2,465 results on '"Evans, Robert"'
Search Results
2. Using test particle sum rules to construct accurate functionals in classical Density Functional Theory
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Gül, Melih, Roth, Roland, and Evans, Robert
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Condensed Matter - Soft Condensed Matter ,Condensed Matter - Statistical Mechanics - Abstract
Fundamental Measure Theory (FMT) is a successful and versatile approach for describing the properties of the hard-sphere fluid and hard-sphere mixtures within the framework of classical density functional theory (DFT). Lutsko [Phys. Rev. E 102, 062137 (2020)] introduced a version of FMT containing two free parameters, to be fixed by additional physical constraints. Whereas Lutsko focused on the stability of crystalline phases, we introduce and employ two statistical mechanical sum rules pertinent for the fluid phase, that are not automatically satisfied by FMT. By minimizing the relative deviation between different routes to calculate the excess chemical potential and the isothermal compressibility we determine the two free parameters of the theory. Our results indicate that requiring consistency with these sum rules can improve the quality of predictions of FMT for properties of the hard-sphere fluid phase. We suggest that employing these (test particle) sum rules, which apply for any interparticle pair-potential, might provide a means of testing the performance and accuracy of general DFT approximations.
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- 2024
3. Neural density functional theory of liquid-gas phase coexistence
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Sammüller, Florian, Schmidt, Matthias, and Evans, Robert
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Condensed Matter - Soft Condensed Matter - Abstract
We use supervised machine learning together with the concepts of classical density functional theory to investigate the effects of interparticle attraction on the pair structure, thermodynamics, bulk liquid-gas coexistence, and associated interfacial phenomena in many-body systems. Local learning of the one-body direct correlation functional is based on Monte Carlo simulations of inhomogeneous systems with randomized thermodynamic conditions, randomized planar shapes of the external potential, and randomized box sizes. Focusing on the prototypical Lennard-Jones system, we test predictions of the resulting neural attractive density functional across a broad spectrum of physical behaviour associated with liquid-gas phase coexistence in bulk and at interfaces. We analyse the bulk radial distribution function $g(r)$ obtained from automatic differentiation and the Ornstein-Zernike route and determine i) the Fisher-Widom line, i.e.\ the crossover of the asymptotic (large distance) decay of $g(r)$ from monotonic to oscillatory, ii) the (Widom) line of maximal correlation length, iii) the line of maximal isothermal compressibility and iv) the spinodal by calculating the poles of the structure factor in the complex plane. The bulk binodal and the density profile of the free liquid-gas interface are obtained from density functional minimization and the corresponding surface tension from functional line integration. We also show that the neural functional describes accurately the phenomena of drying at a hard wall and of capillary evaporation for a liquid confined in a slit pore. Our neural framework yields results that improve significantly upon standard mean-field treatments of interparticle attraction. Comparison with independent simulation results demonstrates a consistent picture of phase separation even when restricting the training to supercritical states only., Comment: 21 pages, 9 figures
- Published
- 2024
4. A 12-week community-based physical activity and mindfulness intervention: health outcomes and markers of autonomic nervous system function (Sweet Hearts biokinetics pilot study)
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Evans, Robert William, Hume, David John, Noorbhai, Mohammed Habib, Van der Schyff, Nasief, and Rauch, H.G. Laurie
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non-communicable diseases ,stress ,sedentary lifestyle ,autonomic nervous system ,heart rate variability ,Diseases of the circulatory (Cardiovascular) system ,RC666-701 - Abstract
The prevalence of non-communicable diseases (NCDs) has reached epidemic proportions in South Africa, coinciding with high levels of sedentary behaviour, urbanisation and stress. The nexus between stress, physical inactivity and non-communicable diseases may be regulated, in part, by changes in the autonomic nervous system (ANS). ANS function may be measured using a proxy of heart rate variability (HRV). Regular physical activity, controlled breathing and stress reduction have been shown to alter HRV. This paper presents preliminary data from a community-based biokinetics physical activity and mindfulness intervention (Sweet Hearts) on HRV. The study’s findings demonstrated favourable changes in measures of heart rate variability (HRV) – specifically in the low frequency (LF) spectrum that is associated with baroreflex function. The implications of these changes, in terms of health outcomes, along with efforts at addressing scalability and sustainability of community-based health promotion interventions may be important targets for future study.
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- 2019
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5. What is the best simulation approach for measuring local density fluctuations near solvo/hydrophobes?
- Author
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Wilding, Nigel B., Evans, Robert, and Turci, Francesco
- Subjects
Condensed Matter - Soft Condensed Matter ,Condensed Matter - Statistical Mechanics - Abstract
Measurements of local density fluctuations are crucial to characterizing the interfacial properties of equilibrium fluids. A specific case that has been well-explored involves the heightened compressibility of water near hydrophobic entities. Commonly, a spatial profile of local fluctuation strength is constructed from measurements of the mean and variance of solvent particle number fluctuations in a set of contiguous sub-volumes of the system adjacent to the solvo/hydrophobe. An alternative measure proposed by Evans and Stewart (J. Phys.: Condens. Matter 27, 194111 (2015)) defines a local compressibility profile in terms of the chemical potential derivative of the spatial number density profile. Using Grand Canonical Monte Carlo simulation, we compare and contrast the efficacy of these two approaches for a Lennard-Jones solvent at spherical and planar solvophobic interfaces, and SPC/E water at a hydrophobic spherical solute. Our principal findings are that: (i) the local compressibility profile $\chi({\bf r})$ of Evans and Stewart is considerably more sensitive to variations in the strength of local density fluctuations than the spatial fluctuation profile $F({\bf r})$ and can resolve much more detailed structure; (ii) while the local compressibility profile is essentially independent of the choice of spatial discretization used to construct the profile, the spatial fluctuation profile exhibits strong systematic dependence on the size of the subvolumes on which the profile is defined. We clarify the origin and nature of this finite-size effect., Comment: 12 pages, 6 figures
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- 2024
6. The Face-to-Face Principle
- Author
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Collins, Harry, Evans, Robert, Innes, Martin, Kennedy, Eric B., Mason-Wilkes, Will, and McLevey, John
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Democracy ,Remote communication ,Social media ,Disinformation ,Trust ,Face-to-face communication ,thema EDItEUR::J Society and Social Sciences::JK Social services and welfare, criminology::JKV Crime and criminology ,thema EDItEUR::J Society and Social Sciences::JB Society and culture: general::JBC Cultural and media studies::JBCT Media studies::JBCT4 Media studies: journalism ,thema EDItEUR::Q Philosophy and Religion::QD Philosophy ,thema EDItEUR::J Society and Social Sciences::JP Politics and government::JPA Political science and theory ,thema EDItEUR::J Society and Social Sciences::JM Psychology ,thema EDItEUR::J Society and Social Sciences::JH Sociology and anthropology::JHB Sociology - Abstract
The internet is changing the way that knowledge is made and shared. Knowledge-making in face-to-face settings is being replaced by information gathering from remote sources, whose origins may be concealed but which can create an illusion of intimacy. Though remote communication is beneficial in many ways – modern societies would fail without it -- and though the tight boundaries of the face-to-face can be used for evil purposes such as criminal conspiracy, if the overall trend to remote communication continues unchecked, it could be disastrous for the future of democracy and the very idea of truth itself. Too much reliance on remote communication threatens the core institutions of democratic societies. We explain the change in technical detail, from a systematic analysis of the workings of the face-to-face to a high level setting-out of its dangerous political implications. The analysis includes field studies, reflexive examination, drawing on the wide experience of the authors, of the stickiness of the face-to-face in our own work and other institutions, and network analysis which explains the illusion of intimacy that can be generated inadvertently or maliciously. We look at the apparent effectiveness of techniques such as blockchain and the limits of their domain. New information is provided about the malicious use of disinformation by foreign powers. We dramatise the dangers to Western pluralist democracy through a personal accounting of the 2020 American election. By drawing out the special features of face-to-face interaction and its constitutive role in creating societies, with science as the icon, the book sets out an agenda for civic education that can protect democratic institutions from the erosion of pluralism and the facile abandonment of trustworthy expertise. The authors conclude by returning to the themes set out at the start of the book, namely the crucial role played by trust in modern societies and the importance of face-to-face interactions in reproducing that trust, and the democratic institutions in which it should be invested.
