Jeremy Graham Frey

Jeremy Graham Frey
University of Southampton · Division of Chemistry

Phd

About

350
Publications
27,120
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3,097
Citations

Publications

Publications (350)
Article
Full-text available
The related problems of chemical reaction optimization and reaction scope search concern the discovery of reaction pathways and conditions that provide the best percentage yield of a target product. The space of possible reaction pathways or conditions is too large to search in full, so identifying a globally optimal set of conditions must instead...
Preprint
Chemical reaction optimisation concerns the discovery of reaction conditions that provide the best percentage yield of the target product. The space of possible reaction conditions is too large to search in full, so identifying a globally optimal set of conditions must instead draw on mathematical methods to identify areas of the space that should...
Article
Full-text available
In the age of big data, it is time to ensure that units are routinely documented for easy, unambiguous exchange of information. In the age of big data, it is time to ensure that units are routinely documented for easy, unambiguous exchange of information.
Article
As the volume of data associated with scientific research has exploded over recent years, the use of digital infrastructures to support this research and the data underpinning it has increased significantly. Physical chemists have been making use of eScience infrastructures since their conception, but in the last five years their usage has increase...
Article
Following the 100 Year Anniversary of IUPAC celebrated in Paris in 2019, Artificial Intelligence was made the focus of the following global 2021 World Chemistry Leadership Meeting (WCLM). Note: The program of WCLM 2021 is available online. A detailed account of WCLM2021 will follow in the next issue of Chem Int. at https://iupac.org/event/wclm2021/...
Article
In November 2020 the Royal Society of Chemistry Chemical Information and Computer Applications interest group (RSC CICAG) ran a five-day meeting entitled Open Chemical Science (https://www.rsc.org/events/detail/42090/open-chemical-science). This event had three intertwined themes, Open Data, Open Access publishing and a series of workshops highligh...
Article
Background The use of artificial intelligence (AI) is growing in food supply chains. The ethical language associated with food supply and technology is contextualised and framed by the meaning given to it by stakeholders. Failure to differentiate between these nuanced meanings can create a barrier to technology adoption and reduce the benefit deriv...
Article
Full-text available
There are a number of issues that inhibit the replication and reproduction of research, and make it hard to utilise existing scientific data to make new discoveries. These include poor data management, competing standards, a lack of consideration of the usability of data, and a disconnect between the publication of science and the data and methods...
Conference Paper
The identification of chemical species in complex fluid materials like biocrude oils, is problem that can be largely solved by a computational optimisation of a molecular design space to expand the limited experimental data. This is specially useful due to the intrinsic difficulties to characterise this bitumen-like materials. We used available exp...
Article
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The growth of machine learning as a tool for research in computational chemistry is well documented. For many years, this growth was heavily driven by the paradigms of supervised and...
Article
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The Internet of Food Things Network⁺ (IoFT) and the Artificial Intelligence and Augmented Intelligence for Automated Investigation for Scientific Discovery Network⁺ (AI3SD) brought together an interdisciplinary multi-institution working group to create an ethical framework for digital collaboration in the food industry. This will enable the explora...
Article
The full potential for a digitally transformed food system has not yet been realized — or indeed imagined. Data flows across, and within, vast but largely decentralized and tiered supply chain networks. Data define internal inputs, bi-directional flows of food, information and finance within the supply chain, and intended and extraneous outputs. Da...
Article
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Even when we all agree to make data usefully available with our publications, the problem remains of how to do this in a reasonable and sensible manner. Just what do we need to do? I suggest a change of perspective: what would you wish other authors had done to make their data easily useful to us?
Article
Full-text available
Precise diagnosis and prognosis are key in prevention and reduction of morbidity and mortality in all types of cancers. Here we show that changes in the collagen fibres in the main histological subtypes of canine mammary gland carcinomas are directly associated with the tumour behaviour and the animal survival time and could become a useful tool in...
Article
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We present nonlinea rmicroscopy imaging results and analysis from canine mammary cancer biopsies. Second harmonic generation imaging allows information of the collagen structure in the extracellular matrix that together with the fluorescence of the cell regions of the biopsies form a base for comprehensive image analysis. We demonstrate an automated...
Article
In today’s world of advancing technology, pervasive and ubiquitous systems have become more common, and have been adapted for many different areas of use. The Internet of Things (IoT) movement has increased in popularity, and there are now many affordable, customisable smart devices available for various purposes. These devices are commonly found i...
Article
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Microscopy with extreme ultraviolet (EUV) light can provide many advantages over optical, hard x-ray or electron-based techniques. However, traditional EUV sources and optics have large disadvantages of scale and cost. Here, we demonstrate the use of a laboratory-scale, coherent EUV source to image biological samples—mouse hippocampal neurons—provi...
Conference Paper
We shall report the latest progress on AWESOME (Airbus Water Emulsification Sensor using Optical Monitoring Equipment), which seeks to use spectrally multiplexed guided and leaky mode Bragg gratings to quantify dissolved (5ppm-v resolution), free and emulsified water contamination at multiple physical points within a fuel tank.
