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3. Book reviews

Author

Oliver, Robin and Burnett, Alan

Published
1992

4. A Stochastic Finite Element Model for the Dynamics of Globular Macromolecules

Author

Oliver, Robin, Read, Daniel J., Harlen, Oliver G., and Harris, Sarah A.

Subjects
Physics - Computational Physics, Physics - Biological Physics
Abstract

We describe a novel coarse-grained simulation method for modelling the dynamics of globular macromolecules, such as proteins. The macromolecule is treated as a continuum that is subject to thermal fluctuations. The model includes a non-linear treatment of elasticity and viscosity with thermal noise that is solved using finite element analysis. We have validated the method by demonstrating that the model provides average kinetic and potential energies that are in agreement with the classical equipartition theorem. In addition, we have performed Fourier analysis on the simulation trajectories obtained for a series of linear beams to confirm that the correct average energies are present in the first two Fourier bending modes. We have then used the new modelling method to simulate the thermal fluctuations of a representative protein over 500ns timescales. Using reasonable parameters for the material properties, we have demonstrated that the overall deformation of the biomolecule is consistent with the results obtained for proteins in general from atomistic molecular dynamics simulations., Comment: 38 pages, 6 figures

Published
2012
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6. A stochastic finite element model for the dynamics of globular proteins

Author

Oliver, Robin, Harris, Sarah, Read, Daniel, and Harlen, Oliver

Subjects
500
Abstract

This thesis concerns a novel coarse graining method for the simulation of the globular proteins. Conventional simulation methods such as molecular dynamics cannot generate sufficient times to reach the important timescales that govern the biology of large biological systems like molecular motors. To address this, I have developed a new coarse graining algorithm drawing on the techniques of continuum mechanics and finite element analysis to build a new simulation technique. The novel part of this algorithm is that the fluctuation dissipation relation for the system can be derived and solved locally. This avoids the need to invert a global resistance matrix to solve for the thermal noise component of the system and reduces the computational expense of the algorithm per time step. I have validated this coarse grained model by performing a variety of tests on the numerical code including spatial and temporal convergence tests using Fourier analysis and beam bending theory. In addition compliance with the equipartition theorem has been confirmed. One key advantage of this method over atomistic techniques is that the coarse grained method does not require any atomic information ab intio. Thus, this method can interface with low resolution imaging techniques such as Small Angle X-Ray Scattering and Cryo-Electron Microscopy. In this thesis, I show how to construct a finite element mesh from both of these sources and run simulations to replicate the results from Small Angle X-Ray Scattering and Cryo-Electron Microscopy experiments. In more detail, I have taken a structure obtained using Small Angle X-ray Scattering, ran simulations and checked that the dynamics do not affect the average X-Ray scattering curve. Furthermore, using experimentally obtained structures and dynamics of the molecular motor dynein I have run simulations to find the elastic parameters that match the experimental data to map the overall dynamics of the dynein motor.

Published
2013

8. A Horizon Scan to support Chemical Pollution related policymaking for sustainable and climate resilient economies

Author

Green, Christopher, primary, Bilyanska, Antoaneta, additional, Bradley, Mags, additional, Dinsdale, Jason, additional, Hutt, Lorraine, additional, Backhaus, Thomas, additional, Boons, Frank, additional, Bott, David, additional, Collins, Chris, additional, Cornell, Sarah E., additional, Craig, Mark, additional, Depledge, Michael, additional, Diderich, Bob, additional, Fuller, Richard, additional, Galloway, Tamara S., additional, Hutchison, Gary R., additional, Ingrey, Nicola, additional, Johnson, Andrew C., additional, Kupka, Rachael, additional, Matthiessen, Peter, additional, Oliver, Robin, additional, Owen, Stewart, additional, Owens, Susan, additional, Pickett, John, additional, Robinson, Sam, additional, Sims, Kerry, additional, Smith, Pete, additional, Sumpter, John P., additional, Tretsiakova‐McNally, Svetlana, additional, Wang, Mengjiao, additional, Welton, Tom, additional, Willis, Katherine J., additional, and Lynch, Iseult, additional