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- 2022
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7. Approaches to Teaching Shakespeare's Othello (review)
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Evans, Robert C.
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- 2011
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8. Distracted Subjects: Madness and Gender in Shakespeare and Early Modern Culture , and: Performing Blackness on English Stages, 1500-1800 (review)
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Evans, Robert C.
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- 2011
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9. Flattery in Shakespeare's Othello : The Relevance of Plutarch and Sir Thomas Elyot
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Evans, Robert C.
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- 2011
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10. Shakespeare and the History of Soliloquies (review)
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Evans, Robert C.
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- 2011
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11. A History of Shakespeare on Screen: A Century of Film and Television , and: Shakespeare, from Stage to Screen (review)
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Evans, Robert C.
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- 2011
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12. Numerical Evidence for a refinement of Deligne's Period Conjecture for Jacobians of Curves
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Evans, Robert, Castillo, Daniel Macias, and Wiersema, Hanneke
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Mathematics - Number Theory ,11G10, 11G40 (primary), 11G30, 11G35 (secondary) - Abstract
Let $A/\mathbb{Q}$ be a Jacobian variety and let $F$ be a totally real, tamely ramified, abelian number field. Given a character $\psi$ of $F/\mathbb{Q}$, Deligne's Period Conjecture asserts the algebraicity of the suitably normalised value $\mathcal{L}(A,\psi,1)$ at $z=1$ of the Hasse-Weil-Artin $L$-function of the $\psi$-twist of $A$. We formulate a conjecture regarding the integrality properties of the family of normalised $L$-values $(\mathcal{L}(A,\psi,1))_{\psi}$, and its relation to the Tate-Shafarevich group of $A$ over $F$. We numerically investigate our conjecture through $p$-adic congruence relations between these values., Comment: 24 pages
- Published
- 2023
13. Understanding the physics of hydrophobic solvation
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Coe, Mary K., Evans, Robert, and Wilding, Nigel B.
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Condensed Matter - Soft Condensed Matter ,Condensed Matter - Statistical Mechanics - Abstract
Simulations of water near extended hydrophobic spherical solutes have revealed the presence of a region of depleted density and accompanying enhanced density fluctuations.The physical origin of both phenomena has remained somewhat obscure. We investigate these effects employing a mesoscopic binding potential analysis, classical density functional theory (DFT) calculations for a simple Lennard-Jones (LJ) solvent and Grand Canonical Monte Carlo (GCMC) simulations of a monatomic water (mw) model. We argue that the density depletion and enhanced fluctuations are near-critical phenomena. Specifically, we show that they can be viewed as remnants of the critical drying surface phase transition that occurs at bulk liquid-vapor coexistence in the macroscopic planar limit, i.e.~as the solute radius $R_s\to\infty$. Focusing on the radial density profile $\rho(r)$ and a sensitive spatial measure of fluctuations, the local compressibility profile $\chi(r)$, our binding potential analysis provides explicit predictions for the manner in which the key features of $\rho(r)$ and $\chi(r)$ scale with $R_s$, the strength of solute-water attraction $\varepsilon_{sf}$, and the deviation from liquid-vapor coexistence of the chemical potential, $\delta\mu$. These scaling predictions are confirmed by our DFT calculations and GCMC simulations. As such our theory provides a firm basis for understanding the physics of hydrophobic solvation., Comment: 18 pages
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- 2022
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14. Othello and Interpretive Traditions (review)
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Evans, Robert C.
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- 2011
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15. Shakespeare at the Cineplex: The Kenneth Branagh Era (review)
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Evans, Robert C.
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- 2011
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16. Measures of Fluctuations for a Liquid Near Critical Drying
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Coe, Mary K., Evans, Robert, and Wilding, Nigel B.
- Subjects
Condensed Matter - Statistical Mechanics - Abstract
We investigate density fluctuations in a liquid close to a solvophobic substrate at which a surface critical drying transition occurs. Using classical density functional theory, we determine three measures of the spatial extent and strength of the fluctuations, i.e., the local compressibility $\chi_{\mu}(z)$, the local thermal susceptibility $\chi_T(z)$ and the reduced density $\chi_*(z)$; $z$ is the distance from the substrate. Whilst the first measure is frequently used, the second and third were introduced very recently by Eckert et.al., Phys. Rev. Lett. 125, 268004 (2020). For state points in the critical drying regime, all three measures, each scaled by its bulk value, exhibit very similar forms and the ratio of $\chi_T(z)$ to $\chi_{\mu}(z)$, for fixed $z$ in the vapour-liquid transition region, is constant. Using a scaling treatment of surface thermodynamics we show that such behaviour is to be expected on general grounds., Comment: 7 pages, 3 figures. Accepted by Physical Review E
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- 2022
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17. Density depletion and enhanced fluctuations in water near hydrophobic solutes: identifying the underlying physics
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Coe, Mary K., Evans, Robert, and Wilding, Nigel B.