Article
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It was highlighted that the original article [1] was missing Additional files 2 and 3.
Preprint
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Understanding the geometry and topology of configuration or conformational spaces of molecules has relevant applications in chemistry and biology such as the proteins folding problem, drug design and the structure activity relationship problem. Despite their relevance, configuration spaces of molecules are only partially understood. In this paper w...
Article
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Bulk water molecular dynamics simulations based on a series of atomistic water potentials (TIP3P, TIP4P/Ew, SPC/E and OPC) are compared using new techniques from the field of topological data analysis. The topological invariants (the different degrees of homology) derived from each simulation frame are used to create a series of persistence diagram...
Article
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Scientific research is increasingly characterised by the volume of documents and data that it produces, from experimental plans and raw data to reports and papers. Researchers frequently struggle to manage and curate these materials, both individually and collectively. Previous studies of Electronic Lab Notebooks (ELNs) in academia and industry hav...
Article
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Introduction: The use of semantic web technologies to aid drug discovery has gained momentum over recent years. Researchers in this domain have realized that semantic web technologies are key to dealing with the high levels of data for drug discovery. These technologies enable us to represent the data in a formal, structured, interoperable and comp...
Article
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Distributed Ledger Technology (DLT), such as blockchain, has the potential to transform supply chains. It can provide a cryptographically secure and immutable record of transactions and associated metadata (origin, contracts, process steps, environmental variations, microbial records, etc.) linked across whole supply chains. The ability to trace fo...
Article
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This work quantifies water contamination in jet fuel (Jet A-1), using silica-based Bragg gratings. The optical sensor geometry exposes the evanescent optical field of a guided mode to enable refractometery. Quantitative analysis is made in addition to the observation of spectral features consistent with emulsification of water droplets and Stokes’...
Article
The intrinsic sampling method (ISM) is a powerful tool that allows the exploration of interfacial properties from molecular simulations by fitting a function that represents the local boundary between two phases. However, owing to the non-physical nature of an “intrinsic” surface, there remains an ambiguity surrounding the comparison of theoretical...
Article
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Topological data analysis is a family of recent mathematical techniques seeking to understand the ‘shape’ of data, and has been used to understand the structure of the descriptor space produced from a standard chemical informatics software from the point of view of solubility. We have used the mapper algorithm, a TDA method that creates low-dimensi...
Article
We present an unexpected finite size effect affecting interfacial molecular simulations that is proportional to the width-to-surface-area ratio of the bulk phase Ll/A. This finite size effect has a significant impact on the variance of surface tension values calculated using the virial summation method. A theoretical derivation of the origin of the...
Article
Full-text available
Computers and computation have become essential to scientific activity and significant amounts of data are now captured digitally or even “born digital”. Consequently, there is more and more incentive to capture the full experiment records using digital tools, such as Electronic Laboratory Notebooks (ELNs), to enable the effective linking and publi...
Article
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Workflows processing data from research activities and driving in silico experiments are becoming an increasingly important method for conducting scientific research. Workflows have the advantage that not only can they be automated and used to process data repeatedly, but they can also be reused – in part or whole – enabling them to be evolved for...
Article
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Coherent diffractive imaging (CDI) has become a standard method on a variety of synchrotron beam lines. The high brilliance short wavelength radiation from these sources can be used to reconstruct attenuation and relative phase of a sample with nanometre resolution via CDI methods. However, the interaction between the sample and high energy ionisin...
Article
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Despite the increasingly digital nature of society there are some areas of research that remain firmly rooted in the past; in this case the laboratory notebook, the last remaining paper component of an experiment. Countless electronic laboratory notebooks (ELNs) have been created in an attempt to digitise record keeping processes in the lab, but no...
Article
The new millennium, now almost 20 years old, has been characterised by a recognition within the research community of the importance of the free flow of research data; not simply in the ability to access the data, but also in the understanding that this valuable resource needs to be reused and built upon. We believe there have been at least two mai...
Article
As an open, inexpensive, collaborative platform, the Web is ideal for facilitating communication among scholars and enabling nearly free access to knowledge. The Web’s potential allows researchers to utilize the digital, networked medium to publish more of their research data in comparison to paper-based journal articles and to publish them in cont...
Article
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The development of an Yb3+-fiber based chirped-pulse amplification system and the performance in the generation of extreme ultraviolet (EUV) radiation by high-harmonic generation is reported. The fiber laser produced 100 µJ, 350 fs output pulses with diffraction limited beam quality at a repetition rate of 16.7 kHz. The system used commercial singl...
Article