Published
2023
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9. A Horizon Scan to Support Chemical Pollution–Related Policymaking for Sustainable and Climate-Resilient Economies

Author

Green, Christopher, Bilyanska, Antoaneta, Bradley, Mags, Dinsdale, Jason, Hutt, Lorraine, Backhaus, Thomas, Boons, Frank, Bott, David, Collins, Chris, Cornell, Sarah E., Craig, Mark, Depledge, Michael, Diderich, Bob, Fuller, Richard, Galloway, Tamara S., Hutchison, Gary R., Ingrey, Nicola, Johnson, Andrew C., Kupka, Rachael, Matthiessen, Peter, Oliver, Robin, Owen, Stewart, Owens, Susan, Pickett, John, Robinson, Sam, Sims, Kerry, Smith, Pete, Sumpter, John P., Tretsiakova-McNally, Svetlana, Wang, Mengjiao, Welton, Tom, Willis, Katherine J., Lynch, Iseult, Green, Christopher, Bilyanska, Antoaneta, Bradley, Mags, Dinsdale, Jason, Hutt, Lorraine, Backhaus, Thomas, Boons, Frank, Bott, David, Collins, Chris, Cornell, Sarah E., Craig, Mark, Depledge, Michael, Diderich, Bob, Fuller, Richard, Galloway, Tamara S., Hutchison, Gary R., Ingrey, Nicola, Johnson, Andrew C., Kupka, Rachael, Matthiessen, Peter, Oliver, Robin, Owen, Stewart, Owens, Susan, Pickett, John, Robinson, Sam, Sims, Kerry, Smith, Pete, Sumpter, John P., Tretsiakova-McNally, Svetlana, Wang, Mengjiao, Welton, Tom, Willis, Katherine J., and Lynch, Iseult

Abstract

While chemicals are vital to modern society through materials, agriculture, textiles, new technology, medicines, and consumer goods, their use is not without risks. Unfortunately, our resources seem inadequate to address the breadth of chemical challenges to the environment and human health. Therefore, it is important we use our intelligence and knowledge wisely to prepare for what lies ahead. The present study used a Delphi-style approach to horizon-scan future chemical threats that need to be considered in the setting of chemicals and environmental policy, which involved a multidisciplinary, multisectoral, and multinational panel of 25 scientists and practitioners (mainly from the United Kingdom, Europe, and other industrialized nations) in a three-stage process. Fifteen issues were shortlisted (from a nominated list of 48), considered by the panel to hold global relevance. The issues span from the need for new chemical manufacturing (including transitioning to non-fossil-fuel feedstocks); challenges from novel materials, food imports, landfills, and tire wear; and opportunities from artificial intelligence, greater data transparency, and the weight-of-evidence approach. The 15 issues can be divided into three classes: new perspectives on historic but insufficiently appreciated chemicals/issues, new or relatively new products and their associated industries, and thinking through approaches we can use to meet these challenges. Chemicals are one threat among many that influence the environment and human health, and interlinkages with wider issues such as climate change and how we mitigate these were clear in this exercise. The horizon scan highlights the value of thinking broadly and consulting widely, considering systems approaches to ensure that interventions appreciate synergies and avoid harmful trade-offs in other areas. We recommend further collaboration between researchers, industry, regulators, and policymakers to perform horizon scanning to inform policymak

Published
2023
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16. Operational value creation in private equity: exploratory research gauging the divergence in perceived prioritization of private equity´s operational improvement measures in normal and recessionary economic conditions

Author

Bennett, Oliver Robin Paul and Pinho, Paulo Soares de

Subjects
Improvement measures, Operational, Private equity, Recessions, Value creation, Ciências Sociais::Economia e Gestão [Domínio/Área Científica]
Abstract

Empirical research wasconducted detailing, ranking, and evaluatingoperational improvement measuresin Private Equity. Forty-two operational PE experts were surveyed, gaugingthe relative prioritization attributed to these measures in normal and recessionary conditions. Ranking these found a strong focus toward cash preserving strategies in economic down turns. Scatter plot analyses crossing evaluation metrics of Potential Money Multiple Uplift, Complexity, Delivery Risk, Senior Time Commitment found no clear conclusion on PE tendencies toward quick wins or larger plays. Additionally, an operational PE to traditional PE historical performance comparison was conducted finding quite consistent outperformance by operational PE funds from 2000 –2017.