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Condensed Matter - Soft Condensed Matter ,Condensed Matter - Statistical Mechanics - Abstract
We investigate the origin of the density depletion and enhanced density fluctuations that occur in water in the vicinity of an extended hydrophobic solute. We argue that both phenomena are remnants of the critical drying surface phase transition that occurs at liquid-vapor coexistence in the macroscopic planar limit, ie. as the solute radius $R_s\to\infty$. Focusing on the density profile $\rho(r)$ and a sensitive spatial measure of fluctuations, the local compressibility profile $\chi(r)$, we develop a scaling theory which expresses the extent of the density depletion and enhancement in compressibility in terms of $R_s$, the strength of solute-water attraction $\varepsilon_s$, and the deviation from liquid-vapor coexistence $\delta\mu$. Testing the predictions against results of classical density functional theory for a simple solvent and Grand Canonical Monte Carlo simulations of a popular water model, we find that the theory provides a firm physical basis for understanding how water behaves at a hydrophobe., Comment: 5 pages, 4 figures. To appear in Phys. Rev. Lett
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- 2022
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18. Network Analysis of Survey Data to Identify Non-Homogeneous Teacher Self-Efficacy Development in Using Formative Assessment Strategies
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Bruun, Jesper and Evans, Robert Harry
- Abstract
In a European project about formative assessment, Local Working Groups (LWGs) from six participating countries made use of a format for teacher-researcher collaboration. The activities in each LWG involved discussions and reflections about implementation of four assessment formats. A key aim was close collaboration between teachers and researchers to develop teachers' formative assessment practices, which were partially evidenced with changes in attributes of self-efficacy. The research question was: to what extent do working with formative assessment strategies in collaboration with researchers and other teachers differentially affect individual self-efficacy beliefs of practicing teachers across different educational contexts? A 12-item teacher questionnaire, with items selected from a commonly used international instrument for science teaching self-efficacy, was distributed to the participating teachers before and after their work in the LWGs. A novel method of analysis using networks where participants from different LWGs were linked based on the similarities of their answers, revealed differences between empirically identified groups and larger super groups of participants. These analyses showed, for example, that one group of teachers perceived themselves to have knowledge about using formative assessment but did not have the skills to use it effectively. It is suggested that future research and development projects may use this new methodology to pinpoint groups, which seem to respond differently to interventions and modify guidance or instruction accordingly.
- Published
- 2020
19. The Holy Sonnets. Volume 7, Part 1 of The Variorum Edition of the Poetry of John Donne (review)
- Author
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Evans, Robert C.
- Published
- 2008
20. Impact of thinning and pruning on selected wood properties in individual radiata pine trees in New Zealand
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Grace, Jennifer C. and Evans, Robert
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- 2012
21. Bypassing the energy functional in density functional theory: Direct calculation of electronic energies from conditional probability densities
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McCarty, Ryan J., Perchak, Dennis, Pederson, Ryan, Evans, Robert, Qiu, Yiheng, White, Steven R., and Burke, Kieron
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Physics - Chemical Physics ,Physics - Computational Physics - Abstract
Density functional calculations can fail for want of an accurate exchange-correlation approximation. The energy can instead be extracted from a sequence of density functional calculations of conditional probabilities (CP-DFT). Simple CP approximations yield usefully accurate results for two-electron ions, the hydrogen dimer, and the uniform gas at all temperatures. CP-DFT has no self-interaction error for one electron, and correctly dissociates H2, both major challenges. For warm dense matter, classical CP-DFT calculations can overcome the convergence problems of Kohn-Sham DFT., Comment: 6 pages, 3 figures, 2 tables
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- 2020
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22. Artin-twists of abelian varieties : periods, L-values and arithmetic
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Evans, Robert, Burns, David, and Dokchitser, Vladimir
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512 - Published
- 2021
23. A unified description of hydrophilic and superhydrophobic surfaces in terms of the wetting and drying transitions of liquids
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Evans, Robert, Stewart, Maria C., and Wilding, Nigel B.
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Condensed Matter - Statistical Mechanics - Abstract
Clarifying the factors that control the contact angle of a liquid on a solid substrate is a long-standing scientific problem pertinent across physics, chemistry and materials science. Progress has been hampered by the lack of a comprehensive and unified understanding of the physics of wetting and drying phase transitions. Using various theoretical and simulational techniques applied to realistic fluid models, we elucidate how the character of these transitions depends sensitively on both the range of fluid-fluid and substrate-fluid interactions and the temperature. Our calculations uncover previously unrecognised classes of surface phase diagram which differ from that established for simple lattice models and often assumed to be universal. The differences relate both to the topology of the phase diagram and to the nature of the transitions, with a remarkable feature being a difference between drying and wetting transitions which persists even in the approach to the bulk critical point. Most experimental and simulational studies of liquids at a substrate belong to one of these previously unrecognised classes. We predict that while there appears to be nothing particularly special about water with regard to its wetting and drying behavior, superhydrophobic behavior should be more readily observable in experiments conducted at high temperatures than at room temperature., Comment: 10 pages plus SI
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- 2019
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24. Bladder capacity as a benchmark for patient stratification in interstitial cystitis/bladder pain syndrome
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Sandberg, Maxwell, Wolff, Dylan T., Whitman, Wyatt, Badlani, Gopal, Matthews, Catherine A., Evans, Robert, and Walker, Stephen J.
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- 2023
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25. Ethics, nanotechnology and elite sport : the need for a precautionary approach
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Evans, Robert, McNamee, Michael, and Bloodworth, Andrew
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Elite sport is a competitive industry, with athletes continuously striving for innovative ways to gain advantages over their competitors. The increasing impact of sport sciences over recent decades has contributed much to this ethos, and has recently been witnessed in the application of sports engineering, working to integrate new technologies in order to enhance levels of athletic performance and also athlete safety. The application of nanotechnology offers a sport engineer the potential to improve equipment used both in and out of competition. Nevertheless, despite its emerging integration into sports sciences, limited attention has been paid to the ethical impacts this technology may have on elite sport. To address this problem, an eclectic normative approach is pursued, allowing for the range of nanotechnological application to elite sport to be considered, in order to generate critical ethical evaluations in relation to its current and potential use within elite sport. The issues were framed variously through consequentialist and deontological analysis. Three nanotechnological case studies are presented, highlighting potential benefits and disbenefits that nanotechnology may present, and to additionally determine whether, and if so, what, deontologically framed regulatory action were required to govern its use within elite sport. The first case study considered nanotechnology's application to the sport of road cycling; the second considered nanotechnology's application to performance analysis; and the third considered nanotechnology's application to horse race betting. The analysis of the case studies revealed that nanotechnology presents a number of benefits for elite sport, such as improved levels of performance and enhanced safety; but also disbenefits, such as those relating to fairness and corruption. Despite this, it is argued that, at present, nanotechnology does not pose a significant risk to the integrity of sport. But in order to reduce any future risk, the disbenefits should be addressed. A case is consequently argued for the application of a weak version of the Precautionary Principle applied through an original ethical analytical tool, in order to govern the initial integration phase of nanotechnology. The work concludes by outlining more specific regulatory actions that could be taken in order to inform the development of a 'nano' specific regulatory framework, in order to govern nanotechnology's continued long term safe and ethical use within elite sport.
