Shkurti
Ardita Shkurti
David J. BrayDavid J. Bray
David J. Bray
Richard L. AndersonRichard L. Anderson
Richard L. Anderson
EPEdward O. Pyzer-Knapp
Edward O. Pyzer-Knapp