Published
2021

19. Long-term experiments to investigate irreversibility in sorption of pesticides to soil

Author

Suddaby, Laura, Beulke, Sabine, van Beinum, Wendy, Oliver, Robin, Kuet, Sui, and Brown, Colin David

Subjects
complex mixtures
Abstract

Experiments investigated irreversibility in pesticide sorption to soil. Sorption behaviour under abiotic conditions was quantified for chlorotoluron, prometryn and hexaconazole in three soils over periods of up to 274 days. An isotope-exchange procedure was used whereby sorption of 12C- and 14C-pesticide isotopes in shaken suspensions of three soils (7-168 days shaking) was followed by substitution of the isotopes in the liquid phase and a 14-day exchange phase. This was followed by forced isotope exchange where the sorbed 14C material was desorbed by adding an excess of non-radiolabelled compound. Experiments were concluded with solvent extraction and soil combustion to determine remaining radioactivity. The pesticide-soil systems took around four months to approach sorption equilibrium, resulting in strong asymmetry between the profiles of exchange for isotopes of all three compounds. Under the steep concentration gradient of forced isotope exchange, physically entrapped residues were released back into solution and small amounts of radioactivity were still being released at the termination of the experiment. Results were shown not to deviate markedly from ideal behaviour based on the assumption that sorption is fully reversible. Whilst the timescales for release of sorbed residues back into solution were very long, soil combustion at study termination only yielded

Published
2016

21. Joint modelling of repeated measurements and time-to-event outcomes:flexible model specification and exact likelihood inference

Author

Barrett, Jessica, Diggle, Peter John, Henderson, Oliver Robin, Taylor-Robinson, David, Barrett, Jessica, Diggle, Peter John, Henderson, Oliver Robin, and Taylor-Robinson, David

Abstract

Random effects or shared parameter models are commonly advocated for the analysis of combined repeated measurement and event history data, including dropout from longitudinal trials. Their use in practical applications has generally been limited by computational cost and complexity, meaning that only simple special cases can be fitted by using readily available software. We propose a new approach that exploits recent distributional results for the extended skew normal family to allow exact likelihood inference for a flexible class of random-effects models. The method uses a discretization of the timescale for the time-to-event outcome, which is often unavoidable in any case when events correspond to dropout. We place no restriction on the times at which repeated measurements are made. An analysis of repeated lung function measurements in a cystic fibrosis cohort is used to illustrate the method.

Published
2015

22. From bioavailability science to regulation of organic chemicals

Author

Ortega-Calvo, Jose-J., Harmsen, Joop, Parsons, John R., Semple, Kirk T., Aitken, Michael D., Ajao, Charmaine, Eadsforth, Charles, Galay-Burgos, Malyka, Naidu, Ravi, Oliver, Robin, Peijnenburg, Willie J. G. M., Roembke, Joerg, Streck, Georg, Versonnen, Bram, Ortega-Calvo, Jose-J., Harmsen, Joop, Parsons, John R., Semple, Kirk T., Aitken, Michael D., Ajao, Charmaine, Eadsforth, Charles, Galay-Burgos, Malyka, Naidu, Ravi, Oliver, Robin, Peijnenburg, Willie J. G. M., Roembke, Joerg, Streck, Georg, and Versonnen, Bram

Abstract

The bioavailability of organic chemicals in soil and sediment is an important area of scientific investigation for environmental scientists, although this area of study remains only partially recognized by regulators and industries working in the environmental sector. Regulators have recently started to consider bioavailability within retrospective risk assessment frameworks for organic chemicals; by doing so, realistic decision-making with regard to polluted environments can be achieved, rather than relying on the traditional approach of using total-extractable concentrations. However, implementation remains difficult because scientific developments on bioavailability are not always translated into ready-to-use approaches for regulators. Similarly, bioavailability remains largely unexplored within prospective regulatory frameworks that address the approval and regulation of organic chemicals. This article discusses bioavailability concepts and methods, as well as possible pathways for the implementation of bioavailability into risk assessment and regulation; in addition, this article offers a simple, pragmatic and justifiable approach for use within retrospective and prospective risk assessment.