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- 2020
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26. On the decay of the pair correlation function and the line of vanishing excess isothermal compressibility in simple fluids
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Stopper, Daniel, Hansen-Goos, Hendrik, Roth, Roland, and Evans, Robert
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Condensed Matter - Soft Condensed Matter ,Condensed Matter - Statistical Mechanics - Abstract
We re-visit the competition between attractive and repulsive interparticle forces in simple fluids and how this governs and connects the macroscopic phase behavior and structural properties as manifest in pair correlation functions. We focus on the asymptotic decay of the total correlation function $h(r)$ which is, in turn, controlled by the form of the pair direct correlation function $c(r)$. The decay of $r h(r)$ to zero can be either exponential (monotonic) if attraction dominates repulsion and exponentially damped oscillatory otherwise. The Fisher-Widom (FW) line separates the phase diagram into two regions characterized by the two different types of asymptotic decay. We show that there is a new and physically intuitive thermodynamic criterion which approximates well the actual FW line. This new criterion defines a line where the isothermal compressibility takes its ideal gas value $\chi_T=\chi_T^\text{id}$. We test our hypothesis by considering four commonly used models for simple fluids. In all cases the new criterion yields a line in the phase diagram that is close to the actual FW line for the thermodynamic state points that are most relevant. We also investigate (Widom) lines of maximal correlation length, emphasizing the importance of distinguishing between the true and Ornstein-Zernike correlation lengths
- Published
- 2019
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27. On a BSD-type formula for L-values of Artin twists of elliptic curves
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Dokchitser, Vladimir, Evans, Robert, and Wiersema, Hanneke
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Mathematics - Number Theory ,11G40, 11G05, 14G10 - Abstract
This is an investigation into the possible existence and consequences of a Birch-Swinnerton-Dyer-type formula for L-functions of elliptic curves twisted by Artin representations. We translate expected properties of L-functions into purely arithmetic predictions for elliptic curves, and show that these force some peculiar properties of the Tate-Shafarevich group, which do not appear to be tractable by traditional Selmer group techniques. In particular we exhibit settings where the different p-primary components of the Tate-Shafarevich group do not behave independently of one another. We also give examples of "arithmetically identical" settings for elliptic curves twisted by Artin representations, where the associated L-values can nonetheless differ, in contrast to the classical Birch-Swinnerton-Dyer conjecture., Comment: 27 pages, new version
- Published
- 2019
28. Bidirectional titration of yeast gene expression using a pooled CRISPR guide RNA approach
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Bowman, Emily K, Deaner, Matthew, Cheng, Jan-Fang, Evans, Robert, Oberortner, Ernst, Yoshikuni, Yasuo, and Alper, Hal S
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Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Biotechnology ,2.1 Biological and endogenous factors ,Aetiology ,CRISPR-Cas Systems ,Clustered Regularly Interspaced Short Palindromic Repeats ,Gene Expression Regulation ,Fungal ,Gene Library ,Plasmids ,Promoter Regions ,Genetic ,RNA ,Fungal ,RNA ,Guide ,Kinetoplastida ,Saccharomyces cerevisiae ,CRISPR ,graded expression ,synthetic biology ,essential genes ,next-generation sequencing - Abstract
Most classic genetic approaches utilize binary modifications that preclude the identification of key knockdowns for essential genes or other targets that only require moderate modulation. As a complementary approach to these classic genetic methods, we describe a plasmid-based library methodology that affords bidirectional, graded modulation of gene expression enabled by tiling the promoter regions of all 969 genes that comprise the ito977 model of Saccharomyces cerevisiae's metabolic network. When coupled with a CRISPR-dCas9-based modulation and next-generation sequencing, this method affords a library-based, bidirection titration of gene expression across all major metabolic genes. We utilized this approach in two case studies: growth enrichment on alternative sugars, glycerol and galactose, and chemical overproduction of betaxanthins, leading to the identification of unique gene targets. In particular, we identify essential genes and other targets that were missed by classic genetic approaches.
- Published
- 2020
29. An Integrated Computer-Aided Design and Manufacturing Workflow for Synthetic Biology
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Oberortner, Ernst, Evans, Robert, Meng, Xianwei, Nath, Sangeeta, Plahar, Hector, Simirenko, Lisa, Tarver, Angela, Deutsch, Samuel, Hillson, Nathan J, and Cheng, Jan-Fang
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Biochemistry and Cell Biology ,Medicinal and Biomolecular Chemistry ,Chemical Sciences ,Biological Sciences ,Computer-Aided Design ,Software ,Synthetic Biology ,Workflow ,DNA synthesis ,DNA assembly ,Computer-aided design ,Computer-aided manufacturing ,Bioengineering ,Synthetic biology ,Other Chemical Sciences ,Developmental Biology ,Biochemistry and cell biology ,Medicinal and biomolecular chemistry - Abstract
Biological computer-aided design and manufacturing (bioCAD/CAM) tools facilitate the design and build processes of engineering biological systems using iterative design-build-test-learn (DBTL) cycles. In this book chapter, we highlight some of the bioCAD/CAM tools developed and used at the US Department of Energy (DOE) Joint Genome Institute (JGI), Joint BioEnergy Institute (JBEI), and Agile BioFoundry (ABF). We demonstrate the use of these bioCAD/CAM tools on a common workflow for designing and building a multigene pathway in a hierarchical fashion. Each tool presented in this book chapter is specifically tailored to support one or more specific steps in a workflow, can be integrated with the others into design and build workflows, and can be deployed at academic, government, or commercial entities.
- Published
- 2020
30. CRAGE enables rapid activation of biosynthetic gene clusters in undomesticated bacteria.
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Wang, Gaoyan, Zhao, Zhiying, Ke, Jing, Engel, Yvonne, Shi, Yi-Ming, Robinson, David, Bingol, Kerem, Zhang, Zheyun, Bowen, Benjamin, Louie, Katherine, Wang, Bing, Evans, Robert, Miyamoto, Yu, Cheng, Kelly, Kosina, Suzanne, De Raad, Markus, Silva, Leslie, Luhrs, Alicia, Lubbe, Andrea, Hoyt, David W, Francavilla, Charles, Otani, Hiroshi, Deutsch, Samuel, Washton, Nancy M, Rubin, Edward M, Mouncey, Nigel J, Visel, Axel, Northen, Trent, Cheng, Jan-Fang, Bode, Helge B, and Yoshikuni, Yasuo
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Bacteria ,Photorhabdus ,Polyketide Synthases ,Peptide Synthases ,Recombinases ,Genetic Engineering ,Gene Expression Regulation ,Bacterial ,Genes ,Bacterial ,Genome ,Bacterial ,Multigene Family ,Biosynthetic Pathways ,Secondary Metabolism ,Gene Expression Regulation ,Bacterial ,Genes ,Genome ,Microbiology ,Medical Microbiology - Abstract
It is generally believed that exchange of secondary metabolite biosynthetic gene clusters (BGCs) among closely related bacteria is an important driver of BGC evolution and diversification. Applying this idea may help researchers efficiently connect many BGCs to their products and characterize the products' roles in various environments. However, existing genetic tools support only a small fraction of these efforts. Here, we present the development of chassis-independent recombinase-assisted genome engineering (CRAGE), which enables single-step integration of large, complex BGC constructs directly into the chromosomes of diverse bacteria with high accuracy and efficiency. To demonstrate the efficacy of CRAGE, we expressed three known and six previously identified but experimentally elusive non-ribosomal peptide synthetase (NRPS) and NRPS-polyketide synthase (PKS) hybrid BGCs from Photorhabdus luminescens in 25 diverse γ-Proteobacteria species. Successful activation of six BGCs identified 22 products for which diversity and yield were greater when the BGCs were expressed in strains closely related to the native strain than when they were expressed in either native or more distantly related strains. Activation of these BGCs demonstrates the feasibility of exploiting their underlying catalytic activity and plasticity, and provides evidence that systematic approaches based on CRAGE will be useful for discovering and identifying previously uncharacterized metabolites.