Ptychographic Coherent diffractive imaging (PCDI) is a significant advance in imaging allowing the measurement of the full electric field at a sample without use of any imaging optics. So far it has been confined solely to imaging of linear optical responses. In this paper we show that because of the coherence-preserving nature of nonlinear optical...
Article
Full-text available
We demonstrate interference lithography using a high-harmonic source. Extreme ultraviolet (EUV) radiation is produced by high-harmonic generation with 800 nm light from a femtosecond Ti:sapphire laser (40 fs pulses, 1 kHz, 2 W average power) in argon gas. Interference patterns created using Lloyd's mirror setup and monochromatized radiation at the...
Article
This note amends the list of funders in a recent Letter [Opt. Lett.41, 1317 (2016)OPLEDP0146-959210.1364/OL.41.001317].
Article
Ptychography is a scanning coherent diffractive imaging (CDI) technique that relies upon a high level of stability of the illumination during the course of an experiment. This is particularly an issue for coherent short wavelength sources, where the beam intensity is usually tightly focused on the sample in order to maximize the photon flux density...
Article
High harmonic generation (HHG) provides a laboratory scale source of coherent radiation ideally suited to lensless coherent diffractive imaging (CDI) in the EUV and X-ray spectral region. Here we demonstrate transmission EUV ptychography, a scanning variant of CDI, using radiation at a wavelength around 29 nm from an HHG source. Image resolution is...
Article
Full-text available
The way that we recall information is dependent upon both the knowledge in our memories and the conditions under which we recall the information. Electronic Laboratory Notebooks can provide a structured interface for the capture of experiment records through the use of forms and templates. These templates can be useful by providing cues to help res...
Article
Full-text available
The transmembrane anion transport activity of 43 synthetic molecules based on the structure of marine alkaloid tambjamine were assessed in model phospholipid (POPC) liposomes. The anionophoric activity of these molecules showed a parabolic dependence with lipophilicity, with an optimum range for transport efficiency. Using a quantitative structure-...
Conference Paper
The ptychography method for coherent diffractive imaging (CDI) is gaining significant popularity over the last few years in the synchrotron science community because of its advantages over simpler single diffraction CDI schemes. However, for imaging applications in the extreme ultraviolet (XUV), the ability to perform ptychography with table top se...
Conference Paper
We present coherent diffractive imaging with broadband radiation generated from a high harmonic source around 29nm wavelength to image neuron tissue from the mouse hypothalamus to 80nm resolution over a 40nm field of view.
Conference Paper
With the aim of improving imaging using table-top extreme ultraviolet sources, we demonstrate coherent diffraction imaging (CDI) with relative bandwidth of 20%. The coherence properties of the illumination probe are identified using the same imaging setup. The presented methods allows for the use of fewer monochromating optics, obtaining higher flu...
Article
In this paper we take a historical view of e-Science and e-Research developments within the Chemical Sciences at the University of Southampton, showing the development of several stages of the evolving data ecosystem as Chemistry moves into the digital age of the 21st Century. We cover our research on aspects of the representation of chemical infor...
Article
The Southampton chemical information group had its genesis in 2001, when we began an e-Science pilot project to investigate structure-property mapping, combinatorial chemistry, and the Grid. CombeChem instigated a range of activities that have since been underway for more than ten years, in many ways matching the expansion of interest in using the...
Article
User-defined metadata is useful for curating and helping to provide context for experiment records, but our previous investigations have demonstrated that simply providing the facility to add metadata is not enough to ensure that metadata is added, let alone to ensure that the metadata is of high quality. For metadata to be useful it first has to b...
Article
In designing an Electronic Lab Notebook (ELN) there is a balance to be struck between keeping it as general and multidisciplinary as possible for simplicity of use and maintenance and introducing more domain-specific functionality to increase their appeal to target research areas. Here we describe the results of a collaboration between the Royal So...
Article
Names are essential to data manipulation and data interpretation. IUPAC standardizes the names that chemists use in their scholarly works, which it publishes as a suite of terminology, nomenclature and ontology, the IUPAC colour books. Currently, machine-accessible representations of these publications are not available on the Web. In this article,...
Article
Ptychography is a scanning coherent diffractive imaging (CDI) technique that relies upon a high level of stability of the illumination during the course of an experiment. This is particularly an issue for coherent sources where the beam intensity is usually tightly focused on the sample in order to maximize the photon flux density on the illuminate...
Conference Paper
High Harmonic Generation (HHG) is a strongly non-linear process where a high intensity, short pulse laser field is focused into a gas resulting in a spectrum of short wavelength radiation in the extreme ultraviolet (EUV) range generated at harmonic frequencies of the fundamental laser field. The resulting radiation conserves the properties of the d...
Conference Paper
Full-text available
In my talk I will consider what it means to be a “Utility” in the Digital Economy, considering the nature and scale of services provided, the potential for flexibility and personalization as a tension against mass service provision characteristic of traditional Utilities. I will reflect the central importance of data to providers and consumers in t...
Conference Paper
Full-text available
Progress in science depends on access to results and data from earlier work. E-Science and Web 2.0 have in principle provided new tools to enable the communication of data that underpins scientific discovery. Professor Frey will explore the ways in which the open agenda serves to improve productivity and reduce and manage uncertainty and consider i...