Published
2015

25. From Bioavailability Science to Regulation of Organic Chemicals

Author

Ortega-Calvo, Jose-J., primary, Harmsen, Joop, additional, Parsons, John R., additional, Semple, Kirk T., additional, Aitken, Michael D., additional, Ajao, Charmaine, additional, Eadsforth, Charles, additional, Galay-Burgos, Malyka, additional, Naidu, Ravi, additional, Oliver, Robin, additional, Peijnenburg, Willie J. G. M., additional, Römbke, Jörg, additional, Streck, Georg, additional, and Versonnen, Bram, additional

Published
2015
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27. Modulation of the Hsp90 Chaperone Cycle by a Stringent Client Protein

Author

Lorenz, Oliver Robin, primary, Freiburger, Lee, additional, Rutz, Daniel Andreas, additional, Krause, Maike, additional, Zierer, Bettina Karolina, additional, Alvira, Sara, additional, Cuéllar, Jorge, additional, Valpuesta, José María, additional, Madl, Tobias, additional, Sattler, Michael, additional, and Buchner, Johannes, additional

Published
2014
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31. Brides can tone up in six weeks

Author

Oliver, Robin

Subjects
General interest, News, opinion and commentary
Abstract

Ah, the busy bliss of engagement. All the excitement, all the parties, all the dinners out. ... So little time to exercise. So much food. Bridal store owners say it [...]

Published
2005

39. Variation in chlorotoluron photodegradation rates as a result of seasonal changes in the composition of natural waters.

Author

Oliver, Robin G, Wallace, Derek F, and Earll, Mark

Subjects
COMPOSITION of water, PHOTODEGRADATION, SEASONAL temperature variations, PHOTOLYSIS (Chemistry), NITRATES, RISK assessment, INDEPENDENT component analysis
Abstract

BACKGROUND: It is important to understand the degradation of organic molecules in surface waters to ensure that risk assessments, intended to prevent adverse effects on human health and the environment, are robust. One important degradation mechanism in surface waters is photodegradation. This process is generally studied in laboratory test systems, and the significance of the results is then extrapolated to the field. The aim of this work was to assess how fluctuations in the composition of surface water influence the photodegradation rate of chlorotoluron. RESULTS: Photodegradation DT50 values in the lake (mean = 26.0 days) and pond (mean = 26.0 days) were significantly slower than in the river (mean = 6.8 days) and stream (mean = 7.3 days) samples. The DT50 values in the pond and lake samples were similar to the direct photolysis value (mean = 28.6 days). Photodegradation was significantly faster in the stream and river samples, suggesting that indirect photolysis was significant in those waters. Principal component analysis indicated a strong inverse correlation between nitrate concentration and degradation rate. CONCLUSIONS: Nitrate concentration had a strong influence on the rate of photodegradation, with increasing nitrate concentrations sharply reducing the DT50. However, this effect was restricted to a narrow concentration range and levelled off quite quickly, such that further increases in the nitrate concentration had no significant effect on the rate of degradation. Extrapolating photodegradation rates of chlorotoluron from the laboratory to the field should be relatively straightforward, provided the nitrate concentrations in the waters are known. Copyright © 2012 Society of Chemical Industry [ABSTRACT FROM AUTHOR]

Published
2013
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41. Variation in mitochondrial translation products associated with male-sterile cytoplasms in maize

Author

Forde, Brian G., Oliver, Robin J. C., and Leaver, Christopher J.

Abstract

Mitochondria were isolated under sterile conditions from maize lines with normal cytoplasm and with T, C, and S sources of cytoplasmic male sterility. Protein synthesis by these mitochondria was dependent upon the presence of ADP and an oxidizable substrate or an energy generating system and displayed characteristic sensitivity towards inhibitors of protein synthesis. Approximately 20 polypeptides were detected by sodium dodecyl sulfate polyacrylamide gel electrophoresis of the [35S]methionine-labeled mitochondrial translation products. Mitochondria from the T and C cytoplasms were characterized by the synthesis of a single additional or variant polypeptide.These observations are discussed with reference to the possible mechanisms of male sterility and the susceptibility of plants with T cytoplasm to Helminthosporium maydis, race T. Our results also suggest a potentially rapid method of classifying sources of cytoplasmic male sterility that could be used in conjunction with existing methods, which depend on patterns of fertility restoration after an extended breeding program.