- Published
- 2019
31. Composition inversion in mixtures of binary colloids and polymer
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Zhang, Isla, Pinchaipat, Rattachai, Wilding, Nigel B., Faers, Malcolm A., Bartlett, Paul, Evans, Robert, and Royall, C. Patrick
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Condensed Matter - Soft Condensed Matter - Abstract
Understanding the phase behaviour of mixtures continues to pose challenges, even for systems that might be considered "simple". Here we consider a very simple mixture of two colloidal and one non-adsorbing polymer species which can be simplified even further to a size-asymmetrical binary mixture, in which the effective colloid-colloid interactions depend on the polymer concentration. We show that this basic system exhibits surprisingly rich phase behaviour. In particular, we enquire whether such a system features only a liquid-vapor phase separation (as in one-component colloid-polymer mixtures) or whether, additionally, liquid-liquid demixing of two colloidal phases can occur. Particle-resolved experiments show demixing-like behaviour, but when combined with bespoke Monte Carlo simulations, this proves illusory, and we reveal that only a single liquid-vapor transition occurs. Progressive migration of the small particles to the liquid phase as the polymer concentration increases gives rise to composition inversion - a maximum in the large particle concentration in the liquid phase. Near criticality the density fluctuations are found to be dominated by the larger colloids., Comment: submitted to J. Chem. Phys
- Published
- 2018
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32. Trading Zones Revisited
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Collins, Harry, Evans, Robert, and Gorman, Michael
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Physics - History and Philosophy of Physics ,Physics - Physics and Society - Abstract
We describe and then elaborate the model of trading zones first presented in Collins et al 2007, Trading Zones and Interactional Expertise. We believe this expanded version of the model includes some very important but previously overlooked ways for separate language communities to communicate. We illustrate the argument with examples., Comment: 9 pages, 1 Figure
- Published
- 2017
33. Validating genome-wide CRISPR-Cas9 function improves screening in the oleaginous yeast Yarrowia lipolytica.
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Schwartz, Cory, Cheng, Jan-Fang, Evans, Robert, Schwartz, Christopher A, Wagner, James M, Anglin, Scott, Beitz, Adam, Pan, Weihua, Lonardi, Stefano, Blenner, Mark, Alper, Hal S, Yoshikuni, Yasuo, and Wheeldon, Ian
- Subjects
Yarrowia ,Gene Library ,Genes ,Fungal ,CRISPR-Cas Systems ,Gene Editing ,Genes ,Fungal ,Genetics ,Biotechnology ,Clinical Research ,Human Genome ,Generic Health Relevance ,Industrial Biotechnology - Abstract
Genome-wide mutational screens are central to understanding the genetic underpinnings of evolved and engineered phenotypes. The widespread adoption of CRISPR-Cas9 genome editing has enabled such screens in many organisms, but identifying functional sgRNAs still remains a challenge. Here, we developed a methodology to quantify the cutting efficiency of each sgRNA in a genome-scale library, and in doing so improve screens in the biotechnologically important yeast Yarrowia lipolytica. Screening in the presence and absence of native DNA repair enabled high-throughput quantification of sgRNA function leading to the identification of high efficiency sgRNAs that cover 94% of genes. Library validation enhanced the classification of essential genes by identifying inactive guides that create false negatives and mask the effects of successful disruptions. Quantification of guide effectiveness also creates a dataset from which determinants of CRISPR-Cas9 can be identified. Finally, application of the library identified novel mutations for metabolic engineering of high lipid accumulation.
- Published
- 2019
34. Discovery of Hydroxylase Activity for PqqB Provides a Missing Link in the Pyrroloquinoline Quinone Biosynthetic Pathway.
- Author
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Koehn, Eric, Latham, John, Armand, Tara, Evans, Robert, Tu, Xiongying, Wilmot, Carrie, Iavarone, Anthony, and Klinman, Judith
- Subjects
Bacterial Proteins ,Catalysis ,Dihydroxyphenylalanine ,Hydroxylation ,Iron ,Methylobacterium extorquens ,Mixed Function Oxygenases ,Models ,Chemical ,Zinc - Abstract
Understanding the biosynthesis of cofactors is fundamental to the life sciences, yet to date a few important pathways remain unresolved. One example is the redox cofactor pyrroloquinoline quinone (PQQ), which is critical for C1 metabolism in many microorganisms, a disproportionate number of which are opportunistic human pathogens. While the initial and final steps of PQQ biosynthesis, involving PqqD/E and PqqC, have been elucidated, the precise nature and order of the remaining transformations in the pathway are unknown. Here we show evidence that the remaining essential biosynthetic enzyme PqqB is an iron-dependent hydroxylase catalyzing oxygen-insertion reactions that are proposed to produce the quinone moiety of the mature PQQ cofactor. The demonstrated reactions of PqqB are unprecedented within the metallo β-lactamase protein family and expand the catalytic repertoire of nonheme iron hydroxylases. These new findings also generate a nearly complete description of the PQQ biosynthetic pathway.
- Published
- 2019
35. God's agency and the recent past in Carolingian history writing, c.750-900
- Author
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Evans, Robert, McKitterick, Rosamond, and Sowerby, Richard
- Subjects
944 ,Carolingian ,theology ,history writing ,annals ,providence ,early middle ages ,God's agency ,Charlemagne ,The Vikings ,The Franks ,Christianity - Abstract
The historians writing in the Carolingian Empire, with a few important exceptions, frequently ascribed events in recent history to God. Where they have been noticed at all, these statements of God’s agency have usually been explained as political propaganda, to demonstrate God’s favour towards the reigning dynasty. Alternatively, they have been explained by the legacy of late antique Christian historians, from which this language supposedly derived. This thesis aims to demonstrate that this language was a distinctive and innovative feature of the emerging tradition of Carolingian history writing and is best explained in religious terms. It argues that Carolingian historians reflected the emphasis on God’s agency found throughout contemporary culture and that they deliberately reshaped the Christian language bequeathed by their Roman, Anglo-Saxon, and Frankish predecessors. It offers a text-by-text analysis of how God’s agency functioned within each major Carolingian history, to further show the versatility of this language over the period. Taken together, these texts suggest that Carolingian historians wanted to teach their audiences about God’s agency and its implications for their own beliefs, identities, and behaviour. As a result, these histories and their depictions of God’s agency can be seen as a distinctive contribution to Carolingian religious renewal. This thesis thus aims to contribute to our understanding of the relationship between religion, history, and culture in early medieval Europe.
- Published
- 2018
- Full Text
- View/download PDF
36. The standard mean-field treatment of inter-particle attraction in classical DFT is better than one might expect
- Author
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Archer, Andrew J., Chacko, Blesson, and Evans, Robert
- Subjects
Condensed Matter - Soft Condensed Matter ,Condensed Matter - Statistical Mechanics - Abstract
In classical density functional theory (DFT) the part of the Helmholtz free energy functional arising from attractive inter-particle interactions is often treated in a mean-field or van der Waals approximation. On the face of it, this is a somewhat crude treatment as the resulting functional generates the simple random phase approximation (RPA) for the bulk fluid pair direct correlation function. We explain why using standard mean-field DFT to describe inhomogeneous fluid structure and thermodynamics is more accurate than one might expect based on this observation. By considering the pair correlation function $g(x)$ and structure factor $S(k)$ of a one-dimensional model fluid, for which exact results are available, we show that the mean-field DFT, employed within the test-particle procedure, yields results much superior to those from the RPA closure of the bulk Ornstein-Zernike equation. We argue that one should not judge the quality of a DFT based solely on the approximation it generates for the bulk pair direct correlation function., Comment: 9 pages, 3 figures
- Published
- 2017
- Full Text
- View/download PDF
37. Drying and Wetting Transitions of a Lennard-Jones Fluid: Simulations and Density Functional Theory
- Author
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Evans, Robert, Stewart, Maria C., and Wilding, Nigel B.
- Subjects
Condensed Matter - Statistical Mechanics - Abstract
We report a theoretical and simulation study of the drying and wetting phase transitions of a truncated Lennard-Jones fluid at a flat structureless wall. Binding potential calculations predict that the nature of these transitions depends on whether the wall-fluid attraction has a long ranged (LR) power law decay, or is instead truncated, rendering it short ranged (SR). Using grand canonical Monte Carlo simulation and classical density functional theory we examine both cases in detail. We find that for the LR case wetting is first order, while drying is continuous (critical) and occurs exactly at zero attractive wall strength, ie. in the limit of a hard wall. In the SR case, drying is also critical but the order of the wetting transition depends on the truncation range of the wall-fluid potential. We characterize the approach to critical drying and wetting in terms of the density and local compressibility profiles and via the finite-size scaling properties of the probability distribution of the overall density. For the LR case, where the drying point is known exactly, this analysis allows us to estimate the exponent $\nu_\parallel$ which controls the parallel correlation length, i.e. the extent of vapor bubbles at the wall. Surprisingly, the value we obtain is over twice that predicted by mean field and renormalization group calculations, despite the fact that our three dimensional system is at the upper critical dimension where mean field theory for critical exponents is expected to hold. We suggest reasons for this discrepancy., Comment: 22 pages, 19 figures
- Published
- 2017
- Full Text
- View/download PDF
38. Solvent fluctuations around solvophobic, solvophilic and patchy nanostructures and the accompanying solvent mediated interactions
- Author
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Chacko, Blesson, Evans, Robert, and Archer, Andrew J.
- Subjects
Condensed Matter - Soft Condensed Matter ,Condensed Matter - Statistical Mechanics - Abstract
Using classical density functional theory (DFT) we calculate the density profile $\rho({\mathbf r})$ and local compressibility $\chi({\mathbf r})$ of a simple liquid solvent in which a pair of blocks with (microscopic) rectangular cross-section are immersed. We consider blocks that are solvophobic, solvophilic and also ones that have both solvophobic and solvophilic patches. Large values of $\chi({\mathbf r})$ correspond to regions in space where the liquid density is fluctuating most strongly. We seek to elucidate how enhanced density fluctuations correlate with the solvent mediated force between the blocks, as the distance between the blocks and the chemical potential of the liquid reservoir vary. For sufficiently solvophobic blocks, at small block separations and small deviations from bulk gas-liquid coexistence, we observe a strongly attractive (near constant) force, stemming from capillary evaporation to form a low density gas-like intrusion between the blocks. The accompanying $\chi({\mathbf r})$ exhibits structure which reflects the incipient gas-liquid interfaces that develop. We argue that our model system provides a means to understanding the basic physics of solvent mediated interactions between nanostructures, and between objects such as proteins in water, that possess hydrophobic and hydrophilic patches., Comment: 19 pages, 21 figures
- Published
- 2017
- Full Text
- View/download PDF
39. Expertise revisited I: Interactional Expertise
- Author
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Collins, Harry and Evans, Robert
- Subjects
Physics - Physics and Society - Abstract
The notion of interactional expertise is explained starting with its origins and discussing its many applications. Interactional expertise is the ability to understand a technical area purely be deeply immersed in its 'practice-language' without actually practising. One of its many applications is to explain how large sciences are managed., Comment: 39 pages, one table
- Published
- 2016
40. Single-strand annealing between inverted DNA repeats: Pathway choice, participating proteins, and genome destabilizing consequences.
- Author
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Ramakrishnan, Sreejith, Kockler, Zachary, Evans, Robert, Downing, Brandon D, and Malkova, Anna
- Subjects
Saccharomyces cerevisiae ,Saccharomyces cerevisiae Proteins ,DNA ,Single-Stranded ,DNA Repair ,DNA Replication ,Gene Rearrangement ,DNA Repeat Expansion ,Gene Deletion ,Recombination ,Genetic ,Gene Conversion ,Molecular Structure ,Base Sequence ,DNA Breaks ,Double-Stranded ,DNA Breaks ,Double-Stranded ,DNA ,Single-Stranded ,Recombination ,Genetic ,Genetics ,Developmental Biology - Abstract
Double strand DNA breaks (DSBs) are dangerous events that can result from various causes including environmental assaults or the collapse of DNA replication. While the efficient and precise repair of DSBs is essential for cell survival, faulty repair can lead to genetic instability, making the choice of DSB repair an important step. Here we report that inverted DNA repeats (IRs) placed near a DSB can channel its repair from an accurate pathway that leads to gene conversion to instead a break-induced replication (BIR) pathway that leads to genetic instabilities. The effect of IRs is explained by their ability to form unusual DNA structures when present in ssDNA that is formed by DSB resection. We demonstrate that IRs can form two types of unusual DNA structures, and the choice between these structures depends on the length of the spacer separating IRs. In particular, IRs separated by a long (1-kb) spacer are predominantly involved in inter-molecular single-strand annealing (SSA) leading to the formation of inverted dimers; IRs separated by a short (12-bp) spacer participate in intra-molecular SSA, leading to the formation of fold-back (FB) structures. Both of these structures interfere with an accurate DSB repair by gene conversion and channel DSB repair into BIR, which promotes genomic destabilization. We also report that different protein complexes participate in the processing of FBs containing short (12-bp) versus long (1-kb) ssDNA loops. Specifically, FBs with short loops are processed by the MRX-Sae2 complex, whereas the Rad1-Rad10 complex is responsible for the processing of long loops. Overall, our studies uncover the mechanisms of genomic destabilization resulting from re-routing DSB repair into unusual pathways by IRs. Given the high abundance of IRs in the human genome, our findings may contribute to the understanding of IR-mediated genomic destabilization associated with human disease.
- Published
- 2018
41. Chemiluminescent Biosensors for Detection of Second Messenger Cyclic di-GMP
- Author
-
Dippel, Andrew B, Anderson, Wyatt A, Evans, Robert S, Deutsch, Samuel, and Hammond, Ming C
- Subjects
Microbiology ,Biological Sciences ,Chemical Sciences ,Infectious Diseases ,Biotechnology ,Amino Acid Sequence ,Base Sequence ,Biosensing Techniques ,Cyclic GMP ,Escherichia coli ,Escherichia coli Proteins ,Fluorescence ,Luminescent Proteins ,Mutation ,Phylogeny ,Second Messenger Systems ,Organic Chemistry ,Biological sciences ,Chemical sciences - Abstract
Bacteria colonize highly diverse and complex environments, from gastrointestinal tracts to soil and plant surfaces. This colonization process is controlled in part by the intracellular signal cyclic di-GMP, which regulates bacterial motility and biofilm formation. To interrogate cyclic di-GMP signaling networks, a variety of fluorescent biosensors for live cell imaging of cyclic di-GMP have been developed. However, the need for external illumination precludes the use of these tools for imaging bacteria in their natural environments, including in deep tissues of whole organisms and in samples that are highly autofluorescent or photosensitive. The need for genetic encoding also complicates the analysis of clinical isolates and environmental samples. Toward expanding the study of bacterial signaling to these systems, we have developed the first chemiluminescent biosensors for cyclic di-GMP. The biosensor design combines the complementation of split luciferase (CSL) and bioluminescence resonance energy transfer (BRET) approaches. Furthermore, we developed a lysate-based assay for biosensor activity that enabled reliable high-throughput screening of a phylogenetic library of 92 biosensor variants. The screen identified biosensors with very large signal changes (∼40- and 90-fold) as well as biosensors with high affinities for cyclic di-GMP ( KD < 50 nM). These chemiluminescent biosensors then were applied to measure cyclic di-GMP levels in E. coli. The cellular experiments revealed an unexpected challenge for chemiluminescent imaging in Gram negative bacteria but showed promising application in lysates. Taken together, this work establishes the first chemiluminescent biosensors for studying cyclic di-GMP signaling and provides a foundation for using these biosensors in more complex systems.
- Published
- 2018
42. Therapeutic recommendations in HFE hemochromatosis for p.Cys282Tyr (C282Y/C282Y) homozygous genotype.
- Author
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Adams, Paul, Altes, Albert, Brissot, Pierre, Butzeck, Barbara, Cabantchik, Ioav, Cançado, Rodolfo, Distante, Sonia, Evans, Patricia, Evans, Robert, Ganz, Tomas, Girelli, Domenico, Hultcrantz, Rolf, McLaren, Gordon, Marris, Ben, Milman, Nils, Nemeth, Elizabeta, Nielsen, Peter, Pineau, Brigitte, Piperno, Alberto, Porto, Graça, Prince, Dianne, Ryan, John, Sanchez, Mayka, Santos, Paulo, Swinkels, Dorine, Teixeira, Emerência, Toska, Ketil, Vanclooster, Annick, White, Desley, and Contributors and Hemochromatosis International Taskforce
- Subjects
Contributors and Hemochromatosis International Taskforce ,Humans ,Hemochromatosis ,Phlebotomy ,Chelation Therapy ,Diet ,Homozygote ,Female ,Male ,Hemochromatosis Protein ,Gastroenterology & Hepatology ,Clinical Sciences - Abstract
Although guidelines are available for hereditary hemochromatosis, a high percentage of the recommendations within them are not shared between the different guidelines. Our main aim is to provide an objective, simple, brief, and practical set of recommendations about therapeutic aspects of HFE hemochromatosis for p.Cys282Tyr (C282Y/C282Y) homozygous genotype, based on the published scientific studies and guidelines, in a form that is reasonably comprehensible to patients and people without medical training. This final version was approved at the Hemochromatosis International meeting on 12th May 2017 in Los Angeles.
- Published
- 2018
43. Crystal structures reveal metal-binding plasticity at the metallo-β-lactamase active site of PqqB from Pseudomonas putida
- Author
-
Tu, Xiongying, Latham, John A, Klema, Valerie J, Evans, Robert L, Li, Chao, Klinman, Judith P, and Wilmot, Carrie M
- Subjects
Inorganic Chemistry ,Biochemistry and Cell Biology ,Chemical Sciences ,Biological Sciences ,Prevention ,Bacterial Proteins ,Binding Sites ,Catalytic Domain ,Crystallography ,X-Ray ,Humans ,Metals ,Models ,Molecular ,PQQ Cofactor ,Protein Binding ,Protein Conformation ,Pseudomonas Infections ,Pseudomonas putida ,beta-Lactamases ,PQQ ,PqqB ,Metallo-beta-lactamase ,Metal-binding plasticity ,Pyrroloquinoline quinone ,X-ray crystallography ,Metallo-β-lactamase ,Medicinal and Biomolecular Chemistry ,Biophysics ,Biochemistry and cell biology ,Inorganic chemistry - Abstract
PqqB is an enzyme involved in the biosynthesis of pyrroloquinoline quinone and a distal member of the metallo-β-lactamase (MBL) superfamily. PqqB lacks two residues in the conserved signature motif HxHxDH that makes up the key metal-chelating elements that can bind up to two metal ions at the active site of MBLs and other members of its superfamily. Here, we report crystal structures of PqqB bound to Mn2+, Mg2+, Cu2+, and Zn2+. These structures demonstrate that PqqB can still bind metal ions at the canonical MBL active site. The fact that PqqB can adapt its side chains to chelate a wide spectrum of metal ions with different coordination features on a uniform main chain scaffold demonstrates its metal-binding plasticity. This plasticity may provide insights into the structural basis of promiscuous activities found in ensembles of metal complexes within this superfamily. Furthermore, PqqB belongs to a small subclass of MBLs that contain an additional CxCxxC motif that binds a structural Zn2+. Our data support a key role for this motif in dimerization.
- Published
- 2017
44. Critical Drying of Liquids
- Author
-
Evans, Robert, Stewart, Maria C., and Wilding, Nigel B.
- Subjects
Condensed Matter - Statistical Mechanics ,Condensed Matter - Soft Condensed Matter - Abstract
We report a detailed simulation and classical density functional theory study of the drying transition in a realistic model fluid at a smooth substrate. This transition (in which the contact angle $\theta\to 180^\circ$) is shown to be critical for both short ranged and long-ranged substrate-fluid interaction potentials. In the latter case critical drying occurs at exactly zero attractive substrate strength. This observation permits the accurate elucidation of the character of the transition via a finite-size scaling analysis of the density probability function. We find that the critical exponent $\nu_\parallel$ that controls the parallel correlation length, i.e. the extent of vapor bubbles at the wall, is over twice as large as predicted by mean field and renormalization group calculations. We suggest a reason for the discrepancy. Our findings shed new light on fluctuation phenomena in fluids near hydrophobic and solvophobic interfaces., Comment: 5 pages plus supplementary information. To appear in Physical Review Letters
- Published
- 2016
- Full Text
- View/download PDF
45. Direct Observation in 3d of Structural Crossover in Binary Hard Sphere Mixtures
- Author
-
Statt, Antonia, Pinchaipat, Rattachai, Turci, Francesco, Evans, Robert, and Royall, C. Patrick
- Subjects
Condensed Matter - Statistical Mechanics ,Condensed Matter - Soft Condensed Matter - Abstract
For binary fluid mixtures of spherical particles in which the two species are sufficiently different in size, the dominant wavelength of oscillations of the pair correlation functions is predicted to change from roughly the diameter of the large species to that of the small species along a sharp crossover line in the phase diagram [C. Grodon, M. Dijkstra, R. Evans & R. Roth, J.Chem.Phys. 121, 7869 (2004)]. Using particle-resolved colloid experiments in 3d we demonstrate that crossover exists and that its location in the phase diagram is in quantitative agreement with the results of both theory and our Monte-Carlo simulations. In contrast with previous work [J. Baumgartl, R. Dullens, M. Dijkstra, R. Roth & C. Bechinger, Phys.Rev.Lett. 98, 198303 (2007)], where a correspondence was drawn between crossover and percolation of both species, in our 3d study we find that structural crossover is unrelated to percolation.
- Published
- 2016
- Full Text
- View/download PDF
46. Nuclear Magnetic Resonance Structure and Binding Studies of PqqD, a Chaperone Required in the Biosynthesis of the Bacterial Dehydrogenase Cofactor Pyrroloquinoline Quinone
- Author
-
Evans, Robert L, Latham, John A, Xia, Youlin, Klinman, Judith P, and Wilmot, Carrie M
- Subjects
Aetiology ,2.1 Biological and endogenous factors ,Bacterial Proteins ,Binding Sites ,Methylobacterium extorquens ,Models ,Molecular ,Molecular Chaperones ,Nuclear Magnetic Resonance ,Biomolecular ,Oxidoreductases ,PQQ Cofactor ,Protein Conformation ,Medicinal and Biomolecular Chemistry ,Biochemistry and Cell Biology ,Medical Biochemistry and Metabolomics ,Biochemistry & Molecular Biology - Abstract
Biosynthesis of the ribosomally synthesized and post-translationally modified peptide (RiPP), pyrroloquinoline quinone (PQQ), is initiated when the precursor peptide, PqqA, is recognized and bound by the RiPP precursor peptide recognition element (RRE), PqqD, for presentation to the first enzyme in the pathway, PqqE. Unlike other RiPP-producing, postribosomal peptide synthesis (PRPS) pathways in which the RRE is a component domain of the first enzyme, PqqD is predominantly a separate scaffolding protein that forms a ternary complex with the precursor peptide and first tailoring enzyme. As PqqD is a stable, independent RRE, this makes the PQQ pathway an ideal PRPS model system for probing RRE interactions using nuclear magnetic resonance (NMR). Herein, we present both the solution NMR structure of Methylobacterium extorquens PqqD and results of 1H-15N HSQC binding experiments that identify the PqqD residues involved in binding the precursor peptide, PqqA, and the enzyme, PqqE. The reported structural model for an independent RRE, along with the mapped binding surfaces, will inform future efforts both to understand and to manipulate PRPS pathways.
- Published
- 2017
47. 1H, 13C, and 15N resonance assignments and secondary structure information for Methylobacterium extorquens PqqD and the complex of PqqD with PqqA
- Author
-
Evans, Robert L, Latham, John A, Klinman, Judith P, Wilmot, Carrie M, and Xia, Youlin
- Subjects
Biochemistry and Cell Biology ,Biological Sciences ,Biotechnology ,Genetics ,Amino Acid Sequence ,Bacterial Proteins ,Methylobacterium extorquens ,Nuclear Magnetic Resonance ,Biomolecular ,PQQ Cofactor ,Protein Structure ,Secondary ,Pyrroloquinoline quinone biosynthesis ,PQQ ,PqqA ,PqqD ,NMR resonance assignments ,RiPP ,Biophysics ,Biochemistry and cell biology - Abstract
The ribosomally synthesized and post-translationally modified peptide (RiPP), pyrroloquinoline quinone (PQQ), is a dehydrogenase cofactor synthesized by, but not exclusively used by, certain prokaryotes. RiPPs represent a rapidly expanding and diverse class of natural products-many of which have therapeutic potential-and the biosynthetic pathways for these are gaining attention. Five gene products from the pqq operon (PqqA, PqqB, PqqC, PqqD, and PqqE) are essential for PQQ biosynthesis. The substrate is the peptide PqqA, which is presented to the radical SAM enzyme PqqE by the small protein PqqD. PqqA is unstructured in solution, and only binds to PqqE when in complex with PqqD. PqqD is a member of a growing family of RiPP chaperone proteins (or domains in most cases) that present their associated peptide substrates to the initial RiPP biosynthesis enzymes. An X-ray crystal structure exists for dimeric Xanthomonas campestris PqqD (PDB ID: 3G2B), but PqqD is now known to act as a monomer under physiological conditions. In this study, the PqqD truncation from naturally fused Methylobacterium extorquens (Mex) PqqCD was overexpressed in Escherichia coli and MexPqqA was chemically synthesized. Solution NMR (1)H-,(15)N-HSQC chemical shift studies have identified the PqqD residues involved in binding PqqA, and (1)H, (13)C, and (15)N peak assignments for PqqD alone and for PqqD bound to PqqA are reported herein.
- Published
- 2016
48. Quantifying density fluctuations in water at a hydrophobic surface: evidence for critical drying
- Author
-
Evans, Robert and Wilding, Nigel B.
- Subjects
Condensed Matter - Statistical Mechanics - Abstract
Employing smart Monte Carlo sampling techniques within the grand canonical ensemble, we investigate the properties of water at a model hydrophobic substrate. By reducing the strength of substrate-water attraction we find that fluctuations in the local number density, quantified by a rigorous definition of the local compressibility $\chi(z)$, increase rapidly for distances $z$ within $1$ or $2$ molecular diameters from the substrate as the degree of hydrophobicity, measured by the macroscopic contact angle $\theta$, increases. Our simulations provide evidence for a continuous (critical) drying transition as the substrate-water interaction becomes very weak: $\cos(\theta)\to -1$. We speculate that the existence of such a transition might account for earlier simulation observations of strongly enhanced density fluctuations.
- Published
- 2015
- Full Text
- View/download PDF
49. The role of Cryptococcus neoformans derived phospholipase B1 during host infection
- Author
-
Evans, Robert J.
- Subjects
579.5 ,QR Microbiology - Abstract
Cryptococcus neoformans is an opportunistic fungal pathogen and a leading cause of fungal infection related fatalities in immunocompromised hosts. Compared to well-studied; Cryptococcus neoformans virulence factors like the polysaccharide capsule and melanin synthesis, very little is known about phospholipase B1 (Plb1). Plb1 is a phospholipid modifying enzyme that is implicated in multiple stages of cryptococcal pathogenesis. Herein I demonstrate that a Plb 1 deficient strain of C.neoformans has a profound defect in intracellular growth within macrophages. In addition, I show that the Δplb1 strain undergoes a novel morphological change during in vitro and in vivo infection, resulting in a sub-population of very large 'titan cells' that may arise as a result of the mutant's inability to cope within the macrophage. I go on to test whether these phenotypes are due to a reduction in eicosanoid production caused by Plb 1 deficiency. Finally, I present an addition project where I optimise a C. neoforman's intracellular proliferation assay for high throughput analysis via flow cytometry. This work provides a new insight into the function of this unappreciated virulence factor and helps to lay the foundation for new treatment strategies to combat cryptococcosis.
- Published
- 2016
50. An investigation into cutting fluid additives performance during machining processing of Ti-6Al-4V
- Author
-
Ma, Junhui, Mohammadi, Javad, Zhou, Yan, Larsh, Jeff, Januszkiewicz, Kris, Evans, Robert, Zhao, Yixing, Gali, Olufisayo A., and Riahi, Reza A.
- Published
- 2021
- Full Text
- View/download PDF
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