Published
1978
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42. Readers report.

Author

Ottmar, Jerome, Coutsis, Elias, Shanok, Michael E., Wallance, Lawrence A., Oliver, Robin Caton, Stewart, John L., Burton, Stanley C., and Nakagama, Sam I.

Subjects
LETTERS to the editor, DETENTE, ENGINEERS, EMPLOYMENT
Abstract

Several letters to the editor are presented in response to articles in previous issues including "A Case for Détente With South Africa," which appeared in the July 3, 1978 issue, "Unionized Papers Strike Back," which appeared in the July 3, 1978 issue, and "Where the Tax Revolt Goes From Here," which appeared in the June 19, 1978 issue.

Published
1978

43. Readers report.

Author

Kirschner, Robert F., Combs, Joseph, Pelt, M. A., Burlingame, C. F., Oliver, Robin, Nethercott, James W., Plaut, Steven E., Bevel, George C., Lehnerd, A. P., and Pulliam, Kenneth

Subjects
LETTERS to the editor, BUSINESS enterprises, INTERNATIONAL relations, EUROPE-Soviet Union relations, DIVERSIFICATION in industry, PETROLEUM industry
Abstract

Several letters to the editor are presented in response to articles in previous issues related to business, including "Why Europe Speaks Softly to Russia," which appeared in the June 16, 1980 issue of the magazine, "Getty: Spending a Windfall to Diversify Far Out of Oil," published in the June 23, 2980 issue, and "The UAW's Time of Trial," published in the June 16, 1980 issue.

Published
1980

44. Readers report.

Author

Aperans, Gundars, Motyka, Walter W., Smolen, Alan, Young, J. R., Turner, Ruth, Thompson, Frank, Magallanes, Diego Alfredo, Harrison, Dan, Hyatt, Judy, Davids, John H., Ryan, John C., Oliver, Robin, Lurie, Adolph G., and Deutsch, Mark

Subjects
LETTERS to the editor, INTERNATIONAL relations
Abstract

Several letters to the editor are presented in response to articles in previous issues, including "A U. S. Strategy to Stop the Soviets," by Eugen Loebl in the October 29, 1979 issue, "The Double Trouble Besetting Horizon," in the October 22, 1979 issue, and "Turning the Sudan Into the Arabs' Breadbasket," in the September 17, 1979 issue.

Published
1979

45. In Vitro Study of Mitochondrial Protein Synthesis during Mitochondrial Biogenesis in Excised Plant Storage Tissue 1

Author

Forde, Brian G., Oliver, Robin J., and Leaver, Christopher J.

Subjects
Articles
Abstract

Mitochondrial biogenesis was induced in Jerusalem artichoke (Helianthus tuberosus) tuber by aging tissue discs in distilled water for up to 26 hours. Changes in the purified mitochondrial fraction during aging included an increase in both protein content and specific respiratory activity. Using intact isolated mitochondria, conditions were optimized for incorporation of radioactive amino acid into protein. Incorporation was dependent upon the supply of an oxidizable substrate or an external ATP-generating system and showed characteristic sensitivity to inhibitors of protein synthesis. Aging of the tissue resulted in a 3-fold increase in the rate of in vitro incorporation of [(35)S]methionine into mitochondrial protein. An analysis of the free amino acid pool in the mitochondrial fraction showed that the decrease in methionine level during aging of intact tissue was sufficient to account for the increased rate of protein labeling. The activation of mitochondrial biogenesis which occurs after slicing is not dependent on an increase in the capacity of mitochondria to synthesize protein as assayed in vitro.Analysis, by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and autoradiography, showed that isolated mitochondria synthesized about 15 polypeptides in the molecular weight range 8,000 to 55,000. As aging proceeded, significant changes were observed in the relative rates of labeling of three out of the eight major polypeptides synthesized by mitochondria in vitro.

Published
1